GWAS on breast cancer [Easton et al., 2007; Hunter et al., 2007], lung cancer [Amos et al., 2008], prostate cancer [Eeles et al., 2008], colorectal cancer [COGENT Study, 2008], type I diabetes [The WTCCC, 2007] and type II diabetes [Zeggini et al., 2008]. Table 1 describes the design, sample size, genotyped SNP number, and SNP selection criterion for these studies, and the corresponding p-value cutoff choice used in the correction procedure. These diseases were selected based on the availability of one or more high dimensional GWAS with SNP selection criteria that were specified or can be inferred, and the availability of replication study results. We then compared the uncorrected OR estimates, the bias-adjusted estimates, and the replication estimates, and their corresponding CIs. A likelihood ratio based test was used to statistically compare the bias-adjusted estimates and the replication estimates. If the test failed to detect statistical significant difference between them, a combined estimated was given using the bias-adjusted estimate, a procedure that makes appropriate use of the data from both the discovery and the replication stages. We found that the simple bias correction procedure generally produces OR point estimates that are closer to estimates from independent replication studies. Furthermore, the
