Comparative analysis of methodologies for detecting extrachromosomal circular DNA

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 evaluated the performance of 7 analysis pipelines using three simulated datasets, in terms of accuracy, similarity, duplication rate, and computational resource consumption. We also compared the eccDNA detection efficiency of 7 experimental methods through twenty-one real sequencing datasets. Our results identified Circle-Map and CReSIL as the most effective pipelines for eccDNA detection through short-read and long-read sequencing data, respectively. Moreover, third-generation sequencing-based Circle-Seq showed superior efficiency in detecting copy number-amplified eccDNA over 10 kb in length. These results offer valuable insights for researchers in choosing the most suitable methods for eccDNA research.