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At PAG, Affymetrix Strengthens Ag-bio Play, Expands GeneAtlas Menu with 10 New Model Organism Arrays

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By Justin Petrone

SAN DIEGO — Affymetrix this week debuted a menu of 10 new whole-transcript model organism arrays that it hopes will attract more agricultural biotechnology researchers to its platform and encourage adoption of its benchtop GeneAtlas system, for which the arrays are primarily being manufactured.

The launch comes at a time when Affy is intensifying its activity in the agbio market. The firm also launched two genotyping arrays this week, one for rice studies, the other for bovine research.

The company is now offering Arabidopsis, bovine, canine, equine, Medicago, porcine, rhesus, rice, soybean, and zebrafish array strips for use on the GeneAtlas. Affy launched the automated system, which processes strips of four arrays at a time and has a price list of $73,000, last year (BAN 6/9/2009).

Rebecca Brandes, associate director of gene expression, RNA applications, and market development at the Santa Clara, Calif.-based firm, said that Affy is making the new products available for use on the GeneAtlas because the ag-bio research community is adopting array technology on an individual lab basis more than it has in the past.

"Right now, [array processing] is centralized, but [the communities] are trending toward a more decentralized model, so people want to run their own arrays," Brandes said. She spoke to BioArray News during the Plant and Animal Genome Conference, held here this week.

Investigators with smaller projects are interested in running their own chips as they sometimes find themselves waiting for core labs or service providers to provide their data. At the same time these customers are driven by the need to publish, and getting data quickly.

"The GeneAtlas is the right instrument in terms of cost, ease of use, and being able to move from target preparation to pathway analysis," Brandes added. "The idea is to get these communities running their own arrays."

She noted that since the chips are being manufactured in the company's new peg array strip format, customers could also run the arrays in plates on the higher-throughput GeneTitan for high-volume projects. The automated GeneTitan instrument enables customers to process up to 96 arrays at a time.

To process the new arrays on the GeneAtlas, customers must also buy GeneChip WT Terminal Labeling and Controls and Ambion WT Expression Kits, plus a GeneAtlas Hybridization, Wash, and Stain Kit for WT array strips. Pricing for the entire offering is still "under discussion," but Brandes said the company is aiming to be competitive with core labs and service providers.

Pricing is an issue for customers who have traditionally been relying on centralized labs to run their samples. Some labs are known to charge prices in the $900 to $1,000 per-sample range for human expression arrays.

Considering those figures, GeneAtlas users may be able to run up to three times more samples, based on pricing for other products.

According to Brandes, Affy settled on its current list of 10 model organisms because they "serve some of the larger communities" in the ag-bio space. She added that Affy plans to add between 10 and 15 more model organisms to its menu in the future, but did not elaborate.

The company will continue to offer some of the organisms in a cartridge format based on earlier designs done in collaborations with various consortia. To design the new chips, Affy drew upon those older 3' IVT designs and matched them with a "demand for whole-transcript" analysis.

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The menu of array strips that can be run on GeneAtlas is still limited when compared with those available in the older cartridge format, however, and the company is keen to expand the menu of arrays offered for the platform. The GeneAtlas menu currently includes IVT human, mouse, and rat products; IVT custom designs available via the firm's MyGeneChip program; WT human, mouse, rat, and custom designs; and the model organism arrays added this week.

"This is really expanding the GeneAtlas menu," Brandes said. Citing the company's recently announced distribution deal with Thermo Fisher Scientific (see story, this issue), she noted that "having a bigger menu is going to help the adoption of this instrument."

'Embracing Arrays'

Affy's push into the ag-bio space is being met with challenges by rivals. All major array vendors, including Illumina, Agilent Technologies, and Roche NimbleGen, are holding workshops at PAG this week. But while Agilent and NimbleGen are focusing on their target-enrichment offerings, and Illumina is emphasizing its genotyping arrays, Affy has, in the case of the new model organism chips, made an appeal to the expression market, where next-generation sequencing has become an approach of choice.

According to Brandes, while some communities have moved their expression analysis projects to NGS, others "don't have the funding or expertise to sequence or to deal with that data." She said these communities are "barely getting their feet wet in some cases with arrays" and that the standard technology for "a lot" of them is still quantitative real-time PCR.

"Moving to whole-genome [studies] is already a challenge, let alone being able to sequence," Brandes said. She believes that the company's new offering is a "nice fit" for ag-bio researchers who are "not ready to bite off sequencing at the moment" but are looking to do their own experiments.

"A lot of these communities have embraced arrays," she said. "They get good, actionable data, and they want to be able to afford their research without waiting for sequencing to get everything packaged nicely."

Brandes added that the company has seen clients who have left Affy for competitors in recent years but have recently returned given the firm's renewed interest in the ag-bio market.


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

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