[PMID:27776117] [Nature Genetics]

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

“The Mendelian Clinically Applicable Pathogenicity (M-CAP) score is a pathogenicity likelihood score that aims to misclassify no more than 5% of pathogenic variants while aggressively reducing the list of variants of uncertain significance. Much like allele frequency, M-CAP is readily interpreted; if it classifies a variant as benign, then that variant can be trusted to be benign with high confidence. M-CAP uses gradient boosting trees, a supervised learning classifier that excels at analyzing nonlinear interactions between features, and has state-of-the-art performance in a variety of classification tasks. The features M-CAP uses for classification are based on both existing pathogenicity likelihood scores and direct measures of evolutionary conservation, the cross-species analog to frequency within the human population.””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.”


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