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January 10, 2018

Illumina’s Push to Democratize Genomics with the iSeq 100

Illumina's new $20,000 iSeq 100 DNA sequencer.

  • Illumina, the San Diego-based leader in next-gen sequencing (NGS) instrumentation, usually makes a point of releasing its biggest product and business news at the JP Morgan Healthcare Conference, the annual scrum of biotech CEOs, VCs, and investors in San Francisco. Past years have included pronouncements regarding the fabled “$1,000 genome” and the spin out of GRAIL, the lavishly funded liquid biopsy company.

    This year, the big news came in a small package—one cubic foot to be precise. The headline yesterday from Illumina CEO Francis deSouza, who succeeded Jay Flatley (now the firm’s executive chairman), was the unveiling of a new benchtop instrument called the iSeq 100.

    The iSeq 100 (formerly known in development as Firefly) is a compact benchtop system that sells for just under $20,000—significantly less than the $50,000 MiniSeq or Illumina’s higher-end instruments (the NovaSeq is close to $1 million). While the iSeq 100 doesn’t match the $1,000 starting price for Oxford Nanopore Technology’s portable minION device, Illumina touts this new price as one that “puts NGS within reach of virtually any lab.”

    “For under $20,000, any researcher can have access to the accuracy of an Illumina sequencer in their lab,” said deSouza in a statement. “The iSeq 100 offers robustness and reliability for a broad range of applications ranging from germline and somatic tumor profiling to 16S [ribosomal RNA] microbial analysis and targeted gene expression.”

    Speaking to CNBC’s Meg Tirrell today, deSouza explained the iSeq 100 rationale: “It makes the power of genomics … available to a lot more labs than had access to it before. Now there are tens of thousands of labs that can get the accuracy of our sequencing capabilities but for under $20,000. I think it opens up a whole new set of markets where you’ll see smaller labs that are doing applications like identifying hospital-acquired infections or testing for foodborne pathogens. This really democratizes access to the power of genomics.”

    Illumina received backing from Harvard/Broad Institute researcher Pardis Sabeti, an expert in the genetics of infectious diseases. Sabeti said the introduction of the iSeq 100 had the potential to transform infectious disease surveillance, and she looked forward to her team using the instrument in the field (although the company says the machine is “for indoor use” only). “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,” she said.

    The iSeq 100 is the first Illumina instrument to use complementary metal-oxide-semiconductor (CMOS) detection technology, representing a different configuration for the company to deliver accurate data at lower cost. CMOS chips have previously featured in Thermo Fisher Scientific’s Ion Torrent systems.

  • Thermo Partnership

    In other surprising news, Illumina announced a partnership with longtime rival Thermo Fisher Scientific on AmpliSeq. For much of the past decade, Illumina was locked in a fierce battle with Thermo subsidiaries Applied Biosystems and Life Technologies for dominance in the NGS space. Thermo produced at least two platforms—the SOLiD sequencing system from Applied Biosystems and subsequently, the Ion Torrent platform, acquired from Life Technologies—that competed strongly with Illumina’s sequencing-by-synthesis chemistry and platform.

    The ingenuity of the Ion Torrent platform, originally developed by Jonathan Rothberg and colleagues, is that DNA sequence is measured essentially by changes in pH as each nucleotide is added to the growing strand. The accompanying AmpliSeq chemistry is widely regarded as the best-in-class strategy for targeted NGS. Illumina says the new partnership allows it to offer its customers “an ION AmpliSeq chemistry product optimized for use on Illumina’s sequencing systems.”

    “We expect standardization on the AmpliSeq technology will have a profound impact on disease research and encourage greater collaboration among the community,” said Joydeep Goswami, president of Clinical Next-Generation Sequencing and Oncology at Thermo Fisher Scientific, in a statement. “More research customers can now leverage AmpliSeq technology’s benefits, while we continue our commitment to Ion Torrent targeted sequencing solutions for the research market and accelerate our focus and forward momentum in the clinical space.”

    The news drew some gasps on social media. “Illumina and Thermo partnership on AmpliSeq is huge news. Who would have imagined that 5 years ago?” commented University of Birmingham (UK) microbiologist Nick Loman on Twitter.

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