| 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 a single-locus approach. However, the computational burden has been a major hurdle to apply epistasis test at the genome-wide scale due to the large number of single nucleotide polymorphism (SNP) pairs to be tested. We have developed and implemented a series of efficient algorithms, i.e., FastANOVA, FastChi, COE, and TEAM, that support epistasis tests in a wide range of problem settings. These algorithms utilize a permutation test for proper error control. Unlike heuristic approaches, they guarantee to find the optimal solutions. It has been shown theoretically and experimentally that these algorithms significantly speed up the process of epistasis detection. |
