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Affymetrix Introduces Its New Scanner As Agilent Abruptly Ends Arrangement


One of the most symbiotic arrangements between competitors in the microarray space has come to an end. On Monday, Ned Barnholt, Agilent Technologies’ CEO, told BioArray News that it has concluded its long-time scanner manufacturing agreement with Affymetrix.

“We have essentially terminated the agreement,” Barnholt said, adding that the company is no longer manufacturing the scanner.

The five-year-old relationship between the two companies had been scheduled to end by March of this year, so the termination of this odd collaboration between two of the largest microarray players does not come as a complete surprise, but the abrupt ending does indicate a raising of the stakes in the marketplace as the new year begins.

On Monday, with a statement released before most early-birds had checked in, Affymetrix announced the new scanning instrument it will sell in its GeneChip brand product line, replacing the one manufactured by Agilent.

Affymetrix said it will commercially launch the scanner, the GeneChip 3000, at the Lab Automation 2003 conference in San Diego on Feb. 2-4. The scanner is the fourth instrument it has sold in its integrated microarray system. In its present configuration, the scanner is sold with a Dell Computer-manufactured workstation loaded with Affymetrix Microarray Suite software.

The GeneArray scanner, which is manufactured by Agilent Technologies, has been the scanner for the GeneChip system in a contractual manufacturing arrangement that began with Hewlett-Packard in 1997, and extended through the spinout four years ago of Agilent Technologies, until now.

The new Affymetrix scanner is smaller than previous models and is manufactured by Affymetrix’s Boston unit, which has its roots in Genetic MicroSystems, the Woburn, Mass., instrument maker acquired by Affymetrix in September 1999 in a stock transaction valued at $264 million.

Affymetrix CEO Steve Fodor said the new scanner will follow the manufacturing curve for Affymetrix’s microarrays, which are expected to increase in resolution over the next few years, traveling down a path from the 18-micron feature size for the company’s newest chips to 10-micron features within five years. The goal is to represent the entire human genome on one glass chip.

“The new scanner supports the technology and is configured to evolve,” Fodor said in a presentation before a standing-room-only crowd at the JP Morgan H&Q Conference in the Westin St. Francis Hotel in San Francisco this week. The hardware includes a solid-state laser and is adaptable for automation — a feature that will be available, Fodor said, within the year: “It will take lots and lots of chips.”

The company has released a small number of machines to early-access partners who are testing the PC-sized system.

“It puts control of technology going in our hands . . . so we can evolve the system,” said Robert Lipshutz, vice president of business development.

According to Affymetrix, the new scanner can scan current arrays in 5.5 minutes. The scanner will include the company’s scanning system, Flying Objective, an optical architecture that, according to the company, provides consistent excitation and emission paths over the entire scan field. The scanner has a 13x21 inch footprint and uses a solid-state laser, which requires no external power supply or a cooling system.

In 2001, Agilent Technologies launched the G2565AA, a next-generation microarray scanner, which allows automatic imaging of 48 chips at a time. This is a different product than that sold with the Affymetrix GeneChip system.

Agilent told BioArray News that it draws a distinction as clear as a pane of glass between its implementation of microarrays and Affymetrix’s.

“We are dedicated to open standards and our technology is developed in accordance with those standards,” Christina Maehr, an Agilent spokesperson, said. “The scanner is part of a solution — you can’t run an experiment without a scanner to run it on. We think the market is moving toward an open platform, the 1x3 inch glass slide. We think that more than 50 percent of customers are still on the glass slide, and that’s an untapped market. We don’t think academics will be able to make the huge investment that it takes for an Affymetrix system.”

Agilent’s scanner lists for $120,000. Affymetrix did not release a price for its system.

Affymetrix officials told BioArray News that they plan to continue to support the Agilent-manufactured scanners. The company said it will have an upgrade program to help customers make the transition to the GeneChip Scanner 3000. Details will be announced in February.

At least one academic user is not ready to make the leap.

“We do not have any plans to use the new scanner anytime soon,” Shrikant Mane, director of Yale University’s Affymetrix GeneChip Resource laboratory, said in e-mail.


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