The Federal Circuit affirmed a decision of obviousness, and that a patentee not be able to amend claims in an inter partes review proceeding, in an opinion handed down January 29th in Illumina Cambridge Ltd. v. Intelligent Bio-Systems, Inc.  The opinion (or rather the description of the Board's procedures and the history of how the Board arrived at its decision) once again illustrate the flaws in the IPR system established under the Leahy-Smith America Invents Act of 2012.

The case was an appeal from a decision by the Patent Trial and Appeals Board (PTAB) that invalidated all challenged claims of US Patent Nos. 7,057,026 (directed towards nucleotide compositions of matter) and 8,158,346 (directed towards methods of using these compositions).  These reagents and methods were related to "sequencing by synthesis" methods that use non-natural nucleotides (exemplified by a nucleotide with a 3' hydroxyl protecting group) and labeled at the base (deazapurine) with a cleavable linker (disulfides).  In the practice of these "SBS" methods, each nucleotide is incorporated into a growing nucleic acid in a stepwise fashion, wherein at each step the label is released and the 3' hydroxyl protecting group cleaved to permit extension of the nucleotide chain.

A third party filed suit against Illumina, asserting patents owned by Intelligent Bio-Systems, who responded to Illumina's counterclaim of infringement by filing an IPR petition, the District Court staying the underlying litigation until the Office decided the IPR.

Claims 1–8 of the '026 patent and claims 1, 2, 4, 11, 12, 17, 18, and 19 of the '346 patent were challenged in the IPR.  Instead of rebutting the asserted grounds of invalidity (anticipation and obviousness), Illumina filed motions to amend (substitute) the challenged claims.  The Board granted Illumina's motion insofar as it requested cancellation of claims, and then refused to enter the amendments on the basis that Illumina had not established that these claims are patentable over the prior art.

Replacement Claim 9 (for Claim 1) in the '026 patent is representative:

9.  A nucleotide triphosphate or nucleoside molecule, having a 7-deazapurine base that is linked to a detectable label via a cleavable linker, wherein the cleavable linker is attached to the 7-position of the 7-deazapurine base and wherein the cleavable linker contains a disulfide linkage, and wherein the nucleotide triphosphate molecule has a ribose or deoxyribose sugar moiety comprising a protecting group attached via the 2′ or 3′ oxygen atom, and the disulfide linkage of the cleavable linker and the protecting group are cleavable under identical conditions.

Despite the evidence of several changes in this claim, the Board found that the only "new" limitation was that the cleavable linker "contains a disulfide bridge."  The "main issue" to be decided (according to the Board) was whether the use of a disulfide bond was obvious, because all of the other limitations "were found in the prior art" (and used as the basis for instituting the IPR).  Unanswered questions raised by this synopsis of the Board's reasoning are whether these limitations were found in one or several references, and in the latter circumstance whether combination itself was disclosed or obvious.  Regarding the question the Board posed for the parties, the Office found that the disclosed cleavage efficiency (>90%) for both the protecting group and the label linkage could be achieved with a reasonable expectation of success and that the proposed amended claims for the '026 patent would be obvious.  The Board separately found that the proposed substitute claims in the '346 patent (reciting methods for using the compositions as claimed in the '026 patent) were also not patentable over the prior art.

The Federal Circuit affirmed, in a decision by Judge Lourie, joined by Judges Bryson and Stoll.  This decision illustrated once again that the deference mandated by Dickenson v Zurko weighs heavily against the patentee wherever (as here) there is a factual determination involved in the Board's decisions.  The panel followed the Court's In re Gartside precedent, which established the standard of review of the Office's factual findings to be substantial evidence, a relatively lax standard.

Illumina's argument was that the Board failed to consider the combination of limitations introduced in its proposed replacement claims, specifically the use of a disulfide bond and that the disulfide bond and the 3'-hydroxyl protecting group were capable of being cleaved under "a single set of chemical conditions."  Illumina argued that while methods for these different cleavages were known in the prior art, the Board improperly disregarded evidence that the combination was not known.  Intelligent Bio-Systems relied upon the Board's decision to institute that held that all the limitations in the claims were known in the prior art, and that as a result the only art the Board needed to consider was art relating to disulfide linkages.  (This seems improper, under the rubric that the claims and the prior art combination must be considered for all they teach but the Board nevertheless agreed with Intelligent Bioi-System's logic.)

Part of the basis for the panel's ease in affirming is that in an IPR it is the patentee that bears the burden of showing patentability, which is easily rendered into a burden to prove that the claims are not unpatentable (a different and higher burden, because of the differences in presumptions this formulation of the requirement imposes).  In this case, this burden shifting is evidenced by statements in the opinion that "the original claims provided a backdrop for the Board to find that one of skill in the art would have reasonably expected to succeed in using a linker with a disulfide linkage as claimed" and "[t]he heightened standard that Illumina decries is instead properly Illumina's burden to show nonobviousness, proof that one of skill in the art would not have a reasonable expectation of success in using a disulfide linkage."

And the fine distinctions of language are raised by the panel, which notes that "[t]he proposed substitute claims do not require that the linker and the protecting group be cleaved at the same efficiency rates, however, only that they are cleavable under the same conditions."  Regardless of the correctness of the panel's appreciation of the scope of the asserted claim limitations, using this basis for upholding an obviousness determination illustrates the extent to which a patentee is left to hope that it can discern the semantic limitations in its claims that will satisfy the burden imposed in order to be able to amend claims in an IPR.  This conclusion is only enhanced by the statement in the panel decision that "nonobviousness might have been supported by evidence that one of skill in the art would not have expected there to be any set of conditions in which a disulfide linkage has lower cleavage efficiency than a protecting group and is still suitable for SBS."

The panel also opined that Illumina had not shown that the skilled worker would not have had a reasonable expectation of success at achieving the required cleavage efficiency.  Also, the panel noted that the presence of some expert testimony to that effect provided "substantial evidence" for the Board's conclusion, disregarding the existence of contrary evidence in the record and making no mention of whether the Board properly considered the strength of this competing evidence in arriving at its conclusion.

There are many anomalies that arise from the PTO's implementation of the IPR provisions of the AIA, some arising from the language of the statute and some from how the Office has implemented those provisions.  The Office's overriding concern is apparently those statutory provisions that mandate conclusion of IPR proceedings within one year of institution, which has led the Board to utilize the broadest reasonable construction of claim terms (thus expanding the scope of the relevant art) and refuse to permit patentees to amend claims (citing the lack of resources available to the Board to determine whether the amendments result in patentable claims).  The Board's solution to this problem has been to shift the burden of persuasion to the patentee, which is ironic:  in ex parte prosecution of claims not yet vetted by an Examiner, the burdens fall on the Office and the applicant's claims are presumed patentable unless the Examiner can make out a prima facie case.  In IPRs, the burdens are reversed, and patentees having claims already determined to be patentable are required to show that their claims are not unpatentable.  The Office may have arrived at procedures that maximize its efficiency in arriving at decisions within the 12-month time period, but it is an open question whether these procedures arrive at the correct decision.  That of course should be the principal aim of the Office's procedures, which the public has a right to expect but that cases like this one call into serious question.  While a legislative solution has been proposed, and the Supreme Court is considering the proper standard for claim construction in Cuozzo v. Lee, these must provide but cold comfort for Illumina and all the other patentees being deprived of their patent claims under the current PTO regime.

Illumina Cambridge Ltd. v. Intelligent Bio-Systems, Inc. (Fed. Cir. 2016)
Nonprecedential disposition
Panel: Circuit Judges Lourie, Bryson, and Stoll
Opinion by Circuit Judge Lourie