Abstract 6331: NCI’s Clinical Proteomic Tumor Analysis Consortium: A proteogenomic cancer analysis program

The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI’s CPTAC) is an integrative proteogenomic program composed of a Proteogenomic Tumor Characterization Program and a Proteogenomic Translational Research Program (https://proteomics.cancer.gov). The goal of CPTAC is to improve prevention, early detection, diagnosis, and treatment of cancer by enhancing the understanding of the molecular mechanisms of cancer, advancing proteogenome science and technology development through community resources, and accelerating the translation of molecular findings into the clinic. Using state-of-the-art high throughput standardized mass spectrometry-based methods, the Proteogenomic Tumor Characterization Program performs deep comprehensive proteogenomic analysis of cancer types with all data and assays to be released to the research community. CPTAC teams have characterized a plethora of treatment-naïve tumor types including colorectal, ovarian, breast, clear cell renal cell carcinoma, uterine corpus endometrial carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, brain (including adult, pediatric, and adolescent and young adult), head and neck squamous cell carcinoma, and pancreatic ductal adenocarcinoma. In the Proteogenomic Translational Research Program, CPTAC is partnering for the first time with NCI-sponsored clinical trials to support clinically relevant research projects that would elucidate biological mechanisms of therapeutic response, resistance, and/or toxicity. The Proteogenomic Translational Research Program currently explores triple negative breast cancer, high-grade serous ovarian cancer, and acute myeloid leukemia. All mass spectrometry-based proteomic, genomic, and imaging data (histopathology and radiology) are made publicly available at the CPTAC Proteomic Data Commons (https://pdc.cancer.gov), Genomic Data Commons (https://gdc.cancer.gov), and the Cancer Imaging Archive (https://cancerimagingarchive.net) respectively. CPTAC is also supporting development of new proteogenomic data analysis tools (https://proteomics.cancer.gov/resources/computational-tools). In addition, the CPTAC Assay Portal (http://assays.cancer.gov) is a public resource populated with mass spectrometry-based targeted proteomic assays developed by the consortium for quantitatively measuring proteins of interest, including those discovered through comprehensive tumor characterization. Lastly, well-characterized monoclonal antibodies targeting cancer