Our goal is to discover and confirm a number of serum-based tumor biomarkers sufficient to diagnose every breast cancer and ovarian cancer in its most treatable stage. To accomplish this, we utilize a novel proteomics approach and serum samples from a rich and well-characterized specimen repository. Our proteomics approach uses three distinct recombinant antibody libraries that each contain between 10^8- to 10^10 unique binding sequences. We select the sub-libraries that can bind epitomes in serum from cancer patients that are not present in cancer-free control serum. This approach has several advantages over other serum proteomics approaches, including the capability to discover biomarkers resulting from differential post-translational modifications and the ability to purify each target, which facilitates biomarker identification (i.e., sequencing) and functional characterization. This recombinant library panning procedure will discover thousands of candidate biomarkers in need of further confirmation. Although confirmation could proceed with standard ELISA techniques, we intend to use two high-throughput platforms - antibody microarrays and a suspension assay system. These platforms allow us to simultaneously evaluate the entire antibody sub library alongside other antibodies, and to molecularly classify breast and ovarian cancer using serum in a manner directly analogous to how we now routinely use transcript microarrays. Our research design will facilitate the early detection of breast and ovarian cancer. In addition, our research plan contains opportunities for the EDRN as a whole. For example, during our antibody profiling we will invite any EDRN investigators having a putative ovarian or breast cancer biomarker to contribute their reagents to our array. Moreover, during our proposal we will have produced an antibody micro arrays useful for evaluating many research questions relevant to breast and ovarian cancer. We will offer to profile any serum samples from within EDRN using these arrays. All data from these measurements will be given to the researchers who provide the specimens (or the EDRN coordinating center).
