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EXTRA: The Race is On: Agilent, NimbleGen Take Up ABI s Challenge To Make First Whole-Genome Microarray

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The race is on to see who will be the first to release a whole human genome single microarray – and then sell it.

Agilent Technologies today said it will release a single-chip whole human genome microarray later this year, BioArray News has learned.

Additionally, Madison, Wisc.-based Nimblegen, a microarray services provider using its proprietary platform, said today that it already has a single-chip whole human genome microarray available for researchers.

The single-chip whole human genome microarray is regarded as a milestone by which to measure the progress of innovation by companies mass-producing this eight-year-old technology.

The announcements follow last week’s statement by Applera’s Applied Biosystems Group of Foster City, Calif., that it would release a single-chip whole human genome microarray, and instrumentation to support it by the end of the year. The company did not provide details about its promised product other than saying it will have better reproducibility and sensitivity than currently available microarrays because of its 60-mer oligonucleotide format, and a chemiluminescent detection scheme. ABI said its product will be available by the end of the year. The company did not respond to BioArray News requests for more information.

ABI is a gene sequencing powerhouse and this announcement marked its entry into the microarray-based, gene-expression analysis market, joining established players like Affymetrix and Agilent as well as Amersham, which entered the fray last summer with the $20 million purchase of Motorola’s CodeLink microarray product line.

Agilent’s declaration means at least two industrial-scale manufacturers, and a smaller player, are racing to produce a tool that some see as the logical next-generation product for genomic researchers – one that has the potential to cut per-chip pricing, and open new experimental possibilities.

It’s a horse race, an Agilent Technologies executive told BioArray News.

“I believe the introduction of a whole human genome microarray will be a singular achievement and an important milestone for the genomics industry,” said Barney Saunders, vice president and general manager for Agilent’s BioResearch Solutions unit. “Because of that, I was a bit disappointed to see ABI issue its announcement so early, because, 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. I hope that history will give credit for this achievement to the company that first releases a product, as opposed to a press release, regardless of which company that turns out to be.”

Agilent will spot onto one chip the genes it now sells as a two-array 60-mer oligonucleotide set – the Human 1A and 1B, released in June, and add additional content from Incyte and public databases, Saunders said. Agilent said it would not issue a press release to formalize its announcement, but would wait until the yet-to-be-named product is available for purchase.

Agilent produces its arrays on 1x3 glass slides and the product will be readable on standard 1x3 microarray scanners, the company said.

Affymetrix, the microarray market leader, did not take the opportunity to bring its own product to the starting blocks as its reported its second quarter financials last week, but industry observers have no doubt that market pressures, if not pride, will soon persuade the company to make its own entry.

In its annual report, Affymetrix said that its research labs have created a prototype microarray “capable of handling 60 million fragments of DNA.” The company did not respond to a BioArray News request for information on when that might be launched into the market. The company currently offers a two-chip set whole human genome microarray.

Amersham also opted not to step up for this lap of the race, said Trevor Hawkins, vice president development, discovery systems, Amersham Biosciences, who is responsible for setting the strategic direction of the company's genomics business. Hawkins joined Amersham in February 2002, leaving as director of the Department of Energy’s Joint Genome Institute.

“I do not believe that having the entire genome on one microarray is a huge advantage, when what researchers are looking for is quantitative and reproducible information,” he said. “Highly quantitative data, that is our main goal, rather than trying to play the density game.”

NimbleGen Systems

Meanwhile, NimbleGen Systems, a Madison, Wisc., microarray manufacturer and analysis services provider today moved to the front of the pack on the emerging race to produce a single-chip whole human genome microarray by announcing the availability of a long-oligo (60 mer) offering.

The company said today it is ready today to provide researchers with a whole human genome single microarray.

The company said it has beta-testers for the product but would not comment on whether it has realized any revenue from its sale.

As ABI was making its aspirations public last week, Bob Palay, the chairman and the CEO of NimbleGen, which in April closed on a $12.5 million Series D financing round, and his staff gathered in front of a computer screen to craft an announcement, released today, on their single-chip whole human genome array.

“We have it,” Palay told BioArray News. “Our customers have had access to it since early this year.”

NimbleGen, founded in 1999 as a University of Wisconsin-Madison spinoff, is commercializing a patented maskless array synthesizer system for creating custom-designed in situ DNA chips using light projection technology. The company provides outsource services based on its platform.

The company’s human array is composed of almost 200,000 long oligo probes, and an additional 5,000 control probes, all at a length of 60 mers, with average coverage of 5 probes per gene. The chips contain 38,000 transcripts, and predicted genes, derived from the University of California, Santa Cruz Golden Path database are represented. Pseudogenes are not on the chip.

The NimbleGen array is not available as a direct product offering to customers: NimbleGen uses the array as part of a service offering, and said it sends out data within weeks of completing an order. The company would not provide details on pricing.

The company has a scalable manufacturing capacity and has accommodated the manufacture of thousands of arrays at a time.

Palay said at least one customer has ordered the service on an early-access basis on this product and the company didn’t give it a second thought until the ABI announcement.

“The real issue for us is the information value customers get for their experimental dollar,” he said. “We’ve been doing this since the beginning of the year and it never occurred to us that it was important.”

— MOK

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