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National Institute of Environmental Health Sciences

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Publication Detail

Title: Tools for efficient epistasis detection in genome-wide association study.

Authors: Zhang, Xiang; Huang, Shunping; Zou, Fei; Wang, Wei

Published In Source Code Biol Med, (2011 Jan 04)

Abstract: Genome-wide association study (GWAS) aims to find genetic factors underlying complex phenotypic traits, for which epistasis or gene-gene interaction detection is often preferred over single-locus approach. However, the computational burden has been a major hurdle to apply epistasis test in the genome-wide scale due to a large number of single nucleotide polymorphism (SNP) pairs to be tested.We have developed a set of three efficient programs, FastANOVA, COE and TEAM, that support epistasis test in a variety of problem settings in GWAS. These programs utilize permutation test to properly control error rate such as family-wise error rate (FWER) and false discovery rate (FDR). They guarantee to find the optimal solutions, and significantly speed up the process of epistasis detection in GWAS.A web server with user interface and source codes are available at the website http://www.csbio.unc.edu/epistasis/. The source codes are also available at SourceForge http://sourceforge.net/projects/epistasis/.

PubMed ID: 21205316 Exiting the NIEHS site

MeSH Terms: No MeSH terms associated with this publication

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