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CombiMatrix Rolls out Designer Microarray Line: At-home Synthesis Machine on the Way


With the introduction of its CustomArray 902 chip this week, Mulkiteo, Wash.,-based CombiMatrix is bringing to market a platform that will allow users to design and purchase low-density microarrays through the Internet. Within months, customers will additionally be able to purchase a machine to build their own designs in-house.

The company on Monday rolled out the first product in this line, a 1-inch by 3-inch customizable array with approximately 1,000 sites for in situ synthesized oligonucleotides, that will sell for approximately $400, the company said.

“Getting this out on the market is a milestone achievement for CombiMatrix,” said Amit Kumar, the company’s chief executive officer. “We think it is a great product and now we are going to start selling it to customers.”

CombiMatrix, a nine-year-old life sciences business of Newport Beach, Calif.-based Acacia Research, has long considered itself a research and development firm, creating partnerships to design and market products using its semiconductor-based electronic-microarray technology. The company has rapidly made available microarrays for the H5N1 “bird flu” virus and the SARS coronavirus.

But with this announcement, the company now becomes a direct seller of microarray products.

The platform rollout, expected to run over the next two months, will include the introduction of a 13,000-site custom array product, followed by the introduction of a benchtop machine for the manufacture of the arrays.

The 64-employee company is targeting the home-brew market, a large group of potential customers who are familiar with methods of creating and using microarrays and who already have the equipment to use the product line, Kumar said.

“They won’t have to do anything new,” he said. “They can just order a few chips and try them out.”

The product introduction comes at a time when the decade-old microarray industry is poised to surpass an estimated $1 billion a year in revenues. At this point in the market’s evolution, the home-brew users, who produce their own arrays, still grab a majority of market share.

CombiMatrix now goes head-to-head with other companies that have custom array offerings. Additionally, the product line may even compete with a CombiMatrix microarray product, the MatrixArray, which the company designed for Roche Diagnostics. CombiMatrix has completed its development of the product line and delivered it to Roche, but the diagnostics giant has not yet released the product for commercial sale.

The microarray market has recently seen the introduction of pre-printed whole-human genome arrays from Affymetrix and Agilent, and awaits the promised entry of a new gene-expression analysis platform from Applied Biosystems.

“We don’t think we are coming in late,” said Kumar. “We are not competing with Affymetrix, and in fact, we think we are quite complementary to them.”

He said that the introduction of whole-human-genome microarray products should whet researchers’ appetites for a custom product that will allow them to focus on the lists of genes they discover through whole-genome analysis with high-density products.

The CustomArray contains a 22 millimeter by 5.5 millimeter strip holding the oligonucleotide probes on a porous layer atop a ceramic substrate (see illustration, this page.)

The company uses an in situ process to deposit oligonucleotides on the slide and is promising delivery within 10 days. The product will allow users to create probes of any length, up to 80 mers, but expects typical lengths of 40 mers to target labeled DNA or RNA. Features are sized at 92 micrometers. The chips will allow users to mix oligo lengths on the same chip.

The chips will have an expected shelf life of four months when stored at room temperature.

The CustomArray Desktop Synthesizer product, which is expected to be available in April, the company said, will allow users to create eight custom arrays at a time.

The slides require 150 microliters of sample each and have a sensitivity of 1.5 picomolars — a mass ratio of better than 1 in 300,000 molecules, the company said.

According to a company study of 42 arrays, the median correlation coefficient of the non-normalized probe intensities across all 42 arrays was .98, with a median coefficient of variance of 18 percent. Intra-array replicates had a mean coefficient of variance of 11 percent.

Users can submit GenBank accession numbers, gene sequences, or specified probes to create chip designs. The CustomArray platform software designs probes, then the probes are positioned on the CustomArray, followed by the in situ synthesis process, which the company says takes about 24 hours.



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