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Proteogenomic data and resources for pan-cancer analysis

  1. Inventor:
    Li, Yize
    Dou, Yongchao
    Da Veiga Leprevost, Felipe
    Geffen, Yifat
    Calinawan, Anna P
    Aguet, François
    Akiyama, Yo
    Anand, Shankara
    Birger, Chet
    Cao, Song
    Chaudhary, Rekha
    Chilappagari, Padmini
    Cieslik, Marcin
    Colaprico, Antonio
    Zhou, Daniel Cui
    Day, Corbin
    Domagalski, Marcin J
    Esai Selvan, Myvizhi
    Fenyö, David
    Foltz, Steven M
    Francis, Alicia
    Gonzalez-Robles, Tania
    Gümüs, Zeynep H
    Heiman, David
    Holck, Michael
    Hong, Runyu
    Hu, Yingwei
    Jaehnig, Eric J
    Ji, Jiayi
    Jiang, Wen
    Katsnelson, Lizabeth
    Ketchum, Karen A
    Klein, Robert J
    Lei, Jonathan T
    Liang, Wen-Wei
    Liao, Yuxing
    Lindgren, Caleb M
    Ma, Weiping
    Ma, Lei
    MacCoss, Michael J
    Martins Rodrigues, Fernanda
    McKerrow, Wilson
    Nguyen, Ngoc
    Oldroyd, Robert
    Pilozzi, Alexander
    Pugliese, Pietro
    Reva, Boris
    Rudnick, Paul
    Ruggles, Kelly V
    Rykunov, Dmitry
    Savage, Sara R
    Schnaubelt, Michael
    Schraink, Tobias
    Shi, Zhiao
    Singhal, Deepak
    Song, Xiaoyu
    Storrs, Erik
    Terekhanova, Nadezhda V
    Thangudu, Ratna R
    Thiagarajan,Mathangi
    Wang, Liang-Bo
    Wang, Joshua M
    Wang, Ying
    Wen, Bo
    Wu, Yige
    Wyczalkowski, Matthew A
    Xin, Yi
    Yao, Lijun
    Yi, Xinpei
    Zhang, Hui
    Zhang, Qing
    Zuhl, Maya
    Getz, Gad
    Ding, Li
    Nesvizhskii, Alexey I
    Wang, Pei
    Robles, Ana I
    Zhang, Bing
    Payne, Samuel H

  2. Inventor Address

    Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA., Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA., Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA., Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., ICF, Rockville, MD 20850, USA., Department of Computational Medicine 160;& Bioinformatics, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA., Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA., Department of Biology, Brigham Young University, Provo, UT 84602, USA., Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA., Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA., Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA., Tisch Cancer Institute and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA., Department of Sciences and Technologies, University of Sannio, Benevento 82100, Italy., Spectragen Informatics, Bainbridge Island, WA 98110, USA., Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA., Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Cancer Center and Department of Pathology, Mass. General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA., Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA., Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA. Electronic address: roblesa@mail.nih.gov., Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: bing.zhang@bcm.edu., Department of Biology, Brigham Young University, Provo, UT 84602, USA. Electronic address: sam_payne@byu.edu.,
    1. Year: 2023
    2. Date: Aug 14
  2. Published Source: Cancer Cell
    1. 41
    2. 8
    3. Pages: 1397-1406
  4. Patent Type: Review
  1. Abstract:

    The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data. Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.

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External Sources

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  2. DOI: 10.1016/j.ccell.2023.06.009
  3. PMID: 37582339
  4. PII : S1535-6108(23)00219-2

Library Notes

  1. Fiscal Year: FY2022-2023
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