Skip to main content


O'Brien, Katie M.; Cole, Stephen R.; Engel, Lawrence S.; Bensen, Jeannette T.; Poole, Charles L.; Herring, Amy H.; & Millikan, Robert C. (2014). Breast Cancer Subtypes and Previously Established Genetic Risk Factors: A Bayesian Approach. Cancer Epidemiology, Biomarkers & Prevention, 23(1), 84-97. PMCID: PMC3947131


Background: Gene expression analyses indicate that breast cancer is a heterogeneous disease with at least 5 immunohistologic subtypes. Despite growing evidence that these subtypes are etiologically and prognostically distinct, few studies have investigated whether they have divergent genetic risk factors. To help fill in this gap in our understanding, we examined associations between breast cancer subtypes and previously established susceptibility loci among white and African-American women in the Carolina Breast Cancer Study.
Methods: We used Bayesian polytomous logistic regression to estimate odds ratios (ORs) and 95% posterior intervals (PIs) for the association between each of 78 single nucleotide polymorphisms (SNPs) and 5 breast cancer subtypes. Subtypes were defined using 5 immunohistochemical markers: estrogen receptors (ER), progesterone receptors (PR), human epidermal growth factor receptors 1 and 2 (HER1/2) and cytokeratin (CK) 5/6.
Results: Several SNPs in TNRC9/TOX3 were associated with luminal A (ER/PR+, HER2-) or basal-like breast cancer (ER-, PR-, HER2-, HER1 or CK 5/6+), and one SNP (rs3104746) was associated with both. SNPs in FGFR2 were associated with luminal A, luminal B (ER/PR+, HER2+), or HER2+/ER- disease, but none were associated with basal-like disease. We also observed subtype differences in the effects of SNPs in 2q35, 4p, TLR1, MAP3K1, ESR1, CDKN2A/B, ANKRD16, and ZM1Z1.
Discussion: We found evidence that genetic risk factors for breast cancer vary by subtype and further clarified the role of several key susceptibility genes.


Reference Type

Journal Article

Year Published


Journal Title

Cancer Epidemiology, Biomarkers & Prevention


O'Brien, Katie M.
Cole, Stephen R.
Engel, Lawrence S.
Bensen, Jeannette T.
Poole, Charles L.
Herring, Amy H.
Millikan, Robert C.