By Toni Clarke

(Reuters) - Biogen Idec Inc's said on Wednesday its experimental multiple sclerosis drug BG-12 met the main goal of a closely watched clinical trial, sending its shares up 9 percent.

The Weston, Massachusetts-based biotechnology company said that a late-stage trial known as CONFIRM showed that BG-12, when given twice a day, cut the annualized relapse rate in patients with multiple sclerosis by 44 percent at two years versus placebo, and by 51 percent when given three times a day.

Investors had been waiting to see if the results would be comparable to an earlier trial known as DEFINE, which posted unexpectedly strong results showing BG-12 cut the annualized relapse rate by 53 percent when given twice a day. The results of the two trials were sufficiently similar to send the stock soaring.

If approved, BG-12 could significantly strengthen Biogen's position in the increasingly competitive market for multiple sclerosis drugs. It already sells Avonex, which is injected, and Tysabri, which is infused. BG-12 is a pill that would compete with Gilenya, a recently launched pill made by Novartis AG.

The CONFIRM study, unlike DEFINE, also tested BG-12 against Copaxone, a drug made by Teva Pharmaceutical Industries Ltd. Copaxone cut the annualized relapse rate by 29 percent.

Biogen said BG-12 cut the rate of disability progression by 21 percent when given twice a day and by 24 percent given three times a day. That result was not statistically significant and compares negatively with the DEFINE trial, which showed a cut in the rate of disability progression of 38 percent.

Biogen said the lack of statistical significance may be attributable to an unexpectedly low rate of disease progression in the placebo group. It said it is studying the data closely to better understand the figures.

Copaxone cut the rate of disability progression by 7 percent.

Analysts said the data, which will be presented in more detail at a future medical meeting, look promising.

"We believe these data generally "confirm" BG-12's efficacy and clearly show that it's likely a more effective drug than Teva's Copaxone," said Mark Schoenebaum, an analyst at ISI Group, in a research note.

Multiple sclerosis is a chronic, often disabling disease that attacks the central nervous system and can lead to numbness, paralysis and loss of vision. BG-12 is designed to treat relapsing-remitting MS, in which flare-ups are followed by periods of remission. About 85 percent of people with MS are initially diagnosed with this form of the disease.

The most common side effects with BG-12 were flushing and gastrointestinal symptoms such as nausea.

Doug Williams, Biogen's head of research and development, said on a conference call that he does not see the difference in the twice a day and three times a day arms of the trial as meaningful, and that twice a day dosing will be "appropriate."

"I think the risk-benefit profile of BG-12 is quite attractive," he said. "It looks like a first-line therapy to me."

Williams said the company expects to file for approval of the drug in the first half of next year.

Biogen's shares rose 9 percent to $116.65. (Reporting by Toni Clarke in Boston; additional reporting by Lewis Krauskopf in New York and Debra Sherman in Chicago. Editing by Lisa Von Ahn and Maureen Bavdek)