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With New Axon ImageXpress Scanners, Affymetrix Takes Steps to Automation


Axon Instruments and Affymetrix last week announced a collaboration to develop a new instrument for use in the high-throughput analysis of a new generation of Affy’s GeneChips.

The instrument is to be based on Axon’s ImageXpress automated cellular screening platform, and will be used in an experimental-stage high-throughput array system being developed in Affy’s research labs, the companies said.

The ImageXpress instrument scans an entire 384-well plate at full resolution with two fluorescence images per well — in about 20 minutes, Axon says in its sales brochure. The system is designed for high-resolution screening processes. It comes with software and Nikon lenses. It is pictured as a two-monitor configuration, with a computer, and an instrument the size of a very large ice chest.

An Affymetrix spokesman took great care to say that this instrument is completely separate from the GeneChip 3000 scanner that the company announced in January and is now selling.

“One thing that I want to be clear about, up front, [is that] the scanner we have recently launched represents the cornerstone in the future generations of our technology,” John Sowatsky, vice president of Affymetrix’s systems business unit, told BioArray News.

The GeneChip 3000 scanner is the fourth scanner that Affymetrix has sold in its integrated microarray system, and it replaces one that was manufactured by Agilent Technologies in a contractual manufacturing arrangement that began with Agilent parent Hewlett-Packard in 1997, and expired in February. The GeneChip 3000 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. Affymetrix expects to introduce an extension for the system in August that will enable the processing of several dozen GeneChip microarrays simultaneously.

Affymetrix took delivery of three of the ImageXpress instruments, the Axon-Affymetrix press release said. List price for the scanner is $200,000.

Bringing Automation to the GeneChip

The new scanner is part of a research project being developed by Affymetrix and one that the company has just recently started mentioning in public forums.

The company is analyzing how to use its GeneChips in a high-throughput system, such as 96-well microtiter plates. The company has discussed slicing its quartz wafers of microarrays into pieces small enough to fit in the bottom of a plate well, creating an automated system that would be able to conduct large numbers of assays in parallel.

“We believe that these kinds of formats may offer scientists another mechanism for looking at a larger number of samples and a greater amount of genomic information by leveraging 96 microarrays at a time,” said Sowatsky.

While Affymetrix brought a high standard of quality to microarray analysis, the company has yet to create a system that would enable an industrial-scale and automated process. Such a process today would include large-scale drug discovery research, but in the future, it might be clinical trials with large numbers of samples requiring very consistent processing.

Diagnostics are less of an opportunity for this instrument and system, Sowatsky said.

“We are working with partners there, and it’s more likely that they will dictate the instrument platform in those instances,” he said.

Still, the 96-well-and-up system is in its early stages, Sowatsky said.

“We are just beginning to explore it technically and we don’t want to mislead anyone into thinking that we have anything more than a research offering,” he said.

The one thing learned so far is that the new format requires a different type of instrumentation, one that is not created to handle Affy’s little black plastic GeneChip holder.

“We went with Axon because it could be altered for our means,” said Sowatsky. “This was the most expedient way of being able to do some proof of principle on the 3x5 microtiter-based GeneChip arrays. And, if we move forward, there are no commitments to use the Axon scanner as the basis of a commercial platform.”

The press release was a way to make sure that people understood where the company is creating new cartridge formats and different ways to apply its products, he said.

Axon officials were not available for comment.

Getting Small

The 96-well microtiter plate format is a technology that sets a few eyes sparkling in the Santa Clara, Calif., headquarters of Affymetrix. As the company improves its GeneChip manufacturing process, and is able to shrink the features it puts on a microarray, it could cut its wafers smaller and smaller, without a loss of resolution. Or, it could make less dense chips that cost less and can be used as diagnostic instruments, another idea the company is pursuing vigorously.

The chips are ready, according to Sowatsky. “We can do it right now,” he said. “We have basically built microtiter format arrays, now it’s just a matter of scanning it.”

Axon was chosen, he said, because “the company has a good track record in scanners, is local, and was willing to do customization,” Sowatsky said.



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