By Donald Zuhn --
Last month, the U.S. Patent and Trademark Office announced that it had updated the training materials to be used by examiners in the examination of patent applications for compliance with the written description requirement of 35 U.S.C. § 112, first paragraph. The revised training materials supersede and replace the previous set of training materials issued by the Patent Office in 1999. In the updated training materials, the Office explains that the revisions to the materials were necessitated by changes in both the case law and technology since the 1999 training materials were issued. The Office also notes that to the extent that conflicts exist between the 1999 training materials and the new materials, the new materials will control.
Commenting on the new training materials, Commissioner for Patents John Doll stated that the materials "will improve the quality and consistency of patent examination, as well as provide guidance to practitioners for the drafting of patent applications and responses to examiners." According to the Patent Office, the new materials are intended to assist patent examiners in applying the "Guidelines for Examination of Patent Applications Under the 35 U.S.C § 112, first paragraph 'Written Description' Requirement," which were originally published in the Federal Register on January 5, 2001, and which are now incorporated in the M.P.E.P. at § 2163.
The new training materials provide seventeen examples, of which fourteen are specifically related to biotech inventions. In particular, the biotech-specific examples address expressed sequence tags (ESTs) (example 4), a partial protein structure (example 5), DNA hybridization (example 6), allelic variants (example 7), bioinformatics (example 8), protein variants (example 9), a product claimed by its function (example 10), a polynucleotide or polypeptide sequence sharing percent identity with another sequence (example 11), antisense oligonucleotides (example 12), antibodies to a single protein (example 13), antibodies to a genus of proteins (example 14), a genus with widely varying species (example 15), a process claim where novelty resides in the process steps (example 16), and methods of using compounds claimed by functional limitations, methods of identifying compounds, and compounds identified by such methods (example 17). Patent Docs will discuss these examples in a series of articles. Today, we address examples 6 and 11.
Example 6
Example 6 concerns claims that are directed to nucleic acid molecules that hybridize to a recited sequence. This example provides three exemplary claims:
Claim 1: An isolated nucleic acid that encodes a protein that binds to the NDG [newly-discovered growth factor] receptor and stimulates tyrosine kinase activity.
Claim 2: An isolated nucleic acid that encodes a protein that binds to the NDG receptor and stimulates tyrosine kinase activity, and consists of the sequence set forth in SEQ ID NO: 1.
Claim 3: An isolated nucleic acid that encodes a protein that binds to the NDG receptor and stimulates tyrosine kinase activity, wherein the nucleic acid hybridizes under highly stringent conditions to the complement of the sequence set forth in SEQ ID NO: 1.
According to the training materials, the specification, which discloses the nucleotide sequence of SEQ ID NO: 1, satisfies the written description requirement with respect to the full scope of claim 2. However, because claim 1 encompasses a broad genus of isolated nucleic acids, and the specification fails to disclose any information about the structure or location of NDG receptor binding domains in the protein encoded by the nucleotide sequence of SEQ ID NO: 1, the specification fails to satisfy the written description requirement with respect to the full scope of claim 1.
Concerning claim 3, the training materials acknowledge that "nucleic acids that hybridize to the complement of SEQ ID NO: 1 must share many nucleotides in common with SEQ ID NO: 1," and therefore, that "[t]he disclosure of SEQ ID NO: 1 combined with the knowledge in the art regarding hybridization would put one in possession of the genus of nucleic acids that would hybridize under stringent conditions to SEQ ID NO: 1." However, the training materials conclude that the specification fails to satisfy the written description requirement with respect to the full scope claim 3 because the specification does not disclose a recognized correlation between the structure of the protein encoded by the nucleotide sequence of SEQ ID NO: 1 and its function, and without this correlation "those of ordinary skill in the art would not be able to identify without further testing which of those nucleic acids that hybridize to SEQ ID NO: 1 would also encode a polypeptide that binds to NDG receptor and stimulates tyrosine kinase activity."
Example 11
Example 11 concerns claims that are directed to a polynucleotide or polypeptide sequence that shares percent identity with another sequence. The example is divided into two sections, one in which there is no art-recognized structure-function correlation for the claimed sequence (example 11A), and one in which there is an art-recognized structure-function correlation for the claimed sequence (example 11B). The first section of this example provides two exemplary claims:
Claim 1: An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2.
Claim 2: An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2; wherein the polypeptide has activity X.
Despite the specification's disclosure of only a single species encoding the polypeptide of SEQ ID NO: 2 (i.e., SEQ ID NO: 1), and the lack of any teaching in the specification regarding which amino acid residues in SEQ ID NO: 2 are tolerable to change, the training materials indicate that the specification satisfies the written description requirement with respect to the scope of claim 1. According to the training materials, this is so because "[w]ith the aid of a computer, one of skill in the art could have identified all of the nucleic acids that encode a polypeptide with at least 85% sequence identity with SEQ ID NO: 2." However, because the specification lacks any teaching as to which amino acid residues in SEQ ID NO: 2 can be changed while still retaining activity X, and the art lacks any recognized correlation between structure (SEQ ID NO: 2 domains) and function (activity X), the training materials indicate that the specification fails to satisfy the written description requirement with respect to the scope of claim 2. This would seem to suggest that if claim 3 in Example 6 above were rewritten to exclude an activity limitation, claim 3 would satisfy the written description requirement, since a nucleotide sequence hybridizing under highly stringent conditions would be expected to encode a protein having a sequence identity that is greater than 85%.
The second section of Example 11 also provides two exemplary claims:
Claim 1: An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2.
Claim 2. An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2; wherein the polypeptide has activity Y.
The only difference between the hypothetical specification of Example 11A and the hypothetical specification of Example 11B is that the latter identifies two domains that are critical to activity Y (i.e., a binding domain and a catalytic domain). Not surprisingly, the training materials find that the specification satisfies the written description requirement with respect to the scope of claim 1 of Example 11B. With respect to claim 2 of Example 11B, the training materials indicate that the specification, which now discloses two domains responsible for activity Y, satisfies the written description requirement.
This reverses (appropriately) many of the mistaken applications of the WD requirement to address issues of scope in biotech claims. The problem will be two fold. First, examiners take time to incorporate new policy into practice (esp. if they don't agree with it) and second, many will take the position that since WD is met then enablement is met as well. The back and forth/piecemeal approach to addressing scope in biopharm patent prosecution makes the entire process unpredictable. Couple this with the recent appeal of the recently overturned rules packages, the moves by the house and senate to push through greater PTO authority and examination sharing among the US, Europe, and Japan, and we have an uncertain system that is likely to remain ambiguous for at least a few more years. With this level of uncertainty, the fate of the innovation pipeline among rapidly converging industries may well decide to go the trade secret route. Query: Who would this serve? Is the US the only nation with a true open market? If so, will an open marker system tolerate true IP globalism? Where is the voice of the backyard inventors?
The US system is not perfect, but until a complete and unified alternative that protects open marker innovation incentives is offered, is change for change sake worth it?
Posted by: BRS | May 09, 2008 at 06:48 AM