GWAIS-Web: a free and secure web service for ultra-fast and large-scale genome-wide association interaction studies

Genome-wide association interaction studies (GWAIS) are essential for identifying non-additive genetic effects underlying complex diseases, but exhaustive screening of SNP-SNP combinations across millions of variants is computationally demanding. We present GWAIS-Web, a free, ultra-fast, privacy-compliant web service that enables genome-wide screening of pairwise or third-order interactions for large case-control GWAS datasets. GWAIS-Web combines algorithmic advances with GPU- and FPGA-accelerated implementations, achieving speedups of more than three orders of magnitude compared to established CPU-based approaches and reducing analysis runtimes from years to days. The service supports multiple widely used epistasis detection methods, including PLINK's logistic regression test and BOOST, and provides practical options such as LD-based SNP filtering, region-specific analyses and the simultaneous execution of multiple methods within a single run.

GWAIS-Web is freely available at https://hybridcomputing.ikmb.uni-kiel.de. Source code for the stand-alone CPU/GPU implementation and the FPGA extension is provided at https://github.com/ikmb/hybridgwais and https://github.com/ikmb/hybridgwais-fpga.