COVID-19
Computational biomedicine at the forefront of epigenomics The advent of new genetics technologies has exploded in the last decade. Since the unravelling of the human genome project in 2003, and with recent discoveries in the field of epigenetics, we are starting to understand not only how and when genes are expressed, but which post-translational modifications are important in disease, and how we can manipulate them therapeutically. Professor Christopher E Mason has developed new technologies to catalog genetic and epigenetic changes caused by everything from cancers to novel viruses, and these tools have proven invaluable during the COVID-19 pandemic. Since the first discoveries in the field of
large consortium tracking microbial
patients’ samples and swabs from
epigenetics in the 1950s, it has been
changes in urban environments. Initially,
hospital surfaces, etc.”
understood that all the inheritable
we were doing everything by hand, but
changes occurring within a cell cannot
our rapidly growing workload meant
The lab still had to adapt its workflow
be explained simply by the DNA
that we urgently needed a robust
to accommodate the unexpected
sequence itself. We now know that both
platform that could reliably and
increase in throughput due to testing of
environmental and lifestyle changes
continuously process the large numbers
COVID-19 patient samples. Dr Mason
can influence whether genes are
of samples we had coming in. Crucially,
expanded: “Since the beginning of the
expressed or silenced, and these factors
it needed to be something we could
pandemic, we have been involved in
can have potentially damaging effects
easily fit into our lab and allow us to hit
numerous projects, both for getting
on our health, such as making us more
the ground running. I heard about the
new testing methods onto the market
prone to developing certain diseases.
DreamPrep™ NAP workstation through
and for tracking the emergence of new
Professor Christopher E Mason is an
a number of our collaborators, and
strains as a result of viral evolution, to
expert in computational and systems
Tecan has a good reputation in the field,
help understand the implications for
genomics, having worked in the field for
so I contacted the company to see what
disease development, treatment and
over 15 years. He is one of the founding
we could do.”
vaccination. This means that our
directors of the MetaSUB International
workflow has been pretty much 5am to
Consortium. Through his research, he
“We were quickly able to set up and run
10pm every day. We really felt that this
has developed a wide knowledge of the
a high throughput platform using the
was a time where we could be most
epigenome and epitranscriptome –
DreamPrep NAP workstation to extract
useful to the wider society, and so we
DNA- and RNA-level modifications,
and process genetic material collected
worked as much as we could!”
respectively – to gather vast amounts
from either clinical samples, or from the
of data that will allow a better
environment – sewage, public benches,
“The DreamPrep NAP has fitted
understanding of how some of these
city subways, etc. I am very much an
seamlessly into our workflow, saving us
seemingly unrelated pathways interact
omnivore of genetics, so when I’m
time, energy and costs. Without it, I
in disease progression. Dr Mason
looking at viruses, I like to find them all,
don’t think we would have been able to
explained: “I oversee a combination of
which is why we use a shotgun
process anywhere near as many
molecular and computational biology
sequencing approach. This is the real
COVID-19 samples as we did, especially
research programs using ‘wet work’ at
fun part of science – pure discovery –
with the need to reduce the number of
the lab bench and the design of new
and in the environmental samples we’ve
staff we had in the lab at any one time. It
algorithms and machine learning to
been collecting, we’ve seen anywhere
has been a true workhorse, and very
process and make sense of the data
from 30 to 60 percent new species,
reliable, with the preprogrammed
that is generated and discover its
annotating them and tracking their
protocols working well. The support
biomedical meaning.”
evolution as we went. This very broad,
from Tecan has also been very
flexible approach meant that, when the
responsive. Any time we’ve had an issue
“Prior to the COVID-19 pandemic, we
pandemic hit, we were already very well
or questions, we’ve had someone on the
mostly processed cancer and
set up to provide a rapid platform to
phone really quickly, or coming to check
microbiome samples, the latter as part
track SARS-CoV-2 genetic material from
it out, which is essential in this kind of
of a project called MetaSUB, which is a
various sample types, including both
situation,” Dr Mason concluded.
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TECAN JOURNAL 2/2021
