Technological advances in extrachromosomal circular DNA detection

Extrachromosomal circular DNA (eccDNA) is a class of circular DNA molecules that exists independently of chromosomes and plays critical roles in genome plasticity, cancer progression, drug resistance, and adaptive evolution. Recent advances in high-throughput sequencing, computational tools, and CRISPR-based genome editing have revolutionized the detection and functional characterization of eccDNAs. The emergence of single-molecule real-time and Nanopore sequencing technologies has further enabled the investigation of eccDNA at the cellular level. The rapid development of eccDNA research has revealed previously unrecognized dimensions of genome organization and function. In this review, we provide a systematic evaluation of current high-throughput sequencing-based methods for eccDNA detection, discussing their technical principles, strengths, limitations, and applications. Finally, we propose novel visualization strategies to improve data interpretation and highlight future research directions incorporating multi-omics integration and single-cell approaches. This review offers a comprehensive resource and presents an updated perspective for researchers interested in eccDNA biology.