IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-59005-9.html
   My bibliography  Save this article

Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity

Author

Listed:
  • Yixing Dong

    (Lausanne University Hospital; University of Lausanne)

  • Chiara Saglietti

    (Lausanne University Hospital and University of Lausanne)

  • Quentin Bayard

    (Owkin)

  • Almudena Espin Perez

    (Owkin)

  • Sabrina Carpentier

    (Owkin)

  • Daria Buszta

    (Lausanne University Hospital; Swiss Cancer Center Leman)

  • Stephanie Tissot

    (Lausanne University Hospital; Swiss Cancer Center Leman
    Ludwig Insitute for Cancer Research)

  • Rémy Dubois

    (Owkin)

  • Atanas Kamburov

    (Owkin)

  • Senbai Kang

    (Lausanne University Hospital; University of Lausanne)

  • Carla Haignere

    (Owkin)

  • Rita Sarkis

    (Lausanne University Hospital and University of Lausanne)

  • Sylvie Andre

    (Lausanne University Hospital; Swiss Cancer Center Leman
    Ludwig Insitute for Cancer Research
    Agora Translational Research Center)

  • Marina Alexandre Gaveta

    (Lausanne University Hospital; Swiss Cancer Center Leman
    Ludwig Insitute for Cancer Research
    Agora Translational Research Center)

  • Silvia Lopez Lastra

    (Owkin)

  • Nathalie Piazzon

    (Lausanne University Hospital and University of Lausanne)

  • Rita Santos

    (Owkin)

  • Katharina Loga

    (Owkin)

  • Caroline Hoffmann

    (Owkin)

  • George Coukos

    (Lausanne University Hospital; Swiss Cancer Center Leman
    Ludwig Insitute for Cancer Research
    Agora Translational Research Center)

  • Solange Peters

    (Lausanne University Hospital; Swiss Cancer Center Leman)

  • Vassili Soumelis

    (Owkin)

  • Eric Yves Durand

    (Owkin)

  • Laurence Leval

    (Lausanne University Hospital and University of Lausanne)

  • Raphael Gottardo

    (Lausanne University Hospital; University of Lausanne
    Agora Translational Research Center
    Swiss Institute of Bioinformatics
    Ecole Polytechnique Fédérale de)

  • Krisztian Homicsko

    (Lausanne University Hospital; Swiss Cancer Center Leman
    Ludwig Insitute for Cancer Research
    Agora Translational Research Center)

  • Elo Madissoon

    (Owkin)

Abstract

Recent advancements in probe-based, full-transcriptome technologies for FFPE tissues, such as Visium CytAssist, Chromium Flex, and GeoMx DSP, enable analysis of archival samples, facilitating the generation of data from extensive cohorts. However, these methods can be labor-intensive and costly, requiring informed selection based on research objectives. We compare these methods on FFPE tumor samples in Breast, NSCLC and DLBCL showing 1) good-quality, highly reproducible data from all methods; 2) GeoMx data containing cell mixtures despite marker-based preselection; 3) Visium and Chromium outperform GeoMx in discovering tumor heterogeneity and potential drug targets. We recommend the use of Visium and Chromium for high-throughput and discovery projects, while the manually more challenging GeoMx platform with targeted regions remains valuable for specialized questions.

Suggested Citation

  • Yixing Dong & Chiara Saglietti & Quentin Bayard & Almudena Espin Perez & Sabrina Carpentier & Daria Buszta & Stephanie Tissot & Rémy Dubois & Atanas Kamburov & Senbai Kang & Carla Haignere & Rita Sark, 2025. "Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59005-9
    DOI: 10.1038/s41467-025-59005-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-59005-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-59005-9?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:16:y:2025:i:1:d:10.1038_s41467-025-59005-9. 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.