Lending added validation to its technology programs, Genaissance Pharmaceuticals Inc. came to terms with Biogen Inc. in a deal to apply gene variation information to drug development.

“This is validation that pharmacogenomics finally is making its way into products,” Genaissance CEO Gualberto Ruano said.

The companies will apply Genaissance’s HAP technology to Biogen’s development-stage drugs and targets. The agreement adds another large company to Genaissance’s list of partners.

“We have relationships mostly with big pharmaceutical companies we have three [AstraZeneca plc, Johnson & Johnson and Pfizer Inc.],” Ruano said. “We always felt that the biotechnology sector, especially the sector that deals with biologics, would be very amenable to pharmacogenomics. Biologicals have very complex banners of interactions with the patient, and that’s an area where we would expect pharmacogenomics to have the most value to develop biologic products.”

The agreement focuses on pharmacogenomics for research applications as well as the creation of prognostic tests for use in drug marketing. Pairing pharmacogenomics with drugs capitalizes on variations of the human gene for the development of personalized medicines.

“The more targeted your treatment is, the more guidance the treatment will receive,” Ruano said.

New Haven, Conn.-based Genaissance will receive an up-front cash payment, research funding and milestone payments based on predetermined goals. Genaissance will also reserve capacity in its HAP typing facility to process Cambridge, Mass.-based Biogen’s clinical trial samples. In addition, Genaissance will receive downstream payments, assuming successful products are developed.

“We expect that throughout the course of this year we will be in a position to do the initial work, and then this year take it from there to specific drugs in the pipeline of Biogen that would trigger payments to Genaissance,” Ruano said.

Genaissance likens its HAP markers to genomic bar codes that represent the pattern and organization of DNA variability that each individual inherits. Its technology is designed to lead to development of personalized medicines by identifying associations between an individual’s genetic makeup and a drug response.

“The technology platform allows us to look at thousands of genes and apply that to specific clinical outcomes, and that’s where the informatics comes in, which is part of our HAP technology,” Ruano said.

“It will go for a specific process of disease. It will target a specific disease that you have. And this is one of the beauties of the relationship with Biogen they realize that disease is heterogeneous. The question is if you don’t have the diagnostic tools to subcategorize the heterogeneity of disease, how do you do it so that you now have a treatment that is really personalized? And that’s why I think the link between Biogen and Genaissance is so attractive.”

In some respects, the agreement with Biogen is reminiscent to prior deals.

“There are some analogies to the Johnson & Johnson collaboration,” Ruano said, “to move the technology from strictly discovery applications into development and marketing applications. If you look back on our AstraZeneca deal last quarter, that one clearly is more geared toward discovery. This Biogen [deal] is more encompassing of many possible applications of the technology for specific drugs.”

Genaissance also continues to internally develop candidates HAP-Clozapine and HAP-Statin using its genetic markers. The latter is in a Phase II level of development, while HAP-Clozapine is not as advanced, Ruano said.

Shares of Genaissance (NASDAQ:GNSC) rose 35 cents Friday to close at $4.42. Biogen’s stock (NASDAQ:BGEN) closed at $54.60, up 38 cents.