WorldWideScience

Sample records for human pharmacogenomic variations

  1. Diabetic retinopathy: variations in patient therapeutic outcomes and pharmacogenomics

    Directory of Open Access Journals (Sweden)

    Agarwal A

    2014-12-01

    Full Text Available Aniruddha Agarwal, Mohamed K Soliman, Yasir J Sepah, Diana V Do, Quan Dong Nguyen Ocular Imaging Research and Reading Center, Stanley M. Truhlsen Eye Institute, University of Nebraska Medical Center, Omaha, USA Abstract: Diabetes and its microvascular complications in patients poses a significant challenge and constitutes a major health problem. When it comes to manifestations in the eye, each case of diabetic retinopathy (DR is unique, in terms of the phenotype, genotype, and, more importantly, the therapeutic response. It is therefore important to identify factors that distinguish one patient from another. Personalized therapy in DR is a new trend aimed at achieving maximum therapeutic response in patients by identifying genotypic and phenotypic factors that may result in less than optimal response to conventional therapy, and consequently, lead to poorer outcome. With advances in the identification of these genetic markers, such as gene polymorphisms and human leucocyte antigen associations, as well as development of drugs that can target their effects, the future of personalized medicine in DR is promising. In this comprehensive review, data from various studies have been analyzed to present what has been achieved in the field of pharmacogenomics thus far. An insight into future research is also provided. Keywords: personalized medicine, therapeutic variation, genomic markers, genotype, phenotype, VEGF mutation, polymorphism, linkage, mutation, responder

  2. Systems genetics analysis of pharmacogenomics variation during antidepressant treatment

    DEFF Research Database (Denmark)

    Madsen, M. B.; Kogelman, L. J. A.; Kadarmideen, H. N.

    2017-01-01

    Selective serotonin reuptake inhibitors (SSRIs) are the most widely used antidepressants, but the efficacy of the treatment varies significantly among individuals. It is believed that complex genetic mechanisms play a part in this variation. We have used a network based approach to unravel the in...... genes involved in calcium homeostasis. In conclusion, we suggest a difference in genetic interaction networks between initial and subsequent SSRI response.The Pharmacogenomics Journal advance online publication, 18 October 2016; doi:10.1038/tpj.2016.68....

  3. Human immunodeficiency virus therapeutics and pharmacogenomics

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    U Shankarkumar

    2011-01-01

    Full Text Available Pharmacogenomics and pharmacogenetics are promising in development of a personalized treatment approach They are of paramount importance for basic immunology, for peptide based vaccine design (vaccinomics drug monitoring in clinical setting and molecular pathophysiology of multifactorial diseases like cancer, tuberculosis, cardiac disorders, diabetes, asthma, HIV, etc

  4. Pharmacogenetics, pharmacogenomics and airway disease

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    Hall Ian P

    2001-11-01

    Full Text Available Abstract The availability of a draft sequence for the human genome will revolutionise research into airway disease. This review deals with two of the most important areas impinging on the treatment of patients: pharmacogenetics and pharmacogenomics. Considerable inter-individual variation exists at the DNA level in targets for medication, and variability in response to treatment may, in part, be determined by this genetic variation. Increased knowledge about the human genome might also permit the identification of novel therapeutic targets by expression profiling at the RNA (genomics or protein (proteomics level. This review describes recent advances in pharmacogenetics and pharmacogenomics with regard to airway disease.

  5. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

    Science.gov (United States)

    Manolio, Teri A

    2016-10-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so.

  6. Web resources for pharmacogenomics.

    Science.gov (United States)

    Zhang, Guoqing; Zhang, Yunsheng; Ling, Yunchao; Jia, Jia

    2015-02-01

    Pharmacogenomics is the study of the impact of genetic variations or genotypes of individuals on their drug response or drug metabolism. Compared to traditional genomics research, pharmacogenomic research is more closely related to clinical practice. Pharmacogenomic discoveries may effectively assist clinicians and healthcare providers in determining the right drugs and proper dose for each patient, which can help avoid side effects or adverse reactions, and improve the drug therapy. Currently, pharmacogenomic approaches have proven their utility when it comes to the use of cardiovascular drugs, antineoplastic drugs, aromatase inhibitors, and agents used for infectious diseases. The rapid innovation in sequencing technology and genome-wide association studies has led to the development of numerous data resources and dramatically changed the landscape of pharmacogenomic research. Here we describe some of these web resources along with their names, web links, main contents, and our ratings.

  7. Web Resources for Pharmacogenomics

    Institute of Scientific and Technical Information of China (English)

    Guoqing Zhang; Yunsheng Zhang; Yunchao Ling; Jia Jia

    2015-01-01

    Pharmacogenomics is the study of the impact of genetic variations or genotypes of individuals on their drug response or drug metabolism. Compared to traditional genomics research, pharmacogenomic research is more closely related to clinical practice. Pharmacogenomic discoveries may effectively assist clinicians and healthcare providers in determining the right drugs and proper dose for each patient, which can help avoid side effects or adverse reactions, and improve the drug therapy. Currently, pharmacogenomic approaches have proven their utility when it comes to the use of cardiovascular drugs, antineoplastic drugs, aromatase inhibitors, and agents used for infectious diseases. The rapid innovation in sequencing technology and genome-wide association studies has led to the development of numerous data resources and dramatically chan-ged the landscape of pharmacogenomic research. Here we describe some of these web resources along with their names, web links, main contents, and our ratings.

  8. Pharmacogenomics and personalized medicine: a review focused on their application in the Chinese population.

    Science.gov (United States)

    Shu, Wen-ying; Li, Jia-li; Wang, Xue-ding; Huang, Min

    2015-05-01

    The field of pharmacogenomics was initiated in the 1950s and began to thrive after the completion of the human genome project 10 years ago. Thus far, more than 100 drug labels and clinical guidelines referring to pharmacogenomic biomarkers have been published, and several key pharmacogenomic markers for either drug safety or efficacy have been identified and subsequently adopted in clinical practice as pre-treatment genetic tests. However, a tremendous variation of genetic backgrounds exists between different ethnic groups. The application of pharmacogenomics in the Chinese population is still a long way off, since the published guidelines issued by the organizations such as US Food and Drug Administration require further confirmation in the Chinese population. This review highlights important pharmacogenomic discoveries in the Chinese population and compares the Chinese population with other nations regarding the pharmacogenomics of five most commonly used drugs, ie, tacrolimus, cyclosporine A, warfarin, cyclophosphamide and azathioprine.

  9. Pharmacogenomic Testing

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    ... what you want to learn. Search form Search Pharmacogenomic testing You are here Home Testing & Services Testing ... people avoid harmful reactions to medication. What Is Pharmacogenomics? Did you ever wonder why a medicine doesn' ...

  10. Pharmacogenomics of pediatric asthma

    Directory of Open Access Journals (Sweden)

    Gupta Sarika

    2010-01-01

    Full Text Available Context: Asthma is a complex disease with multiple genetic and environmental factors contributing to it. A component of this complexity is a highly variable response to pharmacological therapy. Pharmacogenomics is the study of the role of genetic determinants in the variable response to therapy. A number of examples of possible pharmacogenomic approaches that may prove of value in the management of asthma are discussed below. Evidence Acquisition: A search of PubMed, Google scholar, E-Medicine, BMJ and Mbase was done using the key words "pharmacogenomics of asthma", "pharmacogenomics of β-agonist, glucocorticoids, leukotriene modifiers, theophylline, muscarinic antagonists in asthma". Results: Presently, there are limited examples of gene polymorphism that can influence response to asthma therapy. Polymorphisms that alter response to asthma therapy include Arg16Gly, Gln27Glu, Thr164Ile for β-agonist receptor, polymorphism of glucocorticoid receptor gene, CRHR1 variants and polymorphism of LTC4S, ALOX5. Polymorphic variants of muscarinic receptors, PDE4 and CYP450 gene variants. Conclusion: It was concluded that genetic variation can improve the response to asthma therapy. However, no gene polymorphism has been associated with consistent results in different populations. Therefore, asthma pharmacogenomic studies in different populations with a large number of subjects are required to make possible tailoring the asthma therapy according to the genetic characteristic of individual patient.

  11. Human membrane transporter database: a Web-accessible relational database for drug transport studies and pharmacogenomics.

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    Yan, Q; Sadée, W

    2000-01-01

    The human genome contains numerous genes that encode membrane transporters and related proteins. For drug discovery, development, and targeting, one needs to know which transporters play a role in drug disposition and effects. Moreover, genetic polymorphisms in human membrane transporters may contribute to interindividual differences in the response to drugs. Pharmacogenetics, and, on a genome-wide basis, pharmacogenomics, address the effect of genetic variants on an individual's response to drugs and xenobiotics. However, our knowledge of the relevant transporters is limited at present. To facilitate the study of drug transporters on a broad scale, including the use of microarray technology, we have constructed a human membrane transporter database (HMTD). Even though it is still largely incomplete, the database contains information on more than 250 human membrane transporters, such as sequence, gene family, structure, function, substrate, tissue distribution, and genetic disorders associated with transporter polymorphisms. Readers are invited to submit additional data. Implemented as a relational database, HMTD supports complex biological queries. Accessible through a Web browser user interface via Common Gateway Interface (CGI) and Java Database Connection (JDBC), HMTD also provides useful links and references, allowing interactive searching and downloading of data. Taking advantage of the features of an electronic journal, this paper serves as an interactive tutorial for using the database, which we expect to develop into a research tool.

  12. Strategies for implementation of an effective pharmacogenomics program in pharmacy education.

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    Rao, U Subrahmanyeswara; Mayhew, Susan L; Rao, Prema S

    2015-07-01

    Sequencing of the human genome and the evidence correlating specific genetic variations to diseases have opened up the potential of genomics to more effective and less harmful interventions of human diseases. A wealth of pharmacogenomics knowledge is in place for the practice of precision medicine. However, this knowledge is not fully realized in clinical practice. One reason for this impasse is the lack of in-depth understanding of the potential of pharmacogenomics among the healthcare professionals. Pharmacists are the point-of-care providers and are expected to advise clinicians on matters relating to the implementation of pharmacogenomics in patient care. However, current pharmacogenomics instruction in pharmacy schools fails to produce pharmacists with the required knowledge or practical training in this discipline. In this perspective, we provide several strategies to overcome limitations faced by pharmacy schools. Once implemented, pharmacy schools will produce precision medicine-ready pharmacists.

  13. Frequently Asked Questions about Pharmacogenomics

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    ... Care Specific Genetic Disorders Frequently Asked Questions About Pharmacogenomics Enlarge What is pharmacogenomics? What might pharmacogenomics mean ... page, you will need Adobe Reader. What is pharmacogenomics? Pharmacogenomics uses information about a person's genetic makeup, ...

  14. The emerging era of pharmacogenomics: current successes, future potential, and challenges.

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    Lee, J W; Aminkeng, F; Bhavsar, A P; Shaw, K; Carleton, B C; Hayden, M R; Ross, C J D

    2014-07-01

    The vast range of genetic diversity contributes to a wonderful array of human traits and characteristics. Unfortunately, a consequence of this genetic diversity is large variability in drug response between people, meaning that no single medication is safe and effective in everyone. The debilitating and sometimes deadly consequences of adverse drug reactions (ADRs) are a major and unmet problem of modern medicine. Pharmacogenomics can uncover associations between genetic variation and drug safety and has the potential to predict ADRs in individual patients. Here we review pharmacogenomic successes leading to changes in clinical practice, as well as clinical areas probably to be impacted by pharmacogenomics in the near future. We also discuss some of the challenges, and potential solutions, that remain for the implementation of pharmacogenomic testing into clinical practice for the significant improvement of drug safety.

  15. Asymmetry in scientific method and limits to cross-disciplinary dialogue: toward a shared language and science policy in pharmacogenomics and human disease genetics.

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    Ozdemir, Vural; Williams-Jones, Bryn; Graham, Janice E; Preskorn, Sheldon H; Gripeos, Dimitrios; Glatt, Stephen J; Friis, Robert H; Reist, Christopher; Szabo, Sandor; Lohr, James B; Someya, Toshiyuki

    2007-04-01

    Pharmacogenomics is a hybrid field of experimental science at the intersection of human disease genetics and clinical pharmacology sharing applications of the new genomic technologies. But this hybrid field is not yet stable or fully integrated, nor is science policy in pharmacogenomics fully equipped to resolve the challenges of this emerging hybrid field. The disciplines of human disease genetics and clinical pharmacology contain significant differences in their scientific practices. Whereas clinical pharmacology originates as an experimental science, human disease genetics is primarily observational in nature. The result is a significant asymmetry in scientific method that can differentially impact the degree to which gene-environment interactions are discerned and, by extension, the study sample size required in each discipline. Because the number of subjects enrolled in observational genetic studies of diseases is characteristically viewed as an important criterion of scientific validity and reliability, failure to recognize discipline-specific requirements for sample size may lead to inappropriate dismissal or silencing of meritorious, although smaller-scale, craft-based pharmacogenomic investigations using an experimental study design. Importantly, the recognition that pharmacogenomics is an experimental science creates an avenue for systematic policy response to the ethical imperative to prospectively pursue genetically customized therapies before regulatory approval of pharmaceuticals. To this end, we discuss the critical role of interdisciplinary engagement between medical sciences, policy, and social science. We emphasize the need for development of shared standards across scientific, methodologic, and socioethical epistemologic divides in the hybrid field of pharmacogenomics to best serve the interests of public health.

  16. MicroRNA pharmacogenomics

    DEFF Research Database (Denmark)

    Rukov, Jakob Lewin; Shomron, Noam

    2011-01-01

    polymorphisms, copy number variations or differences in gene expression levels of drug metabolizing or transporting genes and drug targets. In this review paper, we focus instead on microRNAs (miRNAs): small noncoding RNAs, prevalent in metazoans, that negatively regulate gene expression in many cellular...... processes. We discuss how miRNAs, by regulating the expression of pharmacogenomic-related genes, can play a pivotal role in drug efficacy and toxicity and have potential clinical implications for personalized medicine....

  17. Pharmacogenomics and cardiovascular disease

    DEFF Research Database (Denmark)

    Weeke, Peter; Roden, Dan M

    2013-01-01

    Variability in drug responsiveness is a sine qua non of modern therapeutics, and the contribution of genomic variation is increasingly recognized. Investigating the genomic basis for variable responses to cardiovascular therapies has been a model for pharmacogenomics in general and has established...... critical pathways and specific loci modulating therapeutic responses to commonly used drugs such as clopidogrel, warfarin, and statins. In addition, genomic approaches have defined mechanisms and genetic variants underlying important toxicities with these and other drugs. These findings have not only...... resulted in changes to the product labels but also have led to development of initial clinical guidelines that consider how to facilitate incorporating genetic information to the bedside. This review summarizes the state of knowledge in cardiovascular pharmacogenomics and considers how variants described...

  18. Pharmacogenomics in the newborn

    Directory of Open Access Journals (Sweden)

    Mirta Corsello

    2013-06-01

    Full Text Available Genetic variation is an important determinant affecting the individual response to drugs. Considering the high variability in each individual genotype, the development of individualized therapies, according to the intrinsic features of the single patient, represents one of the most challenging problems in pharmacology. Pharmacogenetics analyzes the relationship between drug response and individual genetic differences, while pharmacogenomics analyzes the effect of genetic variations in patients’ response to different drugs. The aim of these two research fields is to predict either drug response or the potential for the development of drug-related side effects. In particular, an important endpoint of pharmacogenomics should be to identify which group of patients responds positively, which patients are nonresponders and who will develop adverse reactions for the same drug and dose. Nevertheless, the utility of the pharmacogenetic and pharmacogenomic information as predictor of the activity of a specific drug-metabolizing enzyme or transporter should be cautiously limited to those developmental periods in which genotype-phenotype concordance is known. This means that in the perinatal period a special attention on the peculiar pharmacokinetic properties typical of this life period should be guaranteed. This means that effective and safe drug administration during fetal and neonatal life should consider the interindividual genotypic variability leading to different expression and activity of various enzymes. Both pharmacogenetics and pharmacogenomics may have a crucial role in the achievement of an individualized medicine. Prospective clinical trials analyzing the utility, safety, and cost-effectiveness of an individualized medicine based on the individual genotype are required.Proceedings of the 9th International Workshop on Neonatology · Cagliari (Italy · October 23rd-26th, 2013 · Learned lessons, changing practice and cutting-edge research

  19. Towards pharmacogenomics knowledge discovery with the semantic web.

    Science.gov (United States)

    Dumontier, Michel; Villanueva-Rosales, Natalia

    2009-03-01

    Pharmacogenomics aims to understand pharmacological response with respect to genetic variation. Essential to the delivery of better health care is the use of pharmacogenomics knowledge to answer questions about therapeutic, pharmacological or genetic aspects. Several XML markup languages have been developed to capture pharmacogenomic and related information so as to facilitate data sharing. However, recent advances in semantic web technologies have presented exciting new opportunities for pharmacogenomics knowledge discovery by representing the information with machine understandable semantics. Progress in this area is illustrated with reference to the personalized medicine project that aims to facilitate pharmacogenomics knowledge discovery through intuitive knowledge capture and sophisticated question answering using automated reasoning over expressive ontologies.

  20. Pharmacogenomics of neuropathic pain

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    Vandana Sharma

    2017-01-01

    Full Text Available Variation in pain sensitivity and analgesic drug response is well recognized among individuals. Pharmacogenomics hypothesis dictates that a patient′s response to a drug or development of adverse drug effects may depend on variation in genetic profile, in particular, the different alleles for the same gene that an individual carries. A review of the role of genetic variations in determining the receptor sensitivity and modulation of pain, response to analgesics drugs and their interactions are presented in this article. It is already known that genomic variations affect the pharmacokinetic and pharmacodynamic properties of various analgesic drugs. Genes related to the expression of mu-opioid receptor, ATP-binding cassette B1 (ABCB1, catechol-O-Methyl Transferase (COMT, Cytochrome P450 enzymes have been widely studied and show some promise in determining the drug response in individuals. Some recent studies on sodium channel mutations (SCN9A, SCN11A have been implicated in congenital insensitivity to pain. Voltage gated ion channels such as sodium, calcium and potassium channels are being targeted for development of novel analgesics. Based on the available research, the clinical implementation of pharmacogenomics for personalized pain medicine is still in its infancy, but is promising. These are opening further opportunities for development of newer analgesics targeting pain receptors and ion channels.

  1. The Pharmacogenomics of Anti-Platelet Intervention (PAPI) Study: Variation in Platelet Response to Clopidogrel and Aspirin.

    Science.gov (United States)

    Bozzi, Laura M; Mitchell, Braxton D; Lewis, Joshua P; Ryan, Kathy A; Herzog, William R; O'Connell, Jeffrey R; Horenstein, Richard B; Shuldiner, Alan R; Yerges-Armstrong, Laura M

    2016-01-01

    Clopidogrel and aspirin are commonly prescribed anti-platelet medications indicated for patients who have experienced, or are at risk for, ischemic cardiovascular events. The Pharmacogenomics of Anti-Platelet Intervention (PAPI) Study was designed to characterize determinants of clopidogrel and dual anti-platelet therapy (DAPT) response in a healthy cohort of Old Order Amish from Lancaster, PA. Following a loading dose, clopidogrel was taken once a day for 7 days. One hour after the last dose of clopidogrel, 325 mg of aspirin was given. Ex vivo platelet aggregometry was performed at baseline, post-clopidogrel, and post-DAPT. Platelet aggregation measurements were significantly lower after both interventions for all agonists tested (p pharmacogenomics studies.

  2. The fallacy of racial pharmacogenomics

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    S.D.J. Pena

    2011-04-01

    Full Text Available Personalized pharmacogenomics aims to use individual genotypes to direct medical treatment. Unfortunately, the loci relevant for the pharmacokinetics and especially the pharmacodynamics of most drugs are still unknown. Moreover, we still do not understand the role that individual genotypes play in modulating the pathogenesis, the clinical course and the susceptibility to drugs of human diseases which, although appearing homogeneous on the surface, may vary from patient to patient. To try to deal with this situation, it has been proposed to use interpopulational variability as a reference for drug development and prescription, leading to the development of "race-targeted drugs". Given the present limitations of genomic knowledge and of the tools needed to fully implement it today, some investigators have proposed to use racial criteria as a palliative measure until personalized pharmacogenomics is fully developed. This was the rationale for the FDA approval of BiDil for treatment of heart failure in African Americans. I will evaluate the efficacy and safety of racial pharmacogenomics here and conclude that it fails on both counts. Next I shall review the perspectives and the predicted rate of development of clinical genomic studies. The conclusion is that "next-generation" genomic sequencing is advancing at a tremendous rate and that true personalized pharmacogenomics, based on individual genotyping, should soon become a clinical reality.

  3. Integrating epigenomics into pharmacogenomic studies

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    Wei Zhang

    2008-11-01

    Full Text Available Wei Zhang, R Stephanie Huang, M Eileen DolanSection of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USAAbstract: The goal of personalized medicine is to recommend drug treatment based on an individual’s genetic makeup. Pharmacogenomic studies utilize two main approaches: candidate gene and whole-genome. Both approaches analyze genetic variants such as single nucleotide polymorphisms (SNPs to identify associations with drug response. In addition to DNA sequence variations, nongenetic but heritable epigenetic systems have also been implicated in regulating gene expression that could influence drug response. The International HapMap Project lymphoblastoid cell lines (LCLs have been used to study genetic determinants responsible for expression variation and drug response. Recent studies have demonstrated that common genetic variants, including both SNPs and copy number variants (CNVs account for a substantial fraction of natural variation in gene expression. Given the critical role played by DNA methylationin gene regulation and the fact that DNA methylation is currently the most studied epigenetic system, we suggest that profiling the variation in DNA methylation in the HapMap samples will provide new insights into the regulation of gene expression as well as the mechanisms of individual drug response at a new level of complexity. Epigenomics will substantially add to our knowledge of how genetics explains gene expression and pharmacogenomics.Keywords: epigenetics, DNA methylation, gene expression, pharmacogenomics, HapMap, drug response

  4. Human immune system variation.

    Science.gov (United States)

    Brodin, Petter; Davis, Mark M

    2017-01-01

    The human immune system is highly variable between individuals but relatively stable over time within a given person. Recent conceptual and technological advances have enabled systems immunology analyses, which reveal the composition of immune cells and proteins in populations of healthy individuals. The range of variation and some specific influences that shape an individual's immune system is now becoming clearer. Human immune systems vary as a consequence of heritable and non-heritable influences, but symbiotic and pathogenic microbes and other non-heritable influences explain most of this variation. Understanding when and how such influences shape the human immune system is key for defining metrics of immunological health and understanding the risk of immune-mediated and infectious diseases.

  5. Pharmacogenetics, pharmacogenomics and ecogenetics.

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    Motulsky, Arno G; Qi, Ming

    2006-02-01

    Pharmacogenetics and pharmacogenomics deal with the role of genetic factors in drug effectiveness and adverse drug reactions. The promise of a personalized medicine is beginning to be explored but requires much more clinical and translational research. Specific DNA abnormalities in some cancers already have led to effective targeted treatments. Racially determined frequency differences in pharmacogenetic traits may affect choice of treatment requiring specific testing rather than basing treatments according to racial designation. The role of genes in variable responses to foreign chemicals (xenobiotics) has been termed ecogenetics or toxicogenetics raising problems in public health and occupational medicine. Nutrigenetics refers to genetic variation in response to nutrients and may affect nutritional requirements and predisposition to chronic disease.

  6. Pharmacogenomics in diabetes mellitus

    DEFF Research Database (Denmark)

    Zhou, Kaixin; Pedersen, Helle Krogh; Dawed, Adem Y.

    2016-01-01

    Genomic studies have greatly advanced our understanding of the multifactorial aetiology of type 2 diabetes mellitus (T2DM) as well as the multiple subtypes of monogenic diabetes mellitus. In this Review, we discuss the existing pharmacogenetic evidence in both monogenic diabetes mellitus and T2DM....... We highlight mechanistic insights from the study of adverse effects and the efficacy of antidiabetic drugs. The identification of extreme sulfonylurea sensitivity in patients with diabetes mellitus owing to heterozygous mutations in HNF1A represents a clear example of how pharmacogenetics can direct...... future pharmacogenomic findings could provide insights into treatment response in diabetes mellitus that, in addition to other areas of human genetics, facilitates drug discovery and drug development for T2DM....

  7. Current clinical evidence on pioglitazone pharmacogenomics

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    Marina eKawaguchi-Suzuki

    2013-11-01

    Full Text Available Pioglitazone is the most widely used thiazolidinedione and acts as an insulin-sensitizer through activation of the Peroxisome Proliferator-Activated Receptor-γ (PPARγ. Pioglitazone is approved for use in the management of type 2 diabetes mellitus, but its use in other therapeutic areas is increasing due to pleiotropic effects. In this hypothesis article, the current clinical evidence on pioglitazone pharmacogenomics is summarized and related to variability in pioglitazone response. How genetic variation in the human genome affects the pharmacokinetics and pharmacodynamics of pioglitazone was examined. For pharmacodynamic effects, hypoglycemic and anti-atherosclerotic effects, risks of fracture or edema, and the increase in body mass index in response to pioglitazone based on genotype were examined. The genes CYP2C8 and PPARG are the most extensively studied to date and selected polymorphisms contribute to respective variability in pioglitazone pharmacokinetics and pharmacodynamics. We hypothesized that genetic variation in pioglitazone pathway genes contributes meaningfully to the clinically observed variability in drug response. To test the hypothesis that genetic variation in PPARG associates with variability in pioglitazone response, we conducted a meta-analysis to synthesize the currently available data on the PPARG p.Pro12Ala polymorphism. The results showed that PPARG 12Ala carriers had a more favorable change in fasting blood glucose from baseline as compared to patients with the wild-type Pro12Pro genotype (p=0.018. Unfortunately, findings for many other genes lack replication in independent cohorts to confirm association; further studies are needed. Also, the biological functionality of these polymorphisms is unknown. Based on current evidence, we propose that pharmacogenomics may provide an important tool to individualize pioglitazone therapy and better optimize therapy in patients with T2DM or other conditions for which pioglitazone

  8. Progressing the utilisation of pharmacogenetics and pharmacogenomics into clinical care.

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    Trent, Ronald J; Cheong, Pak Leng; Chua, Eng Wee; Kennedy, Martin A

    2013-06-01

    Understanding human genetic variation and how it impacts on gene function is a major focus in genomic-based research. Translation of this knowledge into clinical care is exemplified by pharmacogenetics/pharmacogenomics. The identification of particular gene variants that might influence drug uptake, metabolism, distribution or excretion promises a more effective personalised medicine approach in choosing the right drug or its dose for any particular individual. Adverse drug responses can then be avoided or mitigated. An understanding of germline or acquired (somatic) DNA mutations can also be used to identify drugs that are more likely to be therapeutically beneficial. This represents an area of growing interest in the treatment of cancer.

  9. Pediatric perspective on pharmacogenomics.

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    Stevens, Adam; De Leonibus, Chiara; Hanson, Daniel; Whatmore, Andrew; Murray, Philip; Donn, Rachelle; Meyer, Stefan; Chatelain, Pierre; Clayton, Peter

    2013-11-01

    The advances in high-throughput genomic technologies have improved the understanding of disease pathophysiology and have allowed a better characterization of drug response and toxicity based on individual genetic make up. Pharmacogenomics is being recognized as a valid approach used to identify patients who are more likely to respond to medication, or those in whom there is a high probability of developing severe adverse drug reactions. An increasing number of pharmacogenomic studies are being published, most include only adults. A few studies have shown the impact of pharmacogenomics in pediatrics, highlighting a key difference between children and adults, which is the contribution of developmental changes to therapeutic responses across different age groups. This review focuses on pharmacogenomic research in pediatrics, providing examples from common pediatric conditions and emphasizing their developmental context.

  10. Personalized Medicine and Pharmacogenomics

    Science.gov (United States)

    ... medications. Pharmacogenomics is part of a field called personalized medicine — also called individualized or precision medicine — that ... may be part of routine medical care. References Personalized medicine. U.S. Food and Drug Administration. http://www. ...

  11. Progress towards the integration of pharmacogenomics in practice.

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    Mooney, Sean D

    2015-05-01

    Understanding the role genes and genetic variants play in clinical treatment response continues to be an active area of research with the goal of common clinical use. This goal has developed into today's industry of pharmacogenomics, where new drug-gene relationships are discovered and further characterized, published and then curated into national and international resources for use by researchers and clinicians. These efforts have given us insight into what a pharmacogenomic variant is, and how it differs from human disease variants and common polymorphisms. While publications continue to reveal pharmacogenomic relationships between genes and specific classes of drugs, many challenges remain toward the goal of widespread use clinically. First, the clinical guidelines for pharmacogenomic testing are still in their infancy. Second, sequencing technologies are changing rapidly making it somewhat unclear what genetic data will be available to the clinician at the time of care. Finally, what and when to return data to a patient is an area under constant debate. New innovations such as PheWAS approaches and whole genome sequencing studies are enabling a tsunami of new findings. In this review, pharmacogenomic variants, pharmacogenomic resources, interpretation clinical guidelines and challenges, such as WGS approaches, and the impact of pharmacogenomics on drug development and regulatory approval are reviewed.

  12. Pharmacogenomics of antimicrobial agents.

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    Aung, Ar Kar; Haas, David W; Hulgan, Todd; Phillips, Elizabeth J

    2014-01-01

    Antimicrobial efficacy and toxicity varies between individuals owing to multiple factors. Genetic variants that affect drug-metabolizing enzymes may influence antimicrobial pharmacokinetics and pharmacodynamics, thereby determining efficacy and/or toxicity. In addition, many severe immune-mediated reactions have been associated with HLA class I and class II genes. In the last two decades, understanding of pharmacogenomic factors that influence antimicrobial efficacy and toxicity has rapidly evolved, leading to translational success such as the routine use of HLA-B*57:01 screening to prevent abacavir hypersensitivity reactions. This article examines recent advances in the field of antimicrobial pharmacogenomics that potentially affect treatment efficacy and toxicity, and challenges that exist between pharmacogenomic discovery and translation into clinical use.

  13. Pharmacogenomics of the human ABC transporter ABCG2: from functional evaluation to drug molecular design

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    Ishikawa, Toshihisa; Tamura, Ai; Saito, Hikaru; Wakabayashi, Kanako; Nakagawa, Hiroshi

    2005-10-01

    In the post-genome-sequencing era, emerging genomic technologies are shifting the paradigm for drug discovery and development. Nevertheless, drug discovery and development still remain high-risk and high-stakes ventures with long and costly timelines. Indeed, the attrition of drug candidates in preclinical and development stages is a major problem in drug design. For at least 30% of the candidates, this attrition is due to poor pharmacokinetics and toxicity. Thus, pharmaceutical companies have begun to seriously re-evaluate their current strategies of drug discovery and development. In that light, we propose that a transport mechanism-based design might help to create new, pharmacokinetically advantageous drugs, and as such should be considered an important component of drug design strategy. Performing enzyme- and/or cell-based drug transporter, interaction tests may greatly facilitate drug development and allow the prediction of drug-drug interactions. We recently developed methods for high-speed functional screening and quantitative structure-activity relationship analysis to study the substrate specificity of ABC transporters and to evaluate the effect of genetic polymorphisms on their function. These methods would provide a practical tool to screen synthetic and natural compounds, and these data can be applied to the molecular design of new drugs. In this review article, we present an overview on the genetic polymorphisms of human ABC transporter ABCG2 and new camptothecin analogues that can circumvent AGCG2-associated multidrug resistance of cancer.

  14. Ethical and public policy challenges for pharmacogenomics.

    Science.gov (United States)

    Gershon, Elliot S; Alliey-Rodriguez, Ney; Grennan, Kay

    2014-12-01

    It is timely to consider the ethical and social questions raised by progress in pharmacogenomics, based on the current importance of pharmacogenomics for avoidance of predictable side effects of drugs, and for correct choice of medications in certain cancers. It has been proposed that the entire population be genotyped for drug-metabolizing enzyme polymorphisms, as a measure that would prevent many untoward and dangerous drug reactions. Pharmacologic treatment targeting based on genomics of disease can be expected to increase greatly in the coming years. Policy and ethical issues exist on consent for large-scale genomic pharmacogenomic data collection, public vs corporate ownership of genomic research results, testing efficacy and safety of drugs used for rare genomic indications, and accessibility of treatments based on costly research that is applicable to relatively few patients. In major psychiatric disorders and intellectual deficiency, rare and de novo deletion or duplication of chromosomal segments (copy number variation), in the aggregate, are common causes of increased risk. This implies that the policy problems of pharmacogenomics will be particularly important for the psychiatric disorders.

  15. Pharmacogenomics in Oncology Care

    Directory of Open Access Journals (Sweden)

    Kelly K Filipski

    2014-04-01

    Full Text Available Cancer pharmacogenomics have contributed a number of important discoveries to current cancer treatment, changing the paradigm of treatment decisions. Both somatic and germline mutations are utilized to better understand the underlying biology of cancer growth and treatment response. The level of evidence required to fully translate pharmacogenomic discoveries into the clinic has relied heavily on randomized clinical trials. In this review, the use of observational studies, as well as, the use of adaptive trials and next generation sequencing to develop the required level of evidence for clinical implementation are discussed.

  16. Pharmacogenomics and migraine

    DEFF Research Database (Denmark)

    Tfelt-Hansen, Peer; Brøsen, Kim

    2008-01-01

    cases pharmacodynamic variability we mention possible implications for the acute and preventive treatment of migraine. Pharmacogenomics will most likely in the future be one part of our therapeutic armamentarium and will provide a stronger scientific basis for optimizing drug therapy on the basis...

  17. A European Spectrum of Pharmacogenomic Biomarkers: Implications for Clinical Pharmacogenomics

    Science.gov (United States)

    Mizzi, Clint; Dalabira, Eleni; Kumuthini, Judit; Dzimiri, Nduna; Balogh, Istvan; Başak, Nazli; Böhm, Ruwen; Borg, Joseph; Borgiani, Paola; Bozina, Nada; Bruckmueller, Henrike; Burzynska, Beata; Carracedo, Angel; Cascorbi, Ingolf; Deltas, Constantinos; Dolzan, Vita; Fenech, Anthony; Grech, Godfrey; Kasiulevicius, Vytautas; Kádaši, Ľudevít; Kučinskas, Vaidutis; Khusnutdinova, Elza; Loukas, Yiannis L.; Macek, Milan; Makukh, Halyna; Mathijssen, Ron; Mitropoulos, Konstantinos; Mitropoulou, Christina; Novelli, Giuseppe; Papantoni, Ioanna; Pavlovic, Sonja; Saglio, Giuseppe; Setric, Jadranka; Stojiljkovic, Maja; Stubbs, Andrew P.; Squassina, Alessio; Torres, Maria; Turnovec, Marek; van Schaik, Ron H.; Voskarides, Konstantinos; Wakil, Salma M.; Werk, Anneke; del Zompo, Maria; Zukic, Branka; Katsila, Theodora; Lee, Ming Ta Michael; Motsinger-Rief, Alison; Mc Leod, Howard L.; van der Spek, Peter J.; Patrinos, George P.

    2016-01-01

    Pharmacogenomics aims to correlate inter-individual differences of drug efficacy and/or toxicity with the underlying genetic composition, particularly in genes encoding for protein factors and enzymes involved in drug metabolism and transport. In several European populations, particularly in countries with lower income, information related to the prevalence of pharmacogenomic biomarkers is incomplete or lacking. Here, we have implemented the microattribution approach to assess the pharmacogenomic biomarkers allelic spectrum in 18 European populations, mostly from developing European countries, by analyzing 1,931 pharmacogenomics biomarkers in 231 genes. Our data show significant inter-population pharmacogenomic biomarker allele frequency differences, particularly in 7 clinically actionable pharmacogenomic biomarkers in 7 European populations, affecting drug efficacy and/or toxicity of 51 medication treatment modalities. These data also reflect on the differences observed in the prevalence of high-risk genotypes in these populations, as far as common markers in the CYP2C9, CYP2C19, CYP3A5, VKORC1, SLCO1B1 and TPMT pharmacogenes are concerned. Also, our data demonstrate notable differences in predicted genotype-based warfarin dosing among these populations. Our findings can be exploited not only to develop guidelines for medical prioritization, but most importantly to facilitate integration of pharmacogenomics and to support pre-emptive pharmacogenomic testing. This may subsequently contribute towards significant cost-savings in the overall healthcare expenditure in the participating countries, where pharmacogenomics implementation proves to be cost-effective. PMID:27636550

  18. A European Spectrum of Pharmacogenomic Biomarkers: Implications for Clinical Pharmacogenomics.

    Science.gov (United States)

    Mizzi, Clint; Dalabira, Eleni; Kumuthini, Judit; Dzimiri, Nduna; Balogh, Istvan; Başak, Nazli; Böhm, Ruwen; Borg, Joseph; Borgiani, Paola; Bozina, Nada; Bruckmueller, Henrike; Burzynska, Beata; Carracedo, Angel; Cascorbi, Ingolf; Deltas, Constantinos; Dolzan, Vita; Fenech, Anthony; Grech, Godfrey; Kasiulevicius, Vytautas; Kádaši, Ľudevít; Kučinskas, Vaidutis; Khusnutdinova, Elza; Loukas, Yiannis L; Macek, Milan; Makukh, Halyna; Mathijssen, Ron; Mitropoulos, Konstantinos; Mitropoulou, Christina; Novelli, Giuseppe; Papantoni, Ioanna; Pavlovic, Sonja; Saglio, Giuseppe; Setric, Jadranka; Stojiljkovic, Maja; Stubbs, Andrew P; Squassina, Alessio; Torres, Maria; Turnovec, Marek; van Schaik, Ron H; Voskarides, Konstantinos; Wakil, Salma M; Werk, Anneke; Del Zompo, Maria; Zukic, Branka; Katsila, Theodora; Lee, Ming Ta Michael; Motsinger-Rief, Alison; Mc Leod, Howard L; van der Spek, Peter J; Patrinos, George P

    2016-01-01

    Pharmacogenomics aims to correlate inter-individual differences of drug efficacy and/or toxicity with the underlying genetic composition, particularly in genes encoding for protein factors and enzymes involved in drug metabolism and transport. In several European populations, particularly in countries with lower income, information related to the prevalence of pharmacogenomic biomarkers is incomplete or lacking. Here, we have implemented the microattribution approach to assess the pharmacogenomic biomarkers allelic spectrum in 18 European populations, mostly from developing European countries, by analyzing 1,931 pharmacogenomics biomarkers in 231 genes. Our data show significant inter-population pharmacogenomic biomarker allele frequency differences, particularly in 7 clinically actionable pharmacogenomic biomarkers in 7 European populations, affecting drug efficacy and/or toxicity of 51 medication treatment modalities. These data also reflect on the differences observed in the prevalence of high-risk genotypes in these populations, as far as common markers in the CYP2C9, CYP2C19, CYP3A5, VKORC1, SLCO1B1 and TPMT pharmacogenes are concerned. Also, our data demonstrate notable differences in predicted genotype-based warfarin dosing among these populations. Our findings can be exploited not only to develop guidelines for medical prioritization, but most importantly to facilitate integration of pharmacogenomics and to support pre-emptive pharmacogenomic testing. This may subsequently contribute towards significant cost-savings in the overall healthcare expenditure in the participating countries, where pharmacogenomics implementation proves to be cost-effective.

  19. Pharmacogenomics--how close/far are we to practising individualized medicine for children?

    Science.gov (United States)

    Sing, Chor-Wing; Cheung, Ching-Lung; Wong, Ian C K

    2015-03-01

    The translation of pharmacogenomics into clinical practice is a key approach for practising individualized medicine, which aims to maximize drug efficacy and minimize drug toxicity. Since the completion of both the Human Genome Project and the International HapMap project, the development of pharmacogenomics has been greatly facilitated. However, progress in translating pharmacogenomics into clinical practice, especially in paediatric medicine, is unexpectedly slow. Many challenges from different areas remain. This paper discusses the existing applications and the limitations to the implementation of paediatric pharmacogenomics, as well as possible solutions for overcoming these limitations and challenges.

  20. Pharmacometabolomics-aided Pharmacogenomics in Autoimmune Disease.

    Science.gov (United States)

    Katsila, Theodora; Konstantinou, Evangelia; Lavda, Ioanna; Malakis, Harilaos; Papantoni, Ioanna; Skondra, Lamprini; Patrinos, George P

    2016-03-01

    Inter-individual variability has been a major hurdle to optimize disease management. Precision medicine holds promise for improving health and healthcare via tailor-made therapeutic strategies. Herein, we outline the paradigm of "pharmacometabolomics-aided pharmacogenomics" in autoimmune diseases. We envisage merging pharmacometabolomic and pharmacogenomic data (to address the interplay of genomic and environmental influences) with information technologies to facilitate data analysis as well as sense- and decision-making on the basis of synergy between artificial and human intelligence. Humans can detect patterns, which computer algorithms may fail to do so, whereas data-intensive and cognitively complex settings and processes limit human ability. We propose that better-informed, rapid and cost-effective omics studies need the implementation of holistic and multidisciplinary approaches.

  1. Report: Pharmacogenetics, pharmacogenomics and ecogenetics

    Institute of Scientific and Technical Information of China (English)

    MOTULSKY Arno G.; QI Ming

    2006-01-01

    Pharmacogenetics and pharmacogenomics deal with the role of genetic factors in drug effectiveness and adverse drug reactions. The promise of a personalized medicine is beginning to be explored but requires much more clinical and translational research. Specific DNA abnormalities in some cancers already have led to effective targeted treatments. Racially determined frequency differences in pharmacogenetic traits may affect choice of treatment requiring specific testing rather than basing treatments according to racial designation.The role of genes in variable responses to foreign chemicals (xenobiotics) has been termed ecogenetics or toxicogenetics raising problems in public health and occupational medicine. Nutrigenetics refers to genetic variation in response to nutrients and may affect nutritional requirements and predisposition to chronic disease.

  2. From pharmacogenetics and ecogenetics to pharmacogenomics.

    Science.gov (United States)

    Motulsky, Arno G; Motuslky, Arno G

    2002-01-01

    The origin and development of pharmacogenetics are traced with emphasis on early hints by Garrod, Haldane, and later by RJ Williams. The field was delineated by Motulsky in 1957 and described as pharmacogenetics by Vogel in 1959. Kalow's monograph (1962) definitely established the discipline. Resemblance of identical twins in drug metabolism as compared with non identical twins (Vesell, 1970's) established the general importance of polygenic inheritance in disposal of many drugs. Ecogenetics was defined by Brewer in 1971 as dealing with genetic variation affecting the response to any environmental agents with emphasis on xenobiotics. More recent developments have broadened pharmacogenetic approaches to include novel genomic techniques with introduction of the term pharmacogenomics in the 1990's. Genetic and genomic approaches (toxicogenetics and toxicogenomics) are also being applied in the "environmental genome project". The interaction of genetic variation with dietary factors led to the field of Nutritional ecogenetics (Nutrigenomics) which relates the role of genetics to nutritional requirements and nutrition-mediated susceptibility to chronic disease. The total promise of pharmacogenomics is often overstated. The field is likely to have an impact on choice of drug therapy and avoidance of adverse events but is unlikely to lead to a revolution in therapeutics. Aspects of pharmacogenomic approaches and its applications including problems of premature commercialization are discussed.

  3. The pharmacogenomics of statins.

    Science.gov (United States)

    Gelissen, Ingrid C; McLachlan, Andrew J

    2014-10-01

    The statin class of cholesterol-lowering drugs have been used for decades to successfully lower plasma cholesterol concentrations and cardiovascular risk. Adverse effects of statins are generally considered mild, but increase with age of patients and polypharmacy. One aspect of statin therapy that is still difficult for prescribers to predict is the individual's response to statin therapy. Recent advances in the field of pharmacogenomics have indicated variants of candidate genes that affect statin efficacy and safety. In this review, a number of candidates that affect statin pharmacokinetics and pharmacodynamics are discussed. Some of these candidates, in particular those involved in import and efflux of statins, have now been linked to increased risk of side effects. Furthermore, pharmacogenomic studies continue to reveal new players that are involved in the fine-tuning of the complex regulation of cholesterol homeostasis and response to statins.

  4. Pharmacogenomics and modern therapy

    Directory of Open Access Journals (Sweden)

    Rao Monica

    2007-01-01

    Full Text Available Pharmacogenomics is an emerging arena which aims to improve the therapeutic efficacy of a drug based on the genetic profile of a patient. This technology tries to detect the link between the genetic blueprint of a person and the heterogenous response to a drug so as to use this information to maximize the efficacy of the drug. This article explores the genesis of this field along with its benefits and the various techniques used for the same.

  5. Mining the pharmacogenomics literature—a survey of the state of the art

    Science.gov (United States)

    Cohen, K. Bretonnel; Garten, Yael; Shah, Nigam H.

    2012-01-01

    This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011. Pharmacogenomics (or pharmacogenetics) is the field that studies how human genetic variation impacts drug response. Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years. This survey covers efforts dealing with the automatic recognition of relevant named entities (e.g. genes, gene variants and proteins, diseases and other pathological phenomena, drugs and other chemicals relevant for medical treatment), as well as various forms of relations between them. A wide range of text genres is considered, such as scientific publications (abstracts, as well as full texts), patent texts and clinical narratives. We also discuss infrastructure and resources needed for advanced text analytics, e.g. document corpora annotated with corresponding semantic metadata (gold standards and training data), biomedical terminologies and ontologies providing domain-specific background knowledge at different levels of formality and specificity, software architectures for building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensive ways to disseminate and interact with the typically huge amounts of semiformal knowledge structures extracted by text mining tools. Finally, we consider some of the novel applications that have already been developed in the field of pharmacogenomic text mining and point out perspectives for future research. PMID:22833496

  6. Mining the pharmacogenomics literature--a survey of the state of the art.

    Science.gov (United States)

    Hahn, Udo; Cohen, K Bretonnel; Garten, Yael; Shah, Nigam H

    2012-07-01

    This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011. Pharmacogenomics (or pharmacogenetics) is the field that studies how human genetic variation impacts drug response. Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years. This survey covers efforts dealing with the automatic recognition of relevant named entities (e.g. genes, gene variants and proteins, diseases and other pathological phenomena, drugs and other chemicals relevant for medical treatment), as well as various forms of relations between them. A wide range of text genres is considered, such as scientific publications (abstracts, as well as full texts), patent texts and clinical narratives. We also discuss infrastructure and resources needed for advanced text analytics, e.g. document corpora annotated with corresponding semantic metadata (gold standards and training data), biomedical terminologies and ontologies providing domain-specific background knowledge at different levels of formality and specificity, software architectures for building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensive ways to disseminate and interact with the typically huge amounts of semiformal knowledge structures extracted by text mining tools. Finally, we consider some of the novel applications that have already been developed in the field of pharmacogenomic text mining and point out perspectives for future research.

  7. Pharmacogenomics considerations in the control of hypertension.

    Science.gov (United States)

    Lupoli, Sara; Salvi, Erika; Barcella, Matteo; Barlassina, Cristina

    2015-11-01

    The response to antihypertensive therapy is very heterogeneous and the need by the physicians to account for it has driven much interest in pharmacogenomics of antihypertensive drugs. The Human Genome Project and the initiatives in genomics that followed, generated a huge number of genetic data that furnished the tools to explore the genotype-phenotype association in candidate genes and at genome-wide level. In spite of the efforts and the great number of publications, pharmacogenomics of antihypertensive drugs is far from being used in clinical practice. In this review, we analyze the main findings available in PubMed from 2010 to 2015, in relation to the major classes of antihypertensive drugs. We also describe a new Phase II drug that targets two specific hypertension predisposing mechanisms.

  8. Role of pharmacogenomics in the treatment of tuberculosis: a review

    Directory of Open Access Journals (Sweden)

    Ramachandran G

    2012-09-01

    Full Text Available Geetha Ramachandran, Soumya SwaminathanNational Institute for Research in Tuberculosis, Indian Council of Medical Research, Chennai, IndiaBackground: Tuberculosis is one of the major public health problems worldwide. Modern antituberculous treatment can cure most patients; cure rates > 95% are achieved with standard short-course chemotherapy regimens containing isoniazid, rifampicin, pyrazinamide, and ethambutol among patients with drug-susceptible strains of tuberculosis; however, a small proportion do not respond to treatment or develop serious adverse events. Pharmacogenomic studies of drugs used in the treatment of tuberculosis could help us understand intersubject variations in treatment response. In this review, we compiled pharmacogenomic data on antituberculous drugs that were available from different settings that would give a better insight into the role of pharmacogenomics in the treatment of tuberculosis, thereby enhancing the efficacy and limiting the toxicity of existing antituberculosis medications.Methods: The PubMed database was searched from 1960 to the present using the keywords "tuberculosis", "antituberculosis treatment", "isoniazid", "rifampicin", "pyrazinamide", "ethambutol", "pharmacogenomics", and "polymorphism". Abstracts from meetings and review articles were included.Conclusion: Studies conducted in different settings suggest that pharmacogenomics plays a significant role in isoniazid metabolism, and impacts both treatment efficacy and frequency of adverse reactions. Single nucleotide polymorphisms influencing plasma rifampicin concentrations are also reported. No data are available regarding other first-line drugs, ie, ethambutol and pyrazinamide. There is a need to incorporate pharmacogenomics into clinical trials of tuberculosis in order to understand the factors impacting therapeutic success and occurrence of adverse drug effects.Keywords: tuberculosis, antituberculous treatment, pharmacogenomics, polymorphism

  9. Physicians' pharmacogenomics information needs and seeking behavior: a study with case vignettes.

    Science.gov (United States)

    Heale, Bret S E; Khalifa, Aly; Stone, Bryan L; Nelson, Scott; Del Fiol, Guilherme

    2017-08-01

    Genetic testing, especially in pharmacogenomics, can have a major impact on patient care. However, most physicians do not feel that they have sufficient knowledge to apply pharmacogenomics to patient care. Online information resources can help address this gap. We investigated physicians' pharmacogenomics information needs and information-seeking behavior, in order to guide the design of pharmacogenomics information resources that effectively meet clinical information needs. We performed a formative, mixed-method assessment of physicians' information-seeking process in three pharmacogenomics case vignettes. Interactions of 6 physicians' with online pharmacogenomics resources were recorded, transcribed, and analyzed for prominent themes. Quantitative data included information-seeking duration, page navigations, and number of searches entered. We found that participants searched an average of 8 min per case vignette, spent less than 30 s reviewing specific content, and rarely refined search terms. Participants' information needs included a need for clinically meaningful descriptions of test interpretations, a molecular basis for the clinical effect of drug variation, information on the logistics of carrying out a genetic test (including questions related to cost, availability, test turn-around time, insurance coverage, and accessibility of expert support).Also, participants sought alternative therapies that would not require genetic testing. This study of pharmacogenomics information-seeking behavior indicates that content to support their information needs is dispersed and hard to find. Our results reveal a set of themes that information resources can use to help physicians find and apply pharmacogenomics information to the care of their patients.

  10. The HapMap Resource is Providing New Insights into Ourselves and its Application to Pharmacogenomics.

    Science.gov (United States)

    Zhang, Wei; Ratain, Mark J; Dolan, M Eileen

    2008-01-01

    The exploration of quantitative variation in complex traits such as gene expression and drug response in human populations has become one of the major priorities for medical genetics. The International HapMap Project provides a key resource of genotypic data on human lymphoblastoid cell lines derived from four major world populations of European, African, Chinese and Japanese ancestry for researchers to associate with various phenotypic data to find genes affecting health, disease and response to drugs. Recent progress in dissecting genetic contribution to natural variation in gene expression within and among human populations and variation in drug response are two examples in which researchers have utilized the HapMap resource. The HapMap Project provides new insights into the human genome and has applicability to pharmacogenomics studies leading to personalized medicine.

  11. New molecular medicine: Diagnomics and pharmacogenomics

    Science.gov (United States)

    Kauffman, Michael G.

    1999-04-01

    Millennium Predictive Medicine (MPMx), a subsidiary of Millennium Pharmaceuticals, is focusing on the discovery and clinical validation of Diagnomic and Pharmacogenomic Tests which will replace many of the subjective elements of clinical decision making. Diagnomics are molecular diagnostic markers with prognostic and economic impact. While the majority of currently available diagnostics represent data points, Diagnomics allow patients and physicians to make scientifically based, individualized decisions about their disease and its therapy. Pharmacogenomics are diagnostics that specify the use or avoidance of specific therapeutics based on an individual genotype and/or disease subtype. MPMx uses the broad Millennium genomics, proteomics, and bioinformatics technologies in the analysis of human disease and drug response. These technologies permit global and unbiased approaches towards the elucidation of disease pathways and mechanisms at the molecular level. Germline or somatic mutations, RNA levels, or protein levels comprising these pathways and mechanisms are currently being evaluated as markers for disease predisposition, stage, aggressiveness, and likely drug response or drug toxicity. Diagnomic and Pharmacogenomic Tests are part of the new molecular medicine that is transforming clinical practice forma symptom/pathology-based art into a pre-symptom, mechanism- based science.

  12. Pharmacogenomic dosing of warfarin: ready or not?

    Science.gov (United States)

    Lackner, Thomas E

    2008-08-01

    Warfarin is a medication with a narrow therapeutic index, nonlinear intrapatient pharmacokinetics, and high interpatient variability in its dose-response relationship. These characteristics create great difficulty in determining an appropriate dose; sub- or supratherapeutic doses can increase the risk of bleeding and venous thromboembolism complications. Algorithms based on nongenetic factors of patient age, gender, body weight, diseases, diet, smoking, and medication traditionally have been used to determine warfarin dose requirements. However, these formulas account for less than 20% of the variability in warfarin response. Following completion of the Human Genome Project, several genetic variants of CYP2C9 and VKORC1 have been identified that account for a greater proportion of the variability in patient response to warfarin than is explained by nongenetic factors. Moreover, algorithms that analyze both patient genetic and nongenetic factors, i.e., pharmacogenomics, in warfarin response account for 55% to 60% of the variability. This raises the prospect of enhancing the ability to predict warfarin dose requirements and, thereby, improving its safety, effectiveness, and therapy efficiency. This review evaluates the impact of combining genetic and nongenetic factors in accounting for the variability in warfarin response and the prospect that pharmacogenomic algorithms will improve warfarin dosing early in therapy, possibly achieving a more rapid attainment of the therapeutic dose, improving safety, and increasing effectiveness. The most comprehensive and widely available pharmacogenomic algorithms for estimating warfarin dose requirements when initiating therapy, www.WarfarinDosing.org, is reviewed.

  13. Potential applications of pharmacogenomics to heart failure therapies.

    Science.gov (United States)

    Parikh, Kishan S; Ahmad, Tariq; Fiuzat, Mona

    2014-10-01

    Pharmacogenomics explores one drug's varying effects on different patient genotypes. A better understanding of genomic variation's contribution to drug response can impact 4 arenas in heart failure (HF): (1) identification of patients most likely to receive benefit from therapy, (2) risk stratify patients for risk of adverse events, (3) optimize dosing of drugs, and (4) steer future clinical trial design and drug development. In this review, the authors explore the potential applications of pharmacogenomics in patients with HF in the context of these categories.

  14. Genetic variation and human longevity.

    Science.gov (United States)

    Soerensen, Mette

    2012-05-01

    The overall aim of the PhD project was to elucidate the association of human longevity with genetic variation in major candidate genes and pathways of longevity. Based on a thorough literature and database search we chose to apply a pathway approach; to explore variation in genes composing the DNA damage signaling, DNA repair, GH/IGF-1/insulin signaling and pro-/antioxidant pathways. In addition, 16 genes which did not belong to the core of either pathway, however recurrently regarded as candidate genes of longevity (e.g. APOE), were included. In this way a total of 168 genes were selected for investigation. We decided to explore the genetic variation in the form of single nucleotide polymorphisms (SNPs), a highly investigated type of genetic variation. SNPs having potential functional impact (e.g. affecting binding of transcription factors) were identified, so were specific SNPs in the candidate genes previously published to be associated with human longevity. To cover the majority of the common genetic variation in the 168 gene regions (encoding regions plus 5,000 bp upstream and 1,000 downstream) we applied the tagging SNP approach via the HapMap Consortium. Consequently 1,536 SNPs were selected. The majority of the previous publications on genetic variation and human longevity had employed a case-control study design, e.g. comparing centenarians to middle-aged controls. This type of study design is somehow prone to bias introduced by for instance cohort effects, i.e. differences in characteristics of cases and controls, a kind of bias which is avoided when a prospective cohort is under study. Therefore, we chose to investigate 1,200 individuals of the Danish 1905 birth cohort, which have been followed since 1998 when the members were 92-93 years old. The genetic contribution to human longevity has been estimated to be most profound during the late part of life, thus these oldest-old individuals are excellent for investigating such effect. The follow-up survival

  15. Pharmacogenomics of glinides.

    Science.gov (United States)

    Chen, Miao; Hu, Cheng; Jia, Weiping

    2015-01-01

    Glinides, including repaglinide, nateglinide and mitiglinide, are a type of fasting insulin secretagogue that could help to mimic early-phase insulin release, thus providing improved control of the postprandial glucose levels. Glinides stimulate insulin secretion by inhibiting ATP-sensitive potassium channels in the pancreatic β-cell membrane. Although glinides have been widely used clinically and display excellent safety and efficacy, the response to glinides varies among individuals, which is partially due to genetic factors involved in drug absorption, distribution, metabolism and targeting. Several pharmacogenomic studies have demonstrated that variants of genes involved in the pharmacokinetics or pharmacodynamics of glinides are associated with the drug response. Polymorphisms of genes involved in drug metabolism, such as CYP2C9, CYP2C8 and SLCO1B1, may influence the efficacy of glinides and the incidence of adverse effects. In addition, Type 2 diabetes mellitus susceptibility genes, such as KCNQ1, PAX4 and BETA2, also influence the efficacy of glinides. In this article, we review and discuss current pharmacogenomics researches on glinides, and hopefully provide useful data and proof for clinical application.

  16. Pharmacogenomics: Principles & Issues

    Science.gov (United States)

    Hoh, Yin Kiong; Boo, Hong Kwen

    2007-01-01

    Human beings vary in their responses to the drugs prescribed to them. These variations can be due to differences in their age, gender, weight, health status, diet, concurrent therapy and genetic make-up. Recently, it has been estimated that 85% of a patient's response to drugs is due to the genetic make-up of the individual (Snedden, 1999).…

  17. 76 FR 9583 - Draft Guidance for Industry on Clinical Pharmacogenomics: Premarketing Evaluation in Early Phase...

    Science.gov (United States)

    2011-02-18

    ... guidance for industry entitled ``Clinical Pharmacogenomics: Premarketing Evaluation in Early Phase Clinical Studies.'' The draft guidance is intended to assist the pharmaceutical industry and other investigators... HUMAN SERVICES Food and Drug Administration Draft Guidance for Industry on Clinical...

  18. Size variation in Middle Pleistocene humans.

    Science.gov (United States)

    Arsuaga, J L; Carretero, J M; Lorenzo, C; Gracia, A; Martínez, I; Bermúdez de Castro, J M; Carbonell, E

    1997-08-22

    It has been suggested that European Middle Pleistocene humans, Neandertals, and prehistoric modern humans had a greater sexual dimorphism than modern humans. Analysis of body size variation and cranial capacity variation in the large sample from the Sima de los Huesos site in Spain showed instead that the sexual dimorphism is comparable in Middle Pleistocene and modern populations.

  19. Anatomy, Medical Education, and Human Ancestral Variation

    Science.gov (United States)

    Strkalj, Goran; Spocter, Muhammad A.; Wilkinson, A. Tracey

    2011-01-01

    It is argued in this article that the human body both in health and disease cannot be fully understood without adequately accounting for the different levels of human variation. The article focuses on variation due to ancestry, arguing that the inclusion of information pertaining to ancestry in human anatomy teaching materials and courses should…

  20. Anatomy, Medical Education, and Human Ancestral Variation

    Science.gov (United States)

    Strkalj, Goran; Spocter, Muhammad A.; Wilkinson, A. Tracey

    2011-01-01

    It is argued in this article that the human body both in health and disease cannot be fully understood without adequately accounting for the different levels of human variation. The article focuses on variation due to ancestry, arguing that the inclusion of information pertaining to ancestry in human anatomy teaching materials and courses should…

  1. Pharmacogenomics: from cell to clinic (Part 1).

    Science.gov (United States)

    Siest, Gérard; Medeiros, Rui; Melichar, Bohuslav; Stathopoulou, Maria; Van Schaik, Ron H N; Cacabelos, Ramon; Abt, Peter Meier; Monteiro, Carolino; Gurwitz, David; Queiroz, Jao; Mota-Filipe, Helder; Ndiaye, Ndieye Coumba; Visvikis-Siest, Sophie

    2014-04-01

    The second international European Society of Pharmacogenomics and Theranostics (ESPT) conference was organized in Lisbon, Portugal, and attracted 250 participants from 37 different countries. The participants could listen to 50 oral presentations, participate in five lunch symposia and were able to view 83 posters and an exhibition. The first part of this Conference Scene will focus on the pharmacogenomics and biomarkers used in medical oncology, and in particular solid tumors. In addition, this article covers the two keynote conference introductory lectures by Ann K Daly and Magnus Ingelman-Sundberg. The second part of this article will discuss the clinical implementation of pharmacogenomic tests; the role of transports and pharmacogenomics; how stem cells and other new tools are helping the development of pharmacogenomics and drug discovery; and an update on the clinical translation of pharmacogenomics to personalized medicine. Part two of this Conference Scene will be featured in the next issue of Pharmacogenomics.

  2. Pharmacogenetics and pharmacogenomics as tools in cancer therapy.

    Science.gov (United States)

    Rodríguez-Vicente, Ana E; Lumbreras, Eva; Hernández, Jesus M; Martín, Miguel; Calles, Antonio; Otín, Carlos López; Algarra, Salvador Martín; Páez, David; Taron, Miquel

    2016-03-01

    Pharmacogenetics and pharmacogenomics (PGx) are rapidly growing fields that aim to elucidate the genetic basis for the interindividual differences in drug response. PGx approaches have been applied to many anticancer drugs in an effort to identify relevant inherited or acquired genetic variations that may predict patient response to chemotherapy and targeted therapies. In this article, we discuss the advances in the field of cancer pharmacogenetics and pharmacogenomics, driven by the recent technological advances and new revolutionary massive sequencing technologies and their application to elucidate the genetic bases for interindividual drug response and the development of biomarkers able to personalize drug treatments. Specifically, we present recent progress in breast cancer molecular classifiers, cell-free circulating DNA as a prognostic and predictive biomarker in cancer, patient-derived tumor xenograft models, chronic lymphocytic leukemia genomic landscape, and current pharmacogenetic advances in colorectal cancer. This review is based on the lectures presented by the speakers of the symposium "Pharmacogenetics and Pharmacogenomics as Tools in Cancer Therapy" from the VII Conference of the Spanish Pharmacogenetics and Pharmacogenomics Society (SEFF), held in Madrid (Spain) on April 21, 2015.

  3. Pharmacogenovigilance: a pharmacogenomics pharmacovigilance program.

    Science.gov (United States)

    Awada, Zeinab; Zgheib, Nathalie Khoueiry

    2014-04-01

    In this report, we review the importance of pharmacovigilance in detecting postmarketing adverse drug events and the potential for developing pharmacogenovigilance programs by integrating pharmacogenomics with pharmacovigilance. We propose to start developing such a program in primary healthcare systems that use basic features of electronic medical records and have access to large numbers of patients commonly prescribed drugs. Such programs, if carefully designed, may grow over time and hopefully enhance the collection and interpretation of useful data for the clinical applications of pharmacogenomics testing.

  4. Pharmacogenomics: Current State-of-the-Art

    Directory of Open Access Journals (Sweden)

    Daniel F. Carr

    2014-05-01

    Full Text Available The completion of the human genome project 10 years ago was met with great optimism for improving drug therapy through personalized medicine approaches, with the anticipation that an era of genotype-guided patient prescribing was imminent. To some extent this has come to pass and a number of key pharmacogenomics markers of inter-individual drug response, for both safety and efficacy, have been identified and subsequently been adopted in clinical practice as pre-treatment genetic tests. However, the universal application of genetics in treatment guidance is still a long way off. This review will highlight important pharmacogenomic discoveries which have been facilitated by the human genome project and other milestone projects such as the International HapMap and 1000 genomes, and by the continued development of genotyping and sequencing technologies, including rapid point of care pre-treatment genetic testing. However, there are still many challenges to implementation for the many other reported biomarkers which continue to languish within the discovery phase. As technology advances over the next 10 years, and the costs fall, the field will see larger genetic data sets, including affordable whole genome sequences, which will, it is hoped, improve patient outcomes through better diagnostic, prognostic and predictive biomarkers.

  5. A European spectrum of pharmacogenomic biomarkers: Implications for clinical pharmacogenomics

    NARCIS (Netherlands)

    C. Mizzi (Clint); Dalabira, E. (Eleni); Kumuthini, J. (Judit); Dzimiri, N. (Nduna); Balogh, I. (Istvan); Başak, N. (Nazli); Böhm, R. (Ruwen); J. Borg (Joseph); P. Borgiani (P.); N. Bozina (Nada); Bruckmueller, H. (Henrike); Burzynska, B. (Beata); Carracedo, A. (Angel); Cascorbi, I. (Ingolf); C. Deltas (Constantinos); Dolzan, V. (Vita); Fenech, A. (Anthony); G. Grech (Godfrey); Kasiulevicius, V. (Vytautas); Kádaši, L. (Ludevít); V. Kučinskas (Vaidutis); E.K. Khusnutdinova (Elza); Loukas, Y.L. (Yiannis L.); Macek, M. (Milan); H. Makukh (Halyna); Mathijssen, R. (Ron); K. Mitropoulos (Konstantinos); C. Mitropoulou (Christina); Novelli, G. (Giuseppe); I. Papantoni (Ioanna); S. Pavlovic (Sonja); Saglio, G. (Giuseppe); Setric, J. (Jadranka); M. Stojiljkovic (Maja); A. Stubbs (Andrew); A. Squassini (Alessio); Torres, M. (Maria); Turnovec, M. (Marek); R.H.N. van Schaik (Ron); Voskarides, K. (Konstantinos); Wakil, S.M. (Salma M.); Werk, A. (Anneke); Zompo, M.D. (Maria Del); B. Zukic (Branka); T. Katsila (Theodora); M.T.M. Lee (M. T M); Motsinger-Rief, A. (Alison); Leod, H.L.M. (Howard L. Mc); P.J. van der Spek (Peter); G.P. Patrinos (George)

    2016-01-01

    textabstractPharmacogenomics aims to correlate inter-individual differences of drug efficacy and/or toxicity with the underlying genetic composition, particularly in genes encoding for protein factors and enzymes involved in drug metabolism and transport. In several European populations, particularl

  6. A European spectrum of pharmacogenomic biomarkers: Implications for clinical pharmacogenomics

    NARCIS (Netherlands)

    C. Mizzi (Clint); Dalabira, E. (Eleni); J. Kumuthini (Judit); Dzimiri, N. (Nduna); Balogh, I. (Istvan); Başak, N. (Nazli); Böhm, R. (Ruwen); J. Borg (Joseph); P. Borgiani (P.); N. Bozina (Nada); Bruckmueller, H. (Henrike); Burzynska, B. (Beata); Carracedo, A. (Angel); Cascorbi, I. (Ingolf); C. Deltas (Constantinos); V. Dolzan (Vita); Fenech, A. (Anthony); G. Grech (Godfrey); Kasiulevicius, V. (Vytautas); Kádaši, L. (Ludevít); V. Kučinskas (Vaidutis); E.K. Khusnutdinova (Elza); Loukas, Y.L. (Yiannis L.); M. Macek (Milan); H. Makukh (Halyna); A.H.J. Mathijssen (Ron); K. Mitropoulos (Konstantinos); C. Mitropoulou (Christina); Novelli, G. (Giuseppe); I. Papantoni (Ioanna); S. Pavlovic (Sonja); G. Saglio; Setric, J. (Jadranka); M. Stojiljkovic (Maja); A. Stubbs (Andrew); A. Squassini (Alessio); Torres, M. (Maria); Turnovec, M. (Marek); R.H.N. van Schaik (Ron); Voskarides, K. (Konstantinos); Wakil, S.M. (Salma M.); Werk, A. (Anneke); Zompo, M.D. (Maria Del); B. Zukic (Branka); T. Katsila (Theodora); M.T.M. Lee (M. T M); Motsinger-Rief, A. (Alison); Leod, H.L.M. (Howard L. Mc); P.J. van der Spek (Peter); G.P. Patrinos (George)

    2016-01-01

    textabstractPharmacogenomics aims to correlate inter-individual differences of drug efficacy and/or toxicity with the underlying genetic composition, particularly in genes encoding for protein factors and enzymes involved in drug metabolism and transport. In several European populations, particularl

  7. Inconsistency in large pharmacogenomic studies

    DEFF Research Database (Denmark)

    Haibe-Kains, Benjamin; El-Hachem, Nehme; Birkbak, Nicolai Juul;

    2013-01-01

    Two large-scale pharmacogenomic studies were published recently in this journal. Genomic data are well correlated between studies; however, the measured drug response data are highly discordant. Although the source of inconsistencies remains uncertain, it has potential implications for using...

  8. Pharmacogenomics and migraine: possible implications

    DEFF Research Database (Denmark)

    Tfelt-Hansen, P.; Brosen, K.

    2008-01-01

    cases pharmacodynamic variability we mention possible implications for the acute and preventive treatment of migraine. Pharmacogenomics will most likely in the future be one part of our therapeutic armamentarium and will provide a stronger scientific basis for optimizing drug therapy on the basis...

  9. Trans-NCI Pharmacogenomics and Pharmacoepidemiology Working Group (PPWG)

    Science.gov (United States)

    NCI established the Trans-NCI Pharmacogenomics and Pharmacoepidemiology Working Group to support development of a comprehensive and interdisciplinary pharmacoepidemiology and pharmacogenomics cancer research program.

  10. International Conference on Harmonisation; Guidance on E15 Pharmacogenomics Definitions and Sample Coding; Availability. Notice.

    Science.gov (United States)

    2008-04-08

    The Food and Drug Administration (FDA) is announcing the availability of a guidance entitled "E15 Definitions for Genomic Biomarkers, Pharmacogenomics, Pharmacogenetics, Genomic Data and Sample Coding Categories." The guidance was prepared under the auspices of the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). The guidance contains definitions of key terms in the discipline of pharmacogenomics and pharmacogenetics, namely genomic biomarkers, pharmacogenomics, pharmacogenetics, and genomic data and sample coding categories. In the effort to develop harmonized approaches to drug regulation, it is important to ensure that consistent definitions of terminology are being applied across all constituents of the ICH. The guidance is intended to facilitate the integration of the discipline of pharmacogenomics and pharmacogenetics into global drug development and approval processes.

  11. Pharmacometabolomics-aided Pharmacogenomics in Autoimmune Disease

    Directory of Open Access Journals (Sweden)

    Theodora Katsila

    2016-03-01

    Full Text Available Inter-individual variability has been a major hurdle to optimize disease management. Precision medicine holds promise for improving health and healthcare via tailor-made therapeutic strategies. Herein, we outline the paradigm of “pharmacometabolomics-aided pharmacogenomics” in autoimmune diseases. We envisage merging pharmacometabolomic and pharmacogenomic data (to address the interplay of genomic and environmental influences with information technologies to facilitate data analysis as well as sense- and decision-making on the basis of synergy between artificial and human intelligence. Humans can detect patterns, which computer algorithms may fail to do so, whereas data-intensive and cognitively complex settings and processes limit human ability. We propose that better-informed, rapid and cost-effective omics studies need the implementation of holistic and multidisciplinary approaches.

  12. Stakeholder views on pharmacogenomic testing.

    Science.gov (United States)

    Patel, Haridarshan N; Ursan, Iulia D; Zueger, Patrick M; Cavallari, Larisa H; Pickard, A Simon

    2014-02-01

    Pharmacogenomics has an important role in the evolution of personalized medicine, and its widespread uptake may ultimately depend on the interests and perspectives of key players in health care. Our aim was to summarize studies on stakeholder perspectives and attitudes toward pharmacogenomic testing. Thus, we conducted a review of original research studies that reported stakeholder views on pharmacogenomic testing using a structured approach in PubMed, International Pharmaceutical Abstracts, Cumulative Index to Nursing and Allied Health Literature, and EMBASE. A standardized data abstraction form was developed that included stakeholder group of interest-patients, general public, providers, and payers. Stakeholder views regarding barriers to pharmacogenetic implementation were organized into the following themes: ancillary information-related, clinical, economic, educational, ethical or legal, medical mistrust, and practicality. Of 34 studies that met our inclusion criteria, 37 perspectives were reported (15 on providers, 9 on the general public, 9 on patients, and 4 on payers). The most common topics that arose in studies of providers related to clinical usefulness of genetic data (n=11) and educational needs (n=11). Among the general public, the most common concerns were medical mistrust (n=5), insufficient education (n=5), and practicality (n=5). The most prevalent issues from the patient perspective were ethical or legal (n=6) and economic (n=5) issues. Among payers, leading issues were practicality (n=4) and clinical usefulness (n=3). There was overlap in the topics and concerns across stakeholder perspectives, including lack of knowledge about pharmacogenomic testing. Views on issues related to privacy, cost, and test result dissemination varied by stakeholder perspective. Limited research had been conducted in underrepresented groups. Efforts to address the issues raised by stakeholders may facilitate the implementation of pharmacogenomic testing into

  13. Extensive Variation in Chromatin States Across Humans

    KAUST Repository

    Kasowski, M.

    2013-10-17

    The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

  14. Pharmacogenetics and pharmacogenomics in rheumatology.

    Science.gov (United States)

    Szekanecz, Zoltán; Meskó, Bertalan; Poliska, Szilard; Váncsa, Andrea; Szamosi, Szilvia; Végh, Edit; Simkovics, Enikö; Laki, Judit; Kurkó, Júlia; Besenyei, Timea; Mikecz, Katalin; Glant, Tibor T; Nagy, László

    2013-07-01

    Pharmacogenetics and pharmacogenomics deal with possible associations of a single genetic polymorphism or those of multiple gene profiles with responses to drugs. In rheumatology, genes and gene signatures may be associated with altered efficacy and/or safety of anti-inflammatory drugs, disease-modifying antirheumatic drugs (DMARDs) and biologics. In brief, genes of cytochrome P450, other enzymes involved in drug metabolism, transporters and some cytokines have been associated with responses to and toxicity of non-steroidal anti-inflammatory drugs, corticosteroids and DMARDs. The efficacy of biologics may be related to alterations in cytokine, chemokine and FcγR genes. Numerous studies reported multiple genetic signatures in association with responses to biologics; however, data are inconclusive. More, focused studies carried out in larger patient cohorts, using pre-selected genes, may be needed in order to determine the future of pharmacogenetics and pharmacogenomics as tools for personalized medicine in rheumatology.

  15. Liver expression quantitative trait loci: a foundation for pharmacogenomic research

    Directory of Open Access Journals (Sweden)

    Dylan eGlubb

    2012-08-01

    Full Text Available Expression quantitative trait loci (eQTL analysis can provide insights into the genetic regulation of gene expression at a genomic level and this information is proving extremely useful in many different areas of research. As a consequence of the role of the liver in drug metabolism and disposition, the study of eQTLs in primary human liver tissue could provide a foundation for pharmacogenomics. Thus far, four genome-wide eQTL studies have been performed using human livers. Many liver eQTLs have been found to be reproducible and a proportion of these may be specific to the liver. Already these data have been used to interpret and inform clinic genome-wide association studies, providing potential mechanistic evidence for clinical associations and identifying genes which may impact on clinical phenotypes. However, the utility of liver eQTL data has not yet been fully explored or realized in pharmacogenomics. As further liver eQTL research is undertaken, the genetic regulation of gene expression will become much better characterized and this knowledge will create a rational basis for the prospective pharmacogenomic study of many drugs.

  16. Pharmacogenomics of cyclooxygenases.

    Science.gov (United States)

    Agúndez, José A G; Blanca, Miguel; Cornejo-García, José A; García-Martín, Elena

    2015-01-01

    Cyclooxygenases (COX-1 and COX-2) are key enzymes in several physiopathological processes. Many adverse drugs reactions to NSAIDs are attributable to COX-inhibition. The genes coding for these enzymes (PTGS1 and PTGS2) are highly variable, and variations in these genes may underlie the risk of developing, or the clinical evolution of, several diseases and adverse drug reactions. We analyze major variations in the PTGS1 and PTGS2 genes, allele frequencies, functional consequences and population genetics. The most salient clinical associations of PTGS gene variations are related to colorectal cancer and stroke. In many studies, the SNPs interact with NSAIDs use, dietary or environmental factors. We provide an up-to-date catalog of PTGS clinical associations based on case-control studies and genome-wide association studies, and future research suggestions.

  17. A global reference for human genetic variation

    DEFF Research Database (Denmark)

    Auton, Adam; Abecasis, Goncalo R.; M. Altshuler, David;

    2015-01-01

    The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals ...

  18. The landscape of human STR variation.

    Science.gov (United States)

    Willems, Thomas; Gymrek, Melissa; Highnam, Gareth; Mittelman, David; Erlich, Yaniv

    2014-11-01

    Short tandem repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across more than 1000 individuals in Phase 1 of the 1000 Genomes Project. Extensive quality controls show that reliable allelic spectra can be obtained for close to 90% of the STR loci in the genome. We utilize this call set to analyze determinants of STR variation, assess the human reference genome's representation of STR alleles, find STR loci with common loss-of-function alleles, and obtain initial estimates of the linkage disequilibrium between STRs and common SNPs. Overall, these analyses further elucidate the scale of genetic variation beyond classical point mutations.

  19. Pharmacogenomics in cardiovascular disorders: Steps in approaching personalized medicine in cardiovascular medicine

    Directory of Open Access Journals (Sweden)

    Christopher Barone

    2009-09-01

    Full Text Available Christopher Barone, Shaymaa S Mousa, Shaker A MousaThe Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Albany, NY, USAAbstract: Some of the most commonly prescribed medications are those for cardiovascular maladies. The beneficial effects of these medications have been well documented. However, there can be substantial variation in response to these medications among patients, which may be due to genetic variation. For this reason pharmacogenomic studies are emerging across all aspects of cardiovascular medicine. The goal of pharmacogenomics is to tailor treatment to an individual’s genetic makeup in order to improve the benefit-to-risk ratio. This review examines the potential pharmacogenomic parameters which may lead to a future of personalized medicine. For example, it has been found that patients with CYP2C9 and VKORC1 gene variations have a different response to warfarin. Other studies looking at β-blockers, ACE inhibitors, ARBs, diuretics and statins have shown some results linking genetic variations to pharmacologic response. However these studies have not impacted clinical use yet, unlike warfarin findings, as the small retrospective studies need to be followed up by larger prospective studies for definitive results.Keywords: cardiovascular, pharmacogenomics, genetics, cardiovascular medicine, personalized medicine, polymorphism

  20. Challenges and opportunities in pharmacogenomics : studies in cardiovascular disease and asthma

    NARCIS (Netherlands)

    Leusink, M.

    2015-01-01

    A drug that is effective in one group of patients may have a reduced or no effect in other patients. Similarly, the risk for side effects differs between patients. The discipline of pharmacogenomics studies how genetic variation in the population can influence this drug response. In this thesis, we

  1. Big Data Analysis of Human Genome Variations

    KAUST Repository

    Gojobori, Takashi

    2016-01-25

    Since the human genome draft sequence was in public for the first time in 2000, genomic analyses have been intensively extended to the population level. The following three international projects are good examples for large-scale studies of human genome variations: 1) HapMap Data (1,417 individuals) (http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2010-08_phaseII+III/forward/), 2) HGDP (Human Genome Diversity Project) Data (940 individuals) (http://www.hagsc.org/hgdp/files.html), 3) 1000 genomes Data (2,504 individuals) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ If we can integrate all three data into a single volume of data, we should be able to conduct a more detailed analysis of human genome variations for a total number of 4,861 individuals (= 1,417+940+2,504 individuals). In fact, we successfully integrated these three data sets by use of information on the reference human genome sequence, and we conducted the big data analysis. In particular, we constructed a phylogenetic tree of about 5,000 human individuals at the genome level. As a result, we were able to identify clusters of ethnic groups, with detectable admixture, that were not possible by an analysis of each of the three data sets. Here, we report the outcome of this kind of big data analyses and discuss evolutionary significance of human genomic variations. Note that the present study was conducted in collaboration with Katsuhiko Mineta and Kosuke Goto at KAUST.

  2. A global reference for human genetic variation

    DEFF Research Database (Denmark)

    Auton, Adam; Abecasis, Goncalo R.; M. Altshuler, David

    2015-01-01

    The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals...... from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short...... insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications...

  3. Pharmacogenomics of oral antiplatelet drugs.

    Science.gov (United States)

    Yasmina, Alfi; de Boer, Anthonius; Klungel, Olaf H; Deneer, Vera H M

    2014-03-01

    Pharmacogenomics has been implicated in the response variability of antiplatelet drugs in coronary artery disease (CAD), particularly for aspirin and clopidogrel. A large number of studies and several meta-analyses have been published on this topic, but until recently, there have been no clear conclusions and no definite guidelines on the clinical use of pharmacogenetic testing before prescribing antiplatelet drugs for CAD. In this review, the available evidence is summarized. The most consistent results are on clopidogrel, where CYP2C19 loss-of-function alleles are associated with stent thrombosis events. We recommend to genotype for CYP2C19 loss-of-function alleles in patients with CAD who are to undergo percutaneous coronary intervention and stenting, and to adjust the antiplatelet treatment based on the genotyping results.

  4. Pharmacogenomic testing and the prospect of individualized treatment.

    Science.gov (United States)

    Jonas, Daniel E; Wines, Roberta

    2013-01-01

    Pharmacogenomics offers the hope of greater individualization of treatment. Therapies that exemplify the promise of pharmacogenomics include anticoagulation with warfarin and the use of antiplatelet medications (eg, clopidogrel) for secondary prevention after acute coronary syndrome. Good evidence of clinical utility must be obtained before pharmacogenomic testing is widely implemented.

  5. A lay prescription for tailor-made drugs--focus group reflections on pharmacogenomics

    DEFF Research Database (Denmark)

    Almarsdóttir, Anna Birna; Björnsdóttir, Ingunn; Traulsen, Janine Morgall

    2005-01-01

    the consequences of the Human Genome Project over the next 40 years, and asked to give advice to politicians and the pharmaceutical industry. A dominating theme in the focus groups was the expectation that drugs developed based on pharmacogenomics will be more expensive than conventional mass produced drugs...

  6. Virtual Pharmacist: A Platform for Pharmacogenomics.

    Science.gov (United States)

    Cheng, Ronghai; Leung, Ross Ka-Kit; Chen, Yao; Pan, Yidan; Tong, Yin; Li, Zhoufang; Ning, Luwen; Ling, Xuefeng B; He, Jiankui

    2015-01-01

    We present Virtual Pharmacist, a web-based platform that takes common types of high-throughput data, namely microarray SNP genotyping data, FASTQ and Variant Call Format (VCF) files as inputs, and reports potential drug responses in terms of efficacy, dosage and toxicity at one glance. Batch submission facilitates multivariate analysis or data mining of targeted groups. Individual analysis consists of a report that is readily comprehensible to patients and practioners who have basic knowledge in pharmacology, a table that summarizes variants and potential affected drug response according to the US Food and Drug Administration pharmacogenomic biomarker labeled drug list and PharmGKB, and visualization of a gene-drug-target network. Group analysis provides the distribution of the variants and potential affected drug response of a target group, a sample-gene variant count table, and a sample-drug count table. Our analysis of genomes from the 1000 Genome Project underlines the potentially differential drug responses among different human populations. Even within the same population, the findings from Watson's genome highlight the importance of personalized medicine. Virtual Pharmacist can be accessed freely at http://www.sustc-genome.org.cn/vp or installed as a local web server. The codes and documentation are available at the GitHub repository (https://github.com/VirtualPharmacist/vp). Administrators can download the source codes to customize access settings for further development.

  7. Virtual Pharmacist: A Platform for Pharmacogenomics.

    Directory of Open Access Journals (Sweden)

    Ronghai Cheng

    Full Text Available We present Virtual Pharmacist, a web-based platform that takes common types of high-throughput data, namely microarray SNP genotyping data, FASTQ and Variant Call Format (VCF files as inputs, and reports potential drug responses in terms of efficacy, dosage and toxicity at one glance. Batch submission facilitates multivariate analysis or data mining of targeted groups. Individual analysis consists of a report that is readily comprehensible to patients and practioners who have basic knowledge in pharmacology, a table that summarizes variants and potential affected drug response according to the US Food and Drug Administration pharmacogenomic biomarker labeled drug list and PharmGKB, and visualization of a gene-drug-target network. Group analysis provides the distribution of the variants and potential affected drug response of a target group, a sample-gene variant count table, and a sample-drug count table. Our analysis of genomes from the 1000 Genome Project underlines the potentially differential drug responses among different human populations. Even within the same population, the findings from Watson's genome highlight the importance of personalized medicine. Virtual Pharmacist can be accessed freely at http://www.sustc-genome.org.cn/vp or installed as a local web server. The codes and documentation are available at the GitHub repository (https://github.com/VirtualPharmacist/vp. Administrators can download the source codes to customize access settings for further development.

  8. Human Structural Variation: Mechanisms of Chromosome Rearrangements.

    Science.gov (United States)

    Weckselblatt, Brooke; Rudd, M Katharine

    2015-10-01

    Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Genomics and pharmacogenomics of dementia.

    Science.gov (United States)

    Cacabelos, Ramón; Martínez-Bouza, Rocío

    2011-10-01

    activity of genes involved in drug metabolism and genes involved in AD pathogenesis (e.g., APOE). AD patients harboring the APOE-4/4 genotypes are the worst responders to conventional antidementia drugs. To achieve a mature discipline of pharmacogenomics in CNS disorders and dementia it would be convenient to accelerate the following processes: (i) to educate physicians and the public on the use of genetic/genomic screening in daily clinical practice; (ii) to standardize genetic testing for major categories of drugs; (iii) to validate pharmacogenomic information according to drug category and pathology; (iv) to regulate ethical, social, and economic issues; and (v) to incorporate pharmacogenomic procedures both to drugs in development and drugs on the market in order to optimize therapeutics. © 2010 Blackwell Publishing Ltd.

  10. Pharmacogenomics in type II diabetes mellitus management: Steps toward personalized medicine

    Directory of Open Access Journals (Sweden)

    Peter Avery

    2009-09-01

    Full Text Available Peter Avery, Shaymaa S Mousa, Shaker A MousaThe Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Albany, NY, USAAbstract: Advances in genotype technology in the last decade have put the pharmacogenomics revolution at the forefront of future medicine in clinical practice. Discovery of novel gene variations in drug transporters, drug targets, effector proteins and metabolizing enzymes in the form of single-nucleotide polymorphisms (SNPs continue to provide insight into the biological phenomena that govern drug efficacy and toxicity. To date, novel gene discoveries extracted from genome-wide association scans and candidate gene studies in at least four antidiabetic drug classes have helped illuminate possible causes of interindividual variability in response. Inadequate protocol guidelines for pharmacogenomics studies often leads to poorly designed studies, making it hard to formulate a definitive conclusion regarding the clinical relevance of the information at hand. These issues, along with the ethical, social, political, legislative, technological, and economic challenges associated with pharmacogenomics have only delayed its entry to mainstream clinical practice. On the other hand, these issues are being actively pursued and rapid progress is being made in each area which assures the possibility of gaining widespread acceptance in clinical practice.Keywords: pharmacogenomics, genetics, pharmacokinetics, pharmacodynamics, personalized medicine, type 2 diabetes, pharmacotherapy, antidiabetic drugs, efficacy, and safety

  11. Medical education in pharmacogenomics-results from a survey on pharmacogenetic knowledge in healthcare professionals within the European pharmacogenomics clinical implementation project Ubiquitous Pharmacogenomics (U-PGx).

    Science.gov (United States)

    Just, Katja Susanne; Steffens, Michael; Swen, Jesse Joachim; Patrinos, George P; Guchelaar, Henk-Jan; Stingl, Julia Carolin

    2017-07-02

    Due to the diversity within Europe, the implementation of pharmacogenomic testing in clinical practice faces specific challenges. In the context of the European pharmacogenomics implementation project "Ubiquitous Pharmacogenomics" (U-PGx; funded by the European Commission), we studied the current educational background. We developed a questionnaire including 29 questions. It was spread out to healthcare professionals working at the future implementation sites (in Austria, Greece, Italy, Netherlands, Slovenia, Spain and Great Britain) of the U-PGx project in preparation of an educational programme. Aim of the survey was to analyse the current educational situation at the implementation sites. In total, 70 healthcare professionals participated in the survey. Of participants, 84.3% found pharmacogenomics relevant to their current practice, but experience was still rare. More than two-thirds (65.7%) did not order nor recommend a pharmacogenomic test in the past year. This was mainly attributed to not having enough knowledge on pharmacogenomics (40.0%). Needs were identified in application of pharmacogenomics (identifying drugs 41.4%, interpreting test results 37.2%) as well as in underlining mechanisms (better knowledge on drug metabolism 67.1%, better knowledge on basic principles of pharmacogenomics 60.0%). This study analysed the specific attitudes, experience and education on pharmacogenomics of future users. There was a general positive attitude and interest towards pharmacogenomic testing. However, the grade of own experience, and knowledge about application and interpretation of pharmacogenomics caused uncertainty. Thus, education and training programmes may be helpful for implementation of pharmacogenomics at a homogenous level within Europe.

  12. CYP2D6 pharmacogenomics

    Directory of Open Access Journals (Sweden)

    Mohanan Geetha Gopisankar

    2017-10-01

    Full Text Available Cytochromes are proteins that catalyze electron transfer reactions of many metabolic pathways. They are involved in drug metabolism and thus determines the therapeutic safety and efficacy of drugs in patients. Cytochrome P450 in mitochondria accounts for 90% of the oxidative metabolism of clinically used drugs during phase 1 reaction. CYP2D6 is a major gene member of this superfamily as it carries out metabolism of 25% of drugs currently available in the market. Contrary to the concept of specificity of enzyme action these can metabolize substrates of different chemistry. Since its discovery, many have intensively studied this unique hemoprotein and contributed to the elucidation of its molecular properties and physiological functions and also the structure-activity relationships of its substrates and inhibitors. Its activity ranges considerably within a population due to genetic polymorphisms which lead to varied responses to drug intake. Studying such polymorphisms which cause a significant impact in the management of patients and helps to achieve the final target of personalizing medicine. This review briefs about history, structure, and function, molecular genetics, substrates, regulators and inhibitors of CYP2D6 and its clinical pharmacogenomics.

  13. Pharmacogenomics Update in Pancreatic Cancer

    Directory of Open Access Journals (Sweden)

    Aditi Puri

    2014-03-01

    Full Text Available Pancreatic cancer is the fourth leading cause of cancer-related deaths in United States. Despite advances in understandingcancer biology and therapeutics, this malignancy carries a grave prognosis with a poor overall survival rate. This is especiallytrue for patients with locally advanced and metastatic disease that are not amenable to surgical resection. Given advances inhuman genome sequencing and pharmacogenomics, we now better understand the complex genetic makeup of these tumorsand numerous gene mutations have been identified that could be potential targets for drug development. In this review, wediscuss two abstract (Abstracts #208 and #192 presented at the 2014 ASCO Gastrointestinal Cancers Symposium aboutpancreatic cancer genome sequencing and their implications for the future of this disease. We discuss what is known aboutthe genome of pancreatic tumors, including common mutations like KRAS, TP53 and SMAD4, as well as discovery ofadditional mutations. In particular, KRAS2 mutations in a subset of patients with pancreatic cancer are discussed. Whilelimited in size and clinical correlativity, these abstracts provide at least seven novel/targetable mutations and elucidatebiologic differences in tumors with wild type and mutant KRAS. These are important steps in understanding tumor biologyand genetic basis of pancreatic cancer to help develop targeted drug therapies in the fast approaching era of personalizedmedicine.

  14. 药物基因组学与抗癫(癎)药物治疗%Pharmacogenomics and antiepileptic drugs

    Institute of Scientific and Technical Information of China (English)

    吴晔

    2015-01-01

    药物基因组学是在整个基因组水平,通过探讨基因的DNA或RNA的变异与药物效应和不良反应之间的相关性,来研究基因的变异对于个体对药物反应的影响.药物基因组学研究的最终目的是实现个体化治疗.现就药物基因组学在抗癫(癎)药物治疗中的角色进行简述.%Pharmacogenomics is defined as the study of variation in DNA and RNA at the whole genome level,and its effects on drug response including effectiveness and adverse events.Pharmacogenomics is helpful for individualized drug therapy.The role of pharmacogenomics in antiepileptic drugs in therapy of epilepsy was briefly reviewed.

  15. Pharmacogenomics and Nanotechnology Toward Advancing Personalized Medicine

    Science.gov (United States)

    Vizirianakis, Ioannis S.; Amanatiadou, Elsa P.

    The target of personalized medicine to achieve major benefits for all patients in terms of diagnosis and drug delivery can be facilitated by creating a sincere multidisciplinary information-based infrastructure in health care. To this end, nanotechnology, pharmacogenomics, and informatics can advance the utility of personalized medicine, enable clinical translation of genomic knowledge, empower healthcare environment, and finally improve clinical outcomes.

  16. Genetics and pharmacogenomics of diffuse gliomas

    NARCIS (Netherlands)

    Thuijl, H.F. van; Ylstra, B.; Wurdinger, T.; Nieuwenhuizen, D. van; Heimans, J.J.; Wesseling, P.; Reijneveld, J.C.

    2013-01-01

    Rapidly evolving techniques for analysis of the genome provide new opportunities for cancer therapy. For diffuse gliomas this has resulted in molecular markers with potential for personalized therapy. Some drugs that utilize pharmacogenomics are currently being tested in clinical trials. In melanoma

  17. The epigenome, 4D nucleome and next-generation neuropsychiatric pharmacogenomics.

    Science.gov (United States)

    Higgins, Gerald A; Allyn-Feuer, Ari; Handelman, Samuel; Sadee, Wolfgang; Athey, Brian D

    2015-01-01

    The 4D nucleome has the potential to render challenges in neuropsychiatric pharmacogenomics more tractable. The epigenome roadmap consortium has demonstrated the critical role that noncoding regions of the human genome play in determination of human phenotype. Chromosome conformation capture methods have revealed the 4D organization of the nucleus, bringing interactions between distant regulatory elements into close spatial proximity in a periodic manner. These functional interactions have the potential to elucidate mechanisms of CNS drug response and side effects that previously have been unrecognized. This perspective assesses recent advances likely to reveal novel pharmacodynamic regulatory pathways in human brain, charting a future new avenue of pharmacogenomics research, using the spatial and temporal architecture of the human epigenome as its foundation.

  18. The promise of psychiatric pharmacogenomics.

    Science.gov (United States)

    Hamilton, Steven P

    2015-01-01

    Clinicians already face "personalized" medicine every day while experiencing the great variation in toxicities and drug efficacy among individual patients. Pharmacogenetics studies are the platform for discovering the DNA determinants of variability in drug response and tolerability. Research now focuses on the genome after its beginning with analyses of single genes. Therapeutic outcomes from several psychotropic drugs have been weakly linked to specific genetic variants without independent replication. Drug side effects show stronger associations to genetic variants, including human leukocyte antigen loci with carbamazepine-induced dermatologic outcome and MC4R with atypical antipsychotic weight gain. Clinical implementation has proven challenging, with barriers including a lack of replicable prospective evidence for clinical utility required for altering medical care. More recent studies show promising approaches for reducing these barriers to routine incorporation of pharmacogenetics data into clinical care.

  19. Pharmacogenomic insights into treatment and management of statin-induced myopathy

    OpenAIRE

    Peters, Bas JM; Klungel, Olaf H.; Visseren, Frank L.; de Boer, Anthonius; Maitland-van der Zee, Anke-Hilse

    2009-01-01

    Although statins are generally well tolerated, the most common adverse drug reaction from statin therapy is myopathy. This article reviews the current pharmacogenomic knowledge of statin-induced myopathy. Furthermore, we will discuss the importance of recent pharmacogenetic advances for the treatment and management of statin-induced myopathy. Variation in the SLCO1B1 gene is associated with increased incidence of statin-induced myopathy, particularly with simvastatin and less so with other st...

  20. Conference scene: pharmacogenomics: from cell to clinic (part 2).

    Science.gov (United States)

    Siest, Gérard; Medeiros, Rui; Melichar, Bohuslav; Stathopoulou, Maria; Van Schaik, Ron Hn; Cacabelos, Ramon; Abt, Peter Meier; Monteiro, Carolino; Gurwitz, David; Queiroz, Jao; Mota-Filipe, Helder; Ndiaye, Ndeye Coumba; Visvikis-Siest, Sophie

    2014-04-01

    Second International ESPT Meeting Lisbon, Portugal, 26-28 September 2013 The second European Society of Pharmacogenomics and Theranostics (ESPT) conference was organized in Lisbon, Portugal, and attracted 250 participants from 37 different countries. The participants could listen to 50 oral presentations, participate in five lunch symposia and were able to view 83 posters and an exhibition. Part 1 of this Conference Scene was presented in the previous issue of Pharmacogenomics. This second part will focus on: clinical implementation of pharmacogenomics tests; transporters and pharmacogenomics; stem cells and other new tools for pharmacogenomics and drug discovery; from system pharmacogenomics to personalized medicine; and, finally, we will discuss the Posters and Awards that were presented at the conference.

  1. Translating pharmacogenomics: challenges on the road to the clinic.

    Directory of Open Access Journals (Sweden)

    Jesse J Swen

    2007-08-01

    Full Text Available Pharmacogenomics is one of the first clinical applications of the postgenomic era. It promises personalized medicine rather than the established "one size fits all" approach to drugs and dosages. The expected reduction in trial and error should ultimately lead to more efficient and safer drug therapy. In recent years, commercially available pharmacogenomic tests have been approved by the Food and Drug Administration (FDA, but their application in patient care remains very limited. More generally, the implementation of pharmacogenomics in routine clinical practice presents significant challenges. This article presents specific clinical examples of such challenges and discusses how obstacles to implementation of pharmacogenomic testing can be addressed.

  2. Pharmacogenetics and pharmacogenomics: a bridge to individualized cancer therapy.

    Science.gov (United States)

    Weng, Liming; Zhang, Li; Peng, Yan; Huang, R Stephanie

    2013-02-01

    In the past decade, advances in pharmacogenetics and pharmacogenomics (PGx) have gradually unveiled the genetic basis of interindividual differences in drug responses. A large portion of these advances have been made in the field of anticancer therapy. Currently, the US FDA has updated the package inserts of approximately 30 anticancer agents to include PGx information. Given the complexity of this genetic information (e.g., tumor mutation and gene overexpression, chromosomal translocation and germline variations), as well as the variable level of scientific evidence, the FDA recommendation and potential action needed varies among drugs. In this review, we have highlighted some of these PGx discoveries for their scientific values and utility in improving therapeutic efficacy and reducing side effects. Furthermore, examples are also provided for the role of PGx in new anticancer drug development by revealing novel druggable targets.

  3. Child Development and Structural Variation in the Human Genome

    Science.gov (United States)

    Zhang, Ying; Haraksingh, Rajini; Grubert, Fabian; Abyzov, Alexej; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E.

    2013-01-01

    Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects…

  4. Child Development and Structural Variation in the Human Genome

    Science.gov (United States)

    Zhang, Ying; Haraksingh, Rajini; Grubert, Fabian; Abyzov, Alexej; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E.

    2013-01-01

    Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects…

  5. The Pharmacogenomics of Anti-Hypertensive Therapy

    Directory of Open Access Journals (Sweden)

    Sandosh Padmanabhan

    2010-06-01

    Full Text Available Hypertension is a major public health problem, but measures to reduce blood pressure and thus cardiovascular risk are complicated by the high prevalence of treatment resistance, despite the availability of multiple drugs. Drug side-effects contribute considerably to suboptimal blood pressure control. Clinicians must often rely on empirical methods to match patients with effective drug treatment. Hypertension pharmacogenomics seeks to find genetic predictors of response to drugs that lower blood pressure and to translate this knowledge into clinical practice. In this review we summarise the current status of hypertension pharmacogenetics from monogenic hypertension to essential hypertension and discuss the issues that need to be considered in a hypertension pharmacogenomic study.

  6. The pharmacogenetics and pharmacogenomics of asthma therapy

    OpenAIRE

    Tse, Sze Man; Tantisira, Kelan; Weiss, Scott Tillman

    2011-01-01

    Despite the availability of several classes of asthma medications and their overall effectiveness, a significant portion of patients fail to respond to these therapeutic agents. Evidence suggests that genetic factors may partly mediate the heterogeneity in asthma treatment response. This review discusses important findings in asthma pharmacogenetics and pharmacogenomics studies conducted to date, examines limitations of these studies and finally, proposes future research directions in this fi...

  7. Pharmacogenomics in osteoporosis: Steps toward personalized medicine

    Directory of Open Access Journals (Sweden)

    Robert Greene

    2009-09-01

    Full Text Available Robert Greene1, Shaymaa S Mousa, Mohamed Ardawi2, Mohamed Qari2, Shaker A Mousa11The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Albany, NY, USA; 2Center of Excellence in Osteoporosis Research, King Abdul Aziz University, Jeddah, Saudi ArabiaAbstract: Osteoporosis is a complicated and preventable disease with major morbidity complications that affects millions of people. In the last 15 years, there have been numerous studies and research in the new fields of pharmacogenetics and pharmacogenomics related to osteoporosis. Numerous “candidate genes” have been identified and have been found to be associated with osteoporosis as well as the treatment of osteoporosis. Many studies have found conflicting results on different polymorphisms and whether or not they are related to bone mineral density and osteoporosis. There is a need for larger and better designed pharmacogenomic studies related to osteoporosis incorporating a greater variety of candidate genes. The evaluation of osteoporosis and fracture risk is moving from a risk stratification approach to a more individualized approach, in which an individual’s absolute risk of fracture is evaluable as a constellation of the individual’s environmental exposure and genetic makeup. Therefore, the identification of gene variants associated with osteoporosis phenotypes or response to therapy might help individualize the prognosis, treatment, and prevention of fracture. This review focuses on major candidate genes and what needs to be done to take the genetics of osteoporosis and incorporate them into the pharmacogenomics of the management of osteoporosis.Keywords: pharmacogenomics, osteoporosis, VDR, ER-alpha, CYP19 Gene, LRP5, COLIA1, polymorphisms, genetics

  8. Pharmacogenomics in osteoporosis: Steps toward personalized medicine.

    Science.gov (United States)

    Greene, Robert; Mousa, Shaymaa S; Ardawi, Mohamed; Qari, Mohamed; Mousa, Shaker A

    2009-01-01

    Osteoporosis is a complicated and preventable disease with major morbidity complications that affects millions of people. In the last 15 years, there have been numerous studies and research in the new fields of pharmacogenetics and pharmacogenomics related to osteoporosis. Numerous "candidate genes" have been identified and have been found to be associated with osteoporosis as well as the treatment of osteoporosis. Many studies have found conflicting results on different polymorphisms and whether or not they are related to bone mineral density and osteoporosis. There is a need for larger and better designed pharmacogenomic studies related to osteoporosis incorporating a greater variety of candidate genes. The evaluation of osteoporosis and fracture risk is moving from a risk stratification approach to a more individualized approach, in which an individual's absolute risk of fracture is evaluable as a constellation of the individual's environmental exposure and genetic makeup. Therefore, the identification of gene variants associated with osteoporosis phenotypes or response to therapy might help individualize the prognosis, treatment, and prevention of fracture. This review focuses on major candidate genes and what needs to be done to take the genetics of osteoporosis and incorporate them into the pharmacogenomics of the management of osteoporosis.

  9. Pharmacogenomic information in drug labels: European Medicines Agency perspective

    NARCIS (Netherlands)

    Ehmann, F.; Caneva, L.; Prasad, K.; Paulmichl, M.; Maliepaard, M.; Llerena, A.; Ingelman-Sundberg, M.; Papaluca-Amati, M.

    2015-01-01

    Pharmacogenomics (PGx) has a growing impact on healthcare and constitutes one of the major pillars of personalised medicine. For the purpose of improved individualised drug treatment, there is an increasing effort to develop drugs suitable for specific subpopulations and to incorporate pharmacogenom

  10. A global reference for human genetic variation

    DEFF Research Database (Denmark)

    Auton, Adam; Abecasis, Goncalo R.; M. Altshuler, David;

    2015-01-01

    insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications...

  11. Evolutionary perspectives on human height variation

    NARCIS (Netherlands)

    Stulp, Gert; Barrett, Louise

    2016-01-01

    Human height is a highly variable trait, both within and between populations, has a high heritability, and influences the manner in which people behave and are treated in society. Although we know much about human height, this information has rarely been brought together in a comprehensive, systemat

  12. Cyclic Variations in Sustained Human Performance

    Science.gov (United States)

    Aue, William R.; Arruda, James E.; Kass, Steven J.; Stanny, Claudia J.

    2009-01-01

    Biological rhythms play a prominent role in the modulation of human physiology and behavior. [Smith, K., Valentino, D., & Arruda, J. (2003). "Rhythmic oscillations in the performance of a sustained attention task." "Journal of Clinical and Experimental Neuropsychology," 25, 561-570] suggested that sustained human performance may systematically…

  13. History repeats itself: the family medication history and pharmacogenomics.

    Science.gov (United States)

    Smith, Thomas R; Kearney, Elizabeth; Hulick, Peter J; Kisor, David F

    2016-05-01

    Related to many drug gene-product interactions, application of pharmacogenomics can lead to improved medication efficacy while decreasing or avoiding adverse drug reactions. However, utilizing pharmacogenomics without other information does not allow for optimal medication therapy. Currently, there is a lack of documentation of family medication history, in other words, inefficacy and adverse reactions across family members throughout generations. The family medication history can serve as an impetus for pharmacogenomic testing to explain lack of medication efficacy or an adverse drug reaction and pre-emptive testing can drive recognition and documentation of medication response in family members. We propose combining the family medication history via pedigree construction with pharmacogenomics to further optimize medication therapy. We encourage clinicians to combine family medication history with pharmacogenomics.

  14. Development and evaluation of a pharmacogenomics educational program for pharmacists.

    Science.gov (United States)

    Formea, Christine M; Nicholson, Wayne T; McCullough, Kristen B; Berg, Kevin D; Berg, Melody L; Cunningham, Julie L; Merten, Julianna A; Ou, Narith N; Stollings, Joanna L

    2013-02-12

    Objectives. To evaluate hospital and outpatient pharmacists' pharmacogenomics knowledge before and 2 months after participating in a targeted, case-based pharmacogenomics continuing education program.Design. As part of a continuing education program accredited by the Accreditation Council for Pharmacy Education (ACPE), pharmacists were provided with a fundamental pharmacogenomics education program.Evaluation. An 11-question, multiple-choice, electronic survey instrument was distributed to 272 eligible pharmacists at a single campus of a large, academic healthcare system. Pharmacists improved their pharmacogenomics test scores by 0.7 questions (pretest average 46%; posttest average 53%, p=0.0003).Conclusions. Although pharmacists demonstrated improvement, overall retention of educational goals and objectives was marginal. These results suggest that the complex topic of pharmacogenomics requires a large educational effort in order to increase pharmacists' knowledge and comfort level with this emerging therapeutic opportunity.

  15. A Model of Genetic Variation in Human Social Networks

    CERN Document Server

    Fowler, James H; Christakis, Nicholas A

    2008-01-01

    Social networks influence the evolution of cooperation and they exhibit strikingly systematic patterns across a wide range of human contexts. Both of these facts suggest that variation in the topological attributes of human social networks might have a genetic basis. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric social network attributes is unknown. Here we show that three of these attributes (in-degree, transitivity, and centrality) are heritable. We then develop a "mirror network" method to test extant network models and show that none accounts for observed genetic variation in human social networks. We propose an alternative "attract and introduce" model that generates significant heritability as well as other important network features, and we show that this model with two simple forms of heterogeneity is well suited to the modeling of real social networks in humans. These results suggest that natural selection ...

  16. The Evolution of Personality Variation in Humans and Other Animals

    Science.gov (United States)

    Nettle, Daniel

    2006-01-01

    A comprehensive evolutionary framework for understanding the maintenance of heritable behavioral variation in humans is yet to be developed. Some evolutionary psychologists have argued that heritable variation will not be found in important, fitness-relevant characteristics because of the winnowing effect of natural selection. This article…

  17. Practical recommendations for pharmacogenomics-based prescription: 2010 ESF-UB Conference on Pharmacogenetics and Pharmacogenomics

    NARCIS (Netherlands)

    L. Becquemont; A. Alfirevic; U. Amstutz; H. Brauch; E. Jacqz-Aigrain; P. Laurent-Puig; M.A. Molina; M. Niemi; M. Schwab; A.A. Somogyi; E. Thervet; A-H. Maitland-van der Zee; A.B.P. van Kuilenburg; R.H.N. van Schaik; C. Verstuyft; M. Wadelius; A.K. Daly

    2011-01-01

    The present article summarizes the discussions of the 3rd European Science Foundation University of Barcelona (ESF-UB) Conference in Biomedicine on Pharmacogenetics and Pharmacogenomics, which was held in June 2010 in Spain. It was focused on practical applications in routine medical practice. We pr

  18. Human gut microbiota: repertoire and variations

    Directory of Open Access Journals (Sweden)

    Jean-Christophe eLagier

    2012-11-01

    Full Text Available The composition of human gut microbiota and their relationship with the host and, consequently, with human health and disease, presents several challenges to microbiologists. Originally dominated by culture-dependent methods for exploring this ecosystem, the advent of molecular tools has revolutionized our ability to investigate these relationships. However, many biases that have led to contradictory results have been identified. Microbial culturomics, a recent concept based on a use of several culture conditions with identification by MALDI-TOF followed by the genome sequencing of the new species cultured had allowed a complementarity with metagenomics. Culturomics allowed to isolate 31 new bacterial species the largest human virus, the largest bacteria, and the largest Archaea from human. Moreover, some members of this ecosystem, such as Eukaryotes, giant viruses, Archaea and Planctomycetes, have been neglected by the majority of studies. In addition, numerous factors, such as age, geographic provenance, dietary habits, antibiotics or probiotics, can influence the composition of the microbiota. Finally, in addition to the countless biases associated with the study techniques, a considerable limitation to the interpretation of studies of human gut microbiota is associated with funding sources and transparency disclosures. In the future, studies independent of food industry funding and using complementary methods from a broad range of both culture-based and molecular tools will increase our knowledge of the repertoire of this complex ecosystem and host-microbiota mutualism.

  19. Pharmacogenomics of platinum-based chemotherapy sensitivity in NSCLC: toward precision medicine.

    Science.gov (United States)

    Yin, Ji-Ye; Li, Xi; Zhou, Hong-Hao; Liu, Zhao-Qian

    2016-08-01

    Lung cancer is one of the leading causes of cancer-related death in the world. Platinum-based chemotherapy is the first-line treatment for non-small-cell lung cancer (NSCLC), however, the therapeutic efficiency varies remarkably among individuals. A large number of pharmacogenomics studies aimed to identify genetic variations which can be used to predict platinum response. Those studies are leading NSCLC treatment to the new era of precision medicine. In the current review, we provided a comprehensive update on the main recent findings of genetic variations which can be used to predict platinum sensitivity in the NSCLC patients.

  20. Variation.

    Science.gov (United States)

    Hamilton City Board of Education (Ontario).

    Suggestions for studying the topic of variation of individuals and objects (balls) to help develop elementary school students' measurement, comparison, classification, evaluation, and data collection and recording skills are made. General suggestions of variables that can be investigated are made for the study of human variation. Twelve specific…

  1. Statistical Analysis of Variation in the Human Plasma Proteome

    Directory of Open Access Journals (Sweden)

    Todd H. Corzett

    2010-01-01

    Full Text Available Quantifying the variation in the human plasma proteome is an essential prerequisite for disease-specific biomarker detection. We report here on the longitudinal and individual variation in human plasma characterized by two-dimensional difference gel electrophoresis (2-D DIGE using plasma samples from eleven healthy subjects collected three times over a two week period. Fixed-effects modeling was used to remove dye and gel variability. Mixed-effects modeling was then used to quantitate the sources of proteomic variation. The subject-to-subject variation represented the largest variance component, while the time-within-subject variation was comparable to the experimental variation found in a previous technical variability study where one human plasma sample was processed eight times in parallel and each was then analyzed by 2-D DIGE in triplicate. Here, 21 protein spots had larger than 50% CV, suggesting that these proteins may not be appropriate as biomarkers and should be carefully scrutinized in future studies. Seventy-eight protein spots showing differential protein levels between different individuals or individual collections were identified by mass spectrometry and further characterized using hierarchical clustering. The results present a first step toward understanding the complexity of longitudinal and individual variation in the human plasma proteome, and provide a baseline for improved biomarker discovery.

  2. Genetic variation and the de novo assembly of human genomes.

    Science.gov (United States)

    Chaisson, Mark J P; Wilson, Richard K; Eichler, Evan E

    2015-11-01

    The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology. Short-read massively parallel sequencing has revolutionized our ability to discover genetic variation but is insufficient to generate high-quality genome assemblies or resolve most structural variation. Full resolution of variation is only guaranteed by complete de novo assembly of a genome. Here, we review approaches to genome assembly, the nature of gaps or missing sequences, and biases in the assembly process. We describe the challenges of generating a complete de novo genome assembly using current technologies and the impact that being able to perfectly sequence the genome would have on understanding human disease and evolution. Finally, we summarize recent technological advances that improve both contiguity and accuracy and emphasize the importance of complete de novo assembly as opposed to read mapping as the primary means to understanding the full range of human genetic variation.

  3. Food neophobia shows heritable variation in humans.

    Science.gov (United States)

    Knaapila, Antti; Tuorila, Hely; Silventoinen, Karri; Keskitalo, Kaisu; Kallela, Mikko; Wessman, Maija; Peltonen, Leena; Cherkas, Lynn F; Spector, Tim D; Perola, Markus

    2007-08-15

    Food neophobia refers to reluctance to eat unfamiliar foods. We determined the heritability of food neophobia in a family and a twin sample. The family sample consisted of 28 Finnish families (105 females, 50 males, aged 18-78 years, mean age 49 years) and the twin sample of 468 British female twin pairs (211 monozygous and 257 dizygous pairs, aged 17-82 years, mean age 55 years). Food neophobia was measured using the ten-item Food Neophobia Scale (FNS) questionnaire, and its internationally validated six-item modification. The heritability estimate for food neophobia was 69 and 66% in Finnish families (h(2)) and 67 and 66% in British female twins (a(2)+d(2)) using the ten- and six-item versions of the FNS, respectively. The results from both populations suggest that about two thirds of variation in food neophobia is genetically determined.

  4. Genomic variation landscape of the human gut microbiome

    DEFF Research Database (Denmark)

    Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi

    2013-01-01

    Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal...... metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous...... polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates...

  5. Diet, disease and pigment variation in humans.

    Science.gov (United States)

    Khan, R; Khan, B S Razib

    2010-10-01

    There are several hypotheses which explain the de-pigmentation of humans. The most prominent environmental explanation is that reduced endogenous vitamin D production due to diminished radiation at higher latitudes had a deleterious impact on fitness. This drove de-pigmentation as an adaptive response. A model of natural selection explains the high correlations found between low vitamin D levels and ill health, as vitamin D's role in immune response has clear evolutionary implications. But recent genomic techniques have highlighted the likelihood that extreme de-pigmentation in Eurasia is a feature of the last 10,000years, not the Upper Pleistocene, when modern humans first settled northern Eurasia. Additionally the data imply two independent selection events in eastern and western Eurasia. Therefore new parameters must be added to the model of natural selection so as to explain the relatively recent and parallel adaptive responses. I propose a model of gene-culture co-evolution whereby the spread of agriculture both reduced dietary vitamin D sources and led to more powerful selection on immune response because of the rise of infectious diseases with greater population densities. This model explains the persistence of relatively dark-skinned peoples at relatively high latitudes and the existence of relatively light-skinned populations at low latitudes. It also reinforces the importance of vitamin D as a micronutrient because of the evidence of extremely powerful fitness implications in the recent human past of pigmentation. Copyright 2010 Elsevier Ltd. All rights reserved.

  6. Deciphering next-generation pharmacogenomics: an information technology perspective.

    Science.gov (United States)

    Potamias, George; Lakiotaki, Kleanthi; Katsila, Theodora; Lee, Ming Ta Michael; Topouzis, Stavros; Cooper, David N; Patrinos, George P

    2014-07-01

    In the post-genomic era, the rapid evolution of high-throughput genotyping technologies and the increased pace of production of genetic research data are continually prompting the development of appropriate informatics tools, systems and databases as we attempt to cope with the flood of incoming genetic information. Alongside new technologies that serve to enhance data connectivity, emerging information systems should contribute to the creation of a powerful knowledge environment for genotype-to-phenotype information in the context of translational medicine. In the area of pharmacogenomics and personalized medicine, it has become evident that database applications providing important information on the occurrence and consequences of gene variants involved in pharmacokinetics, pharmacodynamics, drug efficacy and drug toxicity will become an integral tool for researchers and medical practitioners alike. At the same time, two fundamental issues are inextricably linked to current developments, namely data sharing and data protection. Here, we discuss high-throughput and next-generation sequencing technology and its impact on pharmacogenomics research. In addition, we present advances and challenges in the field of pharmacogenomics information systems which have in turn triggered the development of an integrated electronic 'pharmacogenomics assistant'. The system is designed to provide personalized drug recommendations based on linked genotype-to-phenotype pharmacogenomics data, as well as to support biomedical researchers in the identification of pharmacogenomics-related gene variants. The provisioned services are tuned in the framework of a single-access pharmacogenomics portal.

  7. Meaningful use of pharmacogenomics in health records: semantics should be made explicit.

    Science.gov (United States)

    Shabo Shvo, Amnon

    2010-01-01

    The recent emphasis on 'meaningful use' of electronic health records in health information technology reforms (e.g., as in the US stimulus package) can leverage the pharmacogenomics field. In order for clinical trials outcomes, based on pharmacogenomics research, to be meaningfully and effectively used in clinical practice there is a need to make health semantics explicit. Often, semantics is merely implicit in both the research and practice worlds and is buried in unstructured and disconnected descriptions of the data or just in the heads of human experts. Meaningful semantics includes rich metadata, but more importantly, the context of each discrete data item and how it relates to other data items in a specific dataset, as well as how it fits within the entire health record of an individual and how it references up-to-date clinical knowledge. Properly-built electronic health records systems based on standards could provide meaningful semantics on the healthcare side, while the fields of research and clinical trials need to come closer to healthcare in its data and knowledge representations in a way that lends itself to personalized medicine. The purpose of this review is to explore how evidence created by pharmacogenomics can be meaningfully delivered to healthcare through new approaches, such as electronic health records systems and information models.

  8. Clinical Application and Evaluation of Pharmacogenomics in Tumor Chemotherapy

    Institute of Scientific and Technical Information of China (English)

    Feng Jifeng

    2014-01-01

    In the treatment of tumor patients, how to select the chemotherapy regimen with better efifcacy, less toxicity and expense is a difficult problem that perplexes clinical doctors for a long time. Pharmacogenetics is to study the influence of genetic factors on pharmacokinetics, whereas pharmacogenomics is to study the relationship between various gene mutations and drug efifcacy and safety. With molecular biology developing, pharmacogenetics and pharmacogenomics are considered to be essential in the reduction of adverse reactions, improvement of efficacy and realization of individualized treatment. In this article, the clinical application and evaluation of pharmacogenomics in tumor chemotherapy were primarily investigated.

  9. Pharmacogenomics of alcohol addiction: Personalizing pharmacologic treatment of alcohol dependence

    Directory of Open Access Journals (Sweden)

    Ragia Georgia

    2014-01-01

    Full Text Available Alcohol dependence is a serious psychiatric disorder with harmful physical, mental and social consequences, and a high probability of a chronic relapsing course. The field of pharmacologic treatment of alcohol dependence and craving is expanding rapidly; the drugs that have been found to reduce relapse rates or drinking in alcohol-dependent patients and are approved for treatment of alcohol dependence are naltrexone, acamprosate and disulfiram, whereas also topiramate appears as a promising therapy. For many patients, however, these treatments are not effective. Evidence from a number of different studies suggests that genetic variation is a significant contributor to interindividual variation of clinical presentation of alcohol problems and response to a given treatment. The aim of the present review is to summarize and discuss the findings on the association between gene polymorphisms and the response to alcohol dependence treatment medications. It is anticipated that future implementation of pharmacogenomics in clinical practice will help personalize alcohol dependence drug treatment, and development personalized hospital pharmacology.

  10. Pharmacogenomics of methadone maintenance treatment.

    Science.gov (United States)

    Somogyi, Andrew A; Barratt, Daniel T; Ali, Robert L; Coller, Janet K

    2014-05-01

    Methadone is the major opioid substitution therapy for opioid dependence. Dosage is highly variable and is often controlled by the patient and prescriber according to local and national policy and guidelines. Nevertheless many genetic factors have been investigated including those affecting its metabolism (CYP2B6-consistent results), efflux transport (P-gp-inconsistent results), target μ-opioid receptor (μ-opioid receptor-inconsistent results) and a host of other receptors (DRD2) and signaling elements (GIRK2 and ARRB2; not replicated). None by themselves have been able to substantially explain dosage variation (the major but not sole end point). When multiple genes have been combined such as ABCB1, CYP2B6, OPRM1 and DRD2 a greater contribution to dosage variation was found but not as yet replicated. As stabilization of dosage needs to be made rapidly, it is imperative that larger internationally based studies be instigated so that genetic contribution to dosage can be properly assessed, which may or may not tailor to different ethnic groups and each country's policy towards an outcome that benefits all.

  11. Global properties and functional complexity of human gene regulatory variation.

    Directory of Open Access Journals (Sweden)

    Daniel J Gaffney

    2013-05-01

    Full Text Available Identification and functional interpretation of gene regulatory variants is a major focus of modern genomics. The application of genetic mapping to molecular and cellular traits has enabled the detection of regulatory variation on genome-wide scales and revealed an enormous diversity of regulatory architecture in humans and other species. In this review I summarise the insights gained and questions raised by a decade of genetic mapping of gene expression variation. I discuss recent extensions of this approach using alternative molecular phenotypes that have revealed some of the biological mechanisms that drive gene expression variation between individuals. Finally, I highlight outstanding problems and future directions for development.

  12. Genetics of resistant hypertension: a novel pharmacogenomics phenotype.

    Science.gov (United States)

    El Rouby, Nihal; Cooper-DeHoff, Rhonda M

    2015-09-01

    Resistant hypertension (RHTN), defined as an uncontrolled blood pressure despite the use of multiple antihypertensive medications, is an increasing clinical problem associated with increased cardiovascular (CV) risk, including stroke and target organ damage. Genetic variability in blood pressure (BP)-regulating genes and pathways may, in part, account for the variability in BP response to antihypertensive agents, when taken alone or in combination, and may contribute to the RHTN phenotype. Pharmacogenomics focuses on the identification of genetic factors responsible for inter-individual variability in drug response. Expanding pharmacogenomics research to include patients with RHTN taking multiple BP-lowering medications may identify genetic markers associated with RHTN. To date, the available evidence surrounding pharmacogenomics in RHTN is limited and primarily focused on candidate genes. In this review, we summarize the most current data in RHTN pharmacogenomics and offer some recommendations on how to advance the field.

  13. Cancer pharmacogenomics, challenges in implementation, and patient-focused perspectives

    Directory of Open Access Journals (Sweden)

    Patel JN

    2016-07-01

    Full Text Available Jai N Patel Department of Cancer Pharmacology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA Abstract: Cancer pharmacogenomics is an evolving landscape and has the potential to significantly impact cancer care and precision medicine. Harnessing and understanding the genetic code of both the patient (germline and the tumor (somatic provides the opportunity for personalized dose and therapy selection for cancer patients. While germline DNA is useful in understanding the pharmacokinetic and pharmacodynamic disposition of a drug, somatic DNA is particularly useful in identifying drug targets and predicting drug response. Molecular profiling of somatic DNA has resulted in the current breadth of targeted therapies available, expanding the armamentarium to battle cancer. This review provides an update on cancer pharmacogenomics and genomics-based medicine, challenges in applying pharmacogenomics to the clinical setting, and patient perspectives on the use of pharmacogenomics to personalize cancer therapy. Keywords: oncology, personalized, pharmacogenetics, germline, somatic, DNA, biomarker

  14. Pharmacogenomic knowledge gaps and educational resource needs among physicians in selected specialties

    Directory of Open Access Journals (Sweden)

    Johansen Taber KA

    2014-07-01

    Full Text Available Katherine A Johansen Taber, Barry D Dickinson Department of Science and Biotechnology, American Medical Association, Chicago, IL, USA Background: The use of pharmacogenomic testing in the clinical setting has the potential to improve the safety and effectiveness of drug therapy, yet studies have revealed that physicians lack knowledge about the topic of pharmacogenomics, and are not prepared to implement it in the clinical setting. This study further explores the pharmacogenomic knowledge deficit and educational resource needs among physicians. Materials and methods: Surveys of primary care physicians, cardiologists, and psychiatrists were conducted. Results: Few physicians reported familiarity with the topic of pharmacogenomics, but more reported confidence in their knowledge about the influence of genetics on drug therapy. Only a small minority had undergone formal training in pharmacogenomics, and a majority reported being unsure what type of pharmacogenomic tests were appropriate to order for the clinical situation. Respondents indicated that an ideal pharmacogenomic educational resource should be electronic and include such components as how to interpret pharmacogenomic test results, recommendations for prescribing, population subgroups most likely to be affected, and contact information for laboratories offering pharmacogenomic testing. Conclusion: Physicians continue to demonstrate pharmacogenomic knowledge gaps, and are unsure about how to use pharmacogenomic testing in clinical practice. Educational resources that are clinically oriented and easily accessible are preferred by physicians, and may best support appropriate clinical implementation of pharmacogenomics. Keywords: pharmacogenomics, knowledge gap, drug response, educational resource

  15. Implementing Pharmacogenomics in Europe: Design and Implementation Strategy of the Ubiquitous Pharmacogenomics Consortium.

    Science.gov (United States)

    van der Wouden, C H; Cambon-Thomsen, A; Cecchin, E; Cheung, K C; Dávila-Fajardo, C L; Deneer, V H; Dolžan, V; Ingelman-Sundberg, M; Jönsson, S; Karlsson, M O; Kriek, M; Mitropoulou, C; Patrinos, G P; Pirmohamed, M; Samwald, M; Schaeffeler, E; Schwab, M; Steinberger, D; Stingl, J; Sunder-Plassmann, G; Toffoli, G; Turner, R M; van Rhenen, M H; Swen, J J; Guchelaar, H-J

    2017-03-01

    Despite scientific and clinical advances in the field of pharmacogenomics (PGx), application into routine care remains limited. Opportunely, several implementation studies and programs have been initiated over recent years. This article presents an overview of these studies and identifies current research gaps. Importantly, one such gap is the undetermined collective clinical utility of implementing a panel of PGx-markers into routine care, because the evidence base is currently limited to specific, individual drug-gene pairs. The Ubiquitous Pharmacogenomics (U-PGx) Consortium, which has been funded by the European Commission's Horizon-2020 program, aims to address this unmet need. In a prospective, block-randomized, controlled clinical study (PREemptive Pharmacogenomic testing for prevention of Adverse drug REactions [PREPARE]), pre-emptive genotyping of a panel of clinically relevant PGx-markers, for which guidelines are available, will be implemented across healthcare institutions in seven European countries. The impact on patient outcomes and cost-effectiveness will be investigated. The program is unique in its multicenter, multigene, multidrug, multi-ethnic, and multihealthcare system approach.

  16. The contribution of subsistence to global human cranial variation.

    Science.gov (United States)

    Noback, Marlijn L; Harvati, Katerina

    2015-03-01

    Diet-related cranial variation in modern humans is well documented on a regional scale, with ample examples of cranial changes related to the agricultural transition. However, the influence of subsistence strategy on global cranial variation is less clear, having been confirmed only for the mandible, and dietary effects beyond agriculture are often neglected. Here we identify global patterns of subsistence-related human cranial shape variation. We analysed a worldwide sample of 15 populations (n = 255) with known subsistence strategies using 3-D landmark datasets designed to capture the shape of different units of the cranium. Results show significant correlations between global cranial shape and diet, especially for temporalis muscle shape and general cranial shape. Importantly, the differences between populations with either a plant- or an animal-based diet are more pronounced than those between agriculturalists and hunter-gatherers, suggesting that the influence of diet as driver of cranial variation is not limited to Holocene transitions to agricultural subsistence. Dental arch shape did not correlate with subsistence pattern, possibly indicating the high plasticity of this region of the face in relation to age, disease and individual use of the dentition. Our results highlight the importance of subsistence strategy as one of the factors underlying the evolution of human geographic cranial variation.

  17. Pharmacogenomic considerations in opioid analgesia

    Directory of Open Access Journals (Sweden)

    Vuilleumier PH

    2012-08-01

    Full Text Available Pascal H Vuilleumier,1 Ulrike M Stamer,1 Ruth Landau21Klinik für Anästhesiologie und Schmerztherapie, Inselspital Universität Bern, Switzerland; 2Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA, USAAbstract: Translating pharmacogenetics to clinical practice has been particularly challenging in the context of pain, due to the complexity of this multifaceted phenotype and the overall subjective nature of pain perception and response to analgesia. Overall, numerous genes involved with the pharmacokinetics and dynamics of opioids response are candidate genes in the context of opioid analgesia. The clinical relevance of CYP2D6 genotyping to predict analgesic outcomes is still relatively unknown; the two extremes in CYP2D6 genotype (ultrarapid and poor metabolism seem to predict pain response and/or adverse effects. Overall, the level of evidence linking genetic variability (CYP2D6 and CYP3A4 to oxycodone response and phenotype (altered biotransformation of oxycodone into oxymorphone and overall clearance of oxycodone and oxymorphone is strong; however, there has been no randomized clinical trial on the benefits of genetic testing prior to oxycodone therapy. On the other hand, predicting the analgesic response to morphine based on pharmacogenetic testing is more complex; though there was hope that simple genetic testing would allow tailoring morphine doses to provide optimal analgesia, this is unlikely to occur. A variety of polymorphisms clearly influence pain perception and behavior in response to pain. However, the response to analgesics also differs depending on the pain modality and the potential for repeated noxious stimuli, the opioid prescribed, and even its route of administration.Keywords: pain perception, opioid analgesia, genetic variation, pharmacogenetics

  18. Genetics of the dentofacial variation in human malocclusion.

    Science.gov (United States)

    Moreno Uribe, L M; Miller, S F

    2015-04-01

    Malocclusions affect individuals worldwide, resulting in compromised function and esthetics. Understanding the etiological factors contributing to the variation in dentofacial morphology associated with malocclusions is the key to develop novel treatment approaches. Advances in dentofacial phenotyping, which is the comprehensive characterization of hard and soft tissue variation in the craniofacial complex, together with the acquisition of large-scale genomic data have started to unravel genetic mechanisms underlying facial variation. Knowledge on the genetics of human malocclusion is limited even though results attained thus far are encouraging, with promising opportunities for future research. This review summarizes the most common dentofacial variations associated with malocclusions and reviews the current knowledge of the roles of genes in the development of malocclusions. Lastly, this review will describe ways to advance malocclusion research, following examples from the expanding fields of phenomics and genomic medicine, which aim to better patient outcomes.

  19. Pharmacogenomics of Acetaminophen in Pediatric Populations: a Moving Target

    Directory of Open Access Journals (Sweden)

    Wanqing eLiu

    2014-10-01

    Full Text Available Acetaminophen (APAP is widely used as an over-the-counter fever reducer and pain reliever. However, the current therapeutic use of APAP is not optimal. The inter-patient variability in both efficacy and toxicity limits the use of this drug. This is particularly an issue in pediatric populations, where tools for predicting drug efficacy and developmental toxicity are not well established. Variability in toxicity between age groups may be accounted for by differences in metabolism, transport, and the genetics behind those differences. While pharmacogenomics has been revolutionizing the paradigm of pharmacotherapy for many drugs, its application in pediatric populations faces significant challenges including given the dynamic ontogenic changes in cellular and systems physiology. In this review we focused on the ontogenesis of the regulatory pathways involved in the disposition of APAP and on the variability between pediatric, adolescent, and adult patients. We also summarize important polymorphisms of the pharmacogenes associated with APAP metabolism. Pharmacogenetic studies in pediatric APAP treatment are also reviewed. We conclude that while a consensus in pharmacogenetic management of APAP in pediatric populations has not been achieved, a systems biology based strategy for comprehensively understanding the ontogenic regulatory pathway as well as the interaction between age and genetic variations are particularly necessary in order to address this question.

  20. Advancing Pharmacogenomics as a Component of Precision Medicine: How, Where, and Who?

    Science.gov (United States)

    Johnson, J A; Weitzel, K W

    2016-02-01

    Pharmacogenomics is an important element of precision medicine. Advances in pharmacogenomics implementation have been made but significant barriers remain, including evidence, reimbursement, and clinician knowledge, among others. Widespread adoption of pharmacogenomics requires overcoming these barriers, a clinician champion group, which we propose will be pharmacists, and an easily accessible setting, which may be the community pharmacy. Whatever the path, it must be evidence-driven and pharmacogenomics must improve drug-related outcomes to become a standard of care.

  1. Pharmacogenomics and epilepsy: the road ahead.

    LENUS (Irish Health Repository)

    Cavalleri, Gianpiero L

    2011-10-01

    Epilepsy is one of the most common, serious neurological disorders, affecting an estimated 50 million people worldwide. The condition is typically treated using antiepileptic drugs of which there are 16 in widespread use. However, there are many different syndrome and seizure types within epilepsy and information guiding clinicians on the most effective drug and dose for individual patients is lacking. Further, all of the antiepileptic drugs have associated adverse reactions, some of which are severe and life-threatening. Here, we review the pharmacogenomic work to date in the context of these issues and comment on key aspects of study design that are required to speed up the identification of clinically relevant genetic factors.

  2. Pharmacogenomics: road to anticancer therapeutics nirvana?

    Science.gov (United States)

    Desai, Apurva A; Innocenti, Federico; Ratain, Mark J

    2003-09-29

    Interindividual differences in the toxicity and response to anticancer therapies are currently observed for essentially all available treatment regimens. Such 'unpredictable' drug responses are particularly dangerous in the context of anticancer agents that have narrow therapeutic indices. Pharmacogenomics attempts to elucidate the inherited basis of interindividual differences in drug response, with the eventual goal of minimizing such variability through the use of 'individualized' treatments. There are several emerging examples of genetic polymorphisms of drug-metabolizing enzymes, DNA repair genes and drug targets that have been shown to influence the toxicity and efficacy of anticancer treatment. This review discusses the role of genetic variants of UGT1A1, TS and EGFR to exemplify the potential impact of phramacogenomics on the field of anticancer therapeutics.

  3. Geomagnetic Variations of Near-polar Regions and Human Health

    Science.gov (United States)

    Tchistova, Z. B.; Kutinov, Y. G.

    to conclude, that geomagnetic and geoelectric fields produced the biological effect, that is correlated with solar activity variations. The result of many years investigation of geomagnetic variations on near-polar territory, the authors found the facts of sharp increasing of intensity of the short wave' variations near the points of fault crossing. Analysis of character of geomagnetic variations can give information on the alleged effects of electromagnetic fields on human health. Spectral analysis shows rhythms with periods of 98, 105, 125, 130, 145, 160, 170, 180, 200, 235, 250, 270, 330, 395 sec. The rhythms with period of 98 -180 sec. coincide with rhythms of human cardiovascular activity. This concurrence entail occurrence of a magnetic resonance.

  4. DNA methylation-based variation between human populations.

    Science.gov (United States)

    Kader, Farzeen; Ghai, Meenu

    2017-02-01

    Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development. Genetic variations, such as single-nucleotide polymorphisms and environmental factors, such as age, dietary folate, socioeconomic status, and smoking, impacts DNA methylation levels, which reciprocally impacts expression of phenotypes. Studies show that it is necessary to address these external influences when attempting to differentiate between populations since the relative impacts of these factors on the human methylome remain uncertain. The present review summarises several reported attempts to establish the contribution of differential DNA methylation to natural human variation, and shows that DNA methylation could represent new opportunities for risk stratification and prevention of several diseases amongst populations world-wide. Variation of methylation patterns between human populations is an exciting prospect which inspires further valuable research to apply the concept in routine medical and forensic casework. However, trans-generational inheritance needs to be quantified to decipher the proportion of variation contributed by DNA methylation. The future holds thorough evaluation of the epigenome to understand quantification, heritability, and the effect of DNA methylation on phenotypes. In addition, methylation profiling of the same ethnic groups across geographical locations will shed light on conserved methylation differences in populations.

  5. The ontogeny of nasal floor shape variation in extant humans.

    Science.gov (United States)

    Nicholas, Christina L; Franciscus, Robert G

    2014-11-01

    Variation in nasal floor topography has generated both neontological and paleontological interest. Three categories of nasal floor shape (Franciscus: J Hum Evol 44 (2003) 699-727) have been used when analyzing this trait in extant humans and fossil Homo: flat, sloped, and depressed (or "bi-level"). Variation in the frequency of these configurations within and among extant and fossil humans has been well-documented (Franciscus: J Hum Evol 44 (2003) 699-727; Wu et al.: Anthropol Sci 120 (2012) 217-226). However, variation in this trait in Homo has been observed primarily in adults, with comparatively small subadult sample sizes and/or large age gradients that may not sufficiently track key ontogenetic changes. In this study, we investigate the ontogeny of nasal floor shape in a relatively large cross-sectional age sample of extant humans (n = 382) ranging from 4.0 months fetal to 21 years post-natal. Results indicate that no fetal or young infant individuals possess a depressed nasal floor, and that a depressed nasal floor, when present (ca. 21% of the sample), does not occur until 3.0 years postnatal. A canonical variates analysis of maxillary shape revealed that individuals with depressed nasal floors were also characterized by relatively taller anterior alveolar regions. This suggests that palate remodeling at about 3.0-3.5 years after birth, under the influence of tooth development, strongly influences nasal floor variation, and that various aspects of dental development, including larger crown/root size, may contribute to the development of a depressed nasal floor. These results in extant humans may help explain the high frequency of this trait found in Neandertal and other archaic Homo maxillae.

  6. Demography and ecology drive variation in cooperation across human populations.

    Science.gov (United States)

    Lamba, Shakti; Mace, Ruth

    2011-08-30

    Recent studies argue that cross-cultural variation in human cooperation supports cultural group selection models of the evolution of large-scale cooperation. However, these studies confound cultural and environmental differences between populations by predominantly sampling one population per society. Here, we test the hypothesis that behavioral variation between populations is driven by environmental differences in demography and ecology. We use a public goods game played with money and a naturalistic measure of behavior involving the distribution of salt, an essential and locally valued resource, to demonstrate significant variation in levels of cooperation across 16 discrete populations of the same small-scale society, the Pahari Korwa of central India. Variation between these populations of the same cultural group is comparable to that found between different cultural groups in previous studies. Demographic factors partly explain this variation; age and a measure of social network size are associated with contributions in the public goods game, while population size and the number of adult sisters residing in the population are associated with decisions regarding salt. That behavioral variation is at least partly contingent on environmental differences between populations questions the existence of stable norms of cooperation. Hence, our findings call for reinterpretation of cross-cultural data on cooperation. Although cultural group selection could theoretically explain the evolution of large-scale cooperation, our results make clear that existing cross-cultural data cannot be taken as empirical support for this hypothesis.

  7. ePGA: A Web-Based Information System for Translational Pharmacogenomics

    Science.gov (United States)

    Lakiotaki, Kleanthi; Kartsaki, Evgenia; Kanterakis, Alexandros; Katsila, Theodora; Patrinos, George P.; Potamias, George

    2016-01-01

    One of the challenges that arise from the advent of personal genomics services is to efficiently couple individual data with state of the art Pharmacogenomics (PGx) knowledge. Existing services are limited to either providing static views of PGx variants or applying a simplistic match between individual genotypes and existing PGx variants. Moreover, there is a considerable amount of haplotype variation associated with drug metabolism that is currently insufficiently addressed. Here, we present a web-based electronic Pharmacogenomics Assistant (ePGA; http://www.epga.gr/) that provides personalized genotype-to-phenotype translation, linked to state of the art clinical guidelines. ePGA's translation service matches individual genotype-profiles with PGx gene haplotypes and infers the corresponding diplotype and phenotype profiles, accompanied with summary statistics. Additional features include i) the ability to customize translation based on subsets of variants of clinical interest, and ii) to update the knowledge base with novel PGx findings. We demonstrate ePGA's functionality on genetic variation data from the 1000 Genomes Project. PMID:27631363

  8. Pharmacogenomics of Drug Metabolizing Enzymes and Transporters:Relevance to Precision Medicine

    Institute of Scientific and Technical Information of China (English)

    Shabbir Ahmed; Zhan Zhou; Jie Zhou; Shu-Qing Chen

    2016-01-01

    The interindividual genetic variations in drug metabolizing enzymes and transporters influence the efficacy and toxicity of numerous drugs. As a fundamental element in precision med-icine, pharmacogenomics, the study of responses of individuals to medication based on their genomic information, enables the evaluation of some specific genetic variants responsible for an individual’s particular drug response. In this article, we review the contributions of genetic polymorphisms to major individual variations in drug pharmacotherapy, focusing specifically on the pharmacoge-nomics of phase-I drug metabolizing enzymes and transporters. Substantial frequency differences in key variants of drug metabolizing enzymes and transporters, as well as their possible functional consequences, have also been discussed across geographic regions. The current effort illustrates the common presence of variability in drug responses among individuals and across all geographic regions. This information will aid health-care professionals in prescribing the most appropriate treatment aimed at achieving the best possible beneficial outcomes while avoiding unwanted effects for a particular patient.

  9. Personal and population genomics of human regulatory variation.

    Science.gov (United States)

    Vernot, Benjamin; Stergachis, Andrew B; Maurano, Matthew T; Vierstra, Jeff; Neph, Shane; Thurman, Robert E; Stamatoyannopoulos, John A; Akey, Joshua M

    2012-09-01

    The characteristics and evolutionary forces acting on regulatory variation in humans remains elusive because of the difficulty in defining functionally important noncoding DNA. Here, we combine genome-scale maps of regulatory DNA marked by DNase I hypersensitive sites (DHSs) from 138 cell and tissue types with whole-genome sequences of 53 geographically diverse individuals in order to better delimit the patterns of regulatory variation in humans. We estimate that individuals likely harbor many more functionally important variants in regulatory DNA compared with protein-coding regions, although they are likely to have, on average, smaller effect sizes. Moreover, we demonstrate that there is significant heterogeneity in the level of functional constraint in regulatory DNA among different cell types. We also find marked variability in functional constraint among transcription factor motifs in regulatory DNA, with sequence motifs for major developmental regulators, such as HOX proteins, exhibiting levels of constraint comparable to protein-coding regions. Finally, we perform a genome-wide scan of recent positive selection and identify hundreds of novel substrates of adaptive regulatory evolution that are enriched for biologically interesting pathways such as melanogenesis and adipocytokine signaling. These data and results provide new insights into patterns of regulatory variation in individuals and populations and demonstrate that a large proportion of functionally important variation lies beyond the exome.

  10. Human footprint variation while performing load bearing tasks.

    Directory of Open Access Journals (Sweden)

    Cara M Wall-Scheffler

    Full Text Available Human footprint fossils have provided essential evidence about the evolution of human bipedalism as well as the social dynamics of the footprint makers, including estimates of speed, sex and group composition. Generally such estimates are made by comparing footprint evidence with modern controls; however, previous studies have not accounted for the variation in footprint dimensions coming from load bearing activities. It is likely that a portion of the hominins who created these fossil footprints were carrying a significant load, such as offspring or foraging loads, which caused variation in the footprint which could extend to variation in any estimations concerning the footprint's maker. To identify significant variation in footprints due to load-bearing tasks, we had participants (N = 30, 15 males and 15 females walk at a series of speeds carrying a 20kg pack on their back, side and front. Paint was applied to the bare feet of each participant to create footprints that were compared in terms of foot length, foot width and foot area. Female foot length and width increased during multiple loaded conditions. An appreciation of footprint variability associated with carrying loads adds an additional layer to our understanding of the behavior and morphology of extinct hominin populations.

  11. Variation in human recombination rates and its genetic determinants.

    Directory of Open Access Journals (Sweden)

    Adi Fledel-Alon

    Full Text Available BACKGROUND: Despite the fundamental role of crossing-over in the pairing and segregation of chromosomes during human meiosis, the rates and placements of events vary markedly among individuals. Characterizing this variation and identifying its determinants are essential steps in our understanding of the human recombination process and its evolution. STUDY DESIGN/RESULTS: Using three large sets of European-American pedigrees, we examined variation in five recombination phenotypes that capture distinct aspects of crossing-over patterns. We found that the mean recombination rate in males and females and the historical hotspot usage are significantly heritable and are uncorrelated with one another. We then conducted a genome-wide association study in order to identify loci that influence them. We replicated associations of RNF212 with the mean rate in males and in females as well as the association of Inversion 17q21.31 with the female mean rate. We also replicated the association of PRDM9 with historical hotspot usage, finding that it explains most of the genetic variance in this phenotype. In addition, we identified a set of new candidate regions for further validation. SIGNIFICANCE: These findings suggest that variation at broad and fine scales is largely separable and that, beyond three known loci, there is no evidence for common variation with large effects on recombination phenotypes.

  12. Transitioning Pharmacogenomics into the Clinical Setting: Training Future Pharmacists

    Science.gov (United States)

    Frick, Amber; Benton, Cristina S.; Scolaro, Kelly L.; McLaughlin, Jacqueline E.; Bradley, Courtney L.; Suzuki, Oscar T.; Wang, Nan; Wiltshire, Tim

    2016-01-01

    Pharmacogenomics, once hailed as a futuristic approach to pharmacotherapy, has transitioned to clinical implementation. Although logistic and economic limitations to clinical pharmacogenomics are being superseded by external measures such as preemptive genotyping, implementation by clinicians has met resistance, partly due to a lack of education. Pharmacists, with extensive training in pharmacology and pharmacotherapy and accessibility to patients, are ideally suited to champion clinical pharmacogenomics. This study aimed to analyze the outcomes of an innovative pharmacogenomic teaching approach. Second-year student pharmacists enrolled in a required, 15-week pharmaceutical care lab course in 2015 completed educational activities including lectures and small group work focusing on practical pharmacogenomics. Reflecting the current landscape of direct-to-consumer (DTC) genomic testing, students were offered 23andMe genotyping. Students completed surveys regarding their attitudes and confidence on pharmacogenomics prior to and following the educational intervention. Paired pre- and post-intervention responses were analyzed with McNemar's test for binary comparisons and the Wilcoxon signed-rank test for Likert items. Responses between genotyped and non-genotyped students were analyzed with Fisher's exact test for binary comparisons and the Mann-Whitney U-test for Likert items. Responses were analyzed for all student pharmacists who voluntarily completed the pre-intervention survey (N = 121, 83% response) and for student pharmacists who completed both pre- and post-intervention surveys (N = 39, 27% response). Of those who completed both pre- and post-intervention surveys, 59% obtained genotyping. Student pharmacists demonstrated a significant increase in their knowledge of pharmacogenomic resources (17.9 vs. 56.4%, p < 0.0001) and confidence in applying pharmacogenomic information to manage patients' drug therapy (28.2 vs. 48.7%, p = 0.01), particularly if the student

  13. Nonneutral mitochondrial DNA variation in humans and chimpanzees

    Energy Technology Data Exchange (ETDEWEB)

    Nachman, M.W.; Aquadro, C.F. [Cornell Univ., Ithaca, NY (United States); Brown, W.M. [Univ. of Michigan, Ann Arbor, MI (United States)] [and others

    1996-03-01

    We sequenced the NADH dehydrogenase subunit 3 (ND3) gene from a sample of 61 humans, five common chimpanzees, and one gorilla to test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution. Within humans and within chimpanzees, the ratio of replacement to silent nucleotide substitutions was higher than observed in comparisons between species, contrary to neutral expectations. To test the generality of this result, we reanalyzed published human RFLP data from the entire mitochondrial genome. Gains of restriction sites relative to a known human mtDNA sequence were used to infer unambiguous nucleotide substitutions. We also compared the complete mtDNA sequences of three humans. Both the RFLP data and the sequence data reveal a higher ratio of replacement to silent nucleotide substitutions within humans than is seen between species. This pattern is observed at most or all human mitochondrial genes and is inconsistent with a strictly neutral model. These data suggest that many mitochondrial protein polymorphisms are slightly deleterious, consistent with studies of human mitochondrial diseases. 59 refs., 2 figs., 8 tabs.

  14. Design, Implementation, and Assessment Approaches Within a Pharmacogenomics Course

    Science.gov (United States)

    Remsberg, Connie M.; Bray, Brenda S.; Wright, Susan K.; Ashmore, Joe; Kabasenche, William; Wang, Shuwen; Lazarus, Philip

    2017-01-01

    Objective. To design and implement a pharmacogenomics course that focuses on analysis and integration of pharmacogenomic data into clinical practice and to explore how participation in the course influences student self-confidence. Design. The Basic and Clinical Pharmacogenomics course content was divided into three modules: genetic-based didactic sessions, genomic techniques and self-genotype/phenotype laboratory exercise, and clinical-based case studies. Student learning assessment included knowledge- and application-based tests and performance on a group project. Assessment. Effectiveness of the course was evaluated using results of student performance on coded test questions, student perceptions on pre- and post-course self-assessments, performance on a group project, and course evaluation results. Student pharmacists successfully demonstrated competency in pharmacogenomics knowledge-based learning, demonstrated their abilities to apply learned skills in clinical-based scenarios, and reported improved confidence in analyzing patient-based genomic testing results. Conclusions. This course appears to have contributed to student learning and positively influenced student self-confidence in pharmacogenomics. PMID:28289301

  15. ENGINES: exploring single nucleotide variation in entire human genomes

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    Salas Antonio

    2011-04-01

    Full Text Available Abstract Background Next generation ultra-sequencing technologies are starting to produce extensive quantities of data from entire human genome or exome sequences, and therefore new software is needed to present and analyse this vast amount of information. The 1000 Genomes project has recently released raw data for 629 complete genomes representing several human populations through their Phase I interim analysis and, although there are certain public tools available that allow exploration of these genomes, to date there is no tool that permits comprehensive population analysis of the variation catalogued by such data. Description We have developed a genetic variant site explorer able to retrieve data for Single Nucleotide Variation (SNVs, population by population, from entire genomes without compromising future scalability and agility. ENGINES (ENtire Genome INterface for Exploring SNVs uses data from the 1000 Genomes Phase I to demonstrate its capacity to handle large amounts of genetic variation (>7.3 billion genotypes and 28 million SNVs, as well as deriving summary statistics of interest for medical and population genetics applications. The whole dataset is pre-processed and summarized into a data mart accessible through a web interface. The query system allows the combination and comparison of each available population sample, while searching by rs-number list, chromosome region, or genes of interest. Frequency and FST filters are available to further refine queries, while results can be visually compared with other large-scale Single Nucleotide Polymorphism (SNP repositories such as HapMap or Perlegen. Conclusions ENGINES is capable of accessing large-scale variation data repositories in a fast and comprehensive manner. It allows quick browsing of whole genome variation, while providing statistical information for each variant site such as allele frequency, heterozygosity or FST values for genetic differentiation. Access to the data mart

  16. Effects of Using Personal Genotype Data on Student Learning and Attitudes in a Pharmacogenomics Course

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    McDonough, Caitrin W.; Elsey, Amanda R.; Burkley, Benjamin; Cavallari, Larisa H.; Johnson, Julie A.

    2016-01-01

    Objective. To evaluate the impact of personal genotyping and a novel educational approach on student attitudes, knowledge, and beliefs regarding pharmacogenomics and genomic medicine. Methods. Two online elective courses (pharmacogenomics and genomic medicine) were offered to student pharmacists at the University of Florida using a flipped-classroom, patient-centered teaching approach. In the pharmacogenomics course, students could be genotyped and apply results to patient cases. Results. Thirty-four and 19 student pharmacists completed the pharmacogenomics and genomic medicine courses, respectively, and 100% of eligible students (n=34) underwent genotyping. Student knowledge improved after the courses. Seventy-four percent (n=25) of students reported better understanding of pharmacogenomics based on having undergone genotyping. Conclusions. Completion of a novel pharmacogenomics elective course sequence that incorporated personal genotyping and genomic medicine was associated with increased student pharmacist knowledge and improved clinical confidence with pharmacogenomics. PMID:27756930

  17. Analytical strategies for discovery and replication of genetic effects in pharmacogenomic studies

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    Kohler JR

    2014-08-01

    Full Text Available Jared R Kohler, Tobias Guennel, Scott L MarshallBioStat Solutions, Inc., Frederick, MD, USAAbstract: In the past decade, the pharmaceutical industry and biomedical research sector have devoted considerable resources to pharmacogenomics (PGx with the hope that understanding genetic variation in patients would deliver on the promise of personalized medicine. With the advent of new technologies and the improved collection of DNA samples, the roadblock to advancements in PGx discovery is no longer the lack of high-density genetic information captured on patient populations, but rather the development, adaptation, and tailoring of analytical strategies to effectively harness this wealth of information. The current analytical paradigm in PGx considers the single-nucleotide polymorphism (SNP as the genomic feature of interest and performs single SNP association tests to discover PGx effects – ie, genetic effects impacting drug response. While it can be straightforward to process single SNP results and to consider how this information may be extended for use in downstream patient stratification, the rate of replication for single SNP associations has been low and the desired success of producing clinically and commercially viable biomarkers has not been realized. This may be due to the fact that single SNP association testing is suboptimal given the complexities of PGx discovery in the clinical trial setting, including: 1 relatively small sample sizes; 2 diverse clinical cohorts within and across trials due to genetic ancestry (potentially impacting the ability to replicate findings; and 3 the potential polygenic nature of a drug response. Subsequently, a shift in the current paradigm is proposed: to consider the gene as the genomic feature of interest in PGx discovery. The proof-of-concept study presented in this manuscript demonstrates that genomic region-based association testing has the potential to improve the power of detecting single SNP or

  18. Cardiovascular Pharmacokinetics, Pharmacodynamics, and Pharmacogenomics for the Clinical Practitioner.

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    Sleder, Anna T; Kalus, James; Lanfear, David E

    2016-01-01

    Current clinical cardiovascular practice requires a clinician to have a strong foundation in multiple aspects of pharmacology. Modern cardiovascular regimens are complex, and optimal management, application of evolving guidelines, and adoption of new therapies build off a more basic understanding of pharmacokinetics and pharmacodynamics. In addition, it is likely time to add a third pillar into this discussion, the expanding field of pharmacogenomics referring to the genetic influences on drug response. This field has increasing applications in medicine and clearly holds significant promise for cardiovascular disease management. Awareness of pharmacogenomic advances and the fundamentals of pharmacokinetics and pharmacodynamics can help the clinician more easily deliver great care. Here we attempt to briefly summarize and simplify key concepts of pharmacokinetics, pharmacodynamics, and pharmacogenomics relevant to the cardiovascular disease practitioner.

  19. Human copy number variation and complex genetic disease.

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    Girirajan, Santhosh; Campbell, Catarina D; Eichler, Evan E

    2011-01-01

    Copy number variants (CNVs) play an important role in human disease and population diversity. Advancements in technology have allowed for the analysis of CNVs in thousands of individuals with disease in addition to thousands of controls. These studies have identified rare CNVs associated with neuropsychiatric diseases such as autism, schizophrenia, and intellectual disability. In addition, copy number polymorphisms (CNPs) are present at higher frequencies in the population, show high diversity in copy number, sequence, and structure, and have been associated with multiple phenotypes, primarily related to immune or environmental response. However, the landscape of copy number variation still remains largely unexplored, especially for smaller CNVs and those embedded within complex regions of the human genome. An integrated approach including characterization of single nucleotide variants and CNVs in a large number of individuals with disease and normal genomes holds the promise of thoroughly elucidating the genetic basis of human disease and diversity.

  20. Genome-Wide Associations of Gene Expression Variation in Humans.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available The exploration of quantitative variation in human populations has become one of the major priorities for medical genetics. The successful identification of variants that contribute to complex traits is highly dependent on reliable assays and genetic maps. We have performed a genome-wide quantitative trait analysis of 630 genes in 60 unrelated Utah residents with ancestry from Northern and Western Europe using the publicly available phase I data of the International HapMap project. The genes are located in regions of the human genome with elevated functional annotation and disease interest including the ENCODE regions spanning 1% of the genome, Chromosome 21 and Chromosome 20q12-13.2. We apply three different methods of multiple test correction, including Bonferroni, false discovery rate, and permutations. For the 374 expressed genes, we find many regions with statistically significant association of single nucleotide polymorphisms (SNPs with expression variation in lymphoblastoid cell lines after correcting for multiple tests. Based on our analyses, the signal proximal (cis- to the genes of interest is more abundant and more stable than distal and trans across statistical methodologies. Our results suggest that regulatory polymorphism is widespread in the human genome and show that the 5-kb (phase I HapMap has sufficient density to enable linkage disequilibrium mapping in humans. Such studies will significantly enhance our ability to annotate the non-coding part of the genome and interpret functional variation. In addition, we demonstrate that the HapMap cell lines themselves may serve as a useful resource for quantitative measurements at the cellular level.

  1. Genome-wide associations of gene expression variation in humans.

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    Barbara E Stranger

    2005-12-01

    Full Text Available The exploration of quantitative variation in human populations has become one of the major priorities for medical genetics. The successful identification of variants that contribute to complex traits is highly dependent on reliable assays and genetic maps. We have performed a genome-wide quantitative trait analysis of 630 genes in 60 unrelated Utah residents with ancestry from Northern and Western Europe using the publicly available phase I data of the International HapMap project. The genes are located in regions of the human genome with elevated functional annotation and disease interest including the ENCODE regions spanning 1% of the genome, Chromosome 21 and Chromosome 20q12-13.2. We apply three different methods of multiple test correction, including Bonferroni, false discovery rate, and permutations. For the 374 expressed genes, we find many regions with statistically significant association of single nucleotide polymorphisms (SNPs with expression variation in lymphoblastoid cell lines after correcting for multiple tests. Based on our analyses, the signal proximal (cis- to the genes of interest is more abundant and more stable than distal and trans across statistical methodologies. Our results suggest that regulatory polymorphism is widespread in the human genome and show that the 5-kb (phase I HapMap has sufficient density to enable linkage disequilibrium mapping in humans. Such studies will significantly enhance our ability to annotate the non-coding part of the genome and interpret functional variation. In addition, we demonstrate that the HapMap cell lines themselves may serve as a useful resource for quantitative measurements at the cellular level.

  2. Large multi-allelic copy number variations in humans

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    Handsaker, Robert E.; Van Doren, Vanessa; Berman, Jennifer R.; Genovese, Giulio; Kashin, Seva; Boettger, Linda M.; McCarroll, Steven A.

    2015-01-01

    Thousands of genome segments appear to be present in widely varying copy number in different human genomes. We developed ways to use increasingly abundant whole genome sequence data to identify the copy numbers, alleles and haplotypes present at most large, multi-allelic CNVs (mCNVs). We analyzed 849 genomes sequenced by the 1000 Genomes Project to identify most large (>5 kb) mCNVs, including 3,878 duplications, of which 1,356 appear to have three or more segregating alleles. We find that mCNVs give rise to most human gene-dosage variation – exceeding sevenfold the contribution of deletions and biallelic duplications – and that this variation in gene dosage generates abundant variation in gene expression. We describe “runaway duplication haplotypes” in which genes, including HPR and ORM1, have mutated to high copy number on specific haplotypes. We describe partially successful initial strategies for analyzing mCNVs via imputation and provide an initial data resource to support such analyses. PMID:25621458

  3. Influence of human genetic variation on nutritional requirements.

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    Stover, Patrick J

    2006-02-01

    Genetic variation is known to affect food tolerances among human subpopulations and may also influence dietary requirements, giving rise to the new field of nutritional genomics and raising the possibility of individualizing nutritional intake for optimal health and disease prevention on the basis of an individual's genome. However, because gene-diet interactions are complex and poorly understood, the use of genomic knowledge to adjust population-based dietary recommendations is not without risk. Whereas current recommendations target most of the population to prevent nutritional deficiencies, inclusion of genomic criteria may indicate subpopulations that may incur differential benefit or risk from generalized recommendations and fortification policies. Current efforts to identify gene alleles that affect nutrient utilization have been enhanced by the identification of genetic variations that have expanded as a consequence of selection under extreme conditions. Identification of genetic variation that arose as a consequence of diet as a selective pressure helps to identify gene alleles that affect nutrient utilization. Understanding the molecular mechanisms underlying gene-nutrient interactions and their modification by genetic variation is expected to result in dietary recommendations and nutritional interventions that optimize individual health.

  4. The role of genetics in pre-eclampsia and potential pharmacogenomic interventions

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    Williams PJ

    2012-01-01

    Full Text Available Paula Juliet Williams, Linda MorganHuman Genetics Research Group, University of Nottingham, Nottingham, UKAbstract: The pregnancy-specific condition pre-eclampsia not only affects the health of mother and baby during pregnancy but also has long-term consequences, increasing the chances of cardiovascular disease in later life. It is accepted that pre-eclampsia has a placental origin, but the pathogenic mechanisms leading to the systemic endothelial dysfunction characteristic of the disorder remain to be determined. In this review we discuss some key factors regarded as important in the development of pre-eclampsia, including immune maladaptation, inadequate placentation, oxidative stress, and thrombosis. Genetic factors influence all of these proposed pathophysiological mechanisms. The inherited nature of pre-eclampsia has been known for many years, and extensive genetic studies have been undertaken in this area. Genetic research offers an attractive strategy for studying the pathogenesis of pre-eclampsia as it avoids the ethical and practical difficulties of conducting basic science research during the preclinical phase of pre-eclampsia when the underlying pathological changes occur. Although pharmacogenomic studies have not yet been conducted in pre-eclampsia, a number of studies investigating treatment for essential hypertension are of relevance to therapies used in pre-eclampsia. The pharmacogenomics of antiplatelet agents, alpha and beta blockers, calcium channel blockers, and magnesium sulfate are discussed in relation to the treatment and prevention of pre-eclampsia. Pharmacogenomics offers the prospect of individualized patient treatment, ensuring swift introduction of optimal treatment whilst minimizing the use of inappropriate or ineffective drugs, thereby reducing the risk of harmful effects to both mother and baby.Keywords: pre-eclampsia, pharmacogenetics, placenta, trophoblast, genetics

  5. Systematic pharmacogenomics analysis of a Malay whole genome: proof of concept for personalized medicine.

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    Mohd Zaki Salleh

    Full Text Available BACKGROUND: With a higher throughput and lower cost in sequencing, second generation sequencing technology has immense potential for translation into clinical practice and in the realization of pharmacogenomics based patient care. The systematic analysis of whole genome sequences to assess patient to patient variability in pharmacokinetics and pharmacodynamics responses towards drugs would be the next step in future medicine in line with the vision of personalizing medicine. METHODS: Genomic DNA obtained from a 55 years old, self-declared healthy, anonymous male of Malay descent was sequenced. The subject's mother died of lung cancer and the father had a history of schizophrenia and deceased at the age of 65 years old. A systematic, intuitive computational workflow/pipeline integrating custom algorithm in tandem with large datasets of variant annotations and gene functions for genetic variations with pharmacogenomics impact was developed. A comprehensive pathway map of drug transport, metabolism and action was used as a template to map non-synonymous variations with potential functional consequences. PRINCIPAL FINDINGS: Over 3 million known variations and 100,898 novel variations in the Malay genome were identified. Further in-depth pharmacogenetics analysis revealed a total of 607 unique variants in 563 proteins, with the eventual identification of 4 drug transport genes, 2 drug metabolizing enzyme genes and 33 target genes harboring deleterious SNVs involved in pharmacological pathways, which could have a potential role in clinical settings. CONCLUSIONS: The current study successfully unravels the potential of personal genome sequencing in understanding the functionally relevant variations with potential influence on drug transport, metabolism and differential therapeutic outcomes. These will be essential for realizing personalized medicine through the use of comprehensive computational pipeline for systematic data mining and analysis.

  6. Ontology-based knowledge discovery in pharmacogenomics.

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    Coulet, Adrien; Smaïl-Tabbone, Malika; Napoli, Amedeo; Devignes, Marie-Dominique

    2011-01-01

    One current challenge in biomedicine is to analyze large amounts of complex biological data for extracting domain knowledge. This work holds on the use of knowledge-based techniques such as knowledge discovery (KD) and knowledge representation (KR) in pharmacogenomics, where knowledge units represent genotype-phenotype relationships in the context of a given treatment. An objective is to design knowledge base (KB, here also mentioned as an ontology) and then to use it in the KD process itself. A method is proposed for dealing with two main tasks: (1) building a KB from heterogeneous data related to genotype, phenotype, and treatment, and (2) applying KD techniques on knowledge assertions for extracting genotype-phenotype relationships. An application was carried out on a clinical trial concerned with the variability of drug response to montelukast treatment. Genotype-genotype and genotype-phenotype associations were retrieved together with new associations, allowing the extension of the initial KB. This experiment shows the potential of KR and KD processes, especially for designing KB, checking KB consistency, and reasoning for problem solving.

  7. Oxytocin receptor genetic variation promotes human trust behavior

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    Frank eKrueger

    2012-02-01

    Full Text Available Given that human trust behavior is heritable and intranasal administration of oxytocin enhances trust, the oxytocin receptor (OXTR gene is an excellent candidate to investigate genetic contributions to individual variations in trust behavior. Although a single-nucleotide polymorphism involving an adenine (A/ guanine (G transition (rs53576 has been associated with socio-emotional phenotypes, its link to trust behavior is unclear. We combined genotyping of healthy male students with the administration of a trust game experiment. Our results show that a naturally occurring genetic variation (rs53576 in the OXTR gene is reliably associated with trust behavior rather than a general increase in trustworthy or risk behaviors. Individuals homozygous for the G allele (GG showed higher trust behavior than individuals with A allele carriers (AA/AG. Although the molecular functionality of this polymorphism is still unknown, future research should clarify how the OXTR gene interacts with other genes and the environment in promoting socio-emotional behaviors.

  8. Progress in the detection of human genome structural variations

    Institute of Scientific and Technical Information of China (English)

    WU XueMei; XIAO HuaSheng

    2009-01-01

    The emerging of high.throughput and high-resolution genomic technologies led to the detection of submicroscopic variants ranging from 1 kb to 3 Mb in the human genome. These variants include copy number variations (CNVs), inversions, insertions, deletions and other complex rearrangements of DNA sequences. This paper briefly reviews the commonly used technologies to discover both genomic structural variants and their potential influences. Particularly, we highlight the array-based, PCR-based and sequencing-based assays, including array-based comparative genomic hybridization (aCGH),representational oligonucleotide microarray analysis (ROMA), multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), paired-end mapping (PEM), and next-generation DNA sequencing technologies. Furthermore, we discuss the limitations and challenges of current assays and give advices on how to make the database of genomic variations more reliable.

  9. Progress in the detection of human genome structural variations

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The emerging of high-throughput and high-resolution genomic technologies led to the detection of submicroscopic variants ranging from 1 kb to 3 Mb in the human genome.These variants include copy number variations(CNVs),inversions,insertions,deletions and other complex rearrangements of DNA sequences.This paper briefly reviews the commonly used technologies to discover both genomic structural variants and their potential influences.Particularly,we highlight the array-based,PCR-based and sequencing-based assays,including array-based comparative genomic hybridization(aCGH),representational oligonucleotide microarray analysis(ROMA),multiplex amplifiable probe hybridization(MAPH),multiplex ligation-dependent probe amplification(MLPA),paired-end mapping(PEM),and next-generation DNA sequencing technologies.Furthermore,we discuss the limitations and challenges of current assays and give advices on how to make the database of genomic variations more reliable.

  10. Pharmacogenomic technologies: a necessary "luxury" for better global public health?

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    Williams-Jones Bryn

    2011-08-01

    Full Text Available Abstract Background Pharmacogenomic technologies aim to redirect drug development to increase safety and efficacy of individual care. There is much hope that their implementation in the drug development process will help respond to population health needs, particularly in developing countries. However, there is also fear that novel pharmacogenomic drugs will remain too costly, be designed for the needs of the wealthy nations, and so constitute an unnecessary "luxury" for most populations. In this paper, we analyse the promise that pharmacogenomic technologies hold for improving global public health and identify strategies and challenges associated with their implementation. Discussion This paper evaluates the capacity of pharmacogenomic technologies to meet six criteria described by the University of Toronto Joint Centre for Bioethics group: 1 impact of the technology, 2 technology appropriateness, 3 capacity to address local burdens, 4 feasibility to be implemented in reasonable time, 5 capacity to reduce the knowledge gap, and 6 capacity for indirect benefits. We argue that the implementation of pharmacogenomic technologies in the drug development process can positively impact population health. However, this positive impact depends on how and for which purposes the technologies are used. We discuss the potential of these technologies to stimulate drug discovery in the case of rare (orphan diseases or neglected diseases, but also to reduce acute adverse drug reactions in infectious disease treatment and prevention, which promises to improve global public health. Conclusions The implementation of pharmacogenomic technologies may lead to the development of drugs that appear to be a "luxury" for populations in need of numerous interventions that are known to have a demonstrable impact on population health (e.g., secure access to potable water, reduction of social inequities, health education. However, our analysis shows that pharmacogenomic

  11. The role of ADME pharmacogenomics in early clinical trials: perspective of the Industry Pharmacogenomics Working Group (I-PWG).

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    Tremaine, Larry; Brian, William; DelMonte, Terrye; Francke, Stephan; Groenen, Peter; Johnson, Keith; Li, Lei; Pearson, Kimberly; Marshall, Jean-Claude

    2015-12-01

    Genetic polymorphisms in metabolizing enzymes and drug transporters have been shown to significantly impact the exposure of drugs having a high dependence on a single mechanism for their absorption, distribution or clearance, such that genotyping can lead to actionable steps in disease treatment. Recently, global regulatory agencies have provided guidance for assessment of pharmacogenomics during early stages of drug development, both in the form of formal guidance and perspectives published in scientific journals. The Industry Pharmacogenomics Working Group (I-PWG), conducted a survey among member companies to assess the practices relating to absorption, distribution, metabolism, excretion pharmacogenomics) during early stages of clinical development, to assess the impact of the recent Regulatory Guidance issued by the US FDA and EMA on Industry practices.

  12. Tailoring therapy for heart failure: the pharmacogenomics of adrenergic receptor signaling

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    Femminella GD

    2014-09-01

    Full Text Available Grazia Daniela Femminella,1 Vincenzo Barrese,2,3 Nicola Ferrara,1,4 Giuseppe Rengo4 1Department of Translational Medical Sciences, Federico II University, Naples, Italy; 2Department of Neuroscience, Reproductive Science and Odontostomatology, Federico II University, Naples, Italy; 3Division of Biomedical Sciences, St George’s University of London, London, UK; 4”Salvatore Maugeri” Foundation – IRCCS – Scientific Institute of Telese Terme, Telese Terme, Benevento, Italy Abstract: Heart failure is one of the leading causes of mortality in Western countries, and β-blockers are a cornerstone of its treatment. However, the response to these drugs is variable among individuals, which might be explained, at least in part, by genetic differences. Pharmacogenomics is the study of genetic contributions to drug response variability in order to provide evidence for a tailored therapy in an individual patient. Several studies have investigated the pharmacogenomics of the adrenergic receptor system and its role in the context of the use of β-blockers in treating heart failure. In this review, we will focus on the most significant polymorphisms described in the literature involving adrenergic receptors and adrenergic receptor-related proteins, as well as genetic variations influencing β-blocker metabolism. Keywords: adrenergic system, polymorphisms, β-blockers, functional recovery

  13. Pharmacogenomics of Drug Response in Type 2 Diabetes: Toward the Definition of Tailored Therapies?

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    Carla Pollastro

    2015-01-01

    Full Text Available Type 2 diabetes is one of the major causes of mortality with rapidly increasing prevalence. Pharmacological treatment is the first recommended approach after failure in lifestyle changes. However, a significant number of patients shows—or develops along time and disease progression—drug resistance. In addition, not all type 2 diabetic patients have the same responsiveness to drug treatment. Despite the presence of nongenetic factors (hepatic, renal, and intestinal, most of such variability is due to genetic causes. Pharmacogenomics studies have described association between single nucleotide variations and drug resistance, even though there are still conflicting results. To date, the most reliable approach to investigate allelic variants is Next-Generation Sequencing that allows the simultaneous analysis, on a genome-wide scale, of nucleotide variants and gene expression. Here, we review the relationship between drug responsiveness and polymorphisms in genes involved in drug metabolism (CYP2C9 and insulin signaling (ABCC8, KCNJ11, and PPARG. We also highlight the advancements in sequencing technologies that to date enable researchers to perform comprehensive pharmacogenomics studies. The identification of allelic variants associated with drug resistance will constitute a solid basis to establish tailored therapeutic approaches in the treatment of type 2 diabetes.

  14. Genome Architecture and Its Roles in Human Copy Number Variation

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    Lu Chen

    2014-12-01

    Full Text Available Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs, are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.

  15. Pharmacogenomics and Herb-Drug Interactions: Merge of Future and Tradition

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    Mou-Ze Liu

    2015-01-01

    Full Text Available The worldwide using of herb products and the increasing potential herb-drug interaction issue has raised enthusiasm on discovering the underlying mechanisms. Previous review indicated that the interactions may be mediated by metabolism enzymes and transporters in pharmacokinetic pathways. On the other hand, an increasing number of studies found that genetic variations showed some influence on herb-drug interaction effects whereas these genetic factors did not draw much attention in history. We highlight that pharmacogenomics may involve the pharmacokinetic or pharmacodynamic pathways to affect herb-drug interaction. We are here to make an updated review focused on some common herb-drug interactions in association with genetic variations, with the aim to help safe use of herbal medicines in different individuals in the clinic.

  16. Human feeding biomechanics: performance, variation, and functional constraints

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    Justin A. Ledogar

    2016-07-01

    Full Text Available The evolution of the modern human (Homo sapiens cranium is characterized by a reduction in the size of the feeding system, including reductions in the size of the facial skeleton, postcanine teeth, and the muscles involved in biting and chewing. The conventional view hypothesizes that gracilization of the human feeding system is related to a shift toward eating foods that were less mechanically challenging to consume and/or foods that were processed using tools before being ingested. This hypothesis predicts that human feeding systems should not be well-configured to produce forceful bites and that the cranium should be structurally weak. An alternate hypothesis, based on the observation that humans have mechanically efficient jaw adductors, states that the modern human face is adapted to generate and withstand high biting forces. We used finite element analysis (FEA to test two opposing mechanical hypotheses: that compared to our closest living relative, chimpanzees (Pan troglodytes, the modern human craniofacial skeleton is (1 less well configured, or (2 better configured to generate and withstand high magnitude bite forces. We considered intraspecific variation in our examination of human feeding biomechanics by examining a sample of geographically diverse crania that differed notably in shape. We found that our biomechanical models of human crania had broadly similar mechanical behavior despite their shape variation and were, on average, less structurally stiff than the crania of chimpanzees during unilateral biting when loaded with physiologically-scaled muscle loads. Our results also show that modern humans are efficient producers of bite force, consistent with previous analyses. However, highly tensile reaction forces were generated at the working (biting side jaw joint during unilateral molar bites in which the chewing muscles were recruited with bilateral symmetry. In life, such a configuration would have increased the risk of joint

  17. Pharmacogenomics and Global Precision Medicine in the Context of Adverse Drug Reactions: Top 10 Opportunities and Challenges for the Next Decade.

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    Alessandrini, Marco; Chaudhry, Mamoonah; Dodgen, Tyren M; Pepper, Michael S

    2016-10-01

    In a move indicative of the enthusiastic support of precision medicine, the U.S. President Barack Obama announced the Precision Medicine Initiative in January 2015. The global precision medicine ecosystem is, thus, receiving generous support from the United States ($215 million), and numerous other governments have followed suit. In the context of precision medicine, drug treatment and prediction of its outcomes have been important for nearly six decades in the field of pharmacogenomics. The field offers an elegant solution for minimizing the effects and occurrence of adverse drug reactions (ADRs). The Clinical Pharmacogenetics Implementation Consortium (CPIC) plays an important role in this context, and it aims at specifically guiding the translation of clinically relevant and evidence-based pharmacogenomics research. In this forward-looking analysis, we make particular reference to several of the CPIC guidelines and their role in guiding the treatment of highly relevant diseases, namely cardiovascular disease, major depressive disorder, cancer, and human immunodeficiency virus, with a view to predicting and managing ADRs. In addition, we provide a list of the top 10 crosscutting opportunities and challenges facing the fields of precision medicine and pharmacogenomics, which have broad applicability independent of the drug class involved. Many of these opportunities and challenges pertain to infrastructure, study design, policy, and science culture in the early 21st century. Ultimately, rational pharmacogenomics study design and the acquisition of comprehensive phenotypic data that proportionately match the genomics data should be an imperative as we move forward toward global precision medicine.

  18. Pharmacogenomics and Global Precision Medicine in the Context of Adverse Drug Reactions: Top 10 Opportunities and Challenges for the Next Decade

    Science.gov (United States)

    Alessandrini, Marco; Chaudhry, Mamoonah; Dodgen, Tyren M.

    2016-01-01

    Abstract In a move indicative of the enthusiastic support of precision medicine, the U.S. President Barack Obama announced the Precision Medicine Initiative in January 2015. The global precision medicine ecosystem is, thus, receiving generous support from the United States ($215 million), and numerous other governments have followed suit. In the context of precision medicine, drug treatment and prediction of its outcomes have been important for nearly six decades in the field of pharmacogenomics. The field offers an elegant solution for minimizing the effects and occurrence of adverse drug reactions (ADRs). The Clinical Pharmacogenetics Implementation Consortium (CPIC) plays an important role in this context, and it aims at specifically guiding the translation of clinically relevant and evidence-based pharmacogenomics research. In this forward-looking analysis, we make particular reference to several of the CPIC guidelines and their role in guiding the treatment of highly relevant diseases, namely cardiovascular disease, major depressive disorder, cancer, and human immunodeficiency virus, with a view to predicting and managing ADRs. In addition, we provide a list of the top 10 crosscutting opportunities and challenges facing the fields of precision medicine and pharmacogenomics, which have broad applicability independent of the drug class involved. Many of these opportunities and challenges pertain to infrastructure, study design, policy, and science culture in the early 21st century. Ultimately, rational pharmacogenomics study design and the acquisition of comprehensive phenotypic data that proportionately match the genomics data should be an imperative as we move forward toward global precision medicine. PMID:27643672

  19. Patterns of cis regulatory variation in diverse human populations.

    Directory of Open Access Journals (Sweden)

    Barbara E Stranger

    Full Text Available The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for

  20. Patterns of cis regulatory variation in diverse human populations.

    Directory of Open Access Journals (Sweden)

    Barbara E Stranger

    Full Text Available The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for

  1. Pharmacogenomics genes show varying perceptibility to microRNA regulation

    DEFF Research Database (Denmark)

    Rukov, Jakob Lewin; Vinther, Jeppe; Shomron, Noam

    2011-01-01

    The aim of pharmacogenomics is to identify individual differences in genome and transcriptome composition and their effect on drug efficacy. MicroRNAs (miRNAs) are short noncoding RNAs that negatively regulate expression of the majority of animal genes, including many genes involved in drug...

  2. Biotechnology, nanotechnology, and pharmacogenomics and pharmaceutical compounding, Part 1.

    Science.gov (United States)

    Allen, Loyd V

    2015-01-01

    The world of pharmaceuticals is changing rapidly as biotechnology continues to grow and nanotechnology appears on the horizon. Biotechnology is gaining in importance in extemporaneous pharmaceutical compounding, and nanotechnology and pharmacogenomics could drastically change the practice of pharmacy. This article discusses biotechnology and the factors to consider when compounding biotechnology drugs.

  3. Pharmacy benefit managers, pharmacies, and pharmacogenomic testing: prescription for progress?

    Science.gov (United States)

    Topol, Eric J

    2010-08-11

    Few would argue that the ability to match individual patients with the safest and most effective drugs and doses would be a major advance for clinical medicine. But while clinicians have been reluctant to routinely use pharmacogenomic analyses to guide their prescribing practices, pharmacy benefit managers and drugstores are proceeding with major pharmacogenetic initiatives.

  4. Early HTA in pharmacogenomics : A case example in cardiovascular drugs

    NARCIS (Netherlands)

    Geenen, J.W.; Baranova, E.V.|info:eu-repo/dai/nl/371570697; Asselbergs, F.W.; De Boer, A.|info:eu-repo/dai/nl/075097346; Maitland-van der Zee, A.|info:eu-repo/dai/nl/255164688; Hövels, Anke|info:eu-repo/dai/nl/310470382

    2016-01-01

    Objectives: ACE inhibitors (ACEi) are commonly used cardiovascular drugs. These drugs can cause the severe and possibly lethal adverse drug reaction (ADR) angioedema in a very small part (0.2%) of the patients. A pharmacogenomic test could be used to identify patients at risk for this severe ADR and

  5. Generating Genome-Scale Candidate Gene Lists for Pharmacogenomics

    DEFF Research Database (Denmark)

    Hansen, Niclas Tue; Brunak, Søren; Altman, R. B.

    2009-01-01

    A critical task in pharmacogenomics is identifying genes that may be important modulators of drug response. High-throughput experimental methods are often plagued by false positives and do not take advantage of existing knowledge. Candidate gene lists can usefully summarize existing knowledge...

  6. The Outlier in All of Us: Why Implementing Pharmacogenomics Could Matter for Everyone.

    Science.gov (United States)

    O'Donnell, P H; Danahey, K; Ratain, M J

    2016-04-01

    The field of pharmacogenomics originally emerged in the 1950s from observations that a few rare individuals had unexpected, severe reactions to drugs. As recently as just 6 years ago, prominent views on the subject had largely remained unchanged, with authors from the US Food and Drug Administration (FDA) citing the purpose of pharmacogenetics as "tailoring treatment for the outliers." It should not be surprising if this is the prevailing view--the best-studied pharmacogenomic drug examples are indeed just that, genetic explanations of extreme responses or susceptibilities among usually a very small fraction of the human population. Thiopurine methyltransferase (TPMT) deficiency as a cause of severe myelosuppression upon treatment with azathioprine or mercaptopurine is found as a heterozygous trait in only ∼ 10% of patients, and homozygous (deficiency) carriers are even more rare--occurring in fewer than 1 in 300 patients. Malignant hyperthermia resulting from inhaled anesthetics and succinylcholine is believed to have a genetic incidence of only about 1 in 2000 people.

  7. Genetic Polymorphisms Analysis of Pharmacogenomic VIP Variants in Miao Ethnic Group of Southwest China.

    Science.gov (United States)

    Jin, Tianbo; Aikemu, Ainiwaer; Zhang, Mingxi; Geng, Tingting; Feng, Tian; Kang, Longli; Luo, Man Lin

    2015-12-03

    BACKGROUND Genetic polymorphisms have a potential clinical role in determining both inter-individual and inter-ethnic differences in drug efficacy, but we have not found any pharmacogenomics information regarding minorities, such as the Miao ethnic group. Our study aimed to screen numbers of the Miao ethnic group for genotype frequencies of VIP variants and to determine differences between the Miao and other human populations worldwide. MATERIAL AND METHODS In this study, we genotyped 66 Very Important Pharmacogene (VIP) variants selected from PharmGKB in 98 unrelated, healthy Miao individuals from the Guizhou province and compared our data with 12 other populations, including 11 populations from the HapMap data set and Xi'an Han Chinese. RESULTS Using the χ2 test, we found that the allele frequencies of the VDR rs1544410 and VKORC1 (rs9934438) variants in the Miao population are quite different from that in other ethnic groups. Furthermore, we found that genotype frequencies of rs1801133 (MTHFR) in the 13 selected populations are significantly different. Population structure and F-statistics (Fst) analysis show that the genetic background of the Miao is relatively close to that of Chinese in metropolitan Denver, CO, USA (CHD). CONCLUSIONS Our results help complete the information provided by the pharmacogenomics database of the Miao ethnic group and provide a theoretical basis for safer drug administration, which may be useful for diagnosing and treating diseases in this population.

  8. 应用细胞系模型研究药物基因组学的进展%Progress in the research of pharmacogenomics by cell line models

    Institute of Scientific and Technical Information of China (English)

    王庚; 孟祥宁; 白静; 傅松滨

    2012-01-01

    With the completion of Human Genome Project,pharmacogenomics has become one of the fastest growing disciplines in the post-genomic era.Previously,identification of the genetic contribution to drug response typically comes from clinical observations and use of classic genetic tools.Recent progress in dissecting genetic contribution to natural variation in drug chemosensitivity through the use of cell line models has been the focus of this review.And we also compare the advantages and disadvantages between clinical cases and cell line models.We hope to discuss whether cell line models can provide new insights into the human genome and have applicability to pharmacogenomics studies leading to individualized treatment.%随着人类基因组计划的完成,药物基因组学逐渐成为后基因组时代中发展最迅猛的学科之一.以前绝大部分药物基因组学的研究都是对临床病例数据进行分析,而近些年越来越多的研究者开始使用细胞系模型研究药物基因组学.该文拟就药物基因组学的发展与该领域中细胞系模型的使用情况及该模型与临床病例相比的优、缺点进行综述,旨在探讨细胞系模型是否可以成为药物基因组学研究的一个有效工具,并最终促进新药开发和临床个体化用药的发展.

  9. Cancer Pharmacogenomics: Integrating Discoveries in Basic, Clinical and Population Sciences to Advance Predictive Cancer Care

    Science.gov (United States)

    Cancer Pharmacogenomics: Integrating Discoveries in Basic, Clinical and Population Sciences to Advance Predictive Cancer Care, a 2010 workshop sponsored by the Epidemiology and Genomics Research Program.

  10. Pharmacogenomics and pharmacogenetics of thiazolidinediones: role in diabetes and cardiovascular risk factors

    Science.gov (United States)

    Della-Morte, David; Palmirotta, Raffaele; Rehni, Ashish K; Pastore, Donatella; Capuani, Barbara; Pacifici, Francesca; De Marchis, Maria Laura; Dave, Kunjan R; Bellia, Alfonso; Fogliame, Giuseppe; Ferroni, Patrizia; Donadel, Giulia; Cacciatore, Francesco; Abete, Pasquale; Dong, Chuanhui; Pileggi, Antonello; Roselli, Mario; Ricordi, Camillo; Sbraccia, Paolo; Guadagni, Fiorella; Rundek, Tatjana; Lauro, Davide

    2015-01-01

    The most important goal in the treatment of patients with diabetes is to prevent the risk of cardiovascular disease (CVD), the first cause of mortality in these subjects. Thiazolidinediones (TZDs), a class of antidiabetic drugs, act as insulin sensitizers increasing insulin-dependent glucose disposal and reducing hepatic glucose output. TZDs including pioglitazone, rosiglitazone and troglitazone, by activating PPAR-γ have shown pleiotropic effects in reducing vascular risk factors and atherosclerosis. However, troglitazone was removed from the market due to its hepatoxicity, and rosiglitazone and pioglitazone both have particular warnings due to being associated with heart diseases. Specific genetic variations in genes involved in the pathways regulated by TDZs have demonstrated to modify the variability in treatment with these drugs, especially in their side effects. Therefore, pharmacogenomics and pharmacogenetics are an important tool in further understand intersubject variability per se but also to assess the therapeutic potential of such variability in drug individualization and therapeutic optimization. PMID:25521362

  11. Pharmacogenomics and pharmacogenetics of thiazolidinediones: role in diabetes and cardiovascular risk factors.

    Science.gov (United States)

    Della-Morte, David; Palmirotta, Raffaele; Rehni, Ashish K; Pastore, Donatella; Capuani, Barbara; Pacifici, Francesca; De Marchis, Maria Laura; Dave, Kunjan R; Bellia, Alfonso; Fogliame, Giuseppe; Ferroni, Patrizia; Donadel, Giulia; Cacciatore, Francesco; Abete, Pasquale; Dong, Chuanhui; Pileggi, Antonello; Roselli, Mario; Ricordi, Camillo; Sbraccia, Paolo; Guadagni, Fiorella; Rundek, Tatjana; Lauro, Davide

    2014-12-01

    The most important goal in the treatment of patients with diabetes is to prevent the risk of cardiovascular disease (CVD), the first cause of mortality in these subjects. Thiazolidinediones (TZDs), a class of antidiabetic drugs, act as insulin sensitizers increasing insulin-dependent glucose disposal and reducing hepatic glucose output. TZDs including pioglitazone, rosiglitazone and troglitazone, by activating PPAR-γ have shown pleiotropic effects in reducing vascular risk factors and atherosclerosis. However, troglitazone was removed from the market due to its hepatoxicity, and rosiglitazone and pioglitazone both have particular warnings due to being associated with heart diseases. Specific genetic variations in genes involved in the pathways regulated by TDZs have demonstrated to modify the variability in treatment with these drugs, especially in their side effects. Therefore, pharmacogenomics and pharmacogenetics are an important tool in further understand intersubject variability per se but also to assess the therapeutic potential of such variability in drug individualization and therapeutic optimization.

  12. Seasonal variations in physical activity and implications for human health.

    Science.gov (United States)

    Shephard, Roy J; Aoyagi, Yukitoshi

    2009-10-01

    This review explores the implications of seasonal changes in physical activity for fitness and human health. Photosensitivity and nutrient shortages mediate animal hibernation via the hypothalamus and changes in leptin and ghrelin concentrations. Opportunities for hunting and crop cultivation determine seasonal activity in under-developed human societies, but in developed societies temperature and rainfall are dominant influences, usually over-riding innate rhythms. Both questionnaire data and objective measurements show that many groups from children to the elderly increase their physical activity from winter to spring or summer. Measurements of maximal oxygen intake and muscle strength commonly show parallel seasonal changes. However, potential effects upon body mass and body fat may be counteracted by changes of food intake; subsistence agriculturists sometimes maintain or increase physical activity at the expense of a decrease in body mass. In developed societies, body fat commonly increases during the winter, with parallel changes in blood lipids, blood pressure and blood coagulability; moreover, these changes are not always fully reversed the following summer. Most developed societies show increased all-cause and cardiac mortalities in the winter. Health consequences of seasonal variations in physical activity including an increased vulnerability to cardiac catastrophe and a year-by-year increase in total body fat seem most likely if the average level of physical activity for the year is low. Public health recommendations should underline the importance of maintaining physical activity during adverse environmental conditions by adapting clothing, modifying behaviour and exploiting any available air-conditioned indoor facilities.

  13. The effect of ancient population bottlenecks on human phenotypic variation.

    Science.gov (United States)

    Manica, Andrea; Amos, William; Balloux, François; Hanihara, Tsunehiko

    2007-07-19

    The origin and patterns of dispersal of anatomically modern humans are the focus of considerable debate. Global genetic analyses have argued for one single origin, placed somewhere in Africa. This scenario implies a rapid expansion, with a series of bottlenecks of small amplitude, which would have led to the observed smooth loss of genetic diversity with increasing distance from Africa. Analyses of cranial data, on the other hand, have given mixed results, and have been argued to support multiple origins of modern humans. Using a large data set of skull measurements and an analytical framework equivalent to that used for genetic data, we show that the loss in genetic diversity has been mirrored by a loss in phenotypic variability. We find evidence for an African origin, placed somewhere in the central/southern part of the continent, which harbours the highest intra-population diversity in phenotypic measurements. We failed to find evidence for a second origin, and we confirm these results on a large genetic data set. Distance from Africa accounts for an average 19-25% of heritable variation in craniometric measurements-a remarkably strong effect for phenotypic measurements known to be under selection.

  14. The pharmacogenomics of pain management: prospects for personalized medicine

    Directory of Open Access Journals (Sweden)

    Ting S

    2016-02-01

    Full Text Available Sonya Ting,1 Stephan Schug2,3 1Department of Anaesthesia, Sir Charles Gairdner Hospital, Perth, WA, Australia; 2Anaesthesiology Unit, School of Medicine and Pharmacology, University of Western Australia, Perth, WA, Australia; 3Department of Anaesthesia and Pain Medicine, Royal Perth Hospital, University of Western Australia Anaesthesiology Unit, Royal Perth Hospital, Perth, WA, Australia Abstract: Pain is a common symptom that can be complex to treat. Analgesic medications are the mainstay treatment, but there is wide interindividual variability in analgesic response and adverse effects. Pharmacogenomics is the study of inherited genetic traits that result in these individual responses to drugs. This narrative review will attempt to cover the current understanding of the pharmacogenomics of pain, examining common genes affecting metabolism of analgesic medications, their distribution throughout the body, and end organ effects. Keywords: cytochrome P450, COMT, pharmacokinetics, pharmacodynamics, inherited traits

  15. Emerging roles for pharmacists in clinical implementation of pharmacogenomics.

    Science.gov (United States)

    Owusu-Obeng, Aniwaa; Weitzel, Kristin W; Hatton, Randy C; Staley, Benjamin J; Ashton, Jennifer; Cooper-Dehoff, Rhonda M; Johnson, Julie A

    2014-10-01

    Pharmacists are uniquely qualified to play essential roles in the clinical implementation of pharmacogenomics. However, specific responsibilities and resources needed for these roles have not been defined. We describe roles for pharmacists that emerged in the clinical implementation of genotype-guided clopidogrel therapy in the University of Florida Health Personalized Medicine Program, summarize preliminary program results, and discuss education, training, and resources needed to support such programs. Planning for University of Florida Health Personalized Medicine Program began in summer 2011 under leadership of a pharmacist, with clinical launch in June 2012 of a clopidogrel-CYP2C19 pilot project aimed at tailoring antiplatelet therapies for patients undergoing percutaneous coronary intervention and stent placement. More than 1000 patients were genotyped in the pilot project in year 1. Essential pharmacist roles and responsibilities that developed and/or emerged required expertise in pharmacy informatics (development of clinical decision support in the electronic medical record), medication safety, medication-use policies and processes, development of group and individual educational strategies, literature analysis, drug information, database management, patient care in targeted areas, logistical issues in genetic testing and follow-up, research and ethical issues, and clinical precepting. In the first 2 years of the program (1 year planning and 1 year postimplementation), a total of 14 different pharmacists were directly and indirectly involved, with effort levels ranging from a few hours per month, to 25-30% effort for the director and associate director, to nearly full-time for residents. Clinical pharmacists are well positioned to implement clinical pharmacogenomics programs, with expertise in pharmacokinetics, pharmacogenomics, informatics, and patient care. Education, training, and practice-based resources are needed to support these roles and to

  16. Pharmacogenomics: the inherited basis for interindividual differences in drug response.

    Science.gov (United States)

    Evans, W E; Johnson, J A

    2001-01-01

    It is well recognized that most medications exhibit wide interpatient variability in their efficacy and toxicity. For many medications, these interindividual differences are due in part to polymorphisms in genes encoding drug metabolizing enzymes, drug transporters, and/or drug targets (e.g., receptors, enzymes). Pharmacogenomics is a burgeoning field aimed at elucidating the genetic basis for differences in drug efficacy and toxicity, and it uses genome-wide approaches to identify the network of genes that govern an individual's response to drug therapy. For some genetic polymorphisms (e.g., thiopurine S-methyltransferase), monogenic traits have a marked effect on pharmacokinetics (e.g., drug metabolism), such that individuals who inherit an enzyme deficiency must be treated with markedly different doses of the affected medications (e.g., 5%-10% of the standard thiopurine dose). Likewise, polymorphisms in drug targets (e.g., beta adrenergic receptor) can alter the sensitivity of patients to treatment (e.g., beta-agonists), changing the pharmacodynamics of drug response. Recognizing that most drug effects are determined by the interplay of several gene products that govern the pharmacokinetics and pharmacodynamics of medications, pharmacogenomics research aims to elucidate these polygenic determinants of drug effects. The ultimate goal is to provide new strategies for optimizing drug therapy based on each patient's genetic determinants of drug efficacy and toxicity. This chapter provides an overview of the current pharmacogenomics literature and offers insights for the potential impact of this field on the safe and effective use of medications.

  17. Warfarin pharmacogenomics: recommendations with available patented clinical technologies.

    Science.gov (United States)

    Borkowski, Andrew A; Kardani, Avni; Mastorides, Stephen M; Thomas, L Brannon

    2014-01-01

    Warfarin pharmacogenomic testing has become a prime example of the utility of personalized molecular testing in the modern clinical laboratory. Warfarin is a commonly used drug for the prevention and treatment of thromboembolic complications in a variety of clinical situations. However, a number of factors lead to a high interindividual variability in dose requirements. Among the primary factors in this variability are genetic polymorphisms in general patient populations, which can account for 35-50% of varying dose requirements among patients. In this review, we discuss the implications of polymorphisms in the cytochrome P-450 enzyme 2C9 (CYP2C9) and Vitamin K Epoxide Reductase Enzyme Complex subunit 1 (VKORC1) as they relate to therapeutic warfarin dosing. We discuss the clinical utility of pharmacogenomics testing as related to warfarin dosing, and propose a clinical model for the implementation of the pharmacogenomic test results. Finally, we provide a brief overview of the currently available commercial testing platforms with discussion of the complexities of utilizing patented methodologies in bringing genetic testing such as this to the clinical laboratory.

  18. Using clinical element models for pharmacogenomic study data standardization.

    Science.gov (United States)

    Zhu, Qian; Freimuth, Robert R; Pathak, Jyotishman; Chute, Christopher G

    2013-01-01

    Standardized representations for pharmacogenomics data are seldom used, which leads to data heterogeneity and hinders data reuse and integration. In this study, we attempted to represent data elements from the Pharmacogenomics Research Network (PGRN) that are related to four categories, patient, drug, disease and laboratory, in a standard way using Clinical Element Models (CEMs), which have been adopted in the Strategic Health IT Advanced Research Project, secondary use of EHR (SHARPn) as a library of common logical models that facilitate consistent data representation, interpretation, and exchange within and across heterogeneous sources and applications. This was accomplished by grouping PGRN data elements into categories based on UMLS semantic type, then mapping each to one or more CEM attributes using a web-based tool that was developed to support curation activities. This study demonstrates the successful application of SHARPn CEMs to the pharmacogenomic domain. It also identified several categories of data elements that are not currently supported by SHARPn CEMs, which represent opportunities for further development and collaboration.

  19. Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis

    DEFF Research Database (Denmark)

    Zielinski, Daniel C.; Filipp, F. V.; Bordbar, A.

    2015-01-01

    Drug side effects cause a significant clinical and economic burden. However, mechanisms of drug action underlying side effect pathogenesis remain largely unknown. Here, we integrate pharmacogenomic and clinical data with a human metabolic network and find that non-pharmacokinetic metabolic pathways...... dysregulated by drugs are linked to the development of side effects. We show such dysregulated metabolic pathways contain genes with sequence variants affecting side effect incidence, play established roles in pathophysiology, have significantly altered activity in corresponding diseases, are susceptible...... to metabolic inhibitors and are effective targets for therapeutic nutrient supplementation. Our results indicate that metabolic dysregulation represents a common mechanism underlying side effect pathogenesis that is distinct from the role of metabolism in drug clearance. We suggest that elucidating...

  20. Clinical practice guidelines for translating pharmacogenomic knowledge to bedside. Focus on anticancer drugs.

    Directory of Open Access Journals (Sweden)

    José A G Agúndez

    2014-08-01

    Full Text Available The development of clinical practice recommendations or guidelines for the clinical use of pharmacogenomics data is an essential issue for improving drug therapy, particularly for drugs with high toxicity and/or narrow therapeutic index such as anticancer drugs. Although pharmacogenomic-based recommendations have been formulated for over 40 anticancer drugs, the number of clinical practice guidelines available is very low. The guidelines already published indicate that pharmacogenomic testing is useful for patient selection, but final dosing adjustment should be carried out on the basis of clinical or analytical parameters rather than on pharmacogenomic information.Patient selection may seem a modest objective, but it constitutes a crucial improvement with regard to the pre-pharmacogenomics situation and it saves patients’ lives. However we should not overstate the current power of pharmacogenomics. At present the pharmacogenomics of anticancer drugs is not sufficiently developed for dose adjustments based on pharmacogenomics only, and no current guidelines recommend such adjustments without considering clinical and/or analytical parameters.

  1. Fast and frugal trees: Translating population-based pharmacogenomics to medication prioritization

    NARCIS (Netherlands)

    Rooij, T. van; Roederer, M.; Wareham, H.T.; Rooij, I.J.E.I. van; McLeod, H.L.; Marsh, S.

    2015-01-01

    Aim: Fast and frugal decision trees (FFTs) can simplify clinical decision making by providing a heuristic approach to contextual guidance. We wanted to use FFTs for pharmacogenomic knowledge translation at point-of-care. Materials & Methods: The Pharmacogenomics for Every Nation Initiative (PGENI),

  2. Pharmacogenomic Biomarkers: an FDA Perspective on Utilization in Biological Product Labeling.

    Science.gov (United States)

    Schuck, Robert N; Grillo, Joseph A

    2016-05-01

    Precision medicine promises to improve both the efficacy and safety of therapeutic products by better informing why some patients respond well to a drug, and some experience adverse reactions, while others do not. Pharmacogenomics is a key component of precision medicine and can be utilized to select optimal doses for patients, more precisely identify individuals who will respond to a treatment and avoid serious drug-related toxicities. Since pharmacogenomic biomarker information can help inform drug dosing, efficacy, and safety, pharmacogenomic data are critically reviewed by FDA staff to ensure effective use of pharmacogenomic strategies in drug development and appropriate incorporation into product labels. Pharmacogenomic information may be provided in drug or biological product labeling to inform health care providers about the impact of genotype on response to a drug through description of relevant genomic markers, functional effects of genomic variants, dosing recommendations based on genotype, and other applicable genomic information. The format and content of labeling for biologic drugs will generally follow that of small molecule drugs; however, there are notable differences in pharmacogenomic information that might be considered useful for biologic drugs in comparison to small molecule drugs. Furthermore, the rapid entry of biologic drugs for treatment of rare genetic diseases and molecularly defined subsets of common diseases will likely lead to increased use of pharmacogenomic information in biologic drug labels in the near future. In this review, we outline the general principles of therapeutic product labeling and discuss the utilization of pharmacogenomic information in biologic drug labels.

  3. Analysis of pharmacogenomic variants associated with population differentiation.

    Directory of Open Access Journals (Sweden)

    Bora Yeon

    Full Text Available In the present study, we systematically investigated population differentiation of drug-related (DR genes in order to identify common genetic features underlying population-specific responses to drugs. To do so, we used the International HapMap project release 27 Data and Pharmacogenomics Knowledge Base (PharmGKB database. First, we compared four measures for assessing population differentiation: the chi-square test, the analysis of variance (ANOVA F-test, Fst, and Nearest Shrunken Centroid Method (NSCM. Fst showed high sensitivity with stable specificity among varying sample sizes; thus, we selected Fst for determining population differentiation. Second, we divided DR genes from PharmGKB into two groups based on the degree of population differentiation as assessed by Fst: genes with a high level of differentiation (HD gene group and genes with a low level of differentiation (LD gene group. Last, we conducted a gene ontology (GO analysis and pathway analysis. Using all genes in the human genome as the background, the GO analysis and pathway analysis of the HD genes identified terms related to cell communication. "Cell communication" and "cell-cell signaling" had the lowest Benjamini-Hochberg's q-values (0.0002 and 0.0006, respectively, and "drug binding" was highly enriched (16.51 despite its relatively high q-value (0.0142. Among the 17 genes related to cell communication identified in the HD gene group, five genes (STX4, PPARD, DCK, GRIK4, and DRD3 contained single nucleotide polymorphisms with Fst values greater than 0.5. Specifically, the Fst values for rs10871454, rs6922548, rs3775289, rs1954787, and rs167771 were 0.682, 0.620, 0.573, 0.531, and 0.510, respectively. In the analysis using DR genes as the background, the HD gene group contained six significant terms. Five were related to reproduction, and one was "Wnt signaling pathway," which has been implicated in cancer. Our analysis suggests that the HD gene group from PharmGKB is

  4. Exploring the distribution of genetic markers of pharmacogenomics relevance in Brazilian and Mexican populations.

    Directory of Open Access Journals (Sweden)

    Vania Bonifaz-Peña

    Full Text Available Studies of pharmacogenomics-related traits are increasingly being performed to identify loci that affect either drug response or susceptibility to adverse drug reactions. However, the effect of the polymorphisms can differ in magnitude or be absent depending on the population being assessed. We used the Affymetrix Drug Metabolizing Enzymes and Transporters (DMET Plus array to characterize the distribution of polymorphisms of pharmacogenetics and pharmacogenomics (PGx relevance in two samples from the most populous Latin American countries, Brazil and Mexico. The sample from Brazil included 268 individuals from the southeastern state of Rio de Janeiro, and was stratified into census categories. The sample from Mexico comprised 45 Native American Zapotecas and 224 self-identified Mestizo individuals from 5 states located in geographically distant regions in Mexico. We evaluated the admixture proportions in the Brazilian and Mexican samples using a panel of Ancestry Informative Markers extracted from the DMET array, which was validated with genome-wide data. A substantial variation in ancestral proportions across census categories in Brazil, and geographic regions in Mexico was identified. We evaluated the extent of genetic differentiation (measured as FST values of the genetic markers of the DMET Plus array between the relevant parental populations. Although the average levels of genetic differentiation are low, there is a long tail of markers showing large frequency differences, including markers located in genes belonging to the Cytochrome P450, Solute Carrier (SLC and UDP-glucuronyltransferase (UGT families as well as other genes of PGx relevance such as ABCC8, ADH1A, CHST3, PON1, PPARD, PPARG, and VKORC1. We show how differences in admixture history may have an important impact in the distribution of allele and genotype frequencies at the population level.

  5. Exploring the Distribution of Genetic Markers of Pharmacogenomics Relevance in Brazilian and Mexican Populations

    Science.gov (United States)

    Bonifaz-Peña, Vania; Contreras, Alejandra V.; Struchiner, Claudio Jose; Roela, Rosimeire A.; Furuya-Mazzotti, Tatiane K.; Chammas, Roger; Rangel-Escareño, Claudia; Uribe-Figueroa, Laura; Gómez-Vázquez, María José; McLeod, Howard L.; Hidalgo-Miranda, Alfredo

    2014-01-01

    Studies of pharmacogenomics-related traits are increasingly being performed to identify loci that affect either drug response or susceptibility to adverse drug reactions. However, the effect of the polymorphisms can differ in magnitude or be absent depending on the population being assessed. We used the Affymetrix Drug Metabolizing Enzymes and Transporters (DMET) Plus array to characterize the distribution of polymorphisms of pharmacogenetics and pharmacogenomics (PGx) relevance in two samples from the most populous Latin American countries, Brazil and Mexico. The sample from Brazil included 268 individuals from the southeastern state of Rio de Janeiro, and was stratified into census categories. The sample from Mexico comprised 45 Native American Zapotecas and 224 self-identified Mestizo individuals from 5 states located in geographically distant regions in Mexico. We evaluated the admixture proportions in the Brazilian and Mexican samples using a panel of Ancestry Informative Markers extracted from the DMET array, which was validated with genome-wide data. A substantial variation in ancestral proportions across census categories in Brazil, and geographic regions in Mexico was identified. We evaluated the extent of genetic differentiation (measured as FST values) of the genetic markers of the DMET Plus array between the relevant parental populations. Although the average levels of genetic differentiation are low, there is a long tail of markers showing large frequency differences, including markers located in genes belonging to the Cytochrome P450, Solute Carrier (SLC) and UDP-glucuronyltransferase (UGT) families as well as other genes of PGx relevance such as ABCC8, ADH1A, CHST3, PON1, PPARD, PPARG, and VKORC1. We show how differences in admixture history may have an important impact in the distribution of allele and genotype frequencies at the population level. PMID:25419701

  6. Genome-environment interactions and prospective technology assessment: evolution from pharmacogenomics to nutrigenomics and ecogenomics.

    Science.gov (United States)

    Ozdemir, Vural; Motulsky, Arno G; Kolker, Eugene; Godard, Béatrice

    2009-02-01

    The relationships between food, nutrition science, and health outcomes have been mapped over the past century. Genomic variation among individuals and populations is a new factor that enriches and challenges our understanding of these complex relationships. Hence, the confluence of nutritional science and genomics-nutrigenomics--was the focus of the OMICS: A Journal of Integrative Biology in December 2008 (Part 1). The 2009 Special Issue (Part 2) concludes the analysis of nutrigenomics research and innovations. Together, these two issues expand the scope and depth of critical scholarship in nutrigenomics, in keeping with an integrated multidisciplinary analysis across the bioscience, omics technology, social, ethical, intellectual property and policy dimensions. Historically, the field of pharmacogenetics provided the first examples of specifically identifiable gene variants predisposing to unexpected responses to drugs since the 1950s. Brewer coined the term ecogenetics in 1971 to broaden the concept of gene-environment interactions from drugs and nutrition to include environmental agents in general. In the mid-1990s, introduction of high-throughput technologies led to the terms pharmacogenomics, nutrigenomics and ecogenomics to describe, respectively, the contribution of genomic variability to differential responses to drugs, food, and environment defined in the broadest sense. The distinctions, if any, between these newer fields (e.g., nutrigenomics) and their predecessors (e.g., nutrigenetics) remain to be delineated. For nutrigenomics, its reliance on genome-wide analyses may lead to detection of new biological mechanisms governing host response to food. Recognizing "genome-environment interactions" as the conceptual thread that connects and runs through pharmacogenomics, nutrigenomics, and ecogenomics may contribute toward anticipatory governance and prospective real-time analysis of these omics fields. Such real-time analysis of omics technologies and

  7. Exploring the distribution of genetic markers of pharmacogenomics relevance in Brazilian and Mexican populations.

    Science.gov (United States)

    Bonifaz-Peña, Vania; Contreras, Alejandra V; Struchiner, Claudio Jose; Roela, Rosimeire A; Furuya-Mazzotti, Tatiane K; Chammas, Roger; Rangel-Escareño, Claudia; Uribe-Figueroa, Laura; Gómez-Vázquez, María José; McLeod, Howard L; Hidalgo-Miranda, Alfredo; Parra, Esteban J; Fernández-López, Juan Carlos; Suarez-Kurtz, Guilherme

    2014-01-01

    Studies of pharmacogenomics-related traits are increasingly being performed to identify loci that affect either drug response or susceptibility to adverse drug reactions. However, the effect of the polymorphisms can differ in magnitude or be absent depending on the population being assessed. We used the Affymetrix Drug Metabolizing Enzymes and Transporters (DMET) Plus array to characterize the distribution of polymorphisms of pharmacogenetics and pharmacogenomics (PGx) relevance in two samples from the most populous Latin American countries, Brazil and Mexico. The sample from Brazil included 268 individuals from the southeastern state of Rio de Janeiro, and was stratified into census categories. The sample from Mexico comprised 45 Native American Zapotecas and 224 self-identified Mestizo individuals from 5 states located in geographically distant regions in Mexico. We evaluated the admixture proportions in the Brazilian and Mexican samples using a panel of Ancestry Informative Markers extracted from the DMET array, which was validated with genome-wide data. A substantial variation in ancestral proportions across census categories in Brazil, and geographic regions in Mexico was identified. We evaluated the extent of genetic differentiation (measured as FST values) of the genetic markers of the DMET Plus array between the relevant parental populations. Although the average levels of genetic differentiation are low, there is a long tail of markers showing large frequency differences, including markers located in genes belonging to the Cytochrome P450, Solute Carrier (SLC) and UDP-glucuronyltransferase (UGT) families as well as other genes of PGx relevance such as ABCC8, ADH1A, CHST3, PON1, PPARD, PPARG, and VKORC1. We show how differences in admixture history may have an important impact in the distribution of allele and genotype frequencies at the population level.

  8. Mine, yours, ours? Sharing data on human genetic variation.

    Directory of Open Access Journals (Sweden)

    Nicola Milia

    Full Text Available The achievement of a robust, effective and responsible form of data sharing is currently regarded as a priority for biological and bio-medical research. Empirical evaluations of data sharing may be regarded as an indispensable first step in the identification of critical aspects and the development of strategies aimed at increasing availability of research data for the scientific community as a whole. Research concerning human genetic variation represents a potential forerunner in the establishment of widespread sharing of primary datasets. However, no specific analysis has been conducted to date in order to ascertain whether the sharing of primary datasets is common-practice in this research field. To this aim, we analyzed a total of 543 mitochondrial and Y chromosomal datasets reported in 508 papers indexed in the Pubmed database from 2008 to 2011. A substantial portion of datasets (21.9% was found to have been withheld, while neither strong editorial policies nor high impact factor proved to be effective in increasing the sharing rate beyond the current figure of 80.5%. Disaggregating datasets for research fields, we could observe a substantially lower sharing in medical than evolutionary and forensic genetics, more evident for whole mtDNA sequences (15.0% vs 99.6%. The low rate of positive responses to e-mail requests sent to corresponding authors of withheld datasets (28.6% suggests that sharing should be regarded as a prerequisite for final paper acceptance, while making authors deposit their results in open online databases which provide data quality control seems to provide the best-practice standard. Finally, we estimated that 29.8% to 32.9% of total resources are used to generate withheld datasets, implying that an important portion of research funding does not produce shared knowledge. By making the scientific community and the public aware of this important aspect, we may help popularize a more effective culture of data sharing.

  9. Mine, Yours, Ours? Sharing Data on Human Genetic Variation

    Science.gov (United States)

    Montinaro, Francesco; Capocasa, Marco; Sanna, Emanuele; Bisol, Giovanni Destro

    2012-01-01

    The achievement of a robust, effective and responsible form of data sharing is currently regarded as a priority for biological and bio-medical research. Empirical evaluations of data sharing may be regarded as an indispensable first step in the identification of critical aspects and the development of strategies aimed at increasing availability of research data for the scientific community as a whole. Research concerning human genetic variation represents a potential forerunner in the establishment of widespread sharing of primary datasets. However, no specific analysis has been conducted to date in order to ascertain whether the sharing of primary datasets is common-practice in this research field. To this aim, we analyzed a total of 543 mitochondrial and Y chromosomal datasets reported in 508 papers indexed in the Pubmed database from 2008 to 2011. A substantial portion of datasets (21.9%) was found to have been withheld, while neither strong editorial policies nor high impact factor proved to be effective in increasing the sharing rate beyond the current figure of 80.5%. Disaggregating datasets for research fields, we could observe a substantially lower sharing in medical than evolutionary and forensic genetics, more evident for whole mtDNA sequences (15.0% vs 99.6%). The low rate of positive responses to e-mail requests sent to corresponding authors of withheld datasets (28.6%) suggests that sharing should be regarded as a prerequisite for final paper acceptance, while making authors deposit their results in open online databases which provide data quality control seems to provide the best-practice standard. Finally, we estimated that 29.8% to 32.9% of total resources are used to generate withheld datasets, implying that an important portion of research funding does not produce shared knowledge. By making the scientific community and the public aware of this important aspect, we may help popularize a more effective culture of data sharing. PMID:22679483

  10. Structural variations of the VWA locus in humans and comparison with non-human primates.

    Science.gov (United States)

    Minaguchi, K; Takenaka, O

    2000-09-11

    The HUMVWA locus was examined in 160 samples from the Japanese population. A total of 142 fragments were sequenced, and the counterpart sequences were also determined in non-human primates. In humans, 10 different alleles were found; they could be grouped into seven allelic classes based on the total number of repeats. No variation was observed in the alleles 17, 18 and 19, which showed consensus sequence structures and in the allele 14, which showed a different structure. New variation was found in alleles 15, 16, and 20, which had differences occurred in a basic (TCTA)(TCTG)(n) repeat in the 5' side. The counterpart fragments were successfully amplified in three species (chimpanzees, gorilla, and orangutan) out of four kinds of anthropoids, three species (rhesus macaques, Japanese macaques, and green monkey) out of four kinds of old world monkeys, but not in one species of either new world monkey or prosimian. The sizes of the fragments distributed from 92 to 180 bp in non-human primates and showed allelic size differences in four species. The sequence of the 5' flanking region followed by primer sequences in humans and anthropoids, which consisted of 19 bp, was identical in all, but differed from that in old world monkeys. The basic repeat motifs of humans and anthropoids consisted of TCTA, TCTG, and TCCA but that of old world monkeys consisted of TCTG, TCCG and TCCA The structures of humans and anthropoids were essentially similar, but with characteristic difference in each species. Differences in the allelic structures of old world monkeys were complex. Seven different alleles were observed in two rhesus and two Japanese macaques and one type of allele was observed in two green monkeys. Duplication of more than two repeat units of 4 bp was found in an allele of an old world monkey. These data illuminate interesting features of mutational changes in STRs during the long generations and also some insight into evolutional aspects of primates.

  11. Anatomical Variations of the Circulus Arteriosus in Cadaveric Human Brains

    Directory of Open Access Journals (Sweden)

    S. A. Gunnal

    2014-01-01

    Full Text Available Objective. Circulus arteriosus/circle of Willis (CW is a polygonal anastomotic channel at the base of the brain which unites the internal carotid and vertebrobasilar system. It maintains the steady and constant supply to the brain. The variations of CW are seen often. The Aim of the present work is to find out the percentage of normal pattern of CW, and the frequency of variations of the CW and to study the morphological and morphometric aspects of all components of CW. Methods. Circulus arteriosus of 150 formalin preserved brains were dissected. Dimensions of all the components forming circles were measured. Variations of all the segments were noted and well photographed. The variations such as aplasia, hypoplasia, duplication, fenestrations, and difference in dimensions with opposite segments were noted. The data collected in the study was analyzed. Results. Twenty-one different types of CW were found in the present study. Normal and complete CW was found in 60%. CW with gross morphological variations was seen in 40%. Maximum variations were seen in the PCoA followed by the ACoA in 50% and 40%, respectively. Conclusion. As it confirms high percentage of variations, all surgical interventions should be preceded by angiography. Awareness of these anatomical variations is important in neurovascular procedures.

  12. Cardiovascular pharmacogenomics and individualized drug therapy

    OpenAIRE

    Pereira, Naveen L.; Weinshilboum, Richard M.

    2009-01-01

    The goal of individualized drug therapy requires physicians to be able to accurately predict an individual’s response to a drug. Both genetic and environmental factors are known to influence drug response. ‘Pharmacogenetics’ is the study of the role of inheritance in variation in drug response phenotypes. Pharmacogenetics is now moving genome-wide to become ‘pharmacogenomics’, resulting in the recognition of novel biomarkers for individual variation in drug response. This article reviews the ...

  13. Atenolol induced HDL-C change in the pharmacogenomic evaluation of antihypertensive responses (PEAR study.

    Directory of Open Access Journals (Sweden)

    Caitrin W McDonough

    Full Text Available We sought to identify novel pharmacogenomic markers for HDL-C response to atenolol in participants with mild to moderate hypertension. We genotyped 768 hypertensive participants from the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR study on the Illumina HumanCVD Beadchip. During PEAR, participants were randomized to receive atenolol or hydrochlorothiazide. Blood pressure and cholesterol levels were evaluated at baseline and after treatment. This study focused on participants treated with atenolol monotherapy. Association with atenolol induced HDL-C change was evaluated in 232 whites and 152 African Americans using linear regression. No SNPs achieved a Bonferroni corrected P-value. However, we identified 13 regions with consistent association across whites and African Americans. The most interesting of these regions were seven with prior associations with HDL-C, other metabolic traits, or functional implications in the lipid pathway: GALNT2, FTO, ABCB1, LRP5, STARD3NL, ESR1, and LIPC. Examples are rs2144300 in GALNT2 in whites (P=2.29x10(-4, β=-1.85 mg/dL and rs12595985 in FTO in African Americans (P=2.90x10(-4, β=4.52 mg/dL, both with consistent regional association (P<0.05 in the other race group. Additionally, baseline GALNT2 expression differed by rs2144300 genotype in whites (P=0.0279. In conclusion, we identified multiple gene regions associated with atenolol induced HDL-C change that were consistent across race groups, several with functional implications or prior associations with HDL-C.

  14. A pharmacogenomic approach to the treatment of children with GH deficiency or Turner syndrome

    Science.gov (United States)

    Clayton, P; Chatelain, P; Tatò, L; Yoo, H W; Ambler, G R; Belgorosky, A; Quinteiro, S; Deal, C; Stevens, A; Raelson, J; Croteau, P; Destenaves, B; Olivier, C

    2013-01-01

    Objective Individual sensitivity to recombinant human GH (r-hGH) is variable. Identification of genetic factors contributing to this variability has potential use for individualization of treatment. The objective of this study was to identify genetic markers and gene expression profiles associated with growth response on r-hGH therapy in treatment-naïve, prepubertal children with GH deficiency (GHD) or Turner syndrome (TS). Design A prospective, multicenter, international, open-label pharmacogenomic study. Methods The associations of genotypes in 103 growth- and metabolism-related genes and baseline gene expression profiles with growth response to r-hGH (cm/year) over the first year were evaluated. Genotype associations were assessed with growth response as a continuous variable and as a categorical variable divided into quartiles. Results Eleven genes in GHD and ten in TS, with two overlapping between conditions, were significantly associated with growth response either as a continuous variable (seven in GHD, two in TS) or as a categorical variable (four more in GHD, eight more in TS). For example, in GHD, GRB10 was associated with high response (≥Q3; P=0.0012), while SOS2 was associated with low response (≤Q1; P=0.006), while in TS, LHX4 was associated with high response (P=0.0003) and PTPN1 with low response (P=0.0037). Differences in expression were identified for one of the growth response-associated genes in GHD (AKT1) and for two in TS (KRAS and MYOD1). Conclusions Carriage of specific growth-related genetic markers is associated with growth response in GHD and TS. These findings indicate that pharmacogenomics could have a role in individualized management of childhood growth disorders. PMID:23761422

  15. Pharmacogenomics in Pediatric Patients: Towards Personalized Medicine

    NARCIS (Netherlands)

    Maagdenberg, Hedy; Vijverberg, Susanne J. H.; Bierings, Marc B.; Carleton, Bruce C.; Arets, Hubertus G. M.; de Boer, Anthonius; Maitland-van der Zee, Anke H.

    2016-01-01

    It is well known that drug responses differ among patients with regard to dose requirements, efficacy, and adverse drug reactions (ADRs). The differences in drug responses are partially explained by genetic variation. This paper highlights some examples of areas in which the different responses (dos

  16. Human genetic variation database, a reference database of genetic variations in the Japanese population

    Science.gov (United States)

    Higasa, Koichiro; Miyake, Noriko; Yoshimura, Jun; Okamura, Kohji; Niihori, Tetsuya; Saitsu, Hirotomo; Doi, Koichiro; Shimizu, Masakazu; Nakabayashi, Kazuhiko; Aoki, Yoko; Tsurusaki, Yoshinori; Morishita, Shinichi; Kawaguchi, Takahisa; Migita, Osuke; Nakayama, Keiko; Nakashima, Mitsuko; Mitsui, Jun; Narahara, Maiko; Hayashi, Keiko; Funayama, Ryo; Yamaguchi, Daisuke; Ishiura, Hiroyuki; Ko, Wen-Ya; Hata, Kenichiro; Nagashima, Takeshi; Yamada, Ryo; Matsubara, Yoichi; Umezawa, Akihiro; Tsuji, Shoji; Matsumoto, Naomichi; Matsuda, Fumihiko

    2016-01-01

    Whole-genome and -exome resequencing using next-generation sequencers is a powerful approach for identifying genomic variations that are associated with diseases. However, systematic strategies for prioritizing causative variants from many candidates to explain the disease phenotype are still far from being established, because the population-specific frequency spectrum of genetic variation has not been characterized. Here, we have collected exomic genetic variation from 1208 Japanese individuals through a collaborative effort, and aggregated the data into a prevailing catalog. In total, we identified 156 622 previously unreported variants. The allele frequencies for the majority (88.8%) were lower than 0.5% in allele frequency and predicted to be functionally deleterious. In addition, we have constructed a Japanese-specific major allele reference genome by which the number of unique mapping of the short reads in our data has increased 0.045% on average. Our results illustrate the importance of constructing an ethnicity-specific reference genome for identifying rare variants. All the collected data were centralized to a newly developed database to serve as useful resources for exploring pathogenic variations. Public access to the database is available at http://www.genome.med.kyoto-u.ac.jp/SnpDB/. PMID:26911352

  17. Pharmacogenomics: Overview of Applications and Relation to Infusion Therapy.

    Science.gov (United States)

    Kisor, David F; Bright, David R; Manion, Chelsea R; Smith, Thomas R

    2016-01-01

    Pharmacogenomics (PGx) describes the relationship between an individual's genes and his or her response to drug therapy. Data are accumulating that indicate that PGx has application in the clinical setting for drugs across therapeutic categories, including drugs that are administered intravenously and are of greater familiarity to infusion nurses. This article provides an overview of the science and presents common examples of PGx as it relates to drug and/or drug dose selection. Additionally, there are brief summaries of the role infusion nurses can play relative to toxicity monitoring, patient education, and other aspects of PGx.

  18. Third Santorini conference pharmacogenomics workshop report: "Pharmacogenomics at the crossroads: what else than good science will be needed for the field to become part of Personalized Medicine?".

    Science.gov (United States)

    Llerena, Adrián; Michel, Gerd; Jeannesson, Elise; Wong, Steven; Manolopoulos, Vangelis G; Hockett, Richard Dean; Boubekeur, Karima; Siest, Gérard; Beaune, Philippe; Haefliger, Carolina; Arnold, Hans Peter; Junien, Claudine; Petrovic, Nenad; Molloy, Roisin; Bekers, Otto; Donnelly, Claudine; Arens, Hans-Juergen; Kaput, Jim; McComb, Joel

    2007-01-01

    This workshop discussed the use of pharmacogenomics knowledge in clinical practice. It was organized in three sections: educational needs, definition of industry as a potential trigger, and regulatory aspects. Regarding pharmacogenomics education, it appears that this is truly lacking, except for patients, who are becoming increasingly educated thanks to the media. Regarding administrators, education is mainly a problem of cost. Indeed, even if cost-effective for society on the whole, pharmacogenomic tests will be expensive for hospitals. Physicians are facing an overabundance of information. They must be helped to bridge the gap between knowledge/research and clinical application. Collaboration between the pharmaceutical industry and the diagnostics industry could be one of the triggers. Moreover, there is a lack of qualification of this information, even though some guidelines are being produced. The Food and Drug Administration organizes workshops that often lead to publications on pharmacogenomic education, genomic data aims and development concepts, which can finally be translated into guidelines. Industry can contribute to pharmacogenomic development, not only through research, but also through marketing activities, which would promote the use of pharmacogenomics by physicians. Legal aspects were also considered in terms of the problem of availability and the degree of qualification of commercial drug tests on the market. The Innovative Medicine Initiative was also presented, which is a public-private partnership to create a biomedical research and development leader to benefit patients and society. Finally, a technical report from the Institute for Prospective Technological Studies on the socioeconomic impact of pharmacogenomics in the EU was presented.

  19. Genetic variation in a member of the laminin gene family affects variation in body composition in Drosophila and humans

    Directory of Open Access Journals (Sweden)

    Hunter Gary R

    2008-08-01

    Full Text Available Abstract Background The objective of the present study was to map candidate loci influencing naturally occurring variation in triacylglycerol (TAG storage using quantitative complementation procedures in Drosophila melanogaster. Based on our results from Drosophila, we performed a human population-based association study to investigate the effect of natural variation in LAMA5 gene on body composition in humans. Results We identified four candidate genes that contributed to differences in TAG storage between two strains of D. melanogaster, including Laminin A (LanA, which is a member of the α subfamily of laminin chains. We confirmed the effects of this gene using a viable LanA mutant and showed that female flies homozygous for the mutation had significantly lower TAG storage, body weight, and total protein content than control flies. Drosophila LanA is closely related to human LAMA5 gene, which maps to the well-replicated obesity-linkage region on chromosome 20q13.2-q13.3. We tested for association between three common single nucleotide polymorphisms (SNPs in the human LAMA5 gene and variation in body composition and lipid profile traits in a cohort of unrelated women of European American (EA and African American (AA descent. In both ethnic groups, we found that SNP rs659822 was associated with weight (EA: P = 0.008; AA: P = 0.05 and lean mass (EA: P= 0.003; AA: P = 0.03. We also found this SNP to be associated with height (P = 0.01, total fat mass (P = 0.01, and HDL-cholesterol (P = 0.003 but only in EA women. Finally, significant associations of SNP rs944895 with serum TAG levels (P = 0.02 and HDL-cholesterol (P = 0.03 were observed in AA women. Conclusion Our results suggest an evolutionarily conserved role of a member of the laminin gene family in contributing to variation in weight and body composition.

  20. Human genetics: international projects and personalized medicine.

    Science.gov (United States)

    Apellaniz-Ruiz, Maria; Gallego, Cristina; Ruiz-Pinto, Sara; Carracedo, Angel; Rodríguez-Antona, Cristina

    2016-03-01

    In this article, we present the progress driven by the recent technological advances and new revolutionary massive sequencing technologies in the field of human genetics. We discuss this knowledge in relation with drug response prediction, from the germline genetic variation compiled in the 1000 Genomes Project or in the Genotype-Tissue Expression project, to the phenome-genome archives, the international cancer projects, such as The Cancer Genome Atlas or the International Cancer Genome Consortium, and the epigenetic variation and its influence in gene expression, including the regulation of drug metabolism. This review is based on the lectures presented by the speakers of the Symposium "Human Genetics: International Projects & New Technologies" from the VII Conference of the Spanish Pharmacogenetics and Pharmacogenomics Society, held on the 20th and 21st of April 2015.

  1. Pharmacogenomics of cisplatin-induced ototoxicity

    Science.gov (United States)

    Mukherjea, Debashree; Rybak, Leonard P

    2011-01-01

    Cisplatin ototoxicity affects different individuals in a widely variable manner. These variations are likely to be explained by genetic differences among those affected. It would be highly advantageous to identify genetic variants that predispose to cisplatin ototoxicity in order to minimize the risk to susceptible subgroups. Although this area of research is very important, only a few studies have rigorously examined the genetic basis for cisplatin-induced susceptibility to hearing loss. This article addresses recent progress in clarifying the incidence of cisplatin ototoxicity and the risk factors and controversies regarding the identifcation of genetic variants associated with cisplatin-induced hearing loss. PMID:21787192

  2. Hypertension pharmacogenomics: in search of personalized treatment approaches.

    Science.gov (United States)

    Cooper-DeHoff, Rhonda M; Johnson, Julie A

    2016-02-01

    Cardiovascular and renal diseases are associated with many risk factors, of which hypertension is one of the most prevalent. Worldwide, blood pressure control is only achieved in ∼50% of those treated for hypertension, despite the availability of a considerable number of antihypertensive drugs from different pharmacological classes. Although many reasons exist for poor blood pressure control, a likely contributor is the inability to predict to which antihypertensive drug an individual is most likely to respond. Hypertension pharmacogenomics and other 'omics' technologies have the potential to identify genetic signals that are predictive of response or adverse outcome to particular drugs, and guide selection of hypertension treatment for a given individual. Continued research in this field will enhance our understanding of how to maximally deploy the various antihypertensive drug classes to optimize blood pressure response at the individual level. This Review summarizes the available literature on the most convincing genetic signals associated with antihypertensive drug responses and adverse cardiovascular outcomes. Future research in this area will be facilitated by enhancing collaboration between research groups through consortia such as the International Consortium for Antihypertensives Pharmacogenomics Studies, with the goal of translating replicated findings into clinical implementation.

  3. Variation in the human Achilles tendon moment arm during walking.

    Science.gov (United States)

    Rasske, Kristen; Thelen, Darryl G; Franz, Jason R

    2017-02-01

    The Achilles tendon (AT) moment arm is an important determinant of ankle moment and power generation during locomotion. Load and depth-dependent variations in the AT moment arm are generally not considered, but may be relevant given the complex triceps surae architecture. We coupled motion analysis and ultrasound imaging to characterize AT moment arms during walking in 10 subjects. Muscle loading during push-off amplified the AT moment arm by 10% relative to heel strike. AT moment arms also varied by 14% over the tendon thickness. In walking, AT moment arms are not strictly dependent on kinematics, but exhibit important load and spatial dependencies.

  4. Pharmacogenomic test that predicts response to inhaled corticosteroids in adults with asthma likely to be cost-saving

    Science.gov (United States)

    Wu, Ann Chen; Gay, Charlene; Rett, Melisa D; Stout, Natasha; Weiss, Scott T; Fuhlbrigge, Anne L

    2015-01-01

    Aim To identify the clinical and economic circumstances under which a pharmacogenomic test that predicts response to inhaled corticosteroids might be a cost-effective option for individuals with asthma. Materials & methods We synthesized published data on clinical and economic outcomes to project 10-year costs, quality-adjusted life-years and cost–effectiveness of pharmacogenomic testing for inhaled corticosteroid response. We assumed the pharmacogenomic test cost was $500 with a sensitivity and specificity of 84 and 98%, respectively. These were varied in sensitivity analyses. Results Both strategies, pharmacogenomic testing for inhaled corticosteroid response and no testing conferred 7.1 quality-adjusted life-years. Compared with no testing, pharmacogenomic testing costs less. Conclusion Pharmacogenomic testing for asthma is cost-saving and noninferior in improving health. PMID:25880024

  5. Should we keep on? Looking into pharmacogenomics of ADHD in adulthood from a different perspective.

    Science.gov (United States)

    Rovaris, Diego L; Mota, Nina R; da Silva, Bruna Santos; Girardi, Pricila; Victor, Marcelo M; Grevet, Eugenio H; Bau, Claiton Hd; Contini, Verônica

    2014-07-01

    A considerable proportion of adults with attention-deficit/hyperactivity disorder (ADHD) do not respond to the treatment with methylphenidate. This scenario could be due to inherited interindividual differences that may alter pharmacologic treatment response. In this sense, in 2012 we conducted a systematic search on PUBMED-indexed literature for articles containing information about pharmacogenomics of ADHD in adults. Five studies were found on methylphenidate pharmacogenomics and the only significant association was reported by one particular study. However, this single association with the SLC6A3 gene was not replicated in two subsequent reports. In the present review, although we could not find additional pharmacogenomics studies, we discuss these up-to-date findings and suggest new approaches for this field. Additionally, using systeomic-oriented databases, we provide a broad picture of new possible candidate genes as well as potential gene-gene interactions to be investigated in pharmacogenomics of persistent ADHD.

  6. Pharmacogenomics of episodic migraine: time has come for a step forward.

    Science.gov (United States)

    Viana, Michele; Terrazzino, Salvatore; Genazzani, Armando A; Grieco, Gaetano S; Cargnin, Sarah; Santorelli, Filippo M; Pierelli, Francesco; Tassorelli, Cristina; Nappi, Giuseppe; Di Lorenzo, Cherubino

    2014-03-01

    Migraine is characterized by heterogeneous behavior in response to drugs. Many resources have been invested in attempting to unravel the genetic basis of migraine, while the role of genetics in responses to currently available drugs has received less attention. We performed a systematic literature search identifying original articles pertaining to pharmacogenomics of episodic migraine. Few primary studies on the pharmacogenomics of symptomatic and preventive medication in episodic migraine were found. The number of patients studied in the individual articles ranged from 40 up to 130. There was a strong heterogeneity among these studies. We believe that pharmacogenomics studies, if properly designed, could contribute towards optimizing the treatment and reducing the burden of migraine, in turn helping patients and optimizing resources. Our knowledge on the pharmacogenomics of migraine is growing too slowly, and concerted measures should be undertaken to speed up the process.

  7. Human genetic variation and the gut microbiome in disease.

    Science.gov (United States)

    Hall, Andrew Brantley; Tolonen, Andrew C; Xavier, Ramnik J

    2017-08-21

    Taxonomic and functional changes to the composition of the gut microbiome have been implicated in multiple human diseases. Recent microbiome genome-wide association studies reveal that variants in many human genes involved in immunity and gut architecture are associated with an altered composition of the gut microbiome. Although many factors can affect the microbial organisms residing in the gut, a number of recent findings support the hypothesis that certain host genetic variants predispose an individual towards microbiome dysbiosis. This condition, in which the normal microbiome population structure is disturbed, is a key feature in disorders of metabolism and immunity.

  8. Human genetic variation: new challenges and opportunities for doping control.

    Science.gov (United States)

    Schneider, Angela J; Fedoruk, Matthew N; Rupert, Jim L

    2012-01-01

    Sport celebrates differences in competitors that lead to the often razor-thin margins between victory and defeat. The source of this variation is the interaction between the environment in which the athletes develop and compete and their genetic make-up. However, a darker side of sports may also be genetically influenced: some anti-doping tests are affected by the athlete's genotype. Genetic variation is an issue that anti-doping authorities must address as more is learned about the interaction between genotype and the responses to prohibited practices. To differentiate between naturally occurring deviations in indirect blood and urine markers from those potentially caused by doping, the "biological-passport" program uses intra-individual variability rather than population values to establish an athlete's expected physiological range. The next step in "personalized" doping control may be the inclusion of genetic data, both for the purposes of documenting an athlete's responses to doping agents and doping-control assays as well facilitating athlete and sample identification. Such applications could benefit "clean" athletes but will come at the expense of risks to privacy. This article reviews the instances where genetics has intersected with doping control, and briefly discusses the potential role, and ethical implications, of genotyping in the struggle to eliminate illicit ergogenic practices.

  9. Regional quantitative histological variations in human oral mucosa.

    Science.gov (United States)

    Ciano, Joseph; Beatty, Brian Lee

    2015-03-01

    Oral mucosa demonstrates regional variations that reflect contact with food during mastication. Though known qualitatively, our aim was to quantitatively assess regions to establish a measurable baseline from which one could compare in pathological and comparative studies, in which the abrasiveness of diets may differ. We assessed variations in the epithelial-connective tissue junction (rete ridges counts), collagen organization within the lamina propria, and elastin composition of the lamina propria of 15 regions of the labial (buccal) gingiva, lingual gingiva, vestibule, and palate. All characteristics varied more between regions within the same individual than between individuals. Lingual gingiva had high rete ridges counts, high level of collagen organization, and moderate elastin composition compared to other regions. The labial gingiva had few rete ridges, high collagen organization, and low elastin. The vestibule had the fewest average of rete ridges, least organized collagen, and high elastin. The hard palate had the highest average of rete ridges, high collagen organization, and the lowest elastin content. The soft palate conversely had the smallest average of rete ridges, moderate collagen organization, and the highest elastin composition. Our results indicate that comparison of these quantitative histological differences is warranted only for collagen organization and elastin composition. Differences in rete ridges counts were not statistically significant. Most histological characteristics observed were not significantly different between dentulous and edentulous cadavers, and the group containing all individuals. An exception was the level of collagen fiber organization within the lamina propria, which was higher in most regions when teeth were present.

  10. Age variations in the properties of human tibial trabecular bone

    DEFF Research Database (Denmark)

    Ding, Ming; Dalstra, M; Danielsen, CC;

    1997-01-01

    We tested in compression specimens of human proximal tibial trabecular bone from 31 normal donors aged from 16 to 83 years and determined the mechanical properties, density and mineral and collagen content. Young's modulus and ultimate stress were highest between 40 and 50 years, whereas ultimate...

  11. Inter-specific variation in avian responses to human disturbance

    Science.gov (United States)

    Daniel T. Blumstein; Esteban Fernandez-Juricic; Patrick A. Zollner; Susan C. Garity

    2005-01-01

    1. Increasing urbanization and recreational activities around and within biodiversity hotspots require an understanding of how to reduce the impacts of human disturbance on more than a single species; however, we lack a general framework to study multiple species. One approach is to expand on knowledge about the theory of anti-predator behaviour to understand and...

  12. Variations in Human Capital Investment Activity by Age.

    Science.gov (United States)

    Simpson, Patricia A.; Greller, Martin M.; Stroh, Linda K.

    2002-01-01

    Late-career workers (ages 50-65) were more likely to participate in credentialing programs, targeted job-related courses, and on-the-job computer training than younger adults and received similar employer support. However, participation might be a consequence of support received. Human capital investment thus is more complex than conventional…

  13. Original article Temperamental variation in learned irrelevance in humans

    Directory of Open Access Journals (Sweden)

    Aleksandra Gruszka

    2015-07-01

    Full Text Available Background Learned irrelevance (LIRR represents one of the mechanisms of attentional set-shifting and refers to the inability to attend to, or to learn about, any aspect of a stimulus previously experienced as irrelevant. Although it has been extensively studied in the context of clinical populations, not much is known about LIRR effects in relation to normal variation in individual differences. The present study was designed to assess how temperamental factors may modulate LIRR. Participants and procedures Sixty-eight healthy volunteers performed a visual discrimination learning task modelled after Wisconsin Card Sorting Test. To test the susceptibility to learned irrelevance, participants were expected to shift their attention either to a dimension that prior to the extra-dimensional shift was completely irrelevant, or to a dimension that was previously partly correlated with reinforcement. Temperamental traits were assessed using the Formal Characteristics of Behaviour-Temperament Inventory (Zawadzki & Strelau, 1997. Intelligence level was stratified according to Raven’s Advanced Progressive Matrices (Raven, Raven, & Court, 2003. Results Low level of Briskness and high level of Perseverance were related to enhanced susceptibility to LIRR. High levels of Activity and Emotional Reactivity were related to the poorer performance on the extra-dimensional set-shifting. No effects of other temperament characteristics or intelligence on LIRR were observed. Conclusions The results confirm a strong variation in LIRR related to individual differences in temperament, which appears to be unrelated to DA function. Our results highlight the importance of considering individual differences in studies on cognitive control.

  14. Exploring emerging technologies using metaphors--a study of orphan drugs and pharmacogenomics.

    Science.gov (United States)

    Boon, Wouter; Moors, Ellen

    2008-05-01

    Due to uncertainties of several aspects of emerging health technologies, there is a need to anticipate these developments early. A first step would be to gather information and develop future visions about the technology. This paper introduces metaphor analysis as a novel way to do this. Specifically, we study the future of pharmacogenomics by comparing this technology with orphan drugs, which are more established and often act as a model with comparable (economic, research organisation, etc.) characteristics. The analysis consists of describing the dominant metaphors used and structurally exploring (dis)similarities between pharmacogenomics and orphan drugs developments. This comparison leads to lessons that can be learnt for the emerging pharmacogenomics future. We carried out a comprehensive literature review, extracting metaphors in a structured way from different areas of the drug research and development pipeline. The paper argues that (1) there are many similarities between orphan drugs and pharmacogenomics, especially in terms of registration, and social and economic impacts; (2) pharmacogenomics developments are regarded both as a future 'poison' and a 'chance', whereas orphan drugs are seen as a 'gift', and at the same time as a large 'problem'; and (3) metaphor analysis proves to be a tool for creating prospective images of pharmacogenomics and other emerging technologies.

  15. The future costs, risks and rewards of drug development: the economics of pharmacogenomics.

    Science.gov (United States)

    Cook, Joseph; Hunter, Graeme; Vernon, John A

    2009-01-01

    This article discusses the evolving field of pharmacogenomics, which is the science of using genomic markers to predict drug response, and how it may impact the future costs, risks and returns to pharmaceutical research and development (R&D). We uncover a number of factors and issues that are likely to influence the expected returns and, hence, the incentive to invest in new pharmaceutical R&D in tandem with the development of pharmacogenomics. Specifically, we identify how pharmacogenomics may lower the cost of drug development by shortening drug development times. Thus, pharmacogenomics may lead to an increase in a drug's effective patent life, and may also increase the demand and adoption rate for new products. For these and other reasons, pharmacogenomics may one day enhance expected future returns to R&D, leading to higher levels of R&D investment and an increased pace of pharmaceutical innovation. Our conclusions must be read with much caution, however, as there is considerable uncertainty as to how the area will evolve, both clinically and economically. The time horizon necessary for the science to develop and be adopted into clinical practice is not clear. Nevertheless, we think the issues and factors outlined in this article shed light on possible future economic outcomes and changes in the industry's structure, conduct and performance. Hopefully, this will provide researchers with avenues to pursue regarding a better understanding of the economics of pharmacogenomics.

  16. Pharmacogenomics of Prostaglandin and Leukotriene Receptors

    Science.gov (United States)

    Cornejo-García, José A.; Perkins, James R.; Jurado-Escobar, Raquel; García-Martín, Elena; Agúndez, José A.; Viguera, Enrique; Pérez-Sánchez, Natalia; Blanca-López, Natalia

    2016-01-01

    Individual genetic background together with environmental effects are thought to be behind many human complex diseases. A number of genetic variants, mainly single nucleotide polymorphisms (SNPs), have been shown to be associated with various pathological and inflammatory conditions, representing potential therapeutic targets. Prostaglandins (PTGs) and leukotrienes (LTs) are eicosanoids derived from arachidonic acid and related polyunsaturated fatty acids that participate in both normal homeostasis and inflammatory conditions. These bioactive lipid mediators are synthesized through two major multistep enzymatic pathways: PTGs by cyclooxygenase and LTs by 5-lipoxygenase. The main physiological effects of PTGs include vasodilation and vascular leakage (PTGE2); mast cell maturation, eosinophil recruitment, and allergic responses (PTGD2); vascular and respiratory smooth muscle contraction (PTGF2), and inhibition of platelet aggregation (PTGI2). LTB4 is mainly involved in neutrophil recruitment, vascular leakage, and epithelial barrier function, whereas cysteinyl LTs (CysLTs) (LTC4, LTD4, and LTE4) induce bronchoconstriction and neutrophil extravasation, and also participate in vascular leakage. PTGs and LTs exert their biological functions by binding to cognate receptors, which belong to the seven transmembrane, G protein-coupled receptor superfamily. SNPs in genes encoding these receptors may influence their functionality and have a role in disease susceptibility and drug treatment response. In this review we summarize SNPs in PTGs and LTs receptors and their relevance in human diseases. We also provide information on gene expression. Finally, we speculate on future directions for this topic. PMID:27708579

  17. PHARMACOGENOMICS OF PROSTAGLANDIN AND LEUKOTRIENE RECEPTORS

    Directory of Open Access Journals (Sweden)

    José Antonio Cornejo-García

    2016-09-01

    Full Text Available Individual genetic background together with environmental effects are thought to be behind many human complex diseases. A number of genetic variants, mainly single nucleotide polymorphisms (SNPs, have been shown to be associated with various pathological and inflammatory conditions, representing potential therapeutic targets. Prostaglandins (PTGs and leukotrienes (LTs are eicosanoids derived from arachidonic acid and related polyunsaturated fatty acids that participate in both normal homeostasis and inflammatory conditions. These bioactive lipid mediators are synthesised through two major multistep enzymatic pathways: PTGs by cyclooxygenase and LTs by 5-lipoxygenase. The main physiological effects of PTGs include vasodilation and vascular leakage (PTGE2; mast cell maturation, eosinophil recruitment and allergic responses (PTGD2; vascular and respiratory smooth muscle contraction (PTGF2, and inhibition of platelet aggregation (PTGI2. LTB4 is mainly involved in neutrophil recruitment, vascular leakage, and epithelial barrier function, whereas cysteinyl LTs (CysLTs (LTC4, LTD4 and LTE4 induce bronchoconstriction and neutrophil extravasation, and also participate in vascular leakage. PTGs and LTs exert their biological functions by binding to cognate receptors, which belong to the seven transmembrane, G protein-coupled receptor superfamily. SNPs in genes encoding these receptors may influence their functionality and have a role in disease susceptibility and drug treatment response. In this review we summarize SNPs in PTGs and LTs receptors and their relevance in human diseases. We also provide information on gene expression. Finally, we speculate on future directions for this topic.

  18. Examining perceptions of the usefulness and usability of a mobile-based system for pharmacogenomics clinical decision support: a mixed methods study

    Directory of Open Access Journals (Sweden)

    Kathrin Blagec

    2016-02-01

    Full Text Available Background. Pharmacogenomic testing has the potential to improve the safety and efficacy of pharmacotherapy, but clinical application of pharmacogenetic knowledge has remained uncommon. Clinical Decision Support (CDS systems could help overcome some of the barriers to clinical implementation. The aim of this study was to evaluate the perception and usability of a web- and mobile-enabled CDS system for pharmacogenetics-guided drug therapy–the Medication Safety Code (MSC system–among potential users (i.e., physicians and pharmacists. Furthermore, this study sought to collect data on the practicability and comprehensibility of potential layouts of a proposed personalized pocket card that is intended to not only contain the machine-readable data for use with the MSC system but also human-readable data on the patient’s pharmacogenomic profile. Methods. We deployed an emergent mixed methods design encompassing (1 qualitative interviews with pharmacists and pharmacy students, (2 a survey among pharmacogenomics experts that included both qualitative and quantitative elements and (3 a quantitative survey among physicians and pharmacists. The interviews followed a semi-structured guide including a hypothetical patient scenario that had to be solved by using the MSC system. The survey among pharmacogenomics experts focused on what information should be printed on the card and how this information should be arranged. Furthermore, the MSC system was evaluated based on two hypothetical patient scenarios and four follow-up questions on the perceived usability. The second survey assessed physicians’ and pharmacists’ attitude towards the MSC system. Results. In total, 101 physicians, pharmacists and PGx experts coming from various relevant fields evaluated the MSC system. Overall, the reaction to the MSC system was positive across all investigated parameters and among all user groups. The majority of participants were able to solve the patient

  19. Clinical utility of pharmacogenomics in the management of hepatitis C

    Directory of Open Access Journals (Sweden)

    Trinks J

    2014-10-01

    Full Text Available Julieta Trinks,1,2 María Laura Hulaniuk,1 María Ana Redal,1,3 Diego Flichman2,4 1Instituto de Ciencias Básicas y Medicina Experimental, Hospital Italiano de Buenos Aires, 2National Scientific and Technical Research Council, 3Instituto Universitario del Hospital Italiano de Buenos Aires, 4Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina Abstract: Hepatitis C virus (HCV was identified for the first time more than 20 years ago. Since then, several studies have highlighted the complicated aspects of this viral infection in relation to its worldwide prevalence, its clinical presentation, and its therapeutic response. Recently, two landmark scientific breakthroughs have moved us closer to the successful eradication of chronic HCV infection. First, response rates in treatment-naïve patients and in prior non-responders to pegylated-interferon-α and ribavirin therapy are increasing as a direct consequence of the development of direct-acting antiviral drugs. Secondly, the discovery of single-nucleotide polymorphisms near the interleukin 28B gene significantly related to spontaneous and treatment-induced HCV clearance represents a milestone in the HCV therapeutic landscape. The implementation of this pharmacogenomics finding as a routine test for HCV-infected patients has enhanced our understanding of viral pathogenesis, has encouraged the design of ground-breaking antiviral treatment regimens, and has become useful for pretreatment decision making. Nowadays, interleukin 28B genotyping is considered to be a key diagnostic tool for the management of HCV-infected patients and will maintain its significance for new combination treatment schemes using direct-acting antiviral agents and even in interferon-free regimens. Such pharmacogenomics insights represent a challenge to clinicians, researchers, and health administrators to transform this information into knowledge with the aim of

  20. Perspectives on human genetic variation from the HapMap Project.

    Science.gov (United States)

    McVean, Gil; Spencer, Chris C A; Chaix, Raphaelle

    2005-10-01

    The completion of the International HapMap Project marks the start of a new phase in human genetics. The aim of the project was to provide a resource that facilitates the design of efficient genome-wide association studies, through characterising patterns of genetic variation and linkage disequilibrium in a sample of 270 individuals across four geographical populations. In total, over one million SNPs have been typed across these genomes, providing an unprecedented view of human genetic diversity. In this review we focus on what the HapMap Project has taught us about the structure of human genetic variation and the fundamental molecular and evolutionary processes that shape it.

  1. Age associated variations in human neutrophil and sperm functioning

    Institute of Scientific and Technical Information of China (English)

    Kaveri Purandhar; Sriram Seshadri

    2013-01-01

    Objective: To determine the functional and biochemical variations in sperm and the neutrophil with the progression of age. Methods: Ninety healthy male subjects were selected in the age group 26-40 for the collection of semen and blood samples were collected. Basic semen analysis, hematogram, differential count serum analysis, seminal plasma and serum biochemistry was performed. Mitochondrial isolation from sperm and neutrophil was done to ascertain mitochondrial markers. Results: Our data shows a significant age-dependent reduction in the levels of mitochondrial Superoxide Dismutase (SOD) and Catalase (CAT) in sperm and the neutrophil. The functional attributes of sperm and neutrophil did not show any specific trend.Conclusion:The decreasing trend of the mitochondrial antioxidants enzymes in the sperm and the neutrophil is an indicative of the reduction in the functioning of sperm and the neutrophil. The antioxidants enzymes of sperm and neutrophil shows similar declining trend with the progression of age suggesting its possible role as a prognostic marker for age related deformities and even in male fertility.

  2. Variation of neck muscle strength along the human cervical spine.

    Science.gov (United States)

    Oi, Nelson; Pandy, Marcus G; Myers, Barry S; Nightingale, Roger W; Chancey, Valeta Carol

    2004-11-01

    The aim of this study was to describe and explain the variation of neck muscle strength along the cervical spine. A three-dimensional model of the head-neck complex was developed to test the hypothesis that the moment-generating capacity of the neck musculature is lower in the upper cervical spine than in the lower cervical spine. The model calculations suggest that the neck muscles can protect the lower cervical spine from injury during extension and lateral bending. The maximum flexor moment developed in the lower cervical spine was 2 times higher than that developed in the upper spine. The model also predicted that the neck musculature is 30% stronger in the lower cervical spine during lateral bending. Peak compressive forces (up to 3 times body weight) were higher in the lower cervical spine. These results are consistent with the clinical finding that extension loading of the neck often leads to injuries in the upper cervical spine. Analysis of the model results showed that neck flexor strength was greater in the lower cervical spine because of the relatively large size of the sternocleidomastoid muscle. The hyoid muscles developed significant flexor moments about the joints of the upper cervical spine, as these muscles had relatively large flexor moment arms; however, this effect was offset by the action of the sternocleidomastoid, which exerted a large extensor moment in the upper spine. Lateral bending strength of the neck muscles was governed by geometry (i.e., moment arms) rather than by muscle size.

  3. Human leukocyte antigen (HLA) pharmacogenomic tests: potential and pitfalls.

    Science.gov (United States)

    Daly, Ann K

    2014-02-01

    Adverse drug reactions involving a range of prescribed drugs and affecting the skin, liver and other organs show strong associations with particular HLA alleles. For some reactions, HLA typing prior to prescription, so that those positive for the risk allele are not given the drug associated with the reaction, shows high positive and negative predictive values. The best example of clinical implementation relates to the hypersensitivity reaction induced by the anti-HIV drug abacavir. When this reaction is phenotyped accurately, 100% of those who develop it are positive for HLA-B*57:01. Drug regulators worldwide now recommend genotyping for HLA-B*57:01 before abacavir is prescribed. Serious skin rashes including Stevens-Johnson syndrome and toxic epidermal necrosis can be induced by carbamazepine and other anticonvulsant drugs. In certain East Asians, these reactions are significantly associated with HLA-B*15:02, and typing for this allele is now recommended prior to carbamazepine prescription in these populations. Other HLA associations have been described for skin rash induced by carbamazepine, allopurinol and nevirapine and for liver injury induced by flucloxacillin, amoxicillin-clavulanate, lapatanib, lumiracoxib and ticlopidine. However, the predictive values for typing HLA alleles associated with these adverse reactions are lower. Clinical implementation therefore seems unlikely. Performing HLA typing is relatively complex compared with genotyping assays for single nucleotide polymorphisms. With emphasis on HLA-B*57:01, the approaches used commonly, including use of sequence-specific oligonucleotide PCR primers and DNA sequencing are considered, together with their successful implementation. Genotyping single nucleotide polymorphisms tagging HLA alleles is a simpler alternative to HLA typing but appears insufficiently accurate for clinical use.

  4. [Variations in human parasitic diseases: malaria and schistosomiasis (author's transl)].

    Science.gov (United States)

    Garin, J P

    1981-01-01

    Until now, not any human vaccine against parasites can't be prepared. However, experimental researches are more and more numerous, with two major aims: Malaria and Schistosomiasis. Three vaccines are considered in Malaria: --sporozoite-vaccine, --merozoite-vaccine, --gametocyte-vaccine. Important advances were realized after the control of new techniques: --in vitro cultivation of malaria parasites, --production of monoclonal antibodies, --industrial breeding of anopheles. But the applications in men still remain a remote object. The vaccines against schistosomiasis can be killed vaccines or live vaccines; the use of radio-vaccines is full of promise. The difficulties of vaccination against protozoal or helminthic parasites are due in part to the misappreciation of real defensive means in the parasited host. A serious progress would be to devise artificial systems drawing near of physiological phenomenons.

  5. Size variation in small-bodied humans from palau, micronesia.

    Directory of Open Access Journals (Sweden)

    Andrew Gallagher

    Full Text Available BACKGROUND: Recent discoveries on Palau are claimed to represent the remains of small-bodied humans that may display evidence insular size reduction. This claim has yet to be statistically validated METHODOLOGY/PRINCIPAL FINDINGS: Published postcranial specimens (n = 16 from Palau were assessed relative to recent small-bodied comparative samples. Resampling statistical approaches were employed to test specific hypotheses relating to body size in the Palau sample. Results confirm that the Palau postcranial sample is indisputably small-bodied. CONCLUSIONS/SIGNIFICANCE: A single, homogenous body size morph is represented in early prehistoric postcrania from Palau. Small body size in early Palauans is an ancestral characteristic and was likely not a consequence of in-situ size reduction. Specimens from Palau have little bearing upon hypothesised insular size reduction in the ancestral lineage of Homo floresiensis.

  6. Genome-wide association studies in pharmacogenomics of antidepressants.

    Science.gov (United States)

    Lin, Eugene; Lane, Hsien-Yuan

    2015-01-01

    Major depressive disorder (MDD) is one of the most common psychiatric disorders worldwide. Doctors must prescribe antidepressants based on educated guesses due to the fact that it is unmanageable to predict the effectiveness of any particular antidepressant in an individual patient. With the recent advent of scientific research, the genome-wide association study (GWAS) is extensively employed to analyze hundreds of thousands of single nucleotide polymorphisms by high-throughput genotyping technologies. In addition to the candidate-gene approach, the GWAS approach has recently been utilized to investigate the determinants of antidepressant response to therapy. In this study, we reviewed GWAS studies, their limitations and future directions with respect to the pharmacogenomics of antidepressants in MDD.

  7. Role of dermatology in pharmacogenomics: drug-induced skin injury.

    Science.gov (United States)

    Borroni, Riccardo G

    2015-01-01

    Different individuals may respond diversely to the same drug, in terms of efficacy and toxicity. Adverse drug reactions cause about 6% of all hospital admissions and account for up to 9% of hospitalization costs. Drug-induced skin injury (DISI) is the most common presentation of adverse drug reactions, ranging from maculopapular eruptions to severe adverse cutaneous drug reactions (SCARs) with mortality of up to 40%. Specific genetic polymorphisms confer susceptibility to different types of DISI. Identifying patients genetically at risk for SCARs is one of the goals of pharmacogenomics. In this article, the aspects of clinical dermatology relevant to the pharmacogenetics of DISI are reviewed. Many SCARs are now preventable, with consequent reduction of morbidity, mortality and healthcare costs.

  8. Pharmacogenomics of multifactorial diseases: a focus on psoriatic arthritis.

    Science.gov (United States)

    Cascella, Raffaella; Strafella, Claudia; Longo, Giuliana; Maccarone, Mara; Borgiani, Paola; Sangiuolo, Federica; Novelli, Giuseppe; Giardina, Emiliano

    2016-06-01

    This review will outline the current pharmacogenomics knowledge about psoriatic arthritis with a special attention to the perspectives and the challenges for its implementation in the clinical practice. To date, different drugs have been developed to contrast the symptoms and the progression of psoriatic arthritis. However, patients have shown high variability of drug response in relation to their genetic makeup. In this context, the advances made in the knowledge and the potentialities of genome-drugs associations paved the path for the development of a precision medicine. In fact, these associations may be successfully combined with the environment information to provide new strategies able to prevent and improve the disease management as well as to enhance the patients quality of life.

  9. Pharmacogenomics: current applications and future prospects towards personalized therapeutics.

    Science.gov (United States)

    Vaiopoulou, A; Gazouli, M; Karikas, G A

    2013-01-01

    Personalized Medicine is more than just a metabolic activity of a person. Pharmacogenomics, pharmacogenetics, pharmacoproteomics, and metabolomics play an important role in the development of personalized medicines. Personalized medicine uses information about a person's genes, proteins, enzyme activities, and cellular environment to diagnose and treat disease, cancer included. A major problem of personalized medicine is the fact that there is no portable bedside and low-cost bioanalytical technology that can be used in close proximity to the patient. This technology could play a significant role in defining the dosage setting for subsets of the population. The success of the personalized therapy is possible through the application of technology, which can provide a bridge between metabolism status and an individual's response to a particular drug and therapeutic modality.

  10. Pharmacogenomics Bias - Systematic distortion of study results by genetic heterogeneity

    Directory of Open Access Journals (Sweden)

    Zietemann, Vera

    2008-04-01

    Full Text Available Background: Decision analyses of drug treatments in chronic diseases require modeling the progression of disease and treatment response beyond the time horizon of clinical or epidemiological studies. In many such models, progression and drug effect have been applied uniformly to all patients; heterogeneity in progression, including pharmacogenomic effects, has been ignored. Objective: We sought to systematically evaluate the existence, direction and relative magnitude of a pharmacogenomics bias (PGX-Bias resulting from failure to adjust for genetic heterogeneity in both treatment response (HT and heterogeneity in progression of disease (HP in decision-analytic studies based on clinical study data. Methods: We performed a systematic literature search in electronic databases for studies regarding the effect of genetic heterogeneity on the validity of study results. Included studies have been summarized in evidence tables. In the case of lacking evidence from published studies we sought to perform our own simulation considering both HT and HP. We constructed two simple Markov models with three basic health states (early-stage disease, late-stage disease, dead, one adjusting and the other not adjusting for genetic heterogeneity. Adjustment was done by creating different disease states for presence (G+ and absence (G- of a dichotomous genetic factor. We compared the life expectancy gains attributable to treatment resulting from both models and defined pharmacogenomics bias as percent deviation of treatment-related life expectancy gains in the unadjusted model from those in the adjusted model. We calculated the bias as a function of underlying model parameters to create generic results. We then applied our model to lipid-lowering therapy with pravastatin in patients with coronary atherosclerosis, incorporating the influence of two TaqIB polymorphism variants (B1 and B2 on progression and drug efficacy as reported in the DNA substudy of the REGRESS

  11. Personalized medicine, genomics, and pharmacogenomics: a primer for nurses.

    Science.gov (United States)

    Blix, Andrew

    2014-08-01

    Personalized medicine is the study of patients' unique environmental influences as well as the totality of their genetic code-their genome-to tailor personalized risk assessments, diagnoses, prognoses, and treatments. The study of how patients' genomes affect responses to medications, or pharmacogenomics, is a related field. Personalized medicine and genomics are particularly relevant in oncology because of the genetic basis of cancer. Nurses need to understand related issues such as the role of genetic and genomic counseling, the ethical and legal questions surrounding genomics, and the growing direct-to-consumer genomics industry. As genomics research is incorporated into health care, nurses need to understand the technology to provide advocacy and education for patients and their families.

  12. State of Art of Cancer Pharmacogenomics in Latin American Populations

    Directory of Open Access Journals (Sweden)

    Andrés López-Cortés

    2017-05-01

    Full Text Available Over the past decades, several studies have shown that tumor-related somatic and germline alterations predicts tumor prognosis, drug response and toxicity. Latin American populations present a vast geno-phenotypic diversity due to the great interethnic and interracial mixing. This genetic flow leads to the appearance of complex characteristics that allow individuals to adapt to endemic environments, such as high altitude or extreme tropical weather. These genetic changes, most of them subtle and unexplored, could establish a mutational profile to develop new pharmacogenomic therapies specific for Latin American populations. In this review, we present the current status of research on somatic and germline alterations in Latin America compared to those found in Caucasian and Asian populations.

  13. Pharmacogenomics and pharmacogenetics of cholesterol-lowering therapy.

    Science.gov (United States)

    Schmitz, Gerd; Drobnik, Wolfgang

    2003-04-01

    Cholesterol-lowering therapy is the central approach in the primary and secondary prevention of cardiovascular disease, the leading cause of death in industrialized countries. 3-Hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors (statins) are currently the most potent and widely used cholesterol-lowering drugs. Large-scale clinical trials unequivocally demonstrated the efficacy of statin treatment in reducing the risk of cardiovascular events. In general, HMG-CoA reductase inhibitors are well tolerated, although in a minority of patients severe adverse effects like myopathy or rhabdomyolysis may develop. The incidence of this potentially life-threatening side effects increases with co-adminstration of drugs that are metabolized via the same pharmacokinetic pathways or at high-dose statin therapy. The recent focus on the pleiotropic effects of statins that are more frequently observed at higher doses and the conclusion drawn from the large statin trials that low-density lipoprotein (LDL)-cholesterol is "the lower the better", may need careful consideration in individuals at risk of adverse drug reactions. On the other hand, not all patients respond to statin therapy with a reduction in coronary heart disease (CHD) risk. It is therefore of interest to develop diagnostic test systems, which would allow to identify patients at increased risk of adverse drug reactions or patients with a lack of therapeutic effect. Beside exogenous factors, genetic variability determines the response of an individual to drug therapy and the analysis of genetic variants affecting pharmacokinetic or pharmacodynamic aspects of drug therapy is the subject of pharmacogenomics. This review summarizes current knowledge of the pharmacology and the pharmacogenomics of statin therapy.

  14. Clinical utility of pharmacogenomics in the management of hepatitis C

    Science.gov (United States)

    Trinks, Julieta; Hulaniuk, María Laura; Redal, María Ana; Flichman, Diego

    2014-01-01

    Hepatitis C virus (HCV) was identified for the first time more than 20 years ago. Since then, several studies have highlighted the complicated aspects of this viral infection in relation to its worldwide prevalence, its clinical presentation, and its therapeutic response. Recently, two landmark scientific breakthroughs have moved us closer to the successful eradication of chronic HCV infection. First, response rates in treatment-naïve patients and in prior non-responders to pegylated-interferon-α and ribavirin therapy are increasing as a direct consequence of the development of direct-acting antiviral drugs. Secondly, the discovery of single-nucleotide polymorphisms near the interleukin 28B gene significantly related to spontaneous and treatment-induced HCV clearance represents a milestone in the HCV therapeutic landscape. The implementation of this pharmacogenomics finding as a routine test for HCV-infected patients has enhanced our understanding of viral pathogenesis, has encouraged the design of ground-breaking antiviral treatment regimens, and has become useful for pretreatment decision making. Nowadays, interleukin 28B genotyping is considered to be a key diagnostic tool for the management of HCV-infected patients and will maintain its significance for new combination treatment schemes using direct-acting antiviral agents and even in interferon-free regimens. Such pharmacogenomics insights represent a challenge to clinicians, researchers, and health administrators to transform this information into knowledge with the aim of elaborating safer and more effective therapeutic strategies specifically designed for each patient. In conclusion, the individualization of treatment regimens for patients with hepatitis C, that may lead to a universal cure in future years, is becoming a reality due to recent developments in biomarker and genomic medicine. In light of these advances, we review the scientific evidence and clinical implications of recent findings related to

  15. Genomic Sequence Variation Markup Language (GSVML).

    Science.gov (United States)

    Nakaya, Jun; Kimura, Michio; Hiroi, Kaei; Ido, Keisuke; Yang, Woosung; Tanaka, Hiroshi

    2010-02-01

    With the aim of making good use of internationally accumulated genomic sequence variation data, which is increasing rapidly due to the explosive amount of genomic research at present, the development of an interoperable data exchange format and its international standardization are necessary. Genomic Sequence Variation Markup Language (GSVML) will focus on genomic sequence variation data and human health applications, such as gene based medicine or pharmacogenomics. We developed GSVML through eight steps, based on case analysis and domain investigations. By focusing on the design scope to human health applications and genomic sequence variation, we attempted to eliminate ambiguity and to ensure practicability. We intended to satisfy the requirements derived from the use case analysis of human-based clinical genomic applications. Based on database investigations, we attempted to minimize the redundancy of the data format, while maximizing the data covering range. We also attempted to ensure communication and interface ability with other Markup Languages, for exchange of omics data among various omics researchers or facilities. The interface ability with developing clinical standards, such as the Health Level Seven Genotype Information model, was analyzed. We developed the human health-oriented GSVML comprising variation data, direct annotation, and indirect annotation categories; the variation data category is required, while the direct and indirect annotation categories are optional. The annotation categories contain omics and clinical information, and have internal relationships. For designing, we examined 6 cases for three criteria as human health application and 15 data elements for three criteria as data formats for genomic sequence variation data exchange. The data format of five international SNP databases and six Markup Languages and the interface ability to the Health Level Seven Genotype Model in terms of 317 items were investigated. GSVML was developed as

  16. Perception of the usefulness of drug/gene pairs and barriers for pharmacogenomics in Latin America.

    Science.gov (United States)

    Quinones, Luis Abel; Lavanderos, Maria Alejandra; Cayun, Juan Pablo; Garcia-Martin, Elena; Agundez, Jose Augusto; Caceres, Dante Daniel; Roco, Angela Margarita; Morales, Jorge E; Herrera, Luisa; Encina, Gonzalo; Isaza, Carlos Alberto; Redal, Maria Ana; Larovere, Laura; Soria, Nestor Walter; Eslava-Schmalbach, Javier; Castaneda-Hernandez, Gilberto; Lopez-Cortes, Andres; Magno, Luiz Alexandre; Lopez, Marisol; Chiurillo, Miguel Angel; Rodeiro, Idania; Castro de Guerra, Dinorah; Teran, Enrique; Estevez-Carrizo, Francisco; Lares-Assef, Ismael

    2014-02-01

    Pharmacogenetics and Pharmacogenomics areas are currently emerging fields focused to manage pharmacotherapy that may prevent undertreatment while avoiding associated drug toxicity in patients. Large international differences in the awareness and in the use of pharmacogenomic testing are presumed, but not well assessed to date. In the present study we review the awareness of Latin American scientific community about pharmacogenomic testing and the perceived barriers for their clinical application. In order to that, we have compiled information from 9 countries of the region using a structured survey which is compared with surveys previously performed in USA and Spain. The most relevant group of barriers was related to the need for clear guidelines for the use of pharmacogenomics in clinical practice, followed by insufficient awareness about pharmacogenomics among clinicians and the absence of regulatory institutions that facilitate the use of pharmacogenetic tests. The higher ranked pairs were TPMT/thioguanine, TPMT/azathioprine, CYP2C9/warfarin, UGT1A1/irinotecan, CYP2D6/amitriptiline, CYP2C19/citalopram and CYP2D6/clozapine. The lower ranked pairs were SLCO1B1/simvastatin, CYP2D6/metoprolol and GP6D/chloroquine. Compared with USA and Spanish surveys, 25 pairs were of lower importance for Latin American respondents. Only CYP2C19/esomeprazole, CYP2C19/omeprazole, CYP2C19/celecoxib and G6PD/dapsone were ranked higher or similarly to the USA and Spanish surveys. Integration of pharmacogenomics in clinical practice needs training of healthcare professionals and citizens, but in addition legal and regulatory guidelines and safeguards will be needed. We propose that the approach offered by pharmacogenomics should be incorporated into the decision-making plans in Latin America.

  17. Identification of species and genetic variation in Taenia isolates from human and swine of North India.

    Science.gov (United States)

    Singh, Satyendra K; Prasad, Kashi N; Singh, Aloukick K; Gupta, Kamlesh K; Chauhan, Ranjeet S; Singh, Amrita; Singh, Avinash; Rai, Ravi P; Pati, Binod K

    2016-10-01

    Taenia solium is the major cause of taeniasis and cysticercosis/neurocysticercosis (NCC) in the developing countries including India, but the existence of other Taenia species and genetic variation have not been studied in India. So, we studied the existence of different Taenia species, and sequence variation in Taenia isolates from human (proglottids and cysticerci) and swine (cysticerci) in North India. Amplification of cytochrome c oxidase subunit 1 gene (cox1) was done by polymerase chain reaction (PCR) followed by sequencing and phylogenetic analysis. We identified two species of Taenia i.e. T. solium and Taenia asiatica in our isolates. T. solium isolates showed similarity with Asian genotype and nucleotide variations from 0.25 to 1.01 %, whereas T. asiatica displayed nucleotide variations ranged from 0.25 to 0.5 %. These findings displayed the minimal genetic variations in North Indian isolates of T. solium and T. asiatica.

  18. [The quality control of preanalytical variations for the determination of lead in samples of human origin].

    Science.gov (United States)

    Zhong, Kun; Wang, Wei; He, Falin; Wang, Zhiguo

    2015-02-01

    The aims of this article was to provide the quality control requirements of preanalytical variation for the determination of lead in samples of human origin, reduce the influence of preanalytical variation on the test results. According to the Clinical and Laboratory Standards Institute documents, control of preanalytical variation in trace element determinations, analytical procedures for the determination of lead in blood and urine and other references and guidelines, the methods of quality control of lead determination had been made, including: the factors needed to be considered before collection, preservation, transportation and other preanalytical factors, the abilities and considerations of laboratory staff, etc.

  19. Natural selection affects multiple aspects of genetic variation at putatively peutral sites across the human genome

    DEFF Research Database (Denmark)

    Lohmueller, Kirk E; Albrechtsen, Anders; Li, Yingrui

    2011-01-01

    A major question in evolutionary biology is how natural selection has shaped patterns of genetic variation across the human genome. Previous work has documented a reduction in genetic diversity in regions of the genome with low recombination rates. However, it is unclear whether other summaries...... affected multiple aspects of linked neutral variation throughout the human genome and that positive selection is not required to explain these observations....... these questions by analyzing three different genome-wide resequencing datasets from European individuals. We document several significant correlations between different genomic features. In particular, we find that average minor allele frequency and diversity are reduced in regions of low recombination...

  20. Ubiquitous Pharmacogenomics (U-PGx): The time for implementation is now. An Horizon2020 program to drive pharmacogenomics into clinical practice.

    Science.gov (United States)

    Cecchin, Erika; Roncato, Rossana; Guchelaar, Hendrik Jan; Toffoli, Giuseppe; and for the Ubiquitous Pharmacogenomics Consortium

    2017-01-02

    Although the clinical validity of a number of pharmacogenetic markers is nowadays a matter of fact, and led authoritative scientific consortia as the Dutch Pharmacogenetic Working Group (DPWG) and the Clinical Pharmacogenomics Implementation Consortium (CPIC) to publish pharmacogenetic guidelines, the clinical implementation in the real life remains challenging. Ubiquitous Pharmacogenomics (U-PGx) program is a coordinated effort that put together scientific and clinical expertise in the pharmacogenomic field, to implement the pre-emptive pharmacogenomic approach in the clinical practice in Europe, and to demonstrate its benefit in both patients clinical outcome and quality of life, with an economic advantage for the healthcare system. The project is conceived as a clinical trial that will compare 4,000 patients, pre-emptively genotyped for a panel of pharmacogenes included in the DPWG guidelines, and treated accordingly, with 4,000 controls treated with the standard of care. All the genetic data will be prospectively collected and fully embedded into the patient's clinical record. An electronic clinical decision support system will be developed to alert physicians and pharmacists when a drug is being prescribed or dispensed to a patient with a risky genotype. U-PGx will test and harmonize this approach in seven healthcare environments (The Netherlands, Spain, UK, Italy, Austria, Greece, Slovenia) to set the basis for a future European Healthcare System where an 'effective treatment optimization will be accessible to every European citizen' (www.upgx.eu).

  1. Pharmacogenomics Implications of Using Herbal Medicinal Plants on African Populations in Health Transition

    Directory of Open Access Journals (Sweden)

    Nicholas E. Thomford

    2015-09-01

    Full Text Available The most accessible points of call for most African populations with respect to primary health care are traditional health systems that include spiritual, religious, and herbal medicine. This review focusses only on the use of herbal medicines. Most African people accept herbal medicines as generally safe with no serious adverse effects. However, the overlap between conventional medicine and herbal medicine is a reality among countries in health systems transition. Patients often simultaneously seek treatment from both conventional and traditional health systems for the same condition. Commonly encountered conditions/diseases include malaria, HIV/AIDS, hypertension, tuberculosis, and bleeding disorders. It is therefore imperative to understand the modes of interaction between different drugs from conventional and traditional health care systems when used in treatment combinations. Both conventional and traditional drug entities are metabolized by the same enzyme systems in the human body, resulting in both pharmacokinetics and pharmacodynamics interactions, whose properties remain unknown/unquantified. Thus, it is important that profiles of interaction between different herbal and conventional medicines be evaluated. This review evaluates herbal and conventional drugs in a few African countries and their potential interaction at the pharmacogenomics level.

  2. Time-related patient data retrieval for the case studies from the pharmacogenomics research network.

    Science.gov (United States)

    Zhu, Qian; Tao, Cui; Ding, Ying; Chute, Christopher G

    2012-11-01

    There are lots of question-based data elements from the pharmacogenomics research network (PGRN) studies. Many data elements contain temporal information. To semantically represent these elements so that they can be machine processiable is a challenging problem for the following reasons: (1) the designers of these studies usually do not have the knowledge of any computer modeling and query languages, so that the original data elements usually are represented in spreadsheets in human languages; and (2) the time aspects in these data elements can be too complex to be represented faithfully in a machine-understandable way. In this paper, we introduce our efforts on representing these data elements using semantic web technologies. We have developed an ontology, CNTRO, for representing clinical events and their temporal relations in the web ontology language (OWL). Here we use CNTRO to represent the time aspects in the data elements. We have evaluated 720 time-related data elements from PGRN studies. We adapted and extended the knowledge representation requirements for EliXR-TIME to categorize our data elements. A CNTRO-based SPARQL query builder has been developed to customize users' own SPARQL queries for each knowledge representation requirement. The SPARQL query builder has been evaluated with a simulated EHR triple store to ensure its functionalities.

  3. Humans and Deep Networks Largely Agree on Which Kinds of Variation Make Object Recognition Harder

    Science.gov (United States)

    Kheradpisheh, Saeed R.; Ghodrati, Masoud; Ganjtabesh, Mohammad; Masquelier, Timothée

    2016-01-01

    View-invariant object recognition is a challenging problem that has attracted much attention among the psychology, neuroscience, and computer vision communities. Humans are notoriously good at it, even if some variations are presumably more difficult to handle than others (e.g., 3D rotations). Humans are thought to solve the problem through hierarchical processing along the ventral stream, which progressively extracts more and more invariant visual features. This feed-forward architecture has inspired a new generation of bio-inspired computer vision systems called deep convolutional neural networks (DCNN), which are currently the best models for object recognition in natural images. Here, for the first time, we systematically compared human feed-forward vision and DCNNs at view-invariant object recognition task using the same set of images and controlling the kinds of transformation (position, scale, rotation in plane, and rotation in depth) as well as their magnitude, which we call “variation level.” We used four object categories: car, ship, motorcycle, and animal. In total, 89 human subjects participated in 10 experiments in which they had to discriminate between two or four categories after rapid presentation with backward masking. We also tested two recent DCNNs (proposed respectively by Hinton's group and Zisserman's group) on the same tasks. We found that humans and DCNNs largely agreed on the relative difficulties of each kind of variation: rotation in depth is by far the hardest transformation to handle, followed by scale, then rotation in plane, and finally position (much easier). This suggests that DCNNs would be reasonable models of human feed-forward vision. In addition, our results show that the variation levels in rotation in depth and scale strongly modulate both humans' and DCNNs' recognition performances. We thus argue that these variations should be controlled in the image datasets used in vision research. PMID:27642281

  4. Humans and deep networks largely agree on which kinds of variation make object recognition harder

    Directory of Open Access Journals (Sweden)

    Saeed Reza Kheradpisheh

    2016-08-01

    Full Text Available View-invariant object recognition is a challenging problem that has attracted much attention among the psychology, neuroscience, and computer vision communities. Humans are notoriously good at it, even if some variations are presumably more difficult to handle than others (e.g. 3D rotations. Humans are thought to solve the problem through hierarchical processing along the ventral stream, which progressively extracts more and more invariant visual features. This feed-forward architecture has inspired a new generation of bio-inspired computer vision systems called deep convolutional neural networks (DCNN, which are currently the best models for object recognition in natural images. Here, for the first time, we systematically compared human feed-forward vision and DCNNs at view-invariant object recognition task using the same set of images and controlling the kinds of transformation (position, scale, rotation in plane, and rotation in depth as well as their magnitude, which we call variation level. We used four object categories: car, ship, motorcycle, and animal. In total, 89 human subjects participated in 10 experiments in which they had to discriminate between two or four categories after rapid presentation with backward masking. We also tested two recent DCNNs (proposed respectively by Hinton's group and Zisserman's group on the same tasks. We found that humans and DCNNs largely agreed on the relative difficulties of each kind of variation: rotation in depth is by far the hardest transformation to handle, followed by scale, then rotation in plane, and finally position (much easier. This suggests that DCNNs would be reasonable models of human feed-forward vision. In addition, our results show that the variation levels in rotation in depth and scale strongly modulate both humans' and DCNNs' recognition performances. We thus argue that these variations should be controlled in the image datasets used in vision research.

  5. A genome wide association study between copy number variation (CNV) and human height in Chinese population

    Institute of Scientific and Technical Information of China (English)

    Xi Li; Liang Zhang; Han Yan; Feng Pan; Zhixin Zhang; Yumei Peng; Qi Zhou; Lina He; Xuezhen Zhu; Jing Cheng; Lishu Zhang; Lijun Tan; Yaozhong Liu; Qing Tian; Hongwen Deng; Xiaogang Liu; Shufeng Lei; Tielin Yang; Xiangding Chen; Fang Zhang; Yue Fang; Yan Guo

    2010-01-01

    Copy number variation (CNV) is a type of genetic variation which may have important roles in phenotypic variability and disease susceptibility. To hunt for genetic variants underlying human height variation, we performed a genome wide CNV association study for human height in 618 Chinese unrelated subjects using Affymetrix 500K array set. After adjusting for age and sex, we found that four CNVs at 6p21.3, 8p23.3-23.2, 9p23 and 16p12.1 were associated with human height (with borderline significant p value: 0.013, 0.011, 0.024, 0.049; respectively). However, after multiple tests correction, none of them was associated with human height. We observed that the gain of copy number (more than 2 copies) at 8p23.3-23.2 was associated with lower height (normal copy number vs. gain of copy number; 161.2 cm vs. 153.7 cm, p = 0.011), which accounted for 0.9% of height variation. Loss of copy number (less than 2 copies) at 6p21.3 was associated with 0.8% lower height (loss of copy number vs. normal copy number: 154.5 cm vs. 161.1 cm, p = 0.013). Since no important genes influencing height located in CNVs at loci of 8p23.3-23.2 and 6p21.3, the two CNVs may cause the structural rearrangements of neighbored important candidate genes, thus regulates the variation of height. Our results expand our knowledge of the genetic factors underlying height variation and the biological regulation of human height.

  6. Use of combinatorial pharmacogenomic testing in two cases from community psychiatry

    Directory of Open Access Journals (Sweden)

    Fields ES

    2016-08-01

    Full Text Available Eve S Fields,1 Raymond A Lorenz,2 Joel G Winner2 1Northwest Center for Community Mental Health, Reston, VA, USA; 2Assurex Health, Mason, OH, USA Abstract: This report describes two cases in which pharmacogenomic testing was utilized to guide medication selection for difficult to treat patients. The first patient is a 29-year old male with bipolar disorder who had severe akathisia due to his long acting injectable antipsychotic. The second patient is a 59-year old female with major depressive disorder who was not ­responding to her medication. In both cases, a proprietary combinatorial pharmacogenomic test was used to inform medication changes and improve patient outcomes. The first patient was switched to a long acting injectable that was not affected by his genetic profile and his adverse effects abated. The second patient had her medications discontinued due to the results of the genetic testing and more intense psychotherapy initiated. While pharmacogenomic testing may be ­helpful in cases such as these presented here, it should never serve as a proxy for a comprehensive biopsychosocial approach. The pharmacogenomic information may be selectively added to this comprehensive approach to support medication treatment. Keywords: pharmacogenomics, adverse effects, risperidone, nortriptyline, paliperidone

  7. Institutional Profile: Golden Helix Institute of Biomedical Research: interdisciplinary research and educational activities in pharmacogenomics and personalized medicine.

    Science.gov (United States)

    Mitropoulos, Konstantinos; Innocenti, Federico; van Schaik, Ron H; Lezhava, Alexander; Tzimas, Giannis; Kollia, Panagoula; Macek, Milan; Fortina, Paolo; Patrinos, George P

    2012-03-01

    The Golden Helix Institute of Biomedical Research is an international nonprofit scientific organization with interdisciplinary research and educational activities in the field of genome medicine in Europe, Asia and Latin America. These activities are supervised by an international scientific advisory council, consisting of world leaders in the field of genomics and translational medicine. Research activities include the regional coordination of the Pharmacogenomics for Every Nation Initiative in Europe, in an effort to integrate pharmacogenomics in developing countries, the development of several national/ethnic genetic databases and related web services and the critical assessment of the impact of genetics and genomic medicine on society in various countries. Educational activities also include the organization of the Golden Helix Symposia(®), which are high-profile scientific research symposia in the field of personalized medicine and the Golden Helix Pharmacogenomics Days, an international educational activity focused on pharmacogenomics, as part of its international pharmacogenomics education and outreach efforts.

  8. Assessing the impact of climate variability and human activities on streamflow variation

    OpenAIRE

    Chang, Jianxia; Zhang, Hongxue; Wang, Yimin; Zhu, Yuelu

    2016-01-01

    Water resources in river systems have been changing under the impact of both climate variability and human activities. Assessing the respective impact on decadal streamflow variation is important for water resource management. By using an elasticity-based method and calibrated TOPMODEL and VIC hydrological models, we quantitatively isolated the relative contributions that human activities and climate variability made to decadal streamflow changes in the Jinghe basin, located...

  9. Assessing the impact of climate variability and human activity to streamflow variation

    OpenAIRE

    Chang, J.; Zhang, H.; Y. Wang; Zhu, Y.

    2015-01-01

    Water resources in river systems have been changing under the impacts of both climate variability and human activities. Assessing the respective impacts on decadal streamflow variation is important for water resources management. By using an elasticity-based method, calibrated TOPMODEL and VIC hydrologic models, we have quantitatively isolated the relative contributions that human activity and climate variability made to decadal streamflow changes in Jinhe b...

  10. Assessing the impact of climate variability and human activities on streamflow variation

    OpenAIRE

    Chang, J.; Zhang, H.; Y. Wang; Zhu, Y.

    2015-01-01

    Water resources in river systems have been changing under the impact of both climate variability and human activities. Assessing the respective impact on decadal streamflow variation is important for water resource management. By using an elasticity-based method and calibrated TOPMODEL and VIC hydrological models, we quantitatively isolated the relative contributions that human activities and climate variability made to decadal streamflow changes in Jinghe basin, located in ...

  11. Perspectives on human genetic variation from the HapMap Project.

    OpenAIRE

    2005-01-01

    ABSTRACT The completion of the International HapMap Project marks the start of a new phase in human genetics. The aim of the project was to provide a resource that facilitates the design of efficient genome-wide association studies, through characterising patterns of genetic variation and linkage disequilibrium in a sample of 270 individuals across four geographical populations. In total, over one million SNPs have been typed across these genomes, providing an unprecedented view of human gene...

  12. Feedforward Object-Vision Models Only Tolerate Small Image Variations Compared to Human

    Directory of Open Access Journals (Sweden)

    Masoud eGhodrati

    2014-07-01

    Full Text Available Invariant object recognition is a remarkable ability of primates' visual system that its underlying mechanism has constantly been under intense investigations. Computational modelling is a valuable tool toward understanding the processes involved in invariant object recognition. Although recent computational models have shown outstanding performances on challenging image databases, they fail to perform well when images with more complex variations of the same object are applied to them. Studies have shown that making sparse representation of objects by extracting more informative visual features through a feedforward sweep can lead to higher recognition performances. Here, however, we show that when the complexity of image variations is high, even this approach results in poor performance compared to humans. To assess the performance of models and humans in invariant object recognition tasks, we built a parametrically controlled image database consisting of several object categories varied in different dimensions and levels, rendered from 3D planes. Comparing the performance of several object recognition models with human observers shows that only in low-level image variations the models perform similar to humans in categorization tasks. Furthermore, the results of our behavioral experiments demonstrate that, even under difficult experimental conditions (i.e. briefly presented masked stimuli with complex image variations, human observers performed outstandingly well, suggesting that the models are still far from resembling humans in invariant object recognition. Taken together, we suggest that learning sparse informative visual features, although desirable, is not a complete solution for future progresses in object-vision modelling. We show that this approach is not of significant help in solving the computational crux of object recognition (that is invariant object recognition when the identity-preserving image variations become more complex.

  13. Human loci involved in drug biotransformation: worldwide genetic variation, population structure, and pharmacogenetic implications.

    Science.gov (United States)

    Maisano Delser, Pierpaolo; Fuselli, Silvia

    2013-05-01

    Understanding the role of inheritance in individual variation in drug response is the focus of pharmacogenetics (PGx). A key part of this understanding is quantifying the role of genetic ancestry in this phenotypic outcome. To provide insight into the relationship between ethnicity and drug response, this study first infers the global distribution of PGx variation and defines its structure. Second, the study evaluates if geographic population structure stems from all PGx loci in general, or if structure is caused by specific genes. Lastly, we identify the genetic variants contributing the greatest proportion of such structure. Our study describes the global genetic structure of PGx loci across the 52 populations of the Human Genome Diversity Cell-Line Panel, the most inclusive set of human populations freely available for studies on human genetic variation. By analysing genetic variation at 1,001 single nucleotide polymorphisms (SNPs) involved in biotransformation of exogenous substances, we describe the between-populations PGx variation, as well geographical groupings of diversity. In addition, with discriminant analysis of principal component (DAPC), we infer how many and which groups of populations are supported by PGx variation, and identify which SNPs actually contribute to the PGx structure between such groups. Our results show that intergenic, synonymous and non-synonymous SNPs show similar levels of genetic variation across the globe. Conversely, loci coding for Cytochrome P450s (mainly metabolizing exogenous substances) show significantly higher levels of genetic diversity between populations than the other gene categories. Overall, genetic variation at PGx loci correlates with geographic distances between populations, and the apportionment of genetic variation is similar to that observed for the rest of the genome. In other words, the pattern of PGx variation has been mainly shaped by the demographic history of our species, as in the case of most of our

  14. Predicting Risk Sensitivity in Humans and Lower Animals: Risk as Variance or Coefficient of Variation

    Science.gov (United States)

    Weber, Elke U.; Shafir, Sharoni; Blais, Ann-Renee

    2004-01-01

    This article examines the statistical determinants of risk preference. In a meta-analysis of animal risk preference (foraging birds and insects), the coefficient of variation (CV), a measure of risk per unit of return, predicts choices far better than outcome variance, the risk measure of normative models. In a meta-analysis of human risk…

  15. Variation in human mate choice: Simultaneously investigating heritability, parental influence, sexual imprinting, and assortative mating

    NARCIS (Netherlands)

    Zietsch, B.P.; Verweij, C.J.H.; Heath, A.C.; Martin, N.G.

    2011-01-01

    Human mate choice is central to individuals' lives and to the evolution of the species, but the basis of variation in mate choice is not well understood. Here we looked at a large community-based sample of twins and their partners and parents (N > 20,000 individuals) to test for genetic and famil

  16. Interindividual variation in binding of benzo[a]pyrene to DNA in cultured human Bronchi

    DEFF Research Database (Denmark)

    Harris, C.C.; Autrup, Herman; Connor, R.

    1976-01-01

    The binding of benzo[a]pyrene to DNA in cultured human bronchus was measured in specimens from 37 patients. The binding values ranged from 2 to 151 picomoles of benzo[a]pyrene per milligram of DNA with an overall mean +/- standard error of 34.2 +/- 5.2. This 75-fold interindividual variation in t...

  17. Intra- and interindividual variation in gene expression in human adipose tissue

    NARCIS (Netherlands)

    van Beek, Esther A.; Bakker, Arjen H.; Kruyt, Philip M.; Hofker, Marten H.; Saris, Wim H.; Keijer, Jaap

    2007-01-01

    Adipose tissue is a highly plastic tissue with an important endocrine and metabolic function. To understand its role in human health and disease, it is necessary to understand the extent of variation and the specific differences within and between different depots and subjects. We employed cDNA micr

  18. Predicting Risk Sensitivity in Humans and Lower Animals: Risk as Variance or Coefficient of Variation

    Science.gov (United States)

    Weber, Elke U.; Shafir, Sharoni; Blais, Ann-Renee

    2004-01-01

    This article examines the statistical determinants of risk preference. In a meta-analysis of animal risk preference (foraging birds and insects), the coefficient of variation (CV), a measure of risk per unit of return, predicts choices far better than outcome variance, the risk measure of normative models. In a meta-analysis of human risk…

  19. Intrapopulational body size variation and cranial capacity variation in Middle Pleistocene humans: the Sima de los Huesos sample (Sierra de Atapuerca, Spain).

    Science.gov (United States)

    Lorenzo, C; Carretero, J M; Arsuaga, J L; Gracia, A; Martínez, I

    1998-05-01

    A sexual dimorphism more marked than in living humans has been claimed for European Middle Pleistocene humans, Neandertals and prehistoric modern humans. In this paper, body size and cranial capacity variation are studied in the Sima de los Huesos Middle Pleistocene sample. This is the largest sample of non-modern humans found to date from one single site, and with all skeletal elements represented. Since the techniques available to estimate the degree of sexual dimorphism in small palaeontological samples are all unsatisfactory, we have used the bootstraping method to asses the magnitude of the variation in the Sima de los Huesos sample compared to modern human intrapopulational variation. We analyze size variation without attempting to sex the specimens a priori. Anatomical regions investigated are scapular glenoid fossa; acetabulum; humeral proximal and distal epiphyses; ulnar proximal epiphysis; radial neck; proximal femur; humeral, femoral, ulnar and tibial shaft; lumbosacral joint; patella; calcaneum; and talar trochlea. In the Sima de los Huesos sample only the humeral midshaft perimeter shows an unusual high variation (only when it is expressed by the maximum ratio, not by the coefficient of variation). In spite of that the cranial capacity range at Sima de los Huesos almost spans the rest of the European and African Middle Pleistocene range. The maximum ratio is in the central part of the distribution of modern human samples. Thus, the hypothesis of a greater sexual dimorphism in Middle Pleistocene populations than in modern populations is not supported by either cranial or postcranial evidence from Sima de los Huesos.

  20. Understanding and monitoring the consequences of human impacts on intraspecific variation.

    Science.gov (United States)

    Mimura, Makiko; Yahara, Tetsukazu; Faith, Daniel P; Vázquez-Domínguez, Ella; Colautti, Robert I; Araki, Hitoshi; Javadi, Firouzeh; Núñez-Farfán, Juan; Mori, Akira S; Zhou, Shiliang; Hollingsworth, Peter M; Neaves, Linda E; Fukano, Yuya; Smith, Gideon F; Sato, Yo-Ichiro; Tachida, Hidenori; Hendry, Andrew P

    2017-02-01

    Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and nongovernmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill-advised because phenotypic and genetic variations within and among populations can have dramatic effects on ecological and evolutionary processes, including responses to environmental change, the maintenance of species diversity, and ecological stability and resilience. At the same time, environmental changes associated with many human activities, such as land use and climate change, have dramatic and often negative impacts on intraspecific variation. We argue for the need for local, regional, and global programs to monitor intraspecific genetic variation. We suggest that such monitoring should include two main strategies: (i) intensive monitoring of multiple types of genetic variation in selected species and (ii) broad-brush modeling for representative species for predicting changes in variation as a function of changes in population size and range extent. Overall, we call for collaborative efforts to initiate the urgently needed monitoring of intraspecific variation.

  1. Variation in the pattern of circle of willis in human brain - A morphological study and review

    Directory of Open Access Journals (Sweden)

    Iman Sinha

    2014-01-01

    Full Text Available Background: Variation of “Circulus Arteriosus” is frequent. Knowledge of the variations of vascular anatomy of Circle of Willis will guide the neurosurgeons during intracranial surgery. Objectives: This is an analytical study, where the aim of our study is to analyze the variations regarding shape, symmetry, length and diameters of the component arteries. The study also includes other variations like absence, duplication and abnormal origin of component arteries. Methods: In the present study 80 specimens of human brains of both sexes, aged between 20-60 years are obtained from voluntary body donation at the Department of Anatomy and fresh corpses undergoing autopsy at the Department of Forensic and State Medicine in a teaching hospital in Kolkata. Careful observation & measurement of the component arteries are done after proper preservation and necessary dissection. The findings are then recorded and analyzed. Results: 62 out of total 80 specimens (77.5% have been found to be complete, symmetrical and having normal length and caliber. 7 specimens (6.25% were incomplete and not heptagonal in shape. Conclusion: Out of 22.5% variations most of the variations are seen in posterior communicating artery (10%, followed by anterior cerebral artery (6.25% and anterior communicating artery (6.25%. Most common type of variation is hypoplasia.

  2. Evaluation of popular drug information resources on clinically useful and actionable pharmacogenomic information*†

    Science.gov (United States)

    Chang, Jennifer S.; Pham, Duyen-Anh; Dang, Maithao T.; Lu, Yiting; VanOsdol, Sheri

    2016-01-01

    Background Pharmacogenomics is the study of how genes affect a person's response to drugs. This descriptive study assessed whether popular drug information resources provide clinically useful pharmacogenomic (PGx) information. Methods Four resources (package inserts, Lexicomp, Micromedex 2.0, and Epocrates) were evaluated for information about twenty-seven drugs. Results There was wide variability of PGx information. Whereas Lexicomp included relevant PGx biomarker information for all 27 drugs, Epocrates did in less than 50% of the drugs. None of the resources had monographs that fully incorporated Clinical Pharmacogenomics Implementation Consortium (CPIC) recommendations in more than 30% of the drugs. Conclusion Lexicomp appears to be most useful PGx drug information resource, but none of the resources are sufficient. PMID:26807054

  3. Demographic and spatio-temporal variation in human plague at a persistent focus in Tanzania

    DEFF Research Database (Denmark)

    Davis, S; Makundi, R H; Machang'u, R S

    2006-01-01

    Human plague in the Western Usambara Mountains in Tanzania has been a public health problem since the first outbreak in 1980. The wildlife reservoir is unknown and eradication measures that have proved effective elsewhere in Tanzania appear to fail in this region. We use census data from 2002...... and hospital records kept since 1986 to describe the temporal, spatial and demographic variation in human plague. A seasonal peak in cases occurs from December to February with the numbers of cases during this peak varying between 0 and 1150. Variation in incidence, calculated for each village as the mean...... number of cases per thousand inhabitants per year, indicates that human plague is concentrated around a group of three neighbouring, relatively isolated, high-altitude villages; Nywelo, Madala and Gologolo. However, there was no evidence that these villages were acting as a source of infection...

  4. Genetic variation in lipid desaturases and its impact on the development of human disease

    Directory of Open Access Journals (Sweden)

    Mutch David M

    2010-06-01

    Full Text Available Abstract Perturbations in lipid metabolism characterize many of the chronic diseases currently plaguing our society, such as obesity, diabetes, and cardiovascular disease. Thus interventions that target plasma lipid levels remain a primary goal to manage these diseases. The determinants of plasma lipid levels are multi-factorial, consisting of both genetic and lifestyle components. Recent evidence indicates that fatty acid desaturases have an important role in defining plasma and tissue lipid profiles. This review will highlight the current state-of-knowledge regarding three desaturases (Scd-1, Fads1 and Fads2 and their potential roles in disease onset and development. Although research in rodent models has provided invaluable insight into the regulation and functions of these desaturases, the extent to which murine research can be translated to humans remains unclear. Evidence emerging from human-based research demonstrates that genetic variation in human desaturase genes affects enzyme activity and, consequently, disease risk factors. Moreover, this genetic variation may have a trans-generational effect via breastfeeding. Therefore inter-individual variation in desaturase function is attributed to both genetic and lifestyle components. As such, population-based research regarding the role of desaturases on disease risk is challenged by this complex gene-lifestyle paradigm. Unravelling the contribution of each component is paramount for understanding the inter-individual variation that exists in plasma lipid profiles, and will provide crucial information to develop personalized strategies to improve health management.

  5. Investigation of variation in gene expression profiling of human blood by extended principle component analysis.

    Directory of Open Access Journals (Sweden)

    Qinghua Xu

    Full Text Available BACKGROUND: Human peripheral blood is a promising material for biomedical research. However, various kinds of biological and technological factors result in a large degree of variation in blood gene expression profiles. METHODOLOGY/PRINCIPAL FINDINGS: Human peripheral blood samples were drawn from healthy volunteers and analysed using the Human Genome U133Plus2 Microarray. We applied a novel approach using the Principle Component Analysis and Eigen-R(2 methods to dissect the overall variation of blood gene expression profiles with respect to the interested biological and technological factors. The results indicated that the predominating sources of the variation could be traced to the individual heterogeneity of the relative proportions of different blood cell types (leukocyte subsets and erythrocytes. The physiological factors like age, gender and BMI were demonstrated to be associated with 5.3% to 9.2% of the total variation in the blood gene expression profiles. We investigated the gene expression profiles of samples from the same donors but with different levels of RNA quality. Although the proportion of variation associated to the RNA Integrity Number was mild (2.1%, the significant impact of RNA quality on the expression of individual genes was observed. CONCLUSIONS: By characterizing the major sources of variation in blood gene expression profiles, such variability can be minimized by modifications to study designs. Increasing sample size, balancing confounding factors between study groups, using rigorous selection criteria for sample quality, and well controlled experimental processes will significantly improve the accuracy and reproducibility of blood transcriptome study.

  6. The clinically relevant pharmacogenomic changes in acute myelogenous leukemia.

    Science.gov (United States)

    Emadi, Ashkan; Karp, Judith E

    2012-08-01

    Acute myelogenous leukemia (AML) is an extremely heterogeneous neoplasm with several clinical, pathological, genetic and molecular subtypes. Combinations of various doses and schedules of cytarabine and different anthracyclines have been the mainstay of treatment for all forms of AMLs in adult patients. Although this combination, with the addition of an occasional third agent, remains effective for treatment of some young-adult patients with de novo AML, the prognosis of AML secondary to myelodysplastic syndromes or myeloproliferative neoplasms, treatment-related AML, relapsed or refractory AML, and AML that occurs in older populations remains grim. Taken into account the heterogeneity of AML, one size does not and should not be tried to fit all. In this article, the authors review currently understood, applicable and relevant findings related to cytarabine and anthracycline drug-metabolizing enzymes and drug transporters in adult patients with AML. To provide a prime-time example of clinical applicability of pharmacogenomics in distinguishing a subset of patients with AML who might be better responders to farnesyltransferase inhibitors, the authors also reviewed findings related to a two-gene transcript signature consisting of high RASGRP1 and low APTX, the ratio of which appears to positively predict clinical response in AML patients treated with farnesyltransferase inhibitors.

  7. A comparison of association methods for cytotoxicity mapping in pharmacogenomics

    Directory of Open Access Journals (Sweden)

    Chad eBrown

    2011-12-01

    Full Text Available Cytotoxicity assays of immortalized lymphoblastoid cell lines (LCLs represent a promising new in vitro approach in pharmacogenomics research. However, previous studies employ- ing LCLs in gene mapping have used simple association methods, which may not adequately capture the true differences in nonlinear response profiles between genotypes. Two common approaches summarize each dose-response curve with either the IC50 or the slope parameter estimates from a hill slope fit and treat these estimates as the response in a linear model. The current study investigates these two methods, as well as four novel methods, and compares their power to detect differences between the response profiles of genotypes under a variety of different alternatives. The four novel methods include two methods that summarize each dose-response by its area under the curve, one method based off of an analysis of variance (ANOVA design and one method that compares hill slope fits for all individuals of each geno- type. The power of each method was found to depend not only on the choice of alternative, but also on the choice for the set of dosages used in cytotoxicity measurements. The ANOVA- based method was found to be the most robust across alternatives and dosage sets for power in detecting differences between genotypes.

  8. A service-based framework for pharmacogenomics data integration

    Science.gov (United States)

    Wang, Kun; Bai, Xiaoying; Li, Jing; Ding, Cong

    2010-08-01

    Data are central to scientific research and practices. The advance of experiment methods and information retrieval technologies leads to explosive growth of scientific data and databases. However, due to the heterogeneous problems in data formats, structures and semantics, it is hard to integrate the diversified data that grow explosively and analyse them comprehensively. As more and more public databases are accessible through standard protocols like programmable interfaces and Web portals, Web-based data integration becomes a major trend to manage and synthesise data that are stored in distributed locations. Mashup, a Web 2.0 technique, presents a new way to compose content and software from multiple resources. The paper proposes a layered framework for integrating pharmacogenomics data in a service-oriented approach using the mashup technology. The framework separates the integration concerns from three perspectives including data, process and Web-based user interface. Each layer encapsulates the heterogeneous issues of one aspect. To facilitate the mapping and convergence of data, the ontology mechanism is introduced to provide consistent conceptual models across different databases and experiment platforms. To support user-interactive and iterative service orchestration, a context model is defined to capture information of users, tasks and services, which can be used for service selection and recommendation during a dynamic service composition process. A prototype system is implemented and cases studies are presented to illustrate the promising capabilities of the proposed approach.

  9. Beyond the clinic: 'direct-to-consumer' genomic profiling services and pharmacogenomics.

    Science.gov (United States)

    Prainsack, Barbara; Vayena, Effy

    2013-03-01

    This article provides an overview of commercial pharmacogenetics and pharmacogenomics testing services offered online. The concept of 'beyond-the-clinic' (BTC) genomic testing is introduced to refer to the variety of formats in which these tests are offered and a typology of BTC models is developed. The authors review such models in relation to tests for individual drug response that are currently on offer. In conclusion, the authors argue that the evolving BTC domain provides opportunities for the pioneering of integrated data repositories, whose gatekeepers are patients or citizens. The authors anticipate that such developments will benefit pharmacogenomics sooner than other areas of medical practice.

  10. Simultaneous inference of selection and population growth from patterns of variation in the human genome

    DEFF Research Database (Denmark)

    Williamson, Scott H.; Hernandez, Ryan; Fledel-Alon, Adi

    2005-01-01

    for patterns of polymorphism in the presence of both population size change and natural selection. If data are available from different functional classes of variation, and a priori information suggests that mutations in one of those classes are selectively neutral, then the putatively neutral class can...... this method to a large polymorphism data set from 301 human genes and find (i) widespread negative selection acting on standing nonsynonymous variation, (ii) that the fitness effects of nonsynonymous mutations are well predicted by several measures of amino acid exchangeability, especially site......-specific methods, and (iii) strong evidence for very recent population growth....

  11. Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems.

    Science.gov (United States)

    Rasmussen-Torvik, L J; Stallings, S C; Gordon, A S; Almoguera, B; Basford, M A; Bielinski, S J; Brautbar, A; Brilliant, M H; Carrell, D S; Connolly, J J; Crosslin, D R; Doheny, K F; Gallego, C J; Gottesman, O; Kim, D S; Leppig, K A; Li, R; Lin, S; Manzi, S; Mejia, A R; Pacheco, J A; Pan, V; Pathak, J; Perry, C L; Peterson, J F; Prows, C A; Ralston, J; Rasmussen, L V; Ritchie, M D; Sadhasivam, S; Scott, S A; Smith, M; Vega, A; Vinks, A A; Volpi, S; Wolf, W A; Bottinger, E; Chisholm, R L; Chute, C G; Haines, J L; Harley, J B; Keating, B; Holm, I A; Kullo, I J; Jarvik, G P; Larson, E B; Manolio, T; McCarty, C A; Nickerson, D A; Scherer, S E; Williams, M S; Roden, D M; Denny, J C

    2014-10-01

    We describe here the design and initial implementation of the eMERGE-PGx project. eMERGE-PGx, a partnership of the Electronic Medical Records and Genomics Network and the Pharmacogenomics Research Network, has three objectives: (i) to deploy PGRNseq, a next-generation sequencing platform assessing sequence variation in 84 proposed pharmacogenes, in nearly 9,000 patients likely to be prescribed drugs of interest in a 1- to 3-year time frame across several clinical sites; (ii) to integrate well-established clinically validated pharmacogenetic genotypes into the electronic health record with associated clinical decision support and to assess process and clinical outcomes of implementation; and (iii) to develop a repository of pharmacogenetic variants of unknown significance linked to a repository of electronic health record-based clinical phenotype data for ongoing pharmacogenomics discovery. We describe site-specific project implementation and anticipated products, including genetic variant and phenotype data repositories, novel variant association studies, clinical decision support modules, clinical and process outcomes, approaches to managing incidental findings, and patient and clinician education methods.

  12. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

    Science.gov (United States)

    Kidd, Jeffrey M; Gravel, Simon; Byrnes, Jake; Moreno-Estrada, Andres; Musharoff, Shaila; Bryc, Katarzyna; Degenhardt, Jeremiah D; Brisbin, Abra; Sheth, Vrunda; Chen, Rong; McLaughlin, Stephen F; Peckham, Heather E; Omberg, Larsson; Bormann Chung, Christina A; Stanley, Sarah; Pearlstein, Kevin; Levandowsky, Elizabeth; Acevedo-Acevedo, Suehelay; Auton, Adam; Keinan, Alon; Acuña-Alonzo, Victor; Barquera-Lozano, Rodrigo; Canizales-Quinteros, Samuel; Eng, Celeste; Burchard, Esteban G; Russell, Archie; Reynolds, Andy; Clark, Andrew G; Reese, Martin G; Lincoln, Stephen E; Butte, Atul J; De La Vega, Francisco M; Bustamante, Carlos D

    2012-10-05

    Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas-70% of the European ancestry in today's African Americans dates back to European gene flow happening only 7-8 generations ago.

  13. Read clouds uncover variation in complex regions of the human genome.

    Science.gov (United States)

    Bishara, Alex; Liu, Yuling; Weng, Ziming; Kashef-Haghighi, Dorna; Newburger, Daniel E; West, Robert; Sidow, Arend; Batzoglou, Serafim

    2015-10-01

    Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies.

  14. Midtarsal break variation in modern humans: Functional causes, skeletal correlates, and paleontological implications.

    Science.gov (United States)

    DeSilva, J M; Bonne-Annee, R; Swanson, Z; Gill, C M; Sobel, M; Uy, J; Gill, S V

    2015-04-01

    The midtarsal break was once treated as a dichotomous, non-overlapping trait present in the foot of non-human primates and absent in humans. Recent work indicates that there is considerable variation in human midfoot dorsiflexion, with some overlap with the ape foot. These findings have called into question the uniqueness of the human lateral midfoot, and the use of osteological features in fossil hominins to characterize the midfoot of our extinct ancestors. Here, we present data on plantar pressure and pedal mechanics in a large sample of adults and children (n = 671) to test functional hypotheses concerning variation in midfoot flexibility. Lateral midfoot peak plantar pressure correlates with both sagittal plane flexion at the lateral tarsometatarsal joint, and dorsiflexion at the hallucal metatarsophalangeal joint. The latter finding suggests that midfoot laxity may compromise hallucal propulsion. Multiple regression statistics indicate that a low arch and pronation of the foot explain 40% of variation in midfoot peak plantar pressure, independent of age and BMI. MRI scans on a small subset of study participants (n = 19) reveals that curvature of the base of the 4th metatarsal correlates with lateral midfoot plantar pressure and that specific anatomies of foot bones do indeed reflect relative midfoot flexibility. However, while the shape of the base of the 4th metatarsal may reliably reflect midfoot mobility in individual hominins, given the wide range of overlapping variation in midfoot flexibility in both apes and humans, we caution against generalizing foot function in extinct hominin species until larger fossils samples are available. © 2015 Wiley Periodicals, Inc.

  15. Variation in calculated human exposure. Comparison of calculations with seven European human exposure models

    NARCIS (Netherlands)

    Swartjes F; ECO

    2003-01-01

    Twenty scenarios, differing with respect to land use, soil type and contaminant, formed the basis for calculating human exposure from soil contaminants with the use of models contributed by seven European countries (one model per country). Here, the human exposures to children and children

  16. Validating the pharmacogenomics of chemotherapy-induced cardiotoxicity: What is missing?

    Science.gov (United States)

    Magdy, Tarek; Burmeister, Brian T; Burridge, Paul W

    2016-12-01

    The cardiotoxicity of certain chemotherapeutic agents is now well-established, and has led to the development of the field of cardio-oncology, increased cardiac screening of cancer patients, and limitation of patients' maximum cumulative chemotherapeutic dose. The effect of chemotherapeutic regimes on the heart largely involves cardiomyocyte death, leading to cardiomyopathy and heart failure, or the induction of arrhythmias. Of these cardiotoxic drugs, those resulting in clinical cardiotoxicity can range from 8 to 26% for doxorubicin, 7-28% for trastuzumab, or 5-30% for paclitaxel. For tyrosine kinase inhibitors, QT prolongation and arrhythmia, ischemia and hypertension have been reported in 2-35% of patients. Furthermore, newly introduced chemotherapeutic agents are commonly used as part of changed combinational regimens with significantly increased incidence of cardiotoxicity. It is widely believed that the mechanism of action of these drugs is often independent of their cardiotoxicity, and the basis for why these drugs specifically affect the heart has yet to be established. The genetic rationale for why certain patients experience cardiotoxicity whilst other patients can tolerate high chemotherapy doses has proven highly illusive. This has led to significant genomic efforts using targeted and genome-wide association studies (GWAS) to divine the pharmacogenomic cause of this predilection. With the advent of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), the putative risk and protective role of single nucleotide polymorphisms (SNPs) can now be validated in a human model. Here we review the state of the art knowledge of the genetic predilection to chemotherapy-induced cardiotoxicity and discuss the future for establishing and validating the role of the genome in this disease.

  17. An analysis on spatial variation of urban human thermal comfort in Hangzhou,China

    Institute of Scientific and Technical Information of China (English)

    WANG Wei-wu; ZHU Li-zhong; WANG Ren-chao

    2004-01-01

    Urban human thermal comfort (UHTC) is affected for interacting of weather condition and underlyingsurface framework of urban area. Urban underlying surface temperature value and Normalized Difference VegetationIndex(NDVI) were calculated using image interpreting and supervised classification technique by ERDAS IMAGEsoftware using 1991 and 1999 Landsat TM images data. Reference to the relational standard of assessing humanthermal comfort and other meteorology data of Hangzhou City in summer, air temperature and relative humidityvariation of different land types of underlying surface were inversed. By choosing discomfort index as an indictor, thespatial distribution characteristic and the spatial variation degree of UHTC were estimated and mapped on a middlescale, that is, in six districts of Hangzhou. The main characteristics of UHTC spatial variation from 1991 to 1999 wererevealed using a GIS-based calculation model. The variation mechanism were analyzed and discussed from theviewpoint of city planning, construction and environmental protection.

  18. Severity of infection and seasonal variation of non-typhoid Salmonelle occurence in humans

    DEFF Research Database (Denmark)

    Gradel, K.O.; Dethlefsen, Claus; Schønheyder, H.C.

    2007-01-01

    Non-typhoid Salmonella infections may present as severe gastroenteritis necessitatinghospitalization and some patients become septic with bacteraemia. We hypothesized that theseasonal variation of non-typhoid Salmonella occurrence in humans diminishes with increasedseverity of infection. We...... examined the seasonal variation of non-typhoid Salmonella infections inthree patient groups with differing severity of infection: outpatients treated for gastroenteritis(n=1490); in-patients treated for gastroenteritis (n=492); and in-patients treated for bacteraemia(n=113). The study was population...... 2·4–4·2) forin-patients with gastroenteritis, and 1·6 (95% CI 1·0–2·8) for in-patients with bacteraemia. We conclude that the role of seasonal variation diminishes with increased severity of non-typhoidSalmonella infection....

  19. Selective constraint on copy number variation in human piwi-interacting RNA Loci.

    Directory of Open Access Journals (Sweden)

    David W Gould

    Full Text Available Piwi-interacting RNAs (piRNAs are a recently discovered class of small non-coding RNA found in animals. PiRNAs are primarily expressed in the germline where their best understood function is to repress transposable elements. Unlike previous studies that investigated the evolution of piRNA-generating loci at the level of nucleotide substitutions, here we studied the evolution of piRNA-generating loci at the level of copy number variation (i.e. duplications and deletions using genome-wide copy number variation data from three human populations. Our analysis shows that at the level of copy number variation there is strong selective constraint and a very high mutation rate in human piRNA-generating loci. Our results differ from a model of positive selection on copy number variation in piRNA-generating loci previously proposed in rodents. We discuss possible reasons for this difference based on the transposable element insertion histories in the rodent and primate lineages.

  20. Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue

    OpenAIRE

    Leopold Parts; Hedman, Åsa K.; Sarah Keildson; Knights, Andrew J.; Cei Abreu-Goodger; Martijn van de Bunt; José Afonso Guerra-Assunção; Nenad Bartonicek; Stijn van Dongen; Reedik Mägi; James Nisbet; Amy Barrett; Mattias Rantalainen; Nica, Alexandra C.; Quail, Michael A

    2012-01-01

    Small RNAs are functional molecules that modulate mRNA transcripts and have been implicated in the aetiology of several common diseases. However, little is known about the extent of their variability within the human population. Here, we characterise the extent, causes, and effects of naturally occurring variation in expression and sequence of small RNAs from adipose tissue in relation to genotype, gene expression, and metabolic traits in the MuTHER reference cohort. We profiled the expressio...

  1. Biological and Analytical Variation of the Human Sweating Response: Implications for Study Design and Analysis

    Science.gov (United States)

    2012-01-01

    information http://www.the-aps.org/publications/ajpregu This infomation is current as of January 24, 2012. ISSN: 0363-6119, ESSN: 1522-1490. Visit our...sweating rate; reproducibility; exercise-heat stress; sweating onset A FUNDAMENTAL CHALLENGE IN the study of human integrative physiology is in the...analysis software. Analytical variation. To determine the ventilated sweat capsule measurement system CVa, measurements of SR were made in an

  2. Assessing endocranial variations in great apes and humans using 3D data from virtual endocasts.

    Science.gov (United States)

    Bienvenu, Thibaut; Guy, Franck; Coudyzer, Walter; Gilissen, Emmanuel; Roualdès, Georges; Vignaud, Patrick; Brunet, Michel

    2011-06-01

    Modern humans are characterized by their large, complex, and specialized brain. Human brain evolution can be addressed through direct evidence provided by fossil hominid endocasts (i.e. paleoneurology), or through indirect evidence of extant species comparative neurology. Here we use the second approach, providing an extant comparative framework for hominid paleoneurological studies. We explore endocranial size and shape differences among great apes and humans, as well as between sexes. We virtually extracted 72 endocasts, sampling all extant great ape species and modern humans, and digitized 37 landmarks on each for 3D generalized Procrustes analysis. All species can be differentiated by their endocranial shape. Among great apes, endocranial shapes vary from short (orangutans) to long (gorillas), perhaps in relation to different facial orientations. Endocranial shape differences among African apes are partly allometric. Major endocranial traits distinguishing humans from great apes are endocranial globularity, reflecting neurological reorganization, and features linked to structural responses to posture and bipedal locomotion. Human endocasts are also characterized by posterior location of foramina rotunda relative to optic canals, which could be correlated to lesser subnasal prognathism compared to living great apes. Species with larger brains (gorillas and humans) display greater sexual dimorphism in endocranial size, while sexual dimorphism in endocranial shape is restricted to gorillas, differences between males and females being at least partly due to allometry. Our study of endocranial variations in extant great apes and humans provides a new comparative dataset for studies of fossil hominid endocasts.

  3. Early modern humans and morphological variation in Southeast Asia: fossil evidence from Tam Pa Ling, Laos.

    Directory of Open Access Journals (Sweden)

    Fabrice Demeter

    Full Text Available Little is known about the timing of modern human emergence and occupation in Eastern Eurasia. However a rapid migration out of Africa into Southeast Asia by at least 60 ka is supported by archaeological, paleogenetic and paleoanthropological data. Recent discoveries in Laos, a modern human cranium (TPL1 from Tam Pa Ling's cave, provided the first evidence for the presence of early modern humans in mainland Southeast Asia by 63-46 ka. In the current study, a complete human mandible representing a second individual, TPL 2, is described using discrete traits and geometric morphometrics with an emphasis on determining its population affinity. The TPL2 mandible has a chin and other discrete traits consistent with early modern humans, but it retains a robust lateral corpus and internal corporal morphology typical of archaic humans across the Old World. The mosaic morphology of TPL2 and the fully modern human morphology of TPL1 suggest that a large range of morphological variation was present in early modern human populations residing in the eastern Eurasia by MIS 3.

  4. Adaptive potential of genomic structural variation in human and mammalian evolution.

    Science.gov (United States)

    Radke, David W; Lee, Charles

    2015-09-01

    Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification.

  5. Comparison of inter- and intraspecies variation in humans and fruit flies

    Directory of Open Access Journals (Sweden)

    Juliann Shih

    2015-03-01

    Full Text Available Variation is essential to species survival and adaptation during evolution. This variation is conferred by the imperfection of biochemical processes, such as mutations and alterations in DNA sequences, and can also be seen within genomes through processes such as the generation of antibodies. Recent sequencing projects have produced multiple versions of the genomes of humans and fruit flies (Drosophila melanogaster. These give us a chance to study how individual gene sequences vary within and between species. Here we arranged human and fly genes in orthologous pairs and compared such within-species variability with their degree of conservation between flies and humans. We observed that a significant number of proteins associated with mRNA translation are highly conserved between species and yet are highly variable within each species. The fact that we observe this in two species whose lineages separated more than 700 million years ago suggests that this is the result of a very ancient process. We hypothesize that this effect might be attributed to a positive selection for variability of virus-interacting proteins that confers a general resistance to viral hijacking of the mRNA translation machinery within populations. Our analysis points to this and to other processes resulting in positive selection for gene variation.

  6. VARIATIONS OF MIDDLE SEGMENTAL ARTERY OF HUMAN KIDNEY AND CLINICAL SIGNIFICANCE

    Directory of Open Access Journals (Sweden)

    Gyan Prakash Mishra

    2015-12-01

    Full Text Available Aim: To assess the arterial pattern of middle segmental artery and its relation with collecting system in the human kidneys. Materials and Methods: We studied 50 fresh human Kidneys by corrosion cast techniques. We used different colour coded moulding granules of butyl butyrate, red for artery, blue for vein and black for collecting system of the human kidneys. 20% solution of butyl butyrate in acetone was injected into renal vessels and ureter of each kidney. Injected kidneys were kept immersed in concentrated Potassium Hydroxide solution for corrosion to obtain the endocasts. These endocasts were cleaned under the running tap water and observed macroscopically. Results: We observed three types of variations in arterial pattern of middle segmental artery namely Middle Segmental Artery Type-1 (MSAT1, Middle Segmental Artery Type-2 (MSAT2, Middle Segmental Artery Type-3 (MSAT3 and they were seen in 29(58%, 14(28%, 6(12% kidneys respectively. We also observed three different variations in relation between middle segmental artery and collecting system namely Middle Segmental Artery Group-1 (MSAG1, Middle Segmental Artery Group-2 (MSAG2, Middle Segmental Artery Group-3 (MSAG3 and they were seen in 32%, 24%, 42% kidneys respectively. Conclusion: Anatomical knowledge of these variations is of valuable contribution for uro-surgeon in performing more and more conservative renal surgeries which lead to preservation of healthy and functional renal parenchyma and prevent intraoperative and post-operative complications.

  7. 78 FR 5816 - Guidance for Industry on Clinical Pharmacogenomics: Premarket Evaluation in Early-Phase Clinical...

    Science.gov (United States)

    2013-01-28

    ... assist the pharmaceutical industry and other investigators engaged in new drug development in evaluating... interested persons engaged in new drug development in evaluating how variations in the human...

  8. Use of combinatorial pharmacogenomic testing in two cases from community psychiatry

    Science.gov (United States)

    Fields, Eve S; Lorenz, Raymond A; Winner, Joel G

    2016-01-01

    This report describes two cases in which pharmacogenomic testing was utilized to guide medication selection for difficult to treat patients. The first patient is a 29-year old male with bipolar disorder who had severe akathisia due to his long acting injectable antipsychotic. The second patient is a 59-year old female with major depressive disorder who was not responding to her medication. In both cases, a proprietary combinatorial pharmacogenomic test was used to inform medication changes and improve patient outcomes. The first patient was switched to a long acting injectable that was not affected by his genetic profile and his adverse effects abated. The second patient had her medications discontinued due to the results of the genetic testing and more intense psychotherapy initiated. While pharmacogenomic testing may be helpful in cases such as these presented here, it should never serve as a proxy for a comprehensive biopsychosocial approach. The pharmacogenomic information may be selectively added to this comprehensive approach to support medication treatment. PMID:27574460

  9. Economic Evaluations of Pharmacogenetic and Pharmacogenomic Screening Tests : A Systematic Review. Second Update of the Literature

    NARCIS (Netherlands)

    Berm, Elizabeth J J; Looff, Margot de; Wilffert, Bob; Boersma, Cornelis; Annemans, Lieven; Vegter, Stefan; van Boven, Job FM; Postma, Maarten J

    2016-01-01

    Objective Due to extended application of pharmacogenetic and pharmacogenomic screening (PGx) tests it is important to assess whether they provide good value for money. This review provides an update of the literature. Methods A literature search was performed in PubMed and papers published between

  10. Interactive Communication in Pharmacogenomics Innovations: User-producer interaction from an innovation and science communication perspective

    NARCIS (Netherlands)

    Verhoeff, R.P.; Moors, E.H.M.; Osseweijer, P.

    2008-01-01

    Pharmacogenomics is a quickly evolving field of research that increasingly impacts individuals and society. As some innovations in biotechnology have experienced strong public opposition during the 1990s, interaction between producers and users of these innovations may help in increasing their succe

  11. Opioid Therapy Pharmacogenomics for Noncancer Pain: Efficacy, Adverse Events, and Costs

    Directory of Open Access Journals (Sweden)

    Yan Xu

    2013-01-01

    Full Text Available Chronic non-cancer pain is a debilitating condition associated with high individual and societal costs. While opioid treatment for pain has been available for centuries, it is associated with high variability in outcome, and a considerable proportion of patients is unable to attain relief from symptoms while suffering adverse events and developing medication dependence. We performed a review of the efficacy of pharmacogenomic markers and their abilities to predict adverse events, dependence, and associated economic costs, focusing on two genes: OPRM1 and CYP2D6. Data sources were articles indexed by PubMed on or before August 6, 2013. Articles were first selected after review of their titles and abstracts, and full papers were read to confirm eligibility. Initially, fifty-two articles were identified. Of these, 17 were relevant to biological actions of pharmacogenomic markers and their effect on therapeutic efficacy, 16 to adverse events, 15 to opioid dependence, and eight to economic costs. In conclusion, increasing costs of opioid therapy have made the advances in pharmacogenomics an attractive solution to personalize care with unclear repercussions related to the impact on costs, morbidity, and outcomes. This intersection of pharmacoeconomics and pharmacogenomics presents a unique platform to further examine current advances in clinical medicine and their utility in cost-effective treatment of chronic pain.

  12. Interactive Communication in Pharmacogenomics Innovations: User-producer interaction from an innovation and science communication perspective

    NARCIS (Netherlands)

    Verhoeff, R.P.; Moors, E.H.M.; Osseweijer, P.

    2008-01-01

    Pharmacogenomics is a quickly evolving field of research that increasingly impacts individuals and society. As some innovations in biotechnology have experienced strong public opposition during the 1990s, interaction between producers and users of these innovations may help in increasing their

  13. Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: a case study.

    Science.gov (United States)

    Zhu, Qian; Freimuth, Robert R; Lian, Zonghui; Bauer, Scott; Pathak, Jyotishman; Tao, Cui; Durski, Matthew J; Chute, Christopher G

    2013-04-01

    The Pharmacogenomics Research Network (PGRN) is a collaborative partnership of research groups funded by NIH to discover and understand how genome contributes to an individual's response to medication. Since traditional biomedical research studies and clinical trials are often conducted independently, common and standardized representations for data are seldom used. This leads to heterogeneity in data representation, which hinders data reuse, data integration and meta-analyses. This study demonstrates harmonization and semantic annotation work for pharmacogenomics data dictionaries collected from PGRN research groups. A semi-automated system was developed to support the harmonization/annotation process, which includes four individual steps, (1) pre-processing PGRN variables; (2) decomposing and normalizing variable descriptions; (3) semantically annotating words and phrases using controlled terminologies; (4) grouping PGRN variables into categories based on the annotation results and semantic types, for total 1514 PGRN variables. Our results demonstrate that there is a significant amount of variability in how pharmacogenomics data is represented and that additional standardization efforts are needed. This represents a critical first step toward identifying and creating data standards for pharmacogenomics studies.

  14. Pharmacogenetics, pharmacogenomics and ayurgenomics for personalized medicine: a paradigm shift.

    Science.gov (United States)

    Gupta, Pooja D

    2015-01-01

    The value of health care can be increased tremendously through individualized medicine. With the promise of individualized medicine, healthcare professionals will be able to better predict disease risk, prevent development of disease and manage treatments more efficiently thereby allowing people to be healthier and active longer. The developments in the area of pharmacogenetics/pharmacogenomics can help the physicians achieve the target of personalized medicine. Personalized medicine will come to mean not just the right drug for the right individual, but the right drug for the specific disease affecting a specific individual. The use of personalized medicine will make clinical trials more efficient by lowering the costs that would arise due to adverse drug effects and prescription of drugs that have been proven ineffective in certain genotypes. The genotypic experiments have laid valuable insights into genetic underpinnings of diseases. However it is being realized that identification of sub-groups within normal controls corresponding to contrasting disease susceptibility could lead to more effective discovery of predictive markers for diseases. However there are no modern methods available to look at the inter-individual differences within ethnically matched healthy populations. Ayurveda, an exquisitely elaborate system of predictive medicine which has been practiced for over 3500 years in India, can help in bridging this gap. In contrast to the contemporary system of medicine, the therapeutic regimen in Ayurveda is implicated on tridoshas and prakriti. According to this system, every individual is born with his or her own basic constitution, which to a great extent regulates inter-individual variability in susceptibility to diseases and response to external environment, diet and drugs. Thus the researchers in India have demonstrated that integration of this stratified approach of Ayurveda into genomics i.e. Ayurgenomics could complement personalized medicine.

  15. Cardiovascular pharmacogenomics; state of current knowledge and implementation in practice.

    Science.gov (United States)

    Shahabi, Payman; Dubé, Marie-Pierre

    2015-04-01

    Pharmacogenomics (PGx) is the science that examines how an individual's genetic make-up affects the safety and efficacy of therapeutic drugs. PGx of response to cardiovascular (CV) medications is of the most successfully translated branches of PGx into the clinical workout. However, the clinical implementation of PGx of CV drugs is yet far beyond the growth of our understanding of the role of genetics in drug therapy. A considerable amount of efforts have been devoted by the regulatory agents like the food and drug administration (FDA) as well as the expert-based networks such as the Clinical Pharmacogenetics Implementation Consortium (CPIC) to overcome the existing barriers. This has been done, at least in part, for some of the most widely prescribed CV drugs, including clopidogrel, warfarin and simvastatin for which the PGx knowledge have been satisfactorily robust to provoke the CPIC to issue the guidelines for these drugs and the FDA to update the drugs' labeling, both strongly recommended the use of genotype-guided dosing for these medications, provided that the genetic data are available. For other drugs, however, studies have produced contradictory results and further large and well-designed clinical trials are required to expand and confirm the clinical utility of their PGx data. This review paper presents the current state of knowledge in the field of PGx of CV medications and describes the facilities assisting to the translation of PGx data into the clinical practice. Afterward, the existing body of PGx literature of the most-commonly used CV medications is comprehensively discussed.

  16. Pharmacogenomics of statins: understanding susceptibility to adverse effects

    Directory of Open Access Journals (Sweden)

    Kitzmiller JP

    2016-10-01

    Full Text Available Joseph P Kitzmiller,1 Eduard B Mikulik,1 Anees M Dauki,2 Chandrama Murkherjee,1 Jasmine A Luzum3 1Department of Biological Chemistry and Pharmacology, College of Medicine, 2College of Pharmacy, The Ohio State University, Columbus, OH, 3Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI, USA Abstract: Statins are a cornerstone of the pharmacologic treatment and prevention of atherosclerotic cardiovascular disease. Atherosclerotic disease is a predominant cause of mortality and morbidity worldwide. Statins are among the most commonly prescribed classes of medications, and their prescribing indications and target patient populations have been significantly expanded in the official guidelines recently published by the American and European expert panels. Adverse effects of statin pharmacotherapy, however, result in significant cost and morbidity and can lead to nonadherence and discontinuation of therapy. Statin-associated muscle symptoms occur in ~10% of patients on statins and constitute the most commonly reported adverse effect associated with statin pharmacotherapy. Substantial clinical and nonclinical research effort has been dedicated to determining whether genetics can provide meaningful insight regarding an individual patient’s risk of statin adverse effects. This contemporary review of the relevant clinical research on polymorphisms in several key genes that affect statin pharmacokinetics (eg, transporters and metabolizing enzymes, statin efficacy (eg, drug targets and pathways, and end-organ toxicity (eg, myopathy pathways highlights several promising pharmacogenomic candidates. However, SLCO1B1 521C is currently the only clinically relevant pharmacogenetic test regarding statin toxicity, and its relevance is limited to simvastatin myopathy. Keywords: cholesterol, myopathy, lipids, muscle toxicity, pharmacokinetics, pharmacogenetics

  17. Pharmacogenomic Study of Clozapine-Induced Agranulocytosis/Granulocytopenia in a Japanese Population.

    Science.gov (United States)

    Saito, Takeo; Ikeda, Masashi; Mushiroda, Taisei; Ozeki, Takeshi; Kondo, Kenji; Shimasaki, Ayu; Kawase, Kohei; Hashimoto, Shuji; Yamamori, Hidenaga; Yasuda, Yuka; Fujimoto, Michiko; Ohi, Kazutaka; Takeda, Masatoshi; Kamatani, Yoichiro; Numata, Shusuke; Ohmori, Tetsuro; Ueno, Shu-Ichi; Makinodan, Manabu; Nishihata, Yosuke; Kubota, Masaharu; Kimura, Takemi; Kanahara, Nobuhisa; Hashimoto, Naoki; Fujita, Kiyoshi; Nemoto, Kiyotaka; Fukao, Taku; Suwa, Taro; Noda, Tetsuro; Yada, Yuji; Takaki, Manabu; Kida, Naoya; Otsuru, Taku; Murakami, Masaru; Takahashi, Atsushi; Kubo, Michiaki; Hashimoto, Ryota; Iwata, Nakao

    2016-10-15

    Clozapine-induced agranulocytosis (CIA)/clozapine-induced granulocytopenia (CIG) (CIAG) is a life-threatening event for schizophrenic subjects treated with clozapine. To examine the genetic factor for CIAG, a genome-wide pharmacogenomic analysis was conducted using 50 subjects with CIAG and 2905 control subjects. We identified a significant association in the human leukocyte antigen (HLA) region (rs1800625, p = 3.46 × 10(-9), odds ratio [OR] = 3.8); therefore, subsequent HLA typing was performed. We detected a significant association of HLA-B*59:01 with CIAG (p = 3.81 × 10(-8), OR = 10.7) and confirmed this association by comparing with an independent clozapine-tolerant control group (n = 380, p = 2.97 × 10(-5), OR = 6.3). As we observed that the OR of CIA (OR: 9.3~15.8) was approximately double that in CIG (OR: 4.4~7.4), we hypothesized that the CIG subjects were a mixed population of those who potentially would develop CIA and those who would not develop CIA (non-CIA). This hypothesis allowed the proportion of the CIG who were non-CIA to be calculated, enabling us to estimate the positive predictive value of the nonrisk allele on non-CIA in CIG subjects. Assuming this model, we estimated that 1) ~50% of CIG subjects would be non-CIA; and 2) ~60% of the CIG subjects without the risk allele would be non-CIA and therefore not expected to develop CIA. Our results suggest that HLA-B*59:01 is a risk factor for CIAG in the Japanese population. Furthermore, if our model is true, the results suggest that rechallenging certain CIG subjects with clozapine may not be always contraindicated. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  18. Inter-chromosomal variation in the pattern of human population genetic structure

    Directory of Open Access Journals (Sweden)

    Baye Tesfaye M

    2011-05-01

    Full Text Available Abstract Emerging technologies now make it possible to genotype hundreds of thousands of genetic variations in individuals, across the genome. The study of loci at finer scales will facilitate the understanding of genetic variation at genomic and geographic levels. We examined global and chromosomal variations across HapMap populations using 3.7 million single nucleotide polymorphisms to search for the most stratified genomic regions of human populations and linked these regions to ontological annotation and functional network analysis. To achieve this, we used five complementary statistical and genetic network procedures: principal component (PC, cluster, discriminant, fixation index (FST and network/pathway analyses. At the global level, the first two PC scores were sufficient to account for major population structure; however, chromosomal level analysis detected subtle forms of population structure within continental populations, and as many as 31 PCs were required to classify individuals into homogeneous groups. Using recommended population ancestry differentiation measures, a total of 126 regions of the genome were catalogued. Gene ontology and networks analyses revealed that these regions included the genes encoding oculocutaneous albinism II (OCA2, hect domain and RLD 2 (HERC2, ectodysplasin A receptor (EDAR and solute carrier family 45, member 2 (SLC45A2. These genes are associated with melanin production, which is involved in the development of skin and hair colour, skin cancer and eye pigmentation. We also identified the genes encoding interferon-γ (IFNG and death-associated protein kinase 1 (DAPK1, which are associated with cell death, inflammatory and immunological diseases. An in-depth understanding of these genomic regions may help to explain variations in adaptation to different environments. Our approach offers a comprehensive strategy for analysing chromosome-based population structure and differentiation, and demonstrates the

  19. Variation at genes influencing facial morphology are not associated with developmental imprecision in human faces.

    Directory of Open Access Journals (Sweden)

    Sonja Windhager

    Full Text Available Facial asymmetries are commonly used as a proxy for human developmental imprecision resulting from inbreeding, and thus reduced genetic heterozygosity. Several environmental factors influence human facial asymmetry (e.g., health care, parasites, but the generalizability of findings on genetic stressors has been limited in humans by sample characteristics (island populations, endogamy and indirect genetic assessment (inference from pedigrees. In a sample of 3215 adult humans from the Rotterdam Study, we therefore studied the relationship of facial asymmetry, estimated from nine mid-facial landmarks, with genetic variation at 102 single nucleotide polymorphism (SNP loci recently associated with facial shape variation. We further tested whether the degree of individual heterozygosity is negatively correlated with facial asymmetry. An ANOVA tree regression did not identify any SNP relating to either fluctuating asymmetry or total asymmetry. In a general linear model, only age and sex--but neither heterozygosity nor any SNP previously reported to covary with facial shape--was significantly related to total or fluctuating asymmetry of the midface. Our study does not corroborate the common assumption in evolutionary and behavioral biology that morphological asymmetries reflect heterozygosity. Our results, however, may be affected by a relatively small degree of inbreeding, a relatively stable environment, and an advanced age in the Rotterdam sample. Further large-scale genetic studies, including gene expression studies, are necessary to validate the genetic and developmental origin of morphological asymmetries.

  20. Role of Pharmacogenomics in Statin Responsiveness; A Review

    Directory of Open Access Journals (Sweden)

    Niusha behdad

    2015-12-01

    Full Text Available Statins have been used for decades as a successful cholesterol-lowering class of medicines. Statins are widely prescribed for the primary and secondary prevention of coronary artery disease. They reduce cardiovascular risk and improve health outcomes in people with cardiovascular disease. Although statins re considered as a safe medicine and are well tolerated by patients, prediction of an individual patient’s response to statin therapy remains unclear. Variation to statin therapy has been attributed to both environmental and genetic factors. In this review, a number of candidate genes that affect statin pharmacokinetics and pharmacodynamics are discussed. Moreover, the association of demographic factors with statin response in related studies is described. In this article we have reviewed the literature concerning pharmacogenetic studies on statin response. Thirty seven English-language clinical trials, prospective or retrospective human investigations, case series, case reports, published between 1998 to 2015, were evaluated. Based on these data, there are some candidate genes that have been established as affecting genes on statin efficacy and suggest that drug therapy, based on individuals’ genetic makeup, may result in a clinically important reduction in variation of statin response.

  1. Natural selection affects multiple aspects of genetic variation at putatively peutral sites across the human genome

    DEFF Research Database (Denmark)

    Lohmueller, Kirk E; Albrechtsen, Anders; Li, Yingrui;

    2011-01-01

    throughout the genome. Further, we show that the widespread presence of weakly deleterious alleles, rather than a small number of strongly positively selected mutations, is responsible for the correlation between neutral genetic diversity and recombination rate. This work suggests that natural selection has......A major question in evolutionary biology is how natural selection has shaped patterns of genetic variation across the human genome. Previous work has documented a reduction in genetic diversity in regions of the genome with low recombination rates. However, it is unclear whether other summaries...... and that human diversity, human-chimp divergence, and average minor allele frequency are reduced near genes. Population genetic simulations show that either positive natural selection acting on favorable mutations or negative natural selection acting against deleterious mutations can explain these correlations...

  2. Variations in Humanized and Defined Culture Conditions Supporting Derivation of New Human Embryonic Stem Cell Lines

    DEFF Research Database (Denmark)

    Fletcher, Judy M; Ferrier, Patricia M; Gardner, John O

    2006-01-01

    and the potential to form cells representative of all three germinal lineages in vitro and in vivo, when transitioned off of feeders onto Laminin or Matrigel. Our study thus demonstrates the capacity to integrate derivation strategies eliminating a requirement for animal immune compliment and serum products......, with a transitional requirement for human feeder cells. This represents another sequential step in the generation of therapeutic grade stem cells with reduced risk of zoonotic pathogen transmission....

  3. Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity.

    Science.gov (United States)

    Gupta, Vinod K; Paul, Sandip; Dutta, Chitra

    2017-01-01

    One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats-Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT). The review focuses on the general trend in the human microbiome evolution-a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota-the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome-nature or nurture, host genetics or his environment. Some of

  4. Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

    Directory of Open Access Journals (Sweden)

    Vinod K. Gupta

    2017-06-01

    Full Text Available One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats—Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT. The review focuses on the general trend in the human microbiome evolution—a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota—the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome—nature or nurture, host genetics

  5. Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

    Science.gov (United States)

    Gupta, Vinod K.; Paul, Sandip; Dutta, Chitra

    2017-01-01

    One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats—Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT). The review focuses on the general trend in the human microbiome evolution—a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota—the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome—nature or nurture, host genetics or his environment

  6. Patterns of genic intolerance of rare copy number variation in 59,898 human exomes.

    Science.gov (United States)

    Ruderfer, Douglas M; Hamamsy, Tymor; Lek, Monkol; Karczewski, Konrad J; Kavanagh, David; Samocha, Kaitlin E; Daly, Mark J; MacArthur, Daniel G; Fromer, Menachem; Purcell, Shaun M

    2016-10-01

    Copy number variation (CNV) affecting protein-coding genes contributes substantially to human diversity and disease. Here we characterized the rates and properties of rare genic CNVs (<0.5% frequency) in exome sequencing data from nearly 60,000 individuals in the Exome Aggregation Consortium (ExAC) database. On average, individuals possessed 0.81 deleted and 1.75 duplicated genes, and most (70%) carried at least one rare genic CNV. For every gene, we empirically estimated an index of relative intolerance to CNVs that demonstrated moderate correlation with measures of genic constraint based on single-nucleotide variation (SNV) and was independently correlated with measures of evolutionary conservation. For individuals with schizophrenia, genes affected by CNVs were more intolerant than in controls. The ExAC CNV data constitute a critical component of an integrated database spanning the spectrum of human genetic variation, aiding in the interpretation of personal genomes as well as population-based disease studies. These data are freely available for download and visualization online.

  7. Donor-dependent variations in hepatic differentiation from human-induced pluripotent stem cells.

    Science.gov (United States)

    Kajiwara, Masatoshi; Aoi, Takashi; Okita, Keisuke; Takahashi, Ryosuke; Inoue, Haruhisa; Takayama, Naoya; Endo, Hiroshi; Eto, Koji; Toguchida, Junya; Uemoto, Shinji; Yamanaka, Shinya

    2012-07-31

    Hepatocytes generated from human induced pluripotent stem cells (hiPSCs) are unprecedented resources for pharmaceuticals and cell therapy. However, the in vitro directed differentiation of human pluripotent stem cells into mature hepatocytes remains challenging. Little attention has so far been paid to variations among hiPSC lines in terms of their hepatic differentiation. In the current study, we developed an improved hepatic differentiation protocol and compared 28 hiPSC lines originated from various somatic cells and derived using retroviruses, Sendai viruses, or episomal plasmids. This comparison indicated that the origins, but not the derivation methods, may be a major determinant of variation in hepatic differentiation. The hiPSC clones derived from peripheral blood cells consistently showed good differentiation efficiency, whereas many hiPSC clones from adult dermal fibroblasts showed poor differentiation. However, when we compared hiPSCs from peripheral blood and dermal fibroblasts from the same individuals, we found that variations in hepatic differentiation were largely attributable to donor differences, rather than to the types of the original cells. These data underscore the importance of donor differences when comparing the differentiation propensities of hiPSC clones.

  8. Landscape and variation of RNA secondary structure across the human transcriptome.

    Science.gov (United States)

    Wan, Yue; Qu, Kun; Zhang, Qiangfeng Cliff; Flynn, Ryan A; Manor, Ohad; Ouyang, Zhengqing; Zhang, Jiajing; Spitale, Robert C; Snyder, Michael P; Segal, Eran; Chang, Howard Y

    2014-01-30

    In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. Here we report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child). This provides a comprehensive RSS map of human coding and non-coding RNAs. We identify unique RSS signatures that demarcate open reading frames and splicing junctions, and define authentic microRNA-binding sites. Comparison of native deproteinized RNA isolated from cells versus refolded purified RNA suggests that the majority of the RSS information is encoded within RNA sequence. Over 1,900 transcribed single nucleotide variants (approximately 15% of all transcribed single nucleotide variants) alter local RNA structure. We discover simple sequence and spacing rules that determine the ability of point mutations to impact RSSs. Selective depletion of 'riboSNitches' versus structurally synonymous variants at precise locations suggests selection for specific RNA shapes at thousands of sites, including 3' untranslated regions, binding sites of microRNAs and RNA-binding proteins genome-wide. These results highlight the potentially broad contribution of RNA structure and its variation to gene regulation.

  9. Effect of speech-intrinsic variations on human and automatic recognition of spoken phonemes.

    Science.gov (United States)

    Meyer, Bernd T; Brand, Thomas; Kollmeier, Birger

    2011-01-01

    The aim of this study is to quantify the gap between the recognition performance of human listeners and an automatic speech recognition (ASR) system with special focus on intrinsic variations of speech, such as speaking rate and effort, altered pitch, and the presence of dialect and accent. Second, it is investigated if the most common ASR features contain all information required to recognize speech in noisy environments by using resynthesized ASR features in listening experiments. For the phoneme recognition task, the ASR system achieved the human performance level only when the signal-to-noise ratio (SNR) was increased by 15 dB, which is an estimate for the human-machine gap in terms of the SNR. The major part of this gap is attributed to the feature extraction stage, since human listeners achieve comparable recognition scores when the SNR difference between unaltered and resynthesized utterances is 10 dB. Intrinsic variabilities result in strong increases of error rates, both in human speech recognition (HSR) and ASR (with a relative increase of up to 120%). An analysis of phoneme duration and recognition rates indicates that human listeners are better able to identify temporal cues than the machine at low SNRs, which suggests incorporating information about the temporal dynamics of speech into ASR systems.

  10. Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome

    Directory of Open Access Journals (Sweden)

    Chadwick Brian P

    2010-11-01

    Full Text Available Abstract Background Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease facioscapulohumeral muscular dystrophy. Nevertheless, many other macrosatellite arrays in the human genome remain poorly characterized. Results Here we describe the organization, tandem repeat copy number variation, transmission stability and expression of four macrosatellite arrays in the human genome: the TAF11-Like array located on chromosomes 5p15.1, the SST1 arrays on 4q28.3 and 19q13.12, the PRR20 array located on chromosome 13q21.1, and the ZAV array at 9q32. All are polymorphic macrosatellite arrays that at least for TAF11-Like and SST1 show evidence of meiotic instability. With the exception of the SST1 array that is ubiquitously expressed, all are expressed at high levels in the testis and to a lesser extent in the brain. Conclusions Our results extend the number of characterized macrosatellite arrays in the human genome and provide the foundation for formulation of hypotheses to begin assessing their functional role in the human genome.

  11. Animal Models of Psychiatric Disorders That Reflect Human Copy Number Variation

    Directory of Open Access Journals (Sweden)

    Jun Nomura

    2012-01-01

    Full Text Available The development of genetic technologies has led to the identification of several copy number variations (CNVs in the human genome. Genome rearrangements affect dosage-sensitive gene expression in normal brain development. There is strong evidence associating human psychiatric disorders, especially autism spectrum disorders (ASDs and schizophrenia to genetic risk factors and accumulated CNV risk loci. Deletions in 1q21, 3q29, 15q13, 17p12, and 22q11, as well as duplications in 16p11, 16p13, and 15q11-13 have been reported as recurrent CNVs in ASD and/or schizophrenia. Chromosome engineering can be a useful technology to reflect human diseases in animal models, especially CNV-based psychiatric disorders. This system, based on the Cre/loxP strategy, uses large chromosome rearrangement such as deletion, duplication, inversion, and translocation. Although it is hard to reflect human pathophysiology in animal models, some aspects of molecular pathways, brain anatomy, cognitive, and behavioral phenotypes can be addressed. Some groups have created animal models of psychiatric disorders, ASD, and schizophrenia, which are based on human CNV. These mouse models display some brain anatomical and behavioral abnormalities, providing insight into human neuropsychiatric disorders that will contribute to novel drug screening for these devastating disorders.

  12. Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

    Directory of Open Access Journals (Sweden)

    Brett eWagner Mackenzie

    2015-02-01

    Full Text Available The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation, with a smaller proportion of variation associated with DNA extraction method (technical variation and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

  13. Variation in macronutrients in human bank milk: influencing factors and implications for human milk banking

    DEFF Research Database (Denmark)

    Michaelsen, K F; Skafte, L; Badsberg, J H;

    1990-01-01

    Protein (P), fat (F), and carbohydrate (C) concentration in expressed human bank milk was determined by infrared analysis of 2,554 samples from 224 mothers. The mean contents of P, F, C, and energy (E, calculated from P, F, and C) were 9.0 g/L, 39.0 g/L, 71.9 g/L, and 696 kcal/L, respectively...... with a high P content, we have developed a "high-protein" milk with a P content of about 12 g/L (true protein) and an E content of about 725 kcal/L. Thus, by continuous monitoring of macronutrient content in human bank milk it is possible to develop a "high-protein" milk with sufficient P and E content....... The main results were as follows: the P and F contents increased slightly with increasing body mass index of the mother, the P content decreased with increasing amounts of milk delivered to the milk bank, and the F content was higher in mothers delivering large amounts of milk. By selecting incoming milk...

  14. A comparison of worldwide phonemic and genetic variation in human populations.

    Science.gov (United States)

    Creanza, Nicole; Ruhlen, Merritt; Pemberton, Trevor J; Rosenberg, Noah A; Feldman, Marcus W; Ramachandran, Sohini

    2015-02-03

    Worldwide patterns of genetic variation are driven by human demographic history. Here, we test whether this demographic history has left similar signatures on phonemes-sound units that distinguish meaning between words in languages-to those it has left on genes. We analyze, jointly and in parallel, phoneme inventories from 2,082 worldwide languages and microsatellite polymorphisms from 246 worldwide populations. On a global scale, both genetic distance and phonemic distance between populations are significantly correlated with geographic distance. Geographically close language pairs share significantly more phonemes than distant language pairs, whether or not the languages are closely related. The regional geographic axes of greatest phonemic differentiation correspond to axes of genetic differentiation, suggesting that there is a relationship between human dispersal and linguistic variation. However, the geographic distribution of phoneme inventory sizes does not follow the predictions of a serial founder effect during human expansion out of Africa. Furthermore, although geographically isolated populations lose genetic diversity via genetic drift, phonemes are not subject to drift in the same way: within a given geographic radius, languages that are relatively isolated exhibit more variance in number of phonemes than languages with many neighbors. This finding suggests that relatively isolated languages are more susceptible to phonemic change than languages with many neighbors. Within a language family, phoneme evolution along genetic, geographic, or cognate-based linguistic trees predicts similar ancestral phoneme states to those predicted from ancient sources. More genetic sampling could further elucidate the relative roles of vertical and horizontal transmission in phoneme evolution.

  15. Genetics in endocrinology: genetic variation in deiodinases: a systematic review of potential clinical effects in humans.

    Science.gov (United States)

    Verloop, Herman; Dekkers, Olaf M; Peeters, Robin P; Schoones, Jan W; Smit, Johannes W A

    2014-09-01

    Iodothyronine deiodinases represent a family of selenoproteins involved in peripheral and local homeostasis of thyroid hormone action. Deiodinases are expressed in multiple organs and thyroid hormone affects numerous biological systems, thus genetic variation in deiodinases may affect multiple clinical endpoints. Interest in clinical effects of genetic variation in deiodinases has clearly increased. We aimed to provide an overview for the role of deiodinase polymorphisms in human physiology and morbidity. In this systematic review, studies evaluating the relationship between deiodinase polymorphisms and clinical parameters in humans were eligible. No restrictions on publication date were imposed. The following databases were searched up to August 2013: Pubmed, EMBASE (OVID-version), Web of Science, COCHRANE Library, CINAHL (EbscoHOST-version), Academic Search Premier (EbscoHOST-version), and ScienceDirect. Deiodinase physiology at molecular and tissue level is described, and finally the role of these polymorphisms in pathophysiological conditions is reviewed. Deiodinase type 1 (D1) polymorphisms particularly show moderate-to-strong relationships with thyroid hormone parameters, IGF1 production, and risk for depression. D2 variants correlate with thyroid hormone levels, insulin resistance, bipolar mood disorder, psychological well-being, mental retardation, hypertension, and risk for osteoarthritis. D3 polymorphisms showed no relationship with inter-individual variation in serum thyroid hormone parameters. One D3 polymorphism was associated with risk for osteoarthritis. Genetic deiodinase profiles only explain a small proportion of inter-individual variations in serum thyroid hormone levels. Evidence suggests a role of genetic deiodinase variants in certain pathophysiological conditions. The value for determination of deiodinase polymorphism in clinical practice needs further investigation. © 2014 European Society of Endocrinology.

  16. Economic evaluation of pharmacogenomics: a value-based approach to pragmatic decision making in the face of complexity.

    Science.gov (United States)

    Snyder, Susan R; Mitropoulou, Christina; Patrinos, George P; Williams, Marc S

    2014-01-01

    Evidence of the value of pharmacogenomic testing is needed to inform policymakers and clinicians for decision making related to adoption and coverage, and to facilitate prioritization for research and development. Pharmacogenomics has an important role in creating a more efficient healthcare system, and this article addresses how economic evaluation can strategically target evidence gaps for public health priorities with examples from pharmacogenomic medicine. This article begins with a review of the need for and use of economic evaluations in value-based decision making for pharmacogenomic testing. Three important gaps are described with examples demonstrating how they can be addressed: (1) projected impact of hypothetical new technology, (2) pre-implementation assessment of a specific technology, and (3) post-implementation assessment from relevant analytical stakeholder perspectives. Additional needs, challenges and approaches specific to pharmacogenomic economic evaluation in the developing world are also identified. These pragmatic approaches can provide much needed evidence to support real-world value-based decision making for pharmacogenomic-based screening and treatment strategies. © 2014 S. Karger AG, Basel.

  17. An ontology-based, mobile-optimized system for pharmacogenomic decision support at the point-of-care.

    Directory of Open Access Journals (Sweden)

    Jose Antonio Miñarro-Giménez

    Full Text Available BACKGROUND: The development of genotyping and genetic sequencing techniques and their evolution towards low costs and quick turnaround have encouraged a wide range of applications. One of the most promising applications is pharmacogenomics, where genetic profiles are used to predict the most suitable drugs and drug dosages for the individual patient. This approach aims to ensure appropriate medical treatment and avoid, or properly manage, undesired side effects. RESULTS: We developed the Medicine Safety Code (MSC service, a novel pharmacogenomics decision support system, to provide physicians and patients with the ability to represent pharmacogenomic data in computable form and to provide pharmacogenomic guidance at the point-of-care. Pharmacogenomic data of individual patients are encoded as Quick Response (QR codes and can be decoded and interpreted with common mobile devices without requiring a centralized repository for storing genetic patient data. In this paper, we present the first fully functional release of this system and describe its architecture, which utilizes Web Ontology Language 2 (OWL 2 ontologies to formalize pharmacogenomic knowledge and to provide clinical decision support functionalities. CONCLUSIONS: The MSC system provides a novel approach for enabling the implementation of personalized medicine in clinical routine.

  18. A train-the-trainer approach to a shared pharmacogenomics curriculum for US colleges and schools of pharmacy.

    Science.gov (United States)

    Lee, Kelly C; Ma, Joseph D; Hudmon, Karen Suchanek; Kuo, Grace M

    2012-12-12

    To assess pharmacy faculty trainers' perceptions of a Web-based train-the-trainer program for PharmGenEd, a shared pharmacogenomics curriculum for health professional students and licensed clinicians. Pharmacy faculty trainers (n=58, representing 39 colleges and schools of pharmacy in the United States and 1 school from Canada) participated in a train-the-trainer program consisting of up to 9 pharmacogenomics topics. Posttraining survey instruments assessed faculty trainers' perceptions toward the training program and the likelihood of their adopting the educational materials as part of their institution's curriculum. Fifty-five percent of faculty trainers reported no prior formal training in pharmacogenomics. There was a significant increase (ptrain licensed health professionals, and 95% indicated that they would recommend the program to other pharmacy faculty members. As a result of participating in the train-the-trainer program in pharmacogenomics, faculty member participants gained confidence in teaching pharmacogenomics to their students, and the majority of participants indicated a high likelihood of adopting the program at their institution. A Web-based train-the-trainer model appears to be a feasible strategy for training pharmacy faculty in pharmacogenomics.

  19. [Influence of human activities on groundwater environment based on coefficient variation method].

    Science.gov (United States)

    Zhao, Wei; Lin, Jian; Wang, Shu-Fang; Liu, Ji-Lai; Chen, Zhong-Rong; Kou, Wen-Jie

    2013-04-01

    Groundwater system in the plain area of Beijing can be divided into six subsystems. Due to the different hydrogeological conditions of the subsystems, the degrees to which human activities affect the subsystems are also diverse. In order to evaluate the influence of human activities on each subsystem, the first and second aquifer with relatively poor water quality were chosen to be the evaluating positions, based on the data of groundwater sampled in September, 2011. With respect to human activities affect index such as total hardness, TDS, sulfate and ammonium, variation coefficient methods were used to calculate the weight of each index. Then scores were obtained for each index with national standard as reference, and superposition calculations were used to gain comprehensive scores, finally the groundwater quality conditions were evaluated. Contrast analyses were used to evaluate the incidence of human activities with groundwater subsystems as evaluation unit and water quality partitions as evaluation factors. The results indicate that the influence of human activities on the first aquifer is greater than that of the second aquifer, the Yongding river groundwater subsystems and the Chaobai river groundwater subsystems are affected more than other groundwater subsystems.

  20. Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics.

    Science.gov (United States)

    ElRakaiby, Marwa; Dutilh, Bas E; Rizkallah, Mariam R; Boleij, Annemarie; Cole, Jason N; Aziz, Ramy K

    2014-07-01

    The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome influence human health, immunity, and different disease states. In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics. We propose a microbiome cloud model, reflecting the temporal and spatial uncertainty of defining an individual's microbiome composition, with examples of how intra-individual variations (such as age and mode of delivery) shape the microbiome structure. Additionally, we discuss how this microbiome cloud concept explains the difficulty to define a core human microbiome and to classify individuals according to their biome types. Detailed examples are presented on microbiome changes related to colorectal cancer, antibiotic administration, and pharmacomicrobiomics, or drug-microbiome interactions, highlighting how an improved understanding of the human microbiome, and alterations thereof, may lead to the development of novel therapeutic agents, the modification of antibiotic policies and implementation, and improved health outcomes. Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed.

  1. Age variations in the properties of human tibial trabecular bone and cartilage

    DEFF Research Database (Denmark)

    Ding, Ming

    2000-01-01

    ) to investigate the age-related and osteoarthrosis-related changes in the mechanical properties of the human tibial cartilage-bone complex; and 3) to evaluate mutual associations among various properties. Normal specimens from human autopsy proximal tibiae were used for investigation of age variations...... in the properties of trabecular bone and the cartilage-bone complex, and osteoarthrotic specimens were used for the investigation of changes in the mechanical properties of the cartilage-bone complex induced by this disease process. The mechanical properties and physical/compositional properties of trabecular bone...... is parallel to the longitudinal loading axis of the tibia. The mechanical properties of the normal cartilage and bone vary with age and respond simultaneously to mechanical loading. Both cartilage and bone in early-stage OA are mechanically inferior to normal, and OA cartilage and bone have lost their unit...

  2. Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

    DEFF Research Database (Denmark)

    Cao, Hongzhi; Hastie, Alex R.; Cao, Dandan

    2014-01-01

    mutations; however, none of the current detection methods are comprehensive, and currently available methodologies are incapable of providing sufficient resolution and unambiguous information across complex regions in the human genome. To address these challenges, we applied a high-throughput, cost......BACKGROUND: Structural variants (SVs) are less common than single nucleotide polymorphisms and indels in the population, but collectively account for a significant fraction of genetic polymorphism and diseases. Base pair differences arising from SVs are on a much higher order (>100 fold) than point...... mapping technology as a comprehensive and cost-effective method for detecting structural variation and studying complex regions in the human genome, as well as deciphering viral integration into the host genome....

  3. Variation in the sequence and modification state of the human insulin gene flanking regions.

    Science.gov (United States)

    Ullrich, A; Dull, T J; Gray, A; Philips, J A; Peter, S

    1982-04-10

    The nucleotide sequence of a highly repetitive sequence region upstream from the human insulin gene is reported. The length of this region varies between alleles in the population, and appears to be stably transmitted to the next generation in a Mendelian fashion. There is no significant correlation between the length of this sequence and two types of diabetes mellitus. We observe variation in the cleavability of a BglI recognition site downstream from the human insulin gene, which is probably due to variable nucleotide modification. This presumed modification state appears not to be inherited, and varies between tissues within an individual and between individuals for a given tissue. Both alleles in a given tissue DNA sample are modified to the same extent.

  4. Genetic variation of Aflatoxin B(1) aldehyde reductase genes (AFAR) in human tumour cells

    DEFF Research Database (Denmark)

    Praml, Christian; Schulz, Wolfgang; Claas, Andreas

    2008-01-01

    . Furthermore, human AFAR1 catalyses the rate limiting step in the synthesis of the neuromodulator gamma-hydroxybutyrate (GHB) and was found elevated in neurodegenerative diseases such as Alzheimer's and dementia with Lewy bodies (DLB). The human AFAR gene family maps to a genomic region in 1p36 of frequent...... samples, we identified nine different amino acid changes; two were in AFAR1 and seven in AFAR2. In AFAR1, we found genetic variation in the proposed substrate-binding amino acid 113, encoding Ala(113) or Thr(113). An AFAR2 variant had a Glu(55) substituted by Lys(55) at a position that is conserved among...... many aldo-keto reductases. This polarity change may have an effect on the proposed substrate binding amino acids nearby (Met(47), Tyr(48), Asp(50)). Further population analyses and functional studies of the nine variants detected may show if these variants are disease-related....

  5. Utilizing population variation, vaccination, and systems biology to study human immunology.

    Science.gov (United States)

    Tsang, John S

    2015-08-01

    The move toward precision medicine has highlighted the importance of understanding biological variability within and across individuals in the human population. In particular, given the prevalent involvement of the immune system in diverse pathologies, an important question is how much and what information about the state of the immune system is required to enable accurate prediction of future health and response to medical interventions. Towards addressing this question, recent studies using vaccination as a model perturbation and systems-biology approaches are beginning to provide a glimpse of how natural population variation together with multiplexed, high-throughput measurement and computational analysis can be used to uncover predictors of immune response quality in humans. Here I discuss recent developments in this emerging field, with emphasis on baseline correlates of vaccination responses, sources of immune-state variability, as well as relevant features of study design, data generation, and computational analysis.

  6. Human MAMLD1 Gene Variations Seem Not Sufficient to Explain a 46,XY DSD Phenotype.

    Directory of Open Access Journals (Sweden)

    Núria Camats

    Full Text Available MAMLD1 is thought to cause disordered sex development in 46,XY patients. But its role is controversial because some MAMLD1 variants are also detected in normal individuals, several MAMLD1 mutations have wild-type activity in functional tests, and the male Mamld1-knockout mouse has normal genitalia and reproduction. Our aim was to search for MAMLD1 variations in 108 46,XY patients with disordered sex development, and to test them functionally. We detected MAMDL1 variations and compared SNP frequencies in controls and patients. We tested MAMLD1 transcriptional activity on promoters involved in sex development and assessed the effect of MAMLD1 on androgen production. MAMLD1 expression in normal steroid-producing tissues and mutant MAMLD1 protein expression were also assessed. Nine MAMLD1 mutations (7 novel were characterized. In vitro, most MAMLD1 variants acted similarly to wild type. Only the L210X mutation showed loss of function in all tests. We detected no effect of wild-type or MAMLD1 variants on CYP17A1 enzyme activity in our cell experiments, and Western blots revealed no significant differences for MAMLD1 protein expression. MAMLD1 was expressed in human adult testes and adrenals. In conclusion, our data support the notion that MAMLD1 sequence variations may not suffice to explain the phenotype in carriers and that MAMLD1 may also have a role in adult life.

  7. Human MAMLD1 Gene Variations Seem Not Sufficient to Explain a 46,XY DSD Phenotype

    Science.gov (United States)

    Audí, Laura; Mullis, Primus E.; Moreno, Francisca; González Casado, Isabel; López-Siguero, Juan Pedro; Corripio, Raquel; Bermúdez de la Vega, José Antonio; Blanco, José Antonio; Flück, Christa E.

    2015-01-01

    MAMLD1 is thought to cause disordered sex development in 46,XY patients. But its role is controversial because some MAMLD1 variants are also detected in normal individuals, several MAMLD1 mutations have wild-type activity in functional tests, and the male Mamld1-knockout mouse has normal genitalia and reproduction. Our aim was to search for MAMLD1 variations in 108 46,XY patients with disordered sex development, and to test them functionally. We detected MAMDL1 variations and compared SNP frequencies in controls and patients. We tested MAMLD1 transcriptional activity on promoters involved in sex development and assessed the effect of MAMLD1 on androgen production. MAMLD1 expression in normal steroid-producing tissues and mutant MAMLD1 protein expression were also assessed. Nine MAMLD1 mutations (7 novel) were characterized. In vitro, most MAMLD1 variants acted similarly to wild type. Only the L210X mutation showed loss of function in all tests. We detected no effect of wild-type or MAMLD1 variants on CYP17A1 enzyme activity in our cell experiments, and Western blots revealed no significant differences for MAMLD1 protein expression. MAMLD1 was expressed in human adult testes and adrenals. In conclusion, our data support the notion that MAMLD1 sequence variations may not suffice to explain the phenotype in carriers and that MAMLD1 may also have a role in adult life. PMID:26580071

  8. ALDH1A2 (RALDH2 genetic variation in human congenital heart disease

    Directory of Open Access Journals (Sweden)

    Mesquita Sonia MF

    2009-11-01

    ALDH1A2 genetic variation is present in TOF patients, suggesting a possible causal role for this gene in rare cases of human CHD, but does not support the hypothesis that variation at the ALDH1A2 locus is a significant modifier of the risk for CHD in humans.

  9. Chrono-proteomics of human saliva: variations of the salivary proteome during human development.

    Science.gov (United States)

    Messana, Irene; Cabras, Tiziana; Iavarone, Federica; Manconi, Barbara; Huang, Liling; Martelli, Claudia; Olianas, Alessandra; Sanna, Maria Teresa; Pisano, Elisabetta; Sanna, Monica; Arba, Morena; D'Alessandro, Alfredo; Desiderio, Claudia; Vitali, Alberto; Pirolli, Davide; Tirone, Chiara; Lio, Alessandra; Vento, Giovanni; Romagnoli, Costantino; Cordaro, Massimo; Manni, Armando; Gallenzi, Patrizia; Fiorita, Antonella; Scarano, Emanuele; Calò, Lea; Passali, Giulio Cesare; Picciotti, Pasqualina Maria; Paludetti, Gaetano; Fanos, Vassilios; Faa, Gavino; Castagnola, Massimo

    2015-04-03

    An important contribution to the variability of any proteome is given by the time dimension that should be carefully considered to define physiological modifications. To this purpose, whole saliva proteome was investigated in a wide age range. Whole saliva was collected from 17 preterm newborns with a postconceptional age at birth of 178-217 days. In these subjects sample collection was performed serially starting immediately after birth and within about 1 year follow-up, gathering a total of 111 specimens. Furthermore, whole saliva was collected from 182 subjects aged between 0 and 17 years and from 23 adults aged between 27 and 57 years. The naturally occurring intact salivary proteome of the 316 samples was analyzed by low- and high-resolution HPLC-ESI-MS platforms. Proteins peculiar of the adults appeared in saliva with different time courses during human development. Acidic proline-rich proteins encoded by PRH2 locus and glycosylated basic proline-rich proteins encoded by PRB3 locus appeared following 180 days of postconceptional age, followed at 7 months (±2 weeks) by histatin 1, statherin, and P-B peptide. The other histatins and acidic proline-rich proteins encoded by PRH1 locus appeared in whole saliva of babies from 1 to 3 weeks after the normal term of delivery, S-type cystatins appeared at 1 year (±3 months), and basic proline-rich proteins appeared at 4 years (±1 year) of age. All of the proteinases involved in the maturation of salivary proteins were more active in preterm than in at-term newborns, on the basis of the truncated forms detected. The activity of the Fam20C kinase, involved in the phosphorylation of various proteins, started around 180 days of postconceptional age, slowly increased reaching values comparable to adults at about 2 years (±6 months) of age. Instead, MAPK14 involved in the phosphorylation of S100A9 was fully active since birth also in preterm newborns.

  10. Analysis of protein-coding genetic variation in 60,706 humans.

    Science.gov (United States)

    Lek, Monkol; Karczewski, Konrad J; Minikel, Eric V; Samocha, Kaitlin E; Banks, Eric; Fennell, Timothy; O'Donnell-Luria, Anne H; Ware, James S; Hill, Andrew J; Cummings, Beryl B; Tukiainen, Taru; Birnbaum, Daniel P; Kosmicki, Jack A; Duncan, Laramie E; Estrada, Karol; Zhao, Fengmei; Zou, James; Pierce-Hoffman, Emma; Berghout, Joanne; Cooper, David N; Deflaux, Nicole; DePristo, Mark; Do, Ron; Flannick, Jason; Fromer, Menachem; Gauthier, Laura; Goldstein, Jackie; Gupta, Namrata; Howrigan, Daniel; Kiezun, Adam; Kurki, Mitja I; Moonshine, Ami Levy; Natarajan, Pradeep; Orozco, Lorena; Peloso, Gina M; Poplin, Ryan; Rivas, Manuel A; Ruano-Rubio, Valentin; Rose, Samuel A; Ruderfer, Douglas M; Shakir, Khalid; Stenson, Peter D; Stevens, Christine; Thomas, Brett P; Tiao, Grace; Tusie-Luna, Maria T; Weisburd, Ben; Won, Hong-Hee; Yu, Dongmei; Altshuler, David M; Ardissino, Diego; Boehnke, Michael; Danesh, John; Donnelly, Stacey; Elosua, Roberto; Florez, Jose C; Gabriel, Stacey B; Getz, Gad; Glatt, Stephen J; Hultman, Christina M; Kathiresan, Sekar; Laakso, Markku; McCarroll, Steven; McCarthy, Mark I; McGovern, Dermot; McPherson, Ruth; Neale, Benjamin M; Palotie, Aarno; Purcell, Shaun M; Saleheen, Danish; Scharf, Jeremiah M; Sklar, Pamela; Sullivan, Patrick F; Tuomilehto, Jaakko; Tsuang, Ming T; Watkins, Hugh C; Wilson, James G; Daly, Mark J; MacArthur, Daniel G

    2016-08-18

    Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.

  11. Targeted Application of Human Genetic Variation Can Improve Red Blood Cell Production from Stem Cells.

    Science.gov (United States)

    Giani, Felix C; Fiorini, Claudia; Wakabayashi, Aoi; Ludwig, Leif S; Salem, Rany M; Jobaliya, Chintan D; Regan, Stephanie N; Ulirsch, Jacob C; Liang, Ge; Steinberg-Shemer, Orna; Guo, Michael H; Esko, Tõnu; Tong, Wei; Brugnara, Carlo; Hirschhorn, Joel N; Weiss, Mitchell J; Zon, Leonard I; Chou, Stella T; French, Deborah L; Musunuru, Kiran; Sankaran, Vijay G

    2016-01-07

    Multipotent and pluripotent stem cells are potential sources for cell and tissue replacement therapies. For example, stem cell-derived red blood cells (RBCs) are a potential alternative to donated blood, but yield and quality remain a challenge. Here, we show that application of insight from human population genetic studies can enhance RBC production from stem cells. The SH2B3 gene encodes a negative regulator of cytokine signaling and naturally occurring loss-of-function variants in this gene increase RBC counts in vivo. Targeted suppression of SH2B3 in primary human hematopoietic stem and progenitor cells enhanced the maturation and overall yield of in-vitro-derived RBCs. Moreover, inactivation of SH2B3 by CRISPR/Cas9 genome editing in human pluripotent stem cells allowed enhanced erythroid cell expansion with preserved differentiation. Our findings therefore highlight the potential for combining human genome variation studies with genome editing approaches to improve cell and tissue production for regenerative medicine.

  12. Changes in neuronal DNA content variation in the human brain during aging.

    Science.gov (United States)

    Fischer, Hans-Georg; Morawski, Markus; Brückner, Martina K; Mittag, Anja; Tarnok, Attila; Arendt, Thomas

    2012-08-01

    The human brain has been proposed to represent a genetic mosaic, containing a small but constant number of neurons with an amount of DNA exceeding the diploid level that appear to be generated through various chromosome segregation defects initially. While a portion of these cells apparently die during development, neurons with abnormal chromosomal copy number have been identified in the mature brain. This genomic alteration might to lead to chromosomal instability affecting neuronal viability and could thus contribute to age-related mental disorders. Changes in the frequency of neurons with such structural genomic variation in the adult and aging brain, however, are unknown. Here, we quantified the frequency of neurons with a more than diploid DNA content in the cerebral cortex of normal human brain and analyzed its changes between the fourth and ninth decades of life. We applied a protocol of slide-based cytometry optimized for DNA quantification of single identified neurons, which allowed to analyze the DNA content of about 500 000 neurons for each brain. On average, 11.5% of cortical neurons showed DNA content above the diploid level. The frequency of neurons with this genomic alteration was highest at younger age and declined with age. Our results indicate that the genomic variation associated with DNA content exceeding the diploid level might compromise viability of these neurons in the aging brain and might thus contribute to susceptibilities for age-related CNS disorders. Alternatively, a potential selection bias of "healthy aging brains" needs to be considered, assuming that DNA content variation above a certain threshold associates with Alzheimer's disease.

  13. Pharmacogenomics In Drug Therapy And Interaction: The Role Of Cytochrome P450

    Directory of Open Access Journals (Sweden)

    Peter Pook

    2008-12-01

    Full Text Available Pharmacogenomics (or pharmacogenetics,the study of the effects of genetic differences on aperson’s response to drugs, can help in optimizing drugefficacy and minimizing adverse drug reactions.Interperson difference in drug metabolism is one of theimportant consequences of such genetic variation. Thisvariation is determined in part by mutations incytochrome P450 enzymes (CYPs. IMU is part of amajor collaborative research project in the area ofphamacogenetics and drug metabolism. Workingtogether with USM and UiTM, our group has, since2000, generated useful population database on geneticpolymorphism of various CYP isoforms. We havesuccessfully genotyped three major ethnic groups,Malay, Indian and Chinese for their allelic frequency ofimportant isoforms. These include CYP2D6, CYP2C9,CYP2C8 and CYP2A6. Data generated so farcollectively have contributed to our effort in mappingand constructing genomic database for Malaysianpopulation.Since early 2002, our research has been focusing ondeveloping in vitro methods in studying the functionalconsequences of genetic polymorphism of CYP enzymes.Using site-directed mutagenesis, CYP mutants, carryingnucleotide changes as reported in known alleles inhuman populations, were generated and expressed inE. coli system, and the expressed recombinant proteinswere characterized using enzyme assays to determinethe functional consequences of mutations. We haveestablished a series of HPLC (high performance liquidchromatography-based and fluorescence-based assaysto investigate CYP activities. Assays that have beendeveloped include tolbutamide methylhydroxylase,paclitaxel 6α-hydroxylase, dextromethorphanO-demethylation, testosterone 6β-hydroxylation andcoumarin 7-hydroxylase assays. These assays serve asactivity markers allowing comparison of catalyticactivities of mutant proteins generated. Another focusof our work is to use the developed assays as a screeningtool to investigate drug-herb interactions. This wasachieved

  14. VARIATIONS OF SACRAL HIATUS IN DRY HUMAN SACRA: AN ANATOMICAL STUDY

    Directory of Open Access Journals (Sweden)

    Rubi Saikia

    2016-07-01

    Full Text Available BACKGROUND Sacrum is a large triangular bone formed by the fusion of 5 sacral vertebrae. It lies obliquely at the posterior part of pelvic cavity between the two hip bones. It encloses a canal called the sacral canal. The lower opening of the sacral canal is called the sacral hiatus. It transmits the 5 th pair of sacral nerves, coccygeal nerves & filum terminale externa. AIMS & OBJECTIVES The aim of the present study is to find out the variations of sacral hiatus in this part of Northeast India. MATERIALS & METHODS The study was carried out in 104 dry human sacra to know the anatomical variations of sacral hiatus. The measurements were carried out with the help of a Vernier calliper, scale & a divider. RESULT & OBSERVATIONS Various shapes of sacral hiatus were observed as follows: Inverted U shaped (53.8%, inverted V shaped (29.8 %, irregular shaped (9.6 %, dumb-bell shaped (5.7 %, bifid (0.9%. The length of the sacral hiatus was found to be between 20-30 mm in 46.1% cases. The apex of the sacral hiatus was at the level of S4 vertebra in 46.1% specimens. The anteroposterior diameter of the sacral canal at the apex of the sacral hiatus ranged from 2-12 mm. CONCLUSIONS Variations of sacral hiatus is very common. The knowledge of such variations will definitely help the anaesthesiologists to take proper step while administering caudal epidural anaesthesia to increase the success rate of caudal epidural block.

  15. Genetic variation of human papillomavirus type 16 in individual clinical specimens revealed by deep sequencing.

    Directory of Open Access Journals (Sweden)

    Iwao Kukimoto

    Full Text Available Viral genetic diversity within infected cells or tissues, called viral quasispecies, has been mostly studied for RNA viruses, but has also been described among DNA viruses, including human papillomavirus type 16 (HPV16 present in cervical precancerous lesions. However, the extent of HPV genetic variation in cervical specimens, and its involvement in HPV-induced carcinogenesis, remains unclear. Here, we employ deep sequencing to comprehensively analyze genetic variation in the HPV16 genome isolated from individual clinical specimens. Through overlapping full-circle PCR, approximately 8-kb DNA fragments covering the whole HPV16 genome were amplified from HPV16-positive cervical exfoliated cells collected from patients with either low-grade squamous intraepithelial lesion (LSIL or invasive cervical cancer (ICC. Deep sequencing of the amplified HPV16 DNA enabled de novo assembly of the full-length HPV16 genome sequence for each of 7 specimens (5 LSIL and 2 ICC samples. Subsequent alignment of read sequences to the assembled HPV16 sequence revealed that 2 LSILs and 1 ICC contained nucleotide variations within E6, E1 and the non-coding region between E5 and L2 with mutation frequencies of 0.60% to 5.42%. In transient replication assays, a novel E1 mutant found in ICC, E1 Q381E, showed reduced ability to support HPV16 origin-dependent replication. In addition, partially deleted E2 genes were detected in 1 LSIL sample in a mixed state with the intact E2 gene. Thus, the methods used in this study provide a fundamental framework for investigating the influence of HPV somatic genetic variation on cervical carcinogenesis.

  16. Organizational Variation in Implementation of an Evidence-Based Human Papillomavirus Intervention.

    Science.gov (United States)

    Carman, Angela L; McGladrey, Margaret L; Goodman Hoover, Anna; Crosby, Richard A

    2015-08-01

    "1-2-3 Pap" is a video-based intervention designed to improve human papillomavirus (HPV) vaccine adherence rates among young women in rural Eastern Kentucky. The efficacy trial for the original intervention linked video exposure with increased likelihood of vaccine series completion among the target audience. Given their historic focus on prevention, local health departments were selected as pilot sites to study implementation of 1-2-3 Pap in a public health setting and identify site-specific variations in its implementation. A mixed-method, pre- and post-comparison pilot study conducted between October 2013 and April 2014 addressed three primary research questions: (1) how specific implementation planning activities using existing organizational resources and processes affect the selection and optimization of dissemination channels for evidence-based public health interventions; (2) what organizational resources, processes, or other attributes facilitate or impede implementation of evidence-based public health interventions; and (3) how variation in dissemination channels corresponds with intervention outcomes. Although analysis conducted in October 2014 found that the pilot study did not generate significant changes in HPV vaccine rates, data yielded from the Organizational Readiness to Change Assessment survey instrument and process evaluation interviews revealed variation in pre-study planning and in the use and coordination of staff, the adaptation of materials provided for implementation, and sites' ability to access HPV vaccine rate data throughout the study. The mixed-method pilot study advances dissemination and implementation science through identification of variation in planning activities and use of organizational resources and processes for implementation of prevention interventions in public health settings. Copyright © 2015 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

  17. Review on Pharmacogenetics and Pharmacogenomics Applied to the Study of Asthma.

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    Sánchez-Martín, Almudena; García-Sánchez, Asunción; Isidoro-García, María

    2016-01-01

    Nearly one-half of asthmatic patients do not respond to the most common therapies. Evidence suggests that genetic factors may be involved in the heterogeneity in therapeutic response and adverse events to asthma therapies. We focus on the three major classes of asthma medication: β-adrenergic receptor agonist, inhaled corticosteroids, and leukotriene modifiers. Pharmacogenetics and pharmacogenomics studies have identified several candidate genes associated with drug response.In this chapter, the main pharmacogenetic and pharmacogenomic studies in addition to the future perspectives in personalized medicine will be reviewed. The ideal treatment of asthma would be a tailored approach to health care in which adverse effects are minimized and the therapeutic benefit for an individual asthmatic is maximized leading to a more cost-effective care.

  18. Pharmacogenomics in Pediatric Oncology: Review of Gene—Drug Associations for Clinical Use †

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    Mlakar, Vid; Huezo-Diaz Curtis, Patricia; Satyanarayana Uppugunduri, Chakradhara Rao; Krajinovic, Maja; Ansari, Marc

    2016-01-01

    During the 3rd congress of the European Society of Pharmacogenomics and Personalised Therapy (ESPT) in Budapest in 2015, a preliminary meeting was held aimed at establishing a pediatric individualized treatment in oncology and hematology committees. The main purpose was to facilitate the transfer and harmonization of pharmacogenetic testing from research into clinics, to bring together basic and translational research and to educate health professionals throughout Europe. The objective of this review was to provide the attendees of the meeting as well as the larger scientific community an insight into the compiled evidence regarding current pharmacogenomics knowledge in pediatric oncology. This preliminary evaluation will help steer the committee’s work and should give the reader an idea at which stage researchers and clinicians are, in terms of personalizing medicine for children with cancer. From the evidence presented here, future recommendations to achieve this goal will also be suggested. PMID:27618021

  19. Tacrolimus Pharmacokinetic and Pharmacogenomic Differences between Adults and Pediatric Solid Organ Transplant Recipients

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    Amy Lu

    2010-09-01

    Full Text Available Tacrolimus is a calcineurin inhibitor immunosuppressant that has seen considerable use in both adult and pediatric solid organ transplant recipients. Though there is much pharmacokinetic data available for tacrolimus in the adult population, the literature available for children is limited. Furthermore, very little is known about the pharmacogenomic differences in the two patient groups. Based on what information is currently available, clinically significant differences may exist between the two populations in terms of absorption, distribution, metabolism and elimination. In addition, inherent physiological differences exist in the young child including: less effective plasma binding proteins, altered expression of intestinal P-glycoprotein, and increased expression of phase 1 metabolizing enzymes, therefore one would expect to see clinically significant differences when administering tacrolimus to a child. This paper examines available literature in an attempt to summarize the potential pharmacokinetic and pharmacogenomic variability that exists between the two populations.

  20. Pharmacogenetics and pharmacogenomics: role of mutational analysis in anti-cancer targeted therapy.

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    Savonarola, A; Palmirotta, R; Guadagni, F; Silvestris, F

    2012-08-01

    The goal of cancer pharmacogenomics is to obtain benefit from personalized approaches of cancer treatment and prevention. Recent advances in genomic research have shed light on the crucial role of genetic variants, mainly involving genes encoding drug-metabolizing enzymes, drug transporters and targets, in driving different treatment responses among individuals, in terms of therapeutic efficacy and safety. Although a considerable amount of new targeted agents have been designed based on a finely understanding of molecular alterations in cancer, a wide gap between pharmacogenomic knowledge and clinical application still persists. This review focuses on the relevance of mutational analyses in predicting individual response to antitumor therapy, in order to improve the translational impact of genetic information on clinical practice.

  1. Pharmacogenomics in Pediatric Oncology: Review of Gene—Drug Associations for Clinical Use

    Directory of Open Access Journals (Sweden)

    Vid Mlakar

    2016-09-01

    Full Text Available During the 3rd congress of the European Society of Pharmacogenomics and Personalised Therapy (ESPT in Budapest in 2015, a preliminary meeting was held aimed at establishing a pediatric individualized treatment in oncology and hematology committees. The main purpose was to facilitate the transfer and harmonization of pharmacogenetic testing from research into clinics, to bring together basic and translational research and to educate health professionals throughout Europe. The objective of this review was to provide the attendees of the meeting as well as the larger scientific community an insight into the compiled evidence regarding current pharmacogenomics knowledge in pediatric oncology. This preliminary evaluation will help steer the committee’s work and should give the reader an idea at which stage researchers and clinicians are, in terms of personalizing medicine for children with cancer. From the evidence presented here, future recommendations to achieve this goal will also be suggested.

  2. HLA DNA sequence variation among human populations: molecular signatures of demographic and selective events.

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    Stéphane Buhler

    Full Text Available Molecular differences between HLA alleles vary up to 57 nucleotides within the peptide binding coding region of human Major Histocompatibility Complex (MHC genes, but it is still unclear whether this variation results from a stochastic process or from selective constraints related to functional differences among HLA molecules. Although HLA alleles are generally treated as equidistant molecular units in population genetic studies, DNA sequence diversity among populations is also crucial to interpret the observed HLA polymorphism. In this study, we used a large dataset of 2,062 DNA sequences defined for the different HLA alleles to analyze nucleotide diversity of seven HLA genes in 23,500 individuals of about 200 populations spread worldwide. We first analyzed the HLA molecular structure and diversity of these populations in relation to geographic variation and we further investigated possible departures from selective neutrality through Tajima's tests and mismatch distributions. All results were compared to those obtained by classical approaches applied to HLA allele frequencies.Our study shows that the global patterns of HLA nucleotide diversity among populations are significantly correlated to geography, although in some specific cases the molecular information reveals unexpected genetic relationships. At all loci except HLA-DPB1, populations have accumulated a high proportion of very divergent alleles, suggesting an advantage of heterozygotes expressing molecularly distant HLA molecules (asymmetric overdominant selection model. However, both different intensities of selection and unequal levels of gene conversion may explain the heterogeneous mismatch distributions observed among the loci. Also, distinctive patterns of sequence divergence observed at the HLA-DPB1 locus suggest current neutrality but old selective pressures on this gene. We conclude that HLA DNA sequences advantageously complement HLA allele frequencies as a source of data used

  3. Size variation in early human mandibles and molars from Klasies River, South Africa: comparison with other middle and late Pleistocene assemblages and with modern humans.

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    Royer, Danielle F; Lockwood, Charles A; Scott, Jeremiah E; Grine, Frederick E

    2009-10-01

    Previous studies of the Middle Stone Age human remains from Klasies River have concluded that they exhibited more sexual dimorphism than extant populations, but these claims have not been assessed statistically. We evaluate these claims by comparing size variation in the best-represented elements at the site, namely the mandibular corpora and M(2)s, to that in samples from three recent human populations using resampling methods. We also examine size variation in these same elements from seven additional middle and late Pleistocene sites: Skhūl, Dolní Vestonice, Sima de los Huesos, Arago, Krapina, Shanidar, and Vindija. Our results demonstrate that size variation in the Klasies assemblage was greater than in recent humans, consistent with arguments that the Klasies people were more dimorphic than living humans. Variation in the Skhūl, Dolní Vestonice, and Sima de los Huesos mandibular samples is also higher than in the recent human samples, indicating that the Klasies sample was not unusual among middle and late Pleistocene hominins. In contrast, the Neandertal samples (Krapina, Shanidar, and Vindija) do not evince relatively high mandibular and molar variation, which may indicate that the level of dimorphism in Neandertals was similar to that observed in extant humans. These results suggest that the reduced levels of dimorphism in Neandertals and living humans may have developed independently, though larger fossil samples are needed to test this hypothesis.

  4. Neoliberal technocracy: explaining how and why the US Food and Drug Administration has championed pharmacogenomics.

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    Hogarth, Stuart

    2015-04-01

    By 2004 the FDA had emerged as a champion of pharmacogenomics as an exemplar for novel approaches to drug development. This was made clear in 2004 when the agency released a wide-ranging report which positioned pharmacogenomics at the heart of a broader regulatory reform agenda. The Critical Path initiative addressed declining productivity of drug development by suggesting that the problem was a mismatch between the rapid pace of discovery in post-genomic biomedicine and the antiquated development process for new drugs. Framing their work in this context, FDA officials reconceptualised their role in the innovation process, in what was the first programmatic statement of a shift from a strictly gate-keeping role to a more collaborative or facilitative role as enablers of innovation. This paper situates the FDA's emergence as a champion of pharmacogenomics in the broader politics of pharmaceutical regulation in the USA. In making a contribution to the pharmaceuticalisation literature this paper will draw on the work of John Abraham who has argued that one of the primary drivers of pharmaceuticalisation has been "deregulatory state policies" and on Williams and colleagues who have argued that the changing relationship between regulatory agencies and the pharmaceutical industry is an important dimension of pharmaceuticalisation. This paper links this to the promotion of pharmaceutical futures such as pharmacogenomics and explores how this shift is also closely related to the trend towards a risk management approach to pharmaceutical regulation. The role of Bush appointees in the development and promotion of the Critical Path agenda is also examined.

  5. Assessing the impact of climate variability and human activity to streamflow variation

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    J. Chang

    2015-06-01

    Full Text Available Water resources in river systems have been changing under the impacts of both climate variability and human activities. Assessing the respective impacts on decadal streamflow variation is important for water resources management. By using an elasticity-based method, calibrated TOPMODEL and VIC hydrologic models, we have quantitatively isolated the relative contributions that human activity and climate variability made to decadal streamflow changes in Jinhe basin located in northwest of China. This is an important watershed of Shaanxi Province that supplies drinking water for a population of over 6 million. The results from the three methods show that both human activity and climatic differences can have major effects on catchment streamflow, and the estimates of climate variability impacts from the hydrological models are similar to those from the elasticity-based method. Compared with the baseline period of 1960–1970, streamflow greatly decreased during 2001–2010. The change impacts of human activity and climate variability in 2001–2010 were about 83.5 and 16.5% of the total reduction respectively when averaged over the three methods. The maximum contribution value of human activity was appeared in 1981–1990 due to the effects of soil and water conservation measures and irrigation water withdrawal, which was 95, 112.5 and 92.4% from TOPMODEL, VIC model and elasticity-based method respectively. The maximum value of the aridity index (E0/P was 1.91 appeared in 1991–2000. Compared with 1960–1970 baseline period, climate variability made the greatest contributions reduction in 1991–2000, which was 47.4, 43.9 and 29.9% from TOPMODEL, VIC model and elasticity-based method respectively. We emphasized various source of errors and uncertainties that may occurre in the hydrological model (parameter and structural uncertainty and elasticity-based method (model parameter in climate change impact studies.

  6. Cardiac lipid levels show diurnal changes and long-term variations in healthy human subjects.

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    Ith, Michael; Stettler, Christoph; Xu, Jian; Boesch, Chris; Kreis, Roland

    2014-11-01

    (1) H-MRS is regularly applied to determine lipid content in ectopic tissue - mostly skeletal muscle and liver - to investigate physiological and/or pathologic conditions, e.g. insulin resistance. Technical developments also allow non-invasive in vivo assessment of cardiac lipids; however, basic data about methodological reliability (repeatability) and physiological variations are scarce. The aim of the presented work was to determine potential diurnal changes of cardiac lipid stores in humans, and to put the results in relation to methodological repeatability and normal physiological day-to-day variations. Optimized cardiac- and respiratory-gated (1) H-MRS was used for non-invasive quantification of intracardiomyocellular lipids (ICCL), creatine, trimethyl-ammonium compounds (TMA), and taurine in nine healthy young men at three time points per day on two days separated by one week. This design allowed determination of (a) diurnal changes, (b) physiological variation over one week and (c) methodological repeatability of the ICCL levels. Comparison of fasted morning to post-absorptive evening measurements revealed a significant 37 ± 19% decrease of ICCL during the day (p = 0.0001). There was a significant linear correlation between ICCL levels in the morning and their decrease during the day (p = 0.015). Methodological repeatability for the ICCL/creatine ratio was excellent, with a coefficient of variance of ~5%, whereas physiological variation was found to be considerably higher (22%) in spite of a standardized physiological preparation protocol. In contrast, TMA levels remained stable over this time period. The proposed (1) H-MRS technique provides a robust way to investigate relevant physiological changes in cardiac metabolites, in particular ICCL. The present results suggest that ICCL reveal a diurnal course, with higher levels in the morning as compared to evening. In addition, a considerable long-term variation of ICCL levels, in both the morning and evening

  7. Pharmacokinetics, Pharmacodynamics, and Pharmacogenomics of Immunosuppressants in Allogeneic Hematopoietic Cell Transplantation: Part II.

    Science.gov (United States)

    McCune, Jeannine S; Bemer, Meagan J; Long-Boyle, Janel

    2016-05-01

    Part I of this article included a pertinent review of allogeneic hematopoietic cell transplantation (alloHCT), the role of postgraft immunosuppression in alloHCT, and the pharmacokinetics, pharmacodynamics, and pharmacogenomics of the calcineurin inhibitors and methotrexate. In this article (Part II), we review the pharmacokinetics, pharmacodynamics, and pharmacogenomics of mycophenolic acid (MPA), sirolimus, and the antithymocyte globulins (ATG). We then discuss target concentration intervention (TCI) of these postgraft immunosuppressants in alloHCT patients, with a focus on current evidence for TCI and on how TCI may improve clinical management in these patients. Currently, TCI using trough concentrations is conducted for sirolimus in alloHCT patients. Several studies demonstrate that MPA plasma exposure is associated with clinical outcomes, with an increasing number of alloHCT patients needing TCI of MPA. Compared with MPA, there are fewer pharmacokinetic/dynamic studies of rabbit ATG and horse ATG in alloHCT patients. Future pharmacokinetic/dynamic research of postgraft immunosuppressants should include '-omics'-based tools: pharmacogenomics may be used to gain an improved understanding of the covariates influencing pharmacokinetics as well as proteomics and metabolomics as novel methods to elucidate pharmacodynamic responses.

  8. Can pharmacogenomics help to improve therapy in patients with high-grade osteosarcoma?

    Science.gov (United States)

    Kager, Leo; Diakos, Christopher; Bielack, Stefan

    2015-07-01

    Current standard treatment of patients with high-grade osteosarcoma (HGOS) includes complete surgical resection of the tumor and chemotherapy, most often with high-dose methotrexate, doxorubicin and cisplatin. With this approach > 60% of patients can be cured. However, conventional anticancer drugs have a narrow therapeutic index, and efficacy and toxicity vary considerably among patients. Pharmacogenomics aim to identify key genomic factors for drug effects (either desired or adverse) in normal host cells (germ-line variants) and cancer cells (somatic variants), and if an association between a genotype and a drug phenotype has been identified, validated and demonstrated to have a large effect size, these genotypes may be used to tailor therapy. In addition, pharmacogenomic models can be used to identify novel therapeutic targets. For example, germ-line variants in genes which potentially influence the disposition of methotrexate and cardiotoxicity of doxorubicin have recently been identified. Moreover, next-generation sequencing combined with several analytical methods has identified the phosphatidylinositol 3-kinase/mammalian target of rapamycin (PI3K/mTOR) pathway as a potential therapeutic target in HGOS. Herein, we discuss whether and how these novel pharmacogenomic insights may help to improve future therapy in HGOS.

  9. Circadian variation of the human metabolome captured by real-time breath analysis.

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    Pablo Martinez-Lozano Sinues

    Full Text Available Circadian clocks play a significant role in the correct timing of physiological metabolism, and clock disruption might lead to pathological changes of metabolism. One interesting method to assess the current state of metabolism is metabolomics. Metabolomics tries to capture the entirety of small molecules, i.e. the building blocks of metabolism, in a given matrix, such as blood, saliva or urine. Using mass spectrometric approaches we and others have shown that a significant portion of the human metabolome in saliva and blood exhibits circadian modulation; independent of food intake or sleep/wake rhythms. Recent advances in mass spectrometry techniques have introduced completely non-invasive breathprinting; a method to instantaneously assess small metabolites in human breath. In this proof-of-principle study, we extend these findings about the impact of circadian clocks on metabolomics to exhaled breath. As previously established, our method allows for real-time analysis of a rich matrix during frequent non-invasive sampling. We sampled the breath of three healthy, non-smoking human volunteers in hourly intervals for 24 hours during total sleep deprivation, and found 111 features in the breath of all individuals, 36-49% of which showed significant circadian variation in at least one individual. Our data suggest that real-time mass spectrometric "breathprinting" has high potential to become a useful tool to understand circadian metabolism, and develop new biomarkers to easily and in real-time assess circadian clock phase and function in experimental and clinical settings.

  10. The New Genomics: What Molecular Databases Can Tell Us About Human Population Variation and Endocrine Disease.

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    Rotwein, Peter

    2017-07-01

    Major recent advances in genetics and genomics present unique opportunities for enhancing our understanding of human physiology and disease predisposition. Here I demonstrate how analysis of genomic information can provide new insights into endocrine systems, using the human growth hormone (GH) signaling pathway as an illustrative example. GH is essential for normal postnatal growth in children, and plays important roles in other biological processes throughout life. GH actions are mediated by the GH receptor, primarily via the JAK2 protein tyrosine kinase and the STAT5B transcription factor, and inactivating mutations in this pathway all lead to impaired somatic growth. Variation in GH signaling genes has been evaluated using DNA sequence data from the Exome Aggregation Consortium, a compendium of information from >60,000 individuals. Results reveal many potential missense and other alterations in the coding regions of GH1, GHR, JAK2, and STAT5B, with most changes being uncommon. The total number of different alleles per gene varied by ~threefold, from 101 for GH1 to 338 for JAK2. Several known disease-linked mutations in GH1, GHR, and JAK2 were present but infrequent in the population; however, three amino acid changes in GHR were sufficiently prevalent (~4% to 44% of chromosomes) to suggest that they are not disease causing. Collectively, these data provide new opportunities to understand how genetically driven variability in GH signaling and action may modify human physiology and disease. Copyright © 2017 Endocrine Society.

  11. Variation in the human cannabinoid receptor CNR1 gene modulates gaze duration for happy faces

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    Chakrabarti Bhismadev

    2011-06-01

    Full Text Available Abstract Background From an early age, humans look longer at preferred stimuli and also typically look longer at facial expressions of emotion, particularly happy faces. Atypical gaze patterns towards social stimuli are common in autism spectrum conditions (ASC. However, it is unknown whether gaze fixation patterns have any genetic basis. In this study, we tested whether variations in the cannabinoid receptor 1 (CNR1 gene are associated with gaze duration towards happy faces. This gene was selected because CNR1 is a key component of the endocannabinoid system, which is involved in processing reward, and in our previous functional magnetic resonance imaging (fMRI study, we found that variations in CNR1 modulate the striatal response to happy (but not disgust faces. The striatum is involved in guiding gaze to rewarding aspects of a visual scene. We aimed to validate and extend this result in another sample using a different technique (gaze tracking. Methods A total of 30 volunteers (13 males and 17 females from the general population observed dynamic emotional expressions on a screen while their eye movements were recorded. They were genotyped for the identical four single-nucleotide polymorphisms (SNPs in the CNR1 gene tested in our earlier fMRI study. Results Two SNPs (rs806377 and rs806380 were associated with differential gaze duration for happy (but not disgust faces. Importantly, the allelic groups associated with a greater striatal response to happy faces in the fMRI study were associated with longer gaze duration at happy faces. Conclusions These results suggest that CNR1 variations modulate the striatal function that underlies the perception of signals of social reward, such as happy faces. This suggests that CNR1 is a key element in the molecular architecture of perception of certain basic emotions. This may have implications for understanding neurodevelopmental conditions marked by atypical eye contact and facial emotion processing

  12. Variations of X chromosome inactivation occur in early passages of female human embryonic stem cells.

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    Tamar Dvash

    Full Text Available X chromosome inactivation (XCI is a dosage compensation mechanism essential for embryonic development and cell physiology. Human embryonic stem cells (hESCs derived from inner cell mass (ICM of blastocyst stage embryos have been used as a model system to understand XCI initiation and maintenance. Previous studies of undifferentiated female hESCs at intermediate passages have shown three possible states of XCI; 1 cells in a pre-XCI state, 2 cells that already exhibit XCI, or 3 cells that never undergo XCI even upon differentiation. In this study, XCI status was assayed in ten female hESC lines between passage 5 and 15 to determine whether XCI variations occur in early passages of hESCs. Our results show that three different states of XCI already exist in the early passages of hESC. In addition, we observe one cell line with skewed XCI and preferential expression of X-linked genes from the paternal allele, while another cell line exhibits random XCI. Skewed XCI in undifferentiated hESCs may be due to clonal selection in culture instead of non-random XCI in ICM cells. We also found that XIST promoter methylation is correlated with silencing of XIST transcripts in early passages of hESCs, even in the pre-XCI state. In conclusion, XCI variations already take place in early passages of hESCs, which may be a consequence of in vitro culture selection during the derivation process. Nevertheless, we cannot rule out the possibility that XCI variations in hESCs may reflect heterogeneous XCI states in ICM cells that stochastically give rise to hESCs.

  13. Human genetic variation in VAC14 regulates Salmonella invasion and typhoid fever through modulation of cholesterol.

    Science.gov (United States)

    Alvarez, Monica I; Glover, Luke C; Luo, Peter; Wang, Liuyang; Theusch, Elizabeth; Oehlers, Stefan H; Walton, Eric M; Tram, Trinh Thi Bich; Kuang, Yu-Lin; Rotter, Jerome I; McClean, Colleen M; Chinh, Nguyen Tran; Medina, Marisa W; Tobin, David M; Dunstan, Sarah J; Ko, Dennis C

    2017-09-12

    Risk, severity, and outcome of infection depend on the interplay of pathogen virulence and host susceptibility. Systematic identification of genetic susceptibility to infection is being undertaken through genome-wide association studies, but how to expeditiously move from genetic differences to functional mechanisms is unclear. Here, we use genetic association of molecular, cellular, and human disease traits and experimental validation to demonstrate that genetic variation affects expression of VAC14, a phosphoinositide-regulating protein, to influence susceptibility to Salmonella enterica serovar Typhi (S Typhi) infection. Decreased VAC14 expression increased plasma membrane cholesterol, facilitating Salmonella docking and invasion. This increased susceptibility at the cellular level manifests as increased susceptibility to typhoid fever in a Vietnamese population. Furthermore, treating zebrafish with a cholesterol-lowering agent, ezetimibe, reduced susceptibility to S Typhi. Thus, coupling multiple genetic association studies with mechanistic dissection revealed how VAC14 regulates Salmonella invasion and typhoid fever susceptibility and may open doors to new prophylactic/therapeutic approaches.

  14. An integrated map of genetic variation from 1.092 human genomes

    DEFF Research Database (Denmark)

    Abecasis, Goncalo R.; Auton, Adam; Brooks, Lisa D.

    2012-01-01

    By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination...... deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding...... consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites...

  15. Predicting risk sensitivity in humans and lower animals: risk as variance or coefficient of variation.

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    Weber, Elke U; Shafir, Sharoni; Blais, Ann-Renee

    2004-04-01

    This article examines the statistical determinants of risk preference. In a meta-analysis of animal risk preference (foraging birds and insects), the coefficient of variation (CV), a measure of risk per unit of return, predicts choices far better than outcome variance, the risk measure of normative models. In a meta-analysis of human risk preference, the superiority of the CV over variance in predicting risk taking is not as strong. Two experiments show that people's risk sensitivity becomes strongly proportional to the CV when they learn about choice alternatives like other animals, by experiential sampling over time. Experience-based choices differ from choices when outcomes and probabilities are numerically described. Zipf's law as an ecological regularity and Weber's law as a psychological regularity may give rise to the CV as a measure of risk.

  16. Natural variation in populations of persistently colonizing bacteria affect human host cell phenotype.

    Science.gov (United States)

    Aras, Rahul A; Lee, Yongchan; Kim, Sung-Kook; Israel, Dawn; Peek, Richard M; Blaser, Martin J

    2003-08-15

    The highly diverse bacterium Helicobacter pylori, which persistently colonizes the human stomach, provides models to study the role of genome plasticity in host adaptation. Within H. pylori populations from 2 colonized individuals, intragenomic recombination between cagA DNA repeat sequences leads to deletion or duplication of tyrosine phosphorylation sites in the CagA protein, which is injected by a type IV secretion system into host cells. Experimental coculture of gastric epithelial cells with the strains containing these naturally occurring CagA phosphorylation site variants induced markedly divergent host cell morphologic responses. Mutants were constructed in which a phosphorylation site was either added or deleted in the expressed CagA protein; coculture studies confirmed that the naturally occurring differences in CagA phosphorylation are responsible for the observed phenotypic variation. These findings indicate that within an individual host, intragenomic recombination between H. pylori repetitive DNA produces strain variants differing in their signals to host cells.

  17. Study on Catchment Runoff Variations and Possible Responds to Climate Change and Human Activities

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    Qin, J.; Chen, Y.

    2016-12-01

    Under the influence of global climate change and human activities,the spatial-temporal distribution of precipitation has changed significantly which drives catchment hydrological processes changes.To better understand the characteristic and causes of runoff variations at different periods which would impacts catchment flood disaster risk, the Utaphao catchment is studied whichis a typical catchment in southern Thailand.Based on daily hydrological data from 1971 to 2014,selecting representative raingauges and stream gauging stations from the catchment as research stations. Using the methods of Mann-Kendall test and serial cluster analysis, this paper studied the characteristics and laws of historical hydrological process in Utaphao catchment, detects the impact of changing environment to watershed hydrological processes,the results show that the runoff and precipitation havesome kinds of changes.

  18. Diurnal Variations of Human Circulating Cell-Free Micro-RNA

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    Heegaard, Niels H H; Carlsen, Anting Liu; Lilje, Berit

    2016-01-01

    A 24-hour light and dark cycle-dependent rhythmicity pervades physiological processes in virtually all living organisms including humans. These regular oscillations are caused by external cues to endogenous, independent biological time-keeping systems (clocks). The rhythm is reflected by gene...... expression that varies in a circadian and specific fashion in different organs and tissues and is regulated largely by dynamic epigenetic and post-transcriptional mechanisms. This leads to well-documented oscillations of specific electrolytes, hormones, metabolites, and plasma proteins in blood samples....... An emerging, important class of gene regulators is short single-stranded RNA (micro-RNA, miRNA) that interferes post-transcriptionally with gene expression and thus may play a role in the circadian variation of gene expression. MiRNAs are promising biomarkers by virtue of their disease-specific tissue...

  19. Morphological variations of a jugular foramen in North Indian human adult skulls

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    Ruchira Sethi

    2011-01-01

    Full Text Available Aims: To assess the size and bridging patterns of jugular foramina of adult human skulls. Materials and Methods: The study was conducted on 56 adult North - Indian skulls procured from Department of Anatomy of Santosh Medical College, Ghaziabad. The jugular foramina were observed by naked eye and with magnifying lens to assess the variations in size and bridging patterns. Results: The jugular foramen was larger on the right side in 53.5% skulls and on the left side in 7.1% skulls. In the remaining skulls (39.4% it was equal on both sides. Complete tripartite division was observed in 10.7% cases. Incomplete division was seen in 7.1% cases on right side and 3.5% cases on the left side. Incomplete division was never observed bilaterally. An additional accessory foramen was observed to be communicating with posterior condylar canal. Conclusion: The variations observed in present study are of immense value to ENT surgeons while performing middle ear surgeries for various jugular foramen tumors. Also, the bridging patterns cause compression to structures passing through this foramen hence accentuating the clinical presentations of Glomus jugulare.

  20. Marked variation in predicted and observed variability of tandem repeat loci across the human genome

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    Shields Denis C

    2008-04-01

    Full Text Available Abstract Background Tandem repeat (TR variants in the human genome play key roles in a number of diseases. However, current models predicting variability are based on limited training sets. We conducted a systematic analysis of TRs of unit lengths 2–12 nucleotides in Whole Genome Shotgun (WGS sequences to define the extent of variation of 209,214 unique repeat loci throughout the genome. Results We applied a multivariate statistical model to predict TR variability. Predicted heterozygosity correlated with heterozygosity in the CEPH polymorphism database (correlation ρ = 0.29, p Conclusion Variability among 2–12-mer TRs in the genome can be modeled by a few parameters, which do not markedly differ according to unit length, consistent with a common mechanism for the generation of variability among such TRs. Analysis of the distributions of observed and predicted variants across the genome showed a general concordance, indicating that the repeat variation dataset does not exhibit strong regional ascertainment biases. This revealed a deficit of variant repeats in chromosomes 19 and Y – likely to reflect a reduction in 2-mer repeats in the former and a reduced level of recombination in the latter – and excesses in chromosomes 6, 13, 20 and 21.

  1. Variations in the concentration of total human milk proteins in the first month of lactation

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    Mladenović Marija

    2007-01-01

    Full Text Available Introduction. Human milk proteins are maximally adapted to physiological needs of a neonate. Thus, depending on the speed of the neonatal growth and development, the content of milk proteins changes, both in quantity and quality. Objective. The study was conducted in order to determine variations of total protein concentrations in milk in the first and third lactation week in lactating mothers of term and preterm neonates. Also, we analyzed the influence of the mode of delivery, neonatal Apgar score and parity on the concentration of human milk proteins in both lactation phases. Method. The study aims were evaluated on the sample of 48 women, of whom 33 were mothers of term neonates and 15 of neonates born between the 34th to 37th gestational weeks. Total protein level of the lactation milk from the middle phase was determined using the standard laboratory method (Lowry et al., 1951, and the obtained differences were analyzed by t-test. Results. Total protein concentration in term colostrum was 17.60-45.17 g/l (X=24.71±5.19, while in preterm colostrum it was 28.39-73.30 g/l (X=39.17±11.08. The total protein level of mature milk in women who had term delivery was 11.90-22.11 g/l (X=16.39±2.96, while in women who had preterm delivery it was 14.50-44.19 g/l (X=23.25±8.96. The obtained results indicated that total protein concentration in women who had preterm delivery was significantly higher than that of women who had term delivery, both in the colostral and mature phase of lactation. (p<0.01. Also, the difference in the protein concentration was statistically highly significant (p<0.01 in the colostral and mature phase of lactation, both in women who had term and preterm delivery. Variations in the total protein level of human milk were not significant, depending on the prematurity stage, the mode and severity of delivery and parity, both in the first and third week of lactation. Conclusion. Our results show that total protein concentration

  2. Extent, causes, and consequences of small RNA expression variation in human adipose tissue.

    Directory of Open Access Journals (Sweden)

    Leopold Parts

    Full Text Available Small RNAs are functional molecules that modulate mRNA transcripts and have been implicated in the aetiology of several common diseases. However, little is known about the extent of their variability within the human population. Here, we characterise the extent, causes, and effects of naturally occurring variation in expression and sequence of small RNAs from adipose tissue in relation to genotype, gene expression, and metabolic traits in the MuTHER reference cohort. We profiled the expression of 15 to 30 base pair RNA molecules in subcutaneous adipose tissue from 131 individuals using high-throughput sequencing, and quantified levels of 591 microRNAs and small nucleolar RNAs. We identified three genetic variants and three RNA editing events. Highly expressed small RNAs are more conserved within mammals than average, as are those with highly variable expression. We identified 14 genetic loci significantly associated with nearby small RNA expression levels, seven of which also regulate an mRNA transcript level in the same region. In addition, these loci are enriched for variants significant in genome-wide association studies for body mass index. Contrary to expectation, we found no evidence for negative correlation between expression level of a microRNA and its target mRNAs. Trunk fat mass, body mass index, and fasting insulin were associated with more than twenty small RNA expression levels each, while fasting glucose had no significant associations. This study highlights the similar genetic complexity and shared genetic control of small RNA and mRNA transcripts, and gives a quantitative picture of small RNA expression variation in the human population.

  3. Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue

    Science.gov (United States)

    Knights, Andrew J.; Abreu-Goodger, Cei; van de Bunt, Martijn; Guerra-Assunção, José Afonso; Bartonicek, Nenad; van Dongen, Stijn; Mägi, Reedik; Nisbet, James; Barrett, Amy; Rantalainen, Mattias; Nica, Alexandra C.; Quail, Michael A.; Small, Kerrin S.; Glass, Daniel; Enright, Anton J.; Winn, John; Deloukas, Panos; Dermitzakis, Emmanouil T.; McCarthy, Mark I.; Spector, Timothy D.; Durbin, Richard; Lindgren, Cecilia M.

    2012-01-01

    Small RNAs are functional molecules that modulate mRNA transcripts and have been implicated in the aetiology of several common diseases. However, little is known about the extent of their variability within the human population. Here, we characterise the extent, causes, and effects of naturally occurring variation in expression and sequence of small RNAs from adipose tissue in relation to genotype, gene expression, and metabolic traits in the MuTHER reference cohort. We profiled the expression of 15 to 30 base pair RNA molecules in subcutaneous adipose tissue from 131 individuals using high-throughput sequencing, and quantified levels of 591 microRNAs and small nucleolar RNAs. We identified three genetic variants and three RNA editing events. Highly expressed small RNAs are more conserved within mammals than average, as are those with highly variable expression. We identified 14 genetic loci significantly associated with nearby small RNA expression levels, seven of which also regulate an mRNA transcript level in the same region. In addition, these loci are enriched for variants significant in genome-wide association studies for body mass index. Contrary to expectation, we found no evidence for negative correlation between expression level of a microRNA and its target mRNAs. Trunk fat mass, body mass index, and fasting insulin were associated with more than twenty small RNA expression levels each, while fasting glucose had no significant associations. This study highlights the similar genetic complexity and shared genetic control of small RNA and mRNA transcripts, and gives a quantitative picture of small RNA expression variation in the human population. PMID:22589741

  4. Diurnal variation in baseline human regional cerebral blood flow demonstrated by PET

    Energy Technology Data Exchange (ETDEWEB)

    Diehl, D.J.; Mintun, M.A.; Moore, R.Y. [Univ. of Pittsburgh, PA (United States)] [and others

    1994-05-01

    We have previously described the diurnal variation in regional cerebral blood flow (rCBF) response to bright light in human subjects as demonstrated by the positron emission tomography (PET) activation method. In this abstract, we report the differences in rCBF (an indicator of differences in regional neuronal activity) between the evening and midday dim light baseline scans which served as the control states in the above bright light activation study. Five right-handed, healthy volunteers underwent both an evening (8pm) and a midday (12N) O-15 water PET scanning session. Each scanning session was preceded by one hour of dim light adaptation (50 lux) and consisted of six rCBF scans at three different light intensities in an AABBCC sequence (A=50 lux, B=2500 lux, C=7000lux). Significant differences in rCBF between the evening and midday 50 lux states were identified using the statistical parametric mapping method developed by Friston et al (p<.001). The evening scans demonstrated areas of greater relative blood flow in the pineal gland, the lateral temporal cortex bilaterally, the right lateral prefrontal cortex, the superior aspect of the anterior cingulate, and the left thalamus. The midday scans showed areas of greater relative blood flow in the visual cortex, the left lateral prefrontal cortex. the inferior aspect of the anterior cingulate, the left parietal cortex and the cerebellum. Our results demonstrate an extensive diurnal variation in baseline human rCBF. This indicates that time of day may be an important variable in conducting and interpreting functional brain imaging studies. Furthermore, these results suggest possible neuroanatomical substrates through which the circadian system may regulate the various physiologic and behavioral processes that manifest circadian rhythms.

  5. Assessing the impact of climate variability and human activities on streamflow variation

    Science.gov (United States)

    Chang, Jianxia; Zhang, Hongxue; Wang, Yimin; Zhu, Yuelu

    2016-04-01

    Water resources in river systems have been changing under the impact of both climate variability and human activities. Assessing the respective impact on decadal streamflow variation is important for water resource management. By using an elasticity-based method and calibrated TOPMODEL and VIC hydrological models, we quantitatively isolated the relative contributions that human activities and climate variability made to decadal streamflow changes in the Jinghe basin, located in the northwest of China. This is an important watershed of the Shaanxi province that supplies drinking water for a population of over 6 million people. The results showed that the maximum value of the moisture index (E0/P) was 1.91 and appeared in 1991-2000, and the decreased speed of streamflow was higher since 1990 compared with 1960-1990. The average annual streamflow from 1990 to 2010 was reduced by 26.96 % compared with the multiyear average value (from 1960 to 2010). The estimates of the impacts of climate variability and human activities on streamflow decreases from the hydrological models were similar to those from the elasticity-based method. The maximum contribution value of human activities was 99 % when averaged over the three methods, and appeared in 1981-1990 due to the effects of soil and water conservation measures and irrigation water withdrawal. Climate variability made the greatest contribution to streamflow reduction in 1991-2000, the values of which was 40.4 %. We emphasized various source of errors and uncertainties that may occur in the hydrological model (parameter and structural uncertainty) and elasticity-based method (model parameter) in climate change impact studies.

  6. Effects of Pharmacogenomics on Individualized Drug Treatment%药物基因组学对个体化药物治疗的影响

    Institute of Scientific and Technical Information of China (English)

    赵可新; 石蕊; 李岑; 王倩; 王声祥; 任艳平; 张睿

    2016-01-01

    Pharmacogenomics is a discipline studying the influence of genetic differences on drug effectiveness .It promises to op-timize the effect of medicine and reduce side effects .It is one of the most effective ways to predict the drug reaction in human body by using pharmacogenomics , which can achieve the goal of precision medicine .With the rapid development of the genetical test technolo-gies, the in vitro individual genome testing projects with the properties of high throughput , and measurable and low cost are better to be applied in medical practice and guiding for making individualized medicine plan .The study elucidated the progress in single nucleotide polymorphism and its clinical application , and focused on the strategic effects of pharmacogenomics on individualized treatment and gene diversity for guiding medicine .%药物基因组学是研究个体患者的遗传差异对药物作用的影响,继而优化药效并减少药物的不良反应的一门学科。利用基因组信息预测个体对药物的反应是实现个体化药物治疗最有效的途径之一,也是实现精准医疗的手段之一。随着基因检测技术的飞速发展,使得高通量、可衡量、低成本的体外个体基因组检测项目越来越多的应用到医疗实践中,指导制订个体化给药方案。本文介绍单核苷酸多态性以及相关临床应用进展,阐述药物基因组学的个体化治疗评价和其根据人体的基因多样性指导医疗的战略性作用。

  7. Application of Method of Variation to Analyze and Predict Human Induced Modifications of Water Resource Systems

    Science.gov (United States)

    Dessu, S. B.; Melesse, A. M.; Mahadev, B.; McClain, M.

    2010-12-01

    Water resource systems have often used gravitational surface and subsurface flows because of their practicality in hydrological modeling and prediction. Activities such as inter/intra-basin water transfer, the use of small pumps and the construction of micro-ponds challenge the tradition of natural rivers as water resource management unit. On the contrary, precipitation is barely affected by topography and plot harvesting in wet regions can be more manageable than diverting from rivers. Therefore, it is indicative to attend to systems where precipitation drives the dynamics while the internal mechanics constitutes spectrum of human activity and decision in a network of plots. The trade-in volume and path of harvested precipitation depends on water balance, energy balance and the kinematics of supply and demand. Method of variation can be used to understand and predict the implication of local excess precipitation harvest and exchange on the natural water system. A system model was developed using the variational form of Euler-Bernoulli’s equation for the Kenyan Mara River basin. Satellite derived digital elevation models, precipitation estimates, and surface properties such as fractional impervious surface area, are used to estimate the available water resource. Four management conditions are imposed in the model: gravitational flow, open water extraction and high water use investment at upstream and downstream respectively. According to the model, the first management maintains the basin status quo while the open source management could induce externality. The high water market at the upstream in the third management offers more than 50% of the basin-wide total revenue to the upper third section of the basin thus may promote more harvesting. The open source and upstream exploitation suggest potential drop of water availability to downstream. The model exposed the latent potential of economic gradient to reconfigure the flow network along the direction where the

  8. Genetic variation in human disease and a new role for copy number variants.

    Science.gov (United States)

    Shelling, Andrew N; Ferguson, Lynnette R

    2007-09-01

    While complex diseases, such as inflammatory bowel disease, do not follow distinctive Mendelian inheritance patterns, there is now considerable evidence from twin and pedigree studies to show that there are significant genetic influences in the development of many such diseases. In times past, this type of information was considered to be interesting, and was used mainly to alert other members of the families that they may also be at increased risk of developing the disease. However, with the ability to evaluate the genetic basis of common disease, this information will have important consequences for the diagnosis, prevention and treatment of the disorder. The genetic basis for common disease is likely to be more complicated than we had previously anticipated, since we now recognise epigenetic causes of disease, and other subtle gene regulatory mechanisms. Copy number variants have been highlighted in this review, as being a phenomenon that we have known about for a long time, but that has not previously been clearly associated with human disease. As complex disease is related to changes in gene expression, any variation in the human genome that alters gene expression is now a candidate for being involved in the disease process.

  9. Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes

    KAUST Repository

    Cui, Peng

    2012-03-23

    Here, we evaluate the contribution of two major biological processes—DNA replication and transcription—to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes.

  10. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

    Science.gov (United States)

    Chen, Lu; Ge, Bing; Casale, Francesco Paolo; Vasquez, Louella; Kwan, Tony; Garrido-Martín, Diego; Watt, Stephen; Yan, Ying; Kundu, Kousik; Ecker, Simone; Datta, Avik; Richardson, David; Burden, Frances; Mead, Daniel; Mann, Alice L; Fernandez, Jose Maria; Rowlston, Sophia; Wilder, Steven P; Farrow, Samantha; Shao, Xiaojian; Lambourne, John J; Redensek, Adriana; Albers, Cornelis A; Amstislavskiy, Vyacheslav; Ashford, Sofie; Berentsen, Kim; Bomba, Lorenzo; Bourque, Guillaume; Bujold, David; Busche, Stephan; Caron, Maxime; Chen, Shu-Huang; Cheung, Warren; Delaneau, Oliver; Dermitzakis, Emmanouil T; Elding, Heather; Colgiu, Irina; Bagger, Frederik O; Flicek, Paul; Habibi, Ehsan; Iotchkova, Valentina; Janssen-Megens, Eva; Kim, Bowon; Lehrach, Hans; Lowy, Ernesto; Mandoli, Amit; Matarese, Filomena; Maurano, Matthew T; Morris, John A; Pancaldi, Vera; Pourfarzad, Farzin; Rehnstrom, Karola; Rendon, Augusto; Risch, Thomas; Sharifi, Nilofar; Simon, Marie-Michelle; Sultan, Marc; Valencia, Alfonso; Walter, Klaudia; Wang, Shuang-Yin; Frontini, Mattia; Antonarakis, Stylianos E; Clarke, Laura; Yaspo, Marie-Laure; Beck, Stephan; Guigo, Roderic; Rico, Daniel; Martens, Joost H A; Ouwehand, Willem H; Kuijpers, Taco W; Paul, Dirk S; Stunnenberg, Hendrik G; Stegle, Oliver; Downes, Kate; Pastinen, Tomi; Soranzo, Nicole

    2016-11-17

    Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14(+) monocytes, CD16(+) neutrophils, and naive CD4(+) T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk.

  11. Time to decide: Diurnal variations on the speed and quality of human decisions.

    Science.gov (United States)

    Leone, María Juliana; Fernandez Slezak, Diego; Golombek, Diego; Sigman, Mariano

    2017-01-01

    Human behavior and physiology exhibit diurnal fluctuations. These rhythms are entrained by light and social cues, with vast individual differences in the phase of entrainment - referred as an individual's chronotype - ranging in a continuum between early larks and late owls. Understanding whether decision-making in real-life situations depends on the relation between time of the day and an individual's diurnal preferences has both practical and theoretical implications. However, answering this question has remained elusive because of the difficulty of measuring precisely the quality of a decision in real-life scenarios. Here we investigate diurnal variations in decision-making as a function of an individual's chronotype capitalizing on a vast repository of human decisions: online chess servers. In a chess game, every player has to make around 40 decisions using a finite time budget and both the time and quality of each decision can be accurately determined. We found reliable diurnal rhythms in activity and decision-making policy. During the morning, players adopt a prevention focus policy (slower and more accurate decisions) which is later modified to a promotion focus (faster but less accurate decisions), without daily changes in performance. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Recombination networks as genetic markers in a human variation study of the Old World.

    Science.gov (United States)

    Javed, Asif; Melé, Marta; Pybus, Marc; Zalloua, Pierre; Haber, Marc; Comas, David; Netea, Mihai G; Balanovsky, Oleg; Balanovska, Elena; Jin, Li; Yang, Yajun; Arunkumar, Ganeshprasad; Pitchappan, Ramasamy; Bertranpetit, Jaume; Calafell, Francesc; Parida, Laxmi

    2012-04-01

    We have analyzed human genetic diversity in 33 Old World populations including 23 populations obtained through Genographic Project studies. A set of 1,536 SNPs in five X chromosome regions were genotyped in 1,288 individuals (mostly males). We use a novel analysis employing subARG network construction with recombining chromosomal segments. Here, a subARG is constructed independently for each of five gene-free regions across the X chromosome, and the results are aggregated across them. For PCA, MDS and ancestry inference with STRUCTURE, the subARG is processed to obtain feature vectors of samples and pairwise distances between samples. The observed population structure, estimated from the five short X chromosomal segments, supports genome-wide frequency-based analyses: African populations show higher genetic diversity, and the general trend of shared variation is seen across the globe from Africa through Middle East, Europe, Central Asia, Southeast Asia, and East Asia in broad patterns. The recombinational analysis was also compared with established methods based on SNPs and haplotypes. For haplotypes, we also employed a fixed-length approach based on information-content optimization. Our recombinational analysis suggested a southern migration route out of Africa, and it also supports a single, rapid human expansion from Africa to East Asia through South Asia.

  13. Common genetic variation in the human CTF1 locus, encoding cardiotrophin-1, determines insulin sensitivity.

    Directory of Open Access Journals (Sweden)

    Stefan Z Lutz

    Full Text Available AIMS/HYPOTHESIS: Recently, cardiotrophin-1, a member of the interleukin-6 family of cytokines was described to protect beta-cells from apoptosis, to improve glucose-stimulated insulin secretion and insulin resistance, and to prevent streptozotocin-induced diabetes in mice. Here, we studied whether common single nucleotide polymorphisms (SNPs in the CTF1 locus, encoding cardiotrophin-1, influence insulin secretion and insulin sensitivity in humans. METHODS: We genotyped 1,771 German subjects for three CTF1 tagging SNPs (rs1046276, rs1458201, and rs8046707. The subjects were metabolically characterized by an oral glucose tolerance test. Subgroups underwent magnetic resonance (MR imaging/spectroscopy and hyperinsulinaemic-euglycaemic clamps. RESULTS: After appropriate adjustment, the minor allele of CTF1 SNP rs8046707 was significantly associated with decreased in vivo measures of insulin sensitivity. The other tested SNPs were not associated with OGTT-derived sensitivity parameters, nor did the three tested SNPs show any association with OGTT-derived parameters of insulin release. In the MR subgroup, SNP rs8046707 was nominally associated with lower visceral adipose tissue. Furthermore, the SNP rs1458201 showed a nominal association with increased VLDL levels. CONCLUSIONS: In conclusion, this study, even though preliminary and awaiting further confirmation by independent replication, provides first evidence that common genetic variation in CTF1 could contribute to insulin sensitivity in humans. Our SNP data indicate an insulin-desensitizing effect of cardiotrophin-1 and underline that cardiotrophin-1 represents an interesting target to influence insulin sensitivity.

  14. Review: A high capacity of the human placenta for genetic and epigenetic variation: implications for assessing pregnancy outcome.

    Science.gov (United States)

    Yuen, R K C; Robinson, W P

    2011-03-01

    Genetic and epigenetic studies of the human placenta can help to clarify the underlying mechanisms of placenta-associated diseases. However, such studies have also revealed a considerable degree of within- and between-placenta variability, which can be attributed to a variety of influences. We illustrate the inherent heterogeneity in the placenta using examples from two types of studies: 1) chromosomal mosaicism and 2) DNA methylation variation. We discuss the factors that may influence the distribution of variation and how, understanding the source of this variation is important for interpreting data used to investigate and predict clinical outcomes.

  15. Evaluation of the interindividual human variation in bioactivation of methyleugenol using physiologically based kinetic modeling and Monte Carlo simulations

    Energy Technology Data Exchange (ETDEWEB)

    Al-Subeihi, Ala' A.A., E-mail: subeihi@yahoo.com [Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen (Netherlands); BEN-HAYYAN-Aqaba International Laboratories, Aqaba Special Economic Zone Authority (ASEZA), P. O. Box 2565, Aqaba 77110 (Jordan); Alhusainy, Wasma; Kiwamoto, Reiko; Spenkelink, Bert [Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen (Netherlands); Bladeren, Peter J. van [Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen (Netherlands); Nestec S.A., Avenue Nestlé 55, 1800 Vevey (Switzerland); Rietjens, Ivonne M.C.M.; Punt, Ans [Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen (Netherlands)

    2015-03-01

    The present study aims at predicting the level of formation of the ultimate carcinogenic metabolite of methyleugenol, 1′-sulfooxymethyleugenol, in the human population by taking variability in key bioactivation and detoxification reactions into account using Monte Carlo simulations. Depending on the metabolic route, variation was simulated based on kinetic constants obtained from incubations with a range of individual human liver fractions or by combining kinetic constants obtained for specific isoenzymes with literature reported human variation in the activity of these enzymes. The results of the study indicate that formation of 1′-sulfooxymethyleugenol is predominantly affected by variation in i) P450 1A2-catalyzed bioactivation of methyleugenol to 1′-hydroxymethyleugenol, ii) P450 2B6-catalyzed epoxidation of methyleugenol, iii) the apparent kinetic constants for oxidation of 1′-hydroxymethyleugenol, and iv) the apparent kinetic constants for sulfation of 1′-hydroxymethyleugenol. Based on the Monte Carlo simulations a so-called chemical-specific adjustment factor (CSAF) for intraspecies variation could be derived by dividing different percentiles by the 50th percentile of the predicted population distribution for 1′-sulfooxymethyleugenol formation. The obtained CSAF value at the 90th percentile was 3.2, indicating that the default uncertainty factor of 3.16 for human variability in kinetics may adequately cover the variation within 90% of the population. Covering 99% of the population requires a larger uncertainty factor of 6.4. In conclusion, the results showed that adequate predictions on interindividual human variation can be made with Monte Carlo-based PBK modeling. For methyleugenol this variation was observed to be in line with the default variation generally assumed in risk assessment. - Highlights: • Interindividual human differences in methyleugenol bioactivation were simulated. • This was done using in vitro incubations, PBK modeling

  16. Clinical Interpretation of Genomic Variations.

    Science.gov (United States)

    Sayitoğlu, Müge

    2016-09-05

    Novel high-throughput sequencing technologies generate large-scale genomic data and are used extensively for disease mapping of monogenic and/or complex disorders, personalized treatment, and pharmacogenomics. Next-generation sequencing is rapidly becoming routine tool for diagnosis and molecular monitoring of patients to evaluate therapeutic efficiency. The next-generation sequencing platforms generate huge amounts of genetic variation data and it remains a challenge to interpret the variations that are identified. Such data interpretation needs close collaboration among bioinformaticians, clinicians, and geneticists. There are several problems that must be addressed, such as the generation of new algorithms for mapping and annotation, harmonization of the terminology, correct use of nomenclature, reference genomes for different populations, rare disease variant databases, and clinical reports.

  17. Quantitative variation in obesity-related traits and insulin precursors linked to the OB gene region on human chromosome 7

    Energy Technology Data Exchange (ETDEWEB)

    Duggirala, R.; Stern, M.P.; Reinhart, L.J. [Univ. of Texas Health Science Center, San Antonio, TX (United States)] [and others

    1996-09-01

    Despite the evidence that human obesity has strong genetic determinants, efforts at identifying specific genes that influence human obesity have largely been unsuccessful. Using the sibship data obtained from 32 low-income Mexican American pedigrees ascertained on a type II diabetic proband and a multipoint variance-components method, we tested for linkage between various obesity-related traits plus associated metabolic traits and 15 markers on human chromosome 7. We found evidence for linkage between markers in the OB gene region and various traits, as follows: D7S514 and extremity skinfolds (LOD = 3.1), human carboxypeptidase A1 (HCPA1) and 32,33-split proinsulin level (LOD = 4.2), and HCPA1 and proinsulin level (LOD = 3.2). A putative susceptibility locus linked to the marker D7S514 explained 56% of the total phenotypic variation in extremity skinfolds. Variation at the HCPA1 locus explained 64% of phenotypic variation in proinsulin level and {approximately}73% of phenotypic variation in split proinsulin concentration, respectively. Weaker evidence for linkage to several other obesity-related traits (e.g., waist circumference, body-mass index, fat mass by bioimpedance, etc.) was observed for a genetic location, which is {approximately}15 cM telomeric to OB. In conclusion, our study reveals that the OB region plays a significant role in determining the phenotypic variation of both insulin precursors and obesity-related traits, at least in Mexican Americans. 66 refs., 3 figs., 4 tabs.

  18. Genetic variation of the RASGRF1 regulatory region affects human hippocampus-dependent memory

    Directory of Open Access Journals (Sweden)

    Adriana eBarman

    2014-04-01

    Full Text Available The guanine nucleotide exchange factor RASGRF1 is an important regulator of intracellular signaling and neural plasticity in the brain. RASGRF1-deficient mice exhibit a complex phenotype with learning deficits and ocular abnormalities. Also in humans, a genome-wide association study has identified the single nucleotide polymorphism (SNP rs8027411 in the putative transcription regulatory region of RASGRF1 as a risk variant of myopia. Here we aimed to assess whether, in line with the RASGRF1 knockout mouse phenotype, rs8027411 might also be associated with human memory function. We performed computer-based neuropsychological learning experiments in two independent cohorts of young, healthy participants. Tests included the Verbal Learning and Memory Test (VLMT and the logical memory section of the Wechsler Memory Scale (WMS. Two sub-cohorts additionally participated in functional magnetic resonance imaging (fMRI studies of hippocampus function. 119 participants performed a novelty encoding task that had previously been shown to engage the hippocampus, and 63 subjects participated in a reward-related memory encoding study. RASGRF1 rs8027411 genotype was indeed associated with memory performance in an allele dosage-dependent manner, with carriers of the T allele (i.e. the myopia risk allele showing better memory performance in the early encoding phase of the VLMT and in the recall phase of the WMS logical memory section. In fMRI, T allele carriers exhibited increased hippocampal activation during presentation of novel images and during encoding of pictures associated with monetary reward. Taken together, our results provide evidence for a role of the RASGRF1 gene locus in hippocampus-dependent memory and, along with the previous association with myopia, point towards pleitropic effects of RASGRF1 genetic variations on complex neural function in humans.

  19. Variation of Floods Characteristics and Their Responses to Climate and Human Activities in Poyang Lake, China

    Institute of Scientific and Technical Information of China (English)

    LI Xianghu; ZHANG Qi

    2015-01-01

    The Poyang Lake is one of the most frequently flooded areas in China.Understanding the changing characteristics of floods as well as the affecting factors is an important prerequisite of flood disaster prevention and mitigation.The present study identified the characteristics variations of historical floods in the Poyang Lake and their tendencies based on the Mann-Kendall (M-K) test,and also investigated the related affecting factors,both from climate and human activities.The results revealed that the highest flood stages,duration as well as hazard coefficient of floods showed a long-term increasing linear trend during the last 60 years with the M-K statistic of 1.49,1.60 and 1.50,respectively.And,a slightly increasing linear trend in the timing of the highest stages indicated the floods occurred later and later during the last six decades.The rainfall during the flood season and subsequent discharges of the Changjiang (Yangtze) River and runoff from the Poyang Lake Basin were mainly responsible for the severe flood situation in the Poyang Lake in the 1990s.In addition,the intensive human activities,including land reclamation and levee construction,also played a supplementary role in increasing severity of major floods.While,the fewer floods in the Poyang Lake after 2000 can be attributed to not only the less rainfall over the Poyang Lake Basin and low discharges of the Changjiang River during flood periods,but also the stronger influences of human activity which increased the floodwater storage of the Poyang Lake than before.

  20. Variations of the angiotensin II type 1 receptor gene are associated with extreme human longevity.

    Science.gov (United States)

    Benigni, Ariela; Orisio, Silvia; Noris, Marina; Iatropoulos, Paraskevas; Castaldi, Davide; Kamide, Kei; Rakugi, Hiromi; Arai, Yasumichi; Todeschini, Marta; Ogliari, Giulia; Imai, Enyu; Gondo, Yasuyuki; Hirose, Nobuyoshi; Mari, Daniela; Remuzzi, Giuseppe

    2013-06-01

    Longevity phenotype in humans results from the influence of environmental and genetic factors. Few gene polymorphisms have been identified so far with a modest effect on lifespan leaving room for the search of other players in the longevity game. It has been recently demonstrated that targeted disruption of the mouse homolog of the human angiotensin II type 1 receptor (AT1R) gene (AGTR1) translates into marked prolongation of animal lifespan (Benigni et al., J Clin Invest 119(3):524-530, 2009). Based on the above study in mice, here we sought to search for AGTR1 variations associated to reduced AT1 receptor protein levels and to prolonged lifespan in humans. AGTR1 was sequenced in 173 Italian centenarians and 376 younger controls. A novel non-synonymous mutation was detected in a centenarian. Two polymorphisms in AGTR1 promoter, rs422858 and rs275653, in complete linkage disequilibrium, were significantly associated with the ability to attain extreme old age. We then replicated the study of rs275653 in a large independent cohort of Japanese origin (598 centenarians and semi-supercentenarians, 422 younger controls) and indeed confirmed its association with exceptional old age. In combined analyses, rs275653 was associated to extreme longevity either at recessive model (P = 0.007, odds ratio (OR) 3.57) or at genotype level (P = 0.015). Significance was maintained after correcting for confounding factors. Fluorescence activated cell sorting analysis revealed that subjects homozygous for the minor allele of rs275653 had less AT1R-positive peripheral blood polymorphonuclear cells. Moreover, rs275653 was associated to lower blood pressure in centenarians. These findings highlight the role of AGTR1 as a possible candidate among longevity-enabling genes.

  1. The architecture of gene regulatory variation across multiple human tissues: the MuTHER study.

    Directory of Open Access Journals (Sweden)

    Alexandra C Nica

    Full Text Available While there have been studies exploring regulatory variation in one or more tissues, the complexity of tissue-specificity in multiple primary tissues is not yet well understood. We explore in depth the role of cis-regulatory variation in three human tissues: lymphoblastoid cell lines (LCL, skin, and fat. The samples (156 LCL, 160 skin, 166 fat were derived simultaneously from a subset of well-phenotyped healthy female twins of the MuTHER resource. We discover an abundance of cis-eQTLs in each tissue similar to previous estimates (858 or 4.7% of genes. In addition, we apply factor analysis (FA to remove effects of latent variables, thus more than doubling the number of our discoveries (1,822 eQTL genes. The unique study design (Matched Co-Twin Analysis--MCTA permits immediate replication of eQTLs using co-twins (93%-98% and validation of the considerable gain in eQTL discovery after FA correction. We highlight the challenges of comparing eQTLs between tissues. After verifying previous significance threshold-based estimates of tissue-specificity, we show their limitations given their dependency on statistical power. We propose that continuous estimates of the proportion of tissue-shared signals and direct comparison of the magnitude of effect on the fold change in expression are essential properties that jointly provide a biologically realistic view of tissue-specificity. Under this framework we demonstrate that 30% of eQTLs are shared among the three tissues studied, while another 29% appear exclusively tissue-specific. However, even among the shared eQTLs, a substantial proportion (10%-20% have significant differences in the magnitude of fold change between genotypic classes across tissues. Our results underline the need to account for the complexity of eQTL tissue-specificity in an effort to assess consequences of such variants for complex traits.

  2. The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

    Science.gov (United States)

    Nica, Alexandra C.; Parts, Leopold; Glass, Daniel; Nisbet, James; Barrett, Amy; Sekowska, Magdalena; Travers, Mary; Potter, Simon; Grundberg, Elin; Small, Kerrin; Hedman, Åsa K.; Bataille, Veronique; Tzenova Bell, Jordana; Surdulescu, Gabriela; Dimas, Antigone S.; Ingle, Catherine; Nestle, Frank O.; di Meglio, Paola; Min, Josine L.; Wilk, Alicja; Hammond, Christopher J.; Hassanali, Neelam; Yang, Tsun-Po; Montgomery, Stephen B.; O'Rahilly, Steve; Lindgren, Cecilia M.; Zondervan, Krina T.; Soranzo, Nicole; Barroso, Inês; Durbin, Richard; Ahmadi, Kourosh; Deloukas, Panos; McCarthy, Mark I.; Dermitzakis, Emmanouil T.; Spector, Timothy D.

    2011-01-01

    While there have been studies exploring regulatory variation in one or more tissues, the complexity of tissue-specificity in multiple primary tissues is not yet well understood. We explore in depth the role of cis-regulatory variation in three human tissues: lymphoblastoid cell lines (LCL), skin, and fat. The samples (156 LCL, 160 skin, 166 fat) were derived simultaneously from a subset of well-phenotyped healthy female twins of the MuTHER resource. We discover an abundance of cis-eQTLs in each tissue similar to previous estimates (858 or 4.7% of genes). In addition, we apply factor analysis (FA) to remove effects of latent variables, thus more than doubling the number of our discoveries (1,822 eQTL genes). The unique study design (Matched Co-Twin Analysis—MCTA) permits immediate replication of eQTLs using co-twins (93%–98%) and validation of the considerable gain in eQTL discovery after FA correction. We highlight the challenges of comparing eQTLs between tissues. After verifying previous significance threshold-based estimates of tissue-specificity, we show their limitations given their dependency on statistical power. We propose that continuous estimates of the proportion of tissue-shared signals and direct comparison of the magnitude of effect on the fold change in expression are essential properties that jointly provide a biologically realistic view of tissue-specificity. Under this framework we demonstrate that 30% of eQTLs are shared among the three tissues studied, while another 29% appear exclusively tissue-specific. However, even among the shared eQTLs, a substantial proportion (10%–20%) have significant differences in the magnitude of fold change between genotypic classes across tissues. Our results underline the need to account for the complexity of eQTL tissue-specificity in an effort to assess consequences of such variants for complex traits. PMID:21304890

  3. Individual variation in macronutrient regulation measured by proton magnetic resonance spectroscopy of human plasma.

    Science.gov (United States)

    Park, Youngja; Kim, Seoung Bum; Wang, Bing; Blanco, Roberto A; Le, Ngoc-Anh; Wu, Shaoxiong; Accardi, Carolyn J; Alexander, R Wayne; Ziegler, Thomas R; Jones, Dean P

    2009-07-01

    Proton nuclear magnetic resonance ((1)H-NMR) spectroscopy of plasma provides a global metabolic profiling method that shows promise for clinical diagnostics. However, cross-sectional studies are complicated by a lack of understanding of intraindividual variation, and this limits experimental design and interpretation of data. The present study determined the diurnal variation detected by (1)H NMR spectroscopy of human plasma. Data reduction methods revealed three time-of-day metabolic patterns, which were associated with morning, afternoon, and night. Major discriminatory regions for these time-of-day patterns included the various kinds of lipid signals (-CH(2)- and -CH(2)OCOR), and the region between 3 and 4 ppm heavily overlapped with amino acids that had alpha-CH and alpha-CH(2). The phasing and duration of time-of-day patterns were variable among individuals, apparently because of individual difference in food processing/digestion and absorption and clearance of macronutrient energy sources (fat, protein, carbohydrate). The times of day that were most consistent among individuals, and therefore most useful for cross-sectional studies, were fasting morning (0830-0930), postprandial afternoon (1430-1630), and nighttime samples (0430-0530). Importantly, the integrated picture of metabolism provided by (1)H-NMR spectroscopy of plasma suggests that this approach is suitable to study complex regulatory processes, including eating patterns/eating disorders, upper gastrointestinal functions (gastric emptying, pancreatic, biliary functions), and absorption/clearance of macronutrients. Hence, (1)H-NMR spectroscopy of plasma could provide a global metabolic tolerance test to assess complex processes involved in disease, including eating disorders and the range of physiological processes causing dysregulation of energy homeostasis.

  4. Diffusion tensor imaging of the human calf: Variation of inter- and intramuscle-specific diffusion parameters.

    Science.gov (United States)

    Schlaffke, Lara; Rehmann, Robert; Froeling, Martijn; Kley, Rudolf; Tegenthoff, Martin; Vorgerd, Matthias; Schmidt-Wilcke, Tobias

    2017-10-01

    To investigate to what extent inter- and intramuscular variations of diffusion parameters of human calf muscles can be explained by age, gender, muscle location, and body mass index (BMI) in a specific age group (20-35 years). Whole calf muscles of 18 healthy volunteers were evaluated. Magnetic resonance imaging (MRI) was performed using a 3T scanner and a 16-channel Torso XL coil. Diffusion-weighted images were acquired to perform fiber tractography and diffusion tensor imaging (DTI) analysis for each muscle of both legs. Fiber tractography was used to separate seven lower leg muscles. Associations between DTI parameters and confounds were evaluated. All muscles were additionally separated in seven identical segments along the z-axis to evaluate intramuscular differences in diffusion parameters. Fractional anisotropy (FA) and mean diffusivity (MD) were obtained for each muscle with low standard deviations (SDs) (SDFA : 0.01-0.02; SDMD : 0.07-0.14(10(-3) )). We found significant differences in FA values of the tibialis anterior muscle (AT) and extensor digitorum longus (EDL) muscles between men and women for whole muscle FA (two-sample t-tests; AT: P = 0.0014; EDL: P = 0.0004). We showed significant intramuscular differences in diffusion parameters between adjacent segments in most calf muscles (P muscle insertions showed higher (SD 0.03-0.06) than muscle bellies (SD 0.01-0.03), no relationships between FA or MD with age or BMI were found. Inter- and intramuscular variations in diffusion parameters of the calf were shown, which are not related to age or BMI in this age group. Differences between muscle belly and insertion should be considered when interpreting datasets not including whole muscles. 3 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2017;46:1137-1148. © 2017 International Society for Magnetic Resonance in Medicine.

  5. Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach

    NARCIS (Netherlands)

    B. Giardine (Belinda); J. Borg (Joseph); D.R. Higgs (Douglas); K.R. Peterson (Kenneth R.); J.N.J. Philipsen (Sjaak); D. Maglott (Donna); B.K. Singleton (Belinda K.); D.J. Anstee (David J.); A.N. Basak (Nazli); B.H. Clark (Bruce); F.C. Costa (Flavia C.); P. Faustino (Paula); H. Fedosyuk (Halyna); A.E. Felice (Alex); A. Francina (Alain); R. Galanello (Renzo); M.V.E. Gallivan (Monica V. E.); M. Georgitsi (Marianthi); R.J. Gibbons (Richard J.); P.C. Giordano (Piero Carlo); C.L. Harteveld (Cornelis); J.D. Hoyer (James D.); M. Jarvis (Martin); P. Joly (Philippe); E. Kanavakis (Emmanuel); P. Kollia (Panagoula); S. Menzel (Stephan); W.G. Miller (William); K. Moradkhani (Kamran); J. Old (John); A. Papachatzpoulou (Adamantia); M.N. Papadakis (Manoussos); P. Papadopoulos (Petros); S. Pavlovic (Sonja); L. Perseu (Lucia); M. Radmilovic (Milena); C. Riemer (Cathy); S. Satta (Stefania); I.A. Schrijver (Ingrid); M. Stojiljkovic (Maja); S.L. Thein; J. Traeger-Synodinos (Joanne); R. Tully (Ray); T. Wada (Takahito); J.S. Waye (John); C. Wiemann (Claudia); B. Zukic (Branka); D.H.K. Chui (David H. K.); H. Wajcman (Henri); R. Hardison (Ross); G.P. Patrinos (George)

    2011-01-01

    textabstractWe developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public

  6. Pharmacogenomics of estrogens on changes in carotid artery intima-medial thickness and coronary arterial calcification: Kronos Early Estrogen Prevention Study.

    Science.gov (United States)

    Miller, Virginia M; Jenkins, Gregory D; Biernacka, Joanna M; Heit, John A; Huggins, Gordon S; Hodis, Howard N; Budoff, Matthew J; Lobo, Rogerio A; Taylor, Hugh S; Manson, JoAnn E; Black, Dennis M; Naftolin, Frederick; Harman, S Mitchell; de Andrade, Mariza

    2016-01-01

    Prior to the initiation of menopausal hormone treatment (MHT), genetic variations in the innate immunity pathway were found to be associated with carotid artery intima-medial thickness (CIMT) and coronary arterial calcification (CAC) in women (n = 606) enrolled in the Kronos Early Estrogen Prevention Study (KEEPS). Whether MHT might affect these associations is unknown. The association of treatment outcomes with variation in the same 764 candidate genes was evaluated in the same KEEPS participants 4 yr after randomization to either oral conjugated equine estrogens (0.45 mg/day), transdermal 17β-estradiol (50 μg/day), each with progesterone (200 mg/day) for 12 days each month, or placebo pills and patch. Twenty SNPs within the innate immunity pathway most related with CIMT after 4 yr were not among those associated with CIMT prior to MHT. In 403 women who completed the study in their assigned treatment group, single nucleotide polymorphisms (SNPs) within the innate immunity pathway were found to alter the treatment effect on 4 yr change in CIMT (i.e., significant interaction between treatment and genetic variation in the innate immunity pathway; P 5 Agatston units after 4 yr. Results of this study suggest that hormonal status may interact with genetic variants to influence cardiovascular phenotypes, specifically, the pharmacogenomic effects within the innate immunity pathway for CIMT.

  7. Genetic variation of the human urinary tract innate immune response and asymptomatic bacteriuria in women.

    Directory of Open Access Journals (Sweden)

    Thomas R Hawn

    Full Text Available BACKGROUND: Although several studies suggest that genetic factors are associated with human UTI susceptibility, the role of DNA variation in regulating early in vivo urine inflammatory responses has not been fully examined. We examined whether candidate gene polymorphisms were associated with altered urine inflammatory profiles in asymptomatic women with or without bacteriuria. METHODOLOGY: We conducted a cross-sectional analysis of asymptomatic bacteriuria (ASB in 1,261 asymptomatic women ages 18-49 years originally enrolled as participants in a population-based case-control study of recurrent UTI and pyelonephritis. We genotyped polymorphisms in CXCR1, CXCR2, TLR1, TLR2, TLR4, TLR5, and TIRAP in women with and without ASB. We collected urine samples and measured levels of uropathogenic bacteria, neutrophils, and chemokines. PRINCIPAL FINDINGS: Polymorphism TLR2_G2258A, a variant associated with decreased lipopeptide-induced signaling, was associated with increased ASB risk (odds ratio 3.44, 95%CI; 1.65-7.17. Three CXCR1 polymorphisms were associated with ASB caused by gram-positive organisms. ASB was associated with urinary CXCL-8 levels, but not CXCL-5, CXCL-6, or sICAM-1 (P< or =0.0001. Urinary levels of CXCL-8 and CXCL-6, but not ICAM-1, were associated with higher neutrophil levels (P< or =0.0001. In addition, polymorphism CXCR1_G827C was associated with increased CXCL-8 levels in women with ASB (P = 0.004. CONCLUSIONS: TLR2 and CXCR1 polymorphisms were associated with ASB and a CXCR1 variant was associated with urine CXCL-8 levels. These results suggest that genetic factors are associated with early in vivo human bladder immune responses prior to the development of symptomatic UTIs.

  8. Transcription factor ATF-3 regulates allele variation phenotypes of the human SLC11A1 gene.

    Science.gov (United States)

    Taka, Styliani; Gazouli, Maria; Politis, Panagotis K; Pappa, Kalliopi I; Anagnou, Nicholas P

    2013-03-01

    Genetic polymorphisms in the human solute carrier family 11 member 1 (SLC11A1) gene predispose to susceptibility to infectious/inflammatory diseases and cancer. Human susceptibility to these diseases exhibits allelic association with a polymorphic regulatory Z-DNA-forming microsatellite of a (GT/AC)n repeat. The carriage of different alleles may influence chromatin remodeling and accessibility by transcription factors. Of particular importance is the binding site for the Activating Protein 1 (AP-1) elements, (ATF-3 and c-Jun), adjacent to the 5' sequence of the Z-DNA-forming polymorphism. The aim of the study was to characterize the transcriptional mechanisms controlling different alleles of SLC11A1 expression by ATF-3 and c-Jun. Allele 2, [T(GT)5AC(GT)5AC(GT)10GGCAGA(G)6], and Allele 3, [T(GT)5AC(GT)5AC(GT)9GGCAGA(G)6], were subcloned into the PGL2Basic vector. Transient transfections of THP-1 cells with the constructs, in the presence or absence of pATF-3 were preformed. Luciferase expression was determined. To document the recruitment of ATF-3 and c-Jun, to the polymorphic promoter alleles in vivo, we performed ChIP assays with transient transfected THP-1 cells treated with or without lipopolyssacharides. Our data documented that ATF-3 suppresses the transcriptional activation of Allele-3, and this suppression is enhanced in the presence of lipopolyssacharides. Our findings suggest that ATF-3 and c-Jun may influence heritable variation in SLC11A1-dependent innate resistance to infection and inflammation both within and between populations.

  9. Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation

    Directory of Open Access Journals (Sweden)

    Shriver Mark D

    2005-06-01

    Full Text Available Abstract Understanding the distribution of human genetic variation is an important foundation for research into the genetics of common diseases. Some of the alleles that modify common disease risk are themselves likely to be common and, thus, amenable to identification using gene-association methods. A problem with this approach is that the large sample sizes required for sufficient statistical power to detect alleles with moderate effect make gene-association studies susceptible to false-positive findings as the result of population stratification 12. Such type I errors can be eliminated by using either family-based association tests or methods that sufficiently adjust for population stratification 345. These methods require the availability of genetic markers that can detect and, thus, control for sources of genetic stratification among populations. In an effort to investigate population stratification and identify appropriate marker panels, we have analysed 11,555 single nucleotide polymorphisms in 203 individuals from 12 diverse human populations. Individuals in each population cluster to the exclusion of individuals from other populations using two clustering methods. Higher-order branching and clustering of the populations are consistent with the geographic origins of populations and with previously published genetic analyses. These data provide a valuable resource for the definition of marker panels to detect and control for population stratification in population-based gene identification studies. Using three US resident populations (European-American, African-American and Puerto Rican, we demonstrate how such studies can proceed, quantifying proportional ancestry levels and detecting significant admixture structure in each of these populations.

  10. Adaptive evolution of interleukin-3 (IL3), a gene associated with brain volume variation in general human populations.

    Science.gov (United States)

    Li, Ming; Huang, Liang; Li, Kaiqin; Huo, Yongxia; Chen, Chunhui; Wang, Jinkai; Liu, Jiewei; Luo, Zhenwu; Chen, Chuansheng; Dong, Qi; Yao, Yong-gang; Su, Bing; Luo, Xiong-jian

    2016-04-01

    Greatly expanded brain volume is one of the most characteristic traits that distinguish humans from other primates. Recent studies have revealed genes responsible for the dramatically enlarged human brain size (i.e., the microcephaly genes), and it has been well documented that many microcephaly genes have undergone accelerated evolution along the human lineage. In addition to being far larger than other primates, human brain volume is also highly variable in general populations. However, the genetic basis underlying human brain volume variation remains elusive and it is not known whether genes regulating human brain volume variation also have experienced positive selection. We have previously shown that genetic variants (near the IL3 gene) on 5q33 were significantly associated with brain volume in Chinese population. Here, we provide further evidence that support the significant association of genetic variants on 5q33 with brain volume. Bioinformatic analyses suggested that rs31480 is likely to be the causal variant among the studied SNPs. Molecular evolutionary analyses suggested that IL3 might have undergone positive selection in primates and humans. Neutrality tests further revealed signatures of positive selection of IL3 in Han Chinese and Europeans. Finally, extended haplotype homozygosity (EHH) and relative EHH analyses showed that the C allele of SNP rs31480 might have experienced recent positive selection in Han Chinese. Our results suggest that IL3 is an important genetic regulator for human brain volume variation and implied that IL3 might have experienced weak or modest positive selection in the evolutionary history of humans, which may be due to its contribution to human brain volume.

  11. Variation in human mate choice: simultaneously investigating heritability, parental influence, sexual imprinting, and assortative mating.

    Science.gov (United States)

    Zietsch, Brendan P; Verweij, Karin J H; Heath, Andrew C; Martin, Nicholas G

    2011-05-01

    Human mate choice is central to individuals' lives and to the evolution of the species, but the basis of variation in mate choice is not well understood. Here we looked at a large community-based sample of twins and their partners and parents ([Formula: see text] individuals) to test for genetic and family environmental influences on mate choice, while controlling for and not controlling for the effects of assortative mating. Key traits were analyzed, including height, body mass index, age, education, income, personality, social attitudes, and religiosity. This revealed near-zero genetic influences on male and female mate choice over all traits and no significant genetic influences on mate choice for any specific trait. A significant family environmental influence was found for the age and income of females' mate choices, possibly reflecting parental influence over mating decisions. We also tested for evidence of sexual imprinting, where individuals acquire mate-choice criteria during development by using their opposite-sex parent as the template of a desirable mate; there was no such effect for any trait. The main discernible pattern of mate choice was assortative mating; we found that partner similarity was due to initial choice rather than convergence and also at least in part to phenotypic matching.

  12. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing

    Science.gov (United States)

    Ferreira, Pedro G.; Oti, Martin; Barann, Matthias; Wieland, Thomas; Ezquina, Suzana; Friedländer, Marc R.; Rivas, Manuel A.; Esteve-Codina, Anna; Estivill, Xavier; Guigó, Roderic; Dermitzakis, Emmanouil; Antonarakis, Stylianos; Meitinger, Thomas; Strom, Tim M.; Palotie, Aarno; François Deleuze, Jean; Sudbrak, Ralf; Lerach, Hans; Gut, Ivo; Syvänen, Ann-Christine; Gyllensten, Ulf; Schreiber, Stefan; Rosenstiel, Philip; Brunner, Han; Veltman, Joris; Hoen, Peter A. C. T.; Jan van Ommen, Gert; Carracedo, Angel; Brazma, Alvis; Flicek, Paul; Cambon-Thomsen, Anne; Mangion, Jonathan; Bentley, David; Hamosh, Ada; Rosenstiel, Philip; Strom, Tim M.; Lappalainen, Tuuli; Guigó, Roderic; Sammeth, Michael

    2016-09-01

    Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing—alternative splice sites, introns, and cleavage sites—which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts.

  13. Systematic variation in gene expression patterns in human cancer cell lines

    Energy Technology Data Exchange (ETDEWEB)

    Ross, Douglas T.; Scherf, Uwe; Eisen, Michael B.; Perou, Charles M.; Rees, Christian; Spellman, Paul; Iyer, Vishwanath; Jeffrey, Stefanie S.; Van de Rijn, Matt; Waltham, Mark; Pergamenschikov, Alexander; Lee, Jeffrey C.F.; Lashkari, Deval; Shalon, Dari; Myers, Timothy G.; Weinstein, John N.; Botstein, David; Brown, Patrick O.

    2000-01-01

    We used cDNA micro arrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute s screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumors from which the cell lines were derived. The consistent relationship between the gene expression patterns and the tissue of origin allowed us to recognize outliers whose previous classification appeared incorrect. Specific features of the gene expression patterns appeared to be related to physiological properties of the cell lines, such as their doubling time in culture, drug metabolism or the interferon response. Comparison of gene expression patterns in the cell lines to those observed in normal breast tissue or in breast tumor specimens revealed features of the expression patterns in the tumors that had recognizable counterparts in specific cell lines, reflecting the tumor, stromal and inflammatory components of the tumor tissue. These results provided a novel molecular characterization of this important group of human cell lines and their relationships to tumors in vivo.

  14. Rare and common regulatory variation in population-scale sequenced human genomes.

    Directory of Open Access Journals (Sweden)

    Stephen B Montgomery

    2011-07-01

    Full Text Available Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation. Here, we investigate the influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1000 genomes project in an African and European population sample and gene expression data from lymphoblastoid cell lines. We detect comparable numbers of expression quantitative trait loci (eQTLs when compared to genotypes obtained from HapMap 3, but as many as 80% of the top expression quantitative trait variants (eQTVs discovered from 1000 genomes data are novel. The properties of the newly discovered variants suggest that mapping common causal regulatory variants is challenging even with full resequencing data; however, we observe significant enrichment of regulatory effects in splice-site and nonsense variants. Using RNA sequencing data, we show that 46.2% of nonsynonymous variants are differentially expressed in at least one individual in our sample, creating widespread potential for interactions between functional protein-coding and regulatory variants. We also use allele-specific expression to identify putative rare causal regulatory variants. Furthermore, we demonstrate that outlier expression values can be due to rare variant effects, and we approximate the number of such effects harboured in an individual by effect size. Our results demonstrate that integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing

    Science.gov (United States)

    Ferreira, Pedro G.; Oti, Martin; Barann, Matthias; Wieland, Thomas; Ezquina, Suzana; Friedländer, Marc R.; Rivas, Manuel A.; Esteve-Codina, Anna; Estivill, Xavier; Guigó, Roderic; Dermitzakis, Emmanouil; Antonarakis, Stylianos; Meitinger, Thomas; Strom, Tim M; Palotie, Aarno; François Deleuze, Jean; Sudbrak, Ralf; Lerach, Hans; Gut, Ivo; Syvänen, Ann-Christine; Gyllensten, Ulf; Schreiber, Stefan; Rosenstiel, Philip; Brunner, Han; Veltman, Joris; Hoen, Peter A.C.T; Jan van Ommen, Gert; Carracedo, Angel; Brazma, Alvis; Flicek, Paul; Cambon-Thomsen, Anne; Mangion, Jonathan; Bentley, David; Hamosh, Ada; Rosenstiel, Philip; Strom, Tim M; Lappalainen, Tuuli; Guigó, Roderic; Sammeth, Michael

    2016-01-01

    Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing—alternative splice sites, introns, and cleavage sites—which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts. PMID:27617755

  17. A New Biophysical Metric for Interrogating the Information Content in Human Genome Sequence Variation: Proof of Concept

    CERN Document Server

    Lindesay, James; Ricks-Santi, Luisel; Hercules, William; Kurian, Philip; Dunston, Georgia M

    2011-01-01

    Various studies have shown an association between single nucleotide polymorphisms (SNPs) and common disease. We hypothesize that information encoded in the structure of SNP haploblock variation illumines molecular pathways and cellular mechanisms involved in the regulation of host adaptation to the environment. We developed and utilized the normalized information content (NIC), a novel metric based on SNP haploblock variation. We found that all SNP haploblocks with statistically low information content contained putative transcription factor binding sites and microRNA motifs. We were able to translate a biophysical, mathematical measure of common variants into a deeper understanding of the life sciences through analysis of biochemical patterns associated with SNP haploblock variation. We submit that this new metric, NIC, may be useful in decoding the functional significance of common variation in the human genome and in analyzing the regulation of molecular pathways involved in host adaptation to environmenta...

  18. Designing a post-genomics knowledge ecosystem to translate pharmacogenomics into public health action.

    Science.gov (United States)

    Dove, Edward S; Faraj, Samer A; Kolker, Eugene; Ozdemir, Vural

    2012-01-01

    Translation of pharmacogenomics to public health action is at the epicenter of the life sciences agenda. Post-genomics knowledge is simultaneously co-produced at multiple scales and locales by scientists, crowd-sourcing and biological citizens. The latter are entrepreneurial citizens who are autonomous, self-governing and increasingly conceptualizing themselves in biological terms, ostensibly taking responsibility for their own health, and engaging in patient advocacy and health activism. By studying these heterogeneous 'scientific cultures', we can locate innovative parameters of collective action to move pharmacogenomics to practice (personalized therapeutics). To this end, we reconceptualize knowledge-based innovation as a complex ecosystem comprising 'actors' and 'narrators'. For robust knowledge translation, we require a nested post-genomics technology governance system composed of first-order narrators (for example, social scientists, philosophers, bioethicists) situated at arm's length from innovation actors (for example, pharmacogenomics scientists). Yet, second-order narrators (for example, an independent and possibly crowd-funded think-tank of citizen scholars, marginalized groups and knowledge end-users) are crucial to prevent first-order narrators from gaining excessive power that can be misused in the course of steering innovations. To operate such 'self-calibrating' and nested innovation ecosystems, we introduce the concept of 'wiki-governance' to enable mutual and iterative learning among innovation actors and first- and second-order narrators. '[A] scientific expert is someone who knows more and more about less and less, until finally knowing (almost) everything about (almost) nothing.' [1] 'Ubuntu: I am because you are.' [2].

  19. Pharmacogenomics and Pancreatic Cancer Treatment. Optimizing Current Therapy and Individualizing Future Therapy

    Directory of Open Access Journals (Sweden)

    Soonmo Peter Kang

    2008-05-01

    Full Text Available Each year, more than 30,000 Americans are diagnosed with pancreatic cancer. We have only made incremental advancements in treatment of pancreatic cancer despite our best efforts. Research has revealed that pancreatic cancer is a genetic disease which is associated with various forms of cancer associated genetic alterations. Identification and understanding of these carcinogenic gene alterations is the base upon which we can overcome drug resistance and develop novel treatment approaches. In this paper, we review current understanding of pharmacogenomics of pancreatic cancer treatment and address future direction of the field.

  20. Pharmacogenomics in lung cancer chemotherapy: a review of what the oncologist should know.

    Science.gov (United States)

    D'Antonio, Chiara; Milano, Annalisa; Righini, Riccardo; Onesti, Concetta Elisa; Bassanelli, Maria; Falcone, Rosa; Paris, Ida; Lauro, Salvatore; Marchetti, Paolo

    2014-10-01

    Lung cancer is the leading cause of cancer-related death around the world; the addition of chemotherapy to treatment of this disease has been shown to significantly increase progression-free survival and overall survival. Despite newer chemotherapies, it is important to personalize the care (treatment and dose) upon each single patient's susceptibility for controlling and reducing adverse side-effects, at best. The present review describes the current status of pharmacogenomics studies regarding germline DNA variants that may alter response and tolerability to chemotherapeutic agents used to treat lung cancer, including perspective studies.

  1. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.

    Science.gov (United States)

    Bartha, István; Carlson, Jonathan M; Brumme, Chanson J; McLaren, Paul J; Brumme, Zabrina L; John, Mina; Haas, David W; Martinez-Picado, Javier; Dalmau, Judith; López-Galíndez, Cecilio; Casado, Concepción; Rauch, Andri; Günthard, Huldrych F; Bernasconi, Enos; Vernazza, Pietro; Klimkait, Thomas; Yerly, Sabine; O'Brien, Stephen J; Listgarten, Jennifer; Pfeifer, Nico; Lippert, Christoph; Fusi, Nicolo; Kutalik, Zoltán; Allen, Todd M; Müller, Viktor; Harrigan, P Richard; Heckerman, David; Telenti, Amalio; Fellay, Jacques

    2013-10-29

    HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (pgenome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host-pathogen interaction. DOI:http://dx.doi.org/10.7554/eLife.01123.001.

  2. Spatiotemporal Impacts of Climate, Land Cover Change and Direct Human Activities on Runoff Variations in the Wei River Basin, China

    Directory of Open Access Journals (Sweden)

    Yunyun Li

    2016-05-01

    Full Text Available Previous studies that quantified variations in runoff have mainly focused on the combined impacts of climate and human activities or climate and land cover change. Few have separated land cover change from human activities, which is critical for effective management of water resources. This study aims to investigate the impact of changing environmental conditions on runoff using the Soil and Water Assessment Tool (SWAT model; we examined three categories: climate, land cover change and direct human activities. The study area was the Wei River Basin, a typical arid to semi-arid basin that was divided into five sub-zones (UZ, MZ, DZ, JZ and BZ. Our results showed the following: (1 the calibrated SWAT model produced satisfactory monthly flow processes over the baseline period from 1978 to 1986; (2 compared to the baseline period, the impact of climatic variations decreased and the impact of direct human activities increased from the 1990s to the 2000s, while the impact of land cover change was generally stable; and (3 climatic variations were the main cause of runoff declines over the entire basin during the 1990s and in the UZ, MZ and JZ areas during the 2000s, while direct human activities were most important in the DZ and BZ areas during the 2000s.

  3. Long-term variations in abundance and distribution of sewage pollution indicator and human pathogenic bacteria along the central west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Rodrigues, V.; Ramaiah, N.; Kakti, S.; Samant, D.

    Safe water quality criteria on the load and types of microbial populations are important for human use from fishery, tourism and navigational viewpoints. To understand the variations in sewage pollution indicator and certain human pathogenic...

  4. Genetic Variation of αENaC Influences Lung Diffusion During Exercise in Humans

    Science.gov (United States)

    Baker, Sarah E.; Wheatley, Courtney M.; Cassuto, Nicholas A.; Foxx-Lupo, William T.; Sprissler, Ryan; Snyder, Eric M.

    2011-01-01

    Exercise, decompensated heart failure, and exposure to high altitude have been shown to cause symptoms of pulmonary edema in some, but not all, subjects, suggesting a genetic component to this response. Epithelial Na+ Channels (ENaC) regulate Na+ and fluid reabsorption in the alveolar airspace in the lung. An increase in number and/or activity of ENaC has been shown to increase lung fluid clearance. Previous work has demonstrated common functional genetic variants of the α-subunit of ENaC, including an A→T substitution at amino acid 663 (αA663T). We sought to determine the influence of the T663 variant of αENaC on lung diffusion at rest and at peak exercise in healthy humans. Thirty healthy subjects were recruited for study and grouped according to their SCNN1A genotype [n= 17vs.13, age=25±7vs.30±10yrs., BMI= 23±4vs.25±4kg/m2, V̇O2peak= 95±30vs.100±31%pred., mean±SD, for AA (homozygous for αA663) vs. AT/TT groups (at least one αT663), respectively]. Measures of the diffusing capacity of the lungs for carbon monoxide (DLCO), the diffusing capacity of the lungs for nitric oxide (DLNO), alveolar volume (VA), and alveolar-capillary membrane conductance (DM) were taken at rest and at peak exercise. Subjects expressing the AA polymorphism of ENaC showed a significantly greater percent increase in DLCO and DLNO, and a significantly greater decrease in systemic vascular resistance from rest to peak exercise than those with the AT/TT variant (DLCO=51±12vs.36±17%, DLNO=51±24vs.32±25%, SVR=−67±3vs.−50±8%, p<0.05). The AA ENaC group also tended to have a greater percent increase in DLCO/VA from rest to peak exercise, although this did not reach statistical significance (49±26vs.33±26%, p=0.08). These results demonstrate that genetic variation of the α-subunit of ENaC at amino acid 663 influences lung diffusion at peak exercise in healthy humans, suggesting differences in alveolar Na+ and, therefore, fluid handling. These findings could be important

  5. Diurnal Variations of Human Circulating Cell-Free Micro-RNA.

    Science.gov (United States)

    Heegaard, Niels H H; Carlsen, Anting Liu; Lilje, Berit; Ng, Kim Lee; Rønne, Mette E; Jørgensen, Henrik L; Sennels, Henriette; Fahrenkrug, Jan

    2016-01-01

    A 24-hour light and dark cycle-dependent rhythmicity pervades physiological processes in virtually all living organisms including humans. These regular oscillations are caused by external cues to endogenous, independent biological time-keeping systems (clocks). The rhythm is reflected by gene expression that varies in a circadian and specific fashion in different organs and tissues and is regulated largely by dynamic epigenetic and post-transcriptional mechanisms. This leads to well-documented oscillations of specific electrolytes, hormones, metabolites, and plasma proteins in blood samples. An emerging, important class of gene regulators is short single-stranded RNA (micro-RNA, miRNA) that interferes post-transcriptionally with gene expression and thus may play a role in the circadian variation of gene expression. MiRNAs are promising biomarkers by virtue of their disease-specific tissue expression and because of their presence as stable entities in the circulation. However, no studies have addressed the putative circadian rhythmicity of circulating, cell-free miRNAs. This question is important both for using miRNAs as biological markers and for clues to miRNA function in the regulation of circadian gene expression. Here, we investigate 92 miRNAs in plasma samples from 24 young male, healthy volunteers repeatedly sampled 9 times during a 24-hour stay in a regulated environment. We demonstrate that a third (26/79) of the measurable plasma miRNAs (using RT-qPCR on a microfluidic system) exhibit a rhythmic behavior and are distributed in two main phase patterns. Some of these miRNAs weakly target known clock genes and many have strong targets in intracellular MAPK signaling pathways. These novel findings highlight the importance of considering bio-oscillations in miRNA biomarker studies and suggest the further study of a set of specific circulating miRNAs in the regulation and functioning of biological clocks.

  6. Effect of variations in peptide sequence on anti-human milk fat globule membrane antibody reactions.

    Science.gov (United States)

    Xing, P X; Reynolds, K; Pietersz, G A; McKenzie, I F

    1991-02-01

    Monoclonal anti-mucine antibodies BC1, BC2 and BC3 produced using human milk fat globule membrane react with a synthetic peptide p1-24 (PDTRPAPGSTAPPAHGVTSAPDTR) representing the repeating amino acid sequence of the mucin core protein. The minimum epitope recognized by these three monoclonal antibodies (mAb) in p1-24 was contained in the five amino acids APDTR. To analyse the variation of position of the epitope, various modifications of the APDTR sequence were made by synthesizing peptides and testing by direct binding and inhibition enzyme-linked immunosorbent assays. Firstly, peptides p13-32 and C-p13-32, in which the epitope APDTR was placed in the middle instead of the C-terminal as in p1-24, were examined. These peptides had a greater reaction with mAb BC1, BC2 and BC3 compared with the reaction with p1-24. Secondly, A-p1-24 and TSA-p1-24 were made wherein two APDTR epitopes were present--these peptides were shown to bind two IgG antibody molecules. Finally, the contribution of each amino acid in the APDTR epitope was studied using the pepscan polyethylene rods, making all 20 of the amino acid substitutions in each position for SAPDTR (the minimum epitope APDTR with an adjacent amino acid S). In the 120 peptides examined there were some 'permissible' substitutions in A, D and T but not in P or R for BC1 and BC2; there were more 'permissible' substitutions for BC3; different substitution patterns were found with each antibody and some substitutions gave an increased reaction compared with the native peptide SAPDTR. The studies are of value in analysing the reaction of antibodies with epitopes expressed in breast cancer and in determining the antigenicity of synthetic peptides.

  7. Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli.

    Science.gov (United States)

    Sakata, Katsumi; Saito, Toshiyuki; Ohyanagi, Hajime; Okumura, Jun; Ishige, Kentaro; Suzuki, Harukazu; Nakamura, Takuji; Komatsu, Setsuko

    2016-10-24

    Soybean (Glycine max) is sensitive to flooding stress, and flood damage at the seedling stage is a barrier to growth. We constructed two mathematical models of the soybean metabolic network, a control model and a flooded model, from metabolic profiles in soybean plants. We simulated the metabolic profiles with perturbations before and after the flooding stimulus using the two models. We measured the variation of state that the system could maintain from a state-space description of the simulated profiles. The results showed a loss of variation of state during the flooding response in the soybean plants. Loss of variation of state was also observed in a human myelomonocytic leukaemia cell transcriptional network in response to a phorbol-ester stimulus. Thus, we detected a loss of variation of state under external stimuli in two biological systems, regardless of the regulation and stimulus types. Our results suggest that a loss of robustness may occur concurrently with the loss of variation of state in biological systems. We describe the possible applications of the quantity of variation of state in plant genetic engineering and cell biology. Finally, we present a hypothetical "external stimulus-induced information loss" model of biological systems.

  8. Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli

    KAUST Repository

    Sakata, Katsumi

    2016-10-24

    Soybean (Glycine max) is sensitive to flooding stress, and flood damage at the seedling stage is a barrier to growth. We constructed two mathematical models of the soybean metabolic network, a control model and a flooded model, from metabolic profiles in soybean plants. We simulated the metabolic profiles with perturbations before and after the flooding stimulus using the two models. We measured the variation of state that the system could maintain from a state–space description of the simulated profiles. The results showed a loss of variation of state during the flooding response in the soybean plants. Loss of variation of state was also observed in a human myelomonocytic leukaemia cell transcriptional network in response to a phorbol-ester stimulus. Thus, we detected a loss of variation of state under external stimuli in two biological systems, regardless of the regulation and stimulus types. Our results suggest that a loss of robustness may occur concurrently with the loss of variation of state in biological systems. We describe the possible applications of the quantity of variation of state in plant genetic engineering and cell biology. Finally, we present a hypothetical “external stimulus-induced information loss” model of biological systems.

  9. Pharmacogenomics and Rational Use of Drugs%药物基因组学与合理用药

    Institute of Scientific and Technical Information of China (English)

    张志勇; 肖翠英; 唐尧

    2001-01-01

    目的:介绍药物基因组学及其在临床制定药物治疗方案中的应用。方法:依据有关文献分析、归纳、总结药物基因组学的发展、研究内容及与个体化给药的关系。结果:药物基因组学研究基因的多态性与药物作用多样性之间的关系。结论:药物基因组学为安全、合理用药提供理论依据。%OBJECTIVE:To introduce pharmacogenomics and its applications in establishing clinical pharmacotherapeutic schemes.METHODS:Based on the analysis of the related literatures,the development and contents of pharmacogenomics and their relationship with individualized medication were summarized.RESULTS:Pharmacogenomics studies the association between gene polymorphisms and the variance of drug effects.CONCLUSION:Pharmacogenomics provides a theoretical basis for medication with safety,effectiveness and rationality.

  10. Patient Decisions to Receive Secondary Pharmacogenomic Findings and Development of a Multidisciplinary Practice Model to Integrate Results Into Patient Care.

    Science.gov (United States)

    Hicks, J Kevin; Shealy, Amy; Schreiber, Allison; Coleridge, Marissa; Noss, Ryan; Natowicz, Marvin; Moran, Rocio; Moss, Timothy; Erwin, Angelika; Eng, Charis

    2017-07-27

    Whole exome sequencing (WES) has the potential of identifying secondary findings that are predictive of poor pharmacotherapy outcomes. The purpose of this study was to investigate patients' wishes regarding the reporting of secondary pharmacogenomic findings. WES results (n = 106 patients) were retrospectively reviewed to determine the number of patients electing to receive secondary pharmacogenomic results. Phenotypes were assigned based on Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines. The percent of patients with a predicted phenotype associated with a gene-based CPIC dosing recommendation was determined. Ninety-nine patients (93.4%) elected to receive secondary pharmacogenomic findings. For each gene-drug pair analyzed, the number of patients with an actionable phenotype ranged from two (2%) to 43 patients (43.4%). Combining all gene-drug pairs, 84 unique patients (84.8%) had an actionable phenotype. A prospective multidisciplinary practice model was developed for integrating secondary pharmacogenomic findings into clinical practice. Our model highlights a unique collaboration between physician-geneticists, pharmacists, and genetic counselors. © 2017 The Authors. Clinical and Translational Science published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

  11. The triad of success in personalised medicine: pharmacogenomics, biotechnology and regulatory issues from a Central European perspective.

    Science.gov (United States)

    Mesko, Bertalan; Zahuczky, Gabor; Nagy, Laszlo

    2012-09-15

    The population of the world has recently passed the 7 billion milestone and as the cost of human genome sequencing is rapidly declining, sequence data of billions of people should be accessible much sooner than anyone would have predicted 10 years ago. This will form the basis of personalised medicine. However it is still not clear, even in principle, whether these data, combined with data of the expression of one's genome in various cells and tissues relevant to different diseases, could be used effectively in clinical medicine and healthcare, or in predicting responses to different therapies. Therefore this is an important issue which needs to be addressed before more resources are wasted on less than informative studies and surveys simply because technologies exist. As a typical example, we have selected and summarise here key studies from the biomedical literature that focus on gene expression profiling of the response to biologic therapies in peripheral blood and biopsy samples in autoimmune diseases such as rheumatoid arthritis, spondylarthropathy, inflammatory bowel diseases and psoriasis. We also present the state of the biotechnology market from a European perspective, discuss how spin-offs leverage the power of genomic technologies and describe how they might contribute to personalised medicine. As ethical, legal and social issues are essential in the area of genomics, we analysed these aspects and present here the European situation with a special focus on Hungary. We propose that the synergy of these three issues: pharmacogenomics, biotechnology and regulatory issues should be considered a triad necessary to succeed in personalised medicine. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Using Pharmacogenomic Databases for Discovering Patient-Target Genes and Small Molecule Candidates to Cancer Therapy

    Science.gov (United States)

    Belizário, José E.; Sangiuliano, Beatriz A.; Perez-Sosa, Marcela; Neyra, Jennifer M.; Moreira, Dayson F.

    2016-01-01

    With multiple omics strategies being applied to several cancer genomics projects, researchers have the opportunity to develop a rational planning of targeted cancer therapy. The investigation of such numerous and diverse pharmacogenomic datasets is a complex task. It requires biological knowledge and skills on a set of tools to accurately predict signaling network and clinical outcomes. Herein, we describe Web-based in silico approaches user friendly for exploring integrative studies on cancer biology and pharmacogenomics. We briefly explain how to submit a query to cancer genome databases to predict which genes are significantly altered across several types of cancers using CBioPortal. Moreover, we describe how to identify clinically available drugs and potential small molecules for gene targeting using CellMiner. We also show how to generate a gene signature and compare gene expression profiles to investigate the complex biology behind drug response using Connectivity Map. Furthermore, we discuss on-going challenges, limitations and new directions to integrate molecular, biological and epidemiological information from oncogenomics platforms to create hypothesis-driven projects. Finally, we discuss the use of Patient-Derived Xenografts models (PDXs) for drug profiling in vivo assay. These platforms and approaches are a rational way to predict patient-targeted therapy response and to develop clinically relevant small molecules drugs.

  13. Bioinformatics for transporter pharmacogenomics and systems biology: data integration and modeling with UML.

    Science.gov (United States)

    Yan, Qing

    2010-01-01

    Bioinformatics is the rational study at an abstract level that can influence the way we understand biomedical facts and the way we apply the biomedical knowledge. Bioinformatics is facing challenges in helping with finding the relationships between genetic structures and functions, analyzing genotype-phenotype associations, and understanding gene-environment interactions at the systems level. One of the most important issues in bioinformatics is data integration. The data integration methods introduced here can be used to organize and integrate both public and in-house data. With the volume of data and the high complexity, computational decision support is essential for integrative transporter studies in pharmacogenomics, nutrigenomics, epigenetics, and systems biology. For the development of such a decision support system, object-oriented (OO) models can be constructed using the Unified Modeling Language (UML). A methodology is developed to build biomedical models at different system levels and construct corresponding UML diagrams, including use case diagrams, class diagrams, and sequence diagrams. By OO modeling using UML, the problems of transporter pharmacogenomics and systems biology can be approached from different angles with a more complete view, which may greatly enhance the efforts in effective drug discovery and development. Bioinformatics resources of membrane transporters and general bioinformatics databases and tools that are frequently used in transporter studies are also collected here. An informatics decision support system based on the models presented here is available at http://www.pharmtao.com/transporter . The methodology developed here can also be used for other biomedical fields.

  14. Clinical significance of pharmacogenomic studies in tardive dyskinesia associated with patients with psychiatric disorders

    Directory of Open Access Journals (Sweden)

    Chang FC

    2014-10-01

    Full Text Available Florence CF Chang, Victor SC Fung Movement Disorders Unit, Department of Neurology, Westmead Hospital, Sydney Medical School, University of Sydney, Sydney, NSW, Australia Abstract: Pharmacogenomics is the study of the effects of genetic polymorphisms on medication pharmacokinetics and pharmacodynamics. It offers advantages in predicting drug efficacy and/or toxicity and has already changed clinical practice in many fields of medicine. Tardive dyskinesia (TD is a movement disorder that rarely remits and poses significant social stigma and physical discomfort for the patient. Pharmacokinetic studies show an association between cytochrome P450 enzyme-determined poor metabolizer status and elevated serum antipsychotic and metabolite levels. However, few prospective studies have shown this to correlate with the occurrence of TD. Many retrospective, case-control and cross-sectional studies have examined the association of cytochrome P450 enzyme, dopamine (receptor, metabolizer and transporter, serotonin (receptor and transporter, and oxidative stress enzyme gene polymorphisms with the occurrence and severity of TD. These studies have produced conflicting and confusing results secondary to heterogeneous inclusion criteria and other patient characteristics that also act as confounding factors. This paper aims to review and summarize the pharmacogenetic findings in antipsychotic-associated TD and assess its clinical significance for psychiatry patients. In addition, we hope to provide insight into areas that need further research. Keywords: pharmacogenomics, tardive dyskinesia, cytochrome P450, pharmacogenetic, schizophrenia

  15. Molecular diagnostics for pharmacogenomic testing of fluoropyrimidine based-therapy: costs, methods and applications.

    Science.gov (United States)

    Di Francia, Raffaele; Berretta, Massimiliano; Catapano, Oriana; Canzoniero, Lorella M T; Formisano, Luigi

    2011-07-01

    Abstract Genetic testing of drug response represents an important goal for targeted therapy. In particular, 5-fluorouracil (5-FU) is the backbone of several chemotherapic protocols for treatment of solid tumors. Unfortunately, in some patients, 5-FU is toxic and causes gastrointestinal and hematologic lesions leading to the suspension of therapy. Some adverse drug responses can be predicted by pharmacogenomics. Recently, several polymorphic traits of different genes involved with 5-FU biotransformation have been reported. Many methods have been used for qualitative and quantitative assessment of the mutational status of these genes, without a precise cost-effectiveness analysis. This article reviews recent findings on the seven germline polymorphic traits of four genes involved in the biotransformation of the 5-FU. In particular, we analyze the most common platforms used to identify the specific genetic alterations and their relative costs. Genotyping can be performed either by custom service laboratories or academic reference laboratories by using either the commercial kits (when available) or "in house" tests. By random selection of 20 certified laboratories out of a total of 71, we estimate that the cost of the analysis/single trait is on average €120.00 as custom genotyping service. "In house" validated tests by PCR-based platforms cost approximately €20.00 per single polimorphism. On the basis of this information, the lab manager can evaluate the advantage and limitations, in terms of costs and applicability, of the most appropriate methods for diagnostics of 5-FU pharmacogenomics tests.

  16. Current strategies to minimize toxicity of oxaliplatin: selection of pharmacogenomic panel tests.

    Science.gov (United States)

    Di Francia, Raffaele; Siesto, Raffaella Stefania; Valente, Daniela; Del Buono, Andrea; Pugliese, Sergio; Cecere, Sabrina; Cavaliere, Carla; Nasti, Guglielmo; Facchini, Gaetano; Berretta, Massimiliano

    2013-11-01

    Oxaliplatin is an anticancer drug routinely used to treat colorectal, gastroesophageal, ovarian, breast, head/neck, and genitourinary cancers. Discontinuation of oxaliplatin treatment is mostly because of peripheral neuropathy, more often than for tumor progression, potentially compromising patient benefit. Several strategies to prevent neurotoxicity have so far been investigated. To overcome this life-threatening side effect, while taking advantage of the antineoplastic activities of oxaliplatin, we describe in detail recent findings on the underlying mechanisms of genetic variants associated with toxicity and resistance to oxaliplatin-based chemotherapy in colorectal cancer. A comprehensive panel of eight polymorphisms, previously validated as significant markers related to oxaliplatin toxicity, is proposed and discussed. In addition, the most common available strategies or methods to prevent/minimize the toxicity were described in detail. Moreover, an early outline evaluation of the genotyping costs and methods was taken in consideration. With the availability of individual pharmacogenomic profiles, the oncologists will have new means to make treatment decisions for their patients that maximize benefit and minimize toxicity. With this purpose in mind, the clinician and lab manager should cooperate to evaluate the advantages and limitations, in terms of costs and applicability, of the most appropriate pharmacogenomic tests for routine incorporation into clinical practice.

  17. 药物基因组学相关P450和ABCB1多态性及SNP检测技术%Pharmacogenomics-related P450 and ABCB1 Polymorphisms and SNP Detection Technology

    Institute of Scientific and Technical Information of China (English)

    眭维国; 张若菡; 陈洁晶; 戴勇

    2011-01-01

    药物基因组学(phamacogenomics)是临床检测遗传差异引起药物应答个体性差异的学科,它涉及药物代谢和有害的药物反应的预测等方面的内容.个性化药物和个性化治疗发展的关键条件是能够快速简便的检测出病人的遗传多态性.文章综述了药物基因相关问题,细胞色素酶P450和ABCB1转运蛋白的遗传多态性以及检测遗传多态性的相关技术.%Pharmacogenomics is the study of the influence of genetic factors on drug action. It is increasingly important for predicting metabolism and adverse reaction to drugs. A key requirement for the development of individualized medicine or personalized therapy is the ability to rapidly and conveniently test the genetic polymorphisms and mutations in patients. This review addresses the social issues in Pharmacogenomics testing, the cytochrome P450, human ACBC1 genetic polymorphismand some new methods for single nucleotide polymorphism ( SNP ) detection.

  18. [Pharmacogenomics and pharmacoproteomics: a strategy for cardio-vascular drugs].

    Science.gov (United States)

    Siest, G; Marteau, J-B; Maumus, S; Berrahmoune, H; Jeannesson, E; Samara, A; Batt, A-M; Visvikis-Siest, S

    2007-05-01

    The development of personalized medicine will require improved knowledge of biological variability, particularly concerning the important impact of each individual's genetic makeup. A five-step strategy can be followed when trying to identify genes and gene products involved in differential responses to cardiovascular drugs: 1) Pharmacokinetic-related genes and phenotypes; (2) Pharmacodynamic targets, genes and products; (3) Cardiovascular diseases and risks depending on specific or large metabolic cycles; (4) Physiological variations of previously identified genes and proteins; (5) Environmental influences on them. After summarizing the most well known genes involved in drug metabolism, we used statins as an example. In addition to their economic impact, statins are generally considered to be of significant importance in terms of public health. Individuals respond differently to these drugs depending on multiple polymorphisms. Applying a pharmacoproteomic strategy, it is important to use available information on peptides, proteins and metabolites, generally gene products, in each of the five steps. A profiling approach dealing with genomics as well as proteomics is useful. In conclusion, the ever growing volume of available data will require an organized interpretation of variations in DNA and mRNA as well as proteins, both on the individual and population level.

  19. Genetic diversity of variants involved in drug response and metabolism in Sri Lankan populations: implications for clinical implementation of pharmacogenomics

    Science.gov (United States)

    Chan, Sze Ling; Samaranayake, Nilakshi; Ross, Colin J.D.; Toh, Meng Tiak; Carleton, Bruce; Hayden, Michael R.; Teo, Yik Ying; Dissanayake, Vajira H.W.

    2016-01-01

    Background Interpopulation differences in drug responses are well documented, and in some cases they correspond to differences in the frequency of associated genetic markers. Understanding the diversity of genetic markers associated with drug response across different global populations is essential to infer population rates of drug response or risk for adverse drug reactions, and to guide implementation of pharmacogenomic testing. Sri Lanka is a culturally and linguistically diverse nation, but little is known about the population genetics of the major Sri Lankan ethnic groups. The objective of this study was to investigate the diversity of pharmacogenomic variants in the major Sri Lankan ethnic groups. Methods We examined the allelic diversity of more than 7000 variants in genes involved in drug biotransformation and response in the three major ethnic populations of Sri Lanka (Sinhalese, Sri Lankan Tamils, and Moors), and compared them with other South Asian, South East Asian, and European populations using Wright’s Fixation Index, principal component analysis, and STRUCTURE analysis. Results We observed overall high levels of similarity within the Sri Lankan populations (median FST=0.0034), and between Sri Lankan and other South Asian populations (median FST=0.0064). Notably, we observed substantial differentiation between Sri Lankan and European populations for important pharmacogenomic variants related to warfarin (VKORC1 rs9923231) and clopidogrel (CYP2C19 rs4986893) response. Conclusion These data expand our understanding of the population structure of Sri Lanka, provide a resource for pharmacogenomic research, and have implications for the clinical use of genetic testing of pharmacogenomic variants in these populations. PMID:26444257

  20. ¹³C MRS reveals a small diurnal variation in the glycogen content of human thigh muscle.

    Science.gov (United States)

    Takahashi, Hideyuki; Kamei, Akiko; Osawa, Takuya; Kawahara, Takashi; Takizawa, Osamu; Maruyama, Katsuya

    2015-06-01

    There is marked diurnal variation in the glycogen content of skeletal muscles of animals, but few studies have addressed such variations in human muscles. (13)C MRS can be used to noninvasively measure the glycogen content of human skeletal muscle, but no study has explored the diurnal variations in this parameter. This study aimed to investigate whether a diurnal variation in glycogen content occurs in human muscles and, if so, to what extent it can be identified using (13)C MRS. Six male volunteers were instructed to maintain their normal diet and not to perform strenuous exercise for at least 3 days before and during the experiment. Muscle glycogen and blood glucose concentrations were measured six times in 24 h under normal conditions in these subjects. The glycogen content in the thigh muscle was determined noninvasively by natural abundance (13)C MRS using a clinical MR system at 3 T. Nutritional analysis revealed that the subjects' mean carbohydrate intake was 463 ± 137 g, being approximately 6.8 ± 2.4 g/kg body weight. The average sleeping time was 5.9 ± 1.0 h. The glycogen content in the thigh muscle at the starting point was 64.8 ± 20.6 mM. Although absolute and relative individual variations in muscle glycogen content were 7.0 ± 2.1 mM and 11.3 ± 4.6%, respectively, no significant difference in glycogen content was observed among the different time points. This study demonstrates that normal food intake (not fat and/or carbohydrate rich), sleep and other daily activities have a negligible influence on thigh muscle glycogen content, and that the diurnal variation of the glycogen content in human muscles is markedly smaller than that in animal muscles. Moreover, the present results also support the reproducibility and availability of (13)C MRS for the evaluation of the glycogen content in human muscles. Copyright © 2015 John Wiley & Sons, Ltd.

  1. A Framework of Knowledge Integration and Discovery for Supporting Pharmacogenomics Target Predication of Adverse Drug Events: A Case Study of Drug-Induced Long QT Syndrome.

    Science.gov (United States)

    Jiang, Guoqian; Wang, Chen; Zhu, Qian; Chute, Christopher G

    2013-01-01

    Knowledge-driven text mining is becoming an important research area for identifying pharmacogenomics target genes. However, few of such studies have been focused on the pharmacogenomics targets of adverse drug events (ADEs). The objective of the present study is to build a framework of knowledge integration and discovery that aims to support pharmacogenomics target predication of ADEs. We integrate a semantically annotated literature corpus Semantic MEDLINE with a semantically coded ADE knowledgebase known as ADEpedia using a semantic web based framework. We developed a knowledge discovery approach combining a network analysis of a protein-protein interaction (PPI) network and a gene functional classification approach. We performed a case study of drug-induced long QT syndrome for demonstrating the usefulness of the framework in predicting potential pharmacogenomics targets of ADEs.

  2. Developing a methodology of bioindication of human-induced effects using seagrass morphological variation in Spermonde Archipelago, South Sulawesi, Indonesia.

    Science.gov (United States)

    Ambo-Rappe, Rohani

    2014-09-15

    Seagrass is particularly susceptible to environmental degradation. The objective of the study is to develop an effective bioindicator to assess human-induced effects using morphological variation and fluctuating asymmetry (FA) of seagrass. Samples were collected from eight islands situated at different distance from mainland with different human population density and therefore expected to experience different level of anthropogenic pressure. Cd, Pb, Cu, Zn, nitrate, and phosphate were measured. Metals were also measured in tissues of seagrass. Metal concentrations in sediment, water, and seagrass did not exceed the quality standards required for marine life. Heterogeneity of FA was found among sites suggesting that there are some factors changing developmental instability of seagrass which is not associated to particular toxicants. This baseline study indicates that the water condition is still natural and shows no signs of metal contamination, therefore it does not cause a detectable stress on morphological variation and FA of seagrass.

  3. TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Genomics Data.

    Science.gov (United States)

    Bouaoun, Liacine; Sonkin, Dmitriy; Ardin, Maude; Hollstein, Monica; Byrnes, Graham; Zavadil, Jiri; Olivier, Magali

    2016-09-01

    TP53 gene mutations are one of the most frequent somatic events in cancer. The IARC TP53 Database (http://p53.iarc.fr) is a popular resource that compiles occurrence and phenotype data on TP53 germline and somatic variations linked to human cancer. The deluge of data coming from cancer genomic studies generates new data on TP53 variations and attracts a growing number of database users for the interpretation of TP53 variants. Here, we present the current contents and functionalities of the IARC TP53 Database and perform a systematic analysis of TP53 somatic mutation data extracted from this database and from genomic data repositories. This analysis showed that IARC has more TP53 somatic mutation data than genomic repositories (29,000 vs. 4,000). However, the more complete screening achieved by genomic studies highlighted some overlooked facts about TP53 mutations, such as the presence of a significant number of mutations occurring outside the DNA-binding domain in specific cancer types. We also provide an update on TP53 inherited variants including the ones that should be considered as neutral frequent variations. We thus provide an update of current knowledge on TP53 variations in human cancer as well as inform users on the efficient use of the IARC TP53 Database.

  4. Application of the adductome approach to assess intertissue DNA damage variations in human lung and esophagus

    Energy Technology Data Exchange (ETDEWEB)

    Kanaly, Robert A. [Department of Technology and Ecology, Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606-8501 (Japan); Department of Environmental Biosciences, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama 236-0027 (Japan); Matsui, Saburo [Department of Technology and Ecology, Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606-8501 (Japan); Hanaoka, Tomoyuki [Epidemiology and Prevention Division, National Cancer Center Research Institute, Tokyo 104-0045 (Japan); Matsuda, Tomonari [Department of Technology and Ecology, Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606-8501 (Japan)], E-mail: matsuda@z05.mbox.media.kyoto-u.ac.jp

    2007-12-01

    Methods for determining the differential susceptibility of human organs to DNA damage have not yet been explored to any large extent due to technical constraints. The development of comprehensive analytical approaches by which to detect intertissue variations in DNA damage susceptibility may advance our understanding of the roles of DNA adducts in cancer etiology and as exposure biomarkers at least. A strategy designed for the detection and comparison of multiple DNA adducts from different tissue samples was applied to assess esophageal and peripherally- and centrally-located lung tissue DNA obtained from the same person. This adductome approach utilized LC/ESI-MS/MS analysis methods designed to detect the neutral loss of 2'-deoxyribose from positively ionized 2'-deoxynucleoside adducts transmitting the [M+H]{sup +} > [M+H-116]{sup +} transition over 374 transitions. In the final analyses, adductome maps were produced which facilitated the visualization of putative DNA adducts and their relative levels of occurrence and allowed for comprehensive comparisons between samples, including a calf thymus DNA negative control. The largest putative adducts were distributed similarly across the samples, however, differences in the relative amounts of putative adducts in lung and esophagus tissue were also revealed. The largest-occurring lung tissue DNA putative adducts were 90% similar (n = 50), while putative adducts in esophagus tissue DNA were shown to be 80 and 84% similar to central and peripheral lung tissue DNA respectively. Seven DNA adducts, N{sup 2}-ethyl-2'-deoxyguanosine (N{sup 2}-ethyl-dG), 1,N{sup 6}-etheno-2'-deoxyadenosine ({epsilon}dA), {alpha}-S- and {alpha}-R-methyl-{gamma}-hydroxy-1,N{sup 2}-propano-2'-deoxyguanosine (1,N{sup 2}-PdG{sub 1}, 1,N{sup 2}-PdG{sub 2}), 3-(2'-deoxyribosyl)-5,6,7,8-tetrahydro-8-hydroxy-pyrimido[1,2-a] purine-(3H)-one (8-OH-PdG) and the two stereoisomers of 3-(2'-deoxyribosyl)-5,6,7,8-tetrahydro

  5. A copy number variation in human NCF1 and its pseudogenes

    Directory of Open Access Journals (Sweden)

    Chambers Isfahan

    2010-02-01

    Full Text Available Abstract Background Neutrophil cytosolic factor-1 (NCF1 is a component of NADPH oxidase. The NCF1 gene colocalizes with two pseudogenes (NCF1B and NCF1C. These two pseudogenes have a GT deletion in exon 2, resulting in a frameshift and an early stop codon. Here, we report a copy number variation (CNV of the NCF1 pseudogenes and their alternative spliced expressions. Results We examined three normal populations (86 individuals. We observed the 2:2:2 pattern (NCF1B:NCF1:NCF1C in only 26 individuals. On average, each African- American has 1.4 ± 0.8 (Mean ± SD copies of NCF1B and 2.3 ± 0.6 copies of NCF1C; each Caucasian has 1.8 ± 0.7 copies of NCF1B and 1.9 ± 0.4 copies of NCF1C; and each Mexican has 1.6 ± 0.6 copies of NCF1B and 1.0 ± 0.4 copies of NCF1C. Mexicans have significantly less NCF1C copies than African-Americans (p = 6e-15 and Caucasians (p = 3e-11. Mendelian transmission of this CNV was observed in two CEPH pedigrees. Moreover, we cloned two alternative spliced transcripts generated from these two pseudogenes that adopt alternative exon-2 instead of their defective exon 2. The NCF1 pseudogene expression responded robustly to PMA induction during macrophage differentiation. NCF1B decreased from 32.9% to 8.3% in the cDNA pool transcribed from 3 gene copies. NCF1Ψs also displayed distinct expression patterns in different human tissues. Conclusions Our results suggest that these two pseudogenes may adopt an alternative exon-2 in different tissues and in response to external stimuli. The GT deletion is insufficient to define them as functionless pseudogenes; this CNV may have biological relevance.

  6. Geometric morphometric analysis of craniofacial variation, ontogeny and modularity in a cross-sectional sample of modern humans

    NARCIS (Netherlands)

    Wellens, H.L.L.; Kuijpers-Jagtman, A.M.; Halazonetis, D.J.

    2013-01-01

    This investigation aimed to quantify craniofacial variation in a sample of modern humans. In all, 187 consecutive orthodontic patients were collected, of which 79 were male (mean age 13.3, SD 3.7, range 7.5-40.8) and 99 were female (mean age 12.3, SD 1.9, range 8.7-19.1). The male and female subgrou

  7. The HapMap Resource is Providing New Insights into Ourselves and its Application to Pharmacogenomics

    OpenAIRE

    2008-01-01

    The exploration of quantitative variation in complex traits such as gene expression and drug response in human populations has become one of the major priorities for medical genetics. The International HapMap Project provides a key resource of genotypic data on human lymphoblastoid cell lines derived from four major world populations of European, African, Chinese and Japanese ancestry for researchers to associate with various phenotypic data to find genes affecting health, disease and respons...

  8. Systematic Regional Variations of GABA, Glutamine, and Glutamate Concentrations Follow Receptor Fingerprints of Human Cingulate Cortex

    NARCIS (Netherlands)

    Dou, Weiqiang; Palomero-Gallagher, Nicola; van Tol, Marie-Jose; Kaufmann, Joern; Zhong, Kai; Bernstein, Hans-Gert; Heinze, Hans-Jochen; Speck, Oliver; Walter, Martin

    2013-01-01

    Magnetic resonance spectroscopy (MRS) of glutamatergic or GABAergic measures in anterior cingulate cortex (ACC) was found altered in psychiatric disorders and predictive of interindividual variations of functional responses in healthy populations. Several ACC subregions have been parcellated into re

  9. Genetics in endocrinology: genetic variation in deiodinases: a systematic review of potential clinical effects in humans

    NARCIS (Netherlands)

    Verloop, H.; Dekkers, O.M.; Peeters, R.P.; Schoones, J.W.; Smit, J.W.

    2014-01-01

    Iodothyronine deiodinases represent a family of selenoproteins involved in peripheral and local homeostasis of thyroid hormone action. Deiodinases are expressed in multiple organs and thyroid hormone affects numerous biological systems, thus genetic variation in deiodinases may affect multiple clini

  10. Modelling human regulatory variation in mouse: finding the function in genome-wide association studies and whole-genome sequencing.

    Directory of Open Access Journals (Sweden)

    Jean-François Schmouth

    Full Text Available An increasing body of literature from genome-wide association studies and human whole-genome sequencing highlights the identification of large numbers of candidate regulatory variants of potential therapeutic interest in numerous diseases. Our relatively poor understanding of the functions of non-coding genomic sequence, and the slow and laborious process of experimental validation of the functional significance of human regulatory variants, limits our ability to fully benefit from this information in our efforts to comprehend human disease. Humanized mouse models (HuMMs, in which human genes are introduced into the mouse, suggest an approach to this problem. In the past, HuMMs have been used successfully to study human disease variants; e.g., the complex genetic condition arising from Down syndrome, common monogenic disorders such as Huntington disease and β-thalassemia, and cancer susceptibility genes such as BRCA1. In this commentary, we highlight a novel method for high-throughput single-copy site-specific generation of HuMMs entitled High-throughput Human Genes on the X Chromosome (HuGX. This method can be applied to most human genes for which a bacterial artificial chromosome (BAC construct can be derived and a mouse-null allele exists. This strategy comprises (1 the use of recombineering technology to create a human variant-harbouring BAC, (2 knock-in of this BAC into the mouse genome using Hprt docking technology, and (3 allele comparison by interspecies complementation. We demonstrate the throughput of the HuGX method by generating a series of seven different alleles for the human NR2E1 gene at Hprt. In future challenges, we consider the current limitations of experimental approaches and call for a concerted effort by the genetics community, for both human and mouse, to solve the challenge of the functional analysis of human regulatory variation.

  11. Progress of pharmacogenomic studies on anti-diabetic drugs%口服降糖药的药物基因组学研究进展

    Institute of Scientific and Technical Information of China (English)

    王婕; 贾伟平

    2009-01-01

    药物基因组学是研究基因组变异与药物疗效、安全性间关系的学科.本文主要介绍临床常用降糖药的药物基因组学研究进展.%Pharmacogenomics aims to identify the effects of genomie variants on drug efficacy and safety. This article summarized the progress of pharmacogenomic study on anti-diabetic drugs.

  12. Expanding role of pharmacogenomics in the management of cardiovascular disorders.

    Science.gov (United States)

    Yip, Vincent Lai Ming; Pirmohamed, Munir

    2013-06-01

    Cardiovascular disease is a leading cause of death worldwide. Many pharmacologic therapies are available that aim to reduce the risk of cardiovascular disease but there is significant inter-individual variation in drug response, including both efficacy and toxicity. Pharmacogenetics aims to personalize medication choice and dosage to ensure that maximum clinical benefit is achieved whilst side effects are minimized. Over the past decade, our knowledge of pharmacogenetics in cardiovascular therapies has increased significantly. The anticoagulant warfarin represents the most advanced application of pharmacogenetics in cardiovascular medicine. Prospective randomized clinical trials are currently underway utilizing dosing algorithms that incorporate genetic polymorphisms in cytochrome P450 (CYP)2C9 and vitamin k epoxide reductase (VKORC1) to determine warfarin dosages. Polymorphisms in CYP2C9 and VKORC1 account for approximately 40 % of the variance in warfarin dose. There is currently significant controversy with regards to pharmacogenetic testing in anti-platelet therapy. Inhibition of platelet aggregation by aspirin in vitro has been associated with polymorphisms in the cyclo-oxygenase (COX)-1 gene. However, COX-1 polymorphisms did not affect clinical outcomes in patients prescribed aspirin therapy. Similarly, CYP2C19 polymorphisms have been associated with clopidogrel resistance in vitro, and have shown an association with stent thrombosis, but not with other cardiovascular outcomes in a consistent manner. Response to statins has been associated with polymorphisms in the cholesterol ester transfer protein (CETP), apolipoprotein E (APOE), 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase, calmin (CLMN) and apolipoprotein-CI (APOC1) genes. Although these genes contribute to the variation in lipid levels during statin therapy, their effects on cardiovascular outcomes requires further investigation. Polymorphisms in the solute carrier organic anion transporter

  13. The rhesus macaque is three times as diverse but more closely equivalent in damaging coding variation as compared to the human

    OpenAIRE

    2012-01-01

    Abstract Background As a model organism in biomedicine, the rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate. Although a draft genome sequence was completed in 2007, there has been no systematic genome-wide comparison of genetic variation of this species to humans. Comparative analysis of functional and nonfunctional diversity in this highly abundant and adaptable non-human primate could inform its use as a model for human biology, and could reveal how variation in pop...

  14. Pharmacogenomics, biochemistry, toxicology, microbiology and cancer research in one go.

    Science.gov (United States)

    Rodrigues-Lima, Fernando; Dairou, Julien; Laurieri, Nicola; Busi, Florent; Dupret, Jean-Marie

    2011-08-01

    Arylamine N-acetyltransferases (NATs) are phase II xenobiotic metabolizing enzymes playing a key role in the detoxification and metabolic activation of aromatic amine xenobiotics. The triennial International NAT Workshop has been an important academic meeting where developments in the study of NATs and aromatic amine metabolism have been presented. The 2010 Workshop took place in University Paris Diderot Paris, France. Topics included: structures and functions of eukaryotic and prokaryotic NATs, gene regulation and expression of human NATs, polymorphisms and their effects, arylamine metabolism and toxicity. Nomenclature issues were also discussed.

  15. Pharmacogenomic study using bio- and nanobioelectrochemistry: Drug-DNA interaction.

    Science.gov (United States)

    Hasanzadeh, Mohammad; Shadjou, Nasrin

    2016-04-01

    Small molecules that bind genomic DNA have proven that they can be effective anticancer, antibiotic and antiviral therapeutic agents that affect the well-being of millions of people worldwide. Drug-DNA interaction affects DNA replication and division; causes strand breaks, and mutations. Therefore, the investigation of drug-DNA interaction is needed to understand the mechanism of drug action as well as in designing DNA-targeted drugs. On the other hand, the interaction between DNA and drugs can cause chemical and conformational modifications and, thus, variation of the electrochemical properties of nucleobases. For this purpose, electrochemical methods/biosensors can be used toward detection of drug-DNA interactions. The present paper reviews the drug-DNA interactions, their types and applications of electrochemical techniques used to study interactions between DNA and drugs or small ligand molecules that are potentially of pharmaceutical interest. The results are used to determine drug binding sites and sequence preference, as well as conformational changes due to drug-DNA interactions. Also, the intention of this review is to give an overview of the present state of the drug-DNA interaction cognition. The applications of electrochemical techniques for investigation of drug-DNA interaction were reviewed and we have discussed the type of qualitative or quantitative information that can be obtained from the use of each technique.

  16. Personalized antiplatelet and anticoagulation therapy: applications and significance of pharmacogenomics

    Science.gov (United States)

    Beitelshees, Amber L; Voora, Deepak; Lewis, Joshua P

    2015-01-01

    In recent years, substantial effort has been made to better understand the influence of genetic factors on the efficacy and safety of numerous medications. These investigations suggest that the use of pharmacogenetic data to inform physician decision-making has great potential to enhance patient care by reducing on-treatment clinical events, adverse drug reactions, and health care-related costs. In fact, integration of such information into the clinical setting may be particularly applicable for antiplatelet and anticoagulation therapeutics, given the increasing body of evidence implicating genetic variation in variable drug response. In this review, we summarize currently available pharmacogenetic information for the most commonly used antiplatelet (ie, clopidogrel and aspirin) and anticoagulation (ie, warfarin) medications. Furthermore, we highlight the currently known role of genetic variability in response to next-generation antiplatelet (prasugrel and ticagrelor) and anticoagulant (dabigatran) agents. While compelling evidence suggests that genetic variants are important determinants of antiplatelet and anticoagulation therapy response, significant barriers to clinical implementation of pharmacogenetic testing exist and are described herein. In addition, we briefly discuss development of new diagnostic targets and therapeutic strategies as well as implications for enhanced patient care. In conclusion, pharmacogenetic testing can provide important information to assist clinicians with prescribing the most personalized and effective antiplatelet and anticoagulation therapy. However, several factors may limit its usefulness and should be considered. PMID:25897256

  17. Variation in elemental composition of human teeth and its application for feasible species identification.

    Science.gov (United States)

    Nganvongpanit, Korakot; Buddhachat, Kittisak; Piboon, Promporn; Euppayo, Thippaporn; Mahakkanukrauh, Pasuk

    2017-02-01

    Identifying human remains is a primary task in forensic science. In this study, we propose a possible new technique, handheld X-ray fluorescence (HHXRF), for determining whether a suspected tooth is an authentic human tooth. A total of 444 teeth obtained from 111 human skulls (male=62, female=49) aged between 30-67 years (51.81±8.37 years) were used as subjects. The teeth were scanned by HHXRF to acquire their elemental profile. Differences in elemental composition were analyzed for different tooth positions (numbers 1-32), between crown and root, and between sexes (male and female); also, the proportion of elements in relation to different human ages was examined. Teeth from 20 different animal species, serving as non-human teeth samples, were used to distinguish between human and non-human teeth through a stepwise discriminant analysis. Our results revealed that different tooth positions, different regions (crown and root) of a tooth, and different sexes demonstrated disparities in the proportion of several elements. The accuracy rate of predicting sex based on the elemental profile of human teeth was 65.5%. Likewise, a dissimilar distribution of elements between human and non-human teeth was observed, leading to a high degree of correctness of 83.2% for distinguishing them. In conclusion, elemental analysis by HHXRF could serve as a promising candidate tool for identifying human teeth in forensic science, but is ineffective for sex determination.

  18. Circadian variation of EEG power spectra in NREM and REM sleep in humans: dissociation from body temperature

    Science.gov (United States)

    Dijk, D. J.

    1999-01-01

    In humans, EEG power spectra in REM and NREM sleep, as well as characteristics of sleep spindles such as their duration, amplitude, frequency and incidence, vary with circadian phase. Recently it has been hypothesized that circadian variations in EEG spectra in humans are caused by variations in brain or body temperature and may not represent phenomena relevant to sleep regulatory processes. To test this directly, a further analysis of EEG power spectra - collected in a forced desynchrony protocol in which sleep episodes were scheduled to a 28-h period while the rhythms of body temperature and plasma melatonin were oscillating at their near 24-h period - was carried out. EEG power spectra were computed for NREM and REM sleep occurring between 90-120 and 270-300 degrees of the circadian melatonin rhythm, i.e. just after the clearance of melatonin from plasma in the 'morning' and just after the 'evening' increase in melatonin secretion. Average body temperatures during scheduled sleep at these two circadian phases were identical (36.72 degrees C). Despite identical body temperatures, the power spectra in NREM sleep were very different at these two circadian phases. EEG activity in the low frequency spindle range was significantly and markedly enhanced after the evening increase in plasma melatonin as compared to the morning phase. For REM sleep, significant differences in power spectra during these two circadian phases, in particular in the alpha range, were also observed. The results confirm that EEG power spectra in NREM and REM sleep vary with circadian phase, suggesting that the direct contribution of temperature to the circadian variation in EEG power spectra is absent or only minor, and are at variance with the hypothesis that circadian variations in EEG power spectra are caused by variations in temperature.

  19. Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies.

    Science.gov (United States)

    Lee, Arthur S; Gutiérrez-Arcelus, María; Perry, George H; Vallender, Eric J; Johnson, Welkin E; Miller, Gregory M; Korbel, Jan O; Lee, Charles

    2008-04-15

    Copy number variants (CNVs) are heritable gains and losses of genomic DNA in normal individuals. While copy number variation is widely studied in humans, our knowledge of CNVs in other mammalian species is more limited. We have designed a custom array-based comparative genomic hybridization (aCGH) platform with 385 000 oligonucleotide probes based on the reference genome sequence of the rhesus macaque (Macaca mulatta), the most widely studied non-human primate in biomedical research. We used this platform to identify 123 CNVs among 10 unrelated macaque individuals, with 24% of the CNVs observed in multiple individuals. We found that segmental duplications were significantly enriched at macaque CNV loci. We also observed significant overlap between rhesus macaque and human CNVs, suggesting that certain genomic regions are prone to recurrent CNV formation and instability, even across a total of approximately 50 million years of primate evolution ( approximately 25 million years in each lineage). Furthermore, for eight of the CNVs that were observed in both humans and macaques, previous human studies have reported a relationship between copy number and gene expression or disease susceptibility. Therefore, the rhesus macaque offers an intriguing, non-human primate outbred model organism with which hypotheses concerning the specific functions of phenotypically relevant human CNVs can be tested.

  20. mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory.

    Science.gov (United States)

    Atkinson, Quentin D; Gray, Russell D; Drummond, Alexei J

    2008-02-01

    The relative timing and size of regional human population growth following our expansion from Africa remain unknown. Human mitochondrial DNA (mtDNA) diversity carries a legacy of our population history. Given a set of sequences, we can use coalescent theory to estimate past population size through time and draw inferences about human population history. However, recent work has challenged the validity of using mtDNA diversity to infer species population sizes. Here we use Bayesian coalescent inference methods, together with a global data set of 357 human mtDNA coding-region sequences, to infer human population sizes through time across 8 major geographic regions. Our estimates of relative population sizes show remarkable concordance with the contemporary regional distribution of humans across Africa, Eurasia, and the Americas, indicating that mtDNA diversity is a good predictor of population size in humans. Plots of population size through time show slow growth in sub-Saharan Africa beginning 143-193 kya, followed by a rapid expansion into Eurasia after the emergence of the first non-African mtDNA lineages 50-70 kya. Outside Africa, the earliest and fastest growth is inferred in Southern Asia approximately 52 kya, followed by a succession of growth phases in Northern and Central Asia (approximately 49 kya), Australia (approximately 48 kya), Europe (approximately 42 kya), the Middle East and North Africa (approximately 40 kya), New Guinea (approximately 39 kya), the Americas (approximately 18 kya), and a second expansion in Europe (approximately 10-15 kya). Comparisons of relative regional population sizes through time suggest that between approximately 45 and 20 kya most of humanity lived in Southern Asia. These findings not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past.

  1. Plasmodium falciparum CS protein - prime malaria vaccine candidate: definition of the human CTL domain and analysis of its variation

    Directory of Open Access Journals (Sweden)

    Denise L. Doolan

    1992-01-01

    Full Text Available Studies in mice have shown that immunity to malaria sporozoites is mediated primarily by citotoxic T lymphocytes (CTL specific for epitopes within the circumsporozoite (CS protein. Humans, had never been shown to generate CTL against any malaria or other parasite protein. The design of a sub-unit vaccine for humans ralies on the epitopes recognized by CTL being identified and polymorphisms therein being defined. We have developed a novel technique using an entire series of overlapping synthetic peptides to define the epitopes of the Plasmodium falciparum CS protein recognized by human CTL and have analyzed the sequence variation of the protein with respect to the identified CTL epitopic domain. We have demonstrated that some humans can indeed generate CTL. against the P. falciparum CS protein. Furthermore, the extent of variation observed for the CTL recognition domain is finite and the combination of peptides necessary for inclusion in a polyvalent vaccine may be small. If ways can be found to increase immune responsiveness, then a vaccine designed to stimulate CS protein-specific CTL activity may prevent malaria.

  2. Personalized antiplatelet and anticoagulation therapy: applications and significance of pharmacogenomics

    Directory of Open Access Journals (Sweden)

    Beitelshees AL

    2015-02-01

    Full Text Available Amber L Beitelshees,1,* Deepak Voora,2,* Joshua P Lewis,1,* 1Program for Personalized and Genomic Medicine and Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA; 2Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke School of Medicine, Durham, NC, USA*All authors contributed equally to this work Abstract: In recent years, substantial effort has been made to better understand the influence of genetic factors on the efficacy and safety of numerous medications. These investigations suggest that the use of pharmacogenetic data to inform physician decision-making has great potential to enhance patient care by reducing on-treatment clinical events, adverse drug reactions, and health care-related costs. In fact, integration of such information into the clinical setting may be particularly applicable for antiplatelet and anticoagulation therapeutics, given the increasing body of evidence implicating genetic variation in variable drug response. In this review, we summarize currently available pharmacogenetic information for the most commonly used antiplatelet (ie, clopidogrel and aspirin and anticoagulation (ie, warfarin medications. Furthermore, we highlight the currently known role of genetic variability in response to next-generation antiplatelet (prasugrel and ticagrelor and anticoagulant (dabigatran agents. While compelling evidence suggests that genetic variants are important determinants of antiplatelet and anticoagulation therapy response, significant barriers to clinical implementation of pharmacogenetic testing exist and are described herein. In addition, we briefly discuss development of new diagnostic targets and therapeutic strategies as well as implications for enhanced patient care. In conclusion, pharmacogenetic testing can provide important information to assist clinicians with prescribing the most personalized and effective antiplatelet and

  3. Pharmacogenomics in the treatment of lung cancer: an update.

    Science.gov (United States)

    Morales-Espinosa, Daniela; García-Román, Silvia; Karachaliou, Niki; Rosell, Rafael

    2015-01-01

    Significant advances have been made in the analysis of the human genome in the first decades of the 21st century and understanding of tumor biology has matured greatly. The identification of tumor-associated mutations and the pathways involved has led to the development of targeted anticancer therapies. However, the challenge now in using chemotherapy to treat nonsmall-cell lung cancer is to identify more molecular markers predictive of drug sensitivity and determine the optimal drug sequences in order to tailor treatment to each patient. This approach could permit selection of patients who could benefit most from a specific type of chemotherapy by matching their tumor and individual genetic profile. Nevertheless, this potential has been limited so far by reliance on the single biomarker approach, though this is now on the way to being overcome through whole genome studies.

  4. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines.

    Science.gov (United States)

    Bock, Christoph; Kiskinis, Evangelos; Verstappen, Griet; Gu, Hongcang; Boulting, Gabriella; Smith, Zachary D; Ziller, Michael; Croft, Gist F; Amoroso, Mackenzie W; Oakley, Derek H; Gnirke, Andreas; Eggan, Kevin; Meissner, Alexander

    2011-02-04

    The developmental potential of human pluripotent stem cells suggests that they can produce disease-relevant cell types for biomedical research. However, substantial variation has been reported among pluripotent cell lines, which could affect their utility and clinical safety. Such cell-line-specific differences must be better understood before one can confidently use embryonic stem (ES) or induced pluripotent stem (iPS) cells in translational research. Toward this goal we have established genome-wide reference maps of DNA methylation and gene expression for 20 previously derived human ES lines and 12 human iPS cell lines, and we have measured the in vitro differentiation propensity of these cell lines. This resource enabled us to assess the epigenetic and transcriptional similarity of ES and iPS cells and to predict the differentiation efficiency of individual cell lines. The combination of assays yields a scorecard for quick and comprehensive characterization of pluripotent cell lines.

  5. Myosin heavy chain isoform expression in human extraocular muscles: longitudinal variation and patterns of expression in global and orbital layers.

    Science.gov (United States)

    Park, Kyung-Ah; Lim, Jeonghee; Sohn, Seongsoo; Oh, Sei Yeul

    2012-05-01

    We investigated the distribution of myosin heavy chain (MyHC) isoforms along the length of the global and orbital layers of human extraocular muscles (EOMs). Whole muscle tissue extracts of human EOMs were cross-sectioned consecutively and separated into orbital and global layers. The extracts from these layers were subjected to electrophoretic analysis, followed by quantification with scanning densitometry. MyHC isoforms displayed different distributions along the lengths of EOMs. In the orbital and global layers of all EOMs except for the superior oblique muscle, MyHCeom was enriched in the central regions. MyHCIIa and MyHCI were most abundant in the proximal and distal ends. A variation in MyHC isoform expression was apparent along the lengths of human EOMs. These results provide a basis for understanding the molecular mechanisms underlying the functional diversity of EOMs. Copyright © 2012 Wiley Periodicals, Inc.

  6. A new biophysical metric for interrogating the information content in human genome sequence variation: Proof of concept.

    Science.gov (United States)

    Lindesay, James; Mason, Tshela E; Ricks-Santi, Luisel; Hercules, William; Kurian, Philip; Dunston, Georgia M

    2012-02-01

    The 21(st) century emergence of genomic medicine is shifting the paradigm in biomedical science from the population phenotype to the individual genotype. In characterizing the biology of disease and health disparities in population genetics, human populations are often defined by the most common alleles in the group. This definition poses difficulties when categorizing individuals in the population who do not have the most common allele(s). Various epidemiological studies have shown an association between common genomic variation, such as single nucleotide polymorphisms (SNPs), and common diseases. We hypothesize that information encoded in the structure of SNP haploblock variation in the human leukocyte antigen-disease related (HLA-DR) region of the genome illumines molecular pathways and cellular mechanisms involved in the regulation of host adaptation to the environment. In this paper we describe the development and application of the normalized information content (NIC) as a novel metric based on SNP haploblock variation. The NIC facilitates translation of biochemical DNA sequence variation into a biophysical quantity derived from Boltzmann's canonical ensemble in statistical physics and used widely in information theory. Our normalization of this information metric allows for comparisons of unlike, or even unrelated, regions of the genome. We report here NIC values calculated for HLA-DR SNP haploblocks constructed by Haploview, a product of the International Haplotype Map Project. These haploblocks were scanned for potential regulatory elements using ConSite and miRBase, publicly available bioinformatics tools. We found that all of the haploblocks with statistically low NIC values contained putative transcription factor binding sites and microRNA motifs, suggesting correlation with genomic regulation. Thus, we were able to relate a mathematical measure of information content in HLA-DR SNP haploblocks to biologically relevant functional knowledge embedded in

  7. Does pharmacogenomics account for variability in control of acute chemotherapy-induced nausea and vomiting with 5-hydroxytryptamine type 3 receptor antagonists?

    Science.gov (United States)

    Trammel, Morgan; Roederer, Mary; Patel, Jai; McLeod, Howard

    2013-06-01

    Chemotherapy-induced nausea and vomiting is one of the most concerning adverse drug effects from cytotoxic chemotherapy. Despite appropriate use of antiemetic guidelines, 20-30 % of patients experience breakthrough nausea and vomiting secondary to chemotherapy. To assess the variability of 5-hydroxytryptamine type 3 receptor antagonist efficacy caused by genetic variation, a review of the available literature was conducted. From the literature, three sources of pharmacogenomic variability were identified: polymorphisms associated with 5-hydroxytryptamine type 3 receptor subunits, drug metabolism via cytochromes P450, and drug transport in the body. Testing for receptor subunit polymorphisms is not applicable to a clinical setting at this time; however, cytochrome P450 2D6 testing is FDA-approved and widely accessible. Cytochrome P450 2D6 ultrarapid metabolizers and poor metabolizers displayed altered antiemetic efficacy when compared with intermediate metabolizers and extensive metabolizers. We postulate that testing for cytochrome P450 2D6 phenotypes may be the most accessible way to provide individualized antiemetic therapy in the future.

  8. Design and Anticipated Outcomes of the eMERGE-PGx Project: A Multi-Center Pilot for Pre-Emptive Pharmacogenomics in Electronic Health Record Systems

    Science.gov (United States)

    Rasmussen-Torvik, Laura J.; Stallings, Sarah C.; Gordon, Adam S.; Almoguera, Berta; Basford, Melissa A.; Bielinski, Suzette J.; Brautbar, Ariel; Brilliant, Murray; Carrell, David S.; Connolly, John; Crosslin, David R.; Doheny, Kimberly F.; Gallego, Carlos J.; Gottesman, Omri; Kim, Daniel Seung; Leppig, Kathleen A.; Li, Rongling; Lin, Simon; Manzi, Shannon; Mejia, Ana R.; Pacheco, Jennifer A.; Pan, Vivian; Pathak, Jyotishman; Perry, Cassandra L.; Peterson, Josh F.; Prows, Cynthia A.; Ralston, James; Rasmussen, Luke V.; Ritchie, Marylyn D.; Sadhasivam, Senthilkumar; Scott, Stuart A.; Smith, Maureen; Vega, Aida; Vinks, Alexander A.; Volpi, Simona; Wolf, Wendy A.; Bottinger, Erwin; Chisholm, Rex L.; Chute, Christopher G.; Haines, Jonathan L.; Harley, John B.; Keating, Brendan; Holm, Ingrid A.; Kullo, Iftikhar J.; Jarvik, Gail P.; Larson, Eric B.; Manolio, Teri; McCarty, Catherine A.; Nickerson, Deborah A.; Scherer, Steven E.; Williams, Marc S.; Roden, Dan M.; Denny, Joshua C.

    2014-01-01

    We describe here the design and initial implementation of the eMERGE-PGx project. eMERGE-PGx, a partnership of the eMERGE and PGRN consortia, has three objectives : 1) Deploy PGRNseq, a next-generation sequencing platform assessing sequence variation in 84 proposed pharmacogenes, in nearly 9,000 patients likely to be prescribed drugs of interest in a 1–3 year timeframe across several clinical sites; 2) Integrate well-established clinically-validated pharmacogenetic genotypes into the electronic health record with associated clinical decision support and assess process and clinical outcomes of implementation; and 3) Develop a repository of pharmacogenetic variants of unknown significance linked to a repository of EHR-based clinical phenotype data for ongoing pharmacogenomics discovery. We describe site-specific project implementation and anticipated products, including genetic variant and phenotype data repositories, novel variant association studies, clinical decision support modules, clinical and process outcomes, approaches to manage incidental findings, and patient and clinician education methods. PMID:24960519

  9. The variation and influencing factors of human%人的差异及其影响因素

    Institute of Scientific and Technical Information of China (English)

    席焕久; 李文慧; 张美芝; 温有锋; 杜雪; 李超

    2011-01-01

    Human variation is the central problem of anthropology, a hotspot and focus on the research of domestic and overseas.The variation shows not only in human biology (including morphology, physiology, biochemistry, drug metabolism, immunology and disease susceptibility, body composition, physical performance, etc.), but also in geographical,temporal, racial and ethnic, character, gender and other aspects.The causes of these differences originats mainly from ecological factors (or environmental factors) and genetic factors.The study of human variation and its influencing factor is significant to anthropology, medicine, forensic medicine, archeology and human ecology and like.%人的差异问题是人类学的中心问题,是国内外研究的热点和重点.人的差异不仅表现在生物学上(包括形态学、生理学、生物化学、药物代谢、免疫学与疾病易感性、体成分、体能等),还表现在地域、时间、种族与民族、性格、性别等多方面.这些差异产生的原因主要来自生态学因素(或环境因素)和遗传因素等.人的差异及其影响因素的研究对人类学、医学、法医学、考古学和人类生态学等都具有重要意义.

  10. Variations of global and continental water balance components as impacted by climate forcing uncertainty and human water use

    Science.gov (United States)

    Müller Schmied, Hannes; Adam, Linda; Eisner, Stephanie; Fink, Gabriel; Flörke, Martina; Kim, Hyungjun; Oki, Taikan; Portmann, Felix Theodor; Reinecke, Robert; Riedel, Claudia; Song, Qi; Zhang, Jing; Döll, Petra

    2016-07-01

    When assessing global water resources with hydrological models, it is essential to know about methodological uncertainties. The values of simulated water balance components may vary due to different spatial and temporal aggregations, reference periods, and applied climate forcings, as well as due to the consideration of human water use, or the lack thereof. We analyzed these variations over the period 1901-2010 by forcing the global hydrological model WaterGAP 2.2 (ISIMIP2a) with five state-of-the-art climate data sets, including a homogenized version of the concatenated WFD/WFDEI data set. Absolute values and temporal variations of global water balance components are strongly affected by the uncertainty in the climate forcing, and no temporal trends of the global water balance components are detected for the four homogeneous climate forcings considered (except for human water abstractions). The calibration of WaterGAP against observed long-term average river discharge Q significantly reduces the impact of climate forcing uncertainty on estimated Q and renewable water resources. For the homogeneous forcings, Q of the calibrated and non-calibrated regions of the globe varies by 1.6 and 18.5 %, respectively, for 1971-2000. On the continental scale, most differences for long-term average precipitation P and Q estimates occur in Africa and, due to snow undercatch of rain gauges, also in the data-rich continents Europe and North America. Variations of Q at the grid-cell scale are large, except in a few grid cells upstream and downstream of calibration stations, with an average variation of 37 and 74 % among the four homogeneous forcings in calibrated and non-calibrated regions, respectively. Considering only the forcings GSWP3 and WFDEI_hom, i.e., excluding the forcing without undercatch correction (PGFv2.1) and the one with a much lower shortwave downward radiation SWD than the others (WFD), Q variations are reduced to 16 and 31 % in calibrated and non

  11. Modelling Landscape Dynamics in a Highland Mediterranean Catchment: Establishing the impact of Climate Variation and Human Activity

    Science.gov (United States)

    van Beek, L. P. H.; Feiken, H.; van Asch, T. W. J.; Bierkens, M. F. P.

    2012-04-01

    The close link between human occupancy and the Mediterranean landscape has long been recognized. Through the exploitation of the various but fragmented resources that these landscapes have to offer, man has been able to secure a living. However, these activities are often marginal and small shifts in population pressure, corresponding land use patterns or climatic variability can have large consequences on the redistribution of water and sediment in these areas. The meso-scale landscape dynamics model, CALEROS, has been developed to simulate the interactions between climate, soil production and erosion, vegetation and land use on geomorphological to human time scales in Mediterranean environments. Starting from an initial landscape consisting of a DTM, soil distribution and underlying lithology, the landscape is free to develop in response to the imposed climate variability and seismicity. In addition to changes in soil distribution and bedrock lowering, this includes the establishment of vegetation as conditioned by a selection of plant functional types and, optionally, population and land use dynamics as conditioned by land use scenarios specifying technological and dietary constraints for different periods. As such CALEROS is well-suited to investigate the relative impacts of climate, land cover and human activities on the hydrological catchment response and the associated sediment fluxes due to soil erosion and mass movements. Within the context of a geo-archeological study on the conservation potential of settlement history in the Contrada Maddalena (~14km2, Calabria, Italy), we apply CALEROS to investigate the relative contributions of climate and man from Neolithic times onwards (5000 BP-present). Model results allow to establish when human impacts become significant over natural variations and to discern shifts in catchment functioning as a result of sudden or climatic variations (e.g., Little Ice Age) as reflected in vegetation patterns and water and

  12. Genetic variation in AKT1 is linked to dopamine-associated prefrontal cortical structure and function in humans

    Science.gov (United States)

    Tan, Hao-Yang; Nicodemus, Kristin K.; Chen, Qiang; Li, Zhen; Brooke, Jennifer K.; Honea, Robyn; Kolachana, Bhaskar S.; Straub, Richard E.; Meyer-Lindenberg, Andreas; Sei, Yoshitasu; Mattay, Venkata S.; Callicott, Joseph H.; Weinberger, Daniel R.

    2008-01-01

    AKT1-dependent molecular pathways control diverse aspects of cellular development and adaptation, including interactions with neuronal dopaminergic signaling. If AKT1 has an impact on dopaminergic signaling, then genetic variation in AKT1 would be associated with brain phenotypes related to cortical dopaminergic function. Here, we provide evidence that a coding variation in AKT1 that affects protein expression in human B lymphoblasts influenced several brain measures related to dopaminergic function. Cognitive performance linked to frontostriatal circuitry, prefrontal physiology during executive function, and frontostriatal gray-matter volume on MRI were altered in subjects with the AKT1 variation. Moreover, on neuroimaging measures with a main effect of the AKT1 genotype, there was significant epistasis with a functional polymorphism (Val158Met) in catechol-O-methyltransferase [COMT], a gene that indexes cortical synaptic dopamine. This genetic interaction was consistent with the putative role of AKT1 in dopaminergic signaling. Supportive of an earlier tentative association of AKT1 with schizophrenia, we also found that this AKT1 variant was associated with risk for schizophrenia. These data implicate AKT1 in modulating human prefrontal-striatal structure and function and suggest that the mechanism of this effect may be coupled to dopaminergic signaling and relevant to the expression of psychosis. PMID:18497887

  13. Husbands' and Wives' Relative Earnings: Exploring Variation by Race, Human Capital, Labor Supply, and Life Stage

    Science.gov (United States)

    Winslow-Bowe, Sarah

    2009-01-01

    Whereas much research has explored the causes and consequences of the gender wage gap, far less has examined earnings differentials within marriage. This article contributes to this literature by utilizing the 2000 wave of the 1979 National Longitudinal Survey of Youth to examine variation in husbands' and wives' relative income by race/ethnicity,…

  14. Genetic variation, expression and ontogeny of sulfotransferase SULT2A1 in humans.

    Science.gov (United States)

    Ekström, L; Rane, A

    2015-08-01

    Sulfotransferases (SULTs) are enzymes involved in the metabolism of several endogenous molecules. The activity and expression exhibit inter- and intra-individual variations due to age and genetic variation. The aims of this study were to compare the gene expression of SULT2A1 in fetal and adult livers, to study the intra-individual tissue distribution, and investigate if expression is associated with a SULT2A1 copy number variation polymorphism. In contrast to other drug metabolizing enzyme systems the expression of SULT2A1 did not differ between fetal and adult liver samples and it was not affected by maternal smoking or gestational age. Gene expression in relation to sex could not be assessed as the sex of the fetuses was unknown. SULT2A1 was consistently expressed in livers and adrenals, being seven times more abundant in adrenals, but was absent in the lungs. The SULT2A1 copy number variation was proportional to gene expression in liver and adrenals. Our results show that SULT2A1 is important in the first trimester; particularly in the adrenals.

  15. Husbands' and Wives' Relative Earnings: Exploring Variation by Race, Human Capital, Labor Supply, and Life Stage

    Science.gov (United States)

    Winslow-Bowe, Sarah

    2009-01-01

    Whereas much research has explored the causes and consequences of the gender wage gap, far less has examined earnings differentials within marriage. This article contributes to this literature by utilizing the 2000 wave of the 1979 National Longitudinal Survey of Youth to examine variation in husbands' and wives' relative income by race/ethnicity,…

  16. Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression

    NARCIS (Netherlands)

    Kumar, Vinod; Westra, Harm-Jan; Karjalainen, Juha; Zhernakova, Daria V.; Esko, Tonu; Hrdlickova, Barbara; Almeida, Rodrigo; Zhernakova, Alexandra; Reinmaa, Eva; Hofker, Marten H.; Fehrmann, Rudolf S. N.; Fu, Jingyuan; Withoff, Sebo; Metspalu, Andres; Franke, Lude; Wijmenga, Cisca; Vosa, Urmo

    2013-01-01

    Recently it has become clear that only a small percentage (7%) of disease-associated single nucleotide polymorphisms (SNPs) are located in protein-coding regions, while the remaining 93% are located in gene regulatory regions or in intergenic regions. Thus, the understanding of how genetic variation

  17. Serial variation in histological character of articular soft tissue in young human adult temporomandibular joint condyles.

    Science.gov (United States)

    Bibb, C A; Pullinger, A G; Baldioceda, F

    1993-04-01

    Histological variation was studied in serial sections, in contrast to previous studies which have generalized from representative sections. The sample consisted of consecutive serial sagittal sections from the central third of nine condyles, plus an accompanying stone cast showing the intact articular surface before sectioning. The thickness of the articular soft tissue and its fibrous connective tissue and cartilage components was measured, and the presence of undifferentiated mesenchymal (UM) cells was assessed by low-power light microscopy. Components of variance analysis showed that section-to-section variation in thickness was of the same order as differences between joints, each explaining approx. 50% of the variance in both connective tissue and cartilage thickness. The fibrous connective tissue contributed as much to the overall variation in soft tissue thickness as did the cartilage component (SD 0.0946 versus 0.0909 mm for the superior sector). Serial UM cell variability was common, and the UM cells were often distributed in islands rather than uniformly across the articular tissue. Condyles with the greatest surface irregularity were characterized by greater serial variability in fibrous connective tissue thickness, more frequent absence of cartilage, and more areas of UM cell depletion. These results suggest that serial variation in histological character may be more important than mean values in the description of surface contours and articular tissue relations in the temporomandibular joint. This should influence the design of future investigations.

  18. Sources of variation in hair cortisol in wild and captive non-human primates.

    Science.gov (United States)

    Fourie, Nicolaas H; Brown, Janine L; Jolly, Clifford J; Phillips-Conroy, Jane E; Rogers, Jeffrey; Bernstein, Robin M

    2016-04-01

    Hair cortisol analysis is a potentially powerful tool for evaluating adrenal function and chronic stress. However, the technique has only recently been applied widely to studies of wildlife, including primates, and there are numerous practical and technical factors that should be considered to ensure good quality data and the validity of results and conclusions. Here we report on various intrinsic and extrinsic sources of variation in hair cortisol measurements in wild and captive primates. Hair samples from both wild and captive primates revealed that age and sex can affect hair cortisol concentrations; these effects need to be controlled for when making comparisons between individual animals or populations. Hair growth rates also showed considerable inter-specific variation among a number of primate species. We describe technical limitations of hair analyses and variation in cortisol concentrations as a function of asynchronous hair growth, anatomical site of collection, and the amount and numbers of hair/s used for cortisol extraction. We discuss these sources of variation and their implications for proper study design and interpretation of results.

  19. Genetic variation in serotonin transporter function affects human fear expression indexed by fear-potentiated startle

    NARCIS (Netherlands)

    Klumpers, F.; Heitland, I.; Oosting, R.S.; Kenemans, J.L.; Baas, J.M.

    2012-01-01

    The serotonin transporter (SERT) plays a crucial role in anxiety. Accordingly, variance in SERT functioning appears to constitute an important pathway to individual differences in anxiety. The current study tested the hypothesis that genetic variation in SERT function is associated with variability

  20. External physical stimulation of the human-fetus during episodes of low heart-rate variation

    NARCIS (Netherlands)

    Visser, G. H. A.; ZEELENBERG, HJ; DEVRIES, JIP; DAWES, GS

    1983-01-01

    The effect of shaking the fetus through the maternal abdomen during episodes of low (nonreactive) fetal heart rate variation was studied in 10 healthy nulliparous women near term. Heart rate monitoring from an abdominal electrocardiogram was combined with real-time scanning for body movements and

  1. Composition and Variation of Macronutrients, Immune Proteins, and Human Milk Oligosaccharides in Human Milk From Nonprofit and Commercial Milk Banks.

    Science.gov (United States)

    Meredith-Dennis, Laura; Xu, Gege; Goonatilleke, Elisha; Lebrilla, Carlito B; Underwood, Mark A; Smilowitz, Jennifer T

    2017-06-01

    When human milk is unavailable, banked milk is recommended for feeding premature infants. Milk banks use processes to eliminate pathogens; however, variability among methods exists. Research aim: The aim of this study was to compare the macronutrient (protein, carbohydrate, fat, energy), immune-protective protein, and human milk oligosaccharide (HMO) content of human milk from three independent milk banks that use pasteurization (Holder vs. vat techniques) or retort sterilization. Randomly acquired human milk samples from three different milk banks ( n = 3 from each bank) were analyzed for macronutrient concentrations using a Fourier transform mid-infrared spectroscopy human milk analyzer. The concentrations of IgA, IgM, IgG, lactoferrin, lysozyme, α-lactalbumin, α antitrypsin, casein, and HMO were analyzed by mass spectrometry. The concentrations of protein and fat were significantly ( p milk samples that had undergone retort sterilization had significantly less immune-protective proteins and total and specific HMOs compared with samples that had undergone Holder and vat pasteurization. These data suggest that further analysis of the effect of retort sterilization on human milk components is needed prior to widespread adoption of this process.

  2. Cytotoxicity and Pharmacogenomics of Medicinal Plants from Traditional Korean Medicine

    Science.gov (United States)

    Kuete, Victor; Seo, Ean-Jeong; Krusche, Benjamin; Oswald, Mira; Schröder, Sven; Greten, Henry Johannes; Lee, Ik-Soo; Efferth, Thomas

    2013-01-01

    Aim. The present study was designed to investigate the cytotoxicity of a panel of 280 Korean medicinal plants belonging to 73 families and 198 species against human CCRF-CEM leukemia cells. Selected phytochemicals were investigated in more detail for their mode of action. Methods. The resazurin assay was used to determine cytotoxicity of the plant extracts. Microarray-based mRNA expression profiling, COMPARE, and hierarchical cluster analyses were applied to identify which genes correlate with sensitivity or resistance to selected phytochemicals of the Korean plants. Results. The results of the resazurin assay showed that cytotoxicity extracts tested at 10 μg/mL from 13 samples inhibited proliferation more than 50% (IC50 plants are Sedum middendorffianum (15.33%) and Lycoris radiata (17.61%). Out of 13 selected phytochemicals from these plants, hopeaphenol and deoxynarciclasine were the most cytotoxic ones. Genes from various functional groups (transcriptional or translational regulation, signal transduction, cellular proliferation, intracellular trafficking, RNA metabolism, endoplasmic/sarcoplasmic reticulum function, etc.) were significantly correlated with response of tumor cell lines to these two compounds. Conclusion. The results provide evidence on the possible use of selected Korean medicinal plants and chemical constituents derived from them for the treatment of tumors. PMID:23935662

  3. Evolutionary developmental pathology and anthropology: A new field linking development, comparative anatomy, human evolution, morphological variations and defects, and medicine.

    Science.gov (United States)

    Diogo, Rui; Smith, Christopher M; Ziermann, Janine M

    2015-11-01

    We introduce a new subfield of the recently created field of Evolutionary-Developmental-Anthropology (Evo-Devo-Anth): Evolutionary-Developmental-Pathology-and-Anthropology (Evo-Devo-P'Anth). This subfield combines experimental and developmental studies of nonhuman model organisms, biological anthropology, chordate comparative anatomy and evolution, and the study of normal and pathological human development. Instead of focusing on other organisms to try to better understand human development, evolution, anatomy, and pathology, it places humans as the central case study, i.e., as truly model organism themselves. We summarize the results of our recent Evo-Devo-P'Anth studies and discuss long-standing questions in each of the broader biological fields combined in this subfield, paying special attention to the links between: (1) Human anomalies and variations, nonpentadactyly, homeotic transformations, and "nearest neighbor" vs. "find and seek" muscle-skeleton associations in limb+facial muscles vs. other head muscles; (2) Developmental constraints, the notion of "phylotypic stage," internalism vs. externalism, and the "logic of monsters" vs. "lack of homeostasis" views about human birth defects; (3) Human evolution, reversions, atavisms, paedomorphosis, and peromorphosis; (4) Scala naturae, Haeckelian recapitulation, von Baer's laws, and parallelism between phylogeny and development, here formally defined as "Phylo-Devo parallelism"; and (5) Patau, Edwards, and Down syndrome (trisomies 13, 18, 21), atavisms, apoptosis, heart malformations, and medical implications.

  4. Incorporation of pharmacogenomics into routine clinical practice: the Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline development process.

    Science.gov (United States)

    Caudle, Kelly E; Klein, Teri E; Hoffman, James M; Muller, Daniel J; Whirl-Carrillo, Michelle; Gong, Li; McDonagh, Ellen M; Sangkuhl, Katrin; Thorn, Caroline F; Schwab, Matthias; Agundez, Jose A G; Freimuth, Robert R; Huser, Vojtech; Lee, Ming Ta Michael; Iwuchukwu, Otito F; Crews, Kristine R; Scott, Stuart A; Wadelius, Mia; Swen, Jesse J; Tyndale, Rachel F; Stein, C Michael; Roden, Dan; Relling, Mary V; Williams, Marc S; Johnson, Samuel G

    2014-02-01

    The Clinical Pharmacogenetics Implementation Consortium (CPIC) publishes genotype-based drug guidelines to help clinicians understand how available genetic test results could be used to optimize drug therapy. CPIC has focused initially on well-known examples of pharmacogenomic associations that have been implemented in selected clinical settings, publishing nine to date. Each CPIC guideline adheres to a standardized format and includes a standard system for grading levels of evidence linking genotypes to phenotypes and assigning a level of strength to each prescribing recommendation. CPIC guidelines contain the necessary information to help clinicians translate patient-specific diplotypes for each gene into clinical phenotypes or drug dosing groups. This paper reviews the development process of the CPIC guidelines and compares this process to the Institute of Medicine's Standards for Developing Trustworthy Clinical Practice Guidelines.

  5. Pharmacogenomics in practice: a case report of personalized inpatient psychiatric care.

    Science.gov (United States)

    Madan, Alok; Walker, Cory R; Weinstein, Benjamin; Fowler, J Christopher

    2015-01-01

    Given variable response to psychotropic intervention, this case highlights the potential of pharmacogenomics to inform medical decision-making in a male with atypical psychosis and depression with longer-standing attentional difficulties. Likely because of his specific COMT polymorphism and intermediate metabolizing liver enzymes, when the patient's stimulant medications were titrated to affect for attentional needs, he became psychotic secondary to a hyperdopaminergic state. Past prescriptions of dopaminergic antidepressant agents (e.g., bupropion) likely would have exacerbated further the problem. The patient's serotonin transporter polymorphism also potentially was associated with SSRI inefficacy and increased side effects. Knowledge of the patient's genetically influenced departure from average response allowed for personalization of pharmacology with clinical improvement across measures of functioning.

  6. Pharmacogenetics and pharmacogenomics for rheumatoid arthritis responsiveness to methotrexate treatment: the 2013 update.

    Science.gov (United States)

    Zhu, Hong; Deng, Fei-Yan; Mo, Xing-Bo; Qiu, Ying-Hua; Lei, Shu-Feng

    2014-03-01

    Rheumatoid arthritis (RA) is a complex, systemic autoimmune disease characterized by chronic inflammation of multiple peripheral joints, which leads to serious destruction of cartilage and bone, progressive deformity and severe disability. Methotrexate (MTX) is one of the first-line drugs commonly used in RA therapy owing to its excellent long-term efficacy and cheapness. However, the efficacy and toxicity of MTX treatment have significant interpatient variability. Genetic factors contribute to this variability. In this review, we have summarized and updated the progress of RA response to MTX treatment since 2009 by focusing on the fields of pharmacogenetics and pharmacogenomics. Identification of genetic factors involved in MTX treatment response will increase the understanding of RA pathology and the development of new personalized treatments.

  7. Pharmacogenomic information in FDA-approved drug labels: Application to pediatric patients.

    Science.gov (United States)

    Green, D J; Mummaneni, P; Kim, I W; Oh, J M; Pacanowski, M; Burckart, G J

    2016-06-01

    Pharmacogenomic (PGx) information is increasingly being incorporated into US Food and Drug Administration-approved drug labels. We reviewed the data source (adults vs. pediatrics) of PGx information in approved drug labels and assessed the suitability of applying adult-derived PGx information and related prescribing recommendations to the care of pediatric patients. We identified 65 drugs with labels containing PGx information and that have also been evaluated in children and found that in the majority of cases (56/65, 86%), the PGx information described was derived from adult studies. The application of PGx information from adults to pediatrics was deemed suitable for 71.4% (n = 40) of the drugs and unclear for 28.6% (n = 16). An ontogeny effect, limited or conflicting data regarding ontogeny of the genetic biomarker, or a difference in the pathophysiology or progression of the adult vs. pediatric disease were the primary reasons for deeming direct application from adults to pediatrics unclear.

  8. Adding pharmacogenomics to the development of new marine-derived anticancer agents

    Directory of Open Access Journals (Sweden)

    Aracil Miguel

    2006-01-01

    Full Text Available Abstract Nature has always been a highly productive tool in the development of anticancer therapies. Renewed interest in the potential of this tool has recently been sparked by the realization that the marine ecosystem can be used for the discovery and development of new compounds with clinical potential in advanced resistant tumors. These compounds can be incorporated into combination approaches in a chronic therapy scenario. Our marine anticancer program is using the sea to develop new agents with activity in resistant solid tumors and to identify new cellular targets for therapeutic intervention. This review describes the integration of different pharmacogenomic tools in the development of Yondelis™, Aplidin® and Kahalalide F, three marine-derived compounds currently in Phase II or III development. Our results are reinforcing the targeted selectivity of these agents and opening the gates for customized therapies in cancer patients in the near future.

  9. Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics.

    Science.gov (United States)

    Percha, Bethany; Altman, Russ B

    2013-01-01

    The biomedical literature presents a uniquely challenging text mining problem. Sentences are long and complex, the subject matter is highly specialized with a distinct vocabulary, and producing annotated training data for this domain is time consuming and expensive. In this environment, unsupervised text mining methods that do not rely on annotated training data are valuable. Here we investigate the use of random indexing, an automated method for producing vector-space semantic representations of words from large, unlabeled corpora, to address the problem of term normalization in sentences describing drugs and genes. We show that random indexing produces similarity scores that capture some of the structure of PHARE, a manually curated ontology of pharmacogenomics concepts. We further show that random indexing can be used to identify likely word candidates for inclusion in the ontology, and can help localize these new labels among classes and roles within the ontology.

  10. Novel therapeutics in metastatic colorectal cancer: molecular insights and pharmacogenomic implications.

    Science.gov (United States)

    Hanna, Diana L; Lenz, Heinz-Josef

    2016-08-01

    Although the survival of metastatic colorectal cancer (mCRC) patients has improved five-fold over the last century, CRC remains a significant global health burden. Impressive strides have been made in identifying new regimens, employing maintenance strategies to limit treatment toxicities, and combining multidisciplinary approaches to achieve cure in oligometastatic disease. Attempts at personalized integration of targeted agents have been limited by the ability to identify molecularly enriched patient populations most likely to benefit. In this review, we discuss novel therapeutics and regimens recently approved and in development for mCRC. In addition, we discuss using older agents in novel combination and maintenance strategies, and highlight evidence for implementing pharmacogenomic data and non-invasive monitoring into the personalized management of mCRC patients.

  11. Pharmacomicrobiomics : the impact of human microbiome variations on systems pharmacology and personalized therapeutics

    NARCIS (Netherlands)

    ElRakaiby, Marwa; Dutilh, Bas E; Rizkallah, Mariam R; Boleij, Annemarie; Cole, Jason N; Aziz, Ramy K

    2014-01-01

    The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome

  12. Pharmacomicrobiomics : the impact of human microbiome variations on systems pharmacology and personalized therapeutics

    NARCIS (Netherlands)

    ElRakaiby, Marwa; Dutilh, Bas E|info:eu-repo/dai/nl/304546313; Rizkallah, Mariam R; Boleij, Annemarie; Cole, Jason N; Aziz, Ramy K

    The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome

  13. Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics

    NARCIS (Netherlands)

    ElRakaiby, M.; Dutilh, B.E.; Rizkallah, M.R.; Boleij, A.; Cole, J.N.; Aziz, R.K.

    2014-01-01

    The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome

  14. Pharmacomicrobiomics : the impact of human microbiome variations on systems pharmacology and personalized therapeutics

    NARCIS (Netherlands)

    ElRakaiby, Marwa; Dutilh, Bas E; Rizkallah, Mariam R; Boleij, Annemarie; Cole, Jason N; Aziz, Ramy K

    2014-01-01

    The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome

  15. Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics