Next-generation characterization of the Cancer Cell Line Encyclopedia

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

doi:10.1038/s41586-019-1186-3

Next-generation characterization of the Cancer Cell Line Encyclopedia

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. LawrenceRehan 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

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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.

Original language	English (US)
Pages (from-to)	503-508
Number of pages	6
Journal	Nature
Volume	569
Issue number	7757
DOIs	https://doi.org/10.1038/s41586-019-1186-3
State	Published - May 23 2019
Externally published	Yes

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Ghandi, M., Huang, F. W., Jané-Valbuena, J., Kryukov, G. V., Lo, C. C., McDonald, E. R., Barretina, J., Gelfand, E. T., Bielski, C. M., Li, H., Hu, K., Andreev-Drakhlin, A. Y., Kim, J., Hess, J. M., Haas, B. J., Aguet, F., Weir, B. A., Rothberg, M. V., Paolella, B. R., ... Sellers, W. R. (2019). Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature, 569(7757), 503-508. https://doi.org/10.1038/s41586-019-1186-3

Ghandi, M, Huang, FW, Jané-Valbuena, J, Kryukov, GV, Lo, CC, McDonald, ER, Barretina, J, Gelfand, ET, Bielski, CM, Li, H, Hu, K, Andreev-Drakhlin, AY, Kim, J, Hess, JM, Haas, BJ, Aguet, F, Weir, BA, Rothberg, MV, Paolella, BR, Lawrence, MS, Akbani, R, Lu, Y, Tiv, HL, Gokhale, PC, de Weck, A, Mansour, AA, Oh, C, Shih, J, Hadi, K, Rosen, Y, Bistline, J, Venkatesan, K, Reddy, A, Sonkin, D, Liu, M, Lehar, J, Korn, JM, Porter, DA, Jones, MD, Golji, J, Caponigro, G, Taylor, JE, Dunning, CM, Creech, AL, Warren, AC, McFarland, JM, Zamanighomi, M, Kauffmann, A, Stransky, N, Imielinski, M, Maruvka, YE, Cherniack, AD, Tsherniak, A, Vazquez, F, Jaffe, JD, Lane, AA, Weinstock, DM, Johannessen, CM, Morrissey, MP, Stegmeier, F, Schlegel, R, Hahn, WC, Getz, G, Mills, GB, Boehm, JS, Golub, TR, Garraway, LA & Sellers, WR 2019, 'Next-generation characterization of the Cancer Cell Line Encyclopedia', Nature, vol. 569, no. 7757, pp. 503-508. https://doi.org/10.1038/s41586-019-1186-3

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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 = "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",

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T1 - Next-generation characterization of the Cancer Cell Line Encyclopedia

AU - Ghandi, Mahmoud

AU - Huang, Franklin W.

AU - Jané-Valbuena, Judit

AU - Kryukov, Gregory V.

AU - Lo, Christopher C.

AU - McDonald, E. Robert

AU - Barretina, Jordi

AU - Gelfand, Ellen T.

AU - Bielski, Craig M.

AU - Li, Haoxin

AU - Hu, Kevin

AU - Andreev-Drakhlin, Alexander Y.

AU - Kim, Jaegil

AU - Hess, Julian M.

AU - Haas, Brian J.

AU - Aguet, François

AU - Weir, Barbara A.

AU - Rothberg, Michael V.

AU - Paolella, Brenton R.

AU - Lawrence, Michael S.

AU - Akbani, Rehan

AU - Lu, Yiling

AU - Tiv, Hong L.

AU - Gokhale, Prafulla C.

AU - de Weck, Antoine

AU - Mansour, Ali Amin

AU - Oh, Coyin

AU - Shih, Juliann

AU - Hadi, Kevin

AU - Rosen, Yanay

AU - Bistline, Jonathan

AU - Venkatesan, Kavitha

AU - Reddy, Anupama

AU - Sonkin, Dmitriy

AU - Liu, Manway

AU - Lehar, Joseph

AU - Korn, Joshua M.

AU - Porter, Dale A.

AU - Jones, Michael D.

AU - Golji, Javad

AU - Caponigro, Giordano

AU - Taylor, Jordan E.

AU - Dunning, Caitlin M.

AU - Creech, Amanda L.

AU - Warren, Allison C.

AU - McFarland, James M.

AU - Zamanighomi, Mahdi

AU - Kauffmann, Audrey

AU - Stransky, Nicolas

AU - Imielinski, Marcin

AU - Maruvka, Yosef E.

AU - Cherniack, Andrew D.

AU - Tsherniak, Aviad

AU - Vazquez, Francisca

AU - Jaffe, Jacob D.

AU - Lane, Andrew A.

AU - Weinstock, David M.

AU - Johannessen, Cory M.

AU - Morrissey, Michael P.

AU - Stegmeier, Frank

AU - Schlegel, Robert

AU - Hahn, William C.

AU - Getz, Gad

AU - Mills, Gordon B.

AU - Boehm, Jesse S.

AU - Golub, Todd R.

AU - Garraway, Levi A.

AU - Sellers, William R.

PY - 2019/5/23

Y1 - 2019/5/23

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AB - 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.

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JO - Nature

JF - Nature

IS - 7757

ER -

Next-generation characterization of the Cancer Cell Line Encyclopedia

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