ArticleNature communications2019
Exploring the landscape of focal amplifications in cancer using AmpliconArchitect.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 245 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
245 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
- Identification of Genome-Wide Chromatin Structural Aberration in Cancer by Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2027Article
- AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes.Nature methods · 2026Article
- A Living Multi-Omics PDX Biobank of High-Risk Sarcomas Reveals ecDNA-Driven Oncogene Amplification in Osteosarcoma and Enables Preclinical Precision Oncology.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Lineage identity governs oncogene dependence in mouse NSCLC models of KRAS inhibitor resistance.Nature genetics · 2026Article
- Circulating tumour DNA and extrachromosomal DNA in prostate and bladder cancer: biology, clinical applications and future perspectives.World journal of urology · 2026Review
- Clustered structural variant hotspots enable oncogenic addiction and plasticity in osteosarcoma.bioRxiv : the preprint server for biology · 2026Article
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- Quantitative and sensitive neuroblastoma minimal residual disease detection using extrachromosomal DNA (ecDNA) breakpoints.bioRxiv : the preprint server for biology · 2026Article
- Article
- Immune pathway activation in gastric cancers with LINE-1 retrotransposon overexpression and homologous recombination deficiency.Experimental & molecular medicine · 2026Article
- Extrachromosomal DNA in urothelial carcinoma: mechanisms and clinical applications.Nature reviews. Urology · 2026Review
- scAmp enables focal gene amplification analysis from single-cell data.Nature communications · 2026Article
- Plasticity of extrachromosomal DNA segregation during drug adaptation.Nature communications · 2026Article
- Examining the role of extrachromosomal DNA in lung cancer.Journal of the National Cancer Institute · 2026Article
- Hybrid extrachromosomal DNA in HPV-driven cancers.Journal of virology · 2026Review
- AI-driven multi-omics deciphering of extrachromosomal circular DNA rescues hidden targets in colorectal cancer.Cell communication and signaling : CCS · 2026Article
- A Conserved Enhancer Locus in Extrachromosomal DNA and Homogeneously Staining Regions Activates MYC Transcription in Group 3 Medulloblastoma.Cancer research · 2026Article
- Article
- A stratified urine-based molecular diagnostic and prognostic model for non-muscle-invasive bladder cancer management.BMC cancer · 2026Article
185 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Focal oncogene amplification and rearrangements drive tumor growth and evolution in multiple cancer types. We present AmpliconArchitect (AA), a tool to reconstruct the fine structure of focally amplified regions using whole genome sequencing (WGS) and validate it extensively on multiple simulated and real datasets, across a wide range of coverage and copy numbers. Analysis of AA-reconstructed amplicons in a pan-cancer dataset reveals many novel properties of copy number amplifications in cancer. These findings support a model in which focal amplifications arise due to the formation and replication of extrachromosomal DNA. Applying AA to 68 viral-mediated cancer samples, we identify a large fraction of amplicons with specific structural signatures suggestive of hybrid, human-viral extrachromosomal DNA. AA reconstruction, integrated with metaphase fluorescence in situ hybridization (FISH) and PacBio sequencing on the cell-line UPCI:SCC090 confirm the extrachromosomal origin and fine structure of a Forkhead box E1 (FOXE1)-containing hybrid amplicon.
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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.