Primary genotype data were obtained for nine breast cancer GWAS in populations of European ancestry (Supplementary Table 1). Standard quality control was performed on all scans as follows. We excluded all individuals with low call rate (<95%) and extremely high or low heterozygosity (P < 1 × 10−5), as well as all individuals evaluated to be of non-European ancestry (>15% non-European component, as determined by multidimensional scaling using the HapMap version 2 CEU, JPT/CHB and YRI populations as a reference). We excluded SNPs with MAF < 1%; call rate < 95%; or call rate < 99% and MAF < 5% and all SNPs with genotype frequencies that departed from Hardy-Weinberg equilibrium at P < 1 × 10−6 in controls or P < 1 × 10−12 in cases. For highly significant SNPs, genotype intensity cluster plots were examined manually to judge reliability, either centrally or by contacting the original investigators.
