Genome-wide association studies using an adaptive two-stage analysis for a case-control design

A new type of test is presented for genome-wide association studies using a case-control design. It is referred to as the adaptive two-stage (ATS) analysis, being based on both the Hardy-Weinberg disequilibrium trend test (HWDTT) and the Cochran-Armitage trend test (CATT). The procedure for the ATS is to screen single-nucleotide polymorphisms (SNPs) using the HWDTT in a first stage, and then test a reduced number of SNPs that pass the screening step in a second stage using the CATT. In the Genetic Analysis Workshop 15 simulated data set, this ATS analysis captured, after Bonferroni correction, the region from 32447.149 kb to 32859.819 kb and the region around 37363.880 kb that are close to the actual trait loci on chromosome 6. We compared the ATS with other ways of combining the p-values of the HWDTT and the CATT, the classical form of Fisher's test and a weighted form of Fisher's test. Results showed that the proposed ATS has good performance and could detect the regions containing a susceptibility locus.