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King's College London - Health: More than a medical matter





Miniature DNA sequencer could read a genome in seconds

27 February 2012

By Ayesha Jadoon

Appeared in BioNews 646

A handheld device for sequencing DNA on the move has been unveiled by UK company Oxford Nanopore. The single-use MinION tool resembles a USB drive in size and shape, and the company hopes it will be put into routine use by clinicians and researchers alike.

Unlike existing sequencing methods, this new technology does not require amplification or manipulation of the DNA - in some cases it will be able to be sequenced directly from the blood. This should produce results quickly, a necessity when testing patients for cancer or checking a fetus for genetic abnormalities, for example.

Oxford Nanopore demonstrated MinION at the Advances in Genome Biology and Technology (AGBT) conference in Marco Island, Florida, as well as a worktop sequencer called GridION, which they claim could sequence the entire human genome in 15 minutes.

The underlying science behind both GridION and MinION is the same. Enzymes bind to the DNA strands, which will guide the DNA into small wells at the bottom of a membrane, each of which contains a tiny tube, each only ten nanometres - a billionth of a metre - in size.

Here, a modified form of a protein called alpha hemolysin 'unzips' the DNA and threads one of the strands through the pore. An electrical current flows through each pout, and the four letters (or bases) that make up DNA disturb this electrical potential in different ways, so the device can determine which base is passing through. This process is called nanopore sensing.

As a proof of principle, the company showed they had sequenced the genome of Phi X, a simple virus with a genome 5000 bases long. Nick Loman, a bioinformatician at the University of Birmingham told New Scientist: 'If you can sequence this genome you should be able to sequence larger genomes'.

Gordon Sanghera, CEO of Oxford Nanopore told Bloomberg that Oxford Nanopore's machines can read strands of tens of thousands of bases with an accuracy comparable to current technology, which only analyses 200 or 300 continues bases.

According to Zoe McDougall of Oxford Nanopore, there is a balance between speed and accuracy. The team is currently trying to reduce error rates, which, at around four percent are considered high. She told the Royal Society of Chemistry that the faster the DNA goes through the pore, the less accurate (noisier) the signal is. However, she noted that every base is 'effectively double-checked a number of times to improve accuracy'.

Both MinION and GridION will be available this year, with MinION costing around £567 ($900) and GridION having different prices according to the speed of the device.

 

SOURCES & REFERENCES
Royal Society of Chemistry | 21 February 2012
 
Oxford Nanopore press release | 20 February 2012
 
Blomberg | 17 February 2012
 
Techworld | 20 February 2012
 
New Scientist | 22 February 2012
 

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