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Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR-Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines.


Mahmoud Ghandi, Franklin W Huang, Judit Jané-Valbuena, Gregory V Kryukov, Christopher C Lo, E Robert McDonald, Jordi Barretina, Ellen T Gelfand, Craig M Bielski, Haoxin Li, Kevin Hu, Alexander Y Andreev-Drakhlin, Jaegil Kim, Julian M Hess, Brian J Haas, François Aguet, Barbara A Weir, Michael V Rothberg, Brenton R Paolella, Michael S Lawrence, Rehan Akbani, Yiling Lu, Hong L Tiv, Prafulla C Gokhale, Antoine de Weck, Ali Amin Mansour, Coyin Oh, Juliann Shih, Kevin Hadi, Yanay Rosen, Jonathan Bistline, Kavitha Venkatesan, Anupama Reddy, Dmitriy Sonkin, Manway Liu, Joseph Lehar, Joshua M Korn, Dale A Porter, Michael D Jones, Javad Golji, Giordano Caponigro, Jordan E Taylor, Caitlin M Dunning, Amanda L Creech, Allison C Warren, James M McFarland, Mahdi Zamanighomi, Audrey Kauffmann, Nicolas Stransky, Marcin Imielinski, Yosef E Maruvka, Andrew D Cherniack, Aviad Tsherniak, Francisca Vazquez, Jacob D Jaffe, Andrew A Lane, David M Weinstock, Cory M Johannessen, Michael P Morrissey, Frank Stegmeier, Robert Schlegel, William C Hahn, Gad Getz, Gordon B Mills, Jesse S Boehm, Todd R Golub, Levi A Garraway, William R Sellers. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature. 2019 May;569(7757):503-508

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PMID: 31068700

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