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Genaissance Wins Patent on Method Linking Genes, Drugs; Will Use in Drug Development

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Genaissance Pharmaceuticals this week said it received the thumbs up from the US Patent and Trademark Office about its patent application for a method to build up predictive haplotypes in association studies.

The patent office sent Genaissance a so-called “Notice of Allowance,” meaning that the patent, entitled “Methods for Obtaining and Using Haplotype Data,” meets all of its criteria and will likely issue in the next few months, according to Genaissance CSO Richard Judson.

The so-called build-up method, incorporated in the company’s DecoGene Informatics System, tests combinations of SNPs, starting with pairs of SNPs and building up to larger haplotypes — most commonly four or five SNPs — and finds the haplotype that gives the best association with a drug response, for example.

“It is a very general method for essentially making use of haplotypes in association studies,” Judson said.

Now that the patent is there, Genaissance hopes that “this will cause other people to come and ask for licenses,” Judson said, but declined to name specific companies. “We believe … that this is the best method there is, and our patent is pretty broad on the method.” The company would probably not immediately seek out competitors using software with uses overlapping with the patent, he said.

Mark Daly, a computational biologist at the Whitehead Institute, said the patent, if indeed as broad as Judson claims, would cover what researchers trying to correlate genotypes with diseases “do every day.” However, he said he had not read the exact claims of the patent.

Genaissance’s DecoGene software, which includes the methods, consists of a database of genotyping data and a number of applications for storing and analyzing the data.

Genaissance has been using the method for analyzing data from clinical trials for four or five years now, according to Judson, and has licensed it to a number of partners as part of pharmaceutical collaborations. The company already licenses the technology to two “very big” pharmaceutical companies and to two smaller drug developers, although Judson declined to name the companies.

Genaissance will not sell licenses to the software as ordinary products, due to the extra infrastructure required, but will continue to make special arrangements with interested parties.

The method has already yielded some research results: For example, the company published an article in Atherosclerosis last month showing that certain haplotypes in the APOE gene correlate with levels of C-reactive protein.

Genaissance also plans to use the method to develop vilazodone, an antidepressant it recently licensed from Merck (see ). Clinical trials are slated to start by the mid-2005.

The outcome in all these cases, Genaissance hopes, will be haplotype-based tests to predict, for example, response to a particular drug. “That’s our business,” Judson said.

As an example, he mentioned a test for TPMT, an enzyme that metabolizes drugs used to treat childhood leukemia. Patients with a certain two-SNP haplotype have an inactive version of the enzyme and require a much lower dose of the drug. A test for this haplotype, originally developed at St. Jude Children’s Research Hospital and now owned by Genaissance, already exists and is widely used in the clinic, Judson said.

Two weeks ago, Genaissance said it filed a patent on genetic markers predicting a person’s disposition to low white blood cell counts after taking clozapine, an anti-psychotic drug.

The company still has two or three other patents for methods used in DecoGen pending, the most important one its haplotype inference program, called HAP Builder. “We are hoping to get an allowance for that sometime this year,” Judson said.

— JK, CW

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