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Application of seventeen two-locus models in genome-wide association studies by two-stage strategy.


ABSTRACT: The goal of this paper is to search for two-locus combinations that are jointly associated with rheumatoid arthritis using the data set of Genetic Analysis Workshop 16 Problem 1. We use a two-stage strategy to reduce the computational burden associated with performing an exhaustive two-locus search across the genome. In the first stage, the full set of 531,689 single-nucleotide polymorphisms was screened using univariate testing. In the second stage, all pairs made from the 500 single-nucleotide polymorphisms with the lowest p-values from the first stage were evaluated under each of 17 two-locus models. Our analyses identified a two-locus combination - rs6939589 and rs11634386 - that proved to be significantly associated with rheumatoid arthritis under a Rec x Rec model (p-value = 0.045 after adjusting for multiple tests and multiple models).

SUBMITTER: Niu A 

PROVIDER: S-EPMC2795923 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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Application of seventeen two-locus models in genome-wide association studies by two-stage strategy.

Niu Adan A   Zhang Zhaogong Z   Sha Qiuying Q  

BMC proceedings 20091215


The goal of this paper is to search for two-locus combinations that are jointly associated with rheumatoid arthritis using the data set of Genetic Analysis Workshop 16 Problem 1. We use a two-stage strategy to reduce the computational burden associated with performing an exhaustive two-locus search across the genome. In the first stage, the full set of 531,689 single-nucleotide polymorphisms was screened using univariate testing. In the second stage, all pairs made from the 500 single-nucleotide  ...[more]

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