Review

. 2023 Aug 14;41(8):1397-1406.

doi: 10.1016/j.ccell.2023.06.009.

Proteogenomic data and resources for pan-cancer analysis

Yize Li¹, Yongchao Dou², Felipe Da Veiga Leprevost³, Yifat Geffen⁴, Anna P Calinawan⁵, François Aguet⁴, Yo Akiyama⁴, Shankara Anand⁴, Chet Birger⁴, Song Cao¹, Rekha Chaudhary⁶, Padmini Chilappagari⁶, Marcin Cieslik⁷, Antonio Colaprico⁸, Daniel Cui Zhou¹, Corbin Day⁹, Marcin J Domagalski⁶, Myvizhi Esai Selvan⁵, David Fenyö¹⁰, Steven M Foltz¹, Alicia Francis⁶, Tania Gonzalez-Robles¹¹, Zeynep H Gümüş⁵, David Heiman⁴, Michael Holck⁶, Runyu Hong¹⁰, Yingwei Hu¹², Eric J Jaehnig², Jiayi Ji¹³, Wen Jiang², Lizabeth Katsnelson¹⁰, Karen A Ketchum⁶, Robert J Klein⁵, Jonathan T Lei², Wen-Wei Liang¹, Yuxing Liao², Caleb M Lindgren⁹, Weiping Ma⁵, Lei Ma⁶, Michael J MacCoss¹⁴, Fernanda Martins Rodrigues¹, Wilson McKerrow¹⁰, Ngoc Nguyen⁶, Robert Oldroyd⁹, Alexander Pilozzi⁶, Pietro Pugliese¹⁵, Boris Reva⁵, Paul Rudnick¹⁶, Kelly V Ruggles¹⁷, Dmitry Rykunov⁵, Sara R Savage², Michael Schnaubelt¹², Tobias Schraink¹¹, Zhiao Shi², Deepak Singhal⁶, Xiaoyu Song¹³, Erik Storrs¹, Nadezhda V Terekhanova¹, Ratna R Thangudu⁶, Mathangi Thiagarajan¹⁸, Liang-Bo Wang¹, Joshua M Wang¹⁰, Ying Wang¹⁰, Bo Wen², Yige Wu¹, Matthew A Wyczalkowski¹, Yi Xin⁶, Lijun Yao¹, Xinpei Yi², Hui Zhang¹², Qing Zhang⁴, Maya Zuhl⁶, Gad Getz¹⁹, Li Ding²⁰, Alexey I Nesvizhskii³, Pei Wang⁵, Ana I Robles²¹, Bing Zhang²², Samuel H Payne²³; Clinical Proteomic Tumor Analysis Consortium

Collaborators, Affiliations

Collaborators

Clinical Proteomic Tumor Analysis Consortium:
Alexander J Lazar, Amanda G Paulovich, Antonio Colaprico, Antonio Iavarone, Arul M Chinnaiyan, Brian J Druker, Chandan Kumar-Sinha, Chelsea J Newton, Chen Huang, D R Mani, Richard D Smith, Emily Huntsman, Eric E Schadt, Eunkyung An, Francesca Petralia, Galen Hostetter, Gilbert S Omenn, Hanbyul Cho, Henry Rodriguez, Hui Zhang, Iga Kolodziejczak, Jared L Johnson, Jasmin Bavarva, Jimin Tan, Karin D Rodland, Karl R Clauser, Karsten Krug, Lewis C Cantley, Maciej Wiznerowicz, Matthew J Ellis, Meenakshi Anurag, Mehdi Mesri, Michael A Gillette, Michael J Birrer, Michele Ceccarelli, Saravana M Dhanasekaran, Nathan Edwards, Nicole Tignor, Özgün Babur, Pietro Pugliese, Sara J C Gosline, Scott D Jewell, Shankha Satpathy, Shrabanti Chowdhury, Stephan Schürer, Steven A Carr, Tao Liu, Tara Hiltke, Tomer M Yaron, Vasileios Stathias, Wenke Liu, Xu Zhang, Yizhe Song, Zhen Zhang

Affiliations

¹ 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.
² 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.
³ Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
⁵ Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁶ ICF, Rockville, MD 20850, USA.
⁷ Department of Computational Medicine & Bioinformatics, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
⁸ 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.
⁹ Department of Biology, Brigham Young University, Provo, UT 84602, USA.
¹⁰ 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.
¹¹ 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.
¹² Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
¹³ Tisch Cancer Institute and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
¹⁴ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
¹⁵ Department of Sciences and Technologies, University of Sannio, Benevento 82100, Italy.
¹⁶ Spectragen Informatics, Bainbridge Island, WA 98110, USA.
¹⁷ 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.
¹⁸ Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
¹⁹ 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.
²⁰ 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.
²¹ Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA. Electronic address: roblesa@mail.nih.gov.
²² 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.
²³ Department of Biology, Brigham Young University, Provo, UT 84602, USA. Electronic address: sam_payne@byu.edu.

PMID: 37582339
PMCID: PMC10506762
DOI: 10.1016/j.ccell.2023.06.009

Review

Proteogenomic data and resources for pan-cancer analysis

Yize Li et al. Cancer Cell. 2023.

. 2023 Aug 14;41(8):1397-1406.

doi: 10.1016/j.ccell.2023.06.009.

Authors

Collaborators

Clinical Proteomic Tumor Analysis Consortium:
Alexander J Lazar, Amanda G Paulovich, Antonio Colaprico, Antonio Iavarone, Arul M Chinnaiyan, Brian J Druker, Chandan Kumar-Sinha, Chelsea J Newton, Chen Huang, D R Mani, Richard D Smith, Emily Huntsman, Eric E Schadt, Eunkyung An, Francesca Petralia, Galen Hostetter, Gilbert S Omenn, Hanbyul Cho, Henry Rodriguez, Hui Zhang, Iga Kolodziejczak, Jared L Johnson, Jasmin Bavarva, Jimin Tan, Karin D Rodland, Karl R Clauser, Karsten Krug, Lewis C Cantley, Maciej Wiznerowicz, Matthew J Ellis, Meenakshi Anurag, Mehdi Mesri, Michael A Gillette, Michael J Birrer, Michele Ceccarelli, Saravana M Dhanasekaran, Nathan Edwards, Nicole Tignor, Özgün Babur, Pietro Pugliese, Sara J C Gosline, Scott D Jewell, Shankha Satpathy, Shrabanti Chowdhury, Stephan Schürer, Steven A Carr, Tao Liu, Tara Hiltke, Tomer M Yaron, Vasileios Stathias, Wenke Liu, Xu Zhang, Yizhe Song, Zhen Zhang

Affiliations

¹ 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.
² 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.
³ Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
⁵ Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁶ ICF, Rockville, MD 20850, USA.
⁷ Department of Computational Medicine & Bioinformatics, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
⁸ 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.
⁹ Department of Biology, Brigham Young University, Provo, UT 84602, USA.
¹⁰ 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.
¹¹ 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.
¹² Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
¹³ Tisch Cancer Institute and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
¹⁴ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
¹⁵ Department of Sciences and Technologies, University of Sannio, Benevento 82100, Italy.
¹⁶ Spectragen Informatics, Bainbridge Island, WA 98110, USA.
¹⁷ 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.
¹⁸ Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
¹⁹ 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.
²⁰ 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.
²¹ Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA. Electronic address: roblesa@mail.nih.gov.
²² 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.
²³ Department of Biology, Brigham Young University, Provo, UT 84602, USA. Electronic address: sam_payne@byu.edu.

PMID: 37582339
PMCID: PMC10506762
DOI: 10.1016/j.ccell.2023.06.009

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.

Keywords: CPTAC; data harmonization; multi-omics; open data; pan-cancer; proteogenomics.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests F.A. is an inventor on a patent application related to SignatureAnalyzer-GPU filed by the Broad Institute and is an employee and shareholder of Illumina Inc. since 8 November 2021.

Figures

**Fig. 1 -. Tumor types and data types of the CPTAC pan-cancer dataset.**
Overview of the available molecular data types for the CPTAC pan-cancer cohort (n=1072, see Table S1 for list of excluded cases and reasons for exclusion from the original data sets). Whole exome, whole genome, transcriptome, proteome, and phosphoproteome data are available for all ten cancer types. Normal samples are available for a subset of tumor types, see Table S1 and S2.

**Fig. 2 -. Demographics of the CPTAC dataset.**
Distributions of selected clinical features among the pan-cancer cohort illustrated in Fig 1. Age is stratified by quartiles. Grade information is not available for BRCA and COAD cohorts. Stage information is not available for the GBM cohort. BMI, Tobacco use, and Alcohol use data is not available for BRCA, COAD, and HGSC cohorts. For survival plots, time starts at diagnosis. Additional clinical features, such as race and ethnicity, are available for exploration on the ProTrack pan-cancer sample dashboard.

**Figure 3 -. Streaming data with APIs.**
Programmatic access to CPTAC proteogenomic data across all cohorts is provided by both a Python and R API.

**Figure 4 -. Web portals to CPTAC data.**
Multiple websites present CPTAC’s proteogenomic data for visual exploration.

See this image and copyright information in PMC

References

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Proteogenomic data and resources for pan-cancer analysis

Collaborators

Affiliations

Proteogenomic data and resources for pan-cancer analysis

Authors

Collaborators

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Medical

Miscellaneous