Proteogenomic data and resources for pan-cancer analysis
Yize Li, Yongchao Dou, Felipe da Veiga Leprevost, Yifat Geffen, Anna Calinawan, François Aguet, Yo Akiyama, Shankara Anand, Chet Birger, Song Cao, Rekha Chaudhary, Padmini Chilappagari, Marcin Cieślik, Antonio Colaprico, Daniel Cui Zhou, Corbin Day, Marcin J. Domagalski, Myvizhi Esai Selvan, David Fenyö, Steven M. Foltz, Alicia Francis, Tania J González-Robles, Zeynep H. Gümüş, David I. Heiman, Michael Holck, Runyu Hong, Yingwei Hu, Eric J. Jaehnig, Jiayi Ji, Wen Jiang, Lizabeth Katsnelson, Karen A. Ketchum, Robert J. Klein, Jonathan T. Lei, Wen-Wei Liang, Yuxing Liao, Caleb M. Lindgren, Weiping Ma, Lei Ma, Michael J. MacCoss, Fernanda Martins Rodrigues, Wilson McKerrow, Ngoc B. Nguyen, Robert Oldroyd, Alexander Pilozzi, Pietro Pugliese, Boris Reva, Paul A. Rudnick, Kelly V. Ruggles, Dmitry Rykunov, Sara R. Savage, Michael Schnaubelt, Tobias Schraink, Zhiao Shi, Deepak Singhal, Xiaoyu Song, Erik Storrs, Nadezhda V. Terekhanova, Ratna R. Thangudu, Mathangi Thiagarajan, Liang-Bo Wang, Joshua M. Wang, Ying Wang, Bo Wen, Yige Wu, Matthew A. Wyczalkowski, Xin Yi, Lijun Yao, Xinpei Yi, Hui Zhang, Qing Zhang, Maya Zuhl, Gad Getz, Li Ding, Alexey I. Nesvizhskii, Pei Wang, Ana I. Robles, Bing Zhang, Samuel Payne, Alexander J. Lazar, Amanda G. Paulovich, Antonio Colaprico, Antonio Iavarone, Arul M. Chinnaiyan, Brian Druker, Chandan Kumar‐Sinha, Chelsea J. Newton, Chen Huang, D.R. Mani, Richard Smith, Emily M. Huntsman, Eric E. Schadt, Eunkyung An, Francesca Petralia, Galen Hostetter, Gilbert S. Omenn, Hanbyul Cho, Henry Rodriguez, Hui Zhang, Iga Kołodziejczak
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.