Comparative analysis of methodologies for detecting extrachromosomal circular DNA

• Published in: Nature communications 2024-10, Vol.15 (1), p.9208-14, Article 9208
• Main Authors: Gao, Xuyuan, Liu, Ke, Luo, Songwen, Tang, Meifang, Liu, Nianping, Jiang, Chen, Fang, Jingwen, Li, Shouzhen, Hou, Yanbing, Guo, Chuang, Qu, Kun
• Format: Article
• Language: English
• Subjects: 38/23; 631/61/212; 631/67/69; Circular DNA; Comparative analysis; Computational Biology - methods; Copy number; Datasets; Deoxyribonucleic acid; DNA; DNA sequencing; DNA, Circular - genetics; Experimental methods; Gene regulation; Gene sequencing; Heterogeneity; High-Throughput Nucleotide Sequencing - methods; Humanities and Social Sciences; Humans; multidisciplinary; Performance evaluation; Pipelines; Redundancy; Research methodology; Resource consumption; Science; Science (multidisciplinary); Sequence Analysis, DNA - methods
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-53496-8

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. Sequencing-based studies have advanced our understanding of the diverse functions of extrachromosomal circular DNA (eccDNA). Here the authors systematically compare the performance of several bioinformatic pipelines and experimental methods that have been developed for eccDNA detection.