Phase II Study Using Genomic & Proteomic Profiling to Influence Treatments for Patients With Metastatic Breast Cancer

DNA contains genetic information that acts as a blueprint for how parts of your body are made and work, determining such things as eye and hair color. DNA is made up of long strands of repeating letters that form a code. The order in which these letters are written is very precise. In the same way that a spelling mistake in a word could change its meaning entirely (for example, mean and meat), a single change in the sequence of DNA can lead to a change in how the body works, which may lead to disease. Currently, researchers and doctors know some of the genetic changes that may result in disease, but they do not know all of the genetic changes that can cause disease. Proteins are the basic building blocks of your body. The parts of your body such as your muscles, your skin, and your organs are made up mostly of proteins. DNA provides the plans, or instructions, for how each protein should be made. If there is a change in your DNA, there may be a change in how a protein is made. Sometimes these changes can lead to disease. To make a protein, the cells in your body take the DNA and make a copy called RNA. The cells read the RNA to make the protein. DNA can be thought of as the original master plan with RNA being photocopies of this plan. The number of copies of RNA can determine the amount of protein that can be made. If the body needs more protein, it can make more RNA but if it needs less protein, it can also shred the RNA so that it cannot be read. The amount of a particular RNA or protein can also be important in how the body works. Too much or too little of a particular protein can also lead to disease. Understanding the relationship between DNA, RNA and proteins can be important in knowing what causes disease and how to treat it. Identification of precisely which treatments to use against a specific patient's tumor is challenging. In this study, four cutting-edge technologies will be used to identify genomic (information we get from DNA and RNA) and proteomic (information we get from proteins) targets for the treatment of your tumor. These four tests will be used together to gather information about your tumor giving doctors and scientists a better understanding of the structure of your tumor and what the best treatment or combination of treatments may be for you. The therapy you receive to treat your tumor will be based on your medical history, previous treatments for your disease if applicable, current state of health, and the findings from these four tests. The therapy you ultimately receive will be selected by your doctor in consultation with a panel of experts in cancer and cancer genomics (the Treatment Selection Committee). The purpose of this study is to examine the impact of targeted therapy for breast cancer based upon proteomic and genomic profiling using four different methods of analysis. * Reverse Phase Protein Microarray will be used to determine how often there are specific proteins that could make the tumor susceptible or resistant to treatment. * Immunohistochemistry will look for specific markers of disease in DNA. * RNA sequencing will be used to help doctors and scientists understand how genes are working. * Low pass whole genome and exome sequencing will be used to help identify variants in DNA. The goal of this study will be to enroll at least 25 women who will receive therapy influenced by the results derived from genomic and proteomic profiling. Up to 30 women will receive treatment suggested by an identified target and up to 10 women will receive treatment that the subject and her doctor choose. The actual treatment of disease will be based upon multiple factors, including current physical condition, prior therapies if applicable, standard labs and tests, and physician's preference. The results from the genomic and proteomic profiling will add to the available information that will be used to aid us in deciding upon the course of therapy.