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Affy to Launch Exon Arrays in Second Half of Year to Stake Claim in Emerging Market

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SAN FRANCISCO — Affymetrix plans to launch a host of new expression arrays in either the third or fourth quarter of this year, an official at the company told BioArray News at the Molecular Medicine Tri-Conference here last week.

Affy currently offers an array for Arabidopsis, a model plant organism, that can generate expression profiles for mRNA transcripts, but the new product line will represent Affy's first foray into the emerging exon array market.

John Blume, the company's vice president of expression research, told conference attendees and later confirmed with BioArray News that Affymetrix intends to introduce exon arrays and other related products before the end of this year.

They will be available "probably sometime in 2005," Blume said.

Exon arrays enable scientists to generate expression profiles for splice variants in a genome. Alternatively spliced mRNA is of interest to researchers and drug makers, and in some cases human diseases have been associated with splice variants.

Blume said that by analyzing the expression of the complete genome with exon arrays, researchers would have a better chance of developing drug targets to be used in diagnosing or crafting therapies for disease

"It's the transcriptome expression, not the gene expression," Blume said during his presentation.

According to Blume, Affymetrix has created exon arrays for the human, mouse, and rat genomes, all which will be made available to customers before the end of the year. Arrays for these organisms will come out at the same time, Blume added.

Blume said that software was being developed with early access customers for exon array use, and that in the future Affy plans to offer splice variant analysis as well as whole transcriptome analysis as part of the offering.

In a conference call with investors last week, Affymetrix CEO Stephen Fodor said the human exon array will contain around 6.5 million probes that will analyze splice variants of approximately 1 million exons. "We believe that this product will fundamentally redefine our understanding of how tens of thousands of genetic elements can code for hundreds of thousands of proteins," said Fodor.

"These new products leverage a 5-micron version of our technology," Fodor said. "To put this in perspective, the current human genome, U133 Expression Array, contains over 1.4 million probes and is an 11 micron product."

Affymetrix denied requests for additional information.

Entering A Competitive Market

Affymetrix is not the first company to set its sights on the market for exon arrays. ExonHit Therapeutics, for example, launched its SpliceArray service earlier this year. An official from the French firm told BioArray News last week that the company had seen increasing demand for the service, which provides customers with analyses of splice variants based on the Agilent microarray platform.

Richard Einstein, ExonHit's vice president of research, said that the service, which is performed out of the company's Gaithersburg, Md., office, has been "doing very well."

ExonHit is a private drug discovery company, and BioArray News was unable to verify any kind of impact the SpliceArray service was having on its revenues.

Unlike Affymetrix, which plans to make the whole human genome available, ExonHit focuses on seven gene families and provides custom arrays based on these genes, Einstein said.

The company, founded in 1997, has so far introduced services for ion channel, G-protein coupled receptor, and nuclear receptor and co-regulator gene families. Einstein told BioArray News that the service would be extended to cover the apoptosis and cytokine gene families in May and June, respectively. Proteases and kinases would be rolled out in July and August, Einstein said.

Einstein said that ExonHit customers, which he declined to name, included academics, a non-profit, and a large pharmaceutical company. Still, Einstein said the company has no plans to commercialize the actual chips.

Another company that also claims to provide technology for the detection of splice variants is Applied Biosystems, which offers PCR-based splice variant TaqMan Gene Expression Assays. While ABI's technology is not array-based, it would also compete with Affy's new exon array product line.

— JP

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