The world of DNA sequencing is buzzing about a startup based in Guilford, CT, and San Francisco called Ion Torrent Systems. This stealthy operation, which is advised by Harvard genomics pioneer George Church and supported by a partner in Seattle, finally pulled off the veil last weekend on a tool that uses semiconductors to generate digital readouts of DNA, in an instrument that costs one-tenth as much as competitors’.
Ion Torrent CEO Jonathan Rothberg, who founded 454 Life Sciences before selling that company to Roche for $140 million in 2007, revealed the new unorthodox approach at the Advances in Genome Biology and Technology meeting in Marco Island, FL. Rothberg gave his 30-minute talk in front of more than 500 of the world’s leading scientists who work in sequencing centers.
The company’s idea is to create an instrument that combines the insights of DNA pioneer Jim Watson with that of semiconductor visionary Gordon Moore, Rothberg said. The technology impressed and surprised a number of genomic scientists who blogged about it, including Daniel MacArthur, Keith Robison, and Luke Jostins.
“There was a lot of buzz. [Rothberg] really impressed people. They may be onto something,” says Todd Smith, the founder and chief science officer of Seattle-based Geospiza, a company that makes software for biologists to analyze genomic data, and a partner of Ion Torrent. “Then again, there are always people who are going to say, ‘Great concept, now show me the data,'”
The new technology attacks the standard mode of sequencing from a completely new angle. The existing heavyweights—Roche, Life Technologies, and Illumina—tag the individual units of DNA with light, or fluorescent, signals. And they use sophisticated lasers and cameras to read the flow of those tags. The tags add some cost, and the cameras make for expensive capital equipment that can run around $500,000, plus the chemicals to keep them running.
Ion Torrent, which has been in stealth mode since 2007, avoids the tags, lasers, and optics. Instead, it has built a proprietary ion sensor which spots hydrogen ions that have an electrical charge associated with each individual base of DNA—represented by the letters A, C, G, and T. Those ions are read as they pass through a tiny pore at the bottom of a sample well. Ion Torrent didn’t respond yesterday to a request for a follow-up interview.
The Ion Torrent machine professes to be able to perform a “run” of sequencing for as little as $500, in one hour of work. But that doesn’t mean it can sequence an entire human genome at that speed and cost, Smith says. One run should generate 150 megabytes of genomic data, based on the blog reviews, which means it would take about 720 runs to get a decent human genome, at a cost about $360,000 and 720 hours of work, Smith says. That really means the Ion Torrent tool isn’t able to crank through as much data in the same amount of time as other machines, making it lower in “throughput,” in its current form, he says.
“So that’s not competitive with the other platforms for whole genome sequences, but it is practical for many other applications. And it can go into labs more easily,” Smith says.
Still, the tool from Ion Torrent is likely to be useful in many ways, Smith says. It might be used by researchers who want a quick, easy genomic readout on other organisms like bacteria or viruses, or certain regions of DNA that are of interest in a specific human tissue, Smith says. Because of the low cost, speed, and simplicity for the user, it could lend itself over time to diagnostic applications, Smith says. And importantly, the low purchase cost of $50,000, compared to $500,000 for other machines, could enable Ion Torrent to “democratize” sequencing by selling its instrument to a broader pool of biologists than just the small group of people who run hard-core sequencing centers. That could unleash the creative juices of many smart scientists who don’t really have easy access to sequencers but could do cool things if they did, Smith says. The machine also is likely to increase its throughput over time, as semiconductor speed and power increases.
The news from Ion Torrent is really just the latest step in the world of DNA sequencing, which has been on a breakneck pace to make sequencing better, faster, and cheaper. Illumina announced in January that it is now possible on its machines to sequence entire human genomes for as little as $10,000. Mountain View, CA-based Complete Genomics says it can do the same job for $5,000, largely because it has a different model in which it doesn’t sell machines, but rather it asks researchers send their samples to a centralized company lab. We’ve also written about other companies that are developing machines that aspire to push the leading edge of speed and cost, including U.K.-based Oxford Nanopore Technologies and Providence, RI-based NABsys.
It all sounds great. But like anything new, Ion Torrent will have to prove that it can do what it says it can do, Smith says.
“There were a lot of people there who were saying they are going to take a serious look at this,” Smith says. “But you also had the world’s best sequence instrument operators there. They’ve built large centers, and they’ve heard everything before from every company. They’re going to ask, ‘Where’s the data?'”
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