Development and application of a computable genotype model in the GA4GH Variation Representation Specification.
Journal
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
ISSN: 2335-6936
Titre abrégé: Pac Symp Biocomput
Pays: United States
ID NLM: 9711271
Informations de publication
Date de publication:
2023
2023
Historique:
entrez:
21
12
2022
pubmed:
22
12
2022
medline:
23
12
2022
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 36540993
pii: 9789811270611_0035
pmc: PMC9782714
mid: NIHMS1853002
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
383-394Subventions
Organisme : NHGRI NIH HHS
ID : R35 HG011949
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG009649
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG006834
Pays : United States
Organisme : Medical Research Council
ID : MC_PC_19024
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : U41 HG006834
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA242954
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG009649
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG009650
Pays : United States
Organisme : NHGRI NIH HHS
ID : R35 HG011899
Pays : United States
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