ArticleFrontiers in genetics2022
Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing.
Article in Frontiers in genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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.
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
8 citing papers in PubMed, 9 citations in OpenAlex.
- ECCFP: A consecutive full pass-based bioinformatic analysis for eccDNA identification from long-read sequencing data.iMetaOmics · 2026Article
- Identification of Extrachromosomal Circular DNA Isolated from Cell Culture Supernatant and Its Potential Applications for Hepatocellular Carcinoma Diagnosis.Asian Pacific journal of cancer prevention : APJCP · 2026Article
- Identification of eccDNA in Extracellular Vesicles Derived from Human Dermal Fibroblasts Through Nanopore Sequencing.International journal of molecular sciences · 2025Article
- Review
- Comparative analysis of methodologies for detecting extrachromosomal circular DNA.Nature communications · 2024Article
- Review
- FLED: a full-length eccDNA detector for long-reads sequencing data.Briefings in bioinformatics · 2023Article
- HPV integration generates a cellular super-enhancer which functions as ecDNA to regulate genome-wide transcription.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Occurrence of extra-chromosomal circular DNA is a phenomenon frequently observed in tumor cells, and the presence of such DNA has been recognized as a marker of adverse outcome across cancer types. We here describe a computational workflow for identification of DNA circles from long-read sequencing data. The workflow is implemented based on the Snakemake workflow management system. Its key step uses a graph-theoretic approach to identify putative circular fragments validated on simulated reads. We then demonstrate robustness of our approach using nanopore sequencing of selectively enriched circular DNA by highly sensitive and specific recovery of plasmids and the mitochondrial genome, which is the only circular DNA in normal human cells. Finally, we show that the workflow facilitates detection of larger circular DNA fragments containing extrachromosomal copies of the MYCN oncogene and the respective breakpoints, which is a potentially useful application in disease monitoring of several cancer types.
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Registered trials
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