Patients diagnosed with basal-like breast cancer face a more aggressive disease course and more dismal prognosis than patients diagnosed with luminal A and luminal B breast cancer molecular subtypes (1-4). Black women are disproportionately diagnosed with basal subtype or triple negative breast cancer for reasons that are not yet understood (3, 4). We mined published microarray data (5, 6) to discover in an unbiased fashion the most distinguishing genetic and transcriptional features of tumors

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... rom patients with basal or basal-like subtype breast cancer and integrated this with DNA sequence information aggregated from across earth to identify sites that are blindly associated with the basal subtype and that harbor imbalance of allelic frequency based on race. We identified a single nucleotide polymorphism, rs7724788, residing within SLC25A46 as among the most significant genetic differences in the tumors of patients with basal-like breast cancer. Allele frequency at this site was significantly different between black women and white women. Analysis of patient survival data revealed that SLC25A46 primary tumor expression was correlated with overall survival in patients with basal-like and luminal A subtype breast cancer. Tumor expression of SLC25A46 was also correlated with overall white but not black women. Sequence variation in the SLC25A46 gene may be important in understanding differences in genetic background that favor development of basal subtype human breast cancer.