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Affy to Debut Benchtop System Next Year to Reach Lower-Throughput Labs


Affymetrix next year will introduce a benchtop instrument that will target "lower-throughput labs with limited capital budgets, users without access to core facilities, price-sensitive markets, and RT-PCR users looking to access the whole genome," according to a company official.

The system, called GeneAtlas, will begin beta trials in the third quarter, and Affy expects to launch it in Q1 2010, according to Jay Kaufman, vice president of product marketing.

GeneAtlas will have a "very attractive price point" and will "enable a lot of people who previously were not able to access a microarray scanner and microarray technology to have very affordable and easy access to a high-quality platform with all the applications that the GCS and GeneTitan can deliver to the research community," he said.

Kaufman, who spoke at Affy's Investor Day Conference in New York last week, did not elaborate on the price. An Affymetrix spokesperson declined this week to discuss how much GeneAtlas may cost, but reiterated that it will be priced at a "level optimized for low- to medium-throughput labs."

Price and throughput have been concerns of Affy users regarding its new higher-throughput GeneTitan platform, launched last year. Several Affy users told BioArray News last year that they were hesitant to adopt such a system because of capital constraints, among other issues (see BAN 10/10/2008).

According to Kaufman, GeneAtlas will join Affy's older GeneChip Scanner 3000 and the automated, high-throughput GeneTitan (see BAN 10/3/2008). In some aspects, GeneAtlas is the lower-throughput offspring of GeneTitan. GeneTitan offers fully automated processing of 96-well- and 24-well-format strips of arrays, a setup described by the firm as "peg arrays" or "array plates" that allow users to process, for example, up to 96 samples at a time.

According to Kaufman, Affy also plans to introduce a 16-well format for GeneTitan later this quarter to "add a degree of flexibility, which is attractive for core labs or service labs" — the main customer target group for the GeneTitan platform.

GeneAtlas, meantime, will enable users to process strips of four arrays using the same assay protocol and automation as GeneTitan. In this way, "lower- to medium-throughput users can get benefit of GeneTitan in terms of automation," Kaufman said.

The spokesperson said Affy's customers and investors "have been made aware that they should expect an ongoing pipeline of innovations, the priority for many being determined by customer demand." Those demands include "ease of use, flexibility, automation, and broader ranges of cost and price points."

Affy also plans to integrate the liquid array technology it acquired with its $25 million purchase of True Materials last year into GeneTitan (see BAN 8/12/2008).

"Liquid arrays" are digitally encoded microparticle-based assays that Affy expects will enable it to enter low- to mid-multiplex markets. The platform consists of a silicon barcode embedded in glass, 15 x 2 x 2 nanometers in size, which is assayed in solution and read by fluorescence 2D imaging.

By making its liquid arrays assays available on GeneTitan, Kaufman said there will be a "seamless transition on one platform from discovery through validation and eventually on to routine testing."

Affy's spokesperson this week declined to comment on whether Affy plans to eventually submit either the GeneTitan or GeneAtlas to the US Food and Drug Administration for 510(k) clearance.

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'Project Falcon'

Affy is also preparing to launch new genotyping applications for use with GeneTitan and GeneAtlas later this year. Affy has said that the genotyping applications will include new content, including new copy-number variation, SNP-allele frequencies, and the on-demand sub-setting of that information (see BAN 1/20/2009).

Keith Jones, Affy's vice president of product development, said that Affy has developed an internal database of validated SNP content that it plans to begin sharing with customers by the end of the year. Using this database, Jones said, customers will be able to order custom strips of SNPs based on their research needs.

According to Jones, who also spoke in New York, Affy has so far taken 8 million SNPs from the dbSNP database and, using its automated genotyping assay, generated genotypes for over 1,300 individuals. This effort, called "Project Falcon" within the company, resulted in a database of validated markers and enabled Affy to assess genetic relationships among the SNPs.

Jones stressed that customers will benefit more from using its validated SNP content than drawing content directly from public databases and projects. For example, Jones said when Affy conducted its screen it found that up to a fifth of the content in dbSNP was nonpolymorphic.

"The 1000 Genomes Project just a few weeks ago released 21 million markers, of which 14 million are unique," said Jones. "We have the ability to validate those SNPs, understand their population frequency, understand their relationship to each other, and then use that information in a very intelligent way, to maximize the genetic content that we can put on our arrays."

Jones said that Affy will use its database to help it decide which catalog products will be launched in the fourth quarter. Additionally, by the end of the year, a "select number of customers will be able to access the database and come up with customer-defined list of SNPs that they would be interested in," he said.

'Fast-Growing' DNA

Affy's effort to reach genotyping customers is directed at two submarkets, according to Jones. He estimated the genome-wide association studies market is currently worth between $200 million and $220 million and is growing at a rate of 5 to 10 percent per year. Targeted genotyping, meantime, is estimated to be worth $175 million and is growing at a rate of 25 percent per year, he said.

According to Affy President and CEO Kevin King, it is this genotyping market where the firm expects to do most of its business in the future. King, who also spoke in New York, told investors that, whereas two-thirds of the company's revenue came from the gene-expression market in 2006, by 2012 the company expects that genotyping will account for more than half of its business.

Between 2006 and 2009, Affy's genotyping business doubled from less than 15 percent of total revenues to about 29 percent, King noted. "Looking out three years from now, we predict that DNA will be the fastest growing portion of our business," he said.

Additionally, Affy predicts that by 2012 80 percent of its business will be in consumables, he said. For example, in 2006 roughly 40 percent of Affy's receipts were from instrument systems, services, and licenses. Over the past three years, Affy has halved that percentage, and it predicts that by 2012 sales related to products other than consumables will account for only 15 percent of its total revenues.

King added that Affy expects to "capture more revenue per sample" as it now provides most of the reagents for its assays itself, and added that sales attributable to its liquid array and Panomics platforms will supplement Affy's growth in the mid- to low-multiplex genotyping arena.

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