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Custom Chips in Focus as Agilent Rolls Out Shared Microarray Design Program


Agilent last week unveiled a shared microarray design program in a bid to gain a greater slice of the academic market and appeal specifically to the needs of consortia sharing data.

The program also marks the beginning of a campaign to expand the firm's custom microarray business, Agilent officials told BioArray News. "This is one of several things we're doing right now with our custom microarray program," said Scott Harrison, custom microarray program manager for the Palo Alto, Calif.-based company.

He said that he could not disclose much more information than that, "but there will be a marketing campaign [to support the shared design program], because Agilent is in the process of reinventing our custom business, and we will be rolling that out over the next six months or so."

The new program will allow researchers to share their custom microarray designs either with designated groups while maintaining control of their intellectual property, or with the scientific community at large. In the case of researchers sharing data with other members of a consortium, Agilent has developed standard contracts that release the firm from the confidentiality restriction for the specific customers that are named, according to Harrison.

"We make it clear in the language of that contract that all we are doing is supplying the array, and the customer still owns that design," he said. "They will only allow us to release it to somebody basically with whom they have a contract," or to a third party who they are confident they can share with while still controlling their IP. "By simplifying the process, we provide a mechanism for it to occur," he said. "You could think of this as a way of enabling collaboration ... [because] they're able to share this information in a controlled environment."

Harrison said the program was launched in response to "missed opportunities" for researchers working with early-stage genomes who wanted to work together, "but the nature of the custom microarray program -- where people are trading confidential information back and forth -- made it very difficult to open the door for multiple parties to work together."

He added, "The contracting aspect was complicated, but also the fact that when people are working in the discovery stage they want to retain control of their intellectual property until they publish or patent. It drove us to develop a contracting mechanism that made this very simple and straightforward to put in place and didn't require a lot of legal review and signatures."

The shared design program enables researchers to order microarrays on demand, and there is no minimum order requirement. But, Harrison said, "What Agilent doesn't do is get involved in standard support of content that would normally occur with a catalog array."

Agilent already has customers for the program, though the firm did not disclose how many. The company said that some of those customers are what drove the firm to develop the program.

One of the program's customers is North Carolina-based firm Icoria, formerly Paradigm Genetics, which has been producing custom microarrays for researchers that are part of the Toxicogenomics Research Consortium, under a contract with NIEHS' National Center for Toxicogenomics. The company worked with researchers at Duke University to develop C. elegans and zebrafish microarrays.

"We entered into a discussion with Agilent to see how we could make these research tools available to the larger research community -- this was a desire not only for us, but also NIEHS as well as the investigators at Duke," said Pat Hurban, director of investigational genomics at Icoria.

Hurban said Icoria started working with Agilent about four years ago "to gain access to some of their technologies, which were particularly well-suited to our research needs at the time, because we had the need to develop custom arrays for the types of model organisms we were working on, and at the time were not well supported by commercial products." He also cited Agilent's ability to quickly make custom arrays as a key decision to work with the firm and get involved in the shared design program.

Agilent declined to provide pricing for the arrays in the shared design program, but Harrison said, "Because we have multiple parties buying the same design, the volume advantages are extended to the larger group, and we can offer much more attractive pricing."

Indeed, pricing is a key issue for researchers in the academic community, and, along with a firm's ability to provide up-to-date data on their chips, could sway a decision about which microarray vendor will get their business, suggested David Baillie, principal investigator of the C. elegans Gene Expression Consortium, and professor in the department of molecular biology and biochemistry at Simon Fraser University, British Columbia. Baillie said the shared design program sounds like a good idea, but he would have to know more details before providing an opinion.

Baillie's lab currently uses a catalog C. elegans array manufactured by Affymetrix, which he believes needs to be updated, and a custom array designed by his consortium and produced by NimbleGen.

Although Agilent said the program is unique to the microarray industry, it follows the launch of Affymetrix's GeneChip Consortia Design Program -- which the microarray market leader announced a year ago at the Plant and Animal Genome Conference (see BAN 01/14/2004). Under this program, Affy said that it would underwrite the design fees required to create novel plant and animal whole-genome arrays, and said that 12 new arrays related to the program were slated for release during 2004.

This week, Affymetrix said that during the past year it launched eight of the plant and animal arrays including chips for grape, soybean, wheat, rice, maize, cow, chicken, and pig research. Affy plans to launch eight more arrays for the program in 2005 including canine, Rhesus macaque, legume, Brassica, tomato, citrus, poplar, and sugar cane.

Affymetrix officials were unable to provide comment for this article by press time.

One of the major differences between the programs is that the Agilent initiative is strictly a custom, not catalog, array operation. "The customers -- the consortia -- are in complete control of the process, because it is their design," Harrison said. "They make the decision of what exactly they want that design to look like, and it becomes the customer's design that Agilent is getting rights to distribute to several parties."

Agilent's ink jet process for printing arrays also lends itself to more frequent revisions of arrays, which may be particularly appealing to consortia. With model organism databases expected to be updated regularly over the next year, Agilent will be able to make revisions as customers demand, Harrison pointed out. He said he expects that once researchers get to the point of publication, they likely will want the array design out in the public domain. It would then be up to Agilent to make a decision about when to revise the chip's content.

The launch of the shared design program comes one week after the firm announced its acquisition of Computational Biology, a developer of ChIP-on-chip technology, which uses chromatin immunoprecipitation to discover how regulatory proteins control gene activity (see BAN 01/12/2005). Agilent officials speculated that applications for the technology could generate $100 million in revenue by 2007.

The purchase of Computational Biology follows the November launch of the firm's fully automated lab-on-a-chip system, an advanced version of the firm's earlier-generation 2100 bioanalyzer, and the purchase of bioinformatics firm Silicon Genetics in August.

Although Agilent has taken great strides over the past year to broaden its pipeline of products and offer customers integrated packages for genomics research, it has maintained that microarrays remain a key part of its growth strategy (see BAN 12/22/2004). Speaking recently at its annual analyst meeting in New York, Chris van Ingen, the head of Agilent's LSCA unit, said, "The microarray market for gene-expression profiling and genotyping is still fluctuating in growth, but the new applications will fuel growth in gene expression higher than 8 to 12 percent."

-- EW

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