Pharmacogenomic allele coverage of genome-wide genotyping arrays: a comparative analysis.

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  • Additional Information
    • Source:
      Publisher: Lippincott Williams & Wilkins Country of Publication: United States NLM ID: 101231005 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1744-6880 (Electronic) Linking ISSN: 17446872 NLM ISO Abbreviation: Pharmacogenet Genomics Subsets: MEDLINE
    • Publication Information:
      Original Publication: Hagerstown, MD : Lippincott Williams & Wilkins, c2005-
    • Subject Terms:
      Alleles* ; Pharmacogenetics*/methods; Humans ; Genotype ; Genotyping Techniques/methods ; Genome-Wide Association Study/methods ; Genome, Human/genetics ; Oligonucleotide Array Sequence Analysis ; Precision Medicine/methods
    • Abstract:
      The use of genome-wide genotyping arrays in pharmacogenomics (PGx) research and clinical implementation applications is increasing but it is unclear which arrays are best suited for these applications. Here, we conduct a comparative coverage analysis of PGx alleles included on genome-wide genotyping arrays, with an emphasis on alleles in genes with PGx-based prescribing guidelines. Genomic manifest files for seven arrays including the Axiom Precision Medicine Diversity Array (PMDA), Axiom PMDA Plus, Axiom PangenomiX, Axiom PangenomiX Plus, Infinium Global Screening Array, Infinium Global Diversity Array (GDA) and Infinium GDA with enhanced PGx (GDA-PGx) Array, were evaluated for coverage of 523 star alleles across 19 pharmacogenes included in prescribing guidelines developed by the Clinical Pharmacogenetic Implementation Consortium and Dutch Pharmacogenomics Working Group. Specific attention was given to coverage of the Association of Molecular Pathology's Tier 1 and Tier 2 allele sets for CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, NUDT15, TPMT and VKORC1 . Coverage of the examined PGx alleles was highest for the Infinium GDA-PGx (88%), Axiom PangenomiX Plus (77%), Axiom PangenomiX (72%) and Axiom PMDA Plus (70%). Three arrays (Infinium GDA-PGx, Axiom PangenomiX Plus and Axiom PMDA Plus) fully covered the Tier 1 alleles and the Axiom PangenomiX array provided full coverage of Tier 2 alleles. In conclusion, PGx allele coverage varied by gene and array. A superior array for all PGx applications was not identified. Future comparative analyses of genotype data produced by these arrays are needed to determine the robustness of the reported coverage estimates.
      (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)
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    • Publication Date:
      Date Created: 20240215 Date Completed: 20240429 Latest Revision: 20240429
    • Publication Date:
      20240429
    • Accession Number:
      10.1097/FPC.0000000000000523
    • Accession Number:
      38359167