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Scope 63 - Small device, big opportunities - sequencing genomes with a MinION

7 August 2017

These days, bench-side laboratory work is intertwined with complex computational work, called bioinformatics. Analysis technologies transform data into meaningful results and open new avenues of research. For the past six months, Dr David Eccles and Dr Jonathan Ewbank have been sequencing the genome of Nippostronglyus brasiliensis. “Nippo” is a parasite with a life-cycle similar to human hookworm, which infects millions of people worldwide. As people with hookworm infection seem to be protected from allergic diseases like asthma, researchers at The Malaghan Institute are interested in understanding more about Nippo.

Sequencing an organism’s genome allows us to understand its unique biology and abilities; for instance, how it infects a host. Dr Eccles and Dr Ewbank use a sequencing device the size of a muesli bar, called MinION, from Oxford Nanopore Technologies. DNA from Nippo is fed into the device and within minutes, it starts reading the DNA sequence.

Previous attempts to sequence Nippo, even a year ago, failed because the established technology could not overcome the complex nature of its genome. “It was like trying to piece together a 10,000-page book using extracts of 100 letters,” describes Dr Ewbank. “Now, we get stretches of 100,000 letters in one go; whole chapters at a time. We can then integrate them back into the whole book, or in this case, the genome.”

With parasitic worms emerging as a potential therapy for diseases like coeliac and asthma, it is crucial to enhance our understanding of their genome and biology. The research findings of this project and others at The Malaghan Institute are contributing in a major way to this goal.