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Carrying on CombiMatrix's Chip Business, CustomArray Sets Sights on Sequence-Capture Market


By Justin Petrone

CustomArray, a six-month-old start up that was founded to continue CombiMatrix's microarray business after the firm restructured, plans new product offerings this quarter in the sequence-capture and microRNA arenas.

CEO Brooke Anderson told BioArray News this week that the Mukilteo, Wash.-based firm believes its sequence-capture approach will be more flexible and more affordable than offerings by established players in the target enrichment market, like Agilent Technologies, Roche NimbleGen, and RainDance Technologies.

Anderson, formerly chief operating officer of CombiMatrix, founded CustomArray to "monetize" CombiMatrix's research-oriented business after it decided last year to abandon its activities in that market, relocate to Irvine, Calif., and focus exclusively on diagnostics (BAN 11/16/2010).

Backed by investors, the firm acquired the assets of the array business, including the B3 custom oligo synthesizer and portable ElectraSense reader, in addition to a menu of gene and microRNA expression arrays. Anderson said the firm's goal is "not only to keep selling them but to enhance those product lines and add new products and to grow as a business."

According to Anderson, the core of CustomArray's new offering is its ability to synthesize pools of oligonucleotides using the B3, a product that CombiMatrix first launched five years ago.

While customers could always synthesize oligos using the instrument, Anderson said that the market for sequence capture is "blossoming" and that CustomArray stands to benefit. "We didn't see it as a very big market in years gone by, but these days with the upsurge of next-generation sequencing, there's a really strong need for it," he said. He added that the oligo pool application could also be useful in markets like gene assembly.

Though the sequence-capture market is dominated by a host of larger competitors, Anderson believes that the firm's niche is in its ability to allow firms to design and make pools on their own at a lower cost, though he declined to discuss pricing for the offering.

"The area where we fit in there is if you have some region you want to target, if that's not a kit that someone already makes, then that needs to be designed and fabricated," Anderson said. "The strength of the CustomArray technology is being able to make a fairly large collection of oligos at a lower price point," he said.

According to Anderson, using the B3, customers can in their own labs synthesize 12,000 different oligos. "That offers a dramatically lower price point and the ability that is opened up for people to iterate those designs, to do a custom area, to target a custom area, to do some sequencing runs on that and then move on to some other region of interest," he said. "That whole dynamic is opened up if you can quickly and inexpensively compare other methods of doing it and make these oligo pools."

CustomArray's oligo pool application is already available, but Anderson said the firm will introduce kits later this quarter to aid the firm's clients with the process. "You can use oligo pooling to make your own kit for targeted sequencing in your own lab right now," he said. "There may be some kits where we do part of that for customers and we are thinking about what kinds of kits we want to provide," he said. Anderson did not elaborate.

He also said that the application will be competitive despite the plummeting costs of next-generation sequencing. I think there will always be an economic case to be made that if you can just focus on a portion of a genome that you are interested in, why would you not want to do that?" he said. "Assuming that your enrichment process or kit has not become more expensive than your sequencing run, it will always be useful if you can do it to select the regions you are interested in."

In the similarly crowded microRNA arena, where firms like Agilent, Affymetrix, Illumina, and others compete, CustomArray is preparing to update its miRNA arrays, first launched in 2005, with a new labeling approach that Anderson said "provides more selectively in the labeling of the microRNA and microarrays." He said the firm's approach will "have a major advantage in the market" and is currently in beta testing ahead of a launch later this quarter. He did not elaborate on the offering.

'Sole Focus'

CustomArray has inherited an installed base of around a dozen B3 synthesizers around the world. Outside the US, Anderson said synthesizers are currently in use in a number of markets such as Australia, China, and Italy. The firm is keen to continue the business relationships CombiMatrix had in the past.

Still, last year's restructuring left some longtime users anxious. "It was a mess," said Massimo Delledonne, director of the center of plant functional genomics at the University of Verona in Italy. Delledonne has been a CombiMatrix user for years and had produced chips for other plant researchers in Italy and abroad. "When we heard about the restructuring, we decided not to do custom chips for others and to save the chips we had at that time," he told BioArray News. Still, he said that he was "happy" with CustomArray and its management, given the firm's focus on the array business.

Anderson said that he understands that "sense of anxiety" that CombiMatrix customers experienced during the transition period, but that CustomArray continues to provide "all of the products and support that CombiMatrix offered."

He noted that the firm, which consists of around 10 employees and consultants, has retained most of the scientists involved in the development of the array platform, but said that the "main difference" between CombiMatrix and CustomArray is that the "oligo microarray platform is our sole focus."

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