While it’s still rare for bioinformatics companies to patent their technologies, a few firms are bucking that tradition. Last week, while Locus Pharmaceuticals announced that it has been granted patent protection for its computational drug design technology (see story, p. 1), Genomatix of Munich, Germany, said it has filed a US patent for a new method of using epigenetic principles in the analysis of gene expression data.
“Patents in software are not a common commodity,” said Genomatix CEO Thomas Werner. One reason for that is the ease with which a patent permits competing firms to write around its claims in order to duplicate the technology without infringing it. In bioinformatics, however, the lack of patents may be due to a dearth of true innovation in the field, according to Werner. “You really need to come up with a new idea to file a patent,” he said. Not surprisingly, he is confident that the company’s technology is a “new pasture that is pretty green because nobody has been grazing there so far.”
Genomatix, launched in 1998 as a spin-off of Germany’s National Research Center for Environment and Health, has built a successful business — and a user base of more than 12,000 worldwide — around its specialty of analyzing transcription regulation. But when it came to analyzing microarray data, Werner said that something very important was being left out of the picture: Focusing on cDNAs to learn about transcription regulation is like “trying to learn about how people drive by looking at the license plates of their cars,” Werner said. “The regulators are the drivers of the genome,” he said, and a good number of these are left unaccounted for in most expression analysis methods.
Werner said that around half of the events on an expression array are post-transcriptional, and the other half are due to promoters, regulation, and epigenetic activation of genes, which Werner defined as “any kind of regulation brought to the genome from elsewhere,” such as changes in chromatin structure or histone acetylation events. “We’ve mastered the specific regulation already, but we’re still missing the whole part of the epigenetics,” he said.
The company set out to apply the methodology it developed for promoter analysis, which focuses on the “context of the elements, not the individual elements themselves,” to glean knowledge about epigenetic principles that “show us, on a larger scale, biologically meaningful groupings on the chips.”
Genomatix is currently using the approach to create a “gene regulatory encyclopedia” of biological pathways and regulatory networks that it will use to support its current software products, as well as a new front-end application, called ChipInspector, which it may release by the end of the year.
Werner said that the recent rise of systems biology research has driven a new wave of interest in gene regulation, which has broadened the user base for the company’s tools well beyond its traditional academic customers. Regulation and regulatory networks — and with that, epigenetics — are gaining interest in pharma, he noted, as companies seek methods for targeting entire pathways rather than single targets. Furthermore, he added, there’s plenty of room for new analysis tools for regulatory regions. After all, he said, “98 percent of the human genome sequence is non-coding … so epigenetics is part [of] the next logical step” in analyzing the complete genome.