ArticleNature communications2024
Comparative analysis of methodologies for detecting extrachromosomal circular DNA.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Multi-omics profiling of recurrence-associated extrachromosomal circular DNA characteristics and its prognostic potential in lung adenocarcinoma.Precision clinical medicine · 2026Article
- Circle-seq analysis reveals the involvement of eccDNAs in salt stress response of bermudagrass (Cynodon dactylon).BMC genomics · 2026Article
- Decoding DNA metabolism and its clinical relevance through the lens of high-throughput sequencing assays.Medical review (2021) · 2026Review
- An enhancement of extrachromosomal circular DNA enrichment and amplification to address the extremely low overlap between replicates.The Journal of biological chemistry · 2026Article
- A Bioinformatics Workflow to Identify eccDNA Using ECCFP From Long-Read Nanopore Sequencing Data.Bio-protocol · 2026Article
- Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination.GigaScience · 2026Article
- Detection of primary cancer types via fragment size selection in circulating cell-free extrachromosomal circular DNA.Genome medicine · 2026Article
- CircleBase V2: an eccDNA annotation platform across cancers and species.Nucleic acids research · 2026Article
- Discovery and validation of GNA12Frontiers in neurology · 2026Article
- Extrachromosomal circular DNA are functional, heritable units that expand genomic plasticity and confer resilience.Frontiers in plant science · 2026Review
- Research Advances of Extrachromosomal Circular DNA in Breast Cancer.Cancer medicine · 2025Review
- PAFAH1B3 Exists in Linear Chromosomal and Extrachromosomal Circular DNA and Promotes HCC Progression via EMT.International journal of molecular sciences · 2025Article
- EccDNA-Driven VPS41 Amplification Alleviates Genotoxic Stress via Lysosomal KAI1 Degradation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress.Nature communications · 2025Article
- Identification of eccDNA in Extracellular Vesicles Derived from Human Dermal Fibroblasts Through Nanopore Sequencing.International journal of molecular sciences · 2025Article
- Extrachromosomal circular DNA drives dynamic genome plasticity: emerging roles in disease progression and clinical potential.Theranostics · 2025Review
- Article
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Extrachromosomal circular DNA (eccDNA) is crucial in oncogene amplification, gene transcription regulation, and intratumor heterogeneity. While various analysis pipelines and experimental methods have been developed for eccDNA identification, their detection efficiencies have not been systematically assessed. To address this, we evaluate the performance of 7 analysis pipelines using seven simulated datasets, in terms of accuracy, identity, duplication rate, and computational resource consumption. We also compare the eccDNA detection efficiency of 7 experimental methods through twenty-one real sequencing datasets. Here, we show that Circle-Map and Circle_finder (bwa-mem-samblaster) outperform the other short-read pipelines. However, Circle_finder (bwa-mem-samblaster) exhibits notable redundancy in its outcomes. CReSIL is the most effective pipeline for eccDNA detection in long-read sequencing data at depths higher than 10X. Moreover, long-read sequencing-based Circle-Seq shows superior efficiency in detecting copy number-amplified eccDNA over 10 kb in length. These results offer valuable insights for researchers in choosing the suitable methods for eccDNA research.
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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.