A molecular test using FFPE tissue from patients to distinguish basal-like breast cancer from other subtypes will be developed and confirmed. The test will be based on a commercial platform, the lysis-on ly quantitative Nuclease Protection Assay (qNPA 1M). Current gene expression signatures described for breast cancer, in particular those for distinguishing basal-like breast cancer from other subtypes, will be incorporated into a profiling qNPA assay along with expressed SNP's and gene fusions associated with breast cancer and miRNA discovered by profiling on a whole transcriptome qNPA microarray. The comparative standard will be a 50 gene signature extensively investigated in the literature, which is the basis for the definition of basallike breast cancer. This signature will be among those incorporated into the profi ling assay. Samples used will include two archived sets for which the ERJPR and HER2 status as well as outcome are defined, one set predominately Caucasian, the other predominately African American. The program will provide a ~qNPA Basal Breast Cancer Classifier', the qNPA BBCC. The significance of the qNPA BBCC test will be low cost, simplicity, specificity, accuracy, reproducibility, sensitivity, robustness, and use of clinical samples as they are collected today from biopsy and surgery - FFPE and H&E stained FFPE. The platronm will be able to run diagnostic tests for other forms of cancer. The qNPA BBCC will identify the basal-like and other subtypes, providing patients information as to the prognosis of their disease and oncologists information for selecting the ~ best therapy' for individual patients. The test will be used to select patients for clinical trials, aid ing in the development of new therapies and potentially serving as a companion diagnostic
