The Federal Circuit basically confirmed in In re Cellect that terminal disclaimers can knock out patent term adjustment (PTA). If you have patent term extension (PTE) and you filed a terminal disclaimer to overcome an obviousness-type double patenting (ODP) rejection, you can get the PTE term tacked onto the disclaimed date. However, in the case of PTA, the court says that PTA term gets added to the life of the patent first and then the terminal disclaimer goes into effect so that you have disclaimed the PTA term and any extended term such that the two patents now expire on the same date regardless of the PTA. In effect, terminal disclaimers may knock out PTA term.
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