A recent In Sequence article indicated that Ion Torrent is enjoying strong initial sales. This bodes well for continued evolution and improvement of the technology, as LIFE will continue to smell revenues and opportunity. Ion has announced a number of improvements, but most aren't scheduled to arrive until the near future.
The challenge is for LIFE to keep executing on their plan. Already some issues have arisen; my own Ion experiment at a service provider is stalled due to a back-ordered template prep reagent (two weeks and counting!). This is a key reason to do pilots on emerging technologies with non-critical (but interesting) samples; I was bitten last fall by another backorder bug (that time, the paired end SOLiD reagents). Of course, this time it is even more complicated, as Ion is making a major change to both the underlying kits and to the software to process the data. It will be worth it if I get results anything like Ion's provided E.coli 314 dataset, which has about 4.5X the data of the original 314 chip spec.
But will this same problem of rolling out improvements persist? I'm really hoping to see the link to the 316 chip become active in the web store by next month. The 316 sports about 5X the number of sensors as the 314 and will presumably give 5X the number of reads. If it can really deliver the same quality of data and that E.coli dataset is not horribly cherry-picked, then the 314 could debut over 2X over its specification. That would be truly impressive and definitely affect designing experiments for the platform (in a good way; more data is always better!).
Similarly, the OneTouch template prep instrument should appear by the end of the summer and could be a big driver of sales for the whole system; if you value your staff's time at $1.5K+ a day (a reasonable ballpark figure for the fully-loaded cost of an employee in Boston or similar U.S. cities), a $5K instrument that saves about 1/4 to 1/2 a day per run is an easy sell. But, if the first boxes don't show up on time or don't perform to spec, then the opportunity to steal a lead on MiSeq will erode. Plus, a big selling point of MiSeq is that the technology is well-tested, and delivery hiccups by Ion will only reinforce that impression. Ditto for the 318 chip; delivered on time it will give Ion a performance edge over MiSeq. Conversely, late delivery will mean lost instrument sales and worse the lost opportunity to sell reagents to those customers.
On the informatics side, there were a number of useful comments on my analysis. In particular, Nils Homer pointed out some tuning I could do on TMAP parameters (which I haven't actually run yet). Nick Loman has generated an interesting take by using the same dataset to try out different assemblers. Nick shows how much you can do in the current environment, but also suggests a strong need for Ion-specific or Ion-tuned assemblers. Also, the fact his lab hasn't run their Ion Torrent yet is telling, reinforcing the notion that Ion customers are being forced to pause by protocol shifts and reagent shortages. Such software won't get written unless developers are motivated and have access to test datasets. In many cases this will be because the developers are in labs with PGMs, but to really grease the skids Ion needs to put more datasets out in the open.
Perhaps least of Ion's worries is the lack of upstream preparation kits and protocols, as there is plenty of interest in the existing applications of fragment sequencing, amplicon sequencing and library QC. Still, it is surprising that LIFE hasn't retrofitted some of the existing SOLiD kits for the Ion; in theory it should just require changing a few oligos. Alternatively, for some applications a few "cheater" oligos could convert another platform's library into an Ion library, at the cost of losing 20-30 bases of read to the other platform's universal sequence.
Ion has a lot of upward potential and is already demonstrating an ability to beat performance targets. But delivery targets are critical too, especially when eager customers are left champing at the bit.