ArticleNature biotechnology2021
Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 75 citations in OpenAlex.
- Wavelet-based whole genome doubling aware single-cell copy number calling.Nucleic acids research · 2026Article
- Chromosomal instability in cancer: sources, consequences and new therapeutic opportunities.Signal transduction and targeted therapy · 2026Review
- 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
- Robust and generalizable CNV detection for single-cell sequencing assays.Nucleic acids research · 2026Article
- Inferring tumor absolute copy number and clonal substructure from single-cell chromatin accessibility.Briefings in bioinformatics · 2026Article
- Benchmarking scRNA-seq Copy Number Inference: A Comprehensive Evaluation and Practitioner's Guide.bioRxiv : the preprint server for biology · 2026Article
- Decoding immunotherapy response through computational modeling.Nature communications · 2026Review
- Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.Genome medicine · 2026Article
- Review
- Single-cell aneuploidy and chromosomal arm imbalances define subclones with divergent transcriptomic phenotypes.NAR genomics and bioinformatics · 2025Article
- Advances in single-cell DNA sequencing enable insights into human somatic mosaicism.Nature reviews. Genetics · 2025Review
- Absolute copy number aware CNV calling of sub-megabase segments in ultra-low coverage single-cell DNA sequencing data.Nucleic acids research · 2025Article
- Cancer subclone detection based on DNA copy number in single-cell and spatial omic sequencing data.Nature methods · 2025Article
- ChromoPattern: characterizing chromosomal rearrangement patterns of copy number alteration in heterogeneous tumor cell populations at single-cell resolution.Briefings in bioinformatics · 2025Article
- Numbat-multiome: inferring copy number variations by combining RNA and chromatin accessibility information from single-cell data.Briefings in bioinformatics · 2025Article
- High-resolution detection of copy number alterations in single cells with HiScanner.Nature communications · 2025Article
- STAT3 Facilitates Super Enhancer Formation to Promote Fibroblast-To-Myofibroblast Differentiation by the Analysis of ATAC-Seq, RNA-Seq and ChIP-Seq.Journal of cellular and molecular medicine · 2025Review
- Discovery of candidate functional non-coding mutations in acute myeloid leukemia using single-cell chromatin accessibility sequencing.Communications biology · 2025Article
- From Multi-Omics to Visualization and Beyond: Bridging Micro and Macro Insights in CAR-T Cell Therapy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- CNRein: an evolution-aware deep reinforcement learning algorithm for single-cell DNA copy number calling.Genome biology · 2025Article
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
Cancer progression is driven by both somatic copy number aberrations (CNAs) and chromatin remodeling, yet little is known about the interplay between these two classes of events in shaping the clonal diversity of cancers. We present Alleloscope, a method for allele-specific copy number estimation that can be applied to single-cell DNA- and/or transposase-accessible chromatin-sequencing (scDNA-seq, ATAC-seq) data, enabling combined analysis of allele-specific copy number and chromatin accessibility. On scDNA-seq data from gastric, colorectal and breast cancer samples, with validation using matched linked-read sequencing, Alleloscope finds pervasive occurrence of highly complex, multiallelic CNAs, in which cells that carry varying allelic configurations adding to the same total copy number coevolve within a tumor. On scATAC-seq from two basal cell carcinoma samples and a gastric cancer cell line, Alleloscope detected multiallelic copy number events and copy-neutral loss-of-heterozygosity, enabling dissection of the contributions of chromosomal instability and chromatin remodeling to tumor evolution.
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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.