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Consistency in large pharmacogenomic studies

Nature volume 540, pages E1–E2 (2016)Cite this article

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

Haibe-Kains et al.1 reported inconsistency between two large-scale pharmacogenomic studies—the Cancer Cell Line Encyclopedia (CCLE)2 and the Cancer Genome Project (CGP)3. Upon careful analysis of the same data, we have come to quite different and much more positive conclusions. Here we highlight the most important reasons for this. There is a Reply to this Comment by Safikhani, Z. et al. Nature 540, http://dx.doi.org/10.1038/nature19839 (2016).

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Figure 1: Limitations of using a correlation metric for the assessment of concordance between the CGP and CCLE drug sensitivity data.

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  • 13 December 2016

    The received date and affiliation details for author P.G. were corrected in the HTML.

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Author information

Authors and Affiliations

  1. Department of Medicine, The University of Chicago, Chicago, 60637, Illinois, USA

    Paul Geeleher, Eric R. Gamazon, Nancy J. Cox & R. Stephanie Huang

  2. Division of Genetic Medicine, Vanderbilt University, Nashville, 37232, Tennessee, USA

    Eric R. Gamazon & Nancy J. Cox

  3. Academic Medical Center, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands

    Eric R. Gamazon

  4. Department of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland

    Cathal Seoighe

Authors
  1. Paul Geeleher
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  2. Eric R. Gamazon
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  3. Cathal Seoighe
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  4. Nancy J. Cox
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  5. R. Stephanie Huang
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Corresponding authors

Correspondence to Nancy J. Cox or R. Stephanie Huang.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

This file shows a summary of the results reported with the Supplementary Data of CGP and CCLE for the 15 compounds assessed by Haibe-Kains et al. These results were obtained from either the CGP web portal (www.cancerrxgene.org) or the supplementary tables S6 & S7 or supplementary figure 9 provided with the publication of the CCLE data. These already published results show a very clear trend of both studies reliably identifying many canonical drug targets. (XLSX 15 kb)

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Geeleher, P., Gamazon, E., Seoighe, C. et al. Consistency in large pharmacogenomic studies. Nature 540, E1–E2 (2016). https://doi.org/10.1038/nature19838

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