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Stratagene Expands ArrayAssist Platform with Copy Number Tool; Tiling Arrays Next in Line

Looking to carve out a niche in the bioinformatics market for high-density arrays, Stratagene has launched a new software package for copy number analysis and intends to follow that up with an application for tiling array analysis later this year.
ArrayAssist Copy Number, which Stratagene launched in late August, follows the January release of ArrayAssist Exon, which was the first in a series of applications for high-density array analysis that the company is planning to build upon its flagship ArrayAssist Expression package.  
“We’re looking at trying to support as many of the higher-density arrays as we possibly can, and that’s why after [ArrayAssist] Exon, copy number was next for us, because we support both the 100K and the 500K arrays from Affymetrix,” David Edwards, director of software solutions at Stratagene, told BioInform.
High-density arrays from Affy and other chip vendors have spurred a new wave of innovation in the microarray field, enabling a wealth of new application areas beyond gene expression — from exon and tiling arrays to ChIP-on-chip and array-CGH.
Stratagene’s goal is to be among the first to market with easy-to-use software in many of these areas. “We’ve decided to focus initially on the places where we feel there isn’t as much commercial support from other software packages,” Edwards said.
In the case of copy number analysis, which detects chromosomal amplifications or deletions and correlates them with phenotypic conditions, Stratagene certainly appears to be ahead of the curve. The only other commercial vendor that Affymetrix lists in its GeneChip-Compatible Solutions Catalog for that area is Partek.
Edwards said that most researchers analyzing chromosomal copy number arrays use Affy’s CNAT copy number tool, CNAG from the University of Tokyo, or dChipSNP from Harvard University. While these tools are strong algorithmically, they are geared toward expert users and do not offer a user-friendly front end — an area where Stratagene feels it has a competitive advantage.
“The way we’ve tried to focus our efforts and to make ourselves a little different than everyone else in the space is really on the end-user biologist,” Edwards said. “We see a need for a workflow that kind of guides the biologist through: ‘What analysis do I do next? What are the best kind of default settings?’”
While gene expression analysis is a standard tool in many labs now, the analytical workflows for new array applications are still in flux, Edwards said. “Copy number analysis isn’t really a done deal, and working with a number of customers and trying to reflect their workflow, I find that it’s a lot more interactive than some of the other types of analysis that are done for standard 3’ IVT.”
The challenge from a software-development perspective, he said, is building a user-friendly package that is flexible enough to evolve as the field progresses. “You want to build something that has the math at the back but doesn’t lock you down,” he said.
Edwards couldn’t provide an estimate for the potential size of the software market for copy number analysis, but he said that it’s a key component in the company’s plan to round out its microarray analysis offering.
While copy number analysis is “obviously not as big as gene expression,” Edwards noted that it’s an important tool in cancer research and other disease areas and is finding a place within the growing systems biology toolkit.
“One of the other reasons we were interested in supporting copy number is we see more and more people doing multiple types of expression analysis, and then trying to look at what genes are coming up in the context of those analyses,” he said. “It fits into a scenario where people do a variety of different experiments.”

“We’ve decided to focus initially on the places where we feel there isn’t as much commercial support from other software packages.”

Edwards said that Stratagene plans to expand ArrayAssist’s capabilities into tiling array analysis and other application areas, and also to support chip platforms from multiple vendors. He said that the company plans to announce formal support for “one of the other very popular chip platforms shortly.”
Stratagene is also planning a fall release for its next version of PathwayArchitect, a pathway analysis package developed in collaboration with Strand Life Sciences. 
Strand is also the co-developer of the ArrayAssist product line, which is built upon its Avadis data-mining platform.
Edwards said that Stratagene’s longer-term software development strategy will likely build upon the strengths of Avadis. While a number of microarray analysis software firms, such as Rosetta Biosoftware and Agilent’s GeneSpring division, have recently launched software packages for proteomics analysis, Edwards said that Stratagene hasn’t decided whether to head down that path or not.
“We’ve got some ideas for tools that are a little bit broader in the systems biology area,” he said. “I think we’ll probably move more into generic biological data analysis tools than something specific.” 

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