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Health
COMPANY UNVEILS DNA SEQUENCING DEVICE MEANT TO BE PORTABLE, DISPOSABLE, AND CHEAP
By Andrew Pollack
New York Times
February 17, 2012
http://www.nytimes.com/2012/02/18/health/oxford-nanopore-unveils-tiny-dna-sequencing-device.html?_r=2
DNA sequencing is becoming both faster and cheaper. Now, it is also becoming tinier.
A British company said on Friday that by the end of the year it would begin selling a disposable gene sequencing device that is the size of a USB memory stick and plugs into a laptop computer to deliver its results.
The device, expected to cost less than $900, could allow small sequencing jobs to be done by researchers who cannot afford the $50,000 to $750,000 needed to buy a sequencing machine.
It might also help doctors to sequence genes at a patient’s bedside, wildlife biologists to study genes in the field, or food inspectors to identify pathogens.
“You don’t need to buy instruments,” Clive G. Brown, the chief technology officer of the company, Oxford Nanopore Technologies, said in an interview. “It’s pay-as-you-go sequencing.”
Oxford presented details of the device, as well as of a new, somewhat larger sequencer that it also plans to begin selling late this year, at the Advances in Genome Biology and Technology conference in Marco Island, Fla., which has become the sequencing industry’s annual boast-fest.
Both the tiny MinIon and the larger GridIon look likely to be the first sequencers to use nanopore sequencing, in which a strand of DNA is read as it is pulled through a microscopic hole, sort of like a noodle being slurped through rounded lips.
Outsiders have not tried the machines, and there can be a big difference between rosy specifications and how well a machine works when it finally reaches the market. Some other sequencers that initially dazzled the field have faltered in the marketplace.
Still, many experts at the conference were dazzled anew.
“If it does work, it will be a game-changer,” said Elaine Mardis, co-director of the genome institute at Washington University in St. Louis. Chad Nusbaum of the Broad Institute in Cambridge, Mass., called it “impressive, credible, possibly amazing.”
Isaac Ro, an analyst at Goldman Sachs, said in a note Friday that the Oxford technology had “impressive performance specs” that suggested it would be a “significant competitor” to Illumina and Life Technologies, the leaders in the sequencing business.
Illumina has a bit of a hedge. In 2009, it invested $18 million in Oxford Nanopore, and owns a 15 percent share. But Illumina does not have the marketing rights to the machines unveiled Friday. Rather, it has the rights to an alternative Oxford technology that is further back in development.
Illumina shares fell nearly 4 percent Friday to $51.82, while Life shares dropped nearly 8 percent to $45.92.
Sequencing involves determining the order of the chemical units of DNA, which are known as bases and are usually represented by the letters A, C, G and T. The order of these bases helps determine inherited traits, like susceptibility to some diseases.
As the cost plummets, sequencing is moving from research laboratories into patient care. Some cancer centers, for instance, sequence genes to determine the best drugs to use.
The growing importance of sequencing in medical care is what motivated Roche to make its current $5.7 billion hostile bid to acquire Illumina. Known mostly for pharmaceuticals, Roche also has a large diagnostics business.
Nanopore sequencing is easy to envision but has been deceptively difficult to carry out, despite two decades of research by universities and companies.
Oxford, which is privately held and based on technology developed by a professor at Oxford University, uses pores made from bacterial proteins. An electric current flows through the pore. The bases interrupt the current in different ways as they go through.
The initial GridIon machines will have 2,000 pores. A machine due in 2013 will have 8,000 pores.
One big advantage of the nanopore sequencing, Dr. Mardis of Washington University said, is that preparing the sample is quick and easy. The technology also offers the promise of being able to read tens of thousands of bases in a stretch. Most sequencers read from around 30 to a few thousand bases at a stretch, and these small fragments then have to be pieced together.
A drawback is that the Oxford machine has a 4 percent error rate, too high for many applications, including diagnosis.
The MinIon, while entailing no capital cost for a machine, can be used only once and will sequence up to one billion bases. That is a cost of up to $1,000 per billion bases.
A GridIon might cost around $30,000, Oxford executives said. The company said that if 20 of the second-generation GridIons were used together, a human genome could be sequenced in 15 minutes at a cost of around $1,500.
By then, however, rival machines might be able to do genomes for that cost or even less. Ion Torrent, a subsidiary of Life Technologies, last month announced it was developing a machine that could do a human genome in a day for $1,000.
“We’re not losing sleep,” Jonathan M. Rothberg, chief executive of Ion Torrent, said Friday. “But they definitely have the Twitter airwaves today.”
2.
PALM-SIZE DNA SEQUENCER MAY THREATEN ILLUMINA, LIFE TECH
By Sharon Begley
Reuters
February 18, 2012
http://in.reuters.com/article/2012/02/18/health-dna-idINDEE81H00920120218
The DNA-sequencing race heated up Friday as privately-held Oxford Nanopore Technologies Ltd. said it developed two new devices that could quickly surpass existing gene decoders and rivals set for release later this year.
The new sequencers will compete against devices from Illumina Inc. and Ion Torrent, a unit of Life Technologies Corp.
Illumina is the target of a $5.7 billion hostile takeover bid from Roche Holding AG, which wants that company's sequencing capabilities. There is growing demand for ways to determine which medicines are best suited to particular patients, known as personalized medicine.
Oxford Nanopore's MinION device is housed in what looks like a USB stick and will sell for about $900. The underlying technology is unique for using an array of 512 nanopores -- holes with diameters of a few nanometers, or 50,000 times smaller than a human hair and about the same size as a DNA molecule -- in a cell membrane. As DNA strands are pulled through the nanopores, they change the electric current flowing across the membrane. Each such change indicates which DNA base has just passed through the pore.
MinION will be capable of sequencing 150,000 DNA bases per hour. The human genome has 3 billion bases.
MinION "will be competitive with current desktop instruments the size of small photocopiers," the company said in a statement on Friday.
Oxford unveiled the devices at the Advances in Genome Biology and Technology meeting in Marco Island, Fla.
The second device, GridION, consists of an array of sequencers, each containing 2,000 nanopores.
That is expected to increase to 8,000 nanopores in the next-generation device. Twenty of these, running simultaneously, could sequence a full human genome in 15 minutes, the company said, describing both devices as "plug-and-play."
Ion Torrent released details of its Ion Proton Sequencer in January, saying the new machine will be able to sequence a complete human genome in a few hours for $1,000 and sell for at least $99,000. Illumina's HiSeq 2500, also announced in January and available later this year, will sequence a human genome in about a day; no price has been announced.
Illumina shares closed 3.9 percent lower on Friday and Life Technologies' shares fell 7.8 percent.
One likely barrier to widespread adoption of the new Nanopore sequencers is their error rate of 4 percent, which is higher than that of most rivals.
"We know what the problem is and we can fix it," Nanopore's Dan Turner told Nick Loman, who blogs at Pathogens: Genes and Genomes.
The Nanopore devices promise to beat existing sequencers in the length of the DNA strand they are able to read: tens of thousands of bases compared with a few hundred in most existing sequencers.
This "read length" is important because it reduces the number of strands that have to be assembled into the precise order in which they exist on a genome, making data analysis easier.
"GridION and MinION are poised to deliver a completely new range of benefits to researchers and clinicians," Dr. Gordon Sanghera, CEO of Oxford Nanopore, said in a statement.
(Reporting By Sharon Begley; editing by Michele Gershberg and Andre Grenon)
3.
OXFORD NANOPORE TO SELL TINY DNA SEQUENCER
By Kristen Hallam
Bloomberg
February 17, 2012
http://www.bloomberg.com/news/2012-02-17/oxford-nanopore-plans-portable-gene-sequencing-device.html
LONDON -- Oxford Nanopore Technologies Ltd. is entering the gene-sequencing race with a new portable device that will allow people to analyze DNA on the go.
The product, called MinION, is about the size of a USB memory stick, the closely held Oxford, England-based company said today. MinION will be ready for sale in the second half of the year at a cost of less than $900. It’s a smaller version of the GridION device that Oxford Nanopore is developing.
Oxford Nanopore is relying on the two products to spur demand for machines that can decode the building blocks of life, helping to identify new targets for medicines and illuminate crop science. The company is jumping into a market led by Life Technologies Corp. (LIFE) and Illumina Inc. (ILMN), which last month said they’ve built products that can sequence a genome in a day. GridION is designed so that computing equipment can be clustered to sequence an entire human genome in as little as 15 minutes.
“The USB stick is an absolute game-changer,” Oxford Nanopore Chief Executive Officer Gordon Sanghera in a telephone interview. “It’s plug-and-play, on-the-go DNA sequencing.”
Life Technologies fell 4.3 percent to $47.66 at 1:15 p.m. in Nasdaq Stock Market trading after dropping as much as 7 percent, the biggest intraday decline since Oct. 7. Illumina dropped 2.9 percent to $52.39 after falling as much as 4.5 percent.
TINY HOLE
The company presented data on the two products today at the Advances in Genome Biology and Technology conference in Florida. The devices use a novel technique known as strand sequencing, in which an entire string of DNA is guided by an enzyme and passes intact through a tiny hole in a cell membrane one-billionth of a meter wide, like a child sucking spaghetti through his mouth.
The strand-sequencing technique relies on an engineered protein or nanopore that creates the hole. As DNA bases, or chemical building blocks, pass through the hole, an electronic chip measures changes in electrical current in the membrane and produces data that, when decoded, identifies the sequence of bases that make up a genome.
That’s different from current techniques, in which 200 or 300 continuous bases of DNA are analyzed, Sanghera said. Oxford Nanopore’s machines can read strands of tens of thousands of bases with an accuracy comparable to technology already on the market, he said.
SPACE AGE
“That is some kind of fantastical, space-age thing,” Sanghera said.
The MinION device can only be used once and can’t decode an entire human genome, according to Oxford Nanopore. Users don’t have to amplify DNA to be able to read it, and the sensitivity is about the same as the larger GridION device, Sanghera said.
“This will result in broader adoption of DNA sequencing,” he said. “This allows non-specialist scientists to extract DNA information back in the field. You just need a laptop and software.”
The GridION system, which is about the size of a videocassette recorder, is designed so that researchers who need quick results can add units of cartridges called nodes that speed processing. Using 20 high-end nodes would allow the entire genome to be sequenced in as little as 15 minutes, Oxford Nanopore said.
'PREGNANT WOMAN'
“Our competitors are like a pregnant woman,” said Zoe McDougall, a company spokeswoman. “It takes nine months to make a baby, and you can’t put nine women on it and get a baby in a month. With our system, you can put nine women on it and make a baby in a month.”
Not all customers want or need such speed, Sanghera said.
“You give flexibility back to the researcher in how they do their experiments,” he said.
Pricing will be “competitive” and will vary, similar to mobile-phone packages tailored to customers’ needs for talk time and data, said Clive Brown, Oxford Nanopore’s chief technology officer.
“There’s no fixed run time on this machine,” Brown said in an interview. “You need pricing elasticity. They all pay same cost per base, but it’s how it’s divided. That’s completely new.”
Life Technologies, based in Carlsbad, California, on Jan. 10 said it is taking orders for its benchtop Ion Proton Sequencer. The machine, available for $149,000, is designed to provide a full transcript of a person’s DNA in a day for $1,000. Illumina, of San Diego, said its HiSeq 2500 will be available in the second half of the year. It didn’t reveal the price.
POTENTIAL BUYERS
Illumina is the target of a $5.7 billion hostile bid by Roche Holding AG of Basel, Switzerland. Illumina’s board unanimously rejected the offer, calling it “grossly inadequate.” Roche is a sponsor of the conference where Oxford Nanopore presented the data on its machines.
Illumina owns 15 percent of Oxford Nanopore and has a partnership with the U.K. company for a technology called exonuclease sequencing, in which the DNA building blocks are separated by an enzyme and pass individually through a nanopore.
While potential buyers have approached Oxford Nanopore, the company hasn’t pursued any offers, Sanghera said.
“Over the last year, we’ve had various companies express interest in us,” Sanghera said. “We remain focused on our strategy, which is to get this technology to our customers.”
SHAREHOLDERS
Oxford Nanopore’s shareholders include IP Group Plc, which owns 21.5 percent, hedge-fund manager Lansdowne Partners LP, and Invesco Perpetual, the U.K. group of mutual funds. The company also has individual shareholders, including company managers, and employees have stock options.
Oxford Nanopore is valued at about $1 billion, said Charles Weston, a London-based analyst at Numis Securities, which advises IP Group, in a note to investors Feb. 1. Weston based the figures on Oxford Nanopore gaining 25 percent of a market that could grow to $6 billion within five years.
“To get a truly accurate assessment of our valuation, we need to understand what markets we can penetrate,” Sanghera said. “We are not displeased with $1 billion; we feel it could be a lot bigger than that.”
Oxford Nanopore, spun out of University of Oxford in 2005, uses sequencing technologies that were initially based on the research of founder and board member Hagan Bayley, a chemistry professor at the university. The company has built on that science through collaborations with researchers at Harvard University, the University of California Santa Cruz, and Boston University, among others, and with internal research, said McDougall, the company spokeswoman.
Early Access
Oxford Nanopore will give early access to a few laboratories to try out the two devices, allowing them to provide feedback and develop applications before the company starts selling the products later this year, Sanghera said.
“The biggest challenge is managing expectations and delivering on the next phase,” Sanghera said. “It feels like you’ve been in a band, and you’ve been doing gigs in grotty little venues, and then you wake up and you’re number one.”
To contact the reporter on this story: Kristen Hallam in London at This e-mail address is being protected from spambots. You need JavaScript enabled to view it
To contact the editor responsible for this story: Phil Serafino at This e-mail address is being protected from spambots. You need JavaScript enabled to view it
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