Illumina Announces iSeq 100, Thermo Fisher Partnership

By Allison Proffitt

January 8, 2018 In the company’s JP Morgan presentation today, Illumina president and CEO Francis deSouza summarized the past year for the sequencing giant, highlighted expected areas of growth—consumer genomics, non-invasive prenatal testing—and announced the launch of the iSeq 100 Sequencing System and library prep partnership with Thermo Fisher.

2017 was a banner year for Illumina deSouza announced. 2017 revenue was about $2.75 billion, driven by the adoption of platforms and growth in both consumer and clinical genomics, he said. The sequencing consumables business grew 30%. The company now has an active install base of 11,000 systems and shipped about 285 of its latest platform, the NovaSeq, announced last year, and 600 NextSeqs. More than 4,000 of the installed systems are connected to BaseSpace Cloud.

As has become tradition, deSouza also announced the newest Illumina platform to join the fold. The iSeq 100 (with a name making Bio-IT World’s 2014 Illumina/JP Morgan lede seem eerily prescient) is actually not new. It’s the research-only next-generation sequencing (NGS) system formerly known as Firefly. Jay Flatley, Illumina’s former CEO, announced Firefly at JP Morgan in 2016, then predicting a mid-2017 ship date, and the instrument was in the hands of beta testers last December. Now officially dubbed iSeq 100, the cartridge-based platform combines the company's sequencing by synthesis (SBS) chemistry and complementary metal-oxide-semiconductor (CMOS) detection technology. It’s an entirely new architecture and boasts a U.S. list price of $19,900. Price per sample ranges from $25 to $115.

Measuring one cubic foot in size, the iSeq 100 delivers NGS discovery power in the most compact format of any Illumina sequencer to date. iSeq can be installed by the user in less than an hour, and generates more than 4 million reads and 1.2 gigabases per run. Runtimes range from 9 to 18 hours depending on the application, deSouza said.

“In the ten years since we launched the GenomeAnalyzer, the iSeq development has now let us launch a system that is 1/20 the size, 1/20 the capital cost, and produces more data per run at a rate that is five times faster,” deSouza said.

DeSouza said that the iSeq platform delivers the same high quality and rival performance as Illumina’s other desktop systems. “This combination of low cost and high accuracy enables a broad range of applications and very attractive price points,” he said.

Thanks to the cartridge architecture, Illumina will be able to extend the performance of the system without changing the hardware, deSouza said, (though architecture obsolescence has never seemed to concern Illumina). He reported that internal R&D teams have already demonstrated 15% faster sequencing already. The CMOS sensors can deliver four to five times more reads, deSouza said. “Ultimately, we believe this will enable outputs in the 10s of [gigabases] with runtimes of just a few hours, allowing higher output applications to be completed in a single shift.”

Initially, Illumina expects customers for the iSeq 100 to come from core and service labs who need to efficiently manage small-batch, quick-turnaround projects. Other existing customers plan to use iSeq for quality control on NGS libraries before higher throughput runs, deSouza reported. In the future, he sees applications monitoring hospital acquired infections, testing for food-borne pathogens, and rapid microbiome sequencing.

"The addition of the iSeq 100 has great potential to transform infectious disease surveillance," said Pardis Sabeti, Professor of Immunology and Infectious Disease at Harvard T.H. Chan School of Public Health and a Broad Institute Member, in a press release issued after deSouza’s presentation. "We anticipate that our lab researchers will use it to focus on infectious disease monitoring. We have seen examples of how Illumina benchtop systems, like the MiSeq, were instrumental in understanding and addressing disease outbreaks. We believe the accuracy of the iSeq 100, coupled with the low cost and small footprint, will allow us to introduce NGS capability where it is needed most."

Thermo Fisher

DeSouza also announced a new agreement with Thermo Fisher Scientific that enables Illumina to sell Ion AmpliSeq technology to researchers who conduct scientific studies on Illumina's next-generation sequencing (NGS) platforms.

Introduced to the market in 2011, Ion AmpliSeq technology was developed to facilitate amplicon sequencing on the Ion Torrent NGS systems. The technology leverages highly multiplexed polymerase chain reaction (PCR) to quickly and easily capture DNA or RNA targets from very limited samples. It has since proven to be a highly desired and effective NGS amplicon sequencing solution for its ease-of-use, scalability, efficient workflow and ability to provide trusted data in multiple NGS research application areas. To date, more than 1,100 Ion AmpliSeq technology studies have been published in peer-reviewed scientific journals.

Illumina’s interest in the technology was driven by the needs of customers, deSouza said. In oncology, in particular, the AmpliSeq technology let researchers work with less than ideal samples.  

“Thermo Fisher has twenty years of experience in PCR amplification chemistries that has enabled them to develop an amplicon library prep that is simple, fast, and robust. The technology has been widely adopted in the oncology space because of the high-quality data achievable with low input and degraded samples, such as FFPE tissue. But until now those customers have not been able to take advantage of Illumina sequencers,” deSouza said. Now Illumina customers will have direct access to the AmpliSeq technology, optimized specifically for Illumina instruments, deSouza said.

Under the agreement, Thermo Fisher will provide Illumina with Ion AmpliSeq technology for research use. Illumina will sell the product directly to its customers under the name AmpliSeq for Illumina. Thermo Fisher will continue to sell Ion AmpliSeq chemistry for both IVD and RUO applications to Ion Torrent NGS customers, and retains the right to make the technology available on other next-generation sequencing platforms.

Illumina customers will have access to ready-to-order panels as well as AmpliSeq algorithms to create custom amplicon assays with Illumina’s DesignStudio, online assay design protocol.

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