Carlsbad-based Isis Pharmaceuticals announced it will earn a $3.5 million milestone payment from Weston, Mass.-based Biogen Idec Inc. for its study of infants with spinal muscular atrophy, a rare genetic condition.

This is an early achievement in a series of deals between the two biopharmaceutical companies — last year, Isis and Biogen Idec penned an agreement that could lead to more than $1 billion in payments if certain clinical and commercialization milestones are reached.

Isis is using its proprietary “antisense” technology, which engineers RNA molecules to deactivate faulty genes, to treat the disease that affects about 30,000 patients in the U.S., Europe and Japan.

— Meghana Keshavan