To identify further loci at which common variants are associated with breast cancer risk, a further 925 SNPs that showed evidence for association in the first two stages of Easton's cohort (combined Ptrend < 0.014) were attempted to genotype in a third stage, 3,878 cases and 3,928 controls from three studies corresponding to stage 2 of CGEMS [Ahmed et al. 2009]. After combination of these data with the original GWAS data, three SNPs had P values < 10−5. These SNPs were then evaluated on 36,141 controls and 33,134 cases. Strong evidence was found for two SNPs, rs4973768 and rs6504950. We performed the bias adjustment using p-value cutoffs of 0.014 and 10−5. For both SNPs, the bias-corrected estimates show good concordance with the replication based estimates (Table 5).
