ArticleCell systems2020
SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing.
Article in Cell systems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Wavelet-based whole genome doubling aware single-cell copy number calling.Nucleic acids research · 2026Article
- CNVeil resolves haplotype-specific copy number and uncovers subclonal architecture hidden from total copy number profiling in single-cell cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- BESTDR Enables Bayesian Quantification of Mechanism-Specific Drug Responses.Cancer research · 2026Article
- CRESCENT: a deep learning framework with multi-scale attention for detecting recurrent copy number alterations.Briefings in bioinformatics · 2026Article
- CNAScope: pan-cancer copy number aberration database with functional annotation and interactive visualization.Nucleic acids research · 2026Article
- Canopy2: Tumor Phylogeny Inference by Bulk DNA and Single-Cell RNA Sequencing.Statistics in biosciences · 2026Article
- Integrative Modeling of Read Depth and B-Allele Frequency Improves Single-Cell Copy Number Calling from Targeted DNA Sequencing Panels.Computational and structural biotechnology journal · 2026Article
- Benchmarking Ploidy Estimation Methods for Bulk and Single-Cell Whole Genome Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Advances in single-cell DNA sequencing enable insights into human somatic mosaicism.Nature reviews. Genetics · 2025Review
- Clinical application of single-cell RNA sequencing in disease and therapy.Clinical and translational medicine · 2025Review
- The dual role of whole-genome duplication: biological mechanisms, functional consequences, and detection advances.Acta biochimica et biophysica Sinica · 2025Review
- High-resolution detection of copy number alterations in single cells with HiScanner.Nature communications · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- CNRein: an evolution-aware deep reinforcement learning algorithm for single-cell DNA copy number calling.Genome biology · 2025Article
- High-resolution detection of copy number alterations in single cells with HiScanner.bioRxiv : the preprint server for biology · 2025Article
- Single-cell copy number calling and event history reconstruction.Bioinformatics (Oxford, England) · 2025Article
- DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogenies.Life science alliance · 2025Article
- Detecting copy-number alterations from single-cell chromatin sequencing data by AtaCNA.Cell reports methods · 2025Article
- HapCNV: A Comprehensive Framework for CNV Detection in Low-input DNA Sequencing Data.bioRxiv : the preprint server for biology · 2025Article
- Inferring Phenotypes of Copy Number Clones in Cancer Populations Using TreeAlign.Methods in molecular biology (Clifton, N.J.) · 2025Article
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Authors and funding
3 authors.
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Abstract
Whole-genome single-cell DNA sequencing (scDNA-seq) enables characterization of copy-number profiles at the cellular level. We propose SCOPE, a normalization and copy-number estimation method for the noisy scDNA-seq data. SCOPE's main features include the following: (1) a Poisson latent factor model for normalization, which borrows information across cells and regions to estimate bias, using in silico identified negative control cells; (2) an expectation-maximization algorithm embedded in the normalization step, which accounts for the aberrant copy-number changes and allows direct ploidy estimation without the need for post hoc adjustment; and (3) a cross-sample segmentation procedure to identify breakpoints that are shared across cells with the same genetic background. We evaluate SCOPE on a diverse set of scDNA-seq data in cancer genomics and show that SCOPE offers accurate copy-number estimates and successfully reconstructs subclonal structure. A record of this paper's transparent peer review process is included in the Supplemental Information.
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