ArticleNature biotechnology2023
Functional analysis of structural variants in single cells using Strand-seq.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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The trial behind it
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
23 citing papers in PubMed, 33 citations in OpenAlex.
- Article
- A genomic and epigenomic lens into the biology of acute lymphoblastic leukaemia.Nature reviews. Cancer · 2026Review
- GEAR Genomics: a user-friendly, open-source web platform enabling interactive genomic analysis for molecular biologists.Nucleic acids research · 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
- Recent advances in single-cell bioinformatics for inferring higher-order chromatin contact maps.BMB reports · 2025Review
- Chromoanagenesis in Osteosarcoma.Biomolecules · 2025Review
- 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
- Nanopore approaches for single-molecule temporal omics: promises and challenges.Nature methods · 2025Review
- Single-cell analysis dissects heterogeneity of leukemias with complex karyotypes.Nature genetics · 2024Article
- 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
- Application of omics in the diagnosis, prognosis, and treatment of acute myeloid leukemia.Biomarker research · 2024Review
- Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells.Nature genetics · 2024Article
- Unlocking the secrets of structural variants in a healthy tissue.Nature genetics · 2024Article
- Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation.Nucleic acids research · 2024Article
- Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements.Nature reviews. Genetics · 2024Review
- Somatic mutation burden in relation to aging and functional life span: implications for cellular reprogramming and rejuvenation.Current opinion in genetics & development · 2023Review
- MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq.Bioinformatics (Oxford, England) · 2023Article
- Nucleosome repositioning in chronic lymphocytic leukemia.Genome research · 2023Article
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Authors and funding
21 authors at 10 institutions in 6 countries.
Funding
Abstract
Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations.
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Registered trials
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.