Next-gen company gives away two $50,000 machines in contest.
By Kevin Davies
May 18, 2010 | Ion Torrent Systems, the new sequencing company founded by Jonathan Rothberg, has announced the winners of two free sequencing instruments, worth about $50,000 apiece.
The winning teams, announced during the GET Conference in April, were headed by John Iafrate and Long Le from Massachusetts General Hospital’s (MGH) pathology department; and Mitchel Sogin from Woods Hole. They were selected from hundreds of entries submitted over two months outlining novel potential applications of the sequencer, scheduled for release later this year.
“It’s really different to start to work in partnership with a company [Ion Torrent] that bears my view of the world—the democratization of sequencing,” said an elated Sogin. “I’ve always thought this is a technology that should be made available to basic research scientists and not restricted to genome centers.”
Rothberg said the two prize winners, dealing with cancer diagnostics and clean water—mirrored the “Watson meets Moore” theme that Ion Torrent has been expounding. Jim Watson has built his career around cancer and human health, while Gordon Moore (through his foundation) has given away more than $1 billion to environmental causes.
At MGH, Le said the lab had been “very interested in next-generation sequencing (NGS) for two years, ever since we started doing cancer genotyping as a broad-based test for routine patient care. We just hadn’t jumped on board.”
The Iafrate lab has been doing cancer genotyping for about a year, with a goal of genotyping cancers not just for key genes but to get a broader snapshot of the genetics of tumors and deliver that information to oncologists, and hopefully into the patient’s medical chart. “The clinicians are very excited about this,” said Iafrate. “It allows them to make rational decisions about these patients.”
The current SNP (single nucleotide polymorphism) genotyping platform takes about six hours, but only detects about 100 hotspot mutations in 20 genes across the cancer genome. “We rapidly run into genes we want to know about,” said Iafrate.
On the other hand, whole-genome sequencing is not the answer. “We’d be overwhelmed with variants of unknown significance,” says Iafrate, adding that the footprint of the benchtop Ion Torrent instrument is ideal.
Iafrate listed several putative advantages of the Ion Torrent Personal Genome Sequencer. “From a data-generation standpoint, the roughly 100 megabases (Mb) [per instrument run] is pretty good, sufficient for what we want to do.” Second, scalability is key. “The instrument cost is roughly an order of magnitude cheaper compared to every other technology,” says Iafrate. “Should we need to scale up to get 100 patients/week, we could buy ten more machines.”
And then there’s the short 1- to 2-hour run time. “Oh my God! That’s phenomenal,” said Iafrate. “The other machines take five days to a week. At the clinical level, we can’t be waiting a week. What if that run fails?”
Data management should be another advantage. “We don’t have a team of 20 bioinformaticians, just one or two,” said Le. “The other advantage is that Ion Torrent has partnered with CLC bio, so we’re getting a license to that software. We see that as a key item to get into the game.”
Iafrate says the goal is “to look at every new cancer diagnostic within our institution, period.” He added that he is “incredibly impressed by the philosophy of the company and its willingness to take a chance on what’s not a large genome center. We’re representing the smaller people!”
The second instrument goes to Mitchel Sogin, the director of the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the Marine Biological Laboratory, Woods Hole in Massachusetts. Explaining this choice, Rothberg said: “Contaminated water kills 13,000 people a day. There is no bigger health problem on earth today.”
Sogin’s lab was part of an international project called the International Census of Marine Microbes (ICOM) including 45 labs and some 1200 sampling sites. His proposal is in some ways a derivative of ICOM. “One application would be to study microbial contamination in fresh water for drinking or recreational waters,” he said. “By sequencing, we could characterize different members of the microbial community and compare to microbial profiles from fecal communities.”
Sogin hopes to build a database to differentiate whether an individual microbe is coming from agricultural or from human fecal contamination. No date has been set for when the winners will take delivery of their instruments, although it will be some time in 2010. •
This article also appeared in the May-June 2010 issue of Bio-IT World Magazine. Subscriptions are free for qualifying individuals. Apply today.