MEGA-V: detection of variant gene sets in patient cohorts.

ABSTRACT

Summary: Detecting significant associations between genetic variants and disease may prove particularly challenging when the variants are rare in the population and/or act together with other variants to cause the disease. We have developed a statistical framework named Mutation Enrichment Gene set Analysis of Variants (MEGA-V) that specifically detects the enrichments of genetic alterations within a process in a cohort of interest. By focusing on the mutations of several genes contributing to the same function rather than on those affecting a single gene, MEGA-V increases the power to detect statistically significant associations. Availability and Implementation MEGA-V is available at https//github.com/ciccalab/MEGA. Contact francesca.ciccarelli@kcl.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.