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Illumina Says It 'Dramatically Underestimated' Exome Chip Demand, Claims 80 Percent Share of Array Market

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This article has been updated to include comments from Affymetrix.

The strong demand Illumina has seen for its family of exome arrays apparently took the company by surprise, an Illumina executive said last week.

Moreover, the firm now believes that the majority of projects run on its BeadChips will move to focused arrays, such as its exome chips, and away from the genome-wide screening tools that have been popular in the past, said Christian Henry, general manager of Illumina's genomic solutions business.

Henry spoke at the RW Baird Growth Stock Conference, which was held in Chicago. The event was also webcast. During his talk, he also claimed that Illumina has a majority share of the microarray market.

"We are the recognized leader in the microarray field with an 80 percent or so market share primarily in DNA genotyping," Henry told investors.

An Affymetrix spokesperson declined to comment specifically on Henry's claim. She said the firm has a "market leading share" for gene expression microarrays and the "second largest share" in both genotyping and the overall microarray market.

"We are growing rapidly in cytogenetics and believe that we hold the number two position in cytogenetics," she added. Agilent Technologies is widely considered to be the leading provider of chromsomal microarrays.

Illumina introduced its exome family of arrays last year. It now offers four chips containing exonic content: the HumanExome BeadChip, the HumanOmniExpressExome BeadChip, the HumanOmni2.5Exome BeadChip, and the HumanOmni5Exome BeadChip (BAN 10/18/2011).

These exome arrays have reinvigorated Illumina's array business. CEO Jay Flatley said during the firm's first quarter earnings call last month that Illumina has shipped enough arrays to survey 1.3 million samples since the exome arrays were launched, the "highest number" in its 13-year history. As each of Illumina's BeadChips contains multiple arrays, Flatley broke out sales by the number of samples that could be run on all the chips Illumina has shipped to date.

The market's reaction to the new chips exceeded the company's expectations.

"This was a product that we originally thought that if we could get 100,000 samples of demand, it would be a productive product for us," said Henry. "We dramatically underestimated the power of the market."

Henry attributed the demand to a need for statistical power to validate discoveries, many of them rare variants that might be associated with a particular disease, in large sample populations.

Using Illumina's exome arrays, "customers can look at a massive scale in terms of number of samples," Henry said. "It is all about the power of statistics in these studies," he added. "The market, needs products that are inexpensive so that it can get that statistical power."

Affy also recently launched an exome array (BAN 2/28/2012).

The firm's spokesperson said that Affy has seen "increasing demand" for the chip, and that its customers have been "particularly impressed" with the array's "significant indel content."

According to Henry, Illumina believes that focused arrays, such as its exome chips, will become its most popular array products in the future, displacing the family of whole-genome Omni arrays it designed for genome-wide association studies, including its flagship HumanOmni5-Quad BeadChip, which it launched last year (BAN 7/26/2011).

"The Omni family has been used in genome-wide association studies and has really driven growth in the array market over the past several years," said Henry. "Now we see these focused products are overtaking them as we determine what we want to look at."

The company had anticipated a second round of association studies that would rely on the rare variation content, much of it selected from the 1000 Genomes Project, made available on its menu of Omni chips. Flatley said during the Q1 call, though, that researchers will most likely transition in coming years to low-pass sequencing to identify causal variants, rather than using whole-genome Omni genotyping chips (BAN 4/24/2012).

Beyond exome arrays, Henry forecast growth in other markets, such as agricultural biotechnology. Specifically, he said that Illumina is seeing demand for arrays covering "pigs and sheep and all of the fruits and vegetables you can think of." The company has seen some initial success in the market, especially with uptake of its bovine-focused genotyping products, as cattle are "high-value" livestock, and the benefit of making better informed breeding decisions offsets the cost of genotyping.

"There is a huge push to understand the genetics behind these [livestock and] crops so that you can get higher yield, you can grow these crops in places where they couldn't grow before, and ultimately you can increase the food supply and production," Henry said of the market.

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