As part of the National Cancer Institute Cancer Genetic Markers of Susceptibility (CGEMS) Project, Hunter et al. [2007] conducted a GWAS of breast cancer by genotyping 528,173 SNPs in 1,145 postmenopausal women of European ancestry with invasive breast cancer and 1,142 controls. The GWAS identified several genomic locations as potentially associated with breast cancer. Of 528,173 SNPs tested, they reported six having the most significant P values [Hunter et al., 2007]. They attempted to replicate the initial associations in the GWAS in an additional independent 1,776 affected individuals and 2,072 controls. We performed the bias adjustment using cutoff 1.5×10−5, the largest observed p-value among the top six SNPs (Table 5). Rs1219648 and rs2420946 were successfully replicated and the bias-corrected ORs are very close to those from the replication study. Rs10510126 failed to show significance in the replication study. Although the corrected OR estimate is smaller than the uncorrected OR, it still overestimates the OR compared to the replication study. All the three SNPs selected from the χ22 test failed to replicate in the follow-up studies. The corrected OR estimates are
