Ductal carcinoma in situ (DCIS); is thought directly to precede invasive breast cancer (IBC). Screening mammography has driven the incidence of this key precursor lesion to >65,000 cases per year. However, little is known about the factors controlling the natural history or risk for recurrence following treatment of a particular patients DCIS. Though the heterogeneity of the disease is well established, no histologic or demographic criteria have been able to stratify DCIS for treatment. We hypothesize that at initial diagnosis there exist biologically distinct subsets of DCIS with associated prognoses that may be recognized by molecular markers. Molecular approaches have been limited by technical design issues related to the types of tissue available for analysis, namely degraded formalin-fixed paraffin embedded (FFPE) specimens and small core biopsy samples. However, new technologies promise to overcome these issues. In the first phase of our investigation, we aimed a) to pilot feasibility studies on the use of FFPE DCIS for molecular analyses including gene expression microarray and b) to pilot feasibility study of selective, high throughput sequencing through the use of "exon capture" on small input material that simulated expected DCIS core biopsy amounts. The results of this work offer specific technical guidelines for the molecular study of DCIS. Moreover, they have enabled the initiation of the second phase of this study, which aims to assess molecular profiles of DCIS recurrence and progression.