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More than 70 common alleles are known to be involved in breast cancer (BC) susceptibility, and several exhibit significant heterogeneity in their associations with different BC subtypes. Although there are differences in the association patterns between  BRCA1  and  BRCA2  mutation carriers and the general population for several loci, no study has comprehensively evaluated the associations of all known BC susceptibility alleles with risk of BC subtypes in  BRCA1  and  BRCA2  carriers.    Methods  We used data from 15,252  BRCA1  and 8,211  BRCA2  carriers to analyze the associations between approximately 200,000 genetic variants on the iCOGS array and risk of BC subtypes defined by estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and triple-negative- (TN) status; morphologic subtypes; histological grade; and nodal involvement.    Results  The estimated BC hazard ratios (HRs) for the 74 known BC alleles in  BRCA1  carriers exhibited moderate correlations with the corresponding odds ratios from the general population. However, their associations with ER-positive BC in  BRCA1  carriers were more consistent with the ER-positive associations in the general population (intraclass correlation (ICC) = 0.61, 95% confidence interval (CI): 0.45 to 0.74), and the same was true when considering ER-negative associations in both groups (ICC = 0.59, 95% CI: 0.42 to 0.72). Similarly, there was strong correlation between the ER-positive associations for  BRCA1  and  BRCA2  carriers (ICC = 0.67, 95% CI: 0.52 to 0.78), whereas ER-positive associations in any one of the groups were generally inconsistent with ER-negative associations in any of the others. After stratifying by ER status in mutation carriers, additional significant associations were observed. Several previously unreported variants exhibited associations at  P  <10 −6  in the analyses by PR status, HER2 status, TN phenotype, morphologic subtypes, histological grade and nodal involvement.    Conclusions  Differences in associations of common BC susceptibility alleles between  BRCA1  and  BRCA2  carriers and the general population are explained to a large extent by differences in the prevalence of ER-positive and ER-negative tumors. Estimates of the risks associated with these variants based on population-based studies are likely to be applicable to mutation carriers after taking ER status into account, which has implications for risk prediction.    Electronic supplementary material  The online version of this article (doi:10.1186/s13058-014-0492-9) contains supplementary material, which is available to authorized users.

Associations of common breast cancer susceptibility alleles with risk of breast cancer subtypes in BRCA1 and BRCA2 mutation carriers