While everyone was waiting for them to come out with the long delayed Ion PII chip, Thermo Fisher decided to instead come out with an all new sequencing platform. And there’s a good chance it’s not the sequencer you’ve been waiting for. And that’s ok with Thermo because you’re probably not the customer they had in mind.
A few weeks ago AllSeq received an invitation to Thermo’s pre-launch media event for the new S5 sequencer. As no details were forthcoming on the new Ion platform, we went digging for ourselves. We turned up a few details which we posted, but in less than 24 hours we were very politely asked to remove the post as it had generated too much interest (supposedly the last thing a company wants for their new product).
Well now that we’ve seen the official presentation, asked our follow up questions and waited for the embargo to lift, we’re ready to blog all the details that are fit to blog.
The new Ion S5 and S5 XL are the latest iterations in the Ion Torrent line of sequencers (with the PGM and the Proton being the first two). So, with all apologies to George Lucas, how come “these aren’t the sequencers you’re looking for”? Because while they replace (or will eventually replace) the PGM and Proton, they don’t generate more data, longer reads, cheaper reads, or improve on read quality. In these categories everything is more or less the same. Instead, they’ve focused on improving one thing – ease of use. And from what we can tell they’ve done a really good job.
They’ve attempted to make everything ‘plug and play’ with RFID-enabled chips and cartridge-based reagents. It takes less than 15 minutes of hands-on time to set up the sequencing run and, when combined with the Ion Chef, less than 45 minutes hands-on time for the entire workflow from DNA to data.
So why the focus on ‘ease of use’? Because they’re going after novice users, especially those involved in clinical sequencing. These are the people who don’t really care about the nuts and bolts of the system (or how long the reads are or how many Gb it can generate). They just want it to work, preferably with the push of a button.
So now for the details. The S5 is essentially a fusion of the PGM and Proton. It runs three types of chips: 520, 530 and 540. The 520 is an updated version of a PGM 318 chip – it generates ~5M reads of up to 400b. The 530 is kind of like a souped-up version of the 318 with 3X the output – 15 to 20M reads of up to 400b. These two chips even use the PGM chemistry (including the upgraded Hi-Q enzymes). The 540 is more or less a PI chip with ~80M reads of up to 200b. And, as you might have guessed, it uses the Proton chemistry. The advantage is you get a wider range of output with just a single machine. While existing users may want to stick with either the PGM or Proton (especially if they have validated protocols worked out), new users will invariably purchase the Ion S5 or the S5 XL. Speaking of which, the XL version runs the same chips with the same specs, but it adds in some extra compute power and server capacity to allow for faster data analysis and more samples per day.
These machines are relatively low cost – $65k for the S5 and $150k for the S5 XL. But to really get all of the ‘ease of use’ benefits, you need to add in the Ion Chef, bringing the cost to $110k and $205k.
As has been the case with the PGM and Proton, Thermo’s focus is really on targeted sequencing – amplicons, gene panels, etc. With the heftier output and increased number of reads of the 540 you also get access to exomes and transcriptomes.
So how will the NGS market react to these two new platforms? Our guess is a collective ‘shrug’ and maybe a few admonishments of ‘too little, too late’. While these platforms definitely improve on the ease of use for Ion chemistry, most of these ‘improvements’ have been available to Illumina customers for a couple of years. But perhaps Thermo’s large sales force pushing the ‘ease of use’ message with the added utility of the Ion AmpliSeq assay will be what it takes to win over the nascent clinical sequencing market. Time will tell. In the meantime, we can still take bets on when the PII will finally launch.
[Edit: For another perspective check out Keith Robison’s blog over at Omics! Omics! Also, Theral Timpson at Mendelspod caught up with Andy Felton of Thermo for a short interview followed by a bit of a ‘counterpoint’ by AllSeq’s CSO Shawn Baker (that’s me).]
I got to have a chat with Theral Timpson at Mendelspod about how the S5 compares with the MiSeq