ArticleNature communications2020
AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 1 of them a synthesis that pooled it.
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Who cites it
65 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA.Frontiers in genetics · 2024Pooled it
- The shared evolutionary capacities of plasmids and extrachromosomal DNA.Nature reviews. Genetics · 2026Review
- Extrachromosomal DNA in urothelial carcinoma: mechanisms and clinical applications.Nature reviews. Urology · 2026Review
- A bibliometric analysis of extrachromosomal DNA in cancer over six decades.Discover oncology · 2026Article
- Targeting extrachromosomal DNA in human cancers.Nature reviews. Drug discovery · 2026Review
- Extrachromosomal DNA Gives Cancer a New Evolutionary Pathway.Research square · 2026Article
- Accurate prediction of ecDNA in interphase cancer cells using deep neural networks.Communications biology · 2026Article
- DeepECC: a deep learning framework for genome-wide identification and analysis of human cancer eccDNAs.Nucleic acids research · 2026Article
- A novel CRISPR-Cas9 nickase-mediated rolling circle amplification (CRIRCA) technique for gene identification and quantitative analysis of extrachromosomal DNA.Journal of advanced research · 2026Article
- Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D.Nature communications · 2025Article
- Emerging hallmarks and the rise of complexities and heterogeneity of tumor.Biochemistry and biophysics reports · 2025Review
- Extrachromosomal DNA-Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma.Cancer discovery · 2025Article
- eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA.Molecular biology and evolution · 2025Article
- ecDNA replication is disorganized and vulnerable to replication stress.Nucleic acids research · 2025Article
- A Guide to Extrachromosomal DNA: Cancer's Dynamic Circular Genome.Cancer discovery · 2025Review
- The Emergence of Nanofluidics for Single-Biomolecule Manipulation and Sensing.Analytical chemistry · 2025Review
- Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies.Cell death discovery · 2025Review
- Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity.Nature communications · 2025Article
- Exploring the potential of extrachromosomal DNA as a novel oncogenic driver.Science China. Life sciences · 2025Review
- Article
5 more citing papers are in PubMed but not listed here.
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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
Oncogene amplification, a major driver of cancer pathogenicity, is often mediated through focal amplification of genomic segments. Recent results implicate extrachromosomal DNA (ecDNA) as the primary driver of focal copy number amplification (fCNA) - enabling gene amplification, rapid tumor evolution, and the rewiring of regulatory circuitry. Resolving an fCNA's structure is a first step in deciphering the mechanisms of its genesis and the fCNA's subsequent biological consequences. We introduce a computational method, AmpliconReconstructor (AR), for integrating optical mapping (OM) of long DNA fragments (>150 kb) with next-generation sequencing (NGS) to resolve fCNAs at single-nucleotide resolution. AR uses an NGS-derived breakpoint graph alongside OM scaffolds to produce high-fidelity reconstructions. After validating its performance through multiple simulation strategies, AR reconstructed fCNAs in seven cancer cell lines to reveal the complex architecture of ecDNA, a breakage-fusion-bridge and other complex rearrangements. By reconstructing the rearrangement signatures associated with an fCNA's generative mechanism, AR enables a more thorough understanding of the origins of fCNAs.
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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.