Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity Article Swipe
Yixing Dong
,
Chiara Saglietti
,
Quentin Bayard
,
Almudena Espín Pérez
,
Sabrina Carpentier
,
Daria Buszta
,
Stéphanie Tissot-Renaud
,
Rémy Dubois
,
Atanas Kamburov
,
Senbai Kang
,
Carla Haignere
,
Rita Sarkis
,
S. André
,
Marina Alexandre Gaveta
,
Silvia Lopez‐Lastra
,
Nathalie Piazzon
,
Rita Santos
,
Katharina von Loga
,
Caroline Hoffmann
,
George Coukos
,
Solange Peters
,
Vassili Soumelis
,
Éric Durand
,
Laurence de Leval
,
Raphaël Gottardo
,
Krisztián Homicskó
,
Elo Madissoon
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1038/s41467-025-59005-9
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1038/s41467-025-59005-9
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.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/s41467-025-59005-9
- https://www.nature.com/articles/s41467-025-59005-9.pdf
- OA Status
- gold
- Cited By
- 5
- References
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- Related Works
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- OpenAlex ID
- https://openalex.org/W4410298458
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4410298458Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1038/s41467-025-59005-9Digital Object Identifier
- Title
-
Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneityWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-05-12Full publication date if available
- Authors
-
Yixing Dong, Chiara Saglietti, Quentin Bayard, Almudena Espín Pérez, Sabrina Carpentier, Daria Buszta, Stéphanie Tissot-Renaud, Rémy Dubois, Atanas Kamburov, Senbai Kang, Carla Haignere, Rita Sarkis, S. André, Marina Alexandre Gaveta, Silvia Lopez‐Lastra, Nathalie Piazzon, Rita Santos, Katharina von Loga, Caroline Hoffmann, George Coukos, Solange Peters, Vassili Soumelis, Éric Durand, Laurence de Leval, Raphaël Gottardo, Krisztián Homicskó, Elo MadissoonList of authors in order
- Landing page
-
https://doi.org/10.1038/s41467-025-59005-9Publisher landing page
- PDF URL
-
https://www.nature.com/articles/s41467-025-59005-9.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://www.nature.com/articles/s41467-025-59005-9.pdfDirect OA link when available
- Concepts
-
Transcriptome, Computer science, Chromium, Computational biology, Throughput, Bioinformatics, Biology, Gene, Gene expression, Chemistry, Genetics, Operating system, Organic chemistry, WirelessTop concepts (fields/topics) attached by OpenAlex
- Cited by
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5Total citation count in OpenAlex
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2025: 5Per-year citation counts (last 5 years)
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27Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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