In order to correct for multiple testing of SNPs in linkage disequilibrium we used Li and Ji's [22] method for calculating the effective number of independent tests from pairwise SNP correlations. Pairwise SNP correlations were obtained from reference genotypes of 1468 subjects in the Busselton study [23]. We estimated that the association tests for the 16,936 highly correlated SNPs we selected in the regions of interest equated to 3,891 independent tests.
