• An Addendum to this article was published on 28 November 2012


The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available1. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of ‘personalized’ therapeutic regimens2.

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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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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

    • Jordi Barretina
    • , Adam A. Margolin
    •  & Michael F. Berger

    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.).

    • Jordi Barretina
    • , Giordano Caponigro
    • , Nicolas Stransky
    • , Kavitha Venkatesan
    • , Adam A. Margolin
    • , Michael P. Morrissey
    • , William R. Sellers
    • , Robert Schlegel
    •  & Levi A. Garraway

    These authors contributed equally to this work.


  1. The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, 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, Massachusetts 02115, 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, Massachusetts 02115, USA

    • Jordi Barretina
    • , Charles Hatton
    • , Emanuele Palescandolo
    • , Laura MacConaill
    • , Matthew Meyerson
    • , Todd R. Golub
    •  & Levi A. Garraway
  4. Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, 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, California 92121, USA

    • Sungjoon Kim
    • , Joseph Thibault
    • , Aaron Shipway
    • , Ingo H. Engels
    • , Nanxin Li
    •  & Jennifer L. Harris
  6. Novartis Institutes for Biomedical Research, Emeryville, California 94608, USA

    • Jill Cheng
    • , Guoying K. Yu
    • , Jianjun Yu
    •  & Vivien Chan
  7. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA

    • Todd R. Golub
  8. Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA

    • Todd R. Golub


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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.

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.

Corresponding authors

Correspondence to Robert Schlegel or Levi A. Garraway.

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    Supplementary Information 1

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    This file contains Supplementary Methods and additional references.

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