Chi8: a GPU program for detecting significant interacting SNPs with the chi-square 8-df test
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 hours 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.

Contact: usman@cs.njit.edu

Source code:

• Chi8 source code

Simulated data:

• Simulated data from BOOST paper

Significant pairs found in WTCCC datasets such that each SNP in the pair is insignificant on its own (by chi-square 2-df test):

• Type 1 diabetes significant SNP pairs
• Rheumatoid arthritis significant SNP pairs
• Crohn's disease significant SNP pairs

Citation: Abdulrhman Aljouie, Mohamadreza Esfandiari, Srividya Ramakrishnan and Usman Roshan, Chi8: a GPU program for detecting significant interacting SNPs with the chi-square 8-df test, accepted to BMC research notes, 2015 (PDF) ( Supplementary material )