Thermo Fisher Clarifies Its Vision for Sequencing with Release of Ion S5 Instruments

By Bio-IT World Staff

September 1, 2015 | Thermo Fisher Scientific, which owns the Ion Torrent line of next-generation sequencing instruments, announced today that two new sequencers are being added to its portfolio. The Ion S5 and Ion S5 XL will make up a new mid-range in the Ion Torrent series, with a price and throughput intermediate between the cut-rate Ion PGM and the workhorse Ion Proton.

The release, however, is about more than filling a gap in Thermo Fisher’s catalogue. The Ion Torrent sequencers, built on a unique technology that measures the electrical output of DNA binding events on a semiconductor, were originally conceived as a way to cheaply read massive and indiscriminate stretches of DNA, up to whole human genomes. The instruments are capable of this kind of sequencing, but since their introduction in 2010, their efficiency has been leapfrogged by Illumina’s HiSeq series, now overwhelmingly the go-to system for broad genomics projects.

On the other hand, users of the Ion PGM and Ion Proton have preferred this technology for targeted sequencing, using both marketed and custom panels to quickly cover selected gene regions. Thermo Fisher’s cancer panels have been deployed for choosing targeted therapies in oncology, and in basic research, Ion Torrent devices have powered facilities like the Mount Sinai genomics lab in Branford, Conn., where a 26,000-gene panel is being used to cover a spectrum of disease-related variants.

“Targeted resequencing is the area we’ve had particular success in, especially for oncology,” Andy Felton, Thermo Fisher’s head of product management for the Ion Torrent line, acknowledged in an interview with Bio-IT World this March (unrelated to the S5 releases). “Our realization over the last year has been that we need to focus on that more ― not that we’re giving up on the exome and genome space, but we want to focus where our strength is and deliver products that really enhance our workflow.”

The Ion S5 and S5 XL are strong fits for that niche. Their sequencing specs are competitive for the price: depending on the chips used, S5 instruments can deliver up to 20 million reads of 400 base pairs, or 80 million reads of 200 base pairs, in each 2.5-hour sequencing run. That’s roughly three times the throughput of an Ion PGM, making the S5 a rapid alternative for the same targeted sequencing applications, while outperforming Illumina’s low-cost MiSeq on volume and quality of data.

In addition, the instruments should be easier to use than previous Ion Torrent devices, an important consideration for the kinds of smaller academic and hospital labs that are most likely to work with targeted panels. The reagents to run the S5 series have been consolidated onto disposable chips, and on-board computing handles the first steps of analysis, a longer process than the sequencing itself. (The amount of computing power is the major difference between the standard S5 and the XL model.) The instruments can also be paired with the Ion Chef device for automated preparation of DNA samples, which the company says will result in just 45 minutes of hands-on time and two pipetting steps from raw sample to sequence.

“We believe that the Ion S5 Systems deliver the best value of any benchtop instruments in the industry,” wrote Ion Torrent General Manager Mark Gardner in a letter introducing the new products. “We built the Ion S5 Systems with process-controlled, easy to use workflows in mind, while retaining maximum application versatility, rendering the Ion S5 Systems an outstanding platform of choice for partners to develop their own assays.”

Meanwhile, Thermo Fisher insists that the P2 chip, a long-planned upgrade to boost the throughput of existing Ion Protons for whole-genome sequencing, is still in active development. Repeated delays, however, may have done irreparable damage to that product. The chip is now more than two years overdue, and even once delivered it will not come close to matching the throughput of Illumina’s most advanced HiSeqs. In light of the major market changes of the past few years, introducing the S5 series is a crucial course correction for Ion Torrent, salvaging its sequencing technology for those applications where it is most competitive. Fortunately for Thermo Fisher, there is strong overlap between the S5’s strengths and the needs of clinical centers, where the market for sequencing is still young and very much up for grabs.

Taking this logic to its extremes, DNA Electronics, the company that originated semiconductor sequencing, is working on handheld chips for ultra-niche genetics, targeting just a small handful of variants at a time. Although semiconductors have not come to dominate population-scale genomics as some predicted they would five years ago, the technology could still be a central part of sequencing’s adoption in routine medicine.