ArticleNature biotechnology2020
Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.
Article in Nature biotechnology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
48 citing papers in PubMed.
- Article
- De Novo Complex Genomic Rearrangement Spanning 2q31.1 in a Proband With Congenital Malformations: Genotype-Phenotype Correlation and Development of a CGR Detection Pipeline.American journal of medical genetics. Part A · 2026Article
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- Recurrent DNA break clusters drive replication-stress-induced copy number variants and genome diversification.Nature communications · 2026Article
- High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq.Nucleic acids research · 2026Article
- Article
- Coordinated control of genome-nuclear lamina interactions by topoisomerase 2B and lamin B receptor.Nucleic acids research · 2025Article
- The reference genome of the human diploid cell line RPE-1.Nature communications · 2025Article
- Review
- Structural variant and nucleosome occupancy dynamics postchemotherapy in a HER2+ breast cancer organoid model.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.Nucleic acids research · 2025Article
- Case Report: Optical genome mapping enables identification of complex balanced chromosomal rearrangements.Frontiers in genetics · 2025Article
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype.Nature genetics · 2024Article
- Multi-omic and single-cell profiling of chromothriptic medulloblastoma reveals genomic and transcriptomic consequences of genome instability.Nature communications · 2024Article
- Single-cell somatic copy number variants in brain using different amplification methods and reference genomes.Communications biology · 2024Article
- Impact and characterization of serial structural variations across humans and great apes.Nature communications · 2024Article
- Simultaneous de novo calling and phasing of genetic variants at chromosome-scale using NanoStrand-seq.Cell discovery · 2024Article
- Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells.Nature genetics · 2024Article
- The two sides of chromosomal instability: drivers and brakes in cancer.Signal transduction and targeted therapy · 2024Review
Corrections and comments
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Authors and funding
23 authors.
Funding
Abstract
Structural variation (SV), involving deletions, duplications, inversions and translocations of DNA segments, is a major source of genetic variability in somatic cells and can dysregulate cancer-related pathways. However, discovering somatic SVs in single cells has been challenging, with copy-number-neutral and complex variants typically escaping detection. Here we describe single-cell tri-channel processing (scTRIP), a computational framework that integrates read depth, template strand and haplotype phase to comprehensively discover SVs in individual cells. We surveyed SV landscapes of 565 single cells, including transformed epithelial cells and patient-derived leukemic samples, to discover abundant SV classes, including inversions, translocations and complex DNA rearrangements. Analysis of the leukemic samples revealed four times more somatic SVs than cytogenetic karyotyping, submicroscopic copy-number alterations, oncogenic copy-neutral rearrangements and a subclonal chromothripsis event. Advancing current methods, single-cell tri-channel processing can directly measure SV mutational processes in individual cells, such as breakage-fusion-bridge cycles, facilitating studies of clonal evolution, genetic mosaicism and SV formation mechanisms, which could improve disease classification for precision medicine.
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