Abstract
Nanopore sensing is a disruptive, revolutionary way in which to sequence nucleic acids, including both native DNA and RNA molecules. First commercialized with the MinIONTM sequencer from Oxford Nanopore TechnologiesTM in 2015, this review article looks at the current state of nanopore sequencing as of June 2022. Covering the unique characteristics of the technology and how it functions, we then go on to look at the ability of the platform to deliver sequencing at all scales—from personal to high-throughput devices—before looking at how the scientific community is applying the technology around the world to answer their biological questions.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Fastest DNA sequencing technique | Guinness World Records. https://www.guinnessworldrecords.com/world-records/675050-fastest%C2%A0dna-sequencing%C2%A0technique. Accessed 30 May 2022
Gorzynski JE, Goenka SD, Shafin K et al (2022) Ultra-rapid nanopore whole genome genetic diagnosis of dilated cardiomyopathy in an adolescent with cardiogenic shock. Circ Genom Precis Med CIRCGEN121003591. https://doi.org/10.1161/circgen.121.003591
First DNA Sequencing in Space a Game Changer | NASA. https://www.nasa.gov/mission_pages/station/research/news/dna_sequencing/. Accessed 3 June 2022
Githinji G, de Laurent ZR, Mohammed KS et al (2021) Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya. Nat Commun 12:4809. https://doi.org/10.1038/s41467-021-25137-x
Yingtaweesittikul H, Ko K, Rahman NA et al (2021) CalmBelt: rapid SARS-CoV-2 genome characterization for outbreak tracking. Front Med 8:790662. https://doi.org/10.3389/fmed.2021.790662
Ranasinghe D, Jayadas TTP, Jayathilaka D et al (2021) Comparison of different sequencing techniques with multiplex real-time PCR for detection to identify SARS-CoV-2 variants of concern. Medrxiv:2021.12.05.21267303. https://doi.org/10.1101/2021.12.05.21267303
Quick J, Loman NJ, Duraffour S et al (2016) Real-time, portable genome sequencing for Ebola surveillance. Nature 530:228–232. https://doi.org/10.1038/nature16996
Faria NR, Quick J, Claro IM et al (2017) Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546:406–410. https://doi.org/10.1038/nature22401
Company history. https://nanoporetech.com/about-us/history. Accessed 3 June 2022
Depledge DP, Srinivas KP, Sadaoka T et al (2019) Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen. Nat Commun 10:754. https://doi.org/10.1038/s41467-019-08734-9
Oxford Nanopore integrates “Remora”: a tool to enable real-time, high-accuracy epigenetic insights with nanopore sequencing software MinKNOW. https://nanoporetech.com/about-us/news/oxford-nanopore-integrates-remora-tool-enable-real-time-high-accuracy-epigenetic. Accessed 5 June 2022
Djirackor L, Halldorsson S, Niehusmann P et al (2021) Intraoperative DNA methylation classification of brain tumors impacts neurosurgical strategy. Neuro-oncol Adv 3:vdab149. https://doi.org/10.1093/noajnl/vdab149
Ebbert MTW, Jensen TD, Jansen-West K et al (2019) Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight. Genome Biol 20:97. https://doi.org/10.1186/s13059-019-1707-2
Dr. Kennda Lynch on Twitter: “A HUGE Thanks to Oxford @nanopore who helped to make my use of the MinION possible!!! Also thanks to @GTSciences, @NewEnglandBIO, and @QIAGENscience who all helped provide equipment, reagents, and support for my trip to Danakil to help film this episode!!”/Twitter. https://twitter.com/marsgirl42/status/1337200697255792641. Accessed 5 June 2022
Quince C, Nurk S, Raguideau S et al (2021) STRONG: metagenomics strain resolution on assembly graphs. Genome Biol 22:214. https://doi.org/10.1186/s13059-021-02419-7
245 Gbases – the highest output record of the PromethION platform to date. https://www.linkedin.com/feed/update/urn:li:activity:6757616979751895041/. Accessed 6 June 2022
Applying portable nanopore sequencing technology to the conservation of the critically endangered kākāpō. https://nanoporetech.com/about-us/news/interview-applying-portable-nanopore-sequencing-technology-conservation-critically. Accessed 6 June 2022
Gowers G, Oliver F, Vince O, Charles J-H et al (2019) Entirely off-grid and solar-powered DNA sequencing of microbial communities during an ice cap traverse expedition. Genes-Basel 10:902. https://doi.org/10.3390/genes10110902
Shinohara Y, Kurniawan YN, Sakai H et al (2021) Nanopore based sequencing enables easy and accurate identification of yeasts in breweries. J I Brewing 127:160–166. https://doi.org/10.1002/jib.639
Sakamoto Y, Zaha S, Suzuki Y et al (2021) Application of long-read sequencing to the detection of structural variants in human cancer genomes. Comput Struct Biotechnol J 19:4207–4216. https://doi.org/10.1016/j.csbj.2021.07.030
Currin A, Swainston N, Dunstan MS et al (2019) Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries. Synth Biol 4:ysz025. https://doi.org/10.1093/synbio/ysz025
Goenka SD, Gorzynski JE, Shafin K et al (2022) Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nat Biotechnol 1–7. https://doi.org/10.1038/s41587-022-01221-5
Owen MJ, Niemi A-K, Dimmock DP et al (2021) Rapid sequencing-based diagnosis of thiamine metabolism dysfunction syndrome. New Engl J Med 384:2159–2161. https://doi.org/10.1056/nejmc2100365
Meyer A, Schloissnig S, Franchini P et al (2021) Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 590:284–289. https://doi.org/10.1038/s41586-021-03198-8
Nowoshilow S, Schloissnig S, Fei J-F et al (2018) The axolotl genome and the evolution of key tissue formation regulators. Nature 554:50–55. https://doi.org/10.1038/nature25458
Hotaling S, Kelley JL, Frandsen PB (2021) Toward a genome sequence for every animal: where are we now? Proc Natl Acad Sci 118:e2109019118. https://doi.org/10.1073/pnas.2109019118
Nurk S, Koren S, Rhie A et al (2022) The complete sequence of a human genome. Science 376:44–53. https://doi.org/10.1126/science.abj6987
COVID-19: Community Timeline. https://nanoporetech.com/covid-19/community-timeline. Accessed 30 May 2022
Freed NE, Vlková M, Faisal MB, Silander OK (2020) Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding. Biol Methods Protoc 5:bpaa014. https://doi.org/10.1093/biomethods/bpaa014
Artic Network. https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html. Accessed 30 May 2022
Stevanovski I, Chintalaphani SR, Gamaarachchi H et al (2022) Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing. Sci Adv 8:eabm5386. https://doi.org/10.1126/sciadv.abm5386
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Pugh, J. (2023). The Current State of Nanopore Sequencing. In: Arakawa, K. (eds) Nanopore Sequencing. Methods in Molecular Biology, vol 2632. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2996-3_1
Download citation
DOI: https://doi.org/10.1007/978-1-0716-2996-3_1
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-2995-6
Online ISBN: 978-1-0716-2996-3
eBook Packages: Springer Protocols