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.; Shankha Satpathy, 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.; Arul Chinnaiyan, M.D., 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.; Diwaker 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.; Brian J. Druker, M.D.; Richard Smith, 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