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FDA Adopts Rosetta’s Syllego Platform to Analyze Genotyping Data Under VXDS

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The US Food and Drug Administration has licensed Rosetta Biosoftware’s Syllego genetic analysis software to keep pace with the rise of genotyping data submitted under its Voluntary eXploratory Data Submission program.
 
The FDA will integrate the software with its in-house informatics system, ArrayTrack.
 
Weida Tong, director of the Center for Toxicoinformatics at the FDA’s National Center for Toxicological Research, told BioInform that the center chose Syllego in order to accomplish two goals. First, he said, the FDA needed a software tool to handle genotyping data, which is a relatively new type of information for the agency’s VXDS program.
 
Secondly, Tong told BioInform, the agency needed the platform for its work with the public/private MicroArray Quality Control Consortium, which earlier this year expanded its scope to identify “best practices” for genome-wide association studies.
 
Sasha Paegle, director of product management and alliances with Rosetta Biosoftware, told BioInform that while the FDA is already using its Resolver gene expression analysis software as part of the VXDS program, the new system serves a different purpose.
 
“Resolver is focused on allowing scientists to manage and analyze gene expression data, whereas the Syllego system is focused on genetic data management,” said Paegle.
 
Paegle said that Rosetta has identified a “large opportunity” for Syellego in the genotyping market.
 
“There have been a number of genome-wide association studies that have been published or are about to be published,” said Paegle. “That means people need to collaborate and make that data comparable ... and there are new groups moving in this direction.”
 
Syllego should appeal to these potential customers, Paegle said, because it allows users to share their analysis results. “The system is really designed to enable these scientists to focus on their questions and be able to communicate their study outcomes,” Paegle said.
 
The VXDS program evolved out of the FDA’s Voluntary Genomics Data Submission program, which the agency launched in 2004 in an effort to encourage pharmaceutical firms to submit microarray data in a no-risk setting. Since then, additional types of omics data have become more common in drug discovery, so the FDA has expanded the scope of the effort.
 

“Resolver is focused on allowing scientists to manage and analyze gene expression data, whereas the Syllego system is focused on genetic data management.”

The FDA’s ArrayTrack database serves as the core of the VXDS program because it is the primary repository for all the data submitted under the program. ArrayTrack includes a number of in-house and commercial analytical packages, including Rosetta Resolver. It is also integrated with several third-party tools such as GeneGo’s Metacore, Pathart’s and Ingenuity’s pathway analysis tools; and JMP Genomics’ statistical analysis tool.
 
Tong said that the FDA also has an agreement to integrate ArrayTrack with Spotfire’s DecisionSite platform.
 
He said that the FDA is currently adding a library of genome-wide association study data to ArrayTrack, and that the agency plans to integrate Syllego with the system once that process is complete.
 
Tong said that the FDA already has three genome-wide association submissions from pharmaceutical firms under VXDS, so it hopes to have the complete analysis system in place “within the next few weeks.”
 
Asked if he foresees any bottlenecks in the integration, Tong said it is too early to tell. “It’s very new and not many pharma companies are using this tool,” he said. “The [feedback] we received from industry is that they have not started to use the Syllego [software platform] yet.”

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