ArticleNature communications2024
Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Innovative technologies and their clinical prospects for early lung cancer screening.Clinical and experimental medicine · 2025Pooled it
- Phase-Separated Nanoarchitecture of Adhesion-Cytoskeleton Force Coupling Reforms Nuclear Spatiotemporal Posture Conformation and Mechanotransduction of Osteosarcoma on Biofunctional Microarrays.Advanced healthcare materials · 2026Article
- DNA Methylation as a Programmable Information Layer: From Molecular Marks to Disease State Engineering.International journal of molecular sciences · 2026Review
- Compact Tabletop Magnetic Resonance Elastography for Mapping Soft Tissue Viscoelasticity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- STGBench: sequencing-level spatial DNA-RNA simulation for multimodal and virtual cell-oriented benchmarking of genomic alterations.Briefings in bioinformatics · 2026Article
- ScSpTITH: a rank-correlation framework for robust quantification of multi-dimensional tumor heterogeneity.Human genetics · 2026Article
- Integrating multi-omics data for next-generation cancer research and precision medicine.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Review
- Plasticity, signaling, and metabolic rewiring in melanoma persister cells.Communications biology · 2026Review
- Organoids glimpse: the nexus for diverse tumor heterogeneity.Frontiers in cell and developmental biology · 2026Review
- Genomic innovations in cancer prevention, diagnosis, prognosis and precision therapeutics.Frontiers in genetics · 2026Review
- Predicting Immunotherapy Outcomes in NSCLC Using RNA and Pathology from Multicenter Clinical Trials.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Applications of artificial intelligence in non-small cell lung cancer: from precision diagnosis to personalized prognosis and therapy.Journal of translational medicine · 2025Review
- Decrypting cancer's spatial code: from single cells to tissue niches.Molecular oncology · 2025Review
- Review
- SpatialSNV: A novel method for identifying and analyzing spatially resolved SNVs in tumor microenvironments.GigaScience · 2025Article
- Computational strategies in tumor phylogenetics: evaluating multimodal integration and methodological trade-offs across study designs.Bioinformatics advances · 2025Review
- Comprehensive analysis reveals MCM4 as a biomarker for guiding therapies and immunomodulatory role in skin cutaneous melanoma.Journal of Cancer · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Spatial and genomic heterogeneity of tumors are crucial factors influencing cancer progression, treatment, and survival. However, a technology for direct mapping the clones in the tumor tissue based on somatic point mutations is lacking. Here, we propose Tumoroscope, the first probabilistic model that accurately infers cancer clones and their localization in close to single-cell resolution by integrating pathological images, whole exome sequencing, and spatial transcriptomics data. In contrast to previous methods, Tumoroscope explicitly addresses the problem of deconvoluting the proportions of clones in spatial transcriptomics spots. Applied to a reference prostate cancer dataset and a newly generated breast cancer dataset, Tumoroscope reveals spatial patterns of clone colocalization and mutual exclusion in sub-areas of the tumor tissue. We further infer clone-specific gene expression levels and the most highly expressed genes for each clone. In summary, Tumoroscope enables an integrated study of the spatial, genomic, and phenotypic organization of tumors.
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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.