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.
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.