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Affymetrix, NimbleGen, CombiMatrix Attack Mid-Density Microarray Market

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Affymetrix moved to address a perceived Achilles’ heel of its microarray platform this week — inflexibile design— in announcing a distribution agreement with NimbleGen Systems of Madison, Wis., to provide custom microarrays for interrogating smaller sets of genes. NimbleGen is able to change designs quickly as it uses a maskless photolithography scheme to build its microarrays.

Meantime, CombiMatrix, the life sciences unit of Newport Beach, Calif.-based Acacia Research, rolled out its next-generation custom microarray for assaying as many as 12,000 transcripts.

Both announcements, coming almost a year after the microarray industry entered into competition to produce and sell single-chip, whole-human-genome microarray assays (see BAN 7/30/2003), indicate an industry trend targeting customers who have identified a focused set of genes, or are using microarrays for investigation of a species with a small genome.

Under an agreement with NimbleGen Systems, Affymetrix will provide customized expression arrays for smaller-scale studies or pilot experiments, the company said in a statement.

Affymetrix did not respond to a BioArray News request for comment.

The product, to be marketed as the NimbleExpress Arrays Program, will be sold and distributed by Affymetrix, and will fit into the latest generation of its proprietary GeneChip instrument platform, Affymetrix said in a statement. It is unclear whether the chips will be compatible with previous generations of the company’s instrumentation and software.

Financial details of the agreement were not disclosed.

Affymetrix has been subject to criticism for the inflexibility of its photolithography-based manufacturing techniques. The complex design processes for retooling the light masks at the root of the company’s microarray manufacturing make it difficult to institute quick changes in its custom microarray products (see BAN 3/10/2004).

The NimbleExpress program requires “nominal upfront fees, and a minimum of 10 arrays,” the company said in a statement. Customers using this program will be able to order custom chips of up to 12,000 transcripts per array. This density range overlaps with that of the 12,000-transcript custom microarray introduced by CombiMatrix, also announced on Monday.

Affymetrix said the chips will require a four-week turnaround time.

The assay on the NimbleExpress array uses Affymetrix’s scheme of multiple pairs of perfect match and mismatch oligos per transcript.

This new program will be complementary to Affymetrix’s existing custom microarray program, which the company in January announced it was retooling to underwrite design fees for research consortia seeking custom microarrays for their species of interest (see BAN 1/14/2004).

NimbleGen, one of the first companies to offer a single-chip, whole-human-genome assay, will manufacture the NimbleExpress chips in its Iceland fabrication facilities. The company’s maskless photolithographic process for the in situ synthesis of microarrays is based on technology originally developed by Texas Instruments for use in projecting video and PowerPoint displays.

The companies utilizing this technology have been involved in a rollup of sorts, with NimbleGen purchasing the assets of microarray developer Light Biology of Dallas, and Invitrogen buying Xeotron of Houston (see BAN 5/26/2004).

For NimbleGen, the deal with Affymetrix offers a new distribution channel for its products, Stan Rose, the company’s chief executive officer, told BioArray News.

“We now have a way to provide NimbleGen technology onto the Affymetrix platform,” Rose said. “That opens up 1,000 customers — [Affymetrix’s installed base of instruments] — and is a validation from the industry leader.”

Rose said changes in the NimbleGen platform to accommodate Affymetrix instrumentation would be minimal. “There is some R&D involved in making these products work for Affymetrix,” he said.

The agreement with the Santa Clara, Calif.-based giant of microarrays is not exclusive, said Rose, who founded the microarray instrument company Genetic Microsystems of Woburn, Mass., which was acquired by Affymetrix in 2000 for $101 million in stock. After that sale, Rose was employed by Affymetrix before taking the helm of NimbleGen in the fall of 2003 (see BAN 10/15/2003).

This latest agreement doesn’t mean that NimbleGen will abandon its other customers, said Rose.

“I think the best way to think about NimbleGen is that we will continue to offer service for those who don’t have access to the Affymetrix platform, and some of the technical capacity that may not be available in the NimbleExpress,” he said.

NimbleGen is developing services to provide microarray-based assays for comparative-genomic-hybridization, as well as other forward-leaning applications such as promoter-region arrays.

Rose said the level of concordance of data from the Affymetrix and NimbleGen’s system is “extremely high.”

He didn’t have any verifiable measurement of that, but said, “you can feel confident in that,” he said.

When asked if Affymetrix had invested in NimbleGen, which is venture-capital backed, Rose said: “No comment.”

He said the company is open to any kinds of arrangements with other firms and that the company continues to feel that it is operating within the intellectual property strictures that so define the industry.

“We do operate our business to respect intellectual property where it exists, and we are comfortable with any licenses that are in place,” he said.

Meantime, in Mulkiteo, Wash., CombiMatrix on Monday launched its 12K CustomArray, which will be available in July, the company said.

The new product follows CombiMatrix’s CustomArray 902 chip, a low density product that has been available since the spring (see BAN 3/3/2004).

The new product is manufactured on a 1-inch by 3-inch ceramic chip and is a customizable array with approximately 12,000 sites for in situ synthesized oligonucleotides. The 902 CustomArray product sells for approximately $400. Pricing was not disclosed for the newest product, the company said.

The synchronistic announcements indicate a customer demand, Jennifer Dent, CombiMatrix’s vice president of business development and sales, told BioArray News.

“I think it actually shows there is a market demand for a mid-density customized microarray,” she said. “In talking to customer groups and different researchers, we hear it again and again. We think a mid-density array will allow us to meet the needs of a broader audience who are studying bacteria, viruses, genomes and screening, as well as looking at toxicity, cancer, and pathways.”

Dent said CombiMatrix’s array products would be sold without a minimum number for purchase, and with a listed turnaround time of 10 days. She said that the company has focused on production of a quick turnaround time, and can usually ship products within five business days and will even scan hybridized arrays for customers.

“Our earliest customers seem to appreciate that they can purchase any amount they like,” she said.

“We have two customers who buy two chips at a time, three times a week on average,” she said. “They are looking for low-expressed genes and are plugging along on their research.”

For CombiMatrix, the test of its products will come in the marketplace, Dent said.

“We are excited to get our product out there in the hands of our customers,” she said. “We are excited to have the customers doing the comparisons, and we are confident that our arrays will outperform the competitors.”

—MOK