The news sent Isis's shares up 9 percent in trade on Monday. Biogen Idec stock was last roughly flat.
The deal is the fourth between the companies in the last two years, and aims to use the "antisense" technology invented by Isis to accelerate discovery of drug targets for neurodegenerative diseases.
Biogen has the option of using the research to develop either antisense drugs, traditional small molecule drugs or antibody-based compounds.
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Antisense drugs aim to interfere at the genetic level to prevent the formation of disease-causing proteins.
"This is a more expansive collaboration in which we will work together over the next several years to use the Isis technology to probe the biology of a disease, develop drug targets and then potentially take those molecules forward," Biogen Chief Executive Officer George Scangos said in a telephone interview.
Biogen is a leader in the market for drugs to treat multiple sclerosis, a progressive neurological disease that can lead to paralysis.
Biogen and Isis are already working to develop an experimental treatment for spinal muscular atrophy which is set to enter late-stage testing in humans. Earlier collaboration has also resulted in an experimental drug for myotonic dystrophy that will soon begin development.
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By next year the companies expect to have drug candidates for three other targets, said Isis CEO Stanley Crooke.
"With the efficiency of antisense we believe we should have a drug moving forward pretty much every year," he said.
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Crooke said the first focus of the new collaboration with Biogen will likely be neurodegenerative disorders, particularly those involved with motor dysfunction.
He put the potential value of the deal for Isis at "several billion dollars," noting that royalty payments for any eventual antisense drugs would be in the double digit percentages, with smaller payments for non-antisense compounds.