By Julia Karow
Life Technologies launched Ion Torrent's Personal Genome Machine this week and kicked off a $7 million competition to encourage users to improve aspects of the system's performance.
Initially, Life Tech will ship the Ion PGM sequencer to "select sites" in North America, Europe, and Asia Pacific, giving delivery preference to customers ordering multiple units, according to the company.
Earlier this month, the company said that the instrument, which will cost $49,500 — not including sample-prep equipment and a server to analyze the data — will generate at least 100,000 reads per run with a read length of 100 to 200 base pairs and an error rate of about 1 percent (In Sequence 12/7/2010).
Pitting users of the new system against its in-house development team, Life Tech is keen on improving the system's performance quickly. The "Life Grand Challenges Contest" that it launched this week includes three $1 million prizes to improve the Ion PGM's sample prep speed, data output, and accuracy. Four more prizes relating to other Life Tech products will be announced in 2011.
To win one of the prizes, contestants must produce results that are twice as good as Ion Torrent's internal record at the time of submission. Thus, as the system's in-house performance increases, the goals for each prize will be adjusted over time.
"We don't have a monopoly on all the good ideas," Jonathan Rothberg, the company's founder, told In Sequence. "This will create a huge incentive for graduate students, undergraduates, and scientists around the world to use our machine and make it better."
Rothberg likened the challenges to the Netflix prize, which awarded $1 million in 2009 to a team outside the company that developed a better algorithm for predicting whether someone would enjoy a movie, based on their movie preferences.
The first contest asks participants to halve the time required to prepare samples for the Ion PGM, either from blood or bacterial colonies, which Rothberg said currently takes about 10 hours using optimized protocols.
For the second prize, contestants need to double the number of bases they can generate from an Ion chip. Currently, the company produces close to 200,000 reads with a read length of 100 to 200 bases and an error rate of about one percent, he said.
The third challenge aims to halve the error rate — currently 1 percent — by improving the data analysis on standard hardware and within time constraints. For this contest, participants will be able to download raw datasets for analysis and do not need to own or have access to a PGM sequencer. Rothberg said Ion Torrent is already able to reduce the error rate with the help of substantial computing power, "but to be practical, you have to be able to do it on a regular computer in less than one hour."
Life Tech will release additional information about the prizes and rules in early 2011, and researchers will be able to register for the contest at the Advances in Genome Biology and Technology meeting in February, Rothberg said. He expects the prizes to be awarded within the next couple of years.
The contests will be held at "neutral sites," he said, at locations that are close to the participant's own that have an Ion PGM machine. As examples, he mentioned Baylor College of Medicine, the Broad Institute, Stanford University, and the Wellcome Trust Sanger Institute, presumably all early users of the system.
"We want to change the way the science is done from the company having all the answers to the community having all the answers," he said. "And we know from the computer industry: the community always does better."
Have topics you'd like to see covered by In Sequence? Email the editor at jkarow [at] genomeweb [.] com.