ArticleNature methods2024
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Benchmarking copy number alteration inference methods for spatial transcriptomics.Nature communications · 2026Article
- HisToSpatialCNV: an interpretable deep learning method predicting spatial copy number variations from histopathology images.Nature biomedical engineering · 2026Article
- Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution.Nature methods · 2026Article
- Tumor evolution: signaling pathways, molecular mechanisms and therapeutic targets.Signal transduction and targeted therapy · 2026Review
- STGBench: sequencing-level spatial DNA-RNA simulation for multimodal and virtual cell-oriented benchmarking of genomic alterations.Briefings in bioinformatics · 2026Article
- Spatial-aware detection of copy number alterations from spatial transcriptomics using SpaCNA.Nature communications · 2026Article
- Single-cell technologies drive mechanistic insights and therapeutic translation in skeletal system research.iScience · 2026Review
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- Multimodal spatial alignment and morphology mapping with MOSAICField.bioRxiv : the preprint server for biology · 2026Article
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- CNAScope: pan-cancer copy number aberration database with functional annotation and interactive visualization.Nucleic acids research · 2026Article
- Organoids glimpse: the nexus for diverse tumor heterogeneity.Frontiers in cell and developmental biology · 2026Review
- Toward Graph-Based Decoding of Tumor Evolution: Spatial Inference of Copy Number Variations.Diagnostics (Basel, Switzerland) · 2025Article
- Large Language Models for Translational Cancer Informatics.JCO clinical cancer informatics · 2025Review
- CLONEID: A Framework for Longitudinal Integration of Phenotypic and Genotypic Data to Monitor and Steer Subclonal Dynamics.bioRxiv : the preprint server for biology · 2025Article
- Unravelling tumour spatiotemporal heterogeneity using spatial multimodal data.Clinical and translational medicine · 2025Review
- Advances in tumor subclone formation and mechanisms of growth and invasion.Journal of translational medicine · 2025Review
- spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis.Cancer research · 2025Article
- Emerging AI approaches for cancer spatial omics.GigaScience · 2025Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Analyzing somatic evolution within a tumor over time and across space is a key challenge in cancer research. Spatially resolved transcriptomics (SRT) measures gene expression at thousands of spatial locations in a tumor, but does not directly reveal genomic aberrations. We introduce CalicoST, an algorithm to simultaneously infer allele-specific copy number aberrations (CNAs) and reconstruct spatial tumor evolution, or phylogeography, from SRT data. CalicoST identifies important classes of CNAs-including copy-neutral loss of heterozygosity and mirrored subclonal CNAs-that are invisible to total copy number analysis. Using nine patients' data from the Human Tumor Atlas Network, CalicoST achieves an average accuracy of 86%, approximately 21% higher than existing methods. CalicoST reconstructs a tumor phylogeography in three-dimensional space for two patients with multiple adjacent slices. CalicoST analysis of multiple SRT slices from a cancerous prostate organ reveals mirrored subclonal CNAs on the two sides of the prostate, forming a bifurcating phylogeography in both genetic and physical space.
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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 Socratic graph.