Ion Torrent Proton Announced: The Chip Is (Not) The Machine

Big announcement today from Life Technologies who have announced the Ion Torrent Proton(tm). This, to all intents and purposes is the PGM-2, the second iteration of their pH-meter-on-a-chip sequencing machine. Indeed it is curious they have dropped the Personal Genome Machine moniker, as this product is the first to explicitly target the $1000 (human) genome market in benchtop format. So what do we know so far?

* Mid-2012 launch for early access customers, Q3 for general release
* $149,000 list price (compared with $50,000 for the PGM)
* Two chips announced
* Ion Proton 1 available at launch – 165m sensors (cf ~12m for the 318 chip and ~1m for the 314 chip)
* Ion Proton 2 in early 2013 – 660m sensors
* Update: 14:28 GMT – According to GenomeWeb, Ion Proton will also require purchase of a $75,000 server

The iPod dock is gone, as have the milking tubes

Eric Olivares over at Seqanswers.com already did the critical calculations. Assuming a 250bp read length you could expect between 3 and 6 exomes at 100x coverage with the Proton 1 chip, and between 1-1.5x whole human genomes at 30x with the Proton 2.

How will this be acheived? Looking at the picture the chip size is visibly larger, but the increase in area (assuming the picture shows normal sized hands!) is not sufficient to account for the increased number of sensors, implying the wells are closer together and/or smaller than existing Ion chips.

Proton chips are bigger than the previous generation

So, what to think about this announcement?

Well, the specs are certainly impressive and this is the first concrete evidence demonstrating continued log-scale improvements using the Ion Torrent technology after the 318 chip, something the Life Tech roadmap has deliberately not spelt out until now.

However, I have to admit to being a bit disappointed that this is an entirely new machine coming in at three times the cost of the original machine. It turns out unlike what we have been told countless times at presentations, the chip is not actually the machine. Whilst no surprise to anyone that has looked at the technology carefully, this may be a disappointment to those who just received or ordered their Ion Torrent PGM and have bought into the marketing wholesale. Are  customers now looking at taking delivery of a machine that has hit its performance ceiling as early as mid-2012? We don’t know how this announcement affects the PGM1 roadmap, it would be nice to get reassurance on this point. Update 14:31 GMTGenomeWeb report an Ion Torrent marketing director as saying “The electronics on the PGM were built to handle chips of 1 million to 10 million sensors”, which seems like confirmation that the 318 chip hits their density ceiling. However read lengths can still increase to generate additional throughput.

This announcement also has resonance for Ion Torrent’s constant comparison to the computer and semiconductor industry. Was it really a wise move to announce a PGM-killer so early into this machines life? I am thinking specifically of the Osborne effect. This is the act of announcing an improved model early, in this case Osborne with their early portable computers, “to reassure current customers that there is improvement or lower cost coming, to increase the interest of the media and investors in the company’s future prospects, and to intimidate or confuse competitors”.  The announcement can actually have the an unintended effect that customers see something better on the horizon and defer their buying decision.

If I was about to buy a PGM, would I now hold off for the Proton? Life Tech will be keen to target the PGM at cheaper “small genome” applications and the Proton at human genome scale, and this will be fine for many users, perhaps those wanting to replace amplicon sequencing done on capillary sequencers with high-throughput instruments. Me personally, I’d always want to buy the most fully-featured instrument available, akin to choosing a new laptop (which you know will be out of date before it is switched on for the first time). In bacteriology we are moving from 16S amplicon studies and whole-genome studies of single isolates to sequencing of entire communities as metagenomes. Such studies benefit from as much throughput as possible.

It will be fascinating to see how this announcement plays out during the year, particularly so close to AGBT where there is reasonable expectation some new “killer” sequencing platforms will be announced.

Have you just bought a PGM? What do you think? Leave a comment below. Also please head over to Seqanswers.com to read more discussion.

Happy New Year!

4 Responses

  1. Jonathan Jacobs
    January 10, 2012 at 5:46 pm |

    We’ve unpacked a PGM two months ago and are just now bringing it online for small genome and amplicon sequencing use. I don’t think it’s a big deal for us – I mean… things always get better, faster, stronger. That’s part of the game. We purchased our PGM for a couple of specific tasks, and for those tasks it will do quite well. Now, for the things that would be pushing the technology – euk transcriptome sequencing or metagenomics – we’ll be back where we were a year ago: stuck with good options a) buy a new platform (not likely unless there is LOTS of long term need), b) outsource the sequencing (much more likely, given that NGS is basically a commodity product now), or c) get our technical staff to tinker around with the protocols to push our existing PGM technology to the limit (less likely than B since we’re in the CRO business, but still possible). In short – for a single PGM lab, it’s no big deal. The PGM is basically no different than our ABI7700HT’s – new, awesome, and sexy (in a geeky sort of way) for a couple weeks but then quickly dated and sort of old news and just another cog in the machine. It does the job it was purchased for – that is what matters.

    I think this announcement is mostly good news for the technology and the market. For big Vendors who invested heavily in PGMs – this could be a problem, but they are also the same folks who are likely to get the best deals from LifeTech on the IonProton – so it could be a good problem.

    Exciting times…

  2. Ion Proton Intensifies Competition in Benchtop Sequencing « Edge Bio – Views From the Edge

    […] If you are a fan of this blog you know that EdgeBio has been an early adopter of the Ion Torrent technology and has walked it through its development curve with rapid and sometimes even surprising success ( Ion Torrent Retrospective). What has most people excited is the rapid turn-around time and the price to generate sequence. Pathogenomics documents this information in their blog. (http://pathogenomics.bham.ac.uk/blog/2012/01/ion-torrent-proton-the-chip-is-not-the-machine/). […]

  3. ion t
    ion t
    January 11, 2012 at 5:54 pm |

    Hi Nick, thanks for your great summary of Ion´s new Proton instrument. You’ve certainly covered a lot of ground on this and we really appreciate the feedback. There still a lot of information you’ve not had access to we’d like to share with you, including how we support our customer base in getting access to the new machine whilst keeping their PGM running and we’d like to encourage every one of our many customers to explore these options with us. The PGM remains the system of choice to targeted genetic analysis; Proton is Ion´s solution to genome sequencing. If you’d like to know more Nick, I’m happy for you to get in touch with me.

  4. 2012 Update to the NGS Field Guide | The Molecular Ecologist

    […] Loman has some nice summaries of the Proton and Nanopore sequencers. Keith Robinson’s OMICS! OMICS! blog on the nanopore sequencers, Ion […]

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