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

Xinyu Zhao; Huan Zhao; Yupeng Liu; Zhiyun Guo

doi:10.1016/j.compbiomed.2023.107680

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

Comput Biol Med. 2023 Dec:167:107680. doi: 10.1016/j.compbiomed.2023.107680. Epub 2023 Nov 10.

Authors

Xinyu Zhao¹, Huan Zhao², Yupeng Liu¹, Zhiyun Guo³

Affiliations

¹ School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
² Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation, Dalian Ocean University, Dalian, 116023, China.
³ School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China. Electronic address: zhiyunguo@swjtu.edu.cn.

PMID: 37976817
DOI: 10.1016/j.compbiomed.2023.107680

Abstract

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.

Keywords: Bioinformatics; Database; Single-cell sequencing; ecDNA.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
DNA* / genetics
Humans
Neoplasms* / genetics
Neoplasms* / pathology
Oncogenes

Substances

DNA