Proteogenomic data and resources for pan-cancer analysis
Yize Li(James S. McDonnell Foundation), Yongchao Dou(Baylor College of Medicine), Felipe da Veiga Leprevost(University of Michigan), Yifat Geffen(Broad Institute), Anna Calinawan(Icahn School of Medicine at Mount Sinai), François Aguet(Broad Institute), Yo Akiyama(Broad Institute), Shankara Anand(Broad Institute), Chet Birger(Broad Institute), Song Cao(James S. McDonnell Foundation), Rekha Chaudhary(ICF International (United States)), Padmini Chilappagari(ICF International (United States)), Marcin Cieślik(University of Michigan), Antonio Colaprico(University of Miami), Daniel Cui Zhou(James S. McDonnell Foundation), Corbin Day(Brigham Young University), Marcin J. Domagalski(ICF International (United States)), Myvizhi Esai Selvan(Icahn School of Medicine at Mount Sinai), David Fenyö(Institute for Systems Biology), Steven M. Foltz(James S. McDonnell Foundation), Alicia Francis(ICF International (United States)), Tania J González-Robles(Institute for Systems Biology), Zeynep H. Gümüş(Icahn School of Medicine at Mount Sinai), David I. Heiman(Broad Institute), Michael Holck(ICF International (United States)), Runyu Hong(Institute for Systems Biology), Yingwei Hu(Johns Hopkins University), Eric J. Jaehnig(Baylor College of Medicine), Jiayi Ji(Icahn School of Medicine at Mount Sinai), Wen Jiang(Baylor College of Medicine), Lizabeth Katsnelson(Institute for Systems Biology), Karen A. Ketchum(ICF International (United States)), Robert J. Klein(Icahn School of Medicine at Mount Sinai), Jonathan T. Lei(Baylor College of Medicine), Wen-Wei Liang(James S. McDonnell Foundation), Yuxing Liao(Baylor College of Medicine), Caleb M. Lindgren(Brigham Young University), Weiping Ma(Icahn School of Medicine at Mount Sinai), Lei Ma(ICF International (United States)), Michael J. MacCoss(University of Washington), Fernanda Martins Rodrigues(James S. McDonnell Foundation), Wilson McKerrow(Institute for Systems Biology), Ngoc B. Nguyen(ICF International (United States)), Robert Oldroyd(Brigham Young University), Alexander Pilozzi(ICF International (United States)), Pietro Pugliese(University of Sannio), Boris Reva(Icahn School of Medicine at Mount Sinai), Paul A. Rudnick, Kelly V. Ruggles(Institute for Systems Biology), Dmitry Rykunov(Icahn School of Medicine at Mount Sinai), Sara R. Savage(Baylor College of Medicine), Michael Schnaubelt(Johns Hopkins University), Tobias Schraink(Institute for Systems Biology), Zhiao Shi(Baylor College of Medicine), Deepak Singhal(ICF International (United States)), Xiaoyu Song(Icahn School of Medicine at Mount Sinai), Erik Storrs(James S. McDonnell Foundation), Nadezhda V. Terekhanova(James S. McDonnell Foundation), Ratna R. Thangudu(ICF International (United States)), Mathangi Thiagarajan(Frederick National Laboratory for Cancer Research), Liang-Bo Wang(James S. McDonnell Foundation), Joshua M. Wang(Institute for Systems Biology), Ying Wang(Institute for Systems Biology), Bo Wen(Baylor College of Medicine), Yige Wu(James S. McDonnell Foundation), Matthew A. Wyczalkowski(James S. McDonnell Foundation), Xin Yi(ICF International (United States)), Lijun Yao(James S. McDonnell Foundation), Xinpei Yi(Baylor College of Medicine), Hui Zhang(Johns Hopkins University), Qing Zhang(Broad Institute), Maya Zuhl(ICF International (United States)), Gad Getz(Broad Institute), Li Ding(James S. McDonnell Foundation), Alexey I. Nesvizhskii(University of Michigan), Pei Wang(Icahn School of Medicine at Mount Sinai), Ana I. Robles(Cancer Clinic), Bing Zhang(Baylor College of Medicine), Samuel Payne(Brigham Young University), Alexander J. Lazar, Amanda G. Paulovich, Antonio Colaprico(University of Miami), Antonio Iavarone(University of Miami), Arul M. Chinnaiyan, Brian Druker, Chandan Kumar‐Sinha, Chelsea J. Newton, Chen Huang, D.R. Mani(Brigham Young University), Richard Smith, Emily M. Huntsman, Eric E. Schadt, Eunkyung An, Francesca Petralia, Galen Hostetter, Gilbert S. Omenn, Hanbyul Cho, Henry Rodriguez, Hui Zhang(Johns Hopkins University), Iga Kołodziejczak(University of Michigan), Jared L. Johnson, Jasmin Bavarva, Jimin Tan(Institute for Systems Biology), Karin Rodland, Karl R. Clauser, Karsten Krug, Lewis C. Cantley, Maciej Wiznerowicz, Matthew J. Ellis, Meenakshi Anurag, Mehdi Mesri, Michael A. Gillette(Johns Hopkins University), Michael J. Birrer(University of Washington), Michele Ceccarelli, Saravana M. Dhanasekaran, Nathan Edwards(Baylor College of Medicine), Nicole Tignor, Özgün Babur, Pietro Pugliese(University of Sannio), Sara J.C. Gosline, Scott D. Jewell, Shankha Satpathy, Shrabanti Chowdhury, Stephan C. Schürer, Steven A. Carr(James S. McDonnell Foundation), Tao Liu, Tara Hiltke, Tomer M. Yaron, Vasileios Stathias, Wenke Liu, Xu Zhang(Baylor College of Medicine), Yizhe Song(Icahn School of Medicine at Mount Sinai), Zhen Zhang(Baylor College of Medicine), Daniel W. Chan
Cited by 222Open Access
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.
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