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Illumina Takes on Roche, Agilent with Higher-Density Array, Two New Chips

Illumina rang in 2008 by introducing a new higher-density array product line that includes two BeadChips, each containing approximately 2.3 million features, that is expected to launch during the first half of the year.
Debuting the products at the JP Morgan Healthcare Conference in San Francisco this week, CEO Jay Flatley said the company has designed a new BeadChip format called HD that uses enhanced signal discrimination together with a new SNP-calling algorithm that increases sample throughput and reduces DNA input requirements.
The new launches will coincide with density upgrades from other array companies, such as Roche NimbleGen, which is rolling out its HD2-format, 2.1-million feature arrays, and Agilent Technologies, which is planning to raise its chip density to 1.1-million features per array some time this year.
Flatley told conference attendees that Illumina plans to launch two initial HD products over the next two quarters. The first, the Human 610-Quad BeadChip, is a four-sample array built on Illumina’s 550,000-SNP HumanHap550, launched in April 2006. He said he expects both to increase customer throughput by as much as 70 percent.
Flatley said that the Human 610-Quad also contains 60,000 copy number-variation markers taken from both public databases as well as proprietary content developed through Illumina’s partnership with DeCode Genetics.
“It essentially puts together the content from our HumanHap550 and the CNV panel together on a single chip and puts four of those collections on one chip,” he said of the 610-Quad. He expects the chip to launch before the end of March.
Illumina has also developed the HD Human1M-Duo BeadChip, an upgraded version of its Human 1M BeadChip that launched last July (see BAN 7/3/2007).


According to Flatley, the Human1M-Duo is a two-sample chip containing 2.4 million variations and updated CNV content in addition to other content-related improvements. ”What we’ve done on this chip is added key content in the CNV area, we’ve added all the recent disease SNPs that have been discovered through whole-genome association studies, we’ve reduced gaps and added additional target SNPs,” Flatley said.
Flatley said that both arrays are the “beginnings of a new family of chips that include greater flexibility and higher customer throughput.” Accompanying the HD product line will be new software designed to handle the additional data.
In a separate statement, John Stuelpnagel, Illumina’s outgoing chief operating officer (see People, this issue) said the company has upgraded its manufacturing capabilities to handle the new HD chips. The new decoding instruments that produce them will “effectively double Illumina's array-manufacturing capacity over the next several quarters,” Stuelpnagel said.
This week, Flatley pledged to increase the content of the arrays in the future. “We continue to increase content. We’ve increased the content of these chips 1,500 percent over the last four years,” he said. “These are dramatic improvements that we expect to continue.”
Illumina did not reply to questions by press time.
Density Boom
Illumina’s move to HD is happening at a time when higher-density chips are being introduced across the array space. Agilent Technologies is working on a density upgrade that could see the firm introduce 1.1-million-feature chips. Meantime, NimbleGen has been upgrading its arrays to its 2.1-million-feature HD2 format.
So far, HD2 arrays have been available from NimbleGen for comparative genomic hybridization and chromatin-immunoprecipitation-on-chip analysis of eukaryotic organisms.

“These are dramatic improvements that we expect to continue.”

Luke Dannenburg, NimbleGen’s epigenetics product manager, told BioArray News in November that his firm plans to expand its current DNA methylation product offering on 2.1-million-probe HD2 arrays by April in the form of whole-genome tiling and CpG island/promoter targeted arrays (see BAN 11/20/2007).


NimbleGen Spokesperson Joleen Rau said this week that NimbleGen plans to upgrade its expression array line to HD2 this quarter. Specifically, 12-plex arrays will become available that contain a dozen 135,000-feature arrays per well, Rau told BioArray News.
However, both Illumina and rival Affymetrix have been mum over the past two quarters about additional density upgrades. Over the past three years they have incrementally introduced higher-density products, culminating with the launch of Affy’s 1.8-million-feature SNP 6.0 array in May 2007 and Illumina’s Human 1M BeadChip two months later
Some analysts and investors have been expecting additional density upgrades, but Illumina remained silent until now, while Affymetrix has been pushing scientists to redesign their whole-genome-association studies to enhance what it calls the statistical power of the results, rather than wait for a new chip (see BAN 10/2/2007).


Beyond being a simple upgrade, though, Illumina’s two new HD products reflect the firm’s strategy of proliferating products for its genotyping chips. Calling product proliferation “integral” to the company’s genotyping strategy, Flatley told conference goers that Illumina launched 14 new genotyping products during 2007, a tactic that has paid off, at least recently.
Total revenues for the three months ended Dec. 31, 2007, for example, swelled 82 percent to $97.5 million from $53.5 million during the same period in 2006. $90 million of those receipts came from a product line that includes the company’s entire chip portfolio (see BAN 10/30/2007).

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