Advancing Breakthrough Therapies for Patients Act of 2012

Advancing Breakthrough Therapies for Patients Act of 2012 - Amends the Federal Food, Drug, and Cosmetic Act to direct the Secretary of Health and Human Services (HHS), at the request of the sponsor of a drug, to expedite the drug's development and review if: (1) it is intended, either alone or in combination, to treat a serious life-threatening disease or condition; and (2) preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over existing therapies on one or more clinically significant endpoints.

Authorizes the drug's sponsor to request the Secretary to designate the drug as a breakthrough therapy. Requires the Secretary, within 60 days of such request, to determine whether the drug meets such criteria and, if so, make such designation, followed by appropriate actions to expedite its development and review for approval.

Directs the Secretary to issue guidance on implementing requirements with respect to breakthrough therapies and to amend promulgated regulations.

Requires the Secretary to contract with an independent entity to evaluate the manner by which the Food and Drug Administration (FDA) has applied the processes for the breakthrough therapy determination, and the impact of such processes on the development and timely availability of innovative treatments for patients affected by serious or life-threatening conditions. Requires an annual report from the Secretary to Congress on drugs for which breakthrough designations were requested and approved.