title: Tools for efficient epistasis detection in genome-wide association study.
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 http://www.csbio.unc.edu/epistasis/. The source codes are also available at SourceForge http://sourceforge.net/projects/epistasis/.
authors.affiliation: Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. xiang@cs.unc.edu.
authors.forename: Xiang
authors.initials: X
authors.lastname: Zhang
authors.forename: Shunping
authors.initials: S
authors.lastname: Huang
authors.forename: Fei
authors.initials: F
authors.lastname: Zou
authors.forename: Wei
authors.initials: W
authors.lastname: Wang