A mini DNA sequencer

Oxford Nanopore Technologies has developed the MinION, a handheld device that works by detecting individual DNA bases that pass through a nanopore. The device has been tested and evaluated by an international consortium coordinated by the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI).

The MinION is a portable technology platform for the direct, electronic analysis of single molecules. It works with consumable flow cells that contain the nanopore-sensing apparatus required to perform experiments and plugs into a PC or laptop that controls the sequencing run. DNA-sequencing users generate long reads, analyse data in real time with a high-speed internet connection and use the device in multiple environments. There are few sensing limits on the length of the DNA sequence that could be read at one go.

The device was initially made available to thousands of laboratories all over the world, which were inspired to contribute to its development through the MinION Access Programme (MAP). The MAP is an early-access community that enables a broad range of people to contribute to developments in analytical tools and applications, share their experiences and collaborate.

“Because the device weighs only 100 g, Oxford Nanopore could share it easily with more than 1000 labs worldwide,” said Mark Akeson of the University of California, Santa Cruz, a co-inventor of nanopore sequencing, consultant to Oxford Nanopore and a MAP participant. “Some of those people are tinkerers who invented new informatics tools or wet lab techniques that improved MinION performance.

“The device performs well now, particularly for viral and bacterial genomes, so you can ship it anywhere and know you’re going to get the same result. We’re looking at a democratisation of sequencing in the not-so-distant future; that is, changing things for people who need to solve critical problems in challenging environments, like tracking Ebola strains during the recent outbreak in West Africa. Another challenging environment is space — the MinION will be the first DNA sequencer tested in space, by NASA on the International Space Station.”

Five laboratories in the UK, the US, Canada and the Netherlands recently conducted two sets of 10 experiments for the same E. coli isolate using a single, shared protocol. The accuracy and reproducibility of the data were consistent between labs and of good quality. A paper providing preliminary analysis of the data generated is available on the Nanopore analysis channel of F1000Research.

“We’ve published the paper in F1000Research before peer review as a baseline for the community, so that everyone can look at the paper and data, go on to do their own analyses, share their results and stimulate discussion,” explained David Buck of Oxford University.

MinION opens up new possibilities for using sequencing technology in the field; for example, in tracking disease outbreaks, testing packaged food or the trafficking of protected species. According to first author Camilla Ip, of Oxford University, it could be used by science teachers in just a few years “to teach science in new, exciting ways that have never been possible before”.

“I’m using the MinION in a project with secondary-school students in Oxford because this technology will probably be so much a part of daily life in a few years’ time that they take it for granted,” she said. “The kids who are about to go to university and join the workforce are the ones who will be creating new smartphone apps that use this sensing device for applications we haven’t yet imagined.”

“Nanopore sequencing will open the door for the development of novel tools and applications to analyse the influx of new data,” added Rebecca Lawrence, managing director of F1000Research. “The Nanopore analysis channel on F1000Research will be a central, open platform on which scientists can publish and discuss new applications and analyse workflows for nanopore sequencing data. People can access and contribute data easily so that the wider life-science community can realise the full potential of this new technology quickly.”

The next phase of analysis is already underway by EMBL-EBI, which is exploring ways to reduce the error rate and pushing to see how small the sample and how long the reads can be.

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