ArticleNature methods2025
Cancer subclone detection based on DNA copy number in single-cell and spatial omic sequencing data.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Benchmarking copy number alteration inference methods for spatial transcriptomics.Nature communications · 2026Article
- Cancer Heterogeneity and Cancer Cell Plasticity: Molecular Mechanisms and Precision Therapy.MedComm · 2026Review
- A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.Cell reports. Medicine · 2026Article
- Single-cell omics data-driven decoding of tumor clonal evolution through reinforcement learning.Genome medicine · 2026Article
- Benchmarking scRNA-seq Copy Number Inference: A Comprehensive Evaluation and Practitioner's Guide.bioRxiv : the preprint server for biology · 2026Article
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- Colorectal cancer relies on an immunosuppressive cellular topography and genomic adaptations for establishing brain metastases.bioRxiv : the preprint server for biology · 2025Article
- A tale of tumors.Nature methods · 2025Article
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics.Nature methods · 2024Article
- A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.bioRxiv : the preprint server for biology · 2024Article
- Joint inference of clonal structure using single-cell genome and transcriptome sequencing data.NAR genomics and bioinformatics · 2024Article
- Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions.Genome biology · 2024Article
- Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI.BMC biology · 2023Article
- Dissecting the tumor microenvironment of epigenetically driven gliomas: Opportunities for single-cell and spatial multiomics.Neuro-oncology advancesReview
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Authors and funding
9 authors.
Funding
Abstract
Somatic mutations such as copy number alterations accumulate during cancer progression, driving intratumor heterogeneity that impacts therapy effectiveness. Understanding the characteristics and spatial distribution of genetically distinct subclones is essential for unraveling tumor evolution and improving cancer treatment. Here we present Clonalscope, a subclone detection method using copy number profiles, applicable to spatial transcriptomics and single-cell sequencing data. Clonalscope implements a nested Chinese Restaurant Process to identify de novo tumor subclones, which can incorporate prior information from matched bulk DNA sequencing data for improved subclone detection and malignant cell labeling. On single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin using sequencing data from gastrointestinal tumors, Clonalscope successfully labeled malignant cells and identified genetically different subclones with thorough validations. On spatial transcriptomics data from various primary and metastasized tumors, Clonalscope labeled malignant spots, traced subclones and identified spatially segregated subclones with distinct differentiation levels and expression of genes associated with drug resistance and survival.
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