The results for the 25 Fabry patients with baseline GL-3 levels of 0.3 or higher -- more severe, and measurable disease -- tell a different story. Here, 64% of patients (7/11) treated with Amigal were classified as a responder compared to 14% of patients (2/14) treated with a placebo. The separation in response rates between Amigal and placebo continues for GL-3 cut points above 0.3 as well.

Amicus designed the phase III study to meet its primary endpoint based on the assumption of a 60-70% response rate in the Amigal arm compared to a 20% or less response rate in the placebo arm. In other words, the study would have succeeded had the overall patient population resembled the 25 patients with baseline GL-3 levels of 0.3 or higher, Amicus believes.

At this point, you should be wondering skeptically if Amicus just picked this GL-3 level cut-off level of 0.3 because it makes the Amigal data look the best. The company says it did not, adding that FDA and independent pathologists have all agreed previously that a GL-3 level of 0.3 represents a starting point for measurable, clinically meaningful Fabry disease. The only reason Amicus didn't exclude patients with GL-3 levels below 0.3 was that kidney biopsies are not routinely performed to screen patients for clinical trials. Amicus tried to use urine levels of GL-3 as a surrogate marker for higher disease burden but it proved to be too permissive.

Looking ahead, Amicus hopes to bolster its argument supporting Amigal's efficacy with an analysis of the trial after 12 months of treatment. The best case for the company would be if patients treated with a full 12 months of Amigal maintain the the response rate observed at six months, or improve further.

According to the study design, placebo patients crossed over to receive Amigal at six months. Amicus hopes to show that the response rates for the placebo-delayed treatment patients at 12 months look similar to the six-month results recorded by the original Amigal-treated patients.

If that happens, Amicus and its partner GlaxoSmithKline ( GSK) expect to seek U.S. Approval for Amigal despite the study failing to hit its primary endpoint. Amicus believes FDA will look at the totality of the data, including the benefit seen in patients with more measurable disease.

-- Reported by Adam Feuerstein in Boston.

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.

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