GAITHERSBURG, Md.--Gene Logic will be the first company to use Affymetrix's GeneChip probe arrays to build large, commercially available gene expression database products, the companies announced last week. The collaboration with Affymetrix was first initiated by Oncormed, which was acquired by Gene Logic last year.
Stephen Push, Gene Logic's vice-president for corporate communications, told BioInform that the gene expression databases created with GeneChip probe arrays will be sold on a nonexclusive basis to pharmaceutical and biotechnology companies.
Gene Logic currently develops customized genomic databases and markets two gene activity reference databases, Gene Express Normal, and Toxicology/Pharmacology Express, for pharmaceutical customers using its patented restriction enzyme analysis of differentially expressed sequences (Reads) technology.
The company said the initial chip-based database will be built by analyzing expression patterns from more than 40,000 human genes and gene fragments in a wide variety of normal and diseased tissues contained in Gene Logic's proprietary tissue repository.
Ultimately, the database is expected to contain hundreds of millions of data points. Gene expression information on laboratory animals may be added to the database as new GeneChip probe arrays become available to analyze these samples, according to Gene Logic.
Reads vs. GeneChip
Doug Dolginow, Gene Logic's vice-president for pharmacogenomics and former president and CEO of Oncormed, said the difference between Reads-based databases and those that will be based on Affymetrix's technology is that of an open versus a closed system.
The GeneChip probe array databases will be closed, containing only genes that have already been discovered and are in the public domain, he said. "The biggest human chip Affymetrix has contains 42,000 genes. If you know that the genes you are interested in are on the chip, it is useful," he explained.
Gene Logic's Reads-based customized gene expression databases contain information about specific tissues. "They allow customers to look at all of the genes expressed in a tissue and between tissues to get a differential display," Dolginow said, adding, "Reads is more useful for our alliance partners who are looking for novel targets."
Gene Logic said it intended to use GeneChip probe arrays to generate additional expression databases for companies interested in specific studies. "We're moving in the direction of using chips whenever possible," added Push, "but in the meantime, Reads is the way to go for specific target discovery."
Because the cost of the GeneChip databases will be carried by a large number of subscribers, they will be less expensive than Gene Logic's exclusive products, the company claimed.
Push added that the two technologies are complementary. Reads will be used for specific target discovery, and GeneChip-based databases will be used for comparisons across a large number of tissues. "For example," he said, "you can use Reads to identify genes that are upregulated for heart disease, and with the GeneChip expression database you can look at other upregulated genes. It can be useful to have that information."
Gene Logic said it will design the new databases in compliance with standards outlined by the Genetic Analysis Technology Consortium, which was established in 1997 by Affymetrix and Molecular Dynamics. That way subscribers can compare data from the Gene Logic databases with data from their own or others' experiments that were conducted using systems that provide data that meet the standards.
Push described the relationship between Affymetrix and Gene Logic as "symbiotic." He remarked, "Affymetrix has been talking for some time about developing databases, but they're not going to do that. They are the preeminent chip manufacturer and we are the preeminent maker of databases. Their chip is an excellent platform for us to generate more information."
Gene Logic will charge annual subscription fees to users of the new databases and will pay Affymetrix annual subscription fees for the use of GeneChip probe arrays. Gene Logic will also buy the probe arrays and related instrumentation and software, and after a commercial milestone has been achieved, pay royalties to Affymetrix on database subscription fees. Push told BioInform that Gene Logic expected to begin seeing revenue from the new gene expression databases in the second half of the year.