I'd love to see the entirety of the letter sent by the FDA. I'd be surprised if it didn't require blinded evaluation and potentially blinded running of the test. Perhaps even the presence of an FDA official since Sarepta has a history of cherry picking and other dubious corporate/scientific practices which would be hard to catch after the fact. (Note that the FDA has had monitors at the Sarepta sites before - probably for similar reasons)
As for how the FDA could use the data - I completely agree with you that it is very uncertain. What threshold are they planning to accept (previously it has been at least 3 percent) and what statistical threshold (given that we are right at the threshold of the test it seems risky to assume they can see anything).
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