Abstract 4537: NCI’s clinical proteomic tumor analysis consortium: A proteogenomic cancer analysis program
Authors: Mesri Mehdi , Boja Emily , Carter Alexis , Hiltke Tara , Kinsinger Chris , Marrero-Oliveras Annette , Robles Ana , Rodriguez Henry ,   CPTAC Investigators
Published: August 2019

Abstract
The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) is an integrative proteogenomic nexus composed of a Proteogenomic Tumor Characterization Program, and a Proteogenomic Translational Research Program. The goal of this multi-faceted program is to: I) comprehensively identify proteins derived from altered genes and related biological processes by applying deep proteogenomic analysis and; II) to determine if novel biological insights can be inferred from this additional facet of molecular information that are not obtained through genomics data alone.
Using high throughput standardized mass spectrometry-based methods, the Proteogenomic Tumor Characterization Program is expanding its deep comprehensive proteogenomic analysis of cancer types with all data and assays to be released to the public. In addition to recently characterized TCGA 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), and lung adenocarcinoma (LUAD) are to be 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 elucidate biological mechanisms of response, resistance, and/or toxicity. The Proteogenomic Translational Research Program explores triple negative breast cancer (TNBC), high-grade serous ovarian cancer (HGSOC), and acute myeloid leukemia (AML).
CPTAC investigators have recently completed proteogenomic analysis of ~ 200 Colorectal, ~ 230 Breast and ~250 Ovarian tumors comprised of both retrospectively and prospectively collected samples that encompass comprehensive interrogation of the proteome and post-translational modifications including phosphoproteome. Raw and processed mass spectrometry-based proteomic, and genomic data are publicly available on the CPTAC Data Portal (http://proteomics.cancer.gov). CPTAC is also supporting development of new proteogenomic analysis tools that help integrate the proteomic data with existing omics data sets, such as the LinkedOmics (http://www.linkedomics.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 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, Alexis Carter, Tara Hiltke, Chris 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 American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4537.