High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs
Fast 3rd order SNP interaction measurement using mutual information measures on FPGAs. High-throughput systolic chain processing element architecture. Sparse contingency tables with counter recovering for optimal resource utilization. >360x/180x faster with a single Virtex7/Kintex7 FPGA compared to Intel 6-core CPU. 34min/68min vs. 8.5 days runtime for 10k SNPs and 5k samples.
epistasis fpga mutual information gwas high performance computing genegene interactions entropy bioinformatics