Beyond gene-disease validity: capturing structured data on inheritance, allelic requirement, disease-relevant variant classes, and disease mechanism for inherited cardiac conditions
Josephs, Katherine S; Roberts, Angharad M; Theotokis, Pantazis; Walsh, Roddy; Ostrowski, Philip J; Edwards, Matthew; Fleming, Andrew; Thaxton, Courtney; Roberts, Jason D; Care, Melanie; Zareba, Wojciech; Adler, Arnon; Sturm, Amy C; Tadros, Rafik; Novelli, Valeria; Owens, Emma; Bronicki, Lucas; Jarinova, Olga; Callewaert, Bert; Peters, Stacey; Lumbers, Tom; Jordan, Elizabeth; Asatryan, Babken; Krishnan, Neesha; Hershberger, Ray E; Chahal, C Anwar A; Landstrom, Andrew P; James, Cynthia; McNally, Elizabeth M; Judge, Daniel P; van Tintelen, Peter; Wilde, Arthur; Gollob, Michael; Ingles, Jodie; Ware, James S
(2023) Genome Medicine, volume 15, issue 1
(Article)
Abstract
BACKGROUND: As the availability of genomic testing grows, variant interpretation will increasingly be performed by genomic generalists, rather than domain-specific experts. Demand is rising for laboratories to accurately classify variants in inherited cardiac condition (ICC) genes, including secondary findings. METHODS: We analyse evidence for inheritance patterns, allelic requirement, disease mechanism
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and disease-relevant variant classes for 65 ClinGen-curated ICC gene-disease pairs. We present this information for the first time in a structured dataset, CardiacG2P, and assess application in genomic variant filtering. RESULTS: For 36/65 gene-disease pairs, loss of function is not an established disease mechanism, and protein truncating variants are not known to be pathogenic. Using the CardiacG2P dataset as an initial variant filter allows for efficient variant prioritisation whilst maintaining a high sensitivity for retaining pathogenic variants compared with two other variant filtering approaches. CONCLUSIONS: Access to evidence-based structured data representing disease mechanism and allelic requirement aids variant filtering and analysis and is a pre-requisite for scalable genomic testing.
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Keywords: Databases, Genetic, Genetic Testing, Genetic Variation, Genomics, Humans, Inheritance Patterns, Inherited cardiac conditions, Inheritance, Variant classification, Allelic requirement, Disease mechanism, Genomic variant filtering, Gene curation, Variant interpretation, Genetics(clinical), Genetics, Molecular Medicine, Molecular Biology, Journal Article
ISSN: 1756-994x
Publisher: BioMed Central
Note: Publisher Copyright: © 2023, BioMed Central Ltd., part of Springer Nature.
(Peer reviewed)