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Tools for efficient epistasis detection in genome-wide association study

Creators: Zhang, Xiang, Huang, Shunping, Zou, Fei, Wang, Wei

  • File Type: pdf | Filesize: 205.1 KB
  • Date Deposited: 2012-08-23
  • Date Created: 2011-01-04

Abstract 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 The source codes are also available at SourceForge