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Oxford Nanopore’s Exciting Sequencing News

 

MinION

Clark Executive Search has often recruited for scientists and doctors with experience in genomics, bioinformatics, and DNA Sequencing. We even had a client that makes DNA sequencing machines where we placed 4 scientists. Since I frequently recruit in this area, I follow the field very closely. Recently there was some news that set all the sequencing scientists aflutter. My twitter feed went berserk with tweets about the news. Quickly written articles appeared everywhere. So what was this important news? Was a new form of life discovered? Did someone find a cure for cancer? No, simply a company, Oxford Nanopore Technologies, that had been in stealth mode for many years, announced to a large gathering of experts in sequencing that they were introducing a new sequencing machine, well actually two machines, and that if their technology works, it would revolutionize how sequencing is handled in the future. Here is a summary of the news as well as links to many of the articles written on the subject:

Oxford Nanopore Technologies made the announcement at the Advances in Genome Biology and Technology (AGBT) conference along with a press release  that they would be introducing their two machines, the MinIon and the GridION, later in 2012. The company states the “GridIon system consists of scalable instruments (nodes) used with consumable cartridges that contain proprietary array chips for the multi-nanopore sensing. Each GridIon node and cartridge is initially designed to deliver tens of GB of sequence data per 24 hour period, with the user choosing whether to run for minutes or days according to the experiment”. Perhaps even more exciting is the announcement of the miniaturized version of the GridION , the MinION: “ a disposable DNA sequencing device the size of a USB memory stick whose low cost, portability and ease of use are designed to make DNA sequencing universally accessible.”

I think Luke Jostins of genomes unzipped summed up in his post “ Making sequencing simpler with nanopores” some of the remarkable capabilities of the technology this way:

“What is really interesting about this new offering is that it manages to get around many of the niggling annoyances involved in sequencing DNA. The sequencers are very small, and stack neatly together – a stack of 20 is about the same size as a HiSeq, giving them a fifth of the footprint per genome sequenced. They use up a lot less power as well, needing about a sixth of the electricity per genome. The low cost of the machines themselves, and the plug-and-play nature of the system, means that scaling up is pretty simple too, and the fact that the machines can handle much of their own computing will keep down IT costs. Most importantly, getting the DNA ready for sequencing is a lot easier, and doesn’t need days of processing and expensive equipment required to prepare DNA for most machines.”

For better understanding of what is being offered, Nick Loman had an exclusive interview with three of the company’s scientists, Dan Turner, Clive Brown, and Zoe McDougall titled “Oxford Nanopore megaton announcement: Why do they need a machine?” In the piece he describes his thoughts on how scientists will have to think differently about these machines. In addition Nick put together a list with links of all the Oxford Nanopore videos about their sequencing technology.

So what is so excitable about this news? Well if you can put 20 of the GridIONs together (sounds like Legos to me) you can sequence the entire human genome in 15 minutes for about $1500 per genome. This is tremendously less time than any other machine and also very affordable. But perhaps the most exciting news was about the smaller MinION machine that would cost less than $900 and be portable. Scientists could take the USB stick out into the field to instantly read DNA or doctors could conceivably test patients right at their bedside.

As noted in a New York Times article  written by Andrew Pollack : “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.”

Matthew Herper of Forbes in his first immediate piece about the new sequencing technology quoted a living legend in the sequencing field: “‘Game changer’ is an understatement,” says George Church of Harvard University. (Church was one of the inventors on one of the patents licensed to Oxford Nanopore that led to the device.” He ticks off the devices specs: Tiny instruments for $900. Able to read DNA in 10,000-letter stretches — compared to a couple hundred for current technologies. Able to sequence a human genome in fifteen minutes (although you’d need 20 of the server-size devices coming in 2013, not just the USB stick.)”

Does all this news sound too good to be true? Some scientists were immediately sounding the alarm that it was too soon to tell if this technology was ready for prime time. Erika Check Hayden wrote for Nature in a piece titled “ Nanopore genome sequencer makes its debut ” that “ The firm has not released any data sequenced from human genomes, so it is unclear how its technology would perform with genomes more complex than those of viruses.”

Perhaps the most vocal criticism came in Matthew Herper’s post over at Forbes titled “ Who Doubts the USB Thumb Drive Sequencer? A Rival”. He mentions that Jonathan Rothberg, who leads Ion Torrent, a company that also makes DNA Sequencers, and hence would be expected to have a slightly biased viewpoint said: “I love technology and science,” Rothberg wrote me in an email. But, he says, “With no data release how do you know this is not cold fusion? If it was robust or scaled why not [sequence] a bacteria? That’s what we first showed at AGBT two years ago.”

And what about the other sequencing companies? How will they fair should Oxford’s technology prove to work out as well as the company press release states? Keith Robison in his wonderfully detailed post titled “ Oxford Nanopore Doesn’t Disappoint” talks about several of the companies that he thinks will suffer if the technology lives up to its hype. He says” I think Oxford is going to cause a lot of discomfort” in the marketplace….Severe pressure will be first felt by others ( like Pacific Biosciences and OpGen) who offered long range information but not as much and for a high entry cost….but for the cost of either instrument you could buy hundreds and hundreds of MinIONs to generate superior data in the same space.” However all is not completely rosy according to Keith. Manufacturing large quantities of  these delicate instruments can be tricky and there might be such demand for the small MinION that fits in a pocket that the company won’t be able to keep up with demand( think Apple with their new products)

Perhaps a good way to end the roundup of articles on this ground breaking technology is a quote from Razib Khan at Discover Magazine from his post “The Nanopore footnote?” He says” I suspect that the specifics of this release will be a footnote due to the inevitable forces of technological progress, exciting as it is in the moment. The precise firm leading the charge, and the details of the technology, are of interest to nerds, but the big picture is that mass-market personal genomics is coming, and soon. How many people on the street can tell you the company which brought television to the mass audience?”

Further reading:

02/14/14 It seems Oxford Nanopore finally is releasing some data on their sequencer. But after two years it still is only in the hands of a few scientists for testing. Over Promise? I think so . “The One and Only Oxford Nanopore talk at ABGT 2014- with real data

06/17/13 Oxford Nanopore Disputes Comments by Illumina CEO

05/13/13 When will Nanopore come out?

11/7/2012 Oxford Nanopore to Reveal New Sequencer

10/28/2012 Nanopores: Fission or Fusion?

7/2/2012 Dale Yuzuki post: ” Oxford Nanopore, the First Nanopore-based Sequencing Technology”

3/26/2012: Wired’s “Can You Really Sequence DNA with a USB Thumb Drive?”

2/28/2012 Careers at Oxford Nanopore Video

technology review: “Why a Portable DNA device Could Yield Better Data

2/27/2012: The Telegraph about an IPO, “Oxford Nanopore considers flotation within 18 months

Bloomberg article about Oxford Nanopore Technologies

BioIT World’s post about Oxford’s new technology 

NewScientist  post Oxford new technology

Omically Speaking ” Beyond the Hype- The Oxford Nano Announcement at AGBT

Xconomy “Oh And More Thing: A Wowser Moment in DNA Sequencing

Eagle Genomics ” Oxford Nanopore and the promise of pay-as-you-go sequencing

Jeremy Leipzig ” AGBT:digesting disposable MinIONs in diaspora

Mike the Mad Biologist “So What Could Nanopore Mean for  Bacterial Genomics?

Gizmodo ” The DNA Sequencing Thumb Drive

PC Advisor ” Oxford Nanopore unveils miniature DNA Sequencer