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Affymetrix and Agilent Turn up the Volume To Market Single Whole Human Genome Chips

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With a statement released released on Thursday morning, Affymetrix last week made its next move in commercializing a single microarray product containing probes that, in toto, represent the known gene content of the human genome.

The Affymetrix announcement, perhaps not coincidentally, came out hours before an announcement by Agilent, which stated that it, too, was in the early stages of commercializing its single microarray, whole-human-genome product.

Industry scientists and researchers said they welcome the tool, with more than one describing it as a means to cast a wide net. in genomic discovery.

Jeffrey Brockman, a senior scientist and microarray group leader for Psychiatric Genomics of Gaithersburg, Md., said his company has evaluated Affymetrix arrays and Agilent’s cDNA arrays in its drug discovery efforts centering around brain diseases.

He said he is using both Agilent’s cDNA arrays and Affymetrix’s rat, mouse, and human catalogue arrays.

“It’s clear that each platform identifies a unique set of genes,” he said. “One platform will not answer all questions.’

But it’s still not clear how many platforms the microarray market, which is estimated to reach $800 million this year, can support.

The competition is just starting to heat up, and it’s centering around this application.

Affymetrix, which is regarded as the market leader in mass-manufactured microarrays with a major-ity share outside of the self-spotting market, said in its Oct. 2 statement that it was ready to take orders for its GeneChip Human Genome U133 Plus 2.0 microarray, a single chip on the company’s proprietary format, which it says contains 1.3 million DNA probes to analyze the expression level of “nearly” 50,000 RNA transcripts and variants.

The arrays, Affymetrix said, would ship this month.

Meantime, Agilent Technologies, the No. 2 player among the companies that mass produce and market micro-arrays, announced that it had already shipped single, whole-genome chips to beta customers.

The Agilent array, the company said, contains 44,000 features and is printed on an 1x3-inch glass slide readable on any microarray scanner.

The dueling press releases clearly demonstrate the kinetics of competition in a market hurtling toward what perhaps may be a record financial quarter.

The whole human genome, arrayed on a single chip represents a technical achievement, and a milestone for an industry that is not a decade old but one that is reaching maturity, despite appearances of a spitting contest among the industry’s largest players.

Meantime, Applied Biosystems, which ignited what some industry analysts are calling the 21st Century Chip Wars with a press release issued in late July (See, BAN 7/30/2003), remained on the sidelines. After issuing a press release promising a whole-human-genome single chip microarray by the end of the year, the company is keeping mum on details of its technology.

Affymetrix Product Details

The Affymetrix HG-U133 pro-duct is the next step beyond Affymetrix’s two-chip microarray set, and contains the probes that represent the company’s decision as to what is important in measuring transcripts from the the human genome. Pricing on the chip will range from $300 to $500, depending on volume purchased, the company told The New York Times. It did not respond to a BioArray News request for comment.

The company said that the content includes 10,000 new probe sets representing 6,500 new genes. The new information has been verified against the latest version of the publicly available genome map, the company said. The probe design strategy of the new array is identical to the two-chip set.

The company is also launching an 11-micron version of its HG-U133A array, which previously has been arrayed at an 18-micron format. The version 2 array contains probe sets identical to the previous product, the company said.

Affymetrix manufactures its microarrays using photolithography, the manufacturing method of the semiconductor industry, using ultraviolet light to deposit, in situ, bases at a length of 25 mers onto a quartz glass substrate.

The new arrays are only readable on the new Affymetrix scanner, which was released in January.

Agilent Product Details

Agilent spots 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 is adding additional content from Incyte and public databases.

The company’s probe design seeks a perfect match to a sequence as its standard in probe design, Doug Amorese, biochemistry/chemistry R&D manager for the com-pany’s BioResearch Solutions group told BioArray News.

“Good [match] is not good enough,” he said.

“What we have done is combined the expertise that we have developed in printing and probe design and validation with a maturing understanding of the human genome to generate a product that represents the genome as well as any product today can,” he said.

Agilent, a Silicon Valley-based spin-off from Hewlett Packard, uses an ink-jet process to manufacture its microarrays, which are printed onto an open-format glass slide, readable in any commercial microarray scanners.

The company is regarded as the No. 2 industrial microarray producer with a product line that, anecdotally, is gaining share in a market where the majority of users spot their own slides.

While Agilent is not identifying its beta customers, no doubt one of them is Paradigm Genetics, which in October 2002, won a five-year contract from the National Institute of Environmental Health Sciences, worth up to $23.9 million, to produce gene expression data for a national reference database on the effects of chemicals on biological systems. The company uses Agilent Technologies’ microarrays.

Others in the Game

Amersham Biosciences, the No. 3 player in the market, has refrained from entering the contest but said last week that it will bring to market a single CodeLink microarray product containing 40,000 probes in 2004.

NimbleGen Systems of Madison, Wisc., offers the whole human genome on an array for its microarray-analysis customers.

And, the European Molecular Biology Laboratory has created its own whole-human-genome microarray, comprised of cDNA probes, with hopes to offer the product to its scientific collaborators.

This rush to a product milestone, however, does not answer questions about the accuracy of the technology, the reproducibility of results, the sensitivity of the assays, and concordance between platforms that scientists as well as the FDA are increasingly echoing.

“Microarrays are a research tool to develop hypothesis, not a hypothesis tester,” said Brockman.

— MOK

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