19 September 2012

2012 Will NOT be The Year of the $1000 Genome

There was a lot of excitement earlier this year when Ion Torrent announced their newest machine, the Proton. It was going to let them continue down the path of rapid technology improvement and let them keep their oft-repeated statement of 10-fold improvement every 6 months. I was pretty skeptical of these claims when they first came out, but the PGM has done a remarkable job of backing them up, going from 10Mb on the 314 chip, to 100Mb on the 316 chip and finally to 1Gb on the 318 chip over a period of 12 months.

As impressive as Ion Torrent’s progress has been, there have been a few hiccups:

  • Contrary to their initial marketing slogan, the chip is no longer the machine. To keep riding the wave of improvements, you have to trade in your original PGM for a much more expensive (but still relatively cheap) Proton. Not surprisingly, there were some grumblings from customers when that little bombshell came out.
  • They have slipped a bit (by about 3 months) on their rapid pace of launching a new chip every 6 months. By their original plan, the PI should have come out in July, but we’re just now seeing it in September.
  • When the Proton was first announced, the PI was targeted for 10Gb, or 2 exomes per chip, and the PII was to offer 10 times the output which would be 100Gb, enough fo a single whole human genome (all for under $1000 for chip+reagents). The only problem is, they’re now redefining “whole human genome” to be 20X coverage, while the industry standard is more like 30X with some pushing for higher coverage of 40X or more. 20X coverage implies that the PII chip will initially only be generating 60Gb per run. Still quite impressive, but another slip from the original roadmap.

So, this means not only will we not have a whole genome on a single chip by the end of the year (due to the 3 month schedule slip), when we do get it, it won’t really be a ‘true’ whole genome run. You’ll probably need to run two chips (or a chip and a half, if you can manage that with indexing), meaning it will cost you more like $2k instead of the holy grail of $1k.

The other thing to note is that the launch of the PII will signal the end of the original ’10-fold improvement every 6 months’ promise. The follow-on chip, the PIII, will take a full 12 months after the launch of the PII, and it will only be about a 2X improvement instead of the 10X improvement we’ve been getting used to.  Still, if they’re able to do what they say, by the middle of 2014 we’ll have the ability to generate ~200Gb in a 2-4 hour run for ~$1000. That, in turn, will surely put a lot of pressure on the market leader, Illumina, to launch some improvements of their own. Chemistry A and B, we’re waiting…