How many nucleotide sequences can be examined in a patent application?

While it may initially be alarming to find a patent application that claims thousands, or tens of thousands of sequences, it is highly unlikely that the application will be granted with more than one, or possibly a few.  The United States Patent Office currently only examines one claimed sequence in each patent application.  However, it is important to note that policies limit the number of sequences examined, but not the number of sequences in the claim set as initially filed.  The limitation to one sequence occurs in the inital stage of the examination process, which often takes place long after the application (with the initial bulk claim set) has published.

Policy in the U.S. – one sequence per application

According to a notice issued by the USPTO (1316 O.G.13, 27 March 2007), for new applications, an examiner has the option to restrict claims such that only a single nucleotide sequence will be examined per application. The examiner, however, does retain the option to examine more than one sequence if he or she deems it appropriate.

This notice rescinded a 1996 notice (1192 O.G. 68, 19 November 1996) on the subject. In that notice (see Section 2434 of the MPEP), the USPTO issued a partial waiver of 37 CFR 1.141 to permit examination of up to 10 independent and distinct nucleotide sequences claimed in a single application.  A similar revision was also made for search and examination of applications filed under the PCT, as a partial waiver of 37 CFR 1.475.

Despite the 1996 Notice, PTO examiners usually examined only a single nucleotide sequence.  The 2007 Notice simply eliminated the opportunity for applicants to argue that claims to multiple nucleotide sequences should be examined together.

While these notices do not specifically mention polypeptide (amino acid) sequences, polypeptide sequences are also generally limited to one sequence per application.

PCT Policy – multiple sequences if sufficiently linked as an inventive concept

For PCT patent applications, the number of sequences examined in an application is limited by Rule 13, Unity of Invention. Rule 13 requires that “the international application shall relate to one invention only or to a group of inventions so linked as to form a single general inventive concept”. For applications claiming multiple nucleic acid sequences, “unity of invention will exist when the polynucleotide molecules, as claimed, share a general inventive concept, i.e., share a technical feature which makes a contribution over the prior art.” Therefore, for applications filed in the United States through the PCT process, more than one sequence can be examined in an application.