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Illumina Aims for Single-Molecule Sequencing, Launches New Business Unit for the Clinical Market


By Monica Heger

is working on a single-molecule sequencing technology, CEO Jay Flatley said today at the JP Morgan Healthcare Conference in San Francisco.

Flatley also discussed a number of other technologies that the company has in its pipeline, as well as a new business unit it has formed to focus on the clinical market, and how he sees the next-gen sequencing market growing over the next few years.

Additionally, he reaffirmed Illumina's strong position in the sequencing market and said that the company's calculations indicate that 90 percent of sequence data is generated on Illumina platforms.

Flatley noted that the Illumina Genome Network, the company's sequencing services business, has been doing well — the company has shipped 900 genomes to customers in the fourth quarter of 2011, he said. This beats Complete Genomics, which shipped only 600 genomes in the fourth quarter and missed its full-year 2011 estimate for genome shipments (see story, this issue).

Despite Illumina's strong position, however, Flatley said the company is pursuing research in technology beyond its sequencing-by-synthesis chemistry, which has formed the basis for all of its instruments to date. According to Flatley, while "we haven't found the limit yet" for sequencing-by-synthesis, the company is working on a number of assays using different chemistry that can be introduced when the limits of sequencing-by-synthesis are reached.

Flatley did not provide many details, but he said that the single-molecule sequencer would be a low-cost device with a low run cost and long reads that utilizes a chemistry that has "advantages over other chemistries that have suffered from low accuracy."

Separately, he said the company has developed another sequencing chemistry with cycle times as low as 10 seconds and high accuracy that can work with both a light-based detection method and lightless detection. The company has already begun using this chemistry internally, although he did not provide a timeline as to when it would be broadly available.

In the meantime, though, Flatley said that Illumina will continue to make improvements to its current platform, such as the upcoming HiSeq 2500 and MiSeq upgrades, which it announced today (see story, this issue). For instance, he said that clusters on the platform could get denser by at least a factor of two. Additionally, the company is continuing to make improvements to its sample-prep technology, and will soon have a kit that will enable sequencing from formalin-fixed paraffin-embedded tissue.

The company also has programs working on long-range haplotyping and longer read lengths. And, Flatley said, within the next two years the company will be able to sequence single cells.

Clinical Market

During the presentation, Flatley also provided some predictions as to where he thought the sequencing market was heading, noting that clinical sequencing is a particularly quick-growing segment.

As a result, the company has set up a new business segment, Translational and Consumer Genomics. Illumina previously said during its 2011 third-quarter earnings call that it planned to establish a clinically focused business unit as part of a restructuring plan that included the layoff of 200 employees (IS 10/25/2011 and 11/1/2011).

During today's presentation, Flatley said that the new business unit would focus on services, the consumer market, CLIA certification and regulations, and business-to-business. The Translational and Consumer Genomics unit could see 75 percent growth in the next few years, he said.

Additionally, he anticipates that at a $1,000 per genome price point, sequencing in clinical trials will be a $24 million market in the next few years, while cancer sequencing will be a $250 million market and newborn sequencing around a $300 million market.

Ultimately, though, "the biggest market will be the consumer market," he said.

Have topics you'd like to see covered by In Sequence? Contact the editor at mheger [at] genomeweb [.] com.

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