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Today, we are very pleased to highlight some exciting new data with regards to genome sequencing. We have just published a short research paper from the Bader lab at the University of Toronto providing the first public example of the Oxford MinION nanopore sequencer being evaluated for utility in the clinic.

For those not familiar with this device, the MinION, created by Oxford Nanopore Technologies, is a portable sequencer designed for molecular analyses that is driven by nanopore technology. However, unlike conventional bench top sequencers the MinION is pocket sized and only as big as a Swiss army knife! What does this device bring to the table? Well above all, it could open the door to new opportunities for easily applying genome sequencing in health care environments as the restrictions of size, mobility and cost are taken out of the equation.

The article itself was published online within 7 days of submission and is currently awaiting peer review. Following the usual F1000Research mantra, the article is fully open access and sharable, and all of the underlying sequencing data is readily available for reuse and download. Through our invited, post-publication peer review model you can track this article and become alerted as referee reports come in and discussion starts – all of which is completely open and transparent. Simply hit the TRACK button at the top of the article to be kept up-to-date.

To date, all other publications using the MinION have focused on bacterial and viral sequencing. So to discuss the work a little further, we have interviewed F1000Research Advisor Gary Bader and his postdoc Ron Ammar who received one of the first devices as part of the MinION Access Program (MAP).

Interview

F1000Research: Being a lab that was part of the MinION Access Program (MAP) did you already have a preconception of how you wanted to apply the device, and what were your expectations of its potential performance?

Gary and Ron: When we applied to the MinION Access Program, our goal was to craft a project leveraging both the affordability of nanopore sequencing and long sequence reads generated in real time by the MinION device. We thought clinical diagnostics would be an appropriate application because the device would satisfy the prerequisites for low cost and rapid outcomes. As well, we selected a clinical application, pharmacogenomics, which assesses genic haplotypes, where the phase of all genetic variants would be important for diagnosis. The long reads allowed us to determine these haplotypes without the need for additional analysis that is common on current sequencing platforms. The only other commercial technology currently capable of this type of analysis is the Pacific Biosciences instrument, which is several orders of magnitude more expensive.

F1000Research: There isn’t much published data on MinION sequencing because the device is still in its test phase. However, your study is important as its the first published case that uses human samples. Can you explain what you sequenced and what its implications are?

Gary and Ron: Nanopore sequencing has the potential to bring DNA sequence-based diagnostics to clinical and laboratory facilities that do not have the budget for large instruments. Currently, only a few hospitals with large research programs are able to purchase and use massively parallel sequencing instruments. However, with the advent of affordable nanopore devices, sequencing tests can be run locally and diagnostic results will be available more rapidly. In anticipation of a revolution in DNA-based diagnostics, we sought to be among the first researchers to investigate the power and pitfalls of nanopore sequencing for human diagnostic applications. For this to happen, advances in sample preparation will be needed and we look forward to their development. As well, we envision that software tools for processing diagnostic data will be open source and available online for institutions to use without the need for a local research program and analysts. All of these would ideally help create a very inexpensive and accessible DNA sequencing platform.

F1000Research: Being in its test phase, it has been reported that the device can be prone to high error rates and some signal and noise issues; was this the case whilst performing your sequencing?

Gary and Ron: We certainly observed high error rates, which have been characterized in our study. However, we also noted that the distribution of errors was relatively uniform across DNA sequence reads, allowing us to build accurate consensus sequences by increasing the depth of coverage. Over the course of the MAP testing program, we have worked on multiple flow cell chemistry versions, and with each iteration of chemistry, the error rates have decreased significantly. We anticipate that this trend will continue until the error rates are low enough to compete with current massively parallel sequencing platforms.

F1000Research: Your lab is primarily computational. How did you get involved in this wet lab project?

Gary and Ron: We are fortunate to be part of an amazing multi-disciplinary and collaborative environment at The Donnelly Centre and the University of Toronto that made this project possible. We were already collaborating with researchers at the Hospital for Sick Children and The Centre for Applied Genomics in Toronto on pharmacogenomics testing in the clinic where we are developing software for genotype interpretation, so we were familiar with the area. Also, our institute’s DNA sequencing facility is located on our floor. It has been noted that computational analysis is now the limiting factor in DNA sequencing, but we already had that part covered. So once we heard about the Oxford Nanopore early access program, we were quickly able to gather collaborators to push our study forward. Nanopore technology is a great illustration of the democratization of DNA sequencing by making an instrument that is very simple to use and significantly more affordable than current-gen sequencers. The sequencing device can be run with only a few pieces of standard lab equipment (specifically, pipettes and a centrifuge) and the pipeline can be processed using a standard laptop. Nanopore-seq certainly lowers the barrier to entry, and we were able to work in the “wet lab” space without prior next generation sequencing experience at the bench.

F1000Research: Once you had generated the data, why did you choose to publish it in F1000Research?

Gary and Ron: We chose F1000Research because we are interested in making our results public as soon as possible. The field is moving very quickly and many researchers are interested to know how nanopore sequencing performs, and our goal was to get data to these scientists in a quick and transparent manner. F1000Research has the advantage of making research available immediately in an open access environment, which includes making all the data available so others can easily reuse and download our data. The peer-review process is also done post-publication and transparently helping foster any potential collaborations. All too often, we’ve experienced delays of six to twelve months in publicly communicating our research findings. We hope publishing early will stimulate constructive discussion on the use of the next generation of sequencing devices in the clinic.

F1000Research: So, what’s next to be sequenced in the Bader lab using the MinION?

Gary and Ron: We’ve got some exciting experiments planned! We hope to use nanopore sequencing to probe questions that are not easily answered with alternative sequencing methods. These include long read RNA-seq validation and sequencing of kilobase-scale repeat regions in the human genome.