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Illumina Passes Terabase Milestone for HiSeq; Customers to Reach 600 Gb per Run this Spring


By Julia Karow

This article was originally published January 12.

Illumina has passed the terabase mark for data generated in a single run on the HiSeq 2000 and plans to enable customers to obtain 600 gigabases per run on the platform this spring, according to a company executive.

During a presentation at the JP Morgan Healthcare Conference in San Francisco last week, Illumina CEO Jay Flatley showed an example in which company researchers generated 1.13 terabases of data in a 14-day run on the HiSeq 2000 with 2 x 150 base reads, about 80 gigabases per day.

Customers will be able to benefit from the improvement this year through a series of software and reagent upgrades, he said. This spring, Illumina plans to release an upgrade that will enable all current users to generate about 600 gigabases per run on the HiSeq 2000, or about half that on the HiSeq 1000. The new kit, which is already used by a number of customers, will be for 2 x 100 base reads instead of 2 x 150 base reads, which is why customers will not initially achieve 1 terabase runs.

With the new kit, customers will be able to sequence five human genomes per run, at about 40x coverage, with a reagent list price "materially below" $5,000 per genome, Flatley said.

The new kit includes "new enzymology" and will also improve the data accuracy, he said. "We have been really focusing on how to eliminate bias in sequencing and made great progress here."

Even at "only" 600 gigabases per HiSeq run, Illumina is leaving behind its closest competitor, Life Technologies' 5500xl SOLiD. When Life Tech introduced the platform in November, it said it would initially deliver more than 180 gigabases of mappable data per run from 2 x 60 base reads, or about 20 to 30 gigabases per day. During the second half of 2011, the output per run is scheduled to increase to 300 gigabases per run, or 35 to 40 gigabases per day. Sequencing a human genome at high coverage will cost high-throughput customers about $3,000 in reagents (IS 11/2/2011).

Flatley claimed that Illumina believes it has "accomplished the first several 1T runs ever done in the world," but that is probably an overstatement. A Complete Genomics spokesperson told In Sequence last week that its standard runs exceed one terabase of high-quality data, and that the company "crossed that milestone when it introduced its commercial sequencing instrument in its sequencing center in May 2010."

In any case, the HiSeq 2000 is likely to remain Illumina's flagship product.

"HiSeq 2000 has been far and away the company's most successful product launch in history," Flatley said. "It really was the growth engine for us in 2010."

He said the company has increased production of the instrument by about 10-fold, compared to the first quarter of 2010, and is now able to fill orders from customers that have been waiting for their instruments. "We now have sufficient manufacturing capacity in place for this system to optimize the backlog over the next couple of quarters," Flatley said. During the fourth quarter, the company shipped about 24 percent more HiSeq instruments than in the previous quarter, he added.

Based on numbers from the fourth quarter, Illumina now expects HiSeq 2000 customers to buy about $350,000 worth of reagents per instrument. Previously, it had estimated $150,000 to $200,000 in annual consumables sales per system (IS 8/3/2010).

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

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