Software review
Tools for efficient epistasis detection in genome-wide association study
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* Corresponding author: Xiang Zhang xiang@cs.unc.edu
1 Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
2 Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Source Code for Biology and Medicine 2011, 6:1 doi:10.1186/1751-0473-6-1
Published: 4 January 2011Abstract
Background
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.
Results
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.
Conclusions
A web server with user interface and source codes are available at the website http://www.csbio.unc.edu/epistasis/ webcite. The source codes are also available at SourceForge http://sourceforge.net/projects/epistasis/ webcite.