@article{a5963da5aab947e1af5ed68cca0b9b1b,
title = "Next-generation characterization of the Cancer Cell Line Encyclopedia",
abstract = "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.",
author = "Mahmoud Ghandi and Huang, {Franklin W.} and Judit Jan{\'e}-Valbuena and Kryukov, {Gregory V.} and Lo, {Christopher C.} and McDonald, {E. Robert} and Jordi Barretina and Gelfand, {Ellen T.} and Bielski, {Craig M.} and Haoxin Li and Kevin Hu and Andreev-Drakhlin, {Alexander Y.} and Jaegil Kim and Hess, {Julian M.} and Haas, {Brian J.} and Fran{\c c}ois Aguet and Weir, {Barbara A.} and Rothberg, {Michael V.} and Paolella, {Brenton R.} and Lawrence, {Michael S.} and Rehan Akbani and Yiling Lu and Tiv, {Hong L.} and Gokhale, {Prafulla C.} and {de Weck}, Antoine and Mansour, {Ali Amin} and Coyin Oh and Juliann Shih and Kevin Hadi and Yanay Rosen and Jonathan Bistline and Kavitha Venkatesan and Anupama Reddy and Dmitriy Sonkin and Manway Liu and Joseph Lehar and Korn, {Joshua M.} and Porter, {Dale A.} and Jones, {Michael D.} and Javad Golji and Giordano Caponigro and Taylor, {Jordan E.} and Dunning, {Caitlin M.} and Creech, {Amanda L.} and Warren, {Allison C.} and McFarland, {James M.} and Mahdi Zamanighomi and Audrey Kauffmann and Nicolas Stransky and Marcin Imielinski and Maruvka, {Yosef E.} and Cherniack, {Andrew D.} and Aviad Tsherniak and Francisca Vazquez and Jaffe, {Jacob D.} and Lane, {Andrew A.} and Weinstock, {David M.} and Johannessen, {Cory M.} and Morrissey, {Michael P.} and Frank Stegmeier and Robert Schlegel and Hahn, {William C.} and Gad Getz and Mills, {Gordon B.} and Boehm, {Jesse S.} and Golub, {Todd R.} and Garraway, {Levi A.} and Sellers, {William R.}",
note = "Funding Information: Competing interests J.M.K., M.D.J., D.A.P., F.S., E.R.M., J.L., R.S., J.B., A.D., K.V., A.R., J.G., G.C., M.L., A.K., M.P.M. and W.R.S. are current or former Novartis employees and/or stock holders. W.R.S. is a Board or SAB member and holds equity in Peloton Therapeutics and Ideaya Biosciences and has consulted for Array, Astex, Ipsen, Sanofi and Servier. B.A.W. is a J&J employee. F.S. and G.V.K. are KSQ Therapeutics employees. N.S. is an employee of Celsius Therapeutics. A.D.C. receives research support from Bayer AG. G.G. receives research support from IBM and Pharmacyclics and is an inventor on patent applications related to MuTect and ABSOLUTE. G.B.M. consults with AstraZeneca, ImmunoMET, Ionis, Nuevolution, PDX Bio, Signalchem Lifesciences, Symphogen and Tarveda, has stock options with Catena Pharmaceuticals, ImmunoMet, SignalChem, Spindle Top Ventures and Tarveda, has sponsored research funding from Adelson Medical Research Foundation, AstraZeneca, Breast Cancer Research Foundation, Immunomet, Komen Research Foundation, Pfizer, Nanostring, Tesaro, travel support from Chrysallis Bio and has licensed technology to Nanostring and Myriad Genetics. T.R.G. is an advisor to GlaxoSmithKline, is a co-founder of Sherlock Biosciences and was a co-founder and advisor to Foundation Medicine. J.K. is a Tesaro employee. W.C.H. is a consultant for Thermo Fisher, AjuIB, Paraxel and MPM Capital, and is a founder and consultant for KSQ Therapeutics. L.A.G. is an employee of Eli Lilly. Funding Information: Acknowledgements We thank the Broad Genomics Platform, C. Clish, H. Bitter, A. Najafi and E. Orlando for their contribution. This work was supported by grants from Novartis and partially by NIH/NCI grants 1U01CA217842-01, 1P50CA217685-01, 5P50CA098258, 1U24CA180922-01, 1R50CA211461-01, CA16672, 1R01CA219943-01, 1U54CA224068-01, NIH U01 CA176058 and R21 DA025720. F.W.H. was supported by the Prostate Cancer Foundation. M.I. was supported by a Burroughs Wellcome Fund Career Award. G.G. was partially supported by the Paul C. Zamecnik, MD, Chair in Oncology at MGH. G.B.M. was supported by the Adelson medical research fund. Drug sensitivity results are in part based on data generated by Cancer Target Discovery and Development (CTD2) Network (https://ocg.cancer.gov/ programs/ctd2/data-portal) established by the National Cancer Institute{\textquoteright}s Office of Cancer Genomics. Publisher Copyright: {\textcopyright} 2019, The Author(s), under exclusive licence to Springer Nature Limited.",
year = "2019",
month = may,
day = "23",
doi = "10.1038/s41586-019-1186-3",
language = "English (US)",
volume = "569",
pages = "503--508",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7757",
}