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.
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. These efforts are providing a catalogue of alterations in the cancer genome and setting the stage for the development of more molecular interventions. CPTAC will leverage its analytical outputs in the coming years by producing a unique continuum that defines the proteins translated from cancer genomes in order to link genotype to proteotype and ultimately to phenotype. This goal will be met through four overarching objectives. They are:
Objective 1: Identify and characterize the protein inventory from tumor and normal tissue biospecimens
Objective 2: Integrate genomic and proteomic data from analysis of common cancer biospecimens
Objective 3: Develop assays against proteins prioritized in the discovery stage as potential biomarker candidates
Objective 4: Perform testing of verification assays in relevant cohorts of biospecimens
At the discovery stage, approaches to integrate genomics and proteomics from a common sample divide into two categories. In the first category, a "targeting genome to proteome" approach, a genome dataset defines the protein sequences (candidates) to be targeted in proteomic measurements. In this approach, proteomic labs will seek to detect and quantify protein products that correspond to splice variants, mutations, insertions, deletions, rearrangements, copy number aberrations, or epigenomic changes detected at the genome level. In the second category, a "mapping proteome to genome" approach, the integration of the genomic and proteomic datasets is delayed until completion of both types of measurements. This approach allows a broader inventory of the detectable proteins in a tumor, including identification of post-translational modifications (PTMs) that may be critical to cell signaling pathways and networks. In addition, it can be used to improve the quality of genome annotations, as it provides confirmation of protein-coding genes (using proteomic information to annotate the genome). The combination of these two approaches is anticipated to produce a more comprehensive inventory of the detectable proteins in a tumor and advance our understanding of cancer biology. The targets identified during the discovery stage will then be configured into multiplexed verification assays that will be tested in relevant cohorts of biospecimens.
For more information about the CPTAC program, download the program flyer (.pdf file).