ArticleNature communications2025
Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Spatial ecotype in tumor immune exclusion: from spatial architecture to therapeutic strategies.Molecular cancer · 2026Review
- Benchmarking cell-type deconvolution in cross-platform transcriptomic data.Genome biology · 2026Article
- Toward comprehensive cellular characterization of H&E slides.Journal of pathology informatics · 2026Article
- Mechanisms and therapeutic targets in distant metastasis of lung adenocarcinoma.Signal transduction and targeted therapy · 2026Article
- Spatial transcriptomics reveals compartment-specific cytotoxic T cell crosstalk with AT2 and goblet cells in advanced COPD.Biomarker research · 2026Article
- Spatiotemporal heterogeneity of neutrophil extracellular traps in hepatocellular carcinoma microenvironment and targeted therapy progress.Journal of translational medicine · 2026Review
- Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.Nature methods · 2026Article
- Review
- Lense: Optimizing data preprocessing in single-cell omics using LLMs.bioRxiv : the preprint server for biology · 2026Article
- Lense: optimizing data preprocessing in single-cell omics using large language models.Briefings in bioinformatics · 2026Article
- Deep learning inference of cell type-specific gene expression from breast tumor histopathology.NPJ precision oncology · 2026Article
- Biomarker exploration for immunotherapy plus chemotherapy following resistance to third-generation EGFR-TKIs in lung adenocarcinoma.BMC cancer · 2026Article
- Longitudinal Imaging of the Premalignant Tumor Microenvironment Reveals Transient Myeloid States Predictive of Tumor Fate.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
27 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.