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Moving Chips to the Clinic - Taking AIM to Track Analysis

Getting a satisfying answer from a microarray experiment requires managing a lot of data, and doing many manipulations of the data. However, researchers have few efficient methods available for keeping track of those critical analysis steps.

"People have just started to realize that what they do to analyze [experimental] images is just as important as the biology they are trying to observe," says Jack Pollard, principal investigator for bioinformatics consulting firm 3rd Millennium.

3rd Millennium recently received a Small Business Innovative Research contract from the Department of Defense to develop what it is calling AIMS — Analysis Information Management System. This system will not only track analytic processes, but it also will connect to a laboratory information management system (LIMS) to link the biological information associated with the samples to the final analysis. The laboratory that is contracting for the system is the Molecular Diagnostics/Pathogenesis Division of Retrovirology at the Walter Reed Army Institute of Research in Rockville, Md.

Many programs store images that are generated during the microarray analysis, but typically the files used to contain them don't contain information about the methods used to generate the images. BioDiscovery's GeneSight is one of the few gene expression analysis tools that has an audit feature, which records specific analytical steps. The company is now offering GeneDirector, which includes GeneSight packaged with a LIMS-type system, CloneTracker for array design and ImaGene for image analysis.

Most labs today use multiple programs for microarray analysis. The system 3rd Millennium is developing will keep track of analysis done with any of the software packages DOD researchers are using. "As they add packages, adjustments have to be made," Pollard says, "but that is not a complicated process." Once this system is completed, 3rd Millennium could adapt it for future clients.

"There's nothing so frustrating as getting a good correlation, and then realizing you don't know how you got there, and you can't repeat it or understand how you derived it," Pollard says. "Until there are data standards for microarrays, and all the packages talk to each other, we're going to have to do a lot of customization."

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