Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations.

ABSTRACT: Mutual Exclusivity analysis of genomic aberrations contributes to the exploration of potential synthetic lethal (SL) relationships thus guiding the nomination of specific cancer cells vulnerabilities. When multiple classes of genomic aberrations and large cohorts of patients are interrogated, exhaustive genome-wide analyses are not computationally feasible with commonly used approaches. Here we present Fast Mutual Exclusivity (FaME), an algorithm based on matrix multiplication that employs a logarithm-based implementation of the Fisher's exact test to achieve fast computation of genome-wide mutual exclusivity tests; we show that brute force testing for mutual exclusivity of hundreds of millions of aberrations combinations can be performed in few minutes. We applied FaME to allele-specific

SUBMITTER: Fedrizzi T 

PROVIDER: S-EPMC8369001 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature