There are three patent interferences between SRPT and what was then RNA and is now BMRN. An interference is when two people claim to have invented the same thing and the Patent Office has to determine who invented it first, because only they get a patent on the thing. The party that is later to invent, even if first to file a patent application and/or receive a patent on the thing, gets nothing. If they were awarded a patent, that patent gets taken away and given to the other party that is determined to be the first one to have invented the thing. This is the old first-to-invent priority system that applies to patents initially filed pre 2013. Patents filed since then are under a strict first-to-file priority system, so interferences are no longer necessary because first-to-invent is irrelevant to who gets the patent under a first-to-file rule.
Two of the SRPT-BMRN interferences deal with composition of matter patents and were started July 2014. In one of those, they have added in a related method patent. The third interference between the parties deals with a method of use patent and was started September 2014. The first two are in the midst of motions and I don't see any decisions having yet been made by the PTO. The third one was actually SRPT's idea, which RNA/BMRN opposed. For the third one to be started, SRPT was required to show that it had some evidence of inventing the method of use before RNA/BMRN, but it failed to provide any (it instead tried to argue RNA didn't invent the thing, which is not what they were required to address). So, as you see with this news, the Patent Office judges assigned to the matter decided this week that they are going to end the third interference, which is a ruling against SRPT. The method of use patent is likely weak regardless, so it's not a big deal. SRPT likely requested the interference because it wanted to stop RNA/BMRN from being issued their patent (at the time the interference was requested, SRPT had an issued patent and RNA/BMRN just had an application).
As SRPT says in its PR, they can (and will) appeal to the Court of Appeals. I don't give them much hope, as the CAFC gives the PTO a lot of respect. But, also as SRPT says, this wasn't really a full fledged fight, so I wouldn't be too quick to draw conclusions regarding the main events, which are the first two interferences. Basically, SRPT made a decision to try to cause trouble for RNA in this third interference, they likely knew their odds were low, but the cost of doing it was even lower relatively speaking. It's rational to spend a dollar getting 100 to 1 odds if the payoff is greater than 100 to 1. Most people don't get this theory of legal behavior, they think losing is always bad, when in reality it's the result of making a rational decision to take a stab at a long shot. The odds of it working, even if unfavorable, were still high enough to make the legal costs worthwhile. Notice, had SRPT never tried to do this third interference, they would have never lost, and this negative news would have never come to light. But had they never tried, they never could have won. In reality, it was a wise gamble, even if it didn't (yet?) pay off. What left is waiting to see what the PTO decides in the other two, more important, interferences.