REVIEW article
Front. Mol. Biosci.
Sec. Molecular Diagnostics and Therapeutics
Volume 12 - 2025 | doi: 10.3389/fmolb.2025.1662587
This article is part of the Research TopicAdvancing Cancer Biology: The Impact and Applications of Long-Read Sequencing TechnologiesView all articles
Advances of Nanopore Direct Sequencing Technology and Bioinformatics Analysis for Cell-free DNA Detection and Its Clinical Applications in Cancer Liquid Biopsy
Provisionally accepted
- 1Gannan Medical University, Ganzhou, China
- 2First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- 3City University of Macau, Taipa, Macao, SAR China
- 4Zhongshan Hospital Fudan University, Shanghai, China
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Cell-free DNA (cfDNA) containing cancer information has become a key biomarker for cancer liquid biopsy. Current next-generation sequencing (NGS) technology for cfDNA detection often fail to capture multiomics information, such as fragmentomics, epigenetics, and genetics, in a single assay. Recently, Oxford Nanopore Technologies (ONT) has demonstrated advantages in acquiring cfDNA's multiomics data by a single sequencing run. In this review, we summarize the recent advancements in library preparation and bioinformatic analyses for cfDNA methylation, copy number variations (CNVs), as well as other biomarkers derived from cfDNA sequencing on the ONT platform. Furthermore, we highlight the latest research progress in the clinical applications of multi-dimensional cfDNA features and outline the future directions of nanopore cfDNA sequencing. Overall, this review updates the understanding of cfDNA detection using nanopore sequencing, providing valuable insights for studies of cfDNA in cancer.
Keywords: nanopore sequencing, cell-free DNA, Methylation, Copy Number Variations, liquid biopsy
Received: 09 Jul 2025; Accepted: 06 Oct 2025.
Copyright: © 2025 Tan, Wu, Zhu, Miao, Xu, Gu, Hu, Xu and Wan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Maohong Hu, humaohong@gmu.cn
Pingping Xu, doctor_xu@hotmail.com
Shaogui Wan, wansg@gmu.edu.cn
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