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

Gennaro Gambardella; Matteo Cereda; Lorena Benedetti; Francesca D Ciccarelli

doi:10.1093/bioinformatics/btw80

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

Gennaro Gambardella, Matteo Cereda, Lorena Benedetti, Francesca D Ciccarelli

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Abstract

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. Supplementary data are available online.

AVAILABILITY: MEGA-V is available at https://github.com/ciccalab/MEGA CONTACT: [email protected].

Original language	English
Pages (from-to)	1248-1249
Number of pages	2
Journal	BIOINFORMATICS
Volume	33
Issue number	8
Early online date	21 Dec 2016
DOIs	https://doi.org/10.1093/bioinformatics/btw80
Publication status	Published - 2017

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MEGA-V detection of variant_GAMBARDELLA_Firstonline21December2016_GOLD VoR (CC-BY)Final published version, 175 KBLicence: CC BY

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title = "MEGA-V: detection of variant gene sets in patient cohorts",

abstract = "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. Supplementary data are available online.AVAILABILITY: MEGA-V is available at https://github.com/ciccalab/MEGA CONTACT: [email protected].",

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AU - Gambardella, Gennaro

AU - Cereda, Matteo

AU - Benedetti, Lorena

AU - Ciccarelli, Francesca D

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AB - 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. Supplementary data are available online.AVAILABILITY: MEGA-V is available at https://github.com/ciccalab/MEGA CONTACT: [email protected].

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

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