The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity (original) (raw)

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Gene Expression Omnibus

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Data have been deposited in the Gene ExpressionOmnibus (GEO) using accession number GSE36139 and are also available at http://www.broadinstitute.org/ccle.

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Acknowledgements

We thank the staff of the Biological Samples Platform, the Genetic Analysis Platform and the Sequencing Platform at the Broad Institute. We thank S. Banerji, J. Che, C .M. Johannessen, A. Su and N. Wagle for advice and discussion. We are grateful for the technical assistance and support of G. Bonamy, R. Brusch III, E. Gelfand, K. Gravelin, T. Huynh, S. Kehoe, K. Matthews, J. Nedzel, L. Niu, R. Pinchback, D. Roby, J. Slind, T. R. Smith, L. Tan, V. Trinh, C. Vickers, G. Yang, Y. Yao and X. Zhang. The Cancer Cell Line Encyclopedia project was enabled by a grant from the Novartis Institutes for Biomedical Research. Additional funding support was provided by the National Cancer Institute (M.M., L.A.G.), the Starr Cancer Consortium (M.F.B., L.A.G.), and the NIH Director’s New Innovator Award (L.A.G.).

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Author notes

  1. Jordi Barretina, Adam A. Margolin & Michael F. Berger
    Present address: Present addresses: Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA (J.B.); Sage Bionetworks, 1100 Fairview Ave. N., Seattle, Washington 98109, USA (A.A.M.); Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA (M.F.B.).,
  2. Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, Adam A. Margolin, Michael P. Morrissey, William R. Sellers, Robert Schlegel and Levi A. Garraway: These authors contributed equally to this work.

Authors and Affiliations

  1. The Broad Institute of Harvard and MIT, Cambridge, 02142, Massachusetts, USA
    Jordi Barretina, Nicolas Stransky, Adam A. Margolin, Gregory V. Kryukov, Lauren Murray, Michael F. Berger, Paula Morais, Adam Korejwa, Judit Jané-Valbuena, Supriya Gupta, Scott Mahan, Carrie Sougnez, Robert C. Onofrio, Ted Liefeld, Wendy Winckler, Michael Reich, Jill P. Mesirov, Stacey B. Gabriel, Gad Getz, Kristin Ardlie, Matthew Meyerson, Todd R. Golub & Levi A. Garraway
  2. Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02115, Massachusetts, USA
    Jordi Barretina, Judit Jané-Valbuena, Matthew Meyerson & Levi A. Garraway
  3. Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02115, Massachusetts, USA
    Jordi Barretina, Charles Hatton, Emanuele Palescandolo, Laura MacConaill, Matthew Meyerson, Todd R. Golub & Levi A. Garraway
  4. Novartis Institutes for Biomedical Research, Cambridge, 02139, Massachusetts, USA
    Giordano Caponigro, Kavitha Venkatesan, Christopher J. Wilson, Joseph Lehár, Dmitriy Sonkin, Anupama Reddy, Manway Liu, John E. Monahan, Jodi Meltzer, Felipa A. Mapa, Eva Bric-Furlong, Pichai Raman, Peter Aspesi, Melanie de Silva, Kalpana Jagtap, Michael D. Jones, Li Wang, Vic E. Myer, Barbara L. Weber, Jeff Porter, Markus Warmuth, Peter Finan, Michael P. Morrissey, William R. Sellers & Robert Schlegel
  5. Genomics Institute of the Novartis Research Foundation, San Diego, 92121, California, USA
    Sungjoon Kim, Joseph Thibault, Aaron Shipway, Ingo H. Engels, Nanxin Li & Jennifer L. Harris
  6. Novartis Institutes for Biomedical Research, Emeryville, 94608, California, USA
    Jill Cheng, Guoying K. Yu, Jianjun Yu & Vivien Chan
  7. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, 02115, Massachusetts, USA
    Todd R. Golub
  8. Howard Hughes Medical Institute, Chevy Chase, 20815, Maryland, USA
    Todd R. Golub

Authors

  1. Jordi Barretina
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  2. Giordano Caponigro
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  3. Nicolas Stransky
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  4. Kavitha Venkatesan
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  5. Adam A. Margolin
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  6. Sungjoon Kim
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  7. Christopher J. Wilson
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  8. Joseph Lehár
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  9. Gregory V. Kryukov
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  10. Dmitriy Sonkin
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  11. Anupama Reddy
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  12. Manway Liu
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  13. Lauren Murray
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  14. Michael F. Berger
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  15. John E. Monahan
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  16. Paula Morais
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  17. Jodi Meltzer
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  18. Adam Korejwa
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  19. Judit Jané-Valbuena
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  20. Felipa A. Mapa
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  21. Joseph Thibault
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  22. Eva Bric-Furlong
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  23. Pichai Raman
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  24. Aaron Shipway
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  25. Ingo H. Engels
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  26. Jill Cheng
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  27. Guoying K. Yu
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  28. Jianjun Yu
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  29. Peter Aspesi
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  30. Melanie de Silva
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  31. Kalpana Jagtap
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  32. Michael D. Jones
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  33. Li Wang
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  34. Charles Hatton
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  35. Emanuele Palescandolo
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  36. Supriya Gupta
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  37. Scott Mahan
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  38. Carrie Sougnez
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  39. Robert C. Onofrio
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  40. Ted Liefeld
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  41. Laura MacConaill
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  42. Wendy Winckler
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  43. Michael Reich
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  44. Nanxin Li
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  45. Jill P. Mesirov
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  46. Stacey B. Gabriel
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  47. Gad Getz
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  48. Kristin Ardlie
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  49. Vivien Chan
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  50. Vic E. Myer
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  51. Barbara L. Weber
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  52. Jeff Porter
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  53. Markus Warmuth
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  54. Peter Finan
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  55. Jennifer L. Harris
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  56. Matthew Meyerson
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  57. Todd R. Golub
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  58. Michael P. Morrissey
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  59. William R. Sellers
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  60. Robert Schlegel
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  61. Levi A. Garraway
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Contributions

For the work described herein, J.B. and G.C. were the lead research scientists; N.S., K.V. and A.M.M. were the lead computational biologists; M.P.M., W.R.S., R.S. and L.A.G. were the senior authors. J.B., G.C., S.K., P.M., J.M., J.T., A.S., N.L. and K.A. performed cell-line procural and processing; P.M. and K.A. performed or directed nucleic acid extraction and quality control; S.G., W.W. and S.B.G. performed or directed genomic data generation; C.J.W., F.A.M., E.B.-F., I.H.E., P.A., M.d.S., K.J. and V.E.M. performed pharmacological data generation; N.S., K.V., G.V.K., A.R., M.F.B., J.C., G.K.Y., M.D.J., T.L., M.R. and G.G. contributed to software development; N.S., K.V., A.A.M., J.L., G.V.K., D.S., A.R., M.L., M.F.B., A.K., P.R., J.C., G.K.Y., J.Y., M.D.J., L.W., C.H., E.P., J.P.M., V.C. and M.P.M. performed computational biology and bioinformatics analysis; J.B., G.C., N.S., L.M., J.E.M., J.J.-V., M.P.M., W.R.S., R.S. and L.A.G. performed biological analysis and interpretation; N.S., K.V., A.A.M., J.L., A.R., M.L., L.M., A.K., J.J.-V., J.C., G.K.Y. and J.Y. prepared figures and tables for the main text and Supplementary Information; J.B., G.C., N.S., K.V., A.A.M., J.L., G.V.K., J.J.-V., M.P.M. and L.A.G. wrote and edited the main text and Supplementary Information; J.B., G.C., N.S., K.V., S.K., C.J.W., J.L., S.M., C.S., R.C.O., T.L., L.McC., W.W., M.R., N.L., S.B.G., K.A. and V.C. performed project management; J.P.M., V.E.M., B.L.W., J.P., M.W., P.F., J.L.H., M.M. and T.R.G. contributed project oversight and advisory roles; and M.P.M., W.R.S., R.S. and L.A.G. provided overall project leadership.

Corresponding authors

Correspondence toRobert Schlegel or Levi A. Garraway.

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Competing interests

Multiple authors are employees of Novartis, Inc., as noted in the affiliations. T.R.G., M.M. and L.A.G. are consultants for and equity holders in Foundation Medicine, Inc. M.M. and L.A.G. are consultants for and receive sponsored research from Novartis, Inc.

Supplementary information

Supplementary Information 1

This file contains Supplementary Figures 1-15 and legends for Supplementary Tables 1-12 (see separate file for Supplementary Tables). (PDF 5034 kb)

Supplementary Information 2

This file contains Supplementary Methods and additional references. (PDF 450 kb)

Supplementary Tables

This file contains Supplementary Tables 1-12 – see Supplementary Information 1 for legends. (XLS 5774 kb)

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Barretina, J., Caponigro, G., Stransky, N. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.Nature 483, 603–607 (2012). https://doi.org/10.1038/nature11003

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