Ion Torrent Throws Another Chip Into the Pot

At the J.P. Morgan conference today, Ion Torrent announced the launch of their second generation chip ("316"), which offers 10X the data generation at apparently 2X the list price (some of this is based on earlier information, which isn't always consistent). Actual chips in the hands of customers is stated to occur in this quarter.

Delivering upgrades to the systems via the consumables rather than new instruments is a big part of the promise of Ion Torrent's system, and so actually delivering the chips is a key part of fulfilling that promise. The GenomeWeb article made no mention of any 3rd generation chip, and certainly it will be the regular release of upgraded chips that will really convince the community that this is for real.

The new chip is described as delivering 100Mb per run, or about 1 million reads of 100 bases each (again, ballpark). It's useful to put that in the context of various possible uses. In my eye, the Ion Torrent still will just not have the number of reads for applications requiring counting tags -- e.g. RNA-Seq or ChIP-Seq. But, for PCR amplicons this would be pretty amazing. Imagine a pool of 100 amplicons; this would mean on average 10K reads per amplicon, which would allow great sensitivity for rare variant detection (either in pooled samples or heterogeneous cancer biopsies). As far as a human genome goes, 100Mb is about 0.025X, so it would not be cost effective (vs. Illumina or SOLiD) or pleasant (imagine snapping all those chips in to the instrument!) to go for 40X human coverage. On the other hand, that is enough to give copy number profiling information. It is also about 2X a human exome chip, which isn't nearly enough either. But, for a small genome it's pretty decent -- certainly good enough for 40+X coverage of many microbes. A de novo project might need other data, but for resequencing of industrial or clinical variants this could be quite interesting.

1M reads is also in the range of what 454 Senior delivers per run. Of course, those are much longer reads -- if you have and need the length you'll care. But given the upfront cost is so much smaller & the per run cost a tiny fraction, it would suggest that the 454 platform is going to quickly be delegated to niche status. Ion Torrent has claimed in interviews that much longer reads have been seen in house, but it isn't clear when these protocols will be rolled out or if they are really robust.

The GenomeWeb item also suggests a reasonably healthy initial uptake of the platform, with 60 orders booked. However, only "early access" customers have gotten any. It is also rumored that Life Tech is strongly encouraging multiple purchases by customers; someone I know with experience in this noted that this was the pattern with their capillary sequencers. On the one hand, this has practical advantages (beyond getting a few more sales), as the rollout can be staged to a smaller number of sites initially. New technologies always have their hiccups. But, on the negative side it does mean that fewer sites will have an opportunity to put the machine through new paces -- and compete in Ion Torrent's Grand Challenges (must write more on that another time).

Ion Torrents haven't started showing up on the wonderful World Sequencer Map yet, but it should be a matter of time. More seriously, no service provider has yet announced support for this platform. That's a pity, since that would enable much wider access to the capabilities. I can't promise I'll be first in line with an order, but I certainly will be if I have a project then that fits the specs for the machine.