IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v504y2013i7480d10.1038_nature12831.html
   My bibliography  Save this article

Inconsistency in large pharmacogenomic studies

Author

Listed:
  • Benjamin Haibe-Kains

    (Institut de Recherches Cliniques de Montréal, University of Montreal, Montreal, Quebec, Canada
    Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada)

  • Nehme El-Hachem

    (Institut de Recherches Cliniques de Montréal, University of Montreal, Montreal, Quebec, Canada)

  • Nicolai Juul Birkbak

    (Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark)

  • Andrew C. Jin

    (Beth Israel Deaconess Medical Center and Harvard Medical School)

  • Andrew H. Beck

    (Beth Israel Deaconess Medical Center and Harvard Medical School)

  • Hugo J. W. L. Aerts

    (Dana-Farber Cancer Institute
    Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School
    Maastricht University, Maastricht 6200 MD, The Netherlands)

  • John Quackenbush

    (Dana-Farber Cancer Institute
    Dana-Farber Cancer Institute)

Abstract

This Analysis compares two large-scale pharmacogenomic data sets that catalogued the sensitivity of a large number of cancer cell lines to approved and potential drugs, and finds that whereas the gene expression data are largely concordant between the two studies, the reported drug sensitivity measures and subsequently their association with genomic features are highly discordant.

Suggested Citation

  • Benjamin Haibe-Kains & Nehme El-Hachem & Nicolai Juul Birkbak & Andrew C. Jin & Andrew H. Beck & Hugo J. W. L. Aerts & John Quackenbush, 2013. "Inconsistency in large pharmacogenomic studies," Nature, Nature, vol. 504(7480), pages 389-393, December.
    • Handle: RePEc:nat:nature:v:504:y:2013:i:7480:d:10.1038_nature12831
    DOI: 10.1038/nature12831
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature12831
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/nature12831?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Paul Geeleher & Nancy Cox & R Stephanie Huang, 2014. "pRRophetic: An R Package for Prediction of Clinical Chemotherapeutic Response from Tumor Gene Expression Levels," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-3, September.
    2. Adrià Fernández-Torras & Miquel Duran-Frigola & Martino Bertoni & Martina Locatelli & Patrick Aloy, 2022. "Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    3. Jurica Levatić & Marina Salvadores & Francisco Fuster-Tormo & Fran Supek, 2022. "Mutational signatures are markers of drug sensitivity of cancer cells," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    4. Xiao-Song Wang & Sanghoon Lee & Han Zhang & Gong Tang & Yue Wang, 2022. "An integral genomic signature approach for tailored cancer therapy using genome-wide sequencing data," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    5. Elisabeth Prince & Jennifer Cruickshank & Wail Ba-Alawi & Kelsey Hodgson & Jillian Haight & Chantal Tobin & Andrew Wakeman & Alona Avoulov & Valentina Topolskaia & Mitchell J. Elliott & Alison P. McGu, 2022. "Biomimetic hydrogel supports initiation and growth of patient-derived breast tumor organoids," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    6. Caitlin E. Mills & Kartik Subramanian & Marc Hafner & Mario Niepel & Luca Gerosa & Mirra Chung & Chiara Victor & Benjamin Gaudio & Clarence Yapp & Ajit J. Nirmal & Nicholas Clark & Peter K. Sorger, 2022. "Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    7. Naiqian Zhang & Haiyun Wang & Yun Fang & Jun Wang & Xiaoqi Zheng & X Shirley Liu, 2015. "Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model," PLOS Computational Biology, Public Library of Science, vol. 11(9), pages 1-18, September.
    8. Nina Kusch & Andreas Schuppert, 2020. "Two-step multi-omics modelling of drug sensitivity in cancer cell lines to identify driving mechanisms," PLOS ONE, Public Library of Science, vol. 15(11), pages 1-22, November.
    9. David A Knowles & Gina Bouchard & Sylvia Plevritis, 2019. "Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features," PLOS Computational Biology, Public Library of Science, vol. 15(5), pages 1-18, May.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:504:y:2013:i:7480:d:10.1038_nature12831. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.