ArticleThe Journal of molecular diagnostics : JMD2022
Analytical Validation of a Computational Method for Pharmacogenetic Genotyping from Clinical Whole Exome Sequencing.
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 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
12 citing papers in PubMed, 13 citations in OpenAlex.
- 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
- Analytical Validation of an Annotation Tool for WGS-Based Pharmacogenomics: Preparing for Clinical Implementation in Pediatric Oncology.Clinical and translational science · 2026Article
- Cohort Study to Determine the Impact of CYP3A5 Genotype on Tacrolimus Dosing Requirements and Trough Concentrations in Heart Transplant Recipients.Pharmacotherapy · 2026Article
- 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
- Geny: a genotyping tool for allelic decomposition of killer cell immunoglobulin-like receptor genes.Frontiers in immunology · 2024Article
- Implementation of Clinical Cytochrome P450 3A Genotyping for Tacrolimus Dosing in a Large Kidney Transplant Program.Journal of clinical pharmacology · 2023Article
- Cytochrome P450 Oxidoreductase (POR) Associated with Severe Paclitaxel-Induced Peripheral Neuropathy in Patients of European Ancestry from ECOG-ACRIN E5103.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Article
- Computational pharmacogenotype extraction from clinical next-generation sequencing.Frontiers in oncology · 2023Article
- An efficient genotyper and star-allele caller for pharmacogenomics.Genome research · 2023Article
- Development of an extensive workflow for comprehensive clinical pharmacogenomic profiling: lessons from a pilot study on 100 whole exome sequencing data.The pharmacogenomics journal · 2022Article
Corrections and comments
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Authors and funding
14 authors at 6 institutions in 2 countries.
Funding
Abstract
Germline whole exome sequencing from molecular tumor boards has the potential to be repurposed to support clinical pharmacogenomics. However, accurately calling pharmacogenomics-relevant genotypes from exome sequencing data remains challenging. Accordingly, this study assessed the analytical validity of the computational tool, Aldy, in calling pharmacogenomics-relevant genotypes from exome sequencing data for 13 major pharmacogenes. Germline DNA from whole blood was obtained for 164 subjects seen at an institutional molecular solid tumor board. All subjects had whole exome sequencing from Ashion Analytics and panel-based genotyping from an institutional pharmacogenomics laboratory. Aldy version 3.3 was operationalized on the LifeOmic Precision Health Cloud with copy number fixed to two copies per gene. Aldy results were compared with those from genotyping for 56 star allele-defining variants within CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, G6PD, NUDT15, SLCO1B1, and TPMT. Read depth was >100× for all variants except CYP3A4∗22. For 75 subjects in the validation cohort, all 3393 Aldy variant calls were concordant with genotyping. Aldy calls for 736 diplotypes containing alleles assessed by both platforms were also concordant. Aldy identified additional star alleles not covered by targeted genotyping for 139 diplotypes. Aldy accurately called variants and diplotypes for 13 major pharmacogenes, except for CYP2D6 variants involving copy number variations, thus allowing repurposing of whole exome sequencing to support clinical pharmacogenomics.
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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.