《生命科学》 2025, 37(9): 1183-1191

基于长读长测序的eccDNA检测方法与生信分析

张堂轩^1,2 , 苗碧元^1,2 , 曾庆松¹ , 万绍贵^1,3,*

¹赣南医科大学基因组学与精准医学研究所，赣州 341000 ²赣南医科大学基础 医学院，赣州 341000 ³赣南医科大学医学技术学院，赣州 341000

摘　要：

染色体外环状DNA (extrachromosomal circular DNA, eccDNA) 是一类独立于染色体存在的环状DNA 分子，广泛分布于真核细胞中，与癌症发生、遗传异质性及治疗耐药性密切相关。当前检测eccDNA的主流方法依赖于高通量测序技术，其中长读长测序凭借其超长读长优势，可精准解析复杂结构eccDNA的完整序列，克服短读长测序因串联重复序列导致的信息丢失问题。本文系统综述了基于长读长测序的eccDNA 检测中的实验富集方法( 如Circle-Seq、3SEP 等) 和生信分析工具，并重点探讨了相关生物信息学工具的分析流程和在断点识别、序列组装及突变分析中的应用进展。尽管现有工具在提升检测灵敏度和准确性方面成效显著，但仍面临假阳性率高、数据利用率低等挑战。未来需进一步优化算法、整合多组学数据，以推动eccDNA 在癌症标志物开发和精准医疗中的转化应用。

通讯作者：万绍贵 , Email:wansg@gmu.edu.cn

eccDNA deteching technology and bioinformatical analysis using long-read sequencing

ZHANG Tang-Xuan^1,2 , MIAO Bi-Yuan^1,2 , ZENG Qing-Song¹ , WAN Shao-Gui^1,3,*

¹Institute of Genomics and Precision Medicine, Gannan Medical University, GanZhou 341000, China ²School of Basic Medicine, Gannan Medical University, GanZhou 341000, China ³School of Medical and Information Engineering, Gannan Medical University, GanZhou 341000, China

Abstract:

Extrachromosomal circular DNA (eccDNA) is a class of circular DNA molecules existing independently of chromosomes, widely distributed in eukaryotic cells and closely associated with cancer development, genetic  heterogeneity, and therapeutic resistance. Current mainstream methods for eccDNA detection rely on highthroughput  sequencing, among which long-read sequencing leverages its ultra-long read length advantages to accurately resolve the complete sequences of complex-structured eccDNA, thereby overcoming the information loss caused by tandem repeats in short-read sequencing. This review systematically summarizes experimental enrichment methods (e.g., Circle-Seq and 3SEP) and bioinformatics analysis tools in eccDNA detection utilizing  long-read sequencing technologies, while highlighting advancements in bioinformatics tools for junction identification, sequence assembly, and mutation analysis. Despite progress in improving sensitivity and accuracy,  challenges such as high false-positive rates and low data utilization persist. Future research should focus on  algorithm optimization and multi-omics integration to advance the  translational application of eccDNA in cancer  biomarker discovery and precision medicine.

Communication Author：WAN Shao-Gui , Email:wansg@gmu.edu.cn