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Affymetrix Tiling Arrays in Early Access; Major Portfolio Expansion Planned in 06

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Affymetrix has made available its new tiling arrays to early-access customers and plans to commercially launch the products — which survey the coding and non-coding regions of the genome — during the first quarter of 2006, according to Affy officials.

Alicia Burt, Affy's senior product manager, wrote via e-mail to BioArray News this week that Affymetrix is gearing up for two "major" launches of tiling array products, which will include a total of 11 distinct products.

"The first launch within the next two months will focus on [Affymetrix's] Human Tiling Array 1.0R Array Set, Mouse Tiling 1.1 Array Set, and supporting reagent kits," Burt wrote in her e-mail. "These 14-array sets feature perfect match/mismatch probe pairs at 35-base-pair resolution across the non-repetitive human and mouse genomes."

A second, much larger tiling array launch is scheduled for the first quarter of 2006. According to Burt, the launch will include products for chromatin immunoprecipitation, including Affy's Human Tiling 2.0R Array Set, Human Promoter 1.0R Array, Mouse Tiling 2.0R Array Set, and Mouse Promoter 1.0R Array. Affymetrix will also launch five products for transcript mapping, Burt said, including the ENCODE01 1.0R Array, a Human Chromosome 21/22 1.0 Array Set, and tiling arrays for Arabidopsis, Schizosaccharomyces pombe, and Saccharomyces cerevisiae.

The product launches will cap a period of major portfolio expansion for Affy. In October, the company released its Human Exon 1.0 ST Array, its GeneChip Mapping 500K Set arrays for SNP genotyping, and the GeneChip Array Station for high-throughput experiments (see BAN 10/5/2005).


"The reality is that this is really the last remaining frontier in genetic research, an area that has not been explored."

According to Burt, the Human Tiling 2.0R Array Set has been available to several early-access customers since October. Burt wrote that the seven-chip set is "targeted at academic researchers doing chromatin immunoprecipitation experiments to study genome-wide protein-DNA interactions."

"The [Human Tiling 2.0R Array Set] is a seven array set designed to interrogate the non-repetitive content in the human genome," Burt wrote. The tiling arrays comprise 25-mer probes and each array in the set has 6.5 million perfect match probes. There are approximately 45.5 million probes on the set," Burt wrote.

BioArray News spoke with Burt about the ENCODE01 array, one of Affy's first tiling arrays in October 2004 (see BAN 10/27/2004).

In her e-mail this week, Burt also said that Affymetrix Laboratories is currently experimenting with a prototype set of ultra-high-resolution tiling arrays.

"This set of 91 arrays includes approximately 295 million probe pairs to interrogate the non-repetitive regions of the human genome," she wrote. "The probes on this array set are spaced at five-base-pair resolution, creating an overlap of approximately 20 base pairs between adjacent probes."

A spokesperson for Affymetrix declined to provide prices for any of the 11 tiling array products set to launch in the first quarter of 2006. "We don't normally disclose pricing because it depends on a number of factors but you can say that Affymetrix offers special pricing for the whole-genome sets," the spokesperson said.

Tiling Arrays on Wall Street

Doug Farrell, Affy's head of investor relations, told investors during the Wall Street Analyst Forum in New York two weeks ago that the Human Tiling 2.0R Array Set became available to early access customers this fall.

Farrell also gave an overview of the motivation behind the new product portfolio.

The "seven-chip set [is] the first tool to enable people to look at the 98 percent of the genome that we know very little about at this point," Farrell said during the forum. He described how after tiling probes across the human genome, Affy found that more than a third of the genome was showing some signs of activity.

"What you would have expected to see if conventional wisdom was right is that 2 percent of those probes would have registered activity, since 2 percent are recognized as coding for proteins," he said. "But what we actually found was that some 35 percent of the genome was being transcribed."

According to Farrell, "there is a huge amount of activity going on outside the coding region and people don't know what it exactly does at this point in time."

"The reality is that this is really the last remaining frontier in genetic research, an area that has not been explored," he said.

— Justin Petrone ([email protected])

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