X. Wan*, C. Yang*, Q. Yang, H. Xue, X. Fan, N. Tang and W. Yu. BOOST: a fast approach to detecting gene-gene interactions in genome-wide case-control studies. The American Journal of Human Genetics, 87(3):325-340, 2010. *Joint first author.


BOolean Operation based Screening and Testing (BOOST) is a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies in a remarkably fast manner. Interaction analyses on seven data sets from the Wellcome Trust Case Control Consortium were carried out. Each analysis took less than 60 hours to completely evaluate all pairs of roughly 360, 000 SNPs on a standard 3.0 GHz desktop with 4G memory running Windows XP system.


The original open-source package is available at:

Our BOOST approach has been incorporated into the most popular GWAS data analysis toolkit PLINK since 1.90 version ( This implementation works on OS X and Linux as well as Windows. It is also able to handle SNPs with missing calls, and supports multithreading and cluster computing.

Sample usage:

plink --bfile [filename] --fast-epistasis boost