“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.”
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 Latest on: Portable DNA sequencing laboratory
via Google News
The Latest on: Portable DNA sequencing laboratory
- A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomeson February 21, 2020 at 2:16 am
... R7.3 flowcell for 48 hours on the MinION portable sequencer (Oxford Nanopore Technologies). Nanopore sequence data are deposited in the European Nucleotide Archives (ENA) and is available through ...
- New online genetics course allows college students to learn DNA Sequencing on a flexible scheduleon February 11, 2020 at 5:13 pm
In order to teach her students DNA sequencing, Wolf says she chose the project ... Long says it is different from doing lab work in an actual lab setting because it is portable and she can do it when ...
- Hong Kong researchers create fastest coronavirus diagnostic test to dateon February 7, 2020 at 3:24 pm
HONG KONG – A team of researchers at Hong Kong University of Science and Technology (HKUST) claim to have invented the world’s fastest portable 2019-nCoV diagnostic ... extraction of viral RNA from ...
- Bay Area Bio-Tech Firms Take Lead In Fight Against Coronaviruson February 6, 2020 at 7:13 pm
The company is testing a new and portable electronic device for DNA sequencing. The device promises ... Until now, samples had to be sent to a lab in Atlanta, which could take a week to provide ...
- Chinese CDC reaches out to young sequencing company for help with the coronavirus outbreakon February 6, 2020 at 9:01 am
In light of this fact, the Chinese CDC (Bejing, China) has recently reached out to a growing DNA sequencing ... than standard sequencing systems. This makes the sequencer incredibly portable and ...
- GenapSys raises $75M to bring its tabletop DNA sequencer to Asia amid coronavirus outbreakon February 6, 2020 at 4:00 am
Just months after collecting $90 million to support the launch of its compact DNA sequencing hardware ... the company said its portable sequencer could be used in a variety of settings.
- From Bench to Clinic—The Potential of New Sequencing Toolson February 4, 2020 at 8:50 am
Beggs’ lab has been testing nanopore-based HLA typing using the portable MinION platform ... instruments that enables direct, real-time DNA or RNA sequencing on smaller, single-use flow cells.
- MGI Launches Benchtop Sequencing Laboratory And Automation Productson February 2, 2020 at 4:00 pm
From DNA to digital library construction, to on-machine sequencing and off-machine reporting ... cell research solutions for all life science laboratories. The current products include the DNBelab C4 ...
- Oxford Nanopore Sequencers Have Left UK for China, to Support Rapid, Near-sample Coronavirus Sequencing for Outbreak Surveillanceon February 2, 2020 at 1:20 pm
Oxford Nanopore is already working to support more than 100 public health laboratories ... MinION is the only portable, real-time device for DNA and RNA sequencing. Each MinION sequencer is ...
- Analyzing DNA in soil could be an effective way of tracking animalson January 13, 2020 at 4:00 pm
A new Stanford study reveals sampling soil for animals' left-behind DNA can provide valuable ... combined with decreasing costs of genetic sequencing and new portable sequencers, makes eDNA ...
via Bing News