An SPA is a means to insure that if everything goes according to plan, that a clear path to NDA approval is assured. Trial design, sufficient patient recruitment for statistical relevance, well defined endpoints are all key.
"The overarching goal of the Special Protocol Assessment Draft Guidance for Industry May 2016 (HHS, FDA, CDER, & CBER) is to improve the quality of new drug applications (NDAs) and biologic license applications (BLAs) by providing more certainty in the clinical protocol design process. Among its several purposes, the Special Protocol Assessment (SPA) affords an opportunity for the FDA and product sponsors to reach agreement, prior to study initiation, on the design of clinical trials intended to form the primary basis for an efficacy claim in a product marketing application. For sponsors, the overall value of an SPA is tied to the benefits gained by receiving preliminary input and agreement from the FDA on protocol design. By reducing uncertainty and thereby mitigating risk for the sponsor, an SPA can serve as a beneficial and valuable"
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