Ion's S5

The Ion Torrent team rolled out a new sequencer line this morning, the S5.  The S5, whose impending release had been tipped on the internet by the leak of a manual, arrives in two models, the standard and the XL, which differ only by on-board computing power and not sequencing metrics.   As has been the trend, Ion's focus is entirely on focused sequencing, and the new lineup emphasizes making targeted sequencing with AmpliSeq and other approaches fast and simple.
The new instrument, which lists for $65K ($150K for the XL model), sports three new chips, which are not interoperable on either the PGM or Proton; certainly for Ion the concept that all upgrades are encased in the consumable is long dead..  The low-end 520 chip offers performance similar to the PGM 318 chip with 200 or 400bp reads.  The mid-range 530 chip offers 3-fold the output of a 318 chip, again with 200 or 400 bp read options. The top-end 540 chip has Proton PI-like characteristics, with only 200bp reads supported.  The fact these straddle the two prior systems is underscored by the fact that the 520 and 530 will use the HiQ enzyme for PGM whereas the 540 will use the HiQ enzyme for Proton.

Reagents are loaded on the system as 3 cartridges, each bearing RFIDs for auto-detection of the cartridge type by the instrument.  Reagents are shelf-stable for 12 months, simplifying reagent management.  Reagents for the 520 and 530 are the same, regardless of which read length is used, again simplifying stocking reagents.  If linked to a $55K Ion Chef sample and template preparation robot, as most customers probably will, then amplified DNA can be sequenced with only 45 minutes of hands-on time and as few as two pipetting steps. In 200 bp mode, the chips can generate from 5M to 80M reads in only 2.5 hours. The boxes also require only standard electrical connections; no gas or water connections are required.

Ion sees huge growth opportunities in the targeted sequencing space, starting with their strong position in cancer (with over 100 publications in peer-reviewed journals but branching out into biosurveillance, infectious diseases, food safety, forensics and other areas.  Ion's promotional materials emphasize the analytical simplification enabled by targeted panels.  This is also where the bigger XL kicks in, able to perform the full on-board analysis (no separate server for either box) in about one third the time of its little sibling.

In the early, heady days of Ion Torrent it was promoted as a disruptive technology that would take on every sequencing challenge.  While there are echos of that past in the new presentation, the reality is that Ion has identified a profitable market segment -- those desiring fast, targeted sequencing -- and is going full bore in this area.  Ion's focus is on expanding the number of off-the-shelf assay panels available for their instrumentation line while making that line simpler and less labor intensive to operate.  While a timetable for FDA clearance was not released, the S5 instruments are clearly aimed at clinical labs.

What about the competition?  MiSeq is the only standing competitor with broad appeal, but in its fastest mode takes 4 hours to deliver very short (1x36bp)  and only around 500Mb (give or take) of these. The repeated feedback when I write these pieces is that for fast, targeted applications Ion is just better.  Potential new entrants such as GnuBio, Genia/Roche and QIAGEN have gone all but silent.  Oxford Nanopore would like to tackle this space and could beat Ion on speed (and by a huge amount on cost), but is still shaking out the kinks in their system and tuning up performance, and in any case will have to convince users that the software exists to filter out the noise in nanopore reads (which can be quite good, the trick is knowing which ones are the good ones even amongst 2D reads).  So Ion has an opportunity to nail down users before these competitors get out of the starting blocks.

The S5 isn't the uber low-cost Ion instrument I dreamed of earlier this year, but it is interesting to note that a combined S5 + Chef purchase will set you back about $120K (in the U.S.), in the same ballpark as the original all-in price for a PGM system (which was about $100K) -- but this offers far more automation.  So while Ion isn't a disruptive technology, it is continuing to refine itself for a key market.

(Note: this entry was prepared using embargoed materials provided by Ion, as well as access to a press presentation which was similarly embargoed).