ArticleFrontiers in oncology2023
Computational pharmacogenotype extraction from clinical next-generation sequencing.
Article in Frontiers in oncology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed, 11 citations in OpenAlex.
- Benchmark of Open-Access Star-Allele Callers to Accurately Assess Haplotypes and Phenotypes in Pharmacogenetic Studies.Clinical pharmacology and therapeutics · 2026Article
- Analytical Validation of an Annotation Tool for WGS-Based Pharmacogenomics: Preparing for Clinical Implementation in Pediatric Oncology.Clinical and translational science · 2026Article
- Pharmacogenomic Calling From Whole-Exome Sequencing in the Taiwanese Population-A Real-World Experience.Molecular genetics & genomic medicine · 2026Article
- Enrichment of Germline Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Pathogenic Variants in Patients With Solid Tumors: Evidence for Increased Cancer Risk.Pediatric pulmonology · 2025Article
- Return of Clinically Actionable Pharmacogenetic Results From Molecular Tumor Board DNA Sequencing Data: Workflow and Estimated Costs.Clinical pharmacology and therapeutics · 2025Article
- Development of a Multifaceted Program for Pharmacogenetics Adoption at an Academic Medical Center: Practical Considerations and Lessons Learned.Clinical pharmacology and therapeutics · 2024Article
- A comprehensive Thai pharmacogenomics database (TPGxD-1): Phenotype prediction and variants identification in 942 whole-genome sequencing data.Clinical and translational science · 2024Article
- Geny: a genotyping tool for allelic decomposition of killer cell immunoglobulin-like receptor genes.Frontiers in immunology · 2024Article
- Targeted haplotyping in pharmacogenomics using Oxford Nanopore Technologies' adaptive sampling.Frontiers in pharmacology · 2023Article
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 2 countries.
Funding
Abstract
Background: Next-generation sequencing (NGS), including whole genome sequencing (WGS) and whole exome sequencing (WES), is increasingly being used for clinic care. While NGS data have the potential to be repurposed to support clinical pharmacogenomics (PGx), current computational approaches have not been widely validated using clinical data. In this study, we assessed the accuracy of the Aldy computational method to extract PGx genotypes from WGS and WES data for 14 and 13 major pharmacogenes, respectively. Methods: Germline DNA was isolated from whole blood samples collected for 264 patients seen at our institutional molecular solid tumor board. DNA was used for panel-based genotyping within our institutional Clinical Laboratory Improvement Amendments- (CLIA-) certified PGx laboratory. DNA was also sent to other CLIA-certified commercial laboratories for clinical WGS or WES. Aldy v3.3 and v4.4 were used to extract PGx genotypes from these NGS data, and results were compared to the panel-based genotyping reference standard that contained 45 star allele-defining variants within Results: Mean WGS read depth was >30x for all variant regions except for Conclusion: Aldy v3.3 and v4.4 called diplotypes for major pharmacogenes from clinical WES and WGS data with >99% accuracy. These findings support the use of Aldy to repurpose clinical NGS data to inform clinical PGx.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.