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GCORE-sib: An efficient gene-gene interaction tool for genome-wide association studies based on discordant sib pairs
Pei-Yuan Sung1, Yi-Ting Wang1, Chao A Hsiung2
1Institute of Statistics, National Tsing Hua University, Hsin-Chu, Taiwan.
Background:
A computationally efficient tool is required for a genome-wide gene-gene interaction analysis that tests an extremely large number of single-nucleotide polymorphism (SNP) interaction pairs in genome-wide association studies (GWAS). Current tools for GWAS interaction analysis are mainly developed for unrelated case-control samples. Relatively fewer tools for interaction analysis are available for complex disease studies with family-based design, and these tools tend to be computationally expensive.
Results:
We developed a fast gene-gene interaction test, GCORE-sib, for discordant sib pairs and implemented the test into an efficient tool. We used simulations to demonstrate that the GCORE-sib has correct type I error rates and has comparable power to that of the regression-based interaction test. We also showed that the GCORE-sib can run more than 10 times faster than the regression-based test. Finally, the GCORE-sib was applied to a GWAS dataset with approximately 2,000 discordant sib pairs, and the GCORE-sib finished testing 19,368,078,382 pairs of SNPs within 6 days.
Conclusions:
An efficient gene-gene interaction tool for discordant sib pairs was developed. It will be very useful for genome-wide gene-gene interaction analysis in GWAS using discordant sib pairs. The tool can be downloaded for free at http://gcore-sib.sourceforge.net .
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