Amgen to Pay Lower Royalties on New Drug : Pharmaceuticals: It costs the Thousand Oaks firm $50 million to alter its agreement with a research center. That will lead to a loss this quarter.

Amgen Inc. said it agreed to pay $50 million to Memorial Sloan-Kettering Cancer Center in exchange for “a substantial reduction” in royalties that Amgen would be required to pay the center on U.S. sales of a new biotechnology drug.

The deal means that Amgen, based in Thousand Oaks, will incur a one-time, after-tax charge of about $46 million against earnings in its fiscal third quarter, which ends Dec. 31, the company said. That will produce a quarterly loss for Amgen, which earned $14.3 million on revenue of $78.8 million in its fiscal second quarter ended Sept. 30, Amgen said.

The drug is Amgen’s recombinant granulocyte colony-stimulating factor, which helps boost white blood cell production for fighting infection. Amgen, which wants to sell the drug as Neupogen, has yet to get Food and Drug Administration approval. It hopes to start marketing the drug early next year.

Memorial Sloan-Kettering is in line for royalties because it helped with the drug’s initial research. Previously, the center’s royalties were set on a sliding scale, rising as U.S. sales of Neupogen rose. Under the new 15-year plan, the New York center will receive a flat 3% of the drug’s annual domestic sales in excess of $350 million, Amgen said.