MvPPT: A Highly Efficient and Sensitive Pathogenicity Prediction Tool for Missense Variants.

ABSTRACT: Next-generation sequencing technologies both boost the discovery of variants in the human genome and exacerbate the challenges of pathogenic variant identification. In this study, we developed Pathogenicity Prediction Tool for missense variants (mvPPT), a highly sensitive and accurate missense variant classifier based on gradient boosting. mvPPT adopts high-confidence training sets with a wide spectrum of variant profiles, and extracts three categories of features, including scores from existing prediction tools, frequencies (allele frequencies, amino acid frequencies, and genotype frequencies), and genomic context. Compared with established predictors, mvPPT achieves superior performance in all test sets, regardless of data source. In addition, our study also provides guidance for trainin

SUBMITTER: Tong SY 

PROVIDER: S-EPMC10626173 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature