• National Cancer Institute
  • National Human Genome Research Institute

The Cancer Genome Atlas

Proteome Characterization Centers

The discovery that proteins and peptides are "leaked" by tumors into clinically accessible bodily fluids such as blood has led to the possibility of monitoring response to treatment or diagnosing cancer at an early stage by collecting these fluids and testing for the presence of cancer-related biomarkers. Accordingly, the National Cancer Institute has launched the Clinical Proteomic Tumor Analysis Consortium (CPTAC) to characterize the proteomic content of tumors.  A key component of CPTAC, the Proteome Characterization Centers (PCCs), will perform this characterization through a 2-step pipeline. In the first stage, the Discovery Step, cancer-specific protein targets from TCGA samples are identified and quantified using technologies that survey the entire proteome. In the second stage, the Verification Step, targeted assays are developed to examine a larger number of biospecimens to ensure appropriate statistical power.

The PCCs add further depth to TCGA’s integrative process. TCGA has analyzed gene expression, but the proteome is an additional layer of data for researchers. These data will provide valuable information linking genotype to proteotype and ultimately to phenotype.

The CPTAC Proteome Characterization Centers, by project title, are:

Cancer Proteomic Center

  • Washington University, St. Louis, Mo.
    Principal Investigators:  
    Matthew J. C. Ellis, M.B., B.Chir, Ph.D.
    R. Reid Townsend, M.D., Ph.D.
  • University of North Carolina, Chapel Hill, N.C.
    Principal Investigator:  
    Xian Chen, Ph.D.
  • Boise State University, Boise, Idaho
    Principal Investigator:  
    Morgan C. Giddings, Ph.D.

Center for Application of Advanced Clinical Proteomic Technologies for Cancer

  • Pacific Northwest National Laboratory, Richland, Wash.
    Principal Investigators:   
    Richard D. Smith, Ph.D.
    Karin D. Rodland, Ph.D.

Proteo-Genomic Discovery, Prioritization and Verification of Cancer Biomarkers

  • The Broad Institute, Cambridge, Mass.
    Principal Investigator:  
    Steven A. Carr, Ph.D.
  • Fred Hutchinson Cancer Research Center, Seattle, Wash.
    Principal Investigator:  
    Amanda G. Paulovich M.D., Ph.D.

Proteome Characterization Center: A GenoProteomics Pipeline for Cancer Biomarkers

  • Johns Hopkins University, Baltimore, Md.
    Principal Investigators:  
    Daniel W. Chan, Ph.D.
    Zhen Zhang, Ph.D.
    Hui Zhang, Ph.D.

Vanderbilt Proteome Characterization Center

  • Vanderbilt University, Nashville, Tenn.
    Principal Investigator:
    Daniel C. Liebler, Ph.D.