Some thoughts on today's Ion World announcements

14 Sep 2012

A few significant announcements from Ion World today (sourced from the press release and #ionworld Tweets) which I've summarised here:

Proton III and Avalanche

The Ion Proton is now shipping and Life Tech plan to ship 100 instruments to customers in September.

The initial chip, Proton I ("PI") will do 60-80m reads and "up to 10Gb" of output from its 110 million sensors. The read length is "between 100 and 200 bases". No mention of 400 base kit for Proton at this time. Proton II (PII) we know has 650 million sensors. The big news is the announcement of a third chip, predictably named Proton III. This will have 1.2bn sensors and could theoretically generate 256Gb of data. It seems this will be enabled by a new emulsion PCR-free technology they are calling Avalanche. Is this related to the long-talked about Wildfire protocol for SOLiD?

The PIII will require Avalanche and so this may suggest that the chip will not have beads and wells, but instead move to some kind of solid-surface technology as used in Illumina sequencing. In turn this may suggest that they have run out of real estate at the PII chip density, and so require the spaces between wells to get further throughput.  But this is pure speculation on my part. Available "within 18 months".

Yes, Chef!

One of the hassles with PGM sequencing right now is that there is a good deal of hands-on to go from a genomic DNA sample to a sequence-ready loaded chip, even with the OneTouch. So it is great news that the Ion Chef (pictured) has been announced which claims to go from library to a loaded chip with only minutes of hands-on time. It presumably replaces the OneTouch (OneTouch 2 for Proton) and is scheduled for some time in first half of 2013.  About the pun-tastic name; awful. Update 14/09: According to Dale Yuzuki's blog, the Ion Chef will be available mid-2013 and will cost about twice the OneTouch, so around $40,000 I think.

Platform Accuracy

Ion Torrent Suite 3.0 is supposed to have dramatic improvements in base-calling. Ion Torrent on Twitter quote Shawn Levy at Hudson Alpha saying: "Concerns about insertion deletion errors are now largely solved". Chad Nusbaum is quoted as saying: "Indel mismatches significantly improved in the new bioinformatics software Torrent suite 3.0" (tweet). This is great news. Certainly the recent E. coli 300bp dataset put out on the Ion Torrent website look a great deal better than that which we got in summer 2011.

On the Ion Proton apparently "consensus accuracy is comparable to that of the Ion PGM™ sequencer" which is a little vague. Apparently the Broad Baylor (thanks NJL_Broad for the correction) have performed 274 runs on the Proton (tweet) which is amazing, but a shame there hasn't been any data released.

How long?!

There seems to be some confusion about how long it takes to sequence on the Proton. Most of the Twitter PR says two hours, but the press release states "two to four hours". Certainly the PGM run-time has been variable depending on the chip type, leading to the development of a run-time calculator.

Well, in summary, this is a pretty exciting set of announcements from Life Tech focusing on some of the platform issues (accuracy and hands-on time). The Proton with Proton II chip and Ion Chef, if it all works and delivers high quality data is a serious prospect. But of course, the proof is in the pudding!

It would be great if some early access users would post some data.

Current Ion Roadmap

There seems to be a little confusion as to what is available now. Here is the roadmap I figured out based on the announcements today:

September 2012 - Ion Proton ships to first customers

end 2012 - 400 base kit available for PGM

March 2013 - PII chip available (assuming 6 months from September 2012)

Mid-2013 - Ion Chef launches (for PGM and Proton)

March 2014 - Avalanche and PIII chip available (assuming 18 months from September 2012)