BCAC cases were women diagnosed with BC7. To define disease status in CIMBA participants, women were censored at the first of the following events: age at BC diagnosis, age at ovarian cancer diagnosis, other cancer, bilateral prophylactic mastectomy or age at study recruitment. Subjects censored at a BC diagnosis were considered as cases.

A control-only analysis was carried out to test the independence between the SNPs and the BRCA1 and BRCA2 mutation carrier status. In BCAC, controls were defined as individuals unaffected by BC at study recruitment35. In CIMBA, participants were considered as controls if they were unaffected at recruitment.

Only women of European ancestry were included. To minimise the chance of observing spurious associations due to differences in the distribution of BC cases in the population by tumour characteristics (defined as unselected BC cases), 3,478 BCAC cases from four studies were excluded because they were included in clinical trials based on breast tumour characteristics as HER-2 receptor status (see Supplementary Table 2). Because all the analyses were adjusted for country, to ensure that the number of subjects in each country stratum was large enough, we excluded the CIMBA data from any country for which there were less than ten BC cases with BRCA1 or BRCA2 mutation. Consequently, data from Poland and Russia were excluded from the BRCA2 analyses (Supplementary Table 3). Finally, duplicate subjects between BCAC and CIMBA were excluded from the BCAC data (114 and 80 subjects from the BRCA1 and BRCA2 case-only analyses, respectively; eight subjects from control-only analyses).

A total of 60,212 BCAC cases and 7,257 BRCA1 mutation carrier cases were available for the BRCA1 case-only analyses and 57,725 BCAC cases and 5097 BRCA2 mutation carrier cases were available for the BRCA2 case-only analyses (Fig. 1). A total of 45,881 BCAC controls and 5,750 BRCA1 mutation carrier controls were available for the BRCA1 control-only analyses and 43,549 BCAC controls and 4,456 BRCA2 mutation carrier controls for the BRCA2 control-only analyses (Fig. 2).

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