The role of objective facial analysis using FDNA in making diagnoses following whole exome analysis. Report of two patients with mutations in the BAF complex genes.

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Gripp, Karen W; Baker, Laura; Telegrafi, Aida; Monaghan, Kristin G

2016-07-01

The genetic basis of numerous intellectual disability (ID) syndromes has recently been identified by applying exome analysis on a research or clinical basis. There is significant clinical overlap of biologically related syndromes, as exemplified by Nicolaides-Baraitser (NCBRS) and Coffin-Siris (CSS) syndrome. Both result from mutations affecting the BAF (mSWI/SNF) complex and belong to the growing category of BAFopathies. In addition to the notable clinical overlap between these BAFopathies, heterogeneity exists for patients clinically diagnosed with one of these conditions. We report two teenagers with ID whose molecular diagnosis of a SMARC2A or ARID1B mutation, respectively, was established through clinical exome analysis. Interestingly, using only the information provided in a single clinically obtained facial photograph from each patient, the facial dysmorphology analysis detected similarities to facial patterns associated with NCBRS as the first suggestion for both individuals, followed by CSS as the second highest ranked in the individual with the ARID1B mutation. Had this information been available to the laboratory performing the exome analysis, it could have been utilized during the variant analysis and reporting process, in conjunction with the written summary provided with each test requisition. While the available massive parallel sequencing technology, variant calling and variant interpretation are constantly evolving, clinical information remains critical for this diagnostic process. When trio analysis is not feasible, additional diagnostic tools may become particularly valuable. Facial dysmorphology analysis data may supplement the clinical phenotype summary and provide data independent of the clinician's personal experience and bias. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Prenatal exome sequencing in anomalous fetuses: new opportunities and challenges.

Science.gov (United States)

Vora, Neeta L; Powell, Bradford; Brandt, Alicia; Strande, Natasha; Hardisty, Emily; Gilmore, Kelly; Foreman, Ann Katherine M; Wilhelmsen, Kirk; Bizon, Chris; Reilly, Jason; Owen, Phil; Powell, Cynthia M; Skinner, Debra; Rini, Christine; Lyerly, Anne D; Boggess, Kim A; Weck, Karen; Berg, Jonathan S; Evans, James P

2017-11-01

PurposeWe investigated the diagnostic and clinical performance of exome sequencing in fetuses with sonographic abnormalities with normal karyotype and microarray and, in some cases, normal gene-specific sequencing.MethodsExome sequencing was performed on DNA from 15 anomalous fetuses and from the peripheral blood of their parents. Parents provided consent to be informed of diagnostic results in the fetus, medically actionable findings in the parents, and their identification as carrier couples for significant autosomal recessive conditions. We assessed the perceptions and understanding of exome sequencing using mixed methods in 15 mother-father dyads.ResultsIn seven (47%) of 15 fetuses, exome sequencing provided a diagnosis or possible diagnosis with identification of variants in the following genes: COL1A1, MUSK, KCTD1, RTTN, TMEM67, PIEZO1 and DYNC2H1. One additional case revealed a de novo nonsense mutation in a novel candidate gene (MAP4K4). The perceived likelihood that exome sequencing would explain the results (5.2 on a 10-point scale) was higher than the approximately 30% diagnostic yield discussed in pretest counseling.ConclusionExome sequencing had diagnostic utility in a highly select population of fetuses where a genetic diagnosis was highly suspected. Challenges related to genetics literacy and variant interpretation must be addressed by highly tailored pre- and posttest genetic counseling.

Exome sequencing of a multigenerational human pedigree.

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Dale J Hedges

2009-12-01

Full Text Available Over the next few years, the efficient use of next-generation sequencing (NGS in human genetics research will depend heavily upon the effective mechanisms for the selective enrichment of genomic regions of interest. Recently, comprehensive exome capture arrays have become available for targeting approximately 33 Mb or approximately 180,000 coding exons across the human genome. Selective genomic enrichment of the human exome offers an attractive option for new experimental designs aiming to quickly identify potential disease-associated genetic variants, especially in family-based studies. We have evaluated a 2.1 M feature human exome capture array on eight individuals from a three-generation family pedigree. We were able to cover up to 98% of the targeted bases at a long-read sequence read depth of > or = 3, 86% at a read depth of > or = 10, and over 50% of all targets were covered with > or = 20 reads. We identified up to 14,284 SNPs and small indels per individual exome, with up to 1,679 of these representing putative novel polymorphisms. Applying the conservative genotype calling approach HCDiff, the average rate of detection of a variant allele based on Illumina 1 M BeadChips genotypes was 95.2% at > or = 10x sequence. Further, we propose an advantageous genotype calling strategy for low covered targets that empirically determines cut-off thresholds at a given coverage depth based on existing genotype data. Application of this method was able to detect >99% of SNPs covered > or = 8x. Our results offer guidance for "real-world" applications in human genetics and provide further evidence that microarray-based exome capture is an efficient and reliable method to enrich for chromosomal regions of interest in next-generation sequencing experiments.

PHARMACOGENETIC TESTING OPPORTUNITIES IN CARDIOLOGY BASED ON EXOME SEQUENCING

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N. V. Shcherbakova

2014-01-01

Full Text Available Aim. To study what cardiac drugs currently have any comments on biomarkers and what information can be obtained by pharmacogenetic testing using data exome sequencing in patients with cardiac diseases.Material and methods. Exome sequencing in random participant of the ATEROGEN IVANOVO study and bioinformatics analysis of the data were performed. Point mutations were annotated using ANNOVAR program, as well as comparison with a number of specialized databases was done on the basis of user protocols.Results. 11 cardiac drugs and 7 genes which variants can influence cardiac drug metabolism were analyzed. According to exome sequencing of the participant we did not reveal allelic variants that require dose regime correction and careful efficacy control.Conclusion. The exome sequencing application is the next step to a wide range of personalized therapy. Future opportunities for improvement of the risk-benefit ratio in each patient are the main purpose of the collection and analysis of pharmacogenetic data.

Clinical exome sequencing reports: current informatics practice and future opportunities.

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Swaminathan, Rajeswari; Huang, Yungui; Astbury, Caroline; Fitzgerald-Butt, Sara; Miller, Katherine; Cole, Justin; Bartlett, Christopher; Lin, Simon

2017-11-01

The increased adoption of clinical whole exome sequencing (WES) has improved the diagnostic yield for patients with complex genetic conditions. However, the informatics practice for handling information contained in whole exome reports is still in its infancy, as evidenced by the lack of a common vocabulary within clinical sequencing reports generated across genetic laboratories. Genetic testing results are mostly transmitted using portable document format, which can make secondary analysis and data extraction challenging. This paper reviews a sample of clinical exome reports generated by Clinical Laboratory Improvement Amendments-certified genetic testing laboratories at tertiary-care facilities to assess and identify common data elements. Like structured radiology reports, which enable faster information retrieval and reuse, structuring genetic information within clinical WES reports would help facilitate integration of genetic information into electronic health records and enable retrospective research on the clinical utility of WES. We identify elements listed as mandatory according to practice guidelines but are currently missing from some of the clinical reports, which might help to organize the data when stored within structured databases. We also highlight elements, such as patient consent, that, although they do not appear within any of the current reports, may help in interpreting some of the information within the reports. Integrating genetic and clinical information would assist the adoption of personalized medicine for improved patient care and outcomes. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Impact of exome sequencing in inflammatory bowel disease

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Cardinale, Christopher J; Kelsen, Judith R; Baldassano, Robert N; Hakonarson, Hakon

2013-01-01

Approaches to understanding the genetic contribution to inflammatory bowel disease (IBD) have continuously evolved from family- and population-based epidemiology, to linkage analysis, and most recently, to genome-wide association studies (GWAS). The next stage in this evolution seems to be the sequencing of the exome, that is, the regions of the human genome which encode proteins. The GWAS approach has been very fruitful in identifying at least 163 loci as being associated with IBD, and now, exome sequencing promises to take our genetic understanding to the next level. In this review we will discuss the possible contributions that can be made by an exome sequencing approach both at the individual patient level to aid with disease diagnosis and future therapies, as well as in advancing knowledge of the pathogenesis of IBD. PMID:24187447

Properties of metallocene complexes during the oxidative crosslinking of air drying coatings

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Stava, Vit; Erben, Milan; Vesely, David; Kalenda, Petr

2007-05-01

Driers are added to air drying paints to accelerate the hardening of spread coating. For decades cobalt octoate has been the most widely used drier because of its good performance at ambient temperature. Recently, several reports describing possible carcinogenity and genotoxicity of cobalt and cobalt salts, such as cobalt sulfate in aerosols, have appeared. It is necessary to reduce the amount of cobalt compounds in coatings industry. Present study deals with the possibility of using ferrocene and its derivatives as driers for air drying coatings. We concentrated particularly on the synergic effect between these metallocene complexes and the cobalt drier. In the first step the kinetics of autooxidation by FTIR spectroscopy in model systems was investigated. Then the metallocene complexes were applied together with cobalt drier to alkyd resin, where their influence on hardness of spread coatings was examined.

Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns

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Alexander H. Li

2017-10-01

Full Text Available Abstract Background Left-sided lesions (LSLs account for an important fraction of severe congenital cardiovascular malformations (CVMs. The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. Methods Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF, and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. Results Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1 as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2. We also identified two genes (DNAH5, OFD1 with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5–6.5. Conclusions Our analytical strategy highlights the utility of bioinformatic resources, including human

Global Carrier Rates of Rare Inherited Disorders Using Population Exome Sequences.

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Kohei Fujikura

Full Text Available Exome sequencing has revealed the causative mutations behind numerous rare, inherited disorders, but it is challenging to find reliable epidemiological values for rare disorders. Here, I provide a genetic epidemiology method to identify the causative mutations behind rare, inherited disorders using two population exome sequences (1000 Genomes and NHLBI. I created global maps of carrier rate distribution for 18 recessive disorders in 16 diverse ethnic populations. Out of a total of 161 mutations associated with 18 recessive disorders, I detected 24 mutations in either or both exome studies. The genetic mapping revealed strong international spatial heterogeneities in the carrier patterns of the inherited disorders. I next validated this methodology by statistically evaluating the carrier rate of one well-understood disorder, sickle cell anemia (SCA. The population exome-based epidemiology of SCA [African (allele frequency (AF = 0.0454, N = 2447, Asian (AF = 0, N = 286, European (AF = 0.000214, N = 4677, and Hispanic (AF = 0.0111, N = 362] was not significantly different from that obtained from a clinical prevalence survey. A pair-wise proportion test revealed no significant differences between the two exome projects in terms of AF (46/48 cases; P > 0.05. I conclude that population exome-based carrier rates can form the foundation for a prospectively maintained database of use to clinical geneticists. Similar modeling methods can be applied to many inherited disorders.

Jannovar: a java library for exome annotation.

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Jäger, Marten; Wang, Kai; Bauer, Sebastian; Smedley, Damian; Krawitz, Peter; Robinson, Peter N

2014-05-01

Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar. © 2014 WILEY PERIODICALS, INC.

Preparation and self-sterilizing properties of Ag@TiO2-styrene-acrylic complex coatings.

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Zhou, Xiang-dong; Chen, Feng; Yang, Jin-tao; Yan, Xiao-hui; Zhong, Ming-qiang

2013-04-01

In this study, we report a simple and cost-effective method for self-sterilized complex coatings obtained by Ag@TiO2 particle incorporation into styrene-acrylic latex. The Ag@TiO2 particles were prepared via a coupling agent modification process. The composite latices characterized by transmission electron microscopy (TEM) study were highly homogeneous at the nanometric scale, and the Ag@TiO2 particles were well dispersed and exhibited an intimate contact between both the organic and inorganic components. The Ag@TiO2 nanoparticles significantly enhanced the absorption in the visible region and engendered a good heat-insulating effect of the complex coatings. Moreover, the Ag@TiO2 nanoparticle incorporation into this polymer matrix renders self-sterilized nanocomposite materials upon light excitation, which are tested against Escherichia coli and Staphylococcus aureus. The complex coatings display an impressive performance in the killing of all micro-organisms with a maximum for a Ag@TiO2 loading concentration of 2-5 wt.%. The weathering endurance of the complex coating was also measured. Copyright © 2012 Elsevier B.V. All rights reserved.

Whole-exome sequencing identified a variant in EFTUD2 gene in establishing a genetic diagnosis.

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Rengasamy Venugopalan, S; Farrow, E G; Lypka, M

2017-06-01

Craniofacial anomalies are complex and have an overlapping phenotype. Mandibulofacial Dysostosis and Oculo-Auriculo-Vertebral Spectrum are conditions that share common craniofacial phenotype and present a challenge in arriving at a diagnosis. In this report, we present a case of female proband who was given a differential diagnosis of Treacher Collins syndrome or Hemifacial Microsomia without certainty. Prior genetic testing reported negative for 22q deletion and FGFR screenings. The objective of this study was to demonstrate the critical role of whole-exome sequencing in establishing a genetic diagnosis of the proband. The participants were 14½-year-old affected female proband/parent trio. Proband/parent trio were enrolled in the study. Surgical tissue sample from the proband and parental blood samples were collected and prepared for whole-exome sequencing. Illumina HiSeq 2500 instrument was used for sequencing (125 nucleotide reads/84X coverage). Analyses of variants were performed using custom-developed software, RUNES and VIKING. Variant analyses following whole-exome sequencing identified a heterozygous de novo pathogenic variant, c.259C>T (p.Gln87*), in EFTUD2 (NM_004247.3) gene in the proband. Previous studies have reported that the variants in EFTUD2 gene were associated with Mandibulofacial Dysostosis with Microcephaly. Patients with facial asymmetry, micrognathia, choanal atresia and microcephaly should be analyzed for variants in EFTUD2 gene. Next-generation sequencing techniques, such as whole-exome sequencing offer great promise to improve the understanding of etiologies of sporadic genetic diseases. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population

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Tae-Joon Park

2015-01-01

Full Text Available Exome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these shortcomings, we present a practical approach for accurate genotype calling using the Illumina Infinium HumanExome BeadChip. We present comparison results and a statistical summary of our genotype data sets. Our data set comprises 14,647 Korean samples. To solve the limitation of automated clustering, we performed manual genotype clustering for the targeted identification of 46,076 variants that were identified using GenomeStudio software. To evaluate the effects of applying custom cluster files, we tested cluster files using 804 independent Korean samples and the same platform. Our study firstly suggests practical guidelines for exome chip quality control in Asian populations and provides valuable insight into an association study using exome chip.

The Highly Conserved COPII Coat Complex Sorts Cargo from the Endoplasmic Reticulum and Targets It to the Golgi

OpenAIRE

Lord, Christopher; Ferro-Novick, Susan; Miller, Elizabeth A.

2013-01-01

Protein egress from the endoplasmic reticulum (ER) is driven by a conserved cytoplasmic coat complex called the COPII coat. The COPII coat complex contains an inner shell (Sec23/Sec24) that sorts cargo into ER-derived vesicles and an outer cage (Sec13/Sec31) that leads to coat polymerization. Once released from the ER, vesicles must tether to and fuse with the target membrane to deliver their protein and lipid contents. This delivery step also depends on the COPII coat, with coat proteins bin...

An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes

DEFF Research Database (Denmark)

Jin, Xin; He, Mingze; Ferguson, Betsy

2012-01-01

-human primate specific reagents that would expedite such research, such as exon-capture tools, are lacking. We evaluated the efficiency of using a human exome capture design for the selective enrichment of exonic regions of non-human primates. We compared the exon sequence recovery in nine chimpanzees, two crab...

Whole exome or genome sequencing: nurses need to prepare families for the possibilities.

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Prows, Cynthia A; Tran, Grace; Blosser, Beverly

2014-12-01

A discussion of whole exome sequencing and the type of possible results patients and families should be aware of before samples are obtained. To find the genetic cause of a rare disorder, whole exome sequencing analyses all known and suspected human genes from a single sample. Over 20,000 detected DNA variants in each individual exome must be considered as possibly causing disease or disregarded as not relevant to the person's disease. In the process, unexpected gene variants associated with known diseases unrelated to the primary purpose of the test may be incidentally discovered. Because family members' DNA samples are often needed, gene variants associated with known genetic diseases or predispositions for diseases can also be discovered in their samples. Discussion paper. PubMed 2009-2013, list of references in retrieved articles, Google Scholar. Nurses need a general understanding of the scope of potential genomic information that may be revealed with whole exome sequencing to provide support and guidance to individuals and families during their decision-making process, while waiting for results and after disclosure. Nurse scientists who want to use whole exome sequencing in their study design and methods must decide early in study development if they will return primary whole exome sequencing research results and if they will give research participants choices about learning incidental research results. It is critical that nurses translate their knowledge about whole exome sequencing into their patient education and patient advocacy roles and relevant programmes of research. © 2014 John Wiley & Sons Ltd.

Evaluation of exome filtering techniques for the analysis of clinically relevant genes.

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Kernohan, Kristin D; Hartley, Taila; Alirezaie, Najmeh; Robinson, Peter N; Dyment, David A; Boycott, Kym M

2018-02-01

A significant challenge facing clinical translation of exome sequencing is meaningful and efficient variant interpretation. Each exome contains ∼500 rare coding variants; laboratories must systematically and efficiently identify which variant(s) contribute to the patient's phenotype. In silico filtering is an approach that reduces analysis time while decreasing the chances of incidental findings. We retrospectively assessed 55 solved exomes using available datasets as in silico filters: Online Mendelian Inheritance in Man (OMIM), Orphanet, Human Phenotype Ontology (HPO), and Radboudumc University Medical Center curated panels. We found that personalized panels produced using HPO terms for each patient had the highest success rate (100%), while producing considerably less variants to assess. HPO panels also captured multiple diagnoses in the same individual. We conclude that custom HPO-derived panels are an efficient and effective way to identify clinically relevant exome variants. © 2017 Wiley Periodicals, Inc.

Antimicrobial coatings on polyethylene terephthalate based on curcumin/cyclodextrin complex embedded in a multilayer polyelectrolyte architecture.

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Shlar, Ilya; Droby, Samir; Rodov, Victor

2018-04-01

Bacterial contamination is a growing concern worldwide. The aim of this work was to develop an antimicrobial coating based on curcumin-cyclodextrin inclusion complex and using polyethylene terephthalate (PET) film as a support matrix. After a pre-treatment aimed to provide sufficient electric charge to the PET surface, it was electrostatically coated with repeated multilayers comprising alternately deposited positively-charged poly-l-lysine (PLL) and negatively-charged poly-l-glutamic acid (PLGA) and carboxymethyl-β-cyclodextrin (CMBCD). The coatings had an architecture (PLL-PLGA) 6 -(PLL-PLGA-PLL-CMBCD) n , with the number of repeated multilayers n varying from 5 to 20. The CMBCD molecules were either covalently cross-linked using carbodiimide crosslinker chemistry or left unbound. The surface morphology, structure and elemental composition of the coatings were analysed by scanning electron microscopy and energy dispersive x-ray spectroscopy. To impart antimicrobial properties to the coatings they were loaded with a natural phenolic compound curcumin forming inclusion complexes with β-cyclodextrin. The non-cross-linked coatings showed bactericidal activity towards Escherichia coli in the dark, and this activity was further enhanced upon illumination with white light. Curcumin was released from the non-cross-linked coatings into an aqueous medium in the form of cyclodextrin inclusion complex. After the cross-linking, the coating lost its dark antimicrobial activity but retained the photodynamic properties. Stabilized cross-linked curcumin-loaded coatings can serve a basis for developing photoactivated antimicrobial surfaces controlling bacterial contamination and spread. Copyright © 2018 Elsevier B.V. All rights reserved.

Exome sequencing for prenatal diagnosis of fetuses with sonographic abnormalities.

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Drury, Suzanne; Williams, Hywel; Trump, Natalie; Boustred, Christopher; Lench, Nicholas; Scott, Richard H; Chitty, Lyn S

2015-10-01

In the absence of aneuploidy or other pathogenic cytogenetic abnormality, fetuses with increased nuchal translucency (NT ≥ 3.5 mm) and/or other sonographic abnormalities have a greater incidence of genetic syndromes, but defining the underlying pathology can be challenging. Here, we investigate the value of whole exome sequencing in fetuses with sonographic abnormalities but normal microarray analysis. Whole exome sequencing was performed on DNA extracted from chorionic villi or amniocytes in 24 fetuses with unexplained ultrasound findings. In the first 14 cases sequencing was initially performed on fetal DNA only. For the remaining 10, the trio of fetus, mother and father was sequenced simultaneously. In 21% (5/24) cases, exome sequencing provided definitive diagnoses (Milroy disease, hypophosphatasia, achondrogenesis type 2, Freeman-Sheldon syndrome and Baraitser-Winter Syndrome). In a further case, a plausible diagnosis of orofaciodigital syndrome type 6 was made. In two others, a single mutation in an autosomal recessive gene was identified, but incomplete sequencing coverage precluded exclusion of the presence of a second mutation. Whole exome sequencing improves prenatal diagnosis in euploid fetuses with abnormal ultrasound scans. In order to expedite interpretation of results, trio sequencing should be employed, but interpretation can still be compromised by incomplete coverage of relevant genes. © 2015 John Wiley & Sons, Ltd.

Lessons learned from whole exome sequencing in multiplex families affected by a complex genetic disorder, intracranial aneurysm.

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Janice L Farlow

Full Text Available Genetic risk factors for intracranial aneurysm (IA are not yet fully understood. Genomewide association studies have been successful at identifying common variants; however, the role of rare variation in IA susceptibility has not been fully explored. In this study, we report the use of whole exome sequencing (WES in seven densely-affected families (45 individuals recruited as part of the Familial Intracranial Aneurysm study. WES variants were prioritized by functional prediction, frequency, predicted pathogenicity, and segregation within families. Using these criteria, 68 variants in 68 genes were prioritized across the seven families. Of the genes that were expressed in IA tissue, one gene (TMEM132B was differentially expressed in aneurysmal samples (n=44 as compared to control samples (n=16 (false discovery rate adjusted p-value=0.023. We demonstrate that sequencing of densely affected families permits exploration of the role of rare variants in a relatively common disease such as IA, although there are important study design considerations for applying sequencing to complex disorders. In this study, we explore methods of WES variant prioritization, including the incorporation of unaffected individuals, multipoint linkage analysis, biological pathway information, and transcriptome profiling. Further studies are needed to validate and characterize the set of variants and genes identified in this study.

Population specific analysis of Yakut exomes

NARCIS (Netherlands)

Zlobin, A. S.; Sharapov, S. Sh.; Guryev, V. P.; Bevova, M. R.; Tsepilov, Y. A.; Sivtseva, T. M.; Boyarskih, U. A.; Sokolova, E. A.; Aulchenko, Y. S.; Filipenko, M. L.; Osakovsky, V. L.

We studied the genetic diversity of the Yakut population using exome sequencing. We performed comparative analysis of the Yakut population and the populations that are included in the "1000 Genomes" project and we identified the alleles specific to the Yakut population. We showed, that the Yakuts

RESEARCH NOTE Genome-based exome-sequencing analysis ...

Indian Academy of Sciences (India)

Navya

2017-02-22

Feb 22, 2017 ... Genome-based exome-sequencing analysis identifies GYG1, DIS3L, DDRGK1 genes ... Cardiology Division, Department of Internal Medicine, Severance .... with p values of <0.05 byanalyzing differences in allele distribution.

ANOMALOUS ELECTRODEPOSITION OF Fe-Ni ALLOY COATING FROM SIMPLE AND COMPLEX BATHS AND ITS MAGNETIC PROPERTY

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M A Islam

2010-03-01

Full Text Available Electrodeposition of Fe-Ni thin films has been carried on copper substrate under various electrodeposition conditions from two simple and six complex baths. Sulfate baths composing of NiSO4. 7H2O, FeSO4.7H2O, H3BO3 and Na2SO4KEYWORDS: Anomalous Electrodeposition, Fe-Ni Coating, Complexing agent, Current Density, Magnetic Property. 1. INTRODUCTION Alloy electrodeposition technologies can extend tremendously the potential of electrochemical deposition processes to provide coatings that require unique mechanical, chemical and physical properties [1]. There has been a great research interest in the development and characterization of iron-nickel (Fe-Ni thin films due to their operational capacity, economic interest, magnetic and other properties [2]. Due to their unique low coefficient of thermal expansion (CTE and soft magnetic properties, Fe-Ni alloys have been used in industrial applications for over 100 years [3]. Typical examples of applications that are based on the low CTE of Fe-Ni alloys include: thermostatic bimetals, glass sealing, integrated circuit packaging, cathode ray tube, shadow masks, membranes for liquid natural gas tankers; applications based on the soft magnetic properties include: read-write heads for magnetic storage, magnetic actuators, magnetic shielding, high performance transformer cores. comprise the simple baths whereas complex baths were prepared by adding ascorbic acid, saccharin and citric acid in simple baths. The effect of bath composition, pH and applied current density on coating appearance, composition, morphology and magnetic property were studied. Wet chemical analysis technique was used to analyze the coating composition whereas SEM and VSM were used to study the deposit morphology and magnetic property respectively. Addition of complexing agents in plating baths suppressed the anomalous nature of Fe-Ni alloy electrodeposition. Coatings obtained from simple baths were characterized by coarse grained non

Whole-Exome Sequencing Identifies One De Novo Variant in the FGD6 Gene in a Thai Family with Autism Spectrum Disorder

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Chuphong Thongnak

2018-01-01

Full Text Available Autism spectrum disorder (ASD has a strong genetic basis, although the genetics of autism is complex and it is unclear. Genetic testing such as microarray or sequencing was widely used to identify autism markers, but they are unsuccessful in several cases. The objective of this study is to identify causative variants of autism in two Thai families by using whole-exome sequencing technique. Whole-exome sequencing was performed with autism-affected children from two unrelated families. Each sample was sequenced on SOLiD 5500xl Genetic Analyzer system followed by combined bioinformatics pipeline including annotation and filtering process to identify candidate variants. Candidate variants were validated, and the segregation study with other family members was performed using Sanger sequencing. This study identified a possible causative variant for ASD, c.2951G>A, in the FGD6 gene. We demonstrated the potential for ASD genetic variants associated with ASD using whole-exome sequencing and a bioinformatics filtering procedure. These techniques could be useful in identifying possible causative ASD variants, especially in cases in which variants cannot be identified by other techniques.

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

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Yang, Yaping; Muzny, Donna M.; Xia, Fan; Niu, Zhiyv; Person, Richard; Ding, Yan; Ward, Patricia; Braxton, Alicia; Wang, Min; Buhay, Christian; Veeraraghavan, Narayanan; Hawes, Alicia; Chiang, Theodore; Leduc, Magalie; Beuten, Joke; Zhang, Jing; He, Weimin; Scull, Jennifer; Willis, Alecia; Landsverk, Megan; Craigen, William J.; Bekheirnia, Mir Reza; Stray-Pedersen, Asbjorg; Liu, Pengfei; Wen, Shu; Alcaraz, Wendy; Cui, Hong; Walkiewicz, Magdalena; Reid, Jeffrey; Bainbridge, Matthew; Patel, Ankita; Boerwinkle, Eric; Beaudet, Arthur L.; Lupski, James R.; Plon, Sharon E.; Gibbs, Richard A.; Eng, Christine M.

2015-01-01

IMPORTANCE Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders. OBJECTIVE To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome. DESIGN, SETTING, AND PATIENTS Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient’s physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay. MAIN OUTCOMES AND MEASURES Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings. RESULTS A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%–31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%–27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%–47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%–25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy

Usability study of clinical exome analysis software: top lessons learned and recommendations.

Science.gov (United States)

Shyr, Casper; Kushniruk, Andre; Wasserman, Wyeth W

2014-10-01

New DNA sequencing technologies have revolutionized the search for genetic disruptions. Targeted sequencing of all protein coding regions of the genome, called exome analysis, is actively used in research-oriented genetics clinics, with the transition to exomes as a standard procedure underway. This transition is challenging; identification of potentially causal mutation(s) amongst ∼10(6) variants requires specialized computation in combination with expert assessment. This study analyzes the usability of user interfaces for clinical exome analysis software. There are two study objectives: (1) To ascertain the key features of successful user interfaces for clinical exome analysis software based on the perspective of expert clinical geneticists, (2) To assess user-system interactions in order to reveal strengths and weaknesses of existing software, inform future design, and accelerate the clinical uptake of exome analysis. Surveys, interviews, and cognitive task analysis were performed for the assessment of two next-generation exome sequence analysis software packages. The subjects included ten clinical geneticists who interacted with the software packages using the "think aloud" method. Subjects' interactions with the software were recorded in their clinical office within an urban research and teaching hospital. All major user interface events (from the user interactions with the packages) were time-stamped and annotated with coding categories to identify usability issues in order to characterize desired features and deficiencies in the user experience. We detected 193 usability issues, the majority of which concern interface layout and navigation, and the resolution of reports. Our study highlights gaps in specific software features typical within exome analysis. The clinicians perform best when the flow of the system is structured into well-defined yet customizable layers for incorporation within the clinical workflow. The results highlight opportunities to

The PsB glycoprotein complex is secreted as a preassembled precursor of the spore coat in Dictyostelium discoideum.

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Watson, N; McGuire, V; Alexander, S

1994-09-01

The PsB glycoprotein in Dictyostelium discoideum is one of a diverse group of developmentally regulated, prespore-cell-specific proteins, that contain a common O-linked oligosaccharide. This post-translational modification is dependent on the wild-type modB allele. The PsB protein exists as part of a multiprotein complex of six different proteins, which have different post-translational modifications and are held together by both covalent and non-covalent interactions (Watson et al. (1993). J. Biol. Chem. 268, 22634-22641). In this study we have used microscopic and biochemical analyses to examine the cellular localization and function of the PsB complex during development. We found that the PsB complex first accumulates in prespore vesicles in slug cells and is secreted later during culmination and becomes localized to both the extracellular matrix of the apical spore mass of mature fruiting bodies and to the inner layer of the spore coat. The PsB associated with the spore coat is covalently bound by disulfide bridges. The PsB protein always exists in a multiprotein complex, but the composition of the PsB complex changes during secretion and spore maturation. Some of the PsB complex proteins have been identified as spore coat proteins. These data demonstrate that some of the proteins that form the spore coat exist as a preassembled precursor complex. The PsB complex is secreted in a developmentally regulated manner during the process of spore differentiation, at which time proteins of the complex, as well as additional spore coat proteins, become covalently associated in at least two forms of extracellular matrix: the interspore matrix and the spore coat. These and other studies show that proteins with modB dependent O-linked oligosaccharides are involved in a wide variety of processes underlying morphogenesis in this organism. These developmental processes are the direct result of cellular mechanisms regulating protein targeting, assembly and secretion, and the

Accurate Local-Ancestry Inference in Exome-Sequenced Admixed Individuals via Off-Target Sequence Reads

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Hu, Youna; Willer, Cristen; Zhan, Xiaowei; Kang, Hyun Min; Abecasis, Gonçalo R.

2013-01-01

Estimates of the ancestry of specific chromosomal regions in admixed individuals are useful for studies of human evolutionary history and for genetic association studies. Previously, this ancestry inference relied on high-quality genotypes from genome-wide association study (GWAS) arrays. These high-quality genotypes are not always available when samples are exome sequenced, and exome sequencing is the strategy of choice for many ongoing genetic studies. Here we show that off-target reads generated during exome-sequencing experiments can be combined with on-target reads to accurately estimate the ancestry of each chromosomal segment in an admixed individual. To reconstruct local ancestry, our method SEQMIX models aligned bases directly instead of relying on hard genotype calls. We evaluate the accuracy of our method through simulations and analysis of samples sequenced by the 1000 Genomes Project and the NHLBI Grand Opportunity Exome Sequencing Project. In African Americans, we show that local-ancestry estimates derived by our method are very similar to those derived with Illumina’s Omni 2.5M genotyping array and much improved in relation to estimates that use only exome genotypes and ignore off-target sequencing reads. Software implementing this method, SEQMIX, can be applied to analysis of human population history or used for genetic association studies in admixed individuals. PMID:24210252

Exome sequencing identifies ZNF644 mutations in high myopia.

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Yi Shi

2011-06-01

Full Text Available Myopia is the most common ocular disorder worldwide, and high myopia in particular is one of the leading causes of blindness. Genetic factors play a critical role in the development of myopia, especially high myopia. Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders. Here we show a successful application of exome sequencing to identify a gene for an autosomal dominant disorder, and we have identified a gene potentially responsible for high myopia in a monogenic form. We captured exomes of two affected individuals from a Han Chinese family with high myopia and performed sequencing analysis by a second-generation sequencer with a mean coverage of 30× and sufficient depth to call variants at ∼97% of each targeted exome. The shared genetic variants of these two affected individuals in the family being studied were filtered against the 1000 Genomes Project and the dbSNP131 database. A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644 was identified as being related to the phenotype of this family. After we performed sequencing analysis of the exons in the ZNF644 gene in 300 sporadic cases of high myopia, we identified an additional five mutations (I587V, R680G, C699Y, 3'UTR+12 C>G, and 3'UTR+592 G>A in 11 different patients. All these mutations were absent in 600 normal controls. The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE. Given that ZNF644 is predicted to be a transcription factor that may regulate genes involved in eye development, mutation may cause the axial elongation of eyeball found in high myopia patients. Our results suggest that ZNF644 might be a causal gene for high myopia in a monogenic form.

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

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Yang, Yaping; Muzny, Donna M.; Reid, Jeffrey G.; Bainbridge, Matthew N.; Willis, Alecia; Ward, Patricia A.; Braxton, Alicia; Beuten, Joke; Xia, Fan; Niu, Zhiyv; Hardison, Matthew; Person, Richard; Bekheirnia, Mir Reza; Leduc, Magalie S.; Kirby, Amelia; Pham, Peter; Scull, Jennifer; Wang, Min; Ding, Yan; Plon, Sharon E.; Lupski, James R.; Beaudet, Arthur L.; Gibbs, Richard A.; Eng, Christine M.

2014-01-01

BACKGROUND Whole-exome sequencing is a diagnostic approach for the identification of molecular defects in patients with suspected genetic disorders. METHODS We developed technical, bioinformatic, interpretive, and validation pipelines for whole-exome sequencing in a certified clinical laboratory to identify sequence variants underlying disease phenotypes in patients. RESULTS We present data on the first 250 probands for whom referring physicians ordered whole-exome sequencing. Patients presented with a range of phenotypes suggesting potential genetic causes. Approximately 80% were children with neurologic pheno-types. Insurance coverage was similar to that for established genetic tests. We identified 86 mutated alleles that were highly likely to be causative in 62 of the 250 patients, achieving a 25% molecular diagnostic rate (95% confidence interval, 20 to 31). Among the 62 patients, 33 had autosomal dominant disease, 16 had auto-somal recessive disease, and 9 had X-linked disease. A total of 4 probands received two nonoverlapping molecular diagnoses, which potentially challenged the clinical diagnosis that had been made on the basis of history and physical examination. A total of 83% of the autosomal dominant mutant alleles and 40% of the X-linked mutant alleles occurred de novo. Recurrent clinical phenotypes occurred in patients with mutations that were highly likely to be causative in the same genes and in different genes responsible for genetically heterogeneous disorders. CONCLUSIONS Whole-exome sequencing identified the underlying genetic defect in 25% of consecutive patients referred for evaluation of a possible genetic condition. (Funded by the National Human Genome Research Institute.) PMID:24088041

Effect of complexing agents and pH on microstructure and tribological properties of Co-W coatings produced by double pulse electrodeposition

International Nuclear Information System (INIS)

Su Fenghua; Liu Cansen; Huang Ping

2012-01-01

The Co-W coatings were produced by double pulse electrodeposition from aqueous bath with cobalt sulphate and sodium tungstate. Effect of complexing agent and pH value in the plating bath on the microstructure, morphology and hardness of the electrodeposited Co-W coatings were investigated using an X-ray diffraction (XRD), scanning electron microscope (SEM) and a Vickers hardness tester, respectively. The friction and wear properties of the Co-W coatings deposited from different baths were evaluated with a ball-on-disk UMT-3MT tribometer. The correlation among the electrodepositing condition that varied with the complexing agent or pH value, the microstructure and the tribological properties of the deposited Co-W coatings were discussed. The results show that the complexing agent and pH value significantly affect the microstructure and tribological properties of the electrodeposited Co-W coatings. The sodium citrate is the best complexing agent to improve the tribological properties of the electrodeposited Co-W coatings at pH 6.0, followed by the sodium gluconate. The Co-W coatings electrodeposited from the near neutral bath can obtain better tribological properties than those deposited from strong acid or strong alkaline bath. The differences of the tribological properties for Co-W coatings from different baths were attributed to their different hardness, crystal structure and morphological characterizations, which can be optimized by the electrodepositing condition, i.e., the complexing agent and pH value in bath.

Exome Array Analysis of Nuclear Lens Opacity.

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Loomis, Stephanie J; Klein, Alison P; Lee, Kristine E; Chen, Fei; Bomotti, Samantha; Truitt, Barbara; Iyengar, Sudha K; Klein, Ronald; Klein, Barbara E K; Duggal, Priya

2018-06-01

Nuclear cataract is the most common subtype of age-related cataract, the leading cause of blindness worldwide. It results from advanced nuclear sclerosis, or opacity in the center of the optic lens, and is affected by both genetic and environmental risk factors, including smoking. We sought to understand the genetic factors associated with nuclear sclerosis through interrogation of rare and low frequency coding variants using exome array data. We analyzed Illumina Human Exome Array data for 1,488 participants of European ancestry in the Beaver Dam Eye Study who were without cataract surgery for association with nuclear sclerosis grade, controlling for age and sex. We performed single-variant regression analysis for 32,138 variants with minor allele frequency (MAF) ≥0.003. In addition, gene-based analysis of 11,844 genes containing at least two variants with MAF nuclear sclerosis, the possible association with the RNF149 gene highlights a potential candidate gene for future studies that aim to understand the genetic architecture of nuclear sclerosis.

Wear Behavior of Uncoated and Coated Tools under Complex Loading Conditions

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M. Wieland

2012-03-01

Full Text Available In automotive industry crash relevant structures of the body in white are manufactured using the direct hot stamping process. Due to the high temperature difference between the hot blank and the cold tool surfaces and the relative movement between the blank and the tool surfaces during the forming operation, high thermal and mechanical loads are applied on the tool leading to excessive wear in terms of adhesion on the tool surfaces. One possibility to reduce wear of hot stamping tools is the application of tool coating systems. In the scope of this work uncoated and coated tools are characterized under complex loading conditions with respect to adhesive layer build-up.

Complex impedance study on nano-CeO2 coating TiO2

International Nuclear Information System (INIS)

Zhang Mei; Wang Honglian; Wang Xidong; Li Wenchao

2006-01-01

Titanium dioxide (TiO 2 ) nanoparticles and cerium dioxide (CeO 2 ) nanoparticles coated titanium dioxide (TiO 2 ) nanoparticles (CeO 2 -TiO 2 nanoparticles) have been successfully synthesized by sol-gel method. The complex impedance of the materials was investigated. The grain resistance, boundary resistance and activation energy of the nanoparticles were calculated according to Arrhenius equation. According to calculating results, the active capacity of pure TiO 2 nanoparticles has been improved because of nano-CeO 2 coating. An optimal CeO 2 content of 4.9 mol% was achieved. The high resolution electron microscopy images of CeO 2 -TiO 2 nanoparticles showed that TiO 2 nanoparticles, as a core, were covered by CeO 2 nanoparticles. The average size of CeO 2 coating TiO 2 nanoparticles was about 70 nm. Scanning electron microscopy observation indicted that CeO 2 nanoparticle coating improved the separation, insulation, and stability the CeO 2 -TiO 2 nanoparticles, which was benefit to the activity of materials

Whole exome analysis identifies dominant COL4A1 mutations in patients with complex ocular phenotypes involving microphthalmia.

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Deml, B; Reis, L M; Maheshwari, M; Griffis, C; Bick, D; Semina, E V

2014-11-01

Anophthalmia/microphthalmia (A/M) is a developmental ocular malformation defined as complete absence or reduction in size of the eye. A/M is a heterogenous disorder with numerous causative genes identified; however, about half the cases lack a molecular diagnosis. We undertook whole exome sequencing in an A/M family with two affected siblings, two unaffected siblings, and unaffected parents; the ocular phenotype was isolated with only mild developmental delay/learning difficulties reported and a normal brain magnetic resonance imaging (MRI) in the proband at 16 months. No pathogenic mutations were identified in 71 known A/M genes. Further analysis identified a shared heterozygous mutation in COL4A1, c.2317G>A, p.(Gly773Arg) that was not seen in the unaffected parents and siblings. Analysis of 24 unrelated A/M exomes identified a novel c.2122G>A, p.(Gly708Arg) mutation in an additional patient with unilateral microphthalmia, bilateral microcornea and Peters anomaly; the mutation was absent in the unaffected mother and the unaffected father was not available. Mutations in COL4A1 have been linked to a spectrum of human disorders; the most consistent feature is cerebrovascular disease with variable ocular anomalies, kidney and muscle defects. This study expands the spectrum of COL4A1 phenotypes and indicates screening in patients with A/M regardless of MRI findings or presumed inheritance pattern. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

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Adalsteinsson, Viktor A; Ha, Gavin; Freeman, Samuel S; Choudhury, Atish D; Stover, Daniel G; Parsons, Heather A; Gydush, Gregory; Reed, Sarah C; Rotem, Denisse; Rhoades, Justin; Loginov, Denis; Livitz, Dimitri; Rosebrock, Daniel; Leshchiner, Ignaty; Kim, Jaegil; Stewart, Chip; Rosenberg, Mara; Francis, Joshua M; Zhang, Cheng-Zhong; Cohen, Ofir; Oh, Coyin; Ding, Huiming; Polak, Paz; Lloyd, Max; Mahmud, Sairah; Helvie, Karla; Merrill, Margaret S; Santiago, Rebecca A; O'Connor, Edward P; Jeong, Seong H; Leeson, Rachel; Barry, Rachel M; Kramkowski, Joseph F; Zhang, Zhenwei; Polacek, Laura; Lohr, Jens G; Schleicher, Molly; Lipscomb, Emily; Saltzman, Andrea; Oliver, Nelly M; Marini, Lori; Waks, Adrienne G; Harshman, Lauren C; Tolaney, Sara M; Van Allen, Eliezer M; Winer, Eric P; Lin, Nancy U; Nakabayashi, Mari; Taplin, Mary-Ellen; Johannessen, Cory M; Garraway, Levi A; Golub, Todd R; Boehm, Jesse S; Wagle, Nikhil; Getz, Gad; Love, J Christopher; Meyerson, Matthew

2017-11-06

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

An integrative variant analysis suite for whole exome next-generation sequencing data

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Challis Danny

2012-01-01

Full Text Available Abstract Background Whole exome capture sequencing allows researchers to cost-effectively sequence the coding regions of the genome. Although the exome capture sequencing methods have become routine and well established, there is currently a lack of tools specialized for variant calling in this type of data. Results Using statistical models trained on validated whole-exome capture sequencing data, the Atlas2 Suite is an integrative variant analysis pipeline optimized for variant discovery on all three of the widely used next generation sequencing platforms (SOLiD, Illumina, and Roche 454. The suite employs logistic regression models in conjunction with user-adjustable cutoffs to accurately separate true SNPs and INDELs from sequencing and mapping errors with high sensitivity (96.7%. Conclusion We have implemented the Atlas2 Suite and applied it to 92 whole exome samples from the 1000 Genomes Project. The Atlas2 Suite is available for download at http://sourceforge.net/projects/atlas2/. In addition to a command line version, the suite has been integrated into the Genboree Workbench, allowing biomedical scientists with minimal informatics expertise to remotely call, view, and further analyze variants through a simple web interface. The existing genomic databases displayed via the Genboree browser also streamline the process from variant discovery to functional genomics analysis, resulting in an off-the-shelf toolkit for the broader community.

Early diagnosis of Werner’s syndrome using exome-wide sequencing in a single, atypical patient

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Eleanor eRaffan

2011-03-01

Full Text Available Genetic diagnosis of inherited metabolic disease is conventionally achieved through syndrome recognition and targeted gene sequencing, but many patients receive no specific diagnosis. Next generation sequencing allied to capture of expressed sequences from genomic DNA now offers a powerful new diagnostic approach. Barriers to routine diagnostic use include cost, and the complexity of interpreting results arising from simultaneous identification of large numbers of variants. We applied exome-wide sequencing to an individual, 16 year old daughter of consanguineous parents with a novel syndrome of short stature, severe insulin resistance, ptosis and microcephaly. Pulldown of expressed sequences from genomic DNA followed by massively parallel sequencing was undertaken. Single nucleotide variants (SNVs were called using SAMtools prior to filtering based on sequence quality and existence in control genomes and exomes. Of 485 genetic variants predicted to alter protein sequence and absent from control data, 24 were homozygous in the patient. One mutation – the p.Arg732X mutation in the WRN gene – has previously been reported in Werner’s syndrome (WS. On re-evaluation of the patient several early features of WS were detected including loss of fat from the extremities and frontal hair thinning. Lymphoblastoid cells from the proband exhibited a defective decatenation checkpoint, consistent with loss of WRN activity. We have thus diagnosed WS some 15 years earlier than average, permitting aggressive prophylactic therapy and screening for WS complications, illustrating the potential of exome-wide sequencing to achieve early diagnosis and change management of rare autosomal recessive disease, even in individual patients of consanguineous parentage with apparently novel syndromes.

Preliminary coating design and coating developments for ATHENA

DEFF Research Database (Denmark)

Jakobsen, Anders Clemen; Ferreira, Desiree Della Monica; Christensen, Finn Erland

2011-01-01

We present initial novel coating design for ATHENA. We make use of both simple bilayer coatings of Ir and B4C and more complex constant period multilayer coatings to enhance the effective area and cover the energy range from 0.1 to 10 keV. We also present the coating technology used...... for these designs and present test results from coatings....

Diagnostic yield of molecular autopsy in patients with sudden arrhythmic death syndrome using targeted exome sequencing

DEFF Research Database (Denmark)

Nunn, Laurence M; Lopes, Luis R; Syrris, Petros

2016-01-01

AIMS: The targeted genetic screening of Sudden Arrhythmic Death Syndrome (SADS) probands in a molecular autopsy has a diagnostic yield of up to 35%. Exome sequencing has the potential to improve this yield. The primary aim of this study is to examine the feasibility and diagnostic utility...... of targeted exome screening in SADS victims, utilizing familial clinical screening whenever possible. METHODS AND RESULTS: To determine the feasibility and diagnostic yield of targeted exome sequencing deoxyribonucleic acid (DNA) was isolated from 59 SADS victims (mean age 25 years, range 1-51 years...... previously published rare (0.02-0.5%) candidate mutations-a total yield of 29%. Co-segregation fully confirmed two private SCN5A Na channel mutations. Variants of unknown significance were detected in a further 34% of probands. CONCLUSION: Molecular autopsy using targeted exome sequencing has a relatively...

Lessons from whole-exome sequencing in MODYX families

DEFF Research Database (Denmark)

Dusatkova, Petra; Fang, Mingyan; Pruhova, Stepanka

2014-01-01

We report the first results from whole-exome sequencing performed in families with Maturity-Onset Diabetes of the Young without a known genetic cause of diabetes (MODYX). This next generation sequencing technique pointed out that routine testing of MODY needs constant awareness and regular re...

How do providers discuss the results of pediatric exome sequencing with families?

Science.gov (United States)

Walser, Sarah A; Werner-Lin, Allison; Mueller, Rebecca; Miller, Victoria A; Biswas, Sawona; Bernhardt, Barbara A

2017-09-01

This study provides preliminary data on the process and content of returning results from exome sequencing offered to children through one of the Clinical Sequencing Exploratory Research (CSER) projects. We recorded 25 sessions where providers returned diagnostic and secondary sequencing results to families. Data interpretation utilized inductive thematic analysis. Typically, providers followed a results report and discussed diagnostic findings using technical genomic and sequencing concepts. We identified four provider processes for returning results: teaching genetic concepts; assessing family response; personalizing findings; and strengthening patient-provider relationships. Sessions should reflect family interest in medical management and next steps, and minimize detailed genomic concepts. As the scope and complexity of sequencing increase, the traditional information-laden counseling model requires revision.

Whole-exome sequencing of a patient with severe and complex hemostatic abnormalities reveals a possible contributing frameshift mutation in C3AR1

DEFF Research Database (Denmark)

Leinøe, Eva; Nielsen, Ove Juul; Jønson, Lars

2016-01-01

-threatening coagulation disorder causing recurrent venous thromboembolic events, severe thrombocytopenia, and subdural hematomas. Whole-exome sequencing revealed a frameshift mutation (C3AR1 c.355-356dup, p.Asp119Alafs*19) resulting in a premature stop codon in C3AR1 (Complement Component 3a Receptor 1). Based...

The cellulose-binding activity of the PsB multiprotein complex is required for proper assembly of the spore coat and spore viability in Dictyostelium discoideum.

Science.gov (United States)

Srinivasan, S; Griffiths, K R; McGuire, V; Champion, A; Williams, K L; Alexander, S

2000-08-01

The terminal event of spore differentiation in the cellular slime mould Dictyostelium discoideum is the assembly of the spore coat, which surrounds the dormant amoeba and allows the organism to survive during extended periods of environmental stress. The spore coat is a polarized extracellular matrix composed of glycoproteins and cellulose. The process of spore coat formation begins by the regulated secretion of spore coat proteins from the prespore vesicles (PSVs). Four of the major spore coat proteins (SP96, PsB/SP85, SP70 and SP60) exist as a preassembled multiprotein complex within the PSVs. This complete complex has an endogenous cellulose-binding activity. Mutant strains lacking either the SP96 or SP70 proteins produce partial complexes that do not have cellulose-binding activity, while mutants lacking SP60 produce a partial complex that retains this activity. Using a combination of immunofluorescence microscopy and biochemical methods we now show that the lack of cellulose-binding activity in the SP96 and SP70 mutants results in abnormally assembled spore coats and spores with greatly reduced viability. In contrast, the SP60 mutant, in which the PsB complex retains its cellulose-binding activity, produces spores with apparently unaltered structure and viability. Thus, it is the loss of the cellulose-binding activity of the PsB complex, rather than the mere loss of individual spore coat proteins, that results in compromised spore coat structure. These results support the idea that the cellulose-binding activity associated with the complete PsB complex plays an active role in the assembly of the spore coat.

Identification of novel single nucleotide polymorphisms associated with acute respiratory distress syndrome by exome-seq.

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Katherine Shortt

Full Text Available Acute respiratory distress syndrome (ARDS is a lung condition characterized by impaired gas exchange with systemic release of inflammatory mediators, causing pulmonary inflammation, vascular leak and hypoxemia. Existing biomarkers have limited effectiveness as diagnostic and therapeutic targets. To identify disease-associating variants in ARDS patients, whole-exome sequencing was performed on 96 ARDS patients, detecting 1,382,399 SNPs. By comparing these exome data to those of the 1000 Genomes Project, we identified a number of single nucleotide polymorphisms (SNP which are potentially associated with ARDS. 50,190SNPs were found in all case subgroups and controls, of which89 SNPs were associated with susceptibility. We validated three SNPs (rs78142040, rs9605146 and rs3848719 in additional ARDS patients to substantiate their associations with susceptibility, severity and outcome of ARDS. rs78142040 (C>T occurs within a histone mark (intron 6 of the Arylsulfatase D gene. rs9605146 (G>A causes a deleterious coding change (proline to leucine in the XK, Kell blood group complex subunit-related family, member 3 gene. rs3848719 (G>A is a synonymous SNP in the Zinc-Finger/Leucine-Zipper Co-Transducer NIF1 gene. rs78142040, rs9605146, and rs3848719 are associated significantly with susceptibility to ARDS. rs3848719 is associated with APACHE II score quartile. rs78142040 is associated with 60-day mortality in the overall ARDS patient population. Exome-seq is a powerful tool to identify potential new biomarkers for ARDS. We selectively validated three SNPs which have not been previously associated with ARDS and represent potential new genetic biomarkers for ARDS. Additional validation in larger patient populations and further exploration of underlying molecular mechanisms are warranted.

Flame Retardant Multilayered Coatings on Acrylic Fabrics Prepared by One-Step Deposition of Chitosan/Montmorillonite Complexes

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Federico Carosio

2018-06-01

Full Text Available Multilayered coatings deposited using the layer-by-layer (LbL assembly technique have attracted great interest in recent years as a sustainable and efficient solution for conferring flame retardant properties to fabrics. The unique structure and interaction established upon the coating assembly are the key factors for successful flame retardant properties. In this study we aimed at the deposition of multilayered coatings comprising chitosan and montmorillonite with a LbL-like structure and interactions by the simple processing of compacted chitosan/montmorillonite complexes obtained by the direct mixing of an oppositely charged solution/suspension. Upon drying, the prepared complex yielded a continuous coating characterized by a brick-and-mortar multi-layered structure, in which oriented clay nanoplatelets were held together by a continuous chitosan matrix. When deposited on acrylic fabrics these coatings were able to suppress the melt-dripping phenomenon, and at 10 and 20% add-ons achieved self-extinguishing behavior within a few seconds after ignition. Cone calorimetry testing revealed an increase in time to ignition (up to +46% and considerable reductions of the rates at which heat is released (up to −62 and −49% for peak of heat release rate and total heat release, respectively. A reduction in the total smoke release (up to −49% was also observed.

Coat/Tether Interactions—Exception or Rule?

Science.gov (United States)

Schröter, Saskia; Beckmann, Sabrina; Schmitt, Hans Dieter

2016-01-01

Coat complexes are important for cargo selection and vesicle formation. Recent evidence suggests that they may also be involved in vesicle targeting. Tethering factors, which form an initial bridge between vesicles and the target membrane, may bind to coat complexes. In this review, we ask whether these coat/tether interactions share some common mechanisms, or whether they are special adaptations to the needs of very specific transport steps. We compare recent findings in two multisubunit tethering complexes, the Dsl1 complex and the HOPS complex, and put them into context with the TRAPP I complex as a prominent example for coat/tether interactions. We explore where coat/tether interactions are found, compare their function and structure, and comment on a possible evolution from a common ancestor of coats and tethers. PMID:27243008

Coat/Tether Interactions-Exception or Rule?

Science.gov (United States)

Schroeter, Saskia; Beckmann, Sabrina; Schmitt, Hans Dieter

2016-01-01

Coat complexes are important for cargo selection and vesicle formation. Recent evidence suggests that they may also be involved in vesicle targeting. Tethering factors, which form an initial bridge between vesicles and the target membrane, may bind to coat complexes. In this review, we ask whether these coat/tether interactions share some common mechanisms, or whether they are special adaptations to the needs of very specific transport steps. We compare recent findings in two multisubunit tethering complexes, the Dsl1 complex and the HOPS complex, and put them into context with the TRAPP I complex as a prominent example for coat/tether interactions. We explore where coat/tether interactions are found, compare their function and structure, and comment on a possible evolution from a common ancestor of coats and tethers.

Exome Sequencing of Bilateral Testicular Germ Cell Tumors Suggests Independent Development Lineages

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Sigmund Brabrand

2015-02-01

Full Text Available Intratubular germ cell neoplasia, the precursor of testicular germ cell tumors (TGCTs, is hypothesized to arise during embryogenesis from developmentally arrested primordial germ cells (PGCs or gonocytes. In early embryonal life, the PGCs migrate from the yolk sac to the dorsal body wall where the cell population separates before colonizing the genital ridges. However, whether the malignant transformation takes place before or after this separation is controversial. We have explored the somatic exome-wide mutational spectra of bilateral TGCT to provide novel insight into the in utero critical time frame of malignant transformation and TGCT pathogenesis. Exome sequencing was performed in five patients with bilateral TGCT (eight tumors, of these three patients in whom both tumors were available (six tumors and two patients each with only one available tumor (two tumors. Selected loci were explored by Sanger sequencing in 71 patients with bilateral TGCT. From the exome-wide mutational spectra, no identical mutations in any of the three bilateral tumor pairs were identified. Exome sequencing of all eight tumors revealed 87 somatic non-synonymous mutations (median 10 per tumor; range 5-21, some in already known cancer genes such as CIITA, NEB, platelet-derived growth factor receptor α (PDGFRA, and WHSC1. SUPT6H was found recurrently mutated in two tumors. We suggest independent development lineages of bilateral TGCT. Thus, malignant transformation into intratubular germ cell neoplasia is likely to occur after the migration of PGCs. We reveal possible drivers of TGCT pathogenesis, such as mutated PDGFRA, potentially with therapeutic implications for TGCT patients.

Genetic variation in an individual human exome.

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Pauline C Ng

2008-08-01

Full Text Available There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized genomics. We focus here on the variants in a person's 'exome,' which is the set of exons in a genome, because the exome is believed to harbor much of the functional variation. We provide an analysis of the approximately 12,500 variants that affect the protein coding portion of an individual's genome. We identified approximately 10,400 nonsynonymous single nucleotide polymorphisms (nsSNPs in this individual, of which approximately 15-20% are rare in the human population. We predict approximately 1,500 nsSNPs affect protein function and these tend be heterozygous, rare, or novel. Of the approximately 700 coding indels, approximately half tend to have lengths that are a multiple of three, which causes insertions/deletions of amino acids in the corresponding protein, rather than introducing frameshifts. Coding indels also occur frequently at the termini of genes, so even if an indel causes a frameshift, an alternative start or stop site in the gene can still be used to make a functional protein. In summary, we reduced the set of approximately 12,500 nonsilent coding variants by approximately 8-fold to a set of variants that are most likely to have major effects on their proteins' functions. This is our first glimpse of an individual's exome and a snapshot of the current state of personalized genomics. The majority of coding variants in this individual are common and appear to be functionally neutral. Our results also indicate that some variants can be used to improve the current NCBI human reference genome. As more genomes are sequenced, many rare variants and non-SNP variants will be discovered. We present an approach to analyze the coding variation in humans by proposing multiple bioinformatic methods to hone in on possible functional variation.

[Identification of novel pathogenic gene mutations in pediatric acute myeloid leukemia by whole-exome resequencing].

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Shiba, Norio

2015-12-01

A new class of gene mutations, identified in the pathogenesis of adult acute myeloid leukemia (AML), includes DNMT3A, IDH1/2, TET2 and EZH2. However, these mutations are rare in pediatric AML cases, indicating that pathogeneses differ between adult and pediatric forms of AML. Meanwhile, the recent development of massively parallel sequencing technologies has provided a new opportunity to discover genetic changes across entire genomes or proteincoding sequences. In order to reveal a complete registry of gene mutations, we performed whole exome resequencing of paired tumor-normal specimens from 19 pediatric AML cases using Illumina HiSeq 2000. In total, 80 somatic mutations or 4.2 mutations per sample were identified. Many of the recurrent mutations identified in this study involved previously reported targets in AML, such as FLT3, CEBPA, KIT, CBL, NRAS, WT1 and EZH2. On the other hand, several genes were newly identified in the current study, including BCORL1 and major cohesin components such as SMC3 and RAD21. Whole exome resequencing revealed a complex array of gene mutations in pediatric AML genomes. Our results indicate that a subset of pediatric AML represents a discrete entity that could be discriminated from its adult counterpart, in terms of the spectrum of gene mutations.

Whole-exome sequencing for diagnosis of hereditary ichthyosis.

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Sitek, J C; Kulseth, M A; Rypdal, K B; Skodje, T; Sheng, Y; Retterstøl, L

2018-02-14

Hereditary ichthyosis constitutes a diverse group of cornification disorders. Identification of the molecular cause facilitates optimal patient care. We wanted to estimate the diagnostic yield of applying whole-exome sequencing (WES) in the routine genetic workup of inherited ichthyosis. During a 3-year-period, all ichthyosis patients, except X-linked and mild vulgar ichthyosis, consecutively admitted to a university hospital clinic were offered WES with subsequent analysis of ichthyosis-related genes as a first-line genetic investigation. Clinical and molecular data have been collected retrospectively. Genetic variants causative for the ichthyosis were identified in 27 of 34 investigated patients (79.4%). In all, 31 causative mutations across 13 genes were disclosed, including 12 novel variants. TGM1 was the most frequently mutated gene, accounting for 43.7% of patients suffering from autosomal recessive congenital ichthyosis (ARCI). Whole-exome sequencing appears an effective tool in disclosing the molecular cause of patients with hereditary ichthyosis seen in clinical practice and should be considered a first-tier genetic test in these patients. © 2018 European Academy of Dermatology and Venereology.

Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies.

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Peter K Joshi

Full Text Available The analysis of less common variants in genome-wide association studies promises to elucidate complex trait genetics but is hampered by low power to reliably detect association. We show that addition of population-specific exome sequence data to global reference data allows more accurate imputation, particularly of less common SNPs (minor allele frequency 1-10% in two very different European populations. The imputation improvement corresponds to an increase in effective sample size of 28-38%, for SNPs with a minor allele frequency in the range 1-3%.

Exome sequencing of bilateral testicular germ cell tumors suggests independent development lineages.

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Brabrand, Sigmund; Johannessen, Bjarne; Axcrona, Ulrika; Kraggerud, Sigrid M; Berg, Kaja G; Bakken, Anne C; Bruun, Jarle; Fosså, Sophie D; Lothe, Ragnhild A; Lehne, Gustav; Skotheim, Rolf I

2015-02-01

Intratubular germ cell neoplasia, the precursor of testicular germ cell tumors (TGCTs), is hypothesized to arise during embryogenesis from developmentally arrested primordial germ cells (PGCs) or gonocytes. In early embryonal life, the PGCs migrate from the yolk sac to the dorsal body wall where the cell population separates before colonizing the genital ridges. However, whether the malignant transformation takes place before or after this separation is controversial. We have explored the somatic exome-wide mutational spectra of bilateral TGCT to provide novel insight into the in utero critical time frame of malignant transformation and TGCT pathogenesis. Exome sequencing was performed in five patients with bilateral TGCT (eight tumors), of these three patients in whom both tumors were available (six tumors) and two patients each with only one available tumor (two tumors). Selected loci were explored by Sanger sequencing in 71 patients with bilateral TGCT. From the exome-wide mutational spectra, no identical mutations in any of the three bilateral tumor pairs were identified. Exome sequencing of all eight tumors revealed 87 somatic non-synonymous mutations (median 10 per tumor; range 5-21), some in already known cancer genes such as CIITA, NEB, platelet-derived growth factor receptor α (PDGFRA), and WHSC1. SUPT6H was found recurrently mutated in two tumors. We suggest independent development lineages of bilateral TGCT. Thus, malignant transformation into intratubular germ cell neoplasia is likely to occur after the migration of PGCs. We reveal possible drivers of TGCT pathogenesis, such as mutated PDGFRA, potentially with therapeutic implications for TGCT patients. Copyright © 2014 Neoplasia Press, Inc. Published by Elsevier Inc. All rights reserved.

Sequencing of 50 human exomes reveals adaptation to high altitude

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Yi, Xin; Liang, Yu; Huerta-Sanchez, Emilia

2010-01-01

Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which repres...... in genetic adaptation to high altitude.......Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which...... represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency...

Coat/tether interactions – exceptions or rule?

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Saskia eSchroeter

2016-05-01

Full Text Available Coat complexes are important for cargo selection and vesicle formation. Recent evidence suggests that they may also be involved in vesicle targeting. Tethering factors, which form an initial bridge between vesicles and the target membrane, may bind to coat complexes. In this review, we ask whether these coat/tether interactions share some common mechanisms, or whether they are special adaptations to the needs of very specific transport steps. We compare recent findings in two multisubunit tethering complexes, the Dsl1 complex and the HOPS complex, and put them into context with the TRAPP I complex as a prominent example for coat/tether interactions. We explore where coat/tether interactions are found, compare their function and structure, and comment on a possible evolution from a common ancestor of coats and tethers.

High prevalence of genetic variants previously associated with Brugada syndrome in new exome data

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Risgaard, B; Jabbari, R; Refsgaard, L

2013-01-01

More than 300 variants in 12 genes have been associated with Brugada syndrome (BrS) which has a prevalence ranging between 1:2000 and 1:100,000. Until recently, there has been little knowledge regarding the distribution of genetic variations in the general population. This problem was partly solved......, when exome data from the NHLI GO Exome Sequencing Project (ESP) was published. In this study, we aimed to report the prevalence of previously BrS-associated variants in the ESP population. We performed a search in ESP for variants previously associated with BrS. In addition, four variants in ESP were...... to a surprisingly high genotype prevalence of 1:23 (274:6258). Genotyping the four common ESP-derived variants CACNA2D1 S709N, SCN5A F2004L, CACNB2 S143F, and CACNB2 T450I in the Danish controls, we found a genotype prevalence comparable with that found in ESP. We suggest that exome data are used in research...

Rapid-Onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD): exome sequencing of trios, monozygotic twins and tumours.

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Barclay, Sarah F; Rand, Casey M; Borch, Lauren A; Nguyen, Lisa; Gray, Paul A; Gibson, William T; Wilson, Richard J A; Gordon, Paul M K; Aung, Zaw; Berry-Kravis, Elizabeth M; Ize-Ludlow, Diego; Weese-Mayer, Debra E; Bech-Hansen, N Torben

2015-08-25

Rapid-onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD) is thought to be a genetic disease caused by de novo mutations, though causative mutations have yet to be identified. We searched for de novo coding mutations among a carefully-diagnosed and clinically homogeneous cohort of 35 ROHHAD patients. We sequenced the exomes of seven ROHHAD trios, plus tumours from four of these patients and the unaffected monozygotic (MZ) twin of one (discovery cohort), to identify constitutional and somatic de novo sequence variants. We further analyzed this exome data to search for candidate genes under autosomal dominant and recessive models, and to identify structural variations. Candidate genes were tested by exome or Sanger sequencing in a replication cohort of 28 ROHHAD singletons. The analysis of the trio-based exomes found 13 de novo variants. However, no two patients had de novo variants in the same gene, and additional patient exomes and mutation analysis in the replication cohort did not provide strong genetic evidence to implicate any of these sequence variants in ROHHAD. Somatic comparisons revealed no coding differences between any blood and tumour samples, or between the two discordant MZ twins. Neither autosomal dominant nor recessive analysis yielded candidate genes for ROHHAD, and we did not identify any potentially causative structural variations. Clinical exome sequencing is highly unlikely to be a useful diagnostic test in patients with true ROHHAD. As ROHHAD has a high risk for fatality if not properly managed, it remains imperative to expand the search for non-exomic genetic risk factors, as well as to investigate other possible mechanisms of disease. In so doing, we will be able to confirm objectively the ROHHAD diagnosis and to contribute to our understanding of obesity, respiratory control, hypothalamic function, and autonomic regulation.

Identification of genetic defects in primary immunodeficiencies by whole exome sequencing

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Christiansen, Mette; Jensen, Jens Magnus Bernth; Veirum, Jens Erik

2014-01-01

to hypogammaglobulinaemia, and increased risk of both infections as well as cancer. We employed whole exome sequencing (WES) to identify mutations associated with primary immunodeficiency in severely affected children. We present WES data on 2 patients with severe immunodeficiency. WES was performed using TruSeq exome kit...... and severe infections including sepsis. Second, we identified compound heterozygote stopgain mutations in RAD52 and a heterozygote mutation in LRRC8A in a 7 year-old girl with T-cell deficiency, reduced T-cell mediated B-cell activity, hypogammaglobulinaemia, prolonged splenomegali and benign adenopathy. RAD......52 has not previously been linked to immunodeficiency and we are currently investigating the functional consequences. Knowledge of the mechanisms underlying immunodeficiencies is a prerequisite for understanding disease pathogenesis. WES allows the demonstration of immune defects that may result from...

Exome sequencing and the management of neurometabolic disorders

OpenAIRE

Tarailo-Graovac, Maja; Shyr, Casper; Ross, Colin J; Horvath, Gabriella A; Salvarinova, Ramona; Ye, Xin C; Zhang, Lin-Hua; Bhavsar, Amit P; Lee, Jessica J Y; Drögemöller, Britt I; Abdelsayed, Mena; Alfadhel, Majid; Armstrong, Linlea; Baumgartner, Matthias R; Burda, Patricie

2016-01-01

BACKGROUND: Whole-exome sequencing has transformed gene discovery and diagnosis in rare diseases. Translation into disease-modifying treatments is challenging, particularly for intellectual developmental disorder. However, the exception is inborn errors of metabolism, since many of these disorders are responsive to therapy that targets pathophysiological features at the molecular or cellular level. METHODS: To uncover the genetic basis of potentially treatable inborn errors of metabolism, ...

Exome Sequencing and the Management of Neurometabolic Disorders

OpenAIRE

Tarailo-Graovac, Maja; Shyr, Casper; Ross, Colin J; Horvath, Gabriella A; Salvarinova, Ramona; Ye, Xin C; Zhang, Lin-Hua; Bhavsar, Amit P; Lee, Jessica J Y; Drögemöller, Britt I; Abdelsayed, Mena; Alfadhel, Majid; Armstrong, Linlea; Baumgartner, Matthias R; Burda, Patricie

2016-01-01

BACKGROUND: Whole-exome sequencing has transformed gene discovery and diagnosis in rare diseases. Translation into disease-modifying treatments is challenging, particularly for intellectual developmental disorder. However, the exception is inborn errors of metabolism, since many of these disorders are responsive to therapy that targets pathophysiological features at the molecular or cellular level.METHODS: To uncover the genetic basis of potentially treatable inborn errors of metabolism, we c...

Exome sequencing in a breast canner family without BRCA mutation

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Noh, Jae Myoung; Choi, Doo Ho; Park, Won; Huh, Seung Jae [Dept. of Radiation Oncology, amsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Ji Hun; Cho, Dae Yeon [LabGenomics Clinical Research Institute, LabGenomics, Seongnam (Korea, Republic of)

2015-06-15

We performed exome sequencing in a breast cancer family without BRCA mutations. A family that three sisters have a history of breast cancer was selected for analysis. There were no family members with breast cancer in the previous generation. Genetic testing for BRCA mutation was negative, even by the multiplex ligation-dependent probe amplification method. Two sisters with breast cancer were selected as affected members, while the mother of the sisters was a non-affected member. Whole exome sequencing was performed on the HiSeq 2000 platform with paired-end reads of 101 bp in the three members. We identified 19,436, 19,468, and 19,345 single-nucleotide polymorphisms (SNPs) in the coding regions. Among them, 8,759, 8,789, and 8,772 were non-synonymous SNPs, respectively. After filtering out 12,843 synonymous variations and 12,105 known variations with indels found in the dbSNP135 or 1000 Genomes Project database, we selected 73 variations in the samples from the affected sisters that did not occur in the sample from the unaffected mother. Using the Sorting Intolerant From Tolerant (SIFT), PolyPhen-2, and MutationTaster algorithms to predict amino acid substitutions, the XCR1, DLL1, TH, ACCS, SPPL3, CCNF, and SRL genes were risky among all three algorithms, while definite candidate genes could not be conclusively determined. Using exome sequencing, we found 7 variants for a breast cancer family without BRCA mutations. Genetic evidence of disease association should be confirmed by future studies.

Identification of rare paired box 3 variant in strabismus by whole exome sequencing

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Hui-Min Gong

2017-08-01

Full Text Available AIM: To identify the potentially pathogenic gene variants that contributes to the etiology of strabismus. METHODS: A Chinese pedigree with strabismus was collected and the exomes of two affected individuals were sequenced using the next-generation sequencing technology. The resulting variants from exome sequencing were filtered by subsequent bioinformatics methods and the candidate mutation was verified as heterozygous in the affected proposita and her mother by sanger sequencing. RESULTS: Whole exome sequencing and filtering identified a nonsynonymous mutation c.434G-T transition in paired box 3 (PAX3 in the two affected individuals, which were predicted to be deleterious by more than 4 bioinformatics programs. This altered amino acid residue was located in the conserved PAX domain of PAX3. This gene encodes a member of the PAX family of transcription factors, which play critical roles during fetal development. Mutations in PAX3 were associated with Waardenburg syndrome with strabismus. CONCLUSION: Our results report that the c.434G-T mutation (p.R145L in PAX3 may contribute to strabismus, expanding our understanding of the causally relevant genes for this disorder.

Substrate-mediated delivery of gene complex nanoparticles via polydopamine coating for enhancing competitiveness of endothelial cells.

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Li, Bo-Chao; Chang, Hao; Ren, Ke-Feng; Ji, Jian

2016-11-01

Substrate-mediated delivery of functional plasmid DNA (pDNA) has been proven to be a promising strategy to promote competitiveness of endothelial cells (ECs) over smooth muscle cells (SMCs), which is beneficial to inducing fast endothelialization of implanted vascular devices. Thus, it is of great importance to develop universal approaches with simplicity and easiness to immobilize DNA complex nanoparticles on substrates. In this study, the bioinspired polydopamine (PDA) coating was employed in immobilization of DNA complex nanoparticles, which were composed of protamine (PrS) and plasmid DNA encoding with hepatocyte growth factor (HGF-pDNA) gene. We demonstrated that the DNA complex nanoparticles can be successfully immobilized onto the PDA surface. Consequently, the HGF expression of both ECs and SMCs were significantly improved when they cultured on the DNA complex nanoparticles-immobilized substrates. Furthermore, EC proliferation was specifically promoted due to bioactivity of HGF, leading to an enhancement of EC competitiveness over SMCs. Our findings demonstrated the substrate-mediated functional gene nanoparticle delivery through PDA coating as a simple and efficient approach. It may hold great potential in the field of interventional cardiovascular implants. Copyright © 2016 Elsevier B.V. All rights reserved.

Whole-exome sequencing reveals GPIHBP1 mutations in infantile colitis with severe hypertriglyceridemia.

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Gonzaga-Jauregui, Claudia; Mir, Sabina; Penney, Samantha; Jhangiani, Shalini; Midgen, Craig; Finegold, Milton; Muzny, Donna M; Wang, Min; Bacino, Carlos A; Gibbs, Richard A; Lupski, James R; Kellermayer, Richard; Hanchard, Neil A

2014-07-01

Severe congenital hypertriglyceridemia (HTG) is a rare disorder caused by mutations in genes affecting lipoprotein lipase (LPL) activity. Here we report a 5-week-old Hispanic girl with severe HTG (12,031 mg/dL, normal limit 150 mg/dL) who presented with the unusual combination of lower gastrointestinal bleeding and milky plasma. Initial colonoscopy was consistent with colitis, which resolved with reduction of triglycerides. After negative sequencing of the LPL gene, whole-exome sequencing revealed novel compound heterozygous mutations in GPIHBP1. Our study broadens the phenotype of GPIHBP1-associated HTG, reinforces the effectiveness of whole-exome sequencing in Mendelian diagnoses, and implicates triglycerides in gastrointestinal mucosal injury.

Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next-generation exome sequencing.

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Lalonde, Emilie; Albrecht, Steffen; Ha, Kevin C H; Jacob, Karine; Bolduc, Nathalie; Polychronakos, Constantin; Dechelotte, Pierre; Majewski, Jacek; Jabado, Nada

2010-08-01

Protein coding genes constitute approximately 1% of the human genome but harbor 85% of the mutations with large effects on disease-related traits. Therefore, efficient strategies for selectively sequencing complete coding regions (i.e., "whole exome") have the potential to contribute our understanding of human diseases. We used a method for whole-exome sequencing coupling Agilent whole-exome capture to the Illumina DNA-sequencing platform, and investigated two unrelated fetuses from nonconsanguineous families with Fowler Syndrome (FS), a stereotyped phenotype lethal disease. We report novel germline mutations in feline leukemia virus subgroup C cellular-receptor-family member 2, FLVCR2, which has recently been shown to cause FS. Using this technology, we identified three types of genetic abnormalities: point-mutations, insertions-deletions, and intronic splice-site changes (first pathogenic report using this technology), in the fetuses who both were compound heterozygotes for the disease. Although revealing a high level of allelic heterogeneity and mutational spectrum in FS, this study further illustrates the successful application of whole-exome sequencing to uncover genetic defects in rare Mendelian disorders. Of importance, we show that we can identify genes underlying rare, monogenic and recessive diseases using a limited number of patients (n=2), in the absence of shared genetic heritage and in the presence of allelic heterogeneity.

New population-based exome data are questioning the pathogenicity of previously cardiomyopathy-associated genetic variants

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Andreasen, Charlotte Hartig; Nielsen, Jonas B; Refsgaard, Lena

2013-01-01

Cardiomyopathies are a heterogeneous group of diseases with various etiologies. We focused on three genetically determined cardiomyopathies: hypertrophic (HCM), dilated (DCM), and arrhythmogenic right ventricular cardiomyopathy (ARVC). Eighty-four genes have so far been associated with these card......Cardiomyopathies are a heterogeneous group of diseases with various etiologies. We focused on three genetically determined cardiomyopathies: hypertrophic (HCM), dilated (DCM), and arrhythmogenic right ventricular cardiomyopathy (ARVC). Eighty-four genes have so far been associated...... with these cardiomyopathies, but the disease-causing effect of reported variants is often dubious. In order to identify possible false-positive variants, we investigated the prevalence of previously reported cardiomyopathy-associated variants in recently published exome data. We searched for reported missense and nonsense...... variants in the NHLBI-Go Exome Sequencing Project (ESP) containing exome data from 6500 individuals. In ESP, we identified 94 variants out of 687 (14%) variants previously associated with HCM, 58 out of 337 (17%) variants associated with DCM, and 38 variants out of 209 (18%) associated with ARVC...

Whole-exome sequencing as a diagnostic tool for distal renal tubular acidosis

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Paula Cristina Barros Pereira

2015-11-01

Full Text Available Objective: Distal renal tubular acidosis (dRTA is characterized by metabolic acidosis due to impaired renal acid excretion. The aim of this study was to demonstrate the genetic diagnosis of four children with dRTA through use of whole-exome sequencing. Methods: Two unrelated families were selected; a total of four children with dRTA and their parents, in order to perform whole-exome sequencing. Hearing was preserved in both children from the first family, but not in the second, wherein a twin pair had severe deafness. Whole-exome sequencing was performed in two pooled samples and findings were confirmed with Sanger sequencing method. Results: Two mutations were identified in the ATP6V0A4 and ATP6V1B1 genes. In the first family, a novel mutation in the exon 13 of the ATP6V0A4 gene with a single nucleotide change GAC → TAC (c.1232G>T was found, which caused a substitution of aspartic acid to tyrosine in position 411. In the second family, a homozygous recurrent mutation with one base-pair insertion (c.1149_1155insC in exon 12 of the ATP6V1B1 gene was detected. Conclusion: These results confirm the value of whole-exome sequencing for the study of rare and complex genetic nephropathies, allowing the identification of novel and recurrent mutations. Furthermore, for the first time the application of this molecular method in renal tubular diseases has been clearly demonstrated. Resumo: Objetivo: A acidose tubular renal distal (ATRd é caracterizada por acidose metabólica devido a excreção renal de ácido prejudicada. O objetivo deste artigo é apresentar o diagnóstico genético de quatro crianças com ATRd utilizando o sequenciamento total do exoma. Métodos: Selecionamos duas famílias não relacionadas, totalizando quatro crianças com ATRd e seus pais, para realizar o sequenciamento total do exoma. A audição foi preservada em ambas as crianças da família um, porém em nenhuma criança da família dois, na qual um par de gêmeas teve

Identification of TP53 as an Acute Lymphocytic Leukemia Susceptibility Gene Through Exome Sequencing

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Powell, Bradford C.; Jiang, Lichun; Muzny, Donna M.; Treviño, Lisa R.; Dreyer, ZoAnn E.; Strong, Louise C.; Wheeler, David A.; Gibbs, Richard A.; Plon, Sharon E.

2014-01-01

Although acute lymphocytic leukemia (ALL) is the most common childhood cancer, genetic predisposition to ALL remains poorly understood. Whole-exome sequencing was performed in an extended kindred in which five individuals had been diagnosed with leukemia. Analysis revealed a nonsense variant of TP53 which has been previously reported in families with sarcomas and other typical Li Fraumeni syndrome-associated cancers but never in a familial leukemia kindred. This unexpected finding enabled identification of an appropriate sibling bone marrow donor and illustrates that exome sequencing will reveal atypical clinical presentations of even well-studied genes. PMID:23255406

Exome sequencing generates high quality data in non-target regions

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Guo Yan

2012-05-01

Full Text Available Abstract Background Exome sequencing using next-generation sequencing technologies is a cost efficient approach to selectively sequencing coding regions of human genome for detection of disease variants. A significant amount of DNA fragments from the capture process fall outside target regions, and sequence data for positions outside target regions have been mostly ignored after alignment. Result We performed whole exome sequencing on 22 subjects using Agilent SureSelect capture reagent and 6 subjects using Illumina TrueSeq capture reagent. We also downloaded sequencing data for 6 subjects from the 1000 Genomes Project Pilot 3 study. Using these data, we examined the quality of SNPs detected outside target regions by computing consistency rate with genotypes obtained from SNP chips or the Hapmap database, transition-transversion (Ti/Tv ratio, and percentage of SNPs inside dbSNP. For all three platforms, we obtained high-quality SNPs outside target regions, and some far from target regions. In our Agilent SureSelect data, we obtained 84,049 high-quality SNPs outside target regions compared to 65,231 SNPs inside target regions (a 129% increase. For our Illumina TrueSeq data, we obtained 222,171 high-quality SNPs outside target regions compared to 95,818 SNPs inside target regions (a 232% increase. For the data from the 1000 Genomes Project, we obtained 7,139 high-quality SNPs outside target regions compared to 1,548 SNPs inside target regions (a 461% increase. Conclusions These results demonstrate that a significant amount of high quality genotypes outside target regions can be obtained from exome sequencing data. These data should not be ignored in genetic epidemiology studies.

Exome sequencing in 32 patients with anophthalmia/microphthalmia and developmental eye defects.

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Slavotinek, A M; Garcia, S T; Chandratillake, G; Bardakjian, T; Ullah, E; Wu, D; Umeda, K; Lao, R; Tang, P L-F; Wan, E; Madireddy, L; Lyalina, S; Mendelsohn, B A; Dugan, S; Tirch, J; Tischler, R; Harris, J; Clark, M J; Chervitz, S; Patwardhan, A; West, J M; Ursell, P; de Alba Campomanes, A; Schneider, A; Kwok, P-Y; Baranzini, S; Chen, R O

2015-11-01

Anophthalmia/microphthalmia (A/M) is a genetically heterogeneous birth defect for which the etiology is unknown in more than 50% of patients. We used exome sequencing with the ACE Exome(TM) (Personalis, Inc; 18 cases) and UCSF Genomics Core (21 cases) to sequence 28 patients with A/M and four patients with varied developmental eye defects. In the 28 patients with A/M, we identified de novo mutations in three patients (OTX2, p.(Gln91His), RARB, p.Arg387Cys and GDF6, p.Ala249Glu) and inherited mutations in STRA6 in two patients. In patients with developmental eye defects, a female with cataracts and cardiomyopathy had a de novo COL4A1 mutation, p.(Gly773Arg), expanding the phenotype associated with COL4A1 to include cardiomyopathy. A male with a chorioretinal defect, microcephaly, seizures and sensorineural deafness had two PNPT1 mutations, p.(Ala507Ser) and c.401-1G>A, and we describe eye defects associated with this gene for the first time. Exome sequencing was efficient for identifying mutations in pathogenic genes for which there is no clinical testing available and for identifying cases that expand phenotypic spectra, such as the PNPT1 and COL4A1-associated disorders described here. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Identification of Heterozygous Single- and Multi-exon Deletions in IL7R by Whole Exome Sequencing.

OpenAIRE

Engelhardt, Karin R; Xu, Yaobo; Grainger, Angela; Germani Batacchi, Mila G C; Swan, David J; Willet, Joseph D P; Abd Hamid, Intan J; Agyeman, Philipp; Barge, Dawn; Bibi, Shahnaz; Jenkins, Lucy; Flood, Terence J; Abinun, Mario; Slatter, Mary A; Gennery, Andrew R

2017-01-01

Purpose We aimed to achieve a retrospective molecular diagnosis by applying state-of-the-art genomic sequencing methods to past patients with T-B+NK+ severe combined immunodeficiency (SCID). We included identification of copy number variations (CNVs) by whole exome sequencing (WES) using the CNV calling method ExomeDepth to detect gene alterations for which routine Sanger sequencing analysis is not suitable, such as large heterozygous deletions. Methods Of a total of 12 undiagnosed patients w...

An Observational Study of Children's Involvement in Informed Consent for Exome Sequencing Research.

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Miller, Victoria A; Werner-Lin, Allison; Walser, Sarah A; Biswas, Sawona; Bernhardt, Barbara A

2017-02-01

The goal of this study was to examine children's involvement in consent sessions for exome sequencing research and associations of involvement with provider and parent communication. Participants included 44 children (8-17 years) from five cohorts who were offered participation in an exome sequencing study. The consent sessions were audiotaped, transcribed, and coded. Providers attempted to facilitate the child's involvement in the majority (73%) of sessions, and most (75%) children also verbally participated. Provider facilitation was strongly associated with likelihood of child participation. These findings underscore that strategies such as asking for children's opinions and soliciting their questions show respect for children and may increase the likelihood that they are engaged and involved in decisions about research participation.

Exome sequencing identifies mutations in ABCD1 and DACH2 in two brothers with a distinct phenotype

OpenAIRE

Zhang, Yanliang; Liu, Yanhui; Li, Ya; Duan, Yong; Zhang, Keyun; Wang, Junwang; Dai, Yong

2014-01-01

Background We report on two brothers with a distinct syndromic phenotype and explore the potential pathogenic cause. Methods Cytogenetic tests and exome sequencing were performed on the two brothers and their parents. Variants detected by exome sequencing were validated by Sanger sequencing. Results The main phenotype of the two brothers included congenital language disorder, growth retardation, intellectual disability, difficulty in standing and walking, and urinary and fecal incontinence. T...

Whole Exome Analysis of Early Onset Alzheimer’s Disease

Science.gov (United States)

2015-04-01

SA, Shan X, Jones BA, Zhao G, Woodward ML, Li X, Zhu Y, McEachern EJ, Silverman MA, Watson NV, Gong CX, Vocadlo DJ1. Pharmacological inhibition of O...ADGC) genotyped on the exome chip, which included 195,039 variants with MAFɚ%. Enrichment analysis of the variant list was conducted using DAVID

Exome Sequencing Identifies Potential Risk Variants for Mendelian Disorders at High Prevalence in Qatar

Science.gov (United States)

Rodriguez-Flores, Juan L.; Fakhro, Khalid; Hackett, Neil R.; Salit, Jacqueline; Fuller, Jennifer; Agosto-Perez, Francisco; Gharbiah, Maey; Malek, Joel A.; Zirie, Mahmoud; Jayyousi, Amin; Badii, Ramin; Al-Marri, Ajayeb Al-Nabet; Chouchane, Lotfi; Stadler, Dora J.; Hunter-Zinck, Haley; Mezey, Jason G.; Crystal, Ronald G.

2013-01-01

Exome sequencing of families of related individuals has been highly successful in identifying genetic polymorphisms responsible for Mendelian disorders. Here, we demonstrate the value of the reverse approach, where we use exome sequencing of a sample of unrelated individuals to analyze allele frequencies of known causal mutations for Mendelian diseases. We sequenced the exomes of 100 individuals representing the three major genetic subgroups of the Qatari population (Q1 Bedouin, Q2 Persian-South Asian, Q3 African) and identified 37 variants in 33 genes with effects on 36 clinically significant Mendelian diseases. These include variants not present in 1000 Genomes and variants at high frequency when compared to 1000 Genomes populations. Several of these Mendelian variants were only segregating in one Qatari subpopulation, where the observed subpopulation specificity trends were confirmed in an independent population of 386 Qataris. Pre-marital genetic screening in Qatar tests for only 4 out of the 37, such that this study provides a set of Mendelian disease variants with potential impact on the epidemiological profile of the population that could be incorporated into the testing program if further experimental and clinical characterization confirms high penetrance. PMID:24123366

Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways

NARCIS (Netherlands)

Cirulli, Elizabeth T.; Lasseigne, Brittany N.; Petrovski, Slavé; Sapp, Peter C.; Dion, Patrick A.; Leblond, Claire S.; Couthouis, Julien; Lu, Yi-Fan; Wang, Quanli; Krueger, Brian J.; Ren, Zhong; Keebler, Jonathan; Han, Yujun; Levy, Shawn E.; Boone, Braden E.; Wimbish, Jack R.; Waite, Lindsay L.; Jones, Angela L.; Carulli, John P.; Day-Williams, Aaron G.; Staropoli, John F.; Xin, Winnie W.; Chesi, Alessandra; Raphael, Alya R.; McKenna-Yasek, Diane; Cady, Janet; de Jong, J. M. B. Vianney; Kenna, Kevin P.; Smith, Bradley N.; Topp, Simon; Miller, Jack; Gkazi, Athina; Al-Chalabi, Ammar; van den Berg, Leonard H.; Veldink, Jan; Silani, Vincenzo; Ticozzi, Nicola; Shaw, Christopher E.; Baloh, Robert H.; Appel, Stanley; Simpson, Ericka; Lagier-Tourenne, Clotilde; Pulst, Stefan M.; Gibson, Summer; Trojanowski, John Q.; Elman, Lauren; McCluskey, Leo; Grossman, Murray; Baas, Frank; ten Asbroek, Anneloor L. M. A.

2015-01-01

Amyotrophic lateral sclerosis (ALS) is a devastating neurological disease with no effective treatment. We report the results of a moderate-scale sequencing study aimed at increasing the number of genes known to contribute to predisposition for ALS. We performed whole-exome sequencing of 2869 ALS

Potentially Treatable Disorder Diagnosed Post Mortem by Exome Analysis in a Boy with Respiratory Distress

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Valentina Imperatore

2016-02-01

Full Text Available We highlight the importance of exome sequencing in solving a clinical case of a child who died at 14 months after a series of respiratory crises. He was the half-brother of a girl diagnosed at 7 years with the early-onset seizure variant of Rett syndrome due to CDKL5 mutation. We performed a test for CDKL5 in the boy, which came back negative. Driven by the mother’s compelling need for a diagnosis, we moved forward performing whole exome sequencing analysis. Surprisingly, two missense mutations in compound heterozygosity were identified in the RAPSN gene encoding a receptor-associated protein with a key role in clustering and anchoring nicotinic acetylcholine receptors at synaptic sites. This gene is responsible for a congenital form of myasthenic syndrome, a disease potentially treatable with cholinesterase inhibitors. Therefore, an earlier diagnosis in this boy would have led to a better clinical management and prognosis. Our study supports the key role of exome sequencing in achieving a definite diagnosis in severe perinatal diseases, an essential step especially when a specific therapy is available.

A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea.

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Bajaj, Deepak; Das, Shouvik; Upadhyaya, Hari D; Ranjan, Rajeev; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C L Laxmipathi; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

2015-01-01

The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.

Exome Sequencing Fails to Identify the Genetic Cause of Aicardi Syndrome

DEFF Research Database (Denmark)

Lund, Caroline; Striano, Pasquale; Sorte, Hanne Sørmo

2016-01-01

Aicardi syndrome (AS) is a well-characterized neurodevelopmental disorder with an unknown etiology. In this study, we performed whole-exome sequencing in 11 female patients with the diagnosis of AS, in order to identify the disease-causing gene. In particular, we focused on detecting variants in ...

Exome-wide association study of endometrial cancer in a multiethnic population.

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Maxine M Chen

Full Text Available Endometrial cancer (EC contributes substantially to total burden of cancer morbidity and mortality in the United States. Family history is a known risk factor for EC, thus genetic factors may play a role in EC pathogenesis. Three previous genome-wide association studies (GWAS have found only one locus associated with EC, suggesting that common variants with large effects may not contribute greatly to EC risk. Alternatively, we hypothesize that rare variants may contribute to EC risk. We conducted an exome-wide association study (EXWAS of EC using the Infinium HumanExome BeadChip in order to identify rare variants associated with EC risk. We successfully genotyped 177,139 variants in a multiethnic population of 1,055 cases and 1,778 controls from four studies that were part of the Epidemiology of Endometrial Cancer Consortium (E2C2. No variants reached global significance in the study, suggesting that more power is needed to detect modest associations between rare genetic variants and risk of EC.

Three-dimensional blade coating of complex fluid

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Singh, Vachitar; Grimaldi, Emma; Sauret, Alban; Dressaire, Emilie

2015-11-01

The application of a layer of non-newtonian fluid on a solid substrate is an important industrial problem involved in polymer or paint coatings, and an everyday life challenge when it comes to spreading peanut butter on a toast. Most experimental and theoretical work has focused on the two-dimensional situation, i.e. the scraping of a fixed blade on a moving substrate to turn a thick layer of liquid into a thin coat. However the spreading of a finite volume of non-newtonian fluid using a blade has received less attention, despite significant practical and fundamental implications. In this study, we investigate experimentally the spreading of a finite volume of a model non-newtonian fluid, carbopol, initially deposited against the fixed blade. As the substrate is translated at constant speed, we characterize the dynamics of spreading and the final shape of the coated layer. We measure and rationalize the influence of the liquid volume, the height and orientation of the blade, and the speed of the substrate on the spreading.

Molecular genetics of the Usher syndrome in Lebanon: identification of 11 novel protein truncating mutations by whole exome sequencing.

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Reddy, Ramesh; Fahiminiya, Somayyeh; El Zir, Elie; Mansour, Ahmad; Megarbane, Andre; Majewski, Jacek; Slim, Rima

2014-01-01

Usher syndrome (USH) is a genetically heterogeneous condition with ten disease-causing genes. The spectrum of genes and mutations causing USH in the Lebanese and Middle Eastern populations has not been described. Consequently, diagnostic approaches designed to screen for previously reported mutations were unlikely to identify the mutations in 11 unrelated families, eight of Lebanese and three of Middle Eastern origins. In addition, six of the ten USH genes consist of more than 20 exons, each, which made mutational analysis by Sanger sequencing of PCR-amplified exons from genomic DNA tedious and costly. The study was aimed at the identification of USH causing genes and mutations in 11 unrelated families with USH type I or II. Whole exome sequencing followed by expanded familial validation by Sanger sequencing. We identified disease-causing mutations in all the analyzed patients in four USH genes, MYO7A, USH2A, GPR98 and CDH23. Eleven of the mutations were novel and protein truncating, including a complex rearrangement in GPR98. Our data highlight the genetic diversity of Usher syndrome in the Lebanese population and the time and cost-effectiveness of whole exome sequencing approach for mutation analysis of genetically heterogeneous conditions caused by large genes.

Molecular genetics of the Usher syndrome in Lebanon: identification of 11 novel protein truncating mutations by whole exome sequencing.

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Ramesh Reddy

Full Text Available Usher syndrome (USH is a genetically heterogeneous condition with ten disease-causing genes. The spectrum of genes and mutations causing USH in the Lebanese and Middle Eastern populations has not been described. Consequently, diagnostic approaches designed to screen for previously reported mutations were unlikely to identify the mutations in 11 unrelated families, eight of Lebanese and three of Middle Eastern origins. In addition, six of the ten USH genes consist of more than 20 exons, each, which made mutational analysis by Sanger sequencing of PCR-amplified exons from genomic DNA tedious and costly. The study was aimed at the identification of USH causing genes and mutations in 11 unrelated families with USH type I or II.Whole exome sequencing followed by expanded familial validation by Sanger sequencing.We identified disease-causing mutations in all the analyzed patients in four USH genes, MYO7A, USH2A, GPR98 and CDH23. Eleven of the mutations were novel and protein truncating, including a complex rearrangement in GPR98.Our data highlight the genetic diversity of Usher syndrome in the Lebanese population and the time and cost-effectiveness of whole exome sequencing approach for mutation analysis of genetically heterogeneous conditions caused by large genes.

Molecular Genetics of the Usher Syndrome in Lebanon: Identification of 11 Novel Protein Truncating Mutations by Whole Exome Sequencing

Science.gov (United States)

Reddy, Ramesh; Fahiminiya, Somayyeh; El Zir, Elie; Mansour, Ahmad; Megarbane, Andre; Majewski, Jacek; Slim, Rima

2014-01-01

Background Usher syndrome (USH) is a genetically heterogeneous condition with ten disease-causing genes. The spectrum of genes and mutations causing USH in the Lebanese and Middle Eastern populations has not been described. Consequently, diagnostic approaches designed to screen for previously reported mutations were unlikely to identify the mutations in 11 unrelated families, eight of Lebanese and three of Middle Eastern origins. In addition, six of the ten USH genes consist of more than 20 exons, each, which made mutational analysis by Sanger sequencing of PCR-amplified exons from genomic DNA tedious and costly. The study was aimed at the identification of USH causing genes and mutations in 11 unrelated families with USH type I or II. Methods Whole exome sequencing followed by expanded familial validation by Sanger sequencing. Results We identified disease-causing mutations in all the analyzed patients in four USH genes, MYO7A, USH2A, GPR98 and CDH23. Eleven of the mutations were novel and protein truncating, including a complex rearrangement in GPR98. Conclusion Our data highlight the genetic diversity of Usher syndrome in the Lebanese population and the time and cost-effectiveness of whole exome sequencing approach for mutation analysis of genetically heterogeneous conditions caused by large genes. PMID:25211151

Few single nucleotide variations in exomes of human cord blood induced pluripotent stem cells.

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Rui-Jun Su

Full Text Available The effect of the cellular reprogramming process per se on mutation load remains unclear. To address this issue, we performed whole exome sequencing analysis of induced pluripotent stem cells (iPSCs reprogrammed from human cord blood (CB CD34(+ cells. Cells from a single donor and improved lentiviral vectors for high-efficiency (2-14% reprogramming were used to examine the effects of three different combinations of reprogramming factors: OCT4 and SOX2 (OS, OS and ZSCAN4 (OSZ, OS and MYC and KLF4 (OSMK. Five clones from each group were subject to whole exome sequencing analysis. We identified 14, 11, and 9 single nucleotide variations (SNVs, in exomes, including untranslated regions (UTR, in the five clones of OSMK, OS, and OSZ iPSC lines. Only 8, 7, and 4 of these, respectively, were protein-coding mutations. An average of 1.3 coding mutations per CB iPSC line is remarkably lower than previous studies using fibroblasts and low-efficiency reprogramming approaches. These data demonstrate that point nucleotide mutations during cord blood reprogramming are negligible and that the inclusion of genome stabilizers like ZSCAN4 during reprogramming may further decrease reprogramming-associated mutations. Our findings provide evidence that CB is a superior source of cells for iPSC banking.

Comparison of whole genome amplification techniques for human single cell exome sequencing.

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Borgström, Erik; Paterlini, Marta; Mold, Jeff E; Frisen, Jonas; Lundeberg, Joakim

2017-01-01

Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells. In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling.

Investigation of the mechanisms of using metal complexation and cellulose nanofiber/sodium alginate layer-by-layer coating for retaining anthocyanin pigments in thermally processed blueberries in aqueous media.

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Jung, Jooyeoun; Cavender, George; Simonsen, John; Zhao, Yanyun

2015-03-25

This study investigated the mechanisms of anthocyanin pigment retention using Fe(3+)-anthocyanin complexation and cellulose nanofiber (CNF)/sodium alginate (SA) layer-by-layer (LBL) coatings on thermally processed blueberries in aqueous media. Anthocyanin pigments were polymerized through complexation with Fe(3+) but readily degraded by heat (93 °C for 7 min) in the aqueous media because of poor stability. CNF/SA LBL coating was successful to retain anthocyanin pigments in thermally processed blueberries. Fruits coated with CNF containing CaCl2 followed by treatment in a SA bath formed a second hydrogel layer onto the CNF layer (LBL coating system) through cross-linking between Ca(2+) and alginic acid. Methyl-cellulose-modified CNF improved the interactions between CNF, the fruit surface, and the SA layer. This study demonstrated that the CNF/SA LBL coating system was effective to retain anthocyanin pigments on thermally processed whole blueberries, whereas no combined benefit of complexation with coating was observed. Results explained the mechanisms of the new approaches for developing colorful and nutritionally enhanced anthocyanin-rich fruit products.

Whole exome sequencing in neurogenetic odysseys: An effective, cost- and time-saving diagnostic approach.

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Marta Córdoba

Full Text Available Diagnostic trajectories for neurogenetic disorders frequently require the use of considerable time and resources, exposing patients and families to so-called "diagnostic odysseys". Previous studies have provided strong evidence for increased diagnostic and clinical utility of whole-exome sequencing in medical genetics. However, specific reports assessing its utility in a setting such as ours- a neurogeneticist led academic group serving in a low-income country-are rare.To assess the diagnostic yield of WES in patients suspected of having a neurogenetic condition and explore the cost-effectiveness of its implementation in a research group located in an Argentinean public hospital.This is a prospective study of the clinical utility of WES in a series of 40 consecutive patients selected from a Neurogenetic Clinic of a tertiary Hospital in Argentina. We evaluated patients retrospectively for previous diagnostic trajectories. Diagnostic yield, clinical impact on management and economic diagnostic burden were evaluated.We demonstrated the clinical utility of Whole Exome Sequencing in our patient cohort, obtaining a diagnostic yield of 40% (95% CI, 24.8%-55.2% among a diverse group of neurological disorders. The average age at the time of WES was 23 (range 3-70. The mean time elapsed from symptom onset to WES was 11 years (range 3-42. The mean cost of the diagnostic workup prior to WES was USD 1646 (USD 1439 to 1853, which is 60% higher than WES cost in our center.WES for neurogenetics proved to be an effective, cost- and time-saving approach for the molecular diagnosis of this heterogeneous and complex group of patients.

Exome analysis in clinical practice: expanding the phenotype of Bartsocas-Papas syndrome.

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Gripp, Karen W; Ennis, Sara; Napoli, Joseph

2013-05-01

Exome analysis has had a dramatic impact on genetic research. We present the application of such newly generated information to patient care. The patient was a female, born with normal growth parameters to nonconsanguineous parents after an uneventful pregnancy. She had bilateral cleft lip/palate and ankyloblepharon. Sparse hair, dysplastic nails and hypohidrosis were subsequently noted. With exception of speech related issues, her development was normal. A clinical diagnosis of ankyloblepharon-ectodermal defects-cleft lip/palate or Hay-Wells syndrome resulted in TP63 sequence analysis. TP63 sequence and deletion/duplication analysis of all coding exons had a normal result, as did chromosome and SNP array analysis. Diagnostic exome analysis revealed a heterozygous nonsense mutation in KRT83 categorized as deleterious and associated with monilethrix. In addition, a homozygous missense variant of unknown clinical significance was reported in RIPK4. Using research based exome analysis, RIPK4 had just a few months prior been identified as pathogenic for Bartsocas-Papas syndrome. While the clinical diagnostic report implied the KRT83 mutation as a more likely cause for the patient's phenotype, clinical correlation, literature review and use of computerized mutation analysis programs allowed us to identify the homozygous RIPK4 (c.488G > A; p.Gly163Asp) mutation as the underlying pathogenic change. Consequently, we expand the phenotype of Bartsocas-Papas syndrome to an attenuated presentation resembling Hay-Wells syndrome, lacking lethality and pterygia. In contrast to the autosomal dominant Hay-Wells syndrome, Bartsocas-Papas syndrome is autosomal recessive, implying a 25% recurrence risk. Copyright © 2013 Wiley Periodicals, Inc.

An inexpensive and fast method for infiltration coating of complex geometry matrices for ISOL production target applications

International Nuclear Information System (INIS)

Kawai, Y.; Alton, G.D.; Bilheux, J.-C.

2005-01-01

An inexpensive, fast, and close to universal infiltration coating technique has been developed for fabricating fast diffusion-release ISOL targets. Targets are fabricated by deposition of finely divided (∼1μm) compound materials in a paint-slurry onto highly permeable, complex structure reticulated-vitreous-carbon-foam (RVCF) matrices, followed by thermal heat treatment. In this article, we describe the coating method and present information on the physical integrity, uniformity of deposition, and matrix adherence of SiC, HfC and UC 2 targets, destined for on-line use as targets at the Holifield Radioactive Ion Beam Facility (HRIBF)

Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides Demonstrates Different Alloreactivity Potential in HLA-Matched and -Mismatched Donor-Recipient Pairs.

Science.gov (United States)

Abdul Razzaq, Badar; Scalora, Allison; Koparde, Vishal N; Meier, Jeremy; Mahmood, Musa; Salman, Salman; Jameson-Lee, Max; Serrano, Myrna G; Sheth, Nihar; Voelkner, Mark; Kobulnicky, David J; Roberts, Catherine H; Ferreira-Gonzalez, Andrea; Manjili, Masoud H; Buck, Gregory A; Neale, Michael C; Toor, Amir A

2016-05-01

Immune reconstitution kinetics and subsequent clinical outcomes in HLA-matched recipients of allogeneic stem cell transplantation (SCT) are variable and difficult to predict. Considering SCT as a dynamical system may allow sequence differences across the exomes of the transplant donors and recipients to be used to simulate an alloreactive T cell response, which may allow better clinical outcome prediction. To accomplish this, whole exome sequencing was performed on 34 HLA-matched SCT donor-recipient pairs (DRPs) and the nucleotide sequence differences translated to peptides. The binding affinity of the peptides to the relevant HLA in each DRP was determined. The resulting array of peptide-HLA binding affinity values in each patient was considered as an operator modifying a hypothetical T cell repertoire vector, in which each T cell clone proliferates in accordance with the logistic equation of growth. Using an iterating system of matrices, each simulated T cell clone's growth was calculated with the steady-state population being proportional to the magnitude of the binding affinity of the driving HLA-peptide complex. Incorporating competition between T cell clones responding to different HLA-peptide complexes reproduces a number of features of clinically observed T cell clonal repertoire in the simulated repertoire, including sigmoidal growth kinetics of individual T cell clones and overall repertoire, Power Law clonal frequency distribution, increase in repertoire complexity over time with increasing clonal diversity, and alteration of clonal dominance when a different antigen array is encountered, such as in SCT. The simulated, alloreactive T cell repertoire was markedly different in HLA-matched DRPs. The patterns were differentiated by rate of growth and steady-state magnitude of the simulated T cell repertoire and demonstrate a possible correlation with survival. In conclusion, exome wide sequence differences in DRPs may allow simulation of donor alloreactive T

Exome Sequencing for cerebral palsies: Opening windows for differential diagnosis

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D. Suresh Bhargav

2017-10-01

Full Text Available DNA sequencing technologies played a critical role in the last two decades in expanding our understanding of genetic spectrum behind neurodevelopmental disorders. Recently, induction MPS in the area of medical genetics provided chance for differential diagnosis and/or reverse phenotyping of cerebral palsies and many other developmental disorders. Here we present how ES through MPS has identified causative mutations and showed scope for further characterization of the neurodevelopmental disorders. Here we report and discuss four cases (5Y to 12Y who were diagnosed as CP with mild or moderate ID. Whole Exome libraries were constructed using Exome RDY panel and sequenced on Ion Proton. The reads generated were aligned to hg19 and variants were annotated and prioritized using Ion Reporter. In Cases-I & II a homozygous mutation in PMM2 gene (NM_000303.2, c.710C>T, p.THR237ARG and a novel nonsense mutation in gene SLC35A2 (NM_005660.2, c.1024C>T, p.Arg342Ter which are known to cause congenital disorder of glycosylation type Ia (MIM: 212065 and type IIm SOMATIC MOSAIC (MIM: 300896 were identified, respectively. In case-III (two male siblings ES identified a novel Frame Shift (FS mutation in APRATAXIN (APTX gene (NM_001195248.1, c.638delG, p.Arg213fs, rs150886026 which are known to cause ATAXIA-OCULOMOTOR APRAXIA 1; AOA1 (MIM: 208920. Brain imaging in Case-IV is suggestive of Joubert syndrome with hearing loss, we identified a missense mutation in AHI1 gene (NM_001134830.1, c.2023G>A, p.Asp675Asn and also a nonsense mutation in gene GJB2 (NM_004004.5, c.71G>A, p.Trp24Ter which explains the hearing impairment in the case. Mutations in cases and parent(s were confirmed on 3500 Genetic Analyzer revealed Autosomal recessive or X-linked dominant and somatic mosaicism pattern of inheritance. Reverse phenotyping was convincing for Case I & II.  Case III phenotype was delineated by the identification of responsible gene /mutation.  Complex phenotype of Case

Integration of 60 000 exomes and ACMG guidelines question the role of Catecholaminergic Polymorphic Ventricular Tachycardia associated variants

DEFF Research Database (Denmark)

Paludan-Müller, Christian; Ahlberg, Gustav; Ghouse, Jonas

2017-01-01

of potential false-positive pathogenic variants was conducted by searching The Exome Aggregation Consortium (ExAC) database (n=60 706) for variants reported to be associated with CPVT. The pathogenicity of the interrogated variants was assessed using guidelines from the American College of Medical Genetics...... and Genomics (ACMG) and in silico prediction tools. Thirty-eight out of 246 variants (15%) previously associated with CPVT were identified in the ExAC database. We predicted the CPVT prevalence to be 1:132. The ACMG standards classified 29% of ExAC variants as pathogenic or likely pathogenic. The in silico...... predictions showed a reduced probability of disease-causing effect for the variants identified in the exome database (P˂0.001). We have observed a large overrepresentation of previously CPVT associated variants in a large exome database. Based on the frequency of CPVT in the general population, it is less...

Whole Exome Sequencing Reveals Genetic Predisposition in a Large Family with Retinitis Pigmentosa

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Juan Wu

2014-01-01

Full Text Available Next-generation sequencing has become more widely used to reveal genetic defect in monogenic disorders. Retinitis pigmentosa (RP, the leading cause of hereditary blindness worldwide, has been attributed to more than 67 disease-causing genes. Due to the extreme genetic heterogeneity, using general molecular screening alone is inadequate for identifying genetic predispositions in susceptible individuals. In order to identify underlying mutation rapidly, we utilized next-generation sequencing in a four-generation Chinese family with RP. Two affected patients and an unaffected sibling were subjected to whole exome sequencing. Through bioinformatics analysis and direct sequencing confirmation, we identified p.R135W transition in the rhodopsin gene. The mutation was subsequently confirmed to cosegregate with the disease in the family. In this study, our results suggest that whole exome sequencing is a robust method in diagnosing familial hereditary disease.

Leveraging the Power of High Performance Computing for Next Generation Sequencing Data Analysis: Tricks and Twists from a High Throughput Exome Workflow

Science.gov (United States)

Wonczak, Stephan; Thiele, Holger; Nieroda, Lech; Jabbari, Kamel; Borowski, Stefan; Sinha, Vishal; Gunia, Wilfried; Lang, Ulrich; Achter, Viktor; Nürnberg, Peter

2015-01-01

Next generation sequencing (NGS) has been a great success and is now a standard method of research in the life sciences. With this technology, dozens of whole genomes or hundreds of exomes can be sequenced in rather short time, producing huge amounts of data. Complex bioinformatics analyses are required to turn these data into scientific findings. In order to run these analyses fast, automated workflows implemented on high performance computers are state of the art. While providing sufficient compute power and storage to meet the NGS data challenge, high performance computing (HPC) systems require special care when utilized for high throughput processing. This is especially true if the HPC system is shared by different users. Here, stability, robustness and maintainability are as important for automated workflows as speed and throughput. To achieve all of these aims, dedicated solutions have to be developed. In this paper, we present the tricks and twists that we utilized in the implementation of our exome data processing workflow. It may serve as a guideline for other high throughput data analysis projects using a similar infrastructure. The code implementing our solutions is provided in the supporting information files. PMID:25942438

Whole-exome sequencing for mutation detection in pediatric disorders of insulin secretion: Maturity onset diabetes of the young and congenital hyperinsulinism.

Science.gov (United States)

Johnson, S R; Leo, P J; McInerney-Leo, A M; Anderson, L K; Marshall, M; McGown, I; Newell, F; Brown, M A; Conwell, L S; Harris, M; Duncan, E L

2018-06-01

To assess the utility of whole-exome sequencing (WES) for mutation detection in maturity-onset diabetes of the young (MODY) and congenital hyperinsulinism (CHI). MODY and CHI are the two commonest monogenic disorders of glucose-regulated insulin secretion in childhood, with 13 causative genes known for MODY and 10 causative genes identified for CHI. The large number of potential genes makes comprehensive screening using traditional methods expensive and time-consuming. Ten subjects with MODY and five with CHI with known mutations underwent WES using two different exome capture kits (Nimblegen SeqCap EZ Human v3.0 Exome Enrichment Kit, Nextera Rapid Capture Exome Kit). Analysis was blinded to previously identified mutations, and included assessment for large deletions. The target capture of five exome capture technologies was also analyzed using sequencing data from >2800 unrelated samples. Four of five MODY mutations were identified using Nimblegen (including a large deletion in HNF1B). Although targeted, one mutation (in INS) had insufficient coverage for detection. Eleven of eleven mutations (six MODY, five CHI) were identified using Nextera Rapid (including the previously missed mutation). On reconciliation, all mutations concorded with previous data and no additional variants in MODY genes were detected. There were marked differences in the performance of the capture technologies. WES can be useful for screening for MODY/CHI mutations, detecting both point mutations and large deletions. However, capture technologies require careful selection. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Promises, pitfalls and practicalities of prenatal whole exome sequencing.

Science.gov (United States)

Best, Sunayna; Wou, Karen; Vora, Neeta; Van der Veyver, Ignatia B; Wapner, Ronald; Chitty, Lyn S

2018-01-01

Prenatal genetic diagnosis provides information for pregnancy and perinatal decision-making and management. In several small series, prenatal whole exome sequencing (WES) approaches have identified genetic diagnoses when conventional tests (karyotype and microarray) were not diagnostic. Here, we review published prenatal WES studies and recent conference abstracts. Thirty-one studies were identified, with diagnostic rates in series of five or more fetuses varying between 6.2% and 80%. Differences in inclusion criteria and trio versus singleton approaches to sequencing largely account for the wide range of diagnostic rates. The data suggest that diagnostic yields will be greater in fetuses with multiple anomalies or in cases preselected following genetic review. Beyond its ability to improve diagnostic rates, we explore the potential of WES to improve understanding of prenatal presentations of genetic disorders and lethal fetal syndromes. We discuss prenatal phenotyping limitations, counselling challenges regarding variants of uncertain significance, incidental and secondary findings, and technical problems in WES. We review the practical, ethical, social and economic issues that must be considered before prenatal WES could become part of routine testing. Finally, we reflect upon the potential future of prenatal genetic diagnosis, including a move towards whole genome sequencing and non-invasive whole exome and whole genome testing. © 2017 John Wiley & Sons, Ltd. © 2017 John Wiley & Sons, Ltd.

Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies.

Science.gov (United States)

Damiati, E; Borsani, G; Giacopuzzi, Edoardo

2016-05-01

The Ion Proton platform allows to perform whole exome sequencing (WES) at low cost, providing rapid turnaround time and great flexibility. Products for WES on Ion Proton system include the AmpliSeq Exome kit and the recently introduced HiQ sequencing chemistry. Here, we used gold standard variants from GIAB consortium to assess the performances in variants identification, characterize the erroneous calls and develop a filtering strategy to reduce false positives. The AmpliSeq Exome kit captures a large fraction of bases (>94 %) in human CDS, ClinVar genes and ACMG genes, but with 2,041 (7 %), 449 (13 %) and 11 (19 %) genes not fully represented, respectively. Overall, 515 protein coding genes contain hard-to-sequence regions, including 90 genes from ClinVar. Performance in variants detection was maximum at mean coverage >120×, while at 90× and 70× we measured a loss of variants of 3.2 and 4.5 %, respectively. WES using HiQ chemistry showed ~71/97.5 % sensitivity, ~37/2 % FDR and ~0.66/0.98 F1 score for indels and SNPs, respectively. The proposed low, medium or high-stringency filters reduced the amount of false positives by 10.2, 21.2 and 40.4 % for indels and 21.2, 41.9 and 68.2 % for SNP, respectively. Amplicon-based WES on Ion Proton platform using HiQ chemistry emerged as a competitive approach, with improved accuracy in variants identification. False-positive variants remain an issue for the Ion Torrent technology, but our filtering strategy can be applied to reduce erroneous variants.

Use of targeted exome sequencing in genetic diagnosis of Chinese familial hypercholesterolemia.

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Wen-Feng Wu

Full Text Available Familial hypercholesterolemia is an autosomal dominant inherited disease characterized by elevated plasma low-density lipoprotein cholesterol (LDL-C. It is mainly caused by mutations of the low-density lipoprotein receptor (LDLR gene. Currently, the methods of whole genome sequencing or whole exome sequencing for screening mutations in familial hypercholesterolemia are not applicable in China due to high cost. We performed targeted exome sequencing of 167 genes implicated in the homozygous phenotype of a proband pedigree to identify candidate mutations, validated them in the family of the proband, studied the functions of the mutant protein, and followed up serum lipid levels after treatment. We discovered that exon 9 c.1268 T>C and exon 8 c.1129 T>G compound heterozygous mutations in the LDLR gene in the proband derived from the mother and father, respectively, in which the mutation of c.1129 T>G has not been reported previously. The mutant LDL-R protein had 57% and 52% binding and internalization functions, respectively, compared with that of the wild type. After 6 months of therapy, the LDL-C level of the proband decreased by more than 50% and the LDL-C of the other family members with heterozygous mutation also reduced to normal. Targeted exome sequencing is an effective method for screening mutation genes in familial hypercholesterolemia. The exon 8 and 9 mutations of the LDLR gene were pedigree mutations. The functions of the mutant LDL-R protein were decreased significantly compared with that of the wild type. Simvastatin plus ezetimibe was proven safe and effective in this preschool-age child.

Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.

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Poultney, Christopher S; Goldberg, Arthur P; Drapeau, Elodie; Kou, Yan; Harony-Nicolas, Hala; Kajiwara, Yuji; De Rubeis, Silvia; Durand, Simon; Stevens, Christine; Rehnström, Karola; Palotie, Aarno; Daly, Mark J; Ma'ayan, Avi; Fromer, Menachem; Buxbaum, Joseph D

2013-10-03

Copy number variation (CNV) is an important determinant of human diversity and plays important roles in susceptibility to disease. Most studies of CNV carried out to date have made use of chromosome microarray and have had a lower size limit for detection of about 30 kilobases (kb). With the emergence of whole-exome sequencing studies, we asked whether such data could be used to reliably call rare exonic CNV in the size range of 1-30 kilobases (kb), making use of the eXome Hidden Markov Model (XHMM) program. By using both transmission information and validation by molecular methods, we confirmed that small CNV encompassing as few as three exons can be reliably called from whole-exome data. We applied this approach to an autism case-control sample (n = 811, mean per-target read depth = 161) and observed a significant increase in the burden of rare (MAF ≤1%) 1-30 kb CNV, 1-30 kb deletions, and 1-10 kb deletions in ASD. CNV in the 1-30 kb range frequently hit just a single gene, and we were therefore able to carry out enrichment and pathway analyses, where we observed enrichment for disruption of genes in cytoskeletal and autophagy pathways in ASD. In summary, our results showed that XHMM provided an effective means to assess small exonic CNV from whole-exome data, indicated that rare 1-30 kb exonic deletions could contribute to risk in up to 7% of individuals with ASD, and implicated a candidate pathway in developmental delay syndromes. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Surface modification of coronary artery stent by Ti-O/Ti-N complex film coating prepared with plasma immersion ion implantation and deposition

International Nuclear Information System (INIS)

Huang, N.; Leng, Y.X.; Yang, P.

2006-01-01

This paper reported the work of surface coating of Ti-O/Ti-N complex films on coronary stents by means of the plasma immersion ion implantation/deposition process. The deformation behavior of the Ti-O/Ti-N coated stainless steel stents was investigated. In vivo investigation of the anticoagulation behavior of Ti-O coated coronary stents was also performed. The results of mechanical characterization of the Ti-O/Ti-N coated stents show that the film has strong binding strength, and to some extent the ability to withstand plastic deformation. The biological response behavior of the coated stent surface was significantly different from the uncoated. The results of implantation of stents into rabbit ventral aorta show no thrombus formation on the surfaces of the Ti-O coated stents, although serious coagulation had occurred on the surfaces of unmodified stents over a period of 4 weeks under conditions with no anticoagulant

Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome

NARCIS (Netherlands)

Albers, Cornelis A.; Cvejic, Ana; Favier, Rémi; Bouwmans, Evelien E.; Alessi, Marie-Christine; Bertone, Paul; Jordan, Gregory; Kettleborough, Ross N. W.; Kiddle, Graham; Kostadima, Myrto; Read, Randy J.; Sipos, Botond; Sivapalaratnam, Suthesh; Smethurst, Peter A.; Stephens, Jonathan; Voss, Katrin; Nurden, Alan; Rendon, Augusto; Nurden, Paquita; Ouwehand, Willem H.

2011-01-01

Gray platelet syndrome (GPS) is a predominantly recessive platelet disorder that is characterized by mild thrombocytopenia with large platelets and a paucity of α-granules; these abnormalities cause mostly moderate but in rare cases severe bleeding. We sequenced the exomes of four unrelated

Molecular defects identified by whole exome sequencing in a child with Fanconi anemia.

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Zheng, Zhaojing; Geng, Juan; Yao, Ru-En; Li, Caihua; Ying, Daming; Shen, Yongnian; Ying, Lei; Yu, Yongguo; Fu, Qihua

2013-11-10

Fanconi anemia is a rare genetic disease characterized by bone marrow failure, multiple congenital malformations, and an increased susceptibility to malignancy. At least 15 genes have been identified that are involved in the pathogenesis of Fanconi anemia. However, it is still a challenge to assign the complementation group and to characterize the molecular defects in patients with Fanconi anemia. In the current study, whole exome sequencing was used to identify the affected gene(s) in a boy with Fanconi anemia. A recurring, non-synonymous mutation was found (c.3971C>T, p.P1324L) as well as a novel frameshift mutation (c.989_995del, p.H330LfsX2) in FANCA gene. Our results indicate that whole exome sequencing may be useful in clinical settings for rapid identification of disease-causing mutations in rare genetic disorders such as Fanconi anemia. © 2013 Elsevier B.V. All rights reserved.

Enhanced photoluminescence from single nitrogen-vacancy defects in nanodiamonds coated with phenol-ionic complexes

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Bray, Kerem; Previdi, Rodolfo; Gibson, Brant C.; Shimoni, Olga; Aharonovich, Igor

2015-03-01

Fluorescent nanodiamonds are attracting major attention in the field of bio-sensing and bio-labeling. In this work we demonstrate a robust approach to achieve an encapsulation of individual nanodiamonds with phenol-ionic complexes that enhance the photoluminescence from single nitrogen vacancy (NV) centers. We show that single NV centres in the coated nanodiamonds also exhibit shorter lifetimes, opening another channel for high resolution sensing. We propose that the nanodiamond encapsulation reduces the non-radiative decay pathways of the NV color centers. Our results provide a versatile and assessable way to enhance photoluminescence from nanodiamond defects that can be used in a variety of sensing and imaging applications.Fluorescent nanodiamonds are attracting major attention in the field of bio-sensing and bio-labeling. In this work we demonstrate a robust approach to achieve an encapsulation of individual nanodiamonds with phenol-ionic complexes that enhance the photoluminescence from single nitrogen vacancy (NV) centers. We show that single NV centres in the coated nanodiamonds also exhibit shorter lifetimes, opening another channel for high resolution sensing. We propose that the nanodiamond encapsulation reduces the non-radiative decay pathways of the NV color centers. Our results provide a versatile and assessable way to enhance photoluminescence from nanodiamond defects that can be used in a variety of sensing and imaging applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07510b

Molecular Diagnostic Experience of Whole-Exome Sequencing in Adult Patients

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Posey, Jennifer E.; Rosenfeld, Jill A.; James, Regis A.; Bainbridge, Matthew; Niu, Zhiyv; Wang, Xia; Dhar, Shweta; Wiszniewski, Wojciech; Akdemir, Zeynep H.C.; Gambin, Tomasz; Xia, Fan; Person, Richard E.; Walkiewicz, Magdalena; Shaw, Chad A.; Sutton, V. Reid; Beaudet, Arthur L.; Muzny, Donna; Eng, Christine M.; Yang, Yaping; Gibbs, Richard A.; Lupski, James R.; Boerwinkle, Eric; Plon, Sharon E.

2015-01-01

Purpose Whole exome sequencing (WES) is increasingly used as a diagnostic tool in medicine, but prior reports focus on predominantly pediatric cohorts with neurologic or developmental disorders. We describe the diagnostic yield and characteristics of whole exome sequencing in adults. Methods We performed a retrospective analysis of consecutive WES reports for adults from a diagnostic laboratory. Phenotype composition was determined using Human Phenotype Ontology terms. Results Molecular diagnoses were reported for 17.5% (85/486) of adults, lower than a primarily pediatric population (25.2%; p=0.0003); the diagnostic rate was higher (23.9%) in those 18–30 years of age compared to patients over 30 years (10.4%; p=0.0001). Dual Mendelian diagnoses contributed to 7% of diagnoses, revealing blended phenotypes. Diagnoses were more frequent among individuals with abnormalities of the nervous system, skeletal system, head/neck, and growth. Diagnostic rate was independent of family history information, and de novo mutations contributed to 61.4% of autosomal dominant diagnoses. Conclusion Early WES experience in adults demonstrates molecular diagnoses in a substantial proportion of patients, informing clinical management, recurrence risk and recommendations for relatives. A positive family history was not predictive, consistent with molecular diagnoses often revealed by de novo events, informing the Mendelian basis of genetic disease in adults. PMID:26633545

Crystal structure of the bacteriophage Qβ coat protein in complex with the RNA operator of the replicase gene.

Science.gov (United States)

Rumnieks, Janis; Tars, Kaspars

2014-03-06

The coat proteins of single-stranded RNA bacteriophages specifically recognize and bind to a hairpin structure in their genome at the beginning of the replicase gene. The interaction serves to repress the synthesis of the replicase enzyme late in infection and contributes to the specific encapsidation of phage RNA. While this mechanism is conserved throughout the Leviviridae family, the coat protein and operator sequences from different phages show remarkable variation, serving as prime examples for the co-evolution of protein and RNA structure. To better understand the protein-RNA interactions in this virus family, we have determined the three-dimensional structure of the coat protein from bacteriophage Qβ bound to its cognate translational operator. The RNA binding mode of Qβ coat protein shares several features with that of the widely studied phage MS2, but only one nucleotide base in the hairpin loop makes sequence-specific contacts with the protein. Unlike in other RNA phages, the Qβ coat protein does not utilize an adenine-recognition pocket for binding a bulged adenine base in the hairpin stem but instead uses a stacking interaction with a tyrosine side chain to accommodate the base. The extended loop between β strands E and F of Qβ coat protein makes contacts with the lower part of the RNA stem, explaining the greater length dependence of the RNA helix for optimal binding to the protein. Consequently, the complex structure allows the proposal of a mechanism by which the Qβ coat protein recognizes and discriminates in favor of its cognate RNA. © 2013.

Exome sequencing identifies highly recurrent MED12 somatic mutations in breast fibroadenoma.

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Lim, Weng Khong; Ong, Choon Kiat; Tan, Jing; Thike, Aye Aye; Ng, Cedric Chuan Young; Rajasegaran, Vikneswari; Myint, Swe Swe; Nagarajan, Sanjanaa; Nasir, Nur Diyana Md; McPherson, John R; Cutcutache, Ioana; Poore, Gregory; Tay, Su Ting; Ooi, Wei Siong; Tan, Veronique Kiak Mien; Hartman, Mikael; Ong, Kong Wee; Tan, Benita K T; Rozen, Steven G; Tan, Puay Hoon; Tan, Patrick; Teh, Bin Tean

2014-08-01

Fibroadenomas are the most common breast tumors in women under 30 (refs. 1,2). Exome sequencing of eight fibroadenomas with matching whole-blood samples revealed recurrent somatic mutations solely in MED12, which encodes a Mediator complex subunit. Targeted sequencing of an additional 90 fibroadenomas confirmed highly frequent MED12 exon 2 mutations (58/98, 59%) that are probably somatic, with 71% of mutations occurring in codon 44. Using laser capture microdissection, we show that MED12 fibroadenoma mutations are present in stromal but not epithelial mammary cells. Expression profiling of MED12-mutated and wild-type fibroadenomas revealed that MED12 mutations are associated with dysregulated estrogen signaling and extracellular matrix organization. The fibroadenoma MED12 mutation spectrum is nearly identical to that of previously reported MED12 lesions in uterine leiomyoma but not those of other tumors. Benign tumors of the breast and uterus, both of which are key target tissues of estrogen, may thus share a common genetic basis underpinned by highly frequent and specific MED12 mutations.

Whole-Exome Sequencing in Adults With Chronic Kidney Disease: A Pilot Study.

Science.gov (United States)

Lata, Sneh; Marasa, Maddalena; Li, Yifu; Fasel, David A; Groopman, Emily; Jobanputra, Vaidehi; Rasouly, Hila; Mitrotti, Adele; Westland, Rik; Verbitsky, Miguel; Nestor, Jordan; Slater, Lindsey M; D'Agati, Vivette; Zaniew, Marcin; Materna-Kiryluk, Anna; Lugani, Francesca; Caridi, Gianluca; Rampoldi, Luca; Mattoo, Aditya; Newton, Chad A; Rao, Maya K; Radhakrishnan, Jai; Ahn, Wooin; Canetta, Pietro A; Bomback, Andrew S; Appel, Gerald B; Antignac, Corinne; Markowitz, Glen S; Garcia, Christine K; Kiryluk, Krzysztof; Sanna-Cherchi, Simone; Gharavi, Ali G

2018-01-16

The utility of whole-exome sequencing (WES) for the diagnosis and management of adult-onset constitutional disorders has not been adequately studied. Genetic diagnostics may be advantageous in adults with chronic kidney disease (CKD), in whom the cause of kidney failure often remains unknown. To study the diagnostic utility of WES in a selected referral population of adults with CKD. Observational cohort. A major academic medical center. 92 adults with CKD of unknown cause or familial nephropathy or hypertension. The diagnostic yield of WES and its potential effect on clinical management. Whole-exome sequencing provided a diagnosis in 22 of 92 patients (24%), including 9 probands with CKD of unknown cause and encompassing 13 distinct genetic disorders. Among these, loss-of-function mutations were identified in PARN in 2 probands with tubulointerstitial fibrosis. PARN mutations have been implicated in a short telomere syndrome characterized by lung, bone marrow, and liver fibrosis; these findings extend the phenotype of PARN mutations to renal fibrosis. In addition, review of the American College of Medical Genetics actionable genes identified a pathogenic BRCA2 mutation in a proband who was diagnosed with breast cancer on follow-up. The results affected clinical management in most identified cases, including initiation of targeted surveillance, familial screening to guide donor selection for transplantation, and changes in therapy. The small sample size and recruitment at a tertiary care academic center limit generalizability of findings among the broader CKD population. Whole-exome sequencing identified diagnostic mutations in a substantial number of adults with CKD of many causes. Further study of the utility of WES in the evaluation and care of patients with CKD in additional settings is warranted. New York State Empire Clinical Research Investigator Program, Renal Research Institute, and National Human Genome Research Institute of the National Institutes of

Exome-wide rare variant analysis identifies TUBA4A mutations associated with familial ALS

NARCIS (Netherlands)

Smith, Bradley N.; Ticozzi, Nicola; Fallini, Claudia; Gkazi, Athina Soragia; Topp, Simon; Kenna, Kevin P.; Scotter, Emma L.; Kost, Jason; Keagle, Pamela; Miller, Jack W.; Calini, Daniela; Vance, Caroline; Danielson, Eric W.; Troakes, Claire; Tiloca, Cinzia; Al-Sarraj, Safa; Lewis, Elizabeth A.; King, Andrew; Colombrita, Claudia; Pensato, Viviana; Castellotti, Barbara; de Belleroche, Jacqueline; Baas, Frank; ten Asbroek, Anneloor L. M. A.; Sapp, Peter C.; McKenna-Yasek, Diane; McLaughlin, Russell L.; Polak, Meraida; Asress, Seneshaw; Esteban-Pérez, Jesús; Muñoz-Blanco, José Luis; Simpson, Michael; van Rheenen, Wouter; Diekstra, Frank P.; Lauria, Giuseppe; Duga, Stefano; Corti, Stefania; Cereda, Cristina; Corrado, Lucia; Sorarù, Gianni; Morrison, Karen E.; Williams, Kelly L.; Nicholson, Garth A.; Blair, Ian P.; Dion, Patrick A.; Leblond, Claire S.; Rouleau, Guy A.; Hardiman, Orla; Veldink, Jan H.; van den Berg, Leonard H.

2014-01-01

Exome sequencing is an effective strategy for identifying human disease genes. However, this methodology is difficult in late-onset diseases where limited availability of DNA from informative family members prohibits comprehensive segregation analysis. To overcome this limitation, we performed an

SNP Analysis and Whole Exome Sequencing: Their Application in the Analysis of a Consanguineous Pedigree Segregating Ataxia

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Sarah L. Nickerson

2015-10-01

Full Text Available Autosomal recessive cerebellar ataxia encompasses a large and heterogeneous group of neurodegenerative disorders. We employed single nucleotide polymorphism (SNP analysis and whole exome sequencing to investigate a consanguineous Maori pedigree segregating ataxia. We identified a novel mutation in exon 10 of the SACS gene: c.7962T>G p.(Tyr2654*, establishing the diagnosis of autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS. Our findings expand both the genetic and phenotypic spectrum of this rare disorder, and highlight the value of high-density SNP analysis and whole exome sequencing as powerful and cost-effective tools in the diagnosis of genetically heterogeneous disorders such as the hereditary ataxias.

Genetics of Infectious and Inflammatory Diseases: Overlapping Discoveries from Association and Exome-Sequencing Studies.

Science.gov (United States)

Langlais, David; Fodil, Nassima; Gros, Philippe

2017-04-26

Genome technologies have defined a complex genetic architecture in major infectious, inflammatory, and autoimmune disorders. High density marker arrays and Immunochips have powered genome-wide association studies (GWAS) that have mapped nearly 450 genetic risk loci in 22 major inflammatory diseases, including a core of common genes that play a central role in pathological inflammation. Whole-exome and whole-genome sequencing have identified more than 265 genes in which mutations cause primary immunodeficiencies and rare forms of severe inflammatory bowel disease. Combined analysis of inflammatory disease GWAS and primary immunodeficiencies point to shared proteins and pathways that are required for immune cell development and protection against infections and are also associated with pathological inflammation. Finally, sequencing of chromatin immunoprecipitates containing specific transcription factors, with parallel RNA sequencing, has charted epigenetic regulation of gene expression by proinflammatory transcription factors in immune cells, providing complementary information to characterize morbid genes at infectious and inflammatory disease loci.

Whole-exome sequencing of a pedigree segregating asthma

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DeWan Andrew T

2012-10-01

Full Text Available Abstract Background Despite the success of genome-wide association studies for asthma, few, if any, definitively causal variants have been identified and there is still a substantial portion of the heritability of the disease yet to be discovered. Some of this “missing heritability” may be accounted for by family-specific coding variants found to be segregating with asthma. Methods To identify family-specific variants segregating with asthma, we recruited one family from a previous study of asthma as reporting multiple asthmatic and non-asthmatic children. We performed whole-exome sequencing on all four children and both parents and identified coding variants segregating with asthma that were not found in other variant databases. Results Ten novel variants were identified that were found in the two affected offspring and affected mother, but absent in the unaffected father and two unaffected offspring. Of these ten, variants in three genes (PDE4DIP, CBLB, and KALRN were deemed of particular interest based on their functional prediction scores and previously reported function or asthma association. We did not identify any common risk variants segregating with asthma, however, we did observe an increase in the number of novel, nonsynonymous variants in asthma candidate genes in the asthmatic children compared to the non-asthmatic children. Conclusions This is the first report applying exome sequencing to identify asthma susceptibility variants. Despite having sequenced only one family segregating asthma, we have identified several potentially functional variants in interesting asthma candidate genes. This will provide the basis for future work in which more families will be sequenced to identify variants across families that cluster within genes.

Targeted Gene Sequencing and Whole-Exome Sequencing in Autopsied Fetuses with Prenatally Diagnosed Kidney Anomalies

DEFF Research Database (Denmark)

Rasmussen, M; Sunde, L; Nielsen, M L

2018-01-01

Identification of fetal kidney anomalies invites questions about underlying causes and recurrence risk in future pregnancies. We therefore investigated the diagnostic yield of next-generation sequencing in fetuses with bilateral kidney anomalies and the correlation between disrupted genes and fetal...... phenotypes. Fetuses with bilateral kidney anomalies were screened using an in-house-designed kidney-gene panel. In families where candidate variants were not identified, whole-exome sequencing was performed. Genes uncovered by this analysis were added to our kidney-panel. We identified likely deleterious...... of nephronophthisis. Exome sequencing identified ROBO1 variants in one family and a GREB1L variant in another family. GREB1L and ROBO1 were added to our kidney-gene panel and additional variants were identified. Next-generation sequencing substantially contributes to identifying causes of fetal kidney anomalies...

Whole-Exome Sequencing in Searching for New Variants Associated With the Development of Parkinson’s Disease

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Marina V. Shulskaya

2018-05-01

Full Text Available Background: Parkinson’s disease (PD is a complex disease with its monogenic forms accounting for less than 10% of all cases. Whole-exome sequencing (WES technology has been used successfully to find mutations in large families. However, because of the late onset of the disease, only small families and unrelated patients are usually available. WES conducted in such cases yields in a large number of candidate variants. There are currently a number of imperfect software tools that allow the pathogenicity of variants to be evaluated.Objectives: We analyzed 48 unrelated patients with an alleged autosomal dominant familial form of PD using WES and developed a strategy for selecting potential pathogenetically significant variants using almost all available bioinformatics resources for the analysis of exonic areas.Methods: DNA sequencing of 48 patients with excluded frequent mutations was performed using an Illumina HiSeq 2500 platform. The possible pathogenetic significance of identified variants and their involvement in the pathogenesis of PD was assessed using SNP and Variation Suite (SVS, Combined Annotation Dependent Depletion (CADD and Rare Exome Variant Ensemble Learner (REVEL software. Functional evaluation was performed using the Pathway Studio database.Results: A significant reduction in the search range from 7082 to 25 variants in 23 genes associated with PD or neuronal function was achieved. Eight (FXN, MFN2, MYOC, NPC1, PSEN1, RET, SCN3A and SPG7 were the most significant.Conclusions: The multistep approach developed made it possible to conduct an effective search for potential pathogenetically significant variants, presumably involved in the pathogenesis of PD. The data obtained need to be further verified experimentally.

Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling.

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Zhang, Guoqiang; Wang, Jianfeng; Yang, Jin; Li, Wenjie; Deng, Yutian; Li, Jing; Huang, Jun; Hu, Songnian; Zhang, Bing

2015-08-05

To promote the clinical application of next-generation sequencing, it is important to obtain accurate and consistent variants of target genomic regions at low cost. Ion Proton, the latest updated semiconductor-based sequencing instrument from Life Technologies, is designed to provide investigators with an inexpensive platform for human whole exome sequencing that achieves a rapid turnaround time. However, few studies have comprehensively compared and evaluated the accuracy of variant calling between Ion Proton and Illumina sequencing platforms such as HiSeq 2000, which is the most popular sequencing platform for the human genome. The Ion Proton sequencer combined with the Ion TargetSeq Exome Enrichment Kit together make up TargetSeq-Proton, whereas SureSelect-Hiseq is based on the Agilent SureSelect Human All Exon v4 Kit and the HiSeq 2000 sequencer. Here, we sequenced exonic DNA from four human blood samples using both TargetSeq-Proton and SureSelect-HiSeq. We then called variants in the exonic regions that overlapped between the two exome capture kits (33.6 Mb). The rates of shared variant loci called by two sequencing platforms were from 68.0 to 75.3% in four samples, whereas the concordance of co-detected variant loci reached 99%. Sanger sequencing validation revealed that the validated rate of concordant single nucleotide polymorphisms (SNPs) (91.5%) was higher than the SNPs specific to TargetSeq-Proton (60.0%) or specific to SureSelect-HiSeq (88.3%). With regard to 1-bp small insertions and deletions (InDels), the Sanger sequencing validated rates of concordant variants (100.0%) and SureSelect-HiSeq-specific (89.6%) were higher than those of TargetSeq-Proton-specific (15.8%). In the sequencing of exonic regions, a combination of using of two sequencing strategies (SureSelect-HiSeq and TargetSeq-Proton) increased the variant calling specificity for concordant variant loci and the sensitivity for variant loci called by any one platform. However, for the

Targeted exome sequencing integrated with clinicopathological information reveals novel and rare mutations in atypical, suspected and unknown cases of Alport syndrome or proteinuria.

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Rajshekhar Chatterjee

Full Text Available We applied customized targeted next-generation exome sequencing (NGS to determine if mutations in genes associated with renal malformations, Alport syndrome (AS or nephrotic syndrome are a potential cause of renal abnormalities in patients with equivocal or atypical presentation. We first sequenced 4,041 exons representing 292 kidney disease genes in a Caucasian woman with a history of congenital vesicoureteral reflux (VUR, recurrent urinary tract infections and hydronephrosis who presented with nephrotic range proteinuria at the age of 45. Her biopsy was remarkable for focal segmental glomerulosclerosis (FSGS, a potential complication of longstanding VUR. She had no family history of renal disease. Her proteinuria improved initially, however, several years later she presented with worsening proteinuria and microhematuria. NGS analysis revealed two deleterious COL4A3 mutations, one novel and the other previously reported in AS, and a novel deleterious SALL2 mutation, a gene linked to renal malformations. Pedigree analysis confirmed that COL4A3 mutations were nonallelic and compound heterozygous. The genomic results in conjunction with subsequent abnormal electron microscopy, Collagen IV minor chain immunohistochemistry and progressive sensorineural hearing loss confirmed AS. We then modified our NGS approach to enable more efficient discovery of variants associated with AS or a subset of FSGS by multiplexing targeted exome sequencing of 19 genes associated with AS or FSGS in 14 patients. Using this approach, we found novel or known COL4A3 or COL4A5 mutations in a subset of patients with clinically diagnosed or suspected AS, APOL1 variants associated with FSGS in African Americans and novel mutations in genes associated with nephrotic syndrome. These studies demonstrate the successful application of targeted capture-based exome sequencing to simultaneously evaluate genetic variations in many genes in patients with complex renal phenotypes and

Whole exome sequencing reveals concomitant mutations of multiple FA genes in individual Fanconi anemia patients.

Science.gov (United States)

Chang, Lixian; Yuan, Weiping; Zeng, Huimin; Zhou, Quanquan; Wei, Wei; Zhou, Jianfeng; Li, Miaomiao; Wang, Xiaomin; Xu, Mingjiang; Yang, Fengchun; Yang, Yungui; Cheng, Tao; Zhu, Xiaofan

2014-05-15

Fanconi anemia (FA) is a rare inherited genetic syndrome with highly variable clinical manifestations. Fifteen genetic subtypes of FA have been identified. Traditional complementation tests for grouping studies have been used generally in FA patients and in stepwise methods to identify the FA type, which can result in incomplete genetic information from FA patients. We diagnosed five pediatric patients with FA based on clinical manifestations, and we performed exome sequencing of peripheral blood specimens from these patients and their family members. The related sequencing data were then analyzed by bioinformatics, and the FANC gene mutations identified by exome sequencing were confirmed by PCR re-sequencing. Homozygous and compound heterozygous mutations of FANC genes were identified in all of the patients. The FA subtypes of the patients included FANCA, FANCM and FANCD2. Interestingly, four FA patients harbored multiple mutations in at least two FA genes, and some of these mutations have not been previously reported. These patients' clinical manifestations were vastly different from each other, as were their treatment responses to androstanazol and prednisone. This finding suggests that heterozygous mutation(s) in FA genes could also have diverse biological and/or pathophysiological effects on FA patients or FA gene carriers. Interestingly, we were not able to identify de novo mutations in the genes implicated in DNA repair pathways when the sequencing data of patients were compared with those of their parents. Our results indicate that Chinese FA patients and carriers might have higher and more complex mutation rates in FANC genes than have been conventionally recognized. Testing of the fifteen FANC genes in FA patients and their family members should be a regular clinical practice to determine the optimal care for the individual patient, to counsel the family and to obtain a better understanding of FA pathophysiology.

A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology.

Science.gov (United States)

Vissers, Lisenka E L M; van Nimwegen, Kirsten J M; Schieving, Jolanda H; Kamsteeg, Erik-Jan; Kleefstra, Tjitske; Yntema, Helger G; Pfundt, Rolph; van der Wilt, Gert Jan; Krabbenborg, Lotte; Brunner, Han G; van der Burg, Simone; Grutters, Janneke; Veltman, Joris A; Willemsen, Michèl A A P

2017-09-01

Implementation of novel genetic diagnostic tests is generally driven by technological advances because they promise shorter turnaround times and/or higher diagnostic yields. Other aspects, including impact on clinical management or cost-effectiveness, are often not assessed in detail prior to implementation. We studied the clinical utility of whole-exome sequencing (WES) in complex pediatric neurology in terms of diagnostic yield and costs. We analyzed 150 patients (and their parents) presenting with complex neurological disorders of suspected genetic origin. In a parallel study, all patients received both the standard diagnostic workup (e.g., cerebral imaging, muscle biopsies or lumbar punctures, and sequential gene-by-gene-based testing) and WES simultaneously. Our unique study design allowed direct comparison of diagnostic yield of both trajectories and provided insight into the economic implications of implementing WES in this diagnostic trajectory. We showed that WES identified significantly more conclusive diagnoses (29.3%) than the standard care pathway (7.3%) without incurring higher costs. Exploratory analysis of WES as a first-tier diagnostic test indicates that WES may even be cost-saving, depending on the extent of other tests being omitted. Our data support such a use of WES in pediatric neurology for disorders of presumed genetic origin.Genet Med advance online publication 23 March 2017.

Cell surface clustering of Cadherin adhesion complex induced by antibody coated beads

Institute of Scientific and Technical Information of China (English)

无

2000-01-01

Cadherin receptors mediate cell-cell adhesion, signal transduction and assembly of cytoskeletons. How a single transmembrane molecule Cadherin can be involved in multiple functions through modulating its binding activities with many membrane adhesion molecules and cytoskeletal components is an unanswered question which can be elucidated by clues from bead experiments. Human lung cells expressing N-Cadherin were examined. After co-incubation with anti-N-Cadherin monoclonal antibody coated beads, cell surface clustering of N-Cadherin was induced. Immunofluorescent detection demonstrated that in addition to Cadherin, β-Catenin, α-Catenin, α-Actinin and Actin fluorescence also aggregated respectively at the membrane site of bead attachment. Myosin heavy chain (MHC), another major component of Actin cytoskeleton, did not aggregate at the membrane site of bead attachment. Adhesion unrelated protein Con A and polylysine conjugated beads did not induce the clustering of adhesion molecules. It is indicated that the Cadherin/Catenins/α-Actinin/Actin complex is formed at Cadherin mediated cell adherens junction; occupancy and cell surface clustering of Cadherin is crucial for the formation of Cadherin adhesion protein complexes.

Ultra-low fouling and high antibody loading zwitterionic hydrogel coatings for sensing and detection in complex media.

Science.gov (United States)

Chou, Ying-Nien; Sun, Fang; Hung, Hsiang-Chieh; Jain, Priyesh; Sinclair, Andrew; Zhang, Peng; Bai, Tao; Chang, Yung; Wen, Ten-Chin; Yu, Qiuming; Jiang, Shaoyi

2016-08-01

For surface-based diagnostic devices to achieve reliable biomarker detection in complex media such as blood, preventing nonspecific protein adsorption and incorporating high loading of biorecognition elements are paramount. In this work, a novel method to produce nonfouling zwitterionic hydrogel coatings was developed to achieve these goals. Poly(carboxybetaine acrylamide) (pCBAA) hydrogel thin films (CBHTFs) prepared with a carboxybetaine diacrylamide crosslinker (CBAAX) were coated on gold and silicon dioxide surfaces via a simple spin coating process. The thickness of CBHTFs could be precisely controlled between 15 and 150nm by varying the crosslinker concentration, and the films demonstrated excellent long-term stability. Protein adsorption from undiluted human blood serum onto the CBHTFs was measured with surface plasmon resonance (SPR). Hydrogel thin films greater than 20nm exhibited ultra-low fouling (crosslinked, purely zwitterionic, carboxybetaine thin film hydrogel (CBHTF) coating platform. The CBHTF on a hydrophilic surface demonstrated long-term stability. By varying the crosslinker content in the spin-coated hydrogel solution, the thickness of CBHTFs could be precisely controlled. Optimized CBHTFs exhibited ultra-low nonspecific protein adsorption below 5ng/cm(2) measured by a surface plasmon resonance (SPR) sensor, and their 3D architecture allowed antibody loading to reach 693ng/cm(2). This strategy provides a facile method to modify SPR biosensor chips with an advanced nonfouling material, and can be potentially expanded to a variety of implantable medical devices and diagnostic biosensors. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Whole-exome sequencing supports genetic heterogeneity in childhood apraxia of speech

OpenAIRE

Worthey, Elizabeth A; Raca, Gordana; Laffin, Jennifer J; Wilk, Brandon M; Harris, Jeremy M; Jakielski, Kathy J; Dimmock, David P; Strand, Edythe A; Shriberg, Lawrence D

2013-01-01

Background Childhood apraxia of speech (CAS) is a rare, severe, persistent pediatric motor speech disorder with associated deficits in sensorimotor, cognitive, language, learning and affective processes. Among other neurogenetic origins, CAS is the disorder segregating with a mutation in FOXP2 in a widely studied, multigenerational London family. We report the first whole-exome sequencing (WES) findings from a cohort of 10 unrelated participants, ages 3 to 19 years, with well-characterized CA...

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

Science.gov (United States)

Samadian, Soroush; Bruce, Jeff P; Pugh, Trevor J

2018-03-01

Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

Directory of Open Access Journals (Sweden)

Soroush Samadian

2018-03-01

Full Text Available Somatic copy number variations (CNVs play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format, lists of non-overlapping genome coordinates for introduction of gains and losses (bed file, and an optional file defining known haplotypes (vcf format. To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total. To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01% while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing

NARCIS (Netherlands)

I. Jansen (Iris); Ye, H. (Hui); Heetveld, S. (Sasja); Lechler, M.C. (Marie C.); Michels, H. (Helen); Seinstra, R.I. (Renée I.); Lubbe, S.J. (Steven J.); Drouet, V. (Valérie); S. Lesage (Suzanne); E. Majounie (Elisa); Gibbs, J.R. (J.Raphael); M.A. Nalls (Michael); M. Ryten (Mina); Botia, J.A. (Juan A.); J. Vandrovcova (Jana); J. Simón-Sánchez (Javier); Castillo-Lizardo, M. (Melissa); P. Rizzu (Patrizia); Blauwendraat, C. (Cornelis); Chouhan, A.K. (Amit K.); Li, Y. (Yarong); Yogi, P. (Puja); N. Amin (Najaf); C.M. van Duijn (Cornelia); Morris, H.R. (Huw R.); Brice, A. (Alexis); A. Singleton (Andrew); David, D.C. (Della C.); Nollen, E.A. (Ellen A.); A. Jain (Ashok); J.M. Shulman; P. Heutink (Peter); D.G. Hernandez (Dena); S. Arepalli (Sampath); J. Brooks (Janet); Price, R. (Ryan); Nicolas, A. (Aude); S. Chong (Sean); M.R. Cookson (Mark); A. Dillman (Allissa); M. Moore (Matt); B.J. Traynor (Bryan); A. Singleton (Andrew); V. Plagnol (Vincent); Nicholas W Wood,; U.-M. Sheerin (Una-Marie); Jose M Bras,; K. Charlesworth (Kate); M. Gardner (Mac); R. Guerreiro (Rita); D. Trabzuni (Danyah); Hardy, J. (John); M. Sharma; M. Saad (Mohamad); Javier Simón-Sánchez,; C. Schulte (Claudia); J.C. Corvol (Jean-Christophe); Dürr, A. (Alexandra); M. Vidailhet (M.); S. Sveinbjörnsdóttir (Sigurlaug); R.A. Barker (Roger); Caroline H Williams-Gray,; Y. Ben-Shlomo; H.W. Berendse (Henk W.); K.D. van Dijk (Karin); D. Berg (Daniela); K. Brockmann; K.D. Wurster (Kathrin); Mätzler, W. (Walter); Gasser, T. (Thomas); M. Martinez (Maria); R.M.A. de Bie (Rob); A. Biffi (Alessandro); D. Velseboer (Daan); B.R. Bloem (Bastiaan); B. Post (Bart); M. Wickremaratchi (Mirdhu); B. van de Warrenburg (Bart); Z. Bochdanovits (Zoltan); M. von Bonin (Malte); H. Pétursson (Hjörvar); O. Riess (Olaf); D.J. Burn (David); Lubbe, S. (Steven); Cooper, J.M. (J Mark); N.H. McNeill (Nathan); Schapira, A. (Anthony); Lungu, C. (Codrin); Chen, H. (Honglei); Dong, J. (Jing); Chinnery, P.F. (Patrick F.); G. Hudson (Gavin); Clarke, C.E. (Carl E.); C. Moorby (Catriona); C. Counsell (Carl); P. Damier (Philippe); J.-F. Dartigues; P. Deloukas (Panagiotis); E. Gray (Emma); T. Edkins (Ted); Hunt, S.E. (Sarah E.); S.C. Potter (Simon); A. Tashakkori-Ghanbaria (Avazeh); G. Deuschl (Günther); D. Lorenz (Delia); D.T. Dexter (David); F. Durif (Frank); J. Evans (Jonathan Mark); Langford, C. (Cordelia); T. Foltynie (Thomas); A.M. Goate (Alison); C. Harris (Clare); J.J. van Hilten (Jacobus); A. Hofman (Albert); J.R. Hollenbeck (John R.); J.L. Holton (Janice); Hu, M. (Michele); X. Huang (Xiaohong); Illig, T. (Thomas); P.V. Jónsson (Pálmi); J.-C. Lambert; S.S. O'Sullivan (Sean); T. Revesz (Tamas); K. Shaw (Karen); A.J. Lees (Andrew); P. Lichtner (Peter); P. Limousin (Patricia); G. Lopez; Escott-Price, V. (Valentina); J. Pearson (Justin); N. Williams (Nigel); E. Mudanohwo (Ese); J.S. Perlmutter (Joel); Pollak, P. (Pierre); F. Rivadeneira Ramirez (Fernando); A.G. Uitterlinden (André); S.J. Sawcer (Stephen); H. Scheffer (Hans); I. Shoulson (Ira); L. Shulman (Lee); Smith, C. (Colin); R. Walker (Robert); C.C.A. Spencer (Chris C.); A. Strange (Amy); H. Stefansson (Hreinn); F. Bettella (Francesco); J-A. Zwart (John-Anker); Stockton, J.D. (Joanna D.); D. Talbot; C.M. Tanner (Carlie); F. Tison (François); S. Winder-Rhodes (Sophie); K.P. Bhatia (Kailash)

2017-01-01

textabstractBackground: Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

NARCIS (Netherlands)

Ellrott, Kyle; Bailey, Matthew H.; Saksena, Gordon; Covington, Kyle R.; Kandoth, Cyriac; Stewart, Chip; Hess, Julian; Ma, Singer; Chiotti, Kami E.; McLellan, Michael; Sofia, Heidi J.; Hutter, Carolyn M.; Getz, Gad; Wheeler, David A.; Ding, Li; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Cho, Juok; DeFreitas, Timothy; Frazer, Scott; Gehlenborg, Nils; Getz, Gad; Heiman, David I.; Kim, Jaegil; Lawrence, Michael S.; Lin, Pei; Meier, Sam; Noble, Michael S.; Saksena, Gordon; Voet, Doug; Zhang, Hailei; Bernard, Brady; Chambwe, Nyasha; Dhankani, Varsha; Knijnenburg, Theo; Kramer, Roger; Leinonen, Kalle; Liu, Yuexin; Miller, Michael; Reynolds, Sheila; Shmulevich, Ilya; Thorsson, Vesteinn; Zhang, Wei; Akbani, Rehan; Broom, Bradley M.; Hegde, Apurva M.; Ju, Zhenlin; Kanchi, Rupa S.; Korkut, Anil; Li, Jun; Liang, Han; Ling, Shiyun; Liu, Wenbin; Lu, Yiling; Mills, Gordon B.; Ng, Kwok Shing; Rao, Arvind; Ryan, Michael; Wang, Jing; Weinstein, John N.; Zhang, Jiexin; Abeshouse, Adam; Armenia, Joshua; Chakravarty, Debyani; Chatila, Walid K.; de Bruijn, Ino; Gao, Jianjiong; Gross, Benjamin E.; Heins, Zachary J.; Kundra, Ritika; La, Konnor; Ladanyi, Marc; Luna, Augustin; Nissan, Moriah G.; Ochoa, Angelica; Phillips, Sarah M.; Reznik, Ed; Sanchez-Vega, Francisco; Sander, Chris; Schultz, Nikolaus; Sheridan, Robert; Sumer, S. Onur; Sun, Yichao; Taylor, Barry S.; Wang, Jioajiao; Zhang, Hongxin; Anur, Pavana; Peto, Myron; Spellman, Paul; Benz, Christopher; Stuart, Joshua M.; Wong, Christopher K.; Yau, Christina; Hayes, D. Neil; Wilkerson, Matthew D.; Ally, Adrian; Balasundaram, Miruna; Bowlby, Reanne; Brooks, Denise; Carlsen, Rebecca; Chuah, Eric; Dhalla, Noreen; Holt, Robert; Jones, Steven J.M.; Kasaian, Katayoon; Lee, Darlene; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen; Robertson, A. Gordon; Sadeghi, Sara; Schein, Jacqueline E.; Sipahimalani, Payal; Tam, Angela; Thiessen, Nina; Tse, Kane; Wong, Tina; Berger, Ashton C.; Beroukhim, Rameen; Cherniack, Andrew D.; Cibulskis, Carrie; Gabriel, Stacey B.; Gao, Galen F.; Ha, Gavin; Meyerson, Matthew; Schumacher, Steven E.; Shih, Juliann; Kucherlapati, Melanie H.; Kucherlapati, Raju S.; Baylin, Stephen; Cope, Leslie; Danilova, Ludmila; Bootwalla, Moiz S.; Lai, Phillip H.; Maglinte, Dennis T.; Van Den Berg, David J.; Weisenberger, Daniel J.; Auman, J. Todd; Balu, Saianand; Bodenheimer, Tom; Fan, Cheng; Hoadley, Katherine A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Corbin D.; Meng, Shaowu; Mieczkowski, Piotr A.; Mose, Lisle E.; Perou, Amy H.; Perou, Charles M.; Roach, Jeffrey; Shi, Yan; Simons, Janae V.; Skelly, Tara; Soloway, Matthew G.; Tan, Donghui; Veluvolu, Umadevi; Fan, Huihui; Hinoue, Toshinori; Laird, Peter W.; Shen, Hui; Zhou, Wanding; Bellair, Michelle; Chang, Kyle; Covington, Kyle; Creighton, Chad J.; Dinh, Huyen; Doddapaneni, Harsha Vardhan; Donehower, Lawrence A.; Drummond, Jennifer; Gibbs, Richard A.; Glenn, Robert; Hale, Walker; Han, Yi; Hu, Jianhong; Korchina, Viktoriya; Lee, Sandra; Lewis, Lora; Li, Wei; Liu, Xiuping; Morgan, Margaret; Morton, Donna; Muzny, Donna; Santibanez, Jireh; Sheth, Margi; Shinbrot, Eve; Wang, Linghua; Wang, Min; Wheeler, David A.; Xi, Liu; Zhao, Fengmei; Hess, Julian; Appelbaum, Elizabeth L.; Bailey, Matthew; Cordes, Matthew G.; Ding, Li; Fronick, Catrina C.; Fulton, Lucinda A.; Fulton, Robert S.; Kandoth, Cyriac; Mardis, Elaine R.; McLellan, Michael D.; Miller, Christopher A.; Schmidt, Heather K.; Wilson, Richard K.; Crain, Daniel; Curley, Erin; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Penny, Robert; Shelton, Candace; Shelton, Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Wise, Lisa; Zmuda, Erik; Corcoran, Niall; Costello, Tony; Hovens, Christopher; Carvalho, Andre L.; de Carvalho, Ana C.; Fregnani, José H.; Longatto-Filho, Adhemar; Reis, Rui M.; Scapulatempo-Neto, Cristovam; Silveira, Henrique C.S.; Vidal, Daniel O.; Burnette, Andrew; Eschbacher, Jennifer; Hermes, Beth; Noss, Ardene; Singh, Rosy; Anderson, Matthew L.; Castro, Patricia D.; Ittmann, Michael; Huntsman, David; Kohl, Bernard; Le, Xuan; Thorp, Richard; Andry, Chris; Duffy, Elizabeth R.; Lyadov, Vladimir; Paklina, Oxana; Setdikova, Galiya; Shabunin, Alexey; Tavobilov, Mikhail; McPherson, Christopher; Warnick, Ronald; Berkowitz, Ross; Cramer, Daniel; Feltmate, Colleen; Horowitz, Neil; Kibel, Adam; Muto, Michael; Raut, Chandrajit P.; Malykh, Andrei; Barnholtz-Sloan, Jill S.; Barrett, Wendi; Devine, Karen; Fulop, Jordonna; Ostrom, Quinn T.; Shimmel, Kristen; Wolinsky, Yingli; Sloan, Andrew E.; De Rose, Agostino; Giuliante, Felice; Goodman, Marc; Karlan, Beth Y.; Hagedorn, Curt H.; Eckman, John; Harr, Jodi; Myers, Jerome; Tucker, Kelinda; Zach, Leigh Anne; Deyarmin, Brenda; Hu, Hai; Kvecher, Leonid; Larson, Caroline; Mural, Richard J.; Somiari, Stella; Vicha, Ales; Zelinka, Tomas; Bennett, Joseph; Iacocca, Mary; Rabeno, Brenda; Swanson, Patricia; Latour, Mathieu; Lacombe, Louis; Têtu, Bernard; Bergeron, Alain; McGraw, Mary; Staugaitis, Susan M.; Chabot, John; Hibshoosh, Hanina; Sepulveda, Antonia; Su, Tao; Wang, Timothy; Potapova, Olga; Voronina, Olga; Desjardins, Laurence; Mariani, Odette; Roman-Roman, Sergio; Sastre, Xavier; Stern, Marc Henri; Cheng, Feixiong; Signoretti, Sabina; Berchuck, Andrew; Bigner, Darell; Lipp, Eric; Marks, Jeffrey; McCall, Shannon; McLendon, Roger; Secord, Angeles; Sharp, Alexis; Behera, Madhusmita; Brat, Daniel J.; Chen, Amy; Delman, Keith; Force, Seth; Khuri, Fadlo; Magliocca, Kelly; Maithel, Shishir; Olson, Jeffrey J.; Owonikoko, Taofeek; Pickens, Alan; Ramalingam, Suresh; Shin, Dong M.; Sica, Gabriel; Van Meir, Erwin G.; Zhang, Hongzheng; Eijckenboom, Wil; Gillis, Ad; Korpershoek, Esther; Looijenga, Leendert; Oosterhuis, Wolter; Stoop, Hans; van Kessel, Kim E.; Zwarthoff, Ellen C.; Calatozzolo, Chiara; Cuppini, Lucia; Cuzzubbo, Stefania; DiMeco, Francesco; Finocchiaro, Gaetano; Mattei, Luca; Perin, Alessandro; Pollo, Bianca; Chen, Chu; Houck, John; Lohavanichbutr, Pawadee; Hartmann, Arndt; Stoehr, Christine; Stoehr, Robert; Taubert, Helge; Wach, Sven; Wullich, Bernd; Kycler, Witold; Murawa, Dawid; Wiznerowicz, Maciej; Chung, Ki; Edenfield, W. Jeffrey; Martin, Julie; Baudin, Eric; Bubley, Glenn; Bueno, Raphael; De Rienzo, Assunta; Richards, William G.; Kalkanis, Steven; Mikkelsen, Tom; Noushmehr, Houtan; Scarpace, Lisa; Girard, Nicolas; Aymerich, Marta; Campo, Elias; Giné, Eva; Guillermo, Armando López; Van Bang, Nguyen; Hanh, Phan Thi; Phu, Bui Duc; Tang, Yufang; Colman, Howard; Evason, Kimberley; Dottino, Peter R.; Martignetti, John A.; Gabra, Hani; Juhl, Hartmut; Akeredolu, Teniola; Stepa, Serghei; Hoon, Dave; Ahn, Keunsoo; Kang, Koo Jeong; Beuschlein, Felix; Breggia, Anne; Birrer, Michael; Bell, Debra; Borad, Mitesh; Bryce, Alan H.; Castle, Erik; Chandan, Vishal; Cheville, John; Copland, John A.; Farnell, Michael; Flotte, Thomas; Giama, Nasra; Ho, Thai; Kendrick, Michael; Kocher, Jean Pierre; Kopp, Karla; Moser, Catherine; Nagorney, David; O'Brien, Daniel; O'Neill, Brian Patrick; Patel, Tushar; Petersen, Gloria; Que, Florencia; Rivera, Michael; Roberts, Lewis; Smallridge, Robert; Smyrk, Thomas; Stanton, Melissa; Thompson, R. Houston; Torbenson, Michael; Yang, Ju Dong; Zhang, Lizhi; Brimo, Fadi; Ajani, Jaffer A.; Angulo Gonzalez, Ana Maria; Behrens, Carmen; Bondaruk, Jolanta; Broaddus, Russell; Czerniak, Bogdan; Esmaeli, Bita; Fujimoto, Junya; Gershenwald, Jeffrey; Guo, Charles; Lazar, Alexander J.; Logothetis, Christopher; Meric-Bernstam, Funda; Moran, Cesar; Ramondetta, Lois; Rice, David; Sood, Anil; Tamboli, Pheroze; Thompson, Timothy; Troncoso, Patricia; Tsao, Anne; Wistuba, Ignacio; Carter, Candace; Haydu, Lauren; Hersey, Peter; Jakrot, Valerie; Kakavand, Hojabr; Kefford, Richard; Lee, Kenneth; Long, Georgina; Mann, Graham; Quinn, Michael; Saw, Robyn; Scolyer, Richard; Shannon, Kerwin; Spillane, Andrew; Stretch, Jonathan; Synott, Maria; Thompson, John; Wilmott, James; Al-Ahmadie, Hikmat; Chan, Timothy A.; Ghossein, Ronald; Gopalan, Anuradha; Levine, Douglas A.; Reuter, Victor; Singer, Samuel; Singh, Bhuvanesh; Tien, Nguyen Viet; Broudy, Thomas; Mirsaidi, Cyrus; Nair, Praveen; Drwiega, Paul; Miller, Judy; Smith, Jennifer; Zaren, Howard; Park, Joong Won; Hung, Nguyen Phi; Kebebew, Electron; Linehan, W. Marston; Metwalli, Adam R.; Pacak, Karel; Pinto, Peter A.; Schiffman, Mark; Schmidt, Laura S.; Vocke, Cathy D.; Wentzensen, Nicolas; Worrell, Robert; Yang, Hannah; Moncrieff, Marc; Goparaju, Chandra; Melamed, Jonathan; Pass, Harvey; Botnariuc, Natalia; Caraman, Irina; Cernat, Mircea; Chemencedji, Inga; Clipca, Adrian; Doruc, Serghei; Gorincioi, Ghenadie; Mura, Sergiu; Pirtac, Maria; Stancul, Irina; Tcaciuc, Diana; Albert, Monique; Alexopoulou, Iakovina; Arnaout, Angel; Bartlett, John; Engel, Jay; Gilbert, Sebastien; Parfitt, Jeremy; Sekhon, Harman; Thomas, George; Rassl, Doris M.; Rintoul, Robert C.; Bifulco, Carlo; Tamakawa, Raina; Urba, Walter; Hayward, Nicholas; Timmers, Henri; Antenucci, Anna; Facciolo, Francesco; Grazi, Gianluca; Marino, Mirella; Merola, Roberta; de Krijger, Ronald; Gimenez-Roqueplo, Anne Paule; Piché, Alain; Chevalier, Simone; McKercher, Ginette; Birsoy, Kivanc; Barnett, Gene; Brewer, Cathy; Farver, Carol; Naska, Theresa; Pennell, Nathan A.; Raymond, Daniel; Schilero, Cathy; Smolenski, Kathy; Williams, Felicia; Morrison, Carl; Borgia, Jeffrey A.; Liptay, Michael J.; Pool, Mark; Seder, Christopher W.; Junker, Kerstin; Omberg, Larsson; Dinkin, Mikhail; Manikhas, George; Alvaro, Domenico; Bragazzi, Maria Consiglia; Cardinale, Vincenzo; Carpino, Guido; Gaudio, Eugenio; Chesla, David; Cottingham, Sandra; Dubina, Michael; Moiseenko, Fedor; Dhanasekaran, Renumathy; Becker, Karl Friedrich; Janssen, Klaus Peter; Slotta-Huspenina, Julia; Abdel-Rahman, Mohamed H.; Aziz, Dina; Bell, Sue; Cebulla, Colleen M.; Davis, Amy; Duell, Rebecca; Elder, J. Bradley; Hilty, Joe; Kumar, Bahavna; Lang, James; Lehman, Norman L.; Mandt, Randy; Nguyen, Phuong; Pilarski, Robert; Rai, Karan; Schoenfield, Lynn; Senecal, Kelly; Wakely, Paul; Hansen, Paul; Lechan, Ronald; Powers, James; Tischler, Arthur; Grizzle, William E.; Sexton, Katherine C.; Kastl, Alison; Henderson, Joel; Porten, Sima; Waldmann, Jens; Fassnacht, Martin; Asa, Sylvia L.; Schadendorf, Dirk; Couce, Marta; Graefen, Markus; Huland, Hartwig; Sauter, Guido; Schlomm, Thorsten; Simon, Ronald; Tennstedt, Pierre; Olabode, Oluwole; Nelson, Mark; Bathe, Oliver; Carroll, Peter R.; Chan, June M.; Disaia, Philip; Glenn, Pat; Kelley, Robin K.; Landen, Charles N.; Phillips, Joanna; Prados, Michael; Simko, Jeffry; Smith-McCune, Karen; VandenBerg, Scott; Roggin, Kevin; Fehrenbach, Ashley; Kendler, Ady; Sifri, Suzanne; Steele, Ruth; Jimeno, Antonio; Carey, Francis; Forgie, Ian; Mannelli, Massimo; Carney, Michael; Hernandez, Brenda; Campos, Benito; Herold-Mende, Christel; Jungk, Christin; Unterberg, Andreas; von Deimling, Andreas; Bossler, Aaron; Galbraith, Joseph; Jacobus, Laura; Knudson, Michael; Knutson, Tina; Ma, Deqin; Milhem, Mohammed; Sigmund, Rita; Godwin, Andrew K.; Madan, Rashna; Rosenthal, Howard G.; Adebamowo, Clement; Adebamowo, Sally N.; Boussioutas, Alex; Beer, David; Giordano, Thomas; Mes-Masson, Anne Marie; Saad, Fred; Bocklage, Therese; Landrum, Lisa; Mannel, Robert; Moore, Kathleen; Moxley, Katherine; Postier, Russel; Walker, Joan; Zuna, Rosemary; Feldman, Michael; Valdivieso, Federico; Dhir, Rajiv; Luketich, James; Mora Pinero, Edna M.; Quintero-Aguilo, Mario; Carlotti, Carlos Gilberto; Dos Santos, Jose Sebastião; Kemp, Rafael; Sankarankuty, Ajith; Tirapelli, Daniela; Catto, James; Agnew, Kathy; Swisher, Elizabeth; Creaney, Jenette; Robinson, Bruce; Shelley, Carl Simon; Godwin, Eryn M.; Kendall, Sara; Shipman, Cassaundra; Bradford, Carol; Carey, Thomas; Haddad, Andrea; Moyer, Jeffey; Peterson, Lisa; Prince, Mark; Rozek, Laura; Wolf, Gregory; Bowman, Rayleen; Fong, Kwun M.; Yang, Ian; Korst, Robert; Rathmell, W. Kimryn; Fantacone-Campbell, J. Leigh; Hooke, Jeffrey A.; Kovatich, Albert J.; Shriver, Craig D.; DiPersio, John; Drake, Bettina; Govindan, Ramaswamy; Heath, Sharon; Ley, Timothy; Van Tine, Brian; Westervelt, Peter; Rubin, Mark A.; Lee, Jung Il; Aredes, Natália D.; Mariamidze, Armaz

2018-01-01

The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a

Functional Plasma-Deposited Coatings

Directory of Open Access Journals (Sweden)

Mykhaylo Pashechko

2017-12-01

Full Text Available The paper focuses on the problem of low adhesion of plasma sprayed coatings to the substrate. The subsequent laser treatment modes and their influence on the coating-substrate interface were studied. This allows to decrease the level of metstability of the coating, thus decreasing its hardness down to 11-12 GPa on the surface and to about 9 GPa on depth of 400 µm. The redistribution of alloying elements through solid and liquid diffusion improves mechanical properties and rises the adhesion up to 450 MPa after remelting and up to 90-110 MPa after laser-aided thermal cycling. At he same time, remelting of coating helps to decrease its porosity down to 1%. Obtained complex of properties also allows to improve wear resistance of coatings and to decrease friction factor.

EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics

Directory of Open Access Journals (Sweden)

Coutant Sophie

2012-09-01

Full Text Available Abstract Background Whole exome sequencing (WES has become the strategy of choice to identify a coding allelic variant for a rare human monogenic disorder. This approach is a revolution in medical genetics history, impacting both fundamental research, and diagnostic methods leading to personalized medicine. A plethora of efficient algorithms has been developed to ensure the variant discovery. They generally lead to ~20,000 variations that have to be narrow down to find the potential pathogenic allelic variant(s and the affected gene(s. For this purpose, commonly adopted procedures which implicate various filtering strategies have emerged: exclusion of common variations, type of the allelics variants, pathogenicity effect prediction, modes of inheritance and multiple individuals for exome comparison. To deal with the expansion of WES in medical genomics individual laboratories, new convivial and versatile software tools have to implement these filtering steps. Non-programmer biologists have to be autonomous combining themselves different filtering criteria and conduct a personal strategy depending on their assumptions and study design. Results We describe EVA (Exome Variation Analyzer, a user-friendly web-interfaced software dedicated to the filtering strategies for medical WES. Thanks to different modules, EVA (i integrates and stores annotated exome variation data as strictly confidential to the project owner, (ii allows to combine the main filters dealing with common variations, molecular types, inheritance mode and multiple samples, (iii offers the browsing of annotated data and filtered results in various interactive tables, graphical visualizations and statistical charts, (iv and finally offers export files and cross-links to external useful databases and softwares for further prioritization of the small subset of sorted candidate variations and genes. We report a demonstrative case study that allowed to identify a new candidate gene

Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy.

NARCIS (Netherlands)

Otto, E.A.; Hurd, T.W.; Airik, R.; Chaki, M.; Zhou, W.; Stoetzel, C.; Patil, S.B.; Levy, S.; Ghosh, A.K.; Murga-Zamalloa, C.A.; Reeuwijk, J. van; Letteboer, S.J.F.; Sang, L.; Giles, R.H.; Liu, Q.; Coene, K.L.M.; Estrada-Cuzcano, A.; Collin, R.W.J.; McLaughlin, H.M.; Held, S.; Kasanuki, J.M.; Ramaswami, G.; Conte, J.; Lopez, I.; Washburn, J.; Macdonald, J.; Hu, J.; Yamashita, Y.; Maher, E.R.; Guay-Woodford, L.M.; Neumann, H.P.; Obermuller, N.; Koenekoop, R.K.; Bergmann, C.; Bei, X.; Lewis, R.A.; Katsanis, N.; Lopes, V.; Williams, D.S.; Lyons, R.H.; Dang, C.V.; Brito, D.A.; Dias, M.B.; Zhang, X.; Cavalcoli, J.D.; Nurnberg, G.; Nurnberg, P.; Pierce, E.A.; Jackson, P.K.; Antignac, C.; Saunier, S.; Roepman, R.; Dollfus, H.; Khanna, H.; Hildebrandt, F.

2010-01-01

Nephronophthisis-related ciliopathies (NPHP-RC) are recessive disorders that feature dysplasia or degeneration occurring preferentially in the kidney, retina and cerebellum. Here we combined homozygosity mapping with candidate gene analysis by performing 'ciliopathy candidate exome capture' followed

Regularized rare variant enrichment analysis for case-control exome sequencing data.

Science.gov (United States)

Larson, Nicholas B; Schaid, Daniel J

2014-02-01

Rare variants have recently garnered an immense amount of attention in genetic association analysis. However, unlike methods traditionally used for single marker analysis in GWAS, rare variant analysis often requires some method of aggregation, since single marker approaches are poorly powered for typical sequencing study sample sizes. Advancements in sequencing technologies have rendered next-generation sequencing platforms a realistic alternative to traditional genotyping arrays. Exome sequencing in particular not only provides base-level resolution of genetic coding regions, but also a natural paradigm for aggregation via genes and exons. Here, we propose the use of penalized regression in combination with variant aggregation measures to identify rare variant enrichment in exome sequencing data. In contrast to marginal gene-level testing, we simultaneously evaluate the effects of rare variants in multiple genes, focusing on gene-based least absolute shrinkage and selection operator (LASSO) and exon-based sparse group LASSO models. By using gene membership as a grouping variable, the sparse group LASSO can be used as a gene-centric analysis of rare variants while also providing a penalized approach toward identifying specific regions of interest. We apply extensive simulations to evaluate the performance of these approaches with respect to specificity and sensitivity, comparing these results to multiple competing marginal testing methods. Finally, we discuss our findings and outline future research. © 2013 WILEY PERIODICALS, INC.

Exome Sequencing Fails to Identify the Genetic Cause of Aicardi Syndrome.

Science.gov (United States)

Lund, Caroline; Striano, Pasquale; Sorte, Hanne Sørmo; Parisi, Pasquale; Iacomino, Michele; Sheng, Ying; Vigeland, Magnus D; Øye, Anne-Marte; Møller, Rikke Steensbjerre; Selmer, Kaja K; Zara, Federico

2016-09-01

Aicardi syndrome (AS) is a well-characterized neurodevelopmental disorder with an unknown etiology. In this study, we performed whole-exome sequencing in 11 female patients with the diagnosis of AS, in order to identify the disease-causing gene. In particular, we focused on detecting variants in the X chromosome, including the analysis of variants with a low number of sequencing reads, in case of somatic mosaicism. For 2 of the patients, we also sequenced the exome of the parents to search for de novo mutations. We did not identify any genetic variants likely to be damaging. Only one single missense variant was identified by the de novo analyses of the 2 trios, and this was considered benign. The failure to identify a disease gene in this study may be due to technical limitations of our study design, including the possibility that the genetic aberration leading to AS is situated in a non-exonic region or that the mutation is somatic and not detectable by our approach. Alternatively, it is possible that AS is genetically heterogeneous and that 11 patients are not sufficient to reveal the causative genes. Future studies of AS should consider designs where also non-exonic regions are explored and apply a sequencing depth so that also low-grade somatic mosaicism can be detected.

Bioinformatics Interpretation of Exome Sequencing: Blood Cancer

Directory of Open Access Journals (Sweden)

Jiwoong Kim

2013-03-01

Full Text Available We had analyzed 10 exome sequencing data and single nucleotide polymorphism chips for blood cancer provided by the PGM21 (The National Project for Personalized Genomic Medicine Award program. We had removed sample G06 because the pair is not correct and G10 because of possible contamination. In-house software somatic copy-number and heterozygosity alteration estimation (SCHALE was used to detect one loss of heterozygosity region in G05. We had discovered 27 functionally important mutations. Network and pathway analyses gave us clues that NPM1, GATA2, and CEBPA were major driver genes. By comparing with previous somatic mutation profiles, we had concluded that the provided data originated from acute myeloid leukemia. Protein structure modeling showed that somatic mutations in IDH2, RASGEF1B, and MSH4 can affect protein structures.

Optical and magneto-optical properties of spin coated films of novel trinuclear bis(oxamato) and bis(oxamidato) type complexes

Energy Technology Data Exchange (ETDEWEB)

Abdulmalic, Mohammad A. [Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Chemie, Straße der Nationen 62, D-09111 Chemnitz (Germany); Fronk, Michael [Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Physik, Reichenhainer Straße 70, D-09107 Chemnitz (Germany); Bräuer, Björn [Stanford Institute of Materials and Energy Science, Stanford University, Stanford, CA 94025 (United States); Zahn, Dietrich R.T. [Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Physik, Reichenhainer Straße 70, D-09107 Chemnitz (Germany); Salvan, Georgeta, E-mail: salvan@physik.tu-chemnitz.de [Technische Universität Chemnitz, Fakultät für Naturwissenschaften, Institut für Physik, Reichenhainer Straße 70, D-09107 Chemnitz (Germany); Eya' ane Meva, Francois [Department of Pharmaceutical Sciences, Faculty of Medicine and Pharmaceutical Sciences, University of Douala, BP 2701 (Cameroon); and others

2016-12-01

This work reports the first example of the spectroscopic measurements of the Magneto-Optical Kerr Effect (MOKE) of films being composed of trinuclear transition metal complexes on a non-transparent substrate at room temperature. The thin films of the tailor-made trinuclear bis(oxamidato) type complex 5 ([Cu{sub 3}(opbo{sup n}Pr{sub 2})(tmcd){sub 2}(NO{sub 3}){sub 2}], opbo{sup n}Pr{sub 2} = o-phenylenebis(N’-{sup n}propyloxamido, tmcd=trans-(1 R,2 R)-N,N,N′,N′-tetramethyl-cyclohexanediamine) and of the bis(oxamato) type complexes 11 ([Cu{sub 2}Ni(opbaCF{sub 3})(pmdta){sub 2}(NO{sub 3}){sub 2}], opbaCF{sub 3} = 4-trifluoromethyl-o-phenylenebis(oxamato), pmdta = N,N,N,′N″,N″-pentamethyldiethylenetriamine) and 12 ([Cu{sub 3}(opba)(bppe){sub 2}(NO{sub 3}){sub 2}] (opba = o-phenylenebis(oxamato), bppe = S-N,N-bis(2-picolyl)−1-phenylethylamine) were fabricated by spin-coating and their thicknesses in the range between 0.5 µm and 2 µm was determined by spectroscopic ellipsometry. Based on the spectroscopic ellipsometry results it was also possible to determine the optical constants of the film and compare them with the absorption of the complexes in solution in order to confirm the complex integrity after the film deposition. The fabrication of high-quality films which exhibit Kerr rotation up to 0.2 mrad (11.5 mdeg) was only possible due to tailor-made synthesis, which allows circumventing intermolecular interactions of the trinuclear complexes during the film formation. - Highlights: • Tailor-made trinuclear bis(oxamidato) and bis(oxamato) type complexes were synthesized. • Thin films (between 0.5 µm and 2 µm) were fabricated by spin-coating. • The film optical constants indicate the complex integrity after the deposition. • Film quality enabled first spectroscopic MOKE measurements of multi-nuclear complexes. • Magneto-optical Kerr rotation up to 11.5 mdeg was observed at RT (in 1.7 T).

Tribological coatings for complex mechanical elements produced by supersonic cluster beam deposition of metal dichalcogenide nanoparticles

Science.gov (United States)

Piazzoni, C.; Buttery, M.; Hampson, M. R.; Roberts, E. W.; Ducati, C.; Lenardi, C.; Cavaliere, F.; Piseri, P.; Milani, P.

2015-07-01

Fullerene-like MoS2 and WS2 nanoparticles can be used as building blocks for the fabrication of fluid and solid lubricants. Metal dichalcogenide films have a very low friction coefficient in vacuum, therefore they have mostly been used as solid lubricants in space and vacuum applications. Unfortunately, their use is significantly hampered by the fact that in the presence of humidity, oxygen and moisture, the low-friction properties of these materials rapidly degrade due to oxidation. The use of closed-cage MoS2 and WS2 nanoparticles may eliminate this problem, although the fabrication of lubricant thin films starting from dichalcogenide nanoparticles is, to date, a difficult task. Here we demonstrate the use of supersonic cluster beam deposition for the coating of complex mechanical elements (angular contact ball bearings) with nanostructured MoS2 and WS2 thin films. We report structural and tribological characterization of the coatings in view of the optimization of tribological performances for aerospace applications.

Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome.

NARCIS (Netherlands)

Krawitz, P.M.; Schweiger, M.R.; Rodelsperger, C.; Marcelis, C.L.M.; Kolsch, U.; Meisel, C.; Stephani, F.; Kinoshita, T.; Murakami, Y.; Bauer, S.; Isau, M.; Fischer, A.; Dahl, A.; Kerick, M.; Hecht, J.; Kohler, S.; Jager, M. de; Grunhagen, J.; Condor, B.J. de; Doelken, S.; Brunner, H.G.; Meinecke, P.; Passarge, E.; Thompson, M.D.; Cole, D.E.; Horn, D.; Roscioli, T.; Mundlos, S.; Robinson, P.N.

2010-01-01

Hyperphosphatasia mental retardation (HPMR) syndrome is an autosomal recessive form of mental retardation with distinct facial features and elevated serum alkaline phosphatase. We performed whole-exome sequencing in three siblings of a nonconsanguineous union with HPMR and performed computational

Template-directed formation of functional complex metal-oxide nanostructures by combination of sol-gel processing and spin coating

International Nuclear Information System (INIS)

Choi, Y.C.; Kim, J.; Bu, S.D.

2006-01-01

We report the template-based formation of functional complex metal-oxide nanostructures by a combination of sol-gel processing and spin coating. This method employs the spin-coating of a sol-gel solution into an anodic aluminum oxide membrane (SSAM). Various metal-oxide nanowires and nanotubes with a high aspect-ratio were prepared. The aspect-ratios of the PbO 2 nanowires and Pb(Zr 0.52 Ti 0.48 )O 3 nanowires were about 300 and 400, respectively, and their diameters were about 50 nm. The fabricated PbTiO 3 nanotubes have a relatively constant wall thickness of about 20 nm with an outer diameter of about 60 nm. The deposition time for all of the fabricated metal-oxide nanowires and nanotubes is less than 120 s, which is far shorter than those required in both the sol-gel dipping and sol-gel electrophoretic methods. These results indicate that the SSAM method can be a versatile pathway to prepare functional complex metal-oxide nanowires and nanotubes with a high aspect-ratio. The possible formation process for the one-dimensional nanostructures by SSAM is discussed

Whole-exome sequencing analysis of Waardenburg syndrome in a Chinese family

Science.gov (United States)

Chen, Dezhong; Zhao, Na; Wang, Jing; Li, Zhuoyu; Wu, Changxin; Fu, Jie; Xiao, Han

2017-01-01

Waardenburg syndrome (WS) is a dominantly inherited, genetically heterogeneous auditory-pigmentary syndrome characterized by non-progressive sensorineural hearing loss and iris discoloration. By whole-exome sequencing (WES), we identified a nonsense mutation (c.598C>T) in PAX3 gene, predicted to be disease causing by in silico analysis. This is the first report of genetically diagnosed case of WS PAX3 c.598C>T nonsense mutation in Chinese ethnic origin by WES and in silico functional prediction methods. PMID:28690861

Whole-exome sequencing analysis of Waardenburg syndrome in a Chinese family.

Science.gov (United States)

Chen, Dezhong; Zhao, Na; Wang, Jing; Li, Zhuoyu; Wu, Changxin; Fu, Jie; Xiao, Han

2017-01-01

Waardenburg syndrome (WS) is a dominantly inherited, genetically heterogeneous auditory-pigmentary syndrome characterized by non-progressive sensorineural hearing loss and iris discoloration. By whole-exome sequencing (WES), we identified a nonsense mutation (c.598C>T) in PAX3 gene, predicted to be disease causing by in silico analysis. This is the first report of genetically diagnosed case of WS PAX3 c.598C>T nonsense mutation in Chinese ethnic origin by WES and in silico functional prediction methods.

Exome sequencing reveals VCP mutations as a cause of familial ALS

OpenAIRE

Johnson, Janel O.; Mandrioli, Jessica; Benatar, Michael; Abramzon, Yevgeniya; Van Deerlin, Vivianna M.; Trojanowski, John Q.; Gibbs, J Raphael; Brunetti, Maura; Gronka, Susan; Wuu, Joanne; Ding, Jinhui; McCluskey, Leo; Martinez-Lage, Maria; Falcone, Dana; Hernandez, Dena G.

2010-01-01

Using exome sequencing, we identified a p.R191Q amino acid change in the valosin-containing protein (VCP) gene in an Italian family with autosomal dominantly inherited amyotrophic lateral sclerosis (ALS). Mutations in VCP have previously been identified in families with Inclusion Body Myopathy, Paget’s disease and Frontotemporal Dementia (IBMPFD). Screening of VCP in a cohort of 210 familial ALS cases and 78 autopsy-proven ALS cases identified four additional mutations including a p.R155H mut...

Cellulose nanofibers use in coated paper

Science.gov (United States)

Richmond, Finley

Cellulose Nanofibers (CNF) are materials that can be obtained by the mechanical breakdown of natural fibers. CNF have the potential to be produced at low cost in a paper mill and may provide novel properties to paper, paper coatings, paints, or other products. However, suspensions have a complex rheology even at low solid contents. To be able to coat, pump, or mix CNF at moderate solids, it is critical to understand the rheology of these suspensions and how they flow in process equipment; current papers only report the rheology up to 6% solids. Few publications are available that describe the coating of CNF onto paper or the use of CNF as an additive into a paper coating. The rheology of CNF suspensions and coatings that contain CNF were characterized with parallel-disk geometry in a controlled stress rheometer. The steady shear viscosity, the complex viscosity, the storage modulus, and the yield stress were determined for the range of solids or concentrations (2.5-10.5%). CNF were coated onto paper with a laboratory rod coater, a size press and a high speed cylindrical laboratory coater (CLC). For each case, the coat weights were measures and the properties of the papers were characterized. CNF water base suspension was found to be a shear thinning with a power law index of around 0.1. Oscillatory tests showed a linear viscoelastic region at low strains and significant storage and loss moduli even at low solids. The Cox Merz rule does not hold for CNF suspensions or coating formulations that contain CNF with complex viscosities that are about 100 times larger than the steady shear viscosities. Paper coating formulations that contain CNF were found to have viscosities and storage and loss moduli that are over ten times larger than coatings that contain starch at similar solids. CNF suspensions were coated on papers with low amount transferred on paper either at high solids or high nip loadings. The amount transferred appears to be controlled by an interaction of

The coat protein complex II, COPII, protein Sec13 directly interacts with presenilin-1

International Nuclear Information System (INIS)

Nielsen, Anders Lade

2009-01-01

Mutations in the human gene encoding presenilin-1, PS1, account for most cases of early-onset familial Alzheimer's disease. PS1 has nine transmembrane domains and a large loop orientated towards the cytoplasm. PS1 locates to cellular compartments as endoplasmic reticulum (ER), Golgi apparatus, vesicular structures, and plasma membrane, and is an integral member of γ-secretase, a protein protease complex with specificity for intra-membranous cleavage of substrates such as β-amyloid precursor protein. Here, an interaction between PS1 and the Sec13 protein is described. Sec13 takes part in coat protein complex II, COPII, vesicular trafficking, nuclear pore function, and ER directed protein sequestering and degradation control. The interaction maps to the N-terminal part of the large hydrophilic PS1 loop and the first of the six WD40-repeats present in Sec13. The identified Sec13 interaction to PS1 is a new candidate interaction for linking PS1 to secretory and protein degrading vesicular circuits.

The coat protein complex II, COPII, protein Sec13 directly interacts with presenilin-1

Energy Technology Data Exchange (ETDEWEB)

Nielsen, Anders Lade, E-mail: aln@humgen.au.dk [Department of Human Genetics, The Bartholin Building, University of Aarhus, DK-8000 Aarhus C (Denmark)

2009-10-23

Mutations in the human gene encoding presenilin-1, PS1, account for most cases of early-onset familial Alzheimer's disease. PS1 has nine transmembrane domains and a large loop orientated towards the cytoplasm. PS1 locates to cellular compartments as endoplasmic reticulum (ER), Golgi apparatus, vesicular structures, and plasma membrane, and is an integral member of {gamma}-secretase, a protein protease complex with specificity for intra-membranous cleavage of substrates such as {beta}-amyloid precursor protein. Here, an interaction between PS1 and the Sec13 protein is described. Sec13 takes part in coat protein complex II, COPII, vesicular trafficking, nuclear pore function, and ER directed protein sequestering and degradation control. The interaction maps to the N-terminal part of the large hydrophilic PS1 loop and the first of the six WD40-repeats present in Sec13. The identified Sec13 interaction to PS1 is a new candidate interaction for linking PS1 to secretory and protein degrading vesicular circuits.

Enhanced photoluminescence from single nitrogen-vacancy defects in nanodiamonds coated with phenol-ionic complexes.

Science.gov (United States)

Bray, Kerem; Previdi, Rodolfo; Gibson, Brant C; Shimoni, Olga; Aharonovich, Igor

2015-03-21

Fluorescent nanodiamonds are attracting major attention in the field of bio-sensing and bio-labeling. In this work we demonstrate a robust approach to achieve an encapsulation of individual nanodiamonds with phenol-ionic complexes that enhance the photoluminescence from single nitrogen vacancy (NV) centers. We show that single NV centres in the coated nanodiamonds also exhibit shorter lifetimes, opening another channel for high resolution sensing. We propose that the nanodiamond encapsulation reduces the non-radiative decay pathways of the NV color centers. Our results provide a versatile and assessable way to enhance photoluminescence from nanodiamond defects that can be used in a variety of sensing and imaging applications.

Bioinspired tannic acid-copper complexes as selective coating for nanofiltration membranes

KAUST Repository

Chakrabarty, Tina

2017-04-27

Bio-polyphenols that are present in tea, date fruits, chockolate and many other plants have been recognized as scaffold material for the manufacture of composite filtration membranes. These phenolic biomolecules possess abundant gallol (1,2,3-trihydroxyphenyl) and catechol (1,2-dihydroxyphenyl) functional groups, which allow the spontaneous formation of a thin polymerized layer at the right pH conditions. Here, we report a facile and cost-effective method to coat porous membranes via the complexation of tannic acid (TA) and cupric acetate (mono hydrate) through co-deposition. The modified membranes were investigated by XPS, ATR/FTIR, water contact angle, SEM and water permeance for a structural and morphological analysis. The obtained results reveal that the modified membranes with TA and cupric acetate (CuII) developed a thin skin layer, which showed excellent hydrophilicity with good water permeance. These membranes were tested with different molecular weight polyethylene glycols (PEG) in aqueous solution; the MWCO was around 600 Daltons.

Irritable bowel syndrome-diarrhea: characterization of genotype by exome sequencing, and phenotypes of bile acid synthesis and colonic transit

Science.gov (United States)

Klee, Eric W.; Shin, Andrea; Carlson, Paula; Li, Ying; Grover, Madhusudan; Zinsmeister, Alan R.

2013-01-01

The study objectives were: to mine the complete exome to identify putative rare single nucleotide variants (SNVs) associated with irritable bowel syndrome (IBS)-diarrhea (IBS-D) phenotype, to assess genes that regulate bile acids in IBS-D, and to explore univariate associations of SNVs with symptom phenotype and quantitative traits in an independent IBS cohort. Using principal components analysis, we identified two groups of IBS-D (n = 16) with increased fecal bile acids: rapid colonic transit or high bile acids synthesis. DNA was sequenced in depth, analyzing SNVs in bile acid genes (ASBT, FXR, OSTα/β, FGF19, FGFR4, KLB, SHP, CYP7A1, LRH-1, and FABP6). Exome findings were compared with those of 50 similar ethnicity controls. We assessed univariate associations of each SNV with quantitative traits and a principal components analysis and associations between SNVs in KLB and FGFR4 and symptom phenotype in 405 IBS, 228 controls and colonic transit in 70 IBS-D, 71 IBS-constipation. Mining the complete exome did not reveal significant associations with IBS-D over controls. There were 54 SNVs in 10 of 11 bile acid-regulating genes, with no SNVs in FGF19; 15 nonsynonymous SNVs were identified in similar proportions of IBS-D and controls. Variations in KLB (rs1015450, downstream) and FGFR4 [rs434434 (intronic), rs1966265, and rs351855 (nonsynonymous)] were associated with colonic transit (rs1966265; P = 0.043), fecal bile acids (rs1015450; P = 0.064), and principal components analysis groups (all 3 FGFR4 SNVs; P transit (P = 0.066). Thus exome sequencing identified additional variants in KLB and FGFR4 associated with bile acids or colonic transit in IBS-D. PMID:24200957

[Exome sequencing revealed Allan-Herndon-Dudley syndrome underlying multiple disabilities].

Science.gov (United States)

Arvio, Maria; Philips, Anju K; Ahvenainen, Minna; Somer, Mirja; Kalscheuer, Vera; Järvelä, Irma

2014-01-01

Normal function of the thyroid gland is the cornerstone of a child's mental development and physical growth. We describe a Finnish family, in which the diagnosis of three brothers became clear after investigations that lasted for more than 30 years. Two of the sons have already died. DNA analysis of the third one, a 16-year-old boy, revealed in exome sequencing of the complete X chromosome a mutation in the SLC16A2 gene, i.e. MCT8, coding for a thyroid hormone transport protein. Allan-Herndon-Dudley syndrome was thus shown to be the cause of multiple disabilities.

Candidate gene analysis and exome sequencing confirm LBX1 as a susceptibility gene for idiopathic scoliosis

DEFF Research Database (Denmark)

Grauers, Anna; Wang, Jingwen; Einarsdottir, Elisabet

2015-01-01

samples from 100 surgically treated idiopathic scoliosis patients. Novel or rare missense, nonsense, or splice site variants were selected for individual genotyping in the 1,739 cases and 1,812 controls. In addition, the 5'UTR, noncoding exon and promoter regions of LBX1, not covered by exome sequencing...... by exome sequencing after filtration and an initial genotyping validation. However, we could not verify any association to idiopathic scoliosis in the large cohort of 1,739 cases and 1,812 controls. We did not find any variants in the 5'UTR, noncoding exon and promoter regions of LBX1. CONCLUSIONS: Here...... that are significantly associated with idiopathic scoliosis in Asian and Caucasian populations, rs11190870 close to the LBX1 gene being the most replicated finding. PURPOSE: The aim of the present study was to investigate the genetics of idiopathic scoliosis in a Scandinavian cohort by performing a candidate gene study...

Coated particle waste form development

International Nuclear Information System (INIS)

Oma, K.H.; Buckwalter, C.Q.; Chick, L.A.

1981-12-01

Coated particle waste forms have been developed as part of the multibarrier concept at Pacific Northwest Laboratory under the Alternative Waste Forms Program for the Department of Energy. Primary efforts were to coat simulated nuclear waste glass marbles and ceramic pellets with low-temperature pyrolytic carbon (LT-PyC) coatings via the process of chemical vapor deposition (CVD). Fluidized bed (FB) coaters, screw agitated coaters (SAC), and rotating tube coaters were used. Coating temperatures were reduced by using catalysts and plasma activation. In general, the LT-PyC coatings did not provide the expected high leach resistance as previously measured for carbon alone. The coatings were friable and often spalled off the substrate. A totally different concept, thermal spray coating, was investigated at PNL as an alternative to CVD coating. Flame spray, wire gun, and plasma gun systems were evaluated using glass, ceramic, and metallic coating materials. Metal plasma spray coatings (Al, Sn, Zn, Pb) provided a two to three orders-of-magnitude increase in chemical durability. Because the aluminum coatings were porous, the superior leach resistance must be due to either a chemical interaction or to a pH buffer effect. Because they are complex, coated waste form processes rank low in process feasibility. Of all the possible coated particle processes, plasma sprayed marbles have the best rating. Carbon coating of pellets by CVD ranked ninth when compared with ten other processes. The plasma-spray-coated marble process ranked sixth out of eleven processes

Gratitude, protective buffering, and cognitive dissonance: How families respond to pediatric whole exome sequencing in the absence of actionable results.

Science.gov (United States)

Werner-Lin, Allison; Zaspel, Lori; Carlson, Mae; Mueller, Rebecca; Walser, Sarah A; Desai, Ria; Bernhardt, Barbara A

2018-03-01

Clinical genome and exome sequencing (CGES) may identify variants leading to targeted management of existing conditions. Yet, CGES often fails to identify pathogenic diagnostic variants and introduces uncertainties by detecting variants of uncertain significance (VUS) and secondary findings. This study investigated how families understand findings and adjust their perspectives on CGES. As part of NIH's Clinical Sequencing Exploratory Research Consortium, children were recruited from clinics at the Children's Hospital of Pennsylvania (CHOP) and offered exome sequencing. Primary pathogenic and possibly pathogenic, and some secondary findings were returned. Investigators digitally recorded results disclosure sessions and conducted 3-month follow up interviews with 10 adolescents and a parent. An interdisciplinary team coded all transcripts. Participants were initially disappointed with findings, yet reactions evolved within disclosure sessions and at 3-month interviews toward acceptance and satisfaction. Families erroneously expected, and prepared extensively, to learn about risk for common conditions. During disclosure sessions, parents and adolescents varied in how they monitored and responded to each others reactions. Several misinterpreted, or overestimated, the utility of findings to attribute meaning and achieve closure for the CGES experience. Participants perceived testing as an opportunity to improve disease management despite results that did not introduce new treatments or diagnoses. Future research may examine whether families experience cognitive dissonance regarding discrepancies between expectations and findings, and how protective buffering minimizes the burden of disappointment on loved ones. As CGES is increasingly integrated into clinical care providers must contend with tempering family expectations and interpretations of findings while managing complex medical care. © 2018 Wiley Periodicals, Inc.

Statistical guidance for experimental design and data analysis of mutation detection in rare monogenic mendelian diseases by exome sequencing.

Directory of Open Access Journals (Sweden)

Degui Zhi

Full Text Available Recently, whole-genome sequencing, especially exome sequencing, has successfully led to the identification of causal mutations for rare monogenic Mendelian diseases. However, it is unclear whether this approach can be generalized and effectively applied to other Mendelian diseases with high locus heterogeneity. Moreover, the current exome sequencing approach has limitations such as false positive and false negative rates of mutation detection due to sequencing errors and other artifacts, but the impact of these limitations on experimental design has not been systematically analyzed. To address these questions, we present a statistical modeling framework to calculate the power, the probability of identifying truly disease-causing genes, under various inheritance models and experimental conditions, providing guidance for both proper experimental design and data analysis. Based on our model, we found that the exome sequencing approach is well-powered for mutation detection in recessive, but not dominant, Mendelian diseases with high locus heterogeneity. A disease gene responsible for as low as 5% of the disease population can be readily identified by sequencing just 200 unrelated patients. Based on these results, for identifying rare Mendelian disease genes, we propose that a viable approach is to combine, sequence, and analyze patients with the same disease together, leveraging the statistical framework presented in this work.

Atypical case of Wolfram syndrome revealed through targeted exome sequencing in a patient with suspected mitochondrial disease.

Science.gov (United States)

Lieber, Daniel S; Vafai, Scott B; Horton, Laura C; Slate, Nancy G; Liu, Shangtao; Borowsky, Mark L; Calvo, Sarah E; Schmahmann, Jeremy D; Mootha, Vamsi K

2012-01-06

Mitochondrial diseases comprise a diverse set of clinical disorders that affect multiple organ systems with varying severity and age of onset. Due to their clinical and genetic heterogeneity, these diseases are difficult to diagnose. We have developed a targeted exome sequencing approach to improve our ability to properly diagnose mitochondrial diseases and apply it here to an individual patient. Our method targets mitochondrial DNA (mtDNA) and the exons of 1,600 nuclear genes involved in mitochondrial biology or Mendelian disorders with multi-system phenotypes, thereby allowing for simultaneous evaluation of multiple disease loci. Targeted exome sequencing was performed on a patient initially suspected to have a mitochondrial disorder. The patient presented with diabetes mellitus, diffuse brain atrophy, autonomic neuropathy, optic nerve atrophy, and a severe amnestic syndrome. Further work-up revealed multiple heteroplasmic mtDNA deletions as well as profound thiamine deficiency without a clear nutritional cause. Targeted exome sequencing revealed a homozygous c.1672C > T (p.R558C) missense mutation in exon 8 of WFS1 that has previously been reported in a patient with Wolfram syndrome. This case demonstrates how clinical application of next-generation sequencing technology can enhance the diagnosis of patients suspected to have rare genetic disorders. Furthermore, the finding of unexplained thiamine deficiency in a patient with Wolfram syndrome suggests a potential link between WFS1 biology and thiamine metabolism that has implications for the clinical management of Wolfram syndrome patients.

Atypical case of Wolfram syndrome revealed through targeted exome sequencing in a patient with suspected mitochondrial disease

Directory of Open Access Journals (Sweden)

Lieber Daniel S

2012-01-01

Full Text Available Abstract Background Mitochondrial diseases comprise a diverse set of clinical disorders that affect multiple organ systems with varying severity and age of onset. Due to their clinical and genetic heterogeneity, these diseases are difficult to diagnose. We have developed a targeted exome sequencing approach to improve our ability to properly diagnose mitochondrial diseases and apply it here to an individual patient. Our method targets mitochondrial DNA (mtDNA and the exons of 1,600 nuclear genes involved in mitochondrial biology or Mendelian disorders with multi-system phenotypes, thereby allowing for simultaneous evaluation of multiple disease loci. Case Presentation Targeted exome sequencing was performed on a patient initially suspected to have a mitochondrial disorder. The patient presented with diabetes mellitus, diffuse brain atrophy, autonomic neuropathy, optic nerve atrophy, and a severe amnestic syndrome. Further work-up revealed multiple heteroplasmic mtDNA deletions as well as profound thiamine deficiency without a clear nutritional cause. Targeted exome sequencing revealed a homozygous c.1672C > T (p.R558C missense mutation in exon 8 of WFS1 that has previously been reported in a patient with Wolfram syndrome. Conclusion This case demonstrates how clinical application of next-generation sequencing technology can enhance the diagnosis of patients suspected to have rare genetic disorders. Furthermore, the finding of unexplained thiamine deficiency in a patient with Wolfram syndrome suggests a potential link between WFS1 biology and thiamine metabolism that has implications for the clinical management of Wolfram syndrome patients.

Detection of 1p36 deletion by clinical exome-first diagnostic approach.

Science.gov (United States)

Watanabe, Miki; Hayabuchi, Yasunobu; Ono, Akemi; Naruto, Takuya; Horikawa, Hideaki; Kohmoto, Tomohiro; Masuda, Kiyoshi; Nakagawa, Ryuji; Ito, Hiromichi; Kagami, Shoji; Imoto, Issei

2016-01-01

Although chromosome 1p36 deletion syndrome is considered clinically recognizable based on characteristic features, the clinical manifestations of patients during infancy are often not consistent with those observed later in life. We report a 4-month-old girl who showed multiple congenital anomalies and developmental delay, but no clinical signs of syndromic disease caused by a terminal deletion in 1p36.32-p36.33 that was first identified by targeted-exome sequencing for molecular diagnosis.

Exome-first approach identified a novel gloss deletion associated with Lowe syndrome.

Science.gov (United States)

Watanabe, Miki; Nakagawa, Ryuji; Kohmoto, Tomohiro; Naruto, Takuya; Suga, Ken-Ichi; Goji, Aya; Horikawa, Hideaki; Masuda, Kiyoshi; Kagami, Shoji; Imoto, Issei

2016-01-01

Lowe syndrome (LS) is an X-linked disorder affecting the eyes, nervous system and kidneys, typically caused by missense or nonsense/frameshift OCRL mutations. We report a 6-month-old male clinically suspected to have LS, but without the Fanconi-type renal dysfunction. Using a targeted-exome sequencing-first approach, LS was diagnosed by the identification of a deletion involving 1.7 Mb at Xq25-q26.1, encompassing the entire OCRL gene and neighboring loci.

Exome sequencing analysis reveals variants in primary immunodeficiency genes in patients with very early onset inflammatory bowel disease.

Science.gov (United States)

Kelsen, Judith R; Dawany, Noor; Moran, Christopher J; Petersen, Britt-Sabina; Sarmady, Mahdi; Sasson, Ariella; Pauly-Hubbard, Helen; Martinez, Alejandro; Maurer, Kelly; Soong, Joanne; Rappaport, Eric; Franke, Andre; Keller, Andreas; Winter, Harland S; Mamula, Petar; Piccoli, David; Artis, David; Sonnenberg, Gregory F; Daly, Mark; Sullivan, Kathleen E; Baldassano, Robert N; Devoto, Marcella

2015-11-01

Very early onset inflammatory bowel disease (VEO-IBD), IBD diagnosed at 5 years of age or younger, frequently presents with a different and more severe phenotype than older-onset IBD. We investigated whether patients with VEO-IBD carry rare or novel variants in genes associated with immunodeficiencies that might contribute to disease development. Patients with VEO-IBD and parents (when available) were recruited from the Children's Hospital of Philadelphia from March 2013 through July 2014. We analyzed DNA from 125 patients with VEO-IBD (age, 3 wk to 4 y) and 19 parents, 4 of whom also had IBD. Exome capture was performed by Agilent SureSelect V4, and sequencing was performed using the Illumina HiSeq platform. Alignment to human genome GRCh37 was achieved followed by postprocessing and variant calling. After functional annotation, candidate variants were analyzed for change in protein function, minor allele frequency less than 0.1%, and scaled combined annotation-dependent depletion scores of 10 or less. We focused on genes associated with primary immunodeficiencies and related pathways. An additional 210 exome samples from patients with pediatric IBD (n = 45) or adult-onset Crohn's disease (n = 20) and healthy individuals (controls, n = 145) were obtained from the University of Kiel, Germany, and used as control groups. Four hundred genes and regions associated with primary immunodeficiency, covering approximately 6500 coding exons totaling more than 1 Mbp of coding sequence, were selected from the whole-exome data. Our analysis showed novel and rare variants within these genes that could contribute to the development of VEO-IBD, including rare heterozygous missense variants in IL10RA and previously unidentified variants in MSH5 and CD19. In an exome sequence analysis of patients with VEO-IBD and their parents, we identified variants in genes that regulate B- and T-cell functions and could contribute to pathogenesis. Our analysis could lead to the

Whole-exome sequencing of individuals from an isolated population implicates rare risk variants in bipolar disorder

DEFF Research Database (Denmark)

Lescai, F; Als, T D; Li, Q

2017-01-01

Bipolar disorder affects about 1% of the world's population, and its estimated heritability is about 75%. Only few whole genome or whole-exome sequencing studies in bipolar disorder have been reported, and no rare coding variants have yet been robustly identified. The use of isolated populations...

Whole Exome Sequencing in Females with Autism Implicates Novel and Candidate Genes

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Merlin G. Butler

2015-01-01

Full Text Available Classical autism or autistic disorder belongs to a group of genetically heterogeneous conditions known as Autism Spectrum Disorders (ASD. Heritability is estimated as high as 90% for ASD with a recently reported compilation of 629 clinically relevant candidate and known genes. We chose to undertake a descriptive next generation whole exome sequencing case study of 30 well-characterized Caucasian females with autism (average age, 7.7 ± 2.6 years; age range, 5 to 16 years from multiplex families. Genomic DNA was used for whole exome sequencing via paired-end next generation sequencing approach and X chromosome inactivation status. The list of putative disease causing genes was developed from primary selection criteria using machine learning-derived classification score and other predictive parameters (GERP2, PolyPhen2, and SIFT. We narrowed the variant list to 10 to 20 genes and screened for biological significance including neural development, function and known neurological disorders. Seventy-eight genes identified met selection criteria ranging from 1 to 9 filtered variants per female. Five females presented with functional variants of X-linked genes (IL1RAPL1, PIR, GABRQ, GPRASP2, SYTL4 with cadherin, protocadherin and ankyrin repeat gene families most commonly altered (e.g., CDH6, FAT2, PCDH8, CTNNA3, ANKRD11. Other genes related to neurogenesis and neuronal migration (e.g., SEMA3F, MIDN, were also identified.

Whole-exome sequencing identifies novel candidate predisposition genes for familial polycythemia vera.

Science.gov (United States)

Hirvonen, Elina A M; Pitkänen, Esa; Hemminki, Kari; Aaltonen, Lauri A; Kilpivaara, Outi

2017-04-20

Polycythemia vera (PV), characterized by massive production of erythrocytes, is one of the myeloproliferative neoplasms. Most patients carry a somatic gain-of-function mutation in JAK2, c.1849G > T (p.Val617Phe), leading to constitutive activation of JAK-STAT signaling pathway. Familial clustering is also observed occasionally, but high-penetrance predisposition genes to PV have remained unidentified. We studied the predisposition to PV by exome sequencing (three cases) in a Finnish PV family with four patients. The 12 shared variants (maximum allowed minor allele frequency  G (p.Phe418Leu) in ZXDC, c.1931C > G (p.Pro644Arg) in ATN1, and c.701G > A (p.Arg234Gln) in LRRC3. We also observed a rare, predicted benign germline variant c.2912C > G (p.Ala971Gly) in BCORL1 in all four patients. Somatic mutations in BCORL1 have been reported in myeloid malignancies. We further screened the variants in eight PV patients in six other Finnish families, but no other carriers were found. Exome sequencing provides a powerful tool for the identification of novel variants, and understanding the familial predisposition of diseases. This is the first report on Finnish familial PV cases, and we identified three novel candidate variants that may predispose to the disease.

Whole-exome re-sequencing in a family quartet identifies POP1 mutations as the cause of a novel skeletal dysplasia.

Directory of Open Access Journals (Sweden)

Evgeny A Glazov

2011-03-01

Full Text Available Recent advances in DNA sequencing have enabled mapping of genes for monogenic traits in families with small pedigrees and even in unrelated cases. We report the identification of disease-causing mutations in a rare, severe, skeletal dysplasia, studying a family of two healthy unrelated parents and two affected children using whole-exome sequencing. The two affected daughters have clinical and radiographic features suggestive of anauxetic dysplasia (OMIM 607095, a rare form of dwarfism caused by mutations of RMRP. However, mutations of RMRP were excluded in this family by direct sequencing. Our studies identified two novel compound heterozygous loss-of-function mutations in POP1, which encodes a core component of the RNase mitochondrial RNA processing (RNase MRP complex that directly interacts with the RMRP RNA domains that are affected in anauxetic dysplasia. We demonstrate that these mutations impair the integrity and activity of this complex and that they impair cell proliferation, providing likely molecular and cellular mechanisms by which POP1 mutations cause this severe skeletal dysplasia.

An Exome Sequencing Study to Assess the Role of Rare Genetic Variation in Pulmonary Fibrosis.

Science.gov (United States)

Petrovski, Slavé; Todd, Jamie L; Durheim, Michael T; Wang, Quanli; Chien, Jason W; Kelly, Fran L; Frankel, Courtney; Mebane, Caroline M; Ren, Zhong; Bridgers, Joshua; Urban, Thomas J; Malone, Colin D; Finlen Copeland, Ashley; Brinkley, Christie; Allen, Andrew S; O'Riordan, Thomas; McHutchison, John G; Palmer, Scott M; Goldstein, David B

2017-07-01

Idiopathic pulmonary fibrosis (IPF) is an increasingly recognized, often fatal lung disease of unknown etiology. The aim of this study was to use whole-exome sequencing to improve understanding of the genetic architecture of pulmonary fibrosis. We performed a case-control exome-wide collapsing analysis including 262 unrelated individuals with pulmonary fibrosis clinically classified as IPF according to American Thoracic Society/European Respiratory Society/Japanese Respiratory Society/Latin American Thoracic Association guidelines (81.3%), usual interstitial pneumonia secondary to autoimmune conditions (11.5%), or fibrosing nonspecific interstitial pneumonia (7.2%). The majority (87%) of case subjects reported no family history of pulmonary fibrosis. We searched 18,668 protein-coding genes for an excess of rare deleterious genetic variation using whole-exome sequence data from 262 case subjects with pulmonary fibrosis and 4,141 control subjects drawn from among a set of individuals of European ancestry. Comparing genetic variation across 18,668 protein-coding genes, we found a study-wide significant (P RTEL1, and PARN. A model qualifying ultrarare, deleterious, nonsynonymous variants implicated TERT and RTEL1, and a model specifically qualifying loss-of-function variants implicated RTEL1 and PARN. A subanalysis of 186 case subjects with sporadic IPF confirmed TERT, RTEL1, and PARN as study-wide significant contributors to sporadic IPF. Collectively, 11.3% of case subjects with sporadic IPF carried a qualifying variant in one of these three genes compared with the 0.3% carrier rate observed among control subjects (odds ratio, 47.7; 95% confidence interval, 21.5-111.6; P = 5.5 × 10 -22 ). We identified TERT, RTEL1, and PARN-three telomere-related genes previously implicated in familial pulmonary fibrosis-as significant contributors to sporadic IPF. These results support the idea that telomere dysfunction is involved in IPF pathogenesis.

Biased HiPIMS technology for superconducting rf accelerating cavities coating

CERN Document Server

G. Rosaz, G.; Sonato, D.; Calatroni, S.; Ehiasarian, A.; Junginger, T.; Taborelli, M.

2016-01-01

In the last few years the interest of the thin film science and technology community on High Impulse Power Magnetron Sputtering (HIPIMS) coatings has steadily increased. HIPIMS literature shows that better thin film morphology, denser and smoother films can be achieved when compared with standard dc Magnetron Sputtering (dcMS) coating technology. Furthermore the capability of HIPIMS to produce a high quantity of ionized species can allow conformal coatings also for complex geometries. CERN already studied the possibility to use such a coating method for SRF accelerating cavities. Results are promising but not better from a RF point of view than dcMS coatings. Thanks to these results the next step is to go towards a biased HiPIMS approach. However the geometry of the cavities leads to complex changes in the coating setup in order to apply a bias voltage. Coating system tweaking and first superconducting properties of biased samples are presented.

Targeted exome sequencing identified novel USH2A mutations in Usher syndrome families.

Directory of Open Access Journals (Sweden)

Xiu-Feng Huang

Full Text Available Usher syndrome (USH is a leading cause of deaf-blindness in autosomal recessive trait. Phenotypic and genetic heterogeneities in USH make molecular diagnosis much difficult. This is a pilot study aiming to develop an approach based on next-generation sequencing to determine the genetic defects in patients with USH or allied diseases precisely and effectively. Eight affected patients and twelve unaffected relatives from five unrelated Chinese USH families, including 2 pseudo-dominant ones, were recruited. A total of 144 known genes of inherited retinal diseases were selected for deep exome resequencing. Through systematic data analysis using established bioinformatics pipeline and segregation analysis, a number of genetic variants were released. Eleven mutations, eight of them were novel, in the USH2A gene were identified. Biparental mutations in USH2A were revealed in 2 families with pseudo-dominant inheritance. A proband was found to have triple mutations, two of them were supposed to locate in the same chromosome. In conclusion, this study revealed the genetic defects in the USH2A gene and demonstrated the robustness of targeted exome sequencing to precisely and rapidly determine genetic defects. The methodology provides a reliable strategy for routine gene diagnosis of USH.

Fracture of niobium-base silicide coated alloy

International Nuclear Information System (INIS)

Davydova, A.D.; Zotov, Yu.P.; Ivashchenko, O.V.; Kushnareva, N.P.; Yarosh, I.P.

1990-01-01

Mechanical properties and character of fracture of Nb-W-Mo-Zr-C alloy composition with complex by composition and structure silicide coating under different states of stage-by-stage coating are studied. Structural features, character of fracture from ductile to quasibrittle transcrystalline one and, respectively, the composition plasticity level are defined by interrelation of fracture processes in coating, matrix plastic flow and possibility and way of stress relaxation on their boundary

Whole-exome sequencing identifies USH2A mutations in a pseudo-dominant Usher syndrome family.

Science.gov (United States)

Zheng, Sui-Lian; Zhang, Hong-Liang; Lin, Zhen-Lang; Kang, Qian-Yan

2015-10-01

Usher syndrome (USH) is an autosomal recessive (AR) multi-sensory degenerative disorder leading to deaf-blindness. USH is clinically subdivided into three subclasses, and 10 genes have been identified thus far. Clinical and genetic heterogeneities in USH make a precise diagnosis difficult. A dominant‑like USH family in successive generations was identified, and the present study aimed to determine the genetic predisposition of this family. Whole‑exome sequencing was performed in two affected patients and an unaffected relative. Systematic data were analyzed by bioinformatic analysis to remove the candidate mutations via step‑wise filtering. Direct Sanger sequencing and co‑segregation analysis were performed in the pedigree. One novel and two known mutations in the USH2A gene were identified, and were further confirmed by direct sequencing and co‑segregation analysis. The affected mother carried compound mutations in the USH2A gene, while the unaffected father carried a heterozygous mutation. The present study demonstrates that whole‑exome sequencing is a robust approach for the molecular diagnosis of disorders with high levels of genetic heterogeneity.

Microstructural evolution of aluminide coatings on Eurofer during heat treatments

International Nuclear Information System (INIS)

Bhanumurthy, K.; Krauss, W.; Konys, J.

2011-01-01

Development of ceramic coatings are essential for the realization of Demo fusion reactor beyond ITER. These functional coatings have to be stable at high temperatures, provide insulating coatings to reduce MHD effects and also act as corrosion barriers to reduce tritium permeation. Some of important development of high temperature coatings are CVD process, powder slurry coatings, hot-dip aluminization and plasma detonation jet processes. Recently Galvono-Al (ECA) process is being used for depositing Al from organic electrolyte, where Al is existing as an toluol-based Al(C x H y ) complex. The deposit is performed under Ar cover gas at 100 deg C with a deposit rate of 10-12 μm/hr. This process is suitable for coating large and complex shaped assemblies and is a well established industrial process for coating Al for wide range of applications including automobile industry. In order to study the effect of high temperature on these coatings, few Al coated on Eurofer specimens were obtained from M/s. Rasant-Alcotec, Germany. The thickness of these coating is around 20 μm. The objective of the presents studies is to subject these coatings to standard heat treatment schedule of Eurofer and study the evolution of microchemistry and microstructure

Studies of decontamination using easy removable coatings technique

International Nuclear Information System (INIS)

Oglaza, J.; Nowak, Z.

1991-01-01

The usefulness of removable coatings for decontamination of steel and epoxy-resin painted surfaces was examined. Natural latex, Revultex, butadiene-styrene latex as well as mixtures of latex with complexing agents and surfactants were used as decontaminating coats. The best decontamination was obtained by removable coatings of natural latex with EDTA additive for all surfaces and radionuclides tested. (author). 16 refs, 5 tabs

Tungsten thick coatings for plasma facing components

International Nuclear Information System (INIS)

Riccardi, B.; Pizzuto, A.; Orsini, A.; Libera, S.; Visca, E.; Bertamini, L.; Casadei, F.; Severini, E.; Montanari, R.; Litunovsky, N.

1998-01-01

The aim of the R and D activity was to realize thick W coatings on CuCrZr hollow bars and to test the mock ups with respect to thermal fatigue. Eight mock ups provided of 4 mm thick W coating were finally manufactured. The bonding integrity between coating and substrate was checked by means of an Ultrasonic apparatus. Characterisation of coatings was performed in order to assess microstructure, impurity content, density, tensile strength, adhesion strength, thermal conductivity and thermal expansion coefficient. Macroscopic residual strain measurements were performed by means of 'hole drilling' technique. The activities performed demonstrated the feasibility of thick Tungsten coatings on geometries with more complex residual strain distribution. These coatings are reliable armour of medium heat flux plasma facing component. (author)

Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome.

Science.gov (United States)

Tsurusaki, Yoshinori; Okamoto, Nobuhiko; Ohashi, Hirofumi; Kosho, Tomoki; Imai, Yoko; Hibi-Ko, Yumiko; Kaname, Tadashi; Naritomi, Kenji; Kawame, Hiroshi; Wakui, Keiko; Fukushima, Yoshimitsu; Homma, Tomomi; Kato, Mitsuhiro; Hiraki, Yoko; Yamagata, Takanori; Yano, Shoji; Mizuno, Seiji; Sakazume, Satoru; Ishii, Takuma; Nagai, Toshiro; Shiina, Masaaki; Ogata, Kazuhiro; Ohta, Tohru; Niikawa, Norio; Miyatake, Satoko; Okada, Ippei; Mizuguchi, Takeshi; Doi, Hiroshi; Saitsu, Hirotomo; Miyake, Noriko; Matsumoto, Naomichi

2012-03-18

By exome sequencing, we found de novo SMARCB1 mutations in two of five individuals with typical Coffin-Siris syndrome (CSS), a rare autosomal dominant anomaly syndrome. As SMARCB1 encodes a subunit of the SWItch/Sucrose NonFermenting (SWI/SNF) complex, we screened 15 other genes encoding subunits of this complex in 23 individuals with CSS. Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B.

Exome sequencing identifies three novel candidate genes implicated in intellectual disability.

Directory of Open Access Journals (Sweden)

Zehra Agha

Full Text Available Intellectual disability (ID is a major health problem mostly with an unknown etiology. Recently exome sequencing of individuals with ID identified novel genes implicated in the disease. Therefore the purpose of the present study was to identify the genetic cause of ID in one syndromic and two non-syndromic Pakistani families. Whole exome of three ID probands was sequenced. Missense variations in two plausible novel genes implicated in autosomal recessive ID were identified: lysine (K-specific methyltransferase 2B (KMT2B, zinc finger protein 589 (ZNF589, as well as hedgehog acyltransferase (HHAT with a de novo mutation with autosomal dominant mode of inheritance. The KMT2B recessive variant is the first report of recessive Kleefstra syndrome-like phenotype. Identification of plausible causative mutations for two recessive and a dominant type of ID, in genes not previously implicated in disease, underscores the large genetic heterogeneity of ID. These results also support the viewpoint that large number of ID genes converge on limited number of common networks i.e. ZNF589 belongs to KRAB-domain zinc-finger proteins previously implicated in ID, HHAT is predicted to affect sonic hedgehog, which is involved in several disorders with ID, KMT2B associated with syndromic ID fits the epigenetic module underlying the Kleefstra syndromic spectrum. The association of these novel genes in three different Pakistani ID families highlights the importance of screening these genes in more families with similar phenotypes from different populations to confirm the involvement of these genes in pathogenesis of ID.

Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Protein Complex, Subunit Alpha (COPA Gene.

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Ben Dorshorst

Full Text Available Coat color in Holstein dairy cattle is primarily controlled by the melanocortin 1 receptor (MC1R gene, a central determinant of black (eumelanin vs. red/brown pheomelanin synthesis across animal species. The major MC1R alleles in Holsteins are Dominant Black (MC1RD and Recessive Red (MC1Re. A novel form of dominant red coat color was first observed in an animal born in 1980. The mutation underlying this phenotype was named Dominant Red and is epistatic to the constitutively activated MC1RD. Here we show that a missense mutation in the coatomer protein complex, subunit alpha (COPA, a gene with previously no known role in pigmentation synthesis, is completely associated with Dominant Red in Holstein dairy cattle. The mutation results in an arginine to cysteine substitution at an amino acid residue completely conserved across eukaryotes. Despite this high level of conservation we show that both heterozygotes and homozygotes are healthy and viable. Analysis of hair pigment composition shows that the Dominant Red phenotype is similar to the MC1R Recessive Red phenotype, although less effective at reducing eumelanin synthesis. RNA-seq data similarly show that Dominant Red animals achieve predominantly pheomelanin synthesis by downregulating genes normally required for eumelanin synthesis. COPA is a component of the coat protein I seven subunit complex that is involved with retrograde and cis-Golgi intracellular coated vesicle transport of both protein and RNA cargo. This suggests that Dominant Red may be caused by aberrant MC1R protein or mRNA trafficking within the highly compartmentalized melanocyte, mimicking the effect of the Recessive Red loss of function MC1R allele.

Analysis of 60 706 Exomes Questions the Role of De Novo Variants Previously Implicated in Cardiac Disease

DEFF Research Database (Denmark)

Paludan-Müller, Christian; Ahlberg, Gustav; Ghouse, Jonas

2017-01-01

BACKGROUND: De novo variants in the exome occur at a rate of 1 per individual per generation, and because of the low reproductive fitness for de novo variants causing severe disease, the likelihood of finding these as standing variations in the general population is low. Therefore, this study...... sought to evaluate the pathogenicity of de novo variants previously associated with cardiac disease based on a large population-representative exome database. METHODS AND RESULTS: We performed a literature search for previous publications on de novo variants associated with severe arrhythmias...... trio studies (>1000 subjects). Of the monogenic variants, 11% (23/211) were present in ExAC, whereas 26% (802/3050) variants believed to increase susceptibility of disease were identified in ExAC. Monogenic de novo variants in ExAC had a total allele count of 109 and with ≈844 expected cases in Ex...

Experimental evaluation of coating delamination in vinyl coated metal forming

International Nuclear Information System (INIS)

Son, Young Ki; Lee, Chan Joo; Kim, Byung Min; Lee, Jung Min; Byoen, Sang Doek; Lee, Soen Bong

2012-01-01

In this paper, a new evaluation and prediction method for coating delamination during sheet metal forming is presented. On the basis of the forming limit diagram (FLD), the current study evaluates the delamination of PET coating by using a cross cut specimen, dome test, and rectangular cup drawing test. Dome test specimens were subjected to biaxial, plane strain, and uniaxial deformation modes. Rectangular cup drawing test specimens were subjected to the deep drawing deformation mode, and compression deformation mode. A vinyl coated metal (VCM) sheet consists of three layers of polymer on the sheet metals: a protective film, a PET layer and a PVC layer. The areas with coating delamination were identified, and the results of the evaluation were plotted according to major and minor strain values, depicting coating delamination. The constructed delamination limit diagram (DLD) can be used to determine the forming limit of VCM during the complex press forming process. ARGUS (GOM) was employed to identify the strain value and deformation mode of the delaminated surface after the press forming. After identifying the areas of delamination, the DLD of the PET coating can be constructed in a format similar to that of the FLD. The forming limit of the VCM sheet can be evaluated using the superimposition of the delamination limit strain of the coating onto the FLD of VCM sheet. The experimental results showed that the proposed test method will support the sheet metal forming process design for VCM sheets. The assessment method presented in this study can be used to determine the delamination limit strain under plastic deformation of other polymer coated metals. The experimental results suggested that the proposed testing method is effective in evaluating delamination for specific applications

Experimental evaluation of coating delamination in vinyl coated metal forming

Energy Technology Data Exchange (ETDEWEB)

Son, Young Ki; Lee, Chan Joo; Kim, Byung Min [Pusan National Univ., Busan (Korea, Republic of); Lee, Jung Min [Korea Institute of Industrial Technology, Busan (Korea, Republic of); Byoen, Sang Doek [HA Digital Engineering Gr., Seongsan Gu (Korea, Republic of); Lee, Soen Bong [Keimyung Univ., Daegu (Korea, Republic of)

2012-10-15

In this paper, a new evaluation and prediction method for coating delamination during sheet metal forming is presented. On the basis of the forming limit diagram (FLD), the current study evaluates the delamination of PET coating by using a cross cut specimen, dome test, and rectangular cup drawing test. Dome test specimens were subjected to biaxial, plane strain, and uniaxial deformation modes. Rectangular cup drawing test specimens were subjected to the deep drawing deformation mode, and compression deformation mode. A vinyl coated metal (VCM) sheet consists of three layers of polymer on the sheet metals: a protective film, a PET layer and a PVC layer. The areas with coating delamination were identified, and the results of the evaluation were plotted according to major and minor strain values, depicting coating delamination. The constructed delamination limit diagram (DLD) can be used to determine the forming limit of VCM during the complex press forming process. ARGUS (GOM) was employed to identify the strain value and deformation mode of the delaminated surface after the press forming. After identifying the areas of delamination, the DLD of the PET coating can be constructed in a format similar to that of the FLD. The forming limit of the VCM sheet can be evaluated using the superimposition of the delamination limit strain of the coating onto the FLD of VCM sheet. The experimental results showed that the proposed test method will support the sheet metal forming process design for VCM sheets. The assessment method presented in this study can be used to determine the delamination limit strain under plastic deformation of other polymer coated metals. The experimental results suggested that the proposed testing method is effective in evaluating delamination for specific applications.

Ranking protective coatings: Laboratory vs. field experience

Science.gov (United States)

Conner, Jeffrey A.; Connor, William B.

1994-12-01

Environmentally protective coatings are used on a wide range of gas turbine components for survival in the harsh operating conditions of engines. A host of coatings are commercially available to protect hot-section components, ranging from simple aluminides to designer metallic overlays and ceramic thermal barrier coatings. A variety of coating-application processes are available, and they range from simple pack cementation processing to complex physical vapor deposition, which requires multimillion dollar facilities. Detailed databases are available for most coatings and coating/process combinations for a range of laboratory tests. Still, the analysis of components actually used in engines often yields surprises when compared against predicted coating behavior from laboratory testing. This paper highlights recent work to develop new laboratory tests that better simulate engine environments. Comparison of in-flight coating performance as well as industrial and factory engine testing on a range of hardware is presented along with laboratory predictions from standard testing and from recently developed cyclic burner-rig testing.

Complex single gene disorders and epilepsy.

LENUS (Irish Health Repository)

Merwick, Aine

2012-09-01

Epilepsy is a heterogeneous group of disorders, often associated with significant comorbidity, such as intellectual disability and skin disorder. The genetic underpinnings of many epilepsies are still being elucidated, and we expect further advances over the coming 5 years, as genetic technology improves and prices fall for whole exome and whole genome sequencing. At present, there are several well-characterized complex epilepsies associated with single gene disorders; we review some of these here. They include well-recognized syndromes such as tuberous sclerosis complex, epilepsy associated with Rett syndrome, some of the progressive myoclonic epilepsies, and novel disorders such as epilepsy associated with mutations in the PCDH 19 gene. These disorders are important in informing genetic testing to confirm a diagnosis and to permit better understanding of the variability in phenotype-genotype correlation.

Induced codeposition of nanocrystalline Co-W coatings and their mechanical properties

International Nuclear Information System (INIS)

Belevskij, Stanislav

2012-01-01

The aim of the research: the complex investigation of induced codeposition mechanism of Co-W coatings obtaining from citrate electrolyte and determining the conditions of electrodeposition that provide the coatings the properties that could compete with the hard chromium electroplating coatings. The scientific novelty and originality of the work: for the first time it is demonstrated that citrate electrolyte used for electrodeposition of Co-W alloy is a mixture of complex compounds, whose composition is determined by the pH. At high pH values, its main component is hetero polynuclear complex with a molecular weight over 1200 g / mol. The totality of the results obtained by different methods (gel-chromatography, voltammetry, the methods of physicochemical hydrodynamics, determination of the composition of coatings, the current efficiency, etc.), can conclude that the chemical composition of electrodeposited Co-W coatings is determined by the hetero polynuclear complex composition on the one hand and the pH near-electrode layer on the other. However, the pH near-electrode layer depends on the rate of the parallel hydrogen evolution reaction (defined by the potential of electrodeposition and the hydrodynamic conditions). The increasing of the pH near-electrode layer shifts the chemical equilibrium toward to the formation of complex products with high molecular weight. It was confirmed the existence of hetero polynuclear Co-W-citrate complex compound, where the atomic ratio of Co:W is equal to 1:1. Solved scientific problem: The experimental proof of the fact that the formation of cobalt-tungsten coatings from citric electrolyte is the result of electrochemical reduction of polynuclear heterometallic complex. The research object is the chemical composition of citrate electrolyte (identification of the contained complexes) and induced codeposition of Co-W coatings from citrate electrolyte. The determination of the influence of the degree of the electrodeposition

Superhydrophobic Ceramic Coatings by Solution Precursor Plasma Spray

Science.gov (United States)

Cai, Yuxuan

Superhydrophobic surfaces exhibit superior water repellent properties, and they have remarkable potential to improve current energy infrastructure. Substantial research has been performed on the production of superhydrophobic coatings. However, superhydrophobic coatings have not yet been adopted in many industries where potential applications exist due to the limited durability of the coating materials and the complex and costly fabrication processes. Here presented a novel coating technique to manufacture ceramic superhydrophobic coatings rapidly and economically. A rare earth oxide (REO) was selected as the coating material due to its hydrophobic nature and strong mechanical properties, and deposited on stainless steel substrates by solution precursor plasma spray (SPPS). The as-sprayed coating demonstrated a hierarchically structured coating topography, which closely resembles superhydrophobic surfaces in nature. Compared to smooth REO surfaces, the SPPS superhydrophobic coating improved the water contact angle by as much as 65° after vacuum treatment at 1 Pa for 48 hours.

Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility

DEFF Research Database (Denmark)

Wessel, Jennifer; Chu, Audrey Y; Willems, Sara M

2015-01-01

Fasting glucose and insulin are intermediate traits for type 2 diabetes. Here we explore the role of coding variation on these traits by analysis of variants on the HumanExome BeadChip in 60,564 non-diabetic individuals and in 16,491 T2D cases and 81,877 controls. We identify a novel association...

Electrochemical Formation of Multilayer SnO2-Sb x O y Coating in Complex Electrolyte.

Science.gov (United States)

Maizelis, Antonina; Bairachniy, Boris

2017-12-01

The multilayer antimony-doped tin dioxide coating was obtained by cathodic deposition of multilayer metal-hydroxide coating with near 100-nm thickness layers on the alloy underlayer accompanied by the anodic oxidation of this coating. The potential regions of deposition of tin, antimony, tin-antimony alloy, and mixture of this metals and their hydroxides in the pyrophosphate-tartrate electrolyte were revealed by the cyclic voltammetric method. The possibility of oxidation of cathodic deposit consisting of tin and Sn(II) hydroxide compounds to the hydrated tin dioxide in the same electrolyte was demonstrated.The operations of alloy underlayer deposition and oxidation of multilayer metal-hydroxide coating were proposed to carry out in the diluted pyrophosphate-tartrate electrolyte, similar to the main electrolyte.The accelerated tests showed higher service life of the titanium electrode with multilayer antimony-doped tin dioxide coating compared to both electrode with single-layer electrodeposited coating and the electrode with the coating obtained using prolonged heat treatment step.

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data

DEFF Research Database (Denmark)

Krøigård, Anne Bruun; Thomassen, Mads; Lænkholm, Anne Vibeke

2016-01-01

a comprehensive evaluation using exome sequencing and targeted deep sequencing data of paired tumor-normal samples from five breast cancer patients to evaluate the performance of nine publicly available somatic variant callers: EBCall, Mutect, Seurat, Shimmer, Indelocator, Somatic Sniper, Strelka, VarScan 2...

Exome sequencing identifies mutations in ABCD1 and DACH2 in two brothers with a distinct phenotype.

Science.gov (United States)

Zhang, Yanliang; Liu, Yanhui; Li, Ya; Duan, Yong; Zhang, Keyun; Wang, Junwang; Dai, Yong

2014-09-19

We report on two brothers with a distinct syndromic phenotype and explore the potential pathogenic cause. Cytogenetic tests and exome sequencing were performed on the two brothers and their parents. Variants detected by exome sequencing were validated by Sanger sequencing. The main phenotype of the two brothers included congenital language disorder, growth retardation, intellectual disability, difficulty in standing and walking, and urinary and fecal incontinence. To the best of our knowledge, no similar phenotype has been reported previously. No abnormalities were detected by G-banding chromosome analysis or array comparative genomic hybridization. However, exome sequencing revealed novel mutations in the ATP-binding cassette, sub-family D member 1 (ABCD1) and Dachshund homolog 2 (DACH2) genes in both brothers. The ABCD1 mutation was a missense mutation c.1126G > C in exon 3 leading to a p.E376Q substitution. The DACH2 mutation was also a missense mutation c.1069A > T in exon 6, leading to a p.S357C substitution. The mother was an asymptomatic heterozygous carrier. Plasma levels of very-long-chain fatty acids were increased in both brothers, suggesting a diagnosis of adrenoleukodystrophy (ALD); however, their phenotype was not compatible with any reported forms of ALD. DACH2 plays an important role in the regulation of brain and limb development, suggesting that this mutation may be involved in the phenotype of the two brothers. The distinct phenotype demonstrated by these two brothers might represent a new form of ALD or a new syndrome. The combination of mutations in ABCD1 and DACH2 provides a plausible mechanism for this phenotype.

Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions.

Science.gov (United States)

Seo, Heewon; Park, Yoomi; Min, Byung Joo; Seo, Myung Eui; Kim, Ju Han

2017-01-01

The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58.2%, 18.7%, and 23.1% of the variants, respectively. We identified four distinct error patterns of variant calling that may be bioinformatically corrected when using different strategies: simplicity region, SNV cluster, peripheral sequence read, and base inversion. Local de novo assembly successfully corrected 201 (38.7%) of the 519 highly likely or likely false positives. We also demonstrate that the two sequencing kits from Thermo Fisher (the Ion PI Sequencing 200 kit V3 and the Ion PI Hi-Q kit) exhibit different error profiles across different error types. A refined calling algorithm with better polymerase may improve the performance of the Ion Proton sequencing platform.

Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions.

Directory of Open Access Journals (Sweden)

Heewon Seo

Full Text Available The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58.2%, 18.7%, and 23.1% of the variants, respectively. We identified four distinct error patterns of variant calling that may be bioinformatically corrected when using different strategies: simplicity region, SNV cluster, peripheral sequence read, and base inversion. Local de novo assembly successfully corrected 201 (38.7% of the 519 highly likely or likely false positives. We also demonstrate that the two sequencing kits from Thermo Fisher (the Ion PI Sequencing 200 kit V3 and the Ion PI Hi-Q kit exhibit different error profiles across different error types. A refined calling algorithm with better polymerase may improve the performance of the Ion Proton sequencing platform.

Somatic Genetic Variation in Solid Pseudopapillary Tumor of the Pancreas by Whole Exome Sequencing

Directory of Open Access Journals (Sweden)

Meng Guo

2017-01-01

Full Text Available Solid pseudopapillary tumor of the pancreas (SPT is a rare pancreatic disease with a unique clinical manifestation. Although CTNNB1 gene mutations had been universally reported, genetic variation profiles of SPT are largely unidentified. We conducted whole exome sequencing in nine SPT patients to probe the SPT-specific insertions and deletions (indels and single nucleotide polymorphisms (SNPs. In total, 54 SNPs and 41 indels of prominent variations were demonstrated through parallel exome sequencing. We detected that CTNNB1 mutations presented throughout all patients studied (100%, and a higher count of SNPs was particularly detected in patients with older age, larger tumor, and metastatic disease. By aggregating 95 detected variation events and viewing the interconnections among each of the genes with variations, CTNNB1 was identified as the core portion in the network, which might collaborate with other events such as variations of USP9X, EP400, HTT, MED12, and PKD1 to regulate tumorigenesis. Pathway analysis showed that the events involved in other cancers had the potential to influence the progression of the SNPs count. Our study revealed an insight into the variation of the gene encoding region underlying solid-pseudopapillary neoplasm tumorigenesis. The detection of these variations might partly reflect the potential molecular mechanism.

Construction of an Exome-Wide Risk Score for Schizophrenia Based on a Weighted Burden Test.

Science.gov (United States)

Curtis, David

2018-01-01

Polygenic risk scores obtained as a weighted sum of associated variants can be used to explore association in additional data sets and to assign risk scores to individuals. The methods used to derive polygenic risk scores from common SNPs are not suitable for variants detected in whole exome sequencing studies. Rare variants, which may have major effects, are seen too infrequently to judge whether they are associated and may not be shared between training and test subjects. A method is proposed whereby variants are weighted according to their frequency, their annotations and the genes they affect. A weighted sum across all variants provides an individual risk score. Scores constructed in this way are used in a weighted burden test and are shown to be significantly different between schizophrenia cases and controls using a five-way cross-validation procedure. This approach represents a first attempt to summarise exome sequence variation into a summary risk score, which could be combined with risk scores from common variants and from environmental factors. It is hoped that the method could be developed further. © 2017 John Wiley & Sons Ltd/University College London.

Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility

NARCIS (Netherlands)

Wessel, Jennifer; Chu, Audrey Y.; Willems, Sara M.; Wang, Shuai; Yaghootkar, Hanieh; Brody, Jennifer A.; Dauriz, Marco; Hivert, Marie-France; Raghavan, Sridharan; Lipovich, Leonard; Hidalgo, Bertha; Fox, Keolu; Huffman, Jennifer E.; An, Ping; Lu, Yingchang; Rasmussen-Torvik, Laura J.; Grarup, Niels; Ehm, Margaret G.; Li, Li; Baldridge, Abigail S.; Stancakova, Alena; Abrol, Ravinder; Besse, Celine; Boland, Anne; Bork-Jensen, Jette; Fornage, Myriam; Freitag, Daniel F.; Garcia, Melissa E.; Guo, Xiuqing; Hara, Kazuo; Isaacs, Aaron; Jakobsdottir, Johanna; Lange, Leslie A.; Layton, Jill C.; Li, Man; Zhao, Jing Hua; Meidtner, Karina; Morrison, Alanna C.; Nalls, Mike A.; Peters, Marjolein J.; Sabater-Lleal, Maria; Schurmann, Claudia; Silveira, Angela; Smith, Albert V.; Southam, Lorraine; Stoiber, Marcus H.; Strawbridge, Rona J.; Taylor, Kent D.; Varga, Tibor V.; Allin, Kristine H.; Amin, Najaf; Aponte, Jennifer L.; Aung, Tin; Barbieri, Caterina; Bihlmeyer, Nathan A.; Boehnke, Michael; Bombieri, Cristina; Bowden, Donald W.; Burns, Sean M.; Chen, Yuning; Chen, Yii-Deri; Cheng, Ching-Yu; Correa, Adolfo; Czajkowski, Jacek; Dehghan, Abbas; Ehret, Georg B.; Eiriksdottir, Gudny; Escher, Stefan A.; Farmaki, Aliki-Eleni; Franberg, Mattias; Gambaro, Giovanni; Giulianini, Franco; Goddard, William A.; Goel, Anuj; Gottesman, Omri; Grove, Megan L.; Gustafsson, Stefan; Hai, Yang; Hallmans, Goeran; Heo, Jiyoung; Hoffmann, Per; Ikram, Mohammad K.; Jensen, Richard A.; Jorgensen, Marit E.; Jorgensen, Torben; Karaleftheri, Maria; Khor, Chiea C.; Kirkpatrick, Andrea; Kraja, Aldi T.; Kuusisto, Johanna; Lange, Ethan M.; Lee, I. T.; Lee, Wen-Jane; Leong, Aaron; Liao, Jiemin; Liu, Chunyu; Liu, Yongmei; Lindgren, Cecilia M.; Linneberg, Allan; Malerba, Giovanni; Mamakou, Vasiliki; Marouli, Eirini; Maruthur, Nisa M.; Matchan, Angela; McKean-Cowdin, Roberta; McLeod, Olga; Metcalf, Ginger A.; Mohlke, Karen L.; Muzny, Donna M.; Ntalla, Ioanna; Palmer, Nicholette D.; Pasko, Dorota; Peter, Andreas; Rayner, Nigel W.; Renstroem, Frida; Rice, Ken; Sala, Cinzia F.; Sennblad, Bengt; Serafetinidis, Ioannis; Smith, Jennifer A.; Soranzo, Nicole; Speliotes, Elizabeth K.; Stahl, Eli A.; Stirrups, Kathleen; Tentolouris, Nikos; Thanopoulou, Anastasia; Torres, Mina; Traglia, Michela; Tsafantakis, Emmanouil; Javad, Sundas; Yanek, Lisa R.; Zengini, Eleni; Becker, Diane M.; Bis, Joshua C.; Brown, James B.; Cupples, L. Adrienne; Hansen, Torben; Ingelsson, Erik; Karter, Andrew J.; Lorenzo, Carlos; Mathias, Rasika A.; Norris, Jill M.; Peloso, Gina M.; Sheu, Wayne H. -H.; Toniolo, Daniela; Vaidya, Dhananjay; Varma, Rohit; Wagenknecht, Lynne E.; Boeing, Heiner; Bottinger, Erwin P.; Dedoussis, George; Deloukas, Panos; Ferrannini, Ele; Franco, Oscar H.; Franks, Paul W.; Gibbs, Richard A.; Gudnason, Vilmundur; Hamsten, Anders; Harris, Tamara B.; Hattersley, Andrew T.; Hayward, Caroline; Hofman, Albert; Jansson, Jan-Hakan; Langenberg, Claudia; Launer, Lenore J.; Levy, Daniel; Oostra, Ben A.; O'Donnell, Christopher J.; O'Rahilly, Stephen; Padmanabhan, Sandosh; Pankow, James S.; Polasek, Ozren; Province, Michael A.; Rich, Stephen S.; Ridker, Paul M.; Rudan, Igor; Schulze, Matthias B.; Smith, Blair H.; Uitterlinden, Andre G.; Walker, Mark; Watkins, Hugh; Wong, Tien Y.; Zeggini, Eleftheria; Laakso, Markku; Borecki, Ingrid B.; Chasman, Daniel I.; Pedersen, Oluf; Psaty, Bruce M.; Tai, E. Shyong; van Duijn, Cornelia M.; Wareham, Nicholas J.; Waterworth, Dawn M.; Boerwinkle, Eric; Kao, W. H. Linda; Florez, Jose C.; Loos, Ruth J. F.; Wilson, James G.; Frayling, Timothy M.; Siscovick, David S.; Dupuis, Josee; Rotter, Jerome I.; Meigs, James B.; Scott, Robert A.; Goodarzi, Mark O.; Sharp, Stephen J.; Forouhi, Nita G.; Kerrison, Nicola D.; Lucarelli, Debora M. E.; Sims, Matt; Barroso, Ines; McCarthy, Mark I.; Arriola, Larraitz; Balkau, Beverley; Barricarte, Aurelio; Gonzalez, Carlos; Grioni, Sara; Kaaks, Rudolf; Key, Timothy J.; Navarro, Carmen; Nilsson, Peter M.; Overvad, Kim; Palli, Domenico; Panico, Salvatore; Quiros, J. Ramon; Rolandsson, Olov; Sacerdote, Carlotta; Sanchez, Maria-Jose; Slimani, Nadia; Tjonneland, Anne; Tumino, Rosario; van der A, Daphne L.; van der Schouw, Yvonne T.; Riboli, Elio

Fasting glucose and insulin are intermediate traits for type 2 diabetes. Here we explore the role of coding variation on these traits by analysis of variants on the HumanExome BeadChip in 60,564 non-diabetic individuals and in 16,491 T2D cases and 81,877 controls. We identify a novel association of

Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana).

Science.gov (United States)

Pavy, Nathalie; Gagnon, France; Deschênes, Astrid; Boyle, Brian; Beaulieu, Jean; Bousquet, Jean

2016-03-01

Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programmes for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97,075 highly reliable in silico SNPs. These SNPs were distributed across 14,909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2% for in silico SNPs, compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications. © 2015 John Wiley & Sons Ltd.

Thin coatings for heavy industry: Advanced coatings for pipes and valves

Science.gov (United States)

Vernhes, Luc

characteristics suitable for applications such as pipes and valves. From these general objectives, three specific objectives were derived: 1) to select and assess the best candidates for alternatives to hard chromium electroplating, which has been classified by the U.S. Environmental Protection Agency (EPA) as an environmentally unfriendly process; 2) to investigate recurrent failures occurring in the field with thermal sprayed HVOF Cr3C 2-NiCr coating applied to Inconel 718 PH when exposed to supercritical steam lines and thermal shocks in supercritical power plants (determining the root causes of coating failures and assessing potential coating alternatives to alleviate these issues); and 3) to develop new coating architectures, including complex microstructures and interfaces, and to better understand and optimize complex tribomechanical properties. The main results are presented in the form of articles in peer-reviewed journals. In the first article, a variety of chromium-free protective coatings were assessed as alternatives to hard chromium (HC) electroplating, such as nanostructured cobalt-phosphor (NCP) deposited by electroplating and tungsten/tungsten carbide (W/WC) applied by chemical vapor deposition. In order to compare performance across the coatings, a series of laboratory tests were performed, including hardness, microscratch, pin-on-disk, and electrochemical polarization measurements. Mechanical and fatigue resistance were also determined using prototype valves with coated ball under severe tribocorrosion conditions. It was found that W/WC coating exhibits superior wear and corrosion resistance due to high hardness and high pitting resistance, respectively, whereas NCP exhibits better wear resistance than HC with alumina ball as well as low corrosion potential, making it suitable for use as sacrificial protective coating. Both nanostructured coatings exhibited superior tribomechanical and functional characteristics compared to HC. The second article presents an

Identification of Candidate Gene Variants in Korean MODY Families by Whole-Exome Sequencing.

Science.gov (United States)

Shim, Ye Jee; Kim, Jung Eun; Hwang, Su-Kyeong; Choi, Bong Seok; Choi, Byung Ho; Cho, Eun-Mi; Jang, Kyoung Mi; Ko, Cheol Woo

2015-01-01

To date, 13 genes causing maturity-onset diabetes of the young (MODY) have been identified. However, there is a big discrepancy in the genetic locus between Asian and Caucasian patients with MODY. Thus, we conducted whole-exome sequencing in Korean MODY families to identify causative gene variants. Six MODY probands and their family members were included. Variants in the dbSNP135 and TIARA databases for Koreans and the variants with minor allele frequencies >0.5% of the 1000 Genomes database were excluded. We selected only the functional variants (gain of stop codon, frameshifts and nonsynonymous single-nucleotide variants) and conducted a case-control comparison in the family members. The selected variants were scanned for the previously introduced gene set implicated in glucose metabolism. Three variants c.620C>T:p.Thr207Ile in PTPRD, c.559C>G:p.Gln187Glu in SYT9, and c.1526T>G:p.Val509Gly in WFS1 were respectively identified in 3 families. We could not find any disease-causative alleles of known MODY 1-13 genes. Based on the predictive program, Thr207Ile in PTPRD was considered pathogenic. Whole-exome sequencing is a valuable method for the genetic diagnosis of MODY. Further evaluation is necessary about the role of PTPRD, SYT9 and WFS1 in normal insulin release from pancreatic beta cells. © 2015 S. Karger AG, Basel.

mirVAFC: A Web Server for Prioritizations of Pathogenic Sequence Variants from Exome Sequencing Data via Classifications.

Science.gov (United States)

Li, Zhongshan; Liu, Zhenwei; Jiang, Yi; Chen, Denghui; Ran, Xia; Sun, Zhong Sheng; Wu, Jinyu

2017-01-01

Exome sequencing has been widely used to identify the genetic variants underlying human genetic disorders for clinical diagnoses, but the identification of pathogenic sequence variants among the huge amounts of benign ones is complicated and challenging. Here, we describe a new Web server named mirVAFC for pathogenic sequence variants prioritizations from clinical exome sequencing (CES) variant data of single individual or family. The mirVAFC is able to comprehensively annotate sequence variants, filter out most irrelevant variants using custom criteria, classify variants into different categories as for estimated pathogenicity, and lastly provide pathogenic variants prioritizations based on classifications and mutation effects. Case studies using different types of datasets for different diseases from publication and our in-house data have revealed that mirVAFC can efficiently identify the right pathogenic candidates as in original work in each case. Overall, the Web server mirVAFC is specifically developed for pathogenic sequence variant identifications from family-based CES variants using classification-based prioritizations. The mirVAFC Web server is freely accessible at https://www.wzgenomics.cn/mirVAFC/. © 2016 WILEY PERIODICALS, INC.

An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes.

Directory of Open Access Journals (Sweden)

Xin Jin

Full Text Available Non-human primates have emerged as an important resource for the study of human disease and evolution. The characterization of genomic variation between and within non-human primate species could advance the development of genetically defined non-human primate disease models. However, non-human primate specific reagents that would expedite such research, such as exon-capture tools, are lacking. We evaluated the efficiency of using a human exome capture design for the selective enrichment of exonic regions of non-human primates. We compared the exon sequence recovery in nine chimpanzees, two crab-eating macaques and eight Japanese macaques. Over 91% of the target regions were captured in the non-human primate samples, although the specificity of the capture decreased as evolutionary divergence from humans increased. Both intra-specific and inter-specific DNA variants were identified; Sanger-based resequencing validated 85.4% of 41 randomly selected SNPs. Among the short indels identified, a majority (54.6%-77.3% of the variants resulted in a change of 3 base pairs, consistent with expectations for a selection against frame shift mutations. Taken together, these findings indicate that use of a human design exon-capture array can provide efficient enrichment of non-human primate gene regions. Accordingly, use of the human exon-capture methods provides an attractive, cost-effective approach for the comparative analysis of non-human primate genomes, including gene-based DNA variant discovery.

Applications of sol gel ceramic coatings

International Nuclear Information System (INIS)

Barrow, D.

1996-01-01

The sol gel method is a chemical technique in which polycrystalline ceramic films are fabricated from a solution of organometallic precursors. The technique is attractive for many industrial applications because it is a simple (films are processed in air), flexible (can be used to coat complex geometries) and cost effective (does not require expensive equipment) process. In addition, dense, high quality coatings can be achieved at much lower temperatures than is generally required for sintering bulk ceramics. In this paper the conventional sol gel method and the new datec process are reviewed and potential applications of sol gel coatings in automotive, aerospace, petrochemical, nuclear and electronic industries are discussed. (orig.)

Incidental and clinically actionable genetic variants in 1005 whole exomes and genomes from Qatar

Directory of Open Access Journals (Sweden)

Abhinav Jain

2017-10-01

Full Text Available Next generation sequencing (NGS technologies such as whole genome and whole exome sequencing has enabled accurate diagnosis of genetic diseases through identification of variations at the genome wide level. While many large populations have been adequately covered in global sequencing efforts little is known on the genomic architecture of populations from Middle East, and South Asia and Africa. Incidental findings and their prevalence in populations have been extensively studied in populations of Caucasian descent. The recent emphasis on genomics and availability of genome-scale datasets in public domain for ethnic population in the Middle East prompted us to estimate the prevalence of incidental findings for this population. In this study, we used whole genome and exome data for a total 1005 non-related healthy individuals from Qatar population dataset which contained 20,930,177 variants. Systematic analysis of the variants in 59 genes recommended by the American College of Medical Genetics and Genomics for reporting of incidental findings revealed a total of 2 pathogenic and 2 likely pathogenic variants. Our analysis suggests the prevalence of incidental variants in population-scale datasets is approx. 0.6%, much lower than those reported for global populations. Our study underlines the essentiality to study population-scale genomes from ethnic groups to understand systematic differences in genetic variants associated with disease predisposition.

Whole-Exome Sequencing Identifies Rare and Low-Frequency Coding Variants Associated with LDL Cholesterol

Science.gov (United States)

Lange, Leslie A.; Hu, Youna; Zhang, He; Xue, Chenyi; Schmidt, Ellen M.; Tang, Zheng-Zheng; Bizon, Chris; Lange, Ethan M.; Smith, Joshua D.; Turner, Emily H.; Jun, Goo; Kang, Hyun Min; Peloso, Gina; Auer, Paul; Li, Kuo-ping; Flannick, Jason; Zhang, Ji; Fuchsberger, Christian; Gaulton, Kyle; Lindgren, Cecilia; Locke, Adam; Manning, Alisa; Sim, Xueling; Rivas, Manuel A.; Holmen, Oddgeir L.; Gottesman, Omri; Lu, Yingchang; Ruderfer, Douglas; Stahl, Eli A.; Duan, Qing; Li, Yun; Durda, Peter; Jiao, Shuo; Isaacs, Aaron; Hofman, Albert; Bis, Joshua C.; Correa, Adolfo; Griswold, Michael E.; Jakobsdottir, Johanna; Smith, Albert V.; Schreiner, Pamela J.; Feitosa, Mary F.; Zhang, Qunyuan; Huffman, Jennifer E.; Crosby, Jacy; Wassel, Christina L.; Do, Ron; Franceschini, Nora; Martin, Lisa W.; Robinson, Jennifer G.; Assimes, Themistocles L.; Crosslin, David R.; Rosenthal, Elisabeth A.; Tsai, Michael; Rieder, Mark J.; Farlow, Deborah N.; Folsom, Aaron R.; Lumley, Thomas; Fox, Ervin R.; Carlson, Christopher S.; Peters, Ulrike; Jackson, Rebecca D.; van Duijn, Cornelia M.; Uitterlinden, André G.; Levy, Daniel; Rotter, Jerome I.; Taylor, Herman A.; Gudnason, Vilmundur; Siscovick, David S.; Fornage, Myriam; Borecki, Ingrid B.; Hayward, Caroline; Rudan, Igor; Chen, Y. Eugene; Bottinger, Erwin P.; Loos, Ruth J.F.; Sætrom, Pål; Hveem, Kristian; Boehnke, Michael; Groop, Leif; McCarthy, Mark; Meitinger, Thomas; Ballantyne, Christie M.; Gabriel, Stacey B.; O’Donnell, Christopher J.; Post, Wendy S.; North, Kari E.; Reiner, Alexander P.; Boerwinkle, Eric; Psaty, Bruce M.; Altshuler, David; Kathiresan, Sekar; Lin, Dan-Yu; Jarvik, Gail P.; Cupples, L. Adrienne; Kooperberg, Charles; Wilson, James G.; Nickerson, Deborah A.; Abecasis, Goncalo R.; Rich, Stephen S.; Tracy, Russell P.; Willer, Cristen J.; Gabriel, Stacey B.; Altshuler, David M.; Abecasis, Gonçalo R.; Allayee, Hooman; Cresci, Sharon; Daly, Mark J.; de Bakker, Paul I.W.; DePristo, Mark A.; Do, Ron; Donnelly, Peter; Farlow, Deborah N.; Fennell, Tim; Garimella, Kiran; Hazen, Stanley L.; Hu, Youna; Jordan, Daniel M.; Jun, Goo; Kathiresan, Sekar; Kang, Hyun Min; Kiezun, Adam; Lettre, Guillaume; Li, Bingshan; Li, Mingyao; Newton-Cheh, Christopher H.; Padmanabhan, Sandosh; Peloso, Gina; Pulit, Sara; Rader, Daniel J.; Reich, David; Reilly, Muredach P.; Rivas, Manuel A.; Schwartz, Steve; Scott, Laura; Siscovick, David S.; Spertus, John A.; Stitziel, Nathaniel O.; Stoletzki, Nina; Sunyaev, Shamil R.; Voight, Benjamin F.; Willer, Cristen J.; Rich, Stephen S.; Akylbekova, Ermeg; Atwood, Larry D.; Ballantyne, Christie M.; Barbalic, Maja; Barr, R. Graham; Benjamin, Emelia J.; Bis, Joshua; Boerwinkle, Eric; Bowden, Donald W.; Brody, Jennifer; Budoff, Matthew; Burke, Greg; Buxbaum, Sarah; Carr, Jeff; Chen, Donna T.; Chen, Ida Y.; Chen, Wei-Min; Concannon, Pat; Crosby, Jacy; Cupples, L. Adrienne; D’Agostino, Ralph; DeStefano, Anita L.; Dreisbach, Albert; Dupuis, Josée; Durda, J. Peter; Ellis, Jaclyn; Folsom, Aaron R.; Fornage, Myriam; Fox, Caroline S.; Fox, Ervin; Funari, Vincent; Ganesh, Santhi K.; Gardin, Julius; Goff, David; Gordon, Ora; Grody, Wayne; Gross, Myron; Guo, Xiuqing; Hall, Ira M.; Heard-Costa, Nancy L.; Heckbert, Susan R.; Heintz, Nicholas; Herrington, David M.; Hickson, DeMarc; Huang, Jie; Hwang, Shih-Jen; Jacobs, David R.; Jenny, Nancy S.; Johnson, Andrew D.; Johnson, Craig W.; Kawut, Steven; Kronmal, Richard; Kurz, Raluca; Lange, Ethan M.; Lange, Leslie A.; Larson, Martin G.; Lawson, Mark; Lewis, Cora E.; Levy, Daniel; Li, Dalin; Lin, Honghuang; Liu, Chunyu; Liu, Jiankang; Liu, Kiang; Liu, Xiaoming; Liu, Yongmei; Longstreth, William T.; Loria, Cay; Lumley, Thomas; Lunetta, Kathryn; Mackey, Aaron J.; Mackey, Rachel; Manichaikul, Ani; Maxwell, Taylor; McKnight, Barbara; Meigs, James B.; Morrison, Alanna C.; Musani, Solomon K.; Mychaleckyj, Josyf C.; Nettleton, Jennifer A.; North, Kari; O’Donnell, Christopher J.; O’Leary, Daniel; Ong, Frank; Palmas, Walter; Pankow, James S.; Pankratz, Nathan D.; Paul, Shom; Perez, Marco; Person, Sharina D.; Polak, Joseph; Post, Wendy S.; Psaty, Bruce M.; Quinlan, Aaron R.; Raffel, Leslie J.; Ramachandran, Vasan S.; Reiner, Alexander P.; Rice, Kenneth; Rotter, Jerome I.; Sanders, Jill P.; Schreiner, Pamela; Seshadri, Sudha; Shea, Steve; Sidney, Stephen; Silverstein, Kevin; Smith, Nicholas L.; Sotoodehnia, Nona; Srinivasan, Asoke; Taylor, Herman A.; Taylor, Kent; Thomas, Fridtjof; Tracy, Russell P.; Tsai, Michael Y.; Volcik, Kelly A.; Wassel, Chrstina L.; Watson, Karol; Wei, Gina; White, Wendy; Wiggins, Kerri L.; Wilk, Jemma B.; Williams, O. Dale; Wilson, Gregory; Wilson, James G.; Wolf, Phillip; Zakai, Neil A.; Hardy, John; Meschia, James F.; Nalls, Michael; Singleton, Andrew; Worrall, Brad; Bamshad, Michael J.; Barnes, Kathleen C.; Abdulhamid, Ibrahim; Accurso, Frank; Anbar, Ran; Beaty, Terri; Bigham, Abigail; Black, Phillip; Bleecker, Eugene; Buckingham, Kati; Cairns, Anne Marie; Caplan, Daniel; Chatfield, Barbara; Chidekel, Aaron; Cho, Michael; Christiani, David C.; Crapo, James D.; Crouch, Julia; Daley, Denise; Dang, Anthony; Dang, Hong; De Paula, Alicia; DeCelie-Germana, Joan; Drumm, Allen DozorMitch; Dyson, Maynard; Emerson, Julia; Emond, Mary J.; Ferkol, Thomas; Fink, Robert; Foster, Cassandra; Froh, Deborah; Gao, Li; Gershan, William; Gibson, Ronald L.; Godwin, Elizabeth; Gondor, Magdalen; Gutierrez, Hector; Hansel, Nadia N.; Hassoun, Paul M.; Hiatt, Peter; Hokanson, John E.; Howenstine, Michelle; Hummer, Laura K.; Kanga, Jamshed; Kim, Yoonhee; Knowles, Michael R.; Konstan, Michael; Lahiri, Thomas; Laird, Nan; Lange, Christoph; Lin, Lin; Lin, Xihong; Louie, Tin L.; Lynch, David; Make, Barry; Martin, Thomas R.; Mathai, Steve C.; Mathias, Rasika A.; McNamara, John; McNamara, Sharon; Meyers, Deborah; Millard, Susan; Mogayzel, Peter; Moss, Richard; Murray, Tanda; Nielson, Dennis; Noyes, Blakeslee; O’Neal, Wanda; Orenstein, David; O’Sullivan, Brian; Pace, Rhonda; Pare, Peter; Parker, H. Worth; Passero, Mary Ann; Perkett, Elizabeth; Prestridge, Adrienne; Rafaels, Nicholas M.; Ramsey, Bonnie; Regan, Elizabeth; Ren, Clement; Retsch-Bogart, George; Rock, Michael; Rosen, Antony; Rosenfeld, Margaret; Ruczinski, Ingo; Sanford, Andrew; Schaeffer, David; Sell, Cindy; Sheehan, Daniel; Silverman, Edwin K.; Sin, Don; Spencer, Terry; Stonebraker, Jackie; Tabor, Holly K.; Varlotta, Laurie; Vergara, Candelaria I.; Weiss, Robert; Wigley, Fred; Wise, Robert A.; Wright, Fred A.; Wurfel, Mark M.; Zanni, Robert; Zou, Fei; Nickerson, Deborah A.; Rieder, Mark J.; Green, Phil; Shendure, Jay; Akey, Joshua M.; Bustamante, Carlos D.; Crosslin, David R.; Eichler, Evan E.; Fox, P. Keolu; Fu, Wenqing; Gordon, Adam; Gravel, Simon; Jarvik, Gail P.; Johnsen, Jill M.; Kan, Mengyuan; Kenny, Eimear E.; Kidd, Jeffrey M.; Lara-Garduno, Fremiet; Leal, Suzanne M.; Liu, Dajiang J.; McGee, Sean; O’Connor, Timothy D.; Paeper, Bryan; Robertson, Peggy D.; Smith, Joshua D.; Staples, Jeffrey C.; Tennessen, Jacob A.; Turner, Emily H.; Wang, Gao; Yi, Qian; Jackson, Rebecca; Peters, Ulrike; Carlson, Christopher S.; Anderson, Garnet; Anton-Culver, Hoda; Assimes, Themistocles L.; Auer, Paul L.; Beresford, Shirley; Bizon, Chris; Black, Henry; Brunner, Robert; Brzyski, Robert; Burwen, Dale; Caan, Bette; Carty, Cara L.; Chlebowski, Rowan; Cummings, Steven; Curb, J. David; Eaton, Charles B.; Ford, Leslie; Franceschini, Nora; Fullerton, Stephanie M.; Gass, Margery; Geller, Nancy; Heiss, Gerardo; Howard, Barbara V.; Hsu, Li; Hutter, Carolyn M.; Ioannidis, John; Jiao, Shuo; Johnson, Karen C.; Kooperberg, Charles; Kuller, Lewis; LaCroix, Andrea; Lakshminarayan, Kamakshi; Lane, Dorothy; Lasser, Norman; LeBlanc, Erin; Li, Kuo-Ping; Limacher, Marian; Lin, Dan-Yu; Logsdon, Benjamin A.; Ludlam, Shari; Manson, JoAnn E.; Margolis, Karen; Martin, Lisa; McGowan, Joan; Monda, Keri L.; Kotchen, Jane Morley; Nathan, Lauren; Ockene, Judith; O’Sullivan, Mary Jo; Phillips, Lawrence S.; Prentice, Ross L.; Robbins, John; Robinson, Jennifer G.; Rossouw, Jacques E.; Sangi-Haghpeykar, Haleh; Sarto, Gloria E.; Shumaker, Sally; Simon, Michael S.; Stefanick, Marcia L.; Stein, Evan; Tang, Hua; Taylor, Kira C.; Thomson, Cynthia A.; Thornton, Timothy A.; Van Horn, Linda; Vitolins, Mara; Wactawski-Wende, Jean; Wallace, Robert; Wassertheil-Smoller, Sylvia; Zeng, Donglin; Applebaum-Bowden, Deborah; Feolo, Michael; Gan, Weiniu; Paltoo, Dina N.; Sholinsky, Phyliss; Sturcke, Anne

2014-01-01

Elevated low-density lipoprotein cholesterol (LDL-C) is a treatable, heritable risk factor for cardiovascular disease. Genome-wide association studies (GWASs) have identified 157 variants associated with lipid levels but are not well suited to assess the impact of rare and low-frequency variants. To determine whether rare or low-frequency coding variants are associated with LDL-C, we exome sequenced 2,005 individuals, including 554 individuals selected for extreme LDL-C (>98th or <2nd percentile). Follow-up analyses included sequencing of 1,302 additional individuals and genotype-based analysis of 52,221 individuals. We observed significant evidence of association between LDL-C and the burden of rare or low-frequency variants in PNPLA5, encoding a phospholipase-domain-containing protein, and both known and previously unidentified variants in PCSK9, LDLR and APOB, three known lipid-related genes. The effect sizes for the burden of rare variants for each associated gene were substantially higher than those observed for individual SNPs identified from GWASs. We replicated the PNPLA5 signal in an independent large-scale sequencing study of 2,084 individuals. In conclusion, this large whole-exome-sequencing study for LDL-C identified a gene not known to be implicated in LDL-C and provides unique insight into the design and analysis of similar experiments. PMID:24507775

The SEA complex – the beginning

Directory of Open Access Journals (Sweden)

Dokudovskaya S. S.

2012-07-01

Full Text Available The presence of distinctive internal membrane compartments, dynamically connected via selective transport pathways, is a hallmark of eukaryotic cells. Many of the proteins required for formation and maintenance of these compartments share an evolutionary history. We have recently identified a new conserved protein complex – the SEA complex – that possesses proteins with structural characteristics similar to the membrane coating complexes such as the nuclear pore complex (NPC, the COPII vesicle coating complex and HOPS/CORVET tethering complexes. The SEA complex in yeast is dynamically associated to the vacuole. The data on the function of the SEA complex remain extremely limited. Here we will discuss a possible role of the SEA complex based on the data from genetic assays and a number of functional studies in both yeast and other eukaryotes.

Exome Sequencing and Linkage Analysis Identified Novel Candidate Genes in Recessive Intellectual Disability Associated with Ataxia.

Science.gov (United States)

Jazayeri, Roshanak; Hu, Hao; Fattahi, Zohreh; Musante, Luciana; Abedini, Seyedeh Sedigheh; Hosseini, Masoumeh; Wienker, Thomas F; Ropers, Hans Hilger; Najmabadi, Hossein; Kahrizi, Kimia

2015-10-01

Intellectual disability (ID) is a neuro-developmental disorder which causes considerable socio-economic problems. Some ID individuals are also affected by ataxia, and the condition includes different mutations affecting several genes. We used whole exome sequencing (WES) in combination with homozygosity mapping (HM) to identify the genetic defects in five consanguineous families among our cohort study, with two affected children with ID and ataxia as major clinical symptoms. We identified three novel candidate genes, RIPPLY1, MRPL10, SNX14, and a new mutation in known gene SURF1. All are autosomal genes, except RIPPLY1, which is located on the X chromosome. Two are housekeeping genes, implicated in transcription and translation regulation and intracellular trafficking, and two encode mitochondrial proteins. The pathogenesis of these variants was evaluated by mutation classification, bioinformatic methods, review of medical and biological relevance, co-segregation studies in the particular family, and a normal population study. Linkage analysis and exome sequencing of a small number of affected family members is a powerful new technique which can be used to decrease the number of candidate genes in heterogenic disorders such as ID, and may even identify the responsible gene(s).

Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus.

Science.gov (United States)

Bowles, Neil E; Jou, Chuanchau J; Arrington, Cammon B; Kennedy, Brett J; Earl, Aubree; Matsunami, Norisada; Meyers, Lindsay L; Etheridge, Susan P; Saarel, Elizabeth V; Bleyl, Steven B; Yost, H Joseph; Yandell, Mark; Leppert, Mark F; Tristani-Firouzi, Martin; Gruber, Peter J

2015-12-01

Wolff-Parkinson-White (WPW) syndrome is a common cause of supraventricular tachycardia that carries a risk of sudden cardiac death. To date, mutations in only one gene, PRKAG2, which encodes the 5'-AMP-activated protein kinase subunit γ-2, have been identified as causative for WPW. DNA samples from five members of a family with WPW were analyzed by exome sequencing. We applied recently designed prioritization strategies (VAAST/pedigree VAAST) coupled with an ontology-based algorithm (Phevor) that reduced the number of potentially damaging variants to 10: a variant in KCNE2 previously associated with Long QT syndrome was also identified. Of these 11 variants, only MYH6 p.E1885K segregated with the WPW phenotype in all affected individuals and was absent in 10 unaffected family members. This variant was predicted to be damaging by in silico methods and is not present in the 1,000 genome and NHLBI exome sequencing project databases. Screening of a replication cohort of 47 unrelated WPW patients did not identify other likely causative variants in PRKAG2 or MYH6. MYH6 variants have been identified in patients with atrial septal defects, cardiomyopathies, and sick sinus syndrome. Our data highlight the pleiotropic nature of phenotypes associated with defects in this gene. © 2015 Wiley Periodicals, Inc.

Exome Analysis of a Family with Wolff–Parkinson–White Syndrome Identifies a Novel Disease Locus

Science.gov (United States)

Bowles, Neil E.; Jou, Chuanchau J.; Arrington, Cammon B.; Kennedy, Brett J.; Earl, Aubree; Matsunami, Norisada; Meyers, Lindsay L.; Etheridge, Susan P.; Saarel, Elizabeth V.; Bleyl, Steven B.; Yost, H. Joseph; Yandell, Mark; Leppert, Mark F.; Tristani-Firouzi, Martin; Gruber, Peter J.

2016-01-01

Wolff–Parkinson–White (WPW) syndrome is a common cause of supraventricular tachycardia that carries a risk of sudden cardiac death. To date, mutations in only one gene, PRKAG2, which encodes the 5’ -AMP-activated protein kinase subunit γ-2, have been identified as causative for WPW. DNA samples from five members of a family with WPW were analyzed by exome sequencing. We applied recently designed prioritization strategies (VAAST/pedigree VAAST) coupled with an ontology-based algorithm (Phevor) that reduced the number of potentially damaging variants to 10: a variant in KCNE2 previously associated with Long QT syndrome was also identified. Of these 11 variants, only MYH6 p.E1885K segregated with the WPW phenotype in all affected individuals and was absent in 10 unaffected family members. This variant was predicted to be damaging by in silico methods and is not present in the 1,000 genome and NHLBI exome sequencing project databases. Screening of a replication cohort of 47 unrelated WPW patients did not identify other likely causative variants in PRKAG2 or MYH6. MYH6 variants have been identified in patients with atrial septal defects, cardiomyopathies, and sick sinus syndrome. Our data highlight the pleiotropic nature of phenotypes associated with defects in this gene. PMID:26284702

The Number of Candidate Variants in Exome Sequencing for Mendelian Disease under No Genetic Heterogeneity

Directory of Open Access Journals (Sweden)

Jo Nishino

2013-01-01

Full Text Available There has been recent success in identifying disease-causing variants in Mendelian disorders by exome sequencing followed by simple filtering techniques. Studies generally assume complete or high penetrance. However, there are likely many failed and unpublished studies due in part to incomplete penetrance or phenocopy. In this study, the expected number of candidate single-nucleotide variants (SNVs in exome data for autosomal dominant or recessive Mendelian disorders was investigated under the assumption of “no genetic heterogeneity.” All variants were assumed to be under the “null model,” and sample allele frequencies were modeled using a standard population genetics theory. To investigate the properties of pedigree data, full-sibs were considered in addition to unrelated individuals. In both cases, particularly regarding full-sibs, the number of SNVs remained very high without controls. The high efficacy of controls was also confirmed. When controls were used with a relatively large total sample size (e.g., N=20, 50, filtering incorporating of incomplete penetrance and phenocopy efficiently reduced the number of candidate SNVs. This suggests that filtering is useful when an assumption of no “genetic heterogeneity” is appropriate and could provide general guidelines for sample size determination.

Exome sequencing for gene discovery in lethal fetal disorders--harnessing the value of extreme phenotypes.

Science.gov (United States)

Filges, Isabel; Friedman, Jan M

2015-10-01

Massively parallel sequencing has revolutionized our understanding of Mendelian disorders, and many novel genes have been discovered to cause disease phenotypes when mutant. At the same time, next-generation sequencing approaches have enabled non-invasive prenatal testing of free fetal DNA in maternal blood. However, little attention has been paid to using whole exome and genome sequencing strategies for gene identification in fetal disorders that are lethal in utero, because they can appear to be sporadic and Mendelian inheritance may be missed. We present challenges and advantages of applying next-generation sequencing approaches to gene discovery in fetal malformation phenotypes and review recent successful discovery approaches. We discuss the implication and significance of recessive inheritance and cross-species phenotyping in fetal lethal conditions. Whole exome sequencing can be used in individual families with undiagnosed lethal congenital anomaly syndromes to discover causal mutations, provided that prior to data analysis, the fetal phenotype can be correlated to a particular developmental pathway in embryogenesis. Cross-species phenotyping allows providing further evidence for causality of discovered variants in genes involved in those extremely rare phenotypes and will increase our knowledge about normal and abnormal human developmental processes. Ultimately, families will benefit from the option of early prenatal diagnosis. © 2014 John Wiley & Sons, Ltd.

Thermodiffusion Mo-B-Si coating on VN-3 niobium alloy

International Nuclear Information System (INIS)

Kozlov, A.T.; Lazarev, Eh.M.; Monakhova, L.A.; Shestova, V.F.; Romanovich, I.V.

1985-01-01

Protective properties of complex Mo-B-Si-coating on niobium alloy VN-3 (4.7 mass.% Mo, 1.1 mass.% Zr, 0.1 mass.% C) have been studied. It is established, that the complex Mo-B-Si-coating ensures protection from oxidation of niobium alloys in the temperature range of 800-1200 degC for 1000-1500 hr, at 1600 degC - for 10 hr. High heat resistance of Mo-B-Si - coating at 800-1200 degC is determined by the presence of amorphous film of SiOΛ2 over the layer MoSiΛ2 and barrier boride layer on the boundary with the metal protected; decrease in the coating heat resistance at 1600 degC is related to the destruction of boride layer, decomposition of MoSiΛ2 for lower cilicides and loosening of SiOΛ2 film

Biomimetic calcium phosphate coating of additively manufactured porous CoCr implants

Energy Technology Data Exchange (ETDEWEB)

Lindahl, Carl [BIOMATCELL Vinn Excellence Center of Biomaterials and Cell Therapy, Gothenburg (Sweden); Department of Engineering Sciences, Ångstrom Laboratory, Uppsala University, Uppsala (Sweden); Xia, Wei, E-mail: wei.xia@angstrom.uu.se [BIOMATCELL Vinn Excellence Center of Biomaterials and Cell Therapy, Gothenburg (Sweden); Department of Engineering Sciences, Ångstrom Laboratory, Uppsala University, Uppsala (Sweden); Engqvist, Håkan [BIOMATCELL Vinn Excellence Center of Biomaterials and Cell Therapy, Gothenburg (Sweden); Department of Engineering Sciences, Ångstrom Laboratory, Uppsala University, Uppsala (Sweden); Snis, Anders [BIOMATCELL Vinn Excellence Center of Biomaterials and Cell Therapy, Gothenburg (Sweden); Arcam AB, Krokslätts Fabriker 27 A, SE-431 37 Mölndal (Sweden); Lausmaa, Jukka [BIOMATCELL Vinn Excellence Center of Biomaterials and Cell Therapy, Gothenburg (Sweden); Department of Chemistry, Materials and Surfaces, SP Technical Research Institute of Sweden, Borås (Sweden); Palmquist, Anders [BIOMATCELL Vinn Excellence Center of Biomaterials and Cell Therapy, Gothenburg (Sweden); Department of Biomaterials, Sahlgrenska Academy at the University of Gothenburg, Gothenburg (Sweden)

2015-10-30

Highlights: • A route for coating complex shaped electron beam melted implants is presented. • Biomimetic HA coatings were deposited on CoCr alloys using a solution method. • Deposited biomimetic coating was partially crystalline, slightly calcium deficient. • Coating morphology was plate-like with crystallites forming roundish flowers. • Present coating procedure could be useful for porous implants made by EBM. - Abstract: The aim of this work was to study the feasibility to use a biomimetic method to prepare biomimetic hydroxyapatite (HA) coatings on CoCr substrates with short soaking times and to characterize the properties of such coatings. A second objective was to investigate if the coatings could be applied to porous CoCr implants manufactured by electron beam melting (EBM). The coating was prepared by immersing the pretreated CoCr substrates and EBM implants into the phosphate-buffered solution with Ca{sup 2+} in sealed plastic bottles, kept at 60 °C for 3 days. The formed coating was partially crystalline, slightly calcium deficient and composed of plate-like crystallites forming roundish flowers in the size range of 300–500 nm. Cross-section imaging showed a thickness of 300–500 nm. In addition, dissolution tests in Tris–HCl up to 28 days showed that a substantial amount of the coating had dissolved, however, undergoing only minor morphological changes. A uniform coating was formed within the porous network of the additive manufactured implants having similar thickness and morphology as for the flat samples. In conclusion, the present coating procedure allows coatings to be formed on CoCr and could be used for complex shaped, porous implants made by additive manufacturing.

Biomimetic calcium phosphate coating of additively manufactured porous CoCr implants

International Nuclear Information System (INIS)

Lindahl, Carl; Xia, Wei; Engqvist, Håkan; Snis, Anders; Lausmaa, Jukka; Palmquist, Anders

2015-01-01

Highlights: • A route for coating complex shaped electron beam melted implants is presented. • Biomimetic HA coatings were deposited on CoCr alloys using a solution method. • Deposited biomimetic coating was partially crystalline, slightly calcium deficient. • Coating morphology was plate-like with crystallites forming roundish flowers. • Present coating procedure could be useful for porous implants made by EBM. - Abstract: The aim of this work was to study the feasibility to use a biomimetic method to prepare biomimetic hydroxyapatite (HA) coatings on CoCr substrates with short soaking times and to characterize the properties of such coatings. A second objective was to investigate if the coatings could be applied to porous CoCr implants manufactured by electron beam melting (EBM). The coating was prepared by immersing the pretreated CoCr substrates and EBM implants into the phosphate-buffered solution with Ca"2"+ in sealed plastic bottles, kept at 60 °C for 3 days. The formed coating was partially crystalline, slightly calcium deficient and composed of plate-like crystallites forming roundish flowers in the size range of 300–500 nm. Cross-section imaging showed a thickness of 300–500 nm. In addition, dissolution tests in Tris–HCl up to 28 days showed that a substantial amount of the coating had dissolved, however, undergoing only minor morphological changes. A uniform coating was formed within the porous network of the additive manufactured implants having similar thickness and morphology as for the flat samples. In conclusion, the present coating procedure allows coatings to be formed on CoCr and could be used for complex shaped, porous implants made by additive manufacturing.

Extended exome sequencing identifies BACH2 as a novel major risk locus for Addison's disease

OpenAIRE

Eriksson, D.; Bianchi, Matteo; Landegren, Nils; Nordin, Jessika; Dalin, Frida; Mathioudaki, Argyri; Eriksson, G. N.; Hultin-Rosenberg, Lina; Dahlqvist, Johanna; Zetterqvist, H.; Karlsson, Andreas; Hallgren, Anna; Farias, F. H. G.; Murén, Eva; Ahlgren, Kerstin M.

2016-01-01

BackgroundAutoimmune disease is one of the leading causes of morbidity and mortality worldwide. In Addisons disease, the adrenal glands are targeted by destructive autoimmunity. Despite being the most common cause of primary adrenal failure, little is known about its aetiology. MethodsTo understand the genetic background of Addisons disease, we utilized the extensively characterized patients of the Swedish Addison Registry. We developed an extended exome capture array comprising a selected se...

Exome sequences of multiplex, multigenerational families reveal schizophrenia risk loci with potential implications for neurocognitive performance.

Science.gov (United States)

Kos, Mark Z; Carless, Melanie A; Peralta, Juan; Curran, Joanne E; Quillen, Ellen E; Almeida, Marcio; Blackburn, August; Blondell, Lucy; Roalf, David R; Pogue-Geile, Michael F; Gur, Ruben C; Göring, Harald H H; Nimgaonkar, Vishwajit L; Gur, Raquel E; Almasy, Laura

2017-12-01

Schizophrenia is a serious mental illness, involving disruptions in thought and behavior, with a worldwide prevalence of about one percent. Although highly heritable, much of the genetic liability of schizophrenia is yet to be explained. We searched for susceptibility loci in multiplex, multigenerational families affected by schizophrenia, targeting protein-altering variation with in silico predicted functional effects. Exome sequencing was performed on 136 samples from eight European-American families, including 23 individuals diagnosed with schizophrenia or schizoaffective disorder. In total, 11,878 non-synonymous variants from 6,396 genes were tested for their association with schizophrenia spectrum disorders. Pathway enrichment analyses were conducted on gene-based test results, protein-protein interaction (PPI) networks, and epistatic effects. Using a significance threshold of FDR < 0.1, association was detected for rs10941112 (p = 2.1 × 10 -5 ; q-value = 0.073) in AMACR, a gene involved in fatty acid metabolism and previously implicated in schizophrenia, with significant cis effects on gene expression (p = 5.5 × 10 -4 ), including brain tissue data from the Genotype-Tissue Expression project (minimum p = 6.0 × 10 -5 ). A second SNP, rs10378 located in TMEM176A, also shows risk effects in the exome data (p = 2.8 × 10 -5 ; q-value = 0.073). PPIs among our top gene-based association results (p < 0.05; n = 359 genes) reveal significant enrichment of genes involved in NCAM-mediated neurite outgrowth (p = 3.0 × 10 -5 ), while exome-wide SNP-SNP interaction effects for rs10941112 and rs10378 indicate a potential role for kinase-mediated signaling involved in memory and learning. In conclusion, these association results implicate AMACR and TMEM176A in schizophrenia risk, whose effects may be modulated by genes involved in synaptic plasticity and neurocognitive performance. © 2017 Wiley Periodicals, Inc.

Corrosion characteristics of several thermal spray cermet-coating/alloy systems

International Nuclear Information System (INIS)

Ashary, A.A.; Tucker, R.C. Jr.

1991-01-01

The corrosion characteristics of a thermal spray multiphase cermet coating can be quite complex. Factors such as porosity and galvanic effects between different phases in the coating and the substrate, as well as the inherent general and localized corrosion resistance of each phase, can play an important role. The present paper describes the corrosion of several cermet-coating/alloy systems as studied by a potentiodynamic cyclic polarization technique. The corrosion of these coating systems was found to be most often dominated by corrosion of the metallic phases in the coating or of the substrate alloy. (orig.)

TMC-SNPdb: an Indian germline variant database derived from whole exome sequences.

Science.gov (United States)

Upadhyay, Pawan; Gardi, Nilesh; Desai, Sanket; Sahoo, Bikram; Singh, Ankita; Togar, Trupti; Iyer, Prajish; Prasad, Ratnam; Chandrani, Pratik; Gupta, Sudeep; Dutt, Amit

2016-01-01

Cancer is predominantly a somatic disease. A mutant allele present in a cancer cell genome is considered somatic when it's absent in the paired normal genome along with public SNP databases. The current build of dbSNP, the most comprehensive public SNP database, however inadequately represents several non-European Caucasian populations, posing a limitation in cancer genomic analyses of data from these populations. We present the T: ata M: emorial C: entre-SNP D: ata B: ase (TMC-SNPdb), as the first open source, flexible, upgradable, and freely available SNP database (accessible through dbSNP build 149 and ANNOVAR)-representing 114 309 unique germline variants-generated from whole exome data of 62 normal samples derived from cancer patients of Indian origin. The TMC-SNPdb is presented with a companion subtraction tool that can be executed with command line option or using an easy-to-use graphical user interface with the ability to deplete additional Indian population specific SNPs over and above dbSNP and 1000 Genomes databases. Using an institutional generated whole exome data set of 132 samples of Indian origin, we demonstrate that TMC-SNPdb could deplete 42, 33 and 28% false positive somatic events post dbSNP depletion in Indian origin tongue, gallbladder, and cervical cancer samples, respectively. Beyond cancer somatic analyses, we anticipate utility of the TMC-SNPdb in several Mendelian germline diseases. In addition to dbSNP build 149 and ANNOVAR, the TMC-SNPdb along with the subtraction tool is available for download in the public domain at the following:Database URL: http://www.actrec.gov.in/pi-webpages/AmitDutt/TMCSNP/TMCSNPdp.html. © The Author(s) 2016. Published by Oxford University Press.

Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease

DEFF Research Database (Denmark)

Kozlitina, Julia; Smagris, Eriks; Stender, Stefan

2014-01-01

Nonalcoholic fatty liver disease (NAFLD) is the most common form of liver disease. To elucidate the molecular basis of NAFLD, we performed an exome-wide association study of liver fat content. Three variants were associated with higher liver fat levels at the exome-wide significance level of 3.......6 × 10(-7): two in PNPLA3, an established locus for NAFLD, and one (encoding p.Glu167Lys) in TM6SF2, a gene of unknown function. The TM6SF2 variant encoding p.Glu167Lys was also associated with higher circulating levels of alanine transaminase, a marker of liver injury, and with lower levels of low...... knockdown of Tm6sf2 in mice increased liver triglyceride content by threefold and decreased very-low-density lipoprotein (VLDL) secretion by 50%. Taken together, these data indicate that TM6SF2 activity is required for normal VLDL secretion and that impaired TM6SF2 function causally contributes to NAFLD....

Whole-exome sequencing identifies novel compound heterozygous mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa.

Science.gov (United States)

Méndez-Vidal, Cristina; González-Del Pozo, María; Vela-Boza, Alicia; Santoyo-López, Javier; López-Domingo, Francisco J; Vázquez-Marouschek, Carmen; Dopazo, Joaquin; Borrego, Salud; Antiñolo, Guillermo

2013-01-01

Retinitis pigmentosa (RP) is an inherited retinal dystrophy characterized by extreme genetic and clinical heterogeneity. Thus, the diagnosis is not always easily performed due to phenotypic and genetic overlap. Current clinical practices have focused on the systematic evaluation of a set of known genes for each phenotype, but this approach may fail in patients with inaccurate diagnosis or infrequent genetic cause. In the present study, we investigated the genetic cause of autosomal recessive RP (arRP) in a Spanish family in which the causal mutation has not yet been identified with primer extension technology and resequencing. We designed a whole-exome sequencing (WES)-based approach using NimbleGen SeqCap EZ Exome V3 sample preparation kit and the SOLiD 5500×l next-generation sequencing platform. We sequenced the exomes of both unaffected parents and two affected siblings. Exome analysis resulted in the identification of 43,204 variants in the index patient. All variants passing filter criteria were validated with Sanger sequencing to confirm familial segregation and absence in the control population. In silico prediction tools were used to determine mutational impact on protein function and the structure of the identified variants. Novel Usher syndrome type 2A (USH2A) compound heterozygous mutations, c.4325T>C (p.F1442S) and c.15188T>G (p.L5063R), located in exons 20 and 70, respectively, were identified as probable causative mutations for RP in this family. Family segregation of the variants showed the presence of both mutations in all affected members and in two siblings who were apparently asymptomatic at the time of family ascertainment. Clinical reassessment confirmed the diagnosis of RP in these patients. Using WES, we identified two heterozygous novel mutations in USH2A as the most likely disease-causing variants in a Spanish family diagnosed with arRP in which the cause of the disease had not yet been identified with commonly used techniques. Our data

Pellagra-like condition is xeroderma pigmentosum/Cockayne syndrome complex and niacin confers clinical benefit.

Science.gov (United States)

Hijazi, H; Salih, M A; Hamad, M H A; Hassan, H H; Salih, S B M; Mohamed, K A; Mukhtar, M M; Karrar, Z A; Ansari, S; Ibrahim, N; Alkuraya, F S

2015-01-01

An extremely rare pellagra-like condition has been described, which was partially responsive to niacin and associated with a multisystem involvement. The condition was proposed to represent a novel autosomal recessive entity but the underlying mutation remained unknown for almost three decades. The objective of this study was to identify the causal mutation in the pellagra-like condition and investigate the mechanism by which niacin confers clinical benefit. Autozygosity mapping and exome sequencing were used to identify the causal mutation, and comet assay on patient fibroblasts before and after niacin treatment to assess its effect on DNA damage. We identified a single disease locus that harbors a novel mutation in ERCC5, thus confirming that the condition is in fact xeroderma pigmentosum/Cockayne syndrome (XP/CS) complex. Importantly, we also show that the previously described dermatological response to niacin is consistent with a dramatic protective effect against ultraviolet-induced DNA damage in patient fibroblasts conferred by niacin treatment. Our findings show the power of exome sequencing in reassigning previously described novel clinical entities, and suggest a mechanism for the dermatological response to niacin in patients with XP/CS complex. This raises interesting possibilities about the potential therapeutic use of niacin in XP. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Rapid prenatal diagnosis using targeted exome sequencing: a cohort study to assess feasibility and potential impact on prenatal counseling and pregnancy management.

Science.gov (United States)

Chandler, Natalie; Best, Sunayna; Hayward, Jane; Faravelli, Francesca; Mansour, Sahar; Kivuva, Emma; Tapon, Dagmar; Male, Alison; DeVile, Catherine; Chitty, Lyn S

2018-03-29

PurposeUnexpected fetal abnormalities occur in 2-5% of pregnancies. While traditional cytogenetic and microarray approaches achieve diagnosis in around 40% of cases, lack of diagnosis in others impedes parental counseling, informed decision making, and pregnancy management. Postnatally exome sequencing yields high diagnostic rates, but relies on careful phenotyping to interpret genotype results. Here we used a multidisciplinary approach to explore the utility of rapid fetal exome sequencing for prenatal diagnosis using skeletal dysplasias as an exemplar.MethodsParents in pregnancies undergoing invasive testing because of sonographic fetal abnormalities, where multidisciplinary review considered skeletal dysplasia a likely etiology, were consented for exome trio sequencing (both parents and fetus). Variant interpretation focused on a virtual panel of 240 genes known to cause skeletal dysplasias.ResultsDefinitive molecular diagnosis was made in 13/16 (81%) cases. In some cases, fetal ultrasound findings alone were of sufficient severity for parents to opt for termination. In others, molecular diagnosis informed accurate prediction of outcome, improved parental counseling, and enabled parents to terminate or continue the pregnancy with certainty.ConclusionTrio sequencing with expert multidisciplinary review for case selection and data interpretation yields timely, high diagnostic rates in fetuses presenting with unexpected skeletal abnormalities. This improves parental counseling and pregnancy management.Genetics in Medicine advance online publication, 29 March 2018; doi:10.1038/gim.2018.30.

Property Evaluation and Damage Evolution of Environmental Barrier Coatings and Environmental Barrier Coated SiC/SiC Ceramic Matrix Composite Sub-Elements

Science.gov (United States)

Zhu, Dongming; Halbig, Michael; Jaskowiak, Martha; Hurst, Janet; Bhatt, Ram; Fox, Dennis S.

2014-01-01

This paper describes recent development of environmental barrier coatings on SiC/SiC ceramic matrix composites. The creep and fatigue behavior at aggressive long-term high temperature conditions have been evaluated and highlighted. Thermal conductivity and high thermal gradient cyclic durability of environmental barrier coatings have been evaluated. The damage accumulation and complex stress-strain behavior environmental barrier coatings on SiCSiC ceramic matrix composite turbine airfoil subelements during the thermal cyclic and fatigue testing of have been also reported.

Extended exome sequencing identifies BACH2 as a novel major risk locus for Addison's disease.

Science.gov (United States)

Eriksson, D; Bianchi, M; Landegren, N; Nordin, J; Dalin, F; Mathioudaki, A; Eriksson, G N; Hultin-Rosenberg, L; Dahlqvist, J; Zetterqvist, H; Karlsson, Å; Hallgren, Å; Farias, F H G; Murén, E; Ahlgren, K M; Lobell, A; Andersson, G; Tandre, K; Dahlqvist, S R; Söderkvist, P; Rönnblom, L; Hulting, A-L; Wahlberg, J; Ekwall, O; Dahlqvist, P; Meadows, J R S; Bensing, S; Lindblad-Toh, K; Kämpe, O; Pielberg, G R

2016-12-01

Autoimmune disease is one of the leading causes of morbidity and mortality worldwide. In Addison's disease, the adrenal glands are targeted by destructive autoimmunity. Despite being the most common cause of primary adrenal failure, little is known about its aetiology. To understand the genetic background of Addison's disease, we utilized the extensively characterized patients of the Swedish Addison Registry. We developed an extended exome capture array comprising a selected set of 1853 genes and their potential regulatory elements, for the purpose of sequencing 479 patients with Addison's disease and 1394 controls. We identified BACH2 (rs62408233-A, OR = 2.01 (1.71-2.37), P = 1.66 × 10 -15 , MAF 0.46/0.29 in cases/controls) as a novel gene associated with Addison's disease development. We also confirmed the previously known associations with the HLA complex. Whilst BACH2 has been previously reported to associate with organ-specific autoimmune diseases co-inherited with Addison's disease, we have identified BACH2 as a major risk locus in Addison's disease, independent of concomitant autoimmune diseases. Our results may enable future research towards preventive disease treatment. © 2016 The Authors. Journal of Internal Medicine published by John Wiley & Sons Ltd on behalf of Association for Publication of The Journal of Internal Medicine.

ATRX mutation in two adult brothers with non-specific moderate intellectual disability identified by exome sequencing

OpenAIRE

Moncini, S.; Bedeschi, M.F.; Castronovo, P.; Crippa, M.; Calvello, M.; Garghentino, R.R.; Scuvera, G.; Finelli, P.; Venturin, M.

2013-01-01

In this report, we describe two adult brothers affected by moderate non-specific intellectual disability (ID). They showed minor facial anomalies, not clearly ascribable to any specific syndromic patterns, microcephaly, brachydactyly and broad toes. Both brothers presented seizures. Karyotype, subtelomeric and FMR1 analysis were normal in both cases. We performed array-CGH analysis that revealed no copy-number variations potentially associated with ID. Subsequent exome sequence analysis allow...

Whole Exome Sequencing for the differential diagnosis of primary adrenal insufficiency in children

Directory of Open Access Journals (Sweden)

Li F Chan

2015-08-01

Full Text Available Adrenal insufficiency is a rare, but potentially fatal medical condition. In children the cause is most commonly congenital and in recent years a growing number of causative gene mutations have been identified resulting in a myriad of syndromes that share adrenal insufficiency as one of the main characteristics. The evolution of adrenal insufficiency is dependent on the variant and the particular gene affected, meaning rapid and accurate diagnosis is imperative for effective treatment of the patient. Common practice is for candidate genes to be sequenced individually, which is a time consuming process and complicated by overlapping clinical phenotypes. However, with the availability, and increasing cost effectiveness of whole exome sequencing there is the potential for this to become a powerful diagnostic tool. Here we report the results of whole exome sequencing of 43 patients referred to us with a diagnosis of familial glucocorticoid deficiency (FGD who were mutation negative for MC2R, MRAP and STAR the most commonly mutated genes in FGD. WES provided a rapid genetic diagnosis in 17/43 sequenced patients, for the remaining 60% the gene defect may be within intronic/regulatory regions not covered by WES or may be in gene(s representing novel aetiologies. The diagnosis of isolated or familial glucocorticoid deficiency was only confirmed in 3 of the 17 patients, other genetic diagnoses were adrenal hypo- and hyperplasia, Triple A and autoimmune polyendocrinopathy syndrome type I, emphasizing both the difficulty of phenotypically distinguishing between disorders of PAI and the utility of WES as a tool to achieve this.

Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis.

Directory of Open Access Journals (Sweden)

Bernd Timmermann

Full Text Available BACKGROUND: Colorectal cancer (CRC is with approximately 1 million cases the third most common cancer worldwide. Extensive research is ongoing to decipher the underlying genetic patterns with the hope to improve early cancer diagnosis and treatment. In this direction, the recent progress in next generation sequencing technologies has revolutionized the field of cancer genomics. However, one caveat of these studies remains the large amount of genetic variations identified and their interpretation. METHODOLOGY/PRINCIPAL FINDINGS: Here we present the first work on whole exome NGS of primary colon cancers. We performed 454 whole exome pyrosequencing of tumor as well as adjacent not affected normal colonic tissue from microsatellite stable (MSS and microsatellite instable (MSI colon cancer patients and identified more than 50,000 small nucleotide variations for each tissue. According to predictions based on MSS and MSI pathomechanisms we identified eight times more somatic non-synonymous variations in MSI cancers than in MSS and we were able to reproduce the result in four additional CRCs. Our bioinformatics filtering approach narrowed down the rate of most significant mutations to 359 for MSI and 45 for MSS CRCs with predicted altered protein functions. In both CRCs, MSI and MSS, we found somatic mutations in the intracellular kinase domain of bone morphogenetic protein receptor 1A, BMPR1A, a gene where so far germline mutations are associated with juvenile polyposis syndrome, and show that the mutations functionally impair the protein function. CONCLUSIONS/SIGNIFICANCE: We conclude that with deep sequencing of tumor exomes one may be able to predict the microsatellite status of CRC and in addition identify potentially clinically relevant mutations.

Use of whole exome sequencing for the identification of Ito-based arrhythmia mechanism and therapy.

Science.gov (United States)

Sturm, Amy C; Kline, Crystal F; Glynn, Patric; Johnson, Benjamin L; Curran, Jerry; Kilic, Ahmet; Higgins, Robert S D; Binkley, Philip F; Janssen, Paul M L; Weiss, Raul; Raman, Subha V; Fowler, Steven J; Priori, Silvia G; Hund, Thomas J; Carnes, Cynthia A; Mohler, Peter J

2015-05-26

Identified genetic variants are insufficient to explain all cases of inherited arrhythmia. We tested whether the integration of whole exome sequencing with well-established clinical, translational, and basic science platforms could provide rapid and novel insight into human arrhythmia pathophysiology and disease treatment. We report a proband with recurrent ventricular fibrillation, resistant to standard therapeutic interventions. Using whole-exome sequencing, we identified a variant in a previously unidentified exon of the dipeptidyl aminopeptidase-like protein-6 (DPP6) gene. This variant is the first identified coding mutation in DPP6 and augments cardiac repolarizing current (Ito) causing pathological changes in Ito and action potential morphology. We designed a therapeutic regimen incorporating dalfampridine to target Ito. Dalfampridine, approved for multiple sclerosis, normalized the ECG and reduced arrhythmia burden in the proband by >90-fold. This was combined with cilostazol to accelerate the heart rate to minimize the reverse-rate dependence of augmented Ito. We describe a novel arrhythmia mechanism and therapeutic approach to ameliorate the disease. Specifically, we identify the first coding variant of DPP6 in human ventricular fibrillation. These findings illustrate the power of genetic approaches for the elucidation and treatment of disease when carefully integrated with clinical and basic/translational research teams. © 2015 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

An intelligent anticorrosion coating based on pH-responsive supramolecular nanocontainers

International Nuclear Information System (INIS)

Chen Tao; Fu Jiajun

2012-01-01

The hollow mesoporous silica nanoparticles (HMSNs), which have been used as the nanocontainers for the corrosion inhibitor, benzotriazole, were fabricated using the hard-template method. Alkaline-responsive HMSNs based on cucurbit[6]uril (CB[6])/bisammonium supramolecular complex and acid-responsive HMSNs based on α-cyclodextrin (α-CD)/aniline supramolecular complex, which operate in water, have been achieved and characterized by solid-state NMR, thermogravimetry analysis, scanning electron microscopy, transmission electron microscopy and N 2 adsorption-desorption analysis. The two elaborately designed nanocontainers show the pH-controlled encapsulation/release behaviors for benzotriazole molecules. Equal amounts of the alkaline- and acid-responsive nanocontainers were uniformly distributed in the hybrid zirconia-silica sol–gel coating and thus formed the intelligent anticorrosion coating. The self-healing property of AA2024 alloy coated with the intelligent anticorrosion coating is evaluated by electrochemical impedance spectroscopy (EIS). The sol–gel coating doped with the pH-responsive nanocontainers clearly demonstrates long-term corrosion protection performances when compared to the undoped sol–gel coating, which is attributed to the release of corrosion inhibitor from the nanocontainers after feeling the changes of environmental pH values near the corroded areas. (paper)

Microplasma synthesis on aluminum with additions of iron and nickel soluble complexes in electrolyte

Energy Technology Data Exchange (ETDEWEB)

Rogov, A.B., E-mail: alex-lab@bk.ru [Nikolaev Institute of Inorganic Chemistry. 3, Acad. Lavrentiev Ave, Novosibirsk, 630090 (Russian Federation); Mironov, I.V.; Terleeva, O.P.; Slonova, A.I. [Nikolaev Institute of Inorganic Chemistry. 3, Acad. Lavrentiev Ave, Novosibirsk, 630090 (Russian Federation)

2012-10-01

Highlights: Black-Right-Pointing-Pointer Alkaline homogeneous electrolyte with transition metals complexes. Black-Right-Pointing-Pointer Coatings contain metallic iron, nickel and their oxides in alumina-silica matrix. Black-Right-Pointing-Pointer Effect of Fe/Ni ratio on coatings properties and process characteristics. - Abstract: The microplasma synthesis of coatings containing iron and nickel from homogeneous electrolytes has been studied. For stabilization of transition metals in solution, it is proposed to use chelation. It was found that the synthesis of coatings using alternating current leads to the formation of metallic iron and nickel particles in addition to oxide phases. The iron and nickel complexes concentrations ratio in the electrolyte correlates with the coatings composition. Obtained coatings have been studied by scanning electron microscopy with X-ray microanalyser and by X-ray diffraction with Cu and Mo radiation. The metal content in the coating was determined spectrophotometrically from the absorption of iron thiocyanate complexes and nickel dimethylglyoxime complex.

Nanoscale Reinforced, Polymer Derived Ceramic Matrix Coatings

Energy Technology Data Exchange (ETDEWEB)

Rajendra Bordia

2009-07-31

The goal of this project was to explore and develop a novel class of nanoscale reinforced ceramic coatings for high temperature (600-1000 C) corrosion protection of metallic components in a coal-fired environment. It was focused on developing coatings that are easy to process and low cost. The approach was to use high-yield preceramic polymers loaded with nano-size fillers. The complex interplay of the particles in the polymer, their role in controlling shrinkage and phase evolution during thermal treatment, resulting densification and microstructural evolution, mechanical properties and effectiveness as corrosion protection coatings were investigated. Fe-and Ni-based alloys currently used in coal-fired environments do not possess the requisite corrosion and oxidation resistance for next generation of advanced power systems. One example of this is the power plants that use ultra supercritical steam as the working fluid. The increase in thermal efficiency of the plant and decrease in pollutant emissions are only possible by changing the properties of steam from supercritical to ultra supercritical. However, the conditions, 650 C and 34.5 MPa, are too severe and result in higher rate of corrosion due to higher metal temperatures. Coating the metallic components with ceramics that are resistant to corrosion, oxidation and erosion, is an economical and immediate solution to this problem. Good high temperature corrosion protection ceramic coatings for metallic structures must have a set of properties that are difficult to achieve using established processing techniques. The required properties include ease of coating complex shapes, low processing temperatures, thermal expansion match with metallic structures and good mechanical and chemical properties. Nanoscale reinforced composite coatings in which the matrix is derived from preceramic polymers have the potential to meet these requirements. The research was focused on developing suitable material systems and

Analysis of exome sequence in 604 trios for recessive genotypes in schizophrenia.

Science.gov (United States)

Rees, E; Kirov, G; Walters, J T; Richards, A L; Howrigan, D; Kavanagh, D H; Pocklington, A J; Fromer, M; Ruderfer, D M; Georgieva, L; Carrera, N; Gormley, P; Palta, P; Williams, H; Dwyer, S; Johnson, J S; Roussos, P; Barker, D D; Banks, E; Milanova, V; Rose, S A; Chambert, K; Mahajan, M; Scolnick, E M; Moran, J L; Tsuang, M T; Glatt, S J; Chen, W J; Hwu, H-G; Neale, B M; Palotie, A; Sklar, P; Purcell, S M; McCarroll, S A; Holmans, P; Owen, M J; O'Donovan, M C

2015-07-21

Genetic associations involving both rare and common alleles have been reported for schizophrenia but there have been no systematic scans for rare recessive genotypes using fully phased trio data. Here, we use exome sequencing in 604 schizophrenia proband-parent trios to investigate the role of recessive (homozygous or compound heterozygous) nonsynonymous genotypes in the disorder. The burden of recessive genotypes was not significantly increased in probands at either a genome-wide level or in any individual gene after adjustment for multiple testing. At a system level, probands had an excess of nonsynonymous compound heterozygous genotypes (minor allele frequency, MAF ⩽ 1%) in voltage-gated sodium channels (VGSCs; eight in probands and none in parents, P = 1.5 × 10(-)(4)). Previous findings of multiple de novo loss-of-function mutations in this gene family, particularly SCN2A, in autism and intellectual disability provide biological and genetic plausibility for this finding. Pointing further to the involvement of VGSCs in schizophrenia, we found that these genes were enriched for nonsynonymous mutations (MAF ⩽ 0.1%) in cases genotyped using an exome array, (5585 schizophrenia cases and 8103 controls), and that in the trios data, synaptic proteins interacting with VGSCs were also enriched for both compound heterozygosity (P = 0.018) and de novo mutations (P = 0.04). However, we were unable to replicate the specific association with compound heterozygosity at VGSCs in an independent sample of Taiwanese schizophrenia trios (N = 614). We conclude that recessive genotypes do not appear to make a substantial contribution to schizophrenia at a genome-wide level. Although multiple lines of evidence, including several from this study, suggest that rare mutations in VGSCs contribute to the disorder, in the absence of replication of the original findings regarding compound heterozygosity, this conclusion requires evaluation in a larger sample of trios.

Chromatin Remodeling BAF (SWI/SNF Complexes in Neural Development and Disorders

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Godwin Sokpor

2017-08-01

Full Text Available The ATP-dependent BRG1/BRM associated factor (BAF chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders.

Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders

Science.gov (United States)

Sokpor, Godwin; Xie, Yuanbin; Rosenbusch, Joachim; Tuoc, Tran

2017-01-01

The ATP-dependent BRG1/BRM associated factor (BAF) chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders. PMID:28824374

Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders.

Science.gov (United States)

Sokpor, Godwin; Xie, Yuanbin; Rosenbusch, Joachim; Tuoc, Tran

2017-01-01

The ATP-dependent BRG1/BRM associated factor (BAF) chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders.

Exome sequencing unravels unexpected differential diagnoses in individuals with the tentative diagnosis of Coffin-Siris and Nicolaides-Baraitser syndromes.

Science.gov (United States)

Bramswig, Nuria C; Lüdecke, Hermann-Josef; Alanay, Yasemin; Albrecht, Beate; Barthelmie, Alexander; Boduroglu, Koray; Braunholz, Diana; Caliebe, Almuth; Chrzanowska, Krystyna H; Czeschik, Johanna Christina; Endele, Sabine; Graf, Elisabeth; Guillén-Navarro, Encarna; Kiper, Pelin Özlem Simsek; López-González, Vanesa; Parenti, Ilaria; Pozojevic, Jelena; Utine, Gulen Eda; Wieland, Thomas; Kaiser, Frank J; Wollnik, Bernd; Strom, Tim M; Wieczorek, Dagmar

2015-06-01

Coffin-Siris syndrome (CSS) and Nicolaides-Baraitser syndrome (NCBRS) are rare intellectual disability/congenital malformation syndromes that represent distinct entities but show considerable clinical overlap. They are caused by mutations in genes encoding members of the BRG1- and BRM-associated factor (BAF) complex. However, there are a number of patients with the clinical diagnosis of CSS or NCBRS in whom the causative mutation has not been identified. In this study, we performed trio-based whole-exome sequencing (WES) in ten previously described but unsolved individuals with the tentative diagnosis of CSS or NCBRS and found causative mutations in nine out of ten individuals. Interestingly, our WES analysis disclosed overlapping differential diagnoses including Wiedemann-Steiner, Kabuki, and Adams-Oliver syndromes. In addition, most likely causative de novo mutations were identified in GRIN2A and SHANK3. Moreover, trio-based WES detected SMARCA2 and SMARCA4 deletions, which had not been annotated in a previous Haloplex target enrichment and next-generation sequencing of known CSS/NCBRS genes emphasizing the advantages of WES as a diagnostic tool. In summary, we discuss the phenotypic and diagnostic challenges in clinical genetics, establish important differential diagnoses, and emphasize the cardinal features and the broad clinical spectrum of BAF complex disorders and other disorders caused by mutations in epigenetic landscapers.

Exome sequencing of a pedigree with Tourette syndrome or chronic tic disorder.

Science.gov (United States)

Sundaram, Senthil K; Huq, Ahm M; Sun, Zhen; Yu, Wu; Bennett, Lindsey; Wilson, Benjamin J; Behen, Michael E; Chugani, Harry T

2011-05-01

Ten members of a 3-generation pedigree with 7 showing Tourette syndrome/chronic tic phenotype (TS-CTD) were evaluated with whole exome sequencing. We identified 3 novel, nonsynonymous single nucleotide variants in the MRPL3, DNAJC13, and OFCC1 genes that segregated with chronic tic phenotype. These variants were not present in 100 control subjects or in dbSNP/1000 Genomes databases. A novel variant in the 5' untranslated region of the OFCC1 gene was found in 2 TS-CTD patients from a different pedigree. Further studies will clarify the importance of variants in MRPL3, DNAJC13, and OFCC1 genes in TS. Copyright © 2011 American Neurological Association.

Investigation of calcium phosphate coatings for biomedical applications

International Nuclear Information System (INIS)

Yusof Abdullah; Idris Besar; Muhammad Jamal Md Isa; Mohamad Abd Razak; Hyzan Mohd Yusof

1999-01-01

Calcium phosphate is the main constituent of our bone and tooth minerals. The use of this bioactive material for coating implant such as artificial joint prosthesis, therefore, can promote biological fixation and enhance biocompatibility. Our initial work has been focused on the evaluation of experimental conditions of coating preparation and the effects of post-deposition calcium phosphate coatings on stainless steel substrates. The coating layers were produced by the precipitation technique and coatings were carried out in sol-gel by the dipping method. For comparison purposes a wet method was used to obtain a fine calcium phosphate ceramic powder for fabrication of microcrystal suspension used as a coating material. Scanning electron microscopy (SEM), energy dispersive microanalysis (EDS), energy dispersive x-ray fluorescence (EDXRF) and x-ray diffraction (XRD) were used to characterise the morphology, chemical composition and structure of the coatings. The results showed that the dip coating of stainless steel substrates using viscous solutions lead to the formation of porous calcium phosphate layers. These results suggested that fabrication of bioactive calcium phosphate coatings using this route offers significant advantages over the currently used methods due to considerably lower temperature process involved and may produce better result for substrates with complex shapes

First applications of a targeted exome sequencing approach in fetuses with ultrasound abnormalities reveals an important fraction of cases with associated gene defects

Directory of Open Access Journals (Sweden)

Constantinos Pangalos

2016-04-01

Full Text Available Background. Fetal malformations and other structural abnormalities are relatively frequent findings in the course of routine prenatal ultrasonographic examination. Due to their considerable genetic and clinical heterogeneity, the underlying genetic cause is often elusive and the resulting inability to provide a precise diagnosis precludes proper reproductive and fetal risk assessment. We report the development and first applications of an expanded exome sequencing-based test, coupled to a bioinformatics-driven prioritization algorithm, targeting gene disorders presenting with abnormal prenatal ultrasound findings. Methods. We applied the testing strategy to14 euploid fetuses, from 11 on-going pregnancies and three products of abortion, all with various abnormalities or malformations detected through prenatal ultrasound examination. Whole exome sequencing (WES was followed by variant prioritization, utilizing a custom analysis pipeline (Fetalis algorithm, targeting 758 genes associated with genetic disorders which may present with abnormal fetal ultrasound findings. Results. A definitive or highly-likely diagnosis was made in 6 of 14 cases (43%, of which 3 were abortuses (Ellis-van Creveld syndrome, Ehlers-Danlos syndrome and Nemaline myopathy 2 and 3 involved on-going pregnancies (Citrullinemia, Noonan syndrome, PROKR2-related Kallmann syndrome. In the remaining eight on-going pregnancy cases (57%, a ZIC1 variant of unknown clinical significance was detected in one case, while in seven cases testing did not reveal any pathogenic variant(s. Pregnancies were followed-up to birth, resulting in one neonate harboring the PROKR2 mutation, presenting with isolated minor structural cardiac abnormalities, and in seven apparently healthy neonates. Discussion. The expanded targeted exome sequencing-based approach described herein (Fetalis, provides strong evidence suggesting a definite and beneficial increase in our diagnostic capabilities in prenatal

Factors affecting the hot-dip zinc coatings structure

International Nuclear Information System (INIS)

Sere, P.R.; Cuclcasi, J.D.; Elsner, C.I.; Sarli, A.R.

1997-01-01

Coating solidification during hot-dip galvanizing is a very complex process due to Al-Fe, Al-Fe-Zn and Fe-Zn intermetallic compounds development . Fe-Zn intermetallics are brittle and detrimental for the coating ductility, while the diffusion towards the surface of a segregated insoluble alloying such as antimonium causes the sheet darkness. Steel of different roughness were hot-dip galvanized under different operation conditions using a laboratory scale simulator. The effect of steel roughness and process parameters upon coating characteristics were analysed. Experimental results showed that the steel roughness affects the coating thickness, zinc grain size and texture as well as the out-bursts development, while the process parameters affects the Fe 2 Al 5 morphology and antimonium segregation. (Author) 11 refs

Thermally joining and/or coating or thermally separating the workpieces having heat-sensitive coating, comprises restoring coating by thermally coating the coating material after thermally joining and/or coating or thermally separating

OpenAIRE

Riedel, Frank; Winkelmann, Ralf; Puschmann, Markus

2011-01-01

The method for thermally joining and/or coating or thermally separating the workpieces (1), which have a heat-sensitive coating (2), comprises restoring the coating by thermally coating a coating material (3) after thermally joining and/or coating or thermally separating the workpieces. A part of the thermal energy introduced in the workpiece for joining and/or coating or separating or in the workpieces is used for thermally coating the coating material. Two workpieces are welded or soldered ...

Identification of resistance mechanisms in erlotinib-resistant subclones of the non-small cell lung cancer cell line HCC827 by exome sequencing

DEFF Research Database (Denmark)

Jacobsen, Kirstine; Alcaraz, Nicolas; Lund, Rikke Raaen

the SeqCap EZ Human Exome Library v3.0 kit and whole-exome sequencing of these (100 bp paired-end) were performed on an Illumina HiSeq 2000 platform. Using a recently developed in-house analysis pipeline the sequencing data were analyzed. The analysis pipeline includes quality control using Trim......Background: Erlotinib (Tarceva®, Roche) has significantly changed the treatment of non-small cell lung cancer (NSCLC) as 70% of patients show significant tumor regression upon treatment (Santarpia et. al., 2013). However, all patients relapse due to development of acquired resistance, which...... mutations in erlotinib-resistant subclones of the NSCLC cell line, HCC827. Materials & Methods: We established 3 erlotinib-resistant subclones (resistant to 10, 20, 30 µM erlotinib, respectively). DNA libraries of each subclone and the parental HCC827 cell line were prepared in biological duplicates using...

Exome-wide Association Study Identifies GREB1L Mutations in Congenital Kidney Malformations.

Science.gov (United States)

Sanna-Cherchi, Simone; Khan, Kamal; Westland, Rik; Krithivasan, Priya; Fievet, Lorraine; Rasouly, Hila Milo; Ionita-Laza, Iuliana; Capone, Valentina P; Fasel, David A; Kiryluk, Krzysztof; Kamalakaran, Sitharthan; Bodria, Monica; Otto, Edgar A; Sampson, Matthew G; Gillies, Christopher E; Vega-Warner, Virginia; Vukojevic, Katarina; Pediaditakis, Igor; Makar, Gabriel S; Mitrotti, Adele; Verbitsky, Miguel; Martino, Jeremiah; Liu, Qingxue; Na, Young-Ji; Goj, Vinicio; Ardissino, Gianluigi; Gigante, Maddalena; Gesualdo, Loreto; Janezcko, Magdalena; Zaniew, Marcin; Mendelsohn, Cathy Lee; Shril, Shirlee; Hildebrandt, Friedhelm; van Wijk, Joanna A E; Arapovic, Adela; Saraga, Marijan; Allegri, Landino; Izzi, Claudia; Scolari, Francesco; Tasic, Velibor; Ghiggeri, Gian Marco; Latos-Bielenska, Anna; Materna-Kiryluk, Anna; Mane, Shrikant; Goldstein, David B; Lifton, Richard P; Katsanis, Nicholas; Davis, Erica E; Gharavi, Ali G

2017-11-02

Renal agenesis and hypodysplasia (RHD) are major causes of pediatric chronic kidney disease and are highly genetically heterogeneous. We conducted whole-exome sequencing in 202 case subjects with RHD and identified diagnostic mutations in genes known to be associated with RHD in 7/202 case subjects. In an additional affected individual with RHD and a congenital heart defect, we found a homozygous loss-of-function (LOF) variant in SLIT3, recapitulating phenotypes reported with Slit3 inactivation in the mouse. To identify genes associated with RHD, we performed an exome-wide association study with 195 unresolved case subjects and 6,905 control subjects. The top signal resided in GREB1L, a gene implicated previously in Hoxb1 and Shha signaling in zebrafish. The significance of the association, which was p = 2.0 × 10 -5 for novel LOF, increased to p = 4.1 × 10 -6 for LOF and deleterious missense variants combined, and augmented further after accounting for segregation and de novo inheritance of rare variants (joint p = 2.3 × 10 -7 ). Finally, CRISPR/Cas9 disruption or knockdown of greb1l in zebrafish caused specific pronephric defects, which were rescued by wild-type human GREB1L mRNA, but not mRNA containing alleles identified in case subjects. Together, our study provides insight into the genetic landscape of kidney malformations in humans, presents multiple candidates, and identifies SLIT3 and GREB1L as genes implicated in the pathogenesis of RHD. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Whole-exome sequencing supports genetic heterogeneity in childhood apraxia of speech.

Science.gov (United States)

Worthey, Elizabeth A; Raca, Gordana; Laffin, Jennifer J; Wilk, Brandon M; Harris, Jeremy M; Jakielski, Kathy J; Dimmock, David P; Strand, Edythe A; Shriberg, Lawrence D

2013-10-02

Childhood apraxia of speech (CAS) is a rare, severe, persistent pediatric motor speech disorder with associated deficits in sensorimotor, cognitive, language, learning and affective processes. Among other neurogenetic origins, CAS is the disorder segregating with a mutation in FOXP2 in a widely studied, multigenerational London family. We report the first whole-exome sequencing (WES) findings from a cohort of 10 unrelated participants, ages 3 to 19 years, with well-characterized CAS. As part of a larger study of children and youth with motor speech sound disorders, 32 participants were classified as positive for CAS on the basis of a behavioral classification marker using auditory-perceptual and acoustic methods that quantify the competence, precision and stability of a speaker's speech, prosody and voice. WES of 10 randomly selected participants was completed using the Illumina Genome Analyzer IIx Sequencing System. Image analysis, base calling, demultiplexing, read mapping, and variant calling were performed using Illumina software. Software developed in-house was used for variant annotation, prioritization and interpretation to identify those variants likely to be deleterious to neurodevelopmental substrates of speech-language development. Among potentially deleterious variants, clinically reportable findings of interest occurred on a total of five chromosomes (Chr3, Chr6, Chr7, Chr9 and Chr17), which included six genes either strongly associated with CAS (FOXP1 and CNTNAP2) or associated with disorders with phenotypes overlapping CAS (ATP13A4, CNTNAP1, KIAA0319 and SETX). A total of 8 (80%) of the 10 participants had clinically reportable variants in one or two of the six genes, with variants in ATP13A4, KIAA0319 and CNTNAP2 being the most prevalent. Similar to the results reported in emerging WES studies of other complex neurodevelopmental disorders, our findings from this first WES study of CAS are interpreted as support for heterogeneous genetic origins of

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

OpenAIRE

Bruce, Jeff; Pugh, Trevor; Samadian, Soroush

2017-01-01

Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To ad...

Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population

DEFF Research Database (Denmark)

Li, Shengting; Besenbacher, Soren; Li, Yingrui

2014-01-01

In this paper, we mine full mtDNA sequences from an exome capture data set of 2000 Danes, showing that it is possible to get high-quality full-genome sequences of the mitochondrion from this resource. The sample includes 1000 individuals with type 2 diabetes and 1000 controls. We characterise...

Development of high-index optical coating for security holograms

Science.gov (United States)

Ahmed, Nadir A. G.

2000-10-01

Over the past few years security holograms have grown into a complex business to prevent counterfeiting of security cards, banknotes and the like. Rapid advances in holographic technology have led to a growing requirement for optical materials and coating methods to produce such holograms at reasonable costs. These materials have specific refractive indices and are used to fabricate semi- transparent holograms. The present paper describes a coating process to deposit optical coating on flexible films inside a vacuum web metallizer for the production of high quality semi-transparent holograms.

Whole exome sequencing identifies novel mutation in eight Chinese children with isolated tetralogy of Fallot.

Science.gov (United States)

Liu, Lin; Wang, Hong-Dan; Cui, Cun-Ying; Qin, Yun-Yun; Fan, Tai-Bing; Peng, Bang-Tian; Zhang, Lian-Zhong; Wang, Cheng-Zeng

2017-12-05

Tetralogy of Fallot is the most common cyanotic congenital heart disease. However, its pathogenesis remains to be clarified. The purpose of this study was to identify the genetic variants in Tetralogy of Fallot by whole exome sequencing. Whole exome sequencing was performed among eight small families with Tetralogy of Fallot. Differential single nucleotide polymorphisms and small InDels were found by alignment within families and between families and then were verified by Sanger sequencing. Tetralogy of Fallot-related genes were determined by analysis using Gene Ontology /pathway, Online Mendelian Inheritance in Man, PubMed and other databases. A total of sixteen differential single nucleotide polymorphisms loci and eight differential small InDels were discovered. The sixteen differential single nucleotide polymorphisms loci were located on Chr 1, 2, 4, 5, 11, 12, 15, 22 and X. Among the sixteen single nucleotide polymorphisms loci, six has not been reported. The eight differential small InDels were located on Chr 2, 4, 9, 12, 17, 19 and X, whereas of the eight differential small InDels, two has not been reported. Analysis using Gene Ontology /pathway, Online Mendelian Inheritance in Man, PubMed and other databases revealed that PEX5 , NACA , ATXN2 , CELA1 , PCDHB4 and CTBP1 were associated with Tetralogy of Fallot. Our findings identify PEX5 , NACA , ATXN2 , CELA1 , PCDHB4 and CTBP1 mutations as underlying genetic causes of isolated tetralogy of Fallot.

NB Coating Developments with HIPIMS for SRF Applications

CERN Document Server

Terenziani, G; Junginger, T; Santillana, I A; Ehiasarian, A P

2013-01-01

In the last few years the interest of the thin film science and technology community on High Impulse Power Magnetron Sputtering (HIPIMS) coatings has steadily increased. HIPIMS literature shows that better thin film morphology, denser and smoother films can be achieved when compared with standard dc Magnetron Sputtering (dcMS) coating technology [1]. Furthermore the capability of HIPIMS to produce a high quantity of ionized species [2,3] can allow conformal coatings also for complex geometries. A study is under way at CERN to apply this technology for the Nb coating of SRF 1.3-1.5 GHz Cu cavities, and in parallel at SHU the plasma physics and its correlation with film morphology are being investigated [2]. Recent results achieved with this technique are presented in the paper.

ATRX mutation in two adult brothers with non-specific moderate intellectual disability identified by exome sequencing.

Science.gov (United States)

Moncini, S; Bedeschi, M F; Castronovo, P; Crippa, M; Calvello, M; Garghentino, R R; Scuvera, G; Finelli, P; Venturin, M

2013-12-01

In this report, we describe two adult brothers affected by moderate non-specific intellectual disability (ID). They showed minor facial anomalies, not clearly ascribable to any specific syndromic patterns, microcephaly, brachydactyly and broad toes. Both brothers presented seizures. Karyotype, subtelomeric and FMR1 analysis were normal in both cases. We performed array-CGH analysis that revealed no copy-number variations potentially associated with ID. Subsequent exome sequence analysis allowed the identification of the ATRX c.109C>T (p.R37X) mutation in both the affected brothers. Sanger sequencing confirmed the presence of the mutation in the brothers and showed that the mother is a healthy carrier. Mutations in the ATRX gene cause the X-linked alpha thalassemia/mental retardation (ATR-X) syndrome (MIM #301040), a severe clinical condition usually associated with profound ID, facial dysmorphism and alpha thalassemia. However, the syndrome is clinically heterogeneous and some mutations, including the c.109C>T, are associated with a broad phenotypic spectrum, with patients displaying a less severe phenotype with only mild-moderate ID. In the case presented here, exome sequencing provided an effective strategy to achieve the molecular diagnosis of ATR-X syndrome, which otherwise would have been difficult to consider due to the mild non-specific phenotype and the absence of a family history with typical severe cases.

Whole exome analysis identifies frequent CNGA1 mutations in Japanese population with autosomal recessive retinitis pigmentosa.

Directory of Open Access Journals (Sweden)

Satoshi Katagiri

Full Text Available OBJECTIVE: The purpose of this study was to investigate frequent disease-causing gene mutations in autosomal recessive retinitis pigmentosa (arRP in the Japanese population. METHODS: In total, 99 Japanese patients with non-syndromic and unrelated arRP or sporadic RP (spRP were recruited in this study and ophthalmic examinations were conducted for the diagnosis of RP. Among these patients, whole exome sequencing analysis of 30 RP patients and direct sequencing screening of all CNGA1 exons of the other 69 RP patients were performed. RESULTS: Whole exome sequencing of 30 arRP/spRP patients identified disease-causing gene mutations of CNGA1 (four patients, EYS (three patients and SAG (one patient in eight patients and potential disease-causing gene variants of USH2A (two patients, EYS (one patient, TULP1 (one patient and C2orf71 (one patient in five patients. Screening of an additional 69 arRP/spRP patients for the CNGA1 gene mutation revealed one patient with a homozygous mutation. CONCLUSIONS: This is the first identification of CNGA1 mutations in arRP Japanese patients. The frequency of CNGA1 gene mutation was 5.1% (5/99 patients. CNGA1 mutations are one of the most frequent arRP-causing mutations in Japanese patients.

Exome sequencing in an admixed isolated population indicates NFXL1 variants confer a risk for specific language impairment.

Directory of Open Access Journals (Sweden)

Pía Villanueva

2015-03-01

Full Text Available Children affected by Specific Language Impairment (SLI fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile, who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations in the NFXL1 gene that confers a nonsynonymous change (N150K and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10-4, 8 variants tested. Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model.

Composition Effects on Aluminide Oxidation Performance: Objectives for Improved Bond Coats

International Nuclear Information System (INIS)

Pint, BA

2001-01-01

Formerly, the role of metallic coatings on Ni-base superalloys was simply to limit environmental attack of the underlying substrate. However, a new paradigm has been established for metallic coatings adapted as bond coats for thermal barrier coatings. It is no longer sufficient for the coating to just minimize the corrosion rate. The metallic coating must also form a slow-growing external Al(sub 2)O(sub 3) layer beneath the overlying low thermal conductivity ceramic top coat. This thermally grown oxide or scale must have near-perfect adhesion in order to limit spallation of the top coat, thereby achieving a long coating lifetime. While oxidation is not the only concern in complex thermal barrier coating systems, it is, however, a primary factor in developing the next generation of bond coats. Therefore, a set of compositional guidelines for coatings is proposed in order to maximize oxidation performance. These criteria are based on test results of cast alloy compositions to quantify an d understand possible improvements as a basis for further investigations using coatings made by chemical vapor deposited (CVD). Experimental work includes furnace cycle testing and in-depth characterization of the alumina scale, including transmission electron microscopy (TEM)

Fullerene monolayer formation by spray coating

NARCIS (Netherlands)

Cervenka, J.; Flipse, C.F.J.

2010-01-01

Many large molecular complexes are limited in thin film applications by their insufficient thermal stability, which excludes deposition via commonly used vapour phase deposition methods. Here we demonstrate an alternative way of monolayer formation of large molecules by a simple spray coating method

Genomic landscape of ovarian clear cell carcinoma via whole exome sequencing.

Science.gov (United States)

Kim, Se Ik; Lee, Ji Won; Lee, Maria; Kim, Hee Seung; Chung, Hyun Hoon; Kim, Jae-Weon; Park, Noh Hyun; Song, Yong-Sang; Seo, Jeong-Sun

2018-02-01

To analyze whole exome sequencing (WES) data on ovarian clear cell carcinoma (OCCC) in Korean patients via the technique of next generation sequencing (NGS). Genomic profiles were compared between endometriosis-associated OCCC (EMS-OCCC) and Non-EMS-OCCC. We used serum samples and cancer tissues, stored at the Seoul National University Hospital Human Biobank, that were initially collected from women diagnosed with OCCC between 2012 and 2016. In total, 15 patients were enrolled: 5 with pathologically confirmed EMS-OCCC and 10 with Non-EMS-OCCC. We performed NGS WES on 15 fresh frozen OCCC tissues and matched serum samples, enabling comprehensive genomic characterization of OCCC. OCCC was characterized by complex genomic alterations, with a median of 178 exonic mutations (range, 111-25,798) and a median of 343 somatic copy number variations (range, 43-1,820) per tumor sample. In all, 54 somatic mutations were discovered across 14 genes, including PIK3CA (40%), ARID1A (40%), and KRAS (20%) in the 15 Korean OCCCs. Copy number gains in NTRK1 (33%), MYC (40%), and GNAS (47%) and copy number losses in TET2 (73%), TSC1 (67%), BRCA2 (60%), and SMAD4 (47%) were frequent. The significantly altered pathways were associated with proliferation and survival (including the PI3K/AKT, TP53, and ERBB2 pathways) in 87% of OCCCs and with chromatin remodeling in 47% of OCCCs. No significant differences in frequencies of genetic alterations were detected between EMS-OCCC and Non-EMS-OCCC groups. We successfully characterized the genomic landscape of 15 Korean patients with OCCC. We identified potential therapeutic targets for the treatment of this malignancy. Copyright © 2017. Published by Elsevier Inc.

Electrodeposition of nanostructured Sn-Zn coatings

Science.gov (United States)

Salhi, Y.; Cherrouf, S.; Cherkaoui, M.; Abdelouahdi, K.

2016-03-01

The electrodeposition of Sn-Zn coating at ambient temperature was investigated. The bath consists of metal salts SnCl2·2H2O and ZnSO4·7H2O and sodium citrate (NaC6H5Na3O7·2H2O) as complexing agent. To prevent precipitation, the pH is fixed at 5. Reducing tin and zinc through Sncit2- and ZnHcit- complex respectively is confirmed by the presence of two cathodic peaks on the voltammogram. The kinetic of tin (II) reduction process is limited by the SnCit2- dissociation. The SEM and TEM observations have showed that the coating consists of a uniform Sn-Zn layer composed of fine grains on which tin aggregates grow up. XRD revealed peaks corresponding to the hexagonal Zn phase and the tetragonal β-Sn phase.

Surfactant-free electrodeposition of reduced graphene oxide/copper composite coatings with enhanced wear resistance

Science.gov (United States)

Mai, Y. J.; Zhou, M. P.; Ling, H. J.; Chen, F. X.; Lian, W. Q.; Jie, X. H.

2018-03-01

How to uniformly disperse graphene sheets into the electrolyte is one of the main challenges to synthesize graphene enhanced nanocomposites by electrodeposition. A surfactant-free colloidal solution comprised of copper (II)-ethylene diamine tetra acetic acid ([CuIIEDTA]2-) complexes and graphene oxide (GO) sheets is proposed to electrodeposit reduced graphene oxide/copper (RGO/Cu) composite coatings. Anionic [CuIIEDTA]2- complexes stably coexist with negatively charged GO sheets due to the electrostatic repulsion between them, facilitating the electrochemical reduction and uniform dispersion of GO sheets into the copper matrix. The RGO/Cu composite coatings are well characterized by XRD, Raman, SEM and XPS. Their tribological behavior as a function of RGO content in composite coatings and normal loads are investigated. Also the chemical composition and topography of the wear tracks for the composite coatings are analyzed to deduce the lubricating and anti-wear mechanism of RGO/Cu composite coatings.

Exome sequencing identifies SUCO mutations in mesial temporal lobe epilepsy.

Science.gov (United States)

Sha, Zhiqiang; Sha, Longze; Li, Wenting; Dou, Wanchen; Shen, Yan; Wu, Liwen; Xu, Qi

2015-03-30

Mesial temporal lobe epilepsy (mTLE) is the main type and most common medically intractable form of epilepsy. Severity of disease-based stratified samples may help identify new disease-associated mutant genes. We analyzed mRNA expression profiles from patient hippocampal tissue. Three of the seven patients had severe mTLE with generalized-onset convulsions and consciousness loss that occurred over many years. We found that compared with other groups, patients with severe mTLE were classified into a distinct group. Whole-exome sequencing and Sanger sequencing validation in all seven patients identified three novel SUN domain-containing ossification factor (SUCO) mutations in severely affected patients. Furthermore, SUCO knock down significantly reduced dendritic length in vitro. Our results indicate that mTLE defects may affect neuronal development, and suggest that neurons have abnormal development due to lack of SUCO, which may be a generalized-onset epilepsy-related gene. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

The structure of the COPII transport-vesicle coat assembled on membranes.

Science.gov (United States)

Zanetti, Giulia; Prinz, Simone; Daum, Sebastian; Meister, Annette; Schekman, Randy; Bacia, Kirsten; Briggs, John A G

2013-09-17

Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, linking them to the outer COPII components that form a cage around the vesicle. Regulated flexibility in coat architecture is essential for transport of a variety of differently sized cargoes, but structural data on the assembled coat has not been available. We have used cryo-electron tomography and subtomogram averaging to determine the structure of the complete, membrane-assembled COPII coat. We describe a novel arrangement of the outer coat and find that the inner coat can assemble into regular lattices. The data reveal how coat subunits interact with one another and with the membrane, suggesting how coordinated assembly of inner and outer coats can mediate and regulate packaging of vesicles ranging from small spheres to large tubular carriers. DOI:http://dx.doi.org/10.7554/eLife.00951.001.

Cell-derived matrix coatings for polymeric scaffolds.

Science.gov (United States)

Decaris, Martin L; Binder, Bernard Y; Soicher, Matthew A; Bhat, Archana; Leach, J Kent

2012-10-01

Cells in culture deposit a complex extracellular matrix that remains intact following decellularization and possesses the capacity to modulate cell phenotype. The direct application of such decellularized matrices (DMs) to 3D substrates is problematic, as transport issues influence the homogeneous deposition, decellularization, and modification of DM surface coatings. In an attempt to address this shortcoming, we hypothesized that DMs deposited by human mesenchymal stem cells (MSCs) could be transferred to the surface of polymeric scaffolds while maintaining their capacity to direct cell fate. The ability of the transferred DM (tDM)-coated scaffolds to enhance the osteogenic differentiation of undifferentiated and osteogenically induced MSCs under osteogenic conditions in vitro was confirmed. tDM-coated scaffolds increased MSC expression of osteogenic marker genes (BGLAP, IBSP) and intracellular alkaline phosphatase production. In addition, undifferentiated MSCs deposited significantly more calcium when seeded onto tDM-coated scaffolds compared with control scaffolds. MSC-seeded tDM-coated scaffolds subcutaneously implanted in nude rats displayed significantly higher blood vessel density after 2 weeks compared with cells on uncoated scaffolds, but we did not observe significant differences in mineral deposition after 8 weeks. These data demonstrate that DM-coatings produced in 2D culture can be successfully transferred to 3D substrates and retain their capacity to modulate cell phenotype.

Whole-exome sequencing reveals the spectrum of gene mutations and the clonal evolution patterns in paediatric acute myeloid leukaemia.

Science.gov (United States)

Shiba, Norio; Yoshida, Kenichi; Shiraishi, Yuichi; Okuno, Yusuke; Yamato, Genki; Hara, Yusuke; Nagata, Yasunobu; Chiba, Kenichi; Tanaka, Hiroko; Terui, Kiminori; Kato, Motohiro; Park, Myoung-Ja; Ohki, Kentaro; Shimada, Akira; Takita, Junko; Tomizawa, Daisuke; Kudo, Kazuko; Arakawa, Hirokazu; Adachi, Souichi; Taga, Takashi; Tawa, Akio; Ito, Etsuro; Horibe, Keizo; Sanada, Masashi; Miyano, Satoru; Ogawa, Seishi; Hayashi, Yasuhide

2016-11-01

Acute myeloid leukaemia (AML) is a molecularly and clinically heterogeneous disease. Targeted sequencing efforts have identified several mutations with diagnostic and prognostic values in KIT, NPM1, CEBPA and FLT3 in both adult and paediatric AML. In addition, massively parallel sequencing enabled the discovery of recurrent mutations (i.e. IDH1/2 and DNMT3A) in adult AML. In this study, whole-exome sequencing (WES) of 22 paediatric AML patients revealed mutations in components of the cohesin complex (RAD21 and SMC3), BCORL1 and ASXL2 in addition to previously known gene mutations. We also revealed intratumoural heterogeneities in many patients, implicating multiple clonal evolution events in the development of AML. Furthermore, targeted deep sequencing in 182 paediatric AML patients identified three major categories of recurrently mutated genes: cohesion complex genes [STAG2, RAD21 and SMC3 in 17 patients (8·3%)], epigenetic regulators [ASXL1/ASXL2 in 17 patients (8·3%), BCOR/BCORL1 in 7 patients (3·4%)] and signalling molecules. We also performed WES in four patients with relapsed AML. Relapsed AML evolved from one of the subclones at the initial phase and was accompanied by many additional mutations, including common driver mutations that were absent or existed only with lower allele frequency in the diagnostic samples, indicating a multistep process causing leukaemia recurrence. © 2016 John Wiley & Sons Ltd.

Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype.

Science.gov (United States)

Chang, Peter L; Kopania, Emily; Keeble, Sara; Sarver, Brice A J; Larson, Erica; Orth, Annie; Belkhir, Khalid; Boursot, Pierre; Bonhomme, François; Good, Jeffrey M; Dean, Matthew D

2017-10-01

The house mouse is a powerful model to dissect the genetic basis of phenotypic variation, and serves as a model to study human diseases. Despite a wealth of discoveries, most classical laboratory strains have captured only a small fraction of genetic variation known to segregate in their wild progenitors, and existing strains are often related to each other in complex ways. Inbred strains of mice independently derived from natural populations have the potential to increase power in genetic studies with the addition of novel genetic variation. Here, we perform exome-enrichment and high-throughput sequencing (~8× coverage) of 26 wild-derived strains known in the mouse research community as the "Montpellier strains." We identified 1.46 million SNPs in our dataset, approximately 19% of which have not been detected from other inbred strains. This novel genetic variation is expected to contribute to phenotypic variation, as they include 18,496 nonsynonymous variants and 262 early stop codons. Simulations demonstrate that the higher density of genetic variation in the Montpellier strains provides increased power for quantitative genetic studies. Inasmuch as the power to connect genotype to phenotype depends on genetic variation, it is important to incorporate these additional genetic strains into future research programs.

In situ coating nickel organic complexes on free-standing nickel wire films for volumetric-energy-dense supercapacitors.

Science.gov (United States)

Hong, Min; Xu, Shusheng; Yao, Lu; Zhou, Chao; Hu, Nantao; Yang, Zhi; Hu, Jing; Zhang, Liying; Zhou, Zhihua; Wei, Hao; Zhang, Yafei

2018-07-06

A self-free-standing core-sheath structured hybrid membrane electrodes based on nickel and nickel based metal-organic complexes (Ni@Ni-OC) was designed and constructed for high volumetric supercapacitors. The self-standing Ni@Ni-OC film electrode had a high volumetric specific capacity of 1225.5 C cm -3 at 0.3 A cm -3 and an excellent rate capability. Moreover, when countered with graphene-carbon nanotube (G-CNT) film electrode, the as-assembled Ni@Ni-OC//G-CNT hybrid supercapacitor device delivered an extraordinary volumetric capacitance of 85 F cm -3 at 0.5 A cm -3 and an outstanding energy density of 33.8 at 483 mW cm -3 . Furthermore, the hybrid supercapacitor showed no capacitance loss after 10 000 cycles at 2 A cm -3 , indicating its excellent cycle stability. These fascinating performances can be ascribed to its unique core-sheath structure that high capacity nano-porous nickel based metal-organic complexes (Ni-OC) in situ coated on highly conductive Ni wires. The impressive results presented here may pave the way to construct s self-standing membrane electrode for applications in high volumetric-performance energy storage.

European coatings conference - Marine coatings. Proceedings

Energy Technology Data Exchange (ETDEWEB)

NONE

2008-07-01

This volume contains 13 lectures (manuscripts or powerpoint foils) with the following topics: 1. Impact of containerization on polyurethane and polyurea in marine and protective coatings (Malte Homann); 2. The application of combinatorial/high-throughput methods to the development of marine coatings (Bret Chisholm); 3. Progress and perspectives in the AMBIO (advanced nanostructured surfaces for the control of biofouling) Project (James Callow); 4. Release behaviour due to shear and pull-off of silicone coatings with a thickness gradient (James G. Kohl); 5. New liquid rheology additives for high build marine coatings (Andreas Freytag); 6. Effective corrosion protection with polyaniline, polpyrrole and polythiophene as anticorrosice additives for marine paints (Carlos Aleman); 7. Potential applications of sol gel technology for marine applications (Robert Akid); 8: Performance of biocide-free Antifouling Coatings for leisure boats (Bernd Daehne); 9. Novel biocidefree nanostructured antifouling coatings - can nano do the job? (Corne Rentrop); 10. One component high solids, VOC compliant high durability finish technology (Adrian Andrews); 11. High solid coatings - the hybrid solution (Luca Prezzi); 12. Unique organofunctional silicone resins for environmentally friendly high-performance coatings (Dieter Heldmann); 13. Silicone-alkyd paints for marine applications: from battleship-grey to green (Thomas Easton).

The clinical utility of whole-exome sequencing in the context of rare diseases - the changing tides of medical practice.

Science.gov (United States)

Nguyen, M T; Charlebois, K

2015-10-01

Whole-exome sequencing (WES) carries the potential to facilitate the identification of disease causing genes. This is particularly relevant concerning rare diseases, which proves particularly difficult for physicians to diagnose. However, the complexity of this technology renders its applicability onto the clinical setting uncertain. Our study thus aims to understand physicians' perspectives regarding the clinical utility of WES, particularly for providing a diagnosis for patients with rare diseases. Ten semi-structured interviews were conducted with physicians with experience and familiarity with WES, and the major themes that emerged from our interviews were (i) the relevance of WES in diagnosing patients with rare diseases (appropriateness); (ii) the cost-effectiveness of WES (accessibility), (iii) the practical issues related to the clinical implementation of WES (practicability); and (iv) ethical, legal and social issues (acceptability). Our study highlights how the clinical implementation of WES presents additional challenges where rare diseases are taken into consideration. © 2014 The Authors. Clinical Genetics published by John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Tetralogy of Fallot and Hypoplastic Left Heart Syndrome – Complex Clinical Phenotypes Meet Complex Genetic Networks

Science.gov (United States)

Lahm, Harald; Schön, Patric; Doppler, Stefanie; Dreßen, Martina; Cleuziou, Julie; Deutsch, Marcus-André; Ewert, Peter; Lange, Rüdiger; Krane, Markus

2015-01-01

In many cases congenital heart disease (CHD) is represented by a complex phenotype and an array of several functional and morphological cardiac disorders. These malformations will be briefly summarized in the first part focusing on two severe CHD phenotypes, hypoplastic left heart syndrome (HLHS) and tetralogy of Fallot (TOF). In most cases of CHD the genetic origin remains largely unknown, though the complexity of the clinical picture strongly argues against a dysregulation which can be attributed to a single candidate gene but rather suggests a multifaceted polygenetic origin with elaborate interactions. Consistent with this idea, genome-wide approaches using whole exome sequencing, comparative sequence analysis of multiplex families to identify de novo mutations and global technologies to identify single nucleotide polymorphisms, copy number variants, dysregulation of the transcriptome and epigenetic variations have been conducted to obtain information about genetic alterations and potential predispositions possibly linked to the occurrence of a CHD phenotype. In the second part of this review we will summarize and discuss the available literature on identified genetic alterations linked to TOF and HLHS. PMID:26069455

High prevalence of genetic variants previously associated with LQT syndrome in new exome data

DEFF Research Database (Denmark)

Refsgaard, Lena; Holst, Anders G; Sadjadieh, Golnaz

2012-01-01

To date, hundreds of variants in 13 genes have been associated with long QT syndrome (LQTS). The prevalence of LQTS is estimated to be between 1:2000 and 1:5000. The knowledge of genetic variation in the general population has until recently been limited, but newly published data from NHLBI GO...... variants KCNH2 P347S; SCN5A: S216L, V1951L; and CAV3 T78M in the control population (n=704) revealed prevalences comparable to those of ESP. Thus, we identified a much higher prevalence of previously LQTS-associated variants than expected in exome data from population studies. Great caution regarding...

Structure and phase composition of titanium nitride coating on austenitic steel

International Nuclear Information System (INIS)

Dubovitskaya, N.V.; Kolenchenko, L.D.; Larikov, L.N.

1989-01-01

Structure and phase composition of titanium nitride coating deposited on 08Kh18N10T steel substrate using ''Bulat'' device are studied. Use of complex investigation methods permitted despite small coating thickness (1μm) to aquire information on hardness, porosity, to study phase composition in all coating thickness. The surface layer (∼0.1 μm) consists of ε-Ti 2 N, TiN 0.6 , TiC 0.35 , that is formed with carbon participation from oil vacuum. In more deeper layers beside ε-Ti 2 N TiC 0.14 N 0.77 is present. Effect of carbon diffusion from substrate to forming coating is stated. Gradient of element concentrations in the substrate-coating interface causes recrystallization of austenite

Sol-gel coatings of ceramic fibres for composites with ceramic matrix

International Nuclear Information System (INIS)

Maier, B.; Grathwohl, G.; Spallek, M.; Pannhorst, W.

1992-01-01

The aim of this work was to show the feasibility in principle of sol-gel coating of ceramic reinforcement components for composites from technical aspects as well. The complexity of the coating task rises with the transition from individual fibres to bundles of fibres of different thickness to weaves, and finally to composites. (orig.) [de

Exome sequencing identifies compound heterozygous mutations in CYP4V2 in a pedigree with retinitis pigmentosa.

Directory of Open Access Journals (Sweden)

Yun Wang

Full Text Available Retinitis pigmentosa (RP is a heterogeneous group of progressive retinal degenerations characterized by pigmentation and atrophy in the mid-periphery of the retina. Twenty two subjects from a four-generation Chinese family with RP and thin cornea, congenital cataract and high myopia is reported in this study. All family members underwent complete ophthalmologic examinations. Patients of the family presented with bone spicule-shaped pigment deposits in retina, retinal vascular attenuation, retinal and choroidal dystrophy, as well as punctate opacity of the lens, reduced cornea thickness and high myopia. Peripheral venous blood was obtained from all patients and their family members for genetic analysis. After mutation analysis in a few known RP candidate genes, exome sequencing was used to analyze the exomes of 3 patients III2, III4, III6 and the unaffected mother II2. A total of 34,693 variations shared by 3 patients were subjected to several filtering steps against existing variation databases. Identified variations were verified in the rest family members by PCR and Sanger sequencing. Compound heterozygous c.802-8_810del17insGC and c.1091-2A>G mutations of the CYP4V2 gene, known as genetic defects for Bietti crystalline corneoretinal dystrophy, were identified as causative mutations for RP of this family.

Identification of a novel mutation in a Chinese family with Nance-Horan syndrome by whole exome sequencing*

Science.gov (United States)

Hong, Nan; Chen, Yan-hua; Xie, Chen; Xu, Bai-sheng; Huang, Hui; Li, Xin; Yang, Yue-qing; Huang, Ying-ping; Deng, Jian-lian; Qi, Ming; Gu, Yang-shun

2014-01-01

Objective: Nance-Horan syndrome (NHS) is a rare X-linked disorder characterized by congenital nuclear cataracts, dental anomalies, and craniofacial dysmorphisms. Mental retardation was present in about 30% of the reported cases. The purpose of this study was to investigate the genetic and clinical features of NHS in a Chinese family. Methods: Whole exome sequencing analysis was performed on DNA from an affected male to scan for candidate mutations on the X-chromosome. Sanger sequencing was used to verify these candidate mutations in the whole family. Clinical and ophthalmological examinations were performed on all members of the family. Results: A combination of exome sequencing and Sanger sequencing revealed a nonsense mutation c.322G>T (E108X) in exon 1 of NHS gene, co-segregating with the disease in the family. The nonsense mutation led to the conversion of glutamic acid to a stop codon (E108X), resulting in truncation of the NHS protein. Multiple sequence alignments showed that codon 108, where the mutation (c.322G>T) occurred, was located within a phylogenetically conserved region. The clinical features in all affected males and female carriers are described in detail. Conclusions: We report a nonsense mutation c.322G>T (E108X) in a Chinese family with NHS. Our findings broaden the spectrum of NHS mutations and provide molecular insight into future NHS clinical genetic diagnosis. PMID:25091991

Identification of a novel mutation in a Chinese family with Nance-Horan syndrome by whole exome sequencing.

Science.gov (United States)

Hong, Nan; Chen, Yan-hua; Xie, Chen; Xu, Bai-sheng; Huang, Hui; Li, Xin; Yang, Yue-qing; Huang, Ying-ping; Deng, Jian-lian; Qi, Ming; Gu, Yang-shun

2014-08-01

Nance-Horan syndrome (NHS) is a rare X-linked disorder characterized by congenital nuclear cataracts, dental anomalies, and craniofacial dysmorphisms. Mental retardation was present in about 30% of the reported cases. The purpose of this study was to investigate the genetic and clinical features of NHS in a Chinese family. Whole exome sequencing analysis was performed on DNA from an affected male to scan for candidate mutations on the X-chromosome. Sanger sequencing was used to verify these candidate mutations in the whole family. Clinical and ophthalmological examinations were performed on all members of the family. A combination of exome sequencing and Sanger sequencing revealed a nonsense mutation c.322G>T (E108X) in exon 1 of NHS gene, co-segregating with the disease in the family. The nonsense mutation led to the conversion of glutamic acid to a stop codon (E108X), resulting in truncation of the NHS protein. Multiple sequence alignments showed that codon 108, where the mutation (c.322G>T) occurred, was located within a phylogenetically conserved region. The clinical features in all affected males and female carriers are described in detail. We report a nonsense mutation c.322G>T (E108X) in a Chinese family with NHS. Our findings broaden the spectrum of NHS mutations and provide molecular insight into future NHS clinical genetic diagnosis.

Targeted exome sequencing reveals novel USH2A mutations in Chinese patients with simplex Usher syndrome.

Science.gov (United States)

Shu, Hai-Rong; Bi, Huai; Pan, Yang-Chun; Xu, Hang-Yu; Song, Jian-Xin; Hu, Jie

2015-09-16

Usher syndrome (USH) is an autosomal recessive disorder characterized by hearing impairment and vision dysfunction due to retinitis pigmentosa. Phenotypic and genetic heterogeneities of this disease make it impractical to obtain a genetic diagnosis by conventional Sanger sequencing. In this study, we applied a next-generation sequencing approach to detect genetic abnormalities in patients with USH. Two unrelated Chinese families were recruited, consisting of two USH afflicted patients and four unaffected relatives. We selected 199 genes related to inherited retinal diseases as targets for deep exome sequencing. Through systematic data analysis using an established bioinformatics pipeline, all variants that passed filter criteria were validated by Sanger sequencing and co-segregation analysis. A homozygous frameshift mutation (c.4382delA, p.T1462Lfs*2) was revealed in exon20 of gene USH2A in the F1 family. Two compound heterozygous mutations, IVS47 + 1G > A and c.13156A > T (p.I4386F), located in intron 48 and exon 63 respectively, of USH2A, were identified as causative mutations for the F2 family. Of note, the missense mutation c.13156A > T has not been reported so far. In conclusion, targeted exome sequencing precisely and rapidly identified the genetic defects in two Chinese USH families and this technique can be applied as a routine examination for these disorders with significant clinical and genetic heterogeneity.

Process engineering of ceramic composite coatings for fuel cell systems

Energy Technology Data Exchange (ETDEWEB)

Li, G.; Kim, H.; Chen, M.; Yang, Q.; Troczynski, T. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Metals and Materials Engineering

2003-07-01

Researchers at UBCeram at the Department of Metals and Materials Engineering at the University of British Columbia have developed a technology to chemically bond composite sol-gel (CB-CSG) coating onto metallic surfaces of complex or concave shapes. The process has been optimized for electrically resistive coatings and corrosion-resistant coatings. The CSG is sprayed onto metallic surfaces and is heat-treated at 300 degrees C to partially dehydrate the hydroxides. The CSG film is then chemically bonded through reaction of active alumina with metal phosphates, such as aluminium phosphate. A new chromate-free process is being developed to address the issue of coatings porosity. The electrodeposition technique involves polymer particles mixed with suspended fine alumina particles which are co-deposited by electrophoretic means or by electrocoagulation. The composite e-coatings have excellent mechanical properties and are being considered as a protective coating for various components of fuel cell systems. 9 refs., 7 figs.

Electroless deposition of nickel-boron coatings using low frequency ultrasonic agitation: Effect of ultrasonic frequency on the coatings.

Science.gov (United States)

Bonin, L; Bains, N; Vitry, V; Cobley, A J

2017-05-01

The effect of ultrasound on the properties of Nickel-Boron (NiB) coatings was investigated. NiB coatings were fabricated by electroless deposition using either ultrasonic or mechanical agitation. The deposition of Ni occurred in an aqueous bath containing a reducible metal salt (nickel chloride), reducing agent (sodium borohydride), complexing agent (ethylenediamine) and stabilizer (lead tungstate). Due to the instability of the borohydride in acidic, neutral and slightly alkaline media, pH was controlled at pH 12±1 in order to avoid destabilizing the bath. Deposition was performed in three different configurations: one with a classical mechanical agitation at 300rpm and the other two employing ultrasound at a frequency of either 20 or 35kHz. The microstructures of the electroless coatings were characterized by a combination of optical Microscopy and Scanning Electron Microscope (SEM). The chemistry of the coatings was determined by ICP-AES (Inductively Coupled Plasma - Atomic Emission Spectrometry) after dissolution in aqua regia. The mechanical properties of the coatings were established by a combination of roughness measurements, Vickers microhardness and pin-on-disk tribology tests. Lastly, the corrosion properties were analysed by potentiodynamic polarization. The results showed that low frequency ultrasonic agitation could be used to produce coatings from an alkaline NiB bath and that the thickness of coatings obtained could be increased by over 50% compared to those produced using mechanical agitation. Although ultrasonic agitation produced a smoother coating and some alteration of the deposit morphology was observed, the mechanical and corrosion properties were very similar to those found when using mechanical agitation. Copyright © 2017 Elsevier B.V. All rights reserved.

Nanoparticle/Polymer Nanocomposite Bond Coat or Coating

Science.gov (United States)

Miller, Sandi G.

2011-01-01

This innovation addresses the problem of coatings (meant to reduce gas permeation) applied to polymer matrix composites spalling off in service due to incompatibility with the polymer matrix. A bond coat/coating has been created that uses chemically functionalized nanoparticles (either clay or graphene) to create a barrier film that bonds well to the matrix resin, and provides an outstanding barrier to gas permeation. There is interest in applying clay nanoparticles as a coating/bond coat to a polymer matrix composite. Often, nanoclays are chemically functionalized with an organic compound intended to facilitate dispersion of the clay in a matrix. That organic modifier generally degrades at the processing temperature of many high-temperature polymers, rendering the clay useless as a nano-additive to high-temperature polymers. However, this innovation includes the use of organic compounds compatible with hightemperature polymer matrix, and is suitable for nanoclay functionalization, the preparation of that clay into a coating/bondcoat for high-temperature polymers, the use of the clay as a coating for composites that do not have a hightemperature requirement, and a comparable approach to the preparation of graphene coatings/bond coats for polymer matrix composites.

Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing

OpenAIRE

Lohr, Jens G.; Stojanov, Petar; Lawrence, Michael S.; Auclair, Daniel; Chapuy, Bjoern; Sougnez, Carrie; Cruz-Gordillo, Peter; Knoechel, Birgit; Asmann, Yan W.; Slager, Susan L.; Novak, Anne J.; Dogan, Ahmet; Ansell, Stephen M.; Link, Brian K.; Zou, Lihua

2012-01-01

To gain insight into the genomic basis of diffuse large B-cell lymphoma (DLBCL), we performed massively parallel whole-exome sequencing of 55 primary tumor samples from patients with DLBCL and matched normal tissue. We identified recurrent mutations in genes that are well known to be functionally relevant in DLBCL, including MYD88, CARD11, EZH2, and CREBBP. We also identified somatic mutations in genes for which a functional role in DLBCL has not been previously suspected. These genes include...

Characterization of boride-based powders and detonation gun sprayed cermet coatings

International Nuclear Information System (INIS)

Keraenen, J.; Stenberg, T.; Maentylae, T.

1995-01-01

Detonation gun sprayed (DGS) cermet coatings containing complex ternary transition metal boride as hard particles dispersed in a stainless steel or nickel based superalloy matrix have been characterized. Microstructure of the coatings, as well as powders, were studied with optical microscopy, scanning electron microscopy (SEM), X-ray diffraction (XRD) and analytical transmission electron microscopy (AEM). X-ray microanalysis of the coatings were carried out using energy dispersive X-ray spectrometer (EDS) attached to the SEM and AEM. Moreover, abrasion wear resistance of the coatings was evaluated with a rubber wheel abrasion test equipment. The general microstructure of studied coatings appeared to be heterogeneous in the terms of the distribution, size and crystallographic nature of the phases. Nonetheless, very low porosities were obtained and in the coatings the oxide phase as well as the unmelted particles and the formation of oxide phase were avoided by optimization of DGS parameters. So far the abrasive wear resistance of boride-based cermet coatings is not so good as that of the WC-12Co coatings

Preparation and properties of chrome-free colored Ti/Zr based conversion coating on aluminum alloy

Energy Technology Data Exchange (ETDEWEB)

Yi Aihua [School of Materials Science and Engineering, South China University of Technology, Guangzhou 510640 (China); Li Wenfang, E-mail: mewfl@scut.edu.cn [School of Materials Science and Engineering, South China University of Technology, Guangzhou 510640 (China); Du Jun; Mu Songlin [School of Materials Science and Engineering, South China University of Technology, Guangzhou 510640 (China)

2012-06-01

A golden conversion coating on the surface of aluminum alloy was prepared by adding tannic acid and coating-forming accelerator in the treatment solution containing titanium and zirconium ions. The growth process, main component and corrosion resistance of the conversion coating were characterized by EDS, SEM, XRD, XPS, FIIR and electrochemical workstation. The results showed that the main components of the conversion coating were Na{sub 3}AlF{sub 6} and the conversion coating owns a double-layer structure. The outer layer consists of metal-organic complex and the inner layer is mainly made up of Na{sub 3}AlF{sub 6}. The mechanism of the formation of the golden conversion coating can be deemed as nucleation, growth of Na{sub 3}AlF{sub 6} crystal and formation of metal-organic complex. In potentiodynamic polarization test, the corrosion current density decreases to 0.283 {mu}A cm{sup -2} from 5.894 {mu}A cm{sup -2}, which indicates an obvious improvement of corrosion resistance.

Microstructure of vapor deposited coatings on curved substrates

Energy Technology Data Exchange (ETDEWEB)

Rodgers, Theron M.; Zhao, Hengbei; Wadley, Haydn N. G., E-mail: haydn@virginia.edu [Department of Materials Science and Engineering, University of Virginia, 395 McCormick Rd., P.O. Box 400745, Charlottesville, Virginia 22904 (United States)

2015-09-15

Thermal barrier coating systems consisting of a metallic bond coat and ceramic over layer are widely used to extend the life of gas turbine engine components. They are applied using either high-vacuum physical vapor deposition techniques in which vapor atoms rarely experience scattering collisions during propagation to a substrate, or by gas jet assisted (low-vacuum) vapor deposition techniques that utilize scattering from streamlines to enable non-line-of-sight deposition. Both approaches require substrate motion to coat a substrate of complex shape. Here, direct simulation Monte Carlo and kinetic Monte Carlo simulation methods are combined to simulate the deposition of a nickel coating over the concave and convex surfaces of a model airfoil, and the simulation results are compared with those from experimental depositions. The simulation method successfully predicted variations in coating thickness, columnar growth angle, and porosity during both stationary and substrate rotated deposition. It was then used to investigate a wide range of vapor deposition conditions spanning high-vacuum physical vapor deposition to low-vacuum gas jet assisted vapor deposition. The average coating thickness was found to increase initially with gas pressure reaching a maximum at a chamber pressure of 8–10 Pa, but the best coating thickness uniformity was achieved under high vacuum deposition conditions. However, high vacuum conditions increased the variation in the coatings pore volume fraction over the surface of the airfoil. The simulation approach was combined with an optimization algorithm and used to investigate novel deposition concepts to tailor the local coating thickness.

Microstructure of vapor deposited coatings on curved substrates

International Nuclear Information System (INIS)

Rodgers, Theron M.; Zhao, Hengbei; Wadley, Haydn N. G.

2015-01-01

Thermal barrier coating systems consisting of a metallic bond coat and ceramic over layer are widely used to extend the life of gas turbine engine components. They are applied using either high-vacuum physical vapor deposition techniques in which vapor atoms rarely experience scattering collisions during propagation to a substrate, or by gas jet assisted (low-vacuum) vapor deposition techniques that utilize scattering from streamlines to enable non-line-of-sight deposition. Both approaches require substrate motion to coat a substrate of complex shape. Here, direct simulation Monte Carlo and kinetic Monte Carlo simulation methods are combined to simulate the deposition of a nickel coating over the concave and convex surfaces of a model airfoil, and the simulation results are compared with those from experimental depositions. The simulation method successfully predicted variations in coating thickness, columnar growth angle, and porosity during both stationary and substrate rotated deposition. It was then used to investigate a wide range of vapor deposition conditions spanning high-vacuum physical vapor deposition to low-vacuum gas jet assisted vapor deposition. The average coating thickness was found to increase initially with gas pressure reaching a maximum at a chamber pressure of 8–10 Pa, but the best coating thickness uniformity was achieved under high vacuum deposition conditions. However, high vacuum conditions increased the variation in the coatings pore volume fraction over the surface of the airfoil. The simulation approach was combined with an optimization algorithm and used to investigate novel deposition concepts to tailor the local coating thickness

Degradation of nitride coatings in low-pressure gas discharge plasma

Science.gov (United States)

Ivanov, Yurii; Shugurov, Vladimir; Krysina, Olga; Petrikova, Elizaveta; Tolkachev, Oleg

2017-12-01

The paper provides research data on the defect structure, mechanical characteristics, and tribological properties of commercially pure VT1-0 titanium exposed to surface modification on a COMPLEX laboratory electron-ion plasma setup which allows nitriding, coating deposition, and etching in low-pressure gas discharge plasma in a single vacuum cycle. It is shown that preliminary plasma nitriding forms a columnar Ti2N phase in VT1-0 titanium and that subsequent TiN deposition results in a thin nanocrystalline TiN layer. When the coating-substrate system is etched, the coating fails and the tribological properties of the material degrade greatly.

Study on the property of low friction complex graphite-like coating containing tantalum

Science.gov (United States)

Wang, Zuoping; Feng, Lajun; Shen, Wenning

2018-03-01

In order to enhance equipment lifetime under low oil or even dry conditions, tantalum was introduced into the graphite-like coating (GLC) by sputtering mosaic targets. The results showed that the introduction of Ta obviously reduced the friction coefficient and hardness of the GLC, while improved the wearability. When the atomic percentage of Ta was larger than 3%, the steady friction coefficient was lower than 0.01, suggesting the coating exhibited super lubricity. When the content of Ta was about 5.0%, the average friction coefficient was 0.02 by a sliding friction test under load of 20 N in unlubricated condition. Its average friction coefficient reduced by 75%, compared with that of control GLC (0.0825).

Multifunctional methacrylate-based coatings for glass and metal surfaces

Science.gov (United States)

Pospiech, Doris; Jehnichen, Dieter; Starke, Sandra; Müller, Felix; Bünker, Tobias; Wollenberg, Anne; Häußler, Liane; Simon, Frank; Grundke, Karina; Oertel, Ulrich; Opitz, Michael; Kruspe, Rainer

2017-03-01

In order to prevent freshwater biofouling glass and metal surfaces were coated with novel transparent methacrylate-based copolymers. The multifunctionality of the copolymers, such as adhesion to the substrate, surface polarity, mechanical long-term stability in water, and ability to form metal complexes was inserted by the choice of suitable comonomers. The monomer 2-acetoacetoxy ethyl methacrylate (AAMA) was used as complexing unit to produce copper(II) complexes in the coating's upper surface layer. The semifluorinated monomer 1H,1H,2H,2H-perfluorodecyl methacrylate was employed to adjust the surface polarity and wettability. Comprehensive surface characterization techniques, such as X-ray photoelectron spectroscopy (XPS) and contact angle measurements showed that surface compositions and properties can be easily adjusted by varying the concentrations of the comonomers. The formation of copper(II) complexes along the copolymer chains and their stability against washing out with plenty of water was proven by XPS. Copolymers containing semifluorinated comonomers significantly inhibited the growth of Achnanthidium species. Copolymers with copper-loaded AAMA-sequences were able to reduce both the growth of Achnanthidium spec. and Staphylococcus aureus.

Replacement for a Flex Hose Coating at the Space Shuttle Launch Pad

Science.gov (United States)

Whitten, Mary; Vinje, Rubiela; Curran, Jerome; Meneghelli, Barry; Calle, Luz Marina

2009-01-01

Aerocoat AR-7 is a coating that has been used to protect stainless steel flex hoses at NASA's Kennedy Space Center launch complex and hydraulic lines of the mobile launch platform (MLP). This coating has great corrosion control performance and low temperature application. AR-7 was developed by NASA and produced exclusively for NASA but its production has been discontinued due to its high content of volatile organic compounds (VOC) and significant environmental impact. The purpose of this project was to select and evaluate candidate coatings to find a replacement coating that is more environmentally friendly, with similar properties to AR-7. No coatings were identified that perform the same as AR-7 in all areas. Candidate coatings failed in comparison to AR-7 in salt fog, beachside atmospheric exposure, pencil hardness, Mandrel bend, chemical compatibility, adhesion, and ease of application tests. However, two coatings were selected for further evaluation.

Electrocurtain coating process for coating solar mirrors

Science.gov (United States)

Kabagambe, Benjamin; Boyd, Donald W.; Buchanan, Michael J.; Kelly, Patrick; Kutilek, Luke A.; McCamy, James W.; McPheron, Douglas A.; Orosz, Gary R.; Limbacher, Raymond D.

2013-10-15

An electrically conductive protective coating or film is provided over the surface of a reflective coating of a solar mirror by flowing or directing a cation containing liquid and an anion containing liquid onto the conductive surface. The cation and the anion containing liquids are spaced from, and preferably out of contact with one another on the surface of the reflective coating as an electric current is moved through the anion containing liquid, the conductive surface between the liquids and the cation containing liquid to coat the conductive surface with the electrically conductive coating.

Exome sequencing of index patients with retinal dystrophies as a tool for molecular diagnosis.

Directory of Open Access Journals (Sweden)

Marta Corton

Full Text Available Retinal dystrophies (RD are a group of hereditary diseases that lead to debilitating visual impairment and are usually transmitted as a Mendelian trait. Pathogenic mutations can occur in any of the 100 or more disease genes identified so far, making molecular diagnosis a rather laborious process. In this work we explored the use of whole exome sequencing (WES as a tool for identification of RD mutations, with the aim of assessing its applicability in a diagnostic context.We ascertained 12 Spanish families with seemingly recessive RD. All of the index patients underwent mutational pre-screening by chip-based sequence hybridization and resulted to be negative for known RD mutations. With the exception of one pedigree, to simulate a standard diagnostic scenario we processed by WES only the DNA from the index patient of each family, followed by in silico data analysis. We successfully identified causative mutations in patients from 10 different families, which were later verified by Sanger sequencing and co-segregation analyses. Specifically, we detected pathogenic DNA variants (∼50% novel mutations in the genes RP1, USH2A, CNGB3, NMNAT1, CHM, and ABCA4, responsible for retinitis pigmentosa, Usher syndrome, achromatopsia, Leber congenital amaurosis, choroideremia, or recessive Stargardt/cone-rod dystrophy cases.Despite the absence of genetic information from other family members that could help excluding nonpathogenic DNA variants, we could detect causative mutations in a variety of genes known to represent a wide spectrum of clinical phenotypes in 83% of the patients analyzed. Considering the constant drop in costs for human exome sequencing and the relative simplicity of the analyses made, this technique could represent a valuable tool for molecular diagnostics or genetic research, even in cases for which no genotypes from family members are available.

Stochastic Computer Simulation of Cermet Coatings Formation

Directory of Open Access Journals (Sweden)

Oleg P. Solonenko

2015-01-01

Full Text Available An approach to the modeling of the process of the formation of thermal coatings lamellar structure, including plasma coatings, at the spraying of cermet powders is proposed. The approach based on the theoretical fundamentals developed which could be used for rapid and sufficiently accurate prediction of thickness and diameter of cermet splats as well as temperature at interface “flattening quasi-liquid cermet particle-substrate” depending on the key physical parameters (KPPs: temperature, velocity and size of particle, substrate temperature, and concentration of finely dispersed solid inclusions uniformly distributed in liquid metal binder. The results are presented, which concern the development of the computational algorithm and the program complex for modeling the process of laying the splats in the coating with regard to the topology of its surface, which varies dynamically at the spraying, as well as the formation of lamellar structure and porosity of the coating. The results of numerical experiments are presented through the example of thermal spraying the cermet TiC-30 vol.% NiCr powder, illustrating the performance of the developed computational technology.

Simple and high yielding method for preparing tissue specific extracellular matrix coatings for cell culture.

Science.gov (United States)

DeQuach, Jessica A; Mezzano, Valeria; Miglani, Amar; Lange, Stephan; Keller, Gordon M; Sheikh, Farah; Christman, Karen L

2010-09-27

The native extracellular matrix (ECM) consists of a highly complex, tissue-specific network of proteins and polysaccharides, which help regulate many cellular functions. Despite the complex nature of the ECM, in vitro cell-based studies traditionally assess cell behavior on single ECM component substrates, which do not adequately mimic the in vivo extracellular milieu. We present a simple approach for developing naturally derived ECM coatings for cell culture that provide important tissue-specific cues unlike traditional cell culture coatings, thereby enabling the maturation of committed C2C12 skeletal myoblast progenitors and human embryonic stem cells differentiated into cardiomyocytes. Here we show that natural muscle-specific coatings can (i) be derived from decellularized, solubilized adult porcine muscle, (ii) contain a complex mixture of ECM components including polysaccharides, (iii) adsorb onto tissue culture plastic and (iv) promote cell maturation of committed muscle progenitor and stem cells. This versatile method can create tissue-specific ECM coatings, which offer a promising platform for cell culture to more closely mimic the mature in vivo ECM microenvironment.

Adhesion and cleaning of foods with complex structure: Effect of oil content and fluoropolymer coating characteristics on the detachment of cake from baking surfaces

OpenAIRE

Magens, Ole; Liu, Y; Hofmans, JFA; Nelissen, JA; Wilson, David Ian

2017-01-01

The effect of surface coating on the detachment of a complex microstructured food material, was investigated using an improved version of the millimanipulation device described by Ali et al. (2015 $\\textit{Food & Bioproducts Processing}$, Vol. 93, 256–268). The test material was baked sponge cake batter, which contains approximately 27 vol% bubbles in a ‘continuous’ phase of emulsified oil in a flour/syrup suspension. Detachment in the dry state was studied for aluminium, 304 stainless steel ...

Whole-exome sequencing revealed two novel mutations in Usher syndrome.

Science.gov (United States)

Koparir, Asuman; Karatas, Omer Faruk; Atayoglu, Ali Timucin; Yuksel, Bayram; Sagiroglu, Mahmut Samil; Seven, Mehmet; Ulucan, Hakan; Yuksel, Adnan; Ozen, Mustafa

2015-06-01

Usher syndrome is a clinically and genetically heterogeneous autosomal recessive inherited disorder accompanied by hearing loss and retinitis pigmentosa (RP). Since the associated genes are various and quite large, we utilized whole-exome sequencing (WES) as a diagnostic tool to identify the molecular basis of Usher syndrome. DNA from a 12-year-old male diagnosed with Usher syndrome was analyzed by WES. Mutations detected were confirmed by Sanger sequencing. The pathogenicity of these mutations was determined by in silico analysis. A maternally inherited deleterious frameshift mutation, c.14439_14454del in exon 66 and a paternally inherited non-sense c.10830G>A stop-gain SNV in exon 55 of USH2A were found as two novel compound heterozygous mutations. Both of these mutations disrupt the C terminal of USH2A protein. As a result, WES revealed two novel compound heterozygous mutations in a Turkish USH2A patient. This approach gave us an opportunity to have an appropriate diagnosis and provide genetic counseling to the family within a reasonable time. Copyright © 2015 Elsevier B.V. All rights reserved.

Portero versus portador: Spanish interpretation of genomic terminology during whole exome sequencing results disclosure.

Science.gov (United States)

Gutierrez, Amanda M; Robinson, Jill O; Statham, Emily E; Scollon, Sarah; Bergstrom, Katie L; Slashinski, Melody J; Parsons, Donald W; Plon, Sharon E; McGuire, Amy L; Street, Richard L

2017-11-01

Describe modifications to technical genomic terminology made by interpreters during disclosure of whole exome sequencing (WES) results. Using discourse analysis, we identified and categorized interpretations of genomic terminology in 42 disclosure sessions where Spanish-speaking parents received their child's WES results either from a clinician using a medical interpreter, or directly from a bilingual physician. Overall, 76% of genomic terms were interpreted accordantly, 11% were misinterpreted and 13% were omitted. Misinterpretations made by interpreters and bilingual physicians included using literal and nonmedical terminology to interpret genomic concepts. Modifications to genomic terminology made during interpretation highlight the need to standardize bilingual genomic lexicons. We recommend Spanish terms that can be used to refer to genomic concepts.

A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders.

Science.gov (United States)

Stark, Zornitza; Tan, Tiong Y; Chong, Belinda; Brett, Gemma R; Yap, Patrick; Walsh, Maie; Yeung, Alison; Peters, Heidi; Mordaunt, Dylan; Cowie, Shannon; Amor, David J; Savarirayan, Ravi; McGillivray, George; Downie, Lilian; Ekert, Paul G; Theda, Christiane; James, Paul A; Yaplito-Lee, Joy; Ryan, Monique M; Leventer, Richard J; Creed, Emma; Macciocca, Ivan; Bell, Katrina M; Oshlack, Alicia; Sadedin, Simon; Georgeson, Peter; Anderson, Charlotte; Thorne, Natalie; Melbourne Genomics Health Alliance; Gaff, Clara; White, Susan M

2016-11-01

To prospectively evaluate the diagnostic and clinical utility of singleton whole-exome sequencing (WES) as a first-tier test in infants with suspected monogenic disease. Singleton WES was performed as a first-tier sequencing test in infants recruited from a single pediatric tertiary center. This occurred in parallel with standard investigations, including single- or multigene panel sequencing when clinically indicated. The diagnosis rate, clinical utility, and impact on management of singleton WES were evaluated. Of 80 enrolled infants, 46 received a molecular genetic diagnosis through singleton WES (57.5%) compared with 11 (13.75%) who underwent standard investigations in the same patient group. Clinical management changed following exome diagnosis in 15 of 46 diagnosed participants (32.6%). Twelve relatives received a genetic diagnosis following cascade testing, and 28 couples were identified as being at high risk of recurrence in future pregnancies. This prospective study provides strong evidence for increased diagnostic and clinical utility of singleton WES as a first-tier sequencing test for infants with a suspected monogenic disorder. Singleton WES outperformed standard care in terms of diagnosis rate and the benefits of a diagnosis, namely, impact on management of the child and clarification of reproductive risks for the extended family in a timely manner.Genet Med 18 11, 1090-1096.

Exome sequence analysis and follow up genotyping implicates rare ULK1 variants to be involved in susceptibility to schizophrenia

Science.gov (United States)

Al Eissa, Mariam M.; Fiorentino, Alessia; Sharp, Sally I.; O'Brien, Niamh L.; Wolfe, Kate; Giaroli, Giovanni; Curtis, David; Bass, Nicholas J.

2017-01-01

Summary Schizophrenia (SCZ) is a severe, highly heritable psychiatric disorder. Elucidation of the genetic architecture of the disorder will facilitate greater understanding of the altered underlying neurobiological mechanisms. The aim of this study was to identify likely aetiological variants in subjects affected with SCZ. Exome sequence data from a SCZ cas–control sample from Sweden was analysed for likely aetiological variants using a weighted burden test. Suggestive evidence implicated the UNC‐51‐like kinase (ULK1) gene, and it was observed that four rare variants that were more common in the Swedish SCZ cases were also more common in UK10K SCZ cases, as compared to obesity cases. These three missense variants and one intronic variant were genotyped in the University College London cohort of 1304 SCZ cases and 1348 ethnically matched controls. All four variants were more common in the SCZ cases than controls and combining them produced a result significant at P = 0.02. The results presented here demonstrate the importance of following up exome sequencing studies using additional datasets. The roles of ULK1 in autophagy and mTOR signalling strengthen the case that these pathways may be important in the pathophysiology of SCZ. The findings reported here await independent replication. PMID:29148569

Characterization of X chromosome inactivation using integrated analysis of whole-exome and mRNA sequencing.

Directory of Open Access Journals (Sweden)

Szabolcs Szelinger

Full Text Available In females, X chromosome inactivation (XCI is an epigenetic, gene dosage compensatory mechanism by inactivation of one copy of X in cells. Random XCI of one of the parental chromosomes results in an approximately equal proportion of cells expressing alleles from either the maternally or paternally inherited active X, and is defined by the XCI ratio. Skewed XCI ratio is suggestive of non-random inactivation, which can play an important role in X-linked genetic conditions. Current methods rely on indirect, semi-quantitative DNA methylation-based assay to estimate XCI ratio. Here we report a direct approach to estimate XCI ratio by integrated, family-trio based whole-exome and mRNA sequencing using phase-by-transmission of alleles coupled with allele-specific expression analysis. We applied this method to in silico data and to a clinical patient with mild cognitive impairment but no clear diagnosis or understanding molecular mechanism underlying the phenotype. Simulation showed that phased and unphased heterozygous allele expression can be used to estimate XCI ratio. Segregation analysis of the patient's exome uncovered a de novo, interstitial, 1.7 Mb deletion on Xp22.31 that originated on the paternally inherited X and previously been associated with heterogeneous, neurological phenotype. Phased, allelic expression data suggested an 83∶20 moderately skewed XCI that favored the expression of the maternally inherited, cytogenetically normal X and suggested that the deleterious affect of the de novo event on the paternal copy may be offset by skewed XCI that favors expression of the wild-type X. This study shows the utility of integrated sequencing approach in XCI ratio estimation.

Wear-resistant and electromagnetic absorbing behaviors of oleic acid post-modified ferrite-filled epoxy resin composite coating

Science.gov (United States)

Wang, Wenjie; Zang, Chongguang; Jiao, Qingjie

2015-03-01

The post-modified Mn-Zn ferrite was prepared by grafting oleic acid on the surface of Mn-Zn ferrite to inhibit magnetic nanoparticle aggregation. Fourier Transform Infrared (FT-IR) spectroscopy was used to characterize the particle surfaces. The friction and electromagnetic absorbing properties of a thin coating fabricated by dispersing ferrite into epoxy resin (EP) were investigated. The roughness of the coating and water contact angle were measured using the VEECO and water contact angle meter. Friction tests were conducted using a stainless-steel bearing ball and a Rockwell diamond tip, respectively. The complex permittivity and complex permeability of the composite coating were studied in the low frequency (10 MHz-1.5 GHz). Surface modified ferrites are found to improve magnetic particles dispersion in EP resulting in significant compatibility between inorganic and organic materials. Results also indicate that modified ferrite/EP coatings have a lower roughness average value and higher water contact angle than original ferrite/EP coatings. The enhanced tribological properties of the modified ferrite/EP coatings can be seen from the increased coefficient value. The composite coatings with modified ferrite are observed to exhibit better reflection loss compared with the coatings with original ferrite.

Molecular Diagnostic Yield of Chromosomal Microarray Analysis and Whole-Exome Sequencing in Children With Autism Spectrum Disorder.

Science.gov (United States)

Tammimies, Kristiina; Marshall, Christian R; Walker, Susan; Kaur, Gaganjot; Thiruvahindrapuram, Bhooma; Lionel, Anath C; Yuen, Ryan K C; Uddin, Mohammed; Roberts, Wendy; Weksberg, Rosanna; Woodbury-Smith, Marc; Zwaigenbaum, Lonnie; Anagnostou, Evdokia; Wang, Zhuozhi; Wei, John; Howe, Jennifer L; Gazzellone, Matthew J; Lau, Lynette; Sung, Wilson W L; Whitten, Kathy; Vardy, Cathy; Crosbie, Victoria; Tsang, Brian; D'Abate, Lia; Tong, Winnie W L; Luscombe, Sandra; Doyle, Tyna; Carter, Melissa T; Szatmari, Peter; Stuckless, Susan; Merico, Daniele; Stavropoulos, Dimitri J; Scherer, Stephen W; Fernandez, Bridget A

2015-09-01

The use of genome-wide tests to provide molecular diagnosis for individuals with autism spectrum disorder (ASD) requires more study. To perform chromosomal microarray analysis (CMA) and whole-exome sequencing (WES) in a heterogeneous group of children with ASD to determine the molecular diagnostic yield of these tests in a sample typical of a developmental pediatric clinic. The sample consisted of 258 consecutively ascertained unrelated children with ASD who underwent detailed assessments to define morphology scores based on the presence of major congenital abnormalities and minor physical anomalies. The children were recruited between 2008 and 2013 in Newfoundland and Labrador, Canada. The probands were stratified into 3 groups of increasing morphological severity: essential, equivocal, and complex (scores of 0-3, 4-5, and ≥6). All probands underwent CMA, with WES performed for 95 proband-parent trios. The overall molecular diagnostic yield for CMA and WES in a population-based ASD sample stratified in 3 phenotypic groups. Of 258 probands, 24 (9.3%, 95%CI, 6.1%-13.5%) received a molecular diagnosis from CMA and 8 of 95 (8.4%, 95%CI, 3.7%-15.9%) from WES. The yields were statistically different between the morphological groups. Among the children who underwent both CMA and WES testing, the estimated proportion with an identifiable genetic etiology was 15.8% (95%CI, 9.1%-24.7%; 15/95 children). This included 2 children who received molecular diagnoses from both tests. The combined yield was significantly higher in the complex group when compared with the essential group (pairwise comparison, P = .002). [table: see text]. Among a heterogeneous sample of children with ASD, the molecular diagnostic yields of CMA and WES were comparable, and the combined molecular diagnostic yield was higher in children with more complex morphological phenotypes in comparison with the children in the essential category. If replicated in additional populations, these findings may

The chemistry and structure of nickel–tungsten coatings obtained by pulse galvanostatic electrodeposition

International Nuclear Information System (INIS)

Argañaraz, M.P. Quiroga; Ribotta, S.B.; Folquer, M.E.; Zelaya, E.; Llorente, C.; Ramallo-López, J.M.; Benítez, G.; Rubert, A.; Gassa, L.M.; Vela, M.E.; Salvarezza, R.C.

2012-01-01

A detailed characterization of electrodeposited Ni-W coatings prepared by pulse electrodeposition on steel and copper substrates is presented. The coatings were obtained at high current pulse frequency and show high microhardness and absence of brittleness. The surface of the coating consists of nanometer sized crystals forming a cauliflower-like structure protected by a mixture of nickel and tungsten oxides. The cauliflower structure is preserved into the bulk coating that exhibits an average composition ≈70 at% Ni-30 at% W. Different phases are observed in the bulk structure: a W-rich amorphous phase (≈40%) and Ni-rich crystalline phases (≈60%). The crystalline phases consist of crystalline domains ≈7 nm in size of Ni(W) (fcc) solid solution (12 at% W content) and a minor Ni 4 W component (less than 10%). The amorphous phase exhibits a less compact Ni-W structure where some amount of C could also be present. Oxidized W species cannot be detected in the bulk coating, thus discarding the presence of significant amounts of tungsten carbide, tungstates or citrate–tungsten complexes. Our results shed light on controversial points related to the chemical composition and demonstrate the complex structure of this system.

AUDIOME: a tiered exome sequencing-based comprehensive gene panel for the diagnosis of heterogeneous nonsyndromic sensorineural hearing loss.

Science.gov (United States)

Guan, Qiaoning; Balciuniene, Jorune; Cao, Kajia; Fan, Zhiqian; Biswas, Sawona; Wilkens, Alisha; Gallo, Daniel J; Bedoukian, Emma; Tarpinian, Jennifer; Jayaraman, Pushkala; Sarmady, Mahdi; Dulik, Matthew; Santani, Avni; Spinner, Nancy; Abou Tayoun, Ahmad N; Krantz, Ian D; Conlin, Laura K; Luo, Minjie

2018-03-29

PurposeHereditary hearing loss is highly heterogeneous. To keep up with rapidly emerging disease-causing genes, we developed the AUDIOME test for nonsyndromic hearing loss (NSHL) using an exome sequencing (ES) platform and targeted analysis for the curated genes.MethodsA tiered strategy was implemented for this test. Tier 1 includes combined Sanger and targeted deletion analyses of the two most common NSHL genes and two mitochondrial genes. Nondiagnostic tier 1 cases are subjected to ES and array followed by targeted analysis of the remaining AUDIOME genes.ResultsES resulted in good coverage of the selected genes with 98.24% of targeted bases at >15 ×. A fill-in strategy was developed for the poorly covered regions, which generally fell within GC-rich or highly homologous regions. Prospective testing of 33 patients with NSHL revealed a diagnosis in 11 (33%) and a possible diagnosis in 8 cases (24.2%). Among those, 10 individuals had variants in tier 1 genes. The ES data in the remaining nondiagnostic cases are readily available for further analysis.ConclusionThe tiered and ES-based test provides an efficient and cost-effective diagnostic strategy for NSHL, with the potential to reflex to full exome to identify causal changes outside of the AUDIOME test.Genetics in Medicine advance online publication, 29 March 2018; doi:10.1038/gim.2018.48.

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data.

Science.gov (United States)

Krøigård, Anne Bruun; Thomassen, Mads; Lænkholm, Anne-Vibeke; Kruse, Torben A; Larsen, Martin Jakob

2016-01-01

Next generation sequencing is extensively applied to catalogue somatic mutations in cancer, in research settings and increasingly in clinical settings for molecular diagnostics, guiding therapy decisions. Somatic variant callers perform paired comparisons of sequencing data from cancer tissue and matched normal tissue in order to detect somatic mutations. The advent of many new somatic variant callers creates a need for comparison and validation of the tools, as no de facto standard for detection of somatic mutations exists and only limited comparisons have been reported. We have performed a comprehensive evaluation using exome sequencing and targeted deep sequencing data of paired tumor-normal samples from five breast cancer patients to evaluate the performance of nine publicly available somatic variant callers: EBCall, Mutect, Seurat, Shimmer, Indelocator, Somatic Sniper, Strelka, VarScan 2 and Virmid for the detection of single nucleotide mutations and small deletions and insertions. We report a large variation in the number of calls from the nine somatic variant callers on the same sequencing data and highly variable agreement. Sequencing depth had markedly diverse impact on individual callers, as for some callers, increased sequencing depth highly improved sensitivity. For SNV calling, we report EBCall, Mutect, Virmid and Strelka to be the most reliable somatic variant callers for both exome sequencing and targeted deep sequencing. For indel calling, EBCall is superior due to high sensitivity and robustness to changes in sequencing depths.

Active coatings technologies for tailorable military coating systems

Science.gov (United States)

Zunino, J. L., III

2007-04-01

The main objective of the U.S. Army's Active Coatings Technologies Program is to develop technologies that can be used in combination to tailor coatings for utilization on Army Materiel. The Active Coatings Technologies Program, ACT, is divided into several thrusts, including the Smart Coatings Materiel Program, Munitions Coatings Technologies, Active Sensor packages, Systems Health Monitoring, Novel Technology Development, as well as other advanced technologies. The goal of the ACT Program is to conduct research leading to the development of multiple coatings systems for use on various military platforms, incorporating unique properties such as self repair, selective removal, corrosion resistance, sensing, ability to modify coatings' physical properties, colorizing, and alerting logistics staff when tanks or weaponry require more extensive repair. A partnership between the U.S. Army Corrosion Office at Picatinny Arsenal, NJ along with researchers at the New Jersey Institute of Technology, NJ, Clemson University, SC, University of New Hampshire, NH, and University of Massachusetts (Lowell), MA, are developing the next generation of Smart Coatings Materiel via novel technologies such as nanotechnology, Micro-electromechanical Systems (MEMS), meta-materials, flexible electronics, electrochromics, electroluminescence, etc. This paper will provide the reader with an overview of the Active Coatings Technologies Program, including an update of the on-going Smart Coatings Materiel Program, its progress thus far, description of the prototype Smart Coatings Systems and research tasks as well as future nanotechnology concepts, and applications for the Department of Defense.

Rapid-Onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD): exome sequencing of trios, monozygotic twins and tumours

OpenAIRE

Barclay, Sarah F.; Rand, Casey M.; Borch, Lauren A.; Nguyen, Lisa; Gray, Paul A.; Gibson, William T.; Wilson, Richard J. A.; Gordon, Paul M. K.; Aung, Zaw; Berry-Kravis, Elizabeth M.; Ize-Ludlow, Diego; Weese-Mayer, Debra E.; Bech-Hansen, N. Torben

2015-01-01

Background Rapid-onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD) is thought to be a genetic disease caused by de novo mutations, though causative mutations have yet to be identified. We searched for de novo coding mutations among a carefully-diagnosed and clinically homogeneous cohort of 35 ROHHAD patients. Methods We sequenced the exomes of seven ROHHAD trios, plus tumours from four of these patients and the unaffected monozygotic (MZ) twin ...

Exome sequencing identifies pathogenic variants of VPS13B in a patient with familial 16p11.2 duplication

OpenAIRE

Dastan, Jila; Chijiwa, Chieko; Tang, Flamingo; Martell, Sally; Qiao, Ying; Rajcan-Separovic, Evica; Lewis, M. E. Suzanne

2016-01-01

Background The recurrent microduplication of 16p11.2 (dup16p11.2) is associated with a broad spectrum of neurodevelopmental disorders (NDD) confounded by incomplete penetrance and variable expressivity. This inter- and intra-familial clinical variability highlights the importance of personalized genetic counselling in individuals at-risk. Case presentation In this study, we performed whole exome sequencing (WES) to look for other genomic alterations that could explain the clinical variability...

Flow coating apparatus and method of coating

Science.gov (United States)

Hanumanthu, Ramasubrahmaniam; Neyman, Patrick; MacDonald, Niles; Brophy, Brenor; Kopczynski, Kevin; Nair, Wood

2014-03-11

Disclosed is a flow coating apparatus, comprising a slot that can dispense a coating material in an approximately uniform manner along a distribution blade that increases uniformity by means of surface tension and transfers the uniform flow of coating material onto an inclined substrate such as for example glass, solar panels, windows or part of an electronic display. Also disclosed is a method of flow coating a substrate using the apparatus such that the substrate is positioned correctly relative to the distribution blade, a pre-wetting step is completed where both the blade and substrate are completed wetted with a pre-wet solution prior to dispensing of the coating material onto the distribution blade from the slot and hence onto the substrate. Thereafter the substrate is removed from the distribution blade and allowed to dry, thereby forming a coating.

Application of Genetic Algorithm to the Design Optimization of Complex Energy Saving Glass Coating Structure

Science.gov (United States)

Johar, F. M.; Azmin, F. A.; Shibghatullah, A. S.; Suaidi, M. K.; Ahmad, B. H.; Abd Aziz, M. Z. A.; Salleh, S. N.; Shukor, M. Md

2014-04-01

Attenuation of GSM, GPS and personal communication signal leads to poor communication inside the building using regular shapes of energy saving glass coating. Thus, the transmission is very low. A brand new type of band pass frequency selective surface (FSS) for energy saving glass application is presented in this paper for one unit cell. Numerical Periodic Method of Moment approach according to a previous study has been applied to determine the new optimum design of one unit cell energy saving glass coating structure. Optimization technique based on the Genetic Algorithm (GA) is used to obtain an improved in return loss and transmission signal. The unit cell of FSS is designed and simulated using the CST Microwave Studio software at based on industrial, scientific and medical bands (ISM). A unique and irregular shape of an energy saving glass coating structure is obtained with lower return loss and improved transmission coefficient.

Application of genetic algorithm to the design optimization of complex energy saving glass coating structure

International Nuclear Information System (INIS)

Johar, F M; Azmin, F A; Suaidi, M K; Ahmad, B H; Aziz, M Z A Abd; Salleh, S N; Shukor, M Md; Shibghatullah, A S

2014-01-01

Attenuation of GSM, GPS and personal communication signal leads to poor communication inside the building using regular shapes of energy saving glass coating. Thus, the transmission is very low. A brand new type of band pass frequency selective surface (FSS) for energy saving glass application is presented in this paper for one unit cell. Numerical Periodic Method of Moment approach according to a previous study has been applied to determine the new optimum design of one unit cell energy saving glass coating structure. Optimization technique based on the Genetic Algorithm (GA) is used to obtain an improved in return loss and transmission signal. The unit cell of FSS is designed and simulated using the CST Microwave Studio software at based on industrial, scientific and medical bands (ISM). A unique and irregular shape of an energy saving glass coating structure is obtained with lower return loss and improved transmission coefficient.

Advantage of whole exome sequencing over allele-specific and targeted segment sequencing in detection of novel TULP1 mutation in leber congenital amaurosis

DEFF Research Database (Denmark)

Guo, Yiran; Prokudin, Ivan; Yu, Cong

2015-01-01

by targeted segment sequencing of 61 regions in 14 causative genes was performed. Subsequently, exome sequencing was undertaken in the proband, unaffected consanguineous parents and two unaffected siblings. Bioinformatic analysis used two independent pipelines, BWA-GATK and SOAP, followed by Annovar and Snp...

SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function

OpenAIRE

Li, Man; Li, Yong; Weeks, Olivia; Mijatovic, Vladan; Teumer, Alexander; Huffman, Jennifer E; Tromp, Gerard; Fuchsberger, Christian; Gorski, Mathias; Lyytikäinen, Leo-Pekka; Nutile, Teresa; Sedaghat, Sanaz; Sorice, Rossella; Tin, Adrienne; Yang, Qiong

2017-01-01

Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphi...

Soft plasma electrolysis with complex ions for optimizing electrochemical performance

Science.gov (United States)

Kamil, Muhammad Prisla; Kaseem, Mosab; Ko, Young Gun

2017-03-01

Plasma electrolytic oxidation (PEO) was a promising surface treatment for light metals to tailor an oxide layer with excellent properties. However, porous coating structure was generally exhibited due to excessive plasma discharges, restraining its performance. The present work utilized ethylenediaminetetraacetic acid (EDTA) and Cu-EDTA complexing agents as electrolyte additives that alter the plasma discharges to improve the electrochemical properties of Al-1.1Mg alloy coated by PEO. To achieve this purpose, PEO coatings were fabricated under an alternating current in silicate electrolytes containing EDTA and Cu-EDTA. EDTA complexes were found to modify the plasma discharging behaviour during PEO that led to a lower porosity than that without additives. This was attributed to a more homogeneous electrical field throughout the PEO process while the coating growth would be maintained by an excess of dissolved Al due to the EDTA complexes. When Cu-EDTA was used, the number of discharge channels in the coating layer was lower than that with EDTA due to the incorporation of Cu2O and CuO altering the dielectric behaviour. Accordingly, the sample in the electrolyte containing Cu-EDTA constituted superior corrosion resistance to that with EDTA. The electrochemical mechanism for excellent corrosion protection was elucidated in the context of equivalent circuit model.

Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3.

Science.gov (United States)

McClure, Matthew C; Bickhart, Derek; Null, Dan; Vanraden, Paul; Xu, Lingyang; Wiggans, George; Liu, George; Schroeder, Steve; Glasscock, Jarret; Armstrong, Jon; Cole, John B; Van Tassell, Curtis P; Sonstegard, Tad S

2014-01-01

The recent discovery of bovine haplotypes with negative effects on fertility in the Brown Swiss, Holstein, and Jersey breeds has allowed producers to identify carrier animals using commercial single nucleotide polymorphism (SNP) genotyping assays. This study was devised to identify the causative mutations underlying defective bovine embryo development contained within three of these haplotypes (Brown Swiss haplotype 1 and Holstein haplotypes 2 and 3) by combining exome capture with next generation sequencing. Of the 68,476,640 sequence variations (SV) identified, only 1,311 genome-wide SNP were concordant with the haplotype status of 21 sequenced carriers. Validation genotyping of 36 candidate SNP identified only 1 variant that was concordant to Holstein haplotype 3 (HH3), while no variants located within the refined intervals for HH2 or BH1 were concordant. The variant strictly associated with HH3 is a non-synonymous SNP (T/C) within exon 24 of the Structural Maintenance of Chromosomes 2 (SMC2) on Chromosome 8 at position 95,410,507 (UMD3.1). This polymorphism changes amino acid 1135 from phenylalanine to serine and causes a non-neutral, non-tolerated, and evolutionarily unlikely substitution within the NTPase domain of the encoded protein. Because only exome capture sequencing was used, we could not rule out the possibility that the true causative mutation for HH3 might lie in a non-exonic genomic location. Given the essential role of SMC2 in DNA repair, chromosome condensation and segregation during cell division, our findings strongly support the non-synonymous SNP (T/C) in SMC2 as the likely causative mutation. The absence of concordant variations for HH2 or BH1 suggests either the underlying causative mutations lie within a non-exomic region or in exome regions not covered by the capture array.

Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3.

Directory of Open Access Journals (Sweden)

Matthew C McClure

Full Text Available The recent discovery of bovine haplotypes with negative effects on fertility in the Brown Swiss, Holstein, and Jersey breeds has allowed producers to identify carrier animals using commercial single nucleotide polymorphism (SNP genotyping assays. This study was devised to identify the causative mutations underlying defective bovine embryo development contained within three of these haplotypes (Brown Swiss haplotype 1 and Holstein haplotypes 2 and 3 by combining exome capture with next generation sequencing. Of the 68,476,640 sequence variations (SV identified, only 1,311 genome-wide SNP were concordant with the haplotype status of 21 sequenced carriers. Validation genotyping of 36 candidate SNP identified only 1 variant that was concordant to Holstein haplotype 3 (HH3, while no variants located within the refined intervals for HH2 or BH1 were concordant. The variant strictly associated with HH3 is a non-synonymous SNP (T/C within exon 24 of the Structural Maintenance of Chromosomes 2 (SMC2 on Chromosome 8 at position 95,410,507 (UMD3.1. This polymorphism changes amino acid 1135 from phenylalanine to serine and causes a non-neutral, non-tolerated, and evolutionarily unlikely substitution within the NTPase domain of the encoded protein. Because only exome capture sequencing was used, we could not rule out the possibility that the true causative mutation for HH3 might lie in a non-exonic genomic location. Given the essential role of SMC2 in DNA repair, chromosome condensation and segregation during cell division, our findings strongly support the non-synonymous SNP (T/C in SMC2 as the likely causative mutation. The absence of concordant variations for HH2 or BH1 suggests either the underlying causative mutations lie within a non-exomic region or in exome regions not covered by the capture array.

Lotus Dust Mitigation Coating and Molecular Adsorber Coating

Science.gov (United States)

O'Connor, Kenneth M.; Abraham, Nithin S.

2015-01-01

NASA Goddard Space Flight Center has developed two unique coating formulations that will keep surfaces clean and sanitary and contain contaminants.The Lotus Dust Mitigation Coating, modeled after the self-cleaning, water-repellant lotus leaf, disallows buildup of dust, dirt, water, and more on surfaces. This coating, has been successfully tested on painted, aluminum, glass, silica, and some composite surfaces, could aid in keeping medical assets clean.The Molecular Adsorber Coating is a zeolite-based, sprayable molecular adsorber coating, designed to prevent outgassing in materials in vacuums. The coating works well to adsorb volatiles and contaminates in manufacturing and processing, such as in pharmaceutical production. The addition of a biocide would also aid in controlling bacteria levels.

Whole-exome sequencing reveals genetic variants associated with chronic kidney disease characterized by tubulointerstitial damages in North Central Region, Sri Lanka.

Science.gov (United States)

Nanayakkara, Shanika; Senevirathna, S T M L D; Parahitiyawa, Nipuna B; Abeysekera, Tilak; Chandrajith, Rohana; Ratnatunga, Neelakanthi; Hitomi, Toshiaki; Kobayashi, Hatasu; Harada, Kouji H; Koizumi, Akio

2015-09-01

The familial clustering observed in chronic kidney disease of uncertain etiology (CKDu) characterized by tubulointerstitial damages in the North Central Region of Sri Lanka strongly suggests the involvement of genetic factors in its pathogenesis. The objective of the present study is to use whole-exome sequencing to identify the genetic variants associated with CKDu. Whole-exome sequencing of eight CKDu cases and eight controls was performed, followed by direct sequencing of candidate loci in 301 CKDu cases and 276 controls. Association study revealed rs34970857 (c.658G > A/p.V220M) located in the KCNA10 gene encoding a voltage-gated K channel as the most promising SNP with the highest odds ratio of 1.74. Four rare variants were identified in gene encoding Laminin beta2 (LAMB2) which is known to cause congenital nephrotic syndrome. Three out of four variants in LAMB2 were novel variants found exclusively in cases. Genetic investigations provide strong evidence on the presence of genetic susceptibility for CKDu. Possibility of presence of several rare variants associated with CKDu in this population is also suggested.

Optimization of High Porosity Thermal Barrier Coatings Generated with a Porosity Former

Science.gov (United States)

Medřický, Jan; Curry, Nicholas; Pala, Zdenek; Vilemova, Monika; Chraska, Tomas; Johansson, Jimmy; Markocsan, Nicolaie

2015-04-01

Yttria-stabilized zirconia thermal barrier coatings are extensively used in turbine industry; however, increasing performance requirements have begun to make conventional air plasma sprayed coatings insufficient for future needs. Since the thermal conductivity of bulk material cannot be lowered easily; the design of highly porous coatings may be the most efficient way to achieve coatings with low thermal conductivity. Thus the approach of fabrication of coatings with a high porosity level based on plasma spraying of ceramic particles of dysprosia-stabilized zirconia mixed with polymer particles, has been tested. Both polymer and ceramic particles melt in plasma and after impact onto a substrate they form a coating. When the coating is subjected to heat treatment, polymer burns out and a complex structure of pores and cracks is formed. In order to obtain desired porosity level and microstructural features in coatings; a design of experiments, based on changes in spray distance, powder feeding rate, and plasma-forming atmosphere, was performed. Acquired coatings were evaluated for thermal conductivity and thermo-cyclic fatigue, and their morphology was assessed using scanning electron microscopy. It was shown that porosity level can be controlled by appropriate changes in spraying parameters.

Combustion chemical vapor desposited coatings for thermal barrier coating systems

Energy Technology Data Exchange (ETDEWEB)

Hampikian, J.M.; Carter, W.B. [Georgia Institute of Technology, Atlanta, GA (United States)

1995-10-01

The new deposition process, combustion chemical vapor deposition, shows a great deal of promise in the area of thermal barrier coating systems. This technique produces dense, adherent coatings, and does not require a reaction chamber. Coatings can therefore be applied in the open atmosphere. The process is potentially suitable for producing high quality CVD coatings for use as interlayers between the bond coat and thermal barrier coating, and/or as overlayers, on top of thermal barrier coatings.

Antimicrobial peptide coatings for hydroxyapatite:Electrostatic and covalent attachment of antimicrobial peptides to surfaces

OpenAIRE

Townsend, Leigh; Williams, Richard L.; Anuforom, Olachi; Berwick, Matthew R.; Halstead, Fenella; Hughes, Erik; Stamboulis, Artemis; Oppenheim, Beryl; Gough, Julie; Grover, Liam; Scott, Robert A H; Webber, Mark; Peacock, Anna F A; Belli, Antonio; Logan, Ann

2017-01-01

The interface between implanted devices and their host tissue is complex and is often optimized for maximal integration and cell adhesion. However, this also gives a surface suitable for bacterial colonization. We have developed a novel method of modifying the surface at the material-tissue interface with an antimicrobial peptide (AMP) coating to allowcell attachment while inhibiting bacterial colonization. The technology reported here is a dual AMP coating. The dual coating consists ofAMPs c...

Design and optimization of coating structure for the thermal barrier coatings fabricated by atmospheric plasma spraying via finite element method

Directory of Open Access Journals (Sweden)

L. Wang

2014-06-01

Full Text Available The first prerequisite for fabricating the thermal barrier coatings (TBCs with excellent performance is to find an optimized coating structure with high thermal insulation effect and low residual stress. This paper discusses the design and optimization of a suitable coating structure for the TBCs prepared by atmospheric plasma spraying (APS using the finite element method. The design and optimization processes comply with the rules step by step, as the structure develops from a simple to a complex one. The research results indicate that the suitable thicknesses of the bond-coating and top-coating are 60–120 μm and 300–420 μm, respectively, for the single ceramic layer YSZ/NiCoCrAlY APS-TBC. The embedded interlayer (50 wt.%YSZ + 50 wt.%NiCoCrAlY will further reduce the residual stress without sacrificing the thermal insulation effect. The double ceramic layer was further considered which was based on the single ceramic layer TBC. The embedded interlayer and the upper additional ceramic layer will have a best match between the low residual stress and high thermal insulation effect. Finally, the optimized coating structure was obtained, i.e., the La2Ce2O7(LC/YSZ/Interlayer/NiCoCrAlY coating structure with appropriate layer thickness is the best choice. The effective thermal conductivity of this optimized LC/YSZ/IL/BL TBC is 13.2% lower than that of the typical single ceramic layer YSZ/BL TBC.

Tablet coating by injection molding technology - Optimization of coating formulation attributes and coating process parameters.

Science.gov (United States)

Desai, Parind M; Puri, Vibha; Brancazio, David; Halkude, Bhakti S; Hartman, Jeremy E; Wahane, Aniket V; Martinez, Alexander R; Jensen, Keith D; Harinath, Eranda; Braatz, Richard D; Chun, Jung-Hoon; Trout, Bernhardt L

2018-01-01

We developed and evaluated a solvent-free injection molding (IM) coating technology that could be suitable for continuous manufacturing via incorporation with IM tableting. Coating formulations (coating polymers and plasticizers) were prepared using hot-melt extrusion and screened via stress-strain analysis employing a universal testing machine. Selected coating formulations were studied for their melt flow characteristics. Tablets were coated using a vertical injection molding unit. Process parameters like softening temperature, injection pressure, and cooling temperature played a very important role in IM coating processing. IM coating employing polyethylene oxide (PEO) based formulations required sufficient room humidity (>30% RH) to avoid immediate cracks, whereas other formulations were insensitive to the room humidity. Tested formulations based on Eudrajit E PO and Kollicoat IR had unsuitable mechanical properties. Three coating formulations based on hydroxypropyl pea starch, PEO 1,000,000 and Opadry had favorable mechanical (35% elongation, >95×10 4 J/m 3 toughness) and melt flow (>0.4g/min) characteristics, that rendered acceptable IM coats. These three formulations increased the dissolution time by 10, 15 and 35min, respectively (75% drug release), compared to the uncoated tablets (15min). Coated tablets stored in several environmental conditions remained stable to cracking for the evaluated 8-week time period. Copyright © 2017 Elsevier B.V. All rights reserved.

SIGNIFICANCE OF TARGETED EXOME SEQUENCING AND METHODS OF DATA ANALYSIS IN THE DIAGNOSIS OF GENETIC DISORDERS LEADING TO THE DEVELOPMENT OF EPILEPTIC ENCEPHALOPATHY

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Tatyana Victorovna Kozhanova

2017-08-01

Full Text Available Epilepsy is the most common serious neurological disorder, and there is a genetic basis in almost 50% of people with epilepsy. The diagnosis of genetic epilepsies makes to estimate reasons of seizures in the patient. Last decade has shown tremendous growth in gene sequencing technologies, which have made genetic tests available. The aim is to show significance of targeted exome sequencing and methods of data analysis in the diagnosis of hereditary syndromes leading to the development of epileptic encephalopathy. We examined 27 patients with с early EE (resistant to antiepileptic drugs, psychomotor and speech development delay in the psycho-neurological department. Targeted exome sequencing was performed for patients without a previously identified molecular diagnosis using 454 Sequencing GS Junior sequencer (Roche and IlluminaNextSeq 500 platform. As a result of the analysis, specific epilepsy genetic variants were diagnosed in 27 patients. The greatest number of cases was due to mutations in the SCN1A gene (7/27. The structure of mutations for other genes (mutations with a minor allele frequency of less than 0,5% are presented: ALDH7A1 (n=1, CACNA1C (n=1, CDKL5 (n=1, CNTNAP2 (n=2, DLGAP2 (n=2, DOCK7 (n=2, GRIN2B (n=2, HCN1 (n=1, NRXN1 (n=3, PCDH19 (n=1, RNASEH2B (n=2, SLC2A1 (n=1, UBE3A (n=1. The use of the exome sequencing in the genetic practice allows to significantly improve the effectiveness of medical genetic counseling, as it made possible to diagnose certain variants of genetically heterogeneous groups of diseases with similar of clinical manifestations.

Interactions between the glass fiber coating and oxidized carbon nanotubes

Energy Technology Data Exchange (ETDEWEB)

Ku-Herrera, J.J., E-mail: jesuskuh@live.com.mx [Centro de Investigación Científica de Yucatán A.C., Unidad de Materiales, Calle 43 No.130, Col. Chuburná de Hidalgo. C.P., 97200 Mérida, Yucatán (Mexico); Avilés, F., E-mail: faviles@cicy.mx [Centro de Investigación Científica de Yucatán A.C., Unidad de Materiales, Calle 43 No.130, Col. Chuburná de Hidalgo. C.P., 97200 Mérida, Yucatán (Mexico); Nistal, A. [Instituto de Cerámica y Vidrio (ICV-CSIC), Kelsen 5, 28049 Madrid (Spain); Cauich-Rodríguez, J.V. [Centro de Investigación Científica de Yucatán A.C., Unidad de Materiales, Calle 43 No.130, Col. Chuburná de Hidalgo. C.P., 97200 Mérida, Yucatán (Mexico); Rubio, F.; Rubio, J. [Instituto de Cerámica y Vidrio (ICV-CSIC), Kelsen 5, 28049 Madrid (Spain); Bartolo-Pérez, P. [Departamento de Física Aplicada, Cinvestav, Unidad Mérida, C.P., 97310 Mérida, Yucatán (Mexico)

2015-03-01

Graphical abstract: - Highlights: • Oxidized multiwall carbon nanotubes (MWCNTs) were deposited onto E-glass fibers. • The role of the fiber coating on the deposition of MWCNTs on the fibers is studied. • A rather homogeneous deposition of MWCNTs is achieved if the coating is maintained. • Multiple oxygen-containing groups were found in the analysis of the fiber coating. • Evidence of chemical interaction between MWCNTs and the fiber coating was found. - Abstract: Chemically oxidized multiwall carbon nanotubes (MWCNTs) were deposited onto commercial E-glass fibers using a dipping procedure assisted by ultrasonic dispersion. In order to investigate the role of the fiber coating (known as “sizing”), MWCNTs were deposited on the surface of as-received E-glass fibers preserving the proprietary coating as well as onto glass fibers which had the coating deliberately removed. Scanning electron microscopy and Raman spectroscopy were used to assess the distribution of MWCNTs onto the fibers. A rather homogeneous coverage with high density of MWCNTs onto the glass fibers is achieved when the fiber coating is maintained. Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and nuclear magnetic resonance (NMR) analyses of the chemical composition of the glass fiber coating suggest that such coating is a complex mixture with multiple oxygen-containing functional groups such as hydroxyl, carbonyl and epoxy. FTIR and XPS of MWCNTs over the glass fibers and of a mixture of MWCNTs and fiber coating provided evidence that the hydroxyl and carboxyl groups of the oxidized MWCNTs react with the oxygen-containing functional groups of the glass fiber coating, forming hydrogen bonding and through epoxy ring opening. Hydrogen bonding and ester formation between the functional groups of the MWCNTs and the silane contained in the coating are also possible.

Interactions between the glass fiber coating and oxidized carbon nanotubes

International Nuclear Information System (INIS)

Ku-Herrera, J.J.; Avilés, F.; Nistal, A.; Cauich-Rodríguez, J.V.; Rubio, F.; Rubio, J.; Bartolo-Pérez, P.

2015-01-01

Graphical abstract: - Highlights: • Oxidized multiwall carbon nanotubes (MWCNTs) were deposited onto E-glass fibers. • The role of the fiber coating on the deposition of MWCNTs on the fibers is studied. • A rather homogeneous deposition of MWCNTs is achieved if the coating is maintained. • Multiple oxygen-containing groups were found in the analysis of the fiber coating. • Evidence of chemical interaction between MWCNTs and the fiber coating was found. - Abstract: Chemically oxidized multiwall carbon nanotubes (MWCNTs) were deposited onto commercial E-glass fibers using a dipping procedure assisted by ultrasonic dispersion. In order to investigate the role of the fiber coating (known as “sizing”), MWCNTs were deposited on the surface of as-received E-glass fibers preserving the proprietary coating as well as onto glass fibers which had the coating deliberately removed. Scanning electron microscopy and Raman spectroscopy were used to assess the distribution of MWCNTs onto the fibers. A rather homogeneous coverage with high density of MWCNTs onto the glass fibers is achieved when the fiber coating is maintained. Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and nuclear magnetic resonance (NMR) analyses of the chemical composition of the glass fiber coating suggest that such coating is a complex mixture with multiple oxygen-containing functional groups such as hydroxyl, carbonyl and epoxy. FTIR and XPS of MWCNTs over the glass fibers and of a mixture of MWCNTs and fiber coating provided evidence that the hydroxyl and carboxyl groups of the oxidized MWCNTs react with the oxygen-containing functional groups of the glass fiber coating, forming hydrogen bonding and through epoxy ring opening. Hydrogen bonding and ester formation between the functional groups of the MWCNTs and the silane contained in the coating are also possible

Effect of SnO2/SiO2 nano particle dispersant on the performance characteristic of complex multi-doped composite coating produced through electrodeposition on oil and gas storage tap

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P.A.L. Anawe

2018-06-01

Full Text Available The effect of SnO2/SiO2 nano particle dispersant on the performance characteristic of complex zinc multi-doped composite coating produced through electrodeposition is studied. The degradation behaviour in term of wear and chemical corrosion activities were considered as a major factor in service. The wear mass loss was carried out with the help of reciprocating tester. The electrochemical corrosion characteristics were investigated using linear polarization technique in 3.5% simulated sodium chloride media. The outcome of the analysis shows that the developed coating was seen to provide a sound anti wear characteristics in its multidoped state. The corrosion resistance properties were observed to be massive compared to the binary based sample. It is expected that this characteristic will impact on the performance life span of storage tap in oil and gas. Keywords: Zn-SnO2-SiO2, Nanocomposite, Electrodeposition, Coatings and corrosion resistance

Contribution of coated humic acids calculated through their surface coverage on nano iron oxides for ofloxacin and norfloxacin sorption.

Science.gov (United States)

Peng, Hongbo; Liang, Ni; Li, Hao; Chen, Fangyuan; Zhang, Di; Pan, Bo; Xing, Baoshan

2015-09-01

Sorption of organic contaminants on organo-mineral complexes has been investigated extensively, but the sorption contribution of mineral particles was not properly addressed before calculating KOC, especially for ionic organic contaminants. We measured the surface coverage of a humic acid (HA) on nano iron oxides (n-Fe2O3) in a series of synthesized organo-mineral complexes. The contribution of the coated HA to ofloxacin (OFL) and norfloxacin (NOR) sorption in HA-n-Fe2O3 complexes was over 80% of the total sorption with the surface coverage of 36% and fOC of 1.6%. All the coated HA showed higher sorption to NOR and OFL in comparison to the original HA, suggesting HA fractionation and/or physical re-conformation during organo-mineral complex formation. The decreased KOC with multilayer coating may suggest the importance of site-specific interactions for OFL sorption, while the increased KOC with multilayer coating may suggest the importance of partitioning in hydrophobic region for NOR sorption. Copyright © 2015 Elsevier Ltd. All rights reserved.

Coating of the orthopaedic titanium alloys with sol-gel derived hydroxyapatite

International Nuclear Information System (INIS)

Milev, A.; Green, D.; Chai, C.S.; Ben-Nissan, B.

1999-01-01

Hydroxyapatite (HAp) is known to be both biocompatible and bioactive material, however, due to its poor mechanical properties and design limitations is not suitable for applying as a load bearing implant. This could be overcome by using appropriate metallic substrates covered with HAp, derived via different techniques. These coatings allow improved adhesion strength of the load bearing substrate to the bone, resulting in shorter healing periods as well as predictable behaviour of the implant for longer periods of time. There are different techniques of producing HAp appropriate for coating purposes. Due to the small particle size of the grains derived, sol-gel route is preferable where lower sintering temperatures are of primary importance. For better adhesion between substrate and hydroxyapatite coating, the surface of titanium substrate, in this study, was converted to titanium nitride and/or oxynitride. Sintering temperatures of 900 deg C have been used for producing crystalline HAp coatings. The control of sol-gel solutions and the analysis of the coatings were carried out using XRD, SEM and DTA techniques. Results obtained indicate high quality HAp coatings can be produced on titanium substrates especially with complex shapes that benefits over the other coating methods

Joint linkage and association analysis with exome sequence data implicates SLC25A40 in hypertriglyceridemia.

Science.gov (United States)

Rosenthal, Elisabeth A; Ranchalis, Jane; Crosslin, David R; Burt, Amber; Brunzell, John D; Motulsky, Arno G; Nickerson, Deborah A; Wijsman, Ellen M; Jarvik, Gail P

2013-12-05

Hypertriglyceridemia (HTG) is a heritable risk factor for cardiovascular disease. Investigating the genetics of HTG may identify new drug targets. There are ~35 known single-nucleotide variants (SNVs) that explain only ~10% of variation in triglyceride (TG) level. Because of the genetic heterogeneity of HTG, a family study design is optimal for identification of rare genetic variants with large effect size because the same mutation can be observed in many relatives and cosegregation with TG can be tested. We considered HTG in a five-generation family of European American descent (n = 121), ascertained for familial combined hyperlipidemia. By using Bayesian Markov chain Monte Carlo joint oligogenic linkage and association analysis, we detected linkage to chromosomes 7 and 17. Whole-exome sequence data revealed shared, highly conserved, private missense SNVs in both SLC25A40 on chr7 and PLD2 on chr17. Jointly, these SNVs explained 49% of the genetic variance in TG; however, only the SLC25A40 SNV was significantly associated with TG (p = 0.0001). This SNV, c.374A>G, causes a highly disruptive p.Tyr125Cys substitution just outside the second helical transmembrane region of the SLC25A40 inner mitochondrial membrane transport protein. Whole-gene testing in subjects from the Exome Sequencing Project confirmed the association between TG and SLC25A40 rare, highly conserved, coding variants (p = 0.03). These results suggest a previously undescribed pathway for HTG and illustrate the power of large pedigrees in the search for rare, causal variants. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Coated kapok fiber for removal of spilled oil

International Nuclear Information System (INIS)

Wang, Jintao; Zheng, Yian; Wang, Aiqin

2013-01-01

Highlights: ► A low-cost and biodegradable oil absorbent based on kapok fiber was prepared. ► The polymer-coated kapok fiber showed higher oil sorption capacity. ► Coated kapok fiber can be reused and the absorbed oil can be easily recovered. ► Adsorption of oil is spontaneous and exothermic physisorption and chemisorption. -- Abstract: Based on raw kapok fiber, two kinds of oil absorbers with high sorption capacity were prepared by a facile solution–immersion process. The coated polymer with low surface energy and rough fiber surface play important role in the retention of oil. The as-prepared fiber can quickly absorb gasoline, diesel, soybean oil, and paraffin oil up to above 74.5%, 66.8%, 64.4% and 47.8% of oil sorption capacity of raw fiber, respectively. The absorbed oils can be easily recovered by a simple vacuum filtration and the recovered coated-fiber still can be used for several cycles without obvious loss in oil sorption capacity. The thermodynamic study indicates that the adsorption process is spontaneous and exothermic, with complex physisorption and chemisorption. The results suggest that the coated fiber can be used as a low-cost alternative for the removal of oil spilled on water surface

High-Melt Carbon-Carbon Coating for Nozzle Extensions

Science.gov (United States)

Thompson, James

2015-01-01

Carbon-Carbon Advanced Technologies, Inc. (C-CAT), has developed a high-melt coating for use in nozzle extensions in next-generation spacecraft. The coating is composed primarily of carbon-carbon, a carbon-fiber and carbon-matrix composite material that has gained a spaceworthy reputation due to its ability to withstand ultrahigh temperatures. C-CAT's high-melt coating embeds hafnium carbide (HfC) and zirconium diboride (ZrB2) within the outer layers of a carbon-carbon structure. The coating demonstrated enhanced high-temperature durability and suffered no erosion during a test in NASA's Arc Jet Complex. (Test parameters: stagnation heat flux=198 BTD/sq ft-sec; pressure=.265 atm; temperature=3,100 F; four cycles totaling 28 minutes) In Phase I of the project, C-CAT successfully demonstrated large-scale manufacturability with a 40-inch cylinder representing the end of a nozzle extension and a 16-inch flanged cylinder representing the attach flange of a nozzle extension. These demonstrators were manufactured without spalling or delaminations. In Phase II, C-CAT worked with engine designers to develop a nozzle extension stub skirt interfaced with an Aerojet Rocketdyne RL10 engine. All objectives for Phase II were successfully met. Additional nonengine applications for the coating include thermal protection systems (TPS) for next-generation spacecraft and hypersonic aircraft.

Preparation of the antithrombotic and antimicrobial coating through layer-by-layer self-assembly of nattokinase-nanosilver complex and polyethylenimine.

Science.gov (United States)

Wei, Xuetuan; Luo, Mingfang; Liu, Huizhou

2014-04-01

The bifunctional coating with antithrombotic and antimicrobial activity was developed using nattokinase (NK) and nanosilver (AgNPs). Firstly, the adsorption interactions between NK and AgNPs were confirmed, and the composite particles of NK-AgNPs were prepared by adsorption of NK with AgNPs. At 5FU/mL of NK concentration, the saturation adsorption capacity reached 24.35 FU/mg AgNPs with a high activity recovery of 97%, and adsorption by AgNPs also enhanced the heat stability and anticoagulant effect of NK. Based on the electrostatic force driven layer-by-layer self-assembly, the NK-AgNPs were further assembled with polyethylenimine (PEI) to form coating. UV-vis analysis showed that the self-assembly process was regular, and atom force microscopy analysis indicated that NK-AgNPs were uniformly embedded into the coating. The NK-AgNPs-PEI composite coating showed potent antithrombotic activity and antibacterial activity. This study developed a novel strategy to construct the bifunctional coating with antithrombotic and antimicrobial properties, and the coating material showed promising potential to be applied in the medical device. Copyright © 2014 Elsevier B.V. All rights reserved.

Ion-exchange voltammetry of tris(2,2'-bipyridine) nickel(II), cobalt(II), and Co(salen) at polyestersulfonated ionomer coated electrodes in acetonitrile: Reactivity of the electrogenerated low-valent complexes

International Nuclear Information System (INIS)

Buriez, Olivier; Moretto, Ligia M.; Ugo, Paolo

2006-01-01

The electrochemical behaviour of [Ni(bpy) 3 (BF 4 ) 2 ], [Co(bpy) 3 (BF 4 ) 2 ], and Co(salen) (where bpy = 2,2'-bipyridine, and salen N,N'-bis(salicylidene)ethylenediamine) is studied at a glassy carbon electrode modified with the poly(estersulfonate) ionomer Eastman AQ 55 in acetonitrile (MeCN). It is shown that the nickel complex is strongly incorporated into the polymer. The reduction of the divalent nickel compound features a two-electron process leading to a nickel(0) species which is released from the coating because of the lack of electrostatic attraction with the ionomer. Yet, the neutral zerovalent nickel-bipyridine complex is reactive towards ethyl 4-iodobenzoate and di-bromocyclohexane despite the presence of the polymer. The activation of the aryl halide occurs through an oxidative addition, whereas, an electron transfer is involved in the presence of the alkyl halide making the catalyst regeneration much faster in the latter case. The electrochemical study of [Co(bpy) 3 (BF 4 ) 2 ] shows that incorporation of the cobalt complex into the polymer is efficient, provided excess bpy is used. This excess bpy does not interfere with the electrocatalytic activity of the cobalt complex incorporated in the AQ coating and efficient electrocatalysis is observed towards di-bromocyclohexane and benzyl-bromide as substrates. Finally, replacement of the bpy ligand with the macrocycle N,N'-bis(salicylidene)ethylenediamine, salen, leads to the incorporation of the non-charged Co II (salen) complex into the AQ 55 polymer showing the relevancy of hydrophobic interactions. The reaction between the electrogenerated [Co I (salen)] - with 1,2-dibromocyclohexane exhibits a fast inner sphere electron transfer

Exome sequencing finds a novel PCSK1 mutation in a child with generalized malabsorptive diarrhea and diabetes insipidus.

Science.gov (United States)

Yourshaw, Michael; Solorzano-Vargas, R Sergio; Pickett, Lindsay A; Lindberg, Iris; Wang, Jiafang; Cortina, Galen; Pawlikowska-Haddal, Anna; Baron, Howard; Venick, Robert S; Nelson, Stanley F; Martín, Martín G

2013-12-01

Congenital diarrhea disorders are a group of genetically diverse and typically autosomal recessive disorders that have yet to be well characterized phenotypically or molecularly. Diagnostic assessments are generally limited to nutritional challenges and histologic evaluation, and many subjects eventually require a prolonged course of intravenous nutrition. Here we describe next-generation sequencing techniques to investigate a child with perplexing congenital malabsorptive diarrhea and other presumably unrelated clinical problems; this method provides an alternative approach to molecular diagnosis. We screened the diploid genome of an affected individual, using exome sequencing, for uncommon variants that have observed protein-coding consequences. We assessed the functional activity of the mutant protein, as well as its lack of expression using immunohistochemistry. Among several rare variants detected was a homozygous nonsense mutation in the catalytic domain of the proprotein convertase subtilisin/kexin type 1 gene. The mutation abolishes prohormone convertase 1/3 endoprotease activity as well as expression in the intestine. These primary genetic findings prompted a careful endocrine reevaluation of the child at 4.5 years of age, and multiple significant problems were subsequently identified consistent with the known phenotypic consequences of proprotein convertase subtilisin/kexin type 1 (PCSK1) gene mutations. Based on the molecular diagnosis, alternate medical and dietary management was implemented for diabetes insipidus, polyphagia, and micropenis. Whole-exome sequencing provides a powerful diagnostic tool to clinicians managing rare genetic disorders with multiple perplexing clinical manifestations.

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data.

Directory of Open Access Journals (Sweden)

Anne Bruun Krøigård

Full Text Available Next generation sequencing is extensively applied to catalogue somatic mutations in cancer, in research settings and increasingly in clinical settings for molecular diagnostics, guiding therapy decisions. Somatic variant callers perform paired comparisons of sequencing data from cancer tissue and matched normal tissue in order to detect somatic mutations. The advent of many new somatic variant callers creates a need for comparison and validation of the tools, as no de facto standard for detection of somatic mutations exists and only limited comparisons have been reported. We have performed a comprehensive evaluation using exome sequencing and targeted deep sequencing data of paired tumor-normal samples from five breast cancer patients to evaluate the performance of nine publicly available somatic variant callers: EBCall, Mutect, Seurat, Shimmer, Indelocator, Somatic Sniper, Strelka, VarScan 2 and Virmid for the detection of single nucleotide mutations and small deletions and insertions. We report a large variation in the number of calls from the nine somatic variant callers on the same sequencing data and highly variable agreement. Sequencing depth had markedly diverse impact on individual callers, as for some callers, increased sequencing depth highly improved sensitivity. For SNV calling, we report EBCall, Mutect, Virmid and Strelka to be the most reliable somatic variant callers for both exome sequencing and targeted deep sequencing. For indel calling, EBCall is superior due to high sensitivity and robustness to changes in sequencing depths.

A review of hydroxyapatite-based coating techniques: Sol-gel and electrochemical depositions on biocompatible metals.

Science.gov (United States)

Asri, R I M; Harun, W S W; Hassan, M A; Ghani, S A C; Buyong, Z

2016-04-01

New promising techniques for depositing biocompatible hydroxyapatite-based coatings on biocompatible metal substrates for biomedical applications have continuously been exploited for more than two decades. Currently, various experimental deposition processes have been employed. In this review, the two most frequently used deposition processes will be discussed: a sol-gel dip coating and an electrochemical deposition. This study deliberates the surface morphologies and chemical composition, mechanical performance and biological responses of sol-gel dip coating as well as the electrochemical deposition for two different sample conditions, with and without coating. The review shows that sol-gel dip coatings and electrochemical deposition were able to obtain the uniform and homogeneous coating thickness and high adherent biocompatible coatings even in complex shapes. It has been accepted that both coating techniques improve bone strength and initial osseointegration rate. The main advantages and limitations of those techniques of hydroxyapatite-based coatings are presented. Furthermore, the most significant challenges and critical issues are also highlighted. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evolution of egg coats: linking molecular biology and ecology.

Science.gov (United States)

Shu, Longfei; Suter, Marc J-F; Räsänen, Katja

2015-08-01

One central goal of evolutionary biology is to explain how biological diversity emerges and is maintained in nature. Given the complexity of the phenotype and the multifaceted nature of inheritance, modern evolutionary ecological studies rely heavily on the use of molecular tools. Here, we show how molecular tools help to gain insight into the role of egg coats (i.e. the extracellular structures surrounding eggs and embryos) in evolutionary diversification. Egg coats are maternally derived structures that have many biological functions from mediating fertilization to protecting the embryo from environmental hazards. They show great molecular, structural and functional diversity across species, but intraspecific variability and the role of ecology in egg coat evolution have largely been overlooked. Given that much of the variation that influences egg coat function is ultimately determined by their molecular phenotype, cutting-edge molecular tools (e.g. proteomics, glycomics and transcriptomics), combined with functional assays, are needed for rigorous inferences on their evolutionary ecology. Here, we identify key research areas and highlight emerging molecular techniques that can increase our understanding of the role of egg coats in the evolution of biological diversity, from adaptation to speciation. © 2015 John Wiley & Sons Ltd.

A novel ANO3 variant identified in a 53-year-old woman presenting with hyperkinetic dysarthria, blepharospasm, hyperkinesias, and complex motor tics.

Science.gov (United States)

Blackburn, Patrick R; Zimmermann, Michael T; Gass, Jennifer M; Harris, Kimberly G; Cousin, Margot A; Boczek, Nicole J; Ross, Owen A; Klee, Eric W; Brazis, Paul W; Van Gerpen, Jay A; Atwal, Paldeep S

2016-12-05

Cervical dystonias have a variable presentation and underlying etiology, but collectively represent the most common form of focal dystonia. There are a number of known genetic forms of dystonia (DYT1-27); however the heterogeneity of disease presentation does not always make it easy to categorize the disease by phenotype-genotype comparison. In this report, we describe a 53-year-old female who presented initially with hand tremor following a total hip arthroplasty. The patient developed a mixed hyperkinetic disorder consisting of chorea, dystonia affecting the upper extremities, dysarthria, and blepharospasm. Whole exome sequencing of the patient revealed a novel heterozygous missense variant (Chr11(GRCh38): g.26525644C > G; NM_031418.2(ANO3): c.702C > G; NP_113606.2. p.C234W) in exon 7 in the ANO3 gene. ANO3 encodes anoctamin-3, a Ca +2 -dependent phospholipid scramblase expressed in striatal-neurons, that has been implicated in autosomal dominant craniocervical dystonia (Dystonia-24, DYT24, MIM# 615034). To date, only a handful of cases of DYT-24 have been described in the literature. The complex clinical presentation of the patient described includes hyperkinesias, complex motor movements, and vocal tics, which have not been reported in other patients with DYT24. This report highlights the utility of using clinical whole exome sequencing in patients with complex neurological phenotypes that would not normally fit a classical presentation of a defined genetic disease.

Cr-Ni ALLOY ELECTRODEPOSITION AND COMPARISON WITH CONVENTIONAL PURE Cr COATING TECHNIQUE

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M. Moniruzzaman

2012-12-01

Full Text Available Cr coating is widely used as the outer surface of precision parts due to its attractive appearance and superior corrosion resistance properties. It is obtained by electrodeposition via a conventional bath with hexavalent Cr ions. This manufacturing technique has many drawbacks, such as very low efficiency and high operating temperature and it is hazardous to health. In this work, we studied a Cr-Ni alloy deposition technique and compared the alloy coating properties to those with conventional Cr coating. Sequential two-step alloy electrodeposition was also compared. We took varying concentrations of Cr, Ni and complexing agents for the electrodeposition of Cr-Ni alloy and sequential Cr-Ni alloy coating on mild steel. Operating parameters, i.e. current density and temperature, were varied to examine their effects on the coating properties. The coatings thus obtained were characterized by visual observation, corrosion test, microhardness measurement, morphology and chemical analysis. The Cr-Ni alloy coating was found to be more corrosion resistant in 5% NaCl solution and harder than the pure Cr coating obtained by conventional electrodeposition. Toxic gas was produced in a much lower extent in the alloy coating than the conventional Cr coating technique. Again, the two-step Cr-Ni alloy coating was found better in terms of corrosion resistance as well as hardness compared to the Cr-Ni alloy coating. The process was also found to be much more environmentally friendly.

High quality aluminide and thermal barrier coatings deposition for new and service exposed parts by CVD techniques

Energy Technology Data Exchange (ETDEWEB)

Pedraza, F.; Tuohy, C.; Whelan, L.; Kennedy, A.D. [SIFCO Turbine Components, Carrigtwohill, Cork (Ireland)

2004-07-01

In this work, the performance of CVD aluminide coatings is compared to that of coatings deposited by the classical pack cementation technique using standard SIFCO procedures. The CVD coatings always seem to behave better upon exposure to isothermal and cyclic oxidation conditions. This is explained by a longer term stability of CVD coatings, with higher Al amounts in the diffusion zone and less refractory element precipitation in the additive layer. The qualities of Pt/Al coatings by out-of-pack and CVD are also compared as a previous step for further thermal barrier coating deposition. As an example, YSZ thermal barrier coatings are deposited by MO-CVD on Pt/Al CVD bond coats rendering adherent and thick coatings around the surface of turbine blades. This process under development does not require complex manipulation of the component to be coated. (orig.)

A simple, high-yield, apparatus for NEG coating of vacuum beamline elements

International Nuclear Information System (INIS)

Ron, G; Oort, R; Lee, D

2010-01-01

Non-Evaporable Getter (NEG) materials are extremely useful in vacuum systems for achieving Ultra High Vacuum. Recently, these materials have been used to coat the inner surfaces of vacuum components, acting as an internal, passive, vacuum pump. We have constructed a low cost apparatus, which allows coating of very small diameter vacuum tubes, used as differential pumping stages. Despite the relative ease of construction, we are routinely able to achieve high coating yields. We further describe an improvement to our system, which is able to achieve the same yield, at an even lower complexity by using an easily manufactured permanent magnet arrangement. The designs described are extendible to virtually any combination of length and diameter of the components to be coated.

Control of surface topography in biomimetic calcium phosphate coatings.

Science.gov (United States)

Costa, Daniel O; Allo, Bedilu A; Klassen, Robert; Hutter, Jeffrey L; Dixon, S Jeffrey; Rizkalla, Amin S

2012-02-28

The behavior of cells responsible for bone formation, osseointegration, and bone bonding in vivo are governed by both the surface chemistry and topography of scaffold matrices. Bone-like apatite coatings represent a promising method to improve the osteoconductivity and bonding of synthetic scaffold materials to mineralized tissues for regenerative procedures in orthopedics and dentistry. Polycaprolactone (PCL) films were coated with calcium phosphates (CaP) by incubation in simulated body fluid (SBF). We investigated the effect of SBF ion concentration and soaking time on the surface properties of the resulting apatite coatings. CaP coatings were examined by scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectrometry (FTIR), and energy dispersive X-ray spectrometry (EDX). Young's modulus (E(s)) was determined by nanoindentation, and surface roughness was assessed by atomic force microscopy (AFM) and mechanical stylus profilometry. CaP such as carbonate-substituted apatite were deposited onto PCL films. SEM and AFM images of the apatite coatings revealed an increase in topographical complexity and surface roughness with increasing ion concentration of SBF solutions. Young's moduli (E(s)) of various CaP coatings were not significantly different, regardless of the CaP phase or surface roughness. Thus, SBF with high ion concentrations may be used to coat synthetic polymers with CaP layers of different surface topography and roughness to improve the osteoconductivity and bone-bonding ability of the scaffold. © 2012 American Chemical Society

Correlation of optical properties with the fractal microstructure of black molybdenum coatings

Energy Technology Data Exchange (ETDEWEB)

Barrera, Enrique; Gonzalez, Federico [Area de Energia, Division de Ciencias Basicas e Ingenieria, Universidad Autonoma Metropolitana-Iztapalapa, Apartado Postal 55-534, Mexico, D.F. 09340 (Mexico); Rodriguez, Eduardo [Area de Computacion y Sistemas, Division de Ciencias Basicas e Ingenieria, Universidad Autonoma Metropolitana-Iztapalapa, Apartado Postal 55-534, Mexico, D.F. 09340 (Mexico); Alvarez-Ramirez, Jose, E-mail: jjar@xanum.uam.mx [Area de Energia, Division de Ciencias Basicas e Ingenieria, Universidad Autonoma Metropolitana-Iztapalapa, Apartado Postal 55-534, Mexico, D.F. 09340 (Mexico)

2010-01-01

Coating is commonly used for improving the optical properties of surfaces for solar collector applications. The coating morphology depends on the deposition conditions, and this determines the final optical characteristics. Coating morphologies are irregular and of fractal nature, so a suitable approach for its characterization should use methods borrowed from fractal analysis. The aim of this work is to study the fractal characteristics of black molybdenum coatings on copper and to relate the fractal parameters to the optical properties. To this end, coating surfaces were prepared via immersion in a solution of ammonium paramolybdate for different deposition periods. The fractal analysis was carried out for SEM and AFM images of the coating surface and the fractal properties were obtained with a recently developed high-dimensional extension of the well-known detrended fluctuation analysis (DFA). The most salient parameter drawn from the application of the DFA is the Hurst index, a parameter related to the roughness of the coating surface, and the multifractality index, which is related to the non-linearity features of the coating morphology. The results showed that optical properties, including absorptance and emittance, are decreasing functions of the Hurst and multifractality indices. This suggests that coating surfaces with high absorptance and emittance values are related to complex coating morphologies conformed within a non-linear structure.

Pixelated coatings and advanced IR coatings

Science.gov (United States)

Pradal, Fabien; Portier, Benjamin; Oussalah, Meihdi; Leplan, Hervé

2017-09-01

Reosc developed pixelated infrared coatings on detector. Reosc manufactured thick pixelated multilayer stacks on IR-focal plane arrays for bi-spectral imaging systems, demonstrating high filter performance, low crosstalk, and no deterioration of the device sensitivities. More recently, a 5-pixel filter matrix was designed and fabricated. Recent developments in pixelated coatings, shows that high performance infrared filters can be coated directly on detector for multispectral imaging. Next generation space instrument can benefit from this technology to reduce their weight and consumptions.

Multifunctional methacrylate-based coatings for glass and metal surfaces

Energy Technology Data Exchange (ETDEWEB)

Pospiech, Doris, E-mail: pospiech@ipfdd.de [Leibniz-Institut für Polymerforschung Dresden e. V., Dresden (Germany); Jehnichen, Dieter [Leibniz-Institut für Polymerforschung Dresden e. V., Dresden (Germany); Starke, Sandra; Müller, Felix [Leibniz-Institut für Polymerforschung Dresden e. V., Dresden (Germany); Technische Universität Dresden, Organic Chemistry of Polymers, Dresden (Germany); Bünker, Tobias [Leibniz-Institut für Polymerforschung Dresden e. V., Dresden (Germany); Wollenberg, Anne [Leibniz-Institut für Polymerforschung Dresden e. V., Dresden (Germany); Technische Universität Dresden, Organic Chemistry of Polymers, Dresden (Germany); Häußler, Liane; Simon, Frank; Grundke, Karina; Oertel, Ulrich [Leibniz-Institut für Polymerforschung Dresden e. V., Dresden (Germany); Opitz, Michael; Kruspe, Rainer [IDUS Biologisch Analytisches Umweltlabor GmbH, Ottendorf-Okrilla (Germany)

2017-03-31

Highlights: • New methacrylate-based copolymers synthesized by free radical polymerization. • Comonomer AAMA was able to complex Cu (II) ions in solvent annealing procedure. • Coatings had efficient anti-biofouling efficacy. - Abstract: In order to prevent freshwater biofouling glass and metal surfaces were coated with novel transparent methacrylate-based copolymers. The multifunctionality of the copolymers, such as adhesion to the substrate, surface polarity, mechanical long-term stability in water, and ability to form metal complexes was inserted by the choice of suitable comonomers. The monomer 2-acetoacetoxy ethyl methacrylate (AAMA) was used as complexing unit to produce copper(II) complexes in the coating’s upper surface layer. The semifluorinated monomer 1H,1H,2H,2H-perfluorodecyl methacrylate was employed to adjust the surface polarity and wettability. Comprehensive surface characterization techniques, such as X-ray photoelectron spectroscopy (XPS) and contact angle measurements showed that surface compositions and properties can be easily adjusted by varying the concentrations of the comonomers. The formation of copper(II) complexes along the copolymer chains and their stability against washing out with plenty of water was proven by XPS. Copolymers containing semifluorinated comonomers significantly inhibited the growth of Achnanthidium species. Copolymers with copper-loaded AAMA-sequences were able to reduce both the growth of Achnanthidium spec. and Staphylococcus aureus.

Multifunctional methacrylate-based coatings for glass and metal surfaces

International Nuclear Information System (INIS)

Pospiech, Doris; Jehnichen, Dieter; Starke, Sandra; Müller, Felix; Bünker, Tobias; Wollenberg, Anne; Häußler, Liane; Simon, Frank; Grundke, Karina; Oertel, Ulrich; Opitz, Michael; Kruspe, Rainer

2017-01-01

Highlights: • New methacrylate-based copolymers synthesized by free radical polymerization. • Comonomer AAMA was able to complex Cu (II) ions in solvent annealing procedure. • Coatings had efficient anti-biofouling efficacy. - Abstract: In order to prevent freshwater biofouling glass and metal surfaces were coated with novel transparent methacrylate-based copolymers. The multifunctionality of the copolymers, such as adhesion to the substrate, surface polarity, mechanical long-term stability in water, and ability to form metal complexes was inserted by the choice of suitable comonomers. The monomer 2-acetoacetoxy ethyl methacrylate (AAMA) was used as complexing unit to produce copper(II) complexes in the coating’s upper surface layer. The semifluorinated monomer 1H,1H,2H,2H-perfluorodecyl methacrylate was employed to adjust the surface polarity and wettability. Comprehensive surface characterization techniques, such as X-ray photoelectron spectroscopy (XPS) and contact angle measurements showed that surface compositions and properties can be easily adjusted by varying the concentrations of the comonomers. The formation of copper(II) complexes along the copolymer chains and their stability against washing out with plenty of water was proven by XPS. Copolymers containing semifluorinated comonomers significantly inhibited the growth of Achnanthidium species. Copolymers with copper-loaded AAMA-sequences were able to reduce both the growth of Achnanthidium spec. and Staphylococcus aureus.

A multi-step approach for testing non-toxic amphiphilic antifouling coatings against marine microfouling at different levels of biological complexity.

Science.gov (United States)

Zecher, Karsten; Aitha, Vishwa Prasad; Heuer, Kirsten; Ahlers, Herbert; Roland, Katrin; Fiedel, Michael; Philipp, Bodo

2018-03-01

Marine biofouling on artificial surfaces such as ship hulls or fish farming nets causes enormous economic damage. The time for the developmental process of antifouling coatings can be shortened by reliable laboratory assays. For designing such test systems, it is important that toxic effects can be excluded, that multiple parameters can be addressed simultaneously and that mechanistic aspects can be included. In this study, a multi-step approach for testing antifouling coatings was established employing photoautotrophic biofilm formation of marine microorganisms in micro- and mesoscoms. Degree and pattern of biofilm formation was determined by quantification of chlorophyll fluorescence. For the microcosms, co-cultures of diatoms and a heterotrophic bacterium were exposed to fouling-release coatings. For the mesocosms, a novel device was developed that permits parallel quantification of a multitude of coatings under defined conditions with varying degrees of shear stress. Additionally, the antifouling coatings were tested for leaching of potential compounds and finally tested in sea trials. This multistep-approach revealed that the individual steps led to consistent results regarding antifouling activity of the coatings. Furthermore, the novel mesocosm system can be employed for advanced antifouling analysis including metagenomic approaches for determination of microbial diversity attaching to different coatings under changing shear forces. Copyright © 2018 Elsevier B.V. All rights reserved.

Whole-exome sequencing reveals a recurrent mutation in the cathepsin C gene that causes Papillon–Lefevre syndrome in a Saudi family

Directory of Open Access Journals (Sweden)

Yaser Mohammad Alkhiary

2016-09-01

Full Text Available Papillon–Lefevre syndrome (PALS is a rare, autosomal recessive disorder characterized by periodontitis and hyperkeratosis over the palms and soles. Mutations in the cathepsin C gene (CTSC have been recognized as the cause of PALS since the late 1990s. More than 75 mutations in CTSC have been identified, and phenotypic variability between different mutations has been described. Next generation sequencing is widely used for efficient molecular diagnostics in various clinical practices. Here we investigated a large consanguineous Saudi family with four affected and four unaffected individuals. All of the affected individuals suffered from hyperkeratosis over the palms and soles and had anomalies of both primary and secondary dentition. For molecular diagnostics, we combined whole-exome sequencing and genome-wide homozygosity mapping procedures, and identified a recurrent homozygous missense mutation (c.899G>A; p.Gly300Asp in exon 7 of CTSC. Validation of all eight family members by Sanger sequencing confirmed co-segregation of the pathogenic variant (c.899G>A with the disease phenotype. This is the first report of whole-exome sequencing performed for molecular diagnosis of PALS in Saudi Arabia. Our findings provide further insights into the genotype–phenotype correlation of CTSC pathogenicity in PALS.

A study of strontium doped calcium phosphate coatings on AZ31

International Nuclear Information System (INIS)

Singh, Satish S.; Roy, Abhijit; Lee, Boeun E.; Ohodnicki, John; Loghmanian, Autrine; Banerjee, Ipsita; Kumta, Prashant N.

2014-01-01

Calcium phosphate (CaP) coatings have been studied to tailor the uncontrolled non-uniform corrosion of Mg based alloys while simultaneously enhancing bioactivity. The use of immersion techniques to deposit CaP coatings is attractive due to the ability of the approach to coat complex structures. In the current study, AZ31 substrates were subjected to various pretreatment conditions prior to depositing Sr 2+ doped and undoped CaP coatings. It was hypothesized that the bioactivity and corrosion protection of CaP coatings could be improved by doping with Sr 2+ . Heat treatment to elevated temperatures resulted in the diffusion of alloying elements, Mg and Zn, into the pretreated layer. Sr 2+ doped and undoped CaP coatings formed on the pretreated substrates consisted of biphasic mixtures of β-tricalcium phosphate (β-TCP) and hydroxyapatite (HA). Electrochemical corrosion experiments indicated that the extent of Sr 2+ doping and pretreatment both influenced the corrosion protection. Cytotoxicity was evaluated with MC3T3-E1 mouse preosteoblasts and human mesenchymal stem cells (hMSCs). For both cell types, proliferation decreased upon increasing the Sr 2+ concentration. However, both osteogenic gene and protein expression significantly increased upon increasing Sr 2+ concentration. These results suggest that Sr 2+ doped coatings are capable of promoting osteogenic differentiation on degradable Mg alloys, while also enhancing corrosion protection, in comparison to undoped CaP coatings

Polyurethane Organosilicate Nanocomposites as Blood Compatible Coatings

Directory of Open Access Journals (Sweden)

Johnson H. Y. Chung

2012-02-01

. This was thought to be from competitive interactions between clay-heparin that influenced the formation of the ternary complex between heparin, ATIII thrombin. In summary, the feasibility of using PUNC as drug delivery coatings was shown by the good uniformity in the coating, absence of by-products from the coating process, and the release of active molecules without significantly interfering with their activity.

Regulation of expression of a select group of Bacillus anthracis spore coat proteins.

Science.gov (United States)

Aronson, Arthur

2018-04-01

The spore coat of Bacilli is a relatively complex structure comprised of about 70 species of proteins in 2 or 3 layers. While some are involved in assembly or protection, the regulation of many are not well defined so lacZ transcriptional fusions were constructed to six Bacillus anthracis spore coat genes in order to gain insight into their possible functions. The genes were selected on the basis of the location of the encoded proteins within the coat and distribution among spore forming species. Conditions tested were temperature and media either as solid or liquid. The most extensive differences were for the relatively well expressed fusions to the cotH and cotM genes, which were greatest at 30°C on plates of a nutrient rich medium. The cotJ operon was moderately expressed under all conditions although somewhat higher on enriched plates at 30°C. Cot S was low under all conditions except for a substantial increase in biofilm medium. Cot∝ and cotF were essentially invariant with a somewhat greater expression in the more enriched medium. The capacity of a subset of coat genes to respond to various conditions reflects a flexibility in spore coat structure that may be necessary for adaptation to environmental challenges. This could account, at least in part, for the complexity of this structure.

Inorganic nanocrystals as contrast agents in MRI:synthesis, coating and introducing multifunctionality

Science.gov (United States)

Sanchez-Gaytan, Brenda L.; Mieszawska, Aneta J.; Fayad, Zahi A.

2013-01-01

Inorganic nanocrystals have myriad applications in medicine, which includes their use as drug or gene delivery complexes, therapeutic hyperthermia agents, in diagnostic systems and as contrast agents in a wide range of medical imaging techniques. For MRI, nanocrystals can produce contrast themselves, of which iron oxides have been most extensively explored, or be given a coating that generates MR contrast, for example gold nanoparticles coated with gadolinium chelates. These MR-active nanocrystals can be used in imaging of the vasculature, liver and other organs, as well as molecular imaging, cell tracking and theranostics. Due to these exciting applications, synthesizing and rendering these nanocrystals water-soluble and biocompatible is therefore highly desirable. We will discuss aqueous phase and organic phase methods for synthesizing inorganic nanocrystals such as gold, iron oxides and quantum dots. The pros and cons of the various methods will be highlighted. We explore various methods for making nanocrystals biocompatible, i.e. directly synthesizing nanocrystals coated with biocompatible coatings, ligand substitution, amphiphile coating and embedding in carrier matrices that can be made biocompatible. Various examples will be highlighted and their applications explained. These examples signify that synthesizing biocompatible nanocrystals with controlled properties has been achieved by numerous research groups and can be applied for a wide range of applications. Therefore we expect to see reports of preclinical applications of ever more complex MRI-active nanoparticles and their wider exploitation, as well as in novel clinical settings. PMID:23303729

High level waste forms: glass marbles and thermal spray coatings

International Nuclear Information System (INIS)

Treat, R.L.; Oma, K.H.; Slate, S.C.

1982-01-01

A process that converts high-level waste to glass marbles and then coats the marbles has been developed at Pacific Northwest Laboratory (PNL) under sponsorship of the US Department of Energy. The process consists of a joule-heated glass melter, a marble-making device based on a patent issued to Corning Glass Works, and a coating system that includes a plasma spray coater and a marble tumbler. The process was developed under the Alternative Waste Forms Program which strived to improve upon monolithic glass for immobilizing high-level wastes. Coated glass marbles were found to be more leach-resistant, and the marbles, before coating were found to be very homogeneous, highly impact resistant, and conductive to encapsulation in a metal matric for improved heat transfer and containment. Marbles are also ideally suited for quality assurance and recycling. However, the marble process is more complex, and marbles require a larger number of canisters for waste containment and have a higher surface area than do glass monoliths

Vapor deposition on doublet airfoil substrates: Control of coating thickness and microstructure

Energy Technology Data Exchange (ETDEWEB)

Rodgers, Theron M.; Zhao, Hengbei; Wadley, Haydn N. G., E-mail: haydn@virginia.edu [Department of Materials Science and Engineering, University of Virginia, 395 McCormick Rd., P.O. Box 400745, Charlottesville, Virginia 22904 (United States)

2015-11-15

Gas jet assisted vapor deposition processes for depositing coatings are conducted at higher pressures than conventional physical vapor deposition methods, and have shown promise for coating complex shaped substrates including those with non-line-of-sight (NLS) regions on their surface. These regions typically receive vapor atoms at a lower rate and with a wider incident angular distribution than substrate regions in line-of-sight (LS) of the vapor source. To investigate the coating of such substrates, the thickness and microstructure variation along the inner (curved) surfaces of a model doublet airfoil containing both LS and NLS regions has been investigated. Results from atomistic simulations and experiments confirm that the coating's thickness is thinner in flux-shadowed regions than in other regions for all the coating processes investigated. They also indicated that the coatings columnar microstructure and pore volume fraction vary with surface location through the LS to NLS transition zone. A substrate rotation strategy for optimizing the thickness over the entire doublet airfoil surface was investigated, and led to the identification of a process that resulted in only small variation of coating thickness, columnar growth angle, and pore volume fraction on all doublet airfoil surfaces.

[Diagnosis of a case with oculocutaneous albinism type Ⅲ with next generation exome capture sequencing].

Science.gov (United States)

Lyu, Yuqiang; Huang, Jing; Zhang, Kaihui; Liu, Guohua; Gao, Min; Gai, Zhongtao; Liu, Yi

2017-02-10

To explore the clinical and genetic features of a Chinese boy with oculocutaneous albinism. The clinical features of the patient were analyzed. The DNA of the patient and his parents was extracted and sequenced by next generation exome capture sequencing. The nature and impact of detected mutation were predicted and validated. The child has displayed strabismus, poor vision, nystagmus and brown hair. DNA sequencing showed that the patient has carried compound heterozygous mutations of the TYRP1 gene, namely c.1214C>A (p.T405N) and c.1333dupG, which were inherited from his mother and father, respectively. Neither mutation was reported previously. The child has suffered from oculocutaneous albinism type Ⅲ caused by mutations of the TYRP1 gene.

Whole-exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population.

Science.gov (United States)

Yousri, Noha A; Fakhro, Khalid A; Robay, Amal; Rodriguez-Flores, Juan L; Mohney, Robert P; Zeriri, Hassina; Odeh, Tala; Kader, Sara Abdul; Aldous, Eman K; Thareja, Gaurav; Kumar, Manish; Al-Shakaki, Alya; Chidiac, Omar M; Mohamoud, Yasmin A; Mezey, Jason G; Malek, Joel A; Crystal, Ronald G; Suhre, Karsten

2018-01-23

Metabolomics-genome-wide association studies (mGWAS) have uncovered many metabolic quantitative trait loci (mQTLs) influencing human metabolic individuality, though predominantly in European cohorts. By combining whole-exome sequencing with a high-resolution metabolomics profiling for a highly consanguineous Middle Eastern population, we discover 21 common variant and 12 functional rare variant mQTLs, of which 45% are novel altogether. We fine-map 10 common variant mQTLs to new metabolite ratio associations, and 11 common variant mQTLs to putative protein-altering variants. This is the first work to report common and rare variant mQTLs linked to diseases and/or pharmacological targets in a consanguineous Arab cohort, with wide implications for precision medicine in the Middle East.

Whole-exome sequencing links TMCO1 defect syndrome with cerebro-facio-thoracic dysplasia.

Science.gov (United States)

Pehlivan, Davut; Karaca, Ender; Aydin, Hatip; Beck, Christine R; Gambin, Tomasz; Muzny, Donna M; Bilge Geckinli, B; Karaman, Ali; Jhangiani, Shalini N; Gibbs, Richard A; Lupski, James R

2014-09-01

Whole-exome sequencing (WES) is a type of disruptive technology that has tremendous influence on human and clinical genetics research. An efficient and cost-effective method, WES is now widely used as a diagnostic tool for identifying the molecular basis of genetic syndromes that are often challenging to diagnose. Here we report a patient with a clinical diagnosis of cerebro-facio-thoracic dysplasia (CFTD; MIM#213980) in whom we identified a homozygous splice-site mutation in the transmembrane and coiled-coil domains 1 (TMCO1) gene using WES. TMCO1 mutations cause craniofacial dysmorphism, skeletal anomalies characterized by multiple malformations of the vertebrae and ribs, and intellectual disability (MIM#614132). A retrospective review revealed that clinical manifestations of both syndromes are very similar and overlap remarkably. We propose that mutations of TMCO1 are not only responsible for craniofacial dysmorphism, skeletal anomalies and mental retardation syndrome but also for CFTD.

Synthesis of Goethite-Coated Sand and Analysis of its Interactions with Uranium

International Nuclear Information System (INIS)

Vijay A. Loganathan; Sushil R. Kanel; Mark O. Barnett; T. Prabhakar Clement

2007-01-01

Iron(III) oxide coating on soils/sediments is reported to be the most important factor for controlling the sorption of radioactive metals in groundwater systems. Various forms of Fe(III) oxides occur in nature; they exist in both crystalline and amorphous forms. Our review indicated that goethite (α-FeOOH) is one of the most common iron oxides present in subsurface sediments. Therefore, it is important to understand the reactive chemistry of U(VI) with goethite-coated sand (GCS). Our overall objective is to develop scalable reaction models to predict uranium fate and transport in subsurface environment. In this paper, we focus on U(VI) interactions with well-characterized, synthetic goethite-coated sand. The objectives of the present work are to: (1) To identify a standard protocol to synthesize pure goethite-coated sand; (2) To characterize the goethite-coated sand synthesized using various methods; (3) To analyze the interaction of U(VI) with the goethite-coated sand; and (4) To predict the adsorption characteristics using surface complexation models

Poly(3-hydroxybutyrate)/caffeic acid electrospun fibrous materials coated with polyelectrolyte complex and their antibacterial activity and in vitro antitumor effect against HeLa cells

Energy Technology Data Exchange (ETDEWEB)

Ignatova, Milena G. [Laboratory of Bioactive Polymers, Institute of Polymers, Bulgarian Academy of Sciences, Acad. G. Bonchev St, Bl. 103A, BG-1113 Sofia (Bulgaria); Manolova, Nevena E., E-mail: manolova@polymer.bas.bg [Laboratory of Bioactive Polymers, Institute of Polymers, Bulgarian Academy of Sciences, Acad. G. Bonchev St, Bl. 103A, BG-1113 Sofia (Bulgaria); Rashkov, Iliya B. [Laboratory of Bioactive Polymers, Institute of Polymers, Bulgarian Academy of Sciences, Acad. G. Bonchev St, Bl. 103A, BG-1113 Sofia (Bulgaria); Markova, Nadya D. [Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G. Bonchev Bl. 26, BG-1113 Sofia (Bulgaria); Toshkova, Reneta A.; Georgieva, Ani K.; Nikolova, Elena B. [Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Acad. G. Bonchev St, bl. 25, BG-1113 Sofia (Bulgaria)

2016-08-01

The purpose of this work was to investigate the possibility for the preparation of new poly(3-hydroxybutyrate) (PHB)/poly(ethylene glycol) (PEG)-based fibrous materials containing natural phenolic compound caffeic acid (CA) of diverse architectures, as well as to study the impact of the fiber composition on the in vitro CA release profile and on the biological properties of the fibrous materials. The application of the one-pot electrospinning enabled the fabrication of nanofibrous materials from PHB and PEG loaded with the CA. Materials with targeted design were obtained by coating with polyelectrolyte complex of alginate (Alg) and N,N,N-trimethylchitosan (TMCh). Three different processing paths were used to obtain coated mats: (i) with CA incorporated in the PHB/PEG core; (ii) with CA embedded in the Alg layer; and (iii) with CA included in the TMCh layer. The in vitro release of CA was modulated by controlling the composition and the architecture of the nanofibrous mats. The performed microbiological screening and MTT cell viability studies revealed that in contrast to the bare mats, the CA-containing nanofibrous materials were effective in suppressing the growth of the Gram-positive bacteria Staphylococcus aureus and the Gram-negative bacteria Escherichia coli and displayed good cytotoxicity against human cervical HeLa tumor cells. In addition, the proliferation of murine spleen lymphocytes and peritoneal macrophages was increased by the prepared CA-containing nanofibrous materials. The obtained materials are promising for antibacterial wound dressing applications as well as for application in local treatment of cervical tumors. - Highlights: • New caffeic acid-loaded materials from PHB and PEG were prepared by electrospinning. • Different design is achieved by coating and formation of polyelectrolyte complexes. • The control on the architecture of the mats enables modulating caffeic acid release. • The caffeic acid-loaded mats suppress the growth of

Poly(3-hydroxybutyrate)/caffeic acid electrospun fibrous materials coated with polyelectrolyte complex and their antibacterial activity and in vitro antitumor effect against HeLa cells

International Nuclear Information System (INIS)

Ignatova, Milena G.; Manolova, Nevena E.; Rashkov, Iliya B.; Markova, Nadya D.; Toshkova, Reneta A.; Georgieva, Ani K.; Nikolova, Elena B.

2016-01-01

The purpose of this work was to investigate the possibility for the preparation of new poly(3-hydroxybutyrate) (PHB)/poly(ethylene glycol) (PEG)-based fibrous materials containing natural phenolic compound caffeic acid (CA) of diverse architectures, as well as to study the impact of the fiber composition on the in vitro CA release profile and on the biological properties of the fibrous materials. The application of the one-pot electrospinning enabled the fabrication of nanofibrous materials from PHB and PEG loaded with the CA. Materials with targeted design were obtained by coating with polyelectrolyte complex of alginate (Alg) and N,N,N-trimethylchitosan (TMCh). Three different processing paths were used to obtain coated mats: (i) with CA incorporated in the PHB/PEG core; (ii) with CA embedded in the Alg layer; and (iii) with CA included in the TMCh layer. The in vitro release of CA was modulated by controlling the composition and the architecture of the nanofibrous mats. The performed microbiological screening and MTT cell viability studies revealed that in contrast to the bare mats, the CA-containing nanofibrous materials were effective in suppressing the growth of the Gram-positive bacteria Staphylococcus aureus and the Gram-negative bacteria Escherichia coli and displayed good cytotoxicity against human cervical HeLa tumor cells. In addition, the proliferation of murine spleen lymphocytes and peritoneal macrophages was increased by the prepared CA-containing nanofibrous materials. The obtained materials are promising for antibacterial wound dressing applications as well as for application in local treatment of cervical tumors. - Highlights: • New caffeic acid-loaded materials from PHB and PEG were prepared by electrospinning. • Different design is achieved by coating and formation of polyelectrolyte complexes. • The control on the architecture of the mats enables modulating caffeic acid release. • The caffeic acid-loaded mats suppress the growth of

Research and Development on Coatings for Retaining Fission Product Iodine

Energy Technology Data Exchange (ETDEWEB)

Genco, J. M.; Berry, D. A.; Rosenberg, H. S.; Cremeans, G. E.; Morrison, D. L. [Battelle Memorial Institute, Columbus Laboratories, Columbus, OH (United States)

1968-12-15

It is well known that elemental iodine has the propensity for forming charge-transfer complexes with amines. These complexes are stable at ambient temperatures and retain much of this stability at elevated temperatures. Amines also react with methyl iodide and hydrogen iodide to form the quaternary ammonium salts and amine salts, respectively. These chemical properties of amines provide the basis for the development of retentive coatings for fission product iodine. Various amine-containing polymers were studied in steam-air environments at elevated temperatures using dilute quantities of tagged iodine. Both non-condensing and condensing steam conditions were investigated. Several of the polymers showed sorption rates and capacities that would be adequate for the chemical removal of accident-released fission-product iodine and were several times more effective than commercial protective coatings currently being used. The removal capabilities for amine polymers also could be enhanced by impregnating the reactant on a matrix material such as asbestos mat, presumably because the impregnation technique leads to enhanced surface area and porosity. The two most promising coating systems found were 1:10-phenanthroline impregnated upon asbestos and a three component composite film of the co-polymer of Genamid 2000 and Epon 828 as a reactive binder with 1,10-phenanthroline as a reactive filler. The use of a reactive coating as a passive safety system should reduce appreciably the airborne iodine half-life and the hazards associated with iodine release during a nuclear reactor accident. (author)

Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk

Science.gov (United States)

Permuth, Jennifer B.; Pirie, Ailith; Ann Chen, Y.; Lin, Hui-Yi; Reid, Brett M.; Chen, Zhihua; Monteiro, Alvaro; Dennis, Joe; Mendoza-Fandino, Gustavo; Anton-Culver, Hoda; Bandera, Elisa V.; Bisogna, Maria; Brinton, Louise; Brooks-Wilson, Angela; Carney, Michael E.; Chenevix-Trench, Georgia; Cook, Linda S.; Cramer, Daniel W.; Cunningham, Julie M.; Cybulski, Cezary; D’Aloisio, Aimee A.; Anne Doherty, Jennifer; Earp, Madalene; Edwards, Robert P.; Fridley, Brooke L.; Gayther, Simon A.; Gentry-Maharaj, Aleksandra; Goodman, Marc T.; Gronwald, Jacek; Hogdall, Estrid; Iversen, Edwin S.; Jakubowska, Anna; Jensen, Allan; Karlan, Beth Y.; Kelemen, Linda E.; Kjaer, Suzanne K.; Kraft, Peter; Le, Nhu D.; Levine, Douglas A.; Lissowska, Jolanta; Lubinski, Jan; Matsuo, Keitaro; Menon, Usha; Modugno, Rosemary; Moysich, Kirsten B.; Nakanishi, Toru; Ness, Roberta B.; Olson, Sara; Orlow, Irene; Pearce, Celeste L.; Pejovic, Tanja; Poole, Elizabeth M.; Ramus, Susan J.; Anne Rossing, Mary; Sandler, Dale P.; Shu, Xiao-Ou; Song, Honglin; Taylor, Jack A.; Teo, Soo-Hwang; Terry, Kathryn L.; Thompson, Pamela J.; Tworoger, Shelley S.; Webb, Penelope M.; Wentzensen, Nicolas; Wilkens, Lynne R.; Winham, Stacey; Woo, Yin-Ling; Wu, Anna H.; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Phelan, Catherine M.; Schildkraut, Joellen M.; Berchuck, Andrew; Goode, Ellen L.; Pharoah, Paul D. P.; Sellers, Thomas A.

2016-01-01

Rare and low frequency variants are not well covered in most germline genotyping arrays and are understudied in relation to epithelial ovarian cancer (EOC) risk. To address this gap, we used genotyping arrays targeting rarer protein-coding variation in 8,165 EOC cases and 11,619 controls from the international Ovarian Cancer Association Consortium (OCAC). Pooled association analyses were conducted at the variant and gene level for 98,543 variants directly genotyped through two exome genotyping projects. Only common variants that represent or are in strong linkage disequilibrium (LD) with previously-identified signals at established loci reached traditional thresholds for exome-wide significance (P  P≥5.0 ×10 − 7) were detected for rare and low-frequency variants at 16 novel loci. Four rare missense variants were identified (ACTBL2 rs73757391 (5q11.2), BTD rs200337373 (3p25.1), KRT13 rs150321809 (17q21.2) and MC2R rs104894658 (18p11.21)), but only MC2R rs104894668 had a large effect size (OR = 9.66). Genes most strongly associated with EOC risk included ACTBL2 (PAML = 3.23 × 10 − 5; PSKAT-o = 9.23 × 10 − 4) and KRT13 (PAML = 1.67 × 10 − 4; PSKAT-o = 1.07 × 10 − 5), reaffirming variant-level analysis. In summary, this large study identified several rare and low-frequency variants and genes that may contribute to EOC susceptibility, albeit with possible small effects. Future studies that integrate epidemiology, sequencing, and functional assays are needed to further unravel the unexplained heritability and biology of this disease. PMID:27378695

A Combined Linkage and Exome Sequencing Analysis for Electrocardiogram Parameters in the Erasmus Rucphen Family Study.

Science.gov (United States)

Silva, Claudia T; Zorkoltseva, Irina V; Amin, Najaf; Demirkan, Ayşe; van Leeuwen, Elisabeth M; Kors, Jan A; van den Berg, Marten; Stricker, Bruno H; Uitterlinden, André G; Kirichenko, Anatoly V; Witteman, Jacqueline C M; Willemsen, Rob; Oostra, Ben A; Axenovich, Tatiana I; van Duijn, Cornelia M; Isaacs, Aaron

2016-01-01

Electrocardiogram (ECG) measurements play a key role in the diagnosis and prediction of cardiac arrhythmias and sudden cardiac death. ECG parameters, such as the PR, QRS, and QT intervals, are known to be heritable and genome-wide association studies of these phenotypes have been successful in identifying common variants; however, a large proportion of the genetic variability of these traits remains to be elucidated. The aim of this study was to discover loci potentially harboring rare variants utilizing variance component linkage analysis in 1547 individuals from a large family-based study, the Erasmus Rucphen Family Study (ERF). Linked regions were further explored using exome sequencing. Five suggestive linkage peaks were identified: two for QT interval (1q24, LOD = 2.63; 2q34, LOD = 2.05), one for QRS interval (1p35, LOD = 2.52) and two for PR interval (9p22, LOD = 2.20; 14q11, LOD = 2.29). Fine-mapping using exome sequence data identified a C > G missense variant (c.713C > G, p.Ser238Cys) in the FCRL2 gene associated with QT (rs74608430; P = 2.8 × 10 -4 , minor allele frequency = 0.019). Heritability analysis demonstrated that the SNP explained 2.42% of the trait's genetic variability in ERF ( P = 0.02). Pathway analysis suggested that the gene is involved in cytosolic Ca 2+ levels ( P = 3.3 × 10 -3 ) and AMPK stimulated fatty acid oxidation in muscle ( P = 4.1 × 10 -3 ). Look-ups in bioinformatics resources showed that expression of FCRL2 is associated with ARHGAP24 and SETBP1 expression. This finding was not replicated in the Rotterdam study. Combining the bioinformatics information with the association and linkage analyses, FCRL2 emerges as a strong candidate gene for QT interval.

A combined linkage and exome sequencing analysis for electrocardiogram parameters in the Erasmus Rucphen Family study

Directory of Open Access Journals (Sweden)

Claudia Tamar Silva

2016-11-01

Full Text Available Electrocardiogram (ECG measurements play a key role in the diagnosis and prediction of cardiac arrhythmias and sudden cardiac death. ECG parameters, such as the PR, QRS, and QT intervals, are known to be heritable and genome-wide association studies (GWAS of these phenotypes have been successful in identifying common variants; however, a large proportion of the genetic variability of these traits remains to be elucidated. The aim of this study was to discover loci potentially harboring rare variants utilizing variance component linkage analysis in 1547 individuals from a large family-based study, the Erasmus Rucphen Family Study (ERF. Linked regions were further explored using exome sequencing. Five suggestive linkage peaks were identified: two for QT interval (1q24, LOD = 2.63; 2q34, LOD = 2.05, one for QRS interval (1p35, LOD = 2.52 and two for PR interval (9p22, LOD = 2.20; 14q11, LOD = 2.29. Fine-mapping using exome sequence data identified a C > G missense variant (c.713C>G, p.Ser238Cys in the FCRL2 gene associated with QT (rs74608430; P = 2.8 ×10-4, minor allele frequency = 0.019. Heritability analysis demonstrated that the SNP explained 2.42% of the trait’s genetic variability in ERF (P = 0.02. Pathway analysis suggested that the gene is involved in cytosolic Ca2+ levels (P = 3.3 × 10-3 and AMPK stimulated fatty acid oxidation in muscle (P = 4.1 ×10-3. Look-ups in bioinformatics resources showed that expression of FCRL2 is associated with ARHGAP24 and SETBP1 expression. This finding was not replicated in the Rotterdam study. Combining the bioinformatics information with the association and linkage analyses, FCRL2 emerges as a strong candidate gene for QT interval.

Whole exome sequencing identifies RAI1 mutation in a morbidly obese child diagnosed with ROHHAD syndrome.

Science.gov (United States)

Thaker, Vidhu V; Esteves, Kristyn M; Towne, Meghan C; Brownstein, Catherine A; James, Philip M; Crowley, Laura; Hirschhorn, Joel N; Elsea, Sarah H; Beggs, Alan H; Picker, Jonathan; Agrawal, Pankaj B

2015-05-01

The current obesity epidemic is attributed to complex interactions between genetic and environmental factors. However, a limited number of cases, especially those with early-onset severe obesity, are linked to single gene defects. Rapid-onset obesity with hypothalamic dysfunction, hypoventilation and autonomic dysregulation (ROHHAD) is one of the syndromes that presents with abrupt-onset extreme weight gain with an unknown genetic basis. To identify the underlying genetic etiology in a child with morbid early-onset obesity, hypoventilation, and autonomic and behavioral disturbances who was clinically diagnosed with ROHHAD syndrome. Design/Setting/Intervention: The index patient was evaluated at an academic medical center. Whole-exome sequencing was performed on the proband and his parents. Genetic variants were validated by Sanger sequencing. We identified a novel de novo nonsense mutation, c.3265 C>T (p.R1089X), in the retinoic acid-induced 1 (RAI1) gene in the proband. Mutations in the RAI1 gene are known to cause Smith-Magenis syndrome (SMS). On further evaluation, his clinical features were not typical of either SMS or ROHHAD syndrome. This study identifies a de novo RAI1 mutation in a child with morbid obesity and a clinical diagnosis of ROHHAD syndrome. Although extreme early-onset obesity, autonomic disturbances, and hypoventilation are present in ROHHAD, several of the clinical findings are consistent with SMS. This case highlights the challenges in the diagnosis of ROHHAD syndrome and its potential overlap with SMS. We also propose RAI1 as a candidate gene for children with morbid obesity.

Exome sequencing identifies rare deleterious mutations in DNA repair genes FANCC and BLM as potential breast cancer susceptibility alleles.

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Ella R Thompson

2012-09-01

Full Text Available Despite intensive efforts using linkage and candidate gene approaches, the genetic etiology for the majority of families with a multi-generational breast cancer predisposition is unknown. In this study, we used whole-exome sequencing of thirty-three individuals from 15 breast cancer families to identify potential predisposing genes. Our analysis identified families with heterozygous, deleterious mutations in the DNA repair genes FANCC and BLM, which are responsible for the autosomal recessive disorders Fanconi Anemia and Bloom syndrome. In total, screening of all exons in these genes in 438 breast cancer families identified three with truncating mutations in FANCC and two with truncating mutations in BLM. Additional screening of FANCC mutation hotspot exons identified one pathogenic mutation among an additional 957 breast cancer families. Importantly, none of the deleterious mutations were identified among 464 healthy controls and are not reported in the 1,000 Genomes data. Given the rarity of Fanconi Anemia and Bloom syndrome disorders among Caucasian populations, the finding of multiple deleterious mutations in these critical DNA repair genes among high-risk breast cancer families is intriguing and suggestive of a predisposing role. Our data demonstrate the utility of intra-family exome-sequencing approaches to uncover cancer predisposition genes, but highlight the major challenge of definitively validating candidates where the incidence of sporadic disease is high, germline mutations are not fully penetrant, and individual predisposition genes may only account for a tiny proportion of breast cancer families.

Whole-exome sequencing of individuals from an isolated population implicates rare risk variants in bipolar disorder

DEFF Research Database (Denmark)

Lescai, F; Als, T D; Li, Q

2017-01-01

Bipolar disorder affects about 1% of the world's population, and its estimated heritability is about 75%. Only few whole genome or whole-exome sequencing studies in bipolar disorder have been reported, and no rare coding variants have yet been robustly identified. The use of isolated populations...... PITPNM2 missense variant, which is located in a highly significant schizophrenia GWAS locus. Likewise, PIK3C2A identified in the gene-based analysis is located in a combined bipolar and schizophrenia GWAS locus. Our results show support both for existing findings in the literature, as well as for new...... risk genes, and identify rare variants that might provide additional information on the underlying biology of bipolar disorder....

Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders.

Science.gov (United States)

Codina-Solà, Marta; Rodríguez-Santiago, Benjamín; Homs, Aïda; Santoyo, Javier; Rigau, Maria; Aznar-Laín, Gemma; Del Campo, Miguel; Gener, Blanca; Gabau, Elisabeth; Botella, María Pilar; Gutiérrez-Arumí, Armand; Antiñolo, Guillermo; Pérez-Jurado, Luis Alberto; Cuscó, Ivon

2015-01-01

Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders with high heritability. Recent findings support a highly heterogeneous and complex genetic etiology including rare de novo and inherited mutations or chromosomal rearrangements as well as double or multiple hits. We performed whole-exome sequencing (WES) and blood cell transcriptome by RNAseq in a subset of male patients with idiopathic ASD (n = 36) in order to identify causative genes, transcriptomic alterations, and susceptibility variants. We detected likely monogenic causes in seven cases: five de novo (SCN2A, MED13L, KCNV1, CUL3, and PTEN) and two inherited X-linked variants (MAOA and CDKL5). Transcriptomic analyses allowed the identification of intronic causative mutations missed by the usual filtering of WES and revealed functional consequences of some rare mutations. These included aberrant transcripts (PTEN, POLR3C), deregulated expression in 1.7% of mutated genes (that is, SEMA6B, MECP2, ANK3, CREBBP), allele-specific expression (FUS, MTOR, TAF1C), and non-sense-mediated decay (RIT1, ALG9). The analysis of rare inherited variants showed enrichment in relevant pathways such as the PI3K-Akt signaling and the axon guidance. Integrative analysis of WES and blood RNAseq data has proven to be an efficient strategy to identify likely monogenic forms of ASD (19% in our cohort), as well as additional rare inherited mutations that can contribute to ASD risk in a multifactorial manner. Blood transcriptomic data, besides validating 88% of expressed variants, allowed the identification of missed intronic mutations and revealed functional correlations of genetic variants, including changes in splicing, expression levels, and allelic expression.

PsB multiprotein complex of Dictyostelium discoideum. Demonstration of cellulose binding activity and order of protein subunit assembly.

Science.gov (United States)

McGuire, V; Alexander, S

1996-06-14

The differentiated spores of Dictyostelium are surrounded by an extracellular matrix, the spore coat, which protects them from environmental factors allowing them to remain viable for extended periods of time. This presumably is a major evolutionary advantage. This unique extracellular matrix is composed of cellulose and glycoproteins. Previous work has shown that some of these spore coat glycoproteins exist as a preassembled multiprotein complex (the PsB multiprotein complex) which is stored in the prespore vesicles (Watson, N., McGuire, V., and Alexander, S (1994) J. Cell Sci. 107, 2567-2579). Later in development, the complex is synchronously secreted from the prespore vesicles and incorporated into the spore coat. We now have shown that the PsB complex has a specific in vitro cellulose binding activity. The analysis of mutants lacking individual subunits of the PsB complex revealed the relative order of assembly of the subunit proteins and demonstrated that the protein subunits must be assembled for cellulose binding activity. These results provide a biochemical explanation for the localization of this multiprotein complex in the spore coat.

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

Science.gov (United States)

Ramos, Enrique; Levinson, Benjamin T; Chasnoff, Sara; Hughes, Andrew; Young, Andrew L; Thornton, Katherine; Li, Allie; Vallania, Francesco L M; Province, Michael; Druley, Todd E

2012-12-06

Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regions and comparing against unaffected cohorts. However, despite persistent declines in sequencing costs, population-based rare variant detection across large genomic target regions remains cost prohibitive for most investigators. In addition, DNA samples are often precious and hybridization methods typically require large amounts of input DNA. Pooled sample DNA sequencing is a cost and time-efficient strategy for surveying populations of individuals for rare variants. We set out to 1) create a scalable, multiplexing method for custom capture with or without individual DNA indexing that was amenable to low amounts of input DNA and 2) expand the functionality of the SPLINTER algorithm for calling substitutions, insertions and deletions across either candidate genes or the entire exome by integrating the variant calling algorithm with the dynamic programming aligner, Novoalign. We report methodology for pooled hybridization capture with pre-enrichment, indexed multiplexing of up to 48 individuals or non-indexed pooled sequencing of up to 92 individuals with as little as 70 ng of DNA per person. Modified solid phase reversible immobilization bead purification strategies enable no sample transfers from sonication in 96-well plates through adapter ligation, resulting in 50% less library preparation reagent consumption. Custom Y-shaped adapters containing novel 7 base pair index sequences with a Hamming distance of ≥2 were directly ligated onto fragmented source DNA eliminating the need for PCR to incorporate indexes, and was followed by a custom blocking strategy using a single oligonucleotide regardless of index sequence. These results were obtained aligning raw

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing

Directory of Open Access Journals (Sweden)

Ramos Enrique

2012-12-01

Full Text Available Abstract Background Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regions and comparing against unaffected cohorts. However, despite persistent declines in sequencing costs, population-based rare variant detection across large genomic target regions remains cost prohibitive for most investigators. In addition, DNA samples are often precious and hybridization methods typically require large amounts of input DNA. Pooled sample DNA sequencing is a cost and time-efficient strategy for surveying populations of individuals for rare variants. We set out to 1 create a scalable, multiplexing method for custom capture with or without individual DNA indexing that was amenable to low amounts of input DNA and 2 expand the functionality of the SPLINTER algorithm for calling substitutions, insertions and deletions across either candidate genes or the entire exome by integrating the variant calling algorithm with the dynamic programming aligner, Novoalign. Results We report methodology for pooled hybridization capture with pre-enrichment, indexed multiplexing of up to 48 individuals or non-indexed pooled sequencing of up to 92 individuals with as little as 70 ng of DNA per person. Modified solid phase reversible immobilization bead purification strategies enable no sample transfers from sonication in 96-well plates through adapter ligation, resulting in 50% less library preparation reagent consumption. Custom Y-shaped adapters containing novel 7 base pair index sequences with a Hamming distance of ≥2 were directly ligated onto fragmented source DNA eliminating the need for PCR to incorporate indexes, and was followed by a custom blocking strategy using a single oligonucleotide regardless of index sequence

Clinical diagnostic exome evaluation for an infant with a lethal disorder: genetic diagnosis of TARP syndrome and expansion of the phenotype in a patient with a newly reported RBM10 alteration.

Science.gov (United States)

Powis, Zöe; Hart, Alexa; Cherny, Sara; Petrik, Igor; Palmaer, Erika; Tang, Sha; Jones, Carolyn

2017-06-02

Diagnostic Exome Sequencing (DES) has been shown to be an effective tool for diagnosis individuals with suspected genetic conditions. We report a male infant born with multiple anomalies including bilateral dysplastic kidneys, cleft palate, bilateral talipes, and bilateral absence of thumbs and first toes. Prenatal testing including chromosome analysis and microarray did not identify a cause for the multiple congenital anomalies. Postnatal diagnostic exome studies (DES) were utilized to find a molecular diagnosis for the patient. Exome sequencing of the proband, mother, and father showed a previously unreported maternally inherited RNA binding motif protein 10 (RBM10) c.1352_1353delAG (p.E451Vfs*66) alteration. Mutations in RBM10 are associated with TARP syndrome, an X-linked recessive disorder originally described with cardinal features of talipes equinovarus, atrial septal defect, Robin sequence, and persistent left superior vena cava. DES established a molecular genetic diagnosis of TARP syndrome for a neonatal patient with a poor prognosis in whom traditional testing methods were uninformative and allowed for efficient diagnosis and future reproductive options for the parents. Other reported cases of TARP syndrome demonstrate significant variability in clinical phenotype. The reported features in this infant including multiple hemivertebrae, imperforate anus, aplasia of thumbs and first toes have not been reported in previous patients, thus expanding the clinical phenotype for this rare disorder.

Coated Aerogel Beads

Science.gov (United States)

Littman, Howard (Inventor); Plawsky, Joel L. (Inventor); Paccione, John D. (Inventor)

2014-01-01

Methods and apparatus for coating particulate material are provided. The apparatus includes a vessel having a top and a bottom, a vertically extending conduit having an inlet in the vessel and an outlet outside of the vessel, a first fluid inlet in the bottom of the vessel for introducing a transfer fluid, a second fluid inlet in the bottom of the vessel for introducing a coating fluid, and a fluid outlet from the vessel. The method includes steps of agitating a material, contacting the material with a coating material, and drying the coating material to produce a coated material. The invention may be adapted to coat aerogel beads, among other materials. A coated aerogel bead and an aerogel-based insulation material are also disclosed.

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

Energy Technology Data Exchange (ETDEWEB)

Krauthammer, Michael; Kong, Yong; Ha, Byung Hak; Evans, Perry; Bacchiocchi, Antonella; McCusker, James P.; Cheng, Elaine; Davis, Matthew J.; Goh, Gerald; Choi, Murim; Ariyan, Stephan; Narayan, Deepak; Dutton-Regester, Ken; Capatana, Ana; Holman, Edna C.; Bosenberg, Marcus; Sznol, Mario; Kluger, Harriet M.; Brash, Douglas E.; Stern, David F.; Materin, Miguel A.; Lo, Roger S.; Mane, Shrikant; Ma, Shuangge; Kidd, Kenneth K.; Hayward, Nicholas K.; Lifton, Richard P.; Schlessinger, Joseph; Boggon, Titus J.; Halaban, Ruth (Yale-MED); (UCLA); (Queens)

2012-10-11

We characterized the mutational landscape of melanoma, the form of skin cancer with the highest mortality rate, by sequencing the exomes of 147 melanomas. Sun-exposed melanomas had markedly more ultraviolet (UV)-like C>T somatic mutations compared to sun-shielded acral, mucosal and uveal melanomas. Among the newly identified cancer genes was PPP6C, encoding a serine/threonine phosphatase, which harbored mutations that clustered in the active site in 12% of sun-exposed melanomas, exclusively in tumors with mutations in BRAF or NRAS. Notably, we identified a recurrent UV-signature, an activating mutation in RAC1 in 9.2% of sun-exposed melanomas. This activating mutation, the third most frequent in our cohort of sun-exposed melanoma after those of BRAF and NRAS, changes Pro29 to serine (RAC1{sup P29S}) in the highly conserved switch I domain. Crystal structures, and biochemical and functional studies of RAC1{sup P29S} showed that the alteration releases the conformational restraint conferred by the conserved proline, causes an increased binding of the protein to downstream effectors, and promotes melanocyte proliferation and migration. These findings raise the possibility that pharmacological inhibition of downstream effectors of RAC1 signaling could be of therapeutic benefit.

Prescreening whole exome sequencing results from patients with retinal degeneration for variants in genes associated with retinal degeneration

Directory of Open Access Journals (Sweden)

Bryant L

2017-12-01

Full Text Available Laura Bryant,1 Olga Lozynska,1 Albert M Maguire,1–3 Tomas S Aleman,1–3 Jean Bennett1–3 1Center for Advanced Retinal and Ocular Therapeutics (CAROT, FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; 2Department of Ophthalmology, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA; 3Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA Background: Accurate clinical diagnosis and prognosis of retinal degeneration can be aided by the identification of the disease-causing genetic variant. It can confirm the clinical diagnosis as well as inform the clinician of the risk for potential involvement of other organs such as kidneys. It also aids in genetic counseling for affected individuals who want to have a child. Finally, knowledge of disease-causing variants informs laboratory investigators involved in translational research. With the advent of next-generation sequencing, identifying pathogenic mutations is becoming easier, especially the identification of novel pathogenic variants.Methods: We used whole exome sequencing on a cohort of 69 patients with various forms of retinal degeneration and in whom screens for previously identified disease-causing variants had been inconclusive. All potential pathogenic variants were verified by Sanger sequencing and, when possible, segregation analysis of immediate relatives. Potential variants were identified by using a semi-masked approach in which rare variants in candidate genes were identified without knowledge of the clinical diagnosis (beyond “retinal degeneration” or inheritance pattern. After the initial list of genes was prioritized, genetic diagnosis and inheritance pattern were taken into account.Results: We identified the likely pathogenic variants in 64% of the subjects. Seven percent had a single

Whole exome sequencing of a patient with metastatic hidradenocarcinoma and review of the literature

Directory of Open Access Journals (Sweden)

Eva Gupta

2015-02-01

Full Text Available Hidradenocarcinoma is a rare malignancy of the sweat glands with only a few cases reported in literature. The management of these tumors is based on the extent of disease with local disease managed with surgical resection. These can tumors carry a high potential of lymphatic and vascular spread and local and distant metastases are not uncommon. Given the rarity of the tumor and lack of genetic and clinical data about these tumors, there is no consensus on the proper management of metastatic disease. Here in we report the first case of metastatic hidradenocarcinoma with detailed molecular profiling including whole exome sequencing. We identified mutations in multiple genes including two that are potentially targetable: PTCH1 and TCF7L1. Further work is necessary to not only confirm the presence of these mutations but also to confirm the clinical significance.

Whole exome sequencing of a patient with metastatic hidradenocarcinoma and review of the literature.

Science.gov (United States)

Gupta, Eva; Guthrie, Kimberly J; Krishna, Murli; Asmann, Yan; Parker, Alexander S; Joseph, Richard W

2015-02-11

Hidradenocarcinoma is a rare malignancy of the sweat glands with only a few cases reported in literature. The management of these tumors is based on the extent of disease with local disease managed with surgical resection. These can tumors carry a high potential of lymphatic and vascular spread and local and distant metastases are not uncommon. Given the rarity of the tumor and lack of genetic and clinical data about these tumors, there is no consensus on the proper management of metastatic disease. Here in we report the first case of metastatic hidradenocarcinoma with detailed molecular profiling including whole exome sequencing. We identified mutations in multiple genes including two that are potentially targetable: PTCH1 and TCF7L1. Further work is necessary to not only confirm the presence of these mutations but also to confirm the clinical significance.

A combined histology and transcriptome analysis unravels novel questions on Medicago truncatula seed coat

Science.gov (United States)

Abirached-Darmency, Mona

2013-01-01

The seed coat is involved in the determination of seed quality traits such as seed size, seed composition, seed permeability, and hormonal regulation. Understanding seed coat structure is therefore a prerequisite to deciphering the genetic mechanisms that govern seed coat functions. By combining histological and transcriptomic data analyses, cellular and molecular events occurring during Medicago truncatula seed coat development were dissected in order to relate structure to function and pinpoint target genes potentially involved in seed coat traits controlling final seed quality traits. The analyses revealed the complexity of the seed coat transcriptome, which contains >30 000 genes. In parallel, a set of genes showing a preferential expression in seed coat that may be involved in more specific functions was identified. The study describes how seed coat anatomy and morphological changes affect final seed quality such as seed size, seed composition, seed permeability, and hormonal regulation. Putative regulator genes of different processes have been identified as potential candidates for further functional genomic studies to improve agronomical seed traits. The study also raises new questions concerning the implication of seed coat endopolyploidy in cell expansion and the participation of the seed coat in de novo abscisic acid biosynthesis at early seed filling. PMID:23125357

Whole-Exome Sequencing Identifies ALMS1, IQCB1, CNGA3, and MYO7A Mutations in Patients with Leber Congenital Amaurosis

OpenAIRE

Wang, Xia; Wang, Hui; Cao, Ming; Li, Zhe; Chen, Xianfeng; Patenia, Claire; Gore, Athurva; Abboud, Emad B.; Al-Rajhi, Ali A.; Lewis, Richard A.; Lupski, James R.; Mardon, Graeme; Zhang, Kun; Muzny, Donna; Gibbs, Richard A.

2011-01-01

It has been well documented that mutations in the same retinal disease gene can result in different clinical phenotypes due to difference in the mutant allele and/or genetic background. To evaluate this, a set of consanguineous patient families with Leber congenital amaurosis (LCA) that do not carry mutations in known LCA disease genes was characterized through homozygosity mapping followed by targeted exon/whole-exome sequencing to identify genetic variations. Among these families, a total o...

Tunable plasmonic enhancement of light scattering and absorption in graphene-coated subwavelength wires

OpenAIRE

Riso, Máximo; Cuevas, Mauro; Depine, Ricardo A.

2015-01-01

The electromagnetic response of subwavelength wires coated with a graphene monolayer illuminated by a linearly polarized plane waves is investigated. The results show that the scattering and extintion cross-sections of the coated wire can be dramatically enhanced when the incident radiation resonantly excites localized surface plasmons. The enhancements occur for p--polarized incident waves and for excitation frequencies that correspond to complex poles in the coefficients of the multipole ex...

Protective coatings for high temperature alloys state of technology

International Nuclear Information System (INIS)

Goward, G.W.

1976-01-01

Coatings used on nickel- and cobalt-base superalloy blades and vanes in gas turbine engines typify the state of coating technology for high temperature alloys. Coatings formed by interdiffusion of aluminum with the alloys to form layers consisting mainly of intermetallic compounds, such as NiAl and CoAl, were the first systems used for protection of gas turbine airfoils. The protectivity of these systems is derived from the formation of protective alumina scales. In a general way, coating degradation occurs by cyclic oxidation, molten salt hot corrosion and, at higher temperatures, interdiffusion with the substrate. Thermal fatigue properties are governed by the brittle-ductile transition behavior of the intermetallic compounds NiAl and CoAl. Both positive and negative effects occur, depending on the shapes of thermal strain-temperature curves for particular applications. Significant increases in hot corrosion and oxidation resistance have been obtained by the incorporation of noble metals, such as platinum, in aluminide coatings. The so-called MCrAlY overlay coatings, based on nickel, cobalt, iron and combinations thereof with chromium, aluminum and yttrium can be formulated over a wide range of compositions nominally independent of those of substrate alloys. Improved oxidation resistance and, in part, hot corrosion resistance is derived from yttrium which enhances protective oxide adherence. Mechanical properties, principally ductility, and therefore thermal fatigue resistance, can be adjusted to the requirements of specific applications. Incremental improvements in performance of the MCrAlY coatings are expected as research programs define degradation mechanisms in greater detail and more complex compositions are devised. More basic evaluations of mixed metal-ceramic insulative coatings have been initiated to determine if these systems are capable of effecting further increases in airfoil durability

Effect of coating parameters on the microstructure of cerium oxide conversion coatings

Energy Technology Data Exchange (ETDEWEB)

Johnson, Benedict Y.; Edington, Joe; O' Keefe, Matthew J

2003-11-25

The microstructure and morphology of cerium oxide conversion coatings prepared under different deposition conditions were characterized by transmission electron microscopy (TEM). The coatings were formed by a spontaneous reaction between a water-based solution containing CeCl{sub 3} and aluminum alloy 7075-T6 substrates. Microstructural characterization was performed to determine the crystallinity of the coatings and to obtain a better understanding of the deposition parameters on coating microstructure. The results of TEM imaging and electron diffraction analysis indicated that the as-deposited coating was composed of nanocrystalline particles of a previously unreported cerium compound. The particles of the coatings produced using glycerol as an additive were found to be much finer than those of the coatings prepared in the absence of glycerol. This indicates that glycerol may act as a grain refiner and/or growth inhibitor during coating deposition. After deposition, the coated panels were treated for 5 min in a phosphate sealing solution. The sealing treatment converted the as-deposited coating into hydrated cerium phosphate. Panels coated from solutions containing no glycerol followed by phosphate sealing performed poorly in salt fog tests. With glycerol addition, the corrosion resistance of the coatings that were phosphate sealed improved considerably, achieving an average passing rate of 85%.

Characterization of PEI-coated superparamagnetic iron oxide nanoparticles for transfection: Size distribution, colloidal properties and DNA interaction

Energy Technology Data Exchange (ETDEWEB)

Steitz, Benedikt [Laboratory of Powder Technology, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne (Switzerland); Hofmann, Heinrich [Laboratory of Powder Technology, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne (Switzerland); Kamau, Sarah W. [Institute of Veterinary Biochemistry and Molecular Biology, University of Zuerich, Zurich (Switzerland); Hassa, Paul O. [Institute of Veterinary Biochemistry and Molecular Biology, University of Zuerich, Zurich (Switzerland); Hottiger, Michael O. [Institute of Veterinary Biochemistry and Molecular Biology, University of Zuerich, Zurich (Switzerland); Rechenberg, Brigitte von [Musculoskeletal Research Unit, Equine Hospital, Vetsuisse Faculty Zurich, University of Zurich, Winterthurerstr. 260, 8057 Zurich (Switzerland); Hofmann-Amtenbrink, Magarethe [MatSearch, Chemin Jean Pavillard 14, 1009 Pully (Switzerland); Petri-Fink, Alke [Laboratory of Powder Technology, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne (Switzerland)]. E-mail: alke.fink@epfl.ch

2007-04-15

Superparamagnetic iron oxide nanoparticles (SPIONs) were coated with polyethylenimine. Here, we briefly describe the synthesis as well as DNA:PEI:SPION complexes and the characterization of the compounds according to their particle size, {zeta}-potential, morphology, DNA complexing ability, magnetic sedimentation, and colloidal stability. PEI coating of SPIONs led to colloidally stable beads even in high salt concentrations over a wide pH range. DNA plasmids and PCR products encoding for green fluorescent protein were associated with the described beads. The complexes were added to cells and exposed to permanent and pulsating magnetic fields. Presence of these magnetic fields significantly increased the transfection efficiency.

Characterization of PEI-coated superparamagnetic iron oxide nanoparticles for transfection: Size distribution, colloidal properties and DNA interaction

International Nuclear Information System (INIS)

Steitz, Benedikt; Hofmann, Heinrich; Kamau, Sarah W.; Hassa, Paul O.; Hottiger, Michael O.; Rechenberg, Brigitte von; Hofmann-Amtenbrink, Magarethe; Petri-Fink, Alke

2007-01-01

Superparamagnetic iron oxide nanoparticles (SPIONs) were coated with polyethylenimine. Here, we briefly describe the synthesis as well as DNA:PEI:SPION complexes and the characterization of the compounds according to their particle size, ζ-potential, morphology, DNA complexing ability, magnetic sedimentation, and colloidal stability. PEI coating of SPIONs led to colloidally stable beads even in high salt concentrations over a wide pH range. DNA plasmids and PCR products encoding for green fluorescent protein were associated with the described beads. The complexes were added to cells and exposed to permanent and pulsating magnetic fields. Presence of these magnetic fields significantly increased the transfection efficiency

Recent developments in genome and exome-wide analyses of plasma lipids.

Science.gov (United States)

Lange, Leslie A; Willer, Cristen J; Rich, Stephen S

2015-04-01

Genome-wide association scans (GWAS) have identified over 100 human loci associated with variation in lipids. The identification of novel genes and variants that affect lipid levels is made possible by next-generation sequencing, rare variant discovery and analytic advances. The current status of the genetic basis of lipid traits will be presented. Expansion of GWAS sample sizes for lipid traits has not substantially increased the proportion of trait variance explained by common genetic variants (less than 15% of trait variation captured). Although GWAS has discovered novel loci and pathways with putative biological function and impact on cardiovascular disease risk, discovery of the genes in these loci remains challenging. Exome sequencing promises to identify genes with protein-coding variants with a large impact on lipids, as shown for LDL-cholesterol levels associated with novel (PNPLA5) and known (LDLR, PCSK9, APOB) genes. Current results have increased our understanding of the genetic architecture of lipids, expanding the range of effect and frequency for variants identified for lipid traits. Identification of novel lipid-associated gene variants, even if small in effect or rare in the population, could provide important novel drug targets and biological pathways for dyslipidemia.

Analysis of Capillary Coating Die Flow in an Optical Fiber Coating Applicator

OpenAIRE

Kyoungjin Kim

2011-01-01

Viscous heating becomes significant in the high speed resin coating process of glass fibers for optical fiber manufacturing. This study focuses on the coating resin flows inside the capillary coating die of optical fiber coating applicator and they are numerically simulated to examine the effects of viscous heating and subsequent temperature increase in coating resin. Resin flows are driven by fast moving glass fiber and the pressurization at the coating die inlet, while ...

High-Quality Exome Sequencing of Whole-Genome Amplified Neonatal Dried Blood Spot DNA

DEFF Research Database (Denmark)

Poulsen, Jesper Buchhave; Lescai, Francesco; Grove, Jakob

2016-01-01

Stored neonatal dried blood spot (DBS) samples from neonatal screening programmes are a valuable diagnostic and research resource. Combined with information from national health registries they can be used in population-based studies of genetic diseases. DNA extracted from neonatal DBSs can...... be amplified to obtain micrograms of an otherwise limited resource, referred to as whole-genome amplified DNA (wgaDNA). Here we investigate the robustness of exome sequencing of wgaDNA of neonatal DBS samples. We conducted three pilot studies of seven, eight and seven subjects, respectively. For each subject...... we analysed a neonatal DBS sample and corresponding adult whole-blood (WB) reference sample. Different DNA sample types were prepared for each of the subjects. Pilot 1: wgaDNA of 2x3.2mm neonatal DBSs (DBS_2x3.2) and raw DNA extract of the WB reference sample (WB_ref). Pilot 2: DBS_2x3.2, WB...

Surface complexation modeling of the effects of phosphate on uranium(VI) adsorption

Energy Technology Data Exchange (ETDEWEB)

Romero-Gonzalez, M.R.; Cheng, T.; Barnett, M.O. [Auburn Univ., AL (United States). Dept. of Civil Engeneering; Roden, E.E. [Wisconsin Univ., Madison, WI (United States). Dept. of Geology and Geophysics

2007-07-01

Previous published data for the adsorption of U(VI) and/or phosphate onto amorphous Fe(III) oxides (hydrous ferric oxide, HFO) and crystalline Fe(III) oxides (goethite) was examined. These data were then used to test the ability of a commonly-used surface complexation model (SCM) to describe the adsorption of U(VI) and phosphate onto pure amorphous and crystalline Fe(III) oxides and synthetic goethite-coated sand, a surrogate for a natural Fe(III)-coated material, using the component additivity (CA) approach. Our modeling results show that this model was able to describe U(VI) adsorption onto both amorphous and crystalline Fe(III) oxides and also goethite-coated sand quite well in the absence of phosphate. However, because phosphate adsorption exhibits a stronger dependence on Fe(III) oxide type than U(VI) adsorption, we could not use this model to consistently describe phosphate adsorption onto both amorphous and crystalline Fe(III) oxides and goethite-coated sand. However, the effects of phosphate on U(VI) adsorption could be incorporated into the model to describe U(VI) adsorption to both amorphous and crystalline Fe(III) oxides and goethite-coated sand, at least for an initial approximation. These results illustrate both the potential and limitations of using surface complexation models developed from pure systems to describe metal/radionuclide adsorption under more complex conditions. (orig.)

Surface complexation modeling of the effects of phosphate on uranium(VI) adsorption

International Nuclear Information System (INIS)

Romero-Gonzalez, M.R.; Cheng, T.; Barnett, M.O.; Roden, E.E.

2007-01-01

Previous published data for the adsorption of U(VI) and/or phosphate onto amorphous Fe(III) oxides (hydrous ferric oxide, HFO) and crystalline Fe(III) oxides (goethite) was examined. These data were then used to test the ability of a commonly-used surface complexation model (SCM) to describe the adsorption of U(VI) and phosphate onto pure amorphous and crystalline Fe(III) oxides and synthetic goethite-coated sand, a surrogate for a natural Fe(III)-coated material, using the component additivity (CA) approach. Our modeling results show that this model was able to describe U(VI) adsorption onto both amorphous and crystalline Fe(III) oxides and also goethite-coated sand quite well in the absence of phosphate. However, because phosphate adsorption exhibits a stronger dependence on Fe(III) oxide type than U(VI) adsorption, we could not use this model to consistently describe phosphate adsorption onto both amorphous and crystalline Fe(III) oxides and goethite-coated sand. However, the effects of phosphate on U(VI) adsorption could be incorporated into the model to describe U(VI) adsorption to both amorphous and crystalline Fe(III) oxides and goethite-coated sand, at least for an initial approximation. These results illustrate both the potential and limitations of using surface complexation models developed from pure systems to describe metal/radionuclide adsorption under more complex conditions. (orig.)

Effect of SnO2/SiO2 nano particle dispersant on the performance characteristic of complex multi-doped composite coating produced through electrodeposition on oil and gas storage tap

Science.gov (United States)

Anawe, P. A. L.; Fayomi, O. S. I.; Ayoola, A. A.; Popoola, A. P. I.

2018-06-01

The effect of SnO2/SiO2 nano particle dispersant on the performance characteristic of complex zinc multi-doped composite coating produced through electrodeposition is studied. The degradation behaviour in term of wear and chemical corrosion activities were considered as a major factor in service. The wear mass loss was carried out with the help of reciprocating tester. The electrochemical corrosion characteristics were investigated using linear polarization technique in 3.5% simulated sodium chloride media. The outcome of the analysis shows that the developed coating was seen to provide a sound anti wear characteristics in its multidoped state. The corrosion resistance properties were observed to be massive compared to the binary based sample. It is expected that this characteristic will impact on the performance life span of storage tap in oil and gas.

Zein/caseinate/pectin complex nanoparticles: Formation and characterization.

Science.gov (United States)

Chang, Chao; Wang, Taoran; Hu, Qiaobin; Luo, Yangchao

2017-11-01

In this study, pectin was used as coating material to form zein/caseinate/pectin complex nanoparticles through pH adjustment and heating treatment for potential oral delivery applications. The preparation conditions were studied by applying heating treatment at different pHs, either the isoelectric point of zein (pH 6.2) or caseinate (pH 4.6), or consecutively at both pHs. The particulate characteristics, including particle size, polydispersity index, and zeta potential were monitored for complex nanoparticles formed under different preparation conditions. The complex nanoparticles generally exhibited particle size smaller than 200nm with narrow distribution, spherical shape, and strong negative charge. Fourier transform infrared and fluorescence spectroscopy revealed that hydrophobic interactions and hydrogen bonds were involved in the formation of complex nanoparticles, in addition to electrostatic interactions. Fresh colloidal dispersion and freeze-dried powders varied in their morphology, depending on their preparation conditions. Our results suggested that heating pH and sequence significantly affected the morphology of complex nanoparticles, and pectin coating exerted stabilization effect under simulated gastrointestinal conditions. The present study provides insight into the formation of protein/polysaccharide complex nanoparticles under different preparation conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Neocellularization and neovascularization of nanosized bioactive glass-coated decellularized trabecular bone scaffolds

KAUST Repository

Gerhardt, Lutz Christian

2012-09-11

In this study, the in vivo recellularization and neovascularization of nanosized bioactive glass (n-BG)-coated decellu-larized trabecular bone scaffolds were studied in a rat model and quantified using stereological analyses. Based on the highest amount of vascular endothelial growth factor (VEGF) secreted by human fibroblasts grown on n-BG coatings (0-1.245 mg/cm 2), decellularized trabecular bone samples (porosity: 43-81%) were coated with n-BG particles. Grown on n-BG particles at a coating density of 0.263 mg/cm2, human fibroblasts produced 4.3 times more VEGF than on uncoated controls. After 8 weeks of implantation in Sprague-Dawley rats, both uncoated and n-BG-coated samples were well infiltrated with newly formed tissue (47-48%) and blood vessels (3-4%). No significant differences were found in cellularization and vascularization between uncoated bone scaffolds and n-BG-coated scaffolds. This finding indicates that the decellularized bone itself may exhibit growth-promoting properties induced by the highly interconnected pore microarchitecture and/or proteins left behind on decellularized scaffolds. Even if we did not find proangiogenic effects in n-BG-coated bone scaffolds, a bioactive coating is considered to be beneficial to impart osteoinductive and osteoconductive properties to decellularized bone. n-BG-coated bone grafts have thus high clinical potential for the regeneration of complex tissue defects given their ability for recellularization and neovascularization. © 2012 Wiley Periodicals, Inc.

Genetic mapping and exome sequencing identify variants associated with five novel diseases.

Directory of Open Access Journals (Sweden)

Erik G Puffenberger

Full Text Available The Clinic for Special Children (CSC has integrated biochemical and molecular methods into a rural pediatric practice serving Old Order Amish and Mennonite (Plain children. Among the Plain people, we have used single nucleotide polymorphism (SNP microarrays to genetically map recessive disorders to large autozygous haplotype blocks (mean = 4.4 Mb that contain many genes (mean = 79. For some, uninformative mapping or large gene lists preclude disease-gene identification by Sanger sequencing. Seven such conditions were selected for exome sequencing at the Broad Institute; all had been previously mapped at the CSC using low density SNP microarrays coupled with autozygosity and linkage analyses. Using between 1 and 5 patient samples per disorder, we identified sequence variants in the known disease-causing genes SLC6A3 and FLVCR1, and present evidence to strongly support the pathogenicity of variants identified in TUBGCP6, BRAT1, SNIP1, CRADD, and HARS. Our results reveal the power of coupling new genotyping technologies to population-specific genetic knowledge and robust clinical data.

Methods and means for coating paper by film coating

NARCIS (Netherlands)

van der Maarel, Marc; Ter Veer, Arend Berend Cornelis; Vrieling-Smit, Annet; Delnoye, Pierre

2015-01-01

This invention relates to the field of paper coating, more in particular to means and methods for providing paper with at least one layer of pigment using film coating to obtain a well printable surface. Provided is a method for preparing coated paper comprising the steps of: a) providing a

Exome sequencing identifies a novel mutation of the GDI1 gene in a Chinese non-syndromic X-linked intellectual disability family

Directory of Open Access Journals (Sweden)

Yongheng Duan

2017-08-01

Full Text Available Abstract X-linked intellectual disability (XLID has been associated with various genes. Diagnosis of XLID, especially for non-syndromic ones (NS-XLID, is often hampered by the heterogeneity of this disease. Here we report the case of a Chinese family in which three males suffer from intellectual disability (ID. The three patients shared the same phenotype: no typical clinical manifestation other than IQ score ≤ 70. For a genetic diagnosis for this family we carried out whole exome sequencing on the proband, and validated 16 variants of interest in the genomic DNA of all the family members. A missense mutation (c.710G > T, which mapped to exon 6 of the Rab GDP-Dissociation Inhibitor 1 (GDI1 gene, was found segregating with the ID phenotype, and this mutation changes the 237th position in the guanosine diphosphate dissociation inhibitor (GDI protein from glycine to valine (p. Gly237Val. Through molecular dynamics simulations we found that this substitution results in a conformational change of GDI, possibly affecting the Rab-binding capacity of this protein. In conclusion, our study identified a novel GDI1 mutation that is possibly NS-XLID causative, and showed that whole exome sequencing provides advantages for detecting novel ID-associated variants and can greatly facilitate the genetic diagnosis of the disease.

Progress and Challenges of Ultrasonic Testing for Stress in Remanufacturing Laser Cladding Coating

Directory of Open Access Journals (Sweden)

Xiao-Ling Yan

2018-02-01

Full Text Available Stress in laser cladding coating is an important factor affecting the safe operation of remanufacturing components. Ultrasonic testing has become a popular approach in the nondestructive evaluation of stress, because it has the advantages of safety, nondestructiveness, and online detection. This paper provides a review of ultrasonic testing for stress in remanufacturing laser cladding coating. It summarizes the recent research outcomes on ultrasonic testing for stress, and analyzes the mechanism of ultrasonic testing for stress. Remanufacturing laser cladding coating shows typical anisotropic behaviors. The ultrasonic testing signal in laser cladding coating is influenced by many complex factors, such as microstructure, defect, temperature, and surface roughness, among others. At present, ultrasonic testing for stress in laser cladding coating can only be done roughly. This paper discusses the active mechanism of micro/macro factors in the reliability of stress measurement, as well as the impact of stress measurement on the quality and safety of remanufacturing components. Based on the discussion, this paper proposes strategies to nondestructively, rapidly, and accurately measure stress in remanufacturing laser cladding coating.

PREPARING OF THE CHAMELEON COATING BY THE ION JET DEPOSITION METHOD

Directory of Open Access Journals (Sweden)

Jakub Skocdopole

2017-07-01

Full Text Available Preparation of chameleon coatings using an Ionized Jet Deposition (IJD technique is reported in the present paper. IJD is a new flexible method for thin film deposition developed by Noivion, Srl. The chameleon coatings are thin films characterised by a distinct change of their tribological properties according to the external conditions. The deposited films of SiC and TiN materials were examined by the Raman spectroscopy, SEM and XPS. The results of the Raman spectroscopy have proved an amorphous structure of SiC films. The data from XPS on TiN films have shown that the films are heavily oxidized, but also prove that the films are composed of TiN and pure Ti. The SEM provided information about the size of grains and particles constituting the deposited films, which is important for tribological properties of the films. Deposition of the chameleon coating is very complex problem and IJD could be ideal method for preparation of this coating.

Laboratory Investigation of Complex Conductivity and Magnetic Susceptibility on Natural Iron Oxide Coated Sand

Science.gov (United States)

Wang, C.; Slater, L. D.; Day-Lewis, F. D.; Briggs, M. A.

2017-12-01

Redox reactions occurring at the oxic/anoxic interface where groundwater discharges to surface water commonly result in iron oxide deposition that coats sediment grains. With relatively large total surface area, these iron oxide coated sediments serve as a sink for sorption of dissolved contaminants, although this sink may be temporary if redox conditions fluctuate with varied flow conditions. Characterization of the distribution of iron oxides in streambed sediments could provide valuable understanding of biogeochemical reactions and the ability of a natural system to sorb contaminants. Towards developing a field methodology, we conducted laboratory spectral induced polarization (SIP) and magnetic susceptibility (MS) measurements on natural iron oxide coated sand (Fe-sand) with grain sizes ranging from 0.3 to 2.0 mm in order to assess the sensitivity of these measurements to iron oxides in sediments. The Fe-sand was also sorted by sieving into various grain sizes to study the impact of grain size on the polarization mechanisms. The unsorted Fe-sand saturated with 0.01 S/m NaCl solution exhibited a distinct phase response ( > 4 mrad) in the frequency range from 0.001 to 100 Hz whereas regular silica sand was characterized by a phase response less than 1 mrad under the same conditions. The presence of iron oxide substantially increased MS (3.08×10-3 SI) over that of regular sand ( Laboratory results demonstrated that SIP and MS may be well suited to mapping the distribution of iron oxides in streambed sediments associated with anoxic groundwater discharge.

Launch Pad Coatings for Smart Corrosion Control

Science.gov (United States)

Calle, Luz M.; Hintze, Paul E.; Bucherl, Cori N.; Li, Wenyan; Buhrow, Jerry W.; Curran, Jerome P.; Whitten, Mary C.

2010-01-01

Corrosion is the degradation of a material as a result of its interaction with the environment. The environment at the KSC launch pads has been documented by ASM International (formerly American Society for Metals) as the most corrosive in the US. The 70 tons of highly corrosive hydrochloric acid that are generated by the solid rocket boosters during a launch exacerbate the corrosiveness of the environment at the pads. Numerous failures at the pads are caused by the pitting of stainless steels, rebar corrosion, and the degradation of concrete. Corrosion control of launch pad structures relies on the use of coatings selected from the qualified products list (QPL) of the NASA Standard 5008A for Protective Coating of Carbon Steel, Stainless Steel, and Aluminum on Launch Structures, Facilities, and Ground Support Equipment. This standard was developed to establish uniform engineering practices and methods and to ensure the inclusion of essential criteria in the coating of ground support equipment (GSE) and facilities used by or for NASA. This standard is applicable to GSE and facilities that support space vehicle or payload programs or projects and to critical facilities at all NASA locations worldwide. Environmental regulation changes have dramatically reduced the production, handling, use, and availability of conventional protective coatings for application to KSC launch structures and ground support equipment. Current attrition rate of qualified KSC coatings will drastically limit the number of commercial off the shelf (COTS) products available for the Constellation Program (CxP) ground operations (GO). CxP GO identified corrosion detection and control technologies as a critical, initial capability technology need for ground processing of Ares I and Ares V to meet Constellation Architecture Requirements Document (CARD) CxP 70000 operability requirements for reduced ground processing complexity, streamlined integrated testing, and operations phase affordability

LANTHANUM STAINING OF THE SURFACE COAT OF CELLS

Science.gov (United States)

Shea, Stephen M.

1971-01-01

Among the techniques which have been reported to stain the surface coat of cells, for electron microscopy, is lanthanum staining en bloc. Similarly, the presence of the cationic dye, Alcian blue 8GX, in a primary glutaraldehyde fixative has been reported to improve the preservation of the surface coat of cells of many types; however, the preserved coat is not very electron opaque unless thin sections are counterstained. The present paper shows that for several rat tissues lanthanum staining en bloc is an effective electron stain for the cell surface, giving excellent contrast, if combined sequentially with prefixation in an aldehyde fixative containing Alcian blue. The cationic substance cetylpyridinium chloride was found to have a similar effect to that of Alcian blue in enhancing the lanthanum staining of the surface coat material of the brush border of intestinal epithelial cells. The patterns of lanthanum staining obtained for the tissues studied strikingly resemble those reported in the literature where tissues are stained by several standard methods for demonstrating mucosubstances at the ultrastructural level. This fact and the reproduction of the effect of Alcian blue by cetylpyridinium chloride constitute a persuasive empirical argument that the material visualized is a mucopolysaccharide or mucopolysaccharide-protein complex. PMID:4108476

Utility of whole exome sequencing in the diagnosis of Usher syndrome: Report of novel compound heterozygous MYO7A mutations.

Science.gov (United States)

Ramzan, Khushnooda; Al-Owain, Mohammed; Huma, Rozeena; Al-Hazzaa, Selwa A F; Al-Ageel, Sarah; Imtiaz, Faiqa; Al-Sayed, Moeenaldeen

2018-05-01

Next generation sequencing (NGS), such as targeted panel sequencing, whole-exome sequencing and whole-genome sequencing has led to an exponential increase of elucidated genetic causes in both rare diseases, and common but heterogeneous disorders. NGS is applied in both research and clinical settings, and the clinical exome sequencing (CES), which provides not only the sequence variation data but also clinical interpretation, aids in reaching a final conclusion with regards to a genetic diagnosis. Usher syndrome is a group of disorders, characterized by bilateral sensorineural hearing loss, with or without vestibular dysfunction and retinitis pigmentosa. The index patient, a 2-year-old child was initially diagnosed with nonsyndromic hearing impairment. Homozygosity mapping followed by CES was utilized as a diagnostic tool to identify the genetic basis of his hearing loss. A paternally inherited novel insertion, c.198_199insA (p.Val67Serfs*73) and a maternally inherited novel deletion, c.1219_1226del (p.Phe407Aspfs*33) in gene MYO7A were found in compound heterozygous state in the index patient. The result expands the mutational spectrum of MYO7A. In addition it helped in early diagnosis of the syndrome, for planning and adjustments for the patient, and as well as for future family planning. This study highlights the clinical effectiveness of CES for Usher syndrome diagnosis in a child presented with congenital hearing loss. Copyright © 2018. Published by Elsevier B.V.

AlOx Coating of Ultrastable Zeolite Y: A Possible Method for Vanadium Passivation of FCC Catalysts

NARCIS (Netherlands)

Weckhuysen, B.M.; Catana, Gabriela; Grünert, W.; Voort, P. van der; Vansant, E.F.; Schoonheydt, R.A.

2000-01-01

AlOx coating is proposed as a possible method for vanadium passivation of the ultrastable zeolite Y (USY). Two coating methods are discussed: (i) the deposition of the [Al13O4(OH)24(H2O)12]7+ ([Al13]) complex from aqueous solutions and (ii) the anchoring of alumoxane by in situ triisobutylaluminum

Stent Coating Integrity of Durable and Biodegradable Coated Drug Eluting Stents.

Science.gov (United States)

Yazdani, Saami K; Sheehy, Alexander; Pacetti, Stephen; Rittlemeyer, Brandon; Kolodgie, Frank D; Virmani, Renu

2016-10-01

Coatings consisting of a polymer and drug are widely used in drug-eluting stents (DES) and are essential in providing programmable drug release kinetics. Among other factors, stent coating technologies can influence blood compatibility, affect acute and sub-acute healing, and potentially trigger a chronic inflammatory response. The aim of this study was to investigate the short-term (7 and 28 days) and long-term (90 and 180 days) coating integrity of the Xience Prime Everolimus-Eluting Stent (EES), Resolute Zotarolimus-Eluting Stent (ZES), Taxus Paclitaxel-Eluting Stent (PES), and Nobori Biolimus A9-Eluting Stent (BES) in a rabbit ilio-femoral stent model. Stented arteries (n = 48) were harvested and the tissue surrounding the implanted stents digested away with an enzymatic solution. Results demonstrated that the majority of struts of EES were without any coating defects with a few struts showing minor defects. Similarly, for the ZES, most of the struts were without coating defects at all time points except at 180 days. The majority of PES demonstrated mostly webbing and uneven coating. In the BES group, the majority of strut coating showed polymer cracking. Overall, the EES and ZES had fewer coating defects than the PES and BES. Coating defects, however increase over time for the ZES, whereas the percent of coating irregularities remained constant for the EES. These results provide, for the first time, a comparison of the long-term durability of these drug-eluting stent coatings in vivo. © 2016, Wiley Periodicals, Inc.

Development and electrochemical characterization of Ni‐P coated tungsten incorporated electroless nickel coatings

Energy Technology Data Exchange (ETDEWEB)

Shibli, S.M.A., E-mail: smashibli@yahoo.com; Chinchu, K.S.

2016-08-01

Ni‐P-W alloy and composite coatings were prepared by incorporation of sodium tungstate/tungsten and Ni‐P coated tungsten into electroless nickel bath respectively. Good inter-particle interactions among the depositing elements i.e. Ni and P with the incorporating tungsten particles were achieved by means of pre-coated tungsten particle by electroless nickel covering prior to its addition into the electroless bath. The pre-coated tungsten particles got incorporated uniformly into the Ni-P matrix of the coating. The particles and the coatings were characterized at different stages by different techniques including X-ray diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive spectrometry (EDS). The electroless Ni-P coating incorporated with pre-coated tungsten exhibited considerably high hardness, thickness and deposition rate. The performance and corrosion resistance characteristics of the composite coating incorporated with the nickel coated tungsten were found to be superior over other conventional Ni-P-W ternary alloy coatings currently reported. - Highlights: • An amorphous Ni-P coating was effectively formed on tungsten particles. • Electroless ternary Ni-P-W composite coatings were successfully prepared. • Enhancement in the inter-particle interaction in the Ni-P composite matrix was achieved. • Efficient and uniform incorporation of the composite in the internal layer was evident. • The tungsten incorporated coating possessed effective barrier protection.

Ellipsometry of single-layer antireflection coatings on transparent substrates

Science.gov (United States)

Azzam, R. M. A.

2017-11-01

The complex reflection coefficients of p- and s-polarized light and ellipsometric parameters of a transparent substrate of refractive index n2, which is coated by a transparent thin film whose refractive index n1 =√{n2 } satisfies the anti-reflection condition at normal incidence, are considered as functions of film thickness d and angle of incidence ϕ. A unique coated surface, with n1 =√{n2 } and film thickness d equal to half of the film-thickness period Dϕ at angle ϕ and wavelength λ, reflects light of the same wavelength without change of polarization for all incident polarization states. (The reflection Jones matrix of such coated surface is the 2 × 2 identity matrix pre-multiplied by a scalar, hence tanΨ = 1,Δ = 0.) To monitor the deposition of an antireflection coating, the normalized Stokes parameters of obliquely reflected light (e.g. at ϕ =70∘) are measured until predetermined target values of those parameters are detected. This provides a more accurate means of film thickness control than is possible using a micro-balance technique or an intensity reflectance method.

XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing.

Science.gov (United States)

Piton, Amélie; Redin, Claire; Mandel, Jean-Louis

2013-08-08

Because of the unbalanced sex ratio (1.3-1.4 to 1) observed in intellectual disability (ID) and the identification of large ID-affected families showing X-linked segregation, much attention has been focused on the genetics of X-linked ID (XLID). Mutations causing monogenic XLID have now been reported in over 100 genes, most of which are commonly included in XLID diagnostic gene panels. Nonetheless, the boundary between true mutations and rare non-disease-causing variants often remains elusive. The sequencing of a large number of control X chromosomes, required for avoiding false-positive results, was not systematically possible in the past. Such information is now available thanks to large-scale sequencing projects such as the National Heart, Lung, and Blood (NHLBI) Exome Sequencing Project, which provides variation information on 10,563 X chromosomes from the general population. We used this NHLBI cohort to systematically reassess the implication of 106 genes proposed to be involved in monogenic forms of XLID. We particularly question the implication in XLID of ten of them (AGTR2, MAGT1, ZNF674, SRPX2, ATP6AP2, ARHGEF6, NXF5, ZCCHC12, ZNF41, and ZNF81), in which truncating variants or previously published mutations are observed at a relatively high frequency within this cohort. We also highlight 15 other genes (CCDC22, CLIC2, CNKSR2, FRMPD4, HCFC1, IGBP1, KIAA2022, KLF8, MAOA, NAA10, NLGN3, RPL10, SHROOM4, ZDHHC15, and ZNF261) for which replication studies are warranted. We propose that similar reassessment of reported mutations (and genes) with the use of data from large-scale human exome sequencing would be relevant for a wide range of other genetic diseases. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Whole-exome sequencing implicates DGKH as a risk gene for panic disorder in the Faroese population

DEFF Research Database (Denmark)

Gregersen, Noomi; Lescai, Francesco; Liang, Jieqin

2016-01-01

attacks, and genetic factors have been estimated to explain around 40% of the risk. In this study the potential enrichment of PD risk variants was explored based on whole-exome sequencing of 54 patients with PD and 211 control individuals from the Faroese population. No genome-wide significant......The demographic history of the isolated population of the Faroe Islands may have induced enrichment of variants rarely seen in outbred European populations, including enrichment of risk variants for panic disorder (PD). PD is a common mental disorder, characterized by recurring and unprovoked panic...... mental disorders. Additionally, we found an enrichment of PD risk variants in the Faroese population; variants with otherwise low frequency in more outbreed European populations. © 2016 Wiley Periodicals, Inc....

Informed consent for exome sequencing research in families with genetic disease: the emerging issue of incidental findings.

Science.gov (United States)

Bergner, Amanda L; Bollinger, Juli; Raraigh, Karen S; Tichnell, Crystal; Murray, Brittney; Blout, Carrie Lynn; Telegrafi, Aida Bytyci; James, Cynthia A

2014-11-01

Genomic sequencing technology is increasingly used in genetic research. Studies of informed consent for exome and genome sequencing (ES/GS) research have largely involved hypothetical scenarios or healthy individuals enrolling in population-based studies. Studies have yet to explore the consent experiences of adults with inherited disease. We conducted a qualitative interview study of 15 adults recently enrolled in a large-scale ES/GS study (11 affected adults, four parents of affected children). Our study had two goals: (1) to explore three theoretical barriers to consent for ES/GS research (interpretive/technical complexity, possibility of incidental findings, and risks of loss of privacy); and (2) to explore how interviewees experienced the consent process. Interviewees could articulate study goals and processes, describe incidental findings, discuss risks of privacy loss, and reflect on their consent experience. Few expected the study would identify the genetic cause of their condition. All elected to receive incidental findings. Interviewees acknowledged paying little attention to potential implications of incidental findings in light of more pressing goals of supporting research regarding their own medical conditions. Interviewees suggested that experience living with a genetic condition prepared them to adjust to incidental findings. Interviewees also expressed little concern about loss of confidentiality of study data. Some experienced the consent process as very long. None desired reconsent prior to return of study results. Families with inherited disease likely would benefit from a consent process in which study risks and benefits were discussed in the context of prior experiences with genetic research and genetic disease. © 2014 Wiley Periodicals, Inc.

TECHNOLOGICAL PECULIARITIES OF THERMAL BARRIER COATINGS BASED ON ZIRCONIUM DIOXIDE

Directory of Open Access Journals (Sweden)

V. V. Okovity

2016-01-01

Full Text Available A technology for formation of thermal barrier coatings (TBC based on zirconium dioxide has been developed in the paper. The paper investigates structures of phase composition and thermal stability of such developed coatings. Investigation results pertaining to formation of an oxide system ZrO2 – Y2O3, while using plasma spraying and subsequent high-energy processing, which allows to increase resistance of a thermal barrier coating to thermal cycling heat resistance of the coating at temperature of 1100 °C. This leads to longer protection of bottom layer against high-temperature exposure. The methodology is based on complex metallographic, X-ray diffraction and electron microscopy investigations of structural elements in composite plasma coatings of the ZrO2 – Y2O system. Resistance of plasma coatings (Мe – Cr – Al – Y/ZrO2 – Y2O3-type, used as TBC to protect gas turbine engine blades under conditions of frequent thermal cyclings is limited by cleavage of an outer ceramic layer. Structural and electron microprobe investigations have shown that as a result of thermal cycling an outer atmosphere due to porous structure of the ceramic coating layer, migrates to the surface of lower metal coating, causing its oxidation. As a result, the metal-ceramic Al2O3 layer is formed at a metal-ceramic interface and it changes a stress state of the coating that causes a reduction of protective properties. Thus, a high heat resistance of thermal barrier coatings depends on processes occurring at the interface between metal and ceramic coating layers. A laser impact on samples with TBC leads to changes in the structure of the oxide layer of ZrO2 – Y2O3. In this case its initial surface characterized by considerable relief is significantly flattened due to processing and the coating is fractured and it is separated in fragments. As the oxide coating has low thermal conductivity, and the time of laser exposure is about 10–3 sec, a heat flux

Pb, Cu, and Zn distributions at humic acid-coated metal-oxide surfaces

Science.gov (United States)

Wang, Yingge; Michel, F. Marc; Choi, Yongseong; Eng, Peter J.; Levard, Clement; Siebner, Hagar; Gu, Baohua; Bargar, John R.; Brown, Gordon E.

2016-09-01

Mineral surfaces are often coated by natural organic matter (NOM), which has a major influence on metal-ion sorption and sequestration because of the abundance of binding sites in such coatings and the changes they cause in local nanoscale environments. The effects of NOM coatings on mineral surfaces are, however, still poorly understood at the molecular level due to the complexity of these systems. In this study, we have applied long-period X-ray standing wave-fluorescence yield (LP-XSW-FY) spectroscopy to measure the partitioning of naturally present Cu(II) (0.0226%), Zn(II) (0.009%), and Pb(II) (∼0.0004%) between Elliott Soil Humic Acid (ESHA) coatings and three model single-crystal metal-oxide substrates: α-Al2O3 (0 0 0 1), α-Al2O3 (1 -1 0 2), and α-Fe2O3 (0 0 0 1). The competitive sorption effects among these metal ions for binding sites in the ESHA coatings and on the metal-oxide surfaces were investigated as a function of reaction time, calcium content, and solution pH. Pb(II) ions present in the ESHA coatings were found to redistribute to reactive α-Al2O3 (1 -1 0 2) and α-Fe2O3 (0 0 0 1) surfaces after 3 h of reaction (pH = 6.0, [Ca(II)] = 2 mM). Pb(II) partitioning onto these reactive metal-oxide surfaces increased with increasing reaction time (up to 7 d). In addition, the partitioning of Cu(II) and Zn(II) from the ESHA coating to the α-Fe2O3 (0 0 0 1) substrate increased slightly with reaction time (2.4% and 3.7% for Cu(II) and Zn(II), respectively, after 3 h and 6.4% and 7.7% for Cu(II) and Zn(II), respectively, after 72 h of reaction time). However, no changes in the partitioning of Cu(II) and Zn(II) onto the α-Al2O3 (1 -1 0 2) surface were observed with increasing reaction time, suggesting that these ions strongly complex with functional groups in the ESHA coatings. Similar results were obtained for Cu(II) and Zn(II) on the ESHA-coated α-Al2O3 (1 -1 0 2) surfaces in samples without the addition of calcium. However, the amounts of Pb

Factors Influencing Plasma Electrolytic Oxidation(PEO) Coatings on Magnesium Alloys: A Review

Energy Technology Data Exchange (ETDEWEB)

Shim, Gunchoo [KISTI ReSEAT Program, Daejon (Korea, Republic of)

2017-05-15

Magnesium alloys, which possess excellent specific strength and castability, are highly susceptible to corrosion. Although anodizing is widely used to resolve this problem, it requires toxic electrolytes and produces relatively thin and weak surface coatings. Recently, plasma electrolytic oxidation (PEO) has emerged as an alternative to anodizing. Although it is derived from conventional anodizing, it uses eco-friendly electrolytes and forms thicker, denser, and harder coatings on the surface of magnesium alloys. However, PEO is a complex process involving physical, chemical, and electrochemical reactions, and it is influenced by various factors such as the alloy substrate composition, electrolyte/additive composition, and the electrical variables including the mode of power supply, applied voltage/current density, frequency, and duty cycle. In this article, the detailed effects of these parameters on the microstructure and properties of the PEO coatings are reviewed, and methods of improving the coatings are proposed.

Evolution of self-organization in nano-structured PVD coatings under extreme tribological conditions

Energy Technology Data Exchange (ETDEWEB)

Fox-Rabinovich, G., E-mail: gfox@mcmaster.ca [Department of Mechanical Engineering, McMaster University, 1280 Main St. W., Hamilton, ON, Canada L8S 4L7 (Canada); Kovalev, A. [Surface Phenomena Researches Group, CNIICHERMET, 9/23, 2-nd Baumanskaya Street, Moscow 105005 (Russian Federation); Aguirre, M.H. [Laboratory of Advanced Microscopy, Institute of Nanoscience of Aragón, University of Zaragoza, 50018 Zaragoza (Spain); Yamamoto, K. [Materials Research Laboratory, Kobe Steel Ltd, 1-5-5 Takatsuda-dai, Nishi-ku, Kobe 651-2271, Hyogo (Japan); Veldhuis, S. [Department of Mechanical Engineering, McMaster University, 1280 Main St. W., Hamilton, ON, Canada L8S 4L7 (Canada); Gershman, I. [All-Russian Railway Research Institute, 10 Third Mytishchinskaya Street, Moscow 29851 (Russian Federation); Rashkovskiy, A. [Surface Phenomena Researches Group, CNIICHERMET, 9/23, 2-nd Baumanskaya Street, Moscow 105005 (Russian Federation); Endrino, J.L. [Albengoa Research, Energia Solar 1, Palmas Altas, Seville 41014 (Spain); Beake, B. [Micro Materials Limited, Willow House, Yale Business Village, Ellice Way, Wrexham LL13 7YL (United Kingdom); Dosbaeva, G. [Department of Mechanical Engineering, McMaster University, 1280 Main St. W., Hamilton, ON, Canada L8S 4L7 (Canada); Wainstein, D. [Surface Phenomena Researches Group, CNIICHERMET, 9/23, 2-nd Baumanskaya Street, Moscow 105005 (Russian Federation); Yuan, Junifeng; Bunting, J.W. [Department of Mechanical Engineering, McMaster University, 1280 Main St. W., Hamilton, ON, Canada L8S 4L7 (Canada)

2014-04-01

Highlights: • The evolution of self-organization under extreme frictional conditions has been studied. • Comprehensive characterization of the tribo-films was made using various surface analytical techniques. • During the running-in stage, mullite tribo-ceramics predominate on the surface of the nano-multilayer coating, establishing a functional hierarchy within the layer of tribo-films. • It is possible to control tribo-film evolution during self-organization by means of an increase in structural complexity and the non-equilibrium state of the surface engineered layer. - Abstract: The evolution of the self-organization process where dissipative structures are formed under the extreme frictional conditions associated with high performance dry machining of hardened steels has been studied in detail. The emphasis was on the progressive studies of surface transformations within multilayer and monolayer TiAlCrSiYN-based PVD coatings during the running-in stage of wear when self-organization process occurs. The coating layer was characterized by high resolution electron energy-loss spectroscopy (HREELS). It is shown that the nano-multilayer coating possesses higher non-equilibrium structure in comparison to the monolayer. Comprehensive studies of the tribo-films (dissipative structures) formed on the friction surface were made using a number of advanced surface characterization techniques such as X-ray photoelectron spectroscopy (XPS) and X-ray absorption near edge structure (XANES). The data obtained for the tribo-films was combined with the detailed TEM studies of the structural and phase transformations within the underlying coating layer. This data was related to the micro-mechanical characteristics of the coating layer and its wear resistance. It was demonstrated that the evolution of the self-organization process is strongly controlled by the characteristics of the tribo-films formed at different stages of the wear process. Within running-in stage (after

Applicability of near-infrared spectroscopy in the monitoring of film coating and curing process of the prolonged release coated pellets.

Science.gov (United States)

Korasa, Klemen; Hudovornik, Grega; Vrečer, Franc

2016-10-10

Although process analytical technology (PAT) guidance has been introduced to the pharmaceutical industry just a decade ago, this innovative approach has already become an important part of efficient pharmaceutical development, manufacturing, and quality assurance. PAT tools are especially important in technologically complex operations which require strict control of critical process parameters and have significant effect on final product quality. Manufacturing of prolonged release film coated pellets is definitely one of such processes. The aim of the present work was to study the applicability of the at-line near-infrared spectroscopy (NIR) approach in the monitoring of pellet film coating and curing steps. Film coated pellets were manufactured by coating the active ingredient containing pellets with film coating based on polymethacrylate polymers (Eudragit® RS/RL). The NIR proved as a useful tool for the monitoring of the curing process since it was able to determine the extent of the curing and hence predict drug release rate by using partial least square (PLS) model. However, such approach also showed a number of limitations, such as low reliability and high susceptibility to pellet moisture content, and was thus not able to predict drug release from pellets with high moisture content. On the other hand, the at-line NIR was capable to predict the thickness of Eudragit® RS/RL film coating in a wide range (up to 40μm) with good accuracy even in the pellets with high moisture content. To sum up, high applicability of the at-line NIR in the monitoring of the prolonged release pellets production was demonstrated in the present study. The present findings may contribute to more efficient and reliable PAT solutions in the manufacturing of prolonged release dosage forms. Copyright © 2016 Elsevier B.V. All rights reserved.

Thermal spraying of functionally graded calcium phosphate coatings for biomedical implants

Science.gov (United States)

Wang, Y.; Khor, K. A.; Cheang, P.

1998-03-01

Biomedical requirements in a prosthesis are often complex and diverse in nature. Biomaterials for implants have to display a wide range of adaptability to suit the various stages of the bio-integration process of any foreign material into the human body. Often, a combination of materials is needed. The preparation of a functionally graded bioceramic coating composed of essentially calcium phosphate compounds is explored. The coating is graded in accordance to adhesive strength, bioactivity, and bioresorbability. The bond coat on the Ti-6Al-4V stub is deposited with a particle range of the hydroxyapatite (HA) that will provide a high adhesive strength and bioactivity but have poor bioresorption properties. The top coat, however, is composed of predominantly α-tricalcium phosphate (α-TCP) that is highly bioresorbable. This arrangement has the propensity of allowing accelerated bio-integration of the coating by the body tissues as the top layer is rapidly resorbed, leaving the more bioactive intermediate layer to facilitate the much needed bioactive properties for proper osteoconduction. The processing steps and problems are highlighted, as well as the results of post-spray heat treatment.

9Å structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments.

Science.gov (United States)

Dodonova, Svetlana O; Aderhold, Patrick; Kopp, Juergen; Ganeva, Iva; Röhling, Simone; Hagen, Wim J H; Sinning, Irmgard; Wieland, Felix; Briggs, John A G

2017-06-16

COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that recruits the coatomer complex to the membrane, triggering polymerization and budding. The vesicle uncoats before fusion with a target membrane. Coat components are structurally conserved between COPI and clathrin/adaptor proteins. Using cryo-electron tomography and subtomogram averaging, we determined the structure of the COPI coat assembled on membranes in vitro at 9 Å resolution. We also obtained a 2.57 Å resolution crystal structure of βδ-COP. By combining these structures we built a molecular model of the coat. We additionally determined the coat structure in the presence of ArfGAP proteins that regulate coat dissociation. We found that Arf1 occupies contrasting molecular environments within the coat, leading us to hypothesize that some Arf1 molecules may regulate vesicle assembly while others regulate coat disassembly.

A mesomechanical analysis of the deformation and fracture in polycrystalline materials with ceramic porous coatings

Science.gov (United States)

Balokhonov, R. R.; Zinoviev, A. V.; Romanova, V. A.; Batukhtina, E. E.

2015-10-01

The special features inherent in the mesoscale mechanical behavior of a porous ceramic coating-steel substrate composite are investigated. Microstructure of the coated material is accounted for explicitly as initial conditions of a plane strain dynamic boundary-value problem solved by the finite difference method. Using a mechanical analogy method, a procedure for generating a uniform curvilinear finite difference computational mesh is developed to provide a more accurate description of the complex grain boundary geometry. A modified algorithm for generation of polycrystalline microstructure of the substrate is designed on the basis of the cellular automata method. The constitutive equations for a steel matrix incorporate an elastic-plastic model for a material subjected to isotropic hardening. The Hall-Petch relation is used to account for the effect of the grain size on the yield stress and strain hardening history. A brittle fracture model for a ceramic coating relying on the Huber criterion is employed. The model allows for crack nucleation in the regions of triaxial tension. The complex inhomogeneous stress and plastic strain patterns are shown to be due to the presence of interfaces of three types: coating-substrate interface, grain boundaries, and pore surfaces.

Fouling release nanostructured coatings based on PDMS-polyurea segmented copolymers

KAUST Repository

Fang, Jason

2010-05-01

The bulk and surface characteristics of a series of coatings based on PDMS-polyurea segmented copolymers were correlated to their fouling release performance. Incorporation of polyurea segments to PDMS backbone gives rise to phase separation with the extensively hydrogen bonded hard domains creating an interconnected network that imparts mechanical rigidity. Increasing the compositional complexity of the system by including fluorinated or POSS-functionalized chain extenders or through nanoclay intercalation, confers further thermomechanical improvements. In analogy to the bulk morphology, the surface topography also reflects the compositional complexity of the materials, displaying a wide range of motifs. Investigations on settlement and subsequent removal of Ulva sporelings on those nanostructured surfaces indicate that the work required to remove the microorganisms is significantly lower compared to coatings based on standard PDMS homopolymer. All in all, the series of materials considered in this study demonstrate advanced fouling release properties, while exhibiting superior mechanical properties and, thus, long term durability. © 2010 Elsevier Ltd.

Mixed zirconia calcium phosphate coatings for dental implants: Tailoring coating stability and bioactivity potential

International Nuclear Information System (INIS)

Pardun, Karoline; Treccani, Laura; Volkmann, Eike; Streckbein, Philipp; Heiss, Christian; Destri, Giovanni Li; Marletta, Giovanni; Rezwan, Kurosch

2015-01-01

Enhanced coating stability and adhesion are essential for long-term success of orthopedic and dental implants. In this study, the effect of coating composition on mechanical, physico-chemical and biological properties of coated zirconia specimens is investigated. Zirconia discs and dental screw implants are coated using the wet powder spraying (WPS) technique. The coatings are obtained by mixing yttria-stabilized zirconia (TZ) and hydroxyapatite (HA) in various ratios while a pure HA coating served as reference material. Scanning electron microscopy (SEM) and optical profilometer analysis confirm a similar coating morphology and roughness for all studied coatings, whereas the coating stability can be tailored with composition and is probed by insertion and dissections experiments in bovine bone with coated zirconia screw implants. An increasing content of calcium phosphate (CP) resulted in a decrease of mechanical and chemical stability, while the bioactivity increased in simulated body fluid (SBF). In vitro experiments with human osteoblast cells (HOB) revealed that the cells grew well on all samples but are affected by dissolution behavior of the studied coatings. This work demonstrates the overall good mechanical strength, the excellent interfacial bonding and the bioactivity potential of coatings with higher TZ contents, which provide a highly interesting coating for dental implants. - Highlights: • Different ratios of zirconia (TZ) and calcium phosphate (CP) were deposited on zirconia substrates. • Enhancement of TZ content in mixed coatings increased coating stability. • Enhancement of CP content in mixed coatings increased bioactivity. • All tested coating compositions were non-toxic

Mixed zirconia calcium phosphate coatings for dental implants: Tailoring coating stability and bioactivity potential

Energy Technology Data Exchange (ETDEWEB)

Pardun, Karoline [University of Bremen, Advanced Ceramics, Am Biologischen Garten 2, 28359 Bremen (Germany); Treccani, Laura, E-mail: treccani@uni-bremen.de [University of Bremen, Advanced Ceramics, Am Biologischen Garten 2, 28359 Bremen (Germany); Volkmann, Eike [University of Bremen, Advanced Ceramics, Am Biologischen Garten 2, 28359 Bremen (Germany); Streckbein, Philipp [University Hospital, Justus-Liebig-University Giessen, Department of Cranio-Maxillo-Facial Surgery, Klinikstrasse 33, 35385 Giessen (Germany); Heiss, Christian [University Hospital of Giessen-Marburg, Department of Trauma Surgery, Rudolf-Buchheim-Strasse 7, 35385 Giessen, Germany, (Germany); Laboratory of Experimental Surgery, Kerkraderstrasse 9, 35392 Giessen (Germany); Destri, Giovanni Li; Marletta, Giovanni [Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN), Department of Chemistry, University of Catania and CSGI, Viale A. Doria 6, 95125 Catania (Italy); Rezwan, Kurosch [University of Bremen, Advanced Ceramics, Am Biologischen Garten 2, 28359 Bremen (Germany)

2015-03-01

Enhanced coating stability and adhesion are essential for long-term success of orthopedic and dental implants. In this study, the effect of coating composition on mechanical, physico-chemical and biological properties of coated zirconia specimens is investigated. Zirconia discs and dental screw implants are coated using the wet powder spraying (WPS) technique. The coatings are obtained by mixing yttria-stabilized zirconia (TZ) and hydroxyapatite (HA) in various ratios while a pure HA coating served as reference material. Scanning electron microscopy (SEM) and optical profilometer analysis confirm a similar coating morphology and roughness for all studied coatings, whereas the coating stability can be tailored with composition and is probed by insertion and dissections experiments in bovine bone with coated zirconia screw implants. An increasing content of calcium phosphate (CP) resulted in a decrease of mechanical and chemical stability, while the bioactivity increased in simulated body fluid (SBF). In vitro experiments with human osteoblast cells (HOB) revealed that the cells grew well on all samples but are affected by dissolution behavior of the studied coatings. This work demonstrates the overall good mechanical strength, the excellent interfacial bonding and the bioactivity potential of coatings with higher TZ contents, which provide a highly interesting coating for dental implants. - Highlights: • Different ratios of zirconia (TZ) and calcium phosphate (CP) were deposited on zirconia substrates. • Enhancement of TZ content in mixed coatings increased coating stability. • Enhancement of CP content in mixed coatings increased bioactivity. • All tested coating compositions were non-toxic.

Molecular diagnostic experience of whole-exome sequencing in adult patients.

Science.gov (United States)

Posey, Jennifer E; Rosenfeld, Jill A; James, Regis A; Bainbridge, Matthew; Niu, Zhiyv; Wang, Xia; Dhar, Shweta; Wiszniewski, Wojciech; Akdemir, Zeynep H C; Gambin, Tomasz; Xia, Fan; Person, Richard E; Walkiewicz, Magdalena; Shaw, Chad A; Sutton, V Reid; Beaudet, Arthur L; Muzny, Donna; Eng, Christine M; Yang, Yaping; Gibbs, Richard A; Lupski, James R; Boerwinkle, Eric; Plon, Sharon E

2016-07-01

Whole-exome sequencing (WES) is increasingly used as a diagnostic tool in medicine, but prior reports focus on predominantly pediatric cohorts with neurologic or developmental disorders. We describe the diagnostic yield and characteristics of WES in adults. We performed a retrospective analysis of consecutive WES reports for adults from a diagnostic laboratory. Phenotype composition was determined using Human Phenotype Ontology terms. Molecular diagnoses were reported for 17.5% (85/486) of adults, which is lower than that for a primarily pediatric population (25.2%; P = 0.0003); the diagnostic rate was higher (23.9%) for those 18-30 years of age compared to patients older than 30 years (10.4%; P = 0.0001). Dual Mendelian diagnoses contributed to 7% of diagnoses, revealing blended phenotypes. Diagnoses were more frequent among individuals with abnormalities of the nervous system, skeletal system, head/neck, and growth. Diagnostic rate was independent of family history information, and de novo mutations contributed to 61.4% of autosomal dominant diagnoses. Early WES experience in adults demonstrates molecular diagnoses in a substantial proportion of patients, informing clinical management, recurrence risk, and recommendations for relatives. A positive family history was not predictive, consistent with molecular diagnoses often revealed by de novo events, informing the Mendelian basis of genetic disease in adults.Genet Med 18 7, 678-685.

Preparation and comparison of a-C:H coatings using reactive sputter techniques

Energy Technology Data Exchange (ETDEWEB)

Keunecke, M., E-mail: martin.keunecke@ist.fraunhofer.d [Fraunhofer Institute for Surface Engineering and Thin Films (IST), Braunschweig (Germany); Weigel, K.; Bewilogua, K. [Fraunhofer Institute for Surface Engineering and Thin Films (IST), Braunschweig (Germany); Cremer, R.; Fuss, H.-G. [CemeCon AG, Wuerselen (Germany)

2009-12-31

Amorphous hydrogenated carbon (a-C:H) coatings are widely used in several industrial applications. These coatings commonly will be prepared by plasma activated chemical vapor deposition (PACVD). The main method used to prepare a-C:H coating in industrial scale is based on a glow discharge in a hydrocarbon gas like acetylene or methane using a substrate electrode powered with medium frequency (m.f. - some 10 to 300 kHz). Some aims of further development are adhesion improvement, increase of hardness and high coating quality on complex geometries. A relatively new and promising technique to fulfil these requirements is the deposition of a-C:H coatings by a reactive d.c. magnetron sputter deposition from a graphite target with acetylene as reactive gas. An advancement of this technique is the deposition in a pulsed magnetron sputter process. Using these three mentioned techniques a-C:H coatings were prepared in the same deposition machine. For adhesion improvement different interlayer systems were applied. The effect of different substrate bias voltages (d.c. and d.c. pulse) was investigated. By applying the magnetron sputter technique in the d.c. pulse mode, plastic hardness values up to 40 GPa could be reached. Besides hardness other mechanical properties like resistance against abrasive wear were measured and compared. Cross sectional SEM images showed the growth structure of the coatings.

A novel method for the synthesis of monodisperse gold-coated silica nanoparticles

International Nuclear Information System (INIS)

English, Michael D.; Waclawik, Eric R.

2012-01-01

Monodisperse silica nanoparticles were synthesised by the well-known Stober protocol, then dispersed in acetonitrile (ACN) and subsequently added to a bisacetonitrile gold(I) coordination complex ([Au(MeCN) 2 ] + ) in ACN. The silica hydroxyl groups were deprotonated in the presence of ACN, generating a formal negative charge on the siloxy groups. This allowed the [Au(MeCN) 2 ] + complex to undergo ligand exchange with the silica nanoparticles and form a surface coordination complex with reduction to metallic gold (Au 0 ) proceeding by an inner sphere mechanism. The residual [Au(MeCN) 2 ] + complex was allowed to react with water, disproportionating into Au 0 and Au(III), respectively, with the Au 0 adding to the reduced gold already bound on the silica surface. The so-formed metallic gold seed surface was found to be suitable for the conventional reduction of Au(III) to Au 0 by ascorbic acid (ASC). This process generated a thin and uniform gold coating on the silica nanoparticles. The silica NPs batches synthesised were in a size range from 45 to 460 nm. Of these silica NP batches, the size range from 400 to 480 nm were used for the gold-coating experiments.

Origin of Shear Stability and Compressive Ductility Enhancement of Metallic Glasses by Metal Coating

Science.gov (United States)

Sun, B. A.; Chen, S. H.; Lu, Y. M.; Zhu, Z. G.; Zhao, Y. L.; Yang, Y.; Chan, K. C.; Liu, C. T.

2016-01-01

Metallic glasses (MGs) are notorious for the poor macroscopic ductility and to overcome the weakness various intrinsic and extrinsic strategies have been proposed in past decades. Among them, the metal coating is regarded as a flexible and facile approach, yet the physical origin is poorly understood due to the complex nature of shear banding process. Here, we studied the origin of ductile enhancement in the Cu-coating both experimentally and theoretically. By examining serrated shear events and their stability of MGs, we revealed that the thin coating layer plays a key role in stopping the final catastrophic failure of MGs by slowing down shear band dynamics and thus retarding its attainment to a critical instable state. The mechanical analysis on interplay between the coating layer and shear banding process showed the enhanced shear stability mainly comes from the lateral tension of coating layer induced by the surface shear step and the bonding between the coating layer and MGs rather than the layer thickness is found to play a key role in contributing to the shear stability. PMID:27271435

Can deformation of a polymer film with a rigid coating model geophysical processes?

Science.gov (United States)

Volynskii, A. L.; Bazhenov, S. L.

2007-12-01

The structural and mechanical behavior of polymer films with a thin rigid coating is analyzed. The behavior of such systems under applied stress is accompanied by the formation of a regular wavy surface relief and by regular fragmentation of the coating. The above phenomena are shown to be universal. Both phenomena (stress-induced development of a regular wavy surface relief and regular fragmentation of the coating) are provided by the specific features of mechanical stress transfer from a compliant soft support to a rigid thin coating. The above phenomena are associated with a specific structure of the system, which is referred to as “a rigid coating on a soft substratum” system (RCSS). Surface microrelief in RCSS systems is similar to the ocean floor relief in the vicinity of mid-oceanic ridges. Thus, the complex system composed of a young oceanic crust and upper Earth's mantle may be considered as typically “a solid coating on a soft substratum” system. Specific features of the ocean floor relief are analyzed in terms of the approach advanced for the description of the structural mechanical behavior of polymer films with a rigid coating. This analysis allowed to estimate the strength of an ocean floor.

Arc-discharge and magnetron sputtering combined equipment for nanocomposite coating deposition

International Nuclear Information System (INIS)

Koval, N.N.; Borisov, D.P.; Savostikov, V.M.

2005-01-01

It is known that characteristics of nanocomposite coatings produced by reactive magnetron sputtering undergo an essential influence on the following parameters such as original component composition of targets being sputtered, as well as abundance ratio of such components in the coatings deposited, relative content of inert and reactionary gases in a gas mixture used and a value of operating pressure in a chamber, substrate temperature, and a value of substrate bias potential, determining energy of ionized atoms, ionized atoms flow density, i.e. ion current density on a substrate. The multifactor character of production process of nanocomposite coatings with certain physical and mechanical properties demands a purposeful and complex control on all above-mentioned parameters. To solve such a problem, an arc-discharge and magnetron sputtering combined equipment including a vacuum chamber of approximately ∼ 0.5 m 3 with a built-in low-pressure plasma generator made on the basis of non-self-sustained discharge with a thermal cathode and a planar magnetron combined with two sputtered targets has been created. Construction of such a complex set-up provides both an autonomous mode of operation and simultaneous operation of an arc plasma generator and magnetron sputtering system. Magnetron sputtering of either one or two targets simultaneously is provided as well. An arc plasma generator enables ions current density control on a substrate in a wide range due to discharge current varying from 1 to 100 A. Energy of ions is also being controlled in a wide range by a negative bias potential from 0 to 1000 V applied to a substrate. The wide control range of gas plasma density of a arc discharge of approximately 10 9 -10 11 cm -3 and high uniformity of its distribution over the total volume of an operating chamber (about 15% error with regard to the mean value) provides a purposeful and simultaneous control either of magnetron discharge characteristics (operating pressure of

Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease

Science.gov (United States)

van der Crabben, Saskia N.; Hennus, Marije P.; McGregor, Grant A.; Ritter, Deborah I.; Nagamani, Sandesh C.S.; Wells, Owen S.; Harakalova, Magdalena; Chinn, Ivan K.; Alt, Aaron; Vondrova, Lucie; Hochstenbach, Ron; van Montfrans, Joris M.; Terheggen-Lagro, Suzanne W.; van Lieshout, Stef; van Roosmalen, Markus J.; Renkens, Ivo; Duran, Karen; Nijman, Isaac J.; Kloosterman, Wigard P.; Hennekam, Eric; van Hasselt, Peter M.; Wheeler, David A.; Palecek, Jan J.; Lehmann, Alan R.; Oliver, Antony W.; Pearl, Laurence H.; Plon, Sharon E.; Murray, Johanne M.

2016-01-01

The structural maintenance of chromosomes (SMC) family of proteins supports mitotic proliferation, meiosis, and DNA repair to control genomic stability. Impairments in chromosome maintenance are linked to rare chromosome breakage disorders. Here, we have identified a chromosome breakage syndrome associated with severe lung disease in early childhood. Four children from two unrelated kindreds died of severe pulmonary disease during infancy following viral pneumonia with evidence of combined T and B cell immunodeficiency. Whole exome sequencing revealed biallelic missense mutations in the NSMCE3 (also known as NDNL2) gene, which encodes a subunit of the SMC5/6 complex that is essential for DNA damage response and chromosome segregation. The NSMCE3 mutations disrupted interactions within the SMC5/6 complex, leading to destabilization of the complex. Patient cells showed chromosome rearrangements, micronuclei, sensitivity to replication stress and DNA damage, and defective homologous recombination. This work associates missense mutations in NSMCE3 with an autosomal recessive chromosome breakage syndrome that leads to defective T and B cell function and acute respiratory distress syndrome in early childhood. PMID:27427983

High-temperature resistant MeCrAlY+Al coatings obtained by ARC-PVD method on Ni Base superalloys

International Nuclear Information System (INIS)

Swadzba, L.; Maciejny, A.; Mendala, B.; Supernak, W.

1999-01-01

Investigations of obtaining high temperature coatings on the Ni base superalloys by the ARC-PVD method, using exothermic reaction processes between Ni and Al with NiAl intermetallic formation are presented in the article. By the diffusion heating at 1050 o C NiAl high temperature diffusion coating containing 21% at. Al and 50 μm thick was obtained. In the next stage coatings with more complex chemical composition NiCoCrAlY were formed. The two targets were applied for formation of complex NiCoCrAlY coatings. The good consistence between the chemical composition of the targets and the coatings and an uniform distribution of elements in the coatings were shown. Then the surface was covered with aluminium also by the ARC-PVD method. In the vacuum chamber of the equipment a synthesis reaction between NiCoCrAlY and Al with the formation NiAl intermetallics of high Co, Cr, Y content was initiated by the changes in process parameters. The final heat treatment of coatings was conducted in the air and vacuum at 1050 o C. The strong segregation of yttrium in to the oxide scale in the specimens heated in the air was shown. It was possible to obtain NiAl intermetallic phase coatings modified by Co, Cr and Y by the ARC-PVD method. An example of the application of this method for the aircraft engine turbine blades was presented. Method of ARC-PVD gives the possibility chemical composition and high resistance to oxidizing and hot corrosion. (author)

Antibacterial polymer coatings.

Energy Technology Data Exchange (ETDEWEB)

Wilson, Mollye C.; Allen, Ashley N.; Barnhart, Meghan; Tucker, Mark David; Hibbs, Michael R.

2009-09-01

A series of poly(sulfone)s with quaternary ammonium groups and another series with aldehyde groups are synthesized and tested for biocidal activity against vegetative bacteria and spores, respectively. The polymers are sprayed onto substrates as coatings which are then exposed to aqueous suspensions of organisms. The coatings are inherently biocidal and do not release any agents into the environment. The coatings adhere well to both glass and CARC-coated coupons and they exhibit significant biotoxicity. The most effective quaternary ammonium polymers kills 99.9% of both gram negative and gram positive bacteria and the best aldehyde coating kills 81% of the spores on its surface.

Hafnia-Based Nanostructured Thermal Barrier Coatings for Advanced Hydrogen Turbine Technology

Energy Technology Data Exchange (ETDEWEB)

Ramana, Chintalapalle; Choudhuri, Ahsan

2013-01-31

Thermal barrier coatings (TBCs) are critical technologies for future gas turbine engines of advanced coal based power generation systems. TBCs protect engine components and allow further increase in engine temperatures for higher efficiency. In this work, nanostructured HfO{sub 2}-based coatings, namely Y{sub 2}O{sub 3}-stabilized HfO{sub 2} (YSH), Gd{sub 2}O{sub 3}-stabilized HfO{sub 2} (GSH) and Y{sub 2}O{sub 3}-stabilized ZrO{sub 2}-HfO{sub 2} (YSZH) were investigated for potential TBC applications in hydrogen turbines. Experimental efforts are aimed at creating a fundamental understanding of these TBC materials. Nanostructured ceramic coatings of YSH, GSH and YSZH were grown by physical vapor deposition methods. The effects of processing parameters and ceramic composition on the microstructural evolution of YSH, GSH and YSZH nanostructured coatings was studied using combined X-ray diffraction (XRD) and Electron microscopy analyses. Efforts were directed to derive a detailed understanding of crystal-structure, morphology, and stability of the coatings. In addition, thermal conductivity as a function of composition in YSH, YSZH and GSH coatings was determined. Laboratory experiments using accelerated test environments were used to investigate the relative importance of various thermo-mechanical and thermo-chemical failure modes of TBCs. Effects of thermal cycling, oxidation and their complex interactions were evaluated using a syngas combustor rig.

Comparison of TiC coating and TD coating in actual application

International Nuclear Information System (INIS)

Kim, S.K.; Yoo, J.K.

1995-01-01

Large blocks of SKD-11 were treated by CVD-TiC coating process, TD coating process, TD coating process after vacuum heat treating, and vacuum heat treating. Amount of deformation was measured and compared to find the process which gives the least deformation. Wear tests were carried out for specimens treated by each process. Application of CVD-TiC and TD coating to the automotive press mold was studied

Coating possibilities for magnetic switches

International Nuclear Information System (INIS)

Sharp, D.J.; Harjes, H.C.; Mann, G.A.; Morgan, F.A.

1990-01-01

High average power magnetic pulse compression systems are now being considered for use in several applications such as the High Power Radiation Source (HiPoRS) project. Such systems will require high reliability magnetic switches (saturable inductors) that are very efficient and have long lifetimes. One of the weakest components in magnetic switches is their interlaminar insulation. Considerations related to dielectric breakdown, thermal management of compact designs, and economical approaches for achieving these needs must be addressed. Various dielectric insulation and coating materials have been applied to Metglas foil in an attempt to solve the complex technical and practical problems associated with large magnetic switch structures. This work reports various needs, studies, results, and proposals in selecting and evaluating continuous coating approaches for magnetic foil. Techniques such as electrophoretic polymer deposition and surface chemical oxidation are discussed. We also propose continuous photofabrication processes for applying dielectric ribs or spacers to the foil which permit circulation of dielectric liquids for cooling during repetitive operation. 10 refs., 8 figs., 11 tabs

Determination of nanoparticle surface coatings and nanoparticle purity using microscale thermogravimetric analysis.

Science.gov (United States)

Mansfield, Elisabeth; Tyner, Katherine M; Poling, Christopher M; Blacklock, Jenifer L

2014-02-04

The use of nanoparticles in some applications (i.e., nanomedical, nanofiltration, or nanoelectronic) requires small samples with well-known purities and composition. In addition, when nanoparticles are introduced into complex environments (e.g., biological fluids), the particles may become coated with matter, such as proteins or lipid layers. Many of today's analytical techniques are not able to address small-scale samples of nanoparticles to determine purity and the presence of surface coatings. Through the use of an elevated-temperature quartz crystal microbalance (QCM) method we call microscale thermogravimetric analysis, or μ-TGA, the nanoparticle purity, as well as the presence of any surface coatings of nanomaterials, can be measured. Microscale thermogravimetric analysis is used to determine the presence and amount of surface-bound ligand coverage on gold nanoparticles and confirm the presence of a poly(ethylene glycol) coating on SiO2 nanoparticles. Results are compared to traditional analytical techniques to demonstrate reproducibility and validity of μ-TGA for determining the presence of nanoparticle surface coatings. Carbon nanotube samples are also analyzed and compared to conventional TGA. The results demonstrate μ-TGA is a valid method for quantitative determination of the coatings on nanoparticles, and in some cases, can provide purity and compositional data of the nanoparticles themselves.

Whole-exome sequencing of a rare case of familial childhood acute lymphoblastic leukemia reveals putative predisposing mutations in Fanconi anemia genes.

Science.gov (United States)

Spinella, Jean-François; Healy, Jasmine; Saillour, Virginie; Richer, Chantal; Cassart, Pauline; Ouimet, Manon; Sinnett, Daniel

2015-07-23

Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer. While the multi-step model of pediatric leukemogenesis suggests interplay between constitutional and somatic genomes, the role of inherited genetic variability remains largely undescribed. Nonsyndromic familial ALL, although extremely rare, provides the ideal setting to study inherited contributions to ALL. Toward this goal, we sequenced the exomes of a childhood ALL family consisting of mother, father and two non-twinned siblings diagnosed with concordant pre-B hyperdiploid ALL and previously shown to have inherited a rare form of PRDM9, a histone H3 methyltransferase involved in crossing-over at recombination hotspots and Holliday junctions. We postulated that inheritance of additional rare disadvantaging variants in predisposing cancer genes could affect genomic stability and lead to increased risk of hyperdiploid ALL within this family. Whole exomes were captured using Agilent's SureSelect kit and sequenced on the Life Technologies SOLiD System. We applied a data reduction strategy to identify candidate variants shared by both affected siblings. Under a recessive disease model, we focused on rare non-synonymous or frame-shift variants in leukemia predisposing pathways. Though the family was nonsyndromic, we identified a combination of rare variants in Fanconi anemia (FA) genes FANCP/SLX4 (compound heterozygote - rs137976282/rs79842542) and FANCA (rs61753269) and a rare homozygous variant in the Holliday junction resolvase GEN1 (rs16981869). These variants, predicted to affect protein function, were previously identified in familial breast cancer cases. Based on our in-house database of 369 childhood ALL exomes, the sibs were the only patients to carry this particularly rare combination and only a single hyperdiploid patient was heterozygote at both FANCP/SLX4 positions, while no FANCA variant allele carriers were identified. FANCA is the most commonly mutated gene in FA and is essential for

Depth-resolved X-ray residual stress analysis in PVD (Ti, Cr) N hard coatings

CERN Document Server

Genzel, C

2003-01-01

Physical vapour deposition (PVD) of thin hard coatings on TiN basis is usually performed at rather low temperatures (T sub D < 500 C) far from thermal equilibrium, which leads to high intrinsic residual stresses in the growing film. In contrast to the extrinsic thermal residual stresses which can easily be estimated from the difference of the coefficients of thermal expansion between the substrate and the coating, a theoretical prediction of the intrinsic residual stresses is difficult, because their amount as well as their distribution within the film depend in a very complex way on the deposition kinetics. By the example of strongly fibre-textured PVD (Ti, Cr)N coatings which have been prepared under defined variation of the deposition parameters in order to adjust the residual stress distribution within the coatings, the paper compares different X-ray diffraction techniques with respect to their applicability for detecting residual stresses which are non-uniform over the coating thickness. (orig.)

TiN-Coating Effects on Stainless Steel Tribological Behavior Under Dry and Lubricated Conditions

Science.gov (United States)

Zhang, Liqiang; Yang, Huisheng; Pang, Xiaolu; Gao, Kewei; Tran, Hai T.; Volinsky, Alex A.

2014-04-01

The tribological properties of magnetron sputtered titanium nitride coating on 316L steel, sliding against Si3N4 ceramic ball under dry friction and synthetic perspiration lubrication, were investigated. The morphology of the worn surface and the elemental composition of the wear debris were examined by scanning electron microscopy and energy dispersive spectroscopy. TiN coatings and 316L stainless steel had better tribological properties under synthetic perspiration lubrication than under dry friction. Among the three tested materials (316L, 1.6 and 2.4 μm TiN coatings), 2.4 μm TiN coating exhibits the best wear resistance. The difference in wear damage of the three materials is essentially due to the wear mechanisms. For the TiN coating, the damage is attributed to abrasive wear under synthetic perspiration lubrication and the complex interactive mechanisms, including abrasive and adhesive wear, along with plastic deformation, under dry friction.

Investigation of duty cycle effect on corrosion properties of electrodeposited calcium phosphate coatings

Energy Technology Data Exchange (ETDEWEB)

Azem, Funda Ak, E-mail: funda.ak@deu.edu.tr [Dokuz Eylul University, Faculty of Engineering, Department of Metallurgical and Materials Engineering, Buca, 35390 Izmir (Turkey); Delice, Tulay Koc, E-mail: tulaykocdelice@gmail.com [Dokuz Eylul University, The Graduate School of Natural and Applied Sciences, Buca, 35390 Izmir (Turkey); Ungan, Guler, E-mail: gulerungan@hotmail.com [Es Group, Izmir (Turkey); Cakir, Ahmet, E-mail: ahmet.cakir@deu.edu.tr [Dokuz Eylul University, Faculty of Engineering, Department of Metallurgical and Materials Engineering, Buca, 35390 Izmir (Turkey)

2016-11-01

The bioceramic calcium phosphate (CaP) is frequently used for improving bone fixation in titanium medical implants and thus increasing lifetime of the implant. It is known that the application of CaP coatings on metallic implant devices offers the possibility of combining the strength of the metals and the bioactivity of the ceramic materials. Many different techniques are available for producing CaP coatings. Electrochemical deposition method is widely used because of its ease of operation parameters, low temperature requirement, reproducibility and suitability for coating complex structures. This technique allows obtaining CaP coatings which promote bone in growth during the first healing period leading to permanent fixation. Electrochemical pulse technique is an alternative to calcium phosphate deposition techniques usually employed to cover orthopedic or dental titanium implant surfaces. Additionally, pulse electrodeposition technique can produce more uniform and denser CaP coatings on metallic implants. In this study, CaP based coatings were produced by electrochemical pulse technique on Ti6Al4V substrates. The resulting CaP deposits were investigated by means of X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). Corrosion properties of the CaP coatings were also investigated. The results showed that various duty cycle ranges have remarkably effect on morphology, crystallinity and corrosion properties of the produced CaP coatings. - Highlights: • Electrodeposited CaP based coating were produced by pulse deposition technique. • The pulsed electrodeposited coatings produced under 30% and 50% duty cycles were exhibited better corrosion resistance. • Produced coatings consist of irregular flake-like structure and compact network with fine needles.

Exome Sequencing Identifies a Missense Variant in EFEMP1 Co-Segregating in a Family with Autosomal Dominant Primary Open-Angle Glaucoma.

Directory of Open Access Journals (Sweden)

Donna S Mackay

Full Text Available Primary open-angle glaucoma (POAG is a clinically important and genetically heterogeneous cause of progressive vision loss as a result of retinal ganglion cell death. Here we have utilized trio-based, whole-exome sequencing to identify the genetic defect underlying an autosomal dominant form of adult-onset POAG segregating in an African-American family. Exome sequencing identified a novel missense variant (c.418C>T, p.Arg140Trp in exon-5 of the gene coding for epidermal growth factor (EGF containing fibulin-like extracellular matrix protein 1 (EFEMP1 that co-segregated with disease in the family. Linkage and haplotype analyses with microsatellite markers indicated that the disease interval overlapped a known POAG locus (GLC1H on chromosome 2p. The p.Arg140Trp substitution was predicted in silico to have damaging effects on protein function and transient expression studies in cultured cells revealed that the Trp140-mutant protein exhibited increased intracellular accumulation compared with wild-type EFEMP1. In situ hybridization of the mouse eye with oligonucleotide probes detected the highest levels of EFEMP1 transcripts in the ciliary body, cornea, inner nuclear layer of the retina, and the optic nerve head. The recent finding that a common variant near EFEMP1 was associated with optic nerve-head morphology supports the possibility that the EFEMP1 variant identified in this POAG family may be pathogenic.

Effects of Bond Coating on NiCrBSi-Mo Composite Functional Coating Properties in Plasma Spraying NiCrBSi-Mo/Ni Coating

OpenAIRE

DU Ji-yu; LI Fang-yi; LU Hai-yang; SHANG Jian-tong; LI Zhen

2017-01-01

Nickel-based bond coating and composite functional coating were sprayed on leaf blade steel material FV520B successively by using air plasma spraying system. NiCrBSi-Mo powder deposition rate, coating porosity, bonding strength and surface hardness were tested. The results indicate that, for the NiCrBSi-Mo/Ni coating, bond coating with 180-220μm thickness can improve NiCrBSi-Mo powder deposition rate while the surface coating with lower porosity, higher bonding strength and high hardness is p...

Whole-Exome Sequencing Identifies Homozygous AFG3L2 Mutations in a Spastic Ataxia-Neuropathy Syndrome Linked to Mitochondrial m-AAA Proteases

Science.gov (United States)

Martinelli, Paola; Cherukuri, Praveen F.; Teer, Jamie K.; Hansen, Nancy F.; Cruz, Pedro; Mullikin for the NISC Comparative Sequencing Program, James C.; Blakesley, Robert W.; Golas, Gretchen; Kwan, Justin; Sandler, Anthony; Fuentes Fajardo, Karin; Markello, Thomas; Tifft, Cynthia; Blackstone, Craig; Rugarli, Elena I.; Langer, Thomas; Gahl, William A.; Toro, Camilo

2011-01-01

We report an early onset spastic ataxia-neuropathy syndrome in two brothers of a consanguineous family characterized clinically by lower extremity spasticity, peripheral neuropathy, ptosis, oculomotor apraxia, dystonia, cerebellar atrophy, and progressive myoclonic epilepsy. Whole-exome sequencing identified a homozygous missense mutation (c.1847G>A; p.Y616C) in AFG3L2, encoding a subunit of an m-AAA protease. m-AAA proteases reside in the mitochondrial inner membrane and are responsible for removal of damaged or misfolded proteins and proteolytic activation of essential mitochondrial proteins. AFG3L2 forms either a homo-oligomeric isoenzyme or a hetero-oligomeric complex with paraplegin, a homologous protein mutated in hereditary spastic paraplegia type 7 (SPG7). Heterozygous loss-of-function mutations in AFG3L2 cause autosomal-dominant spinocerebellar ataxia type 28 (SCA28), a disorder whose phenotype is strikingly different from that of our patients. As defined in yeast complementation assays, the AFG3L2Y616C gene product is a hypomorphic variant that exhibited oligomerization defects in yeast as well as in patient fibroblasts. Specifically, the formation of AFG3L2Y616C complexes was impaired, both with itself and to a greater extent with paraplegin. This produced an early-onset clinical syndrome that combines the severe phenotypes of SPG7 and SCA28, in additional to other “mitochondrial” features such as oculomotor apraxia, extrapyramidal dysfunction, and myoclonic epilepsy. These findings expand the phenotype associated with AFG3L2 mutations and suggest that AFG3L2-related disease should be considered in the differential diagnosis of spastic ataxias. PMID:22022284

Whole-exome sequencing identifies homozygous AFG3L2 mutations in a spastic ataxia-neuropathy syndrome linked to mitochondrial m-AAA proteases.

Directory of Open Access Journals (Sweden)

Tyler Mark Pierson

2011-10-01

Full Text Available We report an early onset spastic ataxia-neuropathy syndrome in two brothers of a consanguineous family characterized clinically by lower extremity spasticity, peripheral neuropathy, ptosis, oculomotor apraxia, dystonia, cerebellar atrophy, and progressive myoclonic epilepsy. Whole-exome sequencing identified a homozygous missense mutation (c.1847G>A; p.Y616C in AFG3L2, encoding a subunit of an m-AAA protease. m-AAA proteases reside in the mitochondrial inner membrane and are responsible for removal of damaged or misfolded proteins and proteolytic activation of essential mitochondrial proteins. AFG3L2 forms either a homo-oligomeric isoenzyme or a hetero-oligomeric complex with paraplegin, a homologous protein mutated in hereditary spastic paraplegia type 7 (SPG7. Heterozygous loss-of-function mutations in AFG3L2 cause autosomal-dominant spinocerebellar ataxia type 28 (SCA28, a disorder whose phenotype is strikingly different from that of our patients. As defined in yeast complementation assays, the AFG3L2(Y616C gene product is a hypomorphic variant that exhibited oligomerization defects in yeast as well as in patient fibroblasts. Specifically, the formation of AFG3L2(Y616C complexes was impaired, both with itself and to a greater extent with paraplegin. This produced an early-onset clinical syndrome that combines the severe phenotypes of SPG7 and SCA28, in additional to other "mitochondrial" features such as oculomotor apraxia, extrapyramidal dysfunction, and myoclonic epilepsy. These findings expand the phenotype associated with AFG3L2 mutations and suggest that AFG3L2-related disease should be considered in the differential diagnosis of spastic ataxias.

Exome sequencing identifies early gastric carcinoma as an early stage of advanced gastric cancer.

Directory of Open Access Journals (Sweden)

Guhyun Kang

Full Text Available Gastric carcinoma is one of the major causes of cancer-related mortality worldwide. Early detection and treatment leads to an excellent prognosis in patients with early gastric cancer (EGC, whereas the prognosis of patients with advanced gastric cancer (AGC remains poor. It is unclear whether EGCs and AGCs are distinct entities or whether EGCs are the beginning stages of AGCs. We performed whole exome sequencing of four samples from patients with EGC and compared the results with those from AGCs. In both EGCs and AGCs, a total of 268 genes were commonly mutated and independent mutations were additionally found in EGCs (516 genes and AGCs (3104 genes. A higher frequency of C>G transitions was observed in intestinal-type compared to diffuse-type carcinomas (P = 0.010. The DYRK3, GPR116, MCM10, PCDH17, PCDHB1, RDH5 and UNC5C genes are recurrently mutated in EGCs and may be involved in early carcinogenesis.

Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy.

Science.gov (United States)

Ellingson, Marissa S; Hart, Steven N; Kalari, Krishna R; Suman, Vera; Schahl, Kimberly A; Dockter, Travis J; Felten, Sara J; Sinnwell, Jason P; Thompson, Kevin J; Tang, Xiaojia; Vedell, Peter T; Barman, Poulami; Sicotte, Hugues; Eckel-Passow, Jeanette E; Northfelt, Donald W; Gray, Richard J; McLaughlin, Sarah A; Moreno-Aspitia, Alvaro; Ingle, James N; Moyer, Ann M; Visscher, Daniel W; Jones, Katie; Conners, Amy; McDonough, Michelle; Wieben, Eric D; Wang, Liewei; Weinshilboum, Richard; Boughey, Judy C; Goetz, Matthew P

2015-09-01

When sequencing blood and tumor samples to identify targetable somatic variants for cancer therapy, clinically relevant germline variants may be uncovered. We evaluated the prevalence of deleterious germline variants in cancer susceptibility genes in women with breast cancer referred for neoadjuvant chemotherapy and returned clinically actionable results to patients. Exome sequencing was performed on blood samples from women with invasive breast cancer referred for neoadjuvant chemotherapy. Germline variants within 142 hereditary cancer susceptibility genes were filtered and reviewed for pathogenicity. Return of results was offered to patients with deleterious variants in actionable genes if they were not aware of their result through clinical testing. 124 patients were enrolled (median age 51) with the following subtypes: triple negative (n = 43, 34.7%), HER2+ (n = 37, 29.8%), luminal B (n = 31, 25%), and luminal A (n = 13, 10.5%). Twenty-eight deleterious variants were identified in 26/124 (21.0%) patients in the following genes: ATM (n = 3), BLM (n = 1), BRCA1 (n = 4), BRCA2 (n = 8), CHEK2 (n = 2), FANCA (n = 1), FANCI (n = 1), FANCL (n = 1), FANCM (n = 1), FH (n = 1), MLH3 (n = 1), MUTYH (n = 2), PALB2 (n = 1), and WRN (n = 1). 121/124 (97.6%) patients consented to return of research results. Thirteen (10.5%) had actionable variants, including four that were returned to patients and led to changes in medical management. Deleterious variants in cancer susceptibility genes are highly prevalent in patients with invasive breast cancer referred for neoadjuvant chemotherapy undergoing exome sequencing. Detection of these variants impacts medical management.

Non-Cyanide Electrodeposited Ag–PTFE Composite Coating Using Direct or Pulsed Current Deposition

Directory of Open Access Journals (Sweden)

Raymond Sieh

2016-07-01

Full Text Available The effects of FC-4 cationic surfactant on electrodeposited Ag–PTFE composite coating using direct or pulsed currents were studied using scanning electron microscope (SEM, energy dispersive X-ray (EDS, optical microscope, and a linear tribometer. FC-4:PTFE in various ratios were added to a non-cyanide succinimide silver complex bath. Direct or pulsed current method was used at a constant current density to enable comparison between both methods. A high incorporation rate of PTFE was successfully achieved, with pulsed current being highly useful in increasing the amount of PTFE in the composite coating. The study of coating wear under sliding showed that a large majority of the electrodeposited coatings still managed to adhere to the substrate, even after 10 wear cycles of sliding tests. Performance improvements were achieved on all the samples with a coefficient of friction (CoF between 0.06 and 0.12.

In-situ phosphatizing coatings for aerospace, OEM and coil coating applications

Science.gov (United States)

Neuder, Heather Aurelia

The current metal coating process is a multi-step process. The surface is cleaned, primered, dried and then painted. The process is labor intensive and time consuming. The wash primer is a conversion coating, which prepares metal surface for better paint adhesion. The wash primers currently used often contain hexavalent chromium (Cr6+), which seals the pores in the conversion coating. The presence of hexavalent chromium, a known carcinogen, and volatile organic compounds (VOCs) make waste disposal expensive and pose dangers to workers. The novel technique of in-situ phosphatizing coating (ISPC) is a single-step, chrome-free alternative to the present coating practice. Formulation of an ISPC involves predispersal of an in-situ phosphatizing reagent (ISPR) into the paint system to form a stable formulation. The ISPR reacts with the metal surface and bonds with the paint film simultaneously, which eliminates the need for a conversion coating. In acid catalyzed paint systems, such as polyester-melamine paints, the ISPR also catalyzes cross-linking reactions between the melamine and the polyester polyols. ISPCs are formulated using commercially available coating systems including: polyester-melamine, two-component epoxy, polyurethane and high-hydroxy content polyester-melamine coil coating. The ISPCs are applied to metal substrates and their performances are evaluated using electrochemical, thermal and standard American Society for Testing and Materials (ASTM) testing methods. In addition, ISPCs were designed and formulated based on: (1) phosphate chemistry, (2) polymer chemistry, (3) sol-gel chemistry, and (4) the ion-exchange principle. Organo-functionalized silanes, which serve as excellent coupling and dispersion agents, are incorporated into the optimized ISPC formula and evaluated using standard ASTM testing methods and electrochemical spectroscopy. Also, an ion-exchange pigment, which leads to better adhesion by forming a mixed metal silicate surface, is

Exome sequencing identifies CTSK mutations in patients originally diagnosed as intermediate osteopetrosis☆

Science.gov (United States)

Pangrazio, Alessandra; Puddu, Alessandro; Oppo, Manuela; Valentini, Maria; Zammataro, Luca; Vellodi, Ashok; Gener, Blanca; Llano-Rivas, Isabel; Raza, Jamal; Atta, Irum; Vezzoni, Paolo; Superti-Furga, Andrea; Villa, Anna; Sobacchi, Cristina

2014-01-01

Autosomal Recessive Osteopetrosis is a genetic disorder characterized by increased bone density due to lack of resorption by the osteoclasts. Genetic studies have widely unraveled the molecular basis of the most severe forms, while cases of intermediate severity are more difficult to characterize, probably because of a large heterogeneity. Here, we describe the use of exome sequencing in the molecular diagnosis of 2 siblings initially thought to be affected by “intermediate osteopetrosis”, which identified a homozygous mutation in the CTSK gene. Prompted by this finding, we tested by Sanger sequencing 25 additional patients addressed to us for recessive osteopetrosis and found CTSK mutations in 4 of them. In retrospect, their clinical and radiographic features were found to be compatible with, but not typical for, Pycnodysostosis. We sought to identify modifier genes that might have played a role in the clinical manifestation of the disease in these patients, but our results were not informative. In conclusion, we underline the difficulties of differential diagnosis in some patients whose clinical appearance does not fit the classical malignant or benign picture and recommend that CTSK gene be included in the molecular diagnosis of high bone density conditions. PMID:24269275

Cold-Sprayed AZ91D Coating and SiC/AZ91D Composite Coatings

Directory of Open Access Journals (Sweden)

Yingying Wang

2018-03-01

Full Text Available As an emerging coating building technique, cold spraying has many advantages to elaborate Mg alloy workpieces. In this study, AZ91D coatings and AZ91D-based composite coatings were deposited using cold spraying. Coatings were prepared using different gas temperatures to obtain the available main gas temperature. Compressed air was used as the accelerating gas, and although magnesium alloy is oxidation-sensitive, AZ91D coatings with good performance were obtained. The results show that dense coatings can be fabricated until the gas temperature is higher than 500 °C. The deposition efficiency increases greatly with the gas temperature, but it is lower than 10% for all coating specimens. To analyze the effects of compressed air on AZ91D powder particles and the effects of gas temperature on coatings, the phase composition, porosity, cross-sectional microstructure, and microhardness of coatings were characterized. X-ray diffraction and oxygen content analysis clarified that no phase transformation or oxidation occurred on AZ91D powder particles during cold spraying processes with compressed air. The porosity of AZ91D coatings remained between 3.6% and 3.9%. Impact melting was found on deformed AZ91D particles when the gas temperature increased to 550 °C. As-sprayed coatings exhibit much higher microhardness than as-casted bulk magnesium, demonstrating the dense structure of cold-sprayed coatings. To study the effects of ceramic particles on cold-sprayed AZ91D coatings, 15 vol % SiC powder particles were added into the feedstock powder. Lower SiC content in the coating than in the feedstock powder means that the deposition efficiency of the SiC powder particles is lower than the deposition efficiency of AZ91D particles. The addition of SiC particles reduces the porosity and increases the microhardness of cold-sprayed AZ91D coatings. The corrosion behavior of AZ91D coating and SiC reinforced AZ91D composite coating were examined. The Si

Exome sequencing in 53 sporadic cases of schizophrenia identifies 18 putative candidate genes.

Directory of Open Access Journals (Sweden)

Michel Guipponi

Full Text Available Schizophrenia (SCZ is a severe, debilitating mental illness which has a significant genetic component. The identification of genetic factors related to SCZ has been challenging and these factors remain largely unknown. To evaluate the contribution of de novo variants (DNVs to SCZ, we sequenced the exomes of 53 individuals with sporadic SCZ and of their non-affected parents. We identified 49 DNVs, 18 of which were predicted to alter gene function, including 13 damaging missense mutations, 2 conserved splice site mutations, 2 nonsense mutations, and 1 frameshift deletion. The average number of exonic DNV per proband was 0.88, which corresponds to an exonic point mutation rate of 1.7×10(-8 per nucleotide per generation. The non-synonymous-to-synonymous mutation ratio of 2.06 did not differ from neutral expectations. Overall, this study provides a list of 18 putative candidate genes for sporadic SCZ, and when combined with the results of similar reports, identifies a second proband carrying a non-synonymous DNV in the RGS12 gene.

Coffin-Siris syndrome is a SWI/SNF complex disorder.

Science.gov (United States)

Tsurusaki, Y; Okamoto, N; Ohashi, H; Mizuno, S; Matsumoto, N; Makita, Y; Fukuda, M; Isidor, B; Perrier, J; Aggarwal, S; Dalal, A B; Al-Kindy, A; Liebelt, J; Mowat, D; Nakashima, M; Saitsu, H; Miyake, N; Matsumoto, N

2014-06-01

Coffin-Siris syndrome (CSS) is a congenital disorder characterized by intellectual disability, growth deficiency, microcephaly, coarse facial features, and hypoplastic or absent fifth fingernails and/or toenails. We previously reported that five genes are mutated in CSS, all of which encode subunits of the switch/sucrose non-fermenting (SWI/SNF) ATP-dependent chromatin-remodeling complex: SMARCB1, SMARCA4, SMARCE1, ARID1A, and ARID1B. In this study, we examined 49 newly recruited CSS-suspected patients, and re-examined three patients who did not show any mutations (using high-resolution melting analysis) in the previous study, by whole-exome sequencing or targeted resequencing. We found that SMARCB1, SMARCA4, or ARID1B were mutated in 20 patients. By examining available parental samples, we ascertained that 17 occurred de novo. All mutations in SMARCB1 and SMARCA4 were non-truncating (missense or in-frame deletion) whereas those in ARID1B were all truncating (nonsense or frameshift deletion/insertion) in this study as in our previous study. Our data further support that CSS is a SWI/SNF complex disorder. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Hard coatings

International Nuclear Information System (INIS)

Dan, J.P.; Boving, H.J.; Hintermann, H.E.

1993-01-01

Hard, wear resistant and low friction coatings are presently produced on a world-wide basis, by different processes such as electrochemical or electroless methods, spray technologies, thermochemical, CVD and PVD. Some of the most advanced processes, especially those dedicated to thin film depositions, basically belong to CVD or PVD technologies, and will be looked at in more detail. The hard coatings mainly consist of oxides, nitrides, carbides, borides or carbon. Over the years, many processes have been developed which are variations and/or combinations of the basic CVD and PVD methods. The main difference between these two families of deposition techniques is that the CVD is an elevated temperature process (≥ 700 C), while the PVD on the contrary, is rather a low temperature process (≤ 500 C); this of course influences the choice of substrates and properties of the coating/substrate systems. Fundamental aspects of the vapor phase deposition techniques and some of their influences on coating properties will be discussed, as well as the very important interactions between deposit and substrate: diffusions, internal stress, etc. Advantages and limitations of CVD and PVD respectively will briefly be reviewed and examples of applications of the layers will be given. Parallel to the development and permanent updating of surface modification technologies, an effort was made to create novel characterisation methods. A close look will be given to the coating adherence control by means of the scratch test, at the coating hardness measurement by means of nanoindentation, at the coating wear resistance by means of a pin-on-disc tribometer, and at the surface quality evaluation by Atomic Force Microscopy (AFM). Finally, main important trends will be highlighted. (orig.)

Nanosilver-penetrated polyion graphene complex membrane for mediator-free amperometric immunoassay of alpha-fetoprotein using nanosilver-coated silica nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Tang Juan [Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou 350108 (China); Tang Dianping, E-mail: dianping.tang@fzu.edu.c [Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou 350108 (China); Su Biling; Li Qunfang; Qiu Bin [Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou 350108 (China); Chen Guonan, E-mail: gnchen@fzu.edu.c [Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou 350108 (China)

2011-04-15

Research highlights: {yields} We fabricate a polyion graphene complex membrane-based immunosensing platform for sensitive electrochemical immunoassay of alpha-fetoprotein. {yields} Nanosilver-coated silica nanocomposites as bionanolabels. {yields} Graphene nanosheets, single-stranded DNA and silver nanoparticles as matrices. {yields} Direct electron transfer without electron mediator. {yields} Analysis of real samples and method comparison. - Abstract: A facile and sensitive mediator-free electrochemical immunosensor for detection of alpha-fetoprotein (AFP) was designed by using nanosilver-coated silica nanoparticles (Ag-SiO{sub 2}) as bionanolabels. To construct such an electrochemical immunosensor, silver ions/single-stranded DNA/graphene nanosheets were initially immobilized on a gold electrode in turn, then silver ions were in situ reduced to silver nanoparticles with the aid of NaBH{sub 4}, and anti-AFP antibodies conjugated to silver nanoparticles were used. In the presence of AFP analyte, the sandwiched immunocomplex was formed on the electrode surface by using horseradish peroxidase-anti-AFP conjugate-labeled Ag-SiO{sub 2} (HRP-anti-AFP-Ag-SiO{sub 2}) as secondary antibodies. Compared with pure silver nanoparticles, Ag-SiO{sub 2} nanocomposites could provide a large room for the immobilization of HRP-anti-AFP, and improve the electrochemical responses of the immunosensor. Meanwhile, the presence of highly conductive graphene nanosheets and silver nanoparticles provided a good pathway for electron transfer. Under optimal conditions, the immunosensor exhibited good electrochemical responses toward AFP ranging from 0.3 to 200 ng/mL with a detection limit (LOD) of 0.05 ng/mL (at 3{sigma}) in pH 6.0 PBS-H{sub 2}O{sub 2} system. Intra- and inter-assay displayed good precisions with coefficient of variation below 9.5%. In addition, the method was evaluated with 23 clinical serum samples, receiving good correlation with results from commercially available

Nanosilver-penetrated polyion graphene complex membrane for mediator-free amperometric immunoassay of alpha-fetoprotein using nanosilver-coated silica nanoparticles

International Nuclear Information System (INIS)

Tang Juan; Tang Dianping; Su Biling; Li Qunfang; Qiu Bin; Chen Guonan

2011-01-01

Research highlights: → We fabricate a polyion graphene complex membrane-based immunosensing platform for sensitive electrochemical immunoassay of alpha-fetoprotein. → Nanosilver-coated silica nanocomposites as bionanolabels. → Graphene nanosheets, single-stranded DNA and silver nanoparticles as matrices. → Direct electron transfer without electron mediator. → Analysis of real samples and method comparison. - Abstract: A facile and sensitive mediator-free electrochemical immunosensor for detection of alpha-fetoprotein (AFP) was designed by using nanosilver-coated silica nanoparticles (Ag-SiO 2 ) as bionanolabels. To construct such an electrochemical immunosensor, silver ions/single-stranded DNA/graphene nanosheets were initially immobilized on a gold electrode in turn, then silver ions were in situ reduced to silver nanoparticles with the aid of NaBH 4 , and anti-AFP antibodies conjugated to silver nanoparticles were used. In the presence of AFP analyte, the sandwiched immunocomplex was formed on the electrode surface by using horseradish peroxidase-anti-AFP conjugate-labeled Ag-SiO 2 (HRP-anti-AFP-Ag-SiO 2 ) as secondary antibodies. Compared with pure silver nanoparticles, Ag-SiO 2 nanocomposites could provide a large room for the immobilization of HRP-anti-AFP, and improve the electrochemical responses of the immunosensor. Meanwhile, the presence of highly conductive graphene nanosheets and silver nanoparticles provided a good pathway for electron transfer. Under optimal conditions, the immunosensor exhibited good electrochemical responses toward AFP ranging from 0.3 to 200 ng/mL with a detection limit (LOD) of 0.05 ng/mL (at 3σ) in pH 6.0 PBS-H 2 O 2 system. Intra- and inter-assay displayed good precisions with coefficient of variation below 9.5%. In addition, the method was evaluated with 23 clinical serum samples, receiving good correlation with results from commercially available electrochemiluminescent analyzer.

Treatment of high-latency microcapsules containing an aluminium complex with an epoxy-functionalised trialkoxysilane.

Science.gov (United States)

Kamiya, Kazunobu; Suzuki, Noboru

2016-12-01

Some aluminium complexes are excellent catalysts of cationic polymerisation and are used for low-temperature and fast-curing adhesive, used in electronic part mounting. Microencapsulation is a suitable technique for getting high latency of the catalysts and long shelf life of the adhesives. For the higher latency in a cycloaliphatic epoxy compound, the microcapsule surface which retained small amount of aluminium complex was coated with epoxy polymer and the effect was examined. From the X-ray photoelectron spectroscopic results, the surface was recognised to be sufficiently coated and the differential scanning calorimetric analyses showed that the coating did not significantly affect the low-temperature and fast-curing properties of adhesive. After storing the mixture of cycloaliphatic epoxy compound, coated microcapsules, triphenylsilanol and silane coupling agent for 48 h at room temperature, the increase in viscosity was only 0.01 Pa s, resulting in the excellent shelf life.

Anticorrosive coatings: a review

DEFF Research Database (Denmark)

Sørensen, Per Aggerholm; Kiil, Søren; Dam-Johansen, Kim

2009-01-01

of volatile organic compounds (VOCs) have caused significant changes in the anticorrosive coating industry. The requirement for new VOC-compliant coating technologies means that coating manufacturers can no longer rely on the extensive track record of their time-served products to convince consumers...... of their suitability for use. An important aspect in the development of new VOC-compliant, high-performance anticorrosive coating systems is a thorough knowledge of the components in anticorrosive coatings, their interactions, their advantages and limitations, as well as a detailed knowledge on the failure modes......, and inhibitive coatings are outlined. In the past decades, several alternatives to organic solvent-borne coatings have reached the commercial market. This review also presents some of these technologies and discusses some of their advantages and limitations. Finally, some of the mechanisms leading to degradation...

Charged-particle coating

International Nuclear Information System (INIS)

Johnson, W.L.; Crane, J.K.; Hendricks, C.D.

1980-01-01

Advanced target designs require thicker (approx. 300 μm) coatings and better surface finishes that can be produced with current coating techniques. An advanced coating technique is proposed to provide maximum control of the coating flux and optimum manipulation of the shell during processing. In this scheme a small beam of ions or particles of known incident energy are collided with a levitated spherical mandrel. Precise control of the incident energy and angle of the deposition flux optimizes the control of the coating morphology while controlled rotation and noncontact support of the shell minimizes the possibility of particulate or damage generated defects. Almost infinite variability of the incident energy and material in this process provides increased flexibility of the target designs which can be physically realized

Comparison of additive amount used in spin-coated and roll-coated organic solar cells

DEFF Research Database (Denmark)

Cheng, Pei; Lin, Yuze; Zawacka, Natalia Klaudia

2014-01-01

All-polymer and polymer/fullerene inverted solar cells were fabricated by spin-coating and roll-coating processes. The spin-coated small-area (0.04 cm(2)) devices were fabricated on indium tin oxide (ITO) coated glass substrates in nitrogen. The roll-coated large-area (1.0 cm(2)) devices were...

Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes

DEFF Research Database (Denmark)

Lohmueller, Kirk E.; Sparsø, Thomas; Li, Qibin

2013-01-01

number of genes. We applied a series of gene-based tests to detect such susceptibility genes. However, no gene showed a significant association with disease risk after we corrected for the number of genes analyzed. Thus, we could reject a model for the genetic architecture of type 2 diabetes where rare......It has been hypothesized that, in aggregate, rare variants in coding regions of genes explain a substantial fraction of the heritability of common diseases. We sequenced the exomes of 1,000 Danish cases with common forms of type 2 diabetes (including body mass index > 27.5 kg/m2 and hypertension...

Microstructural and electrochemical characterization of Ni/Ti/sub 2/N composite coating for sintered NdFeB permanent magnets

International Nuclear Information System (INIS)

Ali, A.; Ahmad, A.; Deen, K.M.; Ahmad, R.

2009-01-01

Sintered NdFeB magnets have complex microstructure that makes them susceptible to corrosion in humid or moist environments. The paper presents the anticorrosion characteristics of a novel Ni/Ti/sub 2/N composite coating applied through electrodeposition and cathodic arc physical vapour deposition (CAPVD) to sintered NdFeB permanent magnets. The performance of composite coating was evaluated in simulated marine environment with the help of dc polarization techniques. The rate of coating degradation was also determined by employing ac electrochemical impedance spectroscopy (EIS). The coating morphology and surface chemistry were studied with scanning electron microscope (SEM). X-ray diffraction (XRD) was used for identification of component phases in the coating-substrate system. The results showed that the composite coating provided an adequately improved corrosion protection to the sintered NdFeB magnets in the simulated marine environment compared to the earlier reported ceramic and metallic coatings. The composite coating did not damage the magnetic properties of coating-substrate system that remained at par with the ceramic and nickel coating having copper interlayer. (author)

Friction surfaced Stellite6 coatings

International Nuclear Information System (INIS)

Rao, K. Prasad; Damodaram, R.; Rafi, H. Khalid; Ram, G.D. Janaki; Reddy, G. Madhusudhan; Nagalakshmi, R.

2012-01-01

Solid state Stellite6 coatings were deposited on steel substrate by friction surfacing and compared with Stellite6 cast rod and coatings deposited by gas tungsten arc and plasma transferred arc welding processes. Friction surfaced coatings exhibited finer and uniformly distributed carbides and were characterized by the absence of solidification structure and compositional homogeneity compared to cast rod, gas tungsten arc and plasma transferred coatings. Friction surfaced coating showed relatively higher hardness. X-ray diffraction of samples showed only face centered cubic Co peaks while cold worked coating showed hexagonally close packed Co also. - Highlights: ► Stellite6 used as coating material for friction surfacing. ► Friction surfaced (FS) coatings compared with casting, GTA and PTA processes. ► Finer and uniformly distributed carbides in friction surfaced coatings. ► Absence of melting results compositional homogeneity in FS Stellite6 coatings.

Non-Deforming, High-Reflectance X-ray Coatings for Lynx and Other Future Missions

Science.gov (United States)

Windt, David

.1–10 keV band deposited by magnetron sputtering have high density and low roughness, and thus good X-ray performance. However Ir, B4C, and certain other materials have exceedingly high film stress when deposited under conditions for maximum reflectance. Residual film stress in the X-ray reflective coatings can deform thin-shell mirror segments, leading to unacceptable degradation of angular resolution. Coating stress was not an issue for Chandra. But for Lynx, for example, the substrates will be 50x thinner, and so sub-arc-second resolution simply cannot be achieved using thin-shell mirror segments without the development of non-deforming coatings. The second specific aim of this proposal is to develop techniques to mitigate coatingstress-induced deformations in glass and Si shell segments. Two potential solutions will be investigated: a) New deposition methods to control coating thickness uniformity and net film stress in two dimensions will be used to determine if already-developed zero-netstress Ir-based coatings, as well as the new reflective coatings to be developed, can be deposited onto shell segments without inducing unacceptable substrate deformations, a question that has not yet been definitively addressed; if uniform coatings having sufficiently low deformation cannot be realized, then non-uniform coatings will be investigated, where spatial control of net film stress in 2D will compensate for potential non-uniform deformations. If successful, the effectiveness of the approach with more complex interference coatings will also be established. b) A more general (albeit more complex) method of mitigating stress-induced deformations will be investigated, specifically the use of balanced front- and backside coatings, a technique that, if successful, can be used, in principle, with any type of coating (Ir-based, high-energy multilayers, etc.), regardless of its stress state. (The approach is likely incompatible with active correction, however.)

In vivo gene transfer using pDNA/chitosan/chondroitin sulfate ternary complexes: influence of chondroitin sulfate on the stability of freeze-dried complexes and transgene expression in vivo.

Science.gov (United States)

Hagiwara, Kenji; Kishimoto, Satoko; Ishihara, Masayuki; Koyama, Yoshiyuki; Mazda, Osam; Sato, Toshinori

2013-02-01

Chitosan has been investigated as a promising nonviral vector. However, several problems still remain, such as a relatively low transfection efficiency and instability under physiological conditions. We previously demonstrated that a chondroitin sulfate (CS) coating enhanced the transfection efficiency and physicochemical stability of plasmid DNA (pDNA)/chitosan complexes in vitro. In the present study, the effects of coating pDNA/chitosan complexes with CS on the stability in freeze-dry rehydration processes and gene expression in vivo were investigated. Freeze-drying storage at -20 °C, 4 °C, or room temperature, freezing storage at -20 °C, or liquid storage at 4 °C or room temperature, were examined for preservation conditions of pDNA/chitosan/CS ternary complexes by a gel retardation assay, measurements of sizes and zeta potentials, and a luciferase assay. Moreover, to determine the transfection efficiency of the ternary complexes in vivo, suicide gene therapy was carried out in Huh-7-implanted mice using herpes simplex virus thymidine kinase coding pDNA and ganciclovir. The freeze-dried pDNA/chitosan/CS ternary complexes showed sufficient cell transfection ability in vitro and in vivo. In addition, ternary complexes were associated with a significant suppression of tumor growth and a histopathologically high anti-tumor effect by intratumoral injection to tumor-bearing mice. The CS coating enhanced the preservation stability of the pDNA/chitosan complexes after freeze-drying-rehydration and their transgene expression in vivo. Copyright © 2013 John Wiley & Sons, Ltd.

Hybrid Perovskite Thin Film Formation: From Lab Scale Spin Coating to Large Area Blade Coating

KAUST Repository

Munir, Rahim

2017-11-22

understand the key scientific insights through spin coating. We observe high-quality film formation for T > 100oC, namely in conditions which inhibit the formation of the crystalline intermediate complex phases. In doing so, we achieve fast and direct formation of the perovskite phase with solar cells yielding PCE > 17%.

Exome sequencing in schizophrenic patients with high levels of homozygosity identifies novel and extremely rare mutations in the GABA/glutamatergic pathways.

Directory of Open Access Journals (Sweden)

Edoardo Giacopuzzi

Full Text Available Inbreeding is a known risk factor for recessive Mendelian diseases and previous studies have suggested that it could also play a role in complex disorders, such as psychiatric diseases. Recent inbreeding results in the presence of long runs of homozygosity (ROHs along the genome, which are also defined as autozygosity regions. Genetic variants in these regions have two alleles that are identical by descent, thus increasing the odds of bearing rare recessive deleterious mutations due to a homozygous state. A recent study showed a suggestive enrichment of long ROHs in schizophrenic patients, suggesting that recent inbreeding could play a role in the disease. To better understand the impact of autozygosity on schizophrenia risk, we selected, from a cohort of 180 Italian patients, seven subjects with extremely high numbers of large ROHs that were likely due to recent inbreeding and characterized the mutational landscape within their ROHs using Whole Exome Sequencing and, gene set enrichment analysis. We identified a significant overlap (17%; empirical p-value = 0.0171 between genes inside ROHs affected by low frequency functional homozygous variants (107 genes and the group of most promising candidate genes mutated in schizophrenia. Moreover, in four patients, we identified novel and extremely rare damaging mutations in the genes involved in neurodevelopment (MEGF8 and in GABA/glutamatergic synaptic transmission (GAD1, FMN1, ANO2. These results provide insights into the contribution of rare recessive mutations and inbreeding as risk factors for schizophrenia. ROHs that are likely due to recent inbreeding harbor a combination of predisposing low-frequency variants and extremely rare variants that have a high impact on pivotal biological pathways implicated in the disease. In addition, this study confirms that focusing on patients with high levels of homozygosity could be a useful prioritization strategy for discovering new high-impact mutations in

Exome sequencing in schizophrenic patients with high levels of homozygosity identifies novel and extremely rare mutations in the GABA/glutamatergic pathways.

Science.gov (United States)

Giacopuzzi, Edoardo; Gennarelli, Massimo; Minelli, Alessandra; Gardella, Rita; Valsecchi, Paolo; Traversa, Michele; Bonvicini, Cristian; Vita, Antonio; Sacchetti, Emilio; Magri, Chiara

2017-01-01

Inbreeding is a known risk factor for recessive Mendelian diseases and previous studies have suggested that it could also play a role in complex disorders, such as psychiatric diseases. Recent inbreeding results in the presence of long runs of homozygosity (ROHs) along the genome, which are also defined as autozygosity regions. Genetic variants in these regions have two alleles that are identical by descent, thus increasing the odds of bearing rare recessive deleterious mutations due to a homozygous state. A recent study showed a suggestive enrichment of long ROHs in schizophrenic patients, suggesting that recent inbreeding could play a role in the disease. To better understand the impact of autozygosity on schizophrenia risk, we selected, from a cohort of 180 Italian patients, seven subjects with extremely high numbers of large ROHs that were likely due to recent inbreeding and characterized the mutational landscape within their ROHs using Whole Exome Sequencing and, gene set enrichment analysis. We identified a significant overlap (17%; empirical p-value = 0.0171) between genes inside ROHs affected by low frequency functional homozygous variants (107 genes) and the group of most promising candidate genes mutated in schizophrenia. Moreover, in four patients, we identified novel and extremely rare damaging mutations in the genes involved in neurodevelopment (MEGF8) and in GABA/glutamatergic synaptic transmission (GAD1, FMN1, ANO2). These results provide insights into the contribution of rare recessive mutations and inbreeding as risk factors for schizophrenia. ROHs that are likely due to recent inbreeding harbor a combination of predisposing low-frequency variants and extremely rare variants that have a high impact on pivotal biological pathways implicated in the disease. In addition, this study confirms that focusing on patients with high levels of homozygosity could be a useful prioritization strategy for discovering new high-impact mutations in genetically

Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations.

Science.gov (United States)

Hsieh, PingHsun; Hallmark, Brian; Watkins, Joseph; Karafet, Tatiana M; Osipova, Ludmila P; Gutenkunst, Ryan N; Hammer, Michael F

2017-11-01

Siberia is one of the coldest environments on Earth and has great seasonal temperature variation. Long-term settlement in northern Siberia undoubtedly required biological adaptation to severe cold stress, dramatic variation in photoperiod, and limited food resources. In addition, recent archeological studies show that humans first occupied Siberia at least 45,000 years ago; yet our understanding of the demographic history of modern indigenous Siberians remains incomplete. In this study, we use whole-exome sequencing data from the Nganasans and Yakuts to infer the evolutionary history of these two indigenous Siberian populations. Recognizing the complexity of the adaptive process, we designed a model-based test to systematically search for signatures of polygenic selection. Our approach accounts for stochasticity in the demographic process and the hitchhiking effect of classic selective sweeps, as well as potential biases resulting from recombination rate and mutation rate heterogeneity. Our demographic inference shows that the Nganasans and Yakuts diverged ∼12,000-13,000 years ago from East-Asian ancestors in a process involving continuous gene flow. Our polygenic selection scan identifies seven candidate gene sets with Siberian-specific signals. Three of these gene sets are related to diet, especially to fat metabolism, consistent with the hypothesis of adaptation to a fat-rich animal diet. Additional testing rejects the effect of hitchhiking and favors a model in which selection yields small allele frequency changes at multiple unlinked genes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

In vivo bioactivity of titanium and fluorinated apatite coatings for orthopaedic implants: a vibrational study

Science.gov (United States)

Taddei, Paola; Tinti, Anna; Reggiani, Matteo; Monti, Patrizia; Fagnano, Concezio

2003-06-01

The bone integration of implants is a complex process which depends on chemical composition and surface morphology. To accelerate osteointegration, metal implants are coated with porous metal or apatites which have been reported to increase mineralisation, improving prosthesis fixation. To study the influence of composition and morphology on the in vivo bioactivity, titanium screws coated by Plasma Flame Spraying (PFS) with titanium or fluorinated apatite (K690) were implanted in sheep tibia and femur for 10 weeks and studied by micro-Raman and IR spectroscopy. The same techniques, together with thermogravimetry, were used for characterising the pre-coating K690 powder. Contrary to the manufacturer report, the K690 pre-coating revealed to be composed of a partially fluorinated apatite containing impurities of Ca(OH) 2 and CaCO 3. By effect of PFS, the impurities were decomposed and the crystallinity degree of the coating was found to decrease. The vibrational spectra recorded on the implanted screws revealed the presence of newly formed bone; for the K690-coated screws at least, a high level of osteointegration was evidenced.

Preparation and voltammetric characterization of electrodes coated with Langmuir-Schaefer ultrathin films of Nafion®

Directory of Open Access Journals (Sweden)

Bertoncello Paolo

2003-01-01

Full Text Available Ultrathin films of Nafion® perfluorinated polymer were deposited on indium-tin oxide electrodes (ITO by using Langmuir-Schaefer (LS technique, after optimization of the subphase composition conditions. Morphological characteristics of these coatings were obtained by Atomic Force Microscopy (AFM. Nafion® LS films showed a good uniformity and complete coverage of the electrode surface, however a different organization degree of the polymer layer was evidenced with respect to thin films deposited by spin-coating. ITO electrodes modified with Nafion® LS coatings preconcentrate by ion-exchange electroactive cations, such as Ru[(NH36]3+, dissolved in diluted solutions. The electroactive species is retained by the Nafion® LS coated ITO also after transfer of the modified electrode into pure supporting electrolyte. This allowed the use of the ruthenium complex as voltammetric probe to test diffusion phenomena within the Nafion® LS films. Apparent diffusion coefficients (Dapp of Ru[(NH36]3+ incorporated in Nafion® LS films were obtained by voltammetric measurements. Dapp values decrease slightly by increasing the amount of ruthenium complex incorporated in the ultrathin film. They are significantly lower than values typical for recasted Nafion® films, in agreement with the highly condensed nature of the Nafion® LS fims.

The stepwise evolution of the exome during acquisition of docetaxel resistance in breast cancer cells

DEFF Research Database (Denmark)

Hansen, Stine Ninel; Ehlers, Natasja Spring; Zhu, Shida

2016-01-01

Background: Resistance to taxane-based therapy in breast cancer patients is a major clinical problem that may be addressed through insight of the genomic alterations leading to taxane resistance in breast cancer cells. In the current study we used whole exome sequencing to discover somatic genomic...... alterations, evolving across evolutionary stages during the acquisition of docetaxel resistance in breast cancer cell lines. Results: Two human breast cancer in vitro models (MCF-7 and MDA-MB-231) of the step-wise acquisition of docetaxel resistance were developed by exposing cells to 18 gradually increasing...... resistance relevant genomic variation appeared to arise midway towards fully resistant cells corresponding to passage 31 (5 nM docetaxel) for MDA-MB-231 and passage 16 (1.2 nM docetaxel) for MCF-7, and where the cells also exhibited a period of reduced growth rate or arrest, respectively. MCF-7 cell acquired...

Novel inborn error of folate metabolism: identification by exome capture and sequencing of mutations in the MTHFD1 gene in a single proband.

Science.gov (United States)

Watkins, David; Schwartzentruber, Jeremy A; Ganesh, Jaya; Orange, Jordan S; Kaplan, Bernard S; Nunez, Laura Dempsey; Majewski, Jacek; Rosenblatt, David S

2011-09-01

An infant was investigated because of megaloblastic anaemia, atypical hemolytic uraemic syndrome, severe combined immune deficiency, elevated blood levels of homocysteine and methylmalonic acid, and a selective decreased synthesis of methylcobalamin in cultured fibroblasts. Exome sequencing was performed on patient genomic DNA. Two mutations were identified in the MTHFD1 gene, which encodes a protein that catalyses three reactions involved in cellular folate metabolism. This protein is essential for the generation of formyltetrahydrofolate and methylenetetrahydrofolate and important for nucleotide and homocysteine metabolism. One mutation (c.727+1G>A) affects the splice acceptor site of intron 8. The second mutation, c.517C>T (p.R173C), changes a critical arginine residue in the NADP-binding site of the protein. Mutations affecting this arginine have previously been shown to affect enzyme activity. Both parents carry a single mutation and an unaffected sibling carries neither mutation. The combination of two mutations in the MTHFRD1 gene, predicted to have severe consequences, in the patient and their absence in the unaffected sibling, supports causality. This patient represents the first case of an inborn error of folate metabolism affecting the trifunctional MTHFD1 protein. This report reinforces the power of exome capture and sequencing for the discovery of novel genes, even when only a single proband is available for study.

The Influence of Nano-Fibrillated Cellulose as a Coating Component in Paper Coating

Directory of Open Access Journals (Sweden)

Yaxi Xu

2016-03-01

Full Text Available This work investigates nano-fibrillated cellulose (NFC as a component in mineral pigment paper coating. In this work, bleached Eucalyptus pulp was pretreated by TEMPO (2,2,6,6-tetramethyl-1-piperdinyloxy-mediated oxidation. The oxidized pulp was then isolated to obtain NFC by sonication. Aqueous coating colors consisting of calcium carbonate, clay, carboxylated butadiene-styrene latex, additives, and NFC were prepared. The rheology of the coating colors and the surface properties of paper coated with NFC containing coating colors were determined. The rheological properties allowed NFC to be used in small amounts under laboratory conditions. Nano-fibrillated cellulose was found to improve the surface strength and smoothness of the coated paper. The water resistance of coated paper, on the other hand, decreased because of the hydrophilicity of NFC.

Experiments, modeling and simulation of the magnetic behavior of inhomogeneously coated nickel/aluminum hybrid foams

Energy Technology Data Exchange (ETDEWEB)

Jung, A., E-mail: anne.jung@mx.uni-saarland.de [Universität des Saarlandes, Institute of Applied Mechanics, Campus A4 2, 66123 Saarbrücken (Germany); Klis, D., E-mail: d.klis@lte.uni-saarland.de [Universität des Saarlandes, Laboratory for Electromagnetic Theory, Campus C6 3, 66123 Saarbrücken (Germany); Goldschmidt, F., E-mail: f.goldschmidt@mx.uni-saarland.de [Universität des Saarlandes, Institute of Applied Mechanics, Campus A4 2, 66123 Saarbrücken (Germany)

2015-03-15

Open-cell metal foams are used as lightweight construction elements, energy absorbers or as support for catalytic coatings. Coating of open-cell metal foams is not only used for catalytic applications, but it leads also to tremendous increase in stiffness and energy absorption capacity. A non-line of sight coating technique for complex 3D structures is electrodeposition. Unfortunately, due to the 3D porosity and the related problems in mass transport limitation during the deposition, it is not possible to produce homogeneously coated foams. In the present contribution, we present a semi-non-destructive technique applicable to determine the coating thickness distribution of magnetic coatings by measuring the remanent magnetic field of coated foams. In order to have a closer look at the mass transport mechanism, a numerical model was developed to predict the field scans for different coating thickness distributions in the foams. For long deposition times the deposition reaches a steady state whereas a Helmholtz equation is sufficient to predict the coating thickness distribution. The applied current density could be identified as the main influencing parameter. Based on the developed model, it is possible to improve the electrodeposition process and hence the homogeneity in the coating thickness of coated metal foams. This leads to enhanced mechanical properties of the hybrid foams and contributes to better and resource-efficient energy absorbers and lightweight materials. - Highlights: • Production of hybrid foams by electrodeposition of nickel on open-cell metal foams. • Magnetic field scans for visualization of spatial coating thickness distribution. • Modeling of magnetic fields of inhomogeneously coated hybrid foams. • Investigation of mass transport limitation during coating by a Helmholtz equation. • Increasing coating homogeneity by use of low current densities and deposition rates.