Ex parte Bandman (B.P.A.I. 2004)

    By Donald Zuhn --

In an appeal from a final rejection of claims 3, 6, 7, 9, and 12 of U.S. Application No. 09/915,694, the Board of Patent Appeals and Interferences reversed the rejection of the claims under both the written description and enablement requirements of 35 U.S.C. § 112, first paragraph, and entered a new ground of rejection under 35 U.S.C. § 112, second paragraph, for claim 12.

Claims 3 and 12 of the '694 application, which were representative of the subject matter on appeal, recite, inter alia, an isolated polynucleotide encoding a polypeptide comprising a naturally occurring amino acid sequence at least 95% identical to the amino acid sequence of SEQ ID NO: 1 (claim 3) and an isolated polynucleotide comprising a naturally occurring polynucleotide sequence at least 95% identical to the polynucleotide sequence of SEQ ID NO: 2 (claim 12).

The Examiner had rejected claims 3, 6, 7, 9, and 12 for failing to comply with the written description requirement, asserting that the specification provides only a single representative species -- the polynucleotide of SEQ ID NO: 2, and fails to disclose any structure-function relationship in this species.  The Examiner had also rejected claims 3, 6, 7, 9, and 12 for failing to comply with the enablement requirement, asserting that because the specification does not teach the specific amino acids and structural motifs in the proteins encoded by the claimed polynucleotides that are essential for protein activity (specifically, malate dehydrogenase activity), the amount of experimentation required to make the claimed polynucleotides was undue.  Appellants contended that because the claims at issue recite polynucleotides having a naturally occurring polynucleotide sequence, or that encode a polypeptide having a naturally occurring amino acid sequence, "through the process of natural selection, nature will have determined the appropriate amino acid sequences [i.e., those retaining malate dehydrogenase activity]."

With regard to the written description rejection, the Board noted that "[t]he written description requirement . . . does not require a description of the complete structure of every species with a chemical genus" (Ex parte Bandman, No. 2004-2319, slip op. at 3 (B.P.A.I. January 6, 2005)).  The Board also compared the circumstances of the instant case with those faced by the Federal Circuit in Enzo Biochem, Inc. v. Gen-Probe Inc., 296 F.3d 1316 (Fed. Cir. 2002).  In Enzo Biochem, the Federal Circuit determined that an "[a]dequate written description may be present for a genus of nucleic acids based on their hybridization properties, 'if they hybridize under highly stringent conditions to known sequences because such conditions dictate that all species within the genus will be structurally similar'" (Ex parte Bandman, No. 2004-2319, slip op. at 4 (B.P.A.I. January 6, 2005) (citing Enzo Biochem, Inc., 296 F.3d at 1327)).  In the instant case, the Board determined that the genus of molecules defined by the claims was similarly limited and reversed the Examiner's written description rejection.

With regard to the enablement rejection, the Board disagreed with the Examiner's assertion that in order to satisfy this requirement, the specification must provide guidance regarding the specific amino acid residues that are tolerant to change without affecting malate dehydrogenase activity.  Instead, the Board deemed persuasive Appellants' argument that because the claims were limited to naturally occurring sequences, nature will have determined the amino acid residues that are tolerant to change (i.e., naturally occurring variants will presumably retain malate dehydrogenase activity).  In particular, in reversing the Examiner's enablement rejection, the Board determined that the Examiner had not provided sufficient evidence that a naturally occurring polypeptide that is at least 95% identical to the amino acid sequence of SEQ ID NO: 1 or a polypeptide encoded by a naturally occurring polynucleotide sequence that is at least 95% identical to the polynucleotide sequence of SEQ ID NO: 2 would not retain malate dehydrogenase activity.

Although the Board reversed both the written description and enablement rejections, it also entered a new ground of rejection for claim 12 under 35 U.S.C. § 112, second paragraph.  The Board found that the specification provided no guidance that would allow one of ordinary skill in the art to determine, with a reasonable degree of confidence, whether a polynucleotide sequence that is at least 95% identical to the polynucleotide sequence of SEQ ID NO: 2 occurs naturally.  The Board concluded that the metes and bounds of claim 12 were unclear, and therefore, that the claim was indefinite.

Ex parte Bandman (B.P.A.I. 2004)
Panel: Administrative Patent Judges Smith, Grimes, and Green
Opinion by Administrative Patent Judge Green

This article was originally published on Patently-O on June 14, 2005.

Comments

[Naishadh Desai]

I have a question. Suppose that claims 3 and 12 were allowed as written.

Now if I change a fewer than 5% of amino acids or nucleotides in the sequence and want to use them in research/pharmaceutical drug, Do I have to go around cheking every natural malate dehydrogenase to see if I may be infringing these claims? Or for that matter, does the Patentee have to show that a natural variant of my sequnce exists to prove infringement?