Comments on 'An empirical comparison of several recent epistatic interaction detection methods'

The detection of epistasis between different loci helps to provide in-depth understanding of complex diseases. Many methods have been proposed to find epistasis in genome-wide association studies (GWAS). A recent article (Wang et al., 2011) published in Bioinformatics conducted an empirical comparison on five methods [TEAM, BOOST, SNPHarvester, SNPRuler, and Screen and Clean (SC)] in terms of power, type-1 error rate, scalability and completeness. This work will help users to better understand the pros and cons of each method. However, the lack of epistasis definitions may bring some confusions for users to select the appropriate method for their tasks because the tests of epistasis in these methods belong to two different categories, while the comparison is based on the same experimental setting. In this letter, we like to clarify the difference of two epistasis tests.