Methods, bioinformatics tools and databases in ecDNA research: An overview

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 sug-gestions for the current bioinformatics analysis of ecDNA and provide an outlook to the future research.

Automated summary

This article provides a comprehensive overview of the methods, bioinformatics tools, and database resources used in ecDNA research, highlighting their significance in tumor initiation and progression, and offering suggestions for current analysis and future research directions.