Junior Party Broad Files Reply to Sigma-Aldrich Opposition to Substantive Preliminary Motion No. 1 in Interference No. 106,133

By Kevin E. Noonan —

On December 3rd, Junior Party the Broad Institute, Harvard University, and MIT (collectively, Broad) filed its Substantive Preliminary Motion No. 1 in Interference No. 106,133 (which names Sigma-Aldrich as Senior Party), asking the Patent Trial and Appeal Board (PTAB) to substitute the interference Count, pursuant to the provisions of 37 CFR §§ 41.121(a)(1)(i) and 41.208) a)(2). On March 16th Senior Party Sigma-Aldrich filed its Opposition to Broad’s Motion and on April 26th Broad filed its Reply.

As a reminder, Broad’s Proposed Substitute Count takes the “McKelvey” format (comprising in the alternative a claim from one of each Party’s applications in interference); the proposed change is in the portion of the Count reciting Broad’s claims:

Proposed Count No. 3 (numbered presumably for consistency with other pending CRISPR-related interferences):

Sigma-Aldrich Application No. 15/456,204 (as declared)


Claim 2 of Broad Application No. 16/177,403:

52. A method comprising: introducing into, or expressing in, a eukaryotic cell having a DNA molecule,
(I) a Cas9 protein or one or more nucleotide sequences encoding the Cas9 protein;
(II) an RNA or one or more nucleotide sequences encoding the RNA, the RNA comprising: (a) a first RNA comprising a first ribonucleotide sequence and a second ribonucleotide sequence, and (b) a second RNA;
(III) a template polynucleotide;
wherein, the second RNA forms an RNA duplex with the second ribonucleotide sequence, and
wherein, in the eukaryotic cell, the first ribonucleotide sequence directs the Cas9 protein to a target sequence of the DNA molecule, whereby the Cas9 cleaves both strands of the DNA molecule and the cleavage is repaired by integration of the template polynucleotide into the DNA molecule in the eukaryotic cell.

In proposing this Substitute Count, Broad emphasis Sigma-Aldrich’s contentions during prosecution that its invention comprised “cleave + insertion” CRISPR methods in eukaryotic cells which were patentably distinct from embodiments comprising “cleavage only” followed by non-homologous end joining of the cleaved DNA target. In making this Motion, Broad clearly intended to cabin Broad’s claims at risk in the interference to a small subset of those claims.

In support of its Motion, Broadly relied heavily on Sigma-Aldrich’s arguments taking substantially the same position in Interference No. 106,132 against Junior Party the University of California, Berkeley; the University of Vienna; and Emmanuelle Charpentier (collectively, “CVC”) (see “Sigma-Aldrich Files Substantive Preliminary Motion 1 to Change the Count in Interference No. 106,132”), including arguments Sigma-Aldrich has made regarding the propriety of its claims not Being part of other interferences having interfering subject matter limited to “cleavage only” eukaryotic CRISPR methods:

Sigma is properly not a party to those ‘cleavage only’ interferences because all of Sigma’s involved claims are pending directed to the patentably distinct ‘cleavage plus integration’ technological advance in the art.

The first argument in Sigma-Aldrich’s Opposition asking the Board to deny Broad’s Motion No. 1 was procedural, that Claim 52 of US Application No. 16/177,403 (the ‘403 application) had not been determined to be allowed when broad filed its motion (complete with a timeline produced from the ‘403 application’s prosecution history’). In addition, Sigma-Aldrich contended “Broad’s Claim 52 is exceedingly broad for at least eight reasons” (as well as being properly subject to the first-inventor-to-file requirements under the Leahy-Smith America Invents Act (AIA) and thus ineligible for consideration in an interference). Sigma-Aldrich also contended that “Broad never even asserts, let alone demonstrate, that ‘cleavage plus altering gene expression’ is patentably distinct from ‘cleavage plus integration by [Homology-Dependent Recombination] HDR'” (in a footnote providing a tally that “[o]f Broad’s 461 involved patent claims, 340 claims are directed to ‘cleavage plus altering gene expression’ (or an analogous recital), 42 claims are directed to insertion of a ‘template,’ and 8 dependent claims are directed to ‘cleavage plus integration by HDR'”. Finally, Sigma-Aldrich asserted that Broad has neglected to “explain how Claim 52 is patentable over Sigma P1.” Citing Louis v. Okada, 2011 Pat. App. 21 LEXIS 24048, at *10 (BPAI May 25, 2011), Sigma-Aldrich contended that a party in an interference must show that there is a genuine need to change the Count and not make a “change for change’s sake.”

In its Reply, Broad tells the Board that Sigma-Aldrich’s Opposition must fail because the Senior Party did not “meaningfully dispute” any of Broad’s three reasons for moving to substitute the Count, particularly with regard to the issue that the Count as encompasses two distinct inventions (ie, “cleavage + altering gene expression” and “cleavage + integration” of heterologous DNA). Broad defines this scope (of the “commonly-claimed interfering subject matter”) as “use of a CRISPR-Cas9 system in a eukaryotic cell to target and cleave both strands of a DNA molecule, with the cleavage being repaired by integrating a donor polynucleotide sequence (“Donor Template Integration”) (an interpretation that would liberate most (340) of Broad’s claims corresponding to Count 1 of the interference as declared). Broad’s arguments are directed to some degree to the nature of the McKelvey Count itself, wherein distinct Aspects of patentably indistinct inventions are combined (the latter characterization forming the core of Broad’s dispute). Broad also argues regarding the similarity between Sigma Claim 31 and claim 18 from an involved CDC patent in the ‘115 interference (in which Broad mentions in passing it the Board granted them priority).[will] work a tremendous” upon Broad should the Board deny its Motion No. 1 and Sigma-Aldrich be entitled to priority on the half of the Count Broad contends it is entitled, the Reply asserts. Broad also argues that Sigma-Aldrich has not “explain[ed] away” its statements agreeing with the patentable distinction Broad argues exists between the two portions of the McKelvey Count as declared in this interference. And Broad reiterates its argument that the position Sigma-Aldrich takes in its Opposition is contrary to positions it has taken during ex parte prosecution of its applications-in-interference (including US Application 15/456,204) and in Interference No. 106,132. Finally, Broad argues that both its dual-molecule and single-molecule proofs will be excluded if the Board maintains Count 1 as declared, the latter set of proofs having been the basis for prevailing Broad in the ‘115 Interference and hence (according to Broad ) be unjust.

Sigma-Aldrich’s procedural arguments are relegated to a shorter portion of the Reply, regarding whether Claim 52 was in condition for allowance and whether the ‘403 application is entitled to the provisions of the 1952 Patent Act and thus properly within the purview of an interference. Broad dissects the former argument allegation-by-allegation with regard to what Claim 52 recites. And regarding the ‘403 application’s status as a pre-AIA application, Broad argues that AIA §§ 3(n)(1) and 3(n)(2) (the statutory basis for Sigma-Aldrich’s argument) do not apply to priority Claims to a provisional application under 35 USC § 119(e) (although a fair reading of the statute would appreciate that the basis for the distinctions under the AIA relate to the claims in a pre-AIA priority application and provisional applications have no claims, at least not formally). And Broad reminds the Board that Sigma-Aldrich attempted to broach this issue in its own Preliminary Motion but the Board denied that request. On the merits, Broad also contends that any differences between what is disclosed in the ‘403 application and the priority applications, including the Zhang application, do not satisfy the standard to qualify as new matter and hence prohibit pre-AIA status. Broad also rejects Sigma-Aldrich’s attempts to incorporate arguments by reference from its Oppositions to other Broad Preliminary Motions, understanding these efforts to be a way for Sigma-Aldrich’s arguments to exceed the page limit for its Opposition here. Finally, Broad argues that its Claim 52 is patentable to Broad over Sigma’s earliest priority application, US Application No. 61/734,256.

For all these reasons Broad asks the Board to grant its Preliminary Motion No. 1.

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