Carlsbad-based Isis Pharmaceuticals Inc. has entered a $392 million deal with Swiss biotech giant Roche Holding AG to work on new treatments for Huntington’s disease, a rare but devastating degenerative genetic brain disorder.

Isis was paid $30 million upfront, with the rest contingent on achieving certain developmental and commercialization milestones.

The deal will employ Isis’ proprietary “antisense” technology, which engineers RNA molecules to deactivate faulty genes.

This is Isis’ latest in series of deals with larger pharmaceutical companies. It last year teamed up with Biogen Idec in three similar collaborations that totaled over $1 billion, when factoring in future milestone payments. It also partnered with AstraZeneca for $31 million cancer treatment deal.

Isis CEO Stanley T. Crooke said in a December interview that the company’s goal was to continue forging these relationships, focusing on antisense research and leaving commercialization to big pharma.

“We believe that Roche's expertise in developing (central nervous system) drugs, along with their clinical development experience, will greatly enhance our development efforts for this program and allow us to move forward more rapidly," B. Lynne Parshall, chief operating officer of Isis, said in a statement. "By partnering our more complex and nuanced research and development programs earlier in development, like our Huntington's disease CNS program, we add value and resources with partners that bring unique benefits."

Isis employs 345 in Carlsbad, and has a broad pipeline of first-in-class drugs in development — 18 drugs in clinical development and five more in pre-clinical study. Its lead drug, Kynamro, was recently approved by the U.S. Food and Drug Administration.

— SDBJ Staff Report