Illumina reveals chip-based sequencing push

Illumina has used its appearance at the JP Morgan Healthcare Conference to announce a number of additions to its DNA sequencing portfolio, including Project Firefly, its attempt to commercialise a new semiconductor-based sequencing system. The company says it will offer a raw error rate of under 1%, and cost under $30,000, with consumables running at under $100/run for eight samples. The chip-based approach puts them in direct competition with Ion Torrent sequencers. Other announcements include MiniSeq, a benchtop sequencer priced under $50,000, shipping in the first quarter this year. 

SAN FRANCISCO -- In a followup to its Sunday announcement of a major cancer detection initiative, genetic sequencing giant Illumina announced more products, including a semiconductor-based sequencing system to sell for less than $30,000.

Illumina also announced a partnership with Hercules-based Bio-Rad Laboratories to make a product that identifies single cells and tags them for later analysis. This single-cell sequencing approach identifies differing cell types that play roles in various diseases, but is complicated to do.

In addition, Illumina said it is about to begin shipping a new technology to allow mass genotyping of samples, the Infinium XT. This will be used on its existing iScan system. Infinium XT can handle 96 samples at a time, four times as many as the previous maximum of 24. This technology can be used for agricultural genomics and human applications such as personalized medicine, the company said.

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The semiconductor system is intended for smaller labs that want a simple, integrated device, Illumina CEO Jay Flatley said Monday morning at the JP Morgan Healthcare Conference in San Francisco. It’s scheduled to hit the market in the second half of 2017.

Moreover, Project Firefly, as the initiative is called, brings Illumina’s considerable heft in DNA and RNA sequencing technology to the semiconductor realm.

As the largest sequencing company, with a market value of about $24 billion, Illumina is the largest biotech company in San Diego, and one of its largest publicly traded companies.

A number of competitors have developed semiconductor sequencing products but so far have not dislodged Illumina, including Ion Torrent, part of Thermo Fisher Scientific.

Ion Torrent was purchased by Carlsbad’s Life Technologies in 2010; and that company was itself purchased by Thermo Fisher in 2014 for $13.6 billion. Over the last 5 years, the Ion Torrent line has struggled against strong competition from Illumina.

Developed under a program called Project Firefly, the initiative faced and solved difficult technical and financial challenges, Flatley said.

“The huge innovation here is we figured out how to run what fundamentally is a four-channel technology on a one-channel chip,” he said.

Illumina began with a commercially available CMOS chip, and designed custom features into it, Flatley said.

The system is small and inexpensive to operate, said Joel Fellis, associate director of product marketing. The cost per sample is about $100. Targeted users include researchers into cancer and reproductive health.

Another system aimed at the low-end market, called MiniSeq, will be introduced in February, Fellis said. The system uses Illumina’s next-generation sequencing technology and will cost just under $50,000.

MiniSeq produces more data per run than the Project Firefly device will be able to do, Fellis said.