Abstract 5122: NCI's Clinical Proteomic Tumor Analysis Consortium: A proteogenomic cancer analysis program
Authors: Mesri Mehdi , Boja Emily , Hiltke Tara , Kinsinger Christopher R. , Marrero-Oliveras Annette , Robles Ana , Rodriguez Henry ,   CPTAC Investigators
Published: September 2020

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) is an integrative proteogenomic program composed of a Proteogenomic Tumor Characterization Program, and a Proteogenomic Translational Research Program. 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 (data and reagents), 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 public. In addition to retrospectively collected TCGA and prospectively collected CPTAC samples from colon, breast and ovarian cancers, additional prospectively-collected, treatment-naïve tumors including clear cell renal cell carcinoma (CCRCC), uterine corpus endometrial carcinoma (UCEC), lung adenocarcinoma (LUAD), glioblastoma multiforme (GBM), and retrospectively collected pediatric brain cancers have been characterized. 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 (TNBC), high-grade serous ovarian cancer (HGSOC), and acute myeloid leukemia (AML).

Raw and processed mass spectrometry-based proteomic, and genomic data are publicly available at the CPTAC Data Portal (http://proteomics.cancer.gov), and GDC Data Portal (https://portal.gdc.cancer.gov/) respectively. CPTAC is also supporting development of new proteogenomic data analysis tools, such as network visualization tools (http://ccrcc.cptac-network-view.org). 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-specific proteins and peptides are also made available at CPTAC's Antibody Portal (http://antibodies.cancer.gov).

Citation Format: Mehdi Mesri, Emily Boja, Tara Hiltke, Christopher R. Kinsinger, Annette Marrero-Oliveras, Ana Robles, Henry Rodriguez, CPTAC Investigators. NCI's Clinical Proteomic Tumor Analysis Consortium: A proteogenomic cancer analysis program [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5122.