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Agilent Introduces Two Microarrays With a Novel Innovation: Bald Spots

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Agilent Technologies last week introduced rat and Magnaporthe grisea microarray slides to add to its catalog of 60-mer products.

The rat product (Agilent G4130A0) is intended for genome screening and toxicogenomic research applications, and was developed in collaboration with Paradigm Genetics of Research Triangle Park, NC, and the National Institute of Enviromental Health Sciences. The 20,000 rat gene probes on each 1 x 3 slide are based on RefSeq, human and mouse homologs, and genes identified by NIEHS. The arrays sell in a kit of five microarrays and are now available.

The Palo Alto, Calif.-based company also introduced a Magnaporthe grisea (rice blast) array based on genome sequence data, and designed in collaboration with Ralph Dean, an NC State researcher (see, BioArray News, Oct. 25, 2002). This array is expected to be available within eight weeks.

The introduction of new products illustrates Agilent’s approach to the microarray market, one of its top executives told BioArray News.

“Our goal is to create a new Moore’s law in the [microarray] industry,” said Barney Saunders, Agilent vice president and general manager for bio-research solutions. (Moore’s Law, an almost 40-year-old semiconductor industry concept, credits Intel co-founder Gordon Moore, who said that the number of components on a microchip would double approximately every 18 months.)

For Agilent, that means speed and flexibility in its manufacturing process.

The company creates its microarrays in a clean-room facility, in what was once a part of Hewlett-Packard’s facility in Silicon Valley. Its process is based on an application of ink-jet technology to “spray” oligonucleotides onto a glass slide. Thus, a 60-mer slide is like a glass “page” that has been printed 60 times.

Today, the company says it can deliver finished microarrays within 10 to 15 days from receipt of the pattern files.

But, the innovation may be in what is not on the slide, rather than what is on it.

The company is now including on its arrays an empty patch of real estate — about 5 percent on the rat arrays — so users can add their own probes to these areas on otherwise catalog slides.

“It’s not just putting down existing probes that we have selected,” said Saunders. “We can now add a few hundred probes that the researcher is interested in, tuning the chips according to their demands, and respond rapidly to the pace of research.”

The rat chips were created in collaboration with Paradigm Genetics, which just announced that it is offering microarray analysis service as a preferred provider of the Agilent platform (see BioArray News, April 4, 2003 ).

Catalogs, or Custom?

The introduction of Agilent’s 60-mer microarrays at October’s Chips to Hits conference in Philadelphia was “a pivotal moment for our business,” said Saunders. At that time, an Agilent spokeswoman said that the microarrays were a hit, “flying off shelves.”

“There is a tremendous base of researchers that want to buy the best product they can get without going through the hard work of creating it,” Saunders said. “There is a transition in the marketplace, partly relating to the issues in biotech funding, and a large installed-base of 1x3 scanners in the academic and not-for-profit sector. We are seeing a big growth there, and we are delighted by the progress we are making.”

The company currently offers four cDNA microarrays — human 1 &2, rat and mouse — and five 60-mer oligo arrays — rat, arabidopsis, human, mouse, and yeast. The rat array kit lists for $2,250. The rice blast array has not been priced.

AgriBusiness

The new rice blast microarray is a first for the company, as a catalog microarray of a non-traditional model organism, but one that may increase in importance when coupled with the recent announcement that the genome of another filamentous fungi, Neurospora crassa, is almost 95 percent sequenced.

The Neurospora sequencing has been led by researchers from the Whitehead Institute/MIT Center for Genome Research who have spearheaded a two-year effort that involved more than 70 scientists from over 30 universities and research groups representing more than 11 countries.

Rice blast is a pathogen that affects rice, wheat, barley and turf grasses. It is also a highly characterized organism that serves as a model for scientists studying filamentous fungi that cause other cereal and crop diseases.

Agilent obtained the rights to use the gene sequences for the pathogen from the North Carolina State University fungal genomics lab. Financial details were not provided.

The array, in itself, is illustrative of Agilent’s methods in creating new catalog products, according to Saunders.

“Each array is very different, depending on the needs of the community,” said Saunders. “Our approach is to work with key groups, so what we are doing is taking this flexible system and putting down the content that the community really wants — on one array, that’s really important.

“On the rice blast, we worked very closely with a world-class research group, and part of the demand to do the project comes very much from that. We are responding to their desires.”

This particular array is also an outgrowth of Agilent’s emphasis on the agricultural market. The company put together a group to focus on this area a year and a half ago.

“We are leveraging the channel we had through our mature instrumentation base that we had in the [agricultural] industry,” Saunders said. “It’s paying off now with arabidopsis and the interest in the Magnaporthe.”

In the Works

While saying he did not make “forward-looking statements,” Saunders did point to areas of interest for the company. Following are some of his thoughts:

  • On CodeLink. “They are another competitor providing 1x3 arrays, and another incentive to keep on the open architecture. It's great for the industry to have healthy competition.
  • On proteins: “There is an area with a lot of interest. Today, what we offer is gene expression microarrays, that’s what our system is set up for.”
  • On automation: “What Agilent does really well is solution engineering. The 48-slide carousel we introduced helps customers with their workflow. That is a major theme for us.”

— MOK

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