ArticleNature communications2024
Robust analysis of allele-specific copy number alterations from scRNA-seq data with XClone.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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Who cites it
7 citing papers in PubMed.
- Benchmarking copy number alteration inference methods for spatial transcriptomics.Nature communications · 2026Article
- Single-cell profiling of gastric cancer ascites reveals an epithelial-immune dual phenotype signature predictive for anti-PD-1 immunotherapy responses.BMC medicine · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Inferring tumor absolute copy number and clonal substructure from single-cell chromatin accessibility.Briefings in bioinformatics · 2026Article
- Spatial-aware detection of copy number alterations from spatial transcriptomics using SpaCNA.Nature communications · 2026Article
- CLADES: a hybrid NeuralODE-Gillespie approach for unveiling clonal cell fate and differentiation dynamics.Nature communications · 2025Article
- Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets.Briefings in bioinformatics · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Somatic copy number alterations (CNAs) are major mutations that contribute to the development and progression of various cancers. Despite a few computational methods proposed to detect CNAs from single-cell transcriptomic data, the technical sparsity of such data makes it challenging to identify allele-specific CNAs, particularly in complex clonal structures. In this study, we present a statistical method, XClone, that strengthens the signals of read depth and allelic imbalance by effective smoothing on cell neighborhood and gene coordinate graphs to detect haplotype-aware CNAs from scRNA-seq data. By applying XClone to multiple datasets with challenging compositions, we demonstrated its ability to robustly detect different types of allele-specific CNAs and potentially indicate whole genome duplication, therefore enabling the discovery of corresponding subclones and the dissection of their phenotypic impacts.
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Registered trials
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