Dataset Information
An efficient gene-gene interaction test for genome-wide association studies in trio families.
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ABSTRACT: Motivation
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.Results
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.Availability and implementation
GCORE is implemented with C ++ and is available at http://gscore.sourceforge.netContact
rchung@nhri.org.twSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Sung PY
PROVIDER: S-EPMC5939888 | biostudies-literature | 2016 Jun
REPOSITORIES: biostudies-literature
Publications
An efficient gene-gene interaction test for genome-wide association studies in trio families.
Bioinformatics (Oxford, England) 20160211 12
<h4>Motivation</h4>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.<h4>Results</h4>We developed an efficient family-based g ...[more]