4.7 Article

Frequencies of pharmacogenomic alleles across biogeographic groups in a large-scale biobank

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation

Shaohua Fan et al.

Summary: By conducting whole-genome sequencing of indigenous African populations, we identified numerous unreported variants and observed evidence of ancient population structure and introgression events from highly diverged ''ghost'' populations. We also found signatures of local adaptation for traits related to skin color, immune response, height, and metabolic processes.
Article Pharmacology & Pharmacy

Expanded Clinical Pharmacogenetics Implementation Consortium Guideline for Medication Use in the Context of G6PD Genotype

Roseann S. Gammal et al.

Summary: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is associated with the development of acute hemolytic anemia in the presence of oxidative stress. This guideline provides information on using G6PD genotype for diagnosing G6PD deficiency and categorizes medications based on their risk level in individuals with G6PD deficiency. High-risk medications should be avoided, medium-risk medications should be used with caution, and low-risk medications can be used without considering the G6PD phenotype.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2023)

Article Multidisciplinary Sciences

Pharmacogenetic allele variant frequencies: An analysis of the VA's Million Veteran Program (MVP) as a representation of the diversity in US population

Kyriacos Markianos et al.

Summary: We provide allele frequencies of pharmacogenomics relevant variants in different populations in the US. We analyzed genotype data from 658,582 individuals and extracted allele frequencies for single nucleotide variants (SNVs), human leukocyte antigens (HLA) 4-digit alleles, and the complete deletion/duplication of CYP2D6, an important copy number variant (CNV). We compiled distinct allele frequency tables for European, African American, Hispanic, and Asian populations, as well as allele frequencies based on local ancestry reconstruction in African American and Hispanic cohorts.

PLOS ONE (2023)

Article Pharmacology & Pharmacy

How to Run the Pharmacogenomics Clinical Annotation Tool (PharmCAT)

Binglan Li et al.

Summary: Pharmacogenomics (PGx) investigates the genetic influence on drug response and is important for precision medicine. The challenge lies in interpreting PGx testing results for clinical decision support. PharmCAT has been designed to provide automatic interpretations of patient genetic data and generate reports with guideline recommendations. It has introduced new features, such as a VCF Preprocessor and functionalities for PGx research.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2023)

Article Pathology

CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype AnalysisA GeT-RM Collaborative Project

Andrea Gaedigk et al.

Summary: This study demonstrates the utility of NGS for pharmacogenetic testing and reveals the presence of many undiscovered novel alleles.

JOURNAL OF MOLECULAR DIAGNOSTICS (2022)

Article Genetics & Heredity

Pharmacogenetics in developing countries and low resource environments

Said El Shamieh et al.

Summary: Developing countries face challenges in pharmacogenetics research and clinical applications, including fewer researchers and slower clinical implementation progress. To move PGx forward in developing countries, it is recommended to enhance regional and multinational collaborations, upgrade genotyping capabilities, implement next-generation sequencing, and organize specialized training and exchange programs.

HUMAN GENETICS (2022)

Article Biochemistry & Molecular Biology

Dutch Pharmacogenetics Working Group (DPWG) guideline for the gene-drug interaction between CYP2D6 and opioids (codeine, tramadol and oxycodone)

Maja Matic et al.

Summary: The guideline describes the gene-drug interaction between CYP2D6 and the opioids codeine, tramadol and oxycodone, categorizing individuals into different metabolizer types based on genotype. Specific recommendations are provided for each metabolizer type when using these drugs to ensure safe and effective treatment.

EUROPEAN JOURNAL OF HUMAN GENETICS (2022)

Article Medicine, Research & Experimental

Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population

Shefali S. Verma et al.

Summary: This study evaluated the opportunities for genetically guided medication prescribing and determined the frequencies of actionable PGx alleles in an ancestrally diverse biobank population. The results showed that clinically actionable PGx alleles were highly prevalent in the health system and many patients were prescribed medications that could be impacted by their genotype. These findings highlight the potential utility of preemptive genotyping for personalized medication selection and implementation of PGx into routine clinical care.

JOURNAL OF TRANSLATIONAL MEDICINE (2022)

Article Multidisciplinary Sciences

The sequences of 150,119 genomes in the UK Biobank

Bjarni Halldorsson et al.

Summary: A comprehensive understanding of how diversity in the human genome sequence affects phenotypic diversity relies on a reliable characterization of both sequences and phenotypic variation. In this study, whole-genome sequencing of 150,119 individuals from the UK Biobank was performed, leading to insights into the relationship between sequence variation and phenotypic traits. The analysis revealed rare variants with large effects, which were not previously identified through whole-exome sequencing and/or imputation studies.

NATURE (2022)

Article Pharmacology & Pharmacy

Importance of Rare DPYD Genetic Polymorphisms for 5-Fluorouracil Therapy in the Japanese Population

Eiji Hishinuma et al.

Summary: In this study, an in vitro analysis was conducted on 41 DPD allelic variants to investigate changes in enzymatic activity, with 7 variants showing significantly decreased activity and 2 variants displaying no enzymatic activity. Our findings suggest that DPD dimerization is essential for enzymatic activity and these variants may contribute to the observed inter-individual variability in the pharmacokinetics and pharmacodynamics of 5-FU. Additionally, rare DPYD variants, although at low frequencies, could serve as important pharmacogenomic markers associated with severe 5-FU toxicity in the Japanese population.

FRONTIERS IN PHARMACOLOGY (2022)

Article Biochemistry & Molecular Biology

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

Marta Byrska-Bishop et al.

Summary: The 1000 Genomes Project is the largest open resource of whole-genome sequencing data, and a new high-coverage WGS 1kGP resource has been released, improving the sensitivity and accuracy of variant calls and making it more valuable for association studies.
Article Pharmacology & Pharmacy

Global Frequencies of Clinically ImportantHLAAlleles and Their Implications For the Cost-Effectiveness of Preemptive Pharmacogenetic Testing

Yitian Zhou et al.

Summary: Cost-effectiveness of preemptive HLA genotyping varies significantly across countries and regions, with some regions showing lower cost-effectiveness of testing for HLA alleles.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Review Pharmacology & Pharmacy

PharmVar GeneFocus: CYP2C19

Mariana R. Botton et al.

Summary: Genetic variation in the CYP2C19 gene impacts the metabolism of many drugs and is associated with efficacy and safety issues for several commonly prescribed medications. The PharmVar catalogued haplotype information is utilized by the Pharmacogenomics Knowledgebase and CPIC.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Article Pharmacology & Pharmacy

Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline forCYP2C19and Proton Pump Inhibitor Dosing

John J. Lima et al.

Summary: Using CYP2C19 genotype data to guide PPI therapy can help identify patients who may need higher doses for efficacy and those who may benefit from lower doses to reduce the risk of toxicity associated with long-term use at higher plasma concentrations.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Review Pharmacology & Pharmacy

Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline forCYP2C9andHLA-BGenotypes and Phenytoin Dosing: 2020 Update

Jason H. Karnes et al.

Summary: Phenytoin, an antiepileptic drug, is influenced by genetic variations in patients, with individuals carrying the variant allele HLA-B*15:02 having an increased risk of severe skin reactions when receiving phenytoin treatment.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Article Pharmacology & Pharmacy

Pharmacogenetics at Scale: An Analysis of the UK Biobank

Gregory McInnes et al.

Summary: Pharmacogenetics studies the influence of genetic variation on drug response, finding that the majority of individuals may have atypical responses to at least one drug and on average have atypical responses to 10.3 drugs. Nearly a quarter of participants have been prescribed drugs for which they are predicted to have atypical responses.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Editorial Material Genetics & Heredity

Expanding evidence leads to new pharmacogenomics payer coverage

Philip E. Empey et al.

GENETICS IN MEDICINE (2021)

Article Multidisciplinary Sciences

Exome sequencing and analysis of 454,787 UK Biobank participants

Joshua D. Backman et al.

Summary: In this study, whole-exome sequencing was used to identify gene-trait associations in 454,787 individuals, revealing 564 distinct genes with significant trait associations. Rare variant associations were enriched in loci from genome-wide association studies (GWAS) but most were independent of common variant signals.

NATURE (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Pathology

Characterization of Reference Materials with an Association for Molecular Pathology Pharmacogenetics Working Group Tier 2 Status: CYP2C9, CYP2C19, VKORC1, CYP2C Cluster Variant, and GGCX A GeT-RM Collaborative Project

Victoria M. Pratt et al.

Summary: Pharmacogenetic testing is becoming more widely available in clinical and research laboratories, but many tested variants lack quality control and reference materials. To address this issue, the GeT-RM program collaborated with laboratory and research communities to characterize 18 DNA samples from Coriell cell lines, supporting the quality control programs of clinical laboratories conducting pharmacogenetic testing. Multiple tier 2 variants were identified among these samples, providing valuable resources for laboratories performing pharmacogenetic testing.

JOURNAL OF MOLECULAR DIAGNOSTICS (2021)

Article Pharmacology & Pharmacy

An Evidence-Based Framework for Evaluating Pharmacogenomics Knowledge for Personalized Medicine

Michelle Whirl-Carrillo et al.

Summary: Clinical annotations in PharmGKB summarize the association between variant-drug pairs and are assigned a level of evidence. To ensure consistency and transparency, a scoring system has been developed to automate LOE assignment. This system improves the quality and reliability of clinical annotations.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Editorial Material Pharmacology & Pharmacy

Pharmacogene Variation Consortium: A Global Resource and Repository for Pharmacogene Variation

Andrea Gaedigk et al.

Summary: PharmVar, founded in 2017, has provided the research and clinical pharmacogenetics/genomics communities with essential information on flagship pharmacogenes such as CYP2C9, CYP2C19, and CYP2D6 for the past four years. The consortium highlights recent milestones and standardization efforts in this Perspective.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Article Genetics & Heredity

Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank

Joseph D. Szustakowski et al.

Summary: The UK Biobank Exome Sequencing Consortium is a successful collaborative project between UK Biobank and biopharmaceutical companies, providing valuable rare coding variation resources for drug discovery. The project has strengthened academic and industry ties and promoted interaction and learning within the wider research community.

NATURE GENETICS (2021)

Review Pharmacology & Pharmacy

PharmVar GeneFocus: CYP2C19

Mariana R. Botton et al.

Summary: This article introduces the star (*) allele nomenclature for the polymorphic human CYP2C19 gene catalogued by PharmVar, and highlights the impact of CYP2C19 genetic variation on drug metabolism, as well as how haplotype information compiled by PharmVar is utilized by CPIC.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2021)

Article Pharmacology & Pharmacy

Pharmacogenomics Clinical Annotation Tool (PharmCAT)

Katrin Sangkuhl et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2020)

Review Pharmacology & Pharmacy

The Clinical Pharmacogenetics Implementation Consortium: 10 Years Later

Mary V. Relling et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2020)

Editorial Material Pharmacology & Pharmacy

PharmVar and the Landscape of Pharmacogenetic Resources

Andrea Gaedigk et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2020)

Article Biochemistry & Molecular Biology

The International Genome Sample Resource (IGSR) collection of open human genomic variation resources

Susan Fairley et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Pharmacology & Pharmacy

Coverage of pharmacogenetic tests by private health insurance companies

Sharon K. Park et al.

JOURNAL OF THE AMERICAN PHARMACISTS ASSOCIATION (2020)

Article Pharmacology & Pharmacy

Clinical Pharmacogenetics Implementation Consortium Guideline (CPIC) for CYP2C9 and Nonsteroidal Anti-Inflammatory Drugs

Katherine N. Theken et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2020)

Article Genetics & Heredity

The landscape of pharmacogenetic testing in a US managed care population

Heather D. Anderson et al.

GENETICS IN MEDICINE (2020)

Article Multidisciplinary Sciences

Exome sequencing and characterization of 49,960 individuals in the UK Biobank

Cristopher V. Van Hout et al.

NATURE (2020)

Correction Biochemistry & Molecular Biology

The Missing Diversity in Human Genetic Studies (vol 177, pg 26, 2019)

Giorgio Sirugo et al.

Article Pharmacology & Pharmacy

Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2B6 and Efavirenz-Containing Antiretroviral Therapy

Zeruesenay Desta et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2019)

Article Medicine, General & Internal

The All of Us Research Program

NEW ENGLAND JOURNAL OF MEDICINE (2019)

Article Pharmacology & Pharmacy

Standardized Biogeographic Grouping System for Annotating Populations in Pharmacogenetic Research

Rachel Huddart et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2019)

Article Multidisciplinary Sciences

The UK Biobank resource with deep phenotyping and genomic data

Clare Bycroft et al.

NATURE (2018)

Article Pharmacology & Pharmacy

The Pharmacogene Variation (PharmVar) Consortium: Incorporation of the Human Cytochrome P450 (CYP) Allele Nomenclature Database

Andrea Gaedigk et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2018)

Article Public, Environmental & Occupational Health

Overview of the BioBank Japan Project: Study design and profile

Akiko Nagai et al.

JOURNAL OF EPIDEMIOLOGY (2017)

Article Pharmacology & Pharmacy

Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for Pharmacogenetics-Guided Warfarin Dosing: 2017 Update

J. A. Johnson et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2017)

Article Pharmacology & Pharmacy

Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines for CYP2C19 and Voriconazole Therapy

B. Moriyama et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2017)

Article Health Care Sciences & Services

Million Veteran Program: A mega-biobank to study genetic influences on health and disease

John Michael Gaziano et al.

JOURNAL OF CLINICAL EPIDEMIOLOGY (2016)

Editorial Material Medicine, General & Internal

Medical error-the third leading cause of death in the US

Martin A. Makary et al.

BMJ-BRITISH MEDICAL JOURNAL (2016)

Editorial Material Medicine, General & Internal

Medical error-the third leading cause of death in the US

Martin A. Makary et al.

BMJ-BRITISH MEDICAL JOURNAL (2016)

Review Pharmacology & Pharmacy

Preemptive Clinical Pharmacogenetics Implementation: Current Programs in Five US Medical Centers

Henry M. Dunnenberger et al.

ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 55 (2015)

Article Biochemical Research Methods

Unified representation of genetic variants

Adrian Tan et al.

BIOINFORMATICS (2015)

Review Genetics & Heredity

Cystic fibrosis genetics: from molecular understanding to clinical application

Garry R. Cutting

NATURE REVIEWS GENETICS (2015)

Article Genetics & Heredity

PG4KDS: A model for the clinical implementation of pre-emptive pharmacogenetics

James M. Hoffman et al.

AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS (2014)

Article Pharmacology & Pharmacy

Clinical Pharmacogenetics Implementation Consortium (CPIC) Guidelines for Ivacaftor Therapy in the Context of CFTR Genotype

J. P. Clancy et al.

CLINICAL PHARMACOLOGY & THERAPEUTICS (2014)

Article Genetics & Heredity

Prevalence of Clinically Relevant UGT1A Alleles and Haplotypes in African Populations

Laura J. Horsfall et al.

ANNALS OF HUMAN GENETICS (2011)