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Mike Hunkapiller, ABI, Stay Mum On Details of its Expression Array System

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Mike Hunkapiller, president of Applied Biosystems, doesn’t seem to be auditioning for the job of head cheerleader for analysis by microarray hybridization, at least when it comes to the new resequencing technology produced by Affymetrix.

Monday morning, Hunkapiller, wearing the dark blue power suit of an industry leader over the sensible black shoes of a scientist, addressed the pinstripes of the financial world at the UBS Global Life Sciences Conference in New York City.

In response to a question from a financial analyst on Affymetrix’s most recent announcement of a microarray-based resequencing product, he, unsmilingly critiqued the product.

“Sequencing by hybridization is always limited,” he said. “You get gaps in sequencing by this method, and the chips have to be custom designed, which means a startup time of two to three months, and they aren’t providing a large section of the genome.”

However, ABI’s 3730xl system, he said, has a throughput that is orders of magnitude higher.

Expect that same attitude to prevail as the sequencing Goliath begins to compete in the gene-expression analysis marketplace, where it enters with a relatively untested technology platform and promises of cheaper, faster, and better.

In July, ABI splashed into the gene-expression market with an announcement of plans to introduce by year’s end a product it calls its Expression Array system, a microarray instrument with its first consumable, a single microarray chip that contains DNA probes representing the entire human genome. That announcement alone was enough to ignite a race in the industry to create, and sell, similar high density microarrays.

Since then, the company has been notably quiet about technical details of this new platform that it says will use 60-mer probes anchored to a nylon membrane. There was no new information forthcoming from Hunkapiller, who later in the day flew to the GSAC conference in Savannah, Ga. He told BioArray News that the company is following advice and not giving out detailed information on its new gene-expression platform in order, apparently, to abide by US Securities and Exchange Commission regulations on disclosure.

Still, the company has John West, vice president for DNA platforms, out in the field promoting the product before analysts, while the ABI sales force is testing buying sentiment among its customer base.

The only new piece of information on the system was a black-and-white picture in a PowerPoint presentation, providing the sort of view one might get from looking across a room at a large metallic box, the size of a clothes dryer, along with a monitor and PC, with several cardboard product kits arrayed in front of it.

“[The Expression Array System] will have a higher sensitivity of detection than other array systems,” Hunkapiller said. “It will allow users to get data out of a larger number of genes than in today’s systems [which] are buried in [background] noise. And, that’s the level of technical detail we are willing to give right now,” Hunkapiller said.

On a macro level, Hunkapiller said that the company is focusing on creating products will enable researchers to integrate information from one set of experiments with another, and then tie it into the vast databases that are available.

“We are forcing our product developers to think how tools can be used together,” he said. “We didn’t originate the concept, just look at the large research centers that are becoming more prevalent.”

For gene expression, Hunkapiller said the company’s goal is to enable gene expression analysis to go from start to finish on an integrated platform.

The Applied Biosystems Expression Array System will be integrated with Applied Biosystems Sequence Detection System (SDS)-based products for gene expression analysis and the Celera Discovery System online platform.

The company has a commitment to research, said Hunkapiller, a PhD from Cal Tech who joined the company’s R&D ranks in 1983. Still, the 14 percent of sales the company spent on R&D last year, will fall to 10 to 12 percent of sales this year.

“For the last couple of years, we have made a substantial investment to make the tools [that are starting to come to the market now],” he said. “A lot of the products we are developing are still in the early stages of production. I hope we have chosen wisely.”

One thing that Hunkapiller was able to clarify is that the microarray platform being rolled out this year is not based on parent company Applera’s US Patent No. 6,573,089, “Method for using and making a fiber array,” which was granted June 3. That patent, he told BioArray News, represents a next-generation microarray.

If so, the microarray technology that some day rolls out of the ABI labs is a new take on using fiber optic wires and microfluidics as a basis for a mass-produced instrumentation system for gene-expression analysis. The system, which starts by immobilizing oligo probes onto fibers, can use any type of label capable of producing a detectable signal, requires no image, avoids washing, and allows for real-time reading, and can contain 100,000 or more fibers for high-density use.

“The fiber arrays of the invention provide myriad advantages over currently available micro-arrays,” the patent reads.

The ‘089 Applera patent references 13 patents held by David Walt, the Tufts University chemistry professor whose fiber-optic based arrays are commercialized by San Diego-based Illumina.

Walt declined comment.

Maria Schiza, an analytical chemist at the University of South Carolina and an expert on chemical sensing and imaging using novel fiber-optic probe designs, told BioArray News that the technology in the patent seems plausible.

“I think the invention could potentially work reliably as far as one can avoid cross-interaction of the probes and analytes used and also take into consideration the spectral and spatial resolution provided from the optical setup one has,” she said in an e-mail message.

The microarray industry might have to wait a few years to see for itself. Meantime, it is waiting for more information on this generation of ABI’s technology.

— MOK

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