ArticleNature biotechnology2011
DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes.
Article in Nature biotechnology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers.
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Who cites it
107 citing papers in PubMed.
- Biochemical, structural and mutational landscapes of base excision repair enzymes and cancer: from atomic resolution to tumor signatures.International journal of radiation biology · 2026Review
- Aging-Related Mechanisms Underlying Carcinogenesis: Therapeutic Opportunities.Aging and disease · 2025Review
- Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.Cell genomics · 2025Article
- Reconstruction of Segmental Duplication Rates and Associated Genomic Features by Network Analysis.Genome biology and evolution · 2025Article
- Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression.Nature communications · 2025Article
- R-loops acted on by RNase H1 influence DNA replication timing and genome stability in Leishmania.Nature communications · 2025Article
- Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data.Nature communications · 2024Article
- Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.bioRxiv : the preprint server for biology · 2024Article
- Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution.Nature communications · 2024Article
- Article
- Inference of 3D genome architecture by modeling overdispersion of Hi-C data.Bioinformatics (Oxford, England) · 2023Article
- Kronos scRT: a uniform framework for single-cell replication timing analysis.Nature communications · 2022Article
- Somatic structural variant formation is guided by and influences genome architecture.Genome research · 2022Article
- Hotspots of Human Mutation.Trends in genetics : TIG · 2021Review
- Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression.Human genetics · 2021Article
- Replication Stress, Genomic Instability, and Replication Timing: A Complex Relationship.International journal of molecular sciences · 2021Review
- Identifying high-confidence capture Hi-C interactions using CHiCANE.Nature protocols · 2021Article
- Article
- A Tale of Two States: Pluripotency Regulation of Telomeres.Frontiers in cell and developmental biology · 2021Review
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
47 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
Somatic copy-number alterations (SCNA) are a hallmark of many cancer types, but the mechanistic basis underlying their genome-wide patterns remains incompletely understood. Here we integrate data on DNA replication timing, long-range interactions between genomic material, and 331,724 SCNAs from 2,792 cancer samples classified into 26 cancer types. We report that genomic regions of similar replication timing are clustered spatially in the nucleus, that the two boundaries of SCNAs tend to be found in such regions, and that regions replicated early and late display distinct patterns of frequencies of SCNA boundaries, SCNA size and a preference for deletions over insertions. We show that long-range interaction and replication timing data alone can identify a significant proportion of SCNAs in an independent test data set. We propose a model for the generation of SCNAs in cancer, suggesting that data on spatial proximity of regions replicating at the same time can be used to predict the mutational landscapes of cancer genomes.
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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.