1,000x Faster Than PLINK: Genome-Wide Epistasis Detection with Logistic Regression Using Combined FPGA and GPU Accelerators

Authors:
Lars Wienbrandt, Jan Christian Kässens, Matthias Hübenthal, David Ellinghaus
Year of publication:
2018
Volume:
10862
Issue:
-
Issn:
0302-9743
Journal title abbreviated:
LNCS
Journal title long:
Lecture Notes in Computer Science
Abstract:
Logistic regression as implemented in PLINK is a powerful and commonly used framework for assessing gene-gene (GxG) interactions. However, fitting regression models for each pair of markers in a genome-wide dataset is a computationally intensive task. Performing billions of tests with PLINK takes days if not weeks, for which reason pre-filtering techniques and fast epistasis screenings are applied to reduce the computational burden.