SANTA CLARA, Calif.—Affymetrix recently announced a new program that is designed to provide GeneChip users with the assurance that the genetic data they derive from its use can be directly applied to compatible software and informatics tools. Called the GeneChip-compatible Applications Program, the program already counted 19 software providers including Genedata, GeneGo, IMC, Rosetta Biosoftware and Stragene, among others when launched in the middle of September.
"Affymetrix GeneChip technology is being used in a growing number of biomedical research and development applications, which require different software solutions," says Mike Lelivelt, senior manager of the GeneChip-compatible Applications Program at Affymetrix. "The program encourages innovation in new application areas and helps drive standardization across well-established areas, such as gene expression, genotyping, splice variant analysis and copy number assays. The GeneChip-compatible Applications Program ensures that individual customers can select the right software applications for their needs from a set of leading software providers."
But rather than merely a stamp of approval, the GeneChip-compatible program aims to provide hands-on, direct collaboration between Affymterix and software providers who attain this new status. To start, Affymetrix provides tools and technical support to help software providers integrate their product with GeneChip. The company will also work with GeneChip-compatible vendors to create case studies, algorithms and tools for current and even new applications. The results of many of these collaborations are new chip designs or approaches to existing scientific needs. And beyond the science, the program provides a basis for co-promotional activities including cross referencing products on each other's Web sites, educational presentations and more.
One of the original 19 GeneChip-compatible companies is GeneGo, a developer of systems biology technology that includes two products: MetaCore 2.5 designed for target selection and validation and MetaDrug, a toxigenomics platform used for the prediction of human drug metabolism and toxicity. In addition, GeneGo curates a proprietary genomic knowledge base called MetaCore to drive its software applications.
"I think it is important for GeneGo to be working with best-in-breed companies and Affymetrix is both that and the dominant player in the industry," says Julie Bryant, vice president of business development for GeneGo. "So it is really important for us to have a very close working relationship with Affymetrix so that when [researchers] upload those chips that we can map those IDs to our internal database so scientists can see their data overlayed on our maps."
In addition, Bryant points out that Affymetrix is also "moving into the SNP business, so again we have the ability to visualize Affy SNP data as well. That will give researchers a much better understanding of pathways. If you can understand the SNPs and what is happening there and you have expression data and you can concurrently visualize it, it gives you a better story about the pathway, rather than just looking at one set of data independently."
For Affymetrix, working with companies such as GeneGo helps it maintain its industry lead by leveraging GeneChip data with a number of providers working in different verticals within the market or researchers' favorite providers for specific applications.
"GeneGo offers users a friendly software package for visualizing and analyzing expression data on pathways," says Lelivelt. "The pathway analysis space continues to undergo rapid development and we are working with a number of different vendors."