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ESR scientists showcase benefits of collaboration for rapid-DNA sequencing

16 December 2020

DNA profiling
Miles Benton DNA Sequencing Esr
Miles Benton DNA Sequencing Esr

 group of ESR scientists want communities to collaborate on the application of real-time, cost-effective DNA analysis outside of the laboratory.

ESR senior Scientist Miles Benton’s first child was born prematurely and required a lumbar puncture for suspected viral meningitis, leaving he and his wife to sit in the hospital waiting for blood test results.  Dr Benton said to himself, “Is there a faster way to get these urgent results? If there is, why isn’t it accessible to the hospital? And if there isn’t, what can I do about it?”

With the help of the international community and a small but powerful single board computer, Dr Benton made a breakthrough a few weeks ago.

Dr Benton first began working in earnest on solutions to his initial question by looking at UK-based technology company Oxford Nanopore Technologies. What caught Dr Benton’s eye was the MinION, a small mars bar-sized device used to complete real-time analysis of long DNA or RNA fragments. As it turned out, there were others, just like him, working on these issues and more.

“This tech enables people to get results and act faster than ever before to protect health and communities, something that falls right into our wheelhouse at ESR,” Dr Benton says. “I began working on an issue some months ago that has been slowing down efforts for true portability. The challenge was pairing the MinION with fast enough compute and small enough to be powered off batteries.” he says. “Currently, the MinIONs do not have built-in GPUs, preventing them from completing what is known as live-base calling. In other words, you still need to plug them into a computer in order to get your results – but traditional computers with GPUs are relatively expensive, less portable and need regular recharging.

A lot of back and forth on solutions finally led to a breakthrough. “We were able to get live base-calling going on the device,” says Dr Benton. “I publish my work online through a blog so anyone who is interested can see and contribute. I had no idea anyone was even following what I was doing until I started to make some progress. People then started talking and had ways to solve issues based on their experiences, that’s true science in action - the sharing of information to solve collective issues. There is nothing like the excitement of troubleshooting an issue at 3AM NZDT with someone in Switzerland and another person in Italy, and then getting it working and seeing real results almost instantaneously. It’s incredibly powerful and humbling.”

“Building upon this work, we have been able to assemble a NZD$1200 portable kit, weighing less than two kilograms. The beauty of it is that we have strung some technologies and off-the-shelf products together, including a solar panel and an external battery, to mean that a person could conceivably do this without access to mains power. The applications for this kind of portable, real-time technology are immense.

Dr Benton says that ESR is actively looking for projects where this kind of technology can be explored, both with community and other scientists.

“I am far from the only one using these devices,” Dr Benton says. “Currently the MinION has been used in Africa in mobile vans to track viruses such as Ebola and Zika. It has also been taken into the rain forest and people have made makeshift labs set up to sequence and discover new species. It has even been used to sequence DNA in the International Space Station. What we have achieved here is making it more portable, affordable and accessible.  This tool is only limited by the imagination of those who use it – it falls upon us to find new ways of using it in different contexts.”