High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs

Epistasis, the interaction between genes, has become a major topic in molecular and quantitative genetics. It is believed that these interactions play a significant role in genetic variations causing complex diseases. Several algorithms have been employed to detect pairwise interactions in genome-wide association studies (GWAS) but revealing higher order interactions remains a computationally challenging task. State of the art tools are not able to perform exhaustive search for all three-locus interactions in reasonable time even for relatively small input datasets. In this paper we present how a hardware-assisted design can solve this problem and provide fast, efficient and exhaustive third-order epistasis analysis with up-to-date FPGA technology.