GCORE-sib: An efficient gene-gene interaction tool for genome-wide association studies based on discordant sib pairs. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Sung, Pei-Yuan; Wang, Yi-Ting; Hsiung, Chao; Chung, Ren-Hua
• Is Part Of: BMC bioinformatics. Volume 17:Issue 1(2016)
• Page Start: 1
• Page End: 8
• Publication Date: 2016-12
• Subjects: Genome-wide association study -- Gene-gene interaction -- Discordant sib pair; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-016-1145-z
• Languages: English
• ISSNs: 1471-2105

Abstract

Abstract 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 athttp://gcore-sib.sourceforge.net .