Scimex: In the first analysis of its kind, US researchers were able to use a
palm-sized DNA sequencing device to accurately identify a range of
closely-related bacteria and viruses within six hours, demonstrating the
potential for this technology to be used during outbreaks. The low-cost
sequencing device is powered and operated via a USB connection plugged
into a laptop, meaning it could potentially be used for on-site clinical
analyses in remote locations, negating the need for samples to be sent
off to laboratories.
A pocket-sized device that can rapidly determine the sequence of an
organism's DNA has shown its potential in disease detection, according
to a study published in the open access, open data journal GigaScience.
In
the first analysis of its kind, researchers were able to use the device
to accurately identify a range of closely-related bacteria and viruses
within six hours, demonstrating the potential for this technology to be
used as a mobile diagnostic clinic during outbreaks.
The MinION™
'Nanopore sequencer' is a low-cost palm-sized sequencing device from
Oxford Nanopore Technologies that has been made available to some
research groups for testing. It is powered and operated via a USB
connection plugged into a laptop, which means that it could potentially
be used for on-site clinical analyses in remote locations, negating the
need for samples to be sent off to laboratories.
Lead author
Andrew Kilianski from Edgewood Chemical Biological Center, USA, whose
team tested the device in joint collaboration with Signature Science,
LLC, said: "Our findings are important because we have for the first
time communicated to the community that this technology can be
incredibly useful in its current state.
"Being able to
accurately identify and characterize strains of viruses and bacteria
using a mobile platform is attractive to anyone collecting biological
samples in the field. And we expect that as the technology improves, the
sequencing will generally become cheaper, faster and more accurate, and
could have further clinical applications."
The researchers were
able to use the MinION™ to accurately identify and differentiate viral
and bacterial species from samples. Within six hours, the device
generated sufficient data to identify an E. coli sample down to species
level, and three poxviruses (cowpox, vaccinia-MVA, and vaccinia-Lister)
down to strain level. The device was able to distinguish between the two
vaccinia strains despite them being closely related and over 98%
similar to each other.
The technology relies on protein
'nanopores' to determine the sequence of a strand of DNA. At the core of
the protein is a hollow tube only a few nanometres in diameter, through
which a single DNA strands can pass. As the DNA strand passes through
the nanopore, it causes characteristic electrical signatures, from which
bases can be identified, and the sequence of the strand determined.
Despite
MinION™'s observed read error rate of 30%, which is higher than that of
other DNA sequencing methods, the team was able to overcome some of the
current limitations by utilizing an approach based on amplified DNA (an
'amplicon' approach). This allowed them to confidently differentiate
between closely-related strains.
The amplicon approach allows for
the analysis of more complex mixed samples containing a range of
organisms in a short runtime. For whole genome sequencing approaches in
less pure samples, they note that improvements will need to be made as
the technology matures.
The authors state it would be difficult
to accurately characterize pathogens within a complex sample in six
hours without applying the amplicon methodology.