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 Supplementary Note). The iCOGS array comprised 211,155 SNPs. These arrays were used to genotype 114,255 DNA samples from 52 studies participating in BCAC (Supplementary Table 2). After quality control exclusions (Online Methods and Supplementary Table 3), data were obtained for 199,961 SNPs in 52,675 cases and 49,436 controls. The analyses presented here are based on data from subjects of European ancestry (45,290 cases and 41,880 controls from 41 studies) and focus on 29,807 SNPs that were selected on the basis of the GWAS analysis that were successfully genotyped and were not located in regions previously known to be associated with breast cancer.
