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Betting on Flexibility, CombiMatrix Launches Design-on-Demand Arrays


CombiMatrix this week launched its line of Design-on-Demand arrays, a catalog of gene-expression products for more than 1,400 microbial, eukaryotic, and viral genomes.

Among the organisms included in the catalog are Escherichia coli, Arabidopsis, and those responsible for influenza, HIV, anthrax, SARS, West Nile virus, tuberculosis, plague, cholera, and other diseases. According to CombiMatrix, there is no design fee, no set-up fee, and no minimum-order requirement for the arrays.

The new set of arrays is an expansion of the company’s CustomArray products, said Mike Tognotti, director of sales and marketing for CombiMatrix. He said customers have responded positively to the CustomArray products and from the bioinformatics support the firm offers. “We’re just increasing that offering,” said Tognotti.

As with its other CustomArray products, the new arrays are in a standard 1” x 3” slide format and use standard reagents. The price of the Design-on-Demand arrays is $550 per chip, which is the standard charge for the CustomArray products.

Tognotti cited the flexibility and rapid turnaround on manufacturing the arrays as keys to competing in the market. “We can synthesize 12,000 features all at the same time — and that’s just for one array — so we could line up our entire capacity if we wish and design several thousand arrays at one time as well. From a manufacturing standpoint, our technology lends itself to speedy synthesis,” he told BioArray News.

The genomic transcripts for the organisms are from the various public repositories. Tognotti said the firm downloads genomic data from the repositories and uses a proprietary algorithm to make a “nice, stringent design for the researcher.”

The firm is able to “leverage a CMOS semiconductor wafer, and we have an oligo synthesis technology where the arrays are in situ built in the synthesizer,” Tognotti explained. “So, where there are little feature sites on the wafer, we can design an exact oligo sequence and have that oligo sequence built in that exact feature site.”

He said building the arrays is as quick as standard oligonucleotide synthesis. But the difference comes in how the firm performs quality control, where it functionally tests every single probe on every array. “That takes a little bit of extra time,” Tognotti said. “We’ve been able to make these [in as short a time as] four to six days. No one else can do that today.”

Tognotti said that although the 12K CustomArrays, which were introduced this past July as the firm attacked the mid-density microarray market, were designed for any kind of customized product, the technology is particularly well-suited to microorganisms.

“The reason why we choose this organism list is mainly because collectively there is a large market wanting to study these organisms, and most competing companies in our space have neglected to serve this market because of oversight or their technology has limited them to do so on a wide scale,” he said.

He said that although the customers for these kinds of arrays is roughly 65 percent academia, “there are a lot of pharma clients interested in microorganisms, more so than ever.” He also cited the government’s interest in organisms that could be used for bioterrorism — which plays into another part of CombiMatrix’s business. The firm has received a total of nearly $10 million in funding from the US Department of Defense in grants related to the development of biowarfare detection products.

Tognotti said that as researchers perform experiments utilizing the Design-on-Demand arrays there will be a better understanding of the organisms, which “will help fuel better content for what we’re doing in our homeland security initiative. You’ll have places now, like the CDC, that can have something built at a very low access cost and with a lot of flexibility, and their research is going to help everybody else,” he said.

Competition in this niche for Mukilteo, Wash.-based CombiMatrix is likely to be strongest from Affymetrix, which recently introduced 179 NimbleExpress prokaryotic array designs. The arrays are manufactured by NimbleGen for Affymetrix under a pact signed earlier this year that will enable researchers to study the whole-genome expression of many pathogenic organisms such as those responsible for anthrax, influenza, and tuberculosis. Competition could also come from NimbleGen itself, which offers gene expression services based on its maskless array synthesis technology.

But Tognotti pointed again to the flexibility CombiMatrix offers with its arrays. He said of the NimbleGen/Affy partnership, “From what I’ve heard, their system is a little more complicated to get an array built, [and] there are minimum order requirements. Whereas, someone could order one array, if they wish, from us.”

He also noted that the CustomArrays could be read on almost any commercially available scanner, whereas with the NimbleExpress products, there is a set scanner. “We made it really easy, because on campus you’re likely to find an Axon scanner, PE scanner, or an ABI scanner, and all of those could read our chip, but they can’t read the [NimbleExpress] chip,” Tognotti said. “That’s how we’re going to compete — it’s total flexibility, lower cost, and better content.”

He declined to provide an exact number of salespeople that CombiMatrix employs, but said that the firm had recently ramped up its domestic and international sales force, marketing team, bioinformatics staff, and customer support infrastructure. The company is not utilizing any partnerships in the US to sell the arrays, but Tognotti said the firm has a couple of distributors that will help sell the arrays overseas — although he also declined to name them because of ongoing negotiations — as well as its division in Japan, which will sell the arrays there.

During the last quarter, CombiMatrix introduced arrays for drug metabolism, toxicology, and cancer. While the microarray business is a key area for the firm, it also has a biodefense segment that makes detection systems for homeland security purposes; a nanotechnology business that recently signed a collaborative pact with Intel; and a drug-development business that has grown rapidly over the past year through a collaboration with IrsiCaixa, a Spanish non-profit research institute, as well as the acquisition of a majority stake in nascent drug developer Leuchemix (see BAN 10/6/2004).

— EW

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