Read about our asthma and allergy research.
When the complete human genome was first sequenced in 2003, it took more than a decade, required huge machines and cost billions of dollars. Next generation sequencers were a step smaller, faster and cheaper, and were centralised because of the cost.
The new sequencer being trialled by staff at the Malaghan Institute of Medical Research is about the size of a muesli bar and can start producing DNA sequences on site in minutes.
Developed by Oxford Nanopore Technologies, the miniature sequencer connects to a laptop via a USB cable. The genetic sequences are read off as the DNA in a sample is sucked through tiny pores in the MinION device.
DNA sample preparation is also radically simplified (in some cases taking less than 10 minutes), which opens the way for the technology to be applied to many other medical, health and biological problems.
The Malaghan Institute is one of about 4,000 customers worldwide that are using the MinION DNA sequencer.
It's a very impressive device that changes almost everything about how sequencing is done. We don’t have to send samples of DNA away to be sequenced, but can do it here, in real time. It’s not designed for large-scale whole genome sequencing but its size, speed and convenience is revolutionary for the work we are doing.
Our scientists have used the sequencer for a lot of different projects, including identifying variation in mitochondrial genome, assembling the genome of a rodent parasite, Nippostrongylus brasiliensis, and for looking at Interferon gene expression. The technology is now advanced enough that it can be used for almost any genetic discovery, and we look forward to seeing how our research can be enhanced by the use of the MinION sequencer in the future.
Watch a talk from David Eccles about sequencing on the MinION (titled Sequencing that Stimulates the Senses), at TEDxWellington on 5 March 2016.
Related MinION publications (co-authored by researchers from the Institute):
Professor Franca Ronchese has been studying dendritic cells for several years, to understand – at a cellular and molecular level –how they respond to environmental changes, in order to trigger allergies. “Even today, we don’t understand the causes of allergic responses, just their symptoms” says Prof Ronchese. In the team’s latest paper, published in the prestigious Journal of Experimental Medicine, they explored the response of dendritic cells to two allergens – one from a parasite called Nippostrongylus brasiliensis, and dibutyl-phthalate, a chemical plasticizer implicated in allergies in children.
Key to this research project’s success was the use of “omics”, or ‘big data’. To understand how dendritic cells respond to allergens, the team identified and compared every molecule produced by healthy and “allergic” dendritic cells, creating a list of hundreds of changes. “Handling this vast amount of data is a challenge in itself, requiring the use of biostatistics and largecomputers, to store, process and visualise the data,” explained Prof Ronchese.
Their surprising results showed that while the overall immune responses to both the chemical and the parasite allergen were similar, the mechanism behind it was very different. “This is the first time such a study has been carried out,” Prof Ronchese said. “We expected to see more similarities than differences, but that was not the case. This is an initial step on a complex scientific path. There is still a lot to discover and understand about allergies!”
Reference: L.M. Connor et al, “Th2 responses are primed by skin dendritic cells with distinct transcriptional profiles.” J. Exp. Med. 2017, Vol. 214 (3). https://doi.org/10.1084/jem.20160470