Cephalon (Nasdaq: CEPH) and the Food and Drug Administration seem to have had a missed connection. Despite the presence of a special protocol assessment (SPA), which is basically the FDA signing off on the clinical trial design, the agency failed to expand Cephalon's Nuvigil for the treatment of jet lag.

Nuvigil, which is already on the market for other sleep disorders, passed its clinical trial using two different measurements of efficacy -- an objective one and a subjective one. It was the subjective assessment -- the Patient Global Impression of Severity (PGI-S) -- that the FDA seems to have a problem with. Cephalon said that the FDA questioned "the robustness of the PGI-S data," but didn't elaborate further.

Companies enter into SPAs with the FDA in order to gain clarity with the agency over what's required for approval. Since no drug has been approved for treating jet lag, the added time it takes to get one seemed well worth the added clarity. The SPA also helped investors feel more confident that Cephalon was on the right track.

As Cephalon's investors learned though, a SPA isn't a guarantee of success. Encysive Pharmaceuticals had a SPA with the agency before getting rejected three times by the FDA and eventually succumbing to a lowball buyout by Pfizer (NYSE: PFE). More recently Cell Therapeutics (Nasdaq: CTIC) seems to have had its SPA invalidated by the FDA because it stopped the clinical trial early.

We'll have to wait and see why the SPA for Nuvigil didn't hold up. If it's on the FDA side (e.g., "upon further review, we've changed our minds"), investors in companies with SPAs for their phase 3 trials -- Dendreon (Nasdaq: DNDN) and Human Genome Sciences (Nasdaq: HGSI) in particular -- should be seriously worried about their lower-risk drug developers being anything but.

On the other hand, Tim Hanson says now is the time to buy risk.

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Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. Pfizer is a recommendation of the Inside Value newsletter. The Fool has a disclosure policy.