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Consistency in drug response profiling

Nature volume 540, pages E5–E6 (2016)Cite this article

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arising from B. Haibe-Kains et al. Nature 504, 389–393 (2013); 10.1038/nature12831

The comparative analysis by Haibe-Kains et al.1 concluded that data from two large-scale studies of cancer cell lines2,3 showed highly discordant results for drug sensitivity measurements, whereas gene expression data were reasonably concordant. Here, we cross-compared the two original datasets2,3 against our own data of drug response profiles in overlapping cancer cell line panels. Our results indicate that it is possible to achieve concordance between different laboratories for drug response measurements by paying attention to the harmonization of assays and experimental procedures. There is a Reply to this Comment by Safikhani, Z. et al. Nature 540, http://dx.doi.org/10.1038/nature20172 (2016).

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Figure 1: Consistency between drug response profiles across FIMM, CCLE and CGP.

References

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

    Article  CAS  ADS  Google Scholar 

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

    Article  CAS  ADS  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  CAS  ADS  Google Scholar 

  4. Weinstein, J. N. & Lorenzi, P. L. Cancer: Discrepancies in drug sensitivity. Nature 504, 381–383 (2013)

    Article  CAS  ADS  Google Scholar 

  5. Yadav, B. et al. Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies. Sci. Rep. 4, 5193 (2014)

    Article  CAS  Google Scholar 

  6. Pemovska, T. et al. Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov. 3, 1416–1429 (2013)

    Article  CAS  Google Scholar 

  7. Brazma, A. et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 29, 365–371 (2001)

    Article  CAS  Google Scholar 

  8. Levenberg, K. A method for the solution of certain problems in least squares. Q. Appl. Math. 2, 164–168 (1944)

    Article  MathSciNet  Google Scholar 

  9. Marquardt, D. W. An algorithm for least-squares estimation of nonlinear parameters. J. Soc. Ind. Appl. Math. 11, 431–441 (1963)

    Article  MathSciNet  Google Scholar 

  10. Nicola, G., Liu, T. & Gilson, M. K. Public domain databases for medicinal chemistry. J. Med. Chem. 55, 6987–7002 (2012)

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, 00290, Finland

    John Patrick Mpindi, Bhagwan Yadav, Päivi Östling, Prson Gautam, Disha Malani, Astrid Murumägi, Akira Hirasawa, Sara Kangaspeska, Krister Wennerberg, Olli Kallioniemi & Tero Aittokallio

  2. Department of Oncology and Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, 17165, Sweden

    Päivi Östling & Olli Kallioniemi

  3. Department of Obstetrics & Gynecology, Keio University School of Medicine, Tokyo, 160-8582, Japan

    Akira Hirasawa

  4. Department of Mathematics and Statistics, University of Turku, Turku, 20014, Finland

    Tero Aittokallio

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  1. John Patrick Mpindi
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Corresponding author

Correspondence to Tero Aittokallio.

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The authors declare no competing financial interests.

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Mpindi, J., Yadav, B., Östling, P. et al. Consistency in drug response profiling. Nature 540, E5–E6 (2016). https://doi.org/10.1038/nature20171

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