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

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 × Rec model (p-value = 0.045 after adjusting for multiple tests and multiple models).