stages 1 and 2. Under the assumption that the vast majority of 227,876 SNPs are from the null distribution, the 227,876 p-values of the difference in genotype frequency between cases and controls follow a distribution that similar to a uniform distribution between 0 and 1. Therefore, selecting the top 5% SNPs among all the SNPs is approximately equivalent to selecting the SNPs with P < 0.05. So the p-value cutoff point for stage 1 is set to 0.05. At stage 2, we approximately set the p-value cutoff point as 30/12, 711 = 2.3 × 10−3. Using the above two p-value cutoffs, we applied the bias correction method to the 24 SNPs (Table 5). The OR estimates from the replication study were less than the OR estimates from the initial discovery scan, showing some selection bias in the unadjusted estimates. The bias-adjusted OR estimates were weaker than the unadjusted estimates, therefore closer to the replication OR estimates. The selection-adjusted CIs were wider than the unadjusted CIs, and more consistent with those from the replication studies. All the selection adjusted CIs exclude 1, which is consistent with the replication studies. Again, the difference observed between the bias-corrected ORs and the replication study
