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Vision In focus DNA sequencing

DNA sequencing

Dr Matt Loose is delivering world-leading insights into DNA using a palm-held sequencer with a power that belies its size

The science of DNA has come a long way since the hugely expensive and labour-intensive processes used to map the very first human genome in 2001, and it has continued to advance with exhilarating speed.

At the forefront of this revolution is the University of Nottingham, where Dr Matt Loose and his colleagues have recorded the most complete human genome sequence using a single sequencing technology.

Dr Loose, a biologist with a particular interest in how cell modification drives the development of an embryo, was part of the Nottingham team that embraced the MinION technology, made by Oxford Nanopore Technologies, when it emerged four years ago.

“The goal is to understand more about biological diversity,” he said. “Nanopore sequencing promised lower cost and higher read lengths which meant we could look at interesting organisms which are yet to be sequenced, because their genomes are extraordinarily large.”

Read length is crucial. Conventional sequencing technologies are ‘short-read’, generating many thousands of fragments that must be stitched together. Sequencing ‘ultra-long’ strands of DNA means the fragments are hundreds of times larger and so far fewer – speeding up the process and enabling new biological insights.

“With respect to the read length, it’s been fun,” said Dr Loose, who has been working with researchers at the universities of Birmingham and East Anglia, and others in the US and Canada. “A bit of a friendly competition has broken out around the world as to who can sequence the longest molecule… a group in Australia broke the megabase [the million base pair read] and so there was an impromptu Ashes competition with an Ashes trophy for the longest piece of DNA.

“Australia briefly won that, but we took the record back with a 1,320,000 base pair read. It makes assembling genomes a lot easier if you can get molecules of that length, or longer. It will be really interesting to see what the absolute upper read length limits are.”

The ‘Ashes-winning’ read was 8,000 times longer than a typical sequencing read. Future long reads could be generated routinely to yield benefits in healthcare, agriculture, industry and many other areas, with genome sequencing even taking place at GP surgeries to pinpoint illness and personalise treatment.

Matt Loose

Other researchers at Nottingham are using the process to look at viruses, bacterial infections and antibiotic resistance. As well as sequencing previously uncharacterised regions of the genome, the new analysis provides greater insight into regions responsible for functions such as immunity and tumour growth.

Dr Loose said: “It would be very useful to be able to do routine genome sequencing for patients with tumours, which is an expensive and difficult undertaking, but I think that these sequencing technologies will help make it much, much easier.”

Scientists are looking at plant and animal genomes as part of the University’s Future Food Beacon. Many plant genomes are far larger than the human genome and harder to sequence. Sequencing should also help identify pathogens in foodstuffs, disease control in animals, diagnosis of infection, and a vast number of food-related areas.

As scientists around the world push the boundaries of DNA sequencing, the pace of development shows no signs of slowing.

“We’re all talking to each other,” said Dr Loose, “so it’s a real community which has been built. And Nottingham is a key player in that, which is quite exciting.”

Dr Matt Loose is an Associate Professor in the School of Life Sciences, Faculty of Medicine and Health Sciences.

How it works

As DNA passes through a nanopore, a nano-scale hole in a membrane, the Oxford Nanopore Technologies MinION sequencer passes an ionic current across its surface. The molecules of DNA change the current flow in different ways depending on which of the four DNA bases – A, T, G or C – is moving through the nanopore, so this information can be used to identify that molecule.

Holes can be created by proteins puncturing membranes (biological nanopores) or in solid materials (solid-state nanopores).

A current trace can be sequenced to give a complete DNA picture. Taking the longest-ever sequencing read as an example and scaling the sequencing pore to the size of an adult fist, this is the equivalent to analysing a 3.85 km (2.4 mile) long rope of DNA.