Skip to main content
SpringerLink
Log in

Safikhani et al. reply

  • Brief Communications Arising
  • Published:

From Nature

View current issue Submit your manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

References

  1. Geeleher, P., Gamazon, E. R., Seoighe, C., Cox, N. J. & Huang, R. S. Consistency in large pharmacogenomic studies. Nature 540, http://dx.doi.org/10.1038/nature19838 (2016)

  2. Garnett, M. J. et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483, 570–575 (2012)

    Article  ADS  CAS  Google Scholar 

  3. Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012)

    Article  ADS  CAS  Google Scholar 

  4. Haibe-Kains, B. et al. Inconsistency in large pharmacogenomic studies. Nature 504, 389–393 (2013)

    Article  ADS  CAS  Google Scholar 

  5. Safikhani, Z. et al. Revisiting inconsistency in large pharmacogenomic studies. F1000Research http://dx.doi.org/10.12688/f1000research.9611.1 (2016)

  6. Haverty, P. M. et al. Reproducible pharmacogenomic profiling of cancer cell line panels. Nature 533, 333–337 (2016)

    Article  ADS  CAS  Google Scholar 

  7. The Cancer Cell Line Encyclopedia Consortium and Genomics of Drug Sensitivity in Cancer Investigators. Pharmacogenomic agreement between two cancer cell line data sets. Nature 528, 84–87 (2015)

  8. Matthews, B. W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta 405, 442–451 (1975)

    Article  CAS  Google Scholar 

  9. Geeleher, P., Cox, N. J. & Huang, R. S. Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines. Genome Biol. 15, R47 (2014)

    Article  Google Scholar 

  10. Papillon-Cavanagh, S. et al. Comparison and validation of genomic predictors for anticancer drug sensitivity. J. Am. Med. Inform. Assoc. 20, 597–602 (2013)

    Article  Google Scholar 

  11. Dong, Z. et al. Anticancer drug sensitivity prediction in cell lines from baseline gene expression through recursive feature selection. BMC Cancer 15, 489 (2015)

    Article  Google Scholar 

  12. Jang, I. S., Neto, E. C., Guinney, J., Friend, S. H. & Margolin, A. A. Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data. Pac. Symp. Biocomput. 2014, 63–74 (2014)

    Google Scholar 

  13. Cortés-Ciriano, I. et al. Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. Bioinformatics 32, 85–95 (2015)

    PubMed  PubMed Central  Google Scholar 

  14. Goodspeed, A., Heiser, L. M., Gray, J. W. & Costello, J. C. Tumor-derived cell lines as molecular models of cancer pharmacogenomics. Mol. Cancer Res. 14, 3–13 (2015)

    Article  Google Scholar 

  15. Sandve, G. K, Nekrutenko, A., Taylor, J. & Hovig, E. Ten simple rules for reproducible computational research. PLoS Comput. Biol.9, e1003285 (2013).

Download references

Author information

Authors and Affiliations

  1. Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 2M9, Ontario, Canada

    Zhaleh Safikhani, Petr Smirnov, Mark Freeman & Benjamin Haibe-Kains

  2. Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada

    Zhaleh Safikhani & Benjamin Haibe-Kains

  3. Institut de recherches cliniques de Montréal, Montreal, H2W 1R7, Quebec, Canada

    Nehme El-Hachem

  4. Hospital for Sick Children, Toronto, M5G 1X8, Ontario, Canada

    Anna Goldenberg

  5. Department of Computer Science, University of Toronto, Toronto, M5S 2E4, Ontario, Canada

    Anna Goldenberg & Benjamin Haibe-Kains

  6. The Francis Crick Institute, University College London, London, NW1 1AT, UK

    Nicolai J. Birkbak

  7. University College London Cancer Institute, London, WC1E 6BT, UK

    Nicolai J. Birkbak

  8. University College London Cancer Institute, London, WC1E 6BT, UK.,

    Nicolai J. Birkbak

  9. Beth Israel Deaconess Medical Center, Boston, 02215, Massachusetts, USA

    Andrew H. Beck

  10. Harvard Medical School, Boston, 02115, Massachusetts, USA

    Andrew H. Beck & Hugo J. W. L. Aerts

  11. Dana-Farber Cancer Institute, Boston, 02115, Massachusetts, USA

    Hugo J. W. L. Aerts & John Quackenbush

  12. Brigham and Women’s Hospital, Boston, 02115, Massachusetts, USA

    Hugo J. W. L. Aerts

  13. Harvard School of Public Health, Boston, 02115, Massachusetts, USA

    John Quackenbush

  14. Ontario Institute of Cancer Research, Toronto, M5G 1L7, Ontario, Canada

    Benjamin Haibe-Kains

Authors
  1. Zhaleh Safikhani
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nehme El-Hachem
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Petr Smirnov
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mark Freeman
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Anna Goldenberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Nicolai J. Birkbak
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Andrew H. Beck
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hugo J. W. L. Aerts
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. John Quackenbush
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Benjamin Haibe-Kains
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Benjamin Haibe-Kains.

Supplementary information

Supplementary Information

This file contains Supplementary Text and Data, Supplementary Methods, Supplementary Tables 1-2, Supplementary Figures 1-7 and additional references. (PDF 1357 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Safikhani, Z., El-Hachem, N., Smirnov, P. et al. Safikhani et al. reply. Nature 540, E2–E4 (2016). https://doi.org/10.1038/nature19839

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature19839

  • Springer Nature Limited

This article is cited by

Search

Navigation