Abstract: The disclosure describes a tumor subtyping schema for selection of therapies to treat Stage II and Stage III breast cancers.

Abstract: The present invention relates to the identification of marker genes useful in the diagnosis and prognosis of clinically problematic subsets of primary breast cancers. More specifically, the invention relates to the identification of two sets of marker genes that are differentially expressed in and useful for the diagnosis and prognosis of subsets of hormone receptor-negative (HRneg; i.e., ER and PR negative) and triple-negative (Tneg; i.e., ER, PR and HER2 negative) primary breast cancers at highest risk for early metastatic relapse. The invention further provides methods for determining the best course of treatment for patients having one of these clinically problematic subsets of primary breast cancers. The invention also provides methods for identifying compounds that prevent or treat a subtype of breast cancer based on their ability to modulate the activity or expression level of one or more marker genes identified herein.