ArticleThe Journal of molecular diagnostics : JMD2022
CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis: A GeT-RM Collaborative Project.
Article in The Journal of molecular diagnostics : JMD, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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The trial behind it
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Who cites it
30 citing papers in PubMed.
- Characterization of NAT2 Using Long-Read Sequencing: Allele, Diplotype, and Phenotype Call Accuracy Compared to Other Testing Strategies.Clinical pharmacology and therapeutics · 2026Article
- Benchmark of Open-Access Star-Allele Callers to Accurately Assess Haplotypes and Phenotypes in Pharmacogenetic Studies.Clinical pharmacology and therapeutics · 2026Article
- Genome Sequencing Enhances Precision and Clinical Utility of Pharmacogenetic Data Compared to Arrays.Journal of clinical pharmacology · 2026Article
- Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping.Scientific reports · 2025Article
- New Resources to Identify Characterized DNA Reference Materials for Pharmacogenetic (PGx) and Human Leukocyte Antigen (HLA) Testing: The Genetic Testing Reference Material (GeT-RM) Program PGx Search Tool and GeT-RM Consolidated PGx and HLA Table.The Journal of molecular diagnostics : JMD · 2025Article
- French-Speaking Network of Pharmacogenetics (RNPGx) Recommendations for Clinical Use of Mavacamten.Clinical pharmacology and therapeutics · 2025Review
- Leveraging long-read sequencing technologies for pharmacogenomic testing: applications, analytical strategies, challenges, and future perspectives.Frontiers in genetics · 2025Review
- StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data.bioRxiv : the preprint server for biology · 2024Article
- PharmVar GeneFocus: CYP4F2.Clinical pharmacology and therapeutics · 2024Review
- Characterization of Reference Materials for DPYD: A GeT-RM Collaborative Project.The Journal of molecular diagnostics : JMD · 2024Article
- Benchmarking pharmacogenomics genotyping tools: Performance analysis on short-read sequencing samples and depth-dependent evaluation.Clinical and translational science · 2024Article
- A comprehensive Thai pharmacogenomics database (TPGxD-1): Phenotype prediction and variants identification in 942 whole-genome sequencing data.Clinical and translational science · 2024Article
- Influence of novel CYP2C-haplotype on proton pump inhibitor pharmacokinetics in children.Clinical and translational science · 2024Article
- Star allele search: a pharmacogenetic annotation database and user-friendly search tool of publicly available 1000 Genomes Project biospecimens.BMC genomics · 2024Article
- Geny: a genotyping tool for allelic decomposition of killer cell immunoglobulin-like receptor genes.Frontiers in immunology · 2024Article
- Exploratory focused pharmacogenetic testing reveals novel markers associated with risperidone pharmacokinetics in Saudi children with autism.Frontiers in pharmacology · 2024Article
- Development and validation of a pharmacogenomics reporting workflow based on the illumina global screening array chip.Frontiers in pharmacology · 2024Article
- ursaPGx: a new R package to annotate pharmacogenetic star alleles using phased whole-genome sequencing data.Frontiers in bioinformatics · 2024Article
- Frequencies of pharmacogenomic alleles across biogeographic groups in a large-scale biobank.American journal of human genetics · 2023Article
- The Genetic Testing Reference Materials Coordination Program: Over 10 Years of Support for Pharmacogenomic Testing.The Journal of molecular diagnostics : JMD · 2023Article
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
Pharmacogenetic tests typically target selected sequence variants to identify haplotypes that are often defined by star (∗) allele nomenclature. Due to their design, these targeted genotyping assays are unable to detect novel variants that may change the function of the gene product and thereby affect phenotype prediction and patient care. In the current study, 137 DNA samples that were previously characterized by the Genetic Testing Reference Material (GeT-RM) program using a variety of targeted genotyping methods were recharacterized using targeted and whole genome sequencing analysis. Sequence data were analyzed using three genotype calling tools to identify star allele diplotypes for CYP2C8, CYP2C9, and CYP2C19. The genotype calls from next-generation sequencing (NGS) correlated well to those previously reported, except when novel alleles were present in a sample. Six novel alleles and 38 novel suballeles were identified in the three genes due to identification of variants not covered by targeted genotyping assays. In addition, several ambiguous genotype calls from a previous study were resolved using the NGS and/or long-read NGS data. Diplotype calls were mostly consistent between the calling algorithms, although several discrepancies were noted. This study highlights the utility of NGS for pharmacogenetic testing and demonstrates that there are many novel alleles that are yet to be discovered, even in highly characterized genes such as CYP2C9 and CYP2C19.
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