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Filed on behalf of: Senior Party, Broad Paper No. ____ By: Steven R. Trybus By: Raymond N. Nimrod Locke Lord LLP Quinn Emanuel Urquhart & Sullivan, LLP 111 South Wacker Drive 51 Madison Avenue Chicago, IL 60606 New York, NY 10010 Telephone: 312-443-0699 Telephone: 212-849-7000 [email protected] [email protected]

UNITED STATES PATENT AND TRADEMARK OFFICE

BEFORE THE PATENT TRIAL AND APPEAL BOARD

THE REGENTS OF THE UNIVERSITY OF CALIFORNIA, UNIVERSITY

OF VIENNA, and EMMANUELLE CHARPENTIER, Junior Party

(Applications 15/947,680; 15/947,700; 15/947,718; 15/981,807;

15/981,808; 15/981,809; 16/136,159; 16/136,165; 16/136,168; 16/136,175; 16/276,361; 16/276,365; 16/276,368; and 16/276,374),

v.

THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, and PRESIDENT AND FELLOWS OF HARVARD

COLLEGE, Senior Party

(Patents 8,697,359; 8,771,945; 8,795,965; 8,865,406; 8,871,445; 8,889,356;

8,895,308; 8,906,616; 8,932,814; 8,945,839; 8,993,233; 8,999,641; and 9,840,713; and Application 14/704,551).

Patent Interference No. 106,115 (DK)

(Technology Center 1600)

BROAD REPLY 5

(for judgment based on priority)

i INTERFERENCE 106,115

BROAD REPLY 5

TABLE OF CONTENTS 1

I. INTRODUCTION ...............................................................................................................1 3

II. DESCRIPTION OF APPENDICES ....................................................................................5 4

III. ARGUMENT .......................................................................................................................5 5

A. CVC Does Not Meaningfully Challenge The Sufficiency Of Broad’s 6 Priority Proofs ..........................................................................................................5 7

B. CVC’S Attacks On Corroboration Lack Merit ........................................................7 8

C. CVC’s Derivation Claim Is Untimely, Improper, And Nothing More Than 9 A Repackaged Argument Based On The Jinek 2012 Disclosure ............................8 10

D. CVC’s Derivation Claim Fails Because Its Inventors Lacked A Prior, 11 Complete Conception At The Time Of The Alleged Derivation ...........................11 12

1. For The Possession Requirement, CVC Makes Inflammatory and 13 Erroneous Arguments Against Broad’s Prior Arguments .........................11 14

2. For The Definite And Permanent Idea Requirement, CVC Fails To 15 Come To Grips With Its Repeated And Extensive Failures After 16 Communication Of The Alleged Conception ............................................12 17

3. For The Reasonable Expectation Of Success Requirement, CVC 18 Makes Erroneous Legal And Factual Arguments ......................................14 19

(a) CVC Misstates The Conception Law For Claims That 20 Recite A Specific Biological Result ..............................................14 21

(b) CVC’s Arguments Regarding Simultaneous 22 Conception/Reduction To Practice Are Irrelevant And 23 Wrong ............................................................................................14 24

(c) CVC’s New Fact Declarations Come Only From Biased 25 Witnesses And Conflict With The Contemporaneous 26 Record ............................................................................................18 27

E. CVC’s Derivation Claim Fails On The Facts Because Far From 28 Communicating the Complete Invention, The Public Disclosure (Less 29 Than Jinek 2012) Does Not Even Render Dr. Zhang’s Inventions Obvious .........20 30

F. CVC’s Derivation Claim Fails Because Dr. Zhang Knew Of And 31 Successfully Used All Aspects Required For A Functional Eukaryotic 32 CRISPR-Cas9 System—Including tracrRNA—Prior To The Marraffini 33 Communication ......................................................................................................22 34

1. CVC Cannot Erase Dr. Zhang’s Pre-Existing Eukaryotic CRISPR-35 Cas9 System Experience And Knowledge ................................................22 36

2. The Facts Contradict CVC’s Claim That Dr. Zhang Did Not 37 Understand tracrRNA Was Necessary .......................................................24 38

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(a) CVC Intentionally Misreads The Record Regarding Dr. 1 Zhang’s Understanding Of The Role Of tracrRNA .......................25 2

(b) Dr. Zamore’s Opinion On tracrRNA Is Irrelevant And 3 Illogical ..........................................................................................27 4

3. Dr. Zhang Did Not Drop His Prior Dual-Molecule Systems .....................28 5

4. Dr. Zhang Did Not Use Only “Ordinary Skill” And “Routine 6 Techniques” In Creating His Eukaryotic CRISPR-Cas9 System ..............30 7

IV. CONCLUSION ..................................................................................................................30 8

APPENDIX A: LIST OF EXHIBITS CITED ............................................................................ A-1 9

APPENDIX B: STATEMENT OF MATERIAL FACTS ...........................................................B-1 10

BROAD’S FACTS AND CVC’s RESPONSES .............................................................B-1 11

CVC’s FACTS AND BROAD’S RESPONSES............................................................B-17 12

BROAD’S ADDITIONAL FACTS ...............................................................................B-29 13 14 15

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TABLE OF AUTHORITIES 1

Page 2

Cases 3

Alexander v. Williams, 4 342 F.2d 466 (C.C.P.A. 1965) ........................................................................................... 23, 24 5

Applegate v. Scherer, 6 332 F.2d 571 (C.C.P.A. 1964) ..................................................................................... 15, 16, 17 7

Brown v. Regents of Univ. of California, 8 866 F. Supp. 439 (N.D. Cal. 1994) .................................................................................... 17, 18 9

Burroughs Wellcome Co. v. Barr Labs., Inc., 10 40 F.3d 1223 (Fed. Cir. 1994)............................................................................................ 13, 14 11

Cumberland Pharms. Inc. v. Mylan Institutional LLC, 12 846 F.3d 1213 (Fed. Cir. 2017)................................................................................................ 21 13

Dawson v. Dawson, 14 710 F.3d 1347 (Fed. Cir. 2013)................................................................................................ 13 15

Gambro Lundia AB v. Baxter Healthcare Corp., 16 110 F.3d 1573 (Fed. Cir. 1997)................................................................................................ 11 17

Hitzeman v. Rutter, 18 243 F.3d 1345 (Fed. Cir. 2011)................................................................................................ 14 19

Larson v. Johenning, 20 17 U.S.P.Q.2d 1610 (B.P.A.I. 1990).......................................................................................... 8 21

MacMillan v. Moffett, 22 432 F.2d 1237 (C.C.P.A. 1970) ......................................................................................... 16, 17 23

Mead v. McKirnan, 24 585 F.2d 504 (C.C.P.A. 1978) ................................................................................................. 20 25

New England Braiding Co., Inc. v. A.W. Chesterton Co., 26 970 F.2d 878 (Fed. Cir. 1992).................................................................................................. 21 27

Price v. Symsek, 28 988 F.2d 1187 (Fed. Cir. 1993).................................................................................................. 7 29

Regents of Univ. of Cal. v. Broad Inst., Inc., 30 903 F.3d 1286 (Fed. Cir. 2018)............................................................................................ 3, 31 31

Statutory Authorities 32

35 U.S.C. § 102(f) ........................................................................................................................... 1 33

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Rules and Regulations 1

37 C.F.R. § 41.208 .......................................................................................................................... 1 2

Bd. R. 121 ....................................................................................................................................... 1 3

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I. INTRODUCTION 1

CVC’s Opposition to Broad’s Substantive Motion No. 5 confirms that CVC cannot defeat 2

Broad’s showing on priority. Dr. Zhang’s conception and ARTPs are beyond legitimate dispute. 3

Indeed, the very sgRNA experiments relied on as ARTPs were subjected to contemporaneous peer 4

review, found to demonstrate successful editing in eukaryotic cells, and published in the landmark 5

Cong 2013 paper. Faced with this evidence, CVC presents no meaningful arguments against 6

Zhang’s conception or ARTPs. Instead, CVC concocts a misplaced derivation argument to try to 7

take credit for Zhang’s groundbreaking success in eukaryotic cells, which occurred while the CVC 8

inventors were floundering with eukaryotic cells—even with their cadre of cell-specific experts. 9

CVC’s derivation claim fails for many reasons. First, it is untimely and improper. CVC 10

bears the burden of proving derivation under 35 U.S.C. § 102(f), as it would with any other 11

invalidity ground. Under Bd. R. 121 and 37 C.F.R. § 41.208, CVC needed to seek relief based on 12

alleged derivation through a substantive motion. CVC seeks to excuse its failure to do so by 13

pointing to the deposition testimony of Dr. Marraffini who communicated to Zhang an sgRNA 14

construct with a GAAA linker. But CVC has known for years that Zhang’s Cong 2013 15

publication—which included successful experiments with dual-molecule and sgRNA systems—16

acknowledged CVC in connection with the use of the GAAA linker. Ex. 3201 at 820. And Zhang’s 17

declaration submitted here acknowledged learning of Chimera A with its GAAA linker first from 18

Marraffini. Thus, CVC could have sought permission to file an opening or responsive motion on 19

derivation, either of which would have afforded Broad the opportunity to file a full opposition, 20

including opposing declarations. But, to Broad’s prejudice, CVC improperly chose to do neither. 21

Ultimately, however, CVC’s derivation argument is nothing more than a repackaging of 22

its failed argument regarding Jinek 2012, which the PTAB considered as prior art in the 048 23


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Interference for the obviousness inquiry. Ex. 3110, 048 Decision at 14. CVC now relies on a 1

similar disclosure at a June 2012 public conference under § 102(f). But even if every one of CVC’s 2

allegations about what was communicated to Zhang are true (they are not), CVC communicated 3

less information than what is in Jinek 2012—which the PTAB, the Federal Circuit, and multiple 4

Patent Office Examiners have already found does not render obvious the eukaryotic CRISPR-Cas9 5

invention, nor provide a reasonable expectation of success. Shifting the statutory prior art category 6

to § 102(f) does not cure the deficiency. It does not matter if one read Jinek 2012 or heard CVC’s 7

conference disclosure; neither of them disclosed nor rendered obvious the eukaryotic CRISPR-8

Cas9 invention, and thus one could not derive the invention from either. 9

Second, CVC’s derivation argument fails because the CVC inventors did not have a prior 10

complete conception, which is a prerequisite for derivation. CVC’s conception argument fails for 11

three separate and independent reasons: (a) CVC’s inventors lacked a reasonable expectation of 12

success, (b) they lacked a definite and permanent idea of the complete and operative invention, 13

and (c) they lacked possession of a functional eukaryotic CRISPR-Cas9 system. CVC’s primary 14

argument in response is that for establishing conception one can simply ignore that Count 1 15

explicitly recites a biologic result as a claim element. The response is that the Federal Circuit cases 16

involving claims reciting a biologic result uniformly hold to the contrary. 17

CVC also asserts that Broad “lacked candor” and perpetrated a “sham” by arguing in this 18

Interference “that a POSA would have needed to see unique conditions and specific instructions 19

relevant to CRISPR-Cas9” to find possession of Count 1. Paper No. 2567, “Opp.” at 59:8-19. The 20

response is that CVC’s allegations are particularly inappropriate given that the words “unique 21

conditions” and “specific instructions” came from the PTAB’s decision in the 048 Interference 22

based on the state of the art and expectations of a POSA in 2012: 23


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Instead, the evidence cited by Broad shows that because each of the riboswitch, 1 ribozyme, and Group II intron RNA-based systems required specific tailoring of 2 conditions, one skilled in the art would have expected that the CRISPR-Cas9 3 system would have also required its own set of unique conditions. 4

Ex. 3110, 048 Decision at 39:6-10; see also Id. 45:19-22 (“there would not have been specific 5

instructions relevant to CRISPR-Cas9 to give one of ordinary skill in the art a reasonable 6

expectation of success”).1 The Federal Circuit reiterated and agreed with those findings. Regents 7

of Univ. of Cal. v. Broad Inst., Inc., 903 F.3d 1286, 1295 (Fed. Cir. 2018). There was no fabrication 8

by Broad—rather, it is CVC that is fabricating a story inconsistent with the state of the art in 2012 9

and the prior decisions of the PTAB and Federal Circuit. 10

Third, CVC’s derivation argument fails because it cannot establish communication of a 11

complete conception, including the critical claim limitation requiring a system capable of 12

eukaryotic cell function. CVC falsely argues that presentation of the abstract idea of using sgRNA 13

CRISPR-Cas9 in a eukaryotic cell conveys the entirety of the invention of Count 1. For example, 14

CVC argues that “they presented their design of a sgRNA CRISPR-Cas9 system for use in 15

eukaryotic cells—the precise content of Count 1.” Opp. at 1:11-13. CVC even complains it is being 16

“wrongly punish[ed]… for sharing” the sgRNA construct. Id. at 8:14. But CVC suffered no such 17

harm. To the contrary, it obtained several patents not at issue here directed to the sgRNA construct 18

itself. 19

The public disclosure of the in vitro sgRNA construct, however, does not entitle CVC to 20

the eukaryotic invention at issue here or make out a claim of derivation. Count 1 requires more. 21

As the PTAB noted, Count 1 requires a system that is capable of functioning in a eukaryotic cell. 22

Paper No. 877, Decision on Motions at 95:6-15, 102:8-103:2 (“Decision”). In fact, claims directed 23

to functioning eukaryotic CRISPR-Cas9 systems were found in the prior Interference to be non-24

1 All emphases are added in the brief except as otherwise noted.


BROAD REPLY 5

obvious over Jinek 2012, with its disclosure of sgRNA. See Ex. 3110 at 13:14-14:21, 17:3-10. The 1

alleged communication from the June conference adds nothing over Jinek 2012. Thus, Zhang’s 2

invention of the functioning eukaryotic system—an essential element of Count 1—was critical and 3

defeats any possible derivation argument. 4

Fourth, CVC’s derivation argument also fails because, contrary to CVC’s false claim that 5

Zhang “contributed none of the elements of Count 1” (Opp. at 6:23 (emphasis in original)), as of 6

June 2012, Zhang already possessed the elements of Count 1 sufficient for a functioning eukaryotic 7

CRISPR-Cas9 system. CVC, however, attempts to cast Zhang’s pre-June 2012 work as worthless, 8

contending that Zhang “immediately dropped” his dual-molecule system after learning about Jinek 9

2012. Opp. at 18:20-21. That is a fabrication. Zhang continued his successful dual-molecule 10

experiments; indeed, they were the first experiments described in Cong 2013. Moreover, he found 11

his dual-molecule systems had higher efficacy than his chimeric RNA system. Ex. 3201 at 820. 12

Further attempting to erase the relevance of Zhang’s prior dual-molecule work, CVC 13

falsely alleges that Zhang adopted all new CRISPR-Cas9 constructs to implement the chimeric 14

RNA system. For instance, CVC’s expert contends that there is “no evidence that Zhang used 15

EF1α promoter before for expressing cas9, and no evidence that he used a lentivirus-based 16

expression vector before” June 2012. Ex. 5013, Doyon 2d Dec. ¶65. But the record shows Zhang’s 17

repeated use of both in his CRISPR-Cas9 systems starting as early as 2011. 18

Finally, CVC contends Zhang did not understand the necessity of tracrRNA for a 19

functioning system prior to June 2012. The response is that, although not even relevant to the 20

issues here, CVC’s contention is flatly contradicted by the record; Zhang included tracrRNA in all 21

of his systems starting in April 2011. See Ex. 3424, Zhang Dec. ¶71; Ex. 3526. He correctly posited 22

in 2011, based on the Deltcheva publication, that tracrRNA remained part of the RNA duplex in 23


BROAD REPLY 5

the CRISPR-Cas9 cutting complex. See, e.g., Ex. 3424, Zhang Dec. ¶¶66-70. Regrettably, CVC 1

disparages Zhang by attacking his conclusion that tracrRNA remained in the Cas9 cutting complex 2

as “scientifically untenable” and “contradicted by basic science.” Ex. 5014, Zamore Dec. ¶¶5, 3

72. But CVC’s Dr. Charpentier has repeatedly stated her view that the 2011 Deltcheva publication 4

teaches exactly what Zhang concluded. CVC’s attacks on Zhang should be rejected. 5

At root, CVC’s derivation claim is yet another improper attempt by CVC to use its in vitro 6

development of sgRNA with a GAAA linker to sweep up for itself Zhang’s fundamental 7

breakthrough of use of CRISPR-Cas9 in eukaryotic cells—a breakthrough that can be carried out 8

using dual-molecule or sgRNA as Zhang showed. Zhang’s proofs on priority stand essentially 9

unopposed, should be accepted, and CVC’s derivation claim dismissed as improper and meritless. 10

II. DESCRIPTION OF APPENDICES 11

Appendix A is a list of cited exhibits; Appendix B is the Statement of Material Facts. 12

III. ARGUMENT 13

A. CVC Does Not Meaningfully Challenge The Sufficiency Of Broad’s Priority 14 Proofs 15

CVC has not meaningfully challenged Broad’s priority proofs on Zhang’s conception or 16

his ARTPs. CVC does not even dispute that Zhang fully conceived of an embodiment of Count 1 17

on June 26, 2012. MFs 142, 28-37. Instead, it embraces Zhang’s conception, but alleges derivation 18

from CVC. Likewise, CVC does not raise any serious argument about Zhang’s ARTPs. Instead, 19

CVC spends the vast majority of its brief embracing Zhang’s ARTPs, but taking credit for them, 20

by arguing (falsely) that Zhang “reduce[d] CVC’s sgRNA CRISPR-Cas9 invention to practice.” 21

Opp. at heading III.c. 22

CVC half-heartedly addresses Zhang’s July and August ARTPs focusing on the alleged 23

lack of details such as a negative control for the July Surveyor results. Opp. at 47:2-20; 49:19-24


BROAD REPLY 5

50:17. CVC is trying to wish away the forest of evidence by focusing on a single, irrelevant tree. 1

MFs 38-55. Initially, the July 20 experiment had negative controls in the form of unsuccessful uses 2

of the system. MF 143; Ex. 5263, Ellington Tr. 183:4-186:17; Ex. 3430, Ellington Dec. ¶41. 3

Moreover, the results were confirmed when the experiment was repeated, producing two 4

independent, positive Surveyor results. MF 142, 28-43; Exs. 3772, 3566. Subsequent sequencing 5

of the samples2 further confirmed the Surveyor results, thereby showing that Zhang successfully 6

used his CRISPR-Cas9 system to introduce indels into the targets. See MF 142, 42-50; Ex. 3784. 7

Those ARTPs were then described in the Science manuscript (Ex. 3564), which impartial 8

reviewers accepted as showing successful experiments. MFs 53-55, 146. Any supposed missing 9

controls for the July 20 Surveyor are irrelevant in view of the body of compelling evidence.3 10

As to the August ARTPs, CVC primarily alleges the PTAB need not review that evidence 11

because CVC’s zebrafish experiments occurred first. Opp. at 51:21-52:12. But CVC’s zebrafish 12

experiments were a failure and were so recognized at the time. See Paper No. 2569, Broad 13

Opposition 2 at 40-50 (“Broad Opp.”). CVC also alleges a “failure of proof” as to the August 14

ARTPs (Opp. at 52:13-53:8), but CVC does not challenge the primary evidence—a presentation 15

with gels and cleavage data reporting the August results—complete with metadata and supporting 16

2 CVC suggests that the notation of some homopolymer/repetitive identification undermines the

results. Opp. at 50:11-17. But the successful sequencing results were repeated, and the outcome

was identical—proving definitively the indels were not a result of sequencing errors.

3 CVC claims “Cong’s electronic notes document [regarding the July and August ARTPs] has no

metadata associated with it at all.” Opp. at 46:18-19. This is false. Cong included the metadata,

including change history information, in his Declaration. MF 144; Ex. 3425 at ¶¶ 42, 84, 119.


BROAD REPLY 5

contemporaneous emails attaching the presentation. MF 145; Ex. 3793. The idea that Zhang did 1

not perceive these experiments “as a positive result” (Opp. at 52:16) is baseless: he directed Cong 2

to present them to the lab as “key data” relating to the best configurations to use in their 3

experiments with chimeric RNA going forward (Ex. 3793). 4

Finally, CVC does not dispute that Zhang’s October 5 Manuscript memorialized successful 5

ARTPs. MFs 53-55, 65-73, 146. The Manuscript memorializes both the July ARTP in mouse cells 6

and Zhang’s later work in human cells. Ex. 3424, Zhang Dec. ¶¶ 143, 177-212. Those ARTPs were 7

subjected to contemporaneous peer review by impartial experts who noted that Zhang’s system “is 8

functional and efficient in vivo, for cleavage and inducing mutations at the target site,” specifically 9

noting that this included success in his experiments with “chimeric RNA.” MFs 53-55, 65-73, 147; 10

Ex. 3836 at 3. These comments and the acceptance of the manuscript by Science for publication 11

demonstrate Zhang’s successful ARTPs of an embodiment of Count 1. 12

B. CVC’S Attacks On Corroboration Lack Merit 13

With no evidence to seriously challenge Broad’s proofs, CVC instead asserts an alleged 14

failure of corroboration based on the supposed bias of Broad’s witnesses. Opp. at 44:6-46:6. But 15

the testimony of Broad’s witnesses is not the only or even the primary evidence of the ARTPs. 16

There are multiple, contemporaneous, and unchallenged emails, along with contemporaneous gel 17

images and sequencing results with unchallenged metadata, corroborating each ARTP and Zhang’s 18

recognition of success. See, e.g., Exs. 3771-73, 3563, 3581-82, 3922, 3429, 3566, 3582 at 20 and 19

24 (gel and notebook entry); Ex. 3784 (sequencing results); Exs. 3781, 3784, 3830, 3775, 3777, 20

3565-66, 3842, 3791, 3793, 3545-50, 3554-55; Ex. 3429 Schou Dec. (metadata). The testimony of 21

Broad’s witnesses confirms and contextualizes these results, and CVC’s arguments fail under a 22

rule of reason analysis. Price v. Symsek, 988 F.2d 1187, 1195 (Fed. Cir. 1993). 23

Regardless, CVC’s issue with the testimony of the witnesses has no merit. CVC does not 24


BROAD REPLY 5

contend Drs. Kosuri or Cox are inventors of the subject matter of Count 1 or of any of the involved 1

patents or application. Paper No. 1558, CVC Substantive Motion 3 (for improper inventorship), 2

Chart 2 at 7-9. Kosuri confirmed that he has no financial interest in this matter or the involved 3

patents or application (to the contrary, he is employed by the Regents of the University of 4

California as a Professor at UCLA). MF 149; Ex. 5259, Kosuri Tr. 23:20-24:13. Nor does Cox, 5

who is not alleged to be an inventor on any involved patent and has no financial interest in them. 6

MF 150; see Paper No. 23; Paper No. 1558 at 7-9. Additionally, CVC’s arguments with respect to 7

Drs. Cong and Sanjana misapprehend the law of corroboration. It is the subject matter of Count 1 8

and who invented that subject matter that is the touchstone for determining who may provide 9

corroboration. Larson v. Johenning, 17 U.S.P.Q.2d 1610 (B.P.A.I. 1990) (Ex. 3316). Neither Cong 10

nor Sanjana are co-inventors of the subject matter of Count 1 (indeed, CVC does not even contend 11

so)—they are merely named on certain involved patents which claim improvements to that 12

invention.4 Thus, their testimony is a proper part of the web of corroboration. 13

C. CVC’s Derivation Claim Is Untimely, Improper, And Nothing More Than A 14 Repackaged Argument Based On The Jinek 2012 Disclosure 15

Lacking any argument as to insufficiency of Broad’s priority proofs, CVC attempts, 16

without any basis in fact, to raise a derivation claim at this late point. CVC asserts that somehow 17

Marraffini’s communication of public information, presented at a June 2012 bacterial conference 18

and later published as part of Jinek 2012, resulted in a derivation of Count 1 by Zhang. 19

As a threshold matter, CVC’s derivation claim is untimely and improperly raised. CVC 20

bears the burden of proving derivation under 35 U.S.C. §102(f) (Price, 988 F.2d at 1194), in the 21

4 Cong or Sanjana are named only on the 233, 445, 616, 814, and 641 patents, and 551

application.


BROAD REPLY 5

same way it would as to any other invalidity ground. PTAB Rule 121 provides that “[r]elief on the 1

merits of a case must be sought through a substantive or responsive motion.” Paper No. 2, S.O. 2

¶121. Further, 37 C.F.R. §41.208(a)(4) identifies derivation as one such substantive motion. The 3

PTAB rules require prior authorization for substantive motions, but CVC did not timely seek and 4

never obtained such authorization. 5

Instead, CVC improperly raised its derivation claim for the first time in its Opposition, 6

spending nearly 40 of its 60 pages on that baseless claim. This approach improperly deprived 7

Broad of the opportunity to fully oppose an argument that should have been made in a substantive 8

motion, with Broad opposing and entitled to present opposing declarations. The record on 9

derivation now consists of declarations and cross-examination of CVC’s paid experts and three 10

financially-interested co-founders (Marraffini, Barrangou and Sontheimer) of Intellia 11

Therapeutics, a real party in interest and a company that helps fund this Interference. MFs 151-12

153. Intellia readily admits that it is on a mission to invalidate Broad’s patents, having joined an 13

agreement to cooperate in that endeavor. See Ex. 6121. 14

To punctuate the unfairness, CVC makes the incredible assertion that Broad does not 15

dispute Marraffini’s testimony. Opp. at 34:4. Not so. Broad had no opportunity to provide counter 16

declarations, including from Zhang, which would have disputed Marraffini’s biased testimony on 17

topics such as Zhang’s supposed knowledge and alleged conversations between them. Had CVC 18

properly and timely filed a substantive motion—Broad would have not only cross-examined 19

CVC’s witnesses, but also would have submitted affirmative declarations explaining what actually 20

transpired. The PTAB should dismiss CVC’s improperly raised derivation claim, cloaked as an 21

Opposition, because CVC failed to comply with the rules, to the substantial prejudice of Broad. 22

In their March 23, 2021 email to the PTAB regarding whether it was proper to include its 23


BROAD REPLY 5

derivation claim in its opposition, CVC asserted Marraffini’s deposition testimony spurred its 1

derivation claim. Ex. 6061. That is nonsense. Cong 2013 explained long ago that the authors 2

adapted their dual-molecule RNA eukaryotic CRISPR-Cas9 system into a system with chimeric 3

RNA that had been “recently validated in vitro,” citing Jinek 2012. MF 148; Ex. 3201 at 820. 4

Marraffini did not claim to have communicated more than Jinek 2012 to Zhang and indeed he 5

could not have because he had no other CVC information to communicate. In addition, Zhang’s 6

priority declaration again acknowledged CVC with respect to his use of a GAAA linker through 7

Marraffini’s communication. See, e.g., MFs 148, 158; Ex. 3424, Zhang Dec. ¶12. Thus, CVC could 8

have timely sought a responsive motion if it believed the derivation argument to have any merit. 9

Moreover, at bottom, CVC’s derivation claim under §102(f) is nothing more than a 10

repackaging of its failed argument regarding the disclosures in Jinek 2012. But Jinek 2012 did not 11

provide an expectation of success or suffice to demonstrate possession of the invention. As Doudna 12

remarked about that paper, “‘[o]ur [Jinek] 2012 paper was a big success, but there was a problem. 13

We weren’t sure if CRISPR/Cas9 would work in eukaryotes – plant and animal cells.’ Unlike 14

bacteria, plant and animal cells have a cell nucleus, and inside, DNA is stored in a tightly wound 15

form, bound in a structure called chromatin.” Ex. 3287 at 3. Similarly, Dr. Carroll explained 16

contemporaneously that actual experiments were necessary. Ex. 3286 at 1660. 17

Nevertheless, CVC asserts that by making the disclosures of Jinek 2012 public, CVC 18

became entitled to the eukaryotic invention, no matter who actually made the critical breakthrough: 19

creating a functioning eukaryotic system. In the 048 Interference, the PTAB found that functioning 20

eukaryotic CRISPR-Cas9 systems were not obvious over the Jinek 2012 disclosure of sgRNA and 21

in vitro experiments. MF 159; Ex. 3110 at 13:14-14:21, 17:3-10. Shifting the statutory prior art 22

category from §102(a) to §102(f) does not cure the deficiency of the disclosures. It does not matter 23


BROAD REPLY 5

if an inventor read the disclosure of Jinek 2012 or heard CVC’s June 2012 public conference 1

disclosure directly or from one who attended. No one could derive the eukaryotic invention from 2

the public conference any more than from the deficient Jinek 2012 publication. 3

D. CVC’s Derivation Claim Fails Because Its Inventors Lacked A Prior, 4 Complete Conception At The Time Of The Alleged Derivation 5

CVC’s derivation claim also fails because CVC has not shown that it conceived of the 6

subject matter of Count 1 before the communication between Zhang and Marraffini. “To show 7

derivation, the party asserting invalidity must prove both prior conception of the invention by 8

another and communication of that conception to the patentee.” Gambro Lundia AB v. Baxter 9

Healthcare Corp., 110 F.3d 1573, 1576 (Fed. Cir. 1997). Broad’s Opposition 2 details why CVC 10

did not have a conception before any of its ARTPs for multiple separate—and independently 11

fatal—reasons, including that CVC’s inventors lacked: (a) a reasonable expectation of success, (b) 12

a definite and permanent idea of the operative invention, and (c) possession of a functional 13

eukaryotic CRISPR-Cas9 system. See Broad Opp. at 16-39. 14

1. For The Possession Requirement, CVC Makes Inflammatory and 15 Erroneous Arguments Against Broad’s Prior Arguments 16

With respect to possession, CVC accuses Broad of perpetrating a sham by arguing that for 17

possession a POSA would have needed to see “unique conditions and specific instructions relevant 18

to CRISPR-Cas9.” Opp. at 59:8-19. But Broad made that argument based on the PTAB’s explicit 19

findings from the 048 Interference. There, the PTAB analyzed the state of the art in 2012, including 20

prior attempts to adapt prokaryotic systems for use in eukaryotes, and found that for a reasonable 21

expectation of success, a POSA would have needed to see “unique conditions” and “specific 22

instructions” for CRISPR-Cas9. Ex. 3110 at 39:6-10, 45:19-22. 23

Broad and Dr. Mirkin used the same words to describe a POSA’s expectations when 24

hypothetically reviewing CVC’s P1 and P2 disclosures in 2012. See e.g., Ex. 3417, Mirkin Dec. 25


BROAD REPLY 5

¶¶ 50, 116, 147. The reason is that the analysis for possession—like that for expectation of 1

success—assesses the application’s disclosure based on what is known at the time. Thus, here, the 2

PTAB found that CVC’s P1 and P2 applications failed to demonstrate possession of Count 1, 3

stating, for example, “CVC’s arguments fail to persuade us that those of ordinary skill in the art 4

would not have considered specific instructions or conditions for a CRISPR-Cas9 activity in a 5

eukaryotic cell to be necessary.” Paper 877, Decision at 90:6-8. 6

For the possession requirement of conception, CVC does not argue that its inventors knew 7

anything relevant beyond the disclosures in P1 and P2. CVC’s inventors were not aware of 8

“specific instructions or conditions” for eukaryotic CRISPR-Cas9 systems, nor had they conducted 9

successful eukaryotic experiments. CVC notes that two of several vectors that it designed in May 10

2012 were supposedly used in October for an alleged ARTP. Opp. at 32:14-20. But that too is an 11

improper retrospective analysis. See Hitzeman v. Rutter, 243 F.3d 1345, 1357-58 (Fed. Cir. 2011). 12

There was no way of knowing in May 2012 whether those two vectors—even if later used in 13

October (they were not)—would lead to success. Indeed, CVC’s expert human cell collaborators, 14

Drs. Drubin and Cheng, repeatedly failed with those and other vectors. Broad Opp. at 31:21-37:19. 15

It was later changes, including changes to the structure of the sgRNA after discussions with Dr. 16

Church (affiliated with Broad), that led to CVC’s alleged success. This amply demonstrates, even 17

retrospectively, that the vectors did not suffice for success. Id. The vectors were simply part of 18

CVC’s multi-prong approach using multiple techniques with multiple collaborators, with the CVC 19

inventors hoping that one collaborator might somehow find success. See MFs 160-162. CVC did 20

not possess the invention, and conception fails for that reason alone. 21

2. For The Definite And Permanent Idea Requirement, CVC Fails To 22 Come To Grips With Its Repeated And Extensive Failures After 23 Communication Of The Alleged Conception 24

CVC largely ignores the definite and permanent idea requirement for conception and never 25


BROAD REPLY 5

comes to grips with the numerous failures by its expert collaborators to whom CVC conveyed the 1

alleged conception. “Conception is complete only when the idea is so clearly defined in the 2

inventor’s mind that only ordinary skill would be necessary to reduce the invention to practice, 3

without extensive research or experimentation.” Dawson v. Dawson, 710 F.3d 1347, 1352 (Fed. 4

Cir. 2013) (quoting Burroughs Wellcome Co. v. Barr Labs., Inc., 40 F.3d 1223, 1228 (Fed. Cir. 5

1994)). The failures of CVC’s expert collaborators provide real-world evidence that CVC’s ideas 6

were not “so clearly defined,” but rather required extensive research and experimentation. 7

CVC relies, for example, on its April 11 IDS (Ex. 5105) as describing “techniques for 8

introducing sgRNA CRISPR-Cas9 complex into eukaryotic cells citing articles published for ZFN 9

and TALENs.” Opp. at 42 (figure), 3-1. But the IDS, like CVC’s P1 and P2 applications, merely 10

provided laundry lists of options. It provided no guidance specific to eukaryotic CRISPR-Cas9. 11

Indeed, persons with expertise with those systems, such as Drubin and Cheng with ZFNs, failed 12

in every attempt to implement CVC’s sgRNA Chimera A system. Broad Opp. at 33:20-35:1. 13

Similarly, Dr. Doudna, working with Dr. Meyer (who had prior eukaryotic ZFN experience), failed 14

to obtain a functioning system in worms. See MFs 208-09; Ex. 3656. 15

Given the clear blow dealt by these many failures, CVC further turns the conception inquiry 16

on its head by arguing that Zhang’s ability to quickly have an ARTP of the sgRNA variant of his 17

eukaryotic invention shows CVC’s conception was complete. Opp. at 6:1-12. The response is that 18

Zhang’s speed is indicative of his prior work and understanding of the CRISPR system, not CVC’s 19

conception. It is CVC’s months of floundering and failure that confirms CVC’s lack of a 20

conception. Zhang moved expeditiously because he had already proven CRISPR-Cas9 in 21

eukaryotic cells with his dual molecule systems and so was able quickly to also implement the 22

sgRNA variant in eukaryotic cells. CVC couldn’t because it hadn’t. 23


BROAD REPLY 5

3. For The Reasonable Expectation Of Success Requirement, CVC Makes 1 Erroneous Legal And Factual Arguments 2

(a) CVC Misstates The Conception Law For Claims That Recite A 3 Specific Biological Result 4

CVC contends that conception does not require a reasonable expectation of success. CVC 5

again misinterprets the statement in Burroughs, 40 F.3d at 1228 that “an inventor need not know 6

that his invention will work for conception to be complete” to argue that the CVC inventors did 7

not need to have an expectation of success. Opp. at 37:14-41:24. The response is that the Hitzeman 8

court addressed the very statement in Burroughs that CVC relies on and admonished against 9

reading it (as CVC does) to suggest that an inventor need not have a reasonable expectation of 10

success in producing the claimed biological result. Hitzeman, 243 F.3d at 1357-58. The court noted 11

that Burroughs’ statement that CVC relies on pertained to the five patents that did not require the 12

biologic result of increasing a patient’s T-Cell count. Id. at 1358. The sixth patent at issue in 13

Burroughs, however, included claims requiring the biological result. Id. The Federal Circuit found 14

no conception of the invention of that sixth patent because “one skilled in the art would not have 15

expected T-cell count to rise” before experiments with patients. Burroughs, 40 F.3d at 1232. 16

CVC ignores this key distinction between claims reciting a biological result and those that 17

do not. Here, as in Hitzeman, Count 1 “claim[s] the specific result of a biological process” in an 18

unpredictable art. Hitzeman, 243 F.3d at 1358. Accordingly, because CVC “failed to show that [it] 19

had a reasonable expectation that the claimed result of the biological process would occur, [its] 20

conception argument cannot prevail.” Id. 21

(b) CVC’s Arguments Regarding Simultaneous 22 Conception/Reduction To Practice Are Irrelevant And Wrong 23

CVC wrongly argues that CVC need not show successful eukaryotic experiments before 24

having a conception because “simultaneous conception and reduction to practice does not apply” 25


BROAD REPLY 5

here. Opp. at 41:12-16. Specifically, CVC contends that by asserting a derivation claim, the 1

requirement for simultaneous conception/reduction to practice can no longer apply as a matter of 2

law, even in unpredictable arts. CVC’s argument is irrelevant on the facts and wrong on the law. 3

First, simultaneous conception/reduction to practice is irrelevant on the facts. Broad does 4

not allege that one must have an ARTP of Count 1 to have a conception. Rather, Broad asserts that 5

to have a reasonable expectation of success (and to demonstrate possession), one must have had 6

successful eukaryotic CRISPR-Cas9 system experiments showing that the hurdles and 7

uncertainties of engineering such a system could be overcome. As the PTAB found regarding the 8

eukaryotic aspect of the prior 048 Count, “one of ordinary skill in the art would not have reasonably 9

expected success before experiments in eukaryotic cells were done.” Ex. 3110 at 23:3-5. Thus, 10

until one has successful eukaryotic experiments, there can be no reasonable expectation of success. 11

CVC misses the mark with its attempt to equate Broad’s argument with a simultaneous 12

conception/reduction to practice requirement. One can have a conception of Count 1 without an 13

ARTP. For example, Zhang had a conception before his ARTP with sgRNA precisely because he 14

already had conducted dual-molecule experiments showing CRISPR-Cas9 function in eukaryotes. 15

Once he made that demonstration, he had a reasonable expectation of success for the analogous 16

sgRNA system because he reasonably did not expect the GAAA linker to alter his prior success. 17

Thus, simultaneous conception/reduction to practice is not the inquiry; it is whether one has shown 18

a reasonable expectation of success in this unpredictable art. 19

CVC cites Applegate and MacMillan in support of its argument. Neither applies. 20

Applegate is inapposite. The count in Applegate v. Scherer, 332 F.2d 571 (C.C.P.A. 1964) 21

was directed to a method of adding a chemical compound (3-trifluoromethyl-4-nitrophenol) to 22

water containing lampreys to control their population numbers. Id. at 571. Importantly both parties 23


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there admitted that the chemical of the count was similar to a prior art compound (3-bromo-4-1

nitrophenol) to control lampreys—in other words, unlike here, the prior art included a successful 2

demonstration of the proposed analogous system. Id. at 572 (junior party identifying “a similar 3

chemical compound” to senior party for testing; senior party responding “since the substance you 4

offer is similar to [the prior art] compound” they would accept a sample and test it). The senior 5

party performed standard testing on the compound and found that, as predicted by both parties, it 6

was effective like the similar prior art compound. Id. Despite obtaining the entirety of the 7

invention—the chemical compound, the only novel feature of the count—from junior party and 8

not having done any prior work on the relevant compound, the senior party patented the compound 9

for itself. The C.C.P.A. found that priority was properly awarded to junior party. Id. at 574. 10

The Applegate court specifically noted it was not the type of case where “the inventor’s 11

mind cannot formulate a completed invention until he finally performs a successful experiment.” 12

Id. at 573. In contrast, the CRISPR-Cas9 art—unlike the art at issue in Applegate—was 13

unpredictable, required eukaryotic experiments for an expectation of success, and included no 14

published demonstration of an analogous CRISPR-Cas9 system functioning in eukaryotic cells. 15

CVC’s argument about MacMillan is illogical and unworkable. CVC cites MacMillan v. 16

Moffett, 432 F.2d 1237 (C.C.P.A. 1970) for the proposition that the doctrine of simultaneous 17

conception and reduction to practice “does not apply in cases where the issue is originality or 18

derivation.” Opp. at 41:15-21 (quoting MacMillan, 432 F.2d at 1240). But even if simultaneous 19

conception/reduction to practice was applicable here (it is not), MacMillan was merely (mis-20

)summarizing Applegate, which—as noted above—is not applicable, especially because the 21

Applegate court expressly noted that its holding did not apply to cases in unpredictable arts. 22

Applegate, 332 F.2d at 573. 23


BROAD REPLY 5

Moreover, MacMillan found complete conception before communication to the testing 1

party without any reference to derivation. MacMillan, 432 F.2d at 1239-40. And, neither Applegate 2

nor MacMillan found that the simultaneous conception/reduction to practice standard applied on 3

the facts of those cases. Id. at 1240; Applegate, 332 F.2d at 573. The better, more consistent, 4

reading of both cases is that simultaneous conception/reduction to practice did not apply on the 5

facts there because of previous successful demonstrations of analogous systems in the prior art. 6

Finally, at base, CVC’s argument presupposes that merely making an allegation of 7

derivation can change the conception standard. It cannot. Nothing in Applegate nor MacMillan 8

suggests that alleging derivation changes whether an art is unpredictable and so requires prior 9

successful use of at least an analogous system for conception. If a mere allegation could change 10

the standard, parties in cases involving unpredictable art could transform an incomplete conception 11

(without a prior analogous ARTP) into a complete one merely by making a baseless derivation 12

allegation, as CVC does here. That makes no sense and is not the law. 13

Indeed, at the urging of one of the CVC parties, the court in Brown v. Regents of Univ. of 14

California rejected such a nonsensical result in addressing a similar MacMillan-based argument. 15

Brown, 866 F. Supp. 439 (N.D. Cal. 1994). In Brown, the party claiming joint inventorship argued, 16

based on MacMillan, her lack of participation in the ARTP could not bar her joint inventorship 17

claim, because issues of originality were in play (there, joint inventorship; here, derivation). Id. at 18

443. The Brown court, analyzing Applegate and MacMillan in depth, rejected the expansive 19

interpretation of MacMillan that CVC argues here, and reasoned that such arguments “highlight[] 20

the untenability of employing different definitions of ‘conception’ depending upon the context in 21

which the Court considers the issue.” Id. at 444. The court thus rejected MacMillan’s “expansive 22

statements” about derivation’s effect on simultaneous conception/reduction to practice, finding 23


BROAD REPLY 5

“the Federal Circuit would apply the doctrine of simultaneous conception and reduction to practice 1

to cases, such as the instant case, where the issue of originality arises” because “employing 2

different definitions of ‘conception’ depending on the context” was not sustainable. Id. 3

(c) CVC’s New Fact Declarations Come Only From Biased 4 Witnesses And Conflict With The Contemporaneous Record 5

CVC submitted declarations from two fact witnesses, Drs. Barrangou and Sontheimer, on 6

expectation of success. However, both are co-founders (along with Drs. Doudna and Marraffini) 7

of Intellia Therapeutics, a real party in interest and a company that helps fund this Interference. 8

MFs 151-153; Ex. 6212, Barrangou Tr. 25:8-11, 165:19-172:21; Ex. 6214, Sontheimer Tr. 13:2-9

16, 20:22-22:18. Intellia admits that it is on a mission to invalidate the Broad’s patents. See Ex. 10

6121. It is telling that CVC could not submit a single fact declaration from a disinterested scientist 11

stating that he or she had an expectation of success upon reading Jinek 2012 or hearing the June 12

presentation. MF 154. In contrast, Broad submitted public record declarations of several scientists 13

with no financial stake in this proceeding who noted that they contemporaneously read Jinek 2012 14

and had no expectation of success for eukaryotic CRISPR-Cas9 systems. MF 155; see, Ex. 3416 15

Lambowitz Dec. ¶¶20-40; Ex. 3446, Gao Dec. ¶¶3-6; Ex. 3435, Davies Dec. ¶¶5-8. 16

Moreover, Dr. Barrangou’s declaration conflicts with the contemporaneous record. In 17

2012, Barrangou published an article stating that the sgRNA system from Jinek 2012 had 18

“immediate applications” in bacteria, but only that there were “intriguing possibilities” for 19

eukaryotes. MF 163; Ex. 4257 at 838. As the PTAB previously found, “[s]tatements of a 20

‘possibility’ that the system might work” are “not statements that it would be expected to do so.” 21

Ex. 3110 at 22:18-23:1. Barrangou also recalls supposedly supporting conversations with Doudna 22

(Ex. 5016, Barrangou Dec. ¶16), but the contemporaneous statements of Doudna shows that she, 23

like Carroll, had no expectation of success. See, e.g., Ex. 3287 at 3-4. 24


BROAD REPLY 5

Barrangou also now states that “it was not a matter of if—but just a matter of when—the 1

CRISPR-Cas9 system would be used for genome editing.” Ex. 5016, Barrangou Dec. ¶20 2

(emphasis original). That statement by Barrangou, whose expertise is with bacterial cells, conflicts 3

with the contemporaneous published statements of CVC’s prior eukaryotic expert, Carroll, 4

identifying hurdles such RNA degradation, chromatin, toxicity, and others that made it impossible 5

to predict whether CRISPR-Cas9 could ever be adapted for eukaryotic cells. Ex. 3286 at 1660. 6

Barrangou’s 2021 contention that it was “just a matter of when” also conflicts with Marraffini’s 7

published statement that “[e]verything seems very simple now. But at the time, we did not know.” 8

Ex. 4320 at 8. Marraffini also stated “[w]hat if Cas9 is kicked off the human DNA by all these 9

structures that are not present in phages or bacterial chromosomes? It might have not worked.” Id. 10

Sontheimer asserts that at the June 2012 conference, he and other attendees “immediately 11

recognized that the CRISPR-Cas9 system they disclosed was revolutionary for genome editing in 12

eukaryotes” and that Doudna, Barrangou, and he “discussed that those in the field would rush to 13

apply the CVC inventors’ sgRNA CRISPRCas9 system in eukaryotes.” Ex. 5018, Sontheimer Dec. 14

¶19. Yet, conspicuously absent from his detailed notes from the conference is any mention of 15

possible eukaryotic applications. See MF 164; Ex. 5277. Moreover, even Marraffini testified that 16

the June 2012 conference was “a CRISPR biology meeting, so most of the people there are 17

interested in bacteria” and that “I don't recall much talk about gene editing.” MF 166; Ex. 5265, 18

Marraffini Tr. 30:12-15, 31:5-6. 19

CVC’s new proofs do not move the needle. The record firmly establishes that a POSA 20

having knowledge of CVC’s complete work through June 2012, even with full knowledge of 21

CVC’s internal work and the information set forth in P1 and P2, would have not had a reasonable 22

expectation of success. None of CVC’s work through June 2012 shows a working example or 23


BROAD REPLY 5

specific instructions and unique conditions necessary to accommodate the eukaryotic environment. 1

Thus there is no reasonable expectation of success and conception fails on this ground also. 2

E. CVC’s Derivation Claim Fails On The Facts Because Far From 3 Communicating the Complete Invention, The Public Disclosure (Less Than 4 Jinek 2012) Does Not Even Render Dr. Zhang’s Inventions Obvious 5

To make out a derivation claim, CVC would have to show not only a “prior, complete 6

conception of the claimed subject matter” (which it failed to do as set forth above) but also a 7

“communication of the subject matter” that would be sufficient “to enable one of ordinary skill in 8

the art to construct and successfully operate the invention.” Mead v. McKirnan, 585 F.2d 504, 507 9

(C.C.P.A. 1978). CVC wrongly contends that Marraffini’s alleged communication to Zhang of 10

certain in vitro results of Jinek 2012 constitutes such a communication. But this communication is 11

necessarily insufficient to constitute an enabling disclosure of the operative invention because, as 12

the PTAB has already found, the in vitro results of Jinek 2012 would not even render obvious 13

successful use of CRISPR-Cas9 in eukaryotic cells. Ex. 3110 at 2:7-11. 14

CVC does not even attempt to show communication of more than the disclosures of P1 and 15

P2 or Jinek 2012. In fact, even taking CVC’s allegations about what was communicated by 16

Marraffini as true (they are not), Zhang would have received substantially less than either 17

disclosure. CVC attempts to attribute significance to Marraffini’s alleged statement that CRISPR-18

Cas9 would be “an important tool for genome editing in eukaryotes specifically.” Opp. at 36:3-6. 19

But it is no more than Jinek 2012’s forward-looking speculation that CRISPR “could offer 20

considerable potential for gene-targeting and genome-editing applications,” which the PTAB 21

found, based on CVC’s arguments, to be proposing use of the system in eukaryotic cells. MF 167-22

170; Ex. 3110 at 21:3-10; Ex. 3202 at 820. 23

Where, as here, a communication would not even render obvious the claimed invention, it 24

cannot properly form the basis of a derivation claim. As the Federal Circuit has instructed, “[t]o 25


BROAD REPLY 5

invalidate a patent for derivation of invention, a party must demonstrate that the named inventor 1

in the patent acquired knowledge of the claimed invention from another, or at least so much of the 2

claimed invention as would have made it obvious to one of ordinary skill in the art.” New England 3

Braiding Co., Inc. v. A.W. Chesterton Co., 970 F.2d 878, 883 (Fed. Cir. 1992); see also 4

Cumberland Pharms. Inc. v. Mylan Institutional LLC, 846 F.3d 1213, 1218-19 (Fed. Cir. 2017) 5

(“We have held that derivation is not proved by showing conception and communication of an 6

idea different from the claimed invention even where that idea would make the claimed idea 7

obvious.”). Here, Marraffini’s communication does not even render the invention of Count 1 8

obvious and thus cannot form the basis of a derivation claim. At best, Marraffini could have 9

communicated only that CVC had “a general goal” or a “bare hope of a result,” not a proper basis 10

of a derivation claim. See Cumberland, 846 F.3d at 1218-19. 11

Moreover, the alleged communication did not disclose any of the adaptations actually 12

needed to implement a functional eukaryotic CRISPR-Cas9 system. For example, CVC does not 13

even allege that the June 21 CVC presentation that Marraffini heard and conveyed to Zhang 14

included any information regarding delivery methods, promoters, NLSs, codon strategy etc. for 15

adapting a CRISPR-Cas9 sgRNA system to eukaryotic uses. See MF 170; Opp. at 15:21-18:17. 16

That would have been impossible because the CVC inventors did not have any of this information 17

but rather (as reflected in P1 and CVC’s internal records) were simply considering “multiple 18

methods” and “multiple approaches” with no success. Ex. 6207, Jinek Tr. 274:15-16; 272:16-17. 19

Count 1 requires a functioning eukaryotic CRISPR-Cas9 system. Decision at 95. In the 048 20

Interference, claims directed to functioning eukaryotic CRISPR-Cas9 systems were found to be 21

non-obvious over Jinek 2012, with its disclosure of sgRNA. Ex. 3110 at 13:14-14:21, 17:3-10. By 22

putting the sgRNA construct into the prior art, the CVC inventors did not become entitled to the 23


BROAD REPLY 5

eukaryotic invention—the requirement of a functioning eukaryotic system is an essential element 1

of Count 1, and it is critically missing from their alleged communication to Zhang. 2

F. CVC’s Derivation Claim Fails Because Dr. Zhang Knew Of And Successfully 3 Used All Aspects Required For A Functional Eukaryotic CRISPR-Cas9 4 System—Including tracrRNA—Prior To The Marraffini Communication 5

1. CVC Cannot Erase Dr. Zhang’s Pre-Existing Eukaryotic CRISPR-6 Cas9 System Experience And Knowledge 7

CVC’s derivation argument also fails for a more fundamental reason: CVC cannot claim 8

Zhang’s prior work developing a eukaryotic CRISPR-Cas9 system as their own. 9

CVC recognizes that for CVC to have communicated a “complete conception” of Count 1, 10

it must first deprive Zhang of his possession of a eukaryotic CRISPR-Cas9 system before the 11

alleged communication. So CVC tries to turn Zhang into CVC’s lab hand, arguing that “Zhang did 12

not invent any of the invention….” (Opp. at 5:10), that “Zhang contributed none of the elements 13

of Count 1” (id. at 6:23 (emphasis in original)), and that Zhang merely “implement[ed] someone 14

else’s (CVC’s) invention” (id. at 8:13-14) after “obtaining the invention of Count 1 from CVC 15

through Marraffini” (id. at 2:13). 16

The response is that these inflammatory allegations turn the facts on their head. The 17

undisputed facts show that Zhang worked from February 2011 on to develop the ground-breaking 18

eukaryotic CRISPR-Cas9 system disclosed in Cong 2013, and that before June 2012, his system 19

included every element of Count 1—other than a linker (MFs 171-177) a single element that was 20

already well known in the art—as shown below (adapted from Ex. 5013, Doyon 2d Dec. ¶55): 21

Aspect of Count 1 Part of Eukaryotic System From

2011 On

Relevant Cites

Eukaryotic cell comprising a target DNA molecule and a CRISPR-Cas9 system

See, e.g. MF 172; Ex. 3424 at ¶¶ 6-11, 48-113; Exs. 3716 at 6, 3736, 3902, 3526-29, 3530, 3531 at 16, 3535-36, 3735, 3742, 3427 at Appendix A and Exs. 3, 7, Ex. 10


BROAD REPLY 5

Cas9 See, e.g. MF 173; Ex. 3424 at ¶¶ 6-11, 48-113; Exs. 3716 at 6, 3736, 3715, 3533, 3734, 3742, 3526, 3528.

crRNA with a target sequence

See, e.g. MF 174; Ex. 3424 at ¶¶ 6-11, 48-113; Exs. 3716 at 6, 3736, 3902, 3531 at 16, 3708; 3526, 3528.

tracrRNA capable of hybridizing with the crRNA to form a duplex

See, e.g. MF 175; Ex. 3424 at ¶¶ 6-11, 48-113; Exs. 3710, 3845, 3526-29, 3736, 3716 at 6.

crRNA and tracrRNA covalently linked with intervening nucleotides

System is capable of cleaving or editing a target DNA molecule.

See, e.g. MF 176; Ex. 3424 at ¶¶ 6-11, 48-113; Exs. 3902, 3530, 3531 at 16, 3716, 3535-36, 3736, 3902, 3526-29.

The only additional information Zhang learned on June 26 was that the Jinek 2012 co-authors had 1

fused the tracrRNA and crRNA with a known GAAA tetraloop, creating the construct identified 2

as Chimera A, which worked in vitro to cut a synthetic DNA target. Fusing two RNA molecules 3

was well known and routine in the art by 2012 and performing such a fusion with the specific 4

CRISPR-Cas9 RNAs was publicly disclosed by June 21, 2012. See, e.g., Ex. 3444, Breaker 2d 5

Dec. ¶¶ 9-13. Zhang added a GAAA linker to his already functioning system to test it alongside 6

his dual-molecule system which he was optimizing at the time (see Ex. 3751), and he submitted 7

both his dual-molecule CRISPR-Cas9 experiments and those with sgRNA for publication only 8

three months later. See MF 148, 199-201; Ex. 3564. 9

CVC claims Zhang surreptitiously took the entire invention from CVC through Marraffini. 10

But the truth is simpler and in no way nefarious: Zhang included a small, single adaptation that the 11

CVC inventors chose to put into the public domain. He was so far ahead of CVC with the work 12

that mattered—creating a functioning eukaryotic CRISPR-Cas9 system—that he was able to 13

reduce the chimeric RNA system to practice multiple times as memorialized in his complete, 14

groundbreaking manuscript, all while CVC struggled and failed despite their multiple, highly-15

experienced eukaryotic co-collaborators (see Broad Opp. at 11:18-15:5). 16


BROAD REPLY 5

CVC’s own cited case, Alexander v. Williams, 342 F.2d 466 (C.C.P.A. 1965), demonstrates 1

the unfairness that would arise if the creator of a minor change to a system were able to leverage 2

that addition to claim the original advance altogether. In Alexander, the count concerned “a system 3

for controlling fuel flow and stator angle in a jet engine” by, among other ways, mounting two 4

cams on a common shaft. Id. at 466. In Alexander, it was undisputed that the junior party was the 5

first to conceive of all elements of the count and communicated all aspects of the count to the 6

senior party other than the aspect of mounting two cams on a common shaft. Id. at 468-69. The 7

senior party had independently conceived just the feature of using two cams on a common shaft. 8

Id. at 471. Similarly, here, in June 2012 CVC did not have a functioning eukaryotic CRISPR 9

system nor did it know what was necessary to adapt the system successfully; it created only an in 10

vitro sgRNA system. In Alexander, the court found that the senior party could not rightfully be 11

awarded priority because “there is no showing that he invented or suggested the entire invention 12

as embodied in the combination of elements claimed” and even where one contributes an 13

improvement to an invention “he cannot appropriate to himself the entire result of the ingenuity 14

and toil of the originator.” Id. (quotation omitted). Likewise, CVC cannot appropriate to itself the 15

entire result of Zhang’s ingenuity and toil in making a functional eukaryotic CRISPR system by, 16

at most, contributing the aspect of disclosing the use in vitro of a known RNA linker. 17

2. The Facts Contradict CVC’s Claim That Dr. Zhang Did Not 18 Understand tracrRNA Was Necessary 19

Ultimately, despite CVC’s grand claims that Zhang contributed nothing at all, CVC retreats 20

to arguing that he did not understand that tracrRNA was a necessary part of the CRISPR-Cas9 21

cleavage complex, citing their Jinek 2012 work and the reviewer comments expressing surprise 22

that tracrRNA was a necessary part of the complex. Opp. at 13:8-14:14, 1:20-22. Broad does not 23

dispute that CVC was the first party to publicly present experimental confirmation in vitro, but 24


BROAD REPLY 5

that is irrelevant here. What is relevant is that Zhang correctly posited, based on Deltcheva, that 1

tracrRNA was part of the cutting complex, and CVC does not and cannot dispute that Zhang used 2

tracrRNA in every one of his CRISPR-Cas9 experiments from April 2011 onwards. MFs 175, 179; 3

Ex. 3424, Zhang Dec. ¶¶ 6-11, 48-113; Exs. 3710, 3845, 3526-29, 3736, 3716 at 6. His actions 4

speak louder than CVC’s words, and they clearly show Zhang’s awareness of the role of tracrRNA, 5

as would be apparent by the POSA reviewing Charpentier’s Deltcheva 2011 publication. MFs 178, 6

187-192; Ex. 3444, Breaker 2d Dec. ¶8; Ex. 3448, Breaker 3d Dec. ¶¶34-36. 7

(a) CVC Intentionally Misreads The Record Regarding Dr. 8 Zhang’s Understanding Of The Role Of tracrRNA 9

First, CVC mischaracterizes the relevant testimony when it claims that “Marraffini testified 10

that he ‘must have’ told Zhang about the role of tracrRNA in the catalytic DNA-cleavage 11

complex.” Opp. at 16:9-10. CVC omits that Marraffini actually testified that “I don't recall saying 12

that, but if I explained what a single-guide RNA is, I must have said that.” MFs 180-181; Ex. 5265, 13

Marraffini Tr. 29:20-30:3. It is apparent that Marraffini had no present recollection, but instead 14

was just filling in. In that regard, it is telling that prior to this proceeding, Marraffini pursued a 15

claim that he should be added as a co-inventor on Broad’s involved eukaryotic patents. See MFs 16

156-157; Ex. 3946. However, in binding arbitration the arbitrator determined that Marraffini did 17

not contribute to Broad’s eukaryotic inventions and is not a co-inventor. Id.; see also MF 165. 18

Unable to join the Broad patents as an inventor, Marraffini now offers testimony here filling in 19

where the written record does not support his testimony. 20

In any event, it is irrelevant whether Marraffini mentioned the role of tracr because, as 21

Zhang confirmed in his declaration and as the supporting evidence confirms, Zhang already knew 22

of, and was using, tracrRNA in the cutting complex. MFs 175, 178-179, 182-198; Ex. 3424, Zhang 23

Dec. at ¶¶114-15; see, e.g., Exs. 3710, 3526-29, 3736, 3708-09, 3716 at 6. Specifically, Zhang 24


BROAD REPLY 5

understood from Deltcheva that tracrRNA would remain bound to crRNA in the CRISPR-Cas9 1

cutting complex due to lack of any agent to overcome the hybridization forces between them and 2

also given Cas9 would protect the duplex. MF 178; Ex. 3424, Zhang Dec. ¶¶66-69. Accordingly, 3

after reading Deltcheva, he always used tracrRNA for all of his CRISPR-Cas9 experiments starting 4

in April 2011 and thereafter. MF 179; Id. at ¶70; Exs. 3710, 3845, 3526-29, 3736, 3716 at 6. 5

Zhang’s awareness is further corroborated by his October 2011 email exchange with his 6

rotation student. MFs 182-184; Ex. 3710. This exchange started on October 23 when the student 7

noted that in the RNAi field scientists were successfully using mature siRNA rather than 8

unprocessed “pri-miRNA” and suggested that, analogously, they attempt to transfect mature 9

crRNA (and Cas9) in their eukaryotic experiments (i.e., without tracrRNA, because the student 10

did not understand both mature crRNA and tracrRNA are in the cutting complex) (id.): 11

12

Consistent with the CRISPR literature, the student used the term “crRNA” to refer to the mature 13

crRNA and distinguish it from unprocessed crRNA, referred to as “pre-crRNA” in the field. MF 14

182-184. In response, Zhang corrected his student, noting that “transfecting crRNA alone” would 15

not work. Id. Zhang, referring to the mature crRNA mentioned by his rotation student, specifically 16

noted that the crRNA “is loaded onto csn-1 [Cas9] as duplex with the tracrRNA”: 17

18

CVC’s expert Dr. Zamore ignores common grammar and argues the “It” in the phrase “It 19

is loaded” did not refer to the subject in the preceding sentence (mature crRNA)—the nearest 20

antecedent basis—but instead referred back to unprocessed (i.e., not mature) pre-crRNA (called 21


BROAD REPLY 5

“CRISPR array”) in the previous paragraph. See Ex. 5014, Zamore Dec. ¶¶78-80. Zamore’s 1

argument conflicts with basic grammar and ignores context—Zhang’s email was responding to his 2

student’s suggestion to transfect mature crRNA and Cas9 in a manner similar to how RNAi 3

scientists used mature siRNA in experiments. As such, Zhang’s response could not have been 4

referring to unprocessed crRNA as that would be a non-sequitur to his student’s suggestion. 5

(b) Dr. Zamore’s Opinion On tracrRNA Is Irrelevant And Illogical 6

Incredibly, Zamore opines that the bases for Zhang’s conclusion in 2011 that the disclosure 7

of Deltcheva showed tracrRNA remained in the Cas9 cutting complex are “contradicted by basic 8

science” and “scientifically untenable.” Id. at ¶¶5, 72. Zamore argues that a POSA would conclude 9

that tracrRNA was not present in the cleavage complex. But in deposition, Zamore admitted he 10

has no opinion as to “whether someone with more or less knowledge than a POSA” would interpret 11

Deltcheva in a different manner. MF 185; Ex. 6215, Zamore Tr. 168:4-13 He also expressly 12

acknowledged that he had no opinion on whether someone with more experience than a POSA—13

like Zhang—could have come to a different conclusion. MF 186; Id. at 167:20-168:3. 14

Tellingly, Zhang’s understanding in 2011 was proven to be correct for the precise reasons 15

that Zhang identified—i.e., that tracrRNA strongly hybridizes to crRNA during processing and 16

remains bound in the cutting complex. Moreover, other scientists with more experience than a 17

POSA who read Deltcheva have reached the same conclusion. MFs 187-191; see, e.g., Ex. 6119 18

at 3 (Barrangou & Horvath (2017)) (citing Deltcheva: “it was shown… (tracrRNA), is necessary 19

to create a dual RNA guide for Cas9). Indeed, Emmanuelle Charpentier has stated publicly of the 20

Deltcheva experiments that they showed “pretty much everything of what one can understand 21

really with particularity of this enzyme guided by two RNAs.” See MF 188; 22

https://www.youtube.com/watch?v=sqRdLJS5tr0&t=271s at 14:45-15:20; Ex. 3945. And in her 23

published work she cites Deltcheva as teaching that “mature tracrRNA:crRNA duplex remains 24


BROAD REPLY 5

bound to Cas9 and it is ready for the interference stage [i.e. cutting stage].” MF 189; Ex. 3613 at 1

384. In other presentations, Charpentier cites Deltcheva 2011 as showing the role of tracrRNA in 2

the mature cutting complex and credits Jinek 2012 only for its disclosure of sgRNA. MF 190-191; 3

https://www.youtube.com/watch?v=PulYE-yErPU at 30:21, 32:00; Ex. 3947. 4

In his declaration, Zamore attempts to argue that the 2012 POSA would conclude that 5

tracrRNA might leave the cutting complex because some unknown protein in the Cas system might 6

pull it apart from crRNA after processing. Ex. 5014, Zamore Dec. ¶¶43-45. Zamore analogizes the 7

natural RNAi system that provides a separate protein—the Argonaute—capable of unwinding an 8

RNA duplex. Id. at ¶43. But neither Deltcheva nor any other publication taught the existence of 9

any such protein and Zamore could not identify any such protein in the CRISPR-Cas9 system 10

(neither could Dr. Doyon). MF 192-195; Ex. 6215, Zamore Tr. 169:8-171:2; Ex. 6213, Doyon Tr. 11

317:14-19. Moreover, nature provided Argonaute because it was necessary for the system to 12

achieve its function—in the RNAi system, the targeter RNA is bound to a passenger RNA which, 13

if not removed, would block the targeter RNA from hybridizing with its target. MF 196; Ex. 6215 14

at 127:14-128:13. In contrast, it was known, including as taught in Deltcheva, that the CRISPR 15

guide/spacer sequence, which hybridizes to the DNA target sequence, is not hybridized to the 16

tracrRNA and so can function without removal of the tracrRNA. MF 197; Ex. 3214 at Fig. 1(b). 17

3. Dr. Zhang Did Not Drop His Prior Dual-Molecule Systems 18

In another attempt to erase Zhang’s work, CVC asserts that “[u]pon obtaining CVC’s 19

invention of Count 1 via Marraffini, Zhang immediately dropped his pre-crRNA processing 20

experiments.” Opp. at 18:20-21. The response is that no reasonable person could believe this is 21

true; Cong 2013 shows definitively that Zhang never dropped those experiments. See, e.g., MFs 22

148, 199-200; Ex. 3424, Zhang Dec. ¶¶59-175. Zhang not only continued his successful dual-23

molecule experiments using a pre-crRNA array, they are the first experiments described in Cong 24


BROAD REPLY 5

2013. MF 199; Ex 3201 at 820 (“we used the U6 promoter to drive the expression of a pre-crRNA 1

array”). In fact, he showed that the pre-crRNA system worked better than the sgRNA system using 2

a short truncated tracrRNA for many targets. MF 201; id. 3

CVC further contends that Zhang abandoned the CRISPR-Cas9 constructs he had been 4

optimizing and reverted back to TALENs systems. The response is Zhang did no such thing—the 5

constructs Zhang used to reduce Count 1 to practice were all part of his ongoing CRISPR-Cas9 6

research. MFs 202-205. As an initial matter, CVC’s argument that Zhang turned to his prior 7

TALENs systems is illogical as TALENs has no RNA component and thus does not involve 8

delivery, expression, and complexation of both RNA and protein components. See, e.g., Ex. 3448, 9

Breaker 3d Dec. ¶¶93-101. The further response is that for the sgRNA system, Zhang actually used 10

components that he previously used in his eukaryotic CRISPR-Cas9 experiments. MF 202-205. 11

For example, CVC’s expert falsely contends there is “no evidence that Zhang used EF1α 12

promoter before for expressing cas9, and no evidence that he used a lentivirus-based expression 13

vector before” June 2012. Ex. 5013, Doyon 2d Dec. ¶65. The response is Zhang had been using 14

pLenti vectors and EF-1α promotors for his eukaryotic CRISPR system starting in 2011. MFs 202-15

203, 205, 207. His 2011 vectors used an EF-1α promotor to express Cas9 and his successful 16

October 2011 experiments used an EF1α promoter and a lentivirus-based expression vector. See, 17

e.g., Ex. 3427, Sanjana Dec., Ex. 3, pdf pg. 60. Similarly, his NIH grant discloses use of an EF1α 18

promoter and two NLS format—as used for his later sgRNA experiments. MF 205; Ex. 3051 at 8. 19

The other change CVC alleges Zhang made to his system was the adoption of a U6 20

promoter. But this change actually shows that Zhang understood something that CVC’s inventors 21

did not. Specifically, Zhang selected a U6 promoter because it results in adding nucleotides to 22

expressed sgRNA, which would help protect the truncated end of the tracr from degradation—an 23


BROAD REPLY 5

end Zhang perceived, based on Deltcheva and his experience, to be important for loading with 1

Cas9 in the context of a cell. See MF 206; Ex. 3424, Zhang Dec. ¶¶128, 181. CVC’s inventors 2

lacked his experience and, for example, did not even appreciate that a U6 promoter would have 3

this protective effect by adding four nucleotides. Ex. 6204, Doudna Tr. 283:15-20. 4

Thus, the evidence confirms that Zhang used his prior eukaryotic dual-molecule RNA 5

CRISPR-Cas9 experience to adapt a sgRNA CRISPR-Cas9 system using prior validated 6

components, and he knew—unlike CVC—how to deal with obstacles such as RNA degradation. 7

4. Dr. Zhang Did Not Use Only “Ordinary Skill” And “Routine 8 Techniques” In Creating His Eukaryotic CRISPR-Cas9 System 9

Lastly, CVC argues Zhang contributed nothing because he allegedly used “routine 10

techniques” and “ordinary skill.” Opp. Heading III.c. In that regard, CVC characterizes each 11

individual technique as supposedly known or routine, such as the selection of U6 as a known 12

promoter. CVC’s argument again misses the point. While CVC would call every technique 13

“routine” or “known,” it was the selection and combination of numerous techniques—whether 14

allegedly routine or not—that led to Zhang’s success. In fact, CVC itself identifies no less than 12 15

adaptations that Zhang made to his CRISPR-Cas9 system to overcome the numerous eukaryotic 16

challenges. Opp. at 20:20-30:15. CVC wrongly seeks to isolate each one of these adaptations and 17

ask in a vacuum whether each had been used. CVC overlooks that choosing the correct 18

combination of adaptations for the system to work in eukaryotic cells was incredibly difficult and 19

unpredictable, as is evident in the CVC inventors’ own repeated failures attempting to find the 20

right combinations and adaptations that would yield success. MF 208-209; Ex. 3656 at 343. 21

IV. CONCLUSION 22

For the foregoing reasons and those stated in Broad Motion 5, that motion should be 23

granted and Broad should be awarded priority. 24


BROAD REPLY 5

Dated: May 6, 2021 Respectfully submitted, 1

/Raymond N. Nimrod / 2 Raymond N. Nimrod 3 Reg. No. 31,987 4 Quinn Emanuel Urquhart & Sullivan, LLP 5 51 Madison Avenue 6 New York, NY 10010 7 Telephone: 212-849-7000 8 [email protected] 9

Steven R. Trybus 10 Reg. No. 32,760 11 Locke Lord LLP 12 111 South Wacker Drive 13 Chicago, IL 60606 14 Telephone: (312) 443-0699 15 [email protected] 16

Counsel for Senior Party 17

A-1 INTERFERENCE 106,115 BROAD REPLY 5

APPENDIX A: LIST OF EXHIBITS CITED

EX. DESCRIPTION 3051 U.S. Patent Application No. 14/704,551, Ex. 22 to Sanjana Declaration (“NIH

application”) (Ex. 2411) 3110 Paper 893, Decision on Motions 37 C.F.R. § 41.125(a), Interference 106,048,

February 15, 2017. 3201 Cong et al., Multiplex Genome Engineering Using CRISPR/Cas Systems,

339(6121) SCIENCE 819-823 (2013) with Supplemental Material. 3202 Jinek et al., A programmable dual-RNA-guided DNA endonuclease in adaptive

bacterial immunity, 337(6096) SCIENCE 816-821 (2012) with Supplemental Material.

3214 Deltcheva et al., CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III, 471 NATURE 602-607 (2011) with Supplementary Materials.

3286 Dana Carrol, A CRISPR Approach to Gene Targeting, 20 Molec. Therapy 1658 (2012) (Ex. 1152)

3287 “The CRISPR Revolution,” CATALYST MAGAZINE, College of Chemistry, University of California, Berkeley, available at: http://catalyst.berkeley.edu/slideshow/the-crispr-revolution/[19/12/2014 12:40:53] (July 9, 2014) (Ex. 2207)

3316 Larson v. Johenning, 17 U.S.P.Q.2d 1610, Patent Int. No. 101,913 (B.P.A.I. 1990).

3416 Declaration of Alan M. Lambowitz, executed October 5, 2017. 3417 Declaration of Chad A. Mirkin, executed January 9, 2019. 3424 Declaration of Feng Zhang, dated December 17, 2020 3425 Declaration of Le Cong, dated December 17, 2020 3427 Declaration of Neville Sanjana, dated December 14, 2020 3429 Declaration of Lars Schou [Epiq] 3430 Declaration of Andrew Ellington, dated December 18, 2020 3435 Declaration of Benjamin Davies, dated July 17, 2020 3444 Second Declaration of Ronald Breaker, dated December 18, 2020 3446 Declaration of Caixia Gao, dated February 24, 2021 3448 Third Declaration of Ronald Breaker, Ph.D., dated March 26, 2021 3526 Sequence Streptococcus thermophilus LMD9 CRISPR1 region 3527 Sequence tracrRNA (putative) 3528 Sequence Streptococcus thermophilus LMD9 CRISPR1 region 3529 Sequence tracrRNA (putative) 3530 Gel image of the surveyor assay for the NTF3 72 hour time point 3531 Slideshow Presentation by Neville Sanjana, dated December 19, 2011, 18 pages 3533 March 1, 2012 Evernote Record 3535 Image 293F_AAV1GFP_a.pdf 3536 Image 293F_AAV1GFP_b.pdf 3545 EMXCT3-A1-M13R.ab1


EX. DESCRIPTION 3546 EMXCT3-C6-M13R.ab1 3547 EMXCT3-D5-M13R.ab1 3548 EMXCT3-E10-M13R.ab1 3549 EMXCT3-G12-M13R.ab1 3550 EMXCT3-H3-M13R.ab1 3554 Gel 2012-08-27 00hr 12min NLS-Csn1 EMX1 Gel-1 LongEXP_Annote.tif 3555 Gel 2012-08-29 00hr 15min HEMX1_Gel2 LXP Quant_Annote.tif 3563 Gel image 3564 Cong et al., October 5, 2012 Manuscript, CRISPR-Assisted Mammalian

Genome Engineering 3565 Picture of Drawing on Whiteboard 3566 Image of Gel 3581 Gel Image 3582 Le Cong Electronic Notebook 3613 Anaïs Le Rhun et al., CRISPR-Cas in Streptococcus pyogenes, 16 RNA Biol.

380 (2019). 3656 Lo et al., Precise and Heritable Genome Editing in Evolutionarily Diverse

Nematodes Using TALENs and CRISPR/Cas9 to Engineer Insertions and Deletions, 195 Genetics 331-348 (2013).

3708 Email from Feng Zhang to Mike Shao, dated August 7, 2011, with 11 page attachment, 12 pages total

3709 Email from Mike Shao to Feng Zhang, dated August 11, 2011, 5 pages 3710 Email from Feng Zhang to Shuailiang Lin, dated October 24, 2011, 1 page 3713 String of emails between Feng Zhang and Luciano Marraffini in 2012 3715 Email from Feng Zhang to Shuailiang Lin, dated January 3, 2012, 1 page 3716 Email from Feng Zhang to Kiran Musunuru, David Altshuler, Chad Cowan, and

Jennifer Hyne, dated January 7, 2012, with 32 page attachment, 33 pages total 3734 Email from [email protected] to Feng Zhang, dated March 5,

2012, with 4 page attachment, 5 pages total 3735 Email from Shuailiang Lin to Feng Zhang, dated March 22, 2012, 3 pages 3736 Email from Feng Zhang to Shuailiang Lin, dated March 24, 2012, 2 pages 3742 Email from Feng Zhang to Shuailiang Lin, dated April 14, 2012, 5 pages 3771 Email from Le Cong to Feng Zhang, dated July 20, 2012, 1 page 3772 Email from Feng Zhang to Le Cong, dated July 20, 2012, with 2 page

attachment, 3 pages total 3773 Email from Le Cong to Feng Zhang, dated July 21, 2012, 1 pages 3775 Email from Le Cong to Feng Zhang, dated July 22, 2012, 2 pages 3777 Email from Feng Zhang to Le Cong, dated July 23, 2012, 1 page 3781 Email from [email protected] to Le Cong, dated July 30, 2012, 3 pages 3784 Email from Feng Zhang to Le Cong, dated July 31, 2012, with 1 page

attachment, 3 pages total 3791 Email from Feng Zhang to Le Cong, dated August 28, 2012, 3 pages


EX. DESCRIPTION 3793 Email from Le Cong to Feng Zhang, Shuailiang Lin, David Cox, and Michael

Yim, dated August 29, 2012, with 20 page attachment, 21 pages total 3830 Email from Le Cong to Feng Zhang, dated July 31, 2012, 2 pages 3836 Email from Lisa Johnson to Feng Zhang, dated November 19, 2012, with 5

page attachment, 7 pages total 3842 Email from Grace Gao to Le Cong and Feng Zhang, dated July 25, 2012, 2

pages total 3845 Email from Shuailiang Lin to Neville Sanjana, dated October 26, 2011, 1 page 3902 Graphs of results from luciferase experiments in human cells with CRISPR-

hSt1Cas9 system 3922 Gel Image 2012-07-20 22hr 21 min.scn 3945 Image from E. Charpentier’s presentation CRISPR-Cas9: Biology, Mechanisms,

Evolution & Applications https://www.youtube.com/watch?v=sqRdLJS5tr0&t=271s Timecode 15min:20sec

3946 Broad Institute Press Release: "The Rockefeller University and Broad Institute of MIT and Harvard Announce Update to CRISPR-Cas9 Portfolio Filed by Broad" dated January 15, 2018.

3947 Images from E. Charpentier’s presentation Le CRISPR Cas9 - La révolution de l'ingénierie génomique https://www.youtube.com/watch?v=PulYE-yErPU Timecodes 30min:21sec, 32min:00sec

4257 Barrangou, R., “RNA-mediated programmable DNA cleavage,” Nature Biotechology, 30(9):836-838 (2012)

4320 Davies, K., and Marraffini, L., “Major insights into Microbiology: An Interview with Luciano Marraffini,” The CRISPR Journal, 3(1):5-9 (2020)

5013 Second Declaration of Yannick Doyon, Ph.D. 5014 Declaration of Philip D. Zamore, Ph.D. 5016 Declaration of Rodolphe Barrangou, Ph.D. 5018 Declaration of Erik J. Sontheimer, Ph.D. 5105 Email from Martin Jinek to Jennifer Doudna, dated April 11, 2012, with

attachment, 33 pages 5259 Deposition transcript of Sriram Kosuri, Sc.D., with errata, Patent Interference

No. 106,115 (January 29, 2021) 5263 Deposition transcript of Andrew Ellington, Ph.D., Patent Interference No.

106,115 (March 3, 2021) 5265 Deposition transcript of Luciano Marraffini, Ph.D., Patent Interference No.

106,115 (March 11, 2021) 5277 Erik Sontheimer handwritten notes from Martin Jinek and Krzysztof Chylinski

presentation at the CRISPR 2012: 5th Annual CRISPR Research Meeting held at the University of California, Berkeley, CA (June 2012), 1 page

6061 Email from Eldora Ellison to [email protected] et al., dated March 23, 2021, 1 page


EX. DESCRIPTION 6119 Barrangou & Horvath, A decade of discovery: CRISPR functions and

applications, Nature Microbiol. Review Article 2, 17092 (2017) DOI: 10.1038/nmicrobioI.2017.92.

6120 Intellia Therapeutics, Inc. U.S. S.E.C. Form 10-K for Fiscal Year Ended December 31, 2019

6121 Consent to Assignments, Licensing and Common Ownership and Invention Management Agreement for a Programmable DNA Restriction Enzyme for Genome Editing

6204 Deposition Transcript of Jennifer Doudna, Ph.D., January 6, 2021 6207 Transcript of Interview of Martin Jinek, January 14-15, 2021, with

Supplemental Declaration 6212 Deposition Transcript of Rodolphe Barrangou, Ph.D., April 19, 2021 6213 Deposition Transcript of Yannick Doyon, Ph.D., Volume 2, April 22, 2021 6214 Deposition Transcript of Erik Joseph Sontheimer, Ph.D., April 23, 2021 6215 Deposition Transcript of Phillip Zamore, Ph.D., April 26, 2021

B-1 INTERFERENCE 106,115

BROAD REPLY 5

APPENDIX B: STATEMENT OF MATERIAL FACTS 1

BROAD’S FACTS AND CVC’s RESPONSES 2

Broad’s Facts 1–77: 3

1. On February 4, 2011, at a Board of Scientific Counselors meeting, Dr. Zhang heard a talk 4

by Dr. Michael Gilmore, a Harvard microbiologist in which the speaker mentioned the 5

bacterial CRISPR nuclease immune system. Zhang (Ex. 3424) ¶48. 6

Response: Unable to admit or deny. 7

2. After the talk, Dr. Zhang wrote his graduate student Le Cong, reporting his plan “to test 8

[CRISPR] out in mammalian system” and said “Let’s keep this confidential. I have a 9

feeling this could work very well in mammalian systems and completely replace any kind 10

of FokI systems.” Zhang (Ex. 3424) ¶50; Ex. 3832. 11

Response: Admitted that the partial quotations appear in Ex. 3832; otherwise 12

denied. 13

3. In February-April 2011, Dr. Zhang conducted proof-of-concept experiments using his 14

engineered CRISPR systems. Zhang (Ex. 3424) ¶¶ 59-65; Exhibit 3523 at 3; Exhibits 15

3701-03, 3822-23; Exhibit 3902; Appendix E at 5.1. 16

Response: Denied. 17

4. In February-April 2011, Dr. Zhang used what is referred to as a luciferase reporter to test 18

whether his engineered system was operable in eukaryotic cells to cut target DNA. Id. 19


5. Dr. Zhang’s luciferase experiments showed a successful proof of concept that Type II 21

CRISPR-Cas9 systems could be engineered to alter the expression of a gene product in a 22

eukaryotic cell. Id. 23



BROAD REPLY 5

6. By April 2011, Dr. Zhang recognized the three components of the CRISPR system – 1

Cas9, crRNA, and tracrRNA. Zhang (Ex. 3424) ¶¶ 65-77; Ex. 3526. 2

Response: Denied. 3

7. By April 2011, Dr. Zhang also recognized by April 2011 from the 2011 Deltcheva 4

publication that during the CRISPR maturation process, the crRNA hybridized with a 5

second RNA molecule called the tracrRNA. Zhang (Ex. 3424) ¶¶ 6-7, 66-79; Ex. 3214 6

(Deltcheva). 7

Response: Denied. 8

8. Before June 2012, Dr. Zhang understood the RNA guide loaded onto the Cas9 as a RNA 9

duplex consisting of hybridized crRNA and tracrRNA and that the RNA duplex persisted 10

in the cutting complex with Cas9. Ex. 3710, 3845; Zhang (Ex. 3424) ¶¶ 75-79; Sanjana 11

(Ex. 3427) ¶¶5-6; Ex. 3526. Exs. 3526, 3214, 3716 at 30, 3051 Ex. 3716 at 30; Ex. 3051 12


9. Dr. Zhang shared his realization that the RNA guide loaded onto the Cas9 as a RNA 14

duplex consisting of hybridized crRNA and tracrRNA and that the RNA duplex persisted 15

in the cutting complex with Cas9 with his student. Ex. 3710, 3845; Zhang (Ex. 3424) ¶¶ 16

75-79; Sanjana (Ex. 3427) ¶¶ 5-6. 17


10. A file dated April 5, 2011 (Ex. 3526) shows that Dr. Zhang had completed a vector 19

design with the separate tracrRNA component in his engineered system, to express the 20

three components, Cas9, crRNA, and tracrRNA. Zhang Decl. ¶ 71. 21



BROAD REPLY 5

11. In August 2011, Dr. Zhang ordered a single vector to express the RNA components by 1

fusing the sequences encoding the tracrRNA and the pre-crRNA array on the vector. Ex. 2

3708; Zhang (Ex. 3424) ¶¶ 78-79. 3

Response: Denied. 4

12. The single vector ordered by Dr. Zhang in August 2011 was used to target, cleave, and 5

edit an endogenous “NTF3” genomic target in eukaryotic (human) cells. Id. 6

Response: Denied. 7

13. Dr. Zhang contemporaneously recognized the success of the experiment targeting the 8

NTF3 gene in human cells. Zhang (Ex. 3424) ¶¶ 70-82; Sanjana (Ex. 3427) ¶¶ 3-10. 9


14. In October 2011, Dr. Zhang began to explore in silico other orthologs of Cas9, including 11

SpCas9 with a more flexible PAM allowing more targets to be addressed. Zhang (Ex. 12

3424) ¶83. 13


15. Dr. Zhang included in a grant proposal submitted on January 12, 2012 to the National 15

Institutes of Health the CRISPR-Cas9 system as a site-directed nuclease for use in 16

eukaryotic cells. Ex. 3716 at 30; Ex. 3051; Zhang (Ex. 3424) ¶¶ 87-90. 17


16. By January 2012 the Broad Management Committee authorized pursuit of patent rights 19

for Dr. Zhang’s CRISPR work. Ex. 3904 at 3; Zhang (Ex. 3424) ¶¶ 90-91. 20


17. Before March 1, 2012, Dr. Zhang understood that the SpCa9 ortholog was not behaving 22

in the same way as his hSt1Cas9 system did in 2011. Zhang (Ex. 3424) ¶¶ 92-99. 23


BROAD REPLY 5

Response: Denied. 1

18. On March 1, 2012, Dr. Zhang created a design for a human-codon-optimized version of 2

SpCas9. Exs. 3533 and 3734; Zhang Decl. ¶92-99; Cong (Ex. 3425) ¶¶ 5-6. 3

Response: Denied. 4

19. Dr. Zhang had substantial prior successful experience with codon-optimizing proteins 5

from naturally occurring non-mammalian systems for use in mammalian cells. Id. 6

Response: Denied. 7

20. Dr. Zhang designed an hSpCas9 and, before March 3, 2012, ordered it from 8

LifeTechnologies. Exhibits 3533 and 3734, respectively, see also Zhang Decl. ¶ 99-101. 9


21. To ensure that his hSpCas9 design worked as expected and intended, Dr. Zhang designed 11

a frame-shift CRISPR reporter. Exs. 3534-36; Zhang (Ex. 3424) ¶¶ 106-108. 12


22. For this reporter test, Dr. Zhang introduced the reporter vector, including a target and the 14

CRISPR system, into the cell. Id. 15


23. Dr. Zhang’s reporter experiment was successful, and confirming this success gel images 17

dated April 26, 2012 show a green fluorescent signal indicating successful function of the 18

hSpCas9 system in a eukaryotic cell. Exs. 3534-36, Zhang (Ex. 3424) ¶¶ 106-108. 19


24. After the April 2012 reporter experiment, Dr. Zhang proceeded to configure the new 21

hSpCas9 with various NLS and GFP additions, appreciating that if he could improve 22

localization and accumulation in the nucleus of eukaryotic (mammalian) cells, the 23


BROAD REPLY 5

hSpCas9 system could cut genomic targets as he had done previously with the hSt1Cas9 1

system. Zhang (Ex. 3424) ¶¶110-113. 2

Response: Denied. 3

25. In June 2012, Dr. Zhang continued planning experiments using hSpCas9 in mammalian 4

cells. Id.; Exs. 3824-25, 3748. 5

Response: Denied. 6

26. The constructs and vectors of Dr. Zhang’s June 2012 plans were based on the three- 7

component system design with dual-molecule RNA (where the crRNA and the tracrRNA 8

are separate molecules that hybridize to form an RNA duplex). Id. ¶¶ 110-113; Ex. 3824-9

25, 3748. 10


27. Dr. Zhang worked diligently throughout June 2012 and into July preparing various 12

configurations of the components of the hSpCas9 system for expression in eukaryotic 13

(human and mouse) cells. Id. ¶¶ 110-143; Ex. 3824-25, 3748. 14


28. On June 26, 2012, Dr. Zhang received an email from Dr. Luciano Marraffini of 16

Rockefeller University sharing the design of a chimeric RNA that Dr. Marraffini heard 17

about at a public conference. Ex. 3713 at 29; Zhang (Ex. 3424) ¶¶ 12-29, 114-122. 18

Response: Admitted to the extent that Marraffini shared the design of a chimeric 19

RNA that Dr. Marraffini copied from CVC’s unpublished manuscript. 20

29. The chimeric RNA that Dr. Marraffini informed Dr. Zhang about had 26 nucleotides of 21

the longer natural tracrRNA sequence for S. Pyogenes. Zhang (Ex. 3424) ¶114 22

Response: Admitted. 23


BROAD REPLY 5

30. After receiving this information, Dr. Zhang designed additional experiments to use 1

hSpCas9 with chimeric RNA as part of his broader plans to research and optimize the 2

hSpCas9 system in eukaryotic (human and mouse) cells. Ex. 3751, 3770, 3755, 3537, 3

3762; Zhang (Ex. 3424) ¶¶ 20-23; Cong (Ex. 3425) ¶¶ 14-25; see also Zhang (Ex. 3424) 4

¶¶110-113; Exs. 3824-25, 3748. 5

Response: Admitted that Zhang used CVC’s chimeric RNA design (i.e., sgRNA); 6

otherwise denied. 7

31. Because Dr. Zhang had already engineered CRISPR-Cas9 systems with the analogous 8

dual-molecule RNA CRISPR-Cas9 system to function in eukaryotic cells, he expected on 9

June 26, 2012 when he received the email from Dr. Marraffini that he could successfully 10

implement a chimeric RNA system with his engineered CRISPR-hSpCas9 system for use 11

in eukaryotic cells, if the tracrRNA was of sufficient length, e.g., the natural tracrRNA 12

length. Id. at ¶¶ 115, 12-19, 66-108, 114-123. 13


32. As of June 26, Dr. Zhang understood how to implement a chimeric RNA CRISPR-Cas9 15

systems in eukaryotic cells given his prior dual-molecule systems that included all the 16

components. Id. at ¶¶ 116-118. 17


33. As of June 26, Dr. Zhang also understood how to implement a covalent GAAA internal 19

linker between the crRNA and tracrRNA. Zhang (Ex. 3424) ¶¶ 114-127; Exhibit 3643 at 20

Fig. 1B (Plavec 2008); Exhibit 4241 (Ma 2004 – siRNA); Exhibit 3645 (Siolas 2005 – 21

shRNAs); Exhibit 3646 (Ke 2004 – GAAA linker); see generally Breaker Decl. ¶¶ 6-13. 22



BROAD REPLY 5

34. On June 27, 2012, Dr. Zhang sent Le Cong an email with his parameters for designing 1

chimeric guides asking him to select two guides apiece for each of human targets 2

AAVS1, hTH, and hPV and for mouse targets mTH and mPVALB, which were being 3

studied in connection with studies of neuronal and brain function in mammalian cells. 4

Zhang (Ex. 3424) ¶124; Cong (Ex. 3425) ¶¶ 14-19, 123-139; Ex. 3751. 5

Response: Denied. 6

35. The chimeric RNA described in June of 2012 for use with hSpCas9 in the CRISPR 7

system had a GAAA linker between the tracr mate sequence and the tracrRNA. Ex. 3751, 8

3770. 9

Response: Admitted that Ex. 3751 shows a GAAA linker; otherwise denied. 10

36. Dr. Zhang in June 2012 also planned to use a vector to express hSpCas9 and chimeric 11

RNA to target and cleave genomic DNA of interest to him—specifically mTH and mouse 12

N2A cells—as part of the ongoing CRISPR program for mammalian cells. Ex. 3751; 13

Zhang (Ex. 3424) ¶¶ 123-125, 129, 133139-; Ex. 3537, 3762, 3839, 3764, 3766-3770; 14

Cong (Ex. 3425) ¶¶ 14-25; Exs. 3751. 15


37. Dr. Zhang’s email to Le Cong set forth key details, i.e., Dr. Zhang identified the SpCas9 17

ortholog and a PAM sequence as TGG and set out for Le Cong that the chimeric RNA for 18

the experiment started on the left with a crRNA segment (having a guide sequence shown 19

by the repeating N’s followed by a tracr mate segment), a GAAA linker, and a tracrRNA 20

segment having the nucleotides shown. Zhang (Ex. 3424) ¶125; Cong (Ex. 3425) ¶¶ 14-21

25; 22

Response: This statement does not cite a specific email exhibit, so denied. 23


BROAD REPLY 5

38. By July 20, 2012, Dr. Zhang’s engineered hSpCas9 and chimeric RNA system had been 1

used to successfully cleave a genomic target (mTh gene target) in eukaryotic (mouse) 2

cells, as confirmed by a Surveyor assay, thereby reducing to practice an embodiment 3

within the scope of Count 1. Zhang (Ex. 3424) ¶¶ 140-149; Cong (Ex. 3425) ¶¶ 14-30; 4

Exs. 3771-73, 3563, 3581-82, 3922. 5

Response: Denied. 6

39. After receiving the promising Surveyor results on July 20, 2012, Dr. Zhang recognized 7

and appreciated the cleavage product as indicating success, and immediately directed Le 8

Cong to repeat this experiment. Zhang (Ex. 3424) ¶¶ 145-169 (gel), 163-169 9

(sequencing); Cong (Ex. 3425) ¶¶ 31-57; Exs. 3566, 3582 at 20 and 24 (gel and notebook 10

entry); Ex. 3784 (email with sequencing results); Exs. 3781, 3784, 3830, 3775, 3777, 11

3565-66, 3842. 12


40. After the system had been used a second time in another set of mouse cells, again to 14

cleave the DNA target, a second Surveyor assay was conducted. Zhang (Ex. 3424) ¶¶ 15

145-169 (gel), 163-169 (sequencing); Cong (Ex. 3425) ¶¶ 31-57; Exs. 3566, 3582 at 20 16

and 24 (gel and notebook entry); Ex. 3784 (email with sequencing results); Exs. 3781, 17

3784, 3830, 3775, 3777, 3565-66, 3842. 18


41. The resulting gel from the repeat experiment against mTH targets is shown in Exhibit 20

3566, and also in Le Cong’s electronic notebook. Zhang (Ex. 3424) ¶¶ 150-162; Cong 21

(Ex. 3425) ¶¶ 41-43; Exhibit 3582 at 24. 22

Response: Admitted that Ex. 3566 appears to be a gel image; otherwise denied. 23


BROAD REPLY 5

42. The gel regarding the mTH experiments shows a successful result using DNA from the 1

cells from the well of the plate used in lane five—a lane for the mTH1 target—with 2

annotations that Le Cong added shortly thereafter in July 2012 to indicate that the 3

cleavage bands appeared in the locations that were expected for the mTH1 target. Zhang 4

(Ex. 3424) ¶¶ 161-162; Cong (Ex. 3425) ¶¶ 41-43. 5

Response: Denied. 6

43. The repeat July experiment constitutes an actual reduction to practice meeting all of the 7

elements of the Count. See Ellington Decl. ¶¶ 44-50. 8

Response: Denied. 9

44. By July 28, 2012, Le Cong also submitted the colonies (containing the genomic DNA 10

fragments of the mTH target from lane 5) from this result for genome sequencing, which 11

allows precise confirmation of the exact location of any changes to the DNA the samples. 12

Zhang (Ex. 3424) ¶¶ 164-169; Cong (Ex. 3425) ¶¶ 44-58; Exs. 3784, 3781-82, 3830. 13

Response: Admitted that Exs. 3784, 3781-82, and 3830 refer to sequencing; 14

otherwise denied. 15

45. The results of the sequencing analysis of the DNA from the cells of the repeat experiment 16

arrived in the morning of July 31, 2012, and Dr. Zhang analyzed the alignment of the 17

sequencing results. Ex. 3784. 18

Response: Admitted that Ex. 3784 refers to sequencing; otherwise denied. 19

46. Dr. Zhang recognized on July 2012 that two colonies showed deletions at the 20

modification site expected from CRISPR-Cas9 targeting and cleavage of the mTH1 21

target. Zhang (Ex. 3424) ¶¶ 164-169; Cong (Ex. 3425) ¶¶ 44-58; Cox (Ex. 3426) ¶¶ 18-22

24; Exs. 3784, 3566-68, 3830, 3842, 3582, 3784, 3847-48, 3713 at 31. 23


BROAD REPLY 5

Response: Denied. 1

47. Dr. Zhang emailed Le Cong on July 31, 2012 reporting that “there are two clones that had 2

modification” with a screenshot of the results identifying the indels, noting that these 3

results were “very promising.” Ex. 3784; Zhang (Ex. 3424) ¶¶ 164-169; Cong (Ex. 3425) 4

¶¶ 44-58. 5

Response: Admitted that Ex. 3784 includes the partially quoted text; otherwise 6

denied. 7

48. Dr. Zhang also attached to the email of Exhibit 3784 a screen shot of the sequencing 8

results showing the location of the deletion in two clones that had modifications. Id. 9


49. Later on July 31, 2012, Le Cong replied by email to Dr. Zhang stating that “There is a 11

better example in plate 3.” Exs. 3830, 3850; Cong (Ex. 3425) ¶¶ 49, 54; Cox (Ex. 3426) ¶ 12

15-16; Zhang (Ex. 3424) ¶166-175. 13


denied. 15

50. Le Cong’s July 31, 2012 email stated that he was “looking at the sequencing results with 16

David [Cox] :).” Exs. 3830, 3850; Cong (Ex. 3425) ¶¶ 49, 54; Cox (Ex. 3426) ¶ 15-16; 17

Zhang (Ex. 3424) ¶166-175. 18


denied. 20

51. Both Le Cong and David Cox have corroborated these successful results and Dr. Zhang’s 21

contemporaneous recognition that these experiments with hSpCas9 system with a 22

chimeric RNA performed in the Zhang Lab in July 2012 successfully targeted, cleaved, 23


BROAD REPLY 5

and edited mTH1. Cong (Ex. 3425) ¶¶ 48-55; Cox (Ex. 3426) ¶¶ 6-17 (generally); id. at ¶ 1

9 (“On July 24, [2012] I emailed Dr. Zhang and Le Cong and asked for the target 2

sequences for the hSpCas9 system that had been successfully used to cleave genomic 3

DNA in mouse cells”); Exs. 3858, 3829 (July 24- 25, 2012 emails between David Cox 4

and Le Cong (Feng Zhang cc’d)) identifying successful target and chimeric RNA 5

sequence) 6

Response: Denied. 7

52. On July 31, 2012, Dr. Zhang shared his success with the hSpCas9 system with Dr. Sriram 8

Kosuri, a former Harvard colleague, noting “We have this system working in mammalian 9

cells and now trying to put together a paper. Don’t tell anyone yet tho. ;).” Ex. 3783; 10

Kosuri (Ex. 3432) ¶¶ 3-5; Zhang (Ex. 3424) ¶¶ 170-172. 11


denied. 13

53. Dr. Zhang also reported his successful results with his hSpCas9 system in the October 5, 14

2012 Manuscript submitted to Science. Exhibit 3564 at 16; Ex. 3564 at 16; Zhang (Ex. 15

3424) ¶¶ 31-35, 173-179; Cong (Ex. 3425) ¶¶ 8-13, 56-57, 106-113. 16


54. In Figure 2A in that manuscript, Dr. Zhang reproduced his hSpCas9 system with 18

chimeric RNA, showing the same design as initially provided to Le Cong by email (Ex. 19

3751) and further memorialized in the vector map for the vector used in the July 20

experiments (Ex. 3770 at 128 (map for mTH target), 131 (chimeric RNA sequence)). 21



BROAD REPLY 5

55. In the October 5, 2012 Manuscript reports successful tarGeting and cleavage of an mTH 1

target with 0.75% indels. Ex. 3564 at Fig. 2, 12 (Figure Legends, Fig. 2); Zhang (Ex. 2

3424) ¶¶ 173-175; Cong (Ex. 3425) ¶¶ 23-25. 3

Response: Admitted that the text “0.75%” appears in Exhibit 3564 Fig.2, 4

otherwise denied. 5

56. By no later than August 31, 2012, Dr. Zhang also actually reduced the subject matter of 6

Count 1 to practice in human cells (HEK293FT) by targeting the EMX1 gene with his 7

hSpCas9 system with chimeric RNA in successful experiments. Zhang (Ex. 3424) ¶¶ 8

180203; Cong Decl. ¶¶ 66-96; Cox (Ex. 3426) ¶¶ 18-24; see also hang Decl. ¶¶ 198-203; 9

Cong (Ex. 3425) ¶¶ 59-98; Cox (Ex. 3426) ¶¶ 24. 10


57. The August experiments targeting hEMX1 were concluded no later than August 31, 12

2012. Ex. 3545-50; Zhang (Ex. 3424) ¶¶ 180-193; Cong (Ex. 3425) ¶¶ 66-80; Exs. 3850, 13

3544-50, 3587; 14


58. The initial success for the August 2012 experiments targeting hEMX1 was achieved and 16

verified by sequencing by August 20, 2012. Ex. 3545-50; Zhang (Ex. 3424) ¶¶ 180-193; 17

Cong (Ex. 3425) ¶¶ 66-80; Exs. 3850, 3544-50, 3587 18


59. Dr. Zhang directed Le Cong to test various configurations of Dr. Zhang’s hSpCas9 20

system with chimeric RNA in August 2012. Ex. 3850; Zhang (Ex. 3424) ¶¶ 194-203; 21

Cong Decl. ¶¶ 81-94; Ex. 3580. 22



BROAD REPLY 5

60. Le Cong tested various configurations of Dr. Zhang’s hSpCas9 system with chimeric 1

RNA from August 25-27, 2012. Ex. 3850; Zhang (Ex. 3424) ¶¶ 194-203; Cong Decl. ¶¶ 2

81-94; Ex. 3580. 3

Response: Denied. 4

61. Le Cong reported in an August 27, 2012 email to Dr. Zhang that the best configurations 5

of Dr. Zhang’s hSpCas9 system with chimeric RNA “help[ed] quite significantly with 6

cleavage… about [a] 2~3 fold increase…” when compared to configurations using a 7

green fluorescent protein. Id; Exhibit 3791. 8


denied. 10

62. By August 29, 2012, Dr. Zhang directed Le Cong to share with David Cox, among 11

others, the “key data we obtained” by these experiments using Dr. Zhang’s hSpCas9 12

system with chimeric RNA. Ex. 3793 at 1, 6-9; Zhang (Ex. 3424) ¶¶ 198-203; Cong 13

Decl. ¶¶ 90-94; Cox (Ex. 3426) ¶¶ 24. 14


denied. 16

63. On August 29, 2012, Le Cong shared a presentation via email with David Cox and others 17

with Surveyor results with annotated bands showing successful cleavage. Ex. 3793 at 1, 18

6-9. 19


64. By August 28, 2012, Dr. Zhang successfully actually reduced to practice an embodiment 21

of his hSpCas9 system with chimeric RNA, this time targeting the hEXM1.3 target in a 22

human cell (HEK293FT), as Le Cong and David Cox corroborated. Zhang (Ex. 3424) ¶¶ 23


BROAD REPLY 5

198-203; Cong (Ex. 3425) ¶¶ 59-98; Cox (Ex. 3426) ¶¶ 24; Ex. 3793; Ex. 3545-50; Ex. 1

3554-55. 2

Response: Denied. 3

65. As shown in Figure 2B of the October 5, 2012 Manuscript, an embodiment of Dr. 4

Zhang’s hSpCas9 system with chimeric RNA targeting the hEMX1 gene in eukaryotic 5

human cells (HEK293FT) produced an indel percentage of 4.7% (bottom left target 6

label). Exhibit 3564; Exhibit 3564 at Fig. 2B; Zhang (Ex. 3424) ¶¶ 180-183; Cong (Ex. 7

3425) ¶¶ 60-65, 95-96. 8

Response: Admitted that the text “4.7%” appears in Exhibit 3564 Fig. 2, 9


66. By October 5, 2012, the Zhang Lab obtained results for publication in Science 11

demonstrating success of an engineered CRISPR-Cas9 systems with chimeric RNA 12

SpCas9 system in mouse cells against mTH targets. Zhang (Ex. 3424) ¶¶ 176-179; 31-35, 13

173-175 (mTH); Cong (Ex. 3425) ¶¶ 56-58 and 106-113 (mTH). 14



demonstrating success of an engineered CRISPR-Cas9 systems with chimeric RNA 17

SpCas9 system in human cells against hEMX1 targets. Zhang (Ex. 3424) ¶¶ 180-183 18

(hEMX1); Cong (Ex. ¶¶ 60-65 and 95-96 (hEMX1). 19



demonstrating success of an engineered CRISPR-Cas9 systems with dual-molecule 22


BROAD REPLY 5

SpCas9 systems in human cells against an hEMX1 target. Zhang (Ex. 3424) ¶¶ 204-207 1

(dual SpCas9); Cong (Ex. 3425) ¶¶ 97-101 (dual SpCas9). 2

Response: Denied. 3


demonstrating success of an engineered CRISPR-Cas9 systems with dual-molecule 5

hSt1Cas9 systems in human cells against hEMX1 targets. Zhang (Ex. 3424) ¶¶ 208-211 6

(dual St1Cas9); Cong (Ex. ¶¶ 102-105 (dual St1Cas9), 7

Response: Denied. 8

70. On November 19, 2012 Dr. Zhang received the Science reviewers’ comments to the 9

October 5, 2012 Manuscript. Ex. 3836; Zhang (Ex. 3424) ¶¶ 33-35 10


71. The reviewers of the October 5, 2012 Manuscript were impartial scientists who were 12

experts the field. Ex. 3836; Zhang (Ex. 3424) ¶¶ 33-35. 13


72. One reviewer of the October 5, 2012 Manuscript stated that the “results show 15

compellingly and thoroughly that the system they developed based on Cas9, crRNA and 16

tracrRNA, or on Cas9 and chimeric RNA is functional and efficient in vivo, for cleavage 17

and inducing mutations at the target site.” Ex. 3836 at 3. 18


denied. 20

73. Science accepted the October 5 manuscript, and published the work online on January 3, 21

2013. Ex. 3201. 22



BROAD REPLY 5

74. Cong 2013 reported Dr. Zhang’s discovery that cleavage efficiencies in the Cas9 system 1

with the chimeric RNA configuration using a 30-nt tracrRNA segment were inferior to 2

systems using the dual-molecule RNA configuration from expression of the about 89-nt 3

natural tracrRNA length in the eukaryotic cell, as was matured to be about 75-nt in the 4

cell and as in the complex. Ex. 3201 at 2C; Zhang (Ex. 3424) ¶¶ 37-38, 212-214. 5

Response: Denied. 6

75. The Zhang Lab is one of more than 350 academic labs depositing vectors described in 7

their articles with the non-profit organization Addgene to make them available for 8

academic research. Exhibit 3516; Zhang (Ex. 3424) ¶¶ 40-42. 9


76. Of Addgene’s top 15 most requested vectors, seven are CRISPR constructs and all seven 11

were designed by Dr. Zhang. Exhibit 3516 (https://blog.addgene.org/15-years-of-12

addgenethe-top-15-vectors). Id. 13


77. CVC does not allege that the CVC inventors conducted any successful experiments in 15

eukaryotic cells prior to August 9, 2012. CVC Motion 2. 16


18


BROAD REPLY 5

CVC’s FACTS AND BROAD’S RESPONSES 1

78. Prior to June 26, 2012, all of Zhang’s CRISPR experiments with eukaryotic cells 2

involved unprocessed crRNA. Ex. 5264, 48:19-49:8, 51:4-10; Ex. 5265, 23:6-18, 24:17-3

25:3, 29:2030:3, 36:17-37:10; Ex. 5262, 78:12-17, 228:2-8, 229:21-230:7; Ex. 3777; Ex. 4

3424, ¶¶70-71, 79; Ex. 3716, 6; Ex. 5013, ¶¶143-158, A1-A78. 5

Response: Denied. 6

79. Prior to June 26, 2012, none of Zhang’s CRISPR experiments with eukaryotic cells 7

involved a sgRNA CRISPR-Cas9 system as recited in Count 1. Paper 271, 16:6-9; Ex. 8

3401, ¶¶7.7-7.13; Ex. 5262, 78:12-17; Ex. 3427, ¶4; Ex. 3424, ¶¶70-71, 79. 9


80. Prior to June 26, 2012, Zhang did not know the necessary and sufficient components of 11

the CRISPR-Cas9 catalytic DNA-cleavage complex. Ex. 5264, 48:19-49:3; Ex. 5265, 12

23:6-18, 24:17-25:3, 29:20-30:3, 36:17-37:10; Ex. 5262, 78:12-17, 228:2-8, 229:21-13

230:7; Ex. 3777; Ex. 3424, ¶¶70-71, 79; Ex. 3716, 6; Ex. 5013, ¶¶143-158, A1-A78. 14


81. Zhang’s March 2011 luciferase experiment did not include a tracrRNA. Ex. 5262, 78:12-16

17; Ex. 3424, ¶¶70-71; Ex. 5013, ¶¶A7-A38. 17


82. Zhang’s March 2011 luciferase experiment included an unprocessed pre-crRNA array 19

that included a leader sequence, and two, three, or four different Cas genes. Ex. 5013, 20

¶¶A7-A38; Ex. 5264, 49:4-8, 51:4-10; Ex. 3424, ¶79; Ex. 3424, Appx A, exhibit 7. 21


83. Zhang’s March 2011 luciferase experiment was an attempt to induce pre-crRNA 23

processing. Ex. 5013, ¶¶A7-A38; Ex. 3424, ¶¶62-64; Ex. 3424, Appx A, exhibit 7. 24


BROAD REPLY 5

Response: Denied. 1

84. Zhang’s March 2011 luciferase experiment did not include a sgRNA CRISPR-Cas9 2

system as recited in Count 1. Ex. 5262, 78:12-17; Ex. 3424, ¶¶70-71; Ex. 5013, ¶¶A7-3

A38; Ex. 3424, Appx A, exhibit 7. 4


85. Zhang’s March 2011 luciferase experiment failed to show CRISPR-Cas9-mediated 6

targeted DNA cleavage. Ex. 5013, ¶¶A7-A38; Ex. 3424, Appx A, exhibit 7. 7

Response: Denied. 8

86. Zhang’s November 2011 “triple target” Surveyor experiment did not include a sgRNA 9

CRISPR-Cas9 system as recited in Count 1. Ex. 3424, ¶79; Paper 271, 16:6-9; Ex. 3401, 10

¶¶7.7-7.13; Ex. 3427, ¶4; Ex. 3427, Appx. A, Exhibit 5; Ex. 5013, ¶¶A39-A59. 11


87. Zhang’s November 2011 “triple target” Surveyor experiment included an unprocessed 13

pre-crRNA array that included a leader sequence, an unprocessed tracrRNA nucleotides, 14

Cas9, and RNase III. Ex. 3427, Appx. A, exhibit 5; Ex. 5013, ¶¶A39-A59. 15


88. Zhang’s November 2011 “triple target” Surveyor experiment was an attempt to induce 17

pre-crRNA processing. Ex. 3424, ¶79; Ex. 3427, Appx. A, exhibit 5; Ex. 5262, 137:5-13; 18

Ex. 5013, ¶¶A39-A59. 19


89. Zhang’s November 2011 “triple target” Surveyor experiment failed to show CRISPR-21

Cas9-mediated targeted DNA cleavage. Ex. 3427, Appx. A, exhibits 3, 4, 13, 14; Ex. 22

5262, 165:17-166:10; Ex. 5013, ¶¶A39-A59. 23


BROAD REPLY 5

Response: Denied. 1

90. Zhang’s January 2012 NIH grant proposal proposed a CRISPR system to induce pre-2

crRNA processing. Ex. 3427, Appx. A, exhibit 22; Ex. 3716, 6; Ex. 3424, ¶89; Ex. 5013, 3

¶¶A60A64. 4

Response: Denied. 5

91. Zhang’s January 2012 NIH grant proposal did not include a sgRNA CRISPR-Cas9 6

system as recited in Count 1. Ex. 3424, ¶89; Ex. 3716, 6; Ex. 3427, Appx. A, exhibit 22; 7

Ex. 5258, 310:15-311:19; Ex. 5013, ¶¶A60-A64. 8


92. Zhang’s January 2012 NIH grant proposal proposed to include a tracrRNA “to facilitate 10

the processing of guide RNAs.” Ex. 3427, Appx. A, exhibit 22; Ex. 3716, 6; Ex. 5013, 11

¶¶A60-A64. 12

Response: Admitted that the words in the partial, cropped quote appear in Ex. 13

3427, Appx. A, exhibit 22, otherwise denied. 14

93. Zhang’s January 2012 NIH grant proposal proposed that “We will: (a) identify the 15

minimal set of genes and RNA elements that will effectively reconstitute a functional 16

CRISPR system in mammalian cells.” Ex. 3427, Appx. A, exhibit 22; Ex. 3716, 6; Ex. 17

5013, ¶¶A60-A64. 18

Response: Admitted that the words in the partial quote appear in Ex. 3427, Appx. 19

A, exhibit 22, otherwise denied. 20

94. Zhang’s January 2012 NIH grant proposal does not include any of Zhang’s data related to 21

testing CRISPR in eukaryotic cells. Ex. 3427, Appx. A, exhibit 22; Ex. 3716, 6; Ex. 22

5262, 178:2-6, 179:4-8; Ex. 5013, ¶¶A60-A64. 23


BROAD REPLY 5

Response: Denied. 1

95. Zhang’s April 2012 “CRISPR reporter” experiment did not include a sgRNA CRISPR-2

Cas9 system as recited in Count 1. Ex. 3424, ¶¶106-108; Ex. 5013, ¶¶A65-A70. 3


96. U.C. hosted the 5th Annual CRISPR Research Conference at U.C. Berkeley from June 5

20–22, 2012. Ex. 4350, ¶82; Ex. 4351, ¶¶53-54; Ex. 4348, ¶¶112-113; Ex. 4349, ¶¶147-6

148; Ex. 4768; Ex. 5266, 179:21-180:10; Ex. 5256. 7

Response: Denied. 8

97. On June 21, 2012, at the 5th Annual CRISPR Research Conference, Jinek and Chylinski 9

presented CVC’s discovery that Cas9, crRNA, and tracrRNA are the necessary and 10

sufficient components of the Type II CRISPR-Cas9 DNA-cleavage complex. Ex. 4350, 11

¶82; Ex. 4351, ¶¶53-54; Ex. 4348, ¶¶112-113; Ex. 4349, ¶¶147-148; Ex. 4768, 17, 29; 12

Ex. 5266, 179:21-180:10; Ex. 5016, ¶¶11-13; Ex. 5018, ¶¶10-15; Ex. 5265, 23:6-18, 13

24:17-25:3, 29:20-30:3. 14


98. On June 21, 2012, at the 5th Annual CRISPR Research Conference, Jinek and Chylinski 16

presented CVC’s design of a sgRNA CRISPR-Cas9 system. Ex. 4350, ¶82; Ex. 4351, 17

¶¶5354; Ex. 4348, ¶¶112-113; Ex. 4349, ¶¶147-148; Ex. 4768, 25-26; Ex. 5266, 179:21-18

180:10; Ex. 5016, ¶15; Ex. 5018, ¶17-18; Ex. 5265, 23:19-24:9. 19


99. Jinek and Chylinski disclosed at the 5th Annual CRISPR Research Conference that 21

CVC’s sgRNA CRISPR-Cas9 system could be used as a “genome editing tool” for 22


BROAD REPLY 5

“genome engineering in any environment.” Ex. 5266, 187:21-188:13; Ex. 4768, 27; Ex. 1

5016, ¶¶15-20; Ex. 5018, ¶¶17-21. 2


100. Jinek and Chylinski disclosed at the 5th Annual CRISPR Research Conference that 4

CVC’s sgRNA CRISPR-Cas9 system is “robust and versatile” and further showed that 5

the system could target and cleave eukaryotic gene sequences in vitro. Ex. 4768, 27; Ex. 6

5016, ¶¶15-20; Ex. 5018, ¶¶17-21. 7


101. Luciano Marraffini is a third party not involved in this patent interference proceeding. 9

Ex. 5240. 10


102. Marraffini and Zhang worked together as collaborators on applying CRISPR in 12

prokaryotes and eukaryotes beginning in January 2012 and ending in 2013. Ex. 5265, 13

15:8-15, 17:11-17; Ex. 5262, 179:10-22. 14


103. Broad had the opportunity to, but did not cross-examine or otherwise challenge 16

Marraffini’s deposition testimony in this proceeding. Ex. 5265, 72:4-9. 17


104. Marraffini attended the 5th Annual CRISPR Research Conference at UC Berkeley, 19

including Jinek and Chylinski’s presentation on June 21, 2012. Ex. 5256, 4; Ex. 5266, 20

179:21-180:10; Ex. 3713, pp. 27-29; Ex. 5265, 18:20-19:3. 21



BROAD REPLY 5

105. Marraffini served as a reviewer for Science on CVC’s Jinek 2012 draft manuscript (Ex. 1

5254). Ex. 3713, 62; Ex. 5265, 21:13-20, 64:19-22; Ex. 5255, 2. 2


106. The draft Jinek 2012 manuscript that CVC submitted to Science and that Marraffini 4

reviewed included the following statement: “This study describes an alternative 5

methodology based on RNA-programmed Cas9 that could offer considerable potential for 6

genome editing in cells of the three kingdoms of life for biotechnological, biomedical and 7

gene-therapeutic purposes.” Ex. 5254, 12; Ex. 5265, 21:13-20, 64:19-22; Ex. 5255, 2. 8


107. On June 26, 2012, after the 5th Annual CRISPR Research Conference at U.C. Berkeley, 10

Marraffini contacted Zhang and informed him that CVC’s presentation was “important to 11

our project.” Ex. 5265, 26:5-14; Ex. 3713, 27. 12


108. Marraffini testified that, prior to June 26, 2012, he never had “any communications with 14

Dr. Zhang about whether tracr was part of the DNA cutting complex in a CRISPR-Cas9 15

system.” Ex. 5265, 24:17-25:3, 23:6-18, 29:20-30:3, 36:17-37:10; Ex. 3713, 27-29. 16


109. Marraffini testified that, prior to June 26, 2012, he and Zhang had only discussed “the 18

importance of tracr for what [they] knew at the time was generation of RNA guides.” Ex. 19

5265, 24:17-25:3, 23:6-18, 29:20-30:3, 36:17-37:10; Ex. 3713, 27-29. 20



BROAD REPLY 5

110. Marraffini testified that, on June 26, 2012, he told Zhang “about the role of tracr in the 1

[DNA] cutting complex in a CRISPR-Cas9 system.” Ex. 5265, 29:20-30:3; Ex. 3713, 27-2

29. 3

Response: Denied. 4

111. Marraffini testified that, prior to June 26, 2012, he “never had any communications with 5

Dr. Zhang about single-guide RNA in a CRISPR-Cas9 system.” Ex. 5265, 23:19-24:8; 6

Ex. 3713, 27-29. 7


112. On June 26, Marraffini communicated to Zhang CVC’s design of a single molecule guide 9

RNA (sgRNA) for CRISPR-Cas9. Ex. 5265, 64:9-18, 66:7-67:7, 68:13-21; Ex. 3713, 27-10

29. 11


113. Marraffini testified that, on June 26, 2012, he informed Zhang that CVC’s sgRNA design 13

“would be an important tool for genome editing in eukaryotes specifically.” Ex. 5265, 14

68:13-21. 15


114. Marraffini testified that the image of the sgRNA design Marraffini communicated to 17

Zhang via email on June 26, 2012 came from CVC’s Jinek 2012 manuscript Ex. 5265, 18

38:410, 35:16-18; Ex. 3713, 29; Ex. 5013, ¶¶48-53. 19


115. The image of the sgRNA design Marraffini communicated to Zhang via email on June 21

26, 2012 is the same sgRNA design that Jinek and Chylinski presented on June 21, 2012, 22


BROAD REPLY 5

at the 5th Annual CRISPR Research Conference. Ex. 5265, 38:4-10, 35:16-18; Ex. 3713, 1

29; Ex. 4768, 27; Ex. 5013, ¶52. 2


116. The sgRNA design Zhang emailed to Cong on June 27, 2012, is the same sgRNA design 4

Jinek and Chylinski presented at the CRISPR Conference on June 21, 2012. Ex. 5265, 5

38:410, 35:16-18; Ex. 3713, 29; Ex. 4768, 26; Ex., 3751, 1; Ex. 3424, ¶124; Ex. 5013, 6

¶52. 7


117. After learning of CVC’s sgRNA CRISPR-Cas9 system from Marraffini, Zhang applied 9

CVC’s sgRNA CRISPR-Cas9 system in his own experiments in July and August, 2012. 10

Ex. 4768, 26; Ex. 3713, 29; Ex., 3751, 1; Ex. 3424, ¶124; Ex. 5013, ¶¶59-63. Ex. 3537, 3; 11

Ex. 3829; Ex. 3201, Fig. 2B; Ex. 3425, ¶24. 12


118. All of the experimental data reported in the Cong 2013 paper were obtained from 14

experiments performed after June 26, 2012. Ex. 5262, 228:2-8, 229:21-230:7; Ex. 3564; 15

Ex. 3201; Ex. 5013, ¶A75. Ex. 3777; Ex. 3580; Ex. 3577; Ex. 3752, 2. 16


119. The Mali 2013 manuscript was submitted to Science before Cong 2013 published in 18

January 2013. Ex. 3623, 826. 19


120. The Hwang 2013 manuscript was submitted to Nature Biotechnology before Cong 2013 21

published in January 2013. Ex. 4233, 227. 22



BROAD REPLY 5

121. The Cho 2013 manuscript was submitted to Nature Biotechnology before Cong 2013 1

published in January 2013. Ex. 4076, 230. 2


122. The Chen provisional application no. 61/734,256 was filed before Cong 2013 published 4

in January 2013. Ex. 5020. 5


123. Makinen disclosed in 2006 that the U6 promoter was one of the two “most commonly 7

used [promoters] to drive the expression of shRNAs.” Ex. 5024, 434; Ex. 5252, 1284, 8

Fig. 1A; Ex. 5129, 494, Fig. 1A; Ex. 5013, ¶¶68-78. 9


124. By June 26, 2012, the pLKO.1 vector containing a U6 promoter was a publicly known 11

vector in the art. Ex. 5024, 434; Ex. 5252, 1284, Fig. 1A; Ex. 5129, 494, Fig. 1A; Ex. 12

5013, ¶¶68-78. 13


125. By June 26, 2012, the EF1α promoter was a publicly known Pol II promoter used to drive 15

expression of proteins in eukaryotic cells. Ex. 5253, 5322; Ex. 4620, 6; Ex. 5257, 3393; 16

Ex. 5013, ¶¶79-83. 17


126. By June 26, 2012, the viral element, WPRE, was publicly known to have been included 19

in lentiviral expression vectors to increase protein expression. Ex. 5214, Abstract, 2888; 20

Ex. 5257, 3393; Ex. 4620, 6; Ex. 5013, ¶¶79-83. 21



BROAD REPLY 5

127. By June 26, 2012, adding one or more nuclear localization sequences (NLS) to a protein 1

was a known, conventional optimization technique for optimizing protein localization to 2

the nucleus of eukaryotic cells. Ex. 4078; Ex. 4077; Ex. 4113; Ex. 4665, 763; Ex. 4312, 3

methods; Ex. 4384; Ex. 4424; Ex. 5013, ¶¶89-92. 4

Response: Denied. 5

128. By June 26, 2012, codon optimization was a known, conventional technique for 6

optimizing protein expression in eukaryotic cells. Ex. 5258, 71:3-74:1; Ex. 3701; Ex. 7

4396, 20476; Ex. 4397, 9270; Ex. 4110, Abstract, Table 1; Ex. 4111, 115, 122; Ex. 4112, 8

796-798; Ex. 5013, ¶¶84-88. 9


129. Breaker testified that, if making recombinant protein outside of a eukaryotic cell 11

(“premade” protein), “then codon optimization would have no effect on those methods.” 12

Ex. 5264, 88:15-89:1. 13

Response: Admitted that the words in the partial, cropped appear in Exhibit 5264, 14


130. By June 26, 2012, the CVC inventors had identified the necessary and sufficient 16

components of the CRISPR-Cas9 DNA cleavage complex (Cas9, crRNA, and tracrRNA). 17

Paper 1579, 5:22-7:16; Ex. 4381, 23-25; Ex. 4345, ¶42; Ex. 5013, ¶¶45-47. 18


131. By June 26, 2012, the CVC inventors had described in detail the structure of the sgRNA 20

CRISPR-Cas9 system for use in eukaryotic cells as evinced in e.g., Jinek’s laboratory 21

notebook entries. Paper 1579, 7:17-14:1; Ex. 4381, 63-65; Ex. 4345, ¶61; Ex. 5013, ¶¶45-22

47. 23


BROAD REPLY 5

Response: Denied. 1

132. By June 26, 2012, the CVC inventors had constructed a working sgRNA CRISPR-Cas9 2

system and confirmed that it cleaved eukaryotic target DNA sequences in vitro, and 3

described the use of NLS and eukaryotic expression vectors with reference to prior 4

publications using TALENs and ZFNs in zebrafish and mammalian cells, e.g., in CVC’s 5

invention disclosure form. Paper 1579, 14:2-17:10; Ex. 4382, 7; Ex. 4349, ¶¶124-128; 6

Ex. 4603; Ex. 5105, 16-29; Ex. 5013, ¶¶45-47. 7

Response: Denied. 8

133. By June 26, 2012, the CVC inventors had designed and constructed sgRNAs and sgRNA 9

expression vectors for targeting eukaryotic gene sequences (e.g., CLTA, GFP targets). 10

Paper 1579, 17:11-19:9; Ex. 4382, 4-7; Ex. 4349, ¶¶124-128; Ex. 4603; Ex. 4345, ¶¶167-11

172; Ex. 5013, ¶¶45-47. 12


134. By June 26, 2012, the CVC inventors had constructed a Cas9 expression vector with an 14

NLS and expressed it human HEK293T cells to visualize nuclear localization of the Cas9 15

protein. Paper 1579, 18:17-19:4; Ex. 4536; Ex. 4345, ¶173; Ex. 5013, ¶¶45-47. 16


135. By June 26, 2012, the CVC inventors had contacted colleagues Drubin and Cheng at U.C. 18

and agreed to contact Raible at U.V. to microinject CVC’s sgRNA CRISPR-Cas9 system 19

into zebrafish (see e.g., Paper 1579, 27:20-28:17; Ex. 4475; Ex. 4775; Ex. 4776; Ex. 20

4350, ¶62; Ex. 4349, ¶¶75, 78; Ex. 4352, ¶12; Ex. 4799; Ex. 4348, ¶115; Ex. 4351, ¶¶56-21

58; Ex. 4294, ¶¶9-14; Ex. 5013, ¶¶45-47.) 22



BROAD REPLY 5

136. By June 26, 2012, the CVC inventors had filed CVC’s first provisional application, 1

disclosing how to make and use a sgRNA CRISPR-Cas9 system in eukaryotic cells. 2

Paper 1579, 17:12-15; Ex. 3002; Ex. 4036, ¶¶82-194; Ex. 4345, ¶5; Ex. 5013, ¶¶45-47. 3

Response: Denied. 4

137. Cong is a named inventor on multiple of Broad’s involved patents in this proceeding. 5

Paper 23, 5:35, 7:22, 8:8, 9:9, 9:15-10:9, 11:8; Ex. 3001, 1. 6

Response: Admitted Cong is a named inventor on some of Broad’s involved 7

patents, otherwise denied. 8

138. Sanjana is a named inventor on multiple of Broad’s involved patents in this proceeding. 9

Paper 23, 5:35, 7:22, 8:8, 9:9, 9:15-10:9, 11:8; Ex. 3001, 1. 10

Response: Admitted Sanjana is a named inventor on some of Broad’s involved 11

patents, otherwise denied. 12

139. Cong and Cox are both named inventors on Broad’s earliest priority application. Ex. 13

3001, 1, 318. 14


140. Zhang did not show Kosuri any data that Zhang successfully used a sgRNA CRISPR-16

Cas9 system for genome editing in eukaryotic cells. Ex. 5259, 39:19-40:1. 17


141. Appendix 3 depicts a timeline of events. See Appendix 3. 19



BROAD REPLY 5

BROAD’S ADDITIONAL FACTS 1

142. Zhang’s July 20 ARTP experiment was repeated, producing two independent, positive 2

Surveyor results, along with subsequent sequencing. Exs. 3772, 3566, 3784. 3

143. Zhang’s July 20 experiment had negative controls in the form of unsuccessful uses of the 4

system. Ex. 5263, Ellington Tr. 183:4-186:17; Ex. 3430, Ellington Dec. ¶41. 5

144. Le Cong included the metadata information, including change history, for his electronic 6

notebooks in his Declaration showing the relevant entries were made contemporaneously. 7

Ex. 3425 at ¶¶ 42, 84, 119. 8

145. An August presentation containing gels and cleavage data reports the August ARTPs 9

with metadata and supporting contemporaneous emails attaching the presentation. Ex. 10

3793. 11

146. Zhang’s October 5 Manuscript memorialized successful ARTPs, including both the July 12

ARTP in mouse cells and later work in human cells. Exs. 3564; 3424, Zhang Dec. ¶¶ 143, 13

177-212. 14

147. Zhang’s ARTPs were subjected to contemporaneous peer review by impartial experts 15

who noted that Zhang’s system “is functional and efficient in vivo, for cleavage and 16

inducing mutations at the target site,” specifically noting that this included his 17

experiments with “chimeric RNA.” Ex. 3836 at 3. 18

148. Zhang’s Cong 2013 publication included successful experiments with dual-molecule and 19

sgRNA systems and acknowledged CVC in connection with the use of an sgRNA with a 20

GAAA linker. Ex. 3201 at 820. 21

149. Kosuri confirmed that he has no financial interest in the involved Broad patents or 22

application (he is employed by the Regents of the University of California as a Professor 23

at UCLA). Ex. 5259, Kosuri Tr. 23:20-24:13. 24


BROAD REPLY 5

150. Cox is not alleged to be an inventor on any involved patent and has no financial interest 1

in them. See Paper No. 23, Redeclaration; Paper No. 1558 at 7-9. Cong or Sanjana are 2

named only on the 233, 445, 616, 814, and 641 patents, and 551 application. Id. 3

151. Marraffini, Barangou, and Sontheimer are a co-founders of Intellia Thereapeutics and 4

have a financial interest in the outcome of this litigation. Ex. 6212 at 25:8-11, 163:10-22, 5

165:19-172:21; Ex. 6214 at 13:2-16, 20:22-22:18. 6

152. Intellia Therapeutics is a real party in interest that is funding this Interference. Paper 004; 7

see also 6120 at 23, 78. 8

153. Intellia is part of a joint agreement to cooperate in invalidating Broad’s patents. See Ex. 9

6121 at 9 (Section C-1.3(b)). 10

154. CVC did not present any uninterested fact witnesses to support their derivation or 11

reasonable expectation of success allegations. See generally CVC Opp. 12

155. Broad submitted public record declarations of several scientists with no financial stake in 13

this proceeding who noted that they contemporaneously read Jinek 2012 and had no 14

expectation of success for eukaryotic CRISPR-Cas9 systems. See, e.g., Ex. 3416, 15

Lambowitz Dec. ¶¶20-40; Ex. 3446, Gao Dec. ¶¶3-6; Ex. 3435, Davies Dec. ¶¶5-8; see 16

also Ex. 3448, Breaker Third Dec. ¶¶38-174; 3417. 17

156. Prior to this proceeding, Marraffini pursued a claim that he should be added as a co-18

inventor on Broad’s involved eukaryotic patents. See Ex. 3946. 19

157. In binding arbitration, the arbitrator determined that Marraffini did not contribute to 20

Broad’s eukaryotic inventions and is not a co-inventor. Id. 21

158. Zhang acknowledged learning of Chimera A with its GAAA linker first from Marraffini. 22

Ex. 3424 at ¶ 12. 23


BROAD REPLY 5

159. The PTAB, the Federal Circuit, and multiple Patent Office Examiners have already found 1

Jinek 2012 does not render obvious the eukaryotic CRISPR-Cas9 invention, nor provide 2

a reasonable expectation of success. Ex. 3110 at 13:14-14:21, 17:3-10; Regents of Univ. 3

of Cal. v. Broad Inst., Inc., 903 F.3d 1286, 1295 (Fed. Cir. 2018). 4

160. CVC does not argue that its inventors knew anything relevant to possession beyond the 5

disclosures in its P1 and P2 applications. 6

161. The two vectors CVC alleges it designed in May 2012 were used by Drs. Drubin and 7

Cheng, who failed with those and other vectors. 8

162. No information about vectors is alleged to have been communicated to Zhang. 9

163. In 2012, Barrangou published an article stating that the sgRNA system from Jinek 2012 10

had “immediate applications” in bacteria, but only that there were “intriguing 11

possibilities” for eukaryotes. Ex. 4257 at 838, middle column. 12

164. Sontheimer’s notes from the Annual CRISPR 2012 conference do not mention any 13

possible eukaryotic applications. See Ex. 5277. 14

165. Marraffini testified that his collaboration with Zhang was “quite split in terms of he 15

[Zhang] was in charge of doing gene editing in human cells. I was more focusing on gene 16

editing in bacterial cells.” Ex. 5265, Marraffini Tr. 27:4-16. 17

166. Marraffini testified, Ex. 5265, Marraffini Tr. 30:4-20 (objections omitted): 18

Q. Turning back for a moment to the CRISPR conference in June of 2012, 19 do you recall the reaction of any other attendees at the conference to the 20 technology -- sorry -- to the presentation by Dr. Jinek and Dr. Chylinski? 21

A. I think it was very well received, the talk. I think that, again, this is a CRISPR 22 biology meeting, so most of the people there are interested in bacteria and how 23 CRISPR works. So the fact that tracr had this -- what's called in biology a 24 cofactor function for Cas9 cleavage was quite interesting. And, of course, the 25 development of the single-guide RNA was very impressive and very well 26 received. 27

167. Marraffini testified, id. at 30:21-31:6 (objections omitted): 28


BROAD REPLY 5

Q Do you recall whether there was any discussion at the CRISPR 1 conference of the potential role of single-guide RNA for use in 2 eukaryotes? 3

A I -- I don't recall much talk about gene editing. 4

168. Marraffini’s alleged statement that CRISPR-Cas9 would be “an important tool for 5

genome editing in eukaryotes specifically” (Opp. at 36:3-6) communicates no more than 6

Jinek 2012’s statement that CRISPR “could offer considerable potential for gene-7

targeting and genome-editing applications.” Ex. 3202 at 820 8

169. Zhang and Mararaffini’s email communications show they did not discuss whether the 9

sgRNA system would be an important tool for eukaryotes, as Zhang only later asked 10

Marraffini if the CVC group had mentioned targeting in eukaryotic cells (Ex. 3713 at 31): 11

12

170. CVC does not allege that it set forth in the June 21 presentation that Marraffini heard, or 13

that Marraffini communicated to Zhang, any information regarding delivery methods, 14

promoters, NLSs, codon strategy etc. for adapting a CRISPR-Cas9 sgRNA system to 15

eukaryotic uses. See Opp. at 15:21-18:17. 16

171. Before June 2012, Zhang already possessed all of the elements of the Count 1—including 17

a functioning eukaryotic CRISPR-Cas9 system—other than the linker. See, e.g., Ex. 3424 18

at ¶¶ 6-11, 48-113; Exs. 3716 at 6, 3736, 3902, 3526-29, 3530, 3531 at 16, 3535-36, 19

3735, 3742, 3427 at Appendix A and Exs. 3, 7, Ex. 10 20

172. Zhang’s system already functioned in eukaryotic cells comprising a target DNA molecule 21

and a Type II CRISPR-Cas9 system before June 2012. Ex. 3424 at ¶¶ 6-11, 48-113; Exs. 22

3902, 3530, 3531 at 16, 3716, 3535-36, 3736, 3902, 3526-29. 23


BROAD REPLY 5

173. Zhang’s CRISPR-Cas9 system included Cas9 before June 2012. Ex. 3424 at ¶¶ 6-11, 48-1

113; Exs. 3716 at 6, 3736, 3715, 3533, 3734, 3742; 3526, 3528. 2

174. Zhang’s CRISPR-Cas9 system included crRNA with a target sequence before June 2012. 3

Ex. 3424 at ¶¶ 6-11, 48-113; Exs. 3716 at 6, 3736, 3902, 3531 at 16, 3708; 3526, 3528. 4

175. Zhang’s CRISPR-Cas9 system included tracrRNA capable of hybridizing with the 5

crRNA to form a duplex before June 2012. Ex. 3424 at ¶¶ 6-11, 48-113; Exs. 3710, 3845, 6

3526-29, 3736, 3716 at 6. 7

176. Zhang’s CRISPR-Cas9 system was capable of cleaving or editing a target DNA molecule 8

before June 2012. Ex. 3424 at ¶¶ 6-11, 48-113; Exs. 3902, 3530, 3531 at 16, 3716, 3535-9

36, 3736, 3902, 3526-29. 10

177. Fusing two RNA molecules was well known and routine in the art by 2012 and 11

performing such a fusion with the specific CRISPR-Cas9 RNAs was publicly disclosed 12

by June 21, 2012. See, e.g., Ex. 3444, Breaker 2d Dec. ¶¶9-13. 13

178. Zhang understood from the Deltcheva publication that tracrRNA would remain bound to 14

crRNA in the CRISPR-Cas9 cutting complex due to lack of any agent to overcome the 15

hybridization forces between them and also given Cas9 would protect the duplex. Ex. 16

3424 at ¶¶66-69. 17

179. Zhang used tracrRNA in every one of his CRISPR-Cas9 experiments after reading 18

Deltcheva and CVC does not dispute this. Ex. 3424 at ¶ 70. 19

180. When asked if he told Zhang about the role of tracrRNA in the catalytic DNA-cleavage 20

complex, Marraffini testified, Ex. 5265, Marraffini Tr. at 29:20-30:3: 21

Q: As part of that conversation, did you also tell Dr. Zhang about the role 22 of tracr in the cutting complex in a CRISPR-Cas9 system? 23

A: I don't recall saying that, but if I explained what a single-guide RNA is, I 24 must have said that. 25


BROAD REPLY 5

181. Marraffini did not recall much of the conversation including Zhang’s reaction: 1

Q. When you described to Dr. Zhang the single-guide RNA disclosed by 2 Jinek 2012, do you recall what his reaction was? 3

A. I don't recall any specific reaction. Like, I don't think he said much. I 4 believe he was interested in trying it. He didn't disregard it. He was -- I 5 would say that he was interested. It was not a -- something that we -- I 6 remember as a too much -- too much -- too much response from him, but 7 he was interested. And he would – I thought he would try it. 8

Id. at 29:9-19. 9

182. In an October 2011 email exchange with Zhang’s rotation student, the student proposed 10

transfecting mature crRNA (and Cas9) in their eukaryotic experiments (Ex. 3710): 11

12

183. “crRNA” in the October 2011 email (Ex. 3710) refers to mature crRNA and distinguishes 13

it from unprocessed pre-crRNA (“pre-crRNA”/”CRISPR array”). 14

184. Referring to mature crRNA, Zhang wrote back that “transfecting crRNA alone” would 15

not work, noting that crRNA (“It”—the antecedent basis in the prior sentence) “is loaded 16

onto csn-1 [Cas9] as duplex with the tracrRNA” (Ex. 3710): 17

18

185. Zamore testified he has no opinion as to “whether someone with more or less knowledge 19

than a POSA” would interpret Deltcheva in a different manner. Ex. 6215, Zamore Tr. 20

168:4-13. 21

186. Zamore also testified: “[S]omeone with more experience than a POSA, could they have 22

come to a different conclusion than a POSA in reading the Deltcheva paper? A. I haven't 23

formulated an opinion on that.”). Id. at 167:20-168:3 (objections omitted). 24


BROAD REPLY 5

187. Scientists with more experience than a POSA who read Deltcheva et al. 1

contemporaneously concluded that tracrRNA remains bound in the cutting complex. See, 2

e.g., Ex. 6119 at 3 (Barrangou & Horvath (2017)) (citing Deltcheva: “it was shown… 3

(tracrRNA), is necessary to create a dual RNA guide for Cas9”). 4

188. Emmanuelle Charpentier has stated publicly of the Deltcheva experiments that it showed 5

“pretty much everything of what one can understand really with particularity of this 6

enzyme guided by two RNAs.” See 7

https://www.youtube.com/watch?v=sqRdLJS5tr0&t=271s at 14:45-15:20; Ex. 3945. 8

189. In her published work, Charpentier cites Deltcheva as teaching that “mature 9

tracrRNA:crRNA duplex remains bound to Cas9 and it is ready for the interference stage 10

[i.e. cutting stage].” Ex. 3613. 11

190. In her own presentations to the scientific community, Charpentier cites Deltcheva 2011 12

as showing the role of tracrRNA in the mature cutting complex and credits Jinek 2012 13

only for its disclosure of sgRNA. See https://www.youtube.com/watch?v=PulYE-yErPU 14

at 30:21, 32:00; Ex. 3947. 15

191. In a slide in one presentation, Charpentier illustrates tracrRNA bound to the “mature 42 16

nt crRNA,” citing Deltcheva 2011 for this teaching. Id. 17

192. Deltcheva teaches that the hybridized duplex of crRNA and tracrRNA is inserted into 18

Cas9, with Cas9 working as a “molecular anchor” for their interaction. Ex. 3214 at 604 19

(“Here, we propose a model wherein Csn1 acts as a molecular anchor facilitating the 20

base-pairing of tracrRNA with pre-crRNA….”). 21


BROAD REPLY 5

193. Neither Deltcheva nor any other publication taught the existence of a Cas protein that 1

would unwind the tracrRNA-crRNA duplex. Ex. 3214; Ex. 6215, Zamore Tr. 169:8-2

171:2; Ex. 6213, Doyon Tr. 317:14-19. 3

194. Zamore could not identify any protein in the CRISPR-Cas9 system that would unwind 4

the tracrRNA-crRNA duplex. Ex. 6215, Zamore Tr. 169:8-171:2. 5

195. Doyon did not have an opinion about what would allegedly unwind the tracrRNA-crRNA 6

duplex either. Ex. 6213, Doyon Tr. 317:14-19. 7

196. The Argonaute protein was provided by nature because it was necessary to separate the 8

RNA duplex for the system to function; the targeter RNA in the RNAi system is 9

hybridized to a passenger RNA that would otherwise block its function of hybridizing 10

with a target. Ex. 6215 at 127:14-128:13. 11

197. Deltcheva taught that in CRISPR, the guide/spacer sequence, which hybridizes to the 12

DNA target sequence, is not hybridized to the tracrRNA and so can function without 13

removal of the tracrRNA. Id; Ex. 5014 at ¶ 62. 14

198. Zamore does not dispute the strength of the hybridization of the RNA duplex, nor 15

Zhang’s conclusion that there would be significant charge-based bonding between the 16

Cas9 and the duplex. Ex. 5014 at ¶ 66. 17

199. The first experiments described in Cong 2013 are dual-molecule experiments. Ex. 3201 at 18

820 (“we used the U6 promoter to drive the expression of a pre-crRNA array”). 19

200. Figure 1 of the manuscript and of Cong 2013 shows a dual molecule RNA system with 20

pre-crRNA array. See Ex. 3564, Fig. 1; Ex. 3201, Fig. 1. 21


BROAD REPLY 5

1

201. Cong 2013 showed that the pre-crRNA dual molecule system worked better than the 2

sgRNA system with the high degree of tracrRNA truncation on the 3’ end. See Ex. 3201 3

at Fig. 2C. 4

202. Zhang repeatedly used an EF1α promoter for expressing Cas9 before June 2012. See, 5

e.g., Ex. 3427, Sanjana Dec., Ex. 3, pdf pg. 60; Ex. 3051 at 8 6

203. Zhang repeatedly used a lentivirus-based expression vector before June 2012. See, e.g., 7

Ex. 3427, Sanjana Dec., Ex. 3, pdf pg. 60. 8

9

204. Zhang repeatedly used two NLSs before June 2012. See, e.g., Ex. 3051 at 8. 10

205. Zhang’s NIH grant discloses use of an EF1α promoter and two NLS format—as used for 11

his later sgRNA experiments. Ex. 3051 at 8. 12

206. Zhang selected a U6 promoter because it would result in adding nucleotides to the 13

construct, which would help protect the end of the truncated tracrRNA from 14

degradation—an end he perceived, based on Deltcheva and his experience, to be 15

important for loading with Cas9 in the context of a cell. See Ex. 3424, Zhang Dec. ¶¶128, 16

181. 17


BROAD REPLY 5

207. Prior to June 2012, Zhang designed a humanized four-part version of the SpCas9 protein 1

for Golden Gate Cloning, using promoters including the EF1a promoter. Ex. 3533. 2

208. Drs. Doudna and Meyer acknowledged in a 2013 publication that their attempts with 3

sgRNA in 2012 were not successful. Ex. 3656 at 343 (“Our initial attempts at genome 4

editing using Cas9-sgRNA complexes to target the ben-1 locus with three different 5

sgRNAs in multiple experiments were unsuccessful.”). 6

209. Doudna and Meyer used the dual crRNA:tracrRNA RNA guides taught in Cong 2012 for 7

genome editing. Id. 8

9

CERTIFICATE OF FILING AND SERVICE

I hereby certify that on May 6, 2020, a true and complete copy of the foregoing BROAD

REPLY 5 is being filed by 8:00 pm ET via the Interference Web Portal. (SO ¶ 105.3). Pursuant

to agreement of the parties, service copies are being sent by e-mail by 11:00 pm ET, to counsel

for Junior Party as follows:

[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]

/Raymond N. Nimrod / Raymond N. Nimrod Reg. No. 31,987 Counsel for Senior Party Quinn Emanuel Urquhart & Sullivan, LLP 51 Madison Avenue New York, NY 10010 Telephone: 212-849-7000 [email protected]

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