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Rachel Huddart, J Steven Leeder, Russ B Altman, Teri E Klein
No abstract text is available yet for this article.
April 2018: Pharmacogenetics and Genomics
Maria Alvarellos, Chantal Guillemette, Russ B Altman, Teri E Klein
No abstract text is available yet for this article.
March 6, 2018: Pharmacogenetics and Genomics
Bethany Percha, Russ B Altman
Motivation: The biomedical community's collective understanding of how chemicals, genes, and phenotypes interact is distributed across the text of over 24 million research articles. These interactions offer insights into the mechanisms behind higher order biochemical phenomena, such as drug-drug interactions and variations in drug response across individuals. To assist their curation at scale, we must understand what relationship types are possible and map unstructured natural language descriptions onto these structured classes...
February 27, 2018: Bioinformatics
Julia M Barbarino, Michelle Whirl-Carrillo, Russ B Altman, Teri E Klein
As precision medicine becomes increasingly relevant in healthcare, the field of pharmacogenomics (PGx) also continues to gain prominence in the clinical setting. Leading institutions have begun to implement PGx testing and the amount of published PGx literature increases yearly. The Pharmacogenomics Knowledgebase (PharmGKB; is one of the foremost worldwide resources for PGx knowledge, and the organization has been adapting and refocusing its mission along with the current revolution in genomic medicine...
February 23, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
Mengdan Yan, Dianzhen Li, Guige Zhao, Jing Li, Fanglin Niu, Bin Li, Peng Chen, Tianbo Jin
INTRODUCTION: Drug response and target therapeutic dosage are different among individuals. The variability is largely genetically determined. With the development of pharmacogenetics and pharmacogenomics, widespread research have provided us a wealth of information on drug-related genetic polymorphisms, and the very important pharmacogenetic (VIP) variants have been identified for the major populations around the world whereas less is known regarding minorities in China, including the Yi ethnic group...
January 11, 2018: Gene
Bani Tamraz, Yong Huang, Audrey L French, Seble Kassaye, Kathryn Anastos, Marek J Nowicki, Stephen Gange, Deborah R Gustafson, Peter Bacchetti, Ruth M Greenblatt, Pirro G Hysi, Bradley E Aouizerat
Hair provides a direct measure of long-term exposure of atazanavir (ATV). We report the results of the first genome-wide association study (GWAS) of ATV exposure measured in hair in an observational cohort representative of U.S. women living with HIV; the Women's Interagency HIV Study. Approximately 14.1 million SNPs were analyzed in linear regression-based GWAS, with replication, adjusted for non-genetic predictors collected under conditions of actual use of ATV in 398 participants. Lastly, the PharmGKB database was used to identify pharmacogene associations with ATV exposure...
January 9, 2018: Clinical Pharmacology and Therapeutics
A S M Ashique Mahmood, Shruti Rao, Peter McGarvey, Cathy Wu, Subha Madhavan, K Vijay-Shanker
Tumor molecular profiling plays an integral role in identifying genomic anomalies which may help in personalizing cancer treatments, improving patient outcomes and minimizing risks associated with different therapies. However, critical information regarding the evidence of clinical utility of such anomalies is largely buried in biomedical literature. It is becoming prohibitive for biocurators, clinical researchers and oncologists to keep up with the rapidly growing volume and breadth of information, especially those that describe therapeutic implications of biomarkers and therefore relevant for treatment selection...
2017: PloS One
W C Tan-Koi, P C Leow, Y Y Teo
With rapid developments of pharmacogenomics (PGx) and regulatory science, it is important to understand the current PGx integration in product life cycle, impact on clinical practice thus far and opportunities ahead. We conducted a cross-sectional review on PGx-related regulatory documents and implementation guidelines in the United States and Europe. Our review found that although PGx-related guidance in both markets span across the entire product life cycle, the scope of implementation guidelines varies across two continents...
December 5, 2017: Pharmacogenomics Journal
Antonio Solano Román, Verónica Alfaro, Carlos Cruz, Allan Orozco Solano
Motivation: VizGVar was designed to meet the growing need of the research community for improved genomic and proteomic data viewers that benefit from better information visualization. Results: We implemented a new information architecture and applied user centered design principles to provide a new improved way of visualizing genetic information and protein data related to human disease. VizGVar connects the entire database of Ensembl protein motifs, domains, genes and exons with annotated SNPs and somatic variations from PharmGKB and COSMIC...
October 30, 2017: Bioinformatics
Eunyong Ahn, Taesung Park
Functional rare variants in drug-related genes are believed to be highly differentiated between ethnic- or racial populations. However, knowledge of population differentiation (PD) of rare single-nucleotide variants (SNVs), remains widely lacking, with the highest fixation indices, (Fst values), from both rare and common variants annotated to specific genes, having only been marginally used to understand PD at the gene level. In this study, we suggest a new, gene-based PD method, PD of Rare and Common variants (PDRC), for analyzing rare variants, as inspired by Generalized Cochran-Mantel-Haenszel (GCMH) statistics, to identify highly population-differentiated drug response-related genes ("pharmacogenes")...
September 4, 2017: Scientific Reports
Alison E Fohner, Deanna J Brackman, Kathleen M Giacomini, Russ B Altman, Teri E Klein
No abstract text is available yet for this article.
November 2017: Pharmacogenetics and Genomics
Caroline F Thorn, Manish R Sharma, Russ B Altman, Teri E Klein
No abstract text is available yet for this article.
August 2017: Pharmacogenetics and Genomics
Jing Zhu, Michele Klein-Fedyshin, James M Stevenson
Selective serotonin reuptake inhibitors (SSRIs) are first-line pharmacotherapy for mood and anxiety disorders. The common mechanism of drugs in this class is antagonism of the serotonin transporter. Within the serotonin transporter gene SLC6A4, two polymorphic sites termed 5-HTTLPR and STin2 are proposed to have functional consequences and thus have been attractive candidates for pharmacogenetic studies of SSRI efficacy and tolerability. This review summarizes approximately 15 years of study of these polymorphisms as they relate to SSRI tolerability phenotypes...
September 2017: Pharmacotherapy
Mengfei Lu, Cathryn M Lewis, Matthew Traylor
BACKGROUND: Rapid advances in scientific research have led to an increase in public awareness of genetic testing and pharmacogenetics. Direct-to-consumer (DTC) genetic testing companies, such as 23andMe, allow consumers to access their genetic information directly through an online service without the involvement of healthcare professionals. Here, we evaluate the clinical relevance of pharmacogenetic tests reported by 23andMe in their UK tests. METHODS: The research papers listed under each 23andMe report were evaluated, extracting information on effect size, sample size and ethnicity...
June 19, 2017: BMC Medical Genomics
Blaz Skrlj, Janez Konc, Tanja Kunej
Protein interactions (PI) underlie complex biological processes. Protein interaction partners include DNA, RNA, ions, small chemical compounds, and proteins (protein-protein interactions; PPI). Analysis of sequence variants within regions corresponding to experimentally validated PI sites presents novel opportunities for understanding of complex diseases. Such information has not been systematically collected due to the fact that datasets are dispersed throughout databases and publications. Sequence variants and PI regions were obtained from the UniProt database...
April 28, 2017: Molecular Informatics
Li Gong, Marilyn M Giacomini, Craig Giacomini, Michael L Maitland, Russ B Altman, Teri E Klein
No abstract text is available yet for this article.
June 2017: Pharmacogenetics and Genomics
Katrina M Romagnoli, Richard D Boyce, Philip E Empey, Yifan Ning, Solomon Adams, Harry Hochheiser
Objective: To develop and evaluate a pharmacogenomics information resource for pharmacists. Materials and Methods: We built a pharmacogenomics information resource presenting Food and Drug Administration (FDA) drug product labelling information, refined it based on feedback from pharmacists, and conducted a comparative usability evaluation, measuring task completion time, task correctness and perceived usability. Tasks involved hypothetical clinical situations requiring interpretation of pharmacogenomics information to determine optimal prescribing for specific patients...
July 1, 2017: Journal of the American Medical Informatics Association: JAMIA
Ingrid Fricke-Galindo, Adrián LLerena, Marisol López-López
Adverse drug reactions (ADRs) are considered as an important cause of morbidity and mortality. The hypersensitivity reactions are immune-mediated ADRs, which are dose-independent, unpredictable and have been associated with several HLA alleles. The present review aimed to describe HLA alleles that have been associated with different ADRs in populations worldwide, the recommendations of regulatory agencies and pharmacoeconomic information and databases for the study of HLA alleles in pharmacogenetics. A systematic search was performed in June 2016 of articles relevant to this issue in indexed journals and in scientific databases (PubMed and PharmGKB)...
May 24, 2017: Drug Metabolism and Personalized Therapy
Julia M Barbarino, Aniwaa Owusu Obeng, Teri E Klein, Russ B Altman
No abstract text is available yet for this article.
May 2017: Pharmacogenetics and Genomics
Alison E Fohner, Alex Sparreboom, Russ B Altman, Teri E Klein
No abstract text is available yet for this article.
April 2017: Pharmacogenetics and Genomics
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