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For Genotype Data, FDA Adopts Rosetta's Syllego

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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 FDA’s National Center for Toxicological Research, says that the center chose Syllego in order to accomplish two goals. First, he says, 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, 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, he says.

Sasha Paegle, director of product management and alliances with Rosetta Biosoftware, says 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,” says Paegle.

“There have been a number of genome-wide association studies that have been published or are about to be published,” says Paegle. “That means people need to collaborate and make that data comparable ... and there are new groups moving in this direction.”

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.

— Laurie Weigler

Short reads

Symyx Technologies has closed its $123 million all-cash purchase of Elsevier’s MDL Information Systems Business. The company has also established a $25 million backup line of credit for capital and future growth initiatives.

Dutch pharmaceuticals developer Organon has extended and expanded its license of GeneGo’s software and database products. Under the new agreement, Organon has also added a new license for GeneGo’s Metalink software.

InforSense and GenomeQuest are slated to integrate technologies for improved probing of data and sharing of work processes by research domains. InforSense customers will have access to GenomeQuest’s sequence and patent record databases directly through the InforSense platform.

GenoLogics announced that Vanderbilt University’s Jim Ayers Institute for Precancer Detection and Diagnosis has implemented its Proteus laboratory and data management solution. The technology will help the institute in its research of early identification and treatment of colorectal cancer.

Progeniq, the Signapore-based reconfigurable computing applications vendor, has announced that it will join Microsoft’s bioIT Alliance. The focus of the alliance is to accelerate drug discovery and realize the potential of personalized medicine.

Patents

US Patent 7,276,335. Designing compounds specifically inhibiting ribonucleic acid function. Inventor: Paul Schimmel. Assignee: Massachusetts Institute of Technology. Issued: October 2, 2007.

This patent claims a “method for designing compounds specifically targeting RNA sequences, based on the discovery of short, specific sequences within RNA that are critical to function, using modeling of the compound to effect binding to the nucleotide sequences in the RNA in combination with secondary and/or tertiary structure associated with the minor groove of the RNA in the region of the critical sequences.”

US Patent 7,277,798. Methods for extracting similar expression patterns and related biopolymers. Inventors: Tsunehiko Watanabe, Yasuyuki Nozaki, and Ryo Nakashige. Assignee: Hitachi Software Engineering. Issued: October 2, 2007.

The patent covers “methods for extracting similar expression patterns and related biopolymers considering natures that are characteristic of expression data of, for example, genes. ... By comparing the selected segment of the expression pattern with expression patterns of a group of candidate genes or the like, genes having an expression pattern with at least a partial similarity are searched from the group of candidate genes.”

Data point

125 million

The number of functional relationships extracted from PubMed in the ResNet database that comes with Ariadne’s Pathway Studio.

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