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Illumina Launches HiSeq with Half the Output, Single Flow Cell

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This article, originally published Oct. 26, has been updated with information from Illumina's third-quarter earnings call.

By Julia Karow

Illumina released the HiSeq 1000 last week, a sequencer with half the output of the HiSeq 2000.

Priced at approximately $550,000 to $600,000, the new instrument will have an expected throughput of more than 100 gigabases per run at launch, using 100-base paired-end reads. It will also be able to generate 500 million clusters, or a billion paired-end reads per run. Run times range from about two days for 35-base applications to 8 days for 100-base paired-end reads.

By comparison, the HiSeq 2000 has a list price of $690,000, an output of up to 200 gigabases per run using 100-base paired reads, and generates up to a billion clusters, or up to two billion paired-end reads per run. Run times are the same as for the 1000 model.

The GAIIx, priced at around $300,000 including the paired end module following a price cut last week, generates up to 95 gigabases per run at 150-base paired reads and up to 320 million clusters or 640 million paired-end reads. Run times range from 2 to 14 days.

The HiSeq 1000 will have the same architecture, workflow, dual-surface imaging technology, cost per gigabase, and data rate as the HiSeq 2000 but will feature one flow cell instead of two. Customers will be able to upgrade from HiSeq 1000 to HiSeq 2000 at an undisclosed cost in order to double the instrument's output.

Illumina expects to start shipping the new instrument in February or March of 2011 and is currently taking orders for the system.

With HiSeq 1000, Illumina is adding another flavor to its mix of sequencers, which currently includes the Genome Analyzer IIx, Genome Analyzer IIe, HiSeq 2000, and HiScanSQ. The company said last week that it plans to discontinue the GAIIe, which it launched earlier this year. Instead, it is offering the GAIIx at a lower price, as well as second-hand refurbished GAIIx instruments.

Demand for the HiSeq 2000, which Illumina also launched earlier this year, has been greater than expected (see other article, this issue), and the company apparently wants to build on this with the HiSeq 1000.

"We are thrilled with the market’s enthusiasm for our HiSeq 2000 platform, which is enabling sequencing studies on an unprecedented scale," said Jay Flatley, president and CEO of Illumina, in a statement. "With HiSeq 1000, we’re offering researchers an additional entry point into the most powerful and cost-effective sequencing technology available."

In a conference call to discuss the company's third-quarter earnings last week, Flatley said that what prompted the introduction of the HiSeq 1000 was the "very rapid conversion away from the Genome Analyzer to the HiSeq platform."

Following the launch of the HiSeq 2000, orders for the Genome Analyzer decreased faster than Illumina had anticipated, he said, so it decided to launch a second instrument that uses the more advanced HiSeq technology and make the GA a lower-cost version for "price-sensitive customers."

He said upgrading from HiSeq 1000 to 2000 only requires a "minor" hardware change that can be performed at the customer's site.

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