Chi8: A GPU program for detecting significant interacting SNPs with the Chi-square 8-df test

Abdulrhman Al-Jouie, Mohammadreza Esfandiari, Srividya Ramakrishnan, Usman Roshan

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Background: Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics. Findings: We present a program Chi8 that calculates the Chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphics Processing Unit. We analyze each of the seven WTCCC genome-wide association studies that have about 5000 total case and controls and 400,000 SNPs in an average of 9.6 h on a single GPU. We also study the power, false positives, and area under curve of our program on simulated data and provide a comparison to the GBOOST program. Our program source code is freely available from http://www.cs.njit.edu/usman/Chi8.

Original languageEnglish (US)
Article number436
JournalBMC Research Notes
Volume8
Issue number1
DOIs
StatePublished - Sep 14 2015

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)

Keywords

  • Chi-square 8 degrees of freedom
  • Epistasis
  • Genome wide association studies
  • Graphics Processing Unit
  • Interacting SNPs

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