Oh, And One More Thing: A Wowser Moment in DNA Sequencing

2/21/12Follow @xconomy

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the company said it plans to introduce a commercial version of the product in the second half of 2012. PerkinElmer’s Smith noted that Oxford’s chief technologist didn’t actually perform a full genome sequence during a 15-minute stretch on stage, which would have really brought the house down. Still, the speed and portability of the new technology will surely get researchers thinking about all kinds of new experiments. Sequencing microbes during environmental field tests, and point-of-care genomic diagnostic tests, are just a couple of ideas that leap to mind right away, Smith says.

Exciting as the possibilities may be, the Oxford machine, like any other one, isn’t perfect. It has an error rate of about 4 percent, which Smith says is high. “You’ll need extra redundancy and informatics” to help correct the errors, he says.

Smith, who has been coming to the Marco Island conference the past five years, said Oxford is picking up on the buzz that Jonathan Rothberg, the founder of Ion Torrent Systems, stirred up two years ago at this conference. Rothberg, one of the most skilled showmen in the genomics business, famously unveiled his semiconductor-based sequencing machine at Marco Island in 2010. Rothberg memorably stated that the Ion Torrent machine, about the size of a desktop printer, could sequence whole genomes “from the back of a donkey.”

Two years later, we’re talking about a new ballgame, based on dropping a sample of blood onto a device you can stick in your pocket, and which will spit out results in 15 minutes. That’s so cool it would have been sci-fi just three or four years ago. But as Smith rightly points out, a company can only get away with talking about the whiz-bang part of the technology for so long. Quickly, the conversation will shift toward “Hey, what the heck are you going to do with that genomic data?”

“You see this all the time,” Smith says. “The more mature platforms talk about the applications with their machines. The new ones talk about the technology, and the vision it creates. Time will tell in terms of what it delivers.”

Besides all the chatter with Oxford Nanopore, I sought some quick commentary from Marco Island on the news from other major sequencing companies. Here’s what Harvard’s George Church had to say via email.

George Church

Illumina: Illumina, the market leader in sequencing, is defending itself from a hostile takeover bid by Switzerland-based Roche. Complicating matters a bit further, Illumina is an equity investor in Oxford Nanopore, which could end up competing with its workhorse instruments. Church was clearly wondering how the Oxford Nanopore presentation might change the Illumina/Roche drama. “Will Roche consider a (Oxford) Nanopore company?” Church says. He also wonders, “if Illumina matches the LifeTech “$1000 genome” (presumably consumable costs), what will their service price be?”

Life Tech: Life Technologies made news earlier this year with its Ion Proton Sequencer, and its purported ability to produce $1,000 genomes by years’ end, but if it gets there, it will be neck-and-neck with other companies, Church says. “Proton II in late 2012/ early 2013 seems very far off now,” Church says. “There will be a few companies capable of $1000 genome (reagent costs) by then and long reads too.”

Complete Genomics:  Church notes that he’s impressed with the low error rates from the Mountain View, CA-based company. “The long-fragment read (LFR) technology may routinely deliver multi-100kbp (kilobase pairs) haplotypes and less than 1 error in 10M (1E-7). This could be very attractive for clinical applications (note Mayo Clinic deal).

PacBio:  The Menlo Park, CA-based company has hung its hat for a while on its ability to sequence long stretches of DNA, which requires less overlapping and assembly than existing technologies from Illumina and Life Tech. But PacBio has got to be watching Oxford closely as an emerging challenger, based on the claims it made at Marco Island. “Longish hyphenated reads won’t be quite as compelling if the Oxford Nanopore Technologies 100 kbp read-length proves to be robust,” Church says.

Oxford Nanopore: The big question, Church says, is “How many reads does it take to get the 4 percent raw error down to 1E-7 consensus? Any systematic (non-random) errors?”

BGI: The organization formerly known as the Beijing Genomics Institute has taken on some ambitious experiments, but doesn’t appear to be developing its own sequencing instrument technology, Church says. “So far, BGI is a consumer of tech, not a producer. As long as companies like Illumina & Complete Genomics are doing both, and as long as automation keeps increasing, it is not clear how big a niche BGI has in human genomics, but getting better at de novo sequencing may be a good fit for them.”

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