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Agilent Launches New 224K Chips for Array CGH, Other Apps; Plans Methylation and miRNA Arrays


Agilent this month began shipment of its new 244,000-probe arrays for comparative genomic hybridization applications, and the company is looking to capitalize on its new printing technology to branch out into emerging array markets for methylation and microRNA chips, according to a company official.

Agilent officials disclosed in March the firm's intent to launch the higher-density chips by this summer (see BAN 4/4/2005). The density upgrade puts Agilent within striking distance of rivals Affymetrix, which sells SNP arrays with 250,000 probes, and NimbleGen System, whose array CGH arrays have 385,000 probes.

Kevin Meldrum, the manager of Agilent's genomics marketing group, told BioArray News this week that the company had met its deadline for introducing the higher-density arrays and that a launch was underway.

"We just started to ship our first arrays for our [array] CGH applications and we also have products that we are going to be rolling out for other applications over the next month or two as we ramp up the capacity," Meldrum said.

Other products that will be available in higher-density format will be chips for chromatin immunoprecipitation (ChIP)-on-chip applications as well as arrays for gene expression experiments. In addition, Agilent's newest arrays — for DNA methylation and microRNA analysis — could become available in the 244K format over the next six to 12 months, Meldrum said.

"The biggest criticism we've had is that ... it wasn't practical to use Agilent's product to do whole-genome experiments. So I think this puts us in a position to compete very effectively there."

Agilent first revealed its plans to launch a chip for methylation analysis last month. Chris Hopkins, a senior scientist at Agilent, told BioArray News at the time that the company was in the "early stages" of launching a methylation array for CpG islands. He said that the arrays could possibly be launched as soon as this month (see BAN 6/20/2006).

Meldrum this week said that a release date for the methylation arrays is imminent and said that the arrays will target the cancer research market.

"I think people are very interested in cancer markers, for example, and are now starting to correlate changes in methylation patterns with different cancers," he said.

Agilent's move into methylation coincides with similar overtures from competitors as diverse as NimbleGen Systems, an Agilent rival which also plans to release methylation arrays by year-end, and Epigenomics, a German molecular diagnostics shop that is thinking about offering its methylation array analysis as a service (see BAN 6/27/2006).

Agilent also plans to add miRNA arrays to its portfolio. Meldrum said that the firm's plan is "over time to further expand into the microRNA area." While the company doesn't "have a specific commercialization timeline yet for that product," he noted that "it's something we're taking a very close look at."

The miRNA market has seen increased interest from array firms large and small since last November when Invitrogen launched its NCode multi-species miRNA array. Since then Invitrogen has been joined by CombiMatrix and Exiqon, as well as Applied Biosystems, which sells its mirVana miRNA array through its Ambion business.

Meldrum said that effective probe-design algorithms would be a vital component of any miRNA array product offering. "In that particular space you have to be very specific because there's a lot of sequence homology between the miRNAs," he noted.

Meldrum said that Agilent is pursuing the higher-density arrays and emerging applications in order to expand its position in the research market. He noted that the company hasn't been able to provide researchers with whole-genome capabilities until now.

"The biggest criticism we've had is ... it wasn't practical to use Agilent's product to do whole-genome experiments. So I think this puts us in a position to compete very effectively there," he said of the upgrade.

He also predicted that the higher-density chips will provide customers with greater value and might lure academics that are printing their own into Agilent's camp.

"We are starting to get to a price point now where a lot of people that have been making their own arrays will start moving to commercial vendors because the cost will become fairly comparable with the cost of them making their own products today," he explained.

"You still have a large number of academic centers that [are printing their own] and when you put it together in total it's a fairly sizeable volume," he said. "Our primary focus is really on the research market right now."

Writer Version 2.7

Agilent believes it will be able to reduce the cost while raising the amount of content per slide due to its new array printing technology, known in house as Writer Version 2.7. Version 2.7 uses the company's standard inkjet printing technology, but enables the company to cram more content onto a slide.

So — in the case of gene expression — instead of selling a single 44,000-probe array on one slide, Meldrum said the company will now be able to squeeze four arrays onto a slide for gene-expression applications.

He also said that Version 2.7 will enable Agilent to continue to increase the density of its arrays. "We are not done. I think we are going to continue to scale this and we have pretty ambitious plans," he said. He did not provide further details on its plans to scale up its chip density.

In addition, the company's new chip writer is "a heck of a lot more robust and it also is scalable — it gives us the capability to ramp volume quite considerably," Meldrum said.

"As we move forward we will be able to increase the number of features we can put on a piece of glass and use this same writer technology as we kind of move up the curve in increasing our density further," he added.

According to Meldrum, the company will shift all its new applications onto its new readers, "both ones that are commercially available today and those that will be coming out over the next six to 12 months."

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