MinIONs, MAP and MARC: Nanotechnology developments
We're working with the latest in nanopore sequencing technology to push the boundaries of low-cost, portable genomics solutions.
What if we had access to a portable and cheap DNA sequencing platform that could provide us with real-time, streamable data with read lengths comparable to some of our current, large, expensive lab-based systems?
With the MinION, we get just that, and a lot more, for only £700. What are we doing to help advance our understanding of how to make the most out of such a useful piece of kit?
The development of the Oxford Nanopore MinION is one of the most exciting steps forward in next-generation sequencing (NGS) technologies. Its possible applications are endless while offering the possibility of ushering NGS into a new era, where we can perform live sequencing experiments in any possible conceivable environment.
The MinION can slip into a pocket as easily as a USB stick, yet has specifications in many ways comparable to or surpassing our current most popular systems. Though not achieving the throughput of some of the well-established platforms, the MinION is capable of producing very long reads, and can do this at a fraction of the cost - with a single unit costing £700.
According to Richard Leggett, who is leading our bioinformatics efforts into advancing the use of the MinION, “The Earlham Institute is an enthusiastic community member of the MinION Access Programme (MAP) and part of the MinION Analysis and Reference Consortium (MARC).
“Phrase one of MARC included the analysis of the Nanopore data generated by five labs around the world - where we developed enhancements to the MinION tool NanoOK specifically with this data in mind - for example, the ability to perform comparative analysis of multiple Nanopore runs. We are now coming into the second phase of the MARC consortium’s plans, both in an experimental and data analysis role.”
One of the most novel facets of the MinION is how genomic data is recognised and relayed. Using nanotechnology; DNA strands are read through a nanopore, across which is passed an electric current. As DNA bases pass through the pore, a sensor detects changes in the current that results in a signal characteristic of the molecule. These signals are then translated back into genetic code using a service called Metrichor.Dr Leggett has been leading a project into the development of NanoOK - an alignment-based data analysis tool - to help users “get to grips” with Nanopore data in order to enable better, and faster, genome analysis and assembly.
This “base-called” data from Metrichor can then be fed into NanoOK, which provides a “flexible, multi-reference software for pre and post-alignment analysis of nanopore sequencing data, quality and error profiles,” said Dr Leggett.
The data is firstly fed into a sequence aligner, which is then processed by NanoOK in order to produce detailed analysis and graphs, including read length, yield, and quality information. The analysis of error also provides information on the accuracy of the DNA sequencing, which currently stands at around 85-90% with the current version of the flow cells.
One of the most useful applications of the MinION, going forwards, will be in the metagenomic analysis of environmental samples. In particular, we hope to sequence multiple genomes in a variety of environments, from soil and air to water and clinical samples.
However, as Dr Leggett points out, searching for meaningful data amid a plethora of samples is rather like delving into a bag of revels. On the outside, they can look quite similar - but within each chocolate-coated treat, there can lie a surprise.
You never quite know what you are getting - be it a hazelnut treat or a coffee-tinged kick. Thus, it’s crucial that we develop the software tools to enable us to understand the data, something that we are working towards.
Further research into the applications of the MinION is bound to open exciting opportunities in the future, with the availability of real-time sequencing, assembly and the possibility of combining technologies such as the Raspberry Pi computer for low-powered, embedded analysis.
The opportunities for using the MinION are seemingly endless - but this tool is already showing great promise for use in a variety of environments. As well as in-field analysis, the pocket-size device is looking likely to offer incredibly important uses in a hospital setting, with more efficient sequencing of clinical DNA samples to better inform medicine and medical procedures.