17 July 2018
MRCG to pilot sequencing samples directly in the field: at the heart of outbreaks
MRC Unit The Gambia recently acquired two portable sequencing devices to pilot on field samples in the recently established Genomics Facility. These were provided as part of the continued collaboration between Oxford Nanopore and the Francis Crick Institute. The Oxford Nanopore MinION Sequencer is unique in its ability to directly sequence DNA/RNA in the field, yielding rapid, high-quality sequence data for downstream analysis in real time.
A Portable Sequencing device is ideal for field studies and outbreak situations, where genetic information on pathogen strains can help map disease transmission and inform treatment strategies. The long sequencing reads generated with this platform improve the data accuracy, which is beneficial when sequencing highly repetitive pathogen genomes. The MinION device has the potential to offer relatively low-cost genotyping, high mobility for testing, and rapid processing of samples with the ability to display results in real-time.
Abdul K Sesay, Manager, Genomics Facility, was selected to be part of the MinION Access Program (MAP) in 2014. He successfully negotiated with The Francis Crick Institute and the team at Oxford Nanopore, to bring the devices and necessary computing hardware to the MRC Unit The Gambia.
Laboratory Services currently have eight flow cells that will be used in the coming months to sequence a range of organisms in proof of principle experiments with this new device.The MinION works as follows; tiny protein pores are embedded in a synthetic membrane, one in each well. A potential is applied across the membrane and, as a result, a small current runs through the pore. As the (charged) DNA/ RNA molecules traverse the pore they reduce the current.These reductions depend on the shape of the DNA or RNA that is a tell-tale sign for the base identity. Single molecules are sequenced as they pass through the pore and because there is no interaction there is no limit to the length of the molecule that can be sequenced.
Two projects will be used to evaluate the MinION.The first project is, in collaboration with Martin Antonio, Director of World Health Organisation Regional Reference Laboratory for Invasive Bacterial Diseases, and will re-sequence Cerebrospinal fluid specimens collected from suspected meningitis cases during a historical outbreak/ epidemic in the region. The second project to be done in collaboration with Andrew Prentice, Nutrition Theme Leader, will sequence samples and evaluate the differences in the gut microbiome of malnourished children. Head of Laboratory Services, Davis Nwakanma, said “In-house capacity for field deployment of the MinION sequencer, will facilitate MRCG’s research in a significant way. Bringing DNA sequencing close to where disease outbreaks occur, should make it possible to identify the responsible pathogens in real-time and to more quickly implement appropriate interventions. Abdul’s commitment to this important project is commendable and has led to the significant progress made to-date.”