Abstract 1282: NCI's Clinical Proteomic Tumor Analysis Consortium

Mission: The Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of robust, quantitative, proteomic technologies and workflows. Goals: The overarching goal of CPTAC is to improve our ability to diagnose, treat and prevent cancer. To achieve this goal in a scientifically rigorous manner, the National Cancer Institute (NCI) launched CPTAC to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, and provide this data with accompanying assays and protocols to the public. Genomics initiatives such as The Cancer Genome Atlas (TCGA) have characterized and sequenced the genomic alterations from several types of cancer. CPTAC will leverage its analytical outputs by producing a unique continuum that defines the proteins translated from cancer genomes in order to link genotype to proteotype and ultimately to phenotype. Scientific Approach: The structure of CPTAC is designed to facilitate the efficient implementation of a two-step developmental pipeline, Discovery and Verification. The pipeline originates with the CPTAC Resource Center, which will provide a set of high-quality, genomically characterized clinical biospecimens from patients with a single type of cancer. The Discovery Unit of each Proteome Characterization Center (PCC) will use a set of proteomic technologies to comprehensively analyze the protein composition of this set of biospecimens including mapping proteome to genome and detecting and quantifying protein products that correspond to genomic aberrations. All data from the Discovery Units will be shared within the network via the CPTAC Data Center. Based on this aggregate data set, each Discovery Unit will select and prioritize cancer-related proteins for potential use in the verification step. The selected lists of prioritized proteins by the Discovery Units will be consolidated and collectively prioritized. The Verification Unit of each PCC will develop targeted assays against corresponding protein targets as assigned by the verification plan. The Verification Units will then verify the biomarker candidates by performing these assays in clinically relevant cancer biospecimens (provided by the CPTAC Resource Center). Data from these verification studies will be shared via the CPTAC Data Center. These verified proteins will serve as high-value targets to other in