IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v9y2018i1d10.1038_s41467-018-06149-6.html
   My bibliography  Save this article

Gene expression imputation identifies candidate genes and susceptibility loci associated with cutaneous squamous cell carcinoma

Author

Listed:
  • Nilah M. Ioannidis

    (Stanford University School of Medicine
    Stanford University School of Medicine
    Stanford University School of Medicine, Stanford)

  • Wei Wang

    (Stanford University School of Medicine)

  • Nicholas A. Furlotte

    (23andMe, Inc.)

  • David A. Hinds

    (23andMe, Inc.)

  • Carlos D. Bustamante

    (Stanford University School of Medicine
    Stanford University School of Medicine, Stanford)

  • Eric Jorgenson

    (Kaiser Permanente Northern California)

  • Maryam M. Asgari

    (Kaiser Permanente Northern California
    Massachusetts General Hospital)

  • Alice S. Whittemore

    (Stanford University School of Medicine
    Stanford University School of Medicine)

Abstract

Cutaneous squamous cell carcinoma (cSCC) is a common skin cancer with genetic susceptibility loci identified in recent genome-wide association studies (GWAS). Transcriptome-wide association studies (TWAS) using imputed gene expression levels can identify additional gene-level associations. Here we impute gene expression levels in 6891 cSCC cases and 54,566 controls in the Kaiser Permanente Genetic Epidemiology Research in Adult Health and Aging (GERA) cohort and 25,558 self-reported cSCC cases and 673,788 controls from 23andMe. In a discovery-validation study, we identify 19 loci containing 33 genes whose imputed expression levels are associated with cSCC at false discovery rate

Suggested Citation

  • Nilah M. Ioannidis & Wei Wang & Nicholas A. Furlotte & David A. Hinds & Carlos D. Bustamante & Eric Jorgenson & Maryam M. Asgari & Alice S. Whittemore, 2018. "Gene expression imputation identifies candidate genes and susceptibility loci associated with cutaneous squamous cell carcinoma," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06149-6
    DOI: 10.1038/s41467-018-06149-6
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-018-06149-6
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-018-06149-6?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
    ---><---

    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:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06149-6. 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.