In an important case, Wyeth has successfully appealed to the CAFC about how patent term adjustments for delays in examining are calculated.
See http://www.cafc.uscourts.gov/opinions/09-1120.pdf
That the case was brought by Wyeth is not surprising. For a pharmaceutical company, days and weeks of patent protection is big money. I would, however, submit, that the time for a pharmaceutical patent to issue is rarely longer than the time for FDA approval, and thus the damage caused is virtual whereas the compensation by adding a period at the end of the patent term is very real indeed. Consequently I would like to see this adjustment running concurrently with patent term extensions since there is a public interest for pharmaceutical patents to expire eventually, enabling distribution of cheaper generic equivalents.
