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

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Gene Expression Omnibus

Data deposits

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.).

Author information

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

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.

Ethics declarations

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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