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

  • Lars WienbrandtEmail author
  • Jan Christian Kässens
  • Matthias Hübenthal
  • David Ellinghaus
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10861)


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.

Here, we demonstrate that employing a combination of a Xilinx UltraScale KU115 FPGA with an Nvidia Tesla P100 GPU leads to runtimes of only minutes for logistic regression GxG tests on a genome-wide scale. In particular, a dataset of 53,000 samples genotyped at 130,000 SNPs was analyzed in 8 min, resulting in a speedup of more than 1,000 when compared to PLINK v1.9 using 32 threads on a server-grade computing platform. Furthermore, on-the-fly calculation of test statistics, p-values and LD-scores in double-precision make commonly used pre-filtering strategies obsolete.


Genome-wide association study (GWAS) Genome-wide interaction study (GWIS) Gene-gene (GxG) interaction Linkage disequilibrium (LD) BOOST Hardware accelerator Hybrid computing Heterogeneous architecture 


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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Lars Wienbrandt
    • 1
    Email author
  • Jan Christian Kässens
    • 1
  • Matthias Hübenthal
    • 1
  • David Ellinghaus
    • 1
  1. 1.Institute of Clinical Molecular BiologyUniversity Medical Center Schleswig-Holstein, Campus Kiel, Kiel UniversityKielGermany

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