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Affy Inks Deal with Beckman to Provide Custom Target Prep Tools for Its Arrays


By Justin Petrone

Affymetrix and Beckman Coulter have partnered to create an automated tool and protocol for genomic research that will pair Beckman's liquid-handling instrumentation with Affy's menu of array-based assays, the firms said last week.

Under the terms of the deal, Affy and Beckman will co-develop Affy-specific configurations for Beckman's Biomek FX Dual Arm Multichannel-Span 8 Liquid Handler. The companies claim that the combination of the Biomek with Affy's existing array cartridge platform as well its newer GeneTitan instrument will provide a standardized system containing all of the components necessary to run Affy genotyping and gene-expression assays.

According to Affy, the deal with Beckman will help fill a gap for customers performing higher-throughput studies by offering them access to liquid-handing tools designed to work with its next-generation GeneTitan system and older products.

It also comes at a time when other array vendors are looking to provide standardized target-preparation options for their customers as the size of projects increases. Agilent Technologies, for example, said recently that it plans to launch an automated liquid-handling workflow in coming months (see BAN 8/11/2009).

Launched last year, the GeneTitan enables users to run expression-profiling assays in array plates designed to process 16, 24, or 96 samples. Now, the Santa Clara, Calif.-based chip maker plans to launch next-generation genotyping assays for use on the system this fall. Unlike the gene-expression assays which contained legacy content, Affy will enable users to survey newly generated catalog and customizable content using its genotyping assays as part of what both Affy and its rivals predict will be a second round of large genome-wide association studies (see BAN 4/28/2009).

Being able to streamline the front end of its assay workflow is therefore "very important" for Affy, according to President and CEO Kevin King. He said in a statement last week that the Beckman deal will not only provide a "much needed" target prep solution for Affy's installed base of GeneChip cartridge users, but aligns with the firm's goals to reengineer its platform.

"With automated target prep robotics in front of our GeneTitan System, our customers will benefit from walk-away automation from prepared samples all the way through array processing and data generation," King said.

Jay Kaufman, vice president of product marketing at Affy, told BioArray News this week that Affy's GeneTitan customers have been relying on manual target preparation methods, "third-party robotics with custom assay methods that they programmed themselves," and Affy's GeneChip Array Station liquid handler, which the firm launched in 2005 (see BAN 9/21/2005).

Kaufman said that users can now use a custom version of Beckman's Biomek FXp for their target prep work. "We worked with Beckman to create a specific version of this platform that will provide the layout and accessories needed to run any Affymetrix assays," Kaufman said.

Affy is collaborating with Beckman on developing methods that are "specific to its version of the Biomek FXp and specific to our assays," he added without elaborating.

Wing Pang, corporate vice president of discovery products at Beckman, said in a statement that Affy customers will "soon see the fruits of this collaboration with the availability of automated target prep solutions for microarrays that address a wide range of sophisticated genetic analysis assays.”

Beckman already sells an application called ArrayPlex that enables automatic target RNA sample processing for use with Affy cartridge arrays using Affy reagents. Affy gave ArrayPlex "premier application status" in 2007. According to Beckman, the firms have worked together on various projects since 2002.

Under the terms of their latest agreement, Kaufman said that Affy and Beckman will "work in a collaborative manner" to sell the Biomek FXp together with Affy systems by "co-developing and co-hosting marketing collateral with links between our product web pages." He also said that the two firms will "collaborate on advertising, tradeshows, and other customer-focused marketing activities."

Finally, Affy and Beckman will "make this offering seamless to the customer in terms of quoting, ordering, and supporting the Biomek FXp instrument and the target prep methods," Kaufman said.

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While the Biomek FXp is being touted as a fix for higher-throughput projects, Kaufman said that customers that purchase the firm's GeneTitan system have a variety of options to choose from when it comes to target preparation for lower-throughput studies.

"The GeneTitan System is clearly ideal for the high-throughput and high-volume customer, but it also provides enormous benefits and value to the medium-volume lab," Kaufman said. "When running lower-volume array plates, users are able to choose between manual and automated target prep methods," he said.

According to Kaufman, a "substantial portion" of Affy's GeneTitan system installations have been at academic institutions where labor is "well-trained and it’s relatively inexpensive to run target prep manually," rather than using an instrument like the BioMek. Because of the GeneTitan's automated assay processing capabilities, smaller and medium-sized labs have been able to "move their resources from array processing and put them on manual target prep," he added.

Affy has not disclosed how many GeneTitan systems it has placed to date. During the firm's second quarter earnings call, King said that 70 percent of those systems placed since last year's launch have been via a reagent rental program (see BAN 7/28/2009).

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