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 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), performed this characterization for TCGA through a 2-step pipeline. In the first stage, the Discovery Step, cancer-specific protein targets from TCGA samples were identified and quantified using technologies that survey the entire proteome. In the second stage, the Verification Step, targeted assays were developed to examine a larger number of biospecimens to ensure appropriate statistical power.

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

The TCGA's CPTAC Proteome Characterization Centers, by project title, were:

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.

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.