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

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

or

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;
and
    (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 emphasizes 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 intends to cabin Broad's claims at risk in the interference to a small subset of its claims.

In support of its Motion, Broad relies 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. 106,133"), 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 pending 'cleavage only' interferences because all of Sigma's involved claims are directed solely to the patentably distinct 'cleavage plus integration' technological advance in the art.

Broad broadens the scope of what Sigma-Aldrich asserts it is entitled to, excluding "no cleavage, cleavage only, altering gene expression, or other forms of cleavage and repair" reciting claims.  Broad also alludes to what can be characterized as a "quasi-estoppel" argument, that Sigma-Aldrich was able to get their claims allowed based on these arguments distinguishing "cleavage only" and "cleavage + integration" eukaryotic CRISPR embodiments and so should not be permitted to ignore these limitations now.

In its argument, Broad agrees with Sigma-Aldrich that the Count should be changed based on the arguments Sigma-Aldrich made in the '132 interference, raising a possible later argument that Sigma-Aldrich should not be heard in Opposition to substituting the Count (in contrast for example on an Opposition based on how the Count should be substituted).  In making this argument, Broad asserts that Sigma-Aldrich should not be permitted to seek the "anomalous possibility" of being permitted to seek priority over Broad's "cleavage only" claims-in-interference based on the Count of the Interference as declared (and thus, presumably, should not be permitted to oppose Broad's motion on the merits):

Count 1 allows Sigma just that opportunity, to try to claim priority to the entirety of Count 1—which it has represented to the Office covers two separate species inventions—based only on proofs that it allegedly made one of those species—Donor Template Integration.  This is not "consonant with [the] fundamental purpose [of an interference] to determine priority separately as to each common, patentably distinct invention."  Zymogenetics, Inc., [(6,528,050), Junior Party, v. Ludwig Instit. for Cancer Res. and Licentia LTD. (09/852,209), Senior Party, Int'f No. 105,433] 2006 WL 6630888 [(Bd. Pat. App. & Interf. Sept. 26, 2006)].

Broad further argues that maintaining the Count as declared would deny Broad the benefit of its "best proofs," which Broad contends relate to embodiments of eukaryotic CRISPR that (1) do not include a "donor polynucleotide template" (i.e., exogenous DNA to be inserted at the CRISPR cleavage site) and (2) are limited to single molecule sgRNA (rather than the dual-molecule, crRNA and tracrRNA, embodiments, Broad contends its inventors had reduced to practice much earlier than either CVC's sgRNA-limited CRISPR experiments or their own (the latter being subject to CVC's allegations in Interference No. 106,115 that Broad derived from their disclosure; see "CVC Files Reply to Broad's Opposition to CVC's Priority Motion").  For Broad, the Count as declared represents a "Catch-22" wherein it cannot satisfy the Sigma-Aldrich portion of the McKelvey Count because it lacks best proofs of "cleavage + integration" embodiments and cannot satisfy its own portion of the Count because it is limited to sgRNA embodiments.

As to what Broad proposes should happen regarding its claims-in-interference, Junior Party again references Sigma-Aldrich's motions in the '132 Interference and specifically addresses these issues here, specifying "claim 30 of U.S. Patent No. 8,906,616 ("616 patent") . . . , claim 14 of U.S. Patent No. 9,840,713 ("713 patent") . . . , claims 14-16 of U.S. Patent Application Nos. 14/704,551 ("551 application") . . . , and claims 52-54 of the 403 application . . ." as Broad claims corresponding to Proposed Substitute Count 3.

Broad argues and presents evidence in the Appendices to its brief that all of Sigma-Aldrich's involved claims are limited to "cleavage + integration" embodiments of eukaryotic CRISPR while Broad's claims to such embodiments are much more limited, and the remaining Broad claims are not limited in ways that fall within the scope of Proposed Count 3.

Broad then sets forth an extensive explication of Sigma-Aldrich's prosecution history to support its contention that the Count should be substituted consistent with these representations that claims to "cleavage only" and "cleavage + integration" eukaryotic CRISPR embodiments were directed to patentably distinct inventions.

Similarly, Broad sets forth a synopsis of Sigma-Aldrich's arguments in the '132 Interference (having CVC as Junior Party) in support of substituting the Count analogously to what Broad is proposing in its Motion No. 1.

After explicating these factual issues, Broad provides its legal argument in support of substituting the Count based on these arguments:

• "First, as Sigma acknowledged in the '132 Interference, a Count that includes Non-Template activity—such as current Count 1 here—does not reflect the scope of the common interfering subject matter claimed by the parties.

• "Second, 'a showing that an original count encompasses patentably distinct species is a proper basis for redefining the count to limit the interference subject matter to a single patentable invention and thereby exclude from its scope a second patentably distinct invention,' citing Zymogenetics, 2006 WL 6630888 (citing [Lee v. ]McIntyre, 55 USPQ2d [1137, 1142, BPAI 2000)].

• "Third, Count 1 would unfairly exclude Broad's best proofs to the generic eukaryotic subject matter. Broad's best and earliest proofs—like many of its designated claims—are dualRNA and not directed to Donor Template Integration."

Proposed Substitute Count 3 cures these deficiencies, Broad argued.

In addition to asking the Board to substitute the Count, Broad also asks that it be given priority to U.S. provisional application No. 61/736,527 having a filing date of December 12, 2012 (which would not result in Broad becoming Senior Party in view of Sigma-Aldrich's December 6, 2012 priority date).  Broad sets forth its argument for having the benefit of priority to its December 12, 2012 filing date, again based not only on the merits but on Sigma-Aldrich's reliance on the PTO Examiner allowing its '204 claims-in-interference based on Sigma-Aldrich's representation that Broad's '527 priority document satisfied the "relevant limitations," i.e., integrating donor DNA.  Broad further argues that it has properly maintained continuity of its priority claim from its December 12, 2012 priority date through the intermediate applications wherein "cleavage + integration" eukaryotic CRISPR embodiments were expressly disclosed.

Broad contends that Proposed Substitute Count 3 is patentable over the prior art, relying in part on Regents of Univ. of Cali. v. Broad Instit., Inc., 903 F.3d 1286, 1293 (Fed. Cir. 2018).

Finally, Broad sets forth its arguments for claim correspondence of its claims in interference and those claims that do not correspond, and that all Sigma-Aldrich's claims in interference correspond to Proposed Substitute Count 3.