First $1,000 genome, now DNA-sequencing for anyone – what comes next?

I recently received a Facebook message from a good friend. He’s an electrical engineer and likes to think outside the box. He shared an article termed “Portable DNA Sequencer MinION helps build the internet of living things” [1]. Below he wrote „Soon we share DNA instead of internet articles.” I was confused. The title was of no use for me. So I read the article. Apparently a DNA sequencing device called MinION was developed that enables not only researchers but EVERYONE to sequence DNA of living things in our environment (including our own human DNA) and share it on the internet. To me this sounded all too strange. But I got curious. How does this work? Surely this couldn’t be done with the methods that I learned at university? Could I even trust what I read?

I had a closer look at the technology of the device with the same name as these little yellow animation stars – MinION. The manufacturer Oxford Nanopore Technologies produces this small portable device (size of a palm) which makes use of the nanopore sequencing technology. Here, nanopores are placed in a synthetic polymer membrane with high electrical resistance. When a potential is applied, an ionic current is generated through the nanopores. Every time an analyte passes through a pore, the current is disrupted in a characteristic pattern. Based on this pattern, a distinction between different molecules is possible. This also includes the four standard DNA bases adenine, cytosine, guanine and thymine [2].

In contrast to the MinION, conventional sequencers require specialized staff, produce a lot of data, are expensive in terms of computing power and storage capacity and are fairly big. The MinION is not just small and cheap; it can also be connected to a laptop and provides full length reads in real time. Imagine what this can mean for our research! We could use the MinION at site and obtain our results immediately. This would be a nice feature. But more importantly, new fields of application could be established. There are first examples where the device was used for the identification of unknown organisms (sequencing of the genome of a native frog in Tanzania) [3] or in field testing in epidemics (sequencing of Ebola virus genomes from 14 patients in 48 h) [4]. There are plans to use the MinION on Mars to test for the existence of life [5] and I can imagine that it’s boosting metagenomics as well. The chips of the MinION might also find use in quality assurance, e.g. on farms, in food processing or retail to test for the existence of pathogens [6], [7]. This obviously means that cheating becomes a lot harder and hopefully we don’t find any rotten meat or horsemeat in the refrigerated display cases of the supermarkets anymore.

Coming back to the comment of my friend that we soon share DNA instead of articles: I would not have thought of an application like this but Clive G. Brown, chief technology officer at Oxford Nanopore Technologies, points out the possible use by everyone for self-quantification. This basically means that “individuals could track changes in their DNA” [6]. There are two thoughts coming to my mind. Firstly: Why would I want to know? In some cases it’s better to stay unsuspecting. Just picture someone reading out his DNA and suddenly discover that the DNA has actually changed. The person wouldn’t know what to make of this and worry or go to the doctor. But would the doctor know what to do with this information? And secondly: Why would I want to share my sensitive data on the Internet? Brown has a point in saying that we are already doing similar things with the fitness trackers. We share our fitness level or sleeping behavior. So why not share DNA sequences? I don’t like the idea but I’m sure there are people who’d do it. But has anyone ever thought about where this would lead? We go further and further without knowing what the consequences could be. At least this is something beyond my imagination and I bet nobody truly knows.

At the moment, an application like this isn’t possible. There are still some teething troubles, e.g. the sequencing speed is still not as high as expected or necessary for large genomes. And in regions of base repeats the error rate is still very high. This would probably not make a difference to people using the device outside science (they wouldn’t know what this means anyways). But what is important to them is the preparation of the DNA. Till now, the DNA extraction and preparation requires multiple steps and usually lab equipment. But Oxford Nanopore Technologies is already developing the user-friendly portable prepping device called VolTRAX [8].

I guess we will have to wait for improvements of MinION and the release of VolTRAX to see in which fields these devices can be used and if the dream of Brown comes true that people track changes of their DNA and share it on the internet. Future will teach us…

Literature

[1] E. Waltz, “Portable DNA Sequencer MinION Helps Build the Internet of Living Things,” IEEE Spectrum: Technology, Engineering, and Science News, 17-Mar-2016. [Online]. Available: http://spectrum.ieee.org/the-human-os/biomedical/devices/portable-dna-sequencer-minion-help-build-the-internet-of-living-things. [Accessed: 30-May-2016].
[2] “How it works – Science & Technology – Oxford Nanopore Technologies.” [Online]. Available: https://nanoporetech.com/science-technology/how-it-works. [Accessed: 30-May-2016].
[3] “Scientists identify frog through DNA without leaving forest,” Wildtech, 05-May-2015. [Online]. Available: https://wildtech.mongabay.com/2015/05/scientists-identify-frog-through-dna-without-leaving-forest/. [Accessed: 07-Jun-2016].
[4] J. Quick, N. J. Loman, S. Duraffour, J. T. Simpson, E. Severi, L. Cowley, J. A. Bore, R. Koundouno, G. Dudas, A. Mikhail, N. Ouédraogo, B. Afrough, A. Bah, J. H. J. Baum, B. Becker-Ziaja, J. P. Boettcher, M. Cabeza-Cabrerizo, Á. Camino-Sánchez, L. L. Carter, J. Doerrbecker, T. Enkirch, I. G.- Dorival, N. Hetzelt, J. Hinzmann, T. Holm, L. E. Kafetzopoulou, M. Koropogui, A. Kosgey, E. Kuisma, C. H. Logue, A. Mazzarelli, S. Meisel, M. Mertens, J. Michel, D. Ngabo, K. Nitzsche, E. Pallasch, L. V. Patrono, J. Portmann, J. G. Repits, N. Y. Rickett, A. Sachse, K. Singethan, I. Vitoriano, R. L. Yemanaberhan, E. G. Zekeng, T. Racine, A. Bello, A. A. Sall, O. Faye, O. Faye, N. Magassouba, C. V. Williams, V. Amburgey, L. Winona, E. Davis, J. Gerlach, F. Washington, V. Monteil, M. Jourdain, M. Bererd, A. Camara, H. Somlare, A. Camara, M. Gerard, G. Bado, B. Baillet, D. Delaune, K. Y. Nebie, A. Diarra, Y. Savane, R. B. Pallawo, G. J. Gutierrez, N. Milhano, I. Roger, C. J. Williams, F. Yattara, K. Lewandowski, J. Taylor, P. Rachwal, D. J. Turner, G. Pollakis, J. A. Hiscox, D. A. Matthews, M. K. O. Shea, A. M. Johnston, D. Wilson, E. Hutley, E. Smit, A. Di Caro, R. Wölfel, K. Stoecker, E. Fleischmann, M. Gabriel, S. A. Weller, L. Koivogui, B. Diallo, S. Keïta, A. Rambaut, P. Formenty, S. Günther, and M. W. Carroll, “Real-time, portable genome sequencing for Ebola surveillance,” Nature, vol. 530, no. 7589, pp. 228–232, Feb. 2016.
[5] K. Rainey, “Sequencing DNA in the Palm of Your Hand,” NASA, 29-Sep-2015. [Online]. Available: http://www.nasa.gov/mission_pages/station/research/news/biomolecule_sequencer. [Accessed: 07-Jun-2016].
[6] Wired UK, Oxford Nanopore’s Clive Brown: the internet of living things – Full WIRED Health Talk.
[7] “Oxford Nanopore Technologies.” [Online]. Available: https://www.nanoporetech.com/. [Accessed: 07-Jun-2016].
[8] “Voltrax – Products & services – Oxford Nanopore Technologies.” [Online]. Available: https://www.nanoporetech.com/products-services/voltrax. [Accessed: 30-May-2016].

About Aline

Aline is a dedicated PhD student from TU Graz who has the passion to share her knowledge to hungry minds.
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