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The overall objective of CPTAC is to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand the molecular basis of cancer that is not fully elucidated or not possible through genomics and to accelerate the translation of molecular findings into the clinic.  This is to be achieved through enhancing our understanding of cancer genome biology by adding a complementary functional layer of protein biology (a “proteogenome” approach) that refines/prioritizes driver genes, enhances understanding of pathogenesis through proteomic subtyping, illuminates dynamic alterations in posttranslational modifications responsible for the dysregulation of cancer signaling networks and pathways, and improves understanding of drug response and resistance to therapies.

CPTAC operates through three components that coordinate research activities.  Collectively, these components bring together leading centers nationwide that proteogenomically comprehensively characterize cancer types and support clinically-relevant research projects that elucidate biological mechanisms of response in clinical trials.  The three components are:

Proteome Characterization Centers (PCCs). PCCs work as a group to comprehensively characterize NCI-provided treatment-naïve biospecimens (genomically characterized) using high-throughput, analytically validated, standardized state-of-the-art proteomic technologies/workflows, to ensure the reliability and usefulness of the overall data collection effort.

Proteogenomic Translational Research Centers (PTRCs). PTRCs address questions of biology in the context of [in collaboration with] a NCI-sponsored clinical trial, using an integration of proteomics and genomics.  Focus is on understanding [predicting] drug response and resistance to therapies.

Proteogenomic Data Analysis Centers (PGDACs). PGDACs work as a group to integrate, visualize and analyze CPTAC data across different data types (genomics, transcriptomics, and proteomics) to identify potentially cancer-related molecular alterations at a linear sequence, network and pathway level, to elucidate how distinct changes at the protein level are related to abnormalities in cancer genomes. 

All CPTAC investigators collaborate, share data and expertise across the consortium, and participate in consortium activities.  Data (genomics, proteomics, imaging), assays, and reagents are made available to the public as a Community Resource in an effort to accelerate cancer research and advance patient care.