ArticleCommunications biology2020
Single-cell sequencing of genomic DNA resolves sub-clonal heterogeneity in a melanoma cell line.
Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Improving Long-Read Somatic Structural Variant Calling with Pangenome and De Novo Personal Genome Assembly.Cancer research communications · 2026Article
- Robust and generalizable CNV detection for single-cell sequencing assays.Nucleic acids research · 2026Article
- Integrated Single-Cell Whole-Genome Sequencing and Spatial Transcriptomics Reveal Intratumoral Heterogeneity in Ovarian Cancer.Cancer research communications · 2026Article
- Genome-wide biomarker analysis across the full spectrum of HER2-expressing breast cancers to reveal a clonal chromosome 17 imbalance defining unfavourable HER2-low disease.Biomarker research · 2026Article
- Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.Nature biotechnology · 2026Article
- Improving long-read somatic structural variant calling with pangenome and de novo personal genome assembly.bioRxiv : the preprint server for biology · 2025Article
- Conversational Artificial Intelligence for Integrating Social Determinants, Genomics, and Clinical Data in Precision Medicine: Development and Implementation Study of the AI-HOPE-PM System.JMIR bioinformatics and biotechnology · 2025Article
- Integrated single-cell whole genome sequencing and spatial transcriptomics reveal latent intra-tumoral heterogeneity in ovarian cancer.bioRxiv : the preprint server for biology · 2025Article
- Artificial Intelligence-Enhanced Precision Medicine Reveals Prognostic Impact of TGF-Beta Pathway Alterations in FOLFOX-Treated Early-Onset Colorectal Cancer Among Disproportionately Affected Populations.International journal of molecular sciences · 2025Article
- Seq2Karyotype (S2K): A Method forbioRxiv : the preprint server for biology · 2025Article
- Pathway-Specific Genomic Alterations in Pancreatic Cancer Across Populations at Risk.International journal of molecular sciences · 2025Article
- Comparative Genomic Analysis of Key Oncogenic Pathways in Hepatocellular Carcinoma Among Diverse Populations.Cancers · 2025Article
- Molecular Heterogeneity in Early-Onset Colorectal Cancer: Pathway-Specific Insights in High-Risk Populations.medRxiv : the preprint server for health sciences · 2025Article
- Pathway-specific genomic alterations in pancreatic cancer across diverse cohorts.medRxiv : the preprint server for health sciences · 2025Article
- Comparative genomic analysis of key oncogenic pathways in hepatocellular carcinoma among diverse populations.medRxiv : the preprint server for health sciences · 2025Article
- DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogenies.Life science alliance · 2025Article
- Inferring active mutational processes in cancer using single cell sequencing and evolutionary constraints.bioRxiv : the preprint server for biology · 2025Article
- Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data.Nature communications · 2024Article
- Analysis of Whole-Genome as a Novel Strategy for Animal Species Identification.International journal of molecular sciences · 2024Article
- Joint inference of clonal structure using single-cell genome and transcriptome sequencing data.NAR genomics and bioinformatics · 2024Article
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12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We performed shallow single-cell sequencing of genomic DNA across 1475 cells from a cell-line, COLO829, to resolve overall complexity and clonality. This melanoma tumor-line has been previously characterized by multiple technologies and is a benchmark for evaluating somatic alterations. In some of these studies, COLO829 has shown conflicting and/or indeterminate copy number and, thus, single-cell sequencing provides a tool for gaining insight. Following shallow single-cell sequencing, we first identified at least four major sub-clones by discriminant analysis of principal components of single-cell copy number data. Based on clustering, break-point and loss of heterozygosity analysis of aggregated data from sub-clones, we identified distinct hallmark events that were validated within bulk sequencing and spectral karyotyping. In summary, COLO829 exhibits a classical Dutrillaux's monosomic/trisomic pattern of karyotype evolution with endoreduplication, where consistent sub-clones emerge from the loss/gain of abnormal chromosomes. Overall, our results demonstrate how shallow copy number profiling can uncover hidden biological insights.
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