Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life.

Science.gov (United States)

Hao, Da-Cheng; Xiao, Pei-Gen

2015-01-01

Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide. This review presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with the evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of the plant genotype and metabolic phenotype, interaction between medicinal plant genomes and their environment, the correlation between genomic diversity and metabolite diversity, and so on. Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.

Cardiovascular Precision Medicine in the Genomics Era

Directory of Open Access Journals (Sweden)

Alexandra M. Dainis, BS

2018-04-01

Full Text Available Summary: Precision medicine strives to delineate disease using multiple data sources—from genomics to digital health metrics—in order to be more precise and accurate in our diagnoses, definitions, and treatments of disease subtypes. By defining disease at a deeper level, we can treat patients based on an understanding of the molecular underpinnings of their presentations, rather than grouping patients into broad categories with one-size-fits-all treatments. In this review, the authors examine how precision medicine, specifically that surrounding genetic testing and genetic therapeutics, has begun to make strides in both common and rare cardiovascular diseases in the clinic and the laboratory, and how these advances are beginning to enable us to more effectively define risk, diagnose disease, and deliver therapeutics for each individual patient. Key Words: genome sequencing, genomics, precision medicine, targeted therapeutics

The business value and cost-effectiveness of genomic medicine.

Science.gov (United States)

Crawford, James M; Aspinall, Mara G

2012-05-01

Genomic medicine offers the promise of more effective diagnosis and treatment of human diseases. Genome sequencing early in the course of disease may enable more timely and informed intervention, with reduced healthcare costs and improved long-term outcomes. However, genomic medicine strains current models for demonstrating value, challenging efforts to achieve fair payment for services delivered, both for laboratory diagnostics and for use of molecular information in clinical management. Current models of healthcare reform stipulate that care must be delivered at equal or lower cost, with better patient and population outcomes. To achieve demonstrated value, genomic medicine must overcome many uncertainties: the clinical relevance of genomic variation; potential variation in technical performance and/or computational analysis; management of massive information sets; and must have available clinical interventions that can be informed by genomic analysis, so as to attain more favorable cost management of healthcare delivery and demonstrate improvements in cost-effectiveness.

Hepatitis B and hepatitis C viruses: a review of viral genomes, viral induced host immune responses, genotypic distributions and worldwide epidemiology

Directory of Open Access Journals (Sweden)

Umar Saeed

2014-04-01

Full Text Available Hepatitis B and hepatitis C viruses (HCV are frequently propagating blood borne pathogens in global community. Viral hepatitis is primarily associated with severe health complications, such as liver cirrhosis, hepatocellular carcinoma, hepatic fibrosis and steatosis. A literature review was conducted on hepatitis B virus (HBV, HBV genome, genotypic distribution and global epidemiology of HBV, HCV, HCV genome, HCV and host immune responses, HCV genotypic distribution and global epidemiology. The valued information was subjected for review. HBV has strict tissue tropism to liver. The virus infecting hepatocytes produces large amount of hepatitis B surface antigen particles which lack the DNA. It has capability to integrate into host genome. It has been found that genotype C is most emerging genotype associated with more severe liver diseases (cirrhosis. The approximate prevalence rate of genotype C is 27.7% which represents a major threat to future generations. Approximately 8% of population is chronic carrier of HBV in developing countries. The chronic carrier rate of HBV is 2%-7% in Middle East, Eastern and Southern Europe, South America and Japan. Among HCV infected individuals, 15% usually have natural tendency to overcome acute viral infection, where as 85% of individuals were unable to control HCV infection. The internal ribosomal entry site contains highly conserved structures important for binding and appropriate positioning of viral genome inside the host cell. HCV infects only in 1%-10% of hepatocytes, but production of tumor necrosis factor alpha (from CD8+ cells and interferon-gamma cause destruction of both infected cells and non-infected surrounding cells. Almost 11 genotypes and above 100 subtypes of HCV exists worldwide with different geographical distribution. Many efforts are still needed to minimize global burden of these infections. For the complete eradication of HBV (just like small pox and polio via vaccination strategies

A CTAB Procedure Of Total Genomic DNA Extraction For Medicinal Mushrooms

International Nuclear Information System (INIS)

Azhar Mohamad; Muhammad Hussaini Mohd Mustafa; Muhammad Hanif Azhari Noor; Rosnani Abdul Rashid; Hasan Hamdani Hasan Mutaat; Meswan Meskom; Mat Rasol Awang

2014-01-01

Medicinal mushroom is defined as mushrooms used in medicine or medical research. Isolation of intact, high-molecular-mass genomic DNA is essential for many molecular biology applications including Polymerase Chain Reaction (PCR), endonuclease restriction digestion, Southern blot analysis, and genomic library construction. The most important and prerequisite towards reliable molecular biology work is the total genomic DNA of a sample must be in good quality. Five freshly samples of medicinal mushroom were used in this work known as Auriculariapolytricha, Lentinus edode, Pleurotus sayorcaju, Sczhizopyllum commune and Ganodermalucidum. 5 mg of each sample were used to extraction the DNA, prepared in 3 replications and repeated twice. PCR based technique by using ISSR markers were used in checking the amplification ability of the total genomic extraction. A standard Doyle and Doyle protocol for genomic DNA extraction was modified in optimizing the total genomic DNA from the medicinal mushroom.The modification parameters were percentage of CTAB, incubation period and temperature. The results reveal that each sample required a certain combinations of time and period of incubation. Besides, percentage of CTAB in the buffer was found significant in giving a high yielding of extracted total genomic DNA. The extracted total genomic DNA from the medicinal mushroom yielded from 39.7 ng/ μl to 919.1 ng/ μl. The different yield among the samples found to be corresponded to polysaccharide content in the medicinal mushrooms. The objective of this works is to optimize total genomic DNA extraction of medicinal mushrooms towards a high quality intact genomic DNA for molecular activities. (author)

Chinese medicinal herbs for asymptomatic carriers of hepatitis B virus infection

DEFF Research Database (Denmark)

Liu, J P; McIntosh, H; Lin, Haili

2001-01-01

About 350 million people are chronically infected carriers of hepatitis B virus and are at a higher risk of serious illness and death from cirrhosis of the liver and liver cancer. Chinese medicinal herbs have been used widely for more than 2000 years to treat chronic liver disease.......About 350 million people are chronically infected carriers of hepatitis B virus and are at a higher risk of serious illness and death from cirrhosis of the liver and liver cancer. Chinese medicinal herbs have been used widely for more than 2000 years to treat chronic liver disease....

[Development of Plant Metabolomics and Medicinal Plant Genomics].

Science.gov (United States)

Saito, Kazuki

2018-01-01

 A variety of chemicals produced by plants, often referred to as 'phytochemicals', have been used as medicines, food, fuels and industrial raw materials. Recent advances in the study of genomics and metabolomics in plant science have accelerated our understanding of the mechanisms, regulation and evolution of the biosynthesis of specialized plant products. We can now address such questions as how the metabolomic diversity of plants is originated at the levels of genome, and how we should apply this knowledge to drug discovery, industry and agriculture. Our research group has focused on metabolomics-based functional genomics over the last 15 years and we have developed a new research area called 'Phytochemical Genomics'. In this review, the development of a research platform for plant metabolomics is discussed first, to provide a better understanding of the chemical diversity of plants. Then, representative applications of metabolomics to functional genomics in a model plant, Arabidopsis thaliana, are described. The extension of integrated multi-omics analyses to non-model specialized plants, e.g., medicinal plants, is presented, including the identification of novel genes, metabolites and networks for the biosynthesis of flavonoids, alkaloids, sulfur-containing metabolites and terpenoids. Further, functional genomics studies on a variety of medicinal plants is presented. I also discuss future trends in pharmacognosy and related sciences.

Functional RNA structures throughout the Hepatitis C Virus genome.

Science.gov (United States)

Adams, Rebecca L; Pirakitikulr, Nathan; Pyle, Anna Marie

2017-06-01

The single-stranded Hepatitis C Virus (HCV) genome adopts a set of elaborate RNA structures that are involved in every stage of the viral lifecycle. Recent advances in chemical probing, sequencing, and structural biology have facilitated analysis of RNA folding on a genome-wide scale, revealing novel structures and networks of interactions. These studies have underscored the active role played by RNA in every function of HCV and they open the door to new types of RNA-targeted therapeutics. Copyright © 2017 Elsevier B.V. All rights reserved.

Artificial intelligence, physiological genomics, and precision medicine.

Science.gov (United States)

Williams, Anna Marie; Liu, Yong; Regner, Kevin R; Jotterand, Fabrice; Liu, Pengyuan; Liang, Mingyu

2018-04-01

Big data are a major driver in the development of precision medicine. Efficient analysis methods are needed to transform big data into clinically-actionable knowledge. To accomplish this, many researchers are turning toward machine learning (ML), an approach of artificial intelligence (AI) that utilizes modern algorithms to give computers the ability to learn. Much of the effort to advance ML for precision medicine has been focused on the development and implementation of algorithms and the generation of ever larger quantities of genomic sequence data and electronic health records. However, relevance and accuracy of the data are as important as quantity of data in the advancement of ML for precision medicine. For common diseases, physiological genomic readouts in disease-applicable tissues may be an effective surrogate to measure the effect of genetic and environmental factors and their interactions that underlie disease development and progression. Disease-applicable tissue may be difficult to obtain, but there are important exceptions such as kidney needle biopsy specimens. As AI continues to advance, new analytical approaches, including those that go beyond data correlation, need to be developed and ethical issues of AI need to be addressed. Physiological genomic readouts in disease-relevant tissues, combined with advanced AI, can be a powerful approach for precision medicine for common diseases.

Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation

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Harrison, Abby; Lemey, Philippe; Hurles, Matthew; Moyes, Chris; Horn, Susanne; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Toatu, Tebuka; Penny, David; Rambaut, Andrew; Shapiro, Beth

2011-01-01

Hepatitis B virus (HBV) genomes are small, semi-double-stranded DNA circular genomes that contain alternating overlapping reading frames and replicate through an RNA intermediary phase. This complex biology has presented a challenge to estimating an evolutionary rate for HBV, leading to difficulties resolving the evolutionary and epidemiological history of the virus. Here, we re-examine rates of HBV evolution using a novel data set of 112 within-host, transmission history (pedigree) and among-host genomes isolated over 20 years from the indigenous peoples of the South Pacific, combined with 313 previously published HBV genomes. We employ Bayesian phylogenetic approaches to examine several potential causes and consequences of evolutionary rate variation in HBV. Our results reveal rate variation both between genotypes and across the genome, as well as strikingly slower rates when genomes are sampled in the Hepatitis B e antigen positive state, compared to the e antigen negative state. This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements. PMID:21765983

Genomic applications in forensic medicine

DEFF Research Database (Denmark)

Børsting, Claus; Morling, Niels

2016-01-01

Since the 1980s, advances in DNA technology have revolutionized the scope and practice of forensic medicine. From the days of restriction fragment length polymorphisms (RFLPs) to short tandem repeats (STRs), the current focus is on the next generation genome sequencing. It has been almost a decad...

Genomic Medicine Without Borders: Which Strategies Should Developing Countries Employ to Invest in Precision Medicine? A New "Fast-Second Winner" Strategy.

Science.gov (United States)

Mitropoulos, Konstantinos; Cooper, David N; Mitropoulou, Christina; Agathos, Spiros; Reichardt, Jürgen K V; Al-Maskari, Fatima; Chantratita, Wasun; Wonkam, Ambroise; Dandara, Collet; Katsila, Theodora; Lopez-Correa, Catalina; Ali, Bassam R; Patrinos, George P

2017-11-01

Genomic medicine has greatly matured in terms of its technical capabilities, but the diffusion of genomic innovations worldwide faces significant barriers beyond mere access to technology. New global development strategies are sorely needed for biotechnologies such as genomics and their applications toward precision medicine without borders. Moreover, diffusion of genomic medicine globally cannot adhere to a "one-size-fits-all-countries" development strategy, in the same way that drug treatments should be customized. This begs a timely, difficult but crucial question: How should developing countries, and the resource-limited regions of developed countries, invest in genomic medicine? Although a full-scale investment in infrastructure from discovery to the translational implementation of genomic science is ideal, this may not always be feasible in all countries at all times. A simple "transplantation of genomics" from developed to developing countries is unlikely to be feasible. Nor should developing countries be seen as simple recipients and beneficiaries of genomic medicine developed elsewhere because important advances in genomic medicine have materialized in developing countries as well. There are several noteworthy examples of genomic medicine success stories involving resource-limited settings that are contextualized and described in this global genomic medicine innovation analysis. In addition, we outline here a new long-term development strategy for global genomic medicine in a way that recognizes the individual country's pressing public health priorities and disease burdens. We term this approach the "Fast-Second Winner" model of innovation that supports innovation commencing not only "upstream" of discovery science but also "mid-stream," building on emerging highly promising biomarker and diagnostic candidates from the global science discovery pipeline, based on the unique needs of each country. A mid-stream entry into innovation can enhance collective

Hepatic sinusoidal obstruction syndrome caused by herbal medicine: CT and MRI features

International Nuclear Information System (INIS)

Zhou, Hua; Lou, Hai Yan; Wang, Yi Xiang J.; Xu, Xiao Jun; Zhang, Min Ming

2014-01-01

To describe the CT and MRI features of hepatic sinusoidal obstruction syndrome (HSOS) caused by herbal medicine Gynura segetum. The CT and MRI features of 16 consecutive Gynura segetum induced HSOS cases (12 men, 4 women) were analyzed. Eight patients had CT; three patients had MRI, and the remaining five patients had both CT and MRI examinations. Based on their clinical presentations and outcomes, the patients were classified into three categories: mild, moderate, and severe. The severity of the disease was also evaluated radiologically based on the abnormal hepatic patchy enhancement in post-contrast CT or MRI images. Ascites, patchy liver enhancement, and main right hepatic vein narrowing or occlusion were present in all 16 cases. Hepatomegaly and gallbladder wall thickening were present in 14 cases (87.5%, 14/16). Periportal high intensity on T2-weighted images was present in 6 cases (75%, 6/8). Normal liver parenchymal enhancement surrounding the main hepatic vein forming a clover-like sign was observed in 4 cases (25%, 4/16). The extent of patchy liver enhancement was statistically associated with clinical severity classification (kappa = 0.565). Ascites, patchy liver enhancement, and the main hepatic veins narrowing were the most frequent signs of herbal medicine induced HSOS. The grade of abnormal patchy liver enhancement was associated with the clinical severity.

Hepatic sinusoidal obstruction syndrome caused by herbal medicine: CT and MRI features

Energy Technology Data Exchange (ETDEWEB)

Zhou, Hua; Lou, Hai Yan [Dept. of Radiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou (China); Wang, Yi Xiang J. [Dept. of Radiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou (China); Xu, Xiao Jun; Zhang, Min Ming [Dept. of Radiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou (China)

2014-04-15

To describe the CT and MRI features of hepatic sinusoidal obstruction syndrome (HSOS) caused by herbal medicine Gynura segetum. The CT and MRI features of 16 consecutive Gynura segetum induced HSOS cases (12 men, 4 women) were analyzed. Eight patients had CT; three patients had MRI, and the remaining five patients had both CT and MRI examinations. Based on their clinical presentations and outcomes, the patients were classified into three categories: mild, moderate, and severe. The severity of the disease was also evaluated radiologically based on the abnormal hepatic patchy enhancement in post-contrast CT or MRI images. Ascites, patchy liver enhancement, and main right hepatic vein narrowing or occlusion were present in all 16 cases. Hepatomegaly and gallbladder wall thickening were present in 14 cases (87.5%, 14/16). Periportal high intensity on T2-weighted images was present in 6 cases (75%, 6/8). Normal liver parenchymal enhancement surrounding the main hepatic vein forming a clover-like sign was observed in 4 cases (25%, 4/16). The extent of patchy liver enhancement was statistically associated with clinical severity classification (kappa = 0.565). Ascites, patchy liver enhancement, and the main hepatic veins narrowing were the most frequent signs of herbal medicine induced HSOS. The grade of abnormal patchy liver enhancement was associated with the clinical severity.

Genome technologies and personalized dental medicine.

Science.gov (United States)

Eng, G; Chen, A; Vess, T; Ginsburg, G S

2012-04-01

The addition of genomic information to our understanding of oral disease is driving important changes in oral health care. It is anticipated that genome-derived information will promote a deeper understanding of disease etiology and permit earlier diagnosis, allowing for preventative measures prior to disease onset rather than treatment that attempts to repair the diseased state. Advances in genome technologies have fueled expectations for this proactive healthcare approach. Application of genomic testing is expanding and has already begun to find its way into the practice of clinical dentistry. To take full advantage of the information and technologies currently available, it is vital that dental care providers, consumers, and policymakers be aware of genomic approaches to understanding of oral diseases and the application of genomic testing to disease diagnosis and treatment. Ethical, legal, clinical, and educational initiatives are also required to responsibly incorporate genomic information into the practice of dentistry. This article provides an overview of the application of genomic technologies to oral health care and introduces issues that require consideration if we are to realize the full potential of genomics to enable the practice of personalized dental medicine. © 2011 John Wiley & Sons A/S.

Global Implementation of Genomic Medicine: We Are Not Alone

Science.gov (United States)

Manolio, Teri A.; Abramowicz, Marc; Al-Mulla, Fahd; Anderson, Warwick; Balling, Rudi; Berger, Adam C.; Bleyl, Steven; Chakravarti, Aravinda; Chantratita, Wasun; Chisholm, Rex L.; Dissanayake, Vajira H. W.; Dunn, Michael; Dzau, Victor J.; Han, Bok-Ghee; Hubbard, Tim; Kolbe, Anne; Korf, Bruce; Kubo, Michiaki; Lasko, Paul; Leego, Erkki; Mahasirimongkol, Surakameth; Majumdar, Partha P.; Matthijs, Gert; McLeod, Howard L.; Metspalu, Andres; Meulien, Pierre; Miyano, Satoru; Naparstek, Yaakov; O’Rourke, P. Pearl; Patrinos, George P.; Rehm, Heidi L.; Relling, Mary V.; Rennert, Gad; Rodriguez, Laura Lyman; Roden, Dan M.; Shuldiner, Alan R.; Sinha, Sukdev; Tan, Patrick; Ulfendahl, Mats; Ward, Robyn; Williams, Marc S.; Wong, John E.L.; Green, Eric D.; Ginsburg, Geoffrey S.

2016-01-01

Advances in high-throughput genomic technologies coupled with a growing number of genomic results potentially useful in clinical care have led to ground-breaking genomic medicine implementation programs in various nations. Many of these innovative programs capitalize on unique local capabilities arising from the structure of their health care systems or their cultural or political milieu, as well as from unusual burdens of disease or risk alleles. Many such programs are being conducted in relative isolation and might benefit from sharing of approaches and lessons learned in other nations. The National Human Genome Research Institute recently brought together 25 of these groups from around the world to describe and compare projects, examine the current state of implementation and desired near-term capabilities, and identify opportunities for collaboration to promote the responsible implementation of genomic medicine. The wide variety of nascent programs in diverse settings demonstrates that implementation of genomic medicine is expanding globally in varied and highly innovative ways. Opportunities for collaboration abound in the areas of evidence generation, health information technology, education, workforce development, pharmacogenomics, and policy and regulatory issues. Several international organizations that are already facilitating effective research collaborations should engage to ensure implementation proceeds collaboratively without potentially wasteful duplication. Efforts to coalesce these groups around concrete but compelling signature projects, such as global eradication of genetically-mediated drug reactions or developing a truly global genomic variant data resource across a wide number of ethnicities, would accelerate appropriate implementation of genomics to improve clinical care world-wide. PMID:26041702

Frequency and pattern of Chinese herbal medicine prescriptions for chronic hepatitis in Taiwan.

Science.gov (United States)

Chen, Fang-Pey; Kung, Yen-Ying; Chen, Yu-Chun; Jong, Maw-Shiou; Chen, Tzeng-Ji; Chen, Fun-Jou; Hwang, Shinn-Jang

2008-04-17

Chinese herbal medicine (CHM) has been commonly used in treating liver diseases in Asian countries. To conduct a large-scale pharmacoepidemiological study and evaluate the frequency and pattern of CHM prescriptions in treating chronic hepatitis. We obtained the database of traditional Chinese medicine outpatient claims from the national health insurance in Taiwan for the whole 2002. Patients with chronic hepatitis were identified by the corresponding diagnosis of International Classification of Disease among claimed visiting files. Corresponding prescription files were analyzed, and association rule were applied to evaluate the co-prescription of CHM in treating chronic hepatitis. Among the 91,080 subjects treated by CHM for chronic hepatitis, the peak age was in the 40 s, followed by 30 s and 50 s. Male/female ratio was 2.07:1. Long-dan-xie-gan-tang and Saliva miltiorrhiza (Dan-shen) were the most commonly prescribed Chinese herbal formula and single herbal drug, respectively. The most common two-drug prescription was Jia-wei-xia-yao-san plus Saliva miltiorrhiza, and the most common three-drug prescription was Jia-wei-xia-yao-san plus Saliva miltiorrhiza and Artemisia capillaries (Yin-chen-hao). This study showed the utilization pattern of Chinese herbal drugs or formulae in treating chronic hepatitis. Further researches and clinical trials are needed to evaluate the efficacy of these Chinese herbs or its ingredients in treating chronic hepatitis.

Recent advances of genomic testing in perinatal medicine.

Science.gov (United States)

Peters, David G; Yatsenko, Svetlana A; Surti, Urvashi; Rajkovic, Aleksandar

2015-02-01

Rapid progress in genomic medicine in recent years has made it possible to diagnose subtle genetic abnormalities in a clinical setting on routine basis. This has allowed for detailed genotype-phenotype correlations and the identification of the genetic basis of many congenital anomalies. In addition to the availability of chromosomal microarray analysis, exome and whole-genome sequencing on pre- and postnatal samples of cell-free DNA has revolutionized the field of prenatal diagnosis. Incorporation of these technologies in perinatal pathology is bound to play a major role in coming years. In this communication, we briefly present the current experience with use of classical chromosome analysis, fluorescence in situ hybridization, and microarray testing, development of whole-genome analysis by next-generation sequencing technology, offer a detailed review of the history and current status of non-invasive prenatal testing using cell-free DNA, and discuss the advents of these new genomic technologies in perinatal medicine. Copyright © 2014 Elsevier Inc. All rights reserved.

Genome-to-genome analysis highlights the impact of the human innate and adaptive immune systems on the hepatitis C virus

Science.gov (United States)

Ip, Camilla; Magri, Andrea; Von Delft, Annette; Bonsall, David; Chaturvedi, Nimisha; Bartha, Istvan; Smith, David; Nicholson, George; McVean, Gilean; Trebes, Amy; Piazza, Paolo; Fellay, Jacques; Cooke, Graham; Foster, Graham R; Hudson, Emma; McLauchlan, John; Simmonds, Peter; Bowden, Rory; Klenerman, Paul; Barnes, Eleanor; Spencer, Chris C. A.

2018-01-01

Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. We use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals chronically infected with HCV, predominately genotype 3. We show that both HLA alleles and interferon lambda innate immune system genes drive viral genome polymorphism, and that IFNL4 genotypes determine HCV viral load through a mechanism that is dependent on a specific polymorphism in the HCV polyprotein. We highlight the interplay between innate immune responses and the viral genome in HCV control. PMID:28394351

Empowering Mayo Clinic Individualized Medicine with Genomic Data Warehousing

Directory of Open Access Journals (Sweden)

Iain Horton

2017-08-01

Full Text Available Individualized medicine enables better diagnoses and treatment decisions for patients and promotes research in understanding the molecular underpinnings of disease. Linking individual patient’s genomic and molecular information with their clinical phenotypes is crucial to these efforts. To address this need, the Center for Individualized Medicine at Mayo Clinic has implemented a genomic data warehouse and a workflow management system to bring data from institutional electronic health records and genomic sequencing data from both clinical and research bioinformatics sources into the warehouse. The system is the foundation for Mayo Clinic to build a suite of tools and interfaces to support various clinical and research use cases. The genomic data warehouse is positioned to play a key role in enhancing the research capabilities and advancing individualized patient care at Mayo Clinic.

Empowering Mayo Clinic Individualized Medicine with Genomic Data Warehousing.

Science.gov (United States)

Horton, Iain; Lin, Yaxiong; Reed, Gay; Wiepert, Mathieu; Hart, Steven

2017-08-22

Individualized medicine enables better diagnoses and treatment decisions for patients and promotes research in understanding the molecular underpinnings of disease. Linking individual patient's genomic and molecular information with their clinical phenotypes is crucial to these efforts. To address this need, the Center for Individualized Medicine at Mayo Clinic has implemented a genomic data warehouse and a workflow management system to bring data from institutional electronic health records and genomic sequencing data from both clinical and research bioinformatics sources into the warehouse. The system is the foundation for Mayo Clinic to build a suite of tools and interfaces to support various clinical and research use cases. The genomic data warehouse is positioned to play a key role in enhancing the research capabilities and advancing individualized patient care at Mayo Clinic.

Environmental Medicine Genome Bank (EMGB): Current Composition

National Research Council Canada - National Science Library

Sonna, Larry

2000-01-01

The USARIEM Environmental Medicine Genome Bank (EMGB) project is an ongoing effort to identify and characterize genes relevant to environmental injuries and illnesses and to human physical performance...

Genome Editing Redefines Precision Medicine in the Cardiovascular Field

Directory of Open Access Journals (Sweden)

Elda Dzilic

2018-01-01

Full Text Available Genome editing is a powerful tool to study the function of specific genes and proteins important for development or disease. Recent technologies, especially CRISPR/Cas9 which is characterized by convenient handling and high precision, revolutionized the field of genome editing. Such tools have enormous potential for basic science as well as for regenerative medicine. Nevertheless, there are still several hurdles that have to be overcome, but patient-tailored therapies, termed precision medicine, seem to be within reach. In this review, we focus on the achievements and limitations of genome editing in the cardiovascular field. We explore different areas of cardiac research and highlight the most important developments: (1 the potential of genome editing in human pluripotent stem cells in basic research for disease modelling, drug screening, or reprogramming approaches and (2 the potential and remaining challenges of genome editing for regenerative therapies. Finally, we discuss social and ethical implications of these new technologies.

[Genomic research of traditional Chinese medicines in vivo metabolism].

Science.gov (United States)

Xiao, Shui-Ming; Bai, Rui; Zhang, Xiao-Yan

2016-11-01

Gene is the base of in vivo metabolism and effectiveness for traditional Chinese medicines (TCM), and the gene expression, regulation and modification are used as the research directions to perform the TCM multi-component, multi-link and multi-target in vivo metabolism studies, which will improve the research on TCM metabolic proecess, effect target and molecular mechanism. Humans are superorganisms with 1% genes inherited from parents and 99% genes from various parts of the human body, mainly coming from the microorganisms in intestinal flora. These indicate that genetically inherited human genome and "second genome" could affect the TCM in vivo metabolism from inheritance and "environmental" aspects respectively. In the present paper, typical case study was used to discuss related TCM in vivo metabolic genomics research, mainly including TCM genomics research and gut metagenomics research, as well as the personalized medicine evoked from the individual difference of above genomics (metagenomics). Copyright© by the Chinese Pharmaceutical Association.

Personalized Medicine in a New Genomic Era: Ethical and Legal Aspects.

Science.gov (United States)

Shoaib, Maria; Rameez, Mansoor Ali Merchant; Hussain, Syed Ather; Madadin, Mohammed; Menezes, Ritesh G

2017-08-01

The genome of two completely unrelated individuals is quite similar apart from minor variations called single nucleotide polymorphisms which contribute to the uniqueness of each and every person. These single nucleotide polymorphisms are of great interest clinically as they are useful in figuring out the susceptibility of certain individuals to particular diseases and for recognizing varied responses to pharmacological interventions. This gives rise to the idea of 'personalized medicine' as an exciting new therapeutic science in this genomic era. Personalized medicine suggests a unique treatment strategy based on an individual's genetic make-up. Its key principles revolve around applied pharmaco-genomics, pharmaco-kinetics and pharmaco-proteomics. Herein, the ethical and legal aspects of personalized medicine in a new genomic era are briefly addressed. The ultimate goal is to comprehensively recognize all relevant forms of genetic variation in each individual and be able to interpret this information in a clinically meaningful manner within the ambit of ethical and legal considerations. The authors of this article firmly believe that personalized medicine has the potential to revolutionize the current landscape of medicine as it makes its way into clinical practice.

Genome-wide association study of the four-constitution medicine.

Science.gov (United States)

Yin, Chang Shik; Park, Hi Joon; Chung, Joo-Ho; Lee, Hye-Jung; Lee, Byung-Cheol

2009-12-01

Four-constitution medicine (FCM), also known as Sasang constitutional medicine, and the heritage of the long history of individualized acupuncture medicine tradition, is one of the holistic and traditional systems of constitution to appraise and categorize individual differences into four major types. This study first reports a genome-wide association study on FCM, to explore the genetic basis of FCM and facilitate the integration of FCM with conventional individual differences research. Healthy individuals of the Korean population were classified into the four constitutional types (FCTs). A total of 353,202 single nucleotide polymorphisms (SNPs) were typed using whole genome amplified samples, and six-way comparison of FCM types provided lists of significantly differential SNPs. In one-to-one FCT comparisons, 15,944 SNPs were significantly differential, and 5 SNPs were commonly significant in all of the three comparisons. In one-to-two FCT comparisons, 22,616 SNPs were significantly differential, and 20 SNPs were commonly significant in all of the three comparison groups. This study presents the association between genome-wide SNP profiles and the categorization of the FCM, and it could further provide a starting point of genome-based identification and research of the constitutions of FCM.

Are electronic health records ready for genomic medicine?

Science.gov (United States)

Scheuner, Maren T; de Vries, Han; Kim, Benjamin; Meili, Robin C; Olmstead, Sarah H; Teleki, Stephanie

2009-07-01

The goal of this project was to assess genetic/genomic content in electronic health records. Semistructured interviews were conducted with key informants. Questions addressed documentation, organization, display, decision support and security of family history and genetic test information, and challenges and opportunities relating to integrating genetic/genomics content in electronic health records. There were 56 participants: 10 electronic health record specialists, 18 primary care clinicians, 16 medical geneticists, and 12 genetic counselors. Few clinicians felt their electronic record met their current genetic/genomic medicine needs. Barriers to integration were mostly related to problems with family history data collection, documentation, and organization. Lack of demand for genetics content and privacy concerns were also mentioned as challenges. Data elements and functionality requirements that clinicians see include: pedigree drawing; clinical decision support for familial risk assessment and genetic testing indications; a patient portal for patient-entered data; and standards for data elements, terminology, structure, interoperability, and clinical decision support rules. Although most said that there is little impact of genetics/genomics on electronic records today, many stated genetics/genomics would be a driver of content in the next 5-10 years. Electronic health records have the potential to enable clinical integration of genetic/genomic medicine and improve delivery of personalized health care; however, structured and standardized data elements and functionality requirements are needed.

Opening plenary speaker: Human genomics, precision medicine, and advancing human health.

Science.gov (United States)

Green, Eric D

2016-08-01

Starting with the launch of the Human Genome Project in 1990, the past quarter-century has brought spectacular achievements in genomics that dramatically empower the study of human biology and disease. The human genomics enterprise is now in the midst of an important transition, as the growing foundation of genomic knowledge is being used by researchers and clinicians to tackle increasingly complex problems in biomedicine. Of particular prominence is the use of revolutionary new DNA sequencing technologies for generating prodigious amounts of DNA sequence data to elucidate the complexities of genome structure, function, and evolution, as well as to unravel the genomic bases of rare and common diseases. Together, these developments are ushering in the era of genomic medicine. Augmenting the advances in human genomics have been innovations in technologies for measuring environmental and lifestyle information, electronic health records, and data science; together, these provide opportunities of unprecedented scale and scope for investigating the underpinnings of health and disease. To capitalize on these opportunities, U.S. President Barack Obama recently announced a major new research endeavor - the U.S. Precision Medicine Initiative. This bold effort will be framed around several key aims, which include accelerating the use of genomically informed approaches to cancer care, making important policy and regulatory changes, and establishing a large research cohort of >1 million volunteers to facilitate precision medicine research. The latter will include making the partnership with all participants a centerpiece feature in the cohort's design and development. The Precision Medicine Initiative represents a broad-based research program that will allow new approaches for individualized medical care to be rigorously tested, so as to establish a new evidence base for advancing clinical practice and, eventually, human health.

Breast Cancer in Africa: Limitations and Opportunities for Application of Genomic Medicine

Directory of Open Access Journals (Sweden)

Allison Silverstein

2016-01-01

Full Text Available As genomic medicine gains clinical applicability across a spectrum of diseases, insufficient application in low-income settings stands to increase health disparity. Breast cancer screening, diagnosis, and treatment have benefited greatly from genomic medicine in high-income settings. As breast cancer is a leading cause of both cancer incidence and mortality in Africa, attention and resources must be applied to research and clinical initiatives to integrate genomic medicine into breast cancer care. In terms of research, there is a paucity of investigations into genetic determinants of breast cancer specific to African populations, despite consensus in the literature that predisposition and susceptibility genes vary between populations. Therefore, we need targeted strengthening of existing research efforts and support of new initiatives. Results will improve clinical care through screening and diagnosis with genetic testing specific to breast cancer in African populations. Clinically, genomic medicine can provide information capable of improving resource allocation to the population which most stands to benefit from increased screening or tailored treatment modalities. In situations where mammography or chemotherapy options are limited, this information will allow for the greatest impact. Implementation of genomic medicine will face numerous systemic barriers but is essential to improve breast cancer outcomes and survival.

Transfusion medicine

International Nuclear Information System (INIS)

Murawski, K.; Peetoom, F.

1986-01-01

These proceedings contain 24 selections, including papers presented at the conference of American Red Cross held in May 1985, on the Subject of transfusion medicine. Some of the titles are: Fluosol/sup R/-DA in Radiation Therapy; Expression of Cloned Human Factor VIII and the Molecular Basis of Gene Defects that Cause Hemophilia; DNA-Probing Assay in the Detection of Hepatitis B Virus Genome in Human Peripheral Blood Cells; and Monoclonal Antibodies: Convergence of Technology and Application

Expression of the hepatitis B virus genome in chronic hepatitis B carriers and patients with hepatocellular carcinoma

International Nuclear Information System (INIS)

Bowyer, S.M.; Dusheiko, G.M.; Schoub, B.D.; Kew, M.C.

1987-01-01

The authors examined the methylation status of CCGG sites in hepatitis B virus (HBV) DNA to determine whether methylation could be responsible for the selective expression of the HBV surface gene in chronic hepatitis B infection and hepatocellular carcinoma. Infected liver tissue from patients with low levels of viral replication was analyzed for HBV DNA copy number per haploid cell genome. Total cellular DNA, with sufficient HBV DNA, was digested with the restriction endonucleases Msp I and Hpa II, to determine whether the HBV DNA was methylated, or HindIII, to determine whether the HBV DNA was integrated or episomal. The cleavage fragments were analyzed by Southern blotting and hybridization to 32 P-labeled HBV DNA. In replicative chronic hepatitis B, hypomethylation of the HBV genome correlated with HBV expression in both virions and infected tissue. In carriers with nonreplicative infection, it was difficult to ascertain the role of methylation as copy number was low. HBV DNA copy number was also low in 17 out of 29 of the rumor tissues tested and as many as 14 out of 16 of the adjacent non-neoplastic tissues tested. Integrated sequences were hypermethylated in the PLC/PRF/5 cell line and in six of the tumor tissues suggesting that methylation plays a role in HBV gene repression. However, since DNA from five other tumors was hypomethylated, the belief that methylation per se is an absolute determinant of HBV core gene repression does not hold for human hepatocellular carcinoma tissue

Cancer 2015: a longitudinal whole-of-system study of genomic cancer medicine.

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Thomas, David M; Fox, Stephen; Lorgelly, Paula K; Ashley, David; Richardson, Gary; Lipton, Lara; Parisot, John P; Lucas, Mark; McNeil, John; Wright, Michael

2015-12-01

Genomic cancer medicine promises revolutionary change in oncology. The impacts of 'personalized medicine', based upon a molecular classification of cancer and linked to targeted therapies, will extend from individual patient outcomes to the health economy at large. To address the 'whole-of-system' impact of genomic cancer medicine, we have established a prospective cohort of patients with newly diagnosed cancer in the state of Victoria, Australia, about whom we have collected a broad range of clinical, demographic, molecular, and patient-reported data, as well as data on health resource utilization. Our goal is to create a model for investigating public investment in genomic medicine that maximizes the cost:benefit ratio for the Australian community at large. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hepatitis A Virus Genome Organization and Replication Strategy.

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McKnight, Kevin L; Lemon, Stanley M

2018-04-02

Hepatitis A virus (HAV) is a positive-strand RNA virus classified in the genus Hepatovirus of the family Picornaviridae It is an ancient virus with a long evolutionary history and multiple features of its capsid structure, genome organization, and replication cycle that distinguish it from other mammalian picornaviruses. HAV proteins are produced by cap-independent translation of a single, long open reading frame under direction of an inefficient, upstream internal ribosome entry site (IRES). Genome replication occurs slowly and is noncytopathic, with transcription likely primed by a uridylated protein primer as in other picornaviruses. Newly produced quasi-enveloped virions (eHAV) are released from cells in a nonlytic fashion in a unique process mediated by interactions of capsid proteins with components of the host cell endosomal sorting complexes required for transport (ESCRT) system. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus.

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Ansari, M Azim; Pedergnana, Vincent; L C Ip, Camilla; Magri, Andrea; Von Delft, Annette; Bonsall, David; Chaturvedi, Nimisha; Bartha, Istvan; Smith, David; Nicholson, George; McVean, Gilean; Trebes, Amy; Piazza, Paolo; Fellay, Jacques; Cooke, Graham; Foster, Graham R; Hudson, Emma; McLauchlan, John; Simmonds, Peter; Bowden, Rory; Klenerman, Paul; Barnes, Eleanor; Spencer, Chris C A

2017-05-01

Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. Here we use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals who were chronically infected with HCV, predominantly genotype 3. We show that both alleles of genes encoding human leukocyte antigen molecules and genes encoding components of the interferon lambda innate immune system drive viral polymorphism. Additionally, we show that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific amino acid residue in the HCV NS5A protein. These findings highlight the interplay between the innate immune system and the viral genome in HCV control.

Endogenous hepatitis C virus homolog fragments in European rabbit and hare genomes replicate in cell culture.

Directory of Open Access Journals (Sweden)

Eliane Silva

Full Text Available Endogenous retroviruses, non-retroviral RNA viruses and DNA viruses have been found in the mammalian genomes. The origin of Hepatitis C virus (HCV, the major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma in humans, remains unclear since its discovery. Here we show that fragments homologous to HCV structural and non-structural (NS proteins present in the European rabbit (Oryctolagus cuniculus and hare (Lepus europaeus genomes replicate in bovine cell cultures. The HCV genomic homolog fragments were demonstrated by RT-PCR, PCR, mass spectrometry, and replication in bovine cell cultures by immunofluorescence assay (IFA and immunogold electron microscopy (IEM using specific MAbs for HCV NS3, NS4A, and NS5 proteins. These findings may lead to novel research approaches on the HCV origin, genesis, evolution and diversity.

An Alternative Methodological Approach for Cost-Effectiveness Analysis and Decision Making in Genomic Medicine.

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Fragoulakis, Vasilios; Mitropoulou, Christina; van Schaik, Ron H; Maniadakis, Nikolaos; Patrinos, George P

2016-05-01

Genomic Medicine aims to improve therapeutic interventions and diagnostics, the quality of life of patients, but also to rationalize healthcare costs. To reach this goal, careful assessment and identification of evidence gaps for public health genomics priorities are required so that a more efficient healthcare environment is created. Here, we propose a public health genomics-driven approach to adjust the classical healthcare decision making process with an alternative methodological approach of cost-effectiveness analysis, which is particularly helpful for genomic medicine interventions. By combining classical cost-effectiveness analysis with budget constraints, social preferences, and patient ethics, we demonstrate the application of this model, the Genome Economics Model (GEM), based on a previously reported genome-guided intervention from a developing country environment. The model and the attendant rationale provide a practical guide by which all major healthcare stakeholders could ensure the sustainability of funding for genome-guided interventions, their adoption and coverage by health insurance funds, and prioritization of Genomic Medicine research, development, and innovation, given the restriction of budgets, particularly in developing countries and low-income healthcare settings in developed countries. The implications of the GEM for the policy makers interested in Genomic Medicine and new health technology and innovation assessment are also discussed.

The complete chloroplast genome of a medicinal plant Epimedium koreanum Nakai (Berberidaceae).

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Lee, Jung-Hoon; Kim, Kyunghee; Kim, Na-Rae; Lee, Sang-Choon; Yang, Tae-Jin; Kim, Young-Dong

2016-11-01

Epimedium koreanum is a perennial medicinal plant distributed in Eastern Asia. The complete chloroplast genome sequences of E. koreanum was obtained by de novo assembly using whole genome next-generation sequences. The chloroplast genome of E. koreanum was 157 218 bp in length and separated into four distinct regions such as large single copy region (89 600 bp), small single copy region (17 222 bp) and a pair of inverted repeat regions (25 198 bp). The genome contained a total of 112 genes including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that E. koreanum is most closely related to Berberis bealei, a traditional medicinal plant in the Berberidaceae family.

Knowledge, attitudes and barriers regarding vaccination against hepatitis A and B in patients with chronic hepatitis C virus infection: a survey of family medicine and internal medicine physicians in the United States.

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Tenner, C T; Herzog, K; Chaudhari, S; Bini, E J; Weinshel, E H

2012-10-01

Although vaccination against hepatitis A virus (HAV) and hepatitis B virus (HBV) is recommended for all patients with chronic hepatitis C virus (HCV) infection, physician vaccination practices are suboptimal. Since training for family medicine (FM) and internal medicine (IM) physicians differ, we hypothesised that there are differences in knowledge, attitudes and barriers regarding vaccination against HAV and HBV in patients with chronic HCV between these two groups. A two-page questionnaire was mailed to 3000 primary care (FM and IM) physicians randomly selected from the AMA Physician Masterfile in 2005. The survey included questions about physician demographics, knowledge and attitudes regarding vaccination. Among the 3000 physicians surveyed, 1209 (42.2%) returned completed surveys. There were no differences between respondents and non-respondents with regard to age, gender, geographic location or specialty. More FM than IM physicians stated that HCV+ patients should not be vaccinated against HAV (23.7% vs. 11.8%, p infection, physicians often do not test or vaccinate susceptible individuals. Interventions are needed to overcome the barriers identified and improve vaccination rates. © 2012 Blackwell Publishing Ltd.

Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B.

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Krause-Kyora, Ben; Susat, Julian; Key, Felix M; Kühnert, Denise; Bosse, Esther; Immel, Alexander; Rinne, Christoph; Kornell, Sabin-Christin; Yepes, Diego; Franzenburg, Sören; Heyne, Henrike O; Meier, Thomas; Lösch, Sandra; Meller, Harald; Friederich, Susanne; Nicklisch, Nicole; Alt, Kurt W; Schreiber, Stefan; Tholey, Andreas; Herbig, Alexander; Nebel, Almut; Krause, Johannes

2018-05-10

The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genomes by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results show that HBV circulates in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. These ancient virus forms appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses. © 2018, Krause-Kyora et al.

Antiviral potential of medicinal plants against HIV, HSV, influenza, hepatitis, and coxsackievirus: A systematic review.

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Akram, Muhammad; Tahir, Imtiaz Mahmood; Shah, Syed Muhammad Ali; Mahmood, Zahed; Altaf, Awais; Ahmad, Khalil; Munir, Naveed; Daniyal, Muhammad; Nasir, Suhaila; Mehboob, Huma

2018-05-01

Viral infections are being managed therapeutically through available antiviral regimens with unsatisfactory clinical outcomes. The refractory viral infections resistant to available antiviral drugs are alarming threats and a serious health concern. For viral hepatitis, the interferon and vaccine therapies solely are not ultimate solutions due to recurrence of hepatitis C virus. Owing to the growing incidences of viral infections and especially of resistant viral strains, the available therapeutic modalities need to be improved, complemented with the discovery of novel antiviral agents to combat refractory viral infections. It is widely accepted that medicinal plant heritage is nature gifted, precious, and fueled with the valuable resources for treatment of metabolic and infectious disorders. The aims of this review are to assemble the facts and to conclude the therapeutic potential of medicinal plants in the eradication and management of various viral diseases such as influenza, human immunodeficiency virus (HIV), herpes simplex virus (HSV), hepatitis, and coxsackievirus infections, which have been proven in diverse clinical studies. The articles, published in the English language since 1982 to 2017, were included from Web of Science, Cochrane Library, AMED, CISCOM, EMBASE, MEDLINE, Scopus, and PubMed by using relevant keywords including plants possessing antiviral activity, the antiviral effects of plants, and plants used in viral disorders. The scientific literature mainly focusing on plant extracts and herbal products with therapeutic efficacies against experimental models of influenza, HIV, HSV, hepatitis, and coxsackievirus were included in the study. Pure compounds possessing antiviral activity were excluded, and plants possessing activity against viruses other than viruses in inclusion criteria were excluded. Hundreds of plant extracts with antiviral effect were recognized. However, the data from only 36 families investigated through in vitro and in vivo

The current state of funded NIH grants in implementation science in genomic medicine: a portfolio analysis.

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Roberts, Megan C; Clyne, Mindy; Kennedy, Amy E; Chambers, David A; Khoury, Muin J

2017-10-26

PurposeImplementation science offers methods to evaluate the translation of genomic medicine research into practice. The extent to which the National Institutes of Health (NIH) human genomics grant portfolio includes implementation science is unknown. This brief report's objective is to describe recently funded implementation science studies in genomic medicine in the NIH grant portfolio, and identify remaining gaps.MethodsWe identified investigator-initiated NIH research grants on implementation science in genomic medicine (funding initiated 2012-2016). A codebook was adapted from the literature, three authors coded grants, and descriptive statistics were calculated for each code.ResultsForty-two grants fit the inclusion criteria (~1.75% of investigator-initiated genomics grants). The majority of included grants proposed qualitative and/or quantitative methods with cross-sectional study designs, and described clinical settings and primarily white, non-Hispanic study populations. Most grants were in oncology and examined genetic testing for risk assessment. Finally, grants lacked the use of implementation science frameworks, and most examined uptake of genomic medicine and/or assessed patient-centeredness.ConclusionWe identified large gaps in implementation science studies in genomic medicine in the funded NIH portfolio over the past 5 years. To move the genomics field forward, investigator-initiated research grants should employ rigorous implementation science methods within diverse settings and populations.Genetics in Medicine advance online publication, 26 October 2017; doi:10.1038/gim.2017.180.

Coverage of genomic medicine: information gap between lay public and scientists.

Science.gov (United States)

Sugawara, Yuya; Narimatsu, Hiroto; Fukao, Akira

2012-01-01

The sharing of information between the lay public and medical professionals is crucial to the conduct of personalized medicine using genomic information in the near future. Mass media, such as newspapers, can play an important role in disseminating scientific information. However, studies on the role of newspaper coverage of genome-related articles are highly limited. We investigated the coverage of genomic medicine in five major Japanese newspapers (Asahi, Mainichi, Yomiuri, Sankei, and Nikkei) using Nikkei Telecom and articles in scientific journals in PubMed from 1995 to 2009. The number of genome-related articles in all five newspapers temporarily increased in 2000, and began continuously decreasing thereafter from 2001 to 2009. Conversely, there was a continuous increasing trend in the number of genome-related articles in PubMed during this period. The numbers of genome-related articles among the five major newspapers from 1995 to 2009 were significantly different (P = 0.002). Commentaries, research articles, and articles about companies were the most frequent in 2001 and 2003, when the number of genome-related articles transiently increased in the five newspapers. This study highlights the significant gap between newspaper coverage and scientific articles in scientific journals.

Understanding patient and provider perceptions and expectations of genomic medicine.

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Hall, Michael J; Forman, Andrea D; Montgomery, Susan V; Rainey, Kim L; Daly, Mary B

2015-01-01

Advances in genome sequencing technology have fostered a new era of clinical genomic medicine. Genetic counselors, who have begun to support patients undergoing multi-gene panel testing for hereditary cancer risk, will review brief clinical vignettes, and discuss early experiences with clinical genomic testing. Their experiences will frame a discussion about how current testing may challenge patient understanding and expectations toward the evaluation of cancer risk and downstream preventive behaviors. © 2014 Wiley Periodicals, Inc.

Using Genome Sequence to Enable the Design of Medicines and Chemical Probes.

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Angelbello, Alicia J; Chen, Jonathan L; Childs-Disney, Jessica L; Zhang, Peiyuan; Wang, Zi-Fu; Disney, Matthew D

2018-02-28

Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.

The Third International Genomic Medicine Conference (3rd IGMC, 2015: overall activities and outcome highlights

Directory of Open Access Journals (Sweden)

Muhammad Abu-Elmagd

2016-10-01

Full Text Available Abstract The Third International Genomic Medicine Conference (3rd IGMC was organised by the Centre of Excellence in Genomic Medicine Research (CEGMR at the King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia (KSA. This conference is a continuation of a series of meetings, which began with the first International Genomic Medicine Conference (1st IGMC, 2011 followed by the second International Genomic Medicine Conference (2nd IGMC, 2013. The 3rd IGMC meeting presented as a timely opportunity to bring scientists from across the world to gather, discuss, and exchange recent advances in the field of genomics and genetics in general as well as practical information on using these new technologies in different basic and clinical applications. The meeting undoubtedly inspired young male and female Saudi researchers, who attended the conference in large numbers, as evidenced by the oversubscribed oral and poster presentations. The conference also witnessed the launch of the first content for npj Genomic Medicine, a high quality new journal was established in partnership by CEGMR with Springer Nature and published as part of the Nature Partner Journal series. Here, we present a brief summary report of the 2-day meeting including highlights from the oral presentations, poster presentations, workshops, poster prize-winners and comments from the distinguished scientists.

A critique of race-based and genomic medicine.

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Meier, Robert J

2012-03-01

Now that a composite human genome has been sequenced (HGP), research has accelerated to discover precise genetic bases of several chronic health issues, particularly in the realms of cancer and cardiovascular disease. It is anticipated that in the future it will be possible and cost effective to regularly sequence individual genomes, and thereby produce a DNA profile that potentially can be used to assess the health risks for each person with respect to certain genetically predisposed conditions. Coupled with that enormous diagnostic power, it will then depend upon equally rapid research efforts to develop personalized courses of treatment, including that of pharmaceutical therapy. Initial treatment attempts have been made to match drug efficacy and safety to individuals of assigned or self-identified groups according to their genetic ancestry or presumed race. A prime example is that of BiDil, which was the first drug approved by the US FDA for the explicit treatment of heart patients of African American ancestry. This race-based approach to medicine has been met with justifiable criticism, notably on ethical grounds that have long plagued historical applications and misuses of human race classification, and also on questionable science. This paper will assess race-based medical research and practice in light of a more thorough understanding of human genetic variability. Additional concerns will be expressed with regard to the rapidly developing area of pharmacogenomics, promoted to be the future of personalized medicine. Genomic epidemiology will be discussed with several examples of on-going research that hopefully will provide a solid scientific grounding for personalized medicine to build upon.

Full-length genomic sequence of hepatitis B virus genotype C2 isolated from a native Brazilian patient

Directory of Open Access Journals (Sweden)

Mónica Viviana Alvarado-Mora

2011-06-01

Full Text Available The hepatitis B virus (HBV is among the leading causes of chronic hepatitis, cirrhosis and hepatocellular carcinoma. In Brazil, genotype A is the most frequent, followed by genotypes D and F. Genotypes B and C are found in Brazil exclusively among Asian patients and their descendants. The aim of this study was to sequence the entire HBV genome of a Caucasian patient infected with HBV/C2 and to infer the origin of the virus based on sequencing analysis. The sequence of this Brazilian isolate was grouped with four other sequences described in China. The sequence of this patient is the first complete genome of HBV/C2 reported in Brazil.

The NCI Genomic Data Commons as an engine for precision medicine.

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Jensen, Mark A; Ferretti, Vincent; Grossman, Robert L; Staudt, Louis M

2017-07-27

The National Cancer Institute Genomic Data Commons (GDC) is an information system for storing, analyzing, and sharing genomic and clinical data from patients with cancer. The recent high-throughput sequencing of cancer genomes and transcriptomes has produced a big data problem that precludes many cancer biologists and oncologists from gleaning knowledge from these data regarding the nature of malignant processes and the relationship between tumor genomic profiles and treatment response. The GDC aims to democratize access to cancer genomic data and to foster the sharing of these data to promote precision medicine approaches to the diagnosis and treatment of cancer.

Hepatitis A

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... is an inflammation of the liver. One type, hepatitis A, is caused by the hepatitis A virus (HAV). The disease spreads through contact with ... suggest medicines to help relieve your symptoms. The hepatitis A vaccine can prevent HAV. Good hygiene can also ...

In Silico Screening Hepatitis B Virus DNA Polymerase Inhibitors from Medicinal Plants

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Mokhtar Nosrati

2017-08-01

Full Text Available Abstract Background: Hepatitis B virus infection (HBV is a significant global health problem and is a major cause of morbidity and mortality worldwide. Therefore, currently, introducing novel anti Hepatitis B drugs is taken into consideration. This study was planned to in silico screening novel Hepatitis B virus DNA polymerase inhibitors from two medicinal plants Terminalis chebula and Caesalpinia sappan. Materials and Methods: This is a descriptive-analytic study. In the study, three-dimensional structure of the Hepatitis B virus DNA polymerase was predicted using homology modeling method. A set of phytochemicals from mentioned plants were retrieved from Pubchem database in SDF format. In silico screening was carried out using molecular docking between mentioned phytochemicals and modeled polymerase by iGemdock 2.1 software. Results: Results of the study confirmed that all evaluated ligands have appropriate interactions to the polymerase with least toxicity and without genotoxicity potential. Results also showed that most interactions occur in reverse transcriptase domain which located in 354-694 area in the amino acid sequence of tested polymerase. Analysis of energy and amino acids involved in ligand-polymerase interaction revealed that Terchebin, Chebulinic Acid and Terflavin A have more effective interaction with the polymerase in compared to other ligands. Conclusion: Based on the results it can be concluded that evaluated compounds could be good candidates for in vitro and in vivo research in order to develop novel anti- Hepatitis B drugs.

The IGNITE network: a model for genomic medicine implementation and research.

Science.gov (United States)

Weitzel, Kristin Wiisanen; Alexander, Madeline; Bernhardt, Barbara A; Calman, Neil; Carey, David J; Cavallari, Larisa H; Field, Julie R; Hauser, Diane; Junkins, Heather A; Levin, Phillip A; Levy, Kenneth; Madden, Ebony B; Manolio, Teri A; Odgis, Jacqueline; Orlando, Lori A; Pyeritz, Reed; Wu, R Ryanne; Shuldiner, Alan R; Bottinger, Erwin P; Denny, Joshua C; Dexter, Paul R; Flockhart, David A; Horowitz, Carol R; Johnson, Julie A; Kimmel, Stephen E; Levy, Mia A; Pollin, Toni I; Ginsburg, Geoffrey S

2016-01-05

Patients, clinicians, researchers and payers are seeking to understand the value of using genomic information (as reflected by genotyping, sequencing, family history or other data) to inform clinical decision-making. However, challenges exist to widespread clinical implementation of genomic medicine, a prerequisite for developing evidence of its real-world utility. To address these challenges, the National Institutes of Health-funded IGNITE (Implementing GeNomics In pracTicE; www.ignite-genomics.org ) Network, comprised of six projects and a coordinating center, was established in 2013 to support the development, investigation and dissemination of genomic medicine practice models that seamlessly integrate genomic data into the electronic health record and that deploy tools for point of care decision making. IGNITE site projects are aligned in their purpose of testing these models, but individual projects vary in scope and design, including exploring genetic markers for disease risk prediction and prevention, developing tools for using family history data, incorporating pharmacogenomic data into clinical care, refining disease diagnosis using sequence-based mutation discovery, and creating novel educational approaches. This paper describes the IGNITE Network and member projects, including network structure, collaborative initiatives, clinical decision support strategies, methods for return of genomic test results, and educational initiatives for patients and providers. Clinical and outcomes data from individual sites and network-wide projects are anticipated to begin being published over the next few years. The IGNITE Network is an innovative series of projects and pilot demonstrations aiming to enhance translation of validated actionable genomic information into clinical settings and develop and use measures of outcome in response to genome-based clinical interventions using a pragmatic framework to provide early data and proofs of concept on the utility of these

The complete mitochondrial genome of the medicinal fungus Ganoderma applanatum (Polyporales, Basidiomycota).

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Wang, Xin-Cun; Shao, Junjie; Liu, Chang

2016-07-01

We have determined the complete nucleotide sequence of the mitochondrial genome of the medicinal fungus Ganoderma applanatum (Pers.) Pat. using the next-generation sequencing technology. The circular molecule is 119,803 bp long with a GC content of 26.66%. Gene prediction revealed genes encoding 15 conserved proteins, 25 tRNAs, the large and small ribosomal RNAs, all genes are located on the same strand except trnW-CCA. Compared with previously sequenced genomes of G. lucidum, G. meredithiae and G. sinense, the order of the protein and rRNA genes is highly conserved; however, the types of tRNA genes are slightly different. The mitochondrial genome of G. applanatum will contribute to the understanding of the phylogeny and evolution of Ganoderma and Ganodermataceae, the group containing many species with high medicinal values.

Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids.

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Park, Seongjun; Ruhlman, Tracey A; Sabir, Jamal S M; Mutwakil, Mohammed H Z; Baeshen, Mohammed N; Sabir, Meshaal J; Baeshen, Nabih A; Jansen, Robert K

2014-05-28

Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicinally important plant, analyses of the complete plastid and mitochondrial genomes and a nuclear transcriptome from Rhazya provide insights into inter-compartmental transfers between genomes and the patterns of evolution among eight asterid mitochondrial genomes. The 154,841 bp plastid genome is highly conserved with gene content and order identical to the ancestral organization of angiosperms. The 548,608 bp mitochondrial genome exhibits a number of phenomena including the presence of recombinogenic repeats that generate a multipartite organization, transferred DNA from the plastid and nuclear genomes, and bidirectional DNA transfers between the mitochondrion and the nucleus. The mitochondrial genes sdh3 and rps14 have been transferred to the nucleus and have acquired targeting presequences. In the case of rps14, two copies are present in the nucleus; only one has a mitochondrial targeting presequence and may be functional. Phylogenetic analyses of both nuclear and mitochondrial copies of rps14 across angiosperms suggests Rhazya has experienced a single transfer of this gene to the nucleus, followed by a duplication event. Furthermore, the phylogenetic distribution of gene losses and the high level of sequence divergence in targeting presequences suggest multiple, independent transfers of both sdh3 and rps14 across asterids. Comparative analyses of mitochondrial genomes of eight sequenced asterids indicates a complicated evolutionary history in this large angiosperm clade with considerable diversity in genome organization and size, repeat, gene and intron content, and amount of foreign DNA from the plastid and nuclear genomes. Organelle genomes of Rhazya stricta provide valuable information for improving the understanding of mitochondrial genome evolution

Deep sequencing and transcriptome analyses to identify genes involved in secoiridoid biosynthesis in Tibetan medicinal plant Sewertia mussotii

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Swertia mussotii Franch. is an important traditional Tibetan medicinal plant with pharmacological properties useful for the treatment of various ailments, such as hepatitis. Secoiridoids, including swertiamarin, are the major bioactive compounds in S. mussotii. The development of genomic resources ...

Synergy between Medical Informatics and Bioinformatics: Facilitating Genomic Medicine for Future Health Care

Czech Academy of Sciences Publication Activity Database

Martin-Sanchez, F.; Iakovidis, I.; Norager, S.; Maojo, V.; de Groen, P.; Van der Lei, J.; Jones, T.; Abraham-Fuchs, K.; Apweiler, R.; Babic, A.; Baud, R.; Breton, V.; Cinquin, P.; Doupi, P.; Dugas, M.; Eils, R.; Engelbrecht, R.; Ghazal, P.; Jehenson, P.; Kulikowski, C.; Lampe, K.; De Moor, G.; Orphanoudakis, S.; Rossing, N.; Sarachan, B.; Sousa, A.; Spekowius, G.; Thireos, G.; Zahlmann, G.; Zvárová, Jana; Hermosilla, I.; Vicente, F. J.

2004-01-01

Roč. 37, - (2004), s. 30-42 ISSN 1532-0464 Institutional research plan: CEZ:AV0Z1030915 Keywords : bioinformatics * medical informatics * genomics * genomic medicine * biomedical informatics Subject RIV: BD - Theory of Information Impact factor: 1.013, year: 2004

75 FR 26846 - Genomic Medicine Program Advisory Committee; Notice of Meeting

Science.gov (United States)

2010-05-12

... appropriate ethical oversight and protecting the privacy of Veterans; presentations on genomic medicine... make recommendations to the Secretary of Veterans Affairs on using genetic information to optimize...

Framework for development of physician competencies in genomic medicine: report of the Competencies Working Group of the Inter-Society Coordinating Committee for Physician Education in Genomics.

Science.gov (United States)

Korf, Bruce R; Berry, Anna B; Limson, Melvin; Marian, Ali J; Murray, Michael F; O'Rourke, P Pearl; Passamani, Eugene R; Relling, Mary V; Tooker, John; Tsongalis, Gregory J; Rodriguez, Laura L

2014-11-01

Completion of the Human Genome Project, in conjunction with dramatic reductions in the cost of DNA sequencing and advances in translational research, is gradually ushering genomic discoveries and technologies into the practice of medicine. The rapid pace of these advances is opening up a gap between the knowledge available about the clinical relevance of genomic information and the ability of clinicians to include such information in their medical practices. This educational gap threatens to be rate limiting to the clinical adoption of genomics in medicine. Solutions will require not only a better understanding of the clinical implications of genetic discoveries but also training in genomics at all levels of professional development, including for individuals in formal training and others who long ago completed such training. The National Human Genome Research Institute has convened the Inter-Society Coordinating Committee for Physician Education in Genomics (ISCC) to develop and share best practices in the use of genomics in medicine. The ISCC has developed a framework for development of genomics practice competencies that may serve as a starting point for formulation of competencies for physicians in various medical disciplines.

Complementary and Alternative Medicine Use by Patients Chronically Infected with Hepatitis C Virus

Directory of Open Access Journals (Sweden)

Colin P White

2007-01-01

Full Text Available Complementary and alternative medicine (CAM is becoming increasingly popular in North America. The use of CAM is also popular in patients with chronic liver disease but is not well documented. The extent of use of CAM in chronic hepatitis C virus (HCV infected patients was determined, and the demographic and clinical data between users and nonusers of CAM was compared.

Distinct changing profiles of hepatitis A and E virus infection among patients with acute hepatitis in Mongolia: The first report of the full genome sequence of a novel genotype 1 hepatitis E virus strain.

Science.gov (United States)

Tsatsralt-Od, Bira; Primadharsini, Putu Prathiwi; Nishizawa, Tsutomu; Ohnishi, Hiroshi; Nagashima, Shigeo; Takahashi, Masaharu; Jirintai, Suljid; Nyamkhuu, Dulmaa; Okamoto, Hiroaki

2018-01-01

In January 2012, Mongolia started a hepatitis A vaccination program, which has not yet been evaluated. The first occurrence of autochthonous acute hepatitis E in 2013, caused by genotype 4 hepatitis E virus (HEV), suggests the need for a routine study to monitor its prevalence. One hundred fifty-four consecutive patients who were clinically diagnosed with acute hepatitis between 2014 and 2015 in Ulaanbaatar, Mongolia were studied. By serological and molecular testing followed by sequencing and phylogenetic analysis, only one patient (0.6%) was diagnosed with acute hepatitis A, caused by genotype IA hepatitis A virus (HAV), and 32 (20.8%) patients were diagnosed with acute hepatitis E, caused by genotype 1 HEV. The 32 HEV isolates obtained in this study shared 99.5-100% nucleotide identity and were grouped into a cluster separated from those of subtypes 1a to 1f. Upon comparison of p-distances over the entire genome, the distances between one representative HEV isolate (MNE15-072) and 1a-1f strains were 0.071-0.137, while those between 1b and 1c were 0.062-0.070. In conclusion, the prevalence of acute hepatitis A has decreased in Mongolia since the start of the vaccination program, while the monophyletic genotype 1 HEV strain of a probably novel subtype has been prevalent. © 2017 Wiley Periodicals, Inc.

Delivery of genomic medicine for common chronic adult diseases: a systematic review.

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Scheuner, Maren T; Sieverding, Pauline; Shekelle, Paul G

2008-03-19

The greatest public health benefit of advances in understanding the human genome may be realized for common chronic diseases such as cardiovascular disease, diabetes mellitus, and cancer. Attempts to integrate such knowledge into clinical practice are still in the early stages, and as a result, many questions surround the current state of this translation. To synthesize current information on genetic health services for common adult-onset conditions by examining studies that have addressed the outcomes, consumer information needs, delivery, and challenges in integrating these services. MEDLINE articles published between January 2000 and February 2008. Original research articles and systematic reviews dealing with common chronic adult-onset conditions were reviewed. A total of 3371 citations were reviewed, 170 articles retrieved, and 68 articles included in the analysis. Data were independently extracted by one reviewer and checked by another with disagreement resolved by consensus. Variables assessed included study design and 4 key areas: outcomes of genomic medicine, consumer information needs, delivery of genomic medicine, and challenges and barriers to integration of genomic medicine. Sixty-eight articles contributed data to the synthesis: 5 systematic reviews, 8 experimental studies, 35 surveys, 7 pre/post studies, 3 observational studies, and 10 qualitative reports. Three systematic reviews, 4 experimental studies, and 9 additional studies reported on outcomes of genetic services. Generally there were modest positive effects on psychological outcomes such as worry and anxiety, behavioral outcomes have shown mixed results, and clinical outcomes were less well studied. One systematic review, 1 randomized controlled trial, and 14 other studies assessed consumer information needs and found in general that genetics knowledge was reported to be low but that attitudes were generally positive. Three randomized controlled trials and 13 other studies assessed how

Protecting and Evaluating Genomic Privacy in Medical Tests and Personalized Medicine

OpenAIRE

Ayday, Erman; Raisaro, Jean Louis; Rougemont, Jacques; Hubaux, Jean-Pierre

2013-01-01

In this paper, we propose privacy-enhancing technologies for medical tests and personalized medicine methods that use patients' genomic data. Focusing on genetic disease-susceptibility tests, we develop a new architecture (between the patient and the medical unit) and propose a "privacy-preserving disease susceptibility test" (PDS) by using homomorphic encryption and proxy re-encryption. Assuming the whole genome sequencing to be done by a certified institution, we propose to store patients' ...

An exploration of therapeutic evaluation of traditional Chinese medicine in treatment of hepatic fibrosis

Directory of Open Access Journals (Sweden)

XU Lieming

2017-05-01

Full Text Available China has become one of the leading counties in the world to treat hepatic fibrosis with Chinese patent drugs. The therapeutic effect of traditional Chinese medicine (TCM should be evaluated from the aspects of short-term therapeutic effect, long-term therapeutic effect, and effect of relief of symptoms. This article introduces the results of our exploration of the application of liver stiffness measurement to evaluate therapeutic effect, five-year survival rate to assess long-term therapeutic effect, and a “TCM syndrome scale” to evaluate effect of relief of symptoms, suggesting that the Chinese patent drug Fuzheng Huayu capsules/tablets have a marked clinical effect in the treatment of hepatic fibrosis. It is recommended to use serological diagnostic models, conduct prospective studies with long-term follow-up, and analyze the samples and data accumulated over a long period of time, in order to perfect the methods for evaluating the outcome of hepatic fibrosis.

The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine.

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Vassy, Jason L; Lautenbach, Denise M; McLaughlin, Heather M; Kong, Sek Won; Christensen, Kurt D; Krier, Joel; Kohane, Isaac S; Feuerman, Lindsay Z; Blumenthal-Barby, Jennifer; Roberts, J Scott; Lehmann, Lisa Soleymani; Ho, Carolyn Y; Ubel, Peter A; MacRae, Calum A; Seidman, Christine E; Murray, Michael F; McGuire, Amy L; Rehm, Heidi L; Green, Robert C

2014-03-20

Whole genome sequencing (WGS) is already being used in certain clinical and research settings, but its impact on patient well-being, health-care utilization, and clinical decision-making remains largely unstudied. It is also unknown how best to communicate sequencing results to physicians and patients to improve health. We describe the design of the MedSeq Project: the first randomized trials of WGS in clinical care. This pair of randomized controlled trials compares WGS to standard of care in two clinical contexts: (a) disease-specific genomic medicine in a cardiomyopathy clinic and (b) general genomic medicine in primary care. We are recruiting 8 to 12 cardiologists, 8 to 12 primary care physicians, and approximately 200 of their patients. Patient participants in both the cardiology and primary care trials are randomly assigned to receive a family history assessment with or without WGS. Our laboratory delivers a genome report to physician participants that balances the needs to enhance understandability of genomic information and to convey its complexity. We provide an educational curriculum for physician participants and offer them a hotline to genetics professionals for guidance in interpreting and managing their patients' genome reports. Using varied data sources, including surveys, semi-structured interviews, and review of clinical data, we measure the attitudes, behaviors and outcomes of physician and patient participants at multiple time points before and after the disclosure of these results. The impact of emerging sequencing technologies on patient care is unclear. We have designed a process of interpreting WGS results and delivering them to physicians in a way that anticipates how we envision genomic medicine will evolve in the near future. That is, our WGS report provides clinically relevant information while communicating the complexity and uncertainty of WGS results to physicians and, through physicians, to their patients. This project will not only

Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses.

Science.gov (United States)

Bracho, Maria A; Saludes, Verónica; Martró, Elisa; Bargalló, Ana; González-Candelas, Fernando; Ausina, Vicent

2008-06-05

Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region) are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest. We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence. In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.

The complete chloroplast genome sequence of the medicinal plant Andrographis paniculata.

Science.gov (United States)

Ding, Ping; Shao, Yanhua; Li, Qian; Gao, Junli; Zhang, Runjing; Lai, Xiaoping; Wang, Deqin; Zhang, Huiye

2016-07-01

The complete chloroplast genome of Andrographis paniculata, an important medicinal plant with great economic value, has been studied in this article. The genome size is 150,249 bp in length, with 38.3% GC content. A pair of inverted repeats (IRs, 25,300 bp) are separated by a large single copy region (LSC, 82,459 bp) and a small single-copy region (SSC, 17,190 bp). The chloroplast genome contains 114 unique genes, 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. In these genes, 15 genes contained 1 intron and 3 genes comprised of 2 introns.

Systems Medicine: The Future of Medical Genomics, Healthcare, and Wellness.

Science.gov (United States)

Saqi, Mansoor; Pellet, Johann; Roznovat, Irina; Mazein, Alexander; Ballereau, Stéphane; De Meulder, Bertrand; Auffray, Charles

2016-01-01

Recent advances in genomics have led to the rapid and relatively inexpensive collection of patient molecular data including multiple types of omics data. The integration of these data with clinical measurements has the potential to impact on our understanding of the molecular basis of disease and on disease management. Systems medicine is an approach to understanding disease through an integration of large patient datasets. It offers the possibility for personalized strategies for healthcare through the development of a new taxonomy of disease. Advanced computing will be an important component in effectively implementing systems medicine. In this chapter we describe three computational challenges associated with systems medicine: disease subtype discovery using integrated datasets, obtaining a mechanistic understanding of disease, and the development of an informatics platform for the mining, analysis, and visualization of data emerging from translational medicine studies.

Genomic heterogeneity among human and nonhuman strains of hepatitis A virus

International Nuclear Information System (INIS)

Lemon, S.M.; Chao, S.F.; Jansen, R.W.; Binn, L.N.; LeDuc, J.W.

1987-01-01

Cloned cDNA probes derived from the P1 and P2 regions of the genome of HM175 virus, a reference strain of human hepatitis A virus (HAV), failed to hybridize under standard stringency criteria with RNA from PA21 and PA33 viruses, two epizootiologically related HAV strains recovered from naturally infected New World owl monkeys. Hybridization of these probes to PA21 RNA was only evident under reduced stringency conditions. However, cDNA representing the 5' nontranslated region of the MH175 genome hybridized equally to HM175 and PA21 RNA under standard stringency conditions, while a probe derived from the 3', 1400 bases of the genome yielded a reduced hybridization signal with PA21 RNA. In contrast, no differences could be discerned between HM175 virus and three other HAV strains of human origin (GR8, LV374, and MS1) in any region of the genome, unless increased stringency conditions were used. These results suggest that PA21 and PA33 are unique among HAV isolates and may represent a virus native to the owl monkey. Despite extremely poor homology within the P1 region, which encodes capsid polypeptides, monoclonal antibody analysis confirmed that the immunodominant neutralization epitopes of HAV were highly conserved between HM175 and PA21 viruses. These data provide molecular evidence for the existence of HAV strains unique to nonhuman species and indicate that strict conservation of antigenic function may accompany substantial genetic divergence in HAV

The Human Genome Project: big science transforms biology and medicine.

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Hood, Leroy; Rowen, Lee

2013-01-01

The Human Genome Project has transformed biology through its integrated big science approach to deciphering a reference human genome sequence along with the complete sequences of key model organisms. The project exemplifies the power, necessity and success of large, integrated, cross-disciplinary efforts - so-called 'big science' - directed towards complex major objectives. In this article, we discuss the ways in which this ambitious endeavor led to the development of novel technologies and analytical tools, and how it brought the expertise of engineers, computer scientists and mathematicians together with biologists. It established an open approach to data sharing and open-source software, thereby making the data resulting from the project accessible to all. The genome sequences of microbes, plants and animals have revolutionized many fields of science, including microbiology, virology, infectious disease and plant biology. Moreover, deeper knowledge of human sequence variation has begun to alter the practice of medicine. The Human Genome Project has inspired subsequent large-scale data acquisition initiatives such as the International HapMap Project, 1000 Genomes, and The Cancer Genome Atlas, as well as the recently announced Human Brain Project and the emerging Human Proteome Project.

Integrated internist - addiction medicine - hepatology model for hepatitis C management for individuals on methadone maintenance.

Science.gov (United States)

Martinez, A D; Dimova, R; Marks, K M; Beeder, A B; Zeremski, M; Kreek, M J; Talal, A H

2012-01-01

Despite a high prevalence of hepatitis C virus (HCV) among drug users, HCV evaluation and treatment acceptance are extremely low among these patients when referred from drug treatment facilities for HCV management. We sought to increase HCV treatment effectiveness among patients from a methadone maintenance treatment program (MMTP) by maintaining continuity of care. We developed, instituted and retrospectively assessed the effectiveness of an integrated, co-localized care model in which an internist-addiction medicine specialist from MMTP was embedded in the hepatitis clinic. Methadone maintenance treatment program patients were referred, evaluated by the internist and hepatologist in hepatitis clinic and provided HCV treatment with integration between both sites. Of 401 evaluated patients, anti-HCV antibody was detected in 257, 86% of whom were older than 40 years. Hepatitis C virus RNA levels were measured in 222 patients, 65 of whom were aviremic. Of 157 patients with detectable HCV RNA, 125 were eligible for referral to the hepatitis clinic, 76 (61%) of whom accepted and adhered with the referral. Men engaged in MMTP <36 months were significantly less likely to be seen in hepatitis clinic than men in MMTP more than 36 months (odds ratio = 7.7; 95% confidence interval 2.6-22.9) or women. We evaluated liver histology in 63 patients, and 83% had moderate to advanced liver disease. Twenty-four patients initiated treatment with 19 completing and 13 (54%) achieving sustained response. In conclusion, integrated care between the MMTP and the hepatitis clinic improves adherence with HCV evaluation and treatment compared to standard referral practices. © 2010 Blackwell Publishing Ltd.

Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing.

Science.gov (United States)

Li, Hui; Stoddard, Mark B; Wang, Shuyi; Blair, Lily M; Giorgi, Elena E; Parrish, Erica H; Learn, Gerald H; Hraber, Peter; Goepfert, Paul A; Saag, Michael S; Denny, Thomas N; Haynes, Barton F; Hahn, Beatrice H; Ribeiro, Ruy M; Perelson, Alan S; Korber, Bette T; Bhattacharya, Tanmoy; Shaw, George M

2012-01-01

A precise molecular identification of transmitted hepatitis C virus (HCV) genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of 2,922 half or quarter genomes from plasma viral RNA to identify transmitted/founder (T/F) viruses in 17 subjects with acute community-acquired HCV infection. Sequences from 13 of 17 acute subjects, but none of 14 chronic controls, exhibited one or more discrete low diversity viral lineages. Sequences within each lineage generally revealed a star-like phylogeny of mutations that coalesced to unambiguous T/F viral genomes. Numbers of transmitted viruses leading to productive clinical infection were estimated to range from 1 to 37 or more (median = 4). Four acutely infected subjects showed a distinctly different pattern of virus diversity that deviated from a star-like phylogeny. In these cases, empirical analysis and mathematical modeling suggested high multiplicity virus transmission from individuals who themselves were acutely infected or had experienced a virus population bottleneck due to antiviral drug therapy. These results provide new quantitative and qualitative insights into HCV transmission, revealing for the first time virus-host interactions that successful vaccines or treatment interventions will need to overcome. Our findings further suggest a novel experimental strategy for identifying full-length T/F genomes for proteome-wide analyses of HCV biology and adaptation to antiviral drug or immune pressures.

Developing a common framework for evaluating the implementation of genomic medicine interventions in clinical care: the IGNITE Network's Common Measures Working Group.

Science.gov (United States)

Orlando, Lori A; Sperber, Nina R; Voils, Corrine; Nichols, Marshall; Myers, Rachel A; Wu, R Ryanne; Rakhra-Burris, Tejinder; Levy, Kenneth D; Levy, Mia; Pollin, Toni I; Guan, Yue; Horowitz, Carol R; Ramos, Michelle; Kimmel, Stephen E; McDonough, Caitrin W; Madden, Ebony B; Damschroder, Laura J

2018-06-01

PurposeImplementation research provides a structure for evaluating the clinical integration of genomic medicine interventions. This paper describes the Implementing Genomics in Practice (IGNITE) Network's efforts to promote (i) a broader understanding of genomic medicine implementation research and (ii) the sharing of knowledge generated in the network.MethodsTo facilitate this goal, the IGNITE Network Common Measures Working Group (CMG) members adopted the Consolidated Framework for Implementation Research (CFIR) to guide its approach to identifying constructs and measures relevant to evaluating genomic medicine as a whole, standardizing data collection across projects, and combining data in a centralized resource for cross-network analyses.ResultsCMG identified 10 high-priority CFIR constructs as important for genomic medicine. Of those, eight did not have standardized measurement instruments. Therefore, we developed four survey tools to address this gap. In addition, we identified seven high-priority constructs related to patients, families, and communities that did not map to CFIR constructs. Both sets of constructs were combined to create a draft genomic medicine implementation model.ConclusionWe developed processes to identify constructs deemed valuable for genomic medicine implementation and codified them in a model. These resources are freely available to facilitate knowledge generation and sharing across the field.

Complete Mitochondrial Genome of the Medicinal Mushroom Ganoderma lucidum

Science.gov (United States)

Chen, Haimei; Chen, Xiangdong; Lan, Jin; Liu, Chang

2013-01-01

Ganoderma lucidum is one of the well-known medicinal basidiomycetes worldwide. The mitochondrion, referred to as the second genome, is an organelle found in most eukaryotic cells and participates in critical cellular functions. Elucidating the structure and function of this genome is important to understand completely the genetic contents of G. lucidum. In this study, we assembled the mitochondrial genome of G. lucidum and analyzed the differential expressions of its encoded genes across three developmental stages. The mitochondrial genome is a typical circular DNA molecule of 60,630 bp with a GC content of 26.67%. Genome annotation identified genes that encode 15 conserved proteins, 27 tRNAs, small and large rRNAs, four homing endonucleases, and two hypothetical proteins. Except for genes encoding trnW and two hypothetical proteins, all genes were located on the positive strand. For the repeat structure analysis, eight forward, two inverted, and three tandem repeats were detected. A pair of fragments with a total length around 5.5 kb was found in both the nuclear and mitochondrial genomes, which suggests the possible transfer of DNA sequences between two genomes. RNA-Seq data for samples derived from three stages, namely, mycelia, primordia, and fruiting bodies, were mapped to the mitochondrial genome and qualified. The protein-coding genes were expressed higher in mycelia or primordial stages compared with those in the fruiting bodies. The rRNA abundances were significantly higher in all three stages. Two regions were transcribed but did not contain any identified protein or tRNA genes. Furthermore, three RNA-editing sites were detected. Genome synteny analysis showed that significant genome rearrangements occurred in the mitochondrial genomes. This study provides valuable information on the gene contents of the mitochondrial genome and their differential expressions at various developmental stages of G. lucidum. The results contribute to the understanding of the

Procedures of hepatic scintigraphy and improvement of professionals by using anthropomorphic simulator object of liver in nuclear medicine

International Nuclear Information System (INIS)

Ferreira, Fernanda C.L.; Cunha, Cledison J.; Dullius, Marcos A.; Souza, Divanizia N.

2011-01-01

This paper evaluates hepatic scintigraphy procedures and the possibility of professional improvement in nuclear medicine by using three-dimension anthropomorphic simulators representative of adult human liver. For the conformation of anthropomorphic simulator, it was used gypsum and acrylic. Three simulator objects representing cirrhosis livers. The simulator were filled with 99m Tc diluted in water for the obtention of scintigraphic images. Tomographic images were analysed posterior and anterior of simulator representing an organ with more cirrhosis grade. It was observed that the simulators make possible the acquisition of images similar to the real images of liver with hepatic cirrhosis. The simulations of hemangiomas can contribute for continuous education of nuclear medicine professionals, as far the question of image formation is concerned, make possible the parameter study as, for example, the , matrix size energy window, zoom and counting statistic

From Rosalind Franklin to Barack Obama: Data Sharing Challenges and Solutions in Genomics and Personalised Medicine.

Science.gov (United States)

Lawler, Mark; Maughan, Tim

2017-04-01

The collection, storage and use of genomic and clinical data from patients and healthy individuals is a key component of personalised medicine enterprises such as the Precision Medicine Initiative, the Cancer Moonshot and the 100,000 Genomes Project. In order to maximise the value of this data, it is important to embed a culture within the scientific, medical and patient communities that supports the appropriate sharing of genomic and clinical information. However, this aspiration raises a number of ethical, legal and regulatory challenges that need to be addressed. The Global Alliance for Genomics and Health, a worldwide coalition of researchers, healthcare professionals, patients and industry partners, is developing innovative solutions to support the responsible and effective sharing of genomic and clinical data. This article identifies the challenges that a data sharing culture poses and highlights a series of practical solutions that will benefit patients, researchers and society.

Genomics and advances towards precision medicine for head and neck squamous cell carcinoma.

Science.gov (United States)

Van Waes, Carter; Musbahi, Omar

2017-10-01

To provide a review of emerging knowledge from genomics and related basic science, preclinical, and clinical precision medicine studies in head and neck squamous cell carcinoma (HNSCC). The Cancer Genome Atlas Network (TCGA) publications, PubMed-based literature review, and ClinicalTrials.gov. TCGA publications, PubMed, and ClinicalTrials.gov were queried for genomics and related basic science, preclinical, and developmental clinical precision medicine studies in HNSCC. TCGA reported comprehensive genomic analyses of 279 HNSCC, defining the landscape and frequency of chromosomal copy number alterations, mutations, and expressed genes that contribute to pathogenesis, prognosis, and resistance to therapy. This provides a road map for basic science and preclinical studies to identify key pathways in cancer and cells of the tumor microenvironment affected by these alterations, and candidate targets for new small molecule and biologic therapies. Recurrent chromosomal abnormalities, mutations, and expression of genes affecting HNSCC subsets are associated with differences in prognosis, and define molecules, pathways, and deregulated immune responses as candidates for therapy. Activity of molecularly targeted agents appears to be enhanced by rational combinations of these agents and standard therapies targeting the complex alterations that affect multiple pathways and mechanisms in HNSCC. NA.

Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses

Directory of Open Access Journals (Sweden)

Bargalló Ana

2008-06-01

Full Text Available Abstract Background Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest. Results We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence. Conclusion In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.

The Qatar genome: a population-specific tool for precision medicine in the Middle East

Science.gov (United States)

Fakhro, Khalid A; Staudt, Michelle R; Ramstetter, Monica Denise; Robay, Amal; Malek, Joel A; Badii, Ramin; Al-Marri, Ajayeb Al-Nabet; Khalil, Charbel Abi; Al-Shakaki, Alya; Chidiac, Omar; Stadler, Dora; Zirie, Mahmoud; Jayyousi, Amin; Salit, Jacqueline; Mezey, Jason G; Crystal, Ronald G; Rodriguez-Flores, Juan L

2016-01-01

Reaching the full potential of precision medicine depends on the quality of personalized genome interpretation. In order to facilitate precision medicine in regions of the Middle East and North Africa (MENA), a population-specific genome for the indigenous Arab population of Qatar (QTRG) was constructed by incorporating allele frequency data from sequencing of 1,161 Qataris, representing 0.4% of the population. A total of 20.9 million single nucleotide polymorphisms (SNPs) and 3.1 million indels were observed in Qatar, including an average of 1.79% novel variants per individual genome. Replacement of the GRCh37 standard reference with QTRG in a best practices genome analysis workflow resulted in an average of 7* deeper coverage depth (an improvement of 23%) and 756,671 fewer variants on average, a reduction of 16% that is attributed to common Qatari alleles being present in QTRG. The benefit for using QTRG varies across ancestries, a factor that should be taken into consideration when selecting an appropriate reference for analysis. PMID:27408750

The beneficial effects of Kampo medicine Dai-ken-chu-to after hepatic resection: a prospective randomized control study.

Science.gov (United States)

Nishi, Masaki; Shimada, Mitsuo; Uchiyama, Hideaki; Ikegami, Toru; Arakawa, Yusuke; Hanaoka, Jun; Kanemura, Hirofumi; Morine, Yuji; Imura, Satoru; Miyake, Hidenori; Utsunomiya, Toru

2012-10-01

After hepatic resection, delayed flatus and impaired bowel movement often cause problematic postoperative ileus. Kampo medicine, Dai-kenchu-to (DKT), is reported to have a various beneficial effects on bowel systems. The aim of this study was to prospectively evaluate effects of DKT after hepatic resection. Thirty-two patients who underwent hepatic resection between July 2007 and August 2008 in Tokushima University Hospital were prospectively divided into DKT group (n=16) and control group (n=16). In DKT group, 2.5 g of DKT was administered orally three times a day from postoperative day (POD) 1. Blood was examined on POD 1, 3, 5 and 7. Postoperative first flatus, bowel movement and full recovery of oral intake, hospital stays and complications were checked. In DKT group, levels of c-reactive protein and beta-(1-3)-D-glucan on POD 3 were significantly decreased (pDKT group (pDKT suppressed inflammatory reaction, stimulated bowel movement and improved oral intake after hepatic resection, which may decrease serious morbidity after hepatic resection.

Toksisk hepatitis efter indtagelse af kosttilskuddet purshianabark

DEFF Research Database (Denmark)

Jacobsen, Claire; Semb, Synne; Kromann-Andersen, Hans

2009-01-01

Herbal medicinal products can cause toxic hepatitis. This case report presents a patient who developed severe toxic hepatitis with beginning liver failure following four weeks of consumption of the herbal medicinal product Cascara Sagrada. A similar case was reported from the United States. Cascara...... Sagrada is found in 30-40 herbal medicinal products in Denmark. We recommend that herbal medicinal products containing Cascara Sagrada be withdrawn from the market. Udgivelsesdato: 2009-Nov...

Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties.

Science.gov (United States)

Upadhyay, Atul K; Chacko, Anita R; Gandhimathi, A; Ghosh, Pritha; Harini, K; Joseph, Agnel P; Joshi, Adwait G; Karpe, Snehal D; Kaushik, Swati; Kuravadi, Nagesh; Lingu, Chandana S; Mahita, J; Malarini, Ramya; Malhotra, Sony; Malini, Manoharan; Mathew, Oommen K; Mutt, Eshita; Naika, Mahantesha; Nitish, Sathyanarayanan; Pasha, Shaik Naseer; Raghavender, Upadhyayula S; Rajamani, Anantharamanan; Shilpa, S; Shingate, Prashant N; Singh, Heikham Russiachand; Sukhwal, Anshul; Sunitha, Margaret S; Sumathi, Manojkumar; Ramaswamy, S; Gowda, Malali; Sowdhamini, Ramanathan

2015-08-28

Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is 'Tulsi' (or 'Tulasi' or 'Thulasi') and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb, with a genome coverage of 61 % (612 Mb estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum, Krishna and Rama Tulsi and report the relative expression of genes in both the varieties. The pathways leading to the production of medicinally-important specialized metabolites have been studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid, implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry. The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal properties to this herb.

Evidence that personal genome testing enhances student learning in a course on genomics and personalized medicine.

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Keyan Salari

Full Text Available An emerging debate in academic medical centers is not about the need for providing trainees with fundamental education on genomics, but rather the most effective educational models that should be deployed. At Stanford School of Medicine, a novel hands-on genomics course was developed in 2010 that provided students the option to undergo personal genome testing as part of the course curriculum. We hypothesized that use of personal genome testing in the classroom would enhance the learning experience of students. No data currently exist on how such methods impact student learning; thus, we surveyed students before and after the course to determine its impact. We analyzed responses using paired statistics from the 31 medical and graduate students who completed both pre-course and post-course surveys. Participants were stratified by those who did (N = 23 or did not (N = 8 undergo personal genome testing. In reflecting on the experience, 83% of students who underwent testing stated that they were pleased with their decision compared to 12.5% of students who decided against testing (P = 0.00058. Seventy percent of those who underwent personal genome testing self-reported a better understanding of human genetics on the basis of having undergone testing. Further, students who underwent personal genome testing demonstrated an average 31% increase in pre- to post-course scores on knowledge questions (P = 3.5×10(-6; this was significantly higher (P = 0.003 than students who did not undergo testing, who showed a non-significant improvement. Undergoing personal genome testing and using personal genotype data in the classroom enhanced students' self-reported and assessed knowledge of genomics, and did not appear to cause significant anxiety. At least for self-selected students, the incorporation of personal genome testing can be an effective educational tool to teach important concepts of clinical genomic testing.

Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

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Champeimont, Raphaël; Laine, Elodie; Hu, Shuang-Wei; Penin, Francois; Carbone, Alessandra

2016-05-01

A novel computational approach of coevolution analysis allowed us to reconstruct the protein-protein interaction network of the Hepatitis C Virus (HCV) at the residue resolution. For the first time, coevolution analysis of an entire viral genome was realized, based on a limited set of protein sequences with high sequence identity within genotypes. The identified coevolving residues constitute highly relevant predictions of protein-protein interactions for further experimental identification of HCV protein complexes. The method can be used to analyse other viral genomes and to predict the associated protein interaction networks.

Genome network medicine: innovation to overcome huge challenges in cancer therapy.

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Roukos, Dimitrios H

2014-01-01

The post-ENCODE era shapes now a new biomedical research direction for understanding transcriptional and signaling networks driving gene expression and core cellular processes such as cell fate, survival, and apoptosis. Over the past half century, the Francis Crick 'central dogma' of single n gene/protein-phenotype (trait/disease) has defined biology, human physiology, disease, diagnostics, and drugs discovery. However, the ENCODE project and several other genomic studies using high-throughput sequencing technologies, computational strategies, and imaging techniques to visualize regulatory networks, provide evidence that transcriptional process and gene expression are regulated by highly complex dynamic molecular and signaling networks. This Focus article describes the linear experimentation-based limitations of diagnostics and therapeutics to cure advanced cancer and the need to move on from reductionist to network-based approaches. With evident a wide genomic heterogeneity, the power and challenges of next-generation sequencing (NGS) technologies to identify a patient's personal mutational landscape for tailoring the best target drugs in the individual patient are discussed. However, the available drugs are not capable of targeting aberrant signaling networks and research on functional transcriptional heterogeneity and functional genome organization is poorly understood. Therefore, the future clinical genome network medicine aiming at overcoming multiple problems in the new fields of regulatory DNA mapping, noncoding RNA, enhancer RNAs, and dynamic complexity of transcriptional circuitry are also discussed expecting in new innovation technology and strong appreciation of clinical data and evidence-based medicine. The problematic and potential solutions in the discovery of next-generation, molecular, and signaling circuitry-based biomarkers and drugs are explored. © 2013 Wiley Periodicals, Inc.

Analysis of the Complete Chloroplast Genome of a Medicinal Plant, Dianthus superbus var. longicalyncinus, from a Comparative Genomics Perspective.

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Raman, Gurusamy; Park, SeonJoo

2015-01-01

Dianthus superbus var. longicalycinus is an economically important traditional Chinese medicinal plant that is also used for ornamental purposes. In this study, D. superbus was compared to its closely related family of Caryophyllaceae chloroplast (cp) genomes such as Lychnis chalcedonica and Spinacia oleracea. D. superbus had the longest large single copy (LSC) region (82,805 bp), with some variations in the inverted repeat region A (IRA)/LSC regions. The IRs underwent both expansion and constriction during evolution of the Caryophyllaceae family; however, intense variations were not identified. The pseudogene ribosomal protein subunit S19 (rps19) was identified at the IRA/LSC junction, but was not present in the cp genome of other Caryophyllaceae family members. The translation initiation factor IF-1 (infA) and ribosomal protein subunit L23 (rpl23) genes were absent from the Dianthus cp genome. When the cp genome of Dianthus was compared with 31 other angiosperm lineages, the infA gene was found to have been lost in most members of rosids, solanales of asterids and Lychnis of Caryophyllales, whereas rpl23 gene loss or pseudogization had occurred exclusively in Caryophyllales. Nevertheless, the cp genome of Dianthus and Spinacia has two introns in the proteolytic subunit of ATP-dependent protease (clpP) gene, but Lychnis has lost introns from the clpP gene. Furthermore, phylogenetic analysis of individual protein-coding genes infA and rpl23 revealed that gene loss or pseudogenization occurred independently in the cp genome of Dianthus. Molecular phylogenetic analysis also demonstrated a sister relationship between Dianthus and Lychnis based on 78 protein-coding sequences. The results presented herein will contribute to studies of the evolution, molecular biology and genetic engineering of the medicinal and ornamental plant, D. superbus var. longicalycinus.

Analysis of the Complete Chloroplast Genome of a Medicinal Plant, Dianthus superbus var. longicalyncinus, from a Comparative Genomics Perspective.

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Gurusamy Raman

Full Text Available Dianthus superbus var. longicalycinus is an economically important traditional Chinese medicinal plant that is also used for ornamental purposes. In this study, D. superbus was compared to its closely related family of Caryophyllaceae chloroplast (cp genomes such as Lychnis chalcedonica and Spinacia oleracea. D. superbus had the longest large single copy (LSC region (82,805 bp, with some variations in the inverted repeat region A (IRA/LSC regions. The IRs underwent both expansion and constriction during evolution of the Caryophyllaceae family; however, intense variations were not identified. The pseudogene ribosomal protein subunit S19 (rps19 was identified at the IRA/LSC junction, but was not present in the cp genome of other Caryophyllaceae family members. The translation initiation factor IF-1 (infA and ribosomal protein subunit L23 (rpl23 genes were absent from the Dianthus cp genome. When the cp genome of Dianthus was compared with 31 other angiosperm lineages, the infA gene was found to have been lost in most members of rosids, solanales of asterids and Lychnis of Caryophyllales, whereas rpl23 gene loss or pseudogization had occurred exclusively in Caryophyllales. Nevertheless, the cp genome of Dianthus and Spinacia has two introns in the proteolytic subunit of ATP-dependent protease (clpP gene, but Lychnis has lost introns from the clpP gene. Furthermore, phylogenetic analysis of individual protein-coding genes infA and rpl23 revealed that gene loss or pseudogenization occurred independently in the cp genome of Dianthus. Molecular phylogenetic analysis also demonstrated a sister relationship between Dianthus and Lychnis based on 78 protein-coding sequences. The results presented herein will contribute to studies of the evolution, molecular biology and genetic engineering of the medicinal and ornamental plant, D. superbus var. longicalycinus.

Rapid and sensitive approach to simultaneous detection of genomes of hepatitis A, B, C, D and E viruses.

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Kodani, Maja; Mixson-Hayden, Tonya; Drobeniuc, Jan; Kamili, Saleem

2014-10-01

Five viruses have been etiologically associated with viral hepatitis. Nucleic acid testing (NAT) remains the gold standard for diagnosis of viremic stages of infection. NAT methodologies have been developed for all hepatitis viruses; however, a NAT-based assay that can simultaneously detect all five viruses is not available. We designed TaqMan card-based assays for detection of HAV RNA, HBV DNA, HCV RNA, HDV RNA and HEV RNA. The performances of individual assays were evaluated on TaqMan Array Cards (TAC) for detecting five viral genomes simultaneously. Sensitivity and specificity were determined by testing 329 NAT-tested clinical specimens. All NAT-positive samples for HCV (n = 32), HDV (n = 28) and HEV (n = 14) were also found positive in TAC (sensitivity, 100%). Forty-three of 46 HAV-NAT positive samples were also positive in TAC (sensitivity, 94%), while 36 of 39 HBV-NAT positive samples were positive (sensitivity, 92%). No false-positives were detected for HBV (n = 32), HCV (n = 36), HDV (n = 30), and HEV (n = 31) NAT-negative samples (specificity 100%), while 38 of 41 HAV-NAT negative samples were negative by TAC (specificity 93%). TAC assay was concordant with corresponding individual NATs for hepatitis A-E viral genomes and can be used for their detection simultaneously. The TAC assay has potential for use in hepatitis surveillance, for screening of donor specimens and in outbreak situations. Wider availability of TAC-ready assays may allow for customized assays, for improving acute jaundice surveillance and for other purposes for which there is need to identify multiple pathogens rapidly. Published by Elsevier B.V.

Genomics as public health? Community genetics and the challenge of personalised medicine in Cuba.

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Gibbon, Sahra

2009-08-01

Making use of a comparative perspective on the emergence of 'breast cancer genetics' in the different cultural context of the UK and Cuba, this article examines the tensions between the modern promise of genomics as personalised medicine and a commitment to public health. Focusing primarily on the Cuba context and drawing on ethnographic research as part of a collaborative project working with genetic professionals and publics, the article examines the particular technologies, identities and socialities at stake in an emerging and evolving field of genetic medicine. It highlights how long-standing continuities in the commitment to the equitable provision of public health, particularly as this relates to 'family medicine', are central to understanding the scope and expansion of 'community genetics' interventions, even when at the level of local practice, public health is also now subject to the unequal dynamics of economic necessity through the working out of 'lo informal'. Illuminating the different ways agency, risk, responsibility, citizenship and activism get configured by and between publics and health professionals in Cuba, the article reveals the challenges and opportunities posed by predictive genomic medicine in relation to the dynamic and shifting terrain of public health.

A quantitative analysis of the mass media coverage of genomics medicine in China: a call for science journalism in the developing world.

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Zhao, Feifei; Chen, Yan; Ge, Siqi; Yu, Xinwei; Shao, Shuang; Black, Michael; Wang, Youxin; Zhang, Jie; Song, Manshu; Wang, Wei

2014-04-01

Science journalism is a previously neglected but rapidly growing area of scholarship in postgenomics medicine and socio-technical studies of knowledge-based innovations. Science journalism can help evaluate the quantity and quality of information flux between traditional scientific expert communities and the broader public, for example, in personalized medicine education. Newspapers can play a crucial role in science and health communication, and more importantly, in framing public engagement. However, research on the role of newspaper coverage of genomics-related articles has not been readily available in resource-limited settings. As genomics is rapidly expanding worldwide, this gap in newspaper reportage in China is therefore an important issue. In order to bridge this gap, we investigated the coverage of genomics medicine in eight major Chinese national newspapers, using the China Core Newspapers Full-text Database (CCND) and articles in scientific journals in PubMed from 2000 to 2011. Coverage of genomics medicine in these eight official government Chinese newspapers has remained low, with only 12 articles published per newspaper per year between 2000 and 2011. Between 2000 and 2011, over a 40-fold difference was observed in the number of genomics medicine-related articles in PubMed, as compared to that in newspapers. The numbers of genomics-related articles among the eight major newspapers from 2000 to 2011 were significantly different (p=0.001). Commentary/mini reviews and articles about gene therapy for specific diseases were most frequently published in 2006 and 2011. In parallel, we observed that "cancer gene therapy," "new susceptibility gene locus," and "gene technology revolution" were the top three thematic strands addressed in the newspapers, even though their volume remained low. This study reports on the under-representation of newspaper coverage of genomics medicine in China, despite the vast growth of scientific articles in journals in this

Exploration of genetic diversity among medicinally important genus Epimedium species based on genomic and EST-SSR marker.

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Yousaf, Zubaida; Hu, Weiming; Zhang, Yanjun; Zeng, Shaohua; Wang, Ying

2015-01-01

Epimedium species has gained prime importance due to their medicinal and economic values. Therefore, in this study, 26 genomic SSR and 10 EST-SSR markers were developed for 13 medicinal species of the Epimedium genus and one out-group species Vancouveria hexandra W. J. Hooker to explore the existing genetic diversity. A total of 100 alleles by genomic SSR and 65 by EST-SSR were detected. The genomic SSR markers were presented between 2-7 alleles per locus. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.00 to 4.5 and 0.0254 to 2.8108, respectively. Similarly, for EST-SSR, these values were ranged from 3.00 to 4.00 and 1.9650 to 2.7142. The number of alleles for EST-SSR markers ranged from 3 to 10 with an average of 3.51 per loci. It has been concluded that medicinally important species of the genus Epimedium possesses lower intraspecific genetic variation.

Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication

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Michael Niepmann

2018-03-01

Full Text Available Hepatitis C virus (HCV preferentially replicates in the human liver and frequently causes chronic infection, often leading to cirrhosis and liver cancer. HCV is an enveloped virus classified in the genus Hepacivirus in the family Flaviviridae and has a single-stranded RNA genome of positive orientation. The HCV RNA genome is translated and replicated in the cytoplasm. Translation is controlled by the Internal Ribosome Entry Site (IRES in the 5′ untranslated region (5′ UTR, while also downstream elements like the cis-replication element (CRE in the coding region and the 3′ UTR are involved in translation regulation. The cis-elements controlling replication of the viral RNA genome are located mainly in the 5′- and 3′-UTRs at the genome ends but also in the protein coding region, and in part these signals overlap with the signals controlling RNA translation. Many long-range RNA–RNA interactions (LRIs are predicted between different regions of the HCV RNA genome, and several such LRIs are actually involved in HCV translation and replication regulation. A number of RNA cis-elements recruit cellular RNA-binding proteins that are involved in the regulation of HCV translation and replication. In addition, the liver-specific microRNA-122 (miR-122 binds to two target sites at the 5′ end of the viral RNA genome as well as to at least three additional target sites in the coding region and the 3′ UTR. It is involved in the regulation of HCV RNA stability, translation and replication, thereby largely contributing to the hepatotropism of HCV. However, we are still far from completely understanding all interactions that regulate HCV RNA genome translation, stability, replication and encapsidation. In particular, many conclusions on the function of cis-elements in HCV replication have been obtained using full-length HCV genomes or near-full-length replicon systems. These include both genome ends, making it difficult to decide if a cis-element in

Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication.

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Niepmann, Michael; Shalamova, Lyudmila A; Gerresheim, Gesche K; Rossbach, Oliver

2018-01-01

Hepatitis C virus (HCV) preferentially replicates in the human liver and frequently causes chronic infection, often leading to cirrhosis and liver cancer. HCV is an enveloped virus classified in the genus Hepacivirus in the family Flaviviridae and has a single-stranded RNA genome of positive orientation. The HCV RNA genome is translated and replicated in the cytoplasm. Translation is controlled by the Internal Ribosome Entry Site (IRES) in the 5' untranslated region (5' UTR), while also downstream elements like the cis -replication element (CRE) in the coding region and the 3' UTR are involved in translation regulation. The cis -elements controlling replication of the viral RNA genome are located mainly in the 5'- and 3'-UTRs at the genome ends but also in the protein coding region, and in part these signals overlap with the signals controlling RNA translation. Many long-range RNA-RNA interactions (LRIs) are predicted between different regions of the HCV RNA genome, and several such LRIs are actually involved in HCV translation and replication regulation. A number of RNA cis -elements recruit cellular RNA-binding proteins that are involved in the regulation of HCV translation and replication. In addition, the liver-specific microRNA-122 (miR-122) binds to two target sites at the 5' end of the viral RNA genome as well as to at least three additional target sites in the coding region and the 3' UTR. It is involved in the regulation of HCV RNA stability, translation and replication, thereby largely contributing to the hepatotropism of HCV. However, we are still far from completely understanding all interactions that regulate HCV RNA genome translation, stability, replication and encapsidation. In particular, many conclusions on the function of cis -elements in HCV replication have been obtained using full-length HCV genomes or near-full-length replicon systems. These include both genome ends, making it difficult to decide if a cis -element in question acts on HCV

Deep brain stimulation, brain maps and personalized medicine: lessons from the human genome project.

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Fins, Joseph J; Shapiro, Zachary E

2014-01-01

Although the appellation of personalized medicine is generally attributed to advanced therapeutics in molecular medicine, deep brain stimulation (DBS) can also be so categorized. Like its medical counterpart, DBS is a highly personalized intervention that needs to be tailored to a patient's individual anatomy. And because of this, DBS like more conventional personalized medicine, can be highly specific where the object of care is an N = 1. But that is where the similarities end. Besides their differing medical and surgical provenances, these two varieties of personalized medicine have had strikingly different impacts. The molecular variant, though of a more recent vintage has thrived and is experiencing explosive growth, while DBS still struggles to find a sustainable therapeutic niche. Despite its promise, and success as a vetted treatment for drug resistant Parkinson's Disease, DBS has lagged in broadening its development, often encountering regulatory hurdles and financial barriers necessary to mount an adequate number of quality trials. In this paper we will consider why DBS-or better yet neuromodulation-has encountered these challenges and contrast this experience with the more successful advance of personalized medicine. We will suggest that personalized medicine and DBS's differential performance can be explained as a matter of timing and complexity. We believe that DBS has struggled because it has been a journey of scientific exploration conducted without a map. In contrast to molecular personalized medicine which followed the mapping of the human genome and the Human Genome Project, DBS preceded plans for the mapping of the human brain. We believe that this sequence has given personalized medicine a distinct advantage and that the fullest potential of DBS will be realized both as a cartographical or electrophysiological probe and as a modality of personalized medicine.

Test Pricing and Reimbursement in Genomic Medicine: Towards a General Strategy.

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Vozikis, Athanassios; Cooper, David N; Mitropoulou, Christina; Kambouris, Manousos E; Brand, Angela; Dolzan, Vita; Fortina, Paolo; Innocenti, Federico; Lee, Ming Ta Michael; Leyens, Lada; Macek, Milan; Al-Mulla, Fahd; Prainsack, Barbara; Squassina, Alessio; Taruscio, Domenica; van Schaik, Ron H; Vayena, Effy; Williams, Marc S; Patrinos, George P

2016-01-01

This paper aims to provide an overview of the rationale and basic principles guiding the governance of genomic testing services, to clarify their objectives, and allocate and define responsibilities among stakeholders in a health-care system, with a special focus on the EU countries. Particular attention is paid to issues pertaining to pricing and reimbursement policies, the availability of essential genomic tests which differs between various countries owing to differences in disease prevalence and public health relevance, the prescribing and use of genomic testing services according to existing or new guidelines, budgetary and fiscal control, the balance between price and access to innovative testing, monitoring and evaluation for cost-effectiveness and safety, and the development of research capacity. We conclude that addressing the specific items put forward in this article will help to create a robust policy in relation to pricing and reimbursement in genomic medicine. This will contribute to an effective and sustainable health-care system and will prove beneficial to the economy at large. © 2016 S. Karger AG, Basel.

The Complete Chloroplast Genome Sequences of the Medicinal Plant Forsythia suspensa (Oleaceae

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Wenbin Wang

2017-10-01

Full Text Available Forsythia suspensa is an important medicinal plant and traditionally applied for the treatment of inflammation, pyrexia, gonorrhea, diabetes, and so on. However, there is limited sequence and genomic information available for F. suspensa. Here, we produced the complete chloroplast genomes of F. suspensa using Illumina sequencing technology. F. suspensa is the first sequenced member within the genus Forsythia (Oleaceae. The gene order and organization of the chloroplast genome of F. suspensa are similar to other Oleaceae chloroplast genomes. The F. suspensa chloroplast genome is 156,404 bp in length, exhibits a conserved quadripartite structure with a large single-copy (LSC; 87,159 bp region, and a small single-copy (SSC; 17,811 bp region interspersed between inverted repeat (IRa/b; 25,717 bp regions. A total of 114 unique genes were annotated, including 80 protein-coding genes, 30 tRNA, and four rRNA. The low GC content (37.8% and codon usage bias for A- or T-ending codons may largely affect gene codon usage. Sequence analysis identified a total of 26 forward repeats, 23 palindrome repeats with lengths >30 bp (identity > 90%, and 54 simple sequence repeats (SSRs with an average rate of 0.35 SSRs/kb. We predicted 52 RNA editing sites in the chloroplast of F. suspensa, all for C-to-U transitions. IR expansion or contraction and the divergent regions were analyzed among several species including the reported F. suspensa in this study. Phylogenetic analysis based on whole-plastome revealed that F. suspensa, as a member of the Oleaceae family, diverged relatively early from Lamiales. This study will contribute to strengthening medicinal resource conservation, molecular phylogenetic, and genetic engineering research investigations of this species.

Hepatic manifestations of celiac disease

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Hugh James Freeman

2010-05-01

Full Text Available Hugh James FreemanDepartment of Medicine (Gastroenterology, University of British Columbia, Vancouver, British Columbia, CanadaAbstract: Different hepatic and biliary tract disorders may occur with celiac disease. Some have been hypothesized to share genetic or immunopathogenetic factors, such as primary biliary cirrhosis, primary sclerosing cholangitis, and autoimmune hepatitis. Other hepatic changes in celiac disease may occur with malnutrition resulting from impaired nutrient absorption, including hepatic steatosis. In addition, celiac disease may be associated with rare hepatic complications, such as hepatic T-cell lymphoma.Keywords: celiac disease, autoimmune liver disease, primary biliary cirrhosis, fatty liver, gluten-free diet

Use of genome editing tools in human stem cell-based disease modeling and precision medicine.

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Wei, Yu-da; Li, Shuang; Liu, Gai-gai; Zhang, Yong-xian; Ding, Qiu-rong

2015-10-01

Precision medicine emerges as a new approach that takes into account individual variability. The successful conduct of precision medicine requires the use of precise disease models. Human pluripotent stem cells (hPSCs), as well as adult stem cells, can be differentiated into a variety of human somatic cell types that can be used for research and drug screening. The development of genome editing technology over the past few years, especially the CRISPR/Cas system, has made it feasible to precisely and efficiently edit the genetic background. Therefore, disease modeling by using a combination of human stem cells and genome editing technology has offered a new platform to generate " personalized " disease models, which allow the study of the contribution of individual genetic variabilities to disease progression and the development of precise treatments. In this review, recent advances in the use of genome editing in human stem cells and the generation of stem cell models for rare diseases and cancers are discussed.

Was it worth it? Patients' perspectives on the perceived value of genomic-based individualized medicine.

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Halverson, Colin Me; Clift, Kristin E; McCormick, Jennifer B

2016-04-01

The value of genomic sequencing is often understood in terms of its ability to affect diagnosis or treatment. In these terms, successes occur only in a minority of cases. This paper presents views from patients who had exome sequencing done clinically to explore how they perceive the utility of genomic medicine. The authors used semi-structured, qualitative interviews in order to study patients' attitudes toward genomic sequencing in oncology and rare-disease settings. Participants from 37 cases were interviewed. In terms of the testing's key values-regardless of having received what clinicians described as meaningful results-participants expressed four qualities that are separate from traditional views of clinical utility: Participants felt they had been empowered over their own health. They felt they had contributed altruistically to the progress of genomic technology in medicine. They felt their suffering had been legitimated. They also felt a sense of closure, having done everything they could. Patients expressed overwhelmingly positive attitudes toward sequencing. Their rationale was not solely based on the results' clinical utility. It is important for clinicians to understand this non-medical reasoning as it pertains to patient decision-making and informed consent.

First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc Maxim, a Chinese Traditional Medicinal Plant

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Gong Xiao

2013-06-01

Full Text Available Epimedium sagittatum (Sieb. et Zucc Maxim is a member of the Berberidaceae family of basal eudicot plants, widely distributed and used as a traditional medicinal plant in China for therapeutic effects on many diseases with a long history. Recent data shows that E. sagittatum has a relatively large genome, with a haploid genome size of ~4496 Mbp, divided into a small number of only 12 diploid chromosomes (2n = 2x = 12. However, little is known about Epimedium genome structure and composition. Here we present the analysis of 691 kb of high-quality genomic sequence derived from 672 randomly selected plasmid clones of E. sagittatum genomic DNA, representing ~0.0154% of the genome. The sampled sequences comprised at least 78.41% repetitive DNA elements and 2.51% confirmed annotated gene sequences, with a total GC% content of 39%. Retrotransposons represented the major class of transposable element (TE repeats identified (65.37% of all TE repeats, particularly LTR (Long Terminal Repeat retrotransposons (52.27% of all TE repeats. Chromosome analysis and Fluorescence in situ Hybridization of Gypsy-Ty3 retrotransposons were performed to survey the E. sagittatum genome at the cytological level. Our data provide the first insights into the composition and structure of the E. sagittatum genome, and will facilitate the functional genomic analysis of this valuable medicinal plant.

First Insights into the Large Genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Traditional Medicinal Plant

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Liu, Di; Zeng, Shao-Hua; Chen, Jian-Jun; Zhang, Yan-Jun; Xiao, Gong; Zhu, Lin-Yao; Wang, Ying

2013-01-01

Epimedium sagittatum (Sieb. et Zucc) Maxim is a member of the Berberidaceae family of basal eudicot plants, widely distributed and used as a traditional medicinal plant in China for therapeutic effects on many diseases with a long history. Recent data shows that E. sagittatum has a relatively large genome, with a haploid genome size of ~4496 Mbp, divided into a small number of only 12 diploid chromosomes (2n = 2x = 12). However, little is known about Epimedium genome structure and composition. Here we present the analysis of 691 kb of high-quality genomic sequence derived from 672 randomly selected plasmid clones of E. sagittatum genomic DNA, representing ~0.0154% of the genome. The sampled sequences comprised at least 78.41% repetitive DNA elements and 2.51% confirmed annotated gene sequences, with a total GC% content of 39%. Retrotransposons represented the major class of transposable element (TE) repeats identified (65.37% of all TE repeats), particularly LTR (Long Terminal Repeat) retrotransposons (52.27% of all TE repeats). Chromosome analysis and Fluorescence in situ Hybridization of Gypsy-Ty3 retrotransposons were performed to survey the E. sagittatum genome at the cytological level. Our data provide the first insights into the composition and structure of the E. sagittatum genome, and will facilitate the functional genomic analysis of this valuable medicinal plant. PMID:23807511

Clinical and virological improvement of hepatitis B virus-related or hepatitis C virus-related chronic hepatitis with concomitant hepatitis A virus infection.

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Sagnelli, Evangelista; Coppola, Nicola; Pisaturo, Mariantonietta; Pisapia, Raffaella; Onofrio, Mirella; Sagnelli, Caterina; Catuogno, Antonio; Scolastico, Carlo; Piccinino, Felice; Filippini, Pietro

2006-06-01

We evaluated the clinical and virological characteristics of hepatitis A virus infection in persons concomitantly infected with hepatitis B virus (HBV) or hepatitis C virus (HCV). We enrolled 21 patients with acute hepatitis A and chronic hepatitis with no sign of liver cirrhosis, 13 patients who were positive for hepatitis B surface antigen (case B group), 8 patients who were anti-HCV positive (case C group), and 21 patients with acute hepatitis A without a preexisting liver disease (control A group). Two control groups of patients with chronic hepatitis B (control B group) or C (control C group) were also chosen. All control groups were pair-matched by age and sex with the corresponding case group. Fulminant hepatitis A was never observed, and hepatitis A had a severe course in 1 patient in the case B group and in 1 patient in the control A group. Both patients recovered. On admission, HBV DNA was detected in 1 patient in the case B group (7.7%) and in 13 patients (50%) in the control B group; HCV RNA was found in no patient in the case C group and in 16 patients (81.2%) in the control C group. Of 9 patients in the case B group who were followed up for 6 months, 3 became negative for hepatitis B surface antigen and positive for hepatitis B surface antibody, 2 remained positive for hepatitis B surface antigen and negative for HBV DNA, and 4 became positive for HBV DNA with a low viral load [corrected] Of 6 patients in the case C group who were followed up for 6 months, 3 remained negative for HCV RNA, and 3 had persistently low viral loads. Concomitant hepatitis A was always self-limited, associated with a marked inhibition of HBV and HCV genomes, and possibly had a good prognosis for the underlying chronic hepatitis.

Hepatitis C

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... viral load (the amount of HCV in your blood), imaging tests, and biopsy results. Treatment is especially important for people who are showing signs liver fibrosis or scarring. Medicines used to treat hepatitis C ...

A Chinese Herbal Medicine, Jia-Wei-Xiao-Yao-San, Prevents Dimethylnitrosamine-Induced Hepatic Fibrosis in Rats

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Shu-Chen Chien

2014-01-01

Full Text Available Jia-wei-xiao-yao-san (JWXYS is a traditional Chinese herbal medicine that is widely used to treat neuropsychological disorders. Only a few of the hepatoprotective effects of JWXYS have been studied. The aim of this study was to investigate the hepatoprotective effects of JWXYS on dimethylnitrosamine- (DMN- induced chronic hepatitis and hepatic fibrosis in rats and to clarify the mechanism through which JWXYS exerts these effects. After the rats were treated with DMN for 3 weeks, serum glutamic oxaloacetic transaminase (SGOT and serum glutamic pyruvic transaminase (SGPT levels were significantly elevated, whereas the albumin level decreased. Although DMN was continually administered, after the 3 doses of JWXYS were orally administered, the SGOT and SGPT levels significantly decreased and the albumin level was significantly elevated. In addition, JWXYS treatment prevented liver fibrosis induced by DMN. JWXYS exhibited superoxide-dismutase-like activity and dose-dependently inhibited DMN-induced lipid peroxidation and xanthine oxidase activity in the liver of rats. Our findings suggest that JWXYS exerts antifibrotic effects against DMN-induced chronic hepatic injury. The possible mechanism is at least partially attributable to the ability of JWXYS to inhibit reactive-oxygen-species-induced membrane lipid peroxidation.

In situ hybridization studies of hepatitis A viral RNA in patients with acute hepatitis A

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Taylor, M; Goldin, R D; Ladva, S [Department of Histopathology, St. Mary' s Hospital Medical School, Imperial College of Science, Technology and Medicine, London (United Kingdom); Scheuer, P J [Department of Histopathology, Royal Free Hospital and School of Medicine, London (United Kingdom); Thomas, H C [Department of Medicine, St. Mary' s Hospital Medical School, Imperial College of Science, Technology and Medicine, London (United Kingdom)

1994-01-01

In situ hybridization with oligonucleotide probes has been used to localise hepatitis A virus RNA genomic sequences in formalin-fixed and routinely processed human liver biopsies from three patients. Using radiolabelled Sulphur-35 antisense probes, viral genomic sequences were found in all three cases, but signal intensity was greatest in cases 1 and 2 with fulminant hepatitis, and was minimal in the third case of resolving hepatitis biopsied 2 months after acute illness. Localisation showed the viral RNA to be present in hepatocytes, sinusoidal cells and inflammatory cells in and around the portal tracts. Both cases showed signal in similar cell types, but the distribution of staining was predominantly periportal in case 1, whereas lobular staining was more apparent in case 2. Hybridization with sense polarity probes failed to detect any evidence of replicative intermediates of antigenomic viral RNA. The presence of hepatitis A RNA in phagocytic cells was confirmed using immunohistochemistryfor a macrophage marker, CD68, combined with in situ hybridization. In all cases the signal was predominantly cytoplasmic, and this was confirmed with the use of tritiated probes. (au).

In situ hybridization studies of hepatitis A viral RNA in patients with acute hepatitis A

International Nuclear Information System (INIS)

Taylor, M.; Goldin, R.D.; Ladva, S.; Scheuer, P.J.; Thomas, H.C.

1994-01-01

In situ hybridization with oligonucleotide probes has been used to localise hepatitis A virus RNA genomic sequences in formalin-fixed and routinely processed human liver biopsies from three patients. Using radiolabelled Sulphur-35 antisense probes, viral genomic sequences were found in all three cases, but signal intensity was greatest in cases 1 and 2 with fulminant hepatitis, and was minimal in the third case of resolving hepatitis biopsied 2 months after acute illness. Localisation showed the viral RNA to be present in hepatocytes, sinusoidal cells and inflammatory cells in and around the portal tracts. Both cases showed signal in similar cell types, but the distribution of staining was predominantly periportal in case 1, whereas lobular staining was more apparent in case 2. Hybridization with sense polarity probes failed to detect any evidence of replicative intermediates of antigenomic viral RNA. The presence of hepatitis A RNA in phagocytic cells was confirmed using immunohistochemistryfor a macrophage marker, CD68, combined with in situ hybridization. In all cases the signal was predominantly cytoplasmic, and this was confirmed with the use of tritiated probes. (au)

The noncoding human genome and the future of personalised medicine.

Science.gov (United States)

Cowie, Philip; Hay, Elizabeth A; MacKenzie, Alasdair

2015-01-30

Non-coding cis-regulatory sequences act as the 'eyes' of the genome and their role is to perceive, organise and relay cellular communication information to RNA polymerase II at gene promoters. The evolution of these sequences, that include enhancers, silencers, insulators and promoters, has progressed in multicellular organisms to the extent that cis-regulatory sequences make up as much as 10% of the human genome. Parallel evidence suggests that 75% of polymorphisms associated with heritable disease occur within predicted cis-regulatory sequences that effectively alter the 'perception' of cis-regulatory sequences or render them blind to cell communication cues. Cis-regulatory sequences also act as major functional targets of epigenetic modification thus representing an important conduit through which changes in DNA-methylation affects disease susceptibility. The objectives of the current review are (1) to describe what has been learned about identifying and characterising cis-regulatory sequences since the sequencing of the human genome; (2) to discuss their role in interpreting cell signalling pathways pathways; and (3) outline how this role may be altered by polymorphisms and epigenetic changes. We argue that the importance of the cis-regulatory genome for the interpretation of cellular communication pathways cannot be overstated and understanding its role in health and disease will be critical for the future development of personalised medicine.

Pharmacogenetics of hepatitis C: transition from interferon-based therapies to direct-acting antiviral agents

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Kamal SM

2014-06-01

Full Text Available Sanaa M Kamal1,21Department of Medicine, Division of Hepatology, Gastroenterology and Tropical Medicine, Ain Shams Faculty of Medicine, Cairo, Egypt, 2Department of Medicine, Salman Bin Abdul Aziz College of Medicine, Kingdom of Saudi ArabiaAbstract: Hepatitis C virus (HCV has emerged as a major viral pandemic over the past two decades, infecting 170 million individuals, which equates to approximately 3% of the world's population. The prevalence of HCV varies according to geographic region, being highest in developing countries such as Egypt. HCV has a high tendency to induce chronic progressive liver damage in the form of hepatic fibrosis, cirrhosis, or liver cancer. To date, there is no vaccine against HCV infection. Combination therapy comprising PEGylated interferon-alpha and ribavirin has been the standard of care for patients with chronic hepatitis C for more than a decade. However, many patients still do not respond to therapy or develop adverse events. Recently, direct antiviral agents such as protease inhibitors, polymerase inhibitors, or NS5A inhibitors have been used to augment PEGylated interferon and ribavirin, resulting in better efficacy, better tolerance, and a shorter treatment duration. However, most clinical trials have focused on assessing the efficacy and safety of direct antiviral agents in patients with genotype 1, and the response of other HCV genotypes has not been elucidated. Moreover, the prohibitive costs of such triple therapies will limit their use in patients in developing countries where most of the HCV infection exists. Understanding the host and viral factors associated with viral clearance is necessary for individualizing therapy to maximize sustained virologic response rates, prevent progression to liver disease, and increase the overall benefits of therapy with respect to its costs. Genome wide studies have shown significant associations between a set of polymorphisms in the region of the interleukin-28B (IL

Updates on genome-wide association findings in eating disorders and future application to precision medicine.

Science.gov (United States)

Breithaupt, Lauren; Hubel, Christopher; Bulik, Cynthia M

2018-02-22

Heterogeneity, frequent diagnostic fluctuation across presentations, and global concerns with the absence of effective treatments all encourage science that moves the field toward individualized or precision medicine in eating disorders. We review recent advances in psychiatric genetics focusing on genome-wide association studies (GWAS) in eating disorders and enumerate the prospects and challenges of a genomics-driven approach towards personalized intervention. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Genomic Characterization of Metformin Hepatic Response.

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Marcelo R Luizon

2016-11-01

Full Text Available Metformin is used as a first-line therapy for type 2 diabetes (T2D and prescribed for numerous other diseases. However, its mechanism of action in the liver has yet to be characterized in a systematic manner. To comprehensively identify genes and regulatory elements associated with metformin treatment, we carried out RNA-seq and ChIP-seq (H3K27ac, H3K27me3 on primary human hepatocytes from the same donor treated with vehicle control, metformin or metformin and compound C, an AMP-activated protein kinase (AMPK inhibitor (allowing to identify AMPK-independent pathways. We identified thousands of metformin responsive AMPK-dependent and AMPK-independent differentially expressed genes and regulatory elements. We functionally validated several elements for metformin-induced promoter and enhancer activity. These include an enhancer in an ataxia telangiectasia mutated (ATM intron that has SNPs in linkage disequilibrium with a metformin treatment response GWAS lead SNP (rs11212617 that showed increased enhancer activity for the associated haplotype. Expression quantitative trait locus (eQTL liver analysis and CRISPR activation suggest that this enhancer could be regulating ATM, which has a known role in AMPK activation, and potentially also EXPH5 and DDX10, its neighboring genes. Using ChIP-seq and siRNA knockdown, we further show that activating transcription factor 3 (ATF3, our top metformin upregulated AMPK-dependent gene, could have an important role in gluconeogenesis repression. Our findings provide a genome-wide representation of metformin hepatic response, highlight important sequences that could be associated with interindividual variability in glycemic response to metformin and identify novel T2D treatment candidates.

Personalized medicine and human genetic diversity.

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Lu, Yi-Fan; Goldstein, David B; Angrist, Misha; Cavalleri, Gianpiero

2014-07-24

Human genetic diversity has long been studied both to understand how genetic variation influences risk of disease and infer aspects of human evolutionary history. In this article, we review historical and contemporary views of human genetic diversity, the rare and common mutations implicated in human disease susceptibility, and the relevance of genetic diversity to personalized medicine. First, we describe the development of thought about diversity through the 20th century and through more modern studies including genome-wide association studies (GWAS) and next-generation sequencing. We introduce several examples, such as sickle cell anemia and Tay-Sachs disease that are caused by rare mutations and are more frequent in certain geographical populations, and common treatment responses that are caused by common variants, such as hepatitis C infection. We conclude with comments about the continued relevance of human genetic diversity in medical genetics and personalized medicine more generally. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

Chinese Herbal Medicine as an Adjunctive Therapy Ameliorated the Incidence of Chronic Hepatitis in Patients with Breast Cancer: A Nationwide Population-Based Cohort Study

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Kuo-Chin Huang

2017-01-01

Full Text Available We conducted a National Health Insurance Research Database-based Taiwanese nationwide population-based cohort study to evaluate whether Chinese herbal medicine (CHM treatment decreased the incidence of chronic hepatitis in breast cancer patients receiving chemotherapy and/or radiotherapy. A total of 81171 patients were diagnosed with breast cancer within the defined study period. After randomly equal matching, data from 13856 patients were analyzed. Hazard ratios of incidence rate of chronic hepatitis were used to determine the influence and therapeutic potential of CHM in patients with breast cancer. The patients with breast cancer receiving CHM treatment exhibited a significantly decreased incidence rate of chronic hepatitis even across the stratification of age, CCI score, and treatments. The cumulative incidence of chronic hepatitis for a period of seven years after initial breast cancer diagnosis was also reduced in the patients receiving CHM treatment. The ten most commonly used single herbs and formulas were effective in protecting liver function in patients with breast cancer, where Hedyotis diffusa and Jia-Wei-Xiao-Yao-San were the most commonly used herbal agents. In conclusion, our study provided information that western medicine therapy combined with CHM as an adjuvant modality may have a significant impact on liver protection in patients with breast cancer.

Determination of the full-genome sequence of hepatitis E virus (HEV) SAAS-FX17 and use as a reference to identify putative HEV genotype 4 virulence determinants.

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Zhu, Yumin; Yu, Xiaoming; Huang, Fenfen; Yu, Ruisong; Dong, Shijuan; Si, Fusheng; Zhang, Yuanshu; Li, Zhen

2012-11-08

Four major genotypes of hepatitis E virus (HEV), the causative agent of hepatitis E, have so far been recognized. While genotypes 3 and 4 are both zoonotic, the disease symptoms caused by the latter tend to be more severe. To examine if specific nucleotide/amino acid variations between genotypes 3 and 4 play a role in determining the severity of hepatitis E disease, the complete genome of one swine HEV genotype 4 isolate, SAAS-FX17, was determined and compared with other genotype 4 and genotype 3 genomes to identify putative HEV genotype 4 virulence determinants. A total of 42 conformable nt/aa variations between genotype 3 and 4 HEVs were detected, of which 19 were proposed to be potential disease severity determinants for genotype 4 strains. One potential determinant was located in each of the 5'-UTR and 3'-UTR, 3 and 12 within ORF1 and ORF2 respectively, and 2 in the junction region.

Transmission of clonal hepatitis C virus genomes reveals the dominant but transitory role of CD8¿ T cells in early viral evolution

DEFF Research Database (Denmark)

Callendret, Benoît; Bukh, Jens; Eccleston, Heather B

2011-01-01

occurred slowly over several years of chronic infection. Together these observations indicate that during acute hepatitis C, virus evolution was driven primarily by positive selection pressure exerted by CD8(+) T cells. This influence of immune pressure on viral evolution appears to subside as chronic......The RNA genome of the hepatitis C virus (HCV) diversifies rapidly during the acute phase of infection, but the selective forces that drive this process remain poorly defined. Here we examined whether Darwinian selection pressure imposed by CD8(+) T cells is a dominant force driving early amino acid...... replacement in HCV viral populations. This question was addressed in two chimpanzees followed for 8 to 10 years after infection with a well-defined inoculum composed of a clonal genotype 1a (isolate H77C) HCV genome. Detailed characterization of CD8(+) T cell responses combined with sequencing of recovered...

Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax.

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Jiang, Peng; Shi, Feng-Xue; Li, Ming-Rui; Liu, Bao; Wen, Jun; Xiao, Hong-Xing; Li, Lin-Feng

2018-01-01

Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions. Genome-wide scanning of positive selection identified five and 12 genes from the chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes.

Hepatitis B vaccination in travelers

NARCIS (Netherlands)

Sonder, Gerard J. B.

2008-01-01

An increasing number of travelers travel to hepatitis B-endemic countries. In travel medicine, vaccinations should be advised according to risks. The actual incidence of hepatitis B infection in short-term tourists is very low and probably not higher than it is for people who do not travel. There is

Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions.

Science.gov (United States)

Urasaki, Naoya; Takagi, Hiroki; Natsume, Satoshi; Uemura, Aiko; Taniai, Naoki; Miyagi, Norimichi; Fukushima, Mai; Suzuki, Shouta; Tarora, Kazuhiko; Tamaki, Moritoshi; Sakamoto, Moriaki; Terauchi, Ryohei; Matsumura, Hideo

2017-02-01

Bitter gourd (Momordica charantia) is an important vegetable and medicinal plant in tropical and subtropical regions globally. In this study, the draft genome sequence of a monoecious bitter gourd inbred line, OHB3-1, was analyzed. Through Illumina sequencing and de novo assembly, scaffolds of 285.5 Mb in length were generated, corresponding to ∼84% of the estimated genome size of bitter gourd (339 Mb). In this draft genome sequence, 45,859 protein-coding gene loci were identified, and transposable elements accounted for 15.3% of the whole genome. According to synteny mapping and phylogenetic analysis of conserved genes, bitter gourd was more related to watermelon (Citrullus lanatus) than to cucumber (Cucumis sativus) or melon (C. melo). Using RAD-seq analysis, 1507 marker loci were genotyped in an F2 progeny of two bitter gourd lines, resulting in an improved linkage map, comprising 11 linkage groups. By anchoring RAD tag markers, 255 scaffolds were assigned to the linkage map. Comparative analysis of genome sequences and predicted genes determined that putative trypsin-inhibitor and ribosome-inactivating genes were distinctive in the bitter gourd genome. These genes could characterize the bitter gourd as a medicinal plant. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Sequence relationships between the genome and the intracellular RNA species 1,3,6 and 7 of mouse hepatitis virus strain A59

NARCIS (Netherlands)

Horzinek, M.C.; Spaan, W.J.M.; Rottier, P.J.M.; Zeijst, B.A.M. van der

1982-01-01

We have shown by T1 oligonucleotide fingerprinting that the genome of mouse hepatitis virus strain A59 and its intracellular RNA 1 have identical fingerprints and that RNA 1 and the subgenomic RNAs 3, 6, and 7 contain common sequences. To localize the homologous region between the RNAs, we compared

Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma.

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Pectasides, Eirini; Stachler, Matthew D; Derks, Sarah; Liu, Yang; Maron, Steven; Islam, Mirazul; Alpert, Lindsay; Kwak, Heewon; Kindler, Hedy; Polite, Blase; Sharma, Manish R; Allen, Kenisha; O'Day, Emily; Lomnicki, Samantha; Maranto, Melissa; Kanteti, Rajani; Fitzpatrick, Carrie; Weber, Christopher; Setia, Namrata; Xiao, Shu-Yuan; Hart, John; Nagy, Rebecca J; Kim, Kyoung-Mee; Choi, Min-Gew; Min, Byung-Hoon; Nason, Katie S; O'Keefe, Lea; Watanabe, Masayuki; Baba, Hideo; Lanman, Rick; Agoston, Agoston T; Oh, David J; Dunford, Andrew; Thorner, Aaron R; Ducar, Matthew D; Wollison, Bruce M; Coleman, Haley A; Ji, Yuan; Posner, Mitchell C; Roggin, Kevin; Turaga, Kiran; Chang, Paul; Hogarth, Kyle; Siddiqui, Uzma; Gelrud, Andres; Ha, Gavin; Freeman, Samuel S; Rhoades, Justin; Reed, Sarah; Gydush, Greg; Rotem, Denisse; Davison, Jon; Imamura, Yu; Adalsteinsson, Viktor; Lee, Jeeyun; Bass, Adam J; Catenacci, Daniel V

2018-01-01

Gastroesophageal adenocarcinoma (GEA) is a lethal disease where targeted therapies, even when guided by genomic biomarkers, have had limited efficacy. A potential reason for the failure of such therapies is that genomic profiling results could commonly differ between the primary and metastatic tumors. To evaluate genomic heterogeneity, we sequenced paired primary GEA and synchronous metastatic lesions across multiple cohorts, finding extensive differences in genomic alterations, including discrepancies in potentially clinically relevant alterations. Multiregion sequencing showed significant discrepancy within the primary tumor (PT) and between the PT and disseminated disease, with oncogene amplification profiles commonly discordant. In addition, a pilot analysis of cell-free DNA (cfDNA) sequencing demonstrated the feasibility of detecting genomic amplifications not detected in PT sampling. Lastly, we profiled paired primary tumors, metastatic tumors, and cfDNA from patients enrolled in the personalized antibodies for GEA (PANGEA) trial of targeted therapies in GEA and found that genomic biomarkers were recurrently discrepant between the PT and untreated metastases. Divergent primary and metastatic tissue profiling led to treatment reassignment in 32% (9/28) of patients. In discordant primary and metastatic lesions, we found 87.5% concordance for targetable alterations in metastatic tissue and cfDNA, suggesting the potential for cfDNA profiling to enhance selection of therapy. Significance: We demonstrate frequent baseline heterogeneity in targetable genomic alterations in GEA, indicating that current tissue sampling practices for biomarker testing do not effectively guide precision medicine in this disease and that routine profiling of metastatic lesions and/or cfDNA should be systematically evaluated. Cancer Discov; 8(1); 37-48. ©2017 AACR. See related commentary by Sundar and Tan, p. 14 See related article by Janjigian et al., p. 49 This article is highlighted

The Information Technology Infrastructure for the Translational Genomics Core and the Partners Biobank at Partners Personalized Medicine

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Natalie Boutin

2016-01-01

Full Text Available The Biobank and Translational Genomics core at Partners Personalized Medicine requires robust software and hardware. This Information Technology (IT infrastructure enables the storage and transfer of large amounts of data, drives efficiencies in the laboratory, maintains data integrity from the time of consent to the time that genomic data is distributed for research, and enables the management of complex genetic data. Here, we describe the functional components of the research IT infrastructure at Partners Personalized Medicine and how they integrate with existing clinical and research systems, review some of the ways in which this IT infrastructure maintains data integrity and security, and discuss some of the challenges inherent to building and maintaining such infrastructure.

Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine

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Wenming Xiao

2016-04-01

immune-response, tailoring drug therapy and detecting tumors. We believe the precision medicine would largely benefit from bioinformatics solutions, particularly for personal genome assembly.

Hepatitis B

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... which can lower your chances of developing serious health problems. Your doctor may recommend screening for hepatitis B if you ... see a doctor who specializes in liver diseases. Doctors can treat the health problems related to cirrhosis with medicines, surgery, and other ...

Comparative Effectiveness Research, Genomics-Enabled Personalized Medicine, and Rapid Learning Health Care: A Common Bond

Science.gov (United States)

Ginsburg, Geoffrey S.; Kuderer, Nicole M.

2012-01-01

Despite stunning advances in our understanding of the genetics and the molecular basis for cancer, many patients with cancer are not yet receiving therapy tailored specifically to their tumor biology. The translation of these advances into clinical practice has been hindered, in part, by the lack of evidence for biomarkers supporting the personalized medicine approach. Most stakeholders agree that the translation of biomarkers into clinical care requires evidence of clinical utility. The highest level of evidence comes from randomized controlled clinical trials (RCTs). However, in many instances, there may be no RCTs that are feasible for assessing the clinical utility of potentially valuable genomic biomarkers. In the absence of RCTs, evidence generation will require well-designed cohort studies for comparative effectiveness research (CER) that link detailed clinical information to tumor biology and genomic data. CER also uses systematic reviews, evidence-quality appraisal, and health outcomes research to provide a methodologic framework for assessing biologic patient subgroups. Rapid learning health care (RLHC) is a model in which diverse data are made available, ideally in a robust and real-time fashion, potentially facilitating CER and personalized medicine. Nonetheless, to realize the full potential of personalized care using RLHC requires advances in CER and biostatistics methodology and the development of interoperable informatics systems, which has been recognized by the National Cancer Institute's program for CER and personalized medicine. The integration of CER methodology and genomics linked to RLHC should enhance, expedite, and expand the evidence generation required for fully realizing personalized cancer care. PMID:23071236

Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification.

Science.gov (United States)

Li, Hui; Stoddard, Mark B; Wang, Shuyi; Giorgi, Elena E; Blair, Lily M; Learn, Gerald H; Hahn, Beatrice H; Alter, Harvey J; Busch, Michael P; Fierer, Daniel S; Ribeiro, Ruy M; Perelson, Alan S; Bhattacharya, Tanmoy; Shaw, George M

2016-01-01

Despite the recent development of highly effective anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and development of an effective vaccine. A precise molecular identification of transmitted/founder (T/F) HCV genomes that lead to productive clinical infection could play a critical role in vaccine research, as it has for HIV-1. However, the replication schema of these two RNA viruses differ substantially, as do viral responses to innate and adaptive host defenses. These differences raise questions as to the certainty of T/F HCV genome inferences, particularly in cases where multiple closely related sequence lineages have been observed. To clarify these issues and distinguish between competing models of early HCV diversification, we examined seven cases of acute HCV infection in humans and chimpanzees, including three examples of virus transmission between linked donors and recipients. Using single-genome sequencing (SGS) of plasma vRNA, we found that inferred T/F sequences in recipients were identical to viral sequences in their respective donors. Early in infection, HCV genomes generally evolved according to a simple model of random evolution where the coalescent corresponded to the T/F sequence. Closely related sequence lineages could be explained by high multiplicity infection from a donor whose viral sequences had undergone a pretransmission bottleneck due to treatment, immune selection, or recent infection. These findings validate SGS, together with mathematical modeling and phylogenetic analysis, as a novel strategy to infer T/F HCV genome sequences. Despite the recent development of highly effective, interferon-sparing anti-hepatitis C virus (HCV) drugs, the global burden of this pathogen remains immense. Control or eradication of HCV will likely require the broad application of antiviral drugs and the development of an effective

[The interpretation and integration of traditional Chinese phytotherapy into Western-type medicine with the possession of knowledge of the human genome].

Science.gov (United States)

Blázovics, Anna

2018-05-01

The terminology of traditional Chinese medicine (TCM) is hardly interpretable in the context of human genome, therefore the human genome program attracted attention towards the Western practice of medicine in China. In the last two decades, several important steps could be observed in China in relation to the approach of traditional Chinese and Western medicine. The Chinese government supports the realization of information databases for research in order to clarify the molecular biology level to detect associations between gene expression signal transduction pathways and protein-protein interactions, and the effects of bioactive components of Chinese drugs and their effectiveness. The values of TCM are becoming more and more important for Western medicine as well, because molecular biological therapies did not redeem themselves, e.g., in tumor therapy. Orv Hetil. 2018; 159(18): 696-702.

Unravelling the genome of Holy basil: an "incomparable" "elixir of life" of traditional Indian medicine.

Science.gov (United States)

Rastogi, Shubhra; Kalra, Alok; Gupta, Vikrant; Khan, Feroz; Lal, Raj Kishori; Tripathi, Anil Kumar; Parameswaran, Sriram; Gopalakrishnan, Chellappa; Ramaswamy, Gopalakrishna; Shasany, Ajit Kumar

2015-05-28

Ocimum sanctum L. (O. tenuiflorum) family-Lamiaceae is an important component of Indian tradition of medicine as well as culture around the world, and hence is known as "Holy basil" in India. This plant is mentioned in the ancient texts of Ayurveda as an "elixir of life" (life saving) herb and worshipped for over 3000 years due to its healing properties. Although used in various ailments, validation of molecules for differential activities is yet to be fully analyzed, as about 80 % of the patents on this plant are on extracts or the plant parts, and mainly focussed on essential oil components. With a view to understand the full metabolic potential of this plant whole nuclear and chloroplast genomes were sequenced for the first time combining the sequence data from 4 libraries and three NGS platforms. The saturated draft assembly of the genome was about 386 Mb, along with the plastid genome of 142,245 bp, turning out to be the smallest in Lamiaceae. In addition to SSR markers, 136 proteins were identified as homologous to five important plant genomes. Pathway analysis indicated an abundance of phenylpropanoids in O. sanctum. Phylogenetic analysis for chloroplast proteome placed Salvia miltiorrhiza as the nearest neighbor. Comparison of the chemical compounds and genes availability in O. sanctum and S. miltiorrhiza indicated the potential for the discovery of new active molecules. The genome sequence and annotation of O. sanctum provides new insights into the function of genes and the medicinal nature of the metabolites synthesized in this plant. This information is highly beneficial for mining biosynthetic pathways for important metabolites in related species.

Medicinal plants with hepatoprotective activity in Iranian folk medicine

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Majid Asadi-Samani

2015-02-01

Full Text Available There are a number of medicinal combinations in the Iranian traditional medicine which are commonly used as tonic for liver. In this review, we have introduced some medicinal plants that are used mainly for the treatment of liver disorders in Iranian folk medicine, with focus on their hepatoprotective effects particularly against CC14 agent. In this study, online databases including Web of Science, PubMed, Scopus, and Science Direct were searched for papers published from January 1970 to December 2013. Search terms consisted of medicinal plants, traditional medicine, folk medicine, hepatoprotective, Iran, liver, therapeutic uses, compounds, antioxidant, CC14, anti-inflammatory, and antihepatotoxic, hepatitis, alone or in combination. Allium hirtifolium Boiss., Apium graveolens L., Cynara scolymus, Berberis vulgaris L., Calendula officinalis, Nigella sativa L., Taraxacum officinale, Tragopogon porrifolius, Prangos ferulacea L., Allium sativum, Marrubium vulgare, Ammi majus L., Citrullus lanatus Thunb, Agrimonia eupatoria L. and Prunus armeniaca L. are some of the medicinal plants that have been used for the treatment of liver disorders in Iranian folk medicine. Out of several leads obtained from plants containing potential hepatoprotective agents, silymarin, β-sitosterol, betalain, neoandrographolide, phyllanthin, andrographolide, curcumin, picroside, hypophyllanthin, kutkoside, and glycyrrhizin have been demonstrated to have potent hepatoprotective properties. Despite encouraging data on possibility of new discoveries in the near future, the evidence on treating viral hepatitis or other chronic liver diseases by herbal medications is not adequate.

Antibody and immune memory persistence post infant hepatitis B vaccination

Directory of Open Access Journals (Sweden)

Hudu SA

2013-09-01

Full Text Available Shuaibu A Hudu,1,2 Yasmin A Malik,3 Mohd Taib Niazlin,1 Nabil S Harmal,1,4 Ariza Adnan,5 Ahmed S Alshrari,1 Zamberi Sekawi1 1Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Selangor, Malaysia; 2Department of Pathology and Medical Microbiology, College of Health Sciences, Usmanu Danfodiyo University Sokoto, Sokoto State, Nigeria; 3Department of Clinical Science, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Selangor, Malaysia; 4Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen; 5Cluster of Laboratory Medical Sciences, Faculty of Medicine Universiti Teknologi MARA, Sungai Buloh, Selangor, Malaysia Objectives: This study aimed to evaluate the level of hepatitis B immunity among undergraduate students 23 years after commencement of the nationwide hepatitis B childhood immunization program in Malaysia. Methods: A total of 402 serum samples obtained from volunteer undergraduate students were screened for the presence of hepatitis B surface antibodies using qualitative ELISA. Results: Results showed that 62.7% of volunteers had protective anti-hepatitis B surface antigens (≥10 IU/L, of whom 67.9% received three doses of the vaccine. The estimated post-vaccination immunity was found to be at least 20 years, indicating persistent immunity against hepatitis B and a significant association (P < 0.05 with duration of vaccination. Anamnestic response 1 month post-hepatitis B booster was 94.0% and highly significant (P < 0.01. Isolated anti-hepatitis B core antigen (anti-HBc prevalence was found to be 5.0%, all having had a positive anamnestic response. Conclusion: Immunity after primary vaccination with hepatitis B recombinant vaccine persists for at least 20 years post-vaccination, with significant association with the number of vaccinations. Furthermore, the presence of anamnestic response to

Genetic determinants of hepatic steatosis in man

Science.gov (United States)

Hooper, Amanda J.; Adams, Leon A.; Burnett, John R.

2011-01-01

Hepatic steatosis is one of the most common liver disorders in the general population. The main cause of hepatic steatosis is nonalcoholic fatty liver disease (NAFLD), representing the hepatic component of the metabolic syndrome, which is characterized by type 2 diabetes, obesity, and dyslipidemia. Insulin resistance and excess adiposity are considered to play key roles in the pathogenesis of NAFLD. Although the risk factors for NAFLD are well established, the genetic basis of hepatic steatosis is largely unknown. Here we review recent progress on genomic variants and their association with hepatic steatosis and discuss the potential impact of these genetic studies on clinical practice. Identifying the genetic determinants of hepatic steatosis will lead to a better understanding of the pathogenesis and progression of NAFLD. PMID:21245030

Hepatitis E: Molecular Virology and Pathogenesis

Science.gov (United States)

Panda, Subrat K.; Varma, Satya P.K.

2013-01-01

Hepatitis E virus is a single, positive-sense, capped and poly A tailed RNA virus classified under the family Hepeviridae. Enteric transmission, acute self-limiting hepatitis, frequent epidemic and sporadic occurrence, high mortality in affected pregnants are hallmarks of hepatitis E infection. Lack of an efficient culture system and resulting reductionist approaches for the study of replication and pathogenesis of HEV made it to be a less understood agent. Early studies on animal models, sub-genomic expression of open reading frames (ORF) and infectious cDNA clones have helped in elucidating the genome organization, important stages in HEV replication and pathogenesis. The genome contains three ORF's and three untranslated regions (UTR). The 5′ distal ORF, ORF1 is translated by host ribosomes in a cap dependent manner to form the non-structural polyprotein including the viral replicase. HEV replicates via a negative-sense RNA intermediate which helps in the formation of the positive-sense genomic RNA and a single bi-cistronic sub-genomic RNA. The 3′ distal ORF's including the major structural protein pORF2 and the multifunctional host interacting protein pORF3 are translated from the sub-genomic RNA. Pathogenesis in HEV infections is not well articulated, and remains a concern due to the many aspects like host dependent and genotype specific variations. Animal HEV, zoonosis, chronicity in immunosuppressed patients, and rapid decompensation in affected chronic liver diseased patients warrants detailed investigation of the underlying pathogenesis. Recent advances about structure, entry, egress and functional characterization of ORF1 domains has furthered our understanding about HEV. This article is an effort to review our present understanding about molecular biology and pathogenesis of HEV. PMID:25755485

Fine-needle aspirate cytology suggesting hepatic lipidosis in four cats with infiltrative hepatic disease.

Science.gov (United States)

Willard, M D; Weeks, B R; Johnson, M

1999-12-01

Four cats are reported in which cytology smears obtained by ultrasound-guided fine needle aspiration of the liver were interpreted as indicative of hepatic lipidosis. However, histopathology of hepatic tissue samples obtained with Tru-Cut-like needles or wedge biopsy revealed that the cats had inflammatory or neoplastic hepatic disease causing their clinical signs. Fine needle aspiration and cytology may not detect infiltrative lesions, particularly those that are nodular, multifocal, or localised around the portal regions. Fine needle aspirate cytology is a useful diagnostic procedure with many advantages, but care must be taken to avoid diagnosing hepatic lipidosis as the cause of illness when an infiltrative lesion is responsible. Copyright 1999 European Society of Feline Medicine.

Transmission af hepatitis E i Danmark

DEFF Research Database (Denmark)

Lindberg, Jens; Böttiger, Blenda; Norder, Heléne

2009-01-01

A case of acute hepatitis due to hepatitis E virus genotype 3 was diagnosed by serology and genomic sequencing. Phylogenetic analysis demonstrated a strain identical to one isolated from a Swedish pig, which supports the hypothesis that swine serves as reservoirs for HEV infection. The patient did...... not have any recent travel history, had experienced no contact with animals and the origin of the infection remained unknown. We emphasize that health personnel should be aware of acute hepatitis E even among patients without a travel history. Udgivelsesdato: 2009-Jun-22...

Real-World Evidence In Support Of Precision Medicine: Clinico-Genomic Cancer Data As A Case Study.

Science.gov (United States)

Agarwala, Vineeta; Khozin, Sean; Singal, Gaurav; O'Connell, Claire; Kuk, Deborah; Li, Gerald; Gossai, Anala; Miller, Vincent; Abernethy, Amy P

2018-05-01

The majority of US adult cancer patients today are diagnosed and treated outside the context of any clinical trial (that is, in the real world). Although these patients are not part of a research study, their clinical data are still recorded. Indeed, data captured in electronic health records form an ever-growing, rich digital repository of longitudinal patient experiences, treatments, and outcomes. Likewise, genomic data from tumor molecular profiling are increasingly guiding oncology care. Linking real-world clinical and genomic data, as well as information from other co-occurring data sets, could create study populations that provide generalizable evidence for precision medicine interventions. However, the infrastructure required to link, ensure quality, and rapidly learn from such composite data is complex. We outline the challenges and describe a novel approach to building a real-world clinico-genomic database of patients with cancer. This work represents a case study in how data collected during routine patient care can inform precision medicine efforts for the population at large. We suggest that health policies can promote innovation by defining appropriate uses of real-world evidence, establishing data standards, and incentivizing data sharing.

Genome-wide association study identifies variants associated with autoimmune hepatitis type 1.

Science.gov (United States)

de Boer, Ynto S; van Gerven, Nicole M F; Zwiers, Antonie; Verwer, Bart J; van Hoek, Bart; van Erpecum, Karel J; Beuers, Ulrich; van Buuren, Henk R; Drenth, Joost P H; den Ouden, Jannie W; Verdonk, Robert C; Koek, Ger H; Brouwer, Johannes T; Guichelaar, Maureen M J; Vrolijk, Jan M; Kraal, Georg; Mulder, Chris J J; van Nieuwkerk, Carin M J; Fischer, Janett; Berg, Thomas; Stickel, Felix; Sarrazin, Christoph; Schramm, Christoph; Lohse, Ansgar W; Weiler-Normann, Christina; Lerch, Markus M; Nauck, Matthias; Völzke, Henry; Homuth, Georg; Bloemena, Elisabeth; Verspaget, Hein W; Kumar, Vinod; Zhernakova, Alexandra; Wijmenga, Cisca; Franke, Lude; Bouma, Gerd

2014-08-01

Autoimmune hepatitis (AIH) is an uncommon autoimmune liver disease of unknown etiology. We used a genome-wide approach to identify genetic variants that predispose individuals to AIH. We performed a genome-wide association study of 649 adults in The Netherlands with AIH type 1 and 13,436 controls. Initial associations were further analyzed in an independent replication panel comprising 451 patients with AIH type 1 in Germany and 4103 controls. We also performed an association analysis in the discovery cohort using imputed genotypes of the major histocompatibility complex region. We associated AIH with a variant in the major histocompatibility complex region at rs2187668 (P = 1.5 × 10(-78)). Analysis of this variant in the discovery cohort identified HLA-DRB1*0301 (P = 5.3 × 10(-49)) as a primary susceptibility genotype and HLA-DRB1*0401 (P = 2.8 × 10(-18)) as a secondary susceptibility genotype. We also associated AIH with variants of SH2B3 (rs3184504, 12q24; P = 7.7 × 10(-8)) and CARD10 (rs6000782, 22q13.1; P = 3.0 × 10(-6)). In addition, strong inflation of association signal was found with single-nucleotide polymorphisms associated with other immune-mediated diseases, including primary sclerosing cholangitis and primary biliary cirrhosis, but not with single-nucleotide polymorphisms associated with other genetic traits. In a genome-wide association study, we associated AIH type 1 with variants in the major histocompatibility complex region, and identified variants of SH2B3and CARD10 as likely risk factors. These findings support a complex genetic basis for AIH pathogenesis and indicate that part of the genetic susceptibility overlaps with that for other immune-mediated liver diseases. Copyright © 2014 AGA Institute. Published by Elsevier Inc. All rights reserved.

Asymmetric Modification of Hepatitis B Virus (HBV) Genomes by an Endogenous Cytidine Deaminase inside HBV Cores Informs a Model of Reverse Transcription.

Science.gov (United States)

Nair, Smita; Zlotnick, Adam

2018-05-15

Cytidine deaminases inhibit replication of a broad range of DNA viruses by deaminating cytidines on single-stranded DNA (ssDNA) to generate uracil. While several lines of evidence have revealed hepatitis B virus (HBV) genome editing by deamination, it is still unclear which nucleic acid intermediate of HBV is modified. Hepatitis B virus has a relaxed circular double-stranded DNA (rcDNA) genome that is reverse transcribed within virus cores from a RNA template. The HBV genome also persists as covalently closed circular DNA (cccDNA) in the nucleus of an infected cell. In the present study, we found that in HBV-producing HepAD38 and HepG2.2.15 cell lines, endogenous cytidine deaminases edited 10 to 25% of HBV rcDNA genomes, asymmetrically with almost all mutations on the 5' half of the minus strand. This region corresponds to the last half of the minus strand to be protected by plus-strand synthesis. Within this half of the genome, the number of mutations peaks in the middle. Overexpressed APOBEC3A and APOBEC3G could be packaged in HBV capsids but did not change the amount or distribution of mutations. We found no deamination on pregenomic RNA (pgRNA), indicating that an intact genome is encapsidated and deaminated during or after reverse transcription. The deamination pattern suggests a model of rcDNA synthesis in which pgRNA and then newly synthesized minus-sense single-stranded DNA are protected from deaminase by interaction with the virus capsid; during plus-strand synthesis, when enough dsDNA has been synthesized to displace the remaining minus strand from the capsid surface, the single-stranded DNA becomes deaminase sensitive. IMPORTANCE Host-induced mutation of the HBV genome by APOBEC proteins may be a path to clearing the virus. We examined cytidine-to-thymidine mutations in the genomes of HBV particles grown in the presence or absence of overexpressed APOBEC proteins. We found that genomes were subjected to deamination activity during reverse transcription

Evidence for quasispecies distributions in the human hepatitis A virus genome

International Nuclear Information System (INIS)

Sanchez, Gloria; Bosch, Albert; Gomez-Mariano, Gema; Domingo, Esteban; Pinto, Rosa M.

2003-01-01

Nucleotide sequence analysis of multiple molecular clones of the hepatitis A virus (HAV), generated by reverse transcription-PCR of two capsid-coding regions, revealed a degree of heterogeneity compatible with a quasispecies structure in three clinical samples. Passage of plaque-purified reference strain HAV pHM175 43c in FRhK-4 cells documented the generation of a mutant distribution of HAV genomes. The mutant spectra showed mutation frequencies in the range of 1 x 10 -3 to 1 x 10 -4 substitutions per nucleotide, with a dominance of transition over transversion mutations. While in the VP3-coding region, nonsynonymous mutations were predominant; in the VP1-coding region they were uncommon. Around 50% of the amino acid replacements involved residues located at or near antigenic sites. Most of the detected mutations occurred at or in the vicinity of rare codons, suggesting a dynamics of mutation-selection, predominantly at and around rare codons. The results indicate that despite antigenic conservation, HAV replicates as a complex distribution of mutants, a feature of viral quasispecies

Hepatitis E Virus in Cambodia: Prevalence among the General Population and Complete Genome Sequence of Genotype 4.

Science.gov (United States)

Yamada, Hiroko; Takahashi, Kazuaki; Lim, Olline; Svay, Somana; Chuon, Channarena; Hok, Sirany; Do, Son Huy; Fujimoto, Mayumi; Akita, Tomoyuki; Goto, Noboru; Katayama, Keiko; Arai, Masahiro; Tanaka, Junko

2015-01-01

Hepatitis E virus (HEV) is a growing public health problem in many countries. In this study, we investigated HEV seroprevalence among the general population in the Siem Reap province, Cambodia, and performed HEV genetic analysis with the aim to develop an HEV prevention strategy. This seroepidemiological cross-sectional study conducted from 2010 to 2014 included 868 participants from four different locations in Siem Reap province, Cambodia. They answered questionnaires and provided blood samples for the analysis of hepatitis virus infections. Among the participants (360 men and 508 women; age range, 7-90 years), the prevalence of anti-HEV IgG was 18.4% (95% confidence interval: 15.9-21.0); HEV RNA was detected in two participants (0.23%) and was classified as genotype 3 and 4. Full-length genome of the genotype 4 isolate, CVS-Sie10, was sequenced; it contained 7,222 nucleotides and three ORFs and demonstrated high sequence identity with the swine China isolates swGX40 (95.57%), SS19 (94.37%), and swDQ (91.94%). Multivariate logistic regression analysis revealed that men, elderly people, and house workers were risk groups significantly associated with the positivity for anti-HEV IgG. This is the first report on the detection of HEV genotype 4 in humans in Cambodia and on the complete genome sequence of HEV genotype 4 from this country. Our study demonstrates that new HEV infection cases occur frequently among the general population in Cambodia, and effective preventive measures are required.

Hepatitis E Virus in Cambodia: Prevalence among the General Population and Complete Genome Sequence of Genotype 4.

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Hiroko Yamada

Full Text Available Hepatitis E virus (HEV is a growing public health problem in many countries. In this study, we investigated HEV seroprevalence among the general population in the Siem Reap province, Cambodia, and performed HEV genetic analysis with the aim to develop an HEV prevention strategy. This seroepidemiological cross-sectional study conducted from 2010 to 2014 included 868 participants from four different locations in Siem Reap province, Cambodia. They answered questionnaires and provided blood samples for the analysis of hepatitis virus infections. Among the participants (360 men and 508 women; age range, 7-90 years, the prevalence of anti-HEV IgG was 18.4% (95% confidence interval: 15.9-21.0; HEV RNA was detected in two participants (0.23% and was classified as genotype 3 and 4. Full-length genome of the genotype 4 isolate, CVS-Sie10, was sequenced; it contained 7,222 nucleotides and three ORFs and demonstrated high sequence identity with the swine China isolates swGX40 (95.57%, SS19 (94.37%, and swDQ (91.94%. Multivariate logistic regression analysis revealed that men, elderly people, and house workers were risk groups significantly associated with the positivity for anti-HEV IgG. This is the first report on the detection of HEV genotype 4 in humans in Cambodia and on the complete genome sequence of HEV genotype 4 from this country. Our study demonstrates that new HEV infection cases occur frequently among the general population in Cambodia, and effective preventive measures are required.

2015 Philip S. Portoghese Medicinal Chemistry Lectureship. Curing Hepatitis C Virus Infection with Direct-Acting Antiviral Agents: The Arc of a Medicinal Chemistry Triumph.

Science.gov (United States)

Meanwell, Nicholas A

2016-08-25

The development of direct-acting antiviral agents that can cure a chronic hepatitis C virus (HCV) infection after 8-12 weeks of daily, well-tolerated therapy has revolutionized the treatment of this insidious disease. In this article, three of Bristol-Myers Squibb's HCV programs are summarized, each of which produced a clinical candidate: the NS3 protease inhibitor asunaprevir (64), marketed as Sunvepra, the NS5A replication complex inhibitor daclatasvir (117), marketed as Daklinza, and the allosteric NS5B polymerase inhibitor beclabuvir (142), which is in late stage clinical studies. A clinical study with 64 and 117 established for the first time that a chronic HCV infection could be cured by treatment with direct-acting antiviral agents alone in the absence of interferon. The development of small molecule HCV therapeutics, designed by medicinal chemists, has been hailed as "the arc of a medical triumph" but may equally well be described as "the arc of a medicinal chemistry triumph".

Medicina genómica aplicada a la salud pública An overview in genomic medicine and public health

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Ana Burguete

2009-01-01

Full Text Available La genómica, visualizada como una disciplina científica encargada del mapeo, secuenciación y análisis de los genomas, ha facilitado la identificación y comprensión de las formas de organización y función de los genes de los organismos, lo cual ha generado un amplio conocimiento de la estructura y la función de los genomas. La influencia de la genómica en la medicina ha creado una nueva visión acerca de la forma de percibir los episodios patológicos y fisiológicos, tras conocer la influencia de las variaciones genéticas sobre la susceptibilidad a la enfermedad. En la salud pública, mediante la epidemiología genética, el conocimiento genético ha promovido acciones individuales y poblacionales para evaluar el efecto de la distribución de los determinantes genéticos y su interacción con factores ambientales en la etiología de las enfermedades humanas. De modo adicional, la medicina genómica propone nuevos sistemas de diagnóstico, relaciones genéticas y alteraciones alimenticias, respuesta específica a diversos medicamentos y diseño de nuevos fármacos para grupos susceptibles. Sin embargo, los grandes avances de la medicina genómica en el campo de la salud aún son sólo promisorios.Genomics, as a scientific discipline responsible for genome maps, sequencing and functional analysis of genomes, allows for continually expanding knowledge of the structure and function of genomes. The influence of genomics on medicine generates a new perspective for how we perceive health and disease, knowing the influence of genetic variations on susceptibility to disease. In the area of public health, genetic epidemiology translates genetic knowledge into individual and public actions, evaluating the effect of the distribution of genetic determinants and their interaction with environmental factors involved in the etiology of human diseases. In addition, genomic medicine suggests new diagnostic systems, genetic associations and nutritional

Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense

Science.gov (United States)

Zhu, Yingjie; Xu, Jiang; Sun, Chao; Zhou, Shiguo; Xu, Haibin; Nelson, David R.; Qian, Jun; Song, Jingyuan; Luo, Hongmei; Xiang, Li; Li, Ying; Xu, Zhichao; Ji, Aijia; Wang, Lizhi; Lu, Shanfa; Hayward, Alice; Sun, Wei; Li, Xiwen; Schwartz, David C.; Wang, Yitao; Chen, Shilin

2015-01-01

Fungi have evolved powerful genomic and chemical defense systems to protect themselves against genetic destabilization and other organisms. However, the precise molecular basis involved in fungal defense remain largely unknown in Basidiomycetes. Here the complete genome sequence, as well as DNA methylation patterns and small RNA transcriptomes, was analyzed to provide a holistic overview of secondary metabolism and defense processes in the model medicinal fungus, Ganoderma sinense. We reported the 48.96 Mb genome sequence of G. sinense, consisting of 12 chromosomes and encoding 15,688 genes. More than thirty gene clusters involved in the biosynthesis of secondary metabolites, as well as a large array of genes responsible for their transport and regulation were highlighted. In addition, components of genome defense mechanisms, namely repeat-induced point mutation (RIP), DNA methylation and small RNA-mediated gene silencing, were revealed in G. sinense. Systematic bioinformatic investigation of the genome and methylome suggested that RIP and DNA methylation combinatorially maintain G. sinense genome stability by inactivating invasive genetic material and transposable elements. The elucidation of the G. sinense genome and epigenome provides an unparalleled opportunity to advance our understanding of secondary metabolism and fungal defense mechanisms. PMID:26046933

Nursing implications for Hepatic arterial perfusion scintigraphy

International Nuclear Information System (INIS)

Ellender, R.

1999-01-01

Nurses working in Nuclear Medicine assist in Hepatic Artery Catheter (HAC) perfusion studies. This scan is not widely performed in Australia, the St George hospital for example performs approximately five per year. The purpose of this article is firstly to review the indications and rationale of HAC patency studies. Secondly, this article will stress the clinical implications for the Nuclear Medicine Nurse during this study. Emphasis will be placed on the importance of patient education during the procedure. A brief overview of hepatic anatomy and the radiopharmaceuticals administered during the scan is discussed. Finally, a step by step protocol is presented to show how the perfusion/ shunt study is performed. Copyright (1999) The Australian and New Zealand Society of Nuclear Medicine Inc

XTC-induced hepatitis

NARCIS (Netherlands)

Oranje, W.A.; van Pol, V.; van der Wurff, A.A.; Zeijen, R.N.; Stockbrügger, R.W.; Arends, J.W.

1994-01-01

XTC-induced hepatitis. Oranje WA, von Pol P, vd Wurff A, Zeijen RN, Stockbrugger RW, Arends JW. Department of Internal Medicine, University Hospital, Maastricht, Netherlands. An increasing number of severe complications associated with the use of XTC is being reported. After 11 earlier case reports

Genomic research perspectives in Kazakhstan

Directory of Open Access Journals (Sweden)

Ainur Akilzhanova

2014-01-01

Full Text Available Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well

Cambridge Healthtech Institute's 5th Annual Conference: impact of genomics on medicine.

Science.gov (United States)

Zanders, E D

2001-08-01

The recent publications in Nature and Science by the Human Genome Consortium and Celera Genomics, respectively, while being landmark achievements in themselves, have also given pause for thought. A definitive catalogue of human genes is still not available but the broad picture of how humans compare with lower organisms at the genomic level is becoming clearer. The full impact of these findings on the practice of medicine is hard to predict, but research being conducted now, in the early years of the 21st century, will form the basis of future advances in the diagnosis and treatment of disease. Exactly what this will entail is the subject of intense debate, but there are some common starting points that were discussed at this meeting in Munich. The main theme to emerge was the need to move beyond the human genome sequence towards an understanding of proteins and their interactions in complex biological pathways, thereby increasing opportunities for drug discovery through the identification of new targets. The majority of the talks were therefore devoted to the description of technological advances in the analysis of gene and protein expression (and interaction) and in the use of various methods of gene deletion in order to validate individual proteins as drug targets. Perhaps it will still be a few years before it will be possible to report on the application of genomic analyses to routine medical practice at the first point of care for patients but when that happens, the research efforts described here will have been worthwhile.

Evidence for a Complex Mosaic Genome Pattern in a Full-length Hepatitis C Virus Sequence

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R.S. Ross

2008-01-01

Full Text Available The genome of the hepatitis C virus (HCV exhibits a high genetic variability. This remarkable heterogeneity is mainly attributed to the gradual accumulation of mutational changes, whereas the contribution of recombination events to the evolution of HCV remains controversial so far. While performing phylogenetic analyses including a large number of sequences deposited in the GenBank, we encountered a full-length HCV sequence (AY651061 that showed evidence for inter-subtype recombination and was, therefore, subjected to a detailed analysis of its molecular structure. The obtained results indicated that AY651061 does not represent a “simple” HCV 1c isolate, but a complex 1a/1c mosaic genome, showing five putative breakpoints in the core to NS3 regions. To our knowledge, this is the first report on a mosaic HCV full- length sequence with multiple breakpoints. The molecular structure of AY651061 is reminiscent of complex homologous recombinant variants occurring among other members of the flaviviridae family, e.g. GB virus C, dengue virus, and Japanese encephalitis virus. Our finding of a mosaic HCV sequence may have important implications for many fields of current HCV research which merit careful consideration.

The openness of pluripotent epigenome - Defining the genomic integrity of stemness for regenerative medicine

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Xuejun H Parsons

2014-02-01

Full Text Available This article is an editorial, and it doesn't include an abstract. Full text of this article is available in HTML and PDF.Cite this article as: Parsons XH. The openness of pluripotent epigenome - Defining the genomic Integrity of stemness for regenerative medicine. Int J Cancer Ther Oncol 2014; 2(1:020114.DOI: http://dx.doi.org/10.14319/ijcto.0201.14

Personalized medicine: genome, e-health and intelligent systems. Part 1. Genomics and monitoring of clinical data

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B. A. Kobrinskii

2017-01-01

Full Text Available The transition to personalized medicine in practical terms should combine the solution of the genomics problems as the basis for possible diseases and phenotypic manifestations that are markers and early signs of emerging pathological changes. Most diseases have their first principles in childhood. Therefore, in all age groups, it is necessary to monitor the minimum deviations and their dynamics, use mobile devices for this purpose and accumulate the received data. Processing big data (Big Data will provide more informative information. On this basis it will be possible to identify analogs for targeted therapy in similar variants of diseases in large databases of publications on the problem of interest.

Draft Genome Sequence of Pseudomonas sp. EpS/L25, Isolated from the Medicinal Plant Echinacea purpurea and Able To Synthesize Antimicrobial Compounds.

Science.gov (United States)

Presta, Luana; Bosi, Emanuele; Fondi, Marco; Maida, Isabel; Perrin, Elena; Miceli, Elisangela; Maggini, Valentina; Bogani, Patrizia; Firenzuoli, Fabio; Di Pilato, Vincenzo; Rossolini, Gian Maria; Mengoni, Alessio; Fani, Renato

2016-05-05

We announce here the draft genome sequence of Pseudomonas sp. strain EpS/L25, isolated from the stem/leaves of the medicinal plant Echinacea purpurea This genome will allow for comparative genomics in order to identify genes associated with the production of bioactive compounds and antibiotic resistance. Copyright © 2016 Presta et al.

Precision medicine, an approach for development of the future medicine technologies

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Iraj Nabipour

2016-04-01

Full Text Available Precision medicine is an approach in medicine that takes into account individual differences in people's genes, environments, and lifestyle. This field of medicine redefines our understanding of disease onset and progression, treatment response, and health outcomes through the more precise measurement of molecular, environmental, and behavioral factors that contribute to health and disease. Undoubtedly, the advances in omics technologies including genomics, data collection and storage, computational analysis, and mobile health applications over the last decade produced significant progress for precision medicine. In fact, precision medicine is a platform for the growth of personalized medicine, wearable biosensors, mobile health, computational sciences, genomic singularity, and other omics technologies. In the pathway of precision medicine, mathematics and computational sciences will be revolutionized to overcome the challenges in Big Data. By the birth of precision medicine, novel therapeutic strategies for chronic complex diseases such as cardiovascular disease and cancers would be designed in Systems Medicine.

Genome analysis of medicinal Ganoderma spp. with plant-pathogenic and saprotrophic life-styles.

Science.gov (United States)

Kües, Ursula; Nelson, David R; Liu, Chang; Yu, Guo-Jun; Zhang, Jianhui; Li, Jianqin; Wang, Xin-Cun; Sun, Hui

2015-06-01

Ganoderma is a fungal genus belonging to the Ganodermataceae family and Polyporales order. Plant-pathogenic species in this genus can cause severe diseases (stem, butt, and root rot) in economically important trees and perennial crops, especially in tropical countries. Ganoderma species are white rot fungi and have ecological importance in the breakdown of woody plants for nutrient mobilization. They possess effective machineries of lignocellulose-decomposing enzymes useful for bioenergy production and bioremediation. In addition, the genus contains many important species that produce pharmacologically active compounds used in health food and medicine. With the rapid adoption of next-generation DNA sequencing technologies, whole genome sequencing and systematic transcriptome analyses become affordable approaches to identify an organism's genes. In the last few years, numerous projects have been initiated to identify the genetic contents of several Ganoderma species, particularly in different strains of Ganoderma lucidum. In November 2013, eleven whole genome sequencing projects for Ganoderma species were registered in international databases, three of which were already completed with genomes being assembled to high quality. In addition to the nuclear genome, two mitochondrial genomes for Ganoderma species have also been reported. Complementing genome analysis, four transcriptome studies on various developmental stages of Ganoderma species have been performed. Information obtained from these studies has laid the foundation for the identification of genes involved in biological pathways that are critical for understanding the biology of Ganoderma, such as the mechanism of pathogenesis, the biosynthesis of active components, life cycle and cellular development, etc. With abundant genetic information becoming available, a few centralized resources have been established to disseminate the knowledge and integrate relevant data to support comparative genomic analyses of

Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague–Dawley rats and C57BL/6 mice

Energy Technology Data Exchange (ETDEWEB)

Nault, Rance; Kim, Suntae; Zacharewski, Timothy R., E-mail: tzachare@msu.edu

2013-03-01

Although the structure and function of the AhR are conserved, emerging evidence suggests that downstream effects are species-specific. In this study, rat hepatic gene expression data from the DrugMatrix database (National Toxicology Program) were compared to mouse hepatic whole-genome gene expression data following treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). For the DrugMatrix study, male Sprague–Dawley rats were gavaged daily with 20 μg/kg TCDD for 1, 3 and 5 days, while female C57BL/6 ovariectomized mice were examined 1, 3 and 7 days after a single oral gavage of 30 μg/kg TCDD. A total of 649 rat and 1386 mouse genes (|fold change| ≥ 1.5, P1(t) ≥ 0.99) were differentially expressed following treatment. HomoloGene identified 11,708 orthologs represented across the rat Affymetrix 230 2.0 GeneChip (12,310 total orthologs), and the mouse 4 × 44K v.1 Agilent oligonucleotide array (17,578 total orthologs). Comparative analysis found 563 and 922 orthologs differentially expressed in response to TCDD in the rat and mouse, respectively, with 70 responses associated with immune function and lipid metabolism in common to both. Moreover, QRTPCR analysis of Ceacam1, showed divergent expression (induced in rat; repressed in mouse) functionally consistent with TCDD-elicited hepatic steatosis in the mouse but not the rat. Functional analysis identified orthologs involved in nucleotide binding and acetyltransferase activity in rat, while mouse-specific responses were associated with steroid, phospholipid, fatty acid, and carbohydrate metabolism. These results provide further evidence that TCDD elicits species-specific regulation of distinct gene networks, and outlines considerations for future comparisons of publicly available microarray datasets. - Highlights: ► We performed a whole-genome comparison of TCDD-regulated genes in mice and rats. ► Previous species comparisons were extended using data from the DrugMatrix database. ► Less than 15% of TCDD

Recent advances in Hepatitis E virus.

Science.gov (United States)

Meng, X J

2010-03-01

Hepatitis E virus (HEV), the causative agent of hepatitis E, belongs to the family Hepeviridae. At least four major genotypes of HEV have been recognized: genotypes 1 and 2 are restricted to humans and associated with epidemics in developing countries, whereas genotypes 3 and 4 are zoonotic and infect humans and several other animals in both developing and industrialized countries. Besides humans, strains of HEV have been genetically identified from swine, chickens, sika deer, mongeese, and rabbits. The genome of HEV consists of three open reading frames (ORFs): ORF1 codes for nonstructural proteins, ORF2 codes for capsid protein, and ORF3 codes for a small multifunctional protein. The ORF2 and ORF3 proteins are translated from a single bicistronic mRNA and overlap each other but neither overlaps ORF1. The recent determination of the 3D crystal structure of the HEV capsid protein should facilitate the development of vaccines and antivirals. The identification and characterization of animal strains of HEV from pigs and chickens and the demonstrated ability of cross-species infection by swine HEV raise public health concerns for zoonosis. Accumulating evidence indicated that hepatitis E is a zoonotic disease and pigs and more likely other animal species are reservoirs for HEV. This article provides an overview of the recent advances in hepatitis E and its causative agent, including nomenclature and genomic organization, gene expression and functions, 3D structure of the virions, changing perspectives on higher mortality during pregnancy and chronic hepatitis E, animal reservoirs, zoonotic risk, food safety, and novel animal models.

Coinfection of hepatitis E virus and other hepatitis virus in Colombia and its genotypic characterization.

Science.gov (United States)

Peláez, Dioselina; Martínez-Vargas, Daniel; Escalante-Mora, Martha; Palacios-Vivero, Mariel; Contreras-Gómez, Lady

2015-12-04

Hepatitis E virus has emerged as a public health problem, particularly in developing countries. The four genotypes identified in mammals include the G3 found in indigenous hepatitis in countries and regions with high porcine population, and the G1, associated with maternal deaths.  To determine coinfection by hepatitis E virus and the circulating genotypes in Colombia in 1,097 samples using serological markers for hepatitis A, B and C.  Serum samples of 1,097 patients from different regions of Colombia stored at the Laboratorio de Virología of the Instituto Nacional de Salud were selected to detect IgG and IgM anti-hepatitis E virus antibodies. The viral genomes of positive samples were amplified by RT-PCR, and the products were sequenced and phylogenetically analyzed by comparing ORF2 sequences deposited in the GenBank.  IgG anti-hepatitis E virus antibodies were found in 278 samples, IgM in 62, and both markers in 64. Hepatitis E virus and hepatitis A virus coinfection determined by IgG anti-hepatitis E virus was 33.6% and 16.1% by IgM; hepatitis E virus and hepatitis B virus coinfection was 23.4% and 8.1%, and hepatitis E virus and hepatitis C virus coinfection was 35.4% and 5.83%, respectively. Among the 52 positive samples by PCR nine were sequenced and grouped within genotype 3A of the American porcine strain.  The highest seropositivity was observed for hepatitis A and E. The incidence of hepatitis E virus coinfection with other hepatotropic viruses indicated that this pathogen is more frequent than expected. The circulation of genotype 3A implies that this disease may occur in outbreaks and as zoonosis in Colombia.

Prevalence of hepatitis viruses in patients with acute hepatitis and characterization of the detected genotype 4 hepatitis E virus sequences in Mongolia.

Science.gov (United States)

Tsatsralt-Od, Bira; Baasanjav, Nachin; Nyamkhuu, Dulmaa; Ohnishi, Hiroshi; Takahashi, Masaharu; Okamoto, Hiroaki

2016-02-01

Hepatitis E is considered to be a worldwide public health problem. Although the prevalence of hepatitis E virus (HEV) antibodies in healthy individuals is noted to be 11%, no patients with acute hepatitis E have previously been identified in Mongolia. Three hundred two consecutive patients (183 males and 119 females; median age of 22.0 [Interquartile range: 18.3-25.0] years) who were clinically diagnosed with sporadic acute hepatitis during 2012-2013 in Ulaanbaatar, Mongolia, were studied. By serological and/or molecular approaches, 77 (25.5%), 93 (30.8%), 19 (6.3%), 48 (15.9%), and 12 (4.0%) of the patients were diagnosed with acute hepatitis of types A, B, C, D (superinfection of hepatitis delta virus on a background of chronic hepatitis B virus infection) and E, respectively, while the cause of hepatitis was unknown in the remaining 53 patients (17.5%). The 12 hepatitis E patients had no history of travel abroad in the 3 months before the onset of disease, and lived separately in fixed or movable houses with water supplied via pipe, tank or well, denying transmission from a common water supply. The 12 HEV isolates obtained from the patients showed high nucleotide identities of 99.7-100%, and a representative HEV isolate, MNE13-227, was closest to the Chinese isolates of genotype 4, with the highest identity of 97.3% in the 304-nt ORF2 sequence and 92.1% over the entire genome. The present study revealed the occurrence of autochthonous acute hepatitis E in Mongolia, caused by a monophyletic genotype 4 HEV strain. © 2015 Wiley Periodicals, Inc.

Exploring the genetic architecture and improving genomic prediction accuracy for mastitis and milk production traits in dairy cattle by mapping variants to hepatic transcriptomic regions responsive to intra-mammary infection.

Science.gov (United States)

Fang, Lingzhao; Sahana, Goutam; Ma, Peipei; Su, Guosheng; Yu, Ying; Zhang, Shengli; Lund, Mogens Sandø; Sørensen, Peter

2017-05-12

A better understanding of the genetic architecture of complex traits can contribute to improve genomic prediction. We hypothesized that genomic variants associated with mastitis and milk production traits in dairy cattle are enriched in hepatic transcriptomic regions that are responsive to intra-mammary infection (IMI). Genomic markers [e.g. single nucleotide polymorphisms (SNPs)] from those regions, if included, may improve the predictive ability of a genomic model. We applied a genomic feature best linear unbiased prediction model (GFBLUP) to implement the above strategy by considering the hepatic transcriptomic regions responsive to IMI as genomic features. GFBLUP, an extension of GBLUP, includes a separate genomic effect of SNPs within a genomic feature, and allows differential weighting of the individual marker relationships in the prediction equation. Since GFBLUP is computationally intensive, we investigated whether a SNP set test could be a computationally fast way to preselect predictive genomic features. The SNP set test assesses the association between a genomic feature and a trait based on single-SNP genome-wide association studies. We applied these two approaches to mastitis and milk production traits (milk, fat and protein yield) in Holstein (HOL, n = 5056) and Jersey (JER, n = 1231) cattle. We observed that a majority of genomic features were enriched in genomic variants that were associated with mastitis and milk production traits. Compared to GBLUP, the accuracy of genomic prediction with GFBLUP was marginally improved (3.2 to 3.9%) in within-breed prediction. The highest increase (164.4%) in prediction accuracy was observed in across-breed prediction. The significance of genomic features based on the SNP set test were correlated with changes in prediction accuracy of GFBLUP (P layers of biological knowledge to provide novel insights into the biological basis of complex traits, and to improve the accuracy of genomic prediction. The SNP set

Whole-genome analysis of genetic recombination of hepatitis delta virus: molecular domain in delta antigen determining trans-activating efficiency.

Science.gov (United States)

Chao, Mei; Lin, Chia-Chi; Lin, Feng-Ming; Li, Hsin-Pai; Iang, Shan-Bei

2015-12-01

Hepatitis delta virus (HDV) is the only animal RNA virus that has an unbranched rod-like genome with ribozyme activity and is replicated by host RNA polymerase. HDV RNA recombination was previously demonstrated in patients and in cultured cells by analysis of a region corresponding to the C terminus of the delta antigen (HDAg), the only viral-encoded protein. Here, a whole-genome recombination map of HDV was constructed using an experimental system in which two HDV-1 sequences were co-transfected into cultured cells and the recombinants were analysed by sequencing of cloned reverse transcription-PCR products. Fifty homologous recombinants with 60 crossovers mapping to 22 junctions were identified from 200 analysed clones. Small HDAg chimeras harbouring a junction newly detected in the recombination map were then constructed. The results further indicated that the genome-replication level of HDV was sensitive to the sixth amino acid within the N-terminal 22 aa of HDAg. Therefore, the recombination map established in this study provided a tool for not only understanding HDV RNA recombination, but also elucidating the related mechanisms, such as molecular elements responsible for the trans-activation levels of the small HDAg.

The use of Chinese herbal medicine as an adjuvant therapy to reduce incidence of chronic hepatitis in colon cancer patients: A Taiwanese population-based cohort study.

Science.gov (United States)

Lin, Tsai-Hui; Yen, Hung-Rong; Chiang, Jen-Huai; Sun, Mao-Feng; Chang, Hen-Hong; Huang, Sheng-Teng

2017-04-18

There is a decided lack of in-depth studies to evaluate the effectiveness of Chinese Herbal Medicine (CHM) as an adjuvant therapy on the incidence of chronic hepatitis in patients with colon cancer. The aim of this study is to assess whether CHM treatment decreased the incidence of chronic hepatitis in colon cancer patients who received conventional Western medical treatment. A Taiwanese nationwide population-based study of colon cancer patients receiving Western medicine treatment in conjunction with CHM treatment, using data provided by the National Health Insurance (NHI) Research Database, was conducted. A total of 61676 patients were diagnosed with colon cancer in Taiwan within the defined study period, from 1997 to 2010. After randomly equal matching for age, sex, excluding patients younger than 18 years of age, chronic hepatitis before colon cancer diagnosis date, receiving acupuncture and/or moxibustion and taking CHM for less than 30 days, data from 155 patients were analyzed. Hazard ratios of incidence rate of chronic hepatitis were used to determine the influence of CHM and the therapeutic potential of herbal products in treating patients with colon cancer. CHM used for patients with colon cancer exhibited significantly decreased incidence rates of chronic hepatitis [hazard ratio (HR)=0.53; 95% confidence interval (CI):0.38-0.74], with multivariate adjustment, compared to those without CHM use. The protective effect of CHM treatment with statistical significance across the stratification of age, gender, co-morbidity and treatment modality was noted. The cumulative incidence of chronic hepatitis was also reduced in patients with colon cancer receiving CHM treatment during a five-year period. In this study, we provide the ten most used single herbs and herbal formulas that were prescribed for patients with colon cancer; moreover, we identify the eight single herbs and five formulas used in CHM treatment which significantly decreased incidence of chronic

Molecular epidemiology and evolution in an outbreak of fulminant hepatitis B virus.

Science.gov (United States)

Bracho, Maria Alma; Gosalbes, María José; González, Francisco; Moya, Andrés; González-Candelas, Fernando

2006-04-01

In order to establish the transmission pathway for two outbreak patients affected by fulminant hepatitis B (FHB) following a shared period of hospitalization, we sequenced the complete genomes of the hepatitis B viruses (HBV) isolated from them as well as from the suspected common source and 11 additional controls. Phylogenetic and statistical analyses of these sequences revealed that the two FHB patients were indeed infected by a common source and that the fatal development of the disease did not appear to be associated with any mutation previously reported to be related to FHB. These data have also allowed us to estimate the extent and distribution of genetic variability along the genomes of HBV genotype D samples from the same source population. As a result of these analyses, we provide an improved statistical method to individualize the assignment of each suspected patient and the source of an outbreak and information on which genome region to analyze in the molecular epidemiological assessment of hepatitis B virus transmission cases.

Precision medicine for advanced prostate cancer.

Science.gov (United States)

Mullane, Stephanie A; Van Allen, Eliezer M

2016-05-01

Precision cancer medicine, the use of genomic profiling of patient tumors at the point-of-care to inform treatment decisions, is rapidly changing treatment strategies across cancer types. Precision medicine for advanced prostate cancer may identify new treatment strategies and change clinical practice. In this review, we discuss the potential and challenges of precision medicine in advanced prostate cancer. Although primary prostate cancers do not harbor highly recurrent targetable genomic alterations, recent reports on the genomics of metastatic castration-resistant prostate cancer has shown multiple targetable alterations in castration-resistant prostate cancer metastatic biopsies. Therapeutic implications include targeting prevalent DNA repair pathway alterations with PARP-1 inhibition in genomically defined subsets of patients, among other genomically stratified targets. In addition, multiple recent efforts have demonstrated the promise of liquid tumor profiling (e.g., profiling circulating tumor cells or cell-free tumor DNA) and highlighted the necessary steps to scale these approaches in prostate cancer. Although still in the initial phase of precision medicine for prostate cancer, there is extraordinary potential for clinical impact. Efforts to overcome current scientific and clinical barriers will enable widespread use of precision medicine approaches for advanced prostate cancer patients.

A new subtype of hepatitis C virus genotype 1: complete genome and phylogenetic relationships of an Equatorial Guinea isolate.

Science.gov (United States)

Bracho, Maria Alma; Carrillo-Cruz, Francy Yolima; Ortega, Enrique; Moya, Andrés; González-Candelas, Fernando

2006-06-01

Hepatitis C virus (HCV) is the leading cause of chronic liver disease and is associated with hepatocellular carcinoma. However, there have been few studies on the distribution and genetic diversity of HCV isolates in non-developed countries. Here, the complete genome sequence of an HCV genotype 1 isolate from Equatorial Guinea is reported, the first complete HCV-1 genome of African origin. Phylogenetic analysis revealed that this sequence always grouped with sequences of genotype 1, but did not group clearly with any subtype described so far. An analysis of partial NS5B gene sequences with additional sequences of African origin also failed to find close similarities between the new sequence and any previously known isolate. Genetic divergence of the coding region of this new sequence with respect to the recognized subtypes of HCV-1 ranged from 20 to 22%. It is proposed that this isolate is a representative of a new, distinct variant of HCV subtype 1.

Prevention of Post Transfusion Hepatitis Employing Sensitive Assay for Hepatitis B Surface Antigen Screening(Topics in Transfusion Medicine 1990 : Autologous Transfusion and Post-Transfusion Hepatitis)

OpenAIRE

小島, 秀男; 大竹, 幸子; 富樫, 和枝; 石口, 重子; 山田, 恵子; 品田, 章二; Kojima, Hideo; Ohtake, Sachiko; Togashi, Kazue; Ishiguchi, Shigeko; Yamada, Keiko; Shinada, Shoji

1990-01-01

Post transfusion Hepatitis (PTH) is one of serious side effects and some times lead to fulminant hepatic failure in case transfused blood contain very low level (under the sensitivity of usual screening method) of hepatitis B virus (HBV). Redcross blood center and blood transfusion devision of our hospital have been employed reverse passive hemmaglutination method (RPHA) for HBsAg screening. Authors employed EIA for sensitive HBsAg test system and compared with RPHA method. Of 2,255 sera from...

Incubation and Growth of Life Sciences, Medical and Biotechnology Businesses in Proteomics, Genomics, Medicine, and Dentistry

Science.gov (United States)

2007-04-01

Medical and Biotechnology Businesses in Proteomics , Genomics, Medicine, and Dentistry PRINCIPAL INVESTIGATOR: Mark S. Long Brian C...2007 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Incubation and Growth of Life Sciences, Medical and Biotechnology Businesses in Proteomics ...aflatoxins B1 and G1 from Aspergillus flavus. All toxins studied were purchased from Sigma Aldrich and used without further purification. Solutions

Optimizing a method for detection of hepatitis A virus in shellfish and study the effect of gamma radiation on the viral genome

International Nuclear Information System (INIS)

Amri, Islem

2008-01-01

Our work was aimed at detecting the hepatitis A virus (HAV) in bivalve mollusc collected from five shellfish harvesting areas and from a coastal region in Tunisia using RT-Nested-PCR and studying the effect of gamma radiation on HAV genome. Two methods used to recover HAV from mollusc flesh and two methods of extraction of virus RNA were compared in order to determine the most sensitive method. Glycine extraction and extraction of virus RNA using proteinase K were more convenient and then used in this study for detection of HAV in shellfish. The results of molecular analyses: RT-Nested-PCR using primers targeted at the P1 region revealed that 28 % of the samples were positive for HAV. Doses of gamma irradiation ranging between 5 to 30 kGy were used to study the effect of this radiation on HAV genome after the contamination of mollusc flesh with suspension of HAV (derived from stool specimens). HAV specific genomic band was observed for doses between 5 to 20 kGy. We didn't detect HAV genome with doses 25 and 30 kGy. (Author)

Precision Medicine in Gastrointestinal Pathology.

Science.gov (United States)

Wang, David H; Park, Jason Y

2016-05-01

-Precision medicine is the promise of individualized therapy and management of patients based on their personal biology. There are now multiple global initiatives to perform whole-genome sequencing on millions of individuals. In the United States, an early program was the Million Veteran Program, and a more recent proposal in 2015 by the president of the United States is the Precision Medicine Initiative. To implement precision medicine in routine oncology care, genetic variants present in tumors need to be matched with effective clinical therapeutics. When we focus on the current state of precision medicine for gastrointestinal malignancies, it becomes apparent that there is a mixed history of success and failure. -To present the current state of precision medicine using gastrointestinal oncology as a model. We will present currently available targeted therapeutics, promising new findings in clinical genomic oncology, remaining quality issues in genomic testing, and emerging oncology clinical trial designs. -Review of the literature including clinical genomic studies on gastrointestinal malignancies, clinical oncology trials on therapeutics targeted to molecular alterations, and emerging clinical oncology study designs. -Translating our ability to sequence thousands of genes into meaningful improvements in patient survival will be the challenge for the next decade.

Occult hepatitis B virus infection is not associated with disease progression of chronic hepatitis C virus infection.

Science.gov (United States)

Cho, Junhyeon; Lee, Sang Soo; Choi, Yun Suk; Jeon, Yejoo; Chung, Jung Wha; Baeg, Joo Yeong; Si, Won Keun; Jang, Eun Sun; Kim, Jin-Wook; Jeong, Sook-Hyang

2016-11-14

To clarify the prevalence of occult hepatitis B virus (HBV) infection (OBI) and the association between OBI and liver disease progression, defined as development of liver cirrhosis or hepatocellular carcinoma (HCC), worsening of Child-Pugh class, or mortality in cases of chronic hepatitis C virus (HCV) infection. This prospective cohort study enrolled 174 patients with chronic HCV infection (chronic hepatitis, n = 83; cirrhosis, n = 47; HCC, n = 44), and evaluated disease progression during a mean follow-up of 38.7 mo. OBI was defined as HBV DNA positivity in 2 or more different viral genomic regions by nested polymerase chain reaction using 4 sets of primers in the S, C, P and X open reading frame of the HBV genome. The overall OBI prevalence in chronic HCV patients at enrollment was 18.4%, with 16.9%, 25.5% and 13.6% in the chronic hepatitis C, liver cirrhosis and HCC groups, respectively ( P = 0.845). During follow-up, 52 patients showed disease progression, which was independently associated with aspartate aminotransferase > 40 IU/L, Child-Pugh score and sustained virologic response (SVR), but not with OBI positivity. In 136 patients who were not in the SVR state during the study period, OBI positivity was associated with neither disease progression, nor HCC development. The prevalence of OBI in chronic HCV patients was 18.4%, and OBI was not associated with disease progression in South Koreans.

THE DRUG-INDUCED HEPATITIS IN CHILDREN

Directory of Open Access Journals (Sweden)

O. V. Molochkova

2017-01-01

Full Text Available Among toxic lesions of the liver, an important place belongs to medicinal hepatitis. Among patients with hepatitis, drug disease of the liver occurs in 0.7—1.4% of cases, and in the presence of jaundice — in 5%. A family case of sisters 9 and 4-year-old life development  of acute drug hepatitis caused by ibuprofen in a daily dose of 32 mg / kg (total 3.2 g and 25 mg / kg (total 2 g, respectively, was demonstrated in siblings. Hepatitis developed after an acute respiratory infection. Weakness, nausea, vomiting, jaundice of the skin and sclera, pruritus, multiple increase in serum transaminases and markers of cholestasis are revealed. Viral hepatitis and some hereditary liver diseases were excluded. The drug lesion of the liver was of a mixed nature: hepatocellular (cytotoxic and cholestatic. Timely administration of therapy (detoxification, glucocorticosteroids, ursodeoxycholic acid (Ursosan led to a regression of clinical symptoms of the disease and positive dynamics of laboratory indicators.

Current hepatitis B virus infection situation in Indonesia and its genetic diversity.

Science.gov (United States)

Lusida, Maria Inge; Juniastuti; Yano, Yoshihiko

2016-08-28

Indonesia has a moderate to high endemicity of hepatitis B virus (HBV) infection. The risk for chronic HBV infection is highest among those infected during infancy. Since 1997, hepatitis B (HepB) vaccination of newborns has been fully integrated into the National Immunization Program. Although HBV infection has been reduced by the universal newborn HepB immunization program, it continues to occur in Indonesia. The low birth dose coverage and the presence of vaccine escape mutants might contribute to this endemicity among children. Although limited information is available for an analysis of occult HBV infection (OBI), several variations and substitutions in the pre-S/S region have been detected in Indonesian HBV strains. Additionally, persistent infection and disease progression of chronic hepatitis B are related to not only viral factors but also the host genome. Indonesia is one of the most ethnically heterogeneous nations, with Javanese and Sundanese as the two highest ethnic groups. This multi-ethnicity makes genomic research in Indonesia difficult. In this article, we focused on and reviewed the following aspects: the current hepatitis B immunization program and its efficacy, OBI, HBV infection among high-risk patients, such as hemodialysis patients, and research regarding the host genome in Indonesia.

Identification of risk factors for hepatitis B and C in Peshawar, Pakistan

Directory of Open Access Journals (Sweden)

Shafiq M

2015-08-01

Full Text Available Muhammad Shafiq,1 Muhammad Nadeem,2 Zeeshan Sattar,3 Sohaib Mohammad Khan,2 Sheikh Muhammad Faheem,4 Irfan Ahsan,5 Rabia Naheed,6 Tahir Mehmood Khattak,2 Shahzad Akbar,7 Muhammad Talha Khan,3 Muhammad Ilyas Khan,1 Muhammad Zubair Khan8 1Department of Internal Medicine, Khyber Teaching Hospital, University Town, Peshawar, 2Department of General Surgery, Nishtar Medical College and Hospital, Dera Ghazi Khan, Punjab, 3Department of Internal Medicine, Khyber Medical College, University Campus, Peshawar, 4Department of Neurology, King Edward Medical University, Anarkali, Lahore, Pakistan; 5Department of Internal Medicine, Mayo Hospital, Phoenix, AZ, USA; 6Department of Internal Medicine, Fatima Memorial Hospital, Lahore, 7Department of Internal Medicine, Lady Reading Hospital, Andar Shehr, Peshawar, 8Department of Internal Medicine, Hayatabad Medical Complex, Hayat Abad, Pakistan Background: Hepatitis B and C need immediate worldwide attention as the infection rates are too high. More than 240 million people have chronic (long-term liver infections. Every year, about 600,000 people die globally due to the acute or chronic consequences of hepatitis B and more than 350,000 people die from hepatitis C-related liver diseases. Methods: Our study was designed as a case-control, descriptive study. It was conducted through formal interviews by using structured questionnaires. A total of 100 cases were included, with four controls for each case. Results: This study confirms household contact, history of dental work, history of surgery, sexual contact, and history of transfusion (blood and its components as the main risk factors which are responsible for the increased prevalence of hepatitis. Conclusion: The important risk factors, responsible for the high prevalence of hepatitis B and C in our society are household contact, history of dental work, history of surgery, sexual contact, and history of transfusion (blood and its components. The odds ratio of

The influence of the human genome on chronic viral hepatitis outcome A influência do genoma humano no curso das hepatites virais crônicas

Directory of Open Access Journals (Sweden)

Dahir Ramos de Andrade Júnior

2004-06-01

Full Text Available The mechanisms that determine viral clearance or viral persistence in chronic viral hepatitis have yet to be identified. Recent advances in molecular genetics have permitted the detection of variations in immune response, often associated with polymorphism in the human genome. Differences in host susceptibility to infectious disease and disease severity cannot be attributed solely to the virulence of microbial agents. Several recent advances concerning the influence of human genes in chronic viral hepatitis B and C are discussed in this article: a the associations between human leukocyte antigen polymorphism and viral hepatic disease susceptibility or resistance; b protective alleles influencing hepatitis B virus (HBV and hepatitis C virus (HCV evolution; c prejudicial alleles influencing HBV and HCV; d candidate genes associated with HBV and HCV evolution; d other genetic factors that may contribute to chronic hepatitis C evolution (genes influencing hepatic stellate cells, TGF-beta1 and TNF-alpha production, hepatic iron deposits and angiotensin II production, among others. Recent discoveries regarding genetic associations with chronic viral hepatitis may provide clues to understanding the development of end-stage complications such as cirrhosis or hepatocellular carcinoma. In the near future, analysis of the human genome will allow the elucidation of both the natural course of viral hepatitis and its response to therapy.Os mecanismos que determinam o clearance ou a persistência da infecção viral nas hepatites virais crônicas não estão ainda bem identificados. O progresso no conhecimento sobre as ferramentas genéticas moleculares tem permitido detectar variações na resposta imune, que freqüentemente são associadas com polimorfismos do genoma humano. As diferenças na susceptibilidade do hospedeiro para as doenças infecciosas e a intensidade das doenças não podem ser atribuídas apenas à virulência do agente microbiano. Neste

Training future physicians in the era of genomic medicine: trends in undergraduate medical genetics education.

Science.gov (United States)

Plunkett-Rondeau, Jevon; Hyland, Katherine; Dasgupta, Shoumita

2015-11-01

Advances in genomic technologies are transforming medical practice, necessitating the expertise of genomically-literate physicians. This study examined 2013-2014 trends in genetics curricula in US and Canadian medical schools to ascertain whether and how curricula are keeping pace with this rapid evolution. Medical genetics course directors received a 60-item electronic questionnaire covering curriculum design, assessment, remediation of failing grades, and inclusion of specific topics. The response rate was 74%. Most schools teach the majority of genetics during the first 2 years, with an increase in the number of integrated curricula. Only 26% reported formal genetics teaching during years 3 and 4, and most respondents felt the amount of time spent on genetics was insufficient preparation for clinical practice. Most participants are using the Association of Professors of Human and Medical Genetics Core Curriculum(1) as a guide. Topics recently added include personalized medicine (21%) and direct-to-consumer testing (18%), whereas eugenics (17%), linkage analysis (16%), and evolutionary genetics (15%) have been recently eliminated. Remediation strategies were heterogeneous across institutions. These findings provide an important update on how genetics and genomics is taught at US and Canadian medical schools. Continuous improvement of educational initiatives will aid in producing genomically-literate physicians.

[Precision medicine: new opportunities and challenges for molecular epidemiology].

Science.gov (United States)

Song, Jing; Hu, Yonghua

2016-04-01

Since the completion of the Human Genome Project in 2003 and the announcement of the Precision Medicine Initiative by U.S. President Barack Obama in January 2015, human beings have initially completed the " three steps" of " genomics to biology, genomics to health as well as genomics to society". As a new inter-discipline, the emergence and development of precision medicine have relied on the support and promotion from biological science, basic medicine, clinical medicine, epidemiology, statistics, sociology and information science, etc. Meanwhile, molecular epidemiology is considered to be the core power to promote precision medical as a cross discipline of epidemiology and molecular biology. This article is based on the characteristics and research progress of medicine and molecular epidemiology respectively, focusing on the contribution and significance of molecular epidemiology to precision medicine, and exploring the possible opportunities and challenges in the future.

Genetic analysis of an orbital metastasis from a primary hepatic neuroendocrine carcinoma

DEFF Research Database (Denmark)

Rasmussen, Jacob Ø; von Holstein, Sarah L; Prause, Jan U

2014-01-01

and immunohistochemical features, and high-resolution, array-based comparative genomic hybridization demonstrated loss of one copy each of chromosomes 3 and 18, and gain of 1q both in the primary hepatic neuroendocrine carcinoma and in the orbital tumour. The orbital mass was diagnosed as a metastasis from the primary...... hepatic neuroendocrine carcinoma. Primary hepatic neuroendocrine tumours are extremely rare, and the orbit is an extremely rare location for a neuroendocrine carcinoma metastasis. This is the first reported case of an orbital metastasis with origin from a primary hepatic neuroendocrine carcinoma....

Isotope-based medical research in the post genome era: Gene-orchestrated life functions in medicine seen and affected by isotopes. Workshop report

International Nuclear Information System (INIS)

Feinendegen, L.E.

1997-01-01

The US Department of Energy (DOE) and the National Institutes of Health (NIH) conducted a workshop on Isotope-Based Medical Research in the Post Genome Era at NIH, Bethesda, Maryland, November 12--14, 1997. The workshop aimed at identifying the role of stable and radioisotopes for advanced diagnosis and therapy of a wide range of illnesses using the new information that comes from the human genome program. In this sense, the agenda addressed the challenge of functional genomics in humans. The workshop addressed: functional genomics in clinical medicine; new diagnostic potentials; new therapy potentials; challenge to tracer- and effector-pharmaceutical chemistry; and project plans for joint ventures

Isotope-based medical research in the post genome era: Gene-orchestrated life functions in medicine seen and affected by isotopes. Workshop report

Energy Technology Data Exchange (ETDEWEB)

Feinendegen, L.E.

1997-12-31

The US Department of Energy (DOE) and the National Institutes of Health (NIH) conducted a workshop on Isotope-Based Medical Research in the Post Genome Era at NIH, Bethesda, Maryland, November 12--14, 1997. The workshop aimed at identifying the role of stable and radioisotopes for advanced diagnosis and therapy of a wide range of illnesses using the new information that comes from the human genome program. In this sense, the agenda addressed the challenge of functional genomics in humans. The workshop addressed: functional genomics in clinical medicine; new diagnostic potentials; new therapy potentials; challenge to tracer- and effector-pharmaceutical chemistry; and project plans for joint ventures.

Ancient hepatitis B viruses from the Bronze Age to the Medieval period

DEFF Research Database (Denmark)

Mühlemann, Barbara; Jones, Terry C.; Damgaard, Peter de Barros

2018-01-01

Hepatitis B virus (HBV) is a major cause of human hepatitis. There is considerable uncertainty about the timescale of its evolution and its association with humans. Here we present 12 full or partial ancient HBV genomes that are between approximately 0.8 and 4.5 thousand years old. The ancient se...

Genomic profiling toward precision medicine in non-small cell lung cancer: getting beyond EGFR

Directory of Open Access Journals (Sweden)

Richer AL

2015-02-01

Full Text Available Amanda L Richer,1 Jacqueline M Friel,1 Vashti M Carson,2 Landon J Inge,1 Timothy G Whitsett2 1Norton Thoracic Institute, St Joseph’s Hospital and Medical Center, 2Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA Abstract: Lung cancer remains the leading cause of cancer-related mortality worldwide. The application of next-generation genomic technologies has offered a more comprehensive look at the mutational landscape across the different subtypes of non-small cell lung cancer (NSCLC. A number of recurrent mutations such as TP53, KRAS, and epidermal growth factor receptor (EGFR have been identified in NSCLC. While targeted therapeutic successes have been demonstrated in the therapeutic targeting of EGFR and ALK, the majority of NSCLC tumors do not harbor these genomic events. This review looks at the current treatment paradigms for lung adenocarcinomas and squamous cell carcinomas, examining genomic aberrations that dictate therapy selection, as well as novel therapeutic strategies for tumors harboring mutations in KRAS, TP53, and LKB1 which, to date, have been considered “undruggable”. A more thorough understanding of the molecular alterations that govern NSCLC tumorigenesis, aided by next-generation sequencing, will lead to targeted therapeutic options expected to dramatically reduce the high mortality rate observed in lung cancer. Keywords: non-small cell lung cancer, precision medicine, epidermal growth factor receptor, Kirsten rat sarcoma viral oncogene homolog, serine/threonine kinase 11, tumor protein p53

Serendipitous identification of natural intergenotypic recombinants of hepatitis C in Ireland.

LENUS (Irish Health Repository)

Moreau, Isabelle

2006-01-01

BACKGROUND: Recombination between hepatitis C single stranded RNA viruses is a rare event. Natural viable intragenotypic and intergenotypic recombinants between 1b-1a, 1a-1c and 2k-1b, 2i-6p, respectively, have been reported. Diagnostically recombinants represent an intriguing challenge. Hepatitis C genotype is defined by interrogation of the sequence composition of the 5\\' untranslated region [5\\'UTR]. Occasionally, ambiguous specimens require further investigation of the genome, usually by interrogation of the NS5B region. The original purpose of this study was to confirm the existence of a suspected mixed genotype infection of genotypes 2 and 4 by clonal analysis at the NS5B region of the genome in two specimens from two separate individuals. This initial identification of genotype was based on analysis of the 5\\'UTR of the genome by reverse line probe hybridisation [RLPH]. RESULTS: The original diagnosis of a mixed genotype infection was not confirmed by clonal analysis of the NS5B region of the genome. The phylogenetic analysis indicated that both specimens were natural intergenotypic recombinant forms of HCV. The recombination was between genotypes 2k and 1b for both specimens. The recombination break point was identified as occurring within the NS2 region of the genome. CONCLUSION: The viral recombinants identified here resemble the recombinant form originally identified in Russia. The RLPH pattern observed in this study may be a signature indicative of this particular type of intergenotype recombinant of hepatitis C meriting clonal analysis of NS2.

Detecting exact breakpoints of deletions with diversity in hepatitis B viral genomic DNA from next-generation sequencing data.

Science.gov (United States)

Cheng, Ji-Hong; Liu, Wen-Chun; Chang, Ting-Tsung; Hsieh, Sun-Yuan; Tseng, Vincent S

2017-10-01

Many studies have suggested that deletions of Hepatitis B Viral (HBV) are associated with the development of progressive liver diseases, even ultimately resulting in hepatocellular carcinoma (HCC). Among the methods for detecting deletions from next-generation sequencing (NGS) data, few methods considered the characteristics of virus, such as high evolution rates and high divergence among the different HBV genomes. Sequencing high divergence HBV genome sequences using the NGS technology outputs millions of reads. Thus, detecting exact breakpoints of deletions from these big and complex data incurs very high computational cost. We proposed a novel analytical method named VirDelect (Virus Deletion Detect), which uses split read alignment base to detect exact breakpoint and diversity variable to consider high divergence in single-end reads data, such that the computational cost can be reduced without losing accuracy. We use four simulated reads datasets and two real pair-end reads datasets of HBV genome sequence to verify VirDelect accuracy by score functions. The experimental results show that VirDelect outperforms the state-of-the-art method Pindel in terms of accuracy score for all simulated datasets and VirDelect had only two base errors even in real datasets. VirDelect is also shown to deliver high accuracy in analyzing the single-end read data as well as pair-end data. VirDelect can serve as an effective and efficient bioinformatics tool for physiologists with high accuracy and efficient performance and applicable to further analysis with characteristics similar to HBV on genome length and high divergence. The software program of VirDelect can be downloaded at https://sourceforge.net/projects/virdelect/. Copyright © 2017. Published by Elsevier Inc.

Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant.

Science.gov (United States)

Lu, Ling; Li, Chunhua; Yuan, Jie; Lu, Teng; Okamoto, Hiroaki; Murphy, Donald G

2013-03-01

We characterized the full-length genomes of five distinct hepatitis C virus (HCV)-3 isolates. These represent the first complete genomes for subtypes 3g and 3h, the second such genomes for 3k and 3i, and of one novel variant presently not assigned to a subtype. Each genome was determined from 18-25 overlapping fragments. They had lengths of 9579-9660 nt and each contained a single ORF encoding 3020-3025 aa. They were isolated from five patients residing in Canada; four were of Asian origin and one was of Somali origin. Phylogenetic analysis using 64 partial NS5B sequences differentiated 10 assigned subtypes, 3a-3i and 3k, and two additional lineages within genotype 3. From the data of this study, HCV-3 full-length sequences are now available for six of the assigned subtypes and one unassigned. Our findings should add insights to HCV evolutionary studies and clinical applications.

A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica

Directory of Open Access Journals (Sweden)

Krishnan Neeraja M

2012-09-01

Full Text Available Abstract Background The Azadirachta indica (neem tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of A. indica and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. A. indica is the first member of the family Meliaceae to be sequenced using next generation sequencing approach. Results The genome and transcriptomes of A. indica were sequenced using multiple sequencing platforms and libraries. The A. indica genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped A. indica together with Citrus sinensis from the Rutaceae family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in A. indica led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs. Conclusions This study on A. indica genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various Meliaceae family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in A. indica will pave ways for bulk production of environment friendly biopesticides.

A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica

Science.gov (United States)

2012-01-01

Background The Azadirachta indica (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of A. indica and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. A. indica is the first member of the family Meliaceae to be sequenced using next generation sequencing approach. Results The genome and transcriptomes of A. indica were sequenced using multiple sequencing platforms and libraries. The A. indica genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped A. indica together with Citrus sinensis from the Rutaceae family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in A. indica led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs. Conclusions This study on A. indica genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various Meliaceae family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in A. indica will pave ways for bulk production of environment friendly biopesticides. PMID:22958331

[ETHICS, MORALS AND SOCIETY IN PERSONALIZED MEDICINE].

Science.gov (United States)

Flugelman, Anath

2015-09-01

Following the completion of the human genome project, genomic medicine including personalized medicine, widely based on pharmacogenetics and pharmacogenomics, is rapidly developing. This breakthrough should benefit humankind thanks to tailoring the most appropriate prevention, interventions and therapies to each individual, minimizing adverse side effects, based on inter-personal genetic variety and polymorphism. Yet wide spectrum ethical, legal and social issues carry significant implications regarding individuals, families, society and public health. The main issues concern genomic information and autonomy, justice and equity, resources allocation and solidarity, challenging the traditional role of medicine and dealing with unlimited boundaries of knowledge. Those issues are not new nor exceptional to genomic medicine, yet their wide unlimited scope and implications on many aspects of life renders them crucial. These aspects will be discussed in light of Beauchamp and Childress' four principles: non-maleficence, beneficence, autonomy and justice, and main moral philosophies, Kant's autonomy, Utilitarianism which promotes the common good, and Rawls' Theory of Justice.

Modeling Inborn Errors of Hepatic Metabolism Using Induced Pluripotent Stem Cells.

Science.gov (United States)

Pournasr, Behshad; Duncan, Stephen A

2017-11-01

Inborn errors of hepatic metabolism are because of deficiencies commonly within a single enzyme as a consequence of heritable mutations in the genome. Individually such diseases are rare, but collectively they are common. Advances in genome-wide association studies and DNA sequencing have helped researchers identify the underlying genetic basis of such diseases. Unfortunately, cellular and animal models that accurately recapitulate these inborn errors of hepatic metabolism in the laboratory have been lacking. Recently, investigators have exploited molecular techniques to generate induced pluripotent stem cells from patients' somatic cells. Induced pluripotent stem cells can differentiate into a wide variety of cell types, including hepatocytes, thereby offering an innovative approach to unravel the mechanisms underlying inborn errors of hepatic metabolism. Moreover, such cell models could potentially provide a platform for the discovery of therapeutics. In this mini-review, we present a brief overview of the state-of-the-art in using pluripotent stem cells for such studies. © 2017 American Heart Association, Inc.

Spaces of genomics : exploring the innovation journey of genomics in research on common disease

NARCIS (Netherlands)

Bitsch, L.

2013-01-01

Genomics was introduced with big promises and expectations of its future contribution to our society. Medical genomics was introduced as that which would lay the foundation for a revolution in our management of common diseases. Genomics would lead the way towards a future of personalised medicine.

Integration of Structural Dynamics and Molecular Evolution via Protein Interaction Networks: A New Era in Genomic Medicine

Science.gov (United States)

Kumar, Avishek; Butler, Brandon M.; Kumar, Sudhir; Ozkan, S. Banu

2016-01-01

Summary Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. PMID:26684487

Personalized medicine beyond genomics: alternative futures in big data-proteomics, environtome and the social proteome.

Science.gov (United States)

Özdemir, Vural; Dove, Edward S; Gürsoy, Ulvi K; Şardaş, Semra; Yıldırım, Arif; Yılmaz, Şenay Görücü; Ömer Barlas, I; Güngör, Kıvanç; Mete, Alper; Srivastava, Sanjeeva

2017-01-01

No field in science and medicine today remains untouched by Big Data, and psychiatry is no exception. Proteomics is a Big Data technology and a next generation biomarker, supporting novel system diagnostics and therapeutics in psychiatry. Proteomics technology is, in fact, much older than genomics and dates to the 1970s, well before the launch of the international Human Genome Project. While the genome has long been framed as the master or "elite" executive molecule in cell biology, the proteome by contrast is humble. Yet the proteome is critical for life-it ensures the daily functioning of cells and whole organisms. In short, proteins are the blue-collar workers of biology, the down-to-earth molecules that we cannot live without. Since 2010, proteomics has found renewed meaning and international attention with the launch of the Human Proteome Project and the growing interest in Big Data technologies such as proteomics. This article presents an interdisciplinary technology foresight analysis and conceptualizes the terms "environtome" and "social proteome". We define "environtome" as the entire complement of elements external to the human host, from microbiome, ambient temperature and weather conditions to government innovation policies, stock market dynamics, human values, political power and social norms that collectively shape the human host spatially and temporally. The "social proteome" is the subset of the environtome that influences the transition of proteomics technology to innovative applications in society. The social proteome encompasses, for example, new reimbursement schemes and business innovation models for proteomics diagnostics that depart from the "once-a-life-time" genotypic tests and the anticipated hype attendant to context and time sensitive proteomics tests. Building on the "nesting principle" for governance of complex systems as discussed by Elinor Ostrom, we propose here a 3-tiered organizational architecture for Big Data science such as

Genetic gatekeepers: regulating direct-to-consumer genomic services in an era of participatory medicine.

Science.gov (United States)

Palmer, Jessica Elizabeth

2012-01-01

Should consumers be able to obtain information about their own bodies, even if it has no proven medical value? Direct-to-consumer ("DTC") genomic companies offer consumers two services: generation of the consumer's personal genetic sequence, and interpretation of that sequence in light of current research. Concerned that consumers will misunderstand genomic information and make ill-advised health decisions, regulators, legislators and scholars have advocated restricted access to DTC genomic services. The Food and Drug Administration, which has historically refrained from regulating most genetic tests, has announced its intent to treat DTC genomic services as medical devices because they make "medical claims." This Article argues that FDA regulation of genomic services as medical devices would be counterproductive. Clinical laboratories conducting genetic tests are already overseen by a federal regime administered by the Centers for Medicare and Medicaid Services. While consumers and clinicians would benefit from clearer communication of test results and their health implications, FDA's gatekeeping framework is ill-suited to weigh the safety and efficacy of genomic information that is not medically actionable in traditional ways. Playing gatekeeper would burden FDA's resources, conflict with the patient-empowering policies promoted by personalized medicine initiatives, impair individuals' access to information in which they have powerful autonomy interests, weaken novel participatory research infrastructures, and set a poor precedent for the future regulation of medical information. Rather than applying its risk-based regulatory framework to genetic information, FDA should ameliorate regulatory uncertainty by working with the Federal Trade Commission and Centers for Medicare and Medicaid Services to ensure that DTC genomic services deliver analytically valid data, market and implement their services in a truthful manner, and fully disclose the limitations of their

Antiviral activity of Dianthus superbusn L. against hepatitis B virus in ...

African Journals Online (AJOL)

Background: Hepatitis is a viral infection of hepatitis B virus (HBV). Limitations of drug used in the management of it opens the interest related to alternative medicine. The given study deals with the antiviral activity of Dianthus superbusn L. (DSL) against HBV in vitro & in vivo. Material and Methods: In vitro study liver cell line ...

Public health and precision medicine share a goal.

Science.gov (United States)

Vaithinathan, Asokan G; Asokan, Vanitha

2017-05-01

The advances made in genomics and molecular tools aid public health programs in the investigation of outbreaks and control of diseases by taking advantage of the precision medicine. Precision medicine means "segregating the individuals into subpopulations who vary in their disease susceptibility and response to a precise treatment" and not merely designing of drugs or creation of medical devices. By 2017, the United Kingdom 100,000 Genomes Project is expected to sequence 100,000 genomes from 70,000 patients. Similarly, the Precision Medicine Initiative of the United States plans to increase population-based genome sequencing and link it with clinical data. A national cohort of around 1 million people is to be established in the long term, to investigate the genetic and environmental determinants of health and disease, and further integrated to their electronic health records that are optional. Precision public health can be seen as administering the right intervention to the needy population at an appropriate time. Precision medicine originates from a wet-lab while evidence-based medicine is nurtured in a clinic. Linking the quintessential basic science research and clinical practice is necessary. In addition, new technologies to employ and analyze data in an integrated and dynamic way are essential for public health and precision medicine. The transition from evidence-based approach in public health to genomic approach to individuals with a paradigm shift of a "reactive" medicine to a more "proactive" and personalized health care may sound exceptional. However, a population perspective is needed for the precision medicine to succeed. © 2016 Chinese Cochrane Center, West China Hospital of Sichuan University and John Wiley & Sons Australia, Ltd.

Traditional Chinese medicine treatment of liver diseases

Directory of Open Access Journals (Sweden)

WANG Rongbing

2015-01-01

Full Text Available Traditional Chinese medicine (TCM treatment of liver diseases is derived from the regulation of liver function including storing blood and governing the free flow of qi, in which functional systems such as modern digestion, endocrine, and the gut-liver axis are involved, and is established on modern hepatic physiology, pathology, and etiology. To objectively reveal the characteristics and advantages of modern TCM treatment of liver diseases, we analyzed the clinical and research situation of TCM therapy for liver diseases in the last decade and collected major achievements that have been applied in clinical treatment of diseases, published in core journals, and confirmed by major scientific research programs. The results showed TCM combined with antiviral therapy can improve the clinical outcomes of chronic hepatitis B. TCM can help HBV carriers prevent disease progression. Integrated traditional Chinese and Western medicine therapy for acute-on-chronic liver failure can block the deterioration induced by endotoxin. TCM has been widely applied in protecting the liver through nonspecific anti-inflammation, alleviating hepatic fibrosis, and preventing non-alcoholic fatty liver. TCM plays an important role in treating some currently untreatable liver diseases. Therefore, it is our common responsibility to inherit and develop effective principle-method-recipe-medicines and create a better medical care system.

Lamivudine plasma levels in chronic hepatitis B patients

NARCIS (Netherlands)

L.M.M. Wolters (Leonieke); C.J. Geerlings; L.J. van Dijk (Laurens); H.G.M. Niesters (Bert); A.G. Vulto (Arnold); R.A. de Man (Robert)

2003-01-01

textabstractLamivudine has recently been registered for the treatment of chronic hepatitis B patients. The main therapeutic outcome in the studies on which the registration was based was a drop of HBV DNA below 10(7) genome equivalents/ml, the level of detection of the insensitive

Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine.

Science.gov (United States)

Kumar, Avishek; Butler, Brandon M; Kumar, Sudhir; Ozkan, S Banu

2015-12-01

Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hepatitis A virus-encoded miRNAs attenuate the accumulation of viral genomic RNAs in infected cells.

Science.gov (United States)

Shi, Jiandong; Sun, Jing; Wu, Meini; Hu, Ningzhu; Hu, Yunzhang

2016-06-01

The establishment of persistent infection with hepatitis A virus (HAV) is the common result of most HAV/cell culture systems. Previous observations show that the synthesis of viral RNAs is reduced during infection. However, the underlying mechanism is poorly understood. We characterized three HAV-encoded miRNAs in our previous study. In this study, we aim to investigate the impact of these miRNAs on the accumulation of viral RNAs. The results indicated that the synthesis of viral genomic RNAs was dramatically reduced (more than 75 % reduction, P viral miRNA mimics. Conversely, they were significantly increased (more than 3.3-fold addition, P viral miRNA inhibitors. The luciferase reporter assay of miRNA targets showed that viral miRNAs were fully complementary to specific sites of the viral plus or minus strand RNA and strongly inhibited their expressions. Further data showed that the relative abundance of viral genomic RNA fragments that contain miRNA targets was also dramatically reduced (more than 80 % reduction, P viral miRNAs were overexpressed with miRNA mimics. In contrast, they were significantly increased (approximately 2-fold addition, P viral miRNAs were inhibited with miRNA inhibitors. In conclusion, these data suggest a possible mechanism for the reduction of viral RNA synthesis during HAV infection. Thus, we propose that it is likely that RNA virus-derived miRNA could serve as a self-mediated feedback regulator during infection.

Rare inborn errors associated with chronic hepatitis B virus infection

DEFF Research Database (Denmark)

Zhao, Qiang; Peng, Liang; Huang, Weijun

2012-01-01

further studied its expression by immunohistochemistry, real-time polymerase chain reaction, and western blotting. Our results showed that it was strongly expressed by healthy hepatocytes, but its expression was reduced in liver tissues with CHB, hepatitis B viral (HBV) genome-containing HepG2.2.15 cells......, as compared with healthy liver tissues and non-HBV genome-containing HepG2 cells (P = 0.022 and 0.0036, respectively)....

National Human Genome Research Institute

Science.gov (United States)

... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

Functional Genomics Group. Program Description

National Research Council Canada - National Science Library

Burian, Dennis

2008-01-01

.... This article reviews mechanisms of gene regulation and discusses how genomics is changing the way medicine is practiced today as a means of demonstrating that molecular medicine is here to stay...

Insights from early experience of a Rare Disease Genomic Medicine Multidisciplinary Team: a qualitative study.

Science.gov (United States)

Ormondroyd, Elizabeth; Mackley, Michael P; Blair, Edward; Craft, Jude; Knight, Julian C; Taylor, John; Taylor, Jenny C; Wilkie, Andrew Om; Watkins, Hugh

2017-06-01

Whole-exome/whole-genome sequencing (WES/WGS) has the potential to enhance genetic diagnosis of rare disease, and is increasingly becoming part of routine clinical care in mainstream medicine. Effective translation will require ongoing efforts in a number of areas including: selection of appropriate patients, provision of effective consent, pre- and post-test genetic counselling, improving variant interpretation algorithms and practices, and management of secondary findings including those found incidentally and those actively sought. Allied to this is the need for an effective education programme for all members of clinical teams involved in care of patients with rare disease, as well as to maintain public confidence in the use of these technologies. We established a Genomic Medicine Multidisciplinary Team (GM-MDT) in 2014 to build on the experiences of earlier successful research-based WES/WGS studies, to address these needs and to review results including pertinent and secondary findings. Here we report on a qualitative study of decision-making in the GM-MDT combined with analysis of semi-structured interviews with GM-MDT members. Study findings show that members appreciate the clinical and scientific diversity of the GM-MDT and value it for education and oversight. To date, discussions have focussed on case selection including the extent and interpretation of clinical and family history information required to establish likely monogenic aetiology and inheritance model. Achieving a balance between effective use of WES/WGS - prioritising cases in a diverse and highly complex patient population where WES/WGS will be tractable - and meeting the recruitment targets of a large project is considered challenging.

An eMERGE Clinical Center at Partners Personalized Medicine

Directory of Open Access Journals (Sweden)

Jordan W. Smoller

2016-01-01

Full Text Available The integration of electronic medical records (EMRs and genomic research has become a major component of efforts to advance personalized and precision medicine. The Electronic Medical Records and Genomics (eMERGE network, initiated in 2007, is an NIH-funded consortium devoted to genomic discovery and implementation research by leveraging biorepositories linked to EMRs. In its most recent phase, eMERGE III, the network is focused on facilitating implementation of genomic medicine by detecting and disclosing rare pathogenic variants in clinically relevant genes. Partners Personalized Medicine (PPM is a center dedicated to translating personalized medicine into clinical practice within Partners HealthCare. One component of the PPM is the Partners Healthcare Biobank, a biorepository comprising broadly consented DNA samples linked to the Partners longitudinal EMR. In 2015, PPM joined the eMERGE Phase III network. Here we describe the elements of the eMERGE clinical center at PPM, including plans for genomic discovery using EMR phenotypes, evaluation of rare variant penetrance and pleiotropy, and a novel randomized trial of the impact of returning genetic results to patients and clinicians.

Radix Sophorae flavescentis for chronic hepatitis B

DEFF Research Database (Denmark)

Liu, Jianping; Zhu, Minghui; Shi, Rui

2003-01-01

biochemical effects, and improved symptoms and signs compared with non-specific treatment and other herbal medicines. The combination of matrine and interferon-alpha (IFN-alpha), thymosin, or basic treatment showed better effects on viral and liver biochemical responses. The antiviral and biochemical......To evaluate the effects of radix Sophorae fiavescentis for chronic hepatitis B, a systematic review of randomized clinical trials was conducted. Randomized trials comparing extract of radix Sophorae flavescentis versus placebo, no intervention, non-specific treatment, other active medicines...

Moduratory effect of Thai traditional medicine (Yahom Tultavai) on ...

African Journals Online (AJOL)

Recently, several herbs and traditional medicines have been reported to demonstrate herbal-drug interaction with conventional medicines. This study aims to investigate the effect of Yahom Tultavai extracts on hepatic cytochrome P450 enzymes and pentobarbital-induced sleeping in mice. Three extracts of Yahom Tultavai, ...

Making Personalized Health Care Even More Personalized: Insights From Activities of the IOM Genomics Roundtable.

Science.gov (United States)

David, Sean P; Johnson, Samuel G; Berger, Adam C; Feero, W Gregory; Terry, Sharon F; Green, Larry A; Phillips, Robert L; Ginsburg, Geoffrey S

2015-01-01

Genomic research has generated much new knowledge into mechanisms of human disease, with the potential to catalyze novel drug discovery and development, prenatal and neonatal screening, clinical pharmacogenomics, more sensitive risk prediction, and enhanced diagnostics. Genomic medicine, however, has been limited by critical evidence gaps, especially those related to clinical utility and applicability to diverse populations. Genomic medicine may have the greatest impact on health care if it is integrated into primary care, where most health care is received and where evidence supports the value of personalized medicine grounded in continuous healing relationships. Redesigned primary care is the most relevant setting for clinically useful genomic medicine research. Taking insights gained from the activities of the Institute of Medicine (IOM) Roundtable on Translating Genomic-Based Research for Health, we apply lessons learned from the patient-centered medical home national experience to implement genomic medicine in a patient-centered, learning health care system. © 2015 Annals of Family Medicine, Inc.

Genome-wide identification of blood DNA methylation patterns associated with early-onset hepatocellular carcinoma development in hepatitis B carriers.

Science.gov (United States)

Kao, Wei-Yi; Yang, Shu-Han; Liu, Wen-Jie; Yeh, Meng-Yin; Lin, Chih-Lin; Liu, Chun-Jen; Huang, Chi-Jung; Lin, Shi-Ming; Lee, Shou-Dong; Chen, Pei-Jer; Yu, Ming-Whei

2017-02-01

The etiology of early-onset hepatocellular carcinoma (HCC) among hepatitis B virus (HBV) carriers remains unclear. DNA methylation levels in peripheral leukocytes have been associated with different environmental exposures and immune or inflammatory response. We aimed to identify methylation signatures of peripheral leukocytes that could track hepatitis B progression to HCC, especially for early-onset HCC. We first performed an epigenome-wide association analysis on 48 matched case-control pairs in a nested case-control study within a 22-yr follow-up cohort of HBV carriers. Through this analysis we found that progression to early-onset HCC involved methylation variable positions across the genome, in which a substantial proportion displayed significant variation due to HBV viral load, chronic hepatitis status, and/or leukocyte subtype composition, and these associations were significantly enriched among genes in immune pathways. Methylation at probes cg00300879, cg06872964, and cg07080864, that are located within the proximal promoter of CNKSR1, IFI44L, and PENK, respectively, was validated by bisulfite pyrosequencing and findings were replicated in a case-sibling study of early-onset HCC (134 cases vs. 174 sibling controls). Furthermore, a high methylation score, constructed using the three probes, was predictive for the risk of early-onset HCC in two datasets (adjusted-odds ratios = 0.21-0.32, P ≤ 0.0206). This association was also observed for late-onset HCC (adjusted-odds ratio = 0.42-0.47, P ≤ 0.0194) in a nested case-control study (120 cases vs. 178 controls). In prospective analysis, change in the score was detected 5-9 yr before HCC onset. Blood-based methylation profiling provides new insights into the complexity of virus-host interaction underlying HBV-related HCC, holding promise for the disease risk management. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

[Cinnamon rolls are not associated with admission for toxic or alcoholic hepatitis in a Danish liver referral centre].

Science.gov (United States)

Gr Ønbæk, Henning; Borre, Mette

2014-12-08

Cinnamon contains cumarin, which may be toxic to the liver. EU-regulations standardardize the amount of cinnamon in pastry including cinnamon rolls. The aim of the study was to investigate if cinnamon intake from pastry was associated with toxic or alcoholic hepatitis. We registered 58 patients with toxic hepatitis, 38 (66%) women and 20 (34%) men with a median age of 51 (range: 32-80) and 53 (range: 18-78) years, respectively. A total of 22 patients had primarily cholestasis and 36 had hepatitis biochemically. The duration of toxic liver disease from admission to normalization of liver enzymes was similar in the two groups (3.5 ± 3.5 vs 3.6 ± 3.5 months). Toxic hepatitis was most often caused by drugs e.g. NSAID (n = 15; 26%), antibiotics (n = 9; 16%), alternative medicine (n = 7; 12%) and Antabuse (n = 5; 9%). We registered eight patients admitted with severe alcoholic hepatitis, five men and three women, median age of 60 (range: 34-67) years. Alcoholic hepatitis was associated with high alcohol intake. None of the patients with toxic or alcoholic hepatitis reported of excessive intake of cinnamon rolls and there was no evidence of cinnamon added to alcohol of alternative medicine products. Intake of cinnamon from cinnamon rolls is not associated with admission for toxic or alcoholic hepatitis. However, for the diagnosis of toxic liver diseases including alcohol it is very important to have patient information regarding any new drugs, alternative medicine and alcohol intake. Further, other causes of liver diseases should be excluded. not relevant. not relevant.

Acute hepatitis e viral infection in pregnancy and maternal morbidity

International Nuclear Information System (INIS)

Khaskheli, M.N.; Baloch, S.

2015-01-01

To determine the maternal morbidity in pregnant women with acute hepatitis E viral infection. Study Design: Observational, cross-sectional study. Place and Duration of Study: Departments of Obstetrics and Gynaecology and Medicine, Liaquat University of Medical and Health Sciences, Jamshoro, Red Crescent General Hospital and Saint Elizabeth Hospital, Hyderabad, from January 2011 to December 2013. Methodology: The study population was pregnant women with acute hepatitis E infection confirmed by ELIZA technique. Pregnant women with other hepatic viral infections were excluded. All medical and obstetric conditions, and mortality were noted on the predesigned proforma. Results: Out of the total 45 admitted pregnant women with hepatitis E viral infection, 22 women (48.9%) had severe morbidity. The most common were hepatic coma in 8 (36.36%) cases and disseminated intravascular coagulation in 14 (63.63%) cases. Highest mortality rate was seen in women with hepatic coma (100%), while in those with disseminated intravascular coagulation, one out of the 14 cases (7.14%) died. Conclusion: The acute viral hepatitis E infection in pregnant women is associated with maternal morbidities and high mortality rate. (author)

Procedures of hepatic scintigraphy and improvement of professionals by using anthropomorphic simulator object of liver in nuclear medicine; Procedimentos de cintilografia hepatica e aperfeicoamento de profissionais utilizando objeto simulador antropomorfico de figado em medicina nuclear

Energy Technology Data Exchange (ETDEWEB)

Ferreira, Fernanda C.L.; Cunha, Cledison J.; Dullius, Marcos A.; Souza, Divanizia N., E-mail: divanizi@ufs.b [Universidade Federal de Sergipe (UFS), Aracaju, SE (Brazil)

2011-10-26

This paper evaluates hepatic scintigraphy procedures and the possibility of professional improvement in nuclear medicine by using three-dimension anthropomorphic simulators representative of adult human liver. For the conformation of anthropomorphic simulator, it was used gypsum and acrylic. Three simulator objects representing cirrhosis livers. The simulator were filled with {sup 99m}Tc diluted in water for the obtention of scintigraphic images. Tomographic images were analysed posterior and anterior of simulator representing an organ with more cirrhosis grade. It was observed that the simulators make possible the acquisition of images similar to the real images of liver with hepatic cirrhosis. The simulations of hemangiomas can contribute for continuous education of nuclear medicine professionals, as far the question of image formation is concerned, make possible the parameter study as, for example, the , matrix size energy window, zoom and counting statistic

A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae: a traditional herbal medicinal genus

Directory of Open Access Journals (Sweden)

Hanghui Kong

2017-11-01

Full Text Available The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs. While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58–62 simple sequence repeats (SSRs were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.

A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus.

Science.gov (United States)

Kong, Hanghui; Liu, Wanzhen; Yao, Gang; Gong, Wei

2017-01-01

The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A . subgenus Lycoctonum and A . subg. Aconitum . The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius , A. finetianum , and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius , 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum , with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψ rps 19 and Ψ ycf 1 were in the LSC/IR/SSC boundaries, Ψ rps 16 and Ψ inf A in the LSC region, and Ψ ycf 15 in the IRb region. The nucleotide variability ( Pi ) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58-62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum , respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum . Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.

The personalised medicine: a paradigm of evidence-based medicine

Directory of Open Access Journals (Sweden)

Dhavendra Kumar

2011-01-01

Full Text Available The practice of "evidence-based medicine" aims at the conscientious, explicit and judicious use of the current best evidence in making decisions about the individualised patient care. The clinical genetics evolved from translational genetics research and contributes to the clinical care of patients and families through evidence-based health care in managing inherited disorders through accurate diagnosis, molecular pathology and assessing phenotypic correlations. Translational genetics and genomics research has led to the development of powerful tools for clinical diagnosis, assessing individual's genomic profile for disease prediction/prevention, high-throughput genome-wide screening for predisposition and/or protection to complex medical conditions, and discovery and development of new drugs and vaccines. Gene mapping and deciphering pathogenic mutations have helped in unravelling the basic biological mechanisms leading to new drug discovery and development. Targeted pharmacotherapy is now possible for managing the highly penetrant multi-system dominantly inherited conditions. Notable examples include rapamycin (sirolimus in suppressing the mTOR pathway associated hamartomas in dominantly inherited cancer family syndromes and angiotensin converting enzyme receptor blockers (ACE-RB in preventing aortic dilatation in Marfan syndrome and related familial arteriopathies. The translational genomic research is the essential prerequisite for developing sound evidence-based diagnostic, therapeutic and prognostic clinical protocols for the practice of personalised clinical medicine.

A post-genomic surprise. The molecular reinscription of race in science, law and medicine.

Science.gov (United States)

Duster, Troy

2015-03-01

The completion of the first draft of the Human Genome Map in 2000 was widely heralded as the promise and future of genetics-based medicines and therapies - so much so that pundits began referring to the new century as 'The Century of Genetics'. Moreover, definitive assertions about the overwhelming similarities of all humans' DNA (99.9 per cent) by the leaders of the Human Genome Project were trumpeted as the end of racial thinking about racial taxonomies of human genetic differences. But the first decade of the new century brought unwelcomed surprises. First, gene therapies turned out to be far more complicated than any had anticipated - and instead the pharmaceutical industry turned to a focus on drugs that might be 'related' to population differences based upon genetic markers. While the language of 'personalized medicine' dominated this frame, research on racially and ethnically designated populations differential responsiveness to drugs dominated the empirical work in the field. Ancestry testing and 'admixture research' would play an important role in a new kind of molecular reification of racial categories. Moreover, the capacity of the super-computer to map differences reverberated into personal identification that would affect both the criminal justice system and forensic science, and generate new levels of concern about personal privacy. Social scientists in general, and sociologists in particular, have been caught short by these developments - relying mainly on assertions that racial categories are socially constructed, regionally and historically contingent, and politically arbitrary. While these assertions are true, the imprimatur of scientific legitimacy has shifted the burden, since now 'admixture research' can claim that its results get at the 'reality' of human differentiation, not the admittedly flawed social constructions of racial categories. Yet what was missing from this framing of the problem: 'admixture research' is itself based upon socially

Functional genomics and proteomics - the role of nuclear medicine

International Nuclear Information System (INIS)

Haberkorn, U.; Altmann, A.; Eisenhut, M.

2002-01-01

Now that the sequencing of the human genome has been completed, the basic challenges are finding the genes, locating their coding regions and predicting their functions. This will result in a new understanding of human biology as well as in the design of new molecular structures as potential novel diagnostic or drug discovery targets. The assessment of gene function may be performed using the tools of the genome program. These tools represent high-throughput methods used to evaluate changes in the expression of many or all genes of an organism at the same time in order to investigate genetic pathways for normal development and disease. This will lead to a shift in the scientific paradigm: In the pre-proteomics era, functional assignments were derived from hypothesis-driven experiments designed to understand specific cellular processes. The new tools describe proteins on a proteome-wide scale, thereby creating a new way of doing cell research which results in the determination of three-dimensional protein structures and the description of protein networks. These descriptions may then be used for the design of new hypotheses and experiments in the traditional physiological, biochemical and pharmacological sense. The evaluation of genetically manipulated animals or newly designed biomolecules will require a thorough understanding of physiology, biochemistry and pharmacology and the experimental approaches will involve many new technologies, including in vivo imaging with single-photon emission tomography and positron emission tomography. Nuclear medicine procedures may be applied for the determination of gene function and regulation using established and new tracers or using in vivo reporter genes such as enzymes, receptors, antigens or transporters. Pharmacogenomics will identify new surrogate markers for therapy monitoring which may represent potential new tracers for imaging. Also, drug distribution studies for new therapeutic biomolecules are needed, at least

Functional genomics and proteomics - the role of nuclear medicine

Energy Technology Data Exchange (ETDEWEB)

Haberkorn, U. [Heidelberg Univ. (Germany). Abt. fuer Klinische Nuklearmedizin; German Cancer Research Center, Heidelberg (Germany); Altmann, A. [German Cancer Research Center, Heidelberg (Germany); Eisenhut, M. [German Cancer Research Center, Heidelberg (Germany). Dept. of Radiopharmacy

2002-01-01

Now that the sequencing of the human genome has been completed, the basic challenges are finding the genes, locating their coding regions and predicting their functions. This will result in a new understanding of human biology as well as in the design of new molecular structures as potential novel diagnostic or drug discovery targets. The assessment of gene function may be performed using the tools of the genome program. These tools represent high-throughput methods used to evaluate changes in the expression of many or all genes of an organism at the same time in order to investigate genetic pathways for normal development and disease. This will lead to a shift in the scientific paradigm: In the pre-proteomics era, functional assignments were derived from hypothesis-driven experiments designed to understand specific cellular processes. The new tools describe proteins on a proteome-wide scale, thereby creating a new way of doing cell research which results in the determination of three-dimensional protein structures and the description of protein networks. These descriptions may then be used for the design of new hypotheses and experiments in the traditional physiological, biochemical and pharmacological sense. The evaluation of genetically manipulated animals or newly designed biomolecules will require a thorough understanding of physiology, biochemistry and pharmacology and the experimental approaches will involve many new technologies, including in vivo imaging with single-photon emission tomography and positron emission tomography. Nuclear medicine procedures may be applied for the determination of gene function and regulation using established and new tracers or using in vivo reporter genes such as enzymes, receptors, antigens or transporters. Pharmacogenomics will identify new surrogate markers for therapy monitoring which may represent potential new tracers for imaging. Also, drug distribution studies for new therapeutic biomolecules are needed, at least

Genome medicine: gene therapy for the millennium, 30 September-3 October 2001, Rome, Italy.

Science.gov (United States)

Gruenert, D C; Novelli, G; Dallapiccola, B; Colosimo, A

2002-06-01

The recent surge of DNA sequence information resulting from the efforts of agencies interested in deciphering the human genetic code has facilitated technological developments that have been critical in the identification of genes associated with numerous disease pathologies. In addition, these efforts have opened the door to the opportunity to develop novel genetic therapies to treat a broad range of inherited disorders. Through a joint effort by the University of Vermont, the University of Rome, Tor Vergata, University of Rome, La Sapienza, and the CSS Mendel Institute, Rome, an international meeting, 'Genome Medicine: Gene Therapy for the Millennium' was organized. This meeting provided a forum for the discussion of scientific and clinical advances stimulated by the explosion of sequence information generated by the Human Genome Project and the implications these advances have for gene therapy. The meeting had six sessions that focused on the functional evaluation of specific genes via biochemical analysis and through animal models, the development of novel therapeutic strategies involving gene targeting, artificial chromsomes, DNA delivery systems and non-embryonic stem cells, and on the ethical and social implications of these advances.

First identification of a recombinant form of hepatitis C virus in Austrian patients by full-genome next generation sequencing.

Science.gov (United States)

Stelzl, Evelyn; Haas, Bernhard; Bauer, Bernd; Zhang, Sherry; Fiss, Ellen H; Hillman, Grantland; Hamilton, Aaron T; Mehta, Rochak; Heil, Marintha L; Marins, Ed G; Santner, Brigitte I; Kessler, Harald H

2017-01-01

Hepatitis C virus (HCV) intergenotypic recombinant forms have been reported for various HCV genotypes/subtypes in several countries worldwide. In a recent study, four patients living in Austria had been identified to be possibly infected with a recombinant HCV strain. To clarify results and determine the point of recombination, full-genome next-generation sequencing using the Illumina MiSeq v2 300 cycle kit (Illumina, San Diego, CA, USA) was performed in the present study. Samples of all of the patients contained the recombinant HCV strain 2k/1b. The point of recombination was found to be within the HCV NS2 gene between nucleotide positions 3189-3200 based on H77 numbering. While three of four patients were male and had migration background from Chechnya (n = 2) and Azerbaijan (n = 1), the forth patient was a female born in Austria. Three of the four patients including the female had intravenous drug abuse as a risk factor for HCV transmission. While sequencing techniques are limited to a few specialized laboratories, a genotyping assay that uses both ends of the HCV genome should be employed to identify patients infected with a recombinant HCV strain. The correct identification of recombinant strains also has an impact considering the tailored choice of anti-HCV treatment.

First identification of a recombinant form of hepatitis C virus in Austrian patients by full-genome next generation sequencing.

Directory of Open Access Journals (Sweden)

Evelyn Stelzl

Full Text Available Hepatitis C virus (HCV intergenotypic recombinant forms have been reported for various HCV genotypes/subtypes in several countries worldwide. In a recent study, four patients living in Austria had been identified to be possibly infected with a recombinant HCV strain. To clarify results and determine the point of recombination, full-genome next-generation sequencing using the Illumina MiSeq v2 300 cycle kit (Illumina, San Diego, CA, USA was performed in the present study. Samples of all of the patients contained the recombinant HCV strain 2k/1b. The point of recombination was found to be within the HCV NS2 gene between nucleotide positions 3189-3200 based on H77 numbering. While three of four patients were male and had migration background from Chechnya (n = 2 and Azerbaijan (n = 1, the forth patient was a female born in Austria. Three of the four patients including the female had intravenous drug abuse as a risk factor for HCV transmission. While sequencing techniques are limited to a few specialized laboratories, a genotyping assay that uses both ends of the HCV genome should be employed to identify patients infected with a recombinant HCV strain. The correct identification of recombinant strains also has an impact considering the tailored choice of anti-HCV treatment.

ETHICAL ASPECTS OF APPLICATION THE GENOMIC MEDICINE IN SPORT

Directory of Open Access Journals (Sweden)

Biljana Vitošević

2013-07-01

Full Text Available Today's level of knowledge of molecular biology and genetics is able to change the established belief that genetic predisposition is a good natural gift. The application of gene therapy in healthy individuals in order to increase sports performance is considered as manipulation and gene doping, which is actually believed that it could be a precursor to a broader notion of human "genetic enhancement" of physical characteristics such as strength, intelligence, social behavior and general improving the quality of life by genetic make-ap. In this sense, gene doping can have a significant and long-term impact on health and society in general and requires a more detailed ethical analysis and the implementation of preventive measures. The paper discusses the manipulation of genomic medicine in sport in terms of basic ethical principles and represents academic contributions to the study of the prevention, detection and control of this type of doping. Sport can and should keep the leading position in the scale of moral values in society through ethical arguments based on the balance of equality, rights and responsibilities. We cannot prevent the evolution of the sport, but we can and must direct this evolution in a better direction.

Tribbles-1: a novel regulator of hepatic lipid metabolism in humans.

Science.gov (United States)

Bauer, Robert C; Yenilmez, Batuhan O; Rader, Daniel J

2015-10-01

The protein tribbles-1, encoded by the gene TRIB1, is increasingly recognized as a major regulator of multiple cellular and physiological processes in humans. Recent human genetic studies, as well as molecular biological approaches, have implicated this intriguing protein in the aetiology of multiple human diseases, including myeloid leukaemia, Crohn's disease, non-alcoholic fatty liver disease (NAFLD), dyslipidaemia and coronary artery disease (CAD). Genome-wide association studies (GWAS) have repeatedly identified variants at the genomic TRIB1 locus as being significantly associated with multiple plasma lipid traits and cardiovascular disease (CVD) in humans. The involvement of TRIB1 in hepatic lipid metabolism has been validated through viral-mediated hepatic overexpression of the gene in mice; increasing levels of TRIB1 decreased plasma lipids in a dose-dependent manner. Additional studies have implicated TRIB1 in the regulation of hepatic lipogenesis and NAFLD. The exact mechanisms of TRIB1 regulation of both plasma lipids and hepatic lipogenesis remain undetermined, although multiple signalling pathways and transcription factors have been implicated in tribbles-1 function. Recent reports have been aimed at developing TRIB1-based lipid therapeutics. In summary, tribbles-1 is an important modulator of human energy metabolism and metabolic syndromes and worthy of future studies aimed at investigating its potential as a therapeutic target. © 2015 Authors; published by Portland Press Limited.

Hepatitis E as a cause of acute jaundice syndrome in northern Uganda, 2010-2012.

Science.gov (United States)

Gerbi, Gemechu B; Williams, Roxanne; Bakamutumaho, Barnabas; Liu, Stephen; Downing, Robert; Drobeniuc, Jan; Kamili, Saleem; Xu, Fujie; Holmberg, Scott D; Teshale, Eyasu H

2015-02-01

Hepatitis E virus (HEV) is a common cause of acute viral hepatitis in developing countries; however, its contribution to acute jaundice syndrome is not well-described. A large outbreak of hepatitis E occurred in northern Uganda from 2007 to 2009. In response to this outbreak, acute jaundice syndrome surveillance was established in 10 district healthcare facilities to determine the proportion of cases attributable to hepatitis E. Of 347 acute jaundice syndrome cases reported, the majority (42%) had hepatitis E followed by hepatitis B (14%), malaria (10%), hepatitis C (5%), and other/unknown (29%). Of hepatitis E cases, 72% occurred in Kaboong district, and 68% of these cases occurred between May and August of 2011. Residence in Kaabong district was independently associated with hepatitis E (adjusted odds ratio = 13; 95% confidence interval = 7-24). The findings from this surveillance show that an outbreak and sporadic transmission of hepatitis E occur in northern Uganda. © The American Society of Tropical Medicine and Hygiene.

Clinical biochemistry and laboratory medicine in the post-genome era

International Nuclear Information System (INIS)

Efremov, Georgi D.

2001-01-01

The last decades of the 20th century were a period of outstanding scientific achievements. The most significant discovery was the decoding of the human genome (Venter, J. et al., 2001; Dennis, C. et al., 2001; Baltimore, D., 2001). In this article the present view of the post genomic era is presented. The new analytical methods, such as micro arrays, bio chips, and nano technology, the discovery of SNPs, and the analysis of the proteome will lead to a greater understanding of the pathogenesis of inherited and acquired diseases. Their use in clinical chemistry and laboratory medicine, and the future of technological innovations are discussed. In the post genomic era the greatest interest will be devoted to the application of these scientific achievements in the diagnosis, prevention and therapy of human diseases. The advances in human genetics that have occurred during the past 20 years have revolutionized our knowledge of the role played by inheritance in health and disease. It is clear that our DNA determines not only single gene disorders but also interacts with environments to predispose individuals to cancer, allergy, hypertension, heart disease, diabetes, psychiatric disorders and even to some infectious diseases. The study of longevity and the demonstration of genes favouring a long lifespan suggest that such protective systems exist. The study of genetic polymorphisms has made clear that some alleles have beneficial effects. These discoveries will be of great help in our understanding of the interactions between genetics and environment. Gene array analysis has become the method of choice for identifying genes expressed at different levels in different samples. The mRNA expression profiles of normal and tumor tissues, treated and untreated cell cultures, and developmental stages of an organism can be compared quickly and easily with an appropriate array analysis system. A major task after a genome has been fully sequenced is to understand the functions

Hepatitis A viral load in relation to severity of the infection.

Science.gov (United States)

Fujiwara, Keiichi; Kojima, Hiroshige; Yasui, Shin; Okitsu, Koichiro; Yonemitsu, Yutaka; Omata, Masao; Yokosuka, Osamu

2011-02-01

A correlation between hepatitis A virus (HAV) genomes and the clinical severity of hepatitis A has not been established. The viral load in sera of hepatitis A patients was examined to determine the possible association between hepatitis A severity and HAV replication. One hundred sixty-four serum samples from 91 Japanese patients with sporadic hepatitis A, comprising 11 patients with fulminant hepatitis, 10 with severe acute hepatitis, and 70 with self-limited acute hepatitis, were tested for HAV RNA. The sera included 83 serial samples from 20 patients. Viral load was measured by real-time RT-PCR. The detection rates of HAV RNA from fulminant, severe acute, and acute hepatitis were 10/11 (91%), 10/10 (100%), and 55/70 (79%), respectively. Mean values of HAV RNA at admission were 3.48 ± 1.30 logcopies/ml in fulminant, 4.19 ± 1.03 in severe acute, and 2.65 ± 1.64 in acute hepatitis. Patients with severe infection such as fulminant hepatitis and severe acute hepatitis had higher initial viral load than patients with less severe infection (P hepatitis after clinical onset (P = 0.19). HAV RNA was detectable quantitatively in the majority of the sera of hepatitis A cases during the early convalescent phase by real-time PCR. Higher initial viral replication was found in severely infected patients. An excessive host immune response might follow, reducing the viral load rapidly as a result of the destruction of large numbers of HAV-infected hepatocytes, and in turn severe disease might be induced. 2010 Wiley-Liss, Inc.

Cloned genomes of infectious hepatitis C viruses and uses thereof

DEFF Research Database (Denmark)

2007-01-01

The present invention discloses nucleic acid sequences which encode infectious hepatitis C viruses and the use of these sequences, and polypeptides encoded by all or part of these sequences, in the development of vaccines and diagnostics for HCV and in the development of screening assays...

Clinical relevance of precore mutations of hepatitis B virus in chronic liver disease

Directory of Open Access Journals (Sweden)

Chaloska-Ivanova Viktorija

2014-07-01

Full Text Available Introduction: Hepatitis B is one of the most frequent etiological factors for chronic liver diseases worldwide. Recent studies have suggested the important role of the genetic diversity of the virus on natural course of hepatitis B. Hepatitis B e-antigen negative type of chronic hepatitis is associated with mutations in the precore region and basic core promoter of hepatitis B viral genome. Aim of study was to identify precore mutations in viral genome of patients with chronic hepatitis B and to evaluate clinical patterns of liver disease related to this type of hepatitis B. Methods: Sixty seven patients with hepatitis B were included in the study. In order to evaluate the clinical patterns of chronic liver disease related to hepatitis B viral infection, biochemical and virological investigations were done, as well as a quantification of serum viral load. All patients underwent liver biopsy and semiquantification of necroinflammation and/or fibrosis according to Knodell scoring was done. In the group of e antigen-negative patients, molecular analysis was performed in order to identify presence of mutations in precore region of the virus. Results: Study group was divided in 25 HBeAg-positive and 42 HBeAg-negative subjects. Al anin-aminotransferase activity and level of viral load were higher in HBeAg-positive (p < 0.05, but average age and histology activity index were significantly higher in the HBeAg-negative patients (p < 0.01. Precore mutants were found in 38 of 42 patients with HBeAg-negative hepatitis (90%. Fibrosis was found in 30/38 cases with mutations. Discussion: Mutations in precore region of HBV in HBeAg-negative patients were more prevalent in older age and were associated with higher rate of fibrosis in liver tissue, meaning more advanced stage of the disease. This could be a consequence of longer duration of HBV infection or more severe clinical course of the disease. Conclusion: Our results suggest that precore mutations are

Hepatitis C Virus(Topics in Transfusion Medicine 1990 : Autologous Transfusion and Post-Transfusion Hepatitis)

OpenAIRE

渡辺, 勇四郎; 宮村, 達男; Watanabe, Yushiro; Miyamura, Tatsuo

1990-01-01

The agent that causes blood-borne non-A, non-B hepatitis has been identified by M.Houghton and his colleagues. A cDNA of this virus has been cloned and assay system of HCV-antibody has been established. By using this assay system, we have been accumulating new epidemiological and clinical findings. We also isolated HCVcDNA clones from the serum of a Japanese healthy HCV carrier. Nucleotide sequences of these cDNA clones showed high homology with the Houghton's clones. Amino acid homology in t...

Pengembangan Sistem Pakar Untuk Diagnosis Penyakit Hepatitis Berbasis Web Menggunakan Metode Certainty Factor

Directory of Open Access Journals (Sweden)

Ahmad Ramdhani

2015-01-01

Full Text Available Expert System is a computer technology that can help people solving problems which are mostly applied in medicine. Expert System is system that trying to adopt human knowledge to the computer, so the computer can resolve the issue as done by an expert.. In this study, an Expert System to diagnose hepatitis disease consisting of Hepatitis A, Hepatitis B, and Hepatitis C will be created. This expert system to diagnose hepatitis disease is created using PHP programing language and MySQL database using Certainty Factor method. This expert system will ask for an input such as symtomps and blood test, then the result is the possibility of the disease suffered by the patient and an explanation of the disease and its treatment solution. This expert system is able to issue diagnosis results for Hepatitis A, Hepatitis B, and Hepatitis C.. Certainty Factor method can be applied to expert systems with simple disease or not complex, such as acute hepatitis disease that is done in this study.

Liver regenerative medicine: advances and challenges.

Science.gov (United States)

Chistiakov, Dimitry A

2012-01-01

Liver transplantation is the standard care for many end-stage liver diseases. However, donor organs are scarce and some people succumb to liver failure before a donor is found. Liver regenerative medicine is a special interdisciplinary field of medicine focused on the development of new therapies incorporating stem cells, gene therapy and engineered tissues in order to repair or replace the damaged organ. In this review we consider the emerging progress achieved in the hepatic regenerative medicine within the last decade. The review starts with the characterization of liver organogenesis, fetal and adult stem/progenitor cells. Then, applications of primary hepatocytes, embryonic and adult (mesenchymal, hematopoietic and induced pluripotent) stem cells in cell therapy of liver diseases are considered. Current advances and challenges in producing mature hepatocytes from stem/progenitor cells are discussed. A section about hepatic tissue engineering includes consideration of synthetic and natural biomaterials in engineering scaffolds, strategies and achievements in the development of 3D bioactive matrices and 3D hepatocyte cultures, liver microengineering, generating bioartificial liver and prospects for fabrication of the bioengineered liver. Copyright © 2012 S. Karger AG, Basel.

'Personalized medicine': what's in a name?

Science.gov (United States)

Pokorska-Bocci, Anna; Stewart, Alison; Sagoo, Gurdeep S; Hall, Alison; Kroese, Mark; Burton, Hilary

2014-03-01

Over the last decade genomics and other molecular biosciences have enabled new capabilities that, according to many, have the potential to revolutionize medicine and healthcare. These developments have been associated with a range of terminologies, including 'precision', 'personalized', 'individualized' and 'stratified' medicine. In this article, based on a literature review, we examine how the terms have arisen and their various meanings and definitions. We discuss the impact of the new technologies on disease classification, prevention and management. We suggest that although genomics and molecular biosciences will undoubtedly greatly enhance the power of medicine, they will not lead to a conceptually new paradigm of medical care. What is new is the portfolio of modern tools that medicine and healthcare can use for better targeted approaches to health and disease management, and the sociopolitical contexts within which these tools are applied.

[Personal genomics: are we debating the right Issues?].

Science.gov (United States)

Vayena, E; Mauch, F

2012-07-25

The debate about personal genomics and their role in personalized medicine has been, to some extent, hijacked by the controversy about commercially available genomic tests sold directly to consumers. The clinical validity and utility of such tests are currently limited and most medical associations recommend that consumers refrain from testing. Conversely, DTC genomics proponents and particularly the DTC industry argue that there is personal utility in acquiring genomic information. While it is necessary to debate risks and benefits of DTC genomics, we should not lose sight of the increasingly important role that genomics will play in medical practice and public health. Therefore, and in anticipation of this shift we also need to focus on important implications from the use of genomics information such as genetic discrimination, privacy protection and equitable access to health care. Undoubtedly, personal genomics will challenge our social norms maybe more than our medicine. Sticking to the polarization of «to have or not to have DTC genomics» risks to takes us away from the critical issues we need to be debating.

Evolutionary molecular medicine.

Science.gov (United States)

Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

2012-05-01

Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

Counter-attack on viral hepatitis. [Hepatitis A; Hepatitis B

Energy Technology Data Exchange (ETDEWEB)

Prozesky, O W [Pretoria Univ. (South Africa). Dept. of Medical Virology; Jupp, P G; Joubert, J J; Taylor, M B; Grabow, W O.K.

1985-07-01

The most highly developed radioimmunoassay test system in medical virology is proving of exceptional value in research aimed at controlling and eventually eradicating the scourge of human hepatitis. The use of radioimmunoassay in detecting hepatitis A (HAV) and hepatitis B (HBV) viruses is discussed. The hepatitis A virus is an enterovirus which infects the gastrointestinal tract and is usually transmitted by contaminated food, milk or water. Hepatitis B spreads mainly by the parenteral rate. Bedbugs and ticks are considered as possible transmitters of HBV. Another important contribution of radioimmunoassay is the ability to monitor the immune response of persons at risk who are vaccinated against hepatitis B.

Hepatitis B virus DNA integration in hepatocellular carcinoma after interferon-induced disappearance of hepatitis C virus.

Science.gov (United States)

Tamori, Akihiro; Nishiguchi, Shuhei; Shiomi, Susumu; Hayashi, Takehiro; Kobayashi, Sawako; Habu, Daiki; Takeda, Tadashi; Seki, Shuichi; Hirohashi, Kazuhiro; Tanaka, Hiromu; Kubo, Shoji

2005-08-01

Hepatocellular carcinoma (HCC) has been reported in patients in whom hepatitis C virus (HCV) was eliminated by interferon (IFN) therapy. We examined the pathogenesis of HCC in patients with sustained viral response. Operable HCC developed in 7 of 342 patients cured of HCV infection by IFN monotherapy. No patient abused alcohol or had diabetes mellitus or obesity. Resected specimens of HCC were histologically evaluated. DNA extracted from HCC was examined by polymerase chain reaction (PCR) to locate hepatitis B virus (HBV) DNA. HBV integration sites in human genome were identified by cassette-ligation-mediated PCR. HBV DNA was not amplified in serum samples from any of the seven patients with HCC and was found in liver in four patients. In the latter four patients, HBV DNA was integrated into the human genome of HCC. In two of these patients, covalently closed circular HBV (cccHBV) was also detected. The patients with HBV DNA integration were free of HCV for more than 3 yr. In two of the three patients without HBV DNA integration, the surrounding liver showed cirrhosis. The liver of HCC with HBV DNA integration had not progressed to cirrhosis. Three of the four tumors with HBV integration had one integration site each, located at chromosomes 11q12, 11q22-23, and 22q11, respectively. The other tumor had two integration sites, situated at chromosomes 11q13 and 14q32. At chromosome 11q12, HBV DNA was integrated into protein-coding genome, the function of which remains unclear. Integrated HBV DNA may play a role in hepatocarcinogenesis after the clearance of HCV by IFN treatment.

Theories about evolutionary origins of human hepatitis B virus in primates and humans.

Science.gov (United States)

Souza, Breno Frederico de Carvalho Dominguez; Drexler, Jan Felix; Lima, Renato Santos de; Rosário, Mila de Oliveira Hughes Veiga do; Netto, Eduardo Martins

2014-01-01

The human hepatitis B virus causes acute and chronic hepatitis and is considered one of the most serious human health issues by the World Health Organization, causing thousands of deaths per year. There are similar viruses belonging to the Hepadnaviridae family that infect non-human primates and other mammals as well as some birds. The majority of non-human primate virus isolates were phylogenetically close to the human hepatitis B virus, but like the human genotypes, the origins of these viruses remain controversial. However, there is a possibility that human hepatitis B virus originated in primates. Knowing whether these viruses might be common to humans and primates is crucial in order to reduce the risk to humans. To review the existing knowledge about the evolutionary origins of viruses of the Hepadnaviridae family in primates. This review was done by reading several articles that provide information about the Hepadnaviridae virus family in non-human primates and humans and the possible origins and evolution of these viruses. The evolutionary origin of viruses of the Hepadnaviridae family in primates has been dated back to several thousand years; however, recent analyses of genomic fossils of avihepadnaviruses integrated into the genomes of several avian species have suggested a much older origin of this genus. Some hypotheses about the evolutionary origins of human hepatitis B virus have been debated since the '90s. One theory suggested a New World origin because of the phylogenetic co-segregation between some New World human hepatitis B virus genotypes F and H and woolly monkey human hepatitis B virus in basal sister-relationship to the Old World non-human primates and human hepatitis B virus variants. Another theory suggests an Old World origin of human hepatitis B virus, and that it would have been spread following prehistoric human migrations over 100,000 years ago. A third theory suggests a co-speciation of human hepatitis B virus in non-human primate

All about the Human Genome Project (HGP)

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... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits

DEFF Research Database (Denmark)

Speliotes, Elizabeth K; Yerges-Armstrong, Laura M; Wu, Jun

2011-01-01

steatosis, a non-invasive measure of NAFLD, in large population based samples. Using variance components methods, we show that CT hepatic steatosis is heritable (~26%-27%) in family-based Amish, Family Heart, and Framingham Heart Studies (n¿=¿880 to 3,070). By carrying out a fixed-effects meta......-analysis of genome-wide association (GWA) results between CT hepatic steatosis and ~2.4 million imputed or genotyped SNPs in 7,176 individuals from the Old Order Amish, Age, Gene/Environment Susceptibility-Reykjavik study (AGES), Family Heart, and Framingham Heart Studies, we identify variants associated at genome......Nonalcoholic fatty liver disease (NAFLD) clusters in families, but the only known common genetic variants influencing risk are near PNPLA3. We sought to identify additional genetic variants influencing NAFLD using genome-wide association (GWA) analysis of computed tomography (CT) measured hepatic...

Perspectives in molecular imaging through translational research, human medicine, and veterinary medicine.

Science.gov (United States)

Berry, Clifford R; Garg, Predeep

2014-01-01

The concept of molecular imaging has taken off over the past 15 years to the point of the renaming of the Society of Nuclear Medicine (Society of Nuclear Medicine and Molecular Imaging) and Journals (European Journal of Nuclear Medicine and Molecular Imaging) and offering of medical fellowships specific to this area of study. Molecular imaging has always been at the core of functional imaging related to nuclear medicine. Even before the phrase molecular imaging came into vogue, radionuclides and radiopharmaceuticals were developed that targeted select physiological processes, proteins, receptor analogs, antibody-antigen interactions, metabolites and specific metabolic pathways. In addition, with the advent of genomic imaging, targeted genomic therapy, and theranostics, a number of novel radiopharmaceuticals for the detection and therapy of specific tumor types based on unique biological and cellular properties of the tumor itself have been realized. However, molecular imaging and therapeutics as well as the concept of theranostics are yet to be fully realized. The purpose of this review article is to present an overview of the translational approaches to targeted molecular imaging with application to some naturally occurring animal models of human disease. © 2013 Published by Elsevier Inc.

Genetic and hormonal control of hepatic steatosis in female and male mice.

Science.gov (United States)

Norheim, Frode; Hui, Simon T; Kulahcioglu, Emre; Mehrabian, Margarete; Cantor, Rita M; Pan, Calvin; Parks, Brian W; Lusis, Aldons J

2017-01-01

The etiology of nonalcoholic fatty liver disease is complex and influenced by factors such as obesity, insulin resistance, hyperlipidemia, and sex. We now report a study on sex difference in hepatic steatosis in the context of genetic variation using a population of inbred strains of mice. While male mice generally exhibited higher concentration of hepatic TG levels on a high-fat high-sucrose diet, sex differences showed extensive interaction with genetic variation. Differences in percentage body fat were the best predictor of hepatic steatosis among the strains and explained about 30% of the variation in both sexes. The difference in percent gonadal fat and HDL explained 9.6% and 6.7% of the difference in hepatic TGs between the sexes, respectively. Genome-wide association mapping of hepatic TG revealed some striking differences in genetic control of hepatic steatosis between females and males. Gonadectomy increased the hepatic TG to body fat percentage ratio among male, but not female, mice. Our data suggest that the difference between the sexes in hepatic TG can be partly explained by differences in body fat distribution, plasma HDL, and genetic regulation. Future studies are required to understand the molecular interactions between sex, genetics, and the environment. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.

Use of alternative product in patients with chronic viral hepatitis

Directory of Open Access Journals (Sweden)

Mahmut Dulger

2014-09-01

Full Text Available Objectives: Some of the patients with chronic hepatitis use both alternative product and/or antiviral treatment. These herbal products sometimes lead to clinical deterioration. In this study we aimed to determine the purpose of alternative product utilization and rate among the chronic hepatitis B (CHB and C (CHC patients. Methods: This prospective cohort study included 200 consecutive adult patients with chronic hepatitis B and C at the Department of Infectious Diseases, Ondokuz Mayis University, between 1 March 2012 and 30 July 2012. At enrollment, clinical information, demographics, laboratory variables and knowledge about alternative products were recorded. Results: Of the patients 150 had CHB, 50 had CHC. 54% of patients were male. Use of alternative products was 26%. Antiviral treatment rate was 48.5% for all patients. The most used alternative products were artichoke extract and honey. 67.3% of patients were using single alternative product whereas the others were using two or more alternative products. 46.2% of patients who use alternative product provided information about the alternative product usage, but the others did not. Conclusions: Majority of patients used alternative products. More than half of these patients did not give information to their physicians about their use of alternative medicine. Use of alternative product should be asked in all patients with chronic hepatitis. Herbal product usage was detected in majority of patients and also approximately half of these patients did not give information to their doctors about taking alternative medicine. In conclusion, it is necessary to take detailed information about herbal product usage in patients with chronic hepatitis. J Microbiol Infect Dis 2014; 4(3: 102-106

GTCBio's Precision Medicine Conference (July 7-8, 2016 - Boston, Massachusetts, USA).

Science.gov (United States)

Cole, P

2016-09-01

GTCBio's Precision Medicine Conference met this year to outline the many steps forward that precision medicine and individualized genomics has made and the challenges it still faces in technological, modeling, and standards development, interoperability and compatibility advancements, and methods of economic and societal adoption. The conference was split into four sections, 'Overcoming Challenges in the Commercialization of Precision Medicine', 'Implementation of Precision Medicine: Strategies & Technologies', 'Integrating & Interpreting Personal Genomics, Big Data, & Bioinformatics' and 'Incentivizing Precision Medicine: Regulation & Reimbursement', with this report focusing on the final two subjects. Copyright 2016 Prous Science, S.A.U. or its licensors. All rights reserved.

Uracil DNA glycosylase counteracts APOBEC3G-induced hypermutation of hepatitis B viral genomes: excision repair of covalently closed circular DNA.

Directory of Open Access Journals (Sweden)

Kouichi Kitamura

Full Text Available The covalently closed circular DNA (cccDNA of the hepatitis B virus (HBV plays an essential role in chronic hepatitis. The cellular repair system is proposed to convert cytoplasmic nucleocapsid (NC DNA (partially double-stranded DNA into cccDNA in the nucleus. Recently, antiviral cytidine deaminases, AID/APOBEC proteins, were shown to generate uracil residues in the NC-DNA through deamination, resulting in cytidine-to-uracil (C-to-U hypermutation of the viral genome. We investigated whether uracil residues in hepadnavirus DNA were excised by uracil-DNA glycosylase (UNG, a host factor for base excision repair (BER. When UNG activity was inhibited by the expression of the UNG inhibitory protein (UGI, hypermutation of NC-DNA induced by either APOBEC3G or interferon treatment was enhanced in a human hepatocyte cell line. To assess the effect of UNG on the cccDNA viral intermediate, we used the duck HBV (DHBV replication model. Sequence analyses of DHBV DNAs showed that cccDNA accumulated G-to-A or C-to-T mutations in APOBEC3G-expressing cells, and this was extensively enhanced by UNG inhibition. The cccDNA hypermutation generated many premature stop codons in the P gene. UNG inhibition also enhanced the APOBEC3G-mediated suppression of viral replication, including reduction of NC-DNA, pre-C mRNA, and secreted viral particle-associated DNA in prolonged culture. Enhancement of APOBEC3G-mediated suppression by UNG inhibition was not observed when the catalytic site of APOBEC3G was mutated. Transfection experiments of recloned cccDNAs revealed that the combination of UNG inhibition and APOBEC3G expression reduced the replication ability of cccDNA. Taken together, these data indicate that UNG excises uracil residues from the viral genome during or after cccDNA formation in the nucleus and imply that BER pathway activities decrease the antiviral effect of APOBEC3-mediated hypermutation.

Genus Phyllanthus for chronic hepatitis B virus infection

DEFF Research Database (Denmark)

Liu, J; Lin, Haili; McIntosh, H

2001-01-01

To evaluate the efficacy and safety of genus Phyllanthus for chronic hepatitis B virus (HBV) infection we performed a systematic review of randomized clinical trials. Randomized trials comparing genus Phyllanthus vs. placebo, no intervention, general nonspecific treatment, other herbal medicine.......85-17.21) compared with placebo or no intervention. There was no significant difference on clearance of serum HBsAg, HBeAg and HBV DNA between Phyllanthus and IFN. Phyllanthus species were better than nonspecific treatment or other herbal medicines for the clearance of serum HBsAg, HBeAg, HBV DNA, and liver enzyme...

Development of a curriculum in molecular diagnostics, genomics and personalized medicine for dermatology trainees.

Science.gov (United States)

Murphy, Michael J; Shahriari, Neda; Payette, Michael; Mnayer, Laila; Elaba, Zendee

2016-10-01

Results of molecular studies are redefining the diagnosis and management of a wide range of skin disorders. Dermatology training programs maintain a relative gap in relevant teaching. To develop a curriculum in molecular diagnostics, genomics and personalized medicine for dermatology trainees at our institution. The aim is to provide trainees with a specialty-appropriate, working knowledge in clinical molecular dermatology. The Departments of Dermatology and Pathology and Laboratory Medicine collaborated on the design and implementation of educational objectives and teaching modalities for the new curriculum. A multidisciplinary curriculum was developed. It comprises: (i) assigned reading from the medical literature and reference textbook; (ii) review of teaching sets; (iii) two 1 hour lectures; (iv) trainee presentations; (v) 1-week rotation in a clinical molecular pathology and cytogenetics laboratory; and (vi) assessments and feedback. Residents who participated in the curriculum to date have found the experience to be of value. Our curriculum provides a framework for other dermatology residency programs to develop their own specific approach to molecular diagnostics education. Such training will provide a foundation for lifelong learning as molecular testing evolves and becomes integral to the practice of dermatology. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Near-Full Genome Characterisation of Two Natural Intergenotypic 2k/1b Recombinant Hepatitis C Virus Isolates

Directory of Open Access Journals (Sweden)

Victoria L. Demetriou

2011-01-01

Full Text Available Few natural intergenotypic hepatitis C virus (HCV recombinants have been characterised, and only RF1_2k/1b has demonstrated widespread transmission. The near-full length genome sequences for two cases of 2k/1b recombinants (CYHCV037 and CYHCV093 sampled in Cyprus were obtained using strain-specific RT-PCR amplification and sequencing protocols. Sequence analysis confirmed their similarity with the original RF1_2k/1b strain from St. Petersburg, N687. These two isolates significantly contribute to the sequence data available on this recombinant and confirm its increasing spread among individuals from Eastern Europe, and its association with transmission through intravenous drug use. Phylogenetic analyses reveal clustering of the sequence 3′ to the recombination point, not seen in the topology of the 5′ sequences, implying a more complicated evolutionary history than that held to date. The increasing cases of HCV recombinant strains underline the requirement of their contribution to the standardised rules of HCV classification and nomenclature, molecular epidemiology, diagnosis, and treatment.

New-onset ascites as a manifestation of virologic relapse in patients with hepatitis C cirrhosis

Directory of Open Access Journals (Sweden)

Chua DL

2014-01-01

Full Text Available Deborah Lim Chua, Thomas Hahambis, Samuel H SigalDivision of Gastroenterology, Department of Medicine, New York University School of Medicine, New York, NY, USABackground: Chronic hepatitis C is the most common cause of cirrhosis in industrialized countries. Successful treatment of chronic hepatitis C in patients with advanced fibrosis or cirrhosis has significant benefits, including improvements in inflammation, fibrosis, and portal hypertension, with prevention of esophageal varices and clinical decompensation.Case: In this report, we present two patients with well-compensated hepatitis C cirrhosis who achieved an end-of-treatment response on a direct-acting antiviral therapy-based triple regimen for hepatitis C virus, but subsequently presented with new-onset ascites associated with virologic relapse.Conclusion: We propose that the development of ascites in this setting is due to the adverse impact of inflammation of the virologic relapse on portal hypertension. Our observation that ascites formation can be a manifestation of virologic relapse has potentially important clinical implications, as it highlights not only the importance of close monitoring of cirrhotic patients after achieving end-of-treatment response but also the impact of active inflammation on the severity of portal hypertension.Keywords: chronic hepatitis C, cirrhosis, virologic relapse, portal hypertension, ascites

[Complex treatment of patients with cholangiogenic hepatic abscess].

Science.gov (United States)

Nychytaĭlo, M Iu; Skums, A V; Medvets'kyĭ, Ie B; Ohorodnyk, P V; Mashkovs'kyĭ, H Iu; Shkarban, V P; Shkarban, P O; Farzolakh, Mekhraban Jafarlu

2005-07-01

Results of treatment of 47 patients with cholangiogenic hepatic abscess were analyzed. Clinical, laboratory and special methods of investigation were applied for diagnosis. The authors consider ultrasound investigation (USI), computer tomography and the abscess puncture under the USI control with subsequent cytological and bacterial control the decisive methods in diagnosis of hepatic abscess. In complex of treatment of patients miniinvasive technologies were applied--the abscess puncture, its cavity drainage under USI control transcutaneus transhepatic cholangiostomy, endoscopic papillosphincterotomy with lithotripsy and nasobiliary drainage, according to indications. Efficacy of the abscess cavity sanation, using miramistinum and decasan, was proved. In general therapy the directed transport of medicines was applied.

Family genome browser: visualizing genomes with pedigree information.

Science.gov (United States)

Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

2015-07-15

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

18F-FAC PET selectively images hepatic infiltrating CD4 and CD8 T cells in a mouse model of autoimmune hepatitis.

Science.gov (United States)

Salas, Jessica R; Chen, Bao Ying; Wong, Alicia; Cheng, Donghui; Van Arnam, John S; Witte, Owen N; Clark, Peter M

2018-04-26

dexamethasone for treating the autoimmune hepatitis model. Infiltrating leukocytes in liver biopsy samples from patients suffering from autoimmune hepatitis express high levels of dCK, a rate-limiting enzyme in the accumulation of 18 F-FAC. Conclusion: Our data suggests that PET can be used to non-invasively visualize activated leukocytes and inflamed hepatocytes in a mouse model of autoimmune hepatitis. Copyright © 2018 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

[Alternative medicine: really an alternative to academic medicine?].

Science.gov (United States)

Happle, R

2000-06-01

Numerous courses on alternative medicine are regularly advertised in Deutsches Arzteblatt, the organ of the German Medical Association. The present German legislation likewise supports this form of medicine, and this explains why Iscador, an extract of the mistletoe, is found in the Rote Liste, a directory of commercially available medical drugs, under the heading "cytostatic and antimetastatic drugs" although such beneficial effect is unproven. To give another example, a German health insurance fund was sentenced to pay for acupuncture as a treatment for hepatic failure. This judgement is characteristic of the present German judicial system and represents a victory of "oracling irrationalism" (Popper). The astonishing popularity of alternative medicine can be explained by a revival of romanticism. An intellectually fair opposite position has been delineated by Karl Popper in the form of critical rationalism. It is important to realize, however, that our decision to adhere to rational thinking is made in the innermost depth of our heart but not on the basis of rational arguing. Rather, the decision in favor of reason has a moral dimension.

Clinical significance of changes of serum IL-12, TGF-β, CTGF and PDGF levels after treatment with integrated traditional and western medicine in patients with chronic severe hepatitis B

International Nuclear Information System (INIS)

Qian Yue

2010-01-01

Objective: To investigate the relationship between progress of disease process and changes of serum IL-12, TGF-β, CTGF and PDGF levels in patients with chronic severe hepatitis B. Methods: Serum TGF-β (with RIA) and IL-12, connective tissue growth factor (CTGF) platelet-derived growth factor (PDGF) (all with ELISA) levels were determined both before and after integrated traditional and western medicine treatment in 50 patients with chronic severe hepatitis β as well as once in 50 controls. Results: Before treatment the serum levels of IL-12 were significantly higher in patients with chronic severe hepatitis B than those in the controls (P<0.01), while after treatment, the serum levels of IL-12 were only slightly decreased and remained significantly higher than those in the controls (P<0.01). Before treatment the serum levels of TGF-β, CTGF and PDGF were all significantly higher than those in controls (P<0.01). After treatment, the levels all dropped significantly (vs before treatment, P<0.05), but still remained significantly higher than those in controls (TGF-β, P<0.05, CTGF and PDGF, P<0.01). Conclusion: Detection of changes of IL-12, TGF-β, CTGF and PDGF levels after treatment in patients with chronic severe hepatitis B provided a valuable laboratory basis for stu-ding the progress of disease process. (authors)

Personalized medicine: reality and reality checks.

Science.gov (United States)

Leeder, J Steven; Spielberg, Stephen P

2009-05-01

The evolving era of pharmacogenomics and personalized medicine is greeted with optimism by many, but this sentiment is not universally shared. The existence of diametrically opposed opinions concerning the potential benefits and obstacles facing the widespread implementation of genomic medicine should stimulate discussion and guide the design of studies to establish the value of interventions targeted at the level of individual patients. One of the more controversial aspects of personalized medicine is whether the anticipated benefits will be realized at an acceptable cost. Recently released analyses suggest that the returns on investment depend on the particular scenario and are different for different stakeholders. On the other hand, cost is only one of the challenges regarding implementation of personalized medicine. Among these are the development of universal standards for managing genomic information in electronic medical records, improvement in the collection and interpretation of clinical phenotype data, and new strategies to educate practitioners and patients/consumers. The reality is that personalized medicine is upon us; open discourse and periodic reality checks will be necessary as we confront it.

Seroepidemiology of hepatitis A and hepatitis E viruses in Aden, Yemen.

Science.gov (United States)

Bawazir, Amen Ahmed; Hart, C Anthony; Sallam, Tallal A; Parry, Christopher M; Beeching, Nicholas J; Cuevas, Luis E

2010-12-01

The burden of hepatitis A (HAV) and hepatitis E (HEV) infection is unknown in Aden, Yemen. This survey describes the prevalence of antibodies against HAV and HEV among individuals attending primary health care facilities in Aden, Yemen. Five hundred and thirty eight participants, stratified by age and district population size, were enrolled and screened for anti-HAV and 356 for anti-HEV antibodies. The age-standardized seroprevalence of antibodies was 86.6% (95% CI 83.7-89.5) for anti-HAV and 10.7% (95% CI 7.5-13.9) for anti-HEV. The prevalence of anti-HAV and anti-HEV ranged from 53% and 0% in infants to 100% and 15.3% in participants >18 years old, respectively (Phepatitis remains a major public health problem in Aden with trends of hyperendemicity for both infections. Priority should be given to improve water quality, sanitation coverage, and food hygiene and increase public health awareness concerning the risk of contracting infection. Copyright © 2010 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.

The landscape of precision cancer medicine clinical trials in the United States.

Science.gov (United States)

Roper, Nitin; Stensland, Kristian D; Hendricks, Ryan; Galsky, Matthew D

2015-05-01

Advances in tumor biology and multiplex genomic analysis have ushered in the era of precision cancer medicine. Little is currently known, however, about the landscape of prospective "precision cancer medicine" clinical trials in the U.S. We identified all adult interventional cancer trials registered on ClinicalTrials.gov between September 2005 and May 2013. Trials were classified as "precision cancer medicine" if a genomic alteration in a predefined set of 88 genes was required for enrollment. Baseline characteristics were ascertained for each trial. Of the initial 18,797 trials identified, 9094 (48%) were eligible for inclusion: 684 (8%) were classified as precision cancer medicine trials and 8410 (92%) were non-precision cancer medicine trials. Compared with non-precision cancer medicine trials, precision cancer medicine trials were significantly more likely to be phase II [RR 1.19 (1.10-1.29), pPrecision medicine trials required 38 unique genomic alterations for enrollment. The proportion of precision cancer medicine trials compared to the total number of trials increased from 3% in 2006 to 16% in 2013. The proportion of adult cancer clinical trials in the U.S. requiring a genomic alteration for enrollment has increased substantially over the past several years. However, such trials still represent a small minority of studies performed within the cancer clinical trials enterprise and include a small subset of putatively "actionable" alterations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hepatitis C Virus: Viral Quasispecies and Genotypes.

Science.gov (United States)

Tsukiyama-Kohara, Kyoko; Kohara, Michinori

2017-12-22

Hepatitis C virus (HCV) mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs), which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

Feature Hepatitis: Hepatitis Can Strike Anyone

Science.gov (United States)

... Navigation Bar Home Current Issue Past Issues Feature Hepatitis Hepatitis Can Strike Anyone Past Issues / Spring 2009 Table ... from all walks of life are affected by hepatitis, especially hepatitis C, the most common form of ...

Genotyping of Hepatitis C virus isolated from hepatitis patients in Southeast of Iran by taqman realtime PCR

International Nuclear Information System (INIS)

Farivar, T.N.; Johari, P.

2011-01-01

Objectives: To check TaqMan Realtime PCR in detecting genotypes of hepatitis C virus in Iran. Methods: From July 2007 to April 2009, HCV genotyping was done on 52 patients who were referred to Research Centre for infectious Disease and Tropical Medicine, in Bou-Ali Hospital, Zahedan University of Medical Sciences. All these patients had proven hepatitis C infection. Results: Out of 52 anti HCV positive samples, 28(53.84%) had genotype 1, 2 cases (3.88 %) had genotype 2 , 12 (23.08 %) had genotype 3 and 7 (13.4 %) had genotype 4 . Mixed infection with genotypes 1 and 3 was seen in 3 cases (5.77 %). Conclusion: TaqMan probes for detecting genotyping of HCV were successful in picking genotyping of HCV infection especially those with mixed genotypes. (author)

HDVDB: a data warehouse for hepatitis delta virus.

Science.gov (United States)

Singh, Sarita; Gupta, Sunil Kumar; Nischal, Anuradha; Pant, Kamlesh Kumar; Seth, Prahlad Kishore

2015-01-01

Hepatitis Delta Virus (HDV) is an RNA virus and causes delta hepatitis in humans. Although a lot of data is available for HDV, but retrieval of information is a complicated task. Current web database 'HDVDB' provides a comprehensive web-resource for HDV. The database is basically concerned with basic information about HDV and disease caused by this virus, genome structure, pathogenesis, epidemiology, symptoms and prevention, etc. Database also supplies sequence data and bibliographic information about HDV. A tool 'siHDV Predict' to design the effective siRNA molecule to control the activity of HDV, is also integrated in database. It is a user friendly information system available at public domain and provides annotated information about HDV for research scholars, scientists, pharma industry people for further study.

Narrowing the gap of personalized medicine in emerging countries: the case of multiple endocrine neoplasias in Brazil.

Science.gov (United States)

Toledo, Rodrigo A; Sekiya, Tomoko; Longuini, Viviane C; Coutinho, Flavia L; Lourenço, Delmar M; Toledo, Sergio P A

2012-01-01

The finished version of the human genome sequence was completed in 2003, and this event initiated a revolution in medical practice, which is usually referred to as the age of genomic or personalized medicine. Genomic medicine aims to be predictive, personalized, preventive, and also participative (4Ps). It offers a new approach to several pathological conditions, although its impact so far has been more evident in mendelian diseases. This article briefly reviews the potential advantages of this approach, and also some issues that may arise in the attempt to apply the accumulated knowledge from genomic medicine to clinical practice in emerging countries. The advantages of applying genomic medicine into clinical practice are obvious, enabling prediction, prevention, and early diagnosis and treatment of several genetic disorders. However, there are also some issues, such as those related to: (a) the need for approval of a law equivalent to the Genetic Information Nondiscrimination Act, which was approved in 2008 in the USA; (b) the need for private and public funding for genetics and genomics; (c) the need for development of innovative healthcare systems that may substantially cut costs (e.g. costs of periodic medical followup); (d) the need for new graduate and postgraduate curricula in which genomic medicine is emphasized; and (e) the need to adequately inform the population and possible consumers of genetic testing, with reference to the basic aspects of genomic medicine.

Complete chloroplast genome and 45S nrDNA sequences of the medicinal plant species Glycyrrhiza glabra and Glycyrrhiza uralensis.

Science.gov (United States)

Kang, Sang-Ho; Lee, Jeong-Hoon; Lee, Hyun Oh; Ahn, Byoung Ohg; Won, So Youn; Sohn, Seong-Han; Kim, Jung Sun

2017-10-06

Glycyrrhiza uralensis and G. glabra, members of the Fabaceae, are medicinally important species that are native to Asia and Europe. Extracts from these plants are widely used as natural sweeteners because of their much greater sweetness than sucrose. In this study, the three complete chloroplast genomes and five 45S nuclear ribosomal (nr)DNA sequences of these two licorice species and an interspecific hybrid are presented. The chloroplast genomes of G. glabra, G. uralensis and G. glabra × G. uralensis were 127,895 bp, 127,716 bp and 127,939 bp, respectively. The three chloroplast genomes harbored 110 annotated genes, including 76 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The 45S nrDNA sequences were either 5,947 or 5,948 bp in length. Glycyrrhiza glabra and G. glabra × G. uralensis showed two types of nrDNA, while G. uralensis contained a single type. The complete 45S nrDNA sequence unit contains 18S rRNA, ITS1, 5.8S rRNA, ITS2 and 26S rRNA. We identified simple sequence repeat and tandem repeat sequences. We also developed four reliable markers for analysis of Glycyrrhiza diversity authentication.

Ethical Considerations Related to Return of Results from Genomic Medicine Projects: The eMERGE Network (Phase III) Experience

Science.gov (United States)

Fossey, Robyn; Kochan, David; Winkler, Erin; Pacyna, Joel E.; Olson, Janet; Thibodeau, Stephen; Connolly, John J.; Harr, Margaret; Behr, Meckenzie A.; Prows, Cynthia A.; Cobb, Beth; Myers, Melanie F.; Leslie, Nancy D.; Namjou-Khales, Bahram; Milo Rasouly, Hila; Wynn, Julia; Fedotov, Alexander; Chung, Wendy K.; Gharavi, Ali; Williams, Janet L.; Pais, Lynn; Holm, Ingrid; Aufox, Sharon; Smith, Maureen E.; Scrol, Aaron; Leppig, Kathleen; Jarvik, Gail P.; Wiesner, Georgia L.; Li, Rongling; Stroud, Mary; Smoller, Jordan W.; Sharp, Richard R.; Kullo, Iftikhar J.

2018-01-01

We examined the Institutional Review Board (IRB) process at 9 academic institutions in the electronic Medical Records and Genomics (eMERGE) Network, for proposed electronic health record-based genomic medicine studies, to identify common questions and concerns. Sequencing of 109 disease related genes and genotyping of 14 actionable variants is being performed in ~28,100 participants from the 9 sites. Pathogenic/likely pathogenic variants in actionable genes are being returned to study participants. We examined each site’s research protocols, informed-consent materials, and interactions with IRB staff. Research staff at each site completed questionnaires regarding their IRB interactions. The time to prepare protocols for IRB submission, number of revisions and time to approval ranged from 10–261 days, 0–11, and 11–90 days, respectively. IRB recommendations related to the readability of informed consent materials, specifying the full range of potential risks, providing options for receiving limited results or withdrawal, sharing of information with family members, and establishing the mechanisms to answer participant questions. IRBs reviewing studies that involve the return of results from genomic sequencing have a diverse array of concerns, and anticipating these concerns can help investigators to more effectively engage IRBs. PMID:29301385

Hepatic Encephalopathy

Medline Plus

Full Text Available ... Disease Type 1 (von Gierke) Hemochromatosis Hepatic Encephalopathy Hepatitis A Hepatitis B Hepatitis C Intrahepatic Cholestasis of Pregnancy ( ... Disease Type 1 (von Gierke) Hemochromatosis Hepatic Encephalopathy Hepatitis A Hepatitis B Hepatitis C Intrahepatic Cholestasis of Pregnancy ( ...

Genomics education for medical professionals - the current UK landscape.

Science.gov (United States)

Slade, Ingrid; Subramanian, Deepak N; Burton, Hilary

2016-08-01

Genomics education in the UK is at an early stage of development, and its pace of evolution has lagged behind that of the genomics research upon which it is based. As a result, knowledge of genomics and its applications remains limited among non-specialist clinicians. In this review article, we describe the complex landscape for genomics education within the UK, and highlight the large number and variety of organisations that can influence, direct and provide genomics training to medical professionals. Postgraduate genomics education is being shaped by the work of the Health Education England (HEE) Genomics Education Programme, working in conjunction with the Joint Committee on Genomics in Medicine. The success of their work will be greatly enhanced by the full cooperation and engagement of the many groups, societies and organisations involved with medical education and training (such as the royal colleges). Without this cooperation, there is a risk of poor coordination and unnecessary duplication of work. Leadership from an organisation such as the HEE Genomics Education Programme will have a key role in guiding the formulation and delivery of genomics education policy by various stakeholders among the different disciplines in medicine. © 2016 Royal College of Physicians.

Newborn Screening in the Era of Precision Medicine.

Science.gov (United States)

Yang, Lan; Chen, Jiajia; Shen, Bairong

2017-01-01

As newborn screening success stories gained general confirmation during the past 50 years, scientists quickly discovered diagnostic tests for a host of genetic disorders that could be treated at birth. Outstanding progress in sequencing technologies over the last two decades has made it possible to comprehensively profile newborn screening (NBS) and identify clinically relevant genomic alterations. With the rapid developments in whole-genome sequencing (WGS) and whole-exome sequencing (WES) recently, we can detect newborns at the genomic level and be able to direct the appropriate diagnosis to the different individuals at the appropriate time, which is also encompassed in the concept of precision medicine. Besides, we can develop novel interventions directed at the molecular characteristics of genetic diseases in newborns. The implementation of genomics in NBS programs would provide an effective premise for the identification of the majority of genetic aberrations and primarily help in accurate guidance in treatment and better prediction. However, there are some debate correlated with the widespread application of genome sequencing in NBS due to some major concerns such as clinical analysis, result interpretation, storage of sequencing data, and communication of clinically relevant mutations to pediatricians and parents, along with the ethical, legal, and social implications (so-called ELSI). This review is focused on these critical issues and concerns about the expanding role of genomics in NBS for precision medicine. If WGS or WES is to be incorporated into NBS practice, considerations about these challenges should be carefully regarded and tackled properly to adapt the requirement of genome sequencing in the era of precision medicine.

A primer on precision medicine informatics.

Science.gov (United States)

Sboner, Andrea; Elemento, Olivier

2016-01-01

In this review, we describe key components of a computational infrastructure for a precision medicine program that is based on clinical-grade genomic sequencing. Specific aspects covered in this review include software components and hardware infrastructure, reporting, integration into Electronic Health Records for routine clinical use and regulatory aspects. We emphasize informatics components related to reproducibility and reliability in genomic testing, regulatory compliance, traceability and documentation of processes, integration into clinical workflows, privacy requirements, prioritization and interpretation of results to report based on clinical needs, rapidly evolving knowledge base of genomic alterations and clinical treatments and return of results in a timely and predictable fashion. We also seek to differentiate between the use of precision medicine in germline and cancer. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Next Generation DNA Sequencing and the Future of Genomic Medicine

OpenAIRE

Anderson, Matthew W.; Schrijver, Iris

2010-01-01

In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed “next-generation” sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic analysis at a cost feasible for routine clinical diagnostics. However, the ability to more thoroughly interrogate genomic sequence raises a number of important issues with regard to result interpreta...

Prediction in medicine – genome contra envirome

Czech Academy of Sciences Publication Activity Database

Brdička, Radim

2012-01-01

Roč. 151, č. 1 (2012), s. 22-25 ISSN 0008-7335 R&D Projects: GA MZd NS9804 Institutional research plan: CEZ:AV0Z50390703 Keywords : genome * genotype * phenotype Subject RIV: FP - Other Medical Disciplines

Privacy in the Genomic Era

Science.gov (United States)

NAVEED, MUHAMMAD; AYDAY, ERMAN; CLAYTON, ELLEN W.; FELLAY, JACQUES; GUNTER, CARL A.; HUBAUX, JEAN-PIERRE; MALIN, BRADLEY A.; WANG, XIAOFENG

2015-01-01

Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward. PMID:26640318

Privacy in the Genomic Era.

Science.gov (United States)

Naveed, Muhammad; Ayday, Erman; Clayton, Ellen W; Fellay, Jacques; Gunter, Carl A; Hubaux, Jean-Pierre; Malin, Bradley A; Wang, Xiaofeng

2015-09-01

Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.

What does it mean to be genomically literate?: National Human Genome Research Institute Meeting Report.

Science.gov (United States)

Hurle, Belen; Citrin, Toby; Jenkins, Jean F; Kaphingst, Kimberly A; Lamb, Neil; Roseman, Jo Ellen; Bonham, Vence L

2013-08-01

Genomic discoveries will increasingly advance the science of medicine. Limited genomic literacy may adversely impact the public's understanding and use of the power of genetics and genomics in health care and public health. In November 2011, a meeting was held by the National Human Genome Research Institute to examine the challenge of achieving genomic literacy for the general public, from kindergarten to grade 12 to adult education. The role of the media in disseminating scientific messages and in perpetuating or reducing misconceptions was also discussed. Workshop participants agreed that genomic literacy will be achieved only through active engagement between genomics experts and the varied constituencies that comprise the public. This report summarizes the background, content, and outcomes from this meeting, including recommendations for a research agenda to inform decisions about how to advance genomic literacy in our society.

Precision Medicine-Nobody Is Average.

Science.gov (United States)

Vinks, A A

2017-03-01

Medicine gets personal and tailor-made treatments are underway. Hospitals have started to advertise their advanced genomic testing capabilities and even their disruptive technologies to help foster a culture of innovation. The prediction in the lay press is that in decades from now we may look back and see 2017 as the year precision medicine blossomed. It is all part of the Precision Medicine Initiative that takes into account individual differences in people's genes, environments, and lifestyles. © 2017 ASCPT.

Exotic multifaceted medicinal plants of drugs and pharmaceutical ...

African Journals Online (AJOL)

They are sources of drugs and are used in herbal medicine to treat measles, malaria, asthma, eczema, cough, hepatitis, ringworm, ulcer and scabies. These plants are continuously screened and evaluated for their pharmacological properties. Bioactive compounds comprising flavanoids, alkaloids, steroids, terpenoids and ...

Visualization and measurement of ATP levels in living cells replicating hepatitis C virus genome RNA.

Directory of Open Access Journals (Sweden)

Tomomi Ando

Full Text Available Adenosine 5'-triphosphate (ATP is the primary energy currency of all living organisms and participates in a variety of cellular processes. Although ATP requirements during viral lifecycles have been examined in a number of studies, a method by which ATP production can be monitored in real-time, and by which ATP can be quantified in individual cells and subcellular compartments, is lacking, thereby hindering studies aimed at elucidating the precise mechanisms by which viral replication energized by ATP is controlled. In this study, we investigated the fluctuation and distribution of ATP in cells during RNA replication of the hepatitis C virus (HCV, a member of the Flaviviridae family. We demonstrated that cells involved in viral RNA replication actively consumed ATP, thereby reducing cytoplasmic ATP levels. Subsequently, a method to measure ATP levels at putative subcellular sites of HCV RNA replication in living cells was developed by introducing a recently-established Förster resonance energy transfer (FRET-based ATP indicator, called ATeam, into the NS5A coding region of the HCV replicon. Using this method, we were able to observe the formation of ATP-enriched dot-like structures, which co-localize with non-structural viral proteins, within the cytoplasm of HCV-replicating cells but not in non-replicating cells. The obtained FRET signals allowed us to estimate ATP concentrations within HCV replicating cells as ∼5 mM at possible replicating sites and ∼1 mM at peripheral sites that did not appear to be involved in HCV replication. In contrast, cytoplasmic ATP levels in non-replicating Huh-7 cells were estimated as ∼2 mM. To our knowledge, this is the first study to demonstrate changes in ATP concentration within cells during replication of the HCV genome and increased ATP levels at distinct sites within replicating cells. ATeam may be a powerful tool for the study of energy metabolism during replication of the viral genome.

Hepatoprotective Effects of Chinese Medicinal Herbs: A Focus on Anti-Inflammatory and Anti-Oxidative Activities

Directory of Open Access Journals (Sweden)

Puiyan Lam

2016-03-01

Full Text Available The liver is intimately connected to inflammation, which is the innate defense system of the body for removing harmful stimuli and participates in the hepatic wound-healing response. Sustained inflammation and the corresponding regenerative wound-healing response can induce the development of fibrosis, cirrhosis and eventually hepatocellular carcinoma. Oxidative stress is associated with the activation of inflammatory pathways, while chronic inflammation is found associated with some human cancers. Inflammation and cancer may be connected by the effect of the inflammation-fibrosis-cancer (IFC axis. Chinese medicinal herbs display abilities in protecting the liver compared to conventional therapies, as many herbal medicines have been shown as effective anti-inflammatory and anti-oxidative agents. We review the relationship between oxidative stress and inflammation, the development of hepatic diseases, and the hepatoprotective effects of Chinese medicinal herbs via anti-inflammatory and anti-oxidative mechanisms. Moreover, several Chinese medicinal herbs and composite formulae, which have been commonly used for preventing and treating hepatic diseases, including Andrographis Herba, Glycyrrhizae Radix et Rhizoma, Ginseng Radix et Rhizoma, Lycii Fructus, Coptidis Rhizoma, curcumin, xiao-cha-hu-tang and shi-quan-da-bu-tang, were selected for reviewing their hepatoprotective effects with focus on their anti-oxidative and ant-inflammatory activities. This review aims to provide new insight into how Chinese medicinal herbs work in therapeutic strategies for liver diseases.

Bringing Precision Medicine to Community Oncologists.

Science.gov (United States)

2017-01-01

Quest Diagnostics has teamed up with Memorial Sloan Kettering Cancer Center and IBM Watson Health to offer IBM Watson Genomics to its network of community cancer centers and hospitals. This new service aims to advance precision medicine by combining genomic tumor sequencing with the power of cognitive computing. ©2017 American Association for Cancer Research.

Hepatitis C Virus: Viral Quasispecies and Genotypes

Directory of Open Access Journals (Sweden)

Kyoko Tsukiyama-Kohara

2017-12-01

Full Text Available Hepatitis C virus (HCV mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs, which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.

Molecular analysis of hepatitis A virus strains obtained from patients with acute hepatitis A in Mongolia, 2004-2013.

Science.gov (United States)

Tsatsralt-Od, Bira; Baasanjav, Nachin; Nyamkhuu, Dulmaa; Ohnishi, Hiroshi; Takahashi, Masaharu; Kobayashi, Tominari; Nagashima, Shigeo; Nishizawa, Tsutomu; Okamoto, Hiroaki

2016-04-01

Despite the high endemicity of hepatitis A virus (HAV) in Mongolia, the genetic information on those HAV strains is limited. Serum samples obtained from 935 patients with acute hepatitis in Ulaanbaatar, Mongolia during 2004-2013 were tested for the presence of HAV RNA using reverse transcription-PCR with primers targeting the VP1-2B region (481 nucleotides, primer sequences at both ends excluded). Overall, 180 patients (19.3%) had detectable HAV RNA. These 180 isolates shared 94.6-100% identity and formed four phylogenetic clusters within subgenotype IA. One or three representative HAV isolates from each cluster exhibited 2.6-3.9% difference between clusters over the entire genome. Cluster 1 accounted for 65.0% of the total, followed by Cluster 2 (30.6%), Cluster 3 (3.3%), and Cluster 4 (1.1%). Clusters 1 and 2 were predominant throughout the observation period, whereas Cluster 3 was undetectable in 2009 and 2013 and Cluster 4 became undetectable after 2009. The Mongolian HAV isolates were closest to those of Chinese or Japanese origin (97.7-98.5% identities over the entire genome), suggesting the evolution from a common ancestor with those circulating in China and Japan. Further molecular epidemiological analyses of HAV infection are necessary to investigate the factors underlying the spread of HAV and to implement appropriate prevention measures in Mongolia. © 2015 Wiley Periodicals, Inc.

Cardiovascular genomics, personalized medicine, and the National Heart, Lung, and Blood Institute: part I: the beginning of an era.

Science.gov (United States)

O'Donnell, Christopher J; Nabel, Elizabeth G

2008-10-01

The inaugural issue of Circulation: Cardiovascular Genetics arrives at a remarkable time in the history of genetic research and cardiovascular medicine. Despite tremendous progress in knowledge gained, cardiovascular disease(CVD) remains the leading cause of death in the United States,1 and it has overcome infectious diseases as the leading cause of death worldwide.2 In addition, rates of CVD remain higher in black and Hispanic populations in the United States.1 The recent Strategic Plan of the National Heart, Lung,and Blood Institute (NHLBI) emphasizes research areas to fill the significant knowledge gaps needed to improve the diagnosis,treatment, and control of known risk factors and clinically apparent disease. Simultaneously, the NHLBI Strategic Plan recognizes a tremendous opportunity that is available for use of genetic and genomic research to generate new knowledge that might reduce the morbidity and mortality from CVD in US populations.3 Public availability of vast amounts of detailed sequence information about the human genome, completed sequence data on dozens of other animal genomes, and private sector development of high-throughput genetic technologies has transformed in a few short years the conduct of cardiovascular genetics and genomics research from a primary focus on mendelian disorders to a current emphasis on genome-wide association studies (GWAS; Figure1). In this review, we describe the rationale for the current emphasis on large-scale genomic studies, summarize the evolving approaches and progress to date, and identify immediate-term research needs. The National Institutes of Health (NIH) and the NHLBI are supporting a portfolio of large-scale genetic and genomic programs in diverse US populations with the longer-term objective of translating knowledge into the prediction, prevention, and preemption of CVD, as well as lung, sleep, and blood disorders. Underlying this portfolio is a strong commitment to make available participant-level data and

Narrowing the gap of personalized medicine in emerging countries: the case of multiple endocrine neoplasias in Brazil

Directory of Open Access Journals (Sweden)

Rodrigo A. Toledo

2012-01-01

Full Text Available The finished version of the human genome sequence was completed in 2003, and this event initiated a revolution in medical practice, which is usually referred to as the age of genomic or personalized medicine. Genomic medicine aims to be predictive, personalized, preventive, and also participative (4Ps. It offers a new approach to several pathological conditions, although its impact so far has been more evident in mendelian diseases. This article briefly reviews the potential advantages of this approach, and also some issues that may arise in the attempt to apply the accumulated knowledge from genomic medicine to clinical practice in emerging countries. The advantages of applying genomic medicine into clinical practice are obvious, enabling prediction, prevention, and early diagnosis and treatment of several genetic disorders. However, there are also some issues, such as those related to: (a the need for approval of a law equivalent to the Genetic Information Nondiscrimination Act, which was approved in 2008 in the USA; (b the need for private and public funding for genetics and genomics; (c the need for development of innovative healthcare systems that may substantially cut costs (e.g. costs of periodic medical followup; (d the need for new graduate and postgraduate curricula in which genomic medicine is emphasized; and (e the need to adequately inform the population and possible consumers of genetic testing, with reference to the basic aspects of genomic medicine.

Genomics for paediatricians: promises and pitfalls.

Science.gov (United States)

Hammond, Carrie Louise; Willoughby, Josh Matthew; Parker, Michael James

2018-03-24

In recent years, there have been significant advances in genetic technologies, evolving the field of genomics from genetics. This has huge diagnostic potential, as genomic testing increasingly becomes part of mainstream medicine. However, there are numerous potential pitfalls in the interpretation of genomic data. It is therefore essential that we educate clinicians more widely about the appropriate interpretation and utilisation of genomic testing. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

High-Definition Medicine.

Science.gov (United States)

Torkamani, Ali; Andersen, Kristian G; Steinhubl, Steven R; Topol, Eric J

2017-08-24

The foundation for a new era of data-driven medicine has been set by recent technological advances that enable the assessment and management of human health at an unprecedented level of resolution-what we refer to as high-definition medicine. Our ability to assess human health in high definition is enabled, in part, by advances in DNA sequencing, physiological and environmental monitoring, advanced imaging, and behavioral tracking. Our ability to understand and act upon these observations at equally high precision is driven by advances in genome editing, cellular reprogramming, tissue engineering, and information technologies, especially artificial intelligence. In this review, we will examine the core disciplines that enable high-definition medicine and project how these technologies will alter the future of medicine. Copyright © 2017 Elsevier Inc. All rights reserved.

Hepatitis C

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... Workshops Follow Us Home Health Information Liver Disease Hepatitis (Viral) Hepatitis C Related Topics English English Español Section Navigation Hepatitis (Viral) What Is Viral Hepatitis? Hepatitis A Hepatitis B ...

Analyses of a whole-genome inter-clade recombination map of hepatitis delta virus suggest a host polymerase-driven and viral RNA structure-promoted template-switching mechanism for viral RNA recombination

Science.gov (United States)

Chao, Mei; Wang, Tzu-Chi; Lin, Chia-Chi; Yung-Liang Wang, Robert; Lin, Wen-Bin; Lee, Shang-En; Cheng, Ying-Yu; Yeh, Chau-Ting; Iang, Shan-Bei

2017-01-01

The genome of hepatitis delta virus (HDV) is a 1.7-kb single-stranded circular RNA that folds into an unbranched rod-like structure and has ribozyme activity. HDV redirects host RNA polymerase(s) (RNAP) to perform viral RNA-directed RNA transcription. RNA recombination is known to contribute to the genetic heterogeneity of HDV, but its molecular mechanism is poorly understood. Here, we established a whole-genome HDV-1/HDV-4 recombination map using two cloned sequences coexisting in cultured cells. Our functional analyses of the resulting chimeric delta antigens (the only viral-encoded protein) and recombinant genomes provide insights into how recombination promotes the genotypic and phenotypic diversity of HDV. Our examination of crossover distribution and subsequent mutagenesis analyses demonstrated that ribozyme activity on HDV genome, which is required for viral replication, also contributes to the generation of an inter-clade junction. These data provide circumstantial evidence supporting our contention that HDV RNA recombination occurs via a replication-dependent mechanism. Furthermore, we identify an intrinsic asymmetric bulge on the HDV genome, which appears to promote recombination events in the vicinity. We therefore propose a mammalian RNAP-driven and viral-RNA-structure-promoted template-switching mechanism for HDV genetic recombination. The present findings improve our understanding of the capacities of the host RNAP beyond typical DNA-directed transcription. PMID:28977829

The YH database: the first Asian diploid genome database

DEFF Research Database (Denmark)

Li, Guoqing; Ma, Lijia; Song, Chao

2009-01-01

genome consensus. The YH database is currently one of the three personal genome database, organizing the original data and analysis results in a user-friendly interface, which is an endeavor to achieve fundamental goals for establishing personal medicine. The database is available at http://yh.genomics.org.cn....

Evolution of hepatic glucose metabolism: liver-specific glucokinase deficiency explained by parallel loss of the gene for glucokinase regulatory protein (GCKR.

Directory of Open Access Journals (Sweden)

Zhao Yang Wang

Full Text Available Glucokinase (GCK plays an important role in the regulation of carbohydrate metabolism. In the liver, phosphorylation of glucose to glucose-6-phosphate by GCK is the first step for both glycolysis and glycogen synthesis. However, some vertebrate species are deficient in GCK activity in the liver, despite containing GCK genes that appear to be compatible with function in their genomes. Glucokinase regulatory protein (GCKR is the most important post-transcriptional regulator of GCK in the liver; it participates in the modulation of GCK activity and location depending upon changes in glucose levels. In experimental models, loss of GCKR has been shown to associate with reduced hepatic GCK protein levels and activity.GCKR genes and GCKR-like sequences were identified in the genomes of all vertebrate species with available genome sequences. The coding sequences of GCKR and GCKR-like genes were identified and aligned; base changes likely to disrupt coding potential or splicing were also identified.GCKR genes could not be found in the genomes of 9 vertebrate species, including all birds. In addition, in multiple mammalian genomes, whereas GCKR-like gene sequences could be identified, these genes could not predict a functional protein. Vertebrate species that were previously reported to be deficient in hepatic GCK activity were found to have deleted (birds and lizard or mutated (mammals GCKR genes. Our results suggest that mutation of the GCKR gene leads to hepatic GCK deficiency due to the loss of the stabilizing effect of GCKR.

Precision medicine in pediatric oncology: Lessons learned and next steps

Science.gov (United States)

Mody, Rajen J.; Prensner, John R.; Everett, Jessica; Parsons, D. Williams; Chinnaiyan, Arul M.

2017-01-01

The maturation of genomic technologies has enabled new discoveries in disease pathogenesis as well as new approaches to patient care. In pediatric oncology, patients may now receive individualized genomic analysis to identify molecular aberrations of relevance for diagnosis and/or treatment. In this context, several recent clinical studies have begun to explore the feasibility and utility of genomics-driven precision medicine. Here, we review the major developments in this field, discuss current limitations, and explore aspects of the clinical implementation of precision medicine, which lack consensus. Lastly, we discuss ongoing scientific efforts in this arena, which may yield future clinical applications. PMID:27748023

Genome projects and the functional-genomic era.

Science.gov (United States)

Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

2005-12-01

The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

Hepatitis A through E (Viral Hepatitis)

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... Treatment Eating, Diet, & Nutrition Clinical Trials Wilson Disease Hepatitis (Viral) View or Print All Sections What is Viral Hepatitis? Viral hepatitis is an infection that causes liver inflammation ...

Microbial Genomes Multiply

Science.gov (United States)

Doolittle, Russell F.

2002-01-01

The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

In vitro evaluation of novel antiviral activities of 60 medicinal plants extracts against hepatitis B virus.

Science.gov (United States)

Arbab, Ahmed Hassan; Parvez, Mohammad Khalid; Al-Dosari, Mohammed Salem; Al-Rehaily, Adnan Jathlan

2017-07-01

Currently, >35 Saudi Arabian medicinal plants are traditionally used for various liver disorders without a scientific rationale. This is the first experimental evaluation of the anti-hepatitis B virus (HBV) potential of the total ethanolic and sequential organic extracts of 60 candidate medicinal plants. The extracts were tested for toxicity on HepG2.2.15 cells and cytotoxicity concentration (CC 50 ) values were determined. The extracts were further investigated on HepG2.2.15 cells for anti-HBV activities by analyzing the inhibition of HBsAg and HBeAg production in the culture supernatants, and their half maximal inhibitory concentration (IC 50 ) and therapeutic index (TI) values were determined. Of the screened plants, Guiera senegalensis (dichloromethane extract, IC 50 =10.65), Pulicaria crispa (ethyl acetate extract, IC 50 =14.45), Coccinea grandis (total ethanol extract, IC 50 =31.57), Fumaria parviflora (hexane extract, IC 50 =35.44), Capparis decidua (aqueous extract, IC 50 =66.82), Corallocarpus epigeus (total ethanol extract, IC 50 =71.9), Indigofera caerulea (methanol extract, IC 50 =73.21), Abutilon figarianum (dichloromethane extract, IC 50 =99.76) and Acacia oerfota (total ethanol extract, IC 50 =101.46) demonstrated novel anti-HBV activities in a time- and dose-dependent manner. Further qualitative phytochemical analysis of the active extracts revealed the presence of alkaloids, tannins, flavonoids and saponins, which are attributed to antiviral efficacies. In conclusion, P. crispa, G. senegalensis and F. parviflora had the most promising anti-HBV potentials, including those of C. decidua , C. epigeus, A. figarianum , A. oerfota and I. caerulea with marked activities. However, a detailed phytochemical study of these extracts is essential to isolate the active principle(s) responsible for their novel anti-HBV potential.

Significance of occult hbv infection in patients with chronic hepatitis c

International Nuclear Information System (INIS)

Anwar, W.; Sarwar, M.; Saif, M.; Hussain, A.B.; Tariq, W.Z.

2006-01-01

Objective: To determine the frequency of occurrence of occult Hepatitis B infection in chronic hepatitis C patients and its impact (if any) on the effectivity of standard chronic hepatitis C treatment. Design: Quasi-experimental study. Place and Duration of Study: The study was conducted at the Department of Medicine, Military Hospital, Rawalpindi, and Virology Department, Armed Forces Institute of Pathology, Rawalpindi, for a period of nine months from January 2003 to September 2003. Patients and Methods: This study was conducted on 30 HBsAg negative patients with chronic hepatitis C liver disease who were receiving combination therapy with interferon and ribavirin. Occult hepatitis B infection was assessed by carrying out HBV DNA by polymerase chain reaction (PCR) in the sera of these patients. Markers of previous hepatitis B infection Le; anti-HBs and total anti-HBc antibodies were also tested. Response to treatment for hepatitis C (with interferon and ribavirin) was assessed at the end of six months of therapy by measuring ALT levels and HCV RNA by PCR in the serum. Results: In our study only one patient (3.33%) was found to be harbouring HBV DNA in the serum detectable by PCR, with markers of previous HBV infection (both anti HBc antibodies and anti HBs antibodies were positive). A total 14 patients (46.67%) had markers of previous HBV infection, while 16 patients (53.33%) had no such sero markers. Twenty five out of 30 patients (83.33%) responded to treatment and 5 (16.66%) turned out to be non-responders. The single case of occult hepatitis B detected in this study responded to hepatitis C treatment. Conclusion: Occult hepatitis B is not a common occurrence in chronic hepatitis C patients and it did not alter the outcome of treatment for hepatitis C in our study. (author)

Host Innate Immunity against Hepatitis E Virus and Viral Evasion Mechanisms.

Science.gov (United States)

Kang, Sangmin; Myoung, Jinjong

2017-10-28

Hepatitis E virus (HEV) infections cause epidemic or sporadic acute hepatitis, which are mostly self-limiting. However, viral infection in immunocompromised patients and pregnant women may result in serious consequences, such as chronic hepatitis and liver damage, mortality of the latter of which reaches up to 20-30%. Type I interferon (IFN)-induced antiviral immunity is known to be the first-line defense against virus infection. Upon HEV infection in the cell, the virus genome is recognized by pathogen recognition receptors, leading to rapid activation of intracellular signaling cascades. Expression of type I IFN triggers induction of a barrage of IFN-stimulated genes, helping the cells cope with viral infection. Interestingly, some of the HEV-encoded genes seem to be involved in disrupting signaling cascades for antiviral immune responses, and thus crippling cytokine/chemokine production. Antagonistic mechanisms of type I IFN responses by HEV have only recently begun to emerge, and in this review, we summarize known HEV evasion strategies and compare them with those of other hepatitis viruses.

Cellular mRNA decay factors involved in the hepatitis C virus life cycle

OpenAIRE

Mina Ibarra, Leonardo Bruno

2010-01-01

The group of positive strand RNA ((+)RNA) viruses includes numerous plant, animal and human pathogens such as the hepatitis C virus (HCV). Their viral genomes mimic cellular mRNAs, however, besides acting as messengers for translation of viral proteins, they also act as templates for viral replication. Since these two functions are mutually exclusive, a key step in the replication of all (+) RNA viruses is the regulated exit of the genomic RNAs from the cellular translation machinery to the v...

Using web services for linking genomic data to medical information systems.

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Maojo, V; Crespo, J; de la Calle, G; Barreiro, J; Garcia-Remesal, M

2007-01-01

To develop a new perspective for biomedical information systems, regarding the introduction of ideas, methods and tools related to the new scenario of genomic medicine. Technological aspects related to the analysis and integration of heterogeneous clinical and genomic data include mapping clinical and genetic concepts, potential future standards or the development of integrated biomedical ontologies. In this clinicomics scenario, we describe the use of Web services technologies to improve access to and integrate different information sources. We give a concrete example of the use of Web services technologies: the OntoFusion project. Web services provide new biomedical informatics (BMI) approaches related to genomic medicine. Customized workflows will aid research tasks by linking heterogeneous Web services. Two significant examples of these European Commission-funded efforts are the INFOBIOMED Network of Excellence and the Advancing Clinico-Genomic Trials on Cancer (ACGT) integrated project. Supplying medical researchers and practitioners with omics data and biologists with clinical datasets can help to develop genomic medicine. BMI is contributing by providing the informatics methods and technological infrastructure needed for these collaborative efforts.

Intrahepatic detection of insulin receptor substrate 2 in chronic hepatitis c patients

International Nuclear Information System (INIS)

Ahmed, N.; Rashid, A.; Bashir, Q.; Majeed, A.

2017-01-01

To detect hepatic insulin receptor substrate 2 in chronic hepatitis C patients. Study Design: Comparative study. Place and Duration of Study: Center for research in experimental and applied medicine (CREAM), Department of Biochemistry and Molecular Biology, Army Medical College and Holy Family Hospital Rawalpindi, from Dec 2011 to Nov 2012. Diagnosed patients of chronic hepatitis C were included in the study. Known cases of diabetes mellitus, patients with pancreatic disease and liver pathology other than hepatitis C were excluded from the study. Material and Methods: Twenty seropositive non diabetic HCV infected patients and 10 control subjects were recruited. Liver biopsy specimen was obtained from seropositive HCV patients while blood samples were obtained from controls as biopsy sample was not possible from normal controls. Both types of speciens were studied for detection of insulin receptor substrate 2 (IRS-2). Results: No alteration in the content of insulin receptor substrate 2 in both seropositive patients and control samples were detected. Conclusion: Hepatitis C virus has no effect on insulin receptor substrate 2 content thus indicating absence of hepatic insulin resistance in patients with HCV infection. (author)

Physician Knowledge and Attitudes About Hepatitis A and Current Practices Regarding Hepatitis A Vaccination Delivery.

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Nelson, Noele P; Allison, Mandy A; Lindley, Megan C; Brtnikova, Michaela; Crane, Lori A; Beaty, Brenda L; Hurley, Laura P; Kempe, Allison

2017-07-01

To assess physicians': 1) knowledge and attitudes about hepatitis A disease and hepatitis A (HepA) vaccine, 2) child care and school HepA vaccine mandates, 3) practices related to HepA vaccine delivery, 4) factors associated with strongly recommending HepA vaccine to all 1- to 2-year-olds, and 5) feasibility of implementing HepA catch-up vaccination at health maintenance visits. A national survey was conducted among representative networks of pediatricians and family medicine physicians (FMs) from March to June, 2014 via e-mail or mail on the basis of provider preference. Response rates were 81% (356 of 440) among pediatricians and 75% (348 of 464) among FMs. Less than 50% correctly identified that hepatitis A virus (HAV) infection is usually asymptomatic in young children and that morbidity from HAV disease increases with age. Ninety-two percent of pediatricians and 59% of FMs strongly recommend HepA vaccine for all 1- to 2-year-olds. In addition to practice specialty, belief that HepA vaccine is required for kindergarten enrollment was the most robust predictor of strong physician recommendation. Gaps in knowledge regarding HAV infection and hepatitis A recommendations and lack of a strong recommendation for routine HepA vaccination of young children among FMs likely contribute to suboptimal coverage. Closing knowledge gaps and addressing barriers that prevent all physicians from strongly recommending HepA vaccine to 1- to 2-year-olds could help increase HepA vaccine coverage and ultimately improve population protection against HAV infection. Published by Elsevier Inc.

Value of FibroScan in diagnosis of hepatic fibrosis in patients with HBeAg-negative chronic hepatitis B

Directory of Open Access Journals (Sweden)

LUO Junhua

2014-07-01

Full Text Available ObjectiveTo evaluate the value of transient elastography (FibroScan, FS in predicting hepatic fibrosis in patients with HBeAg-negative chronic hepatitis B (CHB. MethodsOne hundred and four patients with HBeAg-negative CHB, who were diagnosed and treated in Hubei Hospital of Traditional Chinese Medicine from June 2011 to May 2013, were enrolled in this study. All patients underwent FS for liver stiffness measurement before liver biopsy. Statistical analysis was applied to compare liver stiffness (kPa with fibrosis stage (determined by liver biopsy. The receiver operating characteristic (ROC curve of FS was constructed, and the area under the ROC curve (AUROC was calculated to analyze the accuracy of live stiffness in predicting significant fibrosis and cirrhosis. Comparison between groups was made by Kruskal-Wallis H test, followed by Mann-Whitney U test for multiple comparisons. The correlation between two variables was analyzed by Spearman rank and Pearson correlation test. ResultsLiver stiffness gradually rose as the degree of hepatic fibrosis increased, with significant differences between groups (P＜0.01 or P＜0.05. Liver stiffness was positively correlated with the stage of hepatic fibrosis (r=0.810, P＜0.01. The AUROC of liver stiffness for detecting liver cirrhosis was 0.956; the cut-off value for diagnosing liver cirrhosis was 13.1 kPa; the sensitivity was 92.7%, and the specificity was 80%. ConclusionFS is a promising noninvasive method for the assessment of hepatic fibrosis in patients with HBeAg-negative CHB; particularly, it has high accuracy in the diagnosis of liver cirrhosis. FS combined with direct or indirect markers may play an important role in differential diagnosis and efficacy evaluation in patients with hepatic fibrosis.

Bioinformatics and Medical Informatics: Collaborations on the Road to Genomic Medicine?

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Maojo, Victor; Kulikowski, Casimir A.

2003-01-01

In this report, the authors compare and contrast medical informatics (MI) and bioinformatics (BI) and provide a viewpoint on their complementarities and potential for collaboration in various subfields. The authors compare MI and BI along several dimensions, including: (1) historical development of the disciplines, (2) their scientific foundations, (3) data quality and analysis, (4) integration of knowledge and databases, (5) informatics tools to support practice, (6) informatics methods to support research (signal processing, imaging and vision, and computational modeling, (7) professional and patient continuing education, and (8) education and training. It is pointed out that, while the two disciplines differ in their histories, scientific foundations, and methodologic approaches to research in various areas, they nevertheless share methods and tools, which provides a basis for exchange of experience in their different applications. MI expertise in developing health care applications and the strength of BI in biological “discovery science” complement each other well. The new field of biomedical informatics (BMI) holds great promise for developing informatics methods that will be crucial in the development of genomic medicine. The future of BMI will be influenced strongly by whether significant advances in clinical practice and biomedical research come about from separate efforts in MI and BI, or from emerging, hybrid informatics subdisciplines at their interface. PMID:12925552

Pharmacogenetics of ribavirin-induced anemia in hepatitis C.

Science.gov (United States)

Ampuero, Javier; Romero-Gómez, Manuel

2016-09-01

Pharmacogenetics assesses inherited genetic differences in drug metabolic pathways and its role in medicine is growing. Ribavirin (RBV) and peginterferon were the standard of care therapy in hepatitis C virus infection during 15 years, with the addition of first-generation protease inhibitors at the beginning of 2010s. New direct-acting agents are the new standard of care, but RBV remains important in some scenarios. The main adverse effect of RBV is anemia, which requires dose reduction and even stopping treatment in some patients. Pharmacogenetics has identified ITPA and SLC28/29 genes to be closely related to RBV-induced anemia. The routine evaluation of these genes could help to identify those patients at risk of developing anemia during the hepatitis C virus treatment.

Hepatitis isquémica Ischemic hepatitis

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Marcos Amuchástegui (h

2006-10-01

Full Text Available La hepatitis isquémica es una complicación sumamente infrecuente de cirugía cardiovascular. Las biopsias muestran necrosis centrolobulillar. El término de "hepatitis" fue propuesto debido al aumento de transaminasas similar a aquellas de origen infeccioso, e "isquémica" por falla en la perfusión hepática. Posteriormente se definió el término de hepatitis isquémica como cuadro de elevación aguda y reversible (dentro de las 72 horas de transaminasas de hasta 20 veces el valor normal, asociado a trastornos en la perfusión hepática, luego de haber excluido otras causas de hepatitis aguda o daño hepatocelular. Se describe el caso de un paciente de 53 años que consulta por dolor epigástrico de 12 h de evolución sin fiebre, náuseas ni vómitos, resistente a la medicación. Tenía antecedentes inmediatos de reemplazo de válvula aórtica, y estaba anticoagulado. Evolucionó con shock y fallo multiorgánico. El examen evidenció marcada ictericia y signos de taponamiento pericárdico, asociado a un aumento considerable de enzimas hepáticas. Un ecocardiograma informó signos de taponamiento cardíaco y ausencia de disección aórtica. Se decidió pericardiocentesis, extrayéndose 970 cc. de líquido sanguinolento, y hemodiálisis, con notable mejoría de su estado hemodinámico. Los valores enzimáticos disminuyeron. Los marcadores virales fueron negativos.Ischemic hepatitis is an uncommon cardiovascular surgery complication. Hepatic biopsies show centrolobulillar necrosis. The term "hepatitis" was proposed because of a raise in hepatic enzymes similar with infectious disease, and "ischemic" because of failure in hepatic perfusion. Ischemic hepatitis was then defined as an acute and reversible elevation of hepatic enzymes (within 72 h, associated with disturbance in hepatic perfusion after excluding other causes of acute hepatitis. A 53 year-old male presented complaining of a 12 h epigastric pain, without nausea or vomiting, resistant

Personalized medicine: a confluence of traditional and contemporary medicine.

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Jafari, Samineh; Abdollahi, Mohammad; Saeidnia, Soodabeh

2014-01-01

Traditional systems of medicine have attained great popularity among patients in recent years. Success of this system in the treatment of disease warrants consideration, particularly in cases for which conventional medicine has been insufficient. This study investigates the similarities in principles and approaches of 3 traditional systems and explores whether conventional medicine is able to exploit the advantages of traditional systems. This study first identifies and explores the advantages of 3 well-known systems-traditional Iranian medicine (TIM), ayurveda, and traditional Chinese medicine (TCM)-that are similar in their basic principles and methods. Second, it clarifies whether and how conventional medicine could exploit the advantages of traditional systems as it modernizes, to become more personalized. Finally, this study investigates the possibility that conventional medicine could benefit from traditional typology to improve its personalization. The acknowledgment of the unity of humans and nature, applying rational methods, and personalized approaches is fundamentally similar in the 3 systems. Additionally, they all promote the holistic view that health is harmony and disease is disharmony of the body. Other similarities include their recognition of the unique nature of every person and their categorization of people into different body types. Although conventional medicine has mostly failed to incorporate the advantages of traditional medicine, its integration with traditional medicine is achievable. For instance, exploiting traditional typologies in genomic and other studies may facilitate personalization of conventional medicine. From its review, the research team concludes that prospects are bright for the integration of traditional and conventional medicines and, consequently, for a dramatic improvement in health systems.

Precision Medicine in Myelodysplastic Syndromes and Leukemias: Lessons from Sequential Mutations.

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Nazha, Aziz; Sekeres, Mikkael A

2017-01-14

Precision medicine can be simply defined as the identification of personalized treatment that matches patient-specific clinical and genomic characteristics. Since the completion of the Human Genome Project in 2003, significant advances have been made in our understanding of the genetic makeup of diseases, especially cancers. The identification of somatic mutations that can drive cancer has led to the development of therapies that specifically target the abnormal proteins derived from these mutations. This has led to a paradigm shift in our treatment methodology. Although some success has been achieved in targeting some genetic abnormalities, several challenges and limitations exist when applying precision-medicine concepts in leukemia and myelodysplastic syndromes. We review the current understanding of genomics in myelodysplastic syndromes (MDS) and leukemias and the limitations of precision-medicine concepts in MDS.

Efficient infectious cell culture systems of the hepatitis C virus (HCV) prototype strains HCV-1 and H77

DEFF Research Database (Denmark)

Li, Yi-Ping; Ramirez, Santseharay; Mikkelsen, Lotte

2015-01-01

UNLABELLED: The first discovered and sequenced hepatitis C virus (HCV) genome and the first in vivo infectious HCV clones originated from the HCV prototype strains HCV-1 and H77, respectively, both widely used in research of this important human pathogen. In the present study, we developed...... efficiently after transfection and subsequent infection of naive Huh7.5 cells, reaching titers of 10(3.5) and 10(4.4) FFU/ml, respectively. IMPORTANCE: Hepatitis C virus (HCV) was discovered in 1989 with the cloning of the prototype strain HCV-1 genome. In 1997, two molecular clones of H77, the other HCV...... prototype strain, were shown to be infectious in chimpanzees, but not in vitro. HCV research was hampered by a lack of infectious cell culture systems, which became available only in 2005 with the discovery of JFH1 (genotype 2a), a genome that could establish infection in Huh7.5 cells. Recently, we...

An integrated clinical and genomic information system for cancer precision medicine.

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Jang, Yeongjun; Choi, Taekjin; Kim, Jongho; Park, Jisub; Seo, Jihae; Kim, Sangok; Kwon, Yeajee; Lee, Seungjae; Lee, Sanghyuk

2018-04-20

Increasing affordability of next-generation sequencing (NGS) has created an opportunity for realizing genomically-informed personalized cancer therapy as a path to precision oncology. However, the complex nature of genomic information presents a huge challenge for clinicians in interpreting the patient's genomic alterations and selecting the optimum approved or investigational therapy. An elaborate and practical information system is urgently needed to support clinical decision as well as to test clinical hypotheses quickly. Here, we present an integrated clinical and genomic information system (CGIS) based on NGS data analyses. Major components include modules for handling clinical data, NGS data processing, variant annotation and prioritization, drug-target-pathway analysis, and population cohort explorer. We built a comprehensive knowledgebase of genes, variants, drugs by collecting annotated information from public and in-house resources. Structured reports for molecular pathology are generated using standardized terminology in order to help clinicians interpret genomic variants and utilize them for targeted cancer therapy. We also implemented many features useful for testing hypotheses to develop prognostic markers from mutation and gene expression data. Our CGIS software is an attempt to provide useful information for both clinicians and scientists who want to explore genomic information for precision oncology.

The Human Genome Project (HGP): dividends and challenges: a ...

African Journals Online (AJOL)

The Human Genome Project (HGP): dividends and challenges: a review. ... Genomic studies have given profound insights into the genetic organization of ... with it will be an essential part of modern medicine and biology for years to come.

Hepatic Encephalopathy

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Full Text Available ... Related Liver Disease Alpha-1 Antitrypsin Deficiency Autoimmune Hepatitis Benign Liver Tumors Biliary Atresia Cirrhosis of the ... Disease Type 1 (von Gierke) Hemochromatosis Hepatic Encephalopathy Hepatitis A Hepatitis B Hepatitis C Intrahepatic Cholestasis of ...

Hepatic Encephalopathy

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Full Text Available ... Hemochromatosis Hepatic Encephalopathy Hepatitis A Hepatitis B Hepatitis C Intrahepatic Cholestasis of Pregnancy (ICP) Jaundice In Newborns ... are the common causes of cirrhosis? Hepatitis B & C Alcohol-related Liver Disease Non-alcoholic Fatty Liver ...

Interprofessional education for personalized medicine through technology-based learning.

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Haga, Susanne B; Mills, Rachel; Aucoin, Julia; Taekman, Jeff

2015-06-01

The delivery of personalized medicine utilizing genetic and genomic technologies is anticipated to involve many medical specialties. Interprofessional education will be key to the delivery of personalized medicine in order to reduce disjointed or uncoordinated clinical care, and optimize effective communication to promote patient understanding and engagement regarding the use of or need for these services. While several health professional organizations have endorsed and/or developed core competencies for genetics and genomics, the lack of interprofessional guidelines and training may hamper the delivery of coordinated personalized medicine. In this perspective, we consider the potential for interprofessional education and training using technology-based approaches, such as virtual simulation and gaming, compared with traditional educational approaches.

Hepatic Encephalopathy

Medline Plus

Full Text Available ... 1 (von Gierke) Hemochromatosis Hepatic Encephalopathy Hepatitis A Hepatitis B Hepatitis C Intrahepatic Cholestasis of Pregnancy (ICP) Jaundice ... diseases. What are the common causes of cirrhosis? Hepatitis B & C Alcohol-related Liver Disease Non-alcoholic Fatty ...

Similar Connotation in Chronic Hepatitis B and Nonalcoholic Fatty Liver Patients with Dampness-Heat Syndrome

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Jianye Dai

2013-01-01

Full Text Available The phenomenon that the same syndrome turns up in different diseases appears in the sight of people around the world, which raises the thought for possibility of “Same Treatment for Different Diseases.” Actually, treatment based on ZHENG classification in Traditional Chinese Medicine could bring revelation for the former finding. The dampness-heat syndrome in chronic hepatitis B and nonalcoholic fatty liver is regarded as the breakthrough point. We discussed the molecular mechanism of similar connotation that exists in chronic hepatitis B and nonalcoholic fatty liver by metabonomics to give the modern understanding of dampness-heat syndrome. Both urine and serum metabolic profiling revealed that obvious differences existed between dampness-heat syndrome and non-dampness-heat syndrome but the commonality was proved to appear in chronic hepatitis B and nonalcoholic fatty liver patients with dampness-heat syndrome. Furthermore, disorder of body fluid metabolism, decline in digestive capacity, and imbalance of intestinal flora were found to be the new guiding for treatment, with the hope to provide the basis for Chinese personalized medicine.

Fatal acute hepatic failure in a family infected with the hepatitis A virus subgenotype IB: A case report.

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Yoshida, Yuichi; Okada, Yohei; Suzuki, Akiko; Kakisaka, Keisuke; Miyamoto, Yasuhiro; Miyasaka, Akio; Takikawa, Yasuhiro; Nishizawa, Tsutomu; Okamoto, Hiroaki

2017-09-01

Hepatitis A viral infection is a well-known cause of subclinical or acute self-limited hepatitis. Few cases of hepatitis A virus (HAV)-associated acute liver failure (ALF) have been reported in low HAV endemic countries annually. To investigate the possible factors that affected the severity of HAV infection, a family cluster infected with the HAV subgenotype IB strain, which is not common in Japan, was described. This family consisted of five members who all were infected with HAV. Four of the five patients hospitalized except for an asymptomatic patient. Two of the five patients, men in their 50s and 60s, developed ALF, and one patient died. Various host factors, including sex (male), age, and a high bilirubin level, may affect the outcomes. Based on viral factors, HAV RNA was higher in the fatal case compared with others, and it decreased within a short period of time. The similarity of the nucleotide sequences was 99.9% among the HAV isolates based on an entire genomic sequence. Deletions and/or insertions on the HAV protein-coding sequences that caused a frameshift were found in surviving cases but not in the fatal case. The rapid clearance of increased HAV and the absence of defective HAV might be closely associated with the onset of liver failure.

Hepatitis E Virus Mutations: Functional and Clinical Relevance

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Hoang van Tong

2016-09-01

Full Text Available Hepatitis E virus (HEV infection is a major cause of acute hepatitis and affects more than 20 million individuals, with three million symptomatic cases and 56,000 recognized HEV-related deaths worldwide. HEV is endemic in developing countries and is gaining importance in developed countries, due to increased number of autochthone cases. Although HEV replication is controlled by the host immune system, viral factors (especially specific viral genotypes and mutants can modulate HEV replication, infection and pathogenesis. Limited knowledge exists on the contribution of HEV genome variants towards pathogenesis, susceptibility and to therapeutic response. Nonsynonymous substitutions can modulate viral proteins structurally and thus dysregulate virus-host interactions. This review aims to compile knowledge and discuss recent advances on the casual role of HEV heterogeneity and its variants on viral morphogenesis, pathogenesis, clinical outcome and antiviral resistance.

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

DEFF Research Database (Denmark)

Sung, Wing-Kin; Zheng, Hancheng; Li, Shuyu

2012-01-01

To survey hepatitis B virus (HBV) integration in liver cancer genomes, we conducted massively parallel sequencing of 81 HBV-positive and 7 HBV-negative hepatocellular carcinomas (HCCs) and adjacent normal tissues. We found that HBV integration is observed more frequently in the tumors (86.4%) than...

Prevalence of hepatitis A virus, hepatitis B virus, hepatitis C virus, hepatitis D virus and hepatitis E virus as causes of acute viral hepatitis in North India: a hospital based study.

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Jain, P; Prakash, S; Gupta, S; Singh, K P; Shrivastava, S; Singh, D D; Singh, J; Jain, A

2013-01-01

Acute viral hepatitis (AVH) is a major public health problem and is an important cause of morbidity and mortality. The aim of the present study is to determine the prevalence of hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV) and hepatitis E virus (HEV) as causes of AVH in a tertiary care hospital of North India. Blood samples and clinical information was collected from cases of AVH referred to the Grade I viral diagnostic laboratory over a 1-year period. Samples were tested for hepatitis B surface antigen, anti-HCV total antibodies, anti-HAV immunoglobulin M (IgM) and anti-HEV IgM by the enzyme-linked immunosorbent assay. PCR for nucleic acid detection of HBV and HCV was also carried out. Those positive for HBV infection were tested for anti-HDV antibodies. Fisher's exact test was used and a P hepatitis cases, 62 (23.22%) patients presented as acute hepatic failure. HAV (26.96%) was identified as the most common cause of acute hepatitis followed by HEV (17.97%), HBV (16.10%) and HCV (11.98%). Co-infections with more than one virus were present in 34 cases; HAV-HEV co-infection being the most common. HEV was the most important cause of acute hepatic failure followed by co-infection with HAV and HEV. An indication towards epidemiological shift of HAV infection from children to adults with a rise in HAV prevalence was seen. To the best of our knowledge, this is the first report indicating epidemiological shift of HAV in Uttar Pradesh.

The role of pharmacogenetics in the treatment of chronic hepatitis C infection.

Science.gov (United States)

Kawaguchi-Suzuki, Marina; Frye, Reginald F

2014-02-01

Hepatitis C virus (HCV) chronically infects 170 million people worldwide. Until recently, combination therapy with peginterferon-α (pegIFN) and ribavirin (RBV) has been the standard of care. However, for many patients, especially those infected with the most common HCV genotype 1 (HCV-1), this treatment has resulted in unsatisfactory treatment response rates. Many clinical factors, including pharmacogenetics, influence the treatment response rate. Genetic variation in the interleukin 28B (IL28B) gene is the major determinant of treatment response, a finding that has been replicated in multiple independent cohorts. This review focuses on the association between pharmacogenetics and conventional pegIFN/RBV therapy in patients infected with HCV non-genotype 1; patients reinfected with HCV after liver transplantation; and patients coinfected with HCV and human immunodeficiency virus. We also review the pharmacogenetic data for boceprevir and telaprevir triple therapy in patients with HCV-1 infection, as well as viral genomic polymorphisms and genetic variants that may protect against anemia. Pharmacogenetic information offers a personalized medicine approach to help clinicians and patients make better informed decisions to maximize response and minimize toxicity for the treatment of chronic HCV infection. © 2013 Pharmacotherapy Publications, Inc.

Opportunities for the Cardiovascular Community in the Precision Medicine Initiative.

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Shah, Svati H; Arnett, Donna; Houser, Steven R; Ginsburg, Geoffrey S; MacRae, Calum; Mital, Seema; Loscalzo, Joseph; Hall, Jennifer L

2016-01-12

The Precision Medicine Initiative recently announced by President Barack Obama seeks to move the field of precision medicine more rapidly into clinical care. Precision medicine revolves around the concept of integrating individual-level data including genomics, biomarkers, lifestyle and other environmental factors, wearable device physiological data, and information from electronic health records to ultimately provide better clinical care to individual patients. The Precision Medicine Initiative as currently structured will primarily fund efforts in cancer genomics with longer-term goals of advancing precision medicine to all areas of health, and will be supported through creation of a 1 million person cohort study across the United States. This focused effort on precision medicine provides scientists, clinicians, and patients within the cardiovascular community an opportunity to work together boldly to advance clinical care; the community needs to be aware and engaged in the process as it progresses. This article provides a framework for potential involvement of the cardiovascular community in the Precision Medicine Initiative, while highlighting significant challenges for its successful implementation. © 2016 American Heart Association, Inc.

Human genomic disease variants: a neutral evolutionary explanation.

Science.gov (United States)

Dudley, Joel T; Kim, Yuseob; Liu, Li; Markov, Glenn J; Gerold, Kristyn; Chen, Rong; Butte, Atul J; Kumar, Sudhir

2012-08-01

Many perspectives on the role of evolution in human health include nonempirical assumptions concerning the adaptive evolutionary origins of human diseases. Evolutionary analyses of the increasing wealth of clinical and population genomic data have begun to challenge these presumptions. In order to systematically evaluate such claims, the time has come to build a common framework for an empirical and intellectual unification of evolution and modern medicine. We review the emerging evidence and provide a supporting conceptual framework that establishes the classical neutral theory of molecular evolution (NTME) as the basis for evaluating disease- associated genomic variations in health and medicine. For over a decade, the NTME has already explained the origins and distribution of variants implicated in diseases and has illuminated the power of evolutionary thinking in genomic medicine. We suggest that a majority of disease variants in modern populations will have neutral evolutionary origins (previously neutral), with a relatively smaller fraction exhibiting adaptive evolutionary origins (previously adaptive). This pattern is expected to hold true for common as well as rare disease variants. Ultimately, a neutral evolutionary perspective will provide medicine with an informative and actionable framework that enables objective clinical assessment beyond convenient tendencies to invoke past adaptive events in human history as a root cause of human disease.

New antivirals for the treatment of chronic hepatitis B.

Science.gov (United States)

Soriano, Vincent; Barreiro, Pablo; Benitez, Laura; Peña, Jose M; de Mendoza, Carmen

2017-07-01

Current treatment with oral nucleos(t)ides entecavir or tenofovir provide sustained suppression of HBV replication and clinical benefit in most chronic hepatitis B virus (HBV) infected persons. However, HBV rebound generally occurs upon drug discontinuation due to persistence of genomic HBV reservoirs as episomic cccDNA and chromosomic integrated HBV-DNA. There is renewed enthusiasm on HBV drug discovery following recent successes with antivirals for hepatitis C and immunotherapies for some cancers. Areas covered: New drugs that target distinct steps of the HBV life cycle are been developed, including inhibitors of viral entry, new polymerase inhibitors, capsid and assembly inhibitors, virus release blockers, and disruptors of cccDNA formation and transcription. Alongside these antivirals, agents that enhance anti-HBV specific immune responses are being tested, including TLR agonists, checkpoint inhibitors and therapeutic vaccines. Expert opinion: The achievement of a 'functional cure' for chronic HBV infection, with sustained HBsAg clearance and undetectable viremia once medications are stopped, represents the next step in the pace towards HBV elimination. Hopefully, the combination of new drugs that eliminate or functionally inactivate the genomic HBV reservoirs (cccDNA and integrated HBV-DNA) along with agents that enhance or activate immune responses against HBV will lead to a 'definitive cure' for chronic HBV infection.

Adult lead poisoning from a herbal medicine

International Nuclear Information System (INIS)

Ibrahim, Abdulsalam S.; Latif, Ali H.

2002-01-01

A 56-year-old Indian lady presented with one week history of abdominal pain, jaundice and chronic polyarthralgia. She had evidence of hemolytic anemia and hepatitis. Her blood lead level was high and a peripheral blood film showed dense basophilic stippling. It is believed that the lead toxicity was due to the use of Indian herbal medicine. (author)

EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

Science.gov (United States)

Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

2015-01-01

Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

Stable expression and replication of hepatitis B virus genome in an integrated state in a human hepatoma cell line transfected with the cloned viral DNA

International Nuclear Information System (INIS)

Tsurimoto, T.; Fujiyama, A.; Matsubara, K.

1987-01-01

A human hepatocellular carcinoma cell line (Huh6-c15) was transfected with a recombinant DNA molecule that consists of tandemly arranged hepatitis B virus (HBV) genome and a neomycin-resistant gene. One clone resistant to G-418 produces and releases surface antigen and e antigen into medium at a high level and accumulates core particles intracellularly. This clone has a chromosomally integrated set of the original recombinant DNA and produces a 3.5-kilobase transcript corresponding to the pregenome RNA as well as HBV DNAs in an extrachromosomal form. Most of these DNAs were in single-stranded or partially double-stranded form and were packaged in the intracellular core particles. In the medium, particles were detected that contained HBV DNA and were morphologically indistinguishable from Dane particles. These results demonstrate that the HBV genome in an integrated state acted as a template for viral gene expression and replication. The cells were maintained for more than 6 months without losing the ability to produce the extrachromosomal HBV DNA and Dane-like particles. Thus, the cells can be used as a model system for analyses of gene expression and DNA replication of HBV in human hepatocytes

The draft genome sequence and annotation of the desert woodrat Neotoma lepida

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Michael Campbell

2016-09-01

Full Text Available We present the de novo draft genome sequence for a vertebrate mammalian herbivore, the desert woodrat (Neotoma lepida. This species is of ecological and evolutionary interest with respect to ingestion, microbial detoxification and hepatic metabolism of toxic plant secondary compounds from the highly toxic creosote bush (Larrea tridentata and the juniper shrub (Juniperus monosperma. The draft genome sequence and annotation have been deposited at GenBank under the accession LZPO01000000.

Failure to incriminate hepatitis B, hepatitis C, and hepatitis E viruses in the aetiology of fulminant non-A non-B hepatitis.

OpenAIRE

Mutimer, D; Shaw, J; Neuberger, J; Skidmore, S; Martin, B; Hubscher, S; McMaster, P; Elias, E

1995-01-01

Sporadic non-A, non-B hepatitis is the most common indication for liver transplantation in patients presenting with fulminant and subacute liver failure. This study used serological, histological, and molecular biological techniques to examine specimens from 23 consecutive patients transplanted for sporadic non-A, non-B hepatitis. No evidence was found of hepatitis C virus, hepatitis E virus, or 'cryptic' hepatitis B virus infection.

Hepatitis

Science.gov (United States)

... most common types of viral hepatitis. What Is Hepatitis A? For kids, hep A is the most common ... they recover, it does not come back. Can Hepatitis A Be Prevented? The following will help keep people ...

From hacking the human genome to editing organs.

Science.gov (United States)

Tobita, Takamasa; Guzman-Lepe, Jorge; Collin de l'Hortet, Alexandra

2015-01-01

In the recent decades, human genome engineering has been one of the major interesting research subjects, essentially because it raises new possibilities for personalized medicine and biotechnologies. With the development of engineered nucleases such as the Zinc Finger Nucleases (ZFNs), the Transcription activator-like effector nucleases (TALENs) and more recently the Clustered Regularly Interspaced short Palindromic Repeats (CRISPR), the field of human genome edition has evolved very rapidly. Every new genetic tool is broadening the scope of applications on human tissues, even before we can completely master each of these tools. In this review, we will present the recent advances regarding human genome edition tools, we will discuss the numerous implications they have in research and medicine, and we will mention the limits and concerns about such technologies.

A Complex Multiherbal Regimen Based on Ayurveda Medicine for the Management of Hepatic Cirrhosis Complicated by Ascites: Nonrandomized, Uncontrolled, Single Group, Open-Label Observational Clinical Study.

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Patel, Manish V; Patel, Kalapi B; Gupta, Shivenarain; Michalsen, Andreas; Stapelfeldt, Elmar; Kessler, Christian S

2015-01-01

Hepatic cirrhosis is one of the leading causes of death worldwide, especially if complicated by ascites. This chronic condition can be related to the classical disease entity jalodara in Traditional Indian Medicine (Ayurveda). The present paper aims to evaluate the general potential of Ayurvedic therapy for overall clinical outcomes in hepatic cirrhosis complicated by ascites (HCcA). In form of a nonrandomized, uncontrolled, single group, open-label observational clinical study, 56 patients fulfilling standardized diagnostic criteria for HCcA were observed during their treatment at the P. D. Patel Ayurveda Hospital, Nadiad, India. Based on Ayurvedic tradition, a standardized treatment protocol was developed and implemented, consisting of oral administration of single and compound herbal preparations combined with purificatory measures as well as dietary and lifestyle regimens. The outcomes were assessed by measuring liver functions through specific clinical features and laboratory parameters and by evaluating the Child-Pugh prognostic grade score. After 6 weeks of treatment and a follow-up period of 18 weeks, the outcomes showed statistically significant and clinically relevant improvements. Further larger and randomized trials on effectiveness, safety, and quality of the Ayurvedic approach in the treatment of HCcA are warranted to support these preliminary findings.

How Genomics Is Shaping Precision Medicine in Oncology

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In laboratories at NCI and around the world, researchers are using advanced genomic technologies to study the differences between cancer cells and normal cells, leading to new and more effective treatments for patients with cancer.

Hepatitis Vaccines

OpenAIRE

Ogholikhan, Sina; Schwarz, Kathleen B.

2016-01-01

Viral hepatitis is a serious health problem all over the world. However, the reduction of the morbidity and mortality due to vaccinations against hepatitis A and hepatitis B has been a major component in the overall reduction in vaccine preventable diseases. We will discuss the epidemiology, vaccine development, and post-vaccination effects of the hepatitis A and B virus. In addition, we discuss attempts to provide hepatitis D vaccine for the 350 million individuals infected with hepatitis B ...

Fuzzy Logic in Medicine and Bioinformatics

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Angela Torres

2006-01-01

Full Text Available The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions and in bioinformatics (comparison of genomes.

Hepatitis Vaccines

Directory of Open Access Journals (Sweden)

Sina Ogholikhan

2016-03-01

Full Text Available Viral hepatitis is a serious health problem all over the world. However, the reduction of the morbidity and mortality due to vaccinations against hepatitis A and hepatitis B has been a major component in the overall reduction in vaccine preventable diseases. We will discuss the epidemiology, vaccine development, and post-vaccination effects of the hepatitis A and B virus. In addition, we discuss attempts to provide hepatitis D vaccine for the 350 million individuals infected with hepatitis B globally. Given the lack of a hepatitis C vaccine, the many challenges facing the production of a hepatitis C vaccine will be shown, along with current and former vaccination trials. As there is no current FDA-approved hepatitis E vaccine, we will present vaccination data that is available in the rest of the world. Finally, we will discuss the existing challenges and questions facing future endeavors for each of the hepatitis viruses, with efforts continuing to focus on dramatically reducing the morbidity and mortality associated with these serious infections of the liver.

Hepatitis Vaccines

Science.gov (United States)

Ogholikhan, Sina; Schwarz, Kathleen B.

2016-01-01

Viral hepatitis is a serious health problem all over the world. However, the reduction of the morbidity and mortality due to vaccinations against hepatitis A and hepatitis B has been a major component in the overall reduction in vaccine preventable diseases. We will discuss the epidemiology, vaccine development, and post-vaccination effects of the hepatitis A and B virus. In addition, we discuss attempts to provide hepatitis D vaccine for the 350 million individuals infected with hepatitis B globally. Given the lack of a hepatitis C vaccine, the many challenges facing the production of a hepatitis C vaccine will be shown, along with current and former vaccination trials. As there is no current FDA-approved hepatitis E vaccine, we will present vaccination data that is available in the rest of the world. Finally, we will discuss the existing challenges and questions facing future endeavors for each of the hepatitis viruses, with efforts continuing to focus on dramatically reducing the morbidity and mortality associated with these serious infections of the liver. PMID:26978406

Primary hepatic artery embolization in pediatric blunt hepatic trauma.

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Ong, Caroline C P; Toh, Luke; Lo, Richard H G; Yap, Te-Lu; Narasimhan, Kannan

2012-12-01

Non-operative management of isolated blunt hepatic trauma is recommended except when hemodynamic instability requires immediate laparotomy. Hepatic artery angioembolization is increasingly used for hepatic injuries with ongoing bleeding as demonstrated by contrast extravasation on the CT scan. It is used primarily or after laparotomy to control ongoing hemorrhage. Hepatic angioembolization as part of multimodality management of hepatic trauma is reported mainly in adults, with few pediatric case reports. We describe our institution experience with primary pediatric hepatic angioembolization and review the literature with regard to indications and complications. Two cases (3 and 8 years old), with high-grade blunt hepatic injuries with contrast extravasation on the CT scan were successfully managed by emergency primary hepatic angioembolization with minimal morbidity and avoided laparotomy. To date, the only reports of pediatric hepatic angioembolization for trauma are 5 cases for acute bleeding and 15 delayed cases for pseudoaneurysm. The role of hepatic angioembolization in the presence of an arterial blush on CT in adults is accepted, but contested in a pediatric series, despite higher transfusion rate and mortality rate. We propose that hepatic angioembolization should be considered adjunct treatment, in lieu of, or in addition to emergency laparotomy for hemostasis in pediatric blunt hepatic injury. Copyright © 2012 Elsevier Inc. All rights reserved.

Hepatic protein phosphatase 1 regulatory subunit 3B (Ppp1r3b) promotes hepatic glycogen synthesis and thereby regulates fasting energy homeostasis.

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Mehta, Minal B; Shewale, Swapnil V; Sequeira, Raymond N; Millar, John S; Hand, Nicholas J; Rader, Daniel J

2017-06-23

Maintenance of whole-body glucose homeostasis is critical to glycemic function. Genetic variants mapping to chromosome 8p23.1 in genome-wide association studies have been linked to glycemic traits in humans. The gene of known function closest to the mapped region, PPP1R3B (protein phosphatase 1 regulatory subunit 3B), encodes a protein (G L ) that regulates glycogen metabolism in the liver. We therefore sought to test the hypothesis that hepatic PPP1R3B is associated with glycemic traits. We generated mice with either liver-specific deletion ( Ppp1r3b Δ hep ) or liver-specific overexpression of Ppp1r3b The Ppp1r3b deletion significantly reduced glycogen synthase protein abundance, and the remaining protein was predominantly phosphorylated and inactive. As a consequence, glucose incorporation into hepatic glycogen was significantly impaired, total hepatic glycogen content was substantially decreased, and mice lacking hepatic Ppp1r3b had lower fasting plasma glucose than controls. The concomitant loss of liver glycogen impaired whole-body glucose homeostasis and increased hepatic expression of glycolytic enzymes in Ppp1r3b Δ hep mice relative to controls in the postprandial state. Eight hours of fasting significantly increased the expression of two critical gluconeogenic enzymes, phosphoenolpyruvate carboxykinase and glucose-6-phosphatase, above the levels in control livers. Conversely, the liver-specific overexpression of Ppp1r3b enhanced hepatic glycogen storage above that of controls and, as a result, delayed the onset of fasting-induced hypoglycemia. Moreover, mice overexpressing hepatic Ppp1r3b upon long-term fasting (12-36 h) were protected from blood ketone-body accumulation, unlike control and Ppp1r3b Δ hep mice. These findings indicate a major role for Ppp1r3b in regulating hepatic glycogen stores and whole-body glucose/energy homeostasis. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Feature Hepatitis: Hepatitis Symptoms, Diagnosis, Treatment & Prevention

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... Navigation Bar Home Current Issue Past Issues Feature Hepatitis Hepatitis: Symptoms, Diagnosis, Treatment & Prevention Past Issues / Spring 2009 ... No appetite Fever Headaches Diagnosis To check for hepatitis viruses, your doctor will test your blood. You ...

CRISPR-Cas: Revolutionising genome engineering

African Journals Online (AJOL)

Within the repeating As, Cs, Gs and Ts of the human genome is the .... Medicine, South African Medical Research Council Extramural Unit for Stem Cell Research and Therapy, ... Second, should we allow embryonic/germline engineering, or.

Drug-Induced Liver Injury Associated with Complementary and Alternative Medicines

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Takahashi, Koji; Kanda, Tatsuo; Yasui, Shin; Haga, Yuki; Kumagai, Junichiro; Sasaki, Reina; Wu, Shuang; Nakamoto, Shingo; Nakamura, Masato; Arai, Makoto; Yokosuka, Osamu

2016-01-01

A 24-year-old man was admitted due to acute hepatitis with unknown etiology. After his condition and laboratory data gradually improved with conservative therapy, he was discharged 1 month later. Two months after his discharge, however, liver dysfunction reappeared. After his mother accidentally revealed that he took complementary and alternative medicine, discontinuation of the therapy caused his condition to improve. Finally, he was diagnosed with a recurrent drug-induced liver injury associated with Japanese complementary and alternative medicine. It is important to take the medical history in detail and consider complementary and alternative medicine as a cause of liver disease. PMID:28100990

Viral Hepatitis

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... Home A-Z Health Topics Viral hepatitis Viral hepatitis > A-Z Health Topics Viral hepatitis (PDF, 90 ... liver. Source: National Cancer Institute Learn more about hepatitis Watch a video. Learn who is at risk ...

Evidence of an Exponential Decay Pattern of the Hepatitis Delta Virus Evolution Rate and Fluctuations in Quasispecies Complexity in Long-Term Studies of Chronic Delta Infection.

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Maria Homs

Full Text Available Chronic HDV infection can cause a severe form of viral hepatitis for which there is no specific treatment. Characterization of the hepatitis B or C viral quasispecies has provided insight into treatment failure and disease recurrence following liver transplantation, has proven useful to understand hepatitis B e antigen seroconversion, and has helped to predict whether hepatitis C infection will resolve or become chronic. It is likely that characterization of the hepatitis delta virus (HDV quasispecies will ultimately have similar value for the management of this infection. This study sought to determine the RNA evolution rates in serum of chronic hepatitis delta (CHD treatment-naïve patients, using next-generation sequencing methods. The region selected for study encompassed nucleotide positions 910 to 1270 of the genome and included the amber/W codon. Amber/W is a substrate of the editing process by the ADAR1 host enzyme and is essential for encoding the 2 delta antigens (HDAg. The amber codon encodes the small (unedited HDAg form and the W codon the large (edited HDAg form. The evolution rate was analyzed taking into account the time elapsed between samples, the percentage of unedited and edited genomes, and the complexity of the viral population. The longitudinal studies included 29 sequential samples from CHD patients followed up for a mean of 11.5 years. In total, 121,116 sequences were analyzed. The HDV evolution rate ranged from 9.5x10-3 to 1.2x10-3 substitutions/site/year and showed a negative correlation with the time elapsed between samples (p<0.05. An accumulation of transition-type changes was found to be responsible for higher evolution rates. The percentages of unedited and edited genomes and the quasispecies complexity showed no relationships with the evolution rate, but the fluctuations in the percentages of genomes and in complexity suggest continuous adaptation of HDV to the host conditions.

Chronic hepatitis C--assessment in civil law: a case study.

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Santos, Bruno Miguel; Sousa, Paula; Mena, Filomena; Costa, Graça Santos; Corte-Real, Francisco; Vieira, Duarte Nuno

2010-02-01

This article describes the case of a 58-year-old man who asked for an assessment of physical damage of a civil nature, having been diagnosed with chronic hepatitis C for which he blamed a blood transfusion, supposedly contaminated with hepatitis C virus (HCV). After studying the documentary information, a number of presuppositions were drawn up with a view to determining the causal nexus, but this could not be proved. The assessment of situations like this is not common in civil law. This article is intended to add to the body of information on the forensic assessment of similar cases. Copyright 2009 Elsevier Ltd and Faculty of Forensic and Legal Medicine. Published by Elsevier Ltd. All rights reserved.

Hepatitis B

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... B Entire Lesson Viral Hepatitis Menu Menu Viral Hepatitis Viral Hepatitis Home For Veterans and the Public Veterans ... in their blood (sometimes referred to as the hepatitis B viral load) and an unusually high level of a ...

Hepatic Encephalopathy

Medline Plus

Full Text Available ... A Hepatitis B Hepatitis C Intrahepatic Cholestasis of Pregnancy (ICP) Jaundice In Newborns Diseases of the Liver ... A Hepatitis B Hepatitis C Intrahepatic Cholestasis of Pregnancy (ICP) Jaundice In Newborns Diseases of the Liver ...

Precision medicine in acute myeloid leukemia: Hope, hype or both?

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Prasad, Vinay; Gale, Robert Peter

2016-09-01

Precision medicine is interchangeably used with personalized medicine, genomic medicine and individualized medicine. Collectively, these terms refer to at least 5 distinct concepts in the context of AML. 1st, using molecular or omics data (e.g. genomics, epigenomics, transcriptomics, proteomics) to delineate or define subtypes of AML. 2nd, using these data to select the best therapy for someone with an AML subtype, such as a person with a FLT3-mutation. 3rd, using these data to monitor therapy-response such as measurable residual disease [MRD]-testing. 4th, using results of MRD-testing to select from amongst therapy-options such as additional chemotherapy or a haematopoietic cell transplant. And 5th, using these data to identify persons with hereditary forms of AML with potential therapy and surveillance implications. Here, we review these 5 conceptions and delineate where precision medicine is likely to afford greatest hope and where instead our rhetoric may constitute hype. Copyright © 2016 Elsevier Ltd. All rights reserved.

Challenges and strategies for implementing genomic services in diverse settings: experiences from the Implementing GeNomics In pracTicE (IGNITE) network.

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Sperber, Nina R; Carpenter, Janet S; Cavallari, Larisa H; J Damschroder, Laura; Cooper-DeHoff, Rhonda M; Denny, Joshua C; Ginsburg, Geoffrey S; Guan, Yue; Horowitz, Carol R; Levy, Kenneth D; Levy, Mia A; Madden, Ebony B; Matheny, Michael E; Pollin, Toni I; Pratt, Victoria M; Rosenman, Marc; Voils, Corrine I; W Weitzel, Kristen; Wilke, Russell A; Ryanne Wu, R; Orlando, Lori A

2017-05-22

To realize potential public health benefits from genetic and genomic innovations, understanding how best to implement the innovations into clinical care is important. The objective of this study was to synthesize data on challenges identified by six diverse projects that are part of a National Human Genome Research Institute (NHGRI)-funded network focused on implementing genomics into practice and strategies to overcome these challenges. We used a multiple-case study approach with each project considered as a case and qualitative methods to elicit and describe themes related to implementation challenges and strategies. We describe challenges and strategies in an implementation framework and typology to enable consistent definitions and cross-case comparisons. Strategies were linked to challenges based on expert review and shared themes. Three challenges were identified by all six projects, and strategies to address these challenges varied across the projects. One common challenge was to increase the relative priority of integrating genomics within the health system electronic health record (EHR). Four projects used data warehousing techniques to accomplish the integration. The second common challenge was to strengthen clinicians' knowledge and beliefs about genomic medicine. To overcome this challenge, all projects developed educational materials and conducted meetings and outreach focused on genomic education for clinicians. The third challenge was engaging patients in the genomic medicine projects. Strategies to overcome this challenge included use of mass media to spread the word, actively involving patients in implementation (e.g., a patient advisory board), and preparing patients to be active participants in their healthcare decisions. This is the first collaborative evaluation focusing on the description of genomic medicine innovations implemented in multiple real-world clinical settings. Findings suggest that strategies to facilitate integration of genomic

Alcohol and Hepatitis

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... Home » Living with Hepatitis » Daily Living: Alcohol Viral Hepatitis Menu Menu Viral Hepatitis Viral Hepatitis Home For ... heavy drinking, most heavy drinkers have developed cirrhosis. Hepatitis C and cirrhosis In general, someone with hepatitis ...

Hepatitis C: Treatment

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... Public Home » Hepatitis C » Hepatitis C Treatment Viral Hepatitis Menu Menu Viral Hepatitis Viral Hepatitis Home For ... Enter ZIP code here Enter ZIP code here Hepatitis C Treatment for Veterans and the Public Treatment ...

Treating hepatitis C: can you teach old dogs new tricks?

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Rice, Charles M; You, Shihyun

2005-12-01

Viruses depend on host-derived factors for their efficient genome replication. Here, we demonstrate that a cellular peptidyl-prolyl cis-trans isomerase (PPIase), cyclophilin B (CyPB), is critical for the efficient replication of the hepatitis C virus genome. CyPB interacted with the HCV RNA polymerase NS5B to directly stimulate its RNA binding activity. Both the RNA interference (RNAi)-mediated reduction of endogenous CyPB expression and the induced loss of NS5B binding to CyPB decreased the levels of HCV replication. Thus, CyPB functions as a stimulatory regulator of NS5B in HCV replication machinery. This regulation mechanism for viral replication identifies CyPB as a target for antiviral therapeutic strategies.

Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers.

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Yuichi Shiraishi

Full Text Available Recent studies applying high-throughput sequencing technologies have identified several recurrently mutated genes and pathways in multiple cancer genomes. However, transcriptional consequences from these genomic alterations in cancer genome remain unclear. In this study, we performed integrated and comparative analyses of whole genomes and transcriptomes of 22 hepatitis B virus (HBV-related hepatocellular carcinomas (HCCs and their matched controls. Comparison of whole genome sequence (WGS and RNA-Seq revealed much evidence that various types of genomic mutations triggered diverse transcriptional changes. Not only splice-site mutations, but also silent mutations in coding regions, deep intronic mutations and structural changes caused splicing aberrations. HBV integrations generated diverse patterns of virus-human fusion transcripts depending on affected gene, such as TERT, CDK15, FN1 and MLL4. Structural variations could drive over-expression of genes such as WNT ligands, with/without creating gene fusions. Furthermore, by taking account of genomic mutations causing transcriptional aberrations, we could improve the sensitivity of deleterious mutation detection in known cancer driver genes (TP53, AXIN1, ARID2, RPS6KA3, and identified recurrent disruptions in putative cancer driver genes such as HNF4A, CPS1, TSC1 and THRAP3 in HCCs. These findings indicate genomic alterations in cancer genome have diverse transcriptomic effects, and integrated analysis of WGS and RNA-Seq can facilitate the interpretation of a large number of genomic alterations detected in cancer genome.

Tenofovir and its potential in the treatment of hepatitis B virus

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Laura Reynaud

2009-02-01

Full Text Available Laura Reynaud, Maria Aurora Carleo, Maria Talamo, Guglielmo BorgiaDepartment of Public Medicine and Social Security – Section of Infectious Disease University of Naples “Federico II”, ItalyAbstract: Recent literature is reviewed about treatment of chronic hepatitis B virus (CHB, focusing on tenofovir disoproxil fumarate (TDF; Viread®, among the nucleotide and nucleoside analogs. TDF pharmacokinetics and pharmacodynamics, activity in respect of hepatitis B virus (HBV multi-drug-resistant mutations, efficacy in treatment-naïve and treatment-experienced patients, and side effects are described. The most predictive response factors to TDF therapy are discussed and all available combination therapies to optimize clinical outcome in the various patient profiles are analyzed, such as compensated and/or decompensated cirrhotic patients. The use of TDF in pregnancy, and prophylaxis after exposure to HBV and post-liver transplantation are also evaluated.Keywords: HBV, chronic hepatitis B, tenofovir, antiviral therapy

Arctigenin protects against liver injury from acute hepatitis by suppressing immune cells in mice.

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Cheng, Xixi; Wang, Huafeng; Yang, Jinlai; Cheng, Yingnan; Wang, Dan; Yang, Fengrui; Li, Yan; Zhou, Dongmei; Wang, Yanxia; Xue, Zhenyi; Zhang, Lijuan; Zhang, Qi; Yang, Luhong; Zhang, Rongxin; Da, Yurong

2018-06-01

As a phenylpropanoid and dibenzylbutyrolactone lignan present in medical plants, such as those used in traditional Chinese herbal medicine, including Arctium lappa (Niubang), arctigenin exhibits antimicrobial, anti-inflammatory, and anticancer activities. In this study, we investigated the protective role of arctigenin in Concanavalin A (ConA)-induced acute hepatitis in mice. Arctigenin remarkably reduced the congestion and necroinflammation of livers, and improved hepatic function (ALT and AST) in ConA-induced acute hepatitis in vivo. The infiltration of CD4 T, NKT and macrophages into the livers was found to be reduced with arctigenin treatment. Arctigenin suppressed ConA-induced T lymphocyte proliferations that might have resulted from enhanced IL-10 production by macrophages and CD4 T cells. These results suggested that arctigenin could be a powerful drug candidate for acute hepatitis through immune suppression. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Occult hepatitis B among Iranian hepatitis C patients

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Ahmad shavakhi

2009-02-01

Full Text Available

• BACKGROUND: Occult hepatitis B is defined as presence of HBV DNA in tissue or serum without hepatitis B surface antigen. The aim of this study is to determine frequency of occult hepatitis B among hepatitis C patients in Tehran and compare the route of transmission and liver enzymes between positive and negative HBV DNA patients.
• METHODS: In a cross sectional study, serum of 103 hepatitis C cases (79.6% men and 20.4% women were analyzed for s, x and core genes via a nested polymerase chain reaction technique.
• RESULTS: HBV DNA was detectable in serum of 20 patients (19.4%. No significant difference in age, sex and route of transmission were seen in HBV DNA positive and negative patients. In HBV DNA positive and negative groups, mean of AST was 73, 47 (p < 0.05 and mean of ALT was 76 and 36 respectively (p < 0.05.
• CONCLUSION: Occult hepatitis B was observed in a considerable number of hepatitis C patients in Tehran. It was associated with elevation in liver enzyme but was not related to route of transmission.
• KEY WORD: Occult hepatitis B, hepatitis C, cirrhosis.

Genome engineering for microbial natural product discovery.

Science.gov (United States)

Choi, Si-Sun; Katsuyama, Yohei; Bai, Linquan; Deng, Zixin; Ohnishi, Yasuo; Kim, Eung-Soo

2018-03-03

The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach. Here, we describe recent developments in the MNP research paradigm, including microbial genome mining, NP BGC activation, and NP overproducing cell factory design. Copyright © 2018 Elsevier Ltd. All rights reserved.

Hepatic artery infusion (HAI) for hepatic metastases in combination with hepatic resection and hepatic radiation

International Nuclear Information System (INIS)

Merrick, H.W.; Dobelbower, R.R.; Ringleint, J.F.; Skeel, R.T.

1986-01-01

Renewed interest in hepatic artery infusion has been stimulated by the development of a totally implantable pump which eliminates many of the problems encountered by the external pumps and catheters. As the potential benefit of hepatic artery infusion would be greater if either all gross disease were removed by prior resection, or alternatively, if non-resectable disease were irradiated in conjunction with hepatic artery infusion, the authors initiated a phase I-II trial to evaluate combined modality therapy

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.

Metformin and metabolic diseases: a focus on hepatic aspects

Science.gov (United States)

Woo, Shih-Lung; Hu, Xiang; Botchlett, Rachel; Chen, Lulu; Huo, Yuqing

2015-01-01

Metformin has been widely used as a first-line anti-diabetic medicine for the treatment of type 2 diabetes (T2D). As a drug that primarily targets the liver, metformin suppresses hepatic glucose production (HGP), serving as the main mechanism by which metformin improves hyperglycemia of T2D. Biochemically, metformin suppresses gluconeogenesis and stimulates glycolysis. Metformin also inhibits glycogenolysis, which is a pathway that critically contributes to elevated HGP. While generating beneficial effects on hyperglycemia, metformin also improves insulin resistance and corrects dyslipidemia in patients with T2D. These beneficial effects of metformin implicate a role for metformin in managing non-alcoholic fatty liver disease. As supported by the results from both human and animal studies, metformin improves hepatic steatosis and suppresses liver inflammation. Mechanistically, the beneficial effects of metformin on hepatic aspects are mediated through both adenosine monophosphate-activated protein kinase (AMPK)-dependent and AMPK-independent pathways. In addition, metformin is generally safe and may also benefit patients with other chronic liver diseases. PMID:25676019

Justice and the Human Genome Project

Energy Technology Data Exchange (ETDEWEB)

Murphy, T.F.; Lappe, M. (eds.)

1992-01-01

Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

Justice and the Human Genome Project

Energy Technology Data Exchange (ETDEWEB)

Murphy, T.F.; Lappe, M. [eds.

1992-12-31

Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

Evidence of intratypic recombination in natural populations of hepatitis C virus

International Nuclear Information System (INIS)

Colina, R.; Garcia-Aguirre, L.; Cristina, J.; Casane, D.; Vasquez, S.; Khan, Baldip

2004-01-01

Hepatitis C virus (HCV) has high genomic variability and, since its discovery, at least six different types and an increasing number of subtypes have been reported. Genotype 1 is the most prevalent genotype found in South America. In the present study, three different genomic regions (5 UTR, core and NS5B) of four HCV strains isolated from Peruvian patients were sequenced in order to investigate the congruence of HCV genotyping for these three genomic regions. Phylogenetic analysis using 5 UTR-core sequences found strain PE22 to be related to subtype 1a. To test the possibility of genetic recombination, phylogenetic studies were carried out, revealing that a crossover event had taken place in the NS5B protein. We discuss the consequences of this observation on HCV genotype classification, laboratory diagnosis and treatment of HCV infection

The Human Genome Project: big science transforms biology and medicine

OpenAIRE

Hood, Leroy; Rowen, Lee

2013-01-01

The Human Genome Project has transformed biology through its integrated big science approach to deciphering a reference human genome sequence along with the complete sequences of key model organisms. The project exemplifies the power, necessity and success of large, integrated, cross-disciplinary efforts - so-called ‘big science’ - directed towards complex major objectives. In this article, we discuss the ways in which this ambitious endeavor led to the development of novel technologies and a...

OCCURRENCE OF SMALL HOMOLOGOUS AND COMPLEMENTARY FRAGMENTS IN HUMAN VIRUS GENOMES AND THEIR POSSIBLE ROLE

Directory of Open Access Journals (Sweden)

E. P. Kharchenko

2017-01-01

Full Text Available With computer analysis occurrence of small homologous and complementary fragments (21 nucleotides in length has been studied in genomes of 14 human viruses causing most dangerous infections. The sample includes viruses with (+ and (– single stranded RNA and DNA-containing hepatitis A virus. Analysis of occurrence of homologous sequences has shown the existence two extreme situations. On the one hand, the same virus contains homologous sequences to almost all other viruses (for example, Ebola virus, severe acute respiratory syndrome-related coronavirus, and mumps virus, and numerous homologous sequences to the same other virus (especially in severe acute respiratory syndrome-related coronavirus to Dengue virus and in Ebola virus to poliovirus. On the other hand, there are rare occurrence and not numerous homologous sequences in genomes of other viruses (rubella virus, hepatitis A virus, and hepatitis B virus. Similar situation exists for occurrence of complementary sequences. Rubella virus, the genome of which has the high content of guanine and cytosine, has no complementary sequences to almost all other viruses. Most viruses have moderate level of occurrence for homologous and complementary sequences. Autocomplementary sequences are numerous in most viruses and one may suggest that the genome of single stranded RNA viruses has branched secondary structure. In addition to possible role in recombination among strains autocomplementary sequences could be regulators of translation rate of virus proteins and determine its optimal proportion in virion assembly with genome and mRNA folding. Occurrence of small homologous and complementary sequences in RNA- and DNA-containing viruses may be the result of multiple recombinations in the past and the present and determine their adaptation and variability. Recombination may take place in coinfection of human and/or common hosts. Inclusion of homologous and complementary sequences into genome could not

Ethical, Legal, and Social Implications of Personalized Genomic Medicine Research: Current Literature and Suggestions for the Future.

Science.gov (United States)

Callier, Shawneequa L; Abudu, Rachel; Mehlman, Maxwell J; Singer, Mendel E; Neuhauser, Duncan; Caga-Anan, Charlisse; Wiesner, Georgia L

2016-11-01

This review identifies the prominent topics in the literature pertaining to the ethical, legal, and social issues (ELSI) raised by research investigating personalized genomic medicine (PGM). The abstracts of 953 articles extracted from scholarly databases and published during a 5-year period (2008-2012) were reviewed. A total of 299 articles met our research criteria and were organized thematically to assess the representation of ELSI issues for stakeholders, health specialties, journals, and empirical studies. ELSI analyses were published in both scientific and ethics journals. Investigational research comprised 45% of the literature reviewed (135 articles) and the remaining 55% (164 articles) comprised normative analyses. Traditional ELSI concerns dominated the discourse including discussions about disclosure of research results. In fact, there was a dramatic increase in the number of articles focused on the disclosure of research results and incidental findings to research participants. Few papers focused on particular disorders, the use of racial categories in research, international communities, or special populations (e.g., adolescents, elderly patients, or ethnic groups). Considering that strategies in personalized medicine increasingly target individuals' unique health conditions, environments, and ancestries, further analysis is needed on how ELSI scholarship can better serve the increasingly global, interdisciplinary, and diverse PGM research community. © 2016 John Wiley & Sons Ltd.

Hepatitis B infection reported with cancer chemotherapy: analyzing the US FDA Adverse Event Reporting System.

Science.gov (United States)

Sanagawa, Akimasa; Hotta, Yuji; Kataoka, Tomoya; Maeda, Yasuhiro; Kondo, Masahiro; Kawade, Yoshihiro; Ogawa, Yoshihiro; Nishikawa, Ryohei; Tohkin, Masahiro; Kimura, Kazunori

2018-04-16

We conducted data mining using the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) database on spontaneously reported adverse events to evaluate the association between anticancer drug therapy and hepatitis B infection. Reports of hepatitis B infection were retrieved from the FAERS database. The reporting odds ratio (ROR) was used to estimate the association between hepatitis B infection and various anticancer agents and drug combinations. We detected statistically significant risk signals of hepatitis B for 33 of 64 anticancer agents by ROR (26 cytotoxicity drugs and seven molecular-targeted drugs). We focused on molecular-targeted drugs and assessed the risk of hepatitis B from specific anticancer drug combinations. The frequency of hepatitis B infection was significantly high for drugs such as rituximab, bortezomib, imatinib, and everolimus. The addition of cyclophosphamide, doxorubicin, and fludarabine to drug combinations additively enhanced the frequency of hepatitis B infection. There were no reports on hepatitis B infection associated with trastuzumab or azacitidine monotherapy. However, trastuzumab-containing regimens (e.g., combinations with docetaxel or paclitaxel) were correlated with the incidence of hepatitis B infection, similar to azacitidine monotherapy. Our findings suggest that the concomitant use of anticancer drugs, such as trastuzumab, taxane, and azacitidine, may contribute to the risk of hepatitis B infection. The unique signals detected from the public database might provide clues to eliminate the threat of HBV in oncology. © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

HIV, hepatitis B, and hepatitis C in Zambia

Directory of Open Access Journals (Sweden)

Kenneth C Kapembwa

2011-01-01

Full Text Available Objectives : Epidemiologic data of HIV and viral hepatitis coinfection are needed in sub-Saharan Africa to guide health policy for hepatitis screening and optimized antiretroviral therapy (ART. Materials and Methods: We screened 323 HIV-infected, ART-eligible adults for hepatitis B surface antigen (HBsAg and hepatitis C antibody (HCV Ab at a tertiary hospital in Lusaka, Zambia. We collected basic demographic, medical, and laboratory data to determine predictors for coinfection. Results: Of 323 enrolled patients, 32 (9.9%; 95% CI=6.7-13.2% were HBsAg positive, while 4 (1.2%; 95% CI=0.03-2.4% were HCV Ab positive. Patients with hepatitis B coinfection were more likely to be 200 IU/L was uncommon and did not differ between the two groups (3.4% vs. 2.3%; P=0.5. We were unable to determine predictors of hepatitis C infection due to the low prevalence of disease. Conclusions: HIV and hepatitis B coinfection was common among patients initiating ART at this tertiary care facility. Routine screening for hepatitis B should be considered for HIV-infected persons in southern Africa.

Hepatitis (For Parents)

Science.gov (United States)

... Staying Safe Videos for Educators Search English Español Hepatitis KidsHealth / For Parents / Hepatitis Print en español Hepatitis What Is Hepatitis? Hepatitis is an inflammation of the liver. The ...

Tyrphostin AG1478 Inhibits Encephalomyocarditis Virus and Hepatitis C Virus by Targeting Phosphatidylinositol 4-Kinase IIIα

NARCIS (Netherlands)

Dorobantu, Cristina M.; Harak, Christian; Klein, Rahel; van der Linden, Lonneke; Strating, Jeroen R. P. M.; van der Schaar, Hilde M.; Lohmann, Volker; van Kuppeveld, Frank J. M.

2016-01-01

Encephalomyocarditis virus (EMCV), like hepatitis C virus (HCV), requires phosphatidylinositol 4-kinase IIIα (PI4KA) for genome replication. Here, we demonstrate that tyrphostin AG1478, a known epidermal growth factor receptor (EGFR) inhibitor, also inhibits PI4KA activity, both in vitro and in

Precision medicine driven by cancer systems biology.

Science.gov (United States)

Filipp, Fabian V

2017-03-01

Molecular insights from genome and systems biology are influencing how cancer is diagnosed and treated. We critically evaluate big data challenges in precision medicine. The melanoma research community has identified distinct subtypes involving chronic sun-induced damage and the mitogen-activated protein kinase driver pathway. In addition, despite low mutation burden, non-genomic mitogen-activated protein kinase melanoma drivers are found in membrane receptors, metabolism, or epigenetic signaling with the ability to bypass central mitogen-activated protein kinase molecules and activating a similar program of mitogenic effectors. Mutation hotspots, structural modeling, UV signature, and genomic as well as non-genomic mechanisms of disease initiation and progression are taken into consideration to identify resistance mutations and novel drug targets. A comprehensive precision medicine profile of a malignant melanoma patient illustrates future rational drug targeting strategies. Network analysis emphasizes an important role of epigenetic and metabolic master regulators in oncogenesis. Co-occurrence of driver mutations in signaling, metabolic, and epigenetic factors highlights how cumulative alterations of our genomes and epigenomes progressively lead to uncontrolled cell proliferation. Precision insights have the ability to identify independent molecular pathways suitable for drug targeting. Synergistic treatment combinations of orthogonal modalities including immunotherapy, mitogen-activated protein kinase inhibitors, epigenetic inhibitors, and metabolic inhibitors have the potential to overcome immune evasion, side effects, and drug resistance.

Transmission of viral hepatitis by blood and blood derivatives: current risks, past heritage.

Science.gov (United States)

Prati, D

2002-11-01

For more than 40 years in the history of transfusion medicine, transmission of viral hepatitis from infected donors to recipients has been a frequent and serious adverse effect of the administration of blood components and plasma derivatives. This epidemic is now over, at least in developed and resource-rich countries. Hence, the attention of clinicians and investigators now focuses mainly on the measures to reduce the residual risk, on the possible emergence of novel or undiscovered agents causing post-transfusion hepatitis, and on the long-term outcome of patients who became infected more than ten years ago. The present article reviews these issues.

Multiple surface antigen mutations in five blood donors with occult hepatitis B virus infection

NARCIS (Netherlands)

Zaaijer, H. L.; Torres, P.; Ontañón, A.; Ponte, L. González; Koppelman, M. H. G. M.; Lelie, P. N.; Hemert, F. J. van; Boot, H. J.

2008-01-01

Occult hepatitis B virus (HBV) infection is characterized by the presence of HBV DNA while the HBV surface antigen (HBsAg) remains undetectable. The HBV genomes in five asymptomatic blood donors with occult HBV infection and low viremia ( <10 to 1,000 HBV DNA copies/mL, genotype D) were studied. An

Multiscale modeling of three-dimensional genome

Science.gov (United States)

Zhang, Bin; Wolynes, Peter

The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.

Ethical Considerations Regarding Classroom Use of Personal Genomic Information

Directory of Open Access Journals (Sweden)

Lisa S. Parker

2014-10-01

Full Text Available Rapidly decreasing costs of genetic technologies—especially next-generation sequencing—and intensifying need for a clinical workforce trained in genomic medicine have increased interest in having students use personal genomic information to motivate and enhance genomics education. Numerous ethical issues attend classroom/pedagogical use of students’ personal genomic information, including their informed decision to participate, pressures to participate, privacy concerns, and psychosocial sequelae of learning genomic information. This paper addresses these issues, advocates explicit discussion of these issues to cultivate students’ ethical reasoning skills, suggests ways to mitigate potential harms, and recommends collection of ethically relevant data regarding pedagogical use of personal genomic information.

Genomic interval engineering of mice identified a novel modulator of triglyceride production

Energy Technology Data Exchange (ETDEWEB)

Zhu, Y.; Jong, M.C.; Frazer, K.A.; Gong, E.; Krauss, R.M.; Cheng, J.F.; Boffelli, D.; Rubin, E.M.

1999-10-01

To accelerate the biological annotation of novel genes discovered in sequenced of mammalian genomes, we are creating large deletions in the mouse genome targeted to include clusters of such genes. Here we describe the targeted deletion of a 450 kb region on mouse chromosome 11 which, based on computational analysis of the deleted murine sequences and human 5q orthologous sequences, codes for nine putative genes. Mice homozygous for the deletion had a variety of abnormalities including severe hypertriglyceridemia, hepatic and cardiac enlargement, growth retardation and premature mortality. Analysis of triglyceride metabolism in these animals demonstrated a several-fold increase in hepatic very-low density lipoprotein (VLDL) triglyceride secretion, the most prevalent mechanism responsible for hypertriglyceridemia in humans. A series of mouse BAC and human YAC transgenes covering different intervals of the 450 kb deleted region were assessed for their ability to complement the deletion induced abnormalities. These studies revealed that OCTN2, a gene recently shown to play a role in carnitine transport, was able to correct the triglyceride abnormalities. The discovery of this previously unappreciated relationship between OCTN2, carnitine and hepatic triglyceride production is of particular importance due to the clinical consequence of hypertriglyceridemia and the paucity of genes known to modulate triglyceride secretion.

Playing with heart and soul…and genomes: sports implications and applications of personal genomics.

Science.gov (United States)

Wagner, Jennifer K

2013-01-01

Whether the integration of genetic/omic technologies in sports contexts will facilitate player success, promote player safety, or spur genetic discrimination depends largely upon the game rules established by those currently designing genomic sports medicine programs. The integration has already begun, but there is not yet a playbook for best practices. Thus far discussions have focused largely on whether the integration would occur and how to prevent the integration from occurring, rather than how it could occur in such a way that maximizes benefits, minimizes risks, and avoids the exacerbation of racial disparities. Previous empirical research has identified members of the personal genomics industry offering sports-related DNA tests, and previous legal research has explored the impact of collective bargaining in professional sports as it relates to the employment protections of the Genetic Information Nondiscrimination Act (GINA). Building upon that research and upon participant observations with specific sports-related DNA tests purchased from four direct-to-consumer companies in 2011 and broader personal genomics (PGx) services, this anthropological, legal, and ethical (ALE) discussion highlights fundamental issues that must be addressed by those developing personal genomic sports medicine programs, either independently or through collaborations with commercial providers. For example, the vulnerability of student-athletes creates a number of issues that require careful, deliberate consideration. More broadly, however, this ALE discussion highlights potential sports-related implications (that ultimately might mitigate or, conversely, exacerbate racial disparities among athletes) of whole exome/genome sequencing conducted by biomedical researchers and clinicians for non-sports purposes. For example, the possibility that exome/genome sequencing of individuals who are considered to be non-patients, asymptomatic, normal, etc. will reveal the presence of variants of

Hepatitis B (HBV)

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... Staying Safe Videos for Educators Search English Español Hepatitis B KidsHealth / For Teens / Hepatitis B What's in ... Prevented? Print en español Hepatitis B What Is Hepatitis B? Hepatitis B is an infection of the ...

Hepatitis A Vaccine

Science.gov (United States)

Twinrix® (as a combination product containing Hepatitis A Vaccine, Hepatitis B Vaccine) ... Why get vaccinated against hepatitis A?Hepatitis A is a serious liver disease. It is caused by the hepatitis A virus (HAV). HAV is spread from ...

77 FR 58913 - Genomic Medicine Program Advisory Committee, Notice of Meeting

Science.gov (United States)

2012-09-24

... incorporation of genomic data, particularly whole genome data, into health care and clinical decision-making... of the public may provide statements (limited to 5 minutes each) during the period reserved for public comments. They may also submit, at the time of the meeting, a 1-2 page summary of their comments...

Association of Oral Lichen Planus with Chronic C Hepatitis. Review of the Data in Literature

Science.gov (United States)

GHEORGHE, Carmen; MIHAI, Lelia; PARLATESCU, Ioanina; TOVARU, Serban

2014-01-01

The relationship between chronic hepatitis C virus infection (HCV) and oral lichen planus (OLP) is a current topic in the field of oral medicine. Many studies of this association have been made over time. The geographic variation of the hepatitis C prevalence proved to be an important factor influencing the statistical results of the studies analyzing the association of the oral plan lichen with the hepatitis C virus. Approaching this issue is not to be neglected. Treatment outcomes in patients with oral lichen planus associated with chronic hepatitis C virus are often unsatisfactory compared to patients suffering from idiopathic oral lichen planus. Also, the evolution of oral lesions is often fluctuating, with repeated periods of relapse according to the degree of liver function decompensation. Background therapy for liver disease itself may influence lichen planus lesions. Thus, during therapy with interferon and ribavirin oral lesions may appear or become acute. PMID:25553136

A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis.

Science.gov (United States)

Yoo, Seungyeul; Wang, Wenhui; Wang, Qin; Fiel, M Isabel; Lee, Eunjee; Hiotis, Spiros P; Zhu, Jun

2017-12-07

Chronic hepatitis B virus (HBV) infection leads to liver fibrosis, which is a major risk factor in hepatocellular carcinoma (HCC) and an independent risk factor of recurrence after HCC tumor resection. The HBV genome can be inserted into the human genome, and chronic inflammation may trigger somatic mutations. However, how HBV integration and other genomic changes contribute to the risk of tumor recurrence with regards to the different degree of liver fibrosis is not clearly understood. We sequenced mRNAs of 21 pairs of tumor and distant non-neoplastic liver tissues of HBV-HCC patients and performed comprehensive genomic analyses of our RNAseq data and public available HBV-HCC sequencing data. We developed a robust pipeline for sensitively identifying HBV integration sites based on sequencing data. Simulations showed that our method outperformed existing methods. Applying it to our data, 374 and 106 HBV host genes were identified in non-neoplastic liver and tumor tissues, respectively. When applying it to other RNA sequencing datasets, consistently more HBV integrations were identified in non-neoplastic liver than in tumor tissues. HBV host genes identified in non-neoplastic liver samples significantly overlapped with known tumor suppressor genes. More significant enrichment of tumor suppressor genes was observed among HBV host genes identified from patients with tumor recurrence, indicating the potential risk of tumor recurrence driven by HBV integration in non-neoplastic liver tissues. We also compared SNPs of each sample with SNPs in a cancer census database and inferred samples' pathogenic SNP loads. Pathogenic SNP loads in non-neoplastic liver tissues were consistently higher than those in normal liver tissues. Additionally, HBV host genes identified in non-neoplastic liver tissues significantly overlapped with pathogenic somatic mutations, suggesting that HBV integration and somatic mutations targeting the same set of genes are important to tumorigenesis. HBV

Human Germline Genome Editing.

Science.gov (United States)

Ormond, Kelly E; Mortlock, Douglas P; Scholes, Derek T; Bombard, Yvonne; Brody, Lawrence C; Faucett, W Andrew; Garrison, Nanibaa' A; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E

2017-08-03

With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Genetic Counselors. These groups, as well as the American Society for Reproductive Medicine, Asia Pacific Society of Human Genetics, British Society for Genetic Medicine, Human Genetics Society of Australasia, Professional Society of Genetic Counselors in Asia, and Southern African Society for Human Genetics, endorsed the final statement. The statement includes the following positions. (1) At this time, given the nature and number of unanswered scientific, ethical, and policy questions, it is inappropriate to perform germline gene editing that culminates in human pregnancy. (2) Currently, there is no reason to prohibit in vitro germline genome editing on human embryos and gametes, with appropriate oversight and consent from donors, to facilitate research on the possible future clinical applications of gene editing. There should be no prohibition on making public funds available to support this research. (3) Future clinical application of human germline genome editing should not proceed unless, at a minimum, there is (a) a compelling medical rationale, (b) an evidence base that supports its clinical use, (c) an ethical justification, and (d) a transparent public process to solicit and incorporate stakeholder input. Copyright © 2017 American Society of Human Genetics. All rights reserved.

Genomic variability associated with the presence of occult hepatitis B virus in HIV co-infected individuals

OpenAIRE

Martin, C. M.; Welge, J. A.; Shire, N. J.; Rouster, S. D.; Shata, M. T.; Sherman, K. E.; Blackard, J. T.

2009-01-01

Occult hepatitis B virus (O-HBV) infection is characterized by the presence of HBV DNA without detectable hepatitis B surface antigen (HBV DNA+/HBsAg−) in the serum. Although O-HBV is more prevalent during HBV/HIV co-infection, analysis of HBV mutations in co-infected patients is limited. In this preliminary study, HBV PreSurface (PreS) and surface (S) regions were amplified from 33 HIV-positive patient serum samples − 27 chronic HBV (C-HBV) and six O-HBV infections. HBV genotype was determin...

Hepatitis C: Managing Pain

Science.gov (United States)

... Pain: Entire Lesson Viral Hepatitis Menu Menu Viral Hepatitis Viral Hepatitis Home For Veterans and the Public Veterans and the Public Home Hepatitis A Hepatitis B Hepatitis C Hepatitis C Home Getting ...

Acute Hepatitis Associated with The Use of Herbal Tea (Fennel and Cumin

Directory of Open Access Journals (Sweden)

Suat Zengin

2014-03-01

Full Text Available Herbal remedies have become increasingly popular throughout the globe as a result of disappointment with conventional medicines. The public often regards them as harmless. However, some of these products or their metabolites can cause adverse effects such as liver damage. In this study, two patients who developed acute hepatitis due to consuming herbal tea are presented. Twenty-six and thirty-year-old two women were admitted to our department with symptoms of nausea, vomiting, anorexia and weakness. Serum alanine aminotransferase and aspartate aminotransferase levels were increased; all serological tests for viral hepatitis and autoimmune disorders were negative. They had consumed an herbal tea containing fennel and cumin to increase lactation everyday for three-four weeks. Discontinuation of the herbal tea resulted in normalization of liver enzymes four-five weeks later. To the best of our knowledge, this is the first report of hepatitis possibly related to use of an herbal tea containing fennel and cumin. This study suggests that herbal tea containing fennel and cumin can cause hepatotoxicity, which could be clinically confused with other causes of acute hepatitis. Clinicians may face with a case of acute hepatitis that is not readily diagnosed, and should question patients about herbal remedy use.

Hypoksisk hepatitis

DEFF Research Database (Denmark)

Amadid, Hanan; Schiødt, Frank Vinholt

2014-01-01

Hypoxic hepatitis (HH), also known as ischaemic hepatitis or shock liver, is an acute liver injury caused by hepatic hypoxia. Cardiac failure, respiratory failure and septic shock are the main underlying conditions. In each of these conditions, several haemodynamic mechanisms lead to hepatic...... hypoxia. A shock state is observed in only 50% of cases. Thus, shock liver and ischaemic hepatitis are misnomers. HH can be a diagnostic pitfall but the diagnosis can be established when three criteria are met. Prognosis is poor and prompt identification and treatment of the underlying conditions...

Role of antiviral therapy in the natural history of hepatitis B virus-related chronic liver disease.

Science.gov (United States)

Russo, Francesco Paolo; Rodríguez-Castro, Kryssia; Scribano, Laura; Gottardo, Giorgia; Vanin, Veronica; Farinati, Fabio

2015-05-18

Hepatitis B virus (HBV) infection is a dynamic state of interactions among HBV, hepatocytes, and the host immune system. Natural history studies of chronic hepatitis B (CHB) infection have shown an association between active viral replication and adverse clinical outcomes such as cirrhosis and hepatocellular carcinoma. The goal of therapy for CHB is to improve quality of life and survival by preventing progression of the disease to cirrhosis, decompensation, end-stage liver disease, hepatocellular carcinoma (HCC) and death. This goal can be achieved if HBV replication is suppressed in a sustained manner. The accompanying reduction in histological activity of CHB lessens the risk of cirrhosis and of HCC, particularly in non-cirrhotic patients. However, CHB infection cannot be completely eradicated, due to the persistence of covalently closed circular DNA in the nucleus of infected hepatocytes, which may explain HBV reactivation. Moreover, the integration of the HBV genome into the host genome may favour oncogenesis, development of HCC and may also contribute to HBV reactivation.

Precision Medicine and the Changing Landscape of Research Ethics.

Science.gov (United States)

Hammer, Marilyn J

2016-03-01

President Barack Obama announced the launch of the National Institutes of Health Precision Medicine Initiative® (PMI) in January 2015. Precision medicine includes the concept of individualized or personalized medicine at a more exact level through advances in science and technology, such as genetics and genomics sequencing. Although many disease processes will be investigated through the precision medicine lens for greater understanding and improved treatment responses, oncology research and translation to practice is leading the initiative's debut, referred to as the near-term focus.

Infrastructure for Personalized Medicine at Partners HealthCare

Directory of Open Access Journals (Sweden)

Scott T. Weiss

2016-02-01

Full Text Available Partners HealthCare Personalized Medicine (PPM is a center within the Partners HealthCare system (founded by Massachusetts General Hospital and Brigham and Women’s Hospital whose mission is to utilize genetics and genomics to improve the care of patients in a cost effective manner. PPM consists of five interconnected components: (1 Laboratory for Molecular Medicine (LMM, a CLIA laboratory performing genetic testing for patients world-wide; (2 Translational Genomics Core (TGC, a core laboratory providing genomic platforms for Partners investigators; (3 Partners Biobank, a biobank of samples (DNA, plasma and serum for 50,000 Consented Partners patients; (4 Biobank Portal, an IT infrastructure and viewer to bring together genotypes, samples, phenotypes (validated diagnoses, radiology, and clinical chemistry from the electronic medical record to Partners investigators. These components are united by (5 a common IT system that brings researchers, clinicians, and patients together for optimal research and patient care.

Asthma pharmacogenetics and the development of genetic profiles for personalized medicine

Directory of Open Access Journals (Sweden)

Ortega VE

2015-01-01

Full Text Available Victor E Ortega, Deborah A Meyers, Eugene R Bleecker Center for Genomics and Personalized Medicine Research, Pulmonary Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA Abstract: Human genetics research will be critical to the development of genetic profiles for personalized or precision medicine in asthma. Genetic profiles will consist of gene variants that predict individual disease susceptibility and risk for progression, predict which pharmacologic therapies will result in a maximal therapeutic benefit, and predict whether a therapy will result in an adverse response and should be avoided in a given individual. Pharmacogenetic studies of the glucocorticoid, leukotriene, and β2-adrenergic receptor pathways have focused on candidate genes within these pathways and, in addition to a small number of genome-wide association studies, have identified genetic loci associated with therapeutic responsiveness. This review summarizes these pharmacogenetic discoveries and the future of genetic profiles for personalized medicine in asthma. The benefit of a personalized, tailored approach to health care delivery is needed in the development of expensive biologic drugs directed at a specific biologic pathway. Prior pharmacogenetic discoveries, in combination with additional variants identified in future studies, will form the basis for future genetic profiles for personalized tailored approaches to maximize therapeutic benefit for an individual asthmatic while minimizing the risk for adverse events. Keywords: asthma, pharmacogenetics, response heterogeneity, single nucleotide polymorphism, genome-wide association study

Genome engineering in human cells.

Science.gov (United States)

Song, Minjung; Kim, Young-Hoon; Kim, Jin-Soo; Kim, Hyongbum

2014-01-01

Genome editing in human cells is of great value in research, medicine, and biotechnology. Programmable nucleases including zinc-finger nucleases, transcription activator-like effector nucleases, and RNA-guided engineered nucleases recognize a specific target sequence and make a double-strand break at that site, which can result in gene disruption, gene insertion, gene correction, or chromosomal rearrangements. The target sequence complexities of these programmable nucleases are higher than 3.2 mega base pairs, the size of the haploid human genome. Here, we briefly introduce the structure of the human genome and the characteristics of each programmable nuclease, and review their applications in human cells including pluripotent stem cells. In addition, we discuss various delivery methods for nucleases, programmable nickases, and enrichment of gene-edited human cells, all of which facilitate efficient and precise genome editing in human cells.

[Ethical considerations in genomic cohort study].

Science.gov (United States)

Choi, Eun Kyung; Kim, Ock-Joo

2007-03-01

During the last decade, genomic cohort study has been developed in many countries by linking health data and genetic data in stored samples. Genomic cohort study is expected to find key genetic components that contribute to common diseases, thereby promising great advance in genome medicine. While many countries endeavor to build biobank systems, biobank-based genome research has raised important ethical concerns including genetic privacy, confidentiality, discrimination, and informed consent. Informed consent for biobank poses an important question: whether true informed consent is possible in population-based genomic cohort research where the nature of future studies is unforeseeable when consent is obtained. Due to the sensitive character of genetic information, protecting privacy and keeping confidentiality become important topics. To minimize ethical problems and achieve scientific goals to its maximum degree, each country strives to build population-based genomic cohort research project, by organizing public consultation, trying public and expert consensus in research, and providing safeguards to protect privacy and confidentiality.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Science.gov (United States)

Ming, Ray; Hou, Shaobin; Feng, Yun; Yu, Qingyi; Dionne-Laporte, Alexandre; Saw, Jimmy H; Senin, Pavel; Wang, Wei; Ly, Benjamin V; Lewis, Kanako L T; Salzberg, Steven L; Feng, Lu; Jones, Meghan R; Skelton, Rachel L; Murray, Jan E; Chen, Cuixia; Qian, Wubin; Shen, Junguo; Du, Peng; Eustice, Moriah; Tong, Eric; Tang, Haibao; Lyons, Eric; Paull, Robert E; Michael, Todd P; Wall, Kerr; Rice, Danny W; Albert, Henrik; Wang, Ming-Li; Zhu, Yun J; Schatz, Michael; Nagarajan, Niranjan; Acob, Ricelle A; Guan, Peizhu; Blas, Andrea; Wai, Ching Man; Ackerman, Christine M; Ren, Yan; Liu, Chao; Wang, Jianmei; Wang, Jianping; Na, Jong-Kuk; Shakirov, Eugene V; Haas, Brian; Thimmapuram, Jyothi; Nelson, David; Wang, Xiyin; Bowers, John E; Gschwend, Andrea R; Delcher, Arthur L; Singh, Ratnesh; Suzuki, Jon Y; Tripathi, Savarni; Neupane, Kabi; Wei, Hairong; Irikura, Beth; Paidi, Maya; Jiang, Ning; Zhang, Wenli; Presting, Gernot; Windsor, Aaron; Navajas-Pérez, Rafael; Torres, Manuel J; Feltus, F Alex; Porter, Brad; Li, Yingjun; Burroughs, A Max; Luo, Ming-Cheng; Liu, Lei; Christopher, David A; Mount, Stephen M; Moore, Paul H; Sugimura, Tak; Jiang, Jiming; Schuler, Mary A; Friedman, Vikki; Mitchell-Olds, Thomas; Shippen, Dorothy E; dePamphilis, Claude W; Palmer, Jeffrey D; Freeling, Michael; Paterson, Andrew H; Gonsalves, Dennis; Wang, Lei; Alam, Maqsudul

2008-04-24

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

Hypothyroidism In Hepatitis C Patients On Pegylated Interferon Therapy.

Science.gov (United States)

Hameed, Muhammad Asim; Mehmood, Asif; Farooq, Muhammad Ahsan; Tayyab, Ghias Un Nabi; Haq Toor, Israr Ul

2016-01-01

Chronic hepatitis has become a major health problem all over the world especially in the third world countries. The most common cause of chronic hepatitis in Pakistan is hepatitis C which can lead Toliver cirrhosis and hepatocellular carcinoma. In Pakistan Pegylated Interferon Alpha is still corner stone of therapy for chronic hepatitis C. One of the major side effects of this therapy is the development of thyroid dysfunction, i.e., hypothyroidism and hyperthyroidism. This study was done to assess the frequency of hypothyroidism in hepatitis C patients after three months of pegylated interferon therapy. This study was conducted from 1st October 2013 to 31st march 2014 at outpatients department (OPD) of Gastroenterology and Hepatology, Lahore General Hospital Lahore. Descriptive case series study design was used. The sample of 200 patients was taken from the patients who visited OPD and fulfil the inclusion criteria of the study. Serum thyroid stimulating hormone level (TSH) was done before and after completion of three months therapy at centre for Nuclear Medicine (CENUM) laboratory, Mayo Hospital, Lahore by immune-radiometric assay (IRMA) and patients having TSH>4.0 mIU/L (normal range: 0.2-4.0 mIU/L) were considered hypothyroid. The mean age of the patients was 36.29±8.5 years. One hundred and twenty-three (61.5%) were male and 77 (38.5%) were female. After 3 months of interferon therapy, 163 (81.5%) patients were euthyroid and 37(18.5%) patients were having thyroid dysfunction. There were total 29 (14.5%) hypothyroid patients; 8 (27.6%) were male and 21 (72.4%) female. It is concluded from this study that frequency of hypothyroidism in patients with chronic hepatitis C was 14.5% after treatment with pegylated interferon therapy for 3 months. Female patients were more prone to develop hypothyroidism as compared to male patients.

Hepatic encephalopathy associated with hepatic lipidosis in llamas (Lama glama).

Science.gov (United States)

Pillitteri, C A; Craig, L E

2013-01-01

Hepatic encephalopathy has been listed as a differential for llamas displaying neurologic signs, but it has not been histopathologically described. This report details the neurologic histopathologic findings associated with 3 cases of hepatic lipidosis with concurrent neurologic signs and compares them to 3 cases of hepatic lipidosis in the absence of neurologic signs and 3 cases without hepatic lipidosis. Brain from all 3 llamas displaying neurologic signs contained Alzheimer type II cells, which were not detected in either subset of llamas without neurologic signs. Astrocytic immunohistochemical staining intensity for glial fibrillary acid protein was decreased in llamas with neurologic signs as compared to 2 of 3 llamas with hepatic lipidosis and without neurologic signs and to 2 of 3 llamas without hepatic lipidosis. Immunohistochemical staining for S100 did not vary between groups. These findings suggest that hepatic encephalopathy may be associated with hepatic lipidosis in llamas.

Usefulness of screening ultrasonography for hepatocellular carcinoma detection: chronic hepatitis versus hepatic cirrhosis caused by hepatitis B virus

International Nuclear Information System (INIS)

Chang, Sam Uel; Choi, Don Gil; Lim, Jae Hoon

2004-01-01

To evaluate the usefulness of screening liver ultrasonography (US) for hepatocellular carcinoma (HCC) detection in patients with chronic hepatitis or hepatic cirrhosis caused by hepatitis B virus (HBV). A retrospective study was performed with 1,189 patients with clinical hepatopathy caused by HBV who underwent screening liver US for HCC detection at least twice. All patients were followed up with liver US examinations (mean, 8.3 times), CT, or MR for at least 3 months (range, 3-102 months; mean, 47 months) for the detection of HCC. The study population was divided into two groups: chronic hepatitis (n=492) and hepatic cirrhosis (n=697), which was further divided into two groups with (n=156) or without (n=541) evident shrinkage. The radiologic examinations that had detected HCC for the first time were analyzed and compared between the groups. Among 20 (4.1%) patients with chronic hepatitis and 132 (18.9%) patients with hepatic cirrhosis diagnosed as HCC, screening US was the modality of detection in 17 (85.0%) of 20 patients with chronic hepatitis and 76 (57.6%) of 132 patients with hepatic cirrhosis (p=0.038, Chi-square test). The detection rate of HCC on screening US between the chronic hepatitis and hepatic cirrhosis with evident shrinkage (51.4%, 19/37) showed a significant difference (p=0.027, Chi-square test). For chronic liver disease caused by HBV, screening US for HCC detection is more useful in patients with chronic hepatitis than with hepatic cirrhosis with evident shrinkage

Anonymizing patient genomic data for public sharing association studies.

Science.gov (United States)

Fernandez-Lozano, Carlos; Lopez-Campos, Guillermo; Seoane, Jose A; Lopez-Alonso, Victoria; Dorado, Julian; Martín-Sanchez, Fernando; Pazos, Alejandro

2013-01-01

The development of personalized medicine is tightly linked with the correct exploitation of molecular data, especially those associated with the genome sequence along with these use of genomic data there is an increasing demand to share these data for research purposes. Transition of clinical data to research is based in the anonymization of these data so the patient cannot be identified, the use of genomic data poses a great challenge because its nature of identifying data. In this work we have analyzed current methods for genome anonymization and propose a one way encryption method that may enable the process of genomic data sharing accessing only to certain regions of genomes for research purposes.

Perinatal hepatitis B virus detection by hepatitis B virus-DNA analysis.

OpenAIRE

De Virgiliis, S; Frau, F; Sanna, G; Turco, M P; Figus, A L; Cornacchia, G; Cao, A

1985-01-01

Maternal transmission of hepatitis B virus infection in relation to the hepatitis B e antigen/antibody system and serum hepatitis B virus-DNA were evaluated. Results indicate that hepatitis B virus-DNA analysis can identify hepatitis B serum antigen positive mothers who may transmit infection to their offspring.

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.

Science.gov (United States)

Jayakodi, Murukarthick; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Nam-Hoon; Park, Jee Young; Jang, Woojong; Lakshmanan, Meiyappan; Mohan, Shobhana V G; Lee, Dong-Yup; Yang, Tae-Jin

2018-04-12

The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page. This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

Genomic technologies in neonatology

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L. N. Chernova

2017-01-01

Full Text Available In recent years, there has been a tremendous trend toward personalized medicine. Advances in the field forced clinicians, including neonatologists, to take a fresh look at prevention, tactics of management and therapy of various diseases. In the center of attention of foreign, and increasingly Russian, researchers and doctors, there are individual genomic data that allow not only to assess the risks of some form of pathology, but also to successfully apply personalized strategies of prediction, prevention and targeted treatment. This article provides a brief review of the latest achievements of genomic technologies in newborns, examines the problems and potential applications of genomics in promoting the concept of personalized medicine in neonatology. The increasing amount of personalized data simply impossible to analyze only by the human mind. In this connection, the need of computers and bioinformatics is obvious. The article reveals the role of translational bioinformatics in the analysis and integration of the results of the accumulated fundamental research into complete clinical decisions. The latest advances in neonatal translational bioinformatics such as clinical decision support systems are considered. It helps to monitor vital parameters of newborns influencing the course of a particular disease, to calculate the increased risks of the development of various pathologies and to select the drugs.

Genomic Biomarkers for Personalized Medicine: Development and Validation in Clinical Studies

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Shigeyuki Matsui

2013-01-01

Full Text Available The establishment of high-throughput technologies has brought substantial advances to our understanding of the biology of many diseases at the molecular level and increasing expectations on the development of innovative molecularly targeted treatments and molecular biomarkers or diagnostic tests in the context of clinical studies. In this review article, we position the two critical statistical analyses of high-dimensional genomic data, gene screening and prediction, in the framework of development and validation of genomic biomarkers or signatures, through taking into consideration the possible different strategies for developing genomic signatures. A wide variety of biomarker-based clinical trial designs to assess clinical utility of a biomarker or a new treatment with a companion biomarker are also discussed.

The Medicinal Values of Culinary-Medicinal Royal Sun Mushroom (Agaricus blazei Murrill

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Hang Wang

2013-01-01

Full Text Available Agaricus blazei Murrill (ABM, a mushroom native to Brazil, is a basidiomycete brown fungus, which is popularly known as “Cogumelo do Sol” in Brazil or “Himematsutake” in Japan, and there has been a prominent increase in the use of ABM for therapeutic and medicinal purposes. ABM is useful against a variety of diseases like cancer, tumor, chronic hepatitis, diabetes, atherosclerosis, hypercholesterolemia, and so on. In this review, we demonstrated various pharmacological effects of ABM, so that we can use different effects of ABM against different diseases and provide reference for the study of ABM in the future.

Noninvasive diagnosis of hepatic fibrosis in chronic hepatitis C

OpenAIRE

Stauber, Rudolf E; Lackner, Carolin

2007-01-01

Assessment of hepatic fibrosis is important for determining prognosis, guiding management decisions, and monitoring disease. Histological evaluation of liver biopsy specimens is currently considered the reference test for staging hepatic fibrosis. Since liver biopsy carries a small but significant risk, noninvasive tests to assess hepatic fibrosis are desirable. This editorial gives an overview on noninvasive methods currently available to determine hepatic fibrosis and their diagnostic accur...

Personomics: The Missing Link in the Evolution from Precision Medicine to Personalized Medicine

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Roy C. Ziegelstein

2017-10-01

Full Text Available Clinical practice guidelines have been developed for many common conditions based on data from randomized controlled trials. When medicine is informed solely by clinical practice guidelines, however, the patient is not treated as an individual, but rather a member of a group. Precision medicine, as defined herein, characterizes unique biological characteristics of the individual or of specimens obtained from an individual to tailor diagnostics and therapeutics to a specific patient. These unique biological characteristics are defined by the tools of precision medicine: genomics, proteomics, metabolomics, epigenomics, pharmacogenomics, and other “-omics.” Personalized medicine, as defined herein, uses additional information about the individual derived from knowing the patient as a person. These unique personal characteristics are defined by tools known as personomics which takes into account an individual’s personality, preferences, values, goals, health beliefs, social support network, financial resources, and unique life circumstances that affect how and when a given health condition will manifest in that person and how that condition will respond to treatment. In this paradigm, precision medicine may be considered a necessary step in the evolution of medical care to personalized medicine, with personomics as the missing link.

Hepatitis B Foundation

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... worldwide 2 Billion People have been infected with Hepatitis B Worldwide The Hepatitis B Foundation is working ... of people living with hepatitis B. Learn About Hepatitis B in 11 Other Languages . Resource Video See ...

What Is Hepatitis?

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... Navigation Alt+1 Content Alt+2 What is hepatitis? Online Q&A Reviewed July 2016 Q: What ... Question and answer archives Submit a question World Hepatitis Day Posters: Eliminate hepatitis World Hepatitis Day 2017 ...

From Metabonomics to Pharmacometabonomics: The Role of Metabolic Profiling in Personalised Medicine

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Jeremy Everett

2016-09-01

Full Text Available Variable patient responses to drugs are a key issue for medicine and for drug discovery and development. Personalised medicine, that is the selection of medicines for subgroups of patients so as to maximise drug efficacy and minimise toxicity, is a key goal of 21st century healthcare. Currently, most personalised medicine paradigms rely on clinical judgement based on the patient’s history, and on the analysis of the patients’ genome to predict drug effects i.e. pharmacogenomics. However, variability in patient responses to drugs is dependent upon many environmental factors to which human genomics is essentially blind. A new paradigm for predicting drug responses based on individual pre-dose metabolite profiles has emerged in the past decade: pharmacometabonomics, which is defined as ‘the prediction of the outcome (for example, efficacy or toxicity of a drug or xenobiotic intervention in an individual based on a mathematical model of pre-intervention metabolite signatures’. The new pharmacometabonomics paradigm is complementary to pharmacogenomics but has the advantage of being sensitive to environmental as well as genomic factors. This review will chart the discovery and development of pharmacometabonomics, and provide examples of its current utility and possible future developments.

From Metabonomics to Pharmacometabonomics: The Role of Metabolic Profiling in Personalized Medicine

Science.gov (United States)

Everett, Jeremy R.

2016-01-01

Variable patient responses to drugs are a key issue for medicine and for drug discovery and development. Personalized medicine, that is the selection of medicines for subgroups of patients so as to maximize drug efficacy and minimize toxicity, is a key goal of twenty-first century healthcare. Currently, most personalized medicine paradigms rely on clinical judgment based on the patient's history, and on the analysis of the patients' genome to predict drug effects i.e., pharmacogenomics. However, variability in patient responses to drugs is dependent upon many environmental factors to which human genomics is essentially blind. A new paradigm for predicting drug responses based on individual pre-dose metabolite profiles has emerged in the past decade: pharmacometabonomics, which is defined as “the prediction of the outcome (for example, efficacy or toxicity) of a drug or xenobiotic intervention in an individual based on a mathematical model of pre-intervention metabolite signatures.” The new pharmacometabonomics paradigm is complementary to pharmacogenomics but has the advantage of being sensitive to environmental as well as genomic factors. This review will chart the discovery and development of pharmacometabonomics, and provide examples of its current utility and possible future developments. PMID:27660611

Protection of the Extracts of Lentinus edodes Mycelia against Carbon-Tetrachloride-Induced Hepatic Injury in Rats

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Mei-Fen Chen

2012-01-01

Full Text Available Lentinus edodes is the medicinal macrofungus showing potential for therapeutic applications in infectious disorders including hepatitis. In an attempt to develop the agent for handling hepatic injury, we used the extracts of Lentinus edodes mycelia (LEM to screen the effect on hepatic injury in rats induced by carbon tetrachloride (CCl4. Intraperitoneal administration of CCl4 not only increased plasma glutamic oxaloacetic transaminase (GOT and glutamic pyruvic transaminase (GPT but also decreased hepatic superoxide dismutase (SOD and glutathione peroxidase (GPx levels in rats. Similar to the positive control silymarin, oral administration (three times daily of this product (LEM for 8 weeks significantly reduced plasma GOT and GPT. Also, the activities of antioxidant enzymes of SOD and GPx were elevated by LEM. in liver from CCl4-treated rats, indicating that mycelium can increase antioxidant-like activity. Moreover, the hepatic mRNA and protein levels of SOD and GPx were both markedly raised by LEM. The obtained results suggest that oral administration of the extracts of Lentinus edodes mycelia (LEM has the protective effect against CCl4-induced hepatic injury in rats, mainly due to an increase in antioxidant-like action.

Comparative analysis of disease activity in patients of chronic hepatitis B virus, with and without super infection with hepatitis D virus; an experience at tertiary care centre

International Nuclear Information System (INIS)

Hassan, K.D.; Mahmood, T.; Farooq, M.U.

2008-01-01

The hepatitis D virus super-infection contributes significantly to the morbidity and mortality of hepatitis B virus infection. The objectives were to describe the incidence of Hepatitis D virus and comparative analysis of disease activity in patients of chronic hepatitis B virus, with and without super-infection of hepatitis D virus. This Cross-sectional comparative study was conducted at Department of Medicine and Gastroenterology Clinic Jinnah Postgraduate Medical Centre, Karachi, Pakistan from February 2007 to July 2007. HBsAg positive patients who attended our Gastroenterology clinic were selected for the study. After screening for Anti-HDV these patients were segregated in to Anti-HDV positive and negative groups. Data was analyzed on SPSS 12. Eighty-four patients were selected. Seventy-three patients who fulfilled the inclusion criteria were enrolled in to the study. Anti-HDV was positive in 23 (31.5%) patients. Among these 23 anti-HDV positive, HDV-RNA was detected in 15 (75%) patients. The differences of age, gender, marital status and area of residence whether rural or urban were not significant between the two groups. HBV-DNA was significantly suppressed in majority of anti- HDV positive patients (p=0.019). Mean serum ALT levels were significantly higher in patients who had HDV infection (p=0.014). HDV infection was common in this series of patients with a frequency of 31.5%. All patients of chronic HBV should be screened for HDV whether they are asymptomatic HBV carriers or have chronic active hepatitis particularly when they have raised serum ALT. (author)

Recombination in hepatitis C virus.

Science.gov (United States)

González-Candelas, Fernando; López-Labrador, F Xavier; Bracho, María Alma

2011-10-01

Hepatitis C virus (HCV) is a Flavivirus with a positive-sense, single-stranded RNA genome of about 9,600 nucleotides. It is a major cause of liver disease, infecting almost 200 million people all over the world. Similarly to most RNA viruses, HCV displays very high levels of genetic diversity which have been used to differentiate six major genotypes and about 80 subtypes. Although the different genotypes and subtypes share basic biological and pathogenic features they differ in clinical outcomes, response to treatment and epidemiology. The first HCV recombinant strain, in which different genome segments derived from parentals of different genotypes, was described in St. Petersburg (Russia) in 2002. Since then, there have been only a few more than a dozen reports including descriptions of HCV recombinants at all levels: between genotypes, between subtypes of the same genotype and even between strains of the same subtype. Here, we review the literature considering the reasons underlying the difficulties for unequivocally establishing recombination in this virus along with the analytical methods necessary to do it. Finally, we analyze the potential consequences, especially in clinical practice, of HCV recombination in light of the coming new therapeutic approaches against this virus.

Detection of Hepatitis B Virus (HBV) Genomes and HBV Drug Resistant Variants by Deep Sequencing Analysis of HBV Genomes in Immune Cell Subsets of HBV Mono-Infected and/or Human Immunodeficiency Virus Type-1 (HIV-1) and HBV Co-Infected Individuals

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Lee, Z.; Nishikawa, S.; Gao, S.; Eksteen, J. B.; Czub, M.; Gill, M. J.; Osiowy, C.; van der Meer, F.; van Marle, G.; Coffin, C. S.

2015-01-01

The hepatitis B virus (HBV) and the human immunodeficiency virus type 1 (HIV-1) can infect cells of the lymphatic system. It is unknown whether HIV-1 co-infection impacts infection of peripheral blood mononuclear cell (PBMC) subsets by the HBV. Aims To compare the detection of HBV genomes and HBV sequences in unsorted PBMCs and subsets (i.e., CD4+ T, CD8+ T, CD14+ monocytes, CD19+ B, CD56+ NK cells) in HBV mono-infected vs. HBV/HIV-1 co-infected individuals. Methods Total PBMC and subsets isolated from 14 HBV mono-infected (4/14 before and after anti-HBV therapy) and 6 HBV/HIV-1 co-infected individuals (5/6 consistently on dual active anti-HBV/HIV therapy) were tested for HBV genomes, including replication indicative HBV covalently closed circular (ccc)-DNA, by nested PCR/nucleic hybridization and/or quantitative PCR. In CD4+, and/or CD56+ subsets from two HBV monoinfected cases, the HBV polymerase/overlapping surface region was analyzed by next generation sequencing. Results All analyzed whole PBMC from HBV monoinfected and HBV/HIV coinfected individuals were HBV genome positive. Similarly, HBV DNA was detected in all target PBMC subsets regardless of antiviral therapy, but was absent from the CD4+ T cell subset from all HBV/HIV-1 positive cases (PHBV monoinfected cases on tenofovir therapy, mutations at residues associated with drug resistance and/or immune escape (i.e., G145R) were detected in a minor percentage of the population. Summary HBV genomes and drug resistant variants were detectable in PBMC subsets from HBV mono-infected individuals. The HBV replicates in PBMC subsets of HBV/HIV-1 patients except the CD4+ T cell subpopulation. PMID:26390290

Diagnostic value of liver scintigraphy in fulminant hepatitis and severe acute hepatitis