Abstract: The present invention provides methods for classifying and for evaluating the prognosis of a subject having breast cancer are provided. The methods include prediction of breast cancer subtype using a supervised algorithm trained to stratify subjects on the basis of breast cancer intrinsic subtype. The prediction model is based on the gene expression profile of the intrinsic genes listed in Table 1. This prediction model can be used to accurately predict the intrinsic subtype of a subject diagnosed with or suspected of having breast cancer.

Abstract: The application describes methods for predicting overall survival in subjects with breast cancer. The application also describes for screening subjects with breast cancer to determine if the breast cancer will be responsive to a breast cancer therapy including gemcitabine. The application further describes methods for treating subjects with breast cancer by screening them for the likelihood of the effectiveness of treating the cancer with a therapy including gemcitabine and administering the therapy in subjects when it is found that gemcitabine is likely to be effective.