Alterations of human leukocyte antigen (HLA) class II molecules are relevant to the development of breast cancer and metastatic progression. However, the role of HLA class II polymorphisms in the pathogenesis and progression of breast cancer is unclear. This study aimed to investigate the association between HLA class II variants and breast cancer susceptibility and prognosis in a Chinese population. Sixteen variants in HLA class II were detected with the Sequenom MassArray® iPLEX System in 216 breast cancer patients and 216 healthy controls. An association analysis based on unconditional logistic regression was carried out to determine the odds ratio (OR) and 95% confidence interval (95% CI) for each SNP. Stratified analysis by oestrogen receptor (ER) and progesterone receptor (PR) status was also performed. Among 16 variants, only seven conformed to Hardy–Weinberg proportions in the controls. None of these seven variants showed statistically significant differences between the case and control groups in this Han Chinese population. However, chr6_32737733, a variant in HLA-DQB1, showed significant associations with both ER-negative and PR-negative breast cancer in the best fit to the dominant model. Furthermore, another significant correlation was seen between chr6_32606112, a variant in HLA-DRB5, and PR positivity. These results indicate that although no breast cancer risk variants in HLA class II were found in this Chinese population, HLA-DQB1 chr6_32737733 may to be involved in determining a poor prognosis, whereas HLA-DRB5 chr6_32606112 may relate to a good prognosis.
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