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Thermo Fisher Launches New Systems to Focus on Plug and Play Targeted Sequencing

NEW YORK (GenomeWeb) – Thermo Fisher intends to focus on the targeted sequencing market with the launch today of its new S5 and S5 XL systems.

The systems are especially geared toward customers just getting into the next-generation sequencing market, with an eventual eye toward community hospitals and small clinical laboratories.

The instruments, which are essentially the same instrument except that analysis on the XL is more than three times faster, are designed to be plug and play with just two pipetting steps, Andy Felton, Thermo Fisher's VP of product management for NGS, said during a company-sponsored workshop held Monday at the firm's South San Francisco, California facilities.

Thermo Fisher plans to focus on targeted sequencing applications in inherited disease, oncology, reproductive health, infectious disease, and forensics. The S5 and S5 XL are research-use only, but Thermo Fisher eventually plans to register them with the US Food and Drug Administration, although it did not provide a timeline for that effort.

Both benchtop instruments utilize the same semiconductor sequencing technology as the Ion Torrent PGM and the Ion Proton with the main differences in the instruments' cartridges and reagents. The instruments make use of an internal pump-based fluidics mechanism and single-use cartridges that contain all the necessary reagents, which negate the use for the external gas and water supplies required by the PGM and Proton.

The company has also configured the Ion Chef to enable AmpliSeq library construction along with template preparation and chip loading. Using the Ion Chef for sample prep and library construction, hands-on time from DNA sample to data is 45 minutes, the firm said.

The S5 has a list price of $65,000 and the S5 XL sells for $150,000. Purchase of the Ion Chef adds an additional $55,000.

Three chips are available for the S5 instruments: the 520, 530, and 540, all of which have 2.5-hour sequencing run times for 200 base single-end reads. The 520 chip generates between 1Gb to 2 Gb of data, or 3 million to 5 million reads with read lengths up to 400 bases. Analysis takes five hours on the S5 and one-and-a-half hours on the XL. The 520 chip is geared primarily toward gene panels.

The 530 chip generates between 3 Gb and 5 Gb of data, or 15 million to 20 million reads with read lengths up to 400 bases. The standard eight-hour analysis time can be shortened to two-and-a-half hours with the XL.

The 540 chip generates between 10 Gb to 15 Gb of data, or 60 million to 80 million reads. It does not yet support 400-base reads. Analysis time is 16.5 hours on the S5 and five hours with the XL. The 540 chip is similar to the PI chip on the Proton, able to sequence exomes and transcriptomes, as well as larger gene panels.

Felton said that the reagent cost per run would be about 1 percent to 3 percent more expensive than the $500 to $1,000 runs on the PGM and Proton systems, depending on the chip used and the number of samples run.

With the Ion Chef's library construction functionality, eight AmpliSeq libraries can be prepared in an eight-hour run.

Thermo Fisher also incorporated the Hi-Q chemistry into the S5 systems, which improves accuracy, particularly for indels. In its internal validation studies, the company achieved a raw read accuracy of 99.1 percent for the 520 chip, 99.2 percent for the 530 chip, and 98.4 percent for the 540 chip.

Felton said that the majority of the errors are still indels, but noted that accuracy does not taper off toward the end of a 400-base read.

He added that the 530 chip would be the "most important" one, offering three times the output of the PGM's 318 chip. In a validation study of the chip on an Escherichia coli genome, the company completed 12 runs, generating between 15 million and 18 million reads per run with a mean read length of 326 bases and 99.2 percent raw accuracy.

Early-access users of the system include Uppsala University; the MD Anderson Cancer Center; NIM Genetics, a Spain-based medical genetics company that offers exome sequencing, noninvasive prenatal testing, and some gene panels using Thermo Fisher's technology; and OncoDNA, a clinical NGS provider affiliated with the Institute of Pathology and Genetics in Gosselies, Belgium.

Felton said that the S5 systems would not replace the Proton or the PGM. He added that the company is still working to develop its PII chip, which it had originally planned to launch in 2014, and then at this year's Advances in Genome Biology and Technology conference said it would launch in the second half of this year. Felton did not give an update to the timeline for the PII launch.

He said that users with validated protocols on the PGM and Proton would likely continue running those protocols on those systems, and Thermo Fisher would continue supporting those systems. But for new users without validated workflows on the PGM or Proton, there would be no reason not to opt for the S5, he added.

Mark Gardner, VP and general manager of NGS at Thermo Fisher, said that users needing a clinical instrument in order to bring an assay through FDA clearance would likely opt for the PGM Dx. The PGM is already registered with the FDA and Thermo Fisher currently has collaborations to develop in vitro diagnostics on that device.

"We will register the [S5] with the FDA, but we're not talking about a timeline for that yet," he said.

Along with the sequencing systems, Thermo Fisher also launched 13 targeted AmpliSeq panels covering 3,000 Mendelian disease genes that it developed as part of the Saudi Human Genome Program, a pharmacogenetics panel targeting 40 genes, and a tuberculosis research panel comprising eight genes.