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Agilent Debuts New Scanner as It Prepares To Launch Next-Generation Array Platform

This article has been corrected to reflect the accurate pricing of Agilent's scanner upgrade.
In advance of rolling out its next-generation, high-density microarray platform later this year, Agilent Technologies this week released a new version of its DNA Microarray Scanner that allows users to scan array images at up to 2-micron resolution.
The debut of the new instrument, which Agilent claims has better resolution and dynamic range than older models, also coincides with new scanner launches from a variety of tools companies, including Tecan, Innopsys, and MDS Analytical Technologies.
Agilent’s impending 1-million-feature microarrays will most likely become available by the end of the year, according to Jeffrey McMillan, the firm’s workflow product manager. Agilent currently sells arrays with up to 244,000 features per slide.
Agilent decided to launch the new scanner ahead of the new arrays in order to give customers time to integrate the system into their existing workflows, and so that they are prepared to handle the new chips when they hit the market.
“Based on the chips that are on the market today, you don’t really need the new scanner,” McMillan told BioArray News this week. “But people are getting themselves prepared for what will happen a few months down the road. Our users would like to get the scanner installed and qualified before they begin running the new generation of arrays because it would be hard to qualify all of those things at the same time.”
The scanner is designed to deliver data from Agilent’s current generation of 65-micron feature arrays, as well as output from the 30-micron features of the impending million-feature arrays. The tool enables users to scan images with resolutions of 10 microns, 5 microns, 3 microns, and 2 microns, McMillan said. Agilent’s previous scanner had 5-micron level resolution capabilities.
Like Agilent’s previous scanner, the new instrument is an open system that enables customers to scan both Agilent and non-Agilent arrays. The scanner works with a pre-existing 48-slide carousel.
McMillan pointed out that because Agilent offers arrays in multipack formats with up to eight individual arrays printed per slide, users hypothetically can scan 384 different arrays at a time using the new scanner.

“It is a solution-engineering approach I see — including optimization of chemistry, protocol, process control, array layout and production, and sophisticated software modules.“

However, the company has chosen to tout its system’s resolution and workflow over its throughput. The new scanner uses SureScan high-resolution technology, which Agilent describes as a combination of the system’s autofocus and high-resolution scanning capabilities plus its internally developed feature-extraction software.
“We don’t just concern ourselves with producing a nice looking image,” said McMillan. “It is about creating that quality image and applying some intelligent image analysis that takes advantage of everything you know about the array. Since we manufacture our arrays, we know our arrays best.”
McMillan also said that the dynamic range of image scans is better than previous versions of the scanner. “We have a feature that has extended dynamic range, which gives you two scans at two different detector gains and incorporates that into a result file,” he said. “With high gain and low gain, you can get entire dynamic range, and you don’t have to worry about scanner range. You can get a 20-bit scan in a single scan.”
Agilent has two ways to deliver the new scanner to customers that have older versions installed. Where available, customers can request an infield upgrade in which an Agilent service technician visits their lab, breaks down the old scanner, and rebuilds it to include the new scanner capabilities. The second option is to ship the system to an Agilent repair center for the upgrade.
According to McMillan, the list price for the upgrade is around $38,000. Customers who wish to purchase the new scanner pay $149,500. The package includes two licenses of image-analysis software that run on Windows 32-bit or 64-bit systems. McMillan added that customers can save 10 percent of the scanner price if they purchase the equivalent value of that discount in Agilent arrays.
The Competition
Agilent said the scanner’s feature-extraction software gives the instrument an advantage over scanners made by rivals like Tecan, Innopsys, and MDS. A new version of software ships with the scanner and is designed to work with the large image files common to high-resolution scans.
Because Agilent customers typically use different software depending on the application — for instance, comparative genomic hybridization software for CGH experiments and GeneSpring for gene expression work — McMillan said the company will integrate these packages with the feature-extraction software in coming months in anticipation of the next-generation array launch.
“If our software knows what the array design is, it can process the arrays more efficiently without asking the user to do anything,” McMillan explained. “For instance, there might be canned analysis for expression work that we can do without the user doing any work. It will all be as seamless as possible. That is how we position ourselves against our competitors.”
These rivals are hoping to meet the demand for next-generation scanners. Over the past month Tecan, MDS, and Innopsys have committed to launching new instruments this summer (see BAN 5/13/2008, BAN 6/3/2008).
Switzerland’s Tecan in September plans to deliver its 2-micron-resolution PowerScanner, which costs around €90,000 ($139,000). Like Agilent’s scanner, the PowerScanner can scan up to 48 slides in one run and is designed to scan higher-density chips.
Sunnyvale, Calif.-based MDS, meantime, plans to debut its Axon GenePix 4400A next month. The system delivers 2.5-micron-resolution and can scan 36 slides in one run. The 4400A will cost between $100,000 and $120,000, according to the firm.
Finally, France’s Innopsys this month will debut its InnoScan 900, a scanner capable of up to 1-micron resolution with an autoloader option that allows users to scan 24 slides in a single run. Innopsys is asking €65,000 for the scanner or €85,000 for the scanner plus the autoloader.
While such factors as throughput and cost will no doubt be important in the minds of customers, most vendors insist that, in the end, the market for next-gen scanners will be driven by overall system performance.
“It is a solution-engineering approach I see — including optimization of chemistry, protocol, process control, array layout and production, and sophisticated software modules, all-in-one dedicated to each other — which can make a package really superior to what several stand-alone systems can provide,” Ralph Beneke, Tecan’s microarray product manager, told BioArray News last week.
McMillan said that Agilent has a similar take on the market. “Our position is that the Agilent scanner is superior, given all the integration that we do with the software and even the downstream-analysis capabilities,” he said. “What we are trying to do is put together an entire workflow, not just put together a scanner.”

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