Discovering joint associations between disease and gene pairs with a novel similarity test.
Ontology highlight
ABSTRACT: Background
Genes in a functional pathway can have complex interactions. A gene might activate or suppress another gene, so it is of interest to test joint associations of gene pairs. To simultaneously detect the joint association between disease and two genes (or two chromosomal regions), we propose a new test with the use of genomic similarities. Our test is designed to detect epistasis in the absence of main effects, main effects in the absence of epistasis, or the presence of both main effects and epistasis.Results
The simulation results show that our similarity test with the matching measure is more powerful than the Pearson's ?² test when the disease mutants were introduced at common haplotypes, but is less powerful when the disease mutants were introduced at rare haplotypes. Our similarity tests with the counting measures are more sensitive to marker informativity and linkage disequilibrium patterns, and thus are often inferior to the similarity test with the matching measure and the Pearson's ?² test.Conclusions
In detecting joint associations between disease and gene pairs, our similarity test is a complementary method to the Pearson's ?² test.
SUBMITTER: Lin WY
PROVIDER: S-EPMC2959050 | biostudies-literature | 2010 Oct
REPOSITORIES: biostudies-literature
Publications
Discovering joint associations between disease and gene pairs with a novel similarity test.
Lin Wan-Yu WY Lee Wen-Chung WC
BMC genetics 20101004
<h4>Background</h4>Genes in a functional pathway can have complex interactions. A gene might activate or suppress another gene, so it is of interest to test joint associations of gene pairs. To simultaneously detect the joint association between disease and two genes (or two chromosomal regions), we propose a new test with the use of genomic similarities. Our test is designed to detect epistasis in the absence of main effects, main effects in the absence of epistasis, or the presence of both mai ...[more]
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