An efficient gene-gene interaction test for genome-wide association studies in trio families.

ABSTRACT: Several efficient gene-gene interaction tests have been developed for unrelated case-control samples in genome-wide association studies (GWAS), making it possible to test tens of billions of interaction pairs of single-nucleotide polymorphisms (SNPs) in a reasonable timeframe. However, current family-based gene-gene interaction tests are computationally expensive and are not applicable to genome-wide interaction analysis.We developed an efficient family-based gene-gene interaction test, GCORE, for trios (i.e. two parents and one affected sib). The GCORE compares interlocus correlations at two SNPs between the transmitted and non-transmitted alleles. We used simulation studies to compare the statistical properties such as type I error rates and power for the GCORE with several other family-based interaction tests under various scenarios. We applied the GCORE to a family-based GWAS for autism consisting of approximately 2000 trios. Testing a total of 22 471 383 013 interaction pairs in the GWAS can be finished in 36?h by the GCORE without large-scale computing resources, demonstrating that the test is practical for genome-wide gene-gene interaction analysis in trios.GCORE is implemented with C?++?and is available at http://[e-mail] data are available at Bioinformatics online.

SUBMITTER: Sung PY 

PROVIDER: S-EPMC5939888 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature