Skip to main content
SpringerLink
Log in

Nanopore Sequencing and Its Clinical Applications

  • Protocol
  • First Online:
Precision Medicine

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2204))

Abstract

Nanopore sequencing is a method for determining the order and modifications of DNA/RNA nucleotides by detecting the electric current variations when DNA/RNA oligonucleotides pass through the nanometer-sized hole (nanopore). Nanopore-based DNA analysis techniques have been commercialized by Oxford Nanopore Technologies, NabSys, and Sequenom, and widely used in scientific researches recently including human genomics, cancer, metagenomics, plant sciences, etc., moreover, it also has potential applications in the field of healthcare due to its fast turn-around time, portable and real-time data analysis. Those features make it a promising technology for the point-of-care testing (POCT) and its potential clinical applications are briefly discussed in this chapter.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Norris AL, Workman RE, Fan YF et al (2016) Nanopore sequencing detects structural variants in cancer[J]. Cancer Biol Ther 17(3):246–253

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Gong L, Wong C, Cheng W et al (2017) Nanopore sequencing reveals high-resolution structural variation in the cancer genome[J]. bioRxiv

    Google Scholar 

  3. Sanchisjuan A, Stephens J, French C et al (2018) Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing[J]. Genome Med 10(1):1–10

    Google Scholar 

  4. https://nanoporetech.com/applications

  5. Miao HF, Zhou JP, Yang Q et al (2018) Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis. Hereditas 155(32)

    Google Scholar 

  6. Mitsuhashi S, Frith MC, Mizuguchi T et al (2019) Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads[J]. Genome Biol 20(1):58

    PubMed  PubMed Central  Google Scholar 

  7. Stancu MC, Van Roosmalen MJ, Renkens I et al (2017) Mapping and phasing of structural variation in patient genomes using nanopore sequencing[J]. Nat Commun 8(1):1326–1338

    Google Scholar 

  8. Au CH, Dona N, Beca B (2019) K. Ip et al. Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing. Cancer Genet 239:22–25

    CAS  PubMed  Google Scholar 

  9. Soda M, Choi YL, Enomoto M et al (2007) Identification of the transforming EML4–ALK fusion gene in non-small-cell lung cancerJ. Nature 448(7153):561–566

    CAS  PubMed  Google Scholar 

  10. Jain M, Olsen HE, Paten B et al (2016) The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics communityJ. Genome Biol 17(1):239

    PubMed  PubMed Central  Google Scholar 

  11. Nanopore Protocol 1D Sequence capture (SQK-LSK108)

    Google Scholar 

  12. Jain M, Fiddes IT, Miga KH et al (2015) Improved data analysis for the MinION nanopore sequencer[J]. Nat Methods 12(4):351

    CAS  PubMed  PubMed Central  Google Scholar 

  13. https://github.com/benedictpaten/marginAlign

  14. Oxford Nanopore Technologies. Incorporating sequence capture into library preparation for MinION GridION and PromethION. Online. Available at: https://nanoporetech.com/resource-centre/incorporating-sequence-capture-library-preparation-minion-gridion-and-promethion. Accessed 29 August, 2019

  15. Leija‐Salazar M et al (2019) Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION. Mol Genet Genomic Med 7(3):e564

    PubMed  PubMed Central  Google Scholar 

  16. Gilpatrick T et al (2019) Targeted nanopore sequencing with Cas9 for studies of methylation, structural variants, and mutations. BioRxiv:604173

    Google Scholar 

  17. Mesri E, Feitelson MA, Munger K (2014) Human viral oncogenesis: a cancer Hallmarks analysis. Cell Host Microbe 15(3):266–282

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Plummer M, Martel CD, Vignat J, Ferlay J, Bray F, Franceschi S (2016) Global burden of cancers attributable to infections in 2012: a synthetic analysis. Lancet Glob Health 4(9):e609–e616

    PubMed  Google Scholar 

  19. Tashiro H, Brenner MK (2017) Immunotherapy against cancer-related viruses. Cell Res 27(1):59–73

    CAS  PubMed  Google Scholar 

  20. Tuna M, Amos CI (2017) Next generation sequencing and its applications in HPV-associated cancers. Oncotarget 8(5):8877

    PubMed  Google Scholar 

  21. Strong MJ, Tina OG, Zhen L, Guorong X, Melody B, Chris P, Kun Z, Taylor CM, Flemington EK (2013) Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin’s diffuse large B-cell lymphoma Cohort by using RNA sequencing. J Virol 87(23):13059–13062

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Tang KW, Alaeimahabadi B, Samuelsson T, Lindh M, Larsson E (2013) The landscape of viral expression and host gene fusion and adaptation in human cancer. Nat Commun 4(2513):2513

    PubMed  PubMed Central  Google Scholar 

  23. Network CGA (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513(7517):202–209

    Google Scholar 

  24. Network CGA (2014) Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507(7492):315–322

    Google Scholar 

  25. Network CGA (2015) Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517(7536):576

    Google Scholar 

  26. Cantalupo PG, Katz JP, Pipas JM (2017) Viral sequences in human cancer. Virology 513:208–216

    PubMed  PubMed Central  Google Scholar 

  27. Hanahan D, Weinberg R (2011) Hallmarks of cancer: the next generation. Cell 144(5):646–674

    CAS  PubMed  Google Scholar 

  28. Agalioti T, Lomvardas S, Parekh AB, Yie J, Maniatis T, Thanos D, Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70

    Google Scholar 

  29. Gutschner T, Diederichs S (2012) The hallmarks of cancer. RNA Biol 9(6):703–719

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Xu M, Zhang WL, Zhu Q, Yao YY, Feng QS, Zhang Z, Peng RJ, Jia WH, He GP, Feng L (2019) Genome-wide profiling of Epstein-Barr virus integration by targeted sequencing in Epstein-Barr virus associated malignancies. Theranostics 9(4):1115

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Murakami Y, Saigo K, Takashima H, Minami M, Okanoue T, Bréchot C, Paterlinibréchot P (2005) Large scaled analysis of hepatitis B virus (HBV) DNA integration in HBV related hepatocellular carcinomas. Gut 54(8):1162–1168

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Pett M, Coleman N (2010) Integration of high-risk human papillomavirus: a key event in cervical carcinogenesis? J Pathol 212(4):356–367

    Google Scholar 

  33. Pinatti LM, Walline HM, Carey TE (2018) Human papillomavirus genome integration and head and neck cancer. J Dent Res 97(6):691–700

    CAS  PubMed  Google Scholar 

  34. Zhang J, Huang T, Zhou Y, Cheng A, Yu J, To KF, Kang W (2018) The oncogenic role of Epstein-Barr virus-encoded microRNAs in Epstein-Barr virus-associated gastric carcinoma. J Cell Mol Med 22(1):38–45

    CAS  PubMed  Google Scholar 

  35. Symons J, Cameron PU, Lewin SR (2018) HIV integration sites and implications for maintenance of the reservoir. Curr Opin HIV and AIDS 13(2):152

    CAS  PubMed  Google Scholar 

  36. Ameur A, Kloosterman WP, Hestand MS (2019) Single-molecule sequencing: towards clinical applications. Trends Biotechnol 37(1):72–85

    CAS  PubMed  Google Scholar 

  37. Madsen EB, Kvist T, Höijer I, Ameur A, Mikkelsen MJ (2018) Xdrop: targeted sequencing of long DNA molecules from low input samples using droplet sorting. bioRxiv:409086

    Google Scholar 

  38. Artesi M, Hahaut V, Ashrafi F, Marçais A, Hermine O, Griebel P, Arsic N, van der Meer F, Burny A, Bron D et al (2019) Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads. bioRxiv:558130

    Google Scholar 

  39. Wang M, Beck CR, English AC, Meng Q, Buhay C, Han Y, Doddapaneni HV, Yu F, Boerwinkle E, Lupski JR (2015) PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. BMC Genomics 16(1):214

    PubMed  PubMed Central  Google Scholar 

  40. Mamanova L, Coffey AJ, Scott CE, et al. (2010) Target-enrichment strategies for next-generation sequencing (vol 7, pg 111) [J]. Nat Methods 7(6):479–479

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Geneis (Beijing) Co., Ltd., Beijing, People’s Republic of China

    Xue Sun, Lei Song, Wenjuan Yang, Lili Zhang, Meng Liu, Xiaoshuang Li, Geng Tian & Weiwei Wang

Authors
  1. Xue Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lei Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wenjuan Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lili Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Meng Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xiaoshuang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Geng Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Weiwei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Weiwei Wang .

Editor information

Editors and Affiliations

  1. Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China

    Tao Huang

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Sun, X. et al. (2020). Nanopore Sequencing and Its Clinical Applications. In: Huang, T. (eds) Precision Medicine. Methods in Molecular Biology, vol 2204. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0904-0_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-0904-0_2

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0903-3

  • Online ISBN: 978-1-0716-0904-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation