Research Article
Open access
Published on 17 March 2025
Download pdf
Zhang,Z. (2025). Nanopore sequencing technology in clinical diagnostics and genomic research: Opportunities and challenges. Journal of Food Science, Nutrition and Health,4(1),1-6.
Export citation

Nanopore sequencing technology in clinical diagnostics and genomic research: Opportunities and challenges

Zhengqi Zhang *,1,
  • 1 Southwest Jiaotong University

* Author to whom correspondence should be addressed.

https://doi.org/10.54254/3029-0821/2025.21485

Abstract

Nanopore sequencing technology, an advanced third-generation sequencing technology, is a revolutionary sequencing method widely used in clinical diagnosis and genomic research because of its features such as real-time sequencing, direct sequencing, long read length and portability. This paper outlines the basic principles and advantages of the technology, and briefly introduces its applications in clinical medicine such as diagnosis of diseases rare and genetic diseases, detection of infectious disease pathogens, public health emergency response, and cancer genomics screening. In genomics, nanopore sequencing is instrumental in genome assembly, structural variation detection, recovery of DNA from ancient organisms, and microbiological research. It enables direct sequencing and analysis of molecules, allowing for the identification of complex structural variations within the genome. This study finds that the technology also suffers from low accuracy, high cost associated with large data volumes, and significant requirements for data processing capabilities. These limitations can potentially be addressed through innovations such as improved nanopore materials and design, and integration with artificial intelligence. Finally, the latest innovations of the technology are analyzed, and the development trend and application prospects are outlooked.

Keywords

nanopore sequencing, clinical diagnostics, genomic research, development trends

[1]. Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Biochemistry, 24, 104-108.

[2]. Baudhuin, L. M. (2012). A new era of genetic testing and its impact on research and clinical care. Clinical Chemistry, 58(6), 1070-1071.

[3]. Liang, F., & Zhang, P. (2015). Nanopore DNA sequencing: Are we there yet? Science Bulletin, 60(3), 296-303.

[4]. Sakmann, B., & Neher, E. (1995). Single-channel Recording. New York: Springer-Verlag.

[5]. Loman, N. J., Quick, J., & Simpson, J. T. (2015). A complete bacterial genome assembled de novo using only nanopore sequencing data. Nature Methods, 12(8), 733-735.

[6]. Hansen, S., Dill, V., Shalaby, M. A., et al. (2019). Serotyping of foot-and-mouth disease virus using Oxford nanopore sequencing. Journal of Virological Methods, 263, 50-53.

[7]. Rang, F. J., Kloosterman, W. P., & de Ridder, J. (2018). From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome Biology, 19(1), 90. https://doi.org/10.1186/s13059-018-1462-9

[8]. van Dijk, E. L., Jaszczyszyn, Y., Naquin, D., et al. (2018). The third revolution in sequencing technology. Trends in Genetics, 34(9), 666-681.

[9]. Laver, T., Harrison, J., O'Neill, P. A., et al. (2015). Assessing the performance of the Oxford Nanopore Technologies MinION. Biomolecular Detection and Quantification, 3, 1-8.

[10]. Fan, S., Du, P., & Guo, J. (2021). Application value and prospect of nanopore sequencing technology in the pathogenic diagnosis of respiratory infections. Chinese Medical Journal, 101(25), 2013-2015. https://doi.org/10.3760/cma.j.cn112137-20201027-02942

[11]. Hansen, S., Dill, V., Shalaby, M.A., et al. (2019). Serotyping of foot-and-mouth disease virus using Oxford nanopore sequencing. Virology Methods, 263, 50-53.

[12]. Schadt, E. E., Turner, S., & Kasarskis, A. (2010). A window into third-generation sequencing. Human Molecular Genetics, 19(R2), R227-240.

[13]. Korlach, J., & Turner, S. W. (2012). Going beyond five bases in DNA sequencing. Current Opinion in Structural Biology, 22(3), 251-261.

[14]. Akbari, V., Garant, J. M., O'Neill, K., et al. (2021). Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase. Genome Biology, 22(1), 68.

[15]. De Coster, W., D'Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018). NanoPack: Visualizing and processing long-read sequencing data. Bioinformatics, 34(15), 2666-2669. https://doi.org/10.1093/bioinformatics/bty149

[16]. Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L., & Carroll, M. W. (2016). Real-time, portable genome sequencing for Ebola surveillance. Nature, 530(7589), 228-232. https://doi.org/10.1038/nature16996

[17]. Ji, P., Aw, T. G., Van Bonn, W., et al. (2020). Evaluation of a portable nanopore-based sequencer for detection of viruses in water. Virology Methods, 278, 113805.

[18]. Gulsuner, M., Walsh, T., Watts, A. C., et al. (2013). Spatial and temporal mapping of de novo mutations in schizophrenia. Cell, 154(3), 518-529. https://doi.org/10.1016/j.cell.2013.06.049

[19]. Zhou, W. Y., Tang, D. S., Li, Y.-B., et al. (2001). Self-organized formation of hexagonal nanopore arrays in anodic alumina. Chinese Physics: English Version.

[20]. Jain, M., Olsen, H. E., Paten, B., & Akeson, M. (2016). The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community. Genome Biology, 17(1), 239. https://doi.org/10.1186/s13059-016-1103-0

[21]. Orlando, L., Ginolhac, A., Raghavan, M., et al. (2011). True single-molecule DNA sequencing of a pleistocene horse bone. Genome Research, 21(10), 1705-1719.

[22]. Mikheyev, A. S., & Tin, M. M. (2014). A first look at the Oxford Nanopore MinION sequencer. Molecular Ecology Resources, 14(6), 1097-1102. https://doi.org/10.1111/1755-0998.12324

[23]. Santos, A., van Aerle, R., Barrientos, L., et al. (2020). Computational methods for 16S metabarcoding studies using Nanopore sequencing data. Journal of Computational and Structural Biotechnology, 18, 296-305.

[24]. Cui, X., Li, Y., Yang, Y., et al. (2020). Application of nanopore sequencing technology in viral infectious disease detection and research. Microbiology and Infection, 15(3), 179-185.

[25]. Bayley, H. (2015). Nanopore sequencing: from imagination to reality. Clinical Chemistry, 61(1), 25-31. https://doi.org/10.1373/clinchem.2014.224360

[26]. Branton, D., Deamer, D. W., Marziali, A., Bayley, H., Benner, S. A., Butler, T., & Turner, S. W. (2008). The potential and challenges of nanopore sequencing. Nature Biotechnology, 26(10), 1146-1153. https://doi.org/10.1038/nbt.1495

Cite this article

Zhang,Z. (2025). Nanopore sequencing technology in clinical diagnostics and genomic research: Opportunities and challenges. Journal of Food Science, Nutrition and Health,4(1),1-6.

Data availability

The datasets used and/or analyzed during the current study will be available from the authors upon reasonable request.

Disclaimer/Publisher's Note

The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of EWA Publishing and/or the editor(s). EWA Publishing and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

About volume

Journal:Journal of Food Science, Nutrition and Health

Volume number: Vol.4
ISSN:3029-0821(Print) / 3029-083X(Online)

© 2024 by the author(s). Licensee EWA Publishing, Oxford, UK. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license. Authors who publish this series agree to the following terms:
1. Authors retain copyright and grant the series right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgment of the work's authorship and initial publication in this series.
2. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the series's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgment of its initial publication in this series.
3. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See Open access policy for details).