M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity

Jagadeesh, Karthik A., Wenger, Aaron M., Berger, Mark J., Guturu, Harendra, Stenson, Peter D., Cooper, David N. ORCID: https://orcid.org/0000-0002-8943-8484, Bernstein, Jonathan A. and Bejerano, Gill 2016. M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. Nature Genetics 48 (12) , pp. 1581-1586. 10.1038/ng.3703

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Abstract

Variant pathogenicity classifiers such as SIFT, PolyPhen-2, CADD, and MetaLR assist in interpretation of the hundreds of rare, missense variants in the typical patient genome by deprioritizing some variants as likely benign. These widely used methods misclassify 26 to 38% of known pathogenic mutations, which could lead to missed diagnoses if the classifiers are trusted as definitive in a clinical setting. We developed M-CAP, a clinical pathogenicity classifier that outperforms existing methods at all thresholds and correctly dismisses 60% of rare, missense variants of uncertain significance in a typical genome at 95% sensitivity.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine
Subjects:	R Medicine > R Medicine (General)
Publisher:	Nature
ISSN:	1061-4036
Date of Acceptance:	26 September 2016
Last Modified:	02 Nov 2022 09:50
URI:	https://orca.cardiff.ac.uk/id/eprint/96541

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