image: MinION is a portable sequencing DNA device. view more
Credit: TGAC
As one of the first research Institutes to take part in the MinION Access Programme (MAP) for portable DNA sequencing, introduced by Oxford Nanopore Technologies, The Genome Analysis Centre (TGAC)'s task force share their experience of the ground breaking trial so far.
One of the first research Institutes to be part of MAP, TGAC plans to use the miniaturised sequencing device to conduct live environmental surveillance; rather than gathering samples to take back to the laboratory, enabling the researchers to deliver real-time experimental genetic data for immediate analysis.
The team of scientists from TGAC's Data Infrastructure and Algorithms and Plant and Microbial Genomics groups trialled the miniaturised sensing system by sequencing environmental samples, containing DNA from hundreds or thousands of different organisms.
The team experimented first with a mock community, where they used a simple set of DNA samples from twenty bacteria, created for the Human Microbiome Project. Having developed their experimental and data methods, they then tested real environmental samples sequencing them on the MinION and Illumina platforms for comparison.
Their aim was to sequence the microscopic biological molecules in the air around us - bacteria, spores and viruses. Many key crop diseases spread via the air as spores, as well as some animal and human diseases. Analysing such samples triggers technical issues, where there are very low levels of biological material present when sequencing DNA from air.
Although the scientists faced challenges working with complex metagenomic (genetic material recovered directly from an environment) samples in live-time, the introduction of the MinION as a potential portable laboratory made a major impact to the research's goal.
"In-field surveillance presents a number of hurdles. With its compact size, cheap device cost, simple library preparation and streaming nature, the MinION provides a significant step towards addressing these challenges," said Dr Richard Leggett, member of the MAP task force and Project Leader in the Data Infrastructure & Algorithms Group at TGAC.
The scientists used the bioinformatics tool, Kontaminant in their research, which was originally developed for screening DNA for contamination from other species and then adapted this tool to analyse metagenomic samples and identify species as they are being sequenced on the MinION. They also developed a tool called NanoOK, which is designed to analyse Nanopore data and help to understand the MinION's error profile.
Dr Leggett and the rest of the task force recently presented the TGAC team's preliminary findings at the world renowned scientific conference, Advances in Genome Biology & Technology (AGBT) at Marco Island in Florida in his talk, titled: 'Towards Real-Time Surveillance Approaches Using Nanopore Sequencers'.
Dr Leggett said: "Our research is still at an early stage, but indications are that the MinION is capable of sequencing complex metagenomic samples. We were able to demonstrate species identification from the mock community using Kontaminant and to run this on a very low-powered computer (the Raspberry Pi), which would be capable of being deployed in-field with the MinION."
The scientists choose the MinION for their area of research due to the cost efficiency, simplicity and streaming nature of the portable sequencing device. Although it does have a significant error profile, taking into account its miniature sequencing capability, it was still able to produce large areas of highly-accurate DNA analyses.
"It's great to be part of the MinION Access Programme, as it has provided us with access to the very latest sequencing technology. Though the MinION is not perfect, current sequencing platforms are just too large and cost too much to purchase to consider deploying in-field," said Dr Leggett.
"The ability to deploy real time monitoring in the field could change agriculture methods and how we look at crop disease outbreaks, as well as human disease epidemics. These are early days, but it looks like a combination of a small low power sequencing device with the correct experimental and computational approaches can spot pathogens," said Dr Matt Clark, head of the MAP task force and Plant and Microbial Genomics Group Leader at TGAC.
In addition to studying metagenomics, the TGAC MAP team are also interested in understanding new technologies such as the MinION and providing the scientific community with tools to help them get the most out of these technologies. The research group will continue to be part of the MAP and will be developing this work further by looking at other research areas for the MinION, with a view to paper publication, tools releases, collaborations and grant applications.
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The work has been a collaborative effort amongst the MAP task force at TGAC: Matthew Clark, Rob Davey, Mario Caccamo, Darren Heavens and Richard Leggett.
Notes to Editors
About TGAC
The Genome Analysis Centre (TGAC) is a world-class research institute focusing on the development of genomics and computational biology. TGAC is based on the Norwich Research Park and receives strategic funding from the Biotechnology and Biological Science Research Council (BBSRC) - £7.4M in 2013/14 - as well as support from other research funders. TGAC is one of eight institutes that receive strategic funding from BBSRC. TGAC operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
TGAC offers state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative Bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a Training programme through courses and workshops, and an Outreach programme targeting schools, teachers and the general public through dialogue and science communication activities. http://www.tgac.ac.uk
About BBSRC
The Biotechnology and Biological Sciences Research Council (BBSRC) invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by UK Government, BBSRC invested over £484M in world-class bioscience in 2013-14. We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.
For more information about BBSRC, our science and our impact: http://www.bbsrc.ac.uk
For more information about BBSRC strategically funded institutes: http://www.bbsrc.ac.uk/institutes