Here's something you don't see every day: Sarepta Therapeutics (NASDAQ:SRPT) and Prosensa (NASDAQ:RNA) were both up big today, 40% and 24%, respectively.

The two Duchenne muscular dystrophy drug companies typically act as polar opposites: What's good for one company is usually viewed as bad for the other because they'll compete for patients if both get their drugs approved.

Continuing to work 
Sarepta shot up today after announcing 120-week data from its endless phase 2 trial. After six months of additional treatment with its Duchenne muscular dystrophy drug, eteplirsen, since the last update, the boys in the trial continue to remain stable.

After treatment for 96 weeks, the patients that could take the test walked 17.5 meters less in six minutes than they did at the start of the trial. In the newest measurement, the decline was only 13.9 meters from baseline. Technically, that's an improvement, but it's probably not significant. Considering the eventual decline for the natural course of the disease, stable is just fine.

Four patients in the trial got placebo for the first 24 weeks to act as a control group, and then started to receive eteplirsen. If you measure from 36 weeks, after the drug would have started working, through week 120, those patients declined 9.5 meters. That's actually a substantial improvement compared to the 96-week data, which had a decline of 18.5 because one of the boys was still recovering from a broken ankle. The fact that he recovered at all is a testament that the drug is working.

Might actually work 
Prosensa is in a much different position than Sarepta, having seen its Duchenne muscular dystrophy drug, drisapersen, fail a phase 3 trial, and its partner, GlaxoSmithKline (NYSE:GSK), hand back rights to the drug.

But the biotech said today that drisapersen seems to be helping boys who are seven better than older boys. In one of the phase 2 trials, the treatment difference -- the difference in decline seen in patients receiving drisapersen compared to placebo -- was 38 meters for the younger subset. In the larger phase 3 trial, the difference was 21 meters. Neither was statistically significant, but if you combine the two trials, you get a treatment difference of 24 meters and enough subjects to conclude that it's statistically significant.

Hand waving? Absolutely -- you've got a subset analysis followed and a meta-analysis. While it makes sense the drug would work better earlier in the disease progression, you have to take the data with a grain of salt. The FDA will almost certainly want a new trial in younger patients to confirm the results.

Of course, when your drug looks dead, any inclination that the drug is working will breathe life into a stock. Prosensa's shares were up 24% today, but it still only has a market cap of $250 million, compared to Sarepta's $1 billion market cap.

Better buy?
For long-term investors, I think Sarepta is a better buy even though it's four times as expensive. With every new report from the ongoing phase 2 trial, investors become even more confident that eteplirsen will pass its phase 3 trial.

With data this good, the FDA might even change its current opinion, and accept the current data for an accelerated approval. While a bit of a long shot, some of today's price increase is probably based on that hope. In the short term, shares could come down a little if Sarepta confirms that the FDA wants a phase 3 trial, leading to a delay in approval by more than a year.

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Fool contributor Brian Orelli has no position in any stocks mentioned. The Motley Fool has no position in any of the stocks mentioned. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.

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