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

Authors

Abdulrhman Al-Jouie, King Saud bin Abdulaziz University for Health Sciences
Mohammadreza Esfandiari, Department of Computer Science
Srividya Ramakrishnan, Cold Spring Harbor Laboratory
Usman Roshan, Department of Computer Science

Document Type

Article

Publication Date

9-14-2015

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 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.

Identifier

84941552115 (Scopus)

Publication Title

BMC Research Notes

External Full Text Location

https://doi.org/10.1186/s13104-015-1392-5

e-ISSN

17560500

PubMed ID

26369336

Issue

1

Volume

8

Recommended Citation

Al-Jouie, Abdulrhman; Esfandiari, Mohammadreza; Ramakrishnan, Srividya; and Roshan, Usman, "Chi8: A GPU program for detecting significant interacting SNPs with the Chi-square 8-df test" (2015). Faculty Publications. 6787.
https://digitalcommons.njit.edu/fac_pubs/6787