ABSTRACT
The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA sequencing outside of laboratory, leading to faster and more accessible DNA-based diagnostics. However, portable DNA sequencing and analysis are challenging for mobile systems, owing to high data throughput and computationally intensive processing performed in environments with unreliable connectivity and power.
In this paper, we provide an analysis of the challenges that mobile systems must address to maximize the potential of portable DNA sequencing, and in situ DNA analysis. We explain the DNA sequencing process and highlight the main differences between traditional and portable DNA sequencing in the context of the actual and envisioned applications. We look at the identified challenges from the perspective of both algorithms and systems design, showing the need for careful co-design.
- M.D. Cao, D. Ganesamoorthy, A.G. Elliott, H. Zhang, M.A. Cooper, and L.J. Coin. Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing. GigaScience, 5(1), 2016.Google Scholar
- S.L. Castro-Wallace, C.Y. Chiu, K.K. John, et al. Nanopore DNA sequencing and genome assembly on the International Space Station. bioRxiv, 2016. hrefGoogle Scholar
- A. Edwards, A.R. Debbonaire, B. Sattler, L.AJ Mur, and A.J. Hodson. Extreme metagenomics using nanopore DNA sequencing: A field report from Svalbard, 78 N. bioRxiv, 2017.Google Scholar
- A. Edwards, A. Soares, S. Rassner, , P. Green, J. Felix, and A. Mitchell. Deep sequencing: Intra-terrestrial metagenomics illustrates the potential of off-grid nanopore DNA sequencing. bioRxiv, 2017.Google Scholar
- N.R. Faria, E.C. Sabino, M.R.T. Nunes, L.C.J. Alcantara, N.J. Loman, and O.G. Pybus. Mobile real-time surveillance of Zika virus in Brazil. Genome Medicine, 8(1), 2016.Google Scholar
- J.L. Gardy and N.J. Loman. Towards a genomics-informed, real-time, global pathogen surveillance system. Nature Reviews Genetics, page nrg.2017.88, 2017.Google Scholar
- F.C. Hewitt, S.L. Guertin, K.L. Ternus, K. Schulte, and D. R. Kadavy. Toward rapid sequenced-based detection and characterization of causative agents of Bacteremia. bioRxiv, 2017.Google Scholar
- S.S. Johnson, E. Zaikova, D.S. Goerlitz, Y. Bai, and S. W. Tighe. Real-time DNA sequencing in the Antarctic Dry Valleys using the Oxford Nanopore sequencer. Journal of Biomolecular Techniques, 28(1), 2017.Google Scholar
- S. Juul, F. Izquierdo, A. Hurst, X. Dai, A. Wright, E. Kulesha, R. Pettett, and Turner. D. J. What's in my pot? Real-time species identification on the MinION. bioRxiv, 2015.Google Scholar
- Metrichor Ltd. Metrichor, an Oxford Nanopore Company. https://metrichor.com/, 2017.Google Scholar
- H. Lu, F. Giordano, and Z. Ning. Oxford Nanopore MinION sequencing and genome assembly. Genomics, Proteomics & Bioinformatics, 14(5), 2016.Google Scholar
- A. Pomerantz, N. Penafiel, A. Arteaga, L. Bustamante, F. Pichardo, L.A. Coloma, C.L. Barrio-Amoros, D. Salazar-Valenzuela, and S. Prost. Real-time DNA barcoding in a remote rainforest using nanopore sequencing. bioRxiv, 2017.Google Scholar
- J. Quick, N.J. Loman, S. Duraffour, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature, 530(7589), 2016.Google Scholar
- C. Quince, A.W. Walker, J.T. Simpson, N. J. Loman, and N. Segata. Shotgun metagenomics, from sampling to analysis. Nature Biotechnology, 35(9), 2017.Google Scholar
- M.R. Stratton, P.J. Campbell, and P.A. Futreal. The cancer genome. Nature, 458(7239), 2009.Google Scholar
- Oxford Nanopore Technologies. Oxford Nanopore. https://nanoporetech.com, 2017.Google Scholar
- Oxford Nanopore Technologies. Voltrax. https://nanoporetech.com/products/voltrax, 2017.Google Scholar
- M.C. Walter, K. Zwirglmaier, P. Vette, S. A. Holowachuk, K. Stoecker, G. H. Genzel, and M. H. Antwerpen. MinION as part of a biomedical rapidly deployable laboratory. Journal of Biotechnology, 250, 2017.Google Scholar
- E. Waltz. Portable DNA sequencer MinION helps build the Internet of Living Things. IEEE Spectrum, 2017.Google Scholar
- R.R. Wick, L.M. Judd, and K.E. Holt. Comparison of Oxford Nanopore basecalling tools. https://github.com/rrwick/Basecalling-comparison, 2017.Google Scholar
Index Terms
- Applications and Challenges of Real-time Mobile DNA Analysis
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