Consortium

CPTAC Teams

The following are the current CPTAC teams, representing a network of Proteome Characterization Centers (PCCs), Proteogenomic Data Analysis Centers (PGDACs), and Proteogenomic Translational Research Centers (PTRCs). Teams are listed alphabetically by institution, with their respective Principal Investigators:

Proteome Characterization Centers (PCCs)

PCCs use state-of-the-art, standardized mass spectrometry-based technologies to perform comprehensive proteomic characterizations on genomically-characterized biospecimens, and quantitative measurements of protein targets of biological/clinical relevance.

• Broad Institute, Cambridge, MA
  Principal Investigators: Steven A. Carr, Ph.D.; Michael Gillette, M.D., Ph.D.
• Johns Hopkins University, Baltimore, MD
  Principal Investigators: Daniel W. Chan, Ph.D.; Hui Zhang, Ph.D.
• Pacific Northwest National Laboratory, Richland, WA
  Principal Investigator: Tao Liu, Ph.D.

Proteogenomic Data Analysis Centers (PGDACs)

PGDACs conduct integration, visualization and analyses using different data types (genomics, transcriptomics, and proteomics, imaging and clinical data) to improve the understanding of genome-proteome relationship and the interplay/regulation of signaling pathways involved in cancer.

• Baylor College of Medicine, Houston, TX
  Principal Investigator: Bing Zhang, Ph.D.
  Additional area of focus: pathway and molecular network visualization.
• Broad Institute, Cambridge, MA
  Principal Investigators: Denkanikota R. Mani, Ph.D.; Gad Getz, Ph.D.
  Additional areas of focus: Automated, comprehensive analysis of cancer proteogenomics data using PANOPLY.
• Icahn School of Medicine at Mount Sinai, New York, NY
  Principal Investigators: Pei Wang, Ph.D.; Avi Ma’ayan, Ph.D.
  Additional areas of focus: data preprocessing and quality control for missing proteomics data, batch effects; global regulatory networks.
• University of Michigan, Ann Arbor, MI
  Principal Investigators: Alexey I. Nesvizhskii, Ph.D.; S. Mohan Dhanasekaran, Ph.D.
  Additional areas of focus: individualized proteogenomics; data independent acquisition (DIA) workflows; quality-control scoring measures to identify genomic/transcriptomic variants expressed at protein level.

Proteogenomic Translational Research Centers (PTRCs)

PTRCs address questions of biology in the context of a clinical trial [NCI-sponsored], using an integration of proteomics and genomics. Focus on understanding drug response and resistance to therapies.

• Fred Hutchinson Cancer Center, Seattle, WA; University of Pittsburgh, Pittsburgh, PA
  Principal Investigators: Amanda Paulovich, M.D., Ph.D.; Diwakar Davar, M.B.B.S, M.Sc.
  Cancer focus: Melanoma
• Mayo Clinic, Rochester, MN; Mayo Clinic Arizona, Scottsdale, AZ
  Principal Investigators: Akhilesh Pandey, M.D., Ph.D.; Rafael Fonseca, M.D.
  Cancer focus: Multiple myeloma
• Oregon Health & Science University, Portland, OR; Pacific Northwest National Laboratory, Richland, WA
  Principal Investigators: Jeffrey Tyner, Ph.D.; Paul Piehowski, Ph.D.
  Cancer focus: Acute myeloid leukemia
• Washington University in St. Louis, St. Louis, MO; Broad Institute, Cambridge, MA
  Principal Investigators: Ramaswamy Govindan, M.D.; Steven Carr, Ph.D.; Michael Gillette, M.D., Ph.D.
  Cancer focus: Lung Cancer

Partners

Tissue Source Sites (TSS)

TSSs deliver clinically annotated biospecimens that are prospectively collected using a protocol with specific requirements for biospecimen quality. These include high total cellularity and controlled ischemic time. Complete cases consist of tumor, blood, and where possible, non‐malignant tissue from the same patient. The network of CPTAC TSS is composed of Baylor College of Medicine; Children’s Hospital of Philadelphia; Corewell Health (formerly Spectrum Health System); Corewell Health William Beaumont University Hospital; Duke University; Fidelis Research; H. Lee Moffitt Cancer Center and Research Institute; Hackensack Meridian Health – Jersey Shore University Medical Center; International Institute for Molecular Oncology; Mayo Clinic Jacksonville; Memorial Sloan Kettering Cancer Center; Morehouse School of Medicine; Phase Clinical Services; Sinai Health System; St. Joseph’s Hospital & Medical Center; University of Calgary; University of Kansas Medical Center; University of Oklahoma; University of Pittsburgh; University of South Florida; University of Texas Health Science Center at San Antonio; University of Texas Southwestern; Washington University in St. Louis.

Biospecimen Core Resource (BCR)

The BCR receives, processes, qualifies, and distributes specimens to Characterization Centers. The current BCR for CPTAC is Van Andel Research Institute Biorepository, Grand Rapids, MI.

Genome Characterization in Partnership with Center for Cancer Genomics

Genomic analysis includes, whole exome, whole genome, total RNA and miRNA sequencing, and methylation array from tumor, blood and non‐malignant tissues, as appropriate.

Data Coordinating Center (DCC)

The CPTAC DCC collects, stores, and makes data available within the network and collates and formats proteomic data for dissemination through the Proteomic Data Commons. The current DCC for CPTAC is ICF, Rockville, MD.

Comprehensive Data Resource (CDR)

The CDR manages CPTAC biospecimen and clinical data, which includes patient clinical and pathology data, digital images, extensive biospecimen annotation surrounding the collection, storage, and processing conditions, and quality assurance/control (QA/QC) measures. CPTAC’s CDR is Leidos Biomedical Research.

Affiliated Institutions

• AstraZeneca Pharmaceuticals, Waltham, MA
• Baylor College of Medicine, Houston, TX
• Brigham Young University, Provo, UT
• Bristol Myers Squibb, New York, NY
• Broad Institute of MIT and Harvard, Cambridge, MA
• Bruker Corporation, Billerica, MA
• Cell Signaling, Danvers, MA
• Cellenion, Lyon, France
• Dana-Farber Cancer Institute, Boston, MA
• ECOG-ACRIN, Philadelphia, PA
• Emory Winship Cancer Institute, Atlanta, GA
• Fred Hutchinson Cancer Research Center, Seattle, WA
• Icahn School of Medicine at Mount Sinai, New York, NY
• ICF, Rockville, MD
• Institute for Systems Biology, Seattle, WA
• Johns Hopkins University, Baltimore, MD
• Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA
• Massachusetts General Hospital, Boston, MA
• Mayo Clinic Arizona, Scottsdale, AZ
• Mayo Clinic, Rochester, MN
• Melanoma Institute Australia, Wollstonecraft, Australia
• Memorial Sloan Kettering Cancer Center, New York, NY
• New York University Grossman School of Medicine, NY, NY
• Oregon Health & Science University, Portland, OR
• Pacific Northwest National Laboratory, Richland, WA
• Seven Bridges Genomics Inc, Charlestown, MA
• SISCAPA Assay Technologies, Washington, DC
• The Children's Hospital of Philadelphia, Philadelphia, PA
• The J. David Gladstone Institutes, San Francisco, CA
• The University of Texas MD Anderson Cancer Center, Houston, TX
• ThermoFisher Scientific, San Jose, CA
• University of California, Irvine, CA
• University of Massachusetts Boston, Boston, MA
• University of Miami, Miami, FL
• University of Michigan, Ann Arbor, MI
• University of Pennsylvania, Philadelphia, PA
• University of Pittsburgh, Pittsburgh, PA
• University of Texas Health Science Center at Houston, Houston, TXsity of Pennsylvania, Philadelphia, PA
• University of Washington, Seattle, WAsity of Pennsylvania, Philadelphia, PA
• Vanderbilt University Medical Center, Nashville, TNsity of Pennsylvania, Philadelphia, PA
• Washington University School of Medicine, St. Louis, MOsity of Pennsylvania, Philadelphia, PA
• sity of Pennsylvania, Philadelphia, PA
• Weill Cornell Medicine, New York, NYsity of Pennsylvania, Philadelphia, PA
• Yale University, New Haven, CT

Additional Partners

• Association for Diagnostics & Laboratory Medicine (ADLM)
  NCI’s OCCPR collaborates with the Association for Diagnostics & Laboratory Medicine (ADLM) via a memorandum of understanding (MOU) to promote and educate the clinical chemistry community in the area of proteomic standards/technologies to further its application in clinical labs.
• Food and Drug Administration
  NCI’s OCCPR and the Food and Drug Administration (FDA) formally collaborate (through a memorandum of understanding - MOU) to accelerate the translations of proteomics technologies and applications into clinical settings. This collaborative partnership has facilitated the FDA to be involved in the Clinical Proteomic Tumor Analysis Consortium’s discovery and confirmatory analytical workflows in the following capacities:
  • Development of open access (mock 510K) regulatory science documents on proteomic technologies
    • Analytical Validation of Protein-Based Multiplex Assays: A Workshop Report by the NCI-FDA Interagency Oncology Task Force on Molecular Diagnostics
    • Protein-Based Multiplex Assays: Mock Presubmissions to the U.S. Food and Drug Administration
  • Development of best practice [CLSI guidance] documents on the design, development, and validation of quantitative assays for targeted proteomic assays by mass spectrometry, and
  • Big Data Crowdsourcing Challenge
• National Institute of Standards and Technology
  NCI’s OCCPR collaborates with the National Institute of Standards and Technology (NIST) to develop mass spectrometry-based technology assessment quality control tools used by the CPTAC teams and the broad research community.
• Uniprot
  NCI’s OCCPR collaborates with UniProt, the leading online protein reference library. In addition to searching for a protein-of-interest in UniProt, which includes cross-reference links to the NCI CPTAC Assay Portal for fit-for-purpose targeted assays, users now have cross-reference links to the NCI CPTAC Antibody Portal for cancer-associated renewable antibodies.
• HUPO
  NCI’s OCCPR has a long-standing collaboration with the Human Proteome Organization (HUPO) that is centered in promoting every step in the road towards translation of proteomic measurements to patient care, from accurate and reliable measurements, to clinical and analytical validation of biomarkers, to regulatory compliance.

Governing Body Committees

OCCPR relies on governing body committees to provide objective and expert advice on the coordination and future direction of the CPTAC Program.

• The Steering Committee (SC) consists of awardees and OCCPR leadership, who formulate, coordinate, and oversee strategic decisions and policies regarding consortium-wide activities.
• The External Scientific Evaluation Panel (ESEP) independently assesses awardee research directions, progress, and strategic plans. The ESEP evaluates CPTAC member research and reviews program metrics, while recommending new research opportunities and priorities to the SC to advance CPTAC goals.
• The Biospecimen Working Group coordinates tissue sample processing and accrual efforts based on programmatic timelines.
• Disease Working Groups are recruited and designated by the CPTAC Steering Committee to identify important biological and clinical questions for a designated cancer type. Questions identified by a DWG serve as a guide on the type of molecular data that should be generated, including analysis of the data produced. DWGs are interdisciplinary and consist of international researchers and physicians.
• Data Working Groups ensure that the proteomic data is uploaded to the data coordinating center, determine and coordinate the use of analysis tools for each disease group to analyze data effectively, and incorporate and harmonize the tools into the proteogenomic analytical pipeline.
• Program Evaluation provides stewardship of the NCI research investment by overseeing program effectiveness and efficiency and ensuring that programmatic components meet CPTAC goals.