Review on GPU accelerated methods for genome-wide SNP-SNP interactions

Abstract

Detecting genome-wide SNP-SNP interactions (epistasis) efficiently is essential to harnessing the vast data now available from modern biobanks. With millions of SNPs and genetic information from hundreds of thousands of individuals, researchers are positioned to uncover new insights into complex disease pathways. However, this data scale brings significant computational and statistical challenges. To address these, recent approaches leverage GPU-based parallel computing for high-throughput, cost-effective analysis and refine algorithms to improve time and memory efficiency. In this survey, we systematically review GPU-accelerated methods for exhaustive epistasis detection, detailing the statistical models used and the computational strategies employed to enhance performance. Our findings indicate substantial speedups with GPU implementations over traditional CPU approaches. We conclude that while GPU-based solutions hold promise for advancing genomic research, continued innovation in both algorithm design and hardware optimization is necessary to meet future data challenges in the field.

Keywords: Epistasis; GPU parallel computing; GWAS; Large biobank; SNP-SNP interaction.