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

ABSTRACT: Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics.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.

SUBMITTER: Al-jouie A

PROVIDER: S-EPMC4568583 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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

Al-jouie Abdulrhman A Esfandiari Mohammadreza M Ramakrishnan Srividya S Roshan Usman U

BMC research notes 20150914

<h4>Background</h4>Determining interacting SNPs in genome-wide association studies is computationally expensive yet of considerable interest in genomics.<h4>Findings</h4>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 ...[more]

PMID: 26369336

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