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

doi:10.1142/9789811270611_0035

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

Quantitative Health Sciences

Research output: Contribution to journal › Conference article › peer-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 language	English (US)
Pages (from-to)	383-394
Number of pages	12
Journal	Pacific Symposium on Biocomputing
Issue number	2023
DOIs	https://doi.org/10.1142/9789811270611_0035
State	Published - 2023
Event	28th Pacific Symposium on Biocomputing, PSB 2023 - Kohala Coast, United States Duration: Jan 3 2023 → Jan 7 2023

Keywords

Allele
GA4GH
Genomics
Genotype
HGVS
Haplotype
VCF
VRS

ASJC Scopus subject areas

Biomedical Engineering
Computational Theory and Mathematics

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10.1142/9789811270611_0035

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Goar, W., Babb, L., Chamala, S., Cline, M., Freimuth, R. R., Hart, R. K., Kuzma, K., Lee, J., Nelson, T., Prlić, A., Riehle, K., Smith, A., Stahl, K., Yates, A. D., Rehm, H. L., & Wagner, A. H. (2023). Development and application of a computable genotype model in the GA4GH Variation Representation Specification. Pacific Symposium on Biocomputing, (2023), 383-394. https://doi.org/10.1142/9789811270611_0035

Goar, W, Babb, L, Chamala, S, Cline, M, Freimuth, RR, Hart, RK, Kuzma, K, Lee, J, Nelson, T, Prlić, A, Riehle, K, Smith, A, Stahl, K, Yates, AD, Rehm, HL & Wagner, AH 2023, 'Development and application of a computable genotype model in the GA4GH Variation Representation Specification', Pacific Symposium on Biocomputing, no. 2023, pp. 383-394. https://doi.org/10.1142/9789811270611_0035

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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.",

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AU - Freimuth, Robert R.

AU - Hart, Reece K.

AU - Kuzma, Kori

AU - Lee, Jennifer

AU - Nelson, Tristan

AU - Prlić, Andreas

AU - Riehle, Kevin

AU - Smith, Anastasia

AU - Stahl, Kathryn

AU - Yates, Andrew D.

AU - Rehm, Heidi L.

AU - Wagner, Alex H.

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AB - 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.

KW - Allele

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KW - HGVS

KW - Haplotype

KW - VCF

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ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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