GWAS have identified multiple loci that modestly, but reproducibly, influence risk of T2D [Diabetes Genetics Initiative, 2007; The WTCCC, 2007; Scott et al., 2007]. A meta-analysis has been recently conducted on data from three independent [Diabetes Genetics Initiative, 2007; The WTCCC, 2007; Scott et al. 2007] cohorts [Zeggini et al., 2008]. They selected 69 SNPs for replication in stage 2, which modeled 22426 additional samples, based on the statistical significance. Of these SNPs, 11 showed P < 0.005 in stage 2 alone and P < 10−5 from the combined stage 1 and stage 2 data. Then they further genotyped these 11 SNPs in a replication stage that evaluated 57,366 additional samples. We approximated the p-value cutoff point by 69/2, 202, 892 = 3.1 × 10−5 at stage 1; and at 10−5 at stage II. The bias-adjusted results for the 11 SNPs are shown in table 7. Again, the bias-adjusted OR estimates and CIs have good consistency with the replication based estimates and CIs.
