BARCELONA, Spain — Seeking to keep up with new higher-density microarray platforms on the market, two large tool vendors last week unveiled new scanners capable of higher-resolution image detection, and more powerful software.
The first shop, Tecan, said it is now taking orders for its PowerScanner, which can scan arrays to the 2-micron level and image millions of features from as many as 48 slides in one run. The tool, which was developed in consultation with Agilent Technologies and NimbleGen, will begin shipping in September.
The second vendor, MDS Analytical Technologies, is taking orders for its Axon 4300A and the Axon 4400A, the second of which can scan arrays at the 2.5-micron level, and is faster and more sensitive than its older 4200A system. These products will begin shipping in July.
For Tecan and MDS, the debuts herald a renewed period of competition in the market for flexible, sensitive, and affordable scanners after years of selling well-established systems.
Tecan, for example, has sold its LS Reloaded scanner since 2004. The LS Reloaded can image arrays to the 6-micron level. But according to Ralph Beneke, microarray product manager for the Swiss company, new chip formats, especially the 2.1-million feature arrays introduced by rival NimbleGen as part of its new HD2 generation of arrays, have forced the company to develop higher-resolution scanners.
“After seven or eight years we have seen the need for new scanners that help in detecting beyond the 5-micron level,” said Beneke, who spoke to BioArray News during Select Biosciences Advances in Microarray Technology conference, held here last week. “There is a consensus that 2-micron-level detection is the minimum acceptable right now.”
Beneke stressed that the PowerScanner is not a replacement for the LS Reloaded, which Tecan will continue to sell and support. The PowerScanner will also cost about the same as the LS Reloaded at around €90,000 ($139,000).
There will be a new version of Tecan’s gridding and feature-intensity extraction software for users of PowerScanner, which will add 5 percent to the cost of the scanner. However, Beneke said that customers are likely to stick with the software they know best and stressed that the new software is not a necessity.
“This is not a must-buy-it when PowerScanner is used, because the .tiff [image file] format is compatible to any other feature-extraction software [available] from [MDS] or Agilent or NimbleGen that [can] handle large image size with millions of features,” said Beneke.
Meantime, MDS has developed its two new scanners to handle the new, high-density formats offered by Agilent and NimbleGen, and will follow systems that have been a market staple.
Varshal Davé, director of microdissection and microarray marketing at MDS, told BioArray News here last week that unlike Tecan’s debut, MDS’ scanners will replace the company’s Axon GenePix 4200A scanner, which it launched in 2003.
Like the 4200A, the GenePix 4300A offers 5-micron-level detection and a throughput of 36 slides per run. The difference is that the new system has improved uniformity, sensitivity, speed, and reliability.
“There is a consensus that 2 micron-level detection is the minimum acceptable right now.”
The 4400A, though, is MDS’ next-generation scanner. The system can scan images at the 2.5-micron-level and has features similar to the 4200A and the 4300A. Davé said that going from 5-micron-level detection to 2.5-micron-level detection took a considerable R&D effort.
“It was a significant development process,” he said. “We had to change several components within the system, including the optical path, mechanical components, the slide-holding mechanism, and the performance of the Y-direction stage in order to increase the speed of the system.”
Like Tecan, MDS also consulted with Agilent and NimbleGen during the development of the Axon 4400A. The company also believes that the 4400A will be able to handle future, higher-density generations of arrays.
“We have been working with a lot of our partners. We validate the performance of the systems with the content providers,” said Davé. “We have done a lot of testing with the NimbleGen HD2 format, for example, and we have come to the conclusion that we meet all current needs and can address future needs as well.”
Part of MDS’ scanner upgrade will include a new version of its software, GenePix Pro 7, which Davé said is MDS’ “first major redesign in years.” He said it is configured to work with Windows XP and Windows Vista 64-bit systems. Earlier versions were compatible with 32-bit computer systems, but Davé said that the scanning of the new, higher-density arrays results in “monstrous image files.”
GenePix Pro 7.0 is also configured to work with multi-pack Agilent arrays and allows users to scan sub-regions of arrays and treat each image like it was an individual scan. “It is just keeping up with the demands of the market,” said Davé.
Tentative pricing for the 4400A is between $100,000 and $120,000. Davé pointed out, though, that unlike some segments of the array market, the next-gen scanner market is likely to be driven more by performance than price.
“Our scanners are some of the higher performance systems of the market, and so they are among the higher priced,” he said. “The high density market right now is more performance-driven, whereas applications outside of the super-high-density chips tend to be more price-driven.”
Innopsys and Agilent
While a number of platform providers have exited the array business over the past year and a half, including GE Healthcare, Applied Biosystems, Nanogen, Plexera, both Tecan’s Beneke and MDS’ Davé said that the tools market, especially the market for scanners, has performed differently, with the entry of several new players and an increase in competition.
“The array provider field will continue to shrink down to a number of between three and five players,” Beneke said. “From an instrument providers’ point of view, if you have an open system, you will see around the same number of systems on the market, between three and five.”
One of Tecan and MDS’ newer rivals is Innopsys, a Paris-based firm that launched its first scanner, the InnoScan 700, in 2006, followed by a 24-slide throughput autoloader last December.
“We launched our first scanners InnoScan 700 in February 2006 and the autoloader version, InnoScan 700 AL last December,” Innoscan CEO Stephane Le Brun told BioArray News this week. While the InnoScan 700 can scan at the 10-micron level, the company in June 2009 plans to launch the InnoScan 900, which will be able to scan arrays to the 1-micron-detection level.
“It has to be noted that 1-micron images are extremely big — 5.74 gigabytes for a full slide,” said Le Brun.
He said that Mapix, the company’s internally developed software, can already manage files of that size. Like the InnoScan 700, the InnoScan 900 will also exist with a 24-slide autoloader function.
“A powerful batch mode in our Mapix software allows users to run 24 slides and to make their gridding and quantification in only one step,” said Le Brun. “In the case of high-resolution slides, the autoloader is of course of interest; you don't have to wait for long scanning time.”
The elephant in the room is Agilent, which, unlike NimbleGen, sells its own internally developed hardware along with its content arrays. Though the company recently released a new version of GeneSpring to accompany its higher-density chips, it has so far been mum on the issue of launching a scanner to succeed its 48-slide scanning DNA Microarray Scanner (see BAN 2/19/2008).
Agilent did not respond to an e-mail seeking comment in time for this publication. According to MDS’ Davé, the main competition in the high-density scanner market is likely to be four-way. “Between Tecan, us, Innopsys, and Agilent, there aren’t that many players serving this market,” he said.