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Illumina Launches Semiconductor Sequencer, Partners With Thermo Fisher, Releases Prelim Earnings

This article has been updated to include additional comments from Illumina about the iSeq instrument.

SAN FRANCISCO (GenomeWeb) – Illumina unveiled on Monday the semiconductor-based sequencing system that it has been developing as part of its previously discussed Firefly project.

In addition, Illumina said that it plans to partner with Thermo Fisher Scientific to make Thermo's AmpliSeq chemistry compatible with Illumina's sequencers. Illumina also released preliminary fourth quarter and full year 2017 revenues ahead of its Q4 earnings call.

Illumina CEO Francis deSouza discussed these items and more in a presentation at the JP Morgan Healthcare Conference held here this week.

Illumina's new sequencing instrument, dubbed iSeq 100, was borne out of the Firefly project that the firm initially announced at the JP Morgan Healthcare conference in 2016.

The iSeq system uses sequencing-by-synthesis chemistry coupled with CMOS detection technology. The instrument measures 1 cubic foot in size and has a list price of $19,900. Per-sample cost is between $25 and $150 and each sequencing run generates around 4 million reads, or 1.2 gigabases of data, with a raw read accuracy of 99.8 percent and run times between 9 hours and 18 hours, depending on the application. The system will begin shipping in the first quarter of 2018.

The iSeq 100 will have a "cartridge-based upgrade roadmap," deSouza said, with improvements to CMOS sensors enabling more reads in less time. Ultimately, deSouza said, the system should be able to generate tens of gigabases of data in a few hours. Such improvements would open up new markets to NGS, including monitoring hospital-acquired infections, testing for foodborne pathogens, and rapid microbiome sequencing.

Previously, Illumina had said that library prep would be automated and require a separate module that would be based on digital microfluidics. However, Kevin Meldrum, senior director of product marketing at Illumina, said in an interview following deSouza's presentation that iSeq would instead be compatible with any existing library prep technologies, including the AmpliSeq technology. The previously described library prep module would have been based on the same underlying technology that Illumina had been developing for its automated library prep instrument NeoPrep, but when it decided to discontinue that last year, it moved ahead with iSeq without the library prep module.

"We're actively considering other external options" for an automated library prep module, Meldrum said. In the meantime, he added that the company is working on making library prep simpler through other advances, citing the launch last year of the Nextera Flex chemistry for whole-genome sequencing. That chemistry uses beads and transposomes to prep DNA and has the advantage of direct sample input — for instance, blood can be an input without having to isolate the nucleic acids. Currently, the chemistry is available only for whole-genome sequencing, but Illumina is also working on enrichment-based methods for exome and targeted sequencing that will be available in the second half of the year.

Christopher Mason, an associate professor at Weill Cornell Medicine who has been  testing a beta version of the iSeq instrument, said that he is excited about the technology because it is moving the field "to that point where you can envision home-based sequencing." He added that in his lab, in one run with 150-base-paired end reads the system generated 6 million reads, or 1.8 gigabases of data, with 97 percent of that data above a Q30 quality score. Total time from sample to data was around 13 hours, he said.

Now, he said, the lab plans to test different types of sequencing libraries including bisulfite sequencing, single-cell RNA sequencing, metagenomics, and human DNA sequencing.

Thermo Fisher partnership; financial outlook

Under the terms of Illumina's newly announced agreement with Thermo Fisher, customers will be able to use Thermo's AmpliSeq technology on Illumina instruments for research use only. Illumina will sell the product directly to its customers under the name AmpliSeq for Illumina.

Thermo will continue to sell its AmpliSeq kits to its own sequencing customers for both research and in vitro diagnostics, and retains the right to make the AmpliSeq technology available on other NGS platforms.

During his JPM presentation, deSouza also said that Illumina expects $775 million in Q4 2017 revenues, 25 percent higher than its Q4 2016 revenues of $619 million, and exceeding its prior guidance. , The company's Q4 sequencing consumables revenues are expected to grow more than 30 percent year over year. For the full year 2017, the firm's revenues increased 15 percent to $2.75 billion from $2.40 billion in 2016, driven by NovaSeq adoption and the growth of consumer and clinical genomics markets.

Illumina has so far shipped 285 NovaSeq instruments with more than 80 shipped in Q4 2017. "NovaSeq is an important part of our clinical strategy," deSouza said.

He added that the clinical NGS market is "at the tip of the adoption curve." Thus far, Illumina has placed 375 of its US Food and Drug Administration-cleared MiSeqDx instruments.

DeSouza said that within the clinical market, Illumina plans to focus on five growth areas: population sequencing, NIPT, oncology, and rare and undiagnosed diseases.

Within oncology, he said the firm has launched an immune oncology program and is currently developing a Tumor TruSight panel consisting of around 500 genes to measure tumor mutational burden and microsatellite instability. The panel will initially be used for immune-oncology clinical trial enrollment, with eventual commercialization as an IVD.

The consumer genomics market "hit an inflection point in 2017," with its biggest impact on Illumina's array business, deSouza said. In total, around 12 million samples have been genotyped on Illumina arrays, with 7 million of those samples genotyped in 2017.

For 2018, the firm projects revenues to grow between 13 percent to 14 percent to $3.11 billion to $3.14 billion with an EPS of $4.14 to $4.24 and non-GAAP EPS of $4.50 to $4.60. DeSouza added that the guidance includes the impact of tax reform.