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Illumina Plans to Streamline HiSeq 2500 Sequencing; Unconcerned by Competition from Oxford Nanopore


By Julia Karow

This article, originally published March 8, has been updated to correct the amount of credit customers receive when ordering reagents online.

Illumina CEO Jay Flatley last week provided more details on plans for the HiSeq 2500, upgrades for MiSeq, the recent takeover bid from Roche, and competition from Oxford Nanopore Technologies.

He made his remarks during a presentation at the Cowen Health Care Conference, which was webcast.

Illumina is now taking orders for the HiSeq 2500. Until the instrument is available, customers can order the HiSeq 2000 with a $50,000 upgrade to HiSeq 2500 included.

Once the HiSeq 2000 and HiSeq 2500 are both on the market, their price difference will be $100,000, Flatley noted, creating an incentive for customers to order a HiSeq 2000 plus upgrade now.

Customers have also begun to order $50,000 upgrades for existing HiSeq 2000s. Most of those orders have come from users with between one and five HiSeqs, he said, and not from genome centers, which are still evaluating how many of their instruments they want to upgrade. Illumina anticipates that between 20 percent and 30 percent of HiSeq 2000 customers will upgrade to the 2500 within the next year.

Flatley said that the data quality in the short-run mode of the 2500, which produces about 120 gigabases of data in a day, is "as good or better" than in the long-run mode, which generates up to 600 gigabases in 10 days, because the sequencing reagents spend less time on the instrument and therefore degrade to a lesser extent.

Reagent kits for the fast-run mode will be more expensive than for the slow mode, but they will cost "nowhere near" twice as much, he said.

He pointed out that the short-run mode can be used not only for whole-genome sequencing but also for exome sequencing or RNA-seq. For example, 20 exomes could be analyzed in a day, or 30 RNA-seq samples in about five hours.

As a result, the short-run HiSeq 2500 will begin to compete with expression microarrays, he predicted, moving RNA expression analysis "increasingly towards sequencing."

Illumina is also working on streamlining sample prep and data analysis for the HiSeq 2500, he said, reducing the total time for a sequencing experiment to about three days.

The company plans to launch PCR-free sample prep kits before the end of the year that will result in lower bias, as well as kits for FFPE samples. Sample prep and sequencing will take about 27 hours following the planned improvements.

It also plans to release a new version of its analysis software, which will result in better accuracy and variant calling, reduce the compute time about six-fold, and require less computing power, so a single server will be sufficient. Data analysis will add another 27 hours to the entire sequencing process.

Reducing the overall assay time to 54 hours "is going to be increasingly important in emerging clinical-type applications," Flatley said.

Starting in the second quarter, Illumina plans to increase reagent prices for the HiSeq 2000 by 8 percent. However, customers can get a 4 percent credit back if they order their reagents online. Also, customers with standing orders will not be affected by the price increase in 2012.


The planned mid-year MiSeq upgrade, which will increase the instrument's output from between 1 gigabase and 1.5 gigabases to between 4 gigabases and 7 gigabases per run, will be a "minor field upgrade" and free to existing customers, Flatley said. It will make the instrument particularly suitable for "high-def cancer panels," he added.

As previously reported, Illumina also plans to launch lower-output kits for MiSeq by mid-year, which Flatley said will result in an output of "a few hundred" megabases of sequence per run.

This week, the company launched the first fixed-content sequencing panel for MiSeq, called the TruSeq Amplicon Cancer Panel. The kit, which takes DNA from FFPE samples, allows researchers to sequence 48 cancer genes in less than two days. It includes "all of the reimbursed genes," Flatley said, as well as others, and allows for single-tube amplification. Users can multiplex up to 96 samples per run, and the kit has "excellent performance" in terms of specificity and uniformity, he said.

Roche's Bid; Oxford Nanopore

Commenting on Roche's takeover bid for Illumina, Flatley reiterated that the company's current $44.50 per share offer is "grossly inadequate," "dramatically undervalues" Illumina, and is "blatantly opportunistic."

Illumina has not yet set the date for its annual shareholder meeting, during which Roche plans to take over the majority of Illumina's board of directors, but Flatley said it has to take place by June 10.

Illumina is currently not negotiating directly with Roche, he said, and its board has not set a purchase price offer "that would cause us to engage, but we'll continue to evaluate any offer that comes forward."

Commenting on Illumina's relationship with Oxford Nanopore Technologies, Flatley said that it owns 15 percent of ONT and has exclusive distribution rights to the firm's exonuclease sequencing technology, "if and when they bring an exo product to market."

With regard to the strand sequencing technology that Oxford plans to commercialize this year, "we have some rights," Flatley said, "but if they decide to distribute it on their own, we do not have rights."

For now, Illumina appears to be unconcerned about competition from Oxford Nanopore. While nanopore sequencing has some advantageous characteristics, "we think it's a ways away from being commercially viable or being competitive directly with Illumina's products," he said.

"Obviously, we're going to continue to monitor what they do and how they're competing with our technology, and we plan to stay ahead."

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

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