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.
All Science Journal Classification (ASJC) codes
- Biochemistry, Genetics and Molecular Biology(all)
- Chi-square 8 degrees of freedom
- Genome wide association studies
- Graphics Processing Unit
- Interacting SNPs