Imputation analysis: We used PLINK to impute genotypes for autosomal SNPs that were present in HapMap Phase II release 23a but not genotyped in our GWA scan. HapMap genotype data from the 90 Asian HapMap subjects that have MAF ≥ 1% and genotyping rate ≥ 95% were used as reference. During the imputation, an information score was generated for each imputed SNP that reflected how confidently genotypes were inferred. Values below 0.80 were taken to be indicative of poor quality and were not analyzed. Besides the 0.61 million observed SNPs, an additional 1.14 million imputed SNPs were tested for association with breast cancer.
