1000× faster than PLINK: Combined FPGA and GPU accelerators for logistic regression-based detection of epistasis

Abstract

Logistic regression as implemented in PLINK is a powerful and commonly used framework for assessing gene-gene interactions. However, fitting regression models for each pair of markers in a genome-wide dataset is a computationally intensive task, for which reason pre-filtering techniques and fast epistasis screenings are applied to reduce the computational burden.We demonstrate that employing a combination of a Xilinx UltraScale FPGA with an Nvidia Tesla GPU leads to runtimes of only minutes for logistic regression tests on a genome-wide scale, resulting in a speedup of more than 1000 up to 1600 when compared to multi-threaded PLINK on a server-grade computing platform.This article is an extended version of our conference paper [1].