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Illumina Says New HumanOmni Chip 'Important Flagship' for Next Round of GWAS


This article has been corrected from a previous version that inaccurately described the content on Illumina's HumanOmni1-Quad and Human660W-Quad BeadChips.

The 4-million feature HumanOmni1-Quad BeadChip that Illumina launched this week is the first of a new family of arrays that include rare variant content generated by the 1000 Genomes Project and other sources.

The array is also intended to replace the firm's existing 1.2-million feature Human1M-Duo BeadChip as its main offering for researchers conducting genome-wide association studies, CEO Jay Flatley said this week.

The HumanOmni1-Quad includes new SNP content from the 1000 Genomes Project and more than 11,000 copy number variants from Wellcome Trust Sanger Institute, the Hospital for Sick Children in Toronto, Harvard Medical School/Brigham and Women's Hospital, and Decode Genetics. Customers can survey four samples on one array using the firm's iScan or BeadArray Reader systems, Illumina said.

According to Flatley, the Omni1-Quad is a "very important flagship product" for the company, which has recently predicted that growth in the GWAS market will slow as customers wait for more rare variant content to become available.

"We think this chip has the best coverage of any chip in the market, and is the beginning of a family of arrays that we will put out there that will contain rare variant content," he said.

Flatley spoke at the Deutsche Bank Healthcare Conference held in Boston. His presentation was webcast.

The Omni1-Quad is being presented as a next-generation array for GWA studies. Flatley called it a "replacement chip" for the 1.2-million-marker Infinium HD Human 1M-Duo BeadChip the San Diego firm launched in the second quarter of 2008 (see BAN 8/12/2008).

The new chip "contains all new content fully optimized on everything we have learned over the past few years," Flatley said. "We have included in excess of 100,000 SNPs and markers from the 1000 Genomes program and we have increased the density in and around gene-centric regions, including all known SNPs known to have disease associations, over a thousand of which have been proven and published."

He added that the product is "very important" because it "kicks off the round of rich-genome-wide association studies" the firm has been forecasting. For example, last month Flatley said during Illumina's first-quarter earnings call that new content from sequencing projects such as the 1000 Genomes Project would "drive a whole new round of rich genome-wide association studies" based on rare variant content (see BAN 4/28/2009).

The Omni1-Quad is being positioned in Illumina's product line to be the "most effective way to interrogate the entire genome," said Flatley. Because the chip will allow users to survey four samples, versus two on the 1M-Duo, the company argues that it can reduce cost for its customers.

While Illumina claims that new content and lower cost are benefits of its array, the firm has also not seen adoption of the 1M-Duo to the extent of other chips. For example, Flatley said that only a fifth to a quarter of Illumina's customers doing GWAS use the 1M-Duo. The rest are still using products like the Human 610-Quad, which offers 610,000 SNPs on a four-sample array, and the Human 660W, which includes more than 550,000 tag SNPs from HapMap data plus 100,000 additional markers that specifically target regions of common copy number variation. The 610-Quad and the 660W were Illumina's top-selling chips last quarter, according to the company (see BAN 4/28/2009).

"We think that many of our customers will now upgrade to the Omni1-Quad," Flatley said this week. Illumina also intends over the next few quarters to introduce a supplemental chip that will contain the new content from the Omni1-Quad, enabling customers that have started GWAS with, say, the 610-Quad, to "go back and take advantage of this new content."

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Moderation in Growth?

Last month, Flatley predicted that demand for its genotyping chips in GWA studies will plateau in 2009 as Illumina users finish up projects with the existing generation of chips and wait to adopt future generations of the firm's arrays.

This week, Flatley said that it is unclear whether the Omni1-Quad would stem that slowdown in growth. "I think this chip serves the goal of getting an initial release of rare content into the market," he said. "There will be a full spectrum of customer behavior. For instance, there are customers who will continue using the arrays they were using before and finishing projects, and there are customers that will start with this new product."

There might be some customers who will hold off for the next generation of arrays. "We think it will be a year to a year and a half until all the content is out there and we arrive at a penultimate array that has the content that everyone will want," he said.

Illumina's rivals in the array market are also looking to get fresh content in customers' hands. For example, Agilent Technologies, which until this year had stayed out of the highly competitive GWAS market, has launched two copy number variation-themed arrays so far this year, with another in the pipeline, based on data generated within the framework of 1000 Genomes (see BAN 4/7/2009).

Affymetrix, meantime, expects to launch a new family of genotyping assays for use on its automated GeneTitan platform in the third quarter (see BAN 4/28/2009).

Preparing to Submit

While Illumina looks to stay ahead in the GWAS market, it is also moving forward in building its diagnostics business.

At the Deutsche Bank conference, Flatley said that the company is "working hard" to prepare its digital microbead-based BeadXpress platform with an accompanying assay for ovarian cancer detection, and hopes to have the platform ready for a 510(k) submission to the US Food and Drug Administration this year. "We are in the late stages of getting it ready for submission," he said.

Separately last week, Chief Financial Officer Christian Henry, speaking at Baird's Growth Stock Conference in Chicago, said that the BeadXpress will be "used in areas such as blood typing, pharmacogenetics, and prenatal testing," and that Illumina plans to partner with external parties that will use the 510(k)-cleared BeadXpress as a platform for their test.

According to Henry, Illumina will file for Clinical Laboratory Improvement Act compliance this quarter. He said that, if cleared, Illumina's CLIA-compliant lab in San Diego will offer "proprietary content from in-licensing markers as well as from our discovery program." He said that there are "all types of traditional targets that will round out our menu of services" at the lab. Illumina has said in the past that it will offer services based on arrays and second-generation sequencing in its CLIA lab as well.

Part of Illumina's push into diagnostics is focused on oncology. At the Baird conference, Henry said that the company's goal is to "become a leader in cancer translational diagnostics." Ovarian and gastric cancers are the firm's main focus at the moment. He said that Illumina plans to sequence 50 tumor-normal pairs in order to discover genetic biomarkers that can later be integrated into translational sequencing or array-based diagnostics.