Zhao Xinyu, Zhao Huan, Liu Yupeng, Guo Zhiyun
School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation, Dalian Ocean University, Dalian, 116023, China.
Comput Biol Med. 2023 Dec;167:107680. doi: 10.1016/j.compbiomed.2023.107680. Epub 2023 Nov 10.
Extrachromosomal DNA (ecDNA), derived from chromosomes, is a cancer-specific circular DNA molecule. EcDNA drives tumor initiation and progression, which is associated with poor clinical outcomes and drug resistance in a wide range of cancers. Although ecDNA was first discovered in 1965, tremendous technological revolutions in recent years have provided crucial new insights into its key biological functions and regulatory mechanisms. Here, we provide a thorough overview of the methods, bioinformatics tools, and database resources used in ecDNA research, mainly focusing on their performance, strengths, and limitations. This study can provide important reference for selecting the most appropriate method in ecDNA research. Furthermore, we offer suggestions for the current bioinformatics analysis of ecDNA and provide an outlook to the future research.
染色体外DNA（ecDNA）源自染色体，是一种癌症特异性环状DNA分子。ecDNA驱动肿瘤的起始和进展，这与多种癌症的不良临床结果和耐药性相关。尽管ecDNA于1965年首次被发现，但近年来的巨大技术变革为其关键生物学功能和调控机制提供了重要的新见解。在此，我们全面概述了ecDNA研究中使用的方法、生物信息学工具和数据库资源，主要关注它们的性能、优势和局限性。本研究可为ecDNA研究中选择最合适的方法提供重要参考。此外，我们对当前ecDNA的生物信息学分析提出建议，并对未来研究进行展望。
