To identify additional susceptibility loci for breast cancer, we first conducted a meta-analysis of 9 breast cancer GWAS in populations of European ancestry, including 10,052 cases and 12,575 controls (Supplementary Table 1). From this analysis, we selected 35,084 SNPs on the basis of evidence of association with breast cancer, derived from a 1-degree-of-freedom trend test, a test weighted for family history, a 2-degrees-of-freedom test and subset analyses based on cases of breast cancer diagnosed before 40 years of age and before 50 years of age (Online Methods). In particular, we were able to select all SNPs or surrogate SNPs with 1-degree-of-freedom Ptrend < 0.008. To evaluate these SNPs, we then designed a custom Illumina iSelect genotyping array (iCOGS) in collaboration with three other consortia studying, in addition to breast cancer risk, susceptibility to ovarian cancer, prostate cancer and breast and ovarian cancers in BRCA1 and BRCA2 mutation carriers (COGS)17–20. The array included, in addition to SNPs selected from GWAS, SNPs selected for fine mapping of known susceptibility loci, functional candidate SNPs and SNPs related to other traits (Online Methods and
