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Reproducible pharmacogenomic profiling of cancer cell line panels

Nature volume 533, pages 333337 (19 May 2016) | Download Citation


The use of large-scale genomic and drug response screening of cancer cell lines depends crucially on the reproducibility of results. Here we consider two previously published screens, plus a later critique of these studies. Using independent data, we show that consistency is achievable, and provide a systematic description of the best laboratory and analysis practices for future studies.

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We thank G. Manning, T. Sandmann, B. Forrest and D. Stokoe for their valuable contributions to improving the manuscript. We also thank L. Shi and J. Wu for work on early phases of gCSI screening; R. Rodriguez, G. Yuen and D. Hascall for help preparing drug plates; Y. Jiang for assistance with drug plate quality control; and S. Selvaraj and M. Yu for banking and quality control of cell lines used in this study. This manuscript contains an analysis of data released by the Broad Institute (CCLE) and by the GDSC members. Those who carried out the original analysis and collection of these data bear no responsibility for the further analysis or interpretation of it. The relevant subset of the CCLE data are included in the supplementary software package with the explicit written consent of the CCLE group. The GDSC data has been included following the GDSC’s instructions for attribution and under their specified open-source license, Creative Commons 3.0.

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Author notes

    • Peter M. Haverty
    •  & Eva Lin

    These authors contributed equally to this work.


  1. Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, USA

    • Peter M. Haverty
    • , Steve Lianoglou
    •  & Richard Bourgon
  2. Department of Discovery Oncology, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, USA

    • Eva Lin
    • , Jenille Tan
    • , Yihong Yu
    • , Billy Lam
    • , Richard M. Neve
    • , Scott Martin
    • , Jeff Settleman
    •  & Robert L. Yauch


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P.M.H. and R.B. drafted the manuscript, prepared figures and tables and designed the factorial screen. P.M.H. and R.B. performed computational analysis and interpreted results. S.L. contributed to the development of elastic net biomarker identification software. J.S. and R.L.Y. contributed to the experimental design, data analysis, and manuscript preparation. S.M. contributed to manuscript preparation and data interpretation. E.L., J.T., Y.Y. and B.L. performed primary cell-based screening experiments. E.L. and R.M.N. designed and managed the cell-based screening experiments.

Competing interests

All authors are employees of Genentech Inc. and may be stockholders of Roche Pharmaceuticals.

Corresponding author

Correspondence to Richard Bourgon.

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    Supplementary Information

    This file contains a Supplementary note and full legends for Supplementary Tables 1-6.

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    Supplementary Data

    This file contains Supplementary Tables 1-6, please refer to the Supplementary Information document for full legends.

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