Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes.

Clare TurnbullA GarrettS ChoiL KingC LovedayB TorrG J BurghelM DurkieA CallawayR RobinsonJ DrummondI BerryA WallaceD EcclesM TischkowitzN WhiffinJ S WareH HansonC Turnbullnull CanVIG-Uk

Published in: Genetics in medicine : official journal of the American College of Medical Genetics (2021)

Against these clinically validated "functional truth sets," there was wide variation in the predictive performance of commonly used in silico tools. Overall, REVEL and Meta-SNP had best balanced accuracy and might potentially be used at stronger evidence weighting than current ACMG/AMP prescription, in particular for predictions of benignity.

Keyphrases

genome wide
molecular docking
papillary thyroid
high throughput
protein kinase
dna methylation
squamous cell carcinoma
gene expression
childhood cancer