Publication Date:
2015-09-15
Description:
Background: Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics.FindingsWe 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.
Electronic ISSN:
1756-0500
Topics:
Biology
,
Medicine
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