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REVEL

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Suggested by: Mahantesh Biradar

Description

The vast majority of novel sequencing variants are rare, but assessment of the contribution of rare variants to complex traits is hampered by low statistical power and limited functional data. Improved methods for predicting the pathogenicity of rare coding variants are needed to facilitate the discovery of disease variants from exome sequencing studies.

REVEL is a new ensemble method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, Polyphen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. REVEL was trained using recently discovered pathogenic and rare neutral missense variants, excluding those previously used to train its constituent tools.
The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. REVEL score distributions for 6182 disease mutations from HGMD, 123,706 putatively neutral variants, and 1,125,160 exome sequence variants (ESVs) reported by ESP, ARIC and KGP are shown in the figure below. Also shown are the sensitivity (true positive rate or recall) and specificity (true negative rate) for all possible REVEL score thresholds.

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Associated keywords

Genome sequencing Genetic Variation

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