This article has been updated from a version posted Sept. 13 to include comments from an Ion Torrent official and market analysts.
Life Technologies' Ion Torrent business said last week at its Ion World customer conference that it has started shipping its Proton sequencing system to customers and that it is developing a third version of the Proton as well as new emulsion-free PCR sample prep technology.
The sequencing system promises 10 gigabases of data per two- to four-hour run, generating between 60 million to 80 million filtered reads with read lengths of 100 to 200 bases. The first version of the chip, PI, is geared toward exomes and transcriptomes and is expected to be able to sequence two exomes per run.
The PII chip, which Ion Torrent plans to start shipping in six months, will enable one 20-fold genome or eight exomes to be sequenced per run.
Additionally, the company said last week that it is developing a new emulsion-free PCR sample prep system called Avalanche, which will enable template prep in 30 minutes for all Ion systems, and a third version of the Proton chip, PIII.
Earlier this year, Life Tech launched an emPCR-free sample prep kit for its SOLiD system, dubbed Wildfire, which replaced emulsion PCR with isothermal amplification. With Wildfire, the amplification step takes 30 minutes and the total sample prep from library construction until sequencing starts takes two hours (IS 6/5/2012).
Maneesh Jain, vice president of business development and marketing at Ion Torrent, told In Sequence that while the Avalanche sample-prep will be different from Wildfire it will also be based on isothermal amplification. The amplification step will take 30 minutes. The entire sample prep step will be longer, although Jain declined to disclose specific details.
The PIII chip will include even more sensors than the first or second versions — 1.2 billion sensors per chip, up from 165 million sensors on the first version of the Proton and 660 million sensors that will be included on PII.
Previously, Andy Felton, senior director of product marketing at Ion Torrent, told In Sequence that the Proton made use of updated complementary metal oxide semiconductor technology, which boosted sensor density on the chip from the 11 million that were achieved on the PGM's 318 chip and 1 million on the 314 chip.
Jain added that Avalanche helped bump the increase in sensor density because it offers a "more efficient way to deliver template to the wells."
The PIII chip will also have significantly greater throughput, at 256 gigabases per run.
Life Technologies also said last week that it plans to submit the Proton to the US Food and Drug Administration for 510(k) clearance, although did not specify a timeframe for doing so. It plans to submit the Ion Torrent PGM system to the FDA this year.
Ion Torrent is also planning several upgrades to automate sample prep, including a version 2 of its One Touch system as well as a new system, dubbed Ion Chef.
One Touch 2 is more suited to customers with lower throughput requirements and will cost around $19,000, Jain said, while Ion Chef will be priced at a little over twice that and is suited for higher-throughput needs.
Jain declined to disclose further details about Ion Chef, but said the company plans to launch that system in the first half of 2013. Both Ion Chef and One Touch 2 will be compatible with Avalanche, he added.
Following news of the Proton launch and the Ion World conference, several market analysts said that while the Proton launch is a positive for Ion Torrent, some key details of the system are lacking.
"We believe the new product announcements and Proton roadmap were key positives," wrote Citi Research analyst Amit Bhalla. Bhalla added, however, that investors "may have wanted more data." Of particular concern to customers, noted Isaac Ro of Goldman Sachs, will be the system's accuracy.
Raw accuracy for the PI chip is expected to be equal to the PGM. While Goldman's "recent checks" suggest that PGM's raw accuracy is "inferior" to the Illumina MiSeq, "presenters at Ion World have suggested it is now nearly equal." Additionally, wrote Ro, "management stated that consensus accuracy is near Q50, although we have not been able to confirm that with users."
Dan Leonard at Leerink Swann added that multiple customers presented data from the Proton at Ion World, and while several have received the instruments, "we're still a little thin on performance achieved to date by customers."
Early-access customers could not be reached for comment by In Sequence before press time.