Systematic integration of protein-affecting mutations, gene fusions, and copy number alterations into a comprehensive somatic mutational profile.

ABSTRACT: Somatic mutations occur as random genetic changes in genes through protein-affecting mutations (PAMs), gene fusions, or copy number alterations (CNAs). Mutations of different types can have a similar phenotypic effect (i.e., allelic heterogeneity) and should be integrated into a unified gene mutation profile. We developed OncoMerge to fill this niche of integrating somatic mutations to capture allelic heterogeneity, assign a function to mutations, and overcome known obstacles in cancer genetics. Application of OncoMerge to TCGA Pan-Cancer Atlas increased detection of somatically mutated genes and improved the prediction of the somatic mutation role as either activating or loss of function. Using integrated somatic mutation matrices increased the power to infer gene regulatory networks and

SUBMITTER: Striker SS 

PROVIDER: S-EPMC10162952 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature