Biogen Idec, the maker of the multiple sclerosis pill Tecfidera, expanded its partnership with Isis Pharmaceuticals Inc. in a deal worth at least $100 million to develop drugs for neurological disorders.

Biogen will pay Carlsbad, California-based Isis $100 million upfront and as much as $220 million per compound in potential milestone payments, the companies said today in a statement. The six-year deal gives Weston, Massachusetts-based Biogen exclusive access to Isis’s antisense technology platform to identify targets and develop drugs for neurological diseases.

“This strategic alliance with Isis builds on our existing relationship and combines the unique strengths of each partner to significantly advance the treatment of serious neurological diseases,” said Douglas Williams, Biogen Idec’s executive vice president of research and development. “Antisense is a validated technology that we believe will help build our pipeline of antisense, small molecule and biologics programs, strengthening our leadership in neurology.”

Biogen operates a big manufacturing facility in RTP where it employs some 1,000 people.

The company opened a new 190,000 square foot building in RTP in December.

Antisense therapy works on the underlying genetic causes of disease, turning genes on or off to fix a defect. The agreement expands on three others Biogen has signed with Isis in the last two years, including one to develop a drug for spinal muscular atrophy.

“This is a more expansive collaboration,” Biogen Chief Executive Officer George Scangos said in a telephone interview. “The teams have worked extraordinarily well together.”

Spinal muscular atrophy is a good example of a disorder on which the companies would collaborate, Stanley Crooke, Isis’s chief executive, said. A rare genetic disorder, the most severe form of SMA is characterized by very little production of a specific protein, and can kill patients before age 2.

Isis rose 14 percent to $31.81 at 4 p.m. New York time, its biggest one-day increase since June 24. Biogen shares gained 1.6 percent to $228.86.

Lou Gehrig’s Disease

The companies may also target diseases such as amyotrophic lateral sclerosis, also known as Lou Gehrig’s disease, Crooke and Scangos said. Biogen had been developing a drug for ALS, dexpramipexole, that failed to show any benefit earlier this year in the last stage of clinical trials.

“Biogen has a pretty aggressive program to understand more about the genetic causes of ALS,” Scangos said. One part of that, an academic group, is “already generating interesting insights into the biology and some potential targets we would hope to be able to take forward.”

The partnership is the first for Isis around an entire therapeutic area, Crooke said. The company doesn’t have a sales force, preferring to make partnerships with larger drugmakers to run late-stage clinical studies and to market its medicines. Its first approved drug, Kynamro, for a rare cholesterol disorder, is marketed by Sanofi’s Genzyme unit.

Isis may try to do more deals similar to this one, Crooke said.

“This is the next step in the evolution of our partnering strategy,” Crooke said. “It makes a lot of sense for us; what we need is to make sure our partners understand our technology, are ready for the drugs when they’re ready for them, and that there are people in the organizations we can trust to do a good job with our assets.”