Let's dig into the latest controversy surrounding Sarepta Therapeutics (SRPT) - Get Report : Do the changes made to a planned clinical trial of eteplirsen in Duchenne muscular dystrophy patients with mutations in exons 45 and 53 have positive or negative implications for the company?

[The ongoing regulatory review of eteplirsen by the U.S. Food and Drug Administration covers a different group of Duchenne patients with mutations at exon 51.]

I say the exon 45/53 study changes are positive but let's hear first from the other side. Jefferies analyst and Sarepta bear Gena Wang:

SRPT extended the ph3 study for exon 45/53 skipping to 2 yrs from 1 yr along with other changes, based on clinicaltrials.gov. In our view, the changes were undertaken likely due to 1) feedback from the FDA and/or 2) mgmt's lack of confidence that clinical efficacy can be achieved at 48 wks; which have overall negative readthrough to eteplirsen. We continue to see a slim chance for meaningful dystrophin improvement at 48 wks and approval for eteplirsen.

Sarepta would not comment, citing a self-imposed quiet period due to the ongoing FDA review of eteplirsen. However, it's safe to assume FDA feedback did play a role in the exon 45/53 study changes.

But ask yourself this: Why would Sarepta agree to make the exon 45/53 study longer and more expensive -- adding another year to treatment -- if the company was not also confident the FDA was likely to grant eteplirsen accelerated approval first?

If Wang is right about FDA rejecting Sarepta's bid for eteplirsen accelerated approval, the company is now in even more trouble because the study most needed to convince regulators to reverse that decision -- the exon 45/53 study -- might never be completed. Sarepta wouldn't put itself in this weakened position voluntarily, nor is it in FDA's interest to raise the risk that Duchenne drug development is stopped altogether.  

The more likely interpretation is the opposite of Wang's viewpoint. The FDA is more amenable to granting accelerated approval to eteplirsen later this summer or in the early fall, even though that affirmative decision will be based on imperfect and admittedly inconclusive clinical data.

Sarepta has long been criticized for failing to conduct a randomized, double-blind, placebo controlled study of eteplirsen. But the exon 45/53 study, as now amended, will be that definitive, confirmatory study. It's a study now designed specifically to provide the clinical data needed to support full approval of eteplirsen, as long as the drug is first granted accelerated approval.

Adam Feuerstein writes regularly for TheStreet. In keeping with company editorial policy, he doesn't own or short individual stocks, although he owns stock in TheStreet. He also doesn't invest in hedge funds or other private investment partnerships. Feuerstein appreciates your feedback; click here to send him an email.