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News of the Month ABI, Agilent, NimbleGen Duel for Whole Genome on Single Chip


Call it the press-release war. In late July, Applied Biosystems kicked it off by announcing the “first system for whole human genome analysis using a single microarray,” a seemingly final step from an unexpected player in the race to produce a single chip holding the entire human genome (market leaders Affymetrix and Agilent Technologies previously had achieved squeezing the genome onto two-chip sets).

But on reading further, ABI’s announcement stated that the company had developed a whole-genome chip but was still pretty far from being able to sell it. ABI expects to send the chip out for customer testing by the fall, and to make a final product available at the end of 2003.

Less than a week later, NimbleGen — a small company based in Madison, Wis. — issued its own press release, announcing that it in fact had developed the first single whole-genome chip, and that its product had been available to customers “since early this year,” according to CEO Robert Palay. (Take that, ABI.)

But there’s a caveat for NimbleGen, too. The company operates solely on a service model, so customers ship samples to Nimble- Gen’s core facility in Reykjavik, Iceland, and get results in several days. (Clients are offered the opportunity to set up their own lab within the core facility, though.) Since customers never get to use the array in-house, odds are they don’t care whether NimbleGen uses one chip or two. And Palay hedged about how much use the chip is actually getting: he declined to provide any estimate of how many users were taking advantage of the human genome chip, citing customers’ need for “confidentiality.”

Both companies’ arrays use 60-mer oligos. ABI, which relies on chemiluminescent detection to analyze the more than 30,000 genes it offers, gave no other specifications for its chip — though it’s expected to run on a proprietary platform developed by ABI, according to Ken Goldman, a Lehman Brothers analyst following the company. NimbleGen’s chip comes on a standard microscope slide and has 38,964 genes represented with an average of 5X coverage per gene. Emile Nuwaysir, director of business development and the scientist who originally worked on the NimbleGen chip, first talked about the product at the June Biochips meeting in Boston. “People in the audience jumped on it,” he recalls.

In the meantime, Agilent emerged from stealth mode to announce that it, too, had been developing a single chip containing the human genome. “While we have kept it quiet, it has long been in Agilent’s plans to release a whole human single microarray and we are well on target to do that before the end of 2003,” says Barney Saunders, vice president and general manager of Agilent’s BioResearch Solutions Unit. With more than 36,000 genes, Agilent’s chip will also use 60-mers on a 1” by 3” slide that can be read on any scanner. “At this point, the race is on,” Saunders adds.

Refusing to be bullied in its own race, ABI contends that its chip will give improved sensitivity over other systems. Lehman’s Goldman anticipates the cost to be about the same as the Affy two-chip set, but expects ABI “to be ahead of the pack with throughput by the end of this year.”

The battle’s far from over. Small as NimbleGen may be, Palay is clearly not missing the opportunity to take on giant ABI. “The people that were planning to use ABI’s [whole-genome chips] — if they would like them before ABI has them ready, we can make them,” he says.

— Meredith Salisbury


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