Abstract
DNA sequencing has reached an unprecedented level with the advent of Oxford Nanopore Technologies’ MinION. The low equipment investment, ease of library preparation, small size, and powered only by a laptop computer enable the portability for on-site sequencing. MinION has had its role in clinical, biosecurity, and environmental fields. Here, we describe the many facets of on-site sequencing with MinION. First, we will present some field works using MinION. We will discuss the requirements for targeted or whole genome sequencing and the challenges faced by each technique. We will also elaborate the bioinformatics procedures available for data analysis in the field. MinION has greatly changed the way we do sequencing by bringing the sequencer closer to the biodiversity. Although numerous limitations exist for MinION to be truly portable, improvements of procedures and equipment will enhance MinION’s role in the field.
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References
Boykin LM, Ghalab A, Rossitto De Marchi B, Savill A, Wainaina JM, Kinene T, et al. Real time portable genome sequencing for global food security. bioRxiv. 2018:1–10.
Brinkmann A, Ergu K, Radoni A, Tufan ZK, Domingo C, Nitsche A. Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics. PLoS Negl Trop Dis. 2017;11(11):1–13.
Castro-Wallace SL, Chiu CY, John KK, Stahl SE, Rubins H, Mcintyre ABR, et al. Nanopore DNA sequencing and genome assembly on the international space station. Sci Rep. 2017;7(18022):1–12. https://doi.org/10.1038/s41598-017-18364-0.
Faria NR, Sabino EC, Nunes MRT, Carlos L, Alcantara J, Loman NJ, Pybus OG. Mobile real-time surveillance of Zika virus in Brazil. Genome Med. 2016;8(97):1–4. https://doi.org/10.1186/s13073-016-0356-2.
Faria N, Kraemer N, Hill S, Goes de Jesus J, de Aguiar R, Iani F, et al. Genomic and epidemiological monitoring of yellow fever virus transmission potential. bioRxiv. 2018:1–35.
Goordial J, Altshuler I, Hindson K, Chan-yam K. In situ field sequencing and life detection in remote (79°26’N) Canadian high Arctic permafrost ice wedge microbial communities. Front Microbiol. 2017;8(2594):1–14. https://doi.org/10.3389/fmicb.2017.02594.
Hardegen J, Latorre-Perez A, Vilanova C, Thomas G, Simeonov C, Porcar M. Liquid co-substrates repower sewage microbiomes. bioRxiv. 2018.
Hayashida K, Kajino K, Hachaambwa L, Namangala B, Sugimoto C. Direct blood dry LAMP: a rapid, stable, and easy diagnostic tool for human African trypanosomiasis. PLoS Negl Trop Dis. 2015;9(3):e0003578. https://doi.org/10.1371/journal.pntd.0003578.
Houldcroft CJ, Beale MA, Breuer J. Clinical and biological insights from viral genome sequencing. Nat Rev Microbiol. 2017;15(3):183–92. https://doi.org/10.1038/nrmicro.2016.182.
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018:1–7. https://doi.org/10.1093/bioinformatics/bty191.
Lu H, Giordano F, Ning Z. Oxford Nanopore MinION sequencing and genome assembly. Genomics, Proteomics Bioinformatics. 2016;14(5):265–79. https://doi.org/10.1016/j.gpb.2016.05.004.
Menegon M, Cantaloni C, Rodriguez-prieto A, Centomo C, Abdelfattah A, Rossato M, et al. On site DNA barcoding by nanopore sequencing. PLoS One. 2017;12(10):1–18.
Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28(12):E63. https://doi.org/10.1093/nar/28.12.e63.
Oxford Nanopore Technologies. New basecaller now performs “raw basecalling”, for improved sequencing accuracy. 2017. Retrieved from https://nanoporetech.com/about-us/news/new-basecaller-now-performs-raw-basecalling-improved-sequencing-accuracy
Pomerantz A, Arteaga A, Bustamante L, Pichardo F, Coloma LA, Salazar-valenzuela D, et al. Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building. GigaScience. 2018;7:1–14. https://doi.org/10.1093/gigascience/giy033.
Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016;530(7589):228–32. https://doi.org/10.1038/nature16996.
Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc. 2017;12(6):1261–76. https://doi.org/10.1038/nprot.2017.066.
Runtuwene LR, Tuda JSB, Mongan AE, Makalowski W, Frith MC, Imwong M, et al. Nanopore sequencing of drug- resistance-associated genes in malaria parasites, Plasmodium falciparum. Sci Rep. 2018;8(8286):1–13. https://doi.org/10.1038/s41598-018-26334-3.
Yamagishi J, Runtu LR, Hayashida K, Mongan AE, Thi AN, Thuy LN, et al. Serotyping dengue virus with isothermal amplification and a portable sequencer, (January), 1–10. 2017. https://doi.org/10.1038/s41598-017-03734-5.
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Runtuwene, L.R., Tuda, J.S.B., Mongan, A.E., Suzuki, Y. (2019). On-Site MinION Sequencing. In: Suzuki, Y. (eds) Single Molecule and Single Cell Sequencing. Advances in Experimental Medicine and Biology, vol 1129. Springer, Singapore. https://doi.org/10.1007/978-981-13-6037-4_10
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DOI: https://doi.org/10.1007/978-981-13-6037-4_10
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