After a split vote by a Food and Drug Administration advisory panel, the agency will have the final say on whether Pfizer's (NYSE: PFE) tafamidis meglumine is approved in the U.S.

The decision won't affect Pfizer all that much, but it could signal a major issue for the drug development industry in general.

For Pfizer, the approval or rejection of tafamidis isn't a big deal because this is no Liptior. It's an orphan drug to treat Transthyretin Familial Amyloid Polyneuropathy, which affects an estimated 2,500 to 3,000 Americans, with a total 8,000 to 10,000 estimated incidence worldwide. The drug is already approved in Europe under the name Vyndaqel.

The advisory panel voted 13-4 that Pfizer didn't prove that tafamidis produces efficacy on a clinical endpoint. But then it flipped 13-4 in the other direction, voting that the drug does provide efficacy for a surrogate endpoint that is reasonably likely to predict a clinical benefit.

Whether the FDA puts more weight on the first vote or decides that a biomarker is good enough is a big deal for the entire industry.

Surrogate endpoints have fallen out of favor with the FDA. That's O.K. for something like Merck's (NYSE: MRK) anacetrapib, where the FDA is requiring clinical outcomes -- heart attacks, strokes, and the like -- rather than just demonstrating that the drug lowers bad cholesterol and raises the good kind. The market is large enough to justify the higher development costs.

But for orphan drugs with limited commercial potential, the ability to use surrogate endpoints is essential to getting the clinical trials done quickly and cheaply.

And this quickly becomes a slippery slope. Should promising cancer drugs like Seattle Genetics' (Nasdaq: SGEN) Adcetris not get accelerated approvals based on progression-free survival or response rate because the surrogate endpoints doesn't always correlate with overall survival? If you want to take it to an extreme, the ultimate clinical outcome for many diseases is overall survival. Should Vertex Pharmaceuticals (Nasdaq: VRTX), Gilead Sciences (Nasdaq: GILD), and others have to prove that their hepatitis C drugs cause patients to live longer after they're rid from the virus? It makes empirical sense that they would, but let's prove it, just to be sure.

It's a big stretch from the FDA rejecting tafamidis to my extreme examples, but it's something investors in the industry should keep their eye on.

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