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Illumina Saw 'Record' Array Orders in Q4, CEO Says at JP Morgan Conference


By Justin Petrone

Despite continued concern over federal funding, as well as pressure from next-generation sequencing, Illumina CEO Jay Flatley said this week that the firm had "record overall microarray orders" during the fourth quarter of 2011.

In particular, he said that Illumina has seen strong demand for its 250,000-marker, 12-sample Infinium HumanExome BeadChip, which launched in November. The chip is the "single most successful array we have ever launched," said Flatley, adding that the firm has to date received orders for enough chips to process a million samples.

Flatley commented on the firm's array business at the JP Morgan Healthcare Conference, held in San Francisco. His presentation was webcast.

The Infinium HumanExome BeadChip is one of three exome-focused arrays that Illumina has introduced. In November, it also launched its 950,000-marker, nine-sample OmniExpressExome BeadChip; and it expects to launch its 5-million-marker, four-sample HumanOmni5Exome BeadChip later this year (BAN 10/18/2011).

A recent survey conducted by investment firm William Blair similarly found demand for exome arrays.

While there "continues to be debate as to the future of genome‐wide association studies … our follow‐up discussions overwhelmingly pointed to excitement for newly launched exome arrays in the research community," analysts Amanda Murphy and Silvia Chao wrote in the report (BAN 12/13/2011).

"While clearly providing different data resolution and answering a different experimental question, the same 1,000-sample experiment using exome sequencing would cost about $1 million, but would cost $80,000 to screen those same samples using Illumina's exome chip," they noted.

Illumina said that orders for the chips were also high during the third quarter, even though the firm's overall array business declined nearly 10 percent when compared with the same period of 2010 (BAN 10/25/2011).

At JP Morgan, Flatley called the success of the firm's exome arrays a "great example of how sequencing and arrays work hand in hand."

Still, he acknowledged that Illumina is facing challenges to its array business, largely tied to the National Institutes of Health budget. Flatley has said previously that about a third of the company's revenues come from researchers whose projects are funded by the NIH.

Flatley said that the reason that the company missed its forecast in the second half of 2011 was this uncertainty around current and future NIH budgets.

"NIH had the lowest grant success rate in the history of the company in 2011 with 15.2 percent of grant applications successfully awarded," said Flatley. This is an issue that will continue to challenge Illumina, he added. Given the failure of the Congressional Joint Select Committee on Deficit Reduction to agree on cuts in line with the US Budget Control Act of 2011, Congress may now agree on a negotiated 8 percent cut in the budget, or, as mandated by law, an across-the-board 8 percent cut. Flatley said that Illumina is most concerned about the latter option.

"A lot of people are concerned with what is going to happen in 2013 with sequestration and the chance of an 8 percent budget cut in the NIH budget," said Flatley. "Our belief is that because of bipartisan support for NIH, the likely outcome is better than eight percent, but it is unlikely that we are going to know that until the time of the elections" in November, he said.

Johns Hopkins Study

Illumina's array business recently got a boost with the announcement of a Johns Hopkins University study on asthma that will sequence 1,000 people to identify the genetic causes of asthma in Americans of African descent.

Illumina will be providing the sequencing for the project, but Flatley said at JP Morgan that the firm also expects the researchers to order about 10,000 of the firm's iSelect custom arrays to follow up on their findings. The National Heart, Lung, and Blood Institute awarded JHU $9.5 million to carry out the four-year study. Principal investigator Kathleen Barnes said in a statement that the researchers have not been able to carry out such a study in the past as the content on most commercially available arrays is drawn from people of European descent.

"One of our biggest barriers as researchers trying to find the underlying genetic roots of disease in minority groups has been the persistent lack of microarray testing tools relevant to each racial profile, especially African-Americans," Barnes, director of JHU's Genetics Research Facility, said in a statement.

Rick Kittles similarly described a dearth of options for researchers who wish to use microarrays to study minority populations. Kittles, who is associate professor of medicine, epidemiology, and biostatistics at the University of Illinois at Chicago, discussed his adoption of Affymetrix's African-American population-focused array for association studies with BioArray News in November (BAN 11/29/2011).

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com