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Updated: Jun 9, 2025
Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
Comparative analysis of methodologies for detecting extrachromosomal circular DNA
Xuyuan Gao1, Ke Liu1, Songwen Luo1
1Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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.
Insights
This study systematically assessed extrachromosomal circular DNA (eccDNA) detection tools. Circle-Map and Circle_finder showed strong performance in short-read analysis, while CReSIL excelled in long-read eccDNA identification.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Extrachromosomal circular DNA (eccDNA) plays a key role in cancer development, influencing oncogene amplification, gene transcription, and tumor heterogeneity.
- Numerous computational pipelines and experimental techniques exist for eccDNA identification, but their comparative performance remains unevaluated.
Purpose of the Study:
- To systematically evaluate the detection efficiency and performance of various bioinformatics pipelines and experimental methods for identifying eccDNA.
- To provide guidance for researchers selecting optimal tools for eccDNA analysis.
Main Methods:
- Performance assessment of 7 short-read and long-read eccDNA analysis pipelines using simulated datasets, focusing on accuracy, identity, duplication rates, and computational demands.
- Comparative analysis of 7 experimental methods for eccDNA detection using 21 real sequencing datasets.
Main Results:
- Circle-Map and Circle_finder (bwa-mem-samblaster) demonstrated superior performance among short-read pipelines, though Circle_finder exhibited redundancy.
- CReSIL emerged as the most effective pipeline for long-read eccDNA detection at sequencing depths >10X.
- Long-read sequencing with Circle-Seq proved highly efficient for detecting copy number-amplified eccDNA longer than 10 kb.
Conclusions:
- The study highlights the strengths and weaknesses of different eccDNA detection methodologies.
- Findings offer crucial insights for researchers to select appropriate bioinformatics and experimental approaches for their specific eccDNA research needs.
