Development and application of a computable genotype model in the GA4GH Variation Representation Specification

Wesley Goar, Lawrence Babb, Srikar Chamala, Melissa Cline, Robert R. Freimuth, Reece K. Hart, Kori Kuzma, Jennifer Lee, Tristan Nelson, Andreas Prlić, Kevin Riehle, Anastasia Smith, Kathryn Stahl, Andrew D. Yates, Heidi L. Rehm, Alex H. Wagner

Research output: Contribution to journalConference articlepeer-review

Abstract

As the diversity of genomic variation data increases with our growing understanding of the role of variation in health and disease, it is critical to develop standards for precise inter-system exchange of these data for research and clinical applications. The Global Alliance for Genomics and Health (GA4GH) Variation Representation Specification (VRS) meets this need through a technical terminology and information model for disambiguating and concisely representing variation concepts. Here we discuss the recent Genotype model in VRS, which may be used to represent the allelic composition of a genetic locus. We demonstrate the use of the Genotype model and the constituent Haplotype model for the precise and interoperable representation of pharmacogenomic diplotypes, HGVS variants, and VCF records using VRS and discuss how this can be leveraged to enable interoperable exchange and search operations between assayed variation and genomic knowledgebases.

Original languageEnglish (US)
Pages (from-to)383-394
Number of pages12
JournalPacific Symposium on Biocomputing
Issue number2023
DOIs
StatePublished - 2023
Event28th Pacific Symposium on Biocomputing, PSB 2023 - Kohala Coast, United States
Duration: Jan 3 2023Jan 7 2023

Keywords

  • Allele
  • GA4GH
  • Genomics
  • Genotype
  • Haplotype
  • HGVS
  • VCF
  • VRS

ASJC Scopus subject areas

  • Medicine(all)

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