TY - JOUR
T1 - Chi8
T2 - A GPU program for detecting significant interacting SNPs with the Chi-square 8-df test
AU - Al-Jouie, Abdulrhman
AU - Esfandiari, Mohammadreza
AU - Ramakrishnan, Srividya
AU - Roshan, Usman
N1 - Publisher Copyright:
© 2015 Al-jouie et al.
PY - 2015/9/14
Y1 - 2015/9/14
N2 - 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.
AB - 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.
KW - Chi-square 8 degrees of freedom
KW - Epistasis
KW - Genome wide association studies
KW - Graphics Processing Unit
KW - Interacting SNPs
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U2 - 10.1186/s13104-015-1392-5
DO - 10.1186/s13104-015-1392-5
M3 - Article
C2 - 26369336
AN - SCOPUS:84941552115
SN - 1756-0500
VL - 8
JO - BMC Research Notes
JF - BMC Research Notes
IS - 1
M1 - 436
ER -