uc's motions

8/20/2019 UC's Motions

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Filed on behalf of Senior Party

THE REGENTS OF THE UNIVERSITY OF CALIFORNIA,UNIVERSITY OF VIENNA, AND EMMANUELLE CHARPENTIER

By: Todd R. Walters, Esq.

Erin M. Dunston, Esq.Travis W. Bliss, Ph.D., Esq.

BUCHANAN I NGERSOLL & R OONEY PC

1737 King Street, Suite 500Alexandria, Virginia 22314-2727

Telephone (703) 836-6620

Facsimile (703) [email protected]

[email protected]

[email protected]

By: Brian A. Fairchild, Ph.D., Esq.

Carmella L. Stephens, Ph.D., Esq.GOODWIN PROCTER LLP Exchange Place, 53 State Street

Boston, Massachusetts 02109Telephone (617) 570-1000

Facsimile (617) 523-1231

[email protected] [email protected]

UNITED STATES PATENT AND TRADEMARK OFFICE

____________________

BEFORE THE PATENT TRIAL AND APPEAL BOARD

____________________

THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF

TECHNOLOGY, and PRESIDENT AND FELLOWS OF HARVARD COLLEGEPatents 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; and 8,999,641,

Junior Party,

v.

THE REGENTS OF THE UNIVERSITY OF CALIFORNIA, UNIVERSITYOF VIENNA, AND EMMANUELLE CHARPENTIER,

Application 13/842,859,

Senior Party.

____________________

Patent Interference 106,048 (DK)

____________________

SENIOR PARTY LIST OF PROPOSED MOTIONS


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Interference No. 106,048

i

TABLE OF CONTENTS

Page

A. THRESHOLD ISSUE ......................................................................................................... 1

1.

Motion 1 for Judgment That All of Broad’s Involved Patents Are Subjectto AIA Prior Art Provisions and Therefore All of Broad’s Claims are

Unpatentable Because Broad Cannot Swear Behind Senior Party’sInvolved ‘859 Application/‘797 Publication ...........................................................1

B. REDEFINING THE INTERFERING SUBJECT MATTER ............................................. 7

2. Motion 2 to Redefine the Scope of This Contested Case − SubstitutingCount 1 with Proposed Count 2 ...............................................................................7

3. Motion 3 (Contingent Upon the Denial of Motion 2 to Redefine the Scope

of This Contested Case) to Redefine the Scope of This Contested Case − Substituting Count 1 with Proposed Count 3 .........................................................10

4. Motion 4 (Contingent Upon the Denial of Motion 2 and the Grant of

Motion 3) to Redefine the Scope of this Contested Case − AddingProposed Count 4 ...................................................................................................11

5. Motion 5 (Contingent Upon the Denial of Motions 2 and 3) to Redefinethe Scope of the Contested Case − Adding a Claim That Corresponds to

Count 1 and De-Designating Senior Party’s Involved Claims as

Corresponding to Count 1 ......................................................................................13

6.

Motion 6 (Contingent Upon the Denial of Motions 2, 3, and 5) to Redefine

the Scope of the Contested Case − Substituting Count 1 with ProposedCount 5 ...................................................................................................................13

C. REQUESTS FOR BENEFIT ............................................................................................ 15

7. Motion 7 to Obtain Benefit to the Senior Party Provisionals for the

Existing Count and All Proposed Counts ..............................................................15

D. BROAD’S CLAIMS ARE UNPATENTABLE ............................................................... 15

8.

Motion 8 for Judgment That All Claims in Each of Broad’s InvolvedPatents Are Anticipated By Senior Party’s ‘797 Publication and/orObvious Over Senior Party’s ‘797 Publication in Combination With the

Prior Art .................................................................................................................15


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9. Motion 9 for Judgment That All Claims in Each of Broad’s Involved

Patents Are Unpatentable Under Obviousness-Type Double Patentingand/or 35 U.S.C §§ 102/103 Over Broad’s Non-Commonly-Owned

Involved Patents .....................................................................................................19

10. Motion 10 for Judgment That All of Broad’s Involved Claims Are

Unpatentable for Lacking Proper Inventorship ......................................................25

11. Motion 11 for Judgment That All of Broad’s Involved Patents Were

Obtained Through Inequitable Conduct .................................................................30

E. PRIORITY OF INVENTION ........................................................................................... 31

12. Motion 12 for Priority of Invention .......................................................................31

F. MISCELLANEOUS ISSUES ........................................................................................... 31


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Pursuant to Part D of the Declaration of Interference (Paper No. 1), 37 C.F.R. §§ 41.1201

and 41.204(b), and ¶¶ 104.2.1, 120, and 204 of the Standing Order (Paper No. 2), Senior Party2

(The Regents of The University Of California, University of Vienna, and Emmanuelle3

Charpentier) identifies below the motions that it presently intends to file, if authorized.4

A. THRESHOLD ISSUE5

1. Motion 1 for Judgment That All of Broad’s Involved Patents Are Subject to6

AIA Prior Art Provisions and Therefore All of Broad’s Claims are7

Unpatentable Because Broad Cannot Swear Behind Senior Party’s Involved8

‘859 Application/‘797 Publication9

Senior Party requests judgment that each of Broad’s involved patents is subject to AIA10

prior art provisions, and thus all of Broad’s claims are unpatentable because Broad is barred from11

antedating Senior Party’s involved ‘859 Application, which published as U.S. Application No.12

2014/0068797 (“the ‘797 Publication”). The subject matter of the Count is disclosed in Senior13

Party’s involved ‘859 Application/’797 Publication. Each of Broad’s claims has been designated14

to correspond to the Count. Thus, the claims are presumptively anticipated by or rendered15

obvious by the Count. Because Broad’s patents are subject to AIA prior art provisions, it cannot16

antedate Senior Party’s involved ‘859 Application/‘797 Publication. Therefore, all of Broad’s17

involved claims are unpatentable over Senior Party’s involved ‘859 Application/‘79718

Publication.1 See 35 U.S.C. § 102(d)(2).19

1 Alternatively, the Board has grounds to issue a Show Cause Order against Broad, requiring

Broad to explain why its claims are not subject to AIA prior art provisions and why Broad’s

claims are patentable over Senior Party’s involved ‘859 Application/‘797 Publication. Should a

Show Cause Order issue, Senior Party requests the opportunity to address Broad’s response to

the Order.


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2

AIA prior art provisions “apply to any patent application that contains or contained at any1

time a claim to a claimed invention that has an effective filing date that is on or after March 16,2

2013 . . . or . . . claims or ever claimed the benefit of an earlier filing date under 35 U.S.C. 120,3

121, or 365 based upon an earlier application that ever contained such a claim.” M.P.E.P.4

§ 2159.02; see also LEAHY-SMITH AMERICA I NVENTS ACT OF 2011, Pub. L. No. 112-29, sec.5

3(n)(1), § 273, 125 Stat. 284, 293 (“the amendments made by this section . . . shall apply to any6

application for patent, and to any patent issuing thereon, that contains or contained at any time -7

(A) a claim to a claimed invention that has an effective filing date as defined in section 100(i) of8

title 35, United States Code, that is on or after the effective date described in this paragraph or9

(B) a specific reference under section 120, 121, or 365(c) of title 35, United States Code, to any10

patent or application that contains or contained at any time such a claim.”).11

Here, each of Broad’s involved patents (U.S. Patent Nos. 8,697,359 (“the ‘359 Patent”);12

8,771,945 (“the ‘945 Patent”); 8,945,839 (“the ‘839 Patent”); 8,889,356 (“the ‘356 Patent”);13



8,993,233 (“the ‘233 Patent”); and 8,999,641 (“the ‘641 Patent”)), the application from which16

each of Broad’s involved patents issued, and/or a parent application to which each of Broad’s17

involved patents claims benefit, contains or contained at some time a claim to subject matter that18

has an effective filing date on or after March 16, 2013, thereby subjecting each of Broad’s19

involved patents to AIA prior art provisions.20

All of Broad’s involved patents issued from transition applications, i.e., applications with21

a filing date on or after March 16, 2013, but which claim priority to one or more applications22

filed before March 16, 2013. Senior Party intends to show that each of Broad’s twelve involved23


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patents contains and/or contained at some time one or more claims that are not supported by a1

Broad application filed prior to March 16, 2013, thus making each of Broad’s involved patents2

subject to AIA prior art provisions. As a result, Broad cannot antedate the Senior Party’s3

involved ‘859 Application/’797 Publication and corresponding provisional applications.4

Broad itself designated nearly all of Broad’s transition applications as being subject to5

AIA at the time of filing. See Application Data Sheets (“ADSs”) filed in U.S. Application Nos.6

14/256,912 (which resulted in the ‘839 Patent); 14/105,031 (which is the parent of the ‘356 and7

‘814 Patents); 14/258,458 (which resulted in the ‘814 Patent); 14/105,035 (which is the parent of8

the ‘965 and ‘445 Patents); 14/104,977 (which is the parent of the ‘406 and ‘308 Patents);9

14/222,930 (which resulted in the ‘406 Patent) (corresponding ADS provided as an example10

below); 14/104,990 (which is the parent of the ‘616 Patent); 14/105,017 (which resulted in the11

‘233 Patent); and 14/226,274 (which resulted in the ‘641 Patent). Excerpts from one such ADS12

are provided below.13


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Application Data Sheet, filed on March 24, 2014 in U.S. Patent Application No. 14/222,930,1

which resulted in Broad’s ‘406 Patent. 2

Thus, Broad itself designated applications in the chain of each of its ‘839; ‘256; ‘814;3

‘965; ‘445; ‘406; ‘308; ‘616; ‘233; and ‘641 Patents as AIA applications. Not only did Broad4

not use transition ADSs in the applications that issued as its involved ‘359 and ‘945 Patents,5

Broad also never indicated to the USPTO whether these applications should be examined under6

AIA.7

Broad subsequently changed its position to try to gain benefit of pre-AIA status by8

amending its statements under 37 C.F.R. §§ 1.55 or 1.78 in the above ADSs, thereby incorrectly9

moving the transition applications from AIA to pre-AIA jurisdiction. Also, during examination10

(erroneously conducted under pre-AIA provisions) of the applications that issued as Broad’s11


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involved patents, Broad responded to applied or expected anticipation and/or obviousness1

rejections over Senior Party’s International Application Publication No. WO 2013/0176772 (the2

disclosure of which is identical to the disclosure of Senior Party’s involved ‘8593

Application/‘797 Publication) by submitting therein a Declaration under 37 C.F.R. § 1.1314

attempting to swear behind Senior Party’s international application. See, e.g., Prosecution5

History in the ‘359 Patent, Declaration under 37 C.F.R. § 1.131, filed January 30, 2014.6

Notwithstanding Broad’s attempt to remove its involved patents from AIA jurisdiction7

and antedate Senior Party’s international application, Senior Party intends to show that each of8

Broad’s involved patents remains subject to AIA prior art provisions because each of Broad’s9

involved patents, the transition applications that issued as the involved patents, and/or a10

transition application to which the involved patents claimed benefit, contains or contained at11

some time a claim that has an effective filing date that is on or after March 16, 2013. Thus, each12

of Broad’s involved patents is subject to AIA, including those patents that issued from transition13

applications or claim benefit to transition applications in which Broad’s counsel originally14

acknowledged AIA jurisdiction. Accordingly, all of the claims of Broad’s involved patents are15

subject to AIA prior art provisions because they issued from applications subject to AIA16

provisions.17

Additionally, all of Broad’s claims are presumptively unpatentable because each claim of18

its involved patents has been designated to correspond to the Count, and is therefore presumed to19

be anticipated and/or obvious over the subject matter of the Count, whose subject matter is20

disclosed in Senior Party’s involved ‘859 Application/’797 Publication. See, e.g., Jones v. Lord21

Corp., Paper No. 48, Interference No. 105,968 (P.T.A.B. March 28, 2014).22


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As currently declared, Broad’s patents are subject to AIA prior art provisions because1

Broad’s involved patents have only been accorded the benefit of the filing date of their2

respective non-provisional applications, each of which was filed after March 16, 2013. Broad3

cannot swear behind Senior Party’s involved ‘859 Application/’797 Publication, whose effective4

prior art date is May 25, 2012, because the disclosure of Senior Party’s involved ‘8595

Application/’797 Publication is entitled to the benefit of each of its provisional applications:6

U.S. Provisional Application No. 61/652,086, filed on May 25, 2012 (“the first Senior Party ‘0867

Provisional”); U.S. Provisional Application No. 61/716,256, filed on October 19, 2012 (“the8

second Senior Party ‘256 Provisional”); U.S. Provisional Application No. 61/757,640, filed9

January 28, 2013 (“the third Senior Party ‘640 Provisional”); and U.S. Provisional Application10

No. 61/765,576, filed February 15, 2013 (“the fourth Senior Party ‘576 Provisional”) (together,11

“the Senior Party’s Provisionals”). Broad should be required to establish that it is entitled to pre-12

AIA status, which Senior Party disputes.13

Senior Party intends to show why each of Broad’s twelve involved patents contains14

and/or contained claims that are not supported by a Broad application filed prior to March 16,15

2013, thus making each claim subject to AIA prior art provisions. It is anticipated that the16

default page limit will not be sufficient to address all twelve of Broad’s involved patents. See17

Standing Order ¶ 121.2. Accordingly, Senior Party requests that increasing default page limits,18

waiving statements of fact, and excluding claim charts from page limits be discussed during the19

initial teleconference.20

21


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B. REDEFINING THE INTERFERING SUBJECT MATTER1

2. Motion 2 to Redefine the Scope of This Contested Case − Substituting Count2

1 with Proposed Count 23

Motion 2 requests that existing Count 1 be substituted with Proposed Count 2, which4

reads as follows:5

A method of cleaving or editing a target DNA molecule or modulating transcription of at6least one gene encoded thereon, the method comprising:7

contacting a target DNA molecule having a target sequence with an engineered8

and/or non-naturally-occurring Type II Clustered Regularly Interspaced9

Short Palindromic Repeats (CRISPR)-CRISPR associated (Cas) (CRISPR-10Cas) system comprising:11

a) a single molecule DNA-targeting RNA, or a guide RNA, comprising12

i) a targeter-RNA2 that hybridizes with the target sequence, and13

ii) an activator-RNA, or a trans-activating CRISPR RNA14

(tracrRNA), that hybridizes with the targeter-RNA to form15

a double-stranded RNA duplex of a protein binding16segment, and17

b) a Cas9 protein,18

wherein i) and ii) are covalently linked to one another,19wherein a) forms a complex with b), thereby targeting the Cas9 protein to the target DNA20

molecule, whereby said target DNA molecule is cleaved or edited or transcription of at21

least one gene encoded by the target DNA molecule is modulated.22

Proposed Count 2 differs from Count 1 by removing the eukaryotic limitation and23

explicitly requiring a single molecule DNA-targeting RNA or guide RNA. Removal of the24

eukaryotic limitation from the count is appropriate because none of Senior Party’s claims require25

2 Existing Count 1 uses the language “targeter RNA or guide sequence.” The “guide sequence”

portion of the targeter-RNA is responsible for hybridization with the target DNA

sequence. However, the “guide sequence” does not include the portion of the targeter-RNA

which is required for hybridization with the activator-RNA or tracrRNA to form a double-

stranded RNA duplex of a protein binding segment. Because the “guide sequence” on its own is

incapable of hybridizing with the activator-RNA or tracrRNA, the term “guide sequence” is not

included in Proposed Count 2 or alternative Proposed Counts 3-5 discussed below.


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performance of the claimed method or application of the claimed system in a eukaryotic cell.1

Moreover, performing the method in a eukaryotic cell would have been obvious to a person of2

ordinary skill in the art in view of a disclosure of performing the method in vitro. Senior Party3

will provide ample evidence of this in its motion. However, the Board appears to have already4

recognized the obviousness of the eukaryotic limitations given that, in declaring this interference,5

the Board recognized that there is an interference-in-fact between the claims of Senior Party6

(whose claims do not require performance of the claimed method or application of the claimed7

system in a eukaryotic cell) and Broad (whose claims do require performance of the claimed8

method or application of the claimed system in a eukaryotic cell). In addition, Proposed Count 29

should be substituted for Count 1 at least because doing so will permit Senior Party to rely upon10

its best proofs, which fall outside of Count 1. See, e.g., Grose v. Plank, 15 U.S.P.Q.2d 1338,11

1341 (B.P.A.I. 1990); see also Louis v. Okada, 59 U.S.P.Q.2d 1073, 1076 (B.P.A.I. 2001).12

Thus, it would be unfair to limit priority proofs to only those methods performed in a eukaryotic13

cell.14

Further, addition of the single molecule DNA-targeting RNA limitation is appropriate15

because all of Senior Party’s involved claims and at least some of Broad’s involved claims are16

directed to the use of a single molecule DNA-targeting RNA, which is a separately patentable17

invention. Senior Party’s claimed single molecule DNA-targeting RNA is a unique format that18

is not found in nature. The single molecule DNA-targeting RNA is separately patentable from19

the double-molecule format, which is encompassed by Count 1. Further, the fact that single20

molecule DNA-targeting RNA is patentably distinct from a double molecule DNA-targeting21

RNA was recognized by the USPTO. See, e.g., Restriction Requirement mailed on February 6,22

2015, in Senior Party’s involved ‘859 Application Prosecution History (the single molecule23


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DNA-targeting RNA of Group II was distinguished from the double molecule DNA-targeting1

RNA of Group IV as being “independent and distinct”); see also Lee v. McIntyre., Paper No. 29,2

at *7, Interference No. 104,461 (B.P.A.I. March 16, 2000) (holding that a count can “be3

narrowed so as to be limited to a single patentable invention”). This is also consistent with the4

notion that “[d]uring the course of an interference, a count may be narrowed to exclude5

patentable subject matter within the scope of a claim designated as corresponding to the count6

where the claim is directed to more than one patentable invention.” Id. at *4; see also Board of7

Patent Appeals and Interferences Answers to Frequently Asked Questions,8

http://www.uspto.gov/web/offices/dcom/bpai/bpaifaq.pdf ; see also Godtfredsen v. Banner , 5989

F.2d 589, 592 (C.C.P.A. 1979). Proposed Count 2 reflects the currently-claimed invention10

common to both Broad and Senior Party. For at least these reasons, Proposed Count 2 should be11

substituted for Count 1.12


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3. Motion 3 (Contingent Upon the Denial of Motion 2 to Redefine the Scope of1

This Contested Case) to Redefine the Scope of This Contested Case − 2

Substituting Count 1 with Proposed Count 33

Motion 3 requests, should Motion 2 be denied, that existing Count 1 be substituted with4

Proposed Count 3, which reads as follows:5

A method of cleaving or editing a target DNA molecule or modulating transcription of at6

least one gene encoded thereon, the method comprising:7

contacting a target DNA molecule having a target sequence with an engineered8and/or non-naturally-occurring Type II Clustered Regularly Interspaced9

Short Palindromic Repeats (CRISPR)-CRISPR associated (Cas) (CRISPR-10

Cas) system comprising:11a) a DNA-targeting RNA comprising12

i) a targeter-RNA that hybridizes with the target sequence, and13

ii) an activator-RNA, or a trans-activating CRISPR RNA (tracrRNA),14

that hybridizes with the targeter-RNA to form a15double-stranded RNA duplex of a protein binding segment,16

and17

b) a Cas9 protein,18wherein said contacting takes place outside of a bacterial cell and outside of an19

archaeal cell, and20

wherein the DNA-targeting RNA forms a complex with the Cas9 protein, thereby21targeting the Cas9 protein to the target DNA molecule, whereby said target DNA22

molecule is cleaved or edited or transcription of at least one gene encoded by the target23

DNA molecule is modulated.24

Proposed Count 3 broadens the Count by replacing the eukaryotic limitation with25

“wherein said contacting takes place outside of a bacterial cell and outside of an archaeal cell.”26

Removal of the eukaryotic limitation from the count is appropriate because none of Senior27

Party’s claims require performance of the claimed method or application of the claimed system28

in a eukaryotic cell. Moreover, performing the method in a eukaryotic cell would have been29

obvious to a person of ordinary skill in the art in view of a disclosure of performing the method30

in vitro. Senior Party will provide ample evidence of this in its motion. However, the Board31

appears to have already recognized the obviousness of the eukaryotic limitations given that, in32

declaring this interference, the Board recognized that there is an interference-in-fact between the33

claims of Senior Party (whose claims do not require performance of the claimed method or34


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application of the claimed system in a eukaryotic cell) and Broad (whose claims do require1

performance of the claimed method or application of the claimed system in a eukaryotic cell).2

Thus, it would be unfair to limit priority proofs to only those methods performed in a eukaryotic3

cell. In addition, Proposed Count 3 should be substituted for Count 1 at least because doing so4

will permit Senior Party to rely upon its best proofs, which fall outside of Count 1. See, e.g.,5

Grose v. Plank , 15 U.S.P.Q.2d 1338, 1341 (B.P.A.I. 1990); see also Louis v. Okada, 596

U.S.P.Q.2d 1073, 1076 (B.P.A.I. 2001). Should Senior Party be permitted to file proposed7

Motion 3, Senior Party intends to request the addition of a claim that would correspond to8

Proposed Count 3. See Standing Order, ¶ 208.2. 9

4. Motion 4 (Contingent Upon the Denial of Motion 2 and the Grant of Motion10

3) to Redefine the Scope of this Contested Case − Adding Proposed Count 411

Motion 4 requests, should Motion 2 be denied and Motion 3 be granted, that Proposed12

Count 4 (whose content is the same as Proposed Count 2) be added, which reads as follows:13

A method of cleaving or editing a target DNA molecule or modulating transcription of at14

least one gene encoded thereon, the method comprising:15contacting a target DNA molecule having a target sequence with an engineered16

and/or non-naturally-occurring Type II Clustered Regularly Interspaced17Short Palindromic Repeats (CRISPR)-CRISPR associated (Cas) (CRISPR-18

Cas) system comprising:19

a) a single molecule DNA-targeting RNA, or a guide RNA, comprising20

i) a targeter-RNA that hybridizes with the target sequence, and21ii) an activator-RNA, or a trans-activating CRISPR RNA22

(tracrRNA), that hybridizes with the targeter-RNA to23

form a double-stranded RNA duplex of a protein binding24segment, and25

b) a Cas9 protein,26

wherein i) and ii) are covalently linked to one another,27

wherein a) forms a complex with b), thereby targeting the Cas9 protein to the target DNA28molecule, whereby said target DNA molecule is cleaved or edited or transcription of at29

least one gene encoded by the target DNA molecule is modulated.30

Proposed Count 4 differs from Count 1 by removing the eukaryotic limitation and31

explicitly requiring a single molecule DNA-targeting RNA. Removal of the eukaryotic32


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limitation from the count is appropriate because none of Senior Party’s claims require1

performance of the claimed method or application of the claimed system in a eukaryotic cell.2

Moreover, performing the method in a eukaryotic cell would have been obvious to a person of3

ordinary skill in the art in view of a disclosure of performing the method in vitro. Senior Party4

will provide ample evidence of this in its motion. However, the Board appears to have already5

recognized the obviousness of the eukaryotic limitations given that, in declaring this interference,6

the Board recognized that there is an interference-in-fact between the claims of Senior Party7

(whose claims do not require performance of the claimed method or application of the claimed8

system in a eukaryotic cell) and Broad (whose claims do require performance of the claimed9

method or application of the claimed system in a eukaryotic cell). Thus, it would be unfair to10

limit priority proofs to only those methods performed in a eukaryotic cell. Proposed Count 411

should be added to Proposed Count 3 at least because all of Senior Party’s involved claims and at12

least some of Broad’s involved claims are directed to the use of a single molecule DNA-targeting13

RNA, which is a separately patentable invention. Senior Party’s claimed single molecule DNA-14

targeting RNA is a unique format that is not found in nature. The single molecule DNA-15

targeting RNA is separately patentable from the double-molecule format, which is encompassed16

by the Count. Further, the fact that single molecule DNA-targeting RNA is patentably distinct17

from a double molecule DNA-targeting RNA was recognized by the USPTO. See, e.g., 18

Restriction Requirement mailed on February 6, 2015, in Senior Party’s involved ‘85919

Application Prosecution History (the single molecule DNA-targeting RNA of Group II was20

distinguished from the double molecule DNA-targeting RNA of Group IV as being “independent21

and distinct”). Proposed Count 4 reflects the currently-claimed invention common to both Broad22

and Senior Party.23


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5. Motion 5 (Contingent Upon the Denial of Motions 2 and 3) to Redefine the1

Scope of the Contested Case − Adding a Claim That Corresponds to Count 12

and De-Designating Senior Party’s Involved Claims as Corresponding to3

Count 14

Each of Senior Party’s involved claims is directed to the use of a single molecule DNA-5

targeting RNA, which is separately patentable from Count 1. Accordingly, proposed Motion 56

seeks authorization for Senior Party to add a claim to its involved ‘859 Application that7

corresponds to Count 1. See Standing Order, ¶ 208.3.2. Proposed Motion 5 also seeks to have8

Senior Party’s currently-involved claims designated as not corresponding to Count 1 because9

those claims are neither anticipated by nor rendered obvious by Count 1. Id. Senior Party’s10

claimed single molecule DNA-targeting RNA is a unique format that is not found in nature. The11

single molecule DNA-targeting RNA is separately patentable from the double-molecule format,12

which is encompassed by Count 1. That Senior Party’s single molecule DNA-targeting RNA is13

patentably distinct from a double molecule DNA-targeting RNA has already been recognized by14

the USPTO. See, e.g., Restriction Requirement mailed on February 6, 2015, in Senior Party’s15

involved ‘859 Application Prosecution History (the single molecule DNA-targeting RNA of16

Group II was distinguished from the double molecule DNA-targeting RNA of Group IV as being17

“independent and distinct”).18

6. Motion 6 (Contingent Upon the Denial of Motions 2, 3, and 5) to Redefine the19

Scope of the Contested Case − Substituting Count 1 with Proposed Count 520

Motion 6 requests, should Motions 2, 3, and 5 be denied, that existing Count 1 be21

substituted with Proposed Count 5. Proposed Count 5 is an alternative Count: Claim 168 of22

Senior Party’s involved ‘859 Application OR Claim 1 of Junior Party’s involved ‘359 Patent.23

24


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Claim 168 of the ‘859 Application OR Claim 1 of the ‘359 Patent

A method of cleaving or editing a target

DNA molecule or modulating transcription

of at least one gene encoded thereon, themethod comprising

A method of altering expression of at least

one gene product comprising

contacting a target DNA molecule having atarget sequence with an engineered and/ornon-naturally-occurring Type II Clustered

Regularly Interspaced Short PalindromicRepeats (CRISPR)—CRISPR associated

(Cas) (CRISPR-Cas) system comprising:

introducing into a eukaryotic cellcontaining and expressing a DNA moleculehaving a target sequence and encoding the

gene product an engineered, non-naturallyoccurring Clustered Regularly Interspaced

Short Palindromic Repeats (CRISPR)--

CRISPR associated (Cas) (CRISPR-Cas)system comprising one or more vectors

comprising:

a) a single molecule DNA-targeting RNA

comprising

i) a targeter-RNA that hybridizes with thetarget sequence, and

ii) an activator-RNA that hybridizes withthe targeter-RNA to form a double-stranded

RNA duplex of a protein-binding segment,

wherein the targeter-RNA and the activator-RNA are covalently linked to one another

with intervening nucleotides; and

a) a first regulatory element operable in a

eukaryotic cell operably linked to at least

one nucleotide sequence encoding aCRISPR-Cas system guide RNA that

hybridizes with the target sequence, and

b) a Cas9 protein, b) a second regulatory element operable ina eukaryotic cell operably linked to a

nucleotide sequence encoding a Type-II

Cas9 protein, wherein components (a) and(b) are located on same or different vectorsof the system,

wherein the single molecule DNA-targeting

RNA forms a complex with the Cas9 protein, thereby targeting the Cas9 protein

to the target DNA molecule,

whereby the guide RNA targets the target

sequence and the Cas9 protein cleaves theDNA molecule,

whereby said target DNA molecule iscleaved or edited or transcription of at least

one gene encoded by the target DNA

molecule is modulated.

whereby expression of the at least one gene product is altered; and,

wherein the Cas9 protein and the guideRNA do not naturally occur together.

Proposed Count 5 includes a representative broad claim from Senior Party’s involved1

‘859 Application and a representative broad claim from Broad’s involved patents. Proposed2

Count 5 should be substituted for Count 1 at least because doing so will permit Senior Party to3


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15

rely upon its best proofs, which fall outside of Count 1. See, e.g., Grose v. Plank , 15 U.S.P.Q.2d1

1338, 1341 (B.P.A.I. 1990); see also Louis v. Okada, 59 U.S.P.Q.2d 1073, 1076 (B.P.A.I. 2001).2

C. REQUESTS FOR BENEFIT3

7.

Motion 7 to Obtain Benefit to the Senior Party Provisionals for the Existing4

Count and All Proposed Counts5

For the existing Count and all four Proposed Counts (Proposed Counts 2-5), Senior Party6

seeks the benefit of the filing date of each of its four Provisionals: the first Senior Party ‘0867

Provisional; the second Senior Party ‘256 Provisional; the third Senior Party ‘640 Provisional;8

and the fourth Senior Party ‘576 Provisional.9

Senior Party intends to request benefit to each of its four provisionals for existing Count10

1 and Proposed Counts 2-5. It is anticipated that the default page limit will not be sufficient to11

explain how each of Senior Party’s four provisional applications includes at least one12

constructive reduction to practice of existing Count 1 and Proposed Counts 2-5. See Standing13

Order ¶¶ 121.2, 208.4.1. Accordingly, Senior Party requests that increasing default page limits,14

waiving statements of fact, and excluding claim charts from page limits be discussed during the15

initial teleconference.16

D. BROAD’S CLAIMS ARE UNPATENTABLE17

8. Motion 8 for Judgment That All Claims in Each of Broad’s Involved Patents18

Are Anticipated By Senior Party’s ‘797 Publication and/or Obvious Over19

Senior Party’s ‘797 Publication in Combination With the Prior Art20

Because each of Broad’s involved patents is subject to AIA prior art provisions, the21

Board should determine that all claims of each of Broad’s involved patents are: (1) anticipated22

by the ‘797 Publication and/or (2) obvious over the ‘797 Publication in combination with one or23

more of at least the following references: Mercier et al., A Transcription Factor Cascade24

Involving Fep1 and the CCAAT-Binding Factor Php4 Regulates Gene Expression In Response25


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16

To Iron Deficiency in the Fission Yeast Schizosaccharomyces pombe, 5(11) EUKARYOT. CELL 1

1866-1861 (November 2006) (“Mercier”), Dai et al., The Transcription Factors GATA4 and2

dHAND Physically Interact to Synergistically Activate Cardiac Gene Expression Through a3

p300-dependent Mechanism, 277(27) J. BIOL. CHEM. 24390-24398 (July 2002) (“Dai”),4

Gustafsson et al., Codon Bias and Heterologous Protein Expression, 22(7) TRENDS5

BIOTECHNOL. 346-353 (July 2004) (“Gustafsson”), METHODS I N CELL BIOLOGY, Protein6

Expression In Animal Cells, Chapters 2, 3, 6, 9 (Michael G. Roth ed., 1994) (“Roth”), Deltcheva7

et al., CRISPR RNA Maturation by Trans-Encoded Small RNA and Host Factor RNase III , 4718

NATURE 602-609 (March 2011) (“Deltcheva”), Sapranauskas et al., The Streptococcus9

thermophilus CRISPR/Cas System Provides Immunity in Escherichia coli, 39(21) NUCL. ACIDS10

R ES. 9275-9282 (November 2011) (“Sapranauskas”), Wang et al., Targeted Gene Addition to a11

Predetermined Site in the Human Genome Using a ZFN-Based Nicking Enzyme, 22(7) GENOME12

R ES. 1316-1326 (July 2012; published online March 2012) (“Wang”), Park et al., Regulation of13

Ribosomal S6 Kinase 2 by Mammalian Target of Rapamycin, 277(35) J. BIOL. CHEM. 31423-14

31429 (August 2002) (“Park”), Lieber, The Mechanism of Double-Strand DNA Break Repair by15

the Nonhomologous DNA End-Joining Pathway, 79 A NNU. R EV. BIOCHEM. 181-211 (July 2010)16

(“Lieber”), Jensen et al., An Update on Targeted Gene Repair in Mammalian Cells: Methods17

and Mechanisms, 18 J. BIOMED. SCI. 10 (February 2011) (“Jensen”), NCBI Staphylococcus18

aureus Cas9 protein sequence, GenBank CCK74173.1 (September 2012) (“NCBI”), Boden et19

al., Efficient Gene Transfer of HIV-1-Specific Short Hairpins RNA into Human Lymphocytic20

Cells Using Recombinant Adeno-Associated Virus Vectors, 9(3) MOL. THER . 396-402 (March21

2004) (“Boden”), MOLECULAR CLONING: A LABORATORY MANUAL, Chpt. 16 (J. Sambrook & D.22

Russell, 3rd

ed. 2011) (“Sambrook”), NUCL. ACIDS CHEM. BIOL. Chpt. 4 (B.M. Blackburn et al., 23


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17

3rd

ed. 2006) (“Blackburn”), I NTRODUCTION TO GENETICS A MOLECULAR APPROACH, Chpt. 6 (T.1

Brown, 2012) (“Brown”), Mahfouz et al., Targeted Transcriptional Repression Using a2

Chimeric TALE-SRDX Repressor Protein, 78(3) PLANT MOL. BIOL. 311-321 (February 2012)3

(“Mahfouz”), Geiβler et al., Transcriptional Activators of Human Genes with Programmable4

DNA-Specificity, 6(5) PLOS O NE e19509 (May 2011) (“Geiβler”), Miller et al., A TALE nuclease5

architecture for efficient genome editing, 29(2) NAT BIOTECHNOL. 143-8. (February 2011)6

(“Miller”); Beerli et al., Toward controlling gene expression at will: specific regulation of the7

erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular8

building blocks, 95(25) PNAS 14628-33 (December 1998) (“Beerli”); Zhang et al., Efficient9

construction of sequence-specific TAL effectors for modulating mammalian transcription, 29(2)10

NAT. BIOTECH. 149-154 (February 2011) (“Zhang”), Sanjana et al., A Transcription Activator-11

like Effector Toolbox for Genome Engineering, 7(1) NAT. PROTOC. 171-192 (January 2012)12

(“Sanjana”), Gordley et al., Synthesis of Programmable Integrases, 106(13) PNAS 5053-5058 13

(March 2009) (“Gordley”), Xu and Bestor, Cytosine Methylation Targetted to Pre-determined14

Sequences, 17(4) NAT. GENET. 376-378 (December 1997) (“Xu”), Blancafort et al., Designing15

Transcription Factor Architectures for Drug Discovery, 66(6) MOL. PHARMACOL. 1361-137116

(December 2004) (“Blancafort”), Schückel et al., A Gene-Fusion Approach to Enabling Plant17

Cytochromes p450 for Biocatalysis, 13(18) CHEMBIOCHEM. 2758-2763 (December 2012;18

published online November 2012) (“Schückel”), Lee et al., Targeted Chromosomal Deletions in19

Human Cells Using Zinc Finger Nucleases, 20(1) GENOME R ES. 81-89 (January 2010) (“Lee”),20

Jansa, et al., The transcript release factor PTRF augments ribosomal gene transcription by21

facilitating reinitiation of RNA polymerase I , 29(2) NUCL. ACIDS R ES. 423-429 (January 2001)22

(“Jansa”), Krauss, et al., Antibody-targeted RNase fusion proteins (immunoRNases) for cancer23


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18

therapy, 9(3) CURR . PHARM. BIOTECHNOL. 231-234 (June 2008) (“Krauss”), Guarna, et al.,1

Factor X fusion proteins: improved production and use in the release in vitro of biologically2

active hirudin from an inactive alpha-factor-hirudin fusion protein, 20(2) PROTEIN EXPR . PURIF.3

133-141 (November 2000) (“Guarna”), Savage, et al., A recombinant single-chain antibody4

interleukin-2 fusion protein, 22(1) CELL BIOPHYSICS 61-77 (January-June 1993) (“Savage”),5

Cong et al., Multiplex Genome Engineering Using CRISPR/Cas Systems, 339(6121) SCIENCE 6

819-823 (February 2013; published online January 2013) (“Cong”), Mali et al., RNA-Guided7

Human Genome Engineering Via Cas9, 339(6121) SCIENCE 823-826 (February 2013; published8

online January 2013) (“Mali”), Jinek et al., RNA-Programmed Genome Editing in Human Cells,9

2 ELIFE e00471 (January 2013) (“Jinek”), Hwang et al., Efficient Genome Editing in Zebrafish10

Using a CRISPR-Cas System, 31(3) NAT. BIOTECHNOL. 227-229 (March 2013) (“Hwang”), Cho11

et al., Targeted Genome Engineering in Human Cells With the Cas9 RNA-Guided Endonuclease, 12

31(3) NAT. BIOTECHNOL. 230-232 (March 2013) (“Cho”), Shen et al., Generation of Gene-13

Modified Mice Via Cas9/RNA-Mediated Gene Targeting, 23(5) CELL R ES. 720-723 (May 2013;14

published online April 2013) (“Shen”), U.S. Patent Application Publication No. 2010/007605715

(“Sontheimer”), U.S. Patent Application Publication No. 2015/0322457 (“Kim”), and U.S.16

Patent Application Publication No. 2016/0017366 (“Chen”) under AIA 35 U.S.C. §§ 102(a)(2)17

and/or 102(a)(1)/102(a)(2)/103.18

The ‘797 Publication claims the benefit of priority to the Senior Party’s Provisionals19

under 35 U.S.C. § 119. Thus, the effective date of the ‘797 Publication as prior art against all of20

Broad’s involved patents is the date of the provisional applications as to the subject matter21

disclosed in the provisional applications. See 35 U.S.C. § 102(d)(2). Broad is barred from22

attempting to antedate the ‘797 Publication because all of Broad’s involved patents are subject to23


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19

AIA provisions. Broad’s involved patents, the applications that issued as Broad’s involved1

patents, and/or an application to which each issued patent claims benefit, contains or contained at2

some time a claim to subject-matter that has an effective filing date that is on or after March 16,3

2013. See LEAHY-SMITH AMERICA I NVENTS ACT OF 2011, Pub. L. No. 112-29, sec. 3(n)(1),4

§ 273, 125 Stat. 284, 293; see also M.P.E.P. § 2159.02.5

Further, all of the secondary references listed above are prior art under AIA 35 U.S.C.6

§ 102(a)(1) because Senior Party intends to show that the earliest effective filing date for all7

claims of each of Broad’s involved patents is after the publication date of each secondary8

reference. Accordingly, each claim of all of Broad’s involved patents is unpatentable over the9

‘797 Publication alone and/or in combination with the secondary references.10

Senior Party intends to show why each of Broad’s involved claims from its twelve11

involved patents is anticipated by and/or would have been obvious in view of the prior art. It is12

expected that the default page limit will not be sufficient to address all of Broad’s involved13

claims and all of the prior art. See Standing Order ¶ 121.2. Accordingly, Senior Party requests14

that increasing default page limits, waiving statements of fact, and excluding claim charts from15

page limits be discussed during the initial teleconference.16

9. Motion 9 for Judgment That All Claims in Each of Broad’s Involved Patents17

Are Unpatentable Under Obviousness-Type Double Patenting and/or 3518

U.S.C §§ 102/103 Over Broad’s Non-Commonly-Owned Involved Patents19

The Board should determine that all of the claims of Broad’s involved ‘359, ‘945, ‘965,20

‘356, and ‘839 Patents, each of which is assigned to The Broad Institute, Inc. and Massachusetts21

Institute of Technology (collectively referred to as “the Broad/MIT patents” – see Table22

provided below), are unpatentable under the judicially-created doctrine of obviousness-type23

double patenting (“ODP”) over one or more of the claims of Broad’s involved ‘406, ‘445, ‘308,24

‘616, ‘814, ‘233, and ‘641 Patents, each of which is assigned to The Broad Institute, Inc.;25


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20

Massachusetts Institute of Technology; and President and Fellows of Harvard College1

(collectively referred to as “the Broad/MIT/Harvard patents”) in view of the prior art, and vice2

versa.3

U.S. Patent No. Recorded Assignees*

8,697,359The Broad Institute, Inc. (“Broad”);

Massachusetts Institute of Technology (“MIT”);

8,771,945 Broad; MIT




8,865,406Broad; MIT;

President and Fellows of Harvard College (“Harvard”);

8,871,445 Broad; MIT; Harvard

8,895,308 Broad; MIT; Harvard8,906,616 Broad; MIT; Harvard




* A confirmatory license to the National Institute of Health; U.S. Dept. of Health and Human

Services was recorded in each of Broad’s involved patents.

Each of the Broad/MIT patents and each of the Broad/MIT/Harvard patents share an4

inventor, Feng Zhang, rendering each patent from one group subject to ODP over each patent5

from the other group. See, e.g., In re Hubbell 709 F.3d 1140 (Fed. Cir. 2013). Broad filed6

terminal disclaimers in an attempt to obviate ODP rejections between Broad/MIT patents and7

Broad/MIT/Harvard patents. Consistent with a finding of ODP, the Board designated all of8

Broad’s claims of each of the involved patents to correspond to the Count, creating the9

presumption that all of Broad’s claims in each of the involved patents are obvious in view of the10

Count and obvious over at least some of the subject matter claimed in at least one other involved11

Broad patent. See, e.g., Jones v. Lord Corp., Paper No. 48, Interference No. 105,968 (P.T.A.B.12

March 28, 2014). Broad’s terminal disclaimers, however, are ineffective to overcome ODP13

between patents of the two different groups because the Broad/MIT patents do not share14


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21

common ownership with the Broad/MIT/Harvard patents. See 37 C.F.R. § 1.321(c). Moreover,1

the lack of common ownership is supported, and further highlighted, by the fact that Rockefeller2

University filed U.S. Patent Application 14/324,960 disputing inventorship and proper3

ownership of two Broad/MIT patents − the ‘359 and ‘945 Patents. Excerpts of Petitions filed4

and Decisions issued in Rockefeller’s patent application are provided below.5

6

Petition Entered on July 24, 2014, and Petition Decision issued on October 30, 2014, in U.S.7

Patent Application No. 14/324,960.8

In addition, Broad has not demonstrated the existence of a joint research agreement under9

37 C.F.R. § 1.321(d) between Broad/MIT and Harvard to otherwise attempt to render a terminal10

disclaimer effective for obviating ODP between patents of the respective groups. To the11

contrary, Broad filed, and the USPTO accepted, terminal disclaimers in almost all of Broad’s12


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22

involved patents that unequivocally state that the terminal disclaimers were not being used for a1

joint research agreement.3 An excerpt from one such terminal disclaimer is provided below.2

Terminal Disclaimer filed on July 2, 2014, and accepted in U.S. Application No. 14/259,420,3

which resulted in the ‘445 Patent.4

While Broad attempted to withdraw and substitute its previously-accepted terminal5

disclaimers with replacement terminal disclaimers that state they are being used for a joint6

3 Original terminal disclaimers were accepted by the USPTO in every one of Broad’s involved

patents, with the exception of Broad’s first-issued ‘359 Patent.


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research agreement, to date those new documents have not been accepted by the USPTO. Nor1

can Broad withdraw its previously-accepted terminal disclaimers. See M.P.E.P. § 1490 VIII.B;2

see also Bayer AG v. Carlsbad Tech. Inc., 298 F.3d 1377, 1381 (Fed Cir. 2002). Further, none3

of the specifications of Broad’s involved patents has been amended as required by statute to4

assert the existence of, and names of parties to, such a joint research agreement. See 35 U.S.C5

§ 103(c) (“the application for patent for the claimed invention discloses or is amended to disclose6

the names of the parties to the joint research agreement.”); see also AIA 35 U.S.C. § 102(c)(3) 7

(“the application for patent for the claimed invention must disclose, or be amended to disclose,8

the names of the parties to the joint research agreement.”). 9

Accordingly, Broad is unable to overcome ODP through a terminal disclaimer. As a10

result, each of the claims of the Broad/MIT patents is unpatentable under ODP over one or more11

of the claims of the Broad/MIT/Harvard patents in view of the prior art, and vice versa.12

In addition, each of the claims of the Broad/MIT patents is unpatentable under 35 U.S.C.13

§§ 102/103 because it is anticipated and/or obvious over the disclosure of the14

Broad/MIT/Harvard patents in view of the prior art. Likewise, each of the claims of the15

Broad/MIT/Harvard patents is unpatentable under 35 U.S.C §§ 102/103 because it is anticipated16

and/or obvious over the disclosure of the Broad/MIT patents in view of the prior art. All claims17

of each of the involved Broad ‘359, ‘945, ‘965, ‘356, and ‘839 Patents (Broad/MIT patents) are18

not entitled to a filing date prior to at least March 16, 2013, because of lack of written description19

support in a pre-March 16, 2013, priority application for at least one limitation in each of their20

issued claims. The disclosures of the involved Broad ‘406, ‘445, ‘308, ‘616, ‘814, ‘233, and21

‘641 Patents (Broad/MIT/Harvard patents), however, are effective as prior art references under22


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35 U.S.C. § 102 as of the filing date of the earliest U.S. provisional application that discloses the1

relevant subject matter and to which the Broad/MIT/Harvard patents claim benefit.2

Additionally, all claims of each of the involved Broad ‘406, ‘445, ‘308, ‘616, ‘814, ‘233,3

and ‘641 Patents (Broad/MIT/Harvard patents) are not entitled to a filing date prior to at least4

March 16, 2013, because of lack of written description support in a pre-March 16, 2013, priority5

application for at least one limitation in each of their issued claims. The disclosures of the6

involved Broad ‘359, ‘945, ‘965, ‘356, and ‘839 Patents (Broad/MIT patents), however, are7

effective as prior art references under 35 U.S.C. § 102 as of the filing date of the earliest U.S.8

provisional application that discloses the relevant subject matter and to which the Broad/MIT9

patents claim benefit.10

Broad cannot remove the Broad/MIT patents or the Broad/MIT/Harvard patents as prior11

art against each other under pre-AIA 35 U.S.C § 103(c) because of lack of common ownership.12

And, Broad cannot remove the Broad/MIT patents or the Broad/MIT/Harvard patents as prior art13

under AIA 35 U.S.C. § 102 against a patent(s) of the other group at least because (1) the14

inventive entities differ between the groups of patents, (2) there is no evidence that the subject15

matter disclosed in patents from either group was obtained from, or disclosed by, the inventor,16

joint inventor, or another party, and (3) the claimed invention in the patents of one group and the17

subject matter disclosed in the patents of the other group, did not have common ownership or a18

joint research agreement (see above) at the effective filing date of the invention. See AIA 3519

U.S.C. § 102.20

Accordingly, each of Broad’s involved patents is unpatentable under ODP and/or 3521

U.S.C. §§ 102/103 over at least one other Broad involved patent.22


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25

Senior Party intends to show why each of Broad’s involved claims from its involved1

twelve patents would have been obvious in view of at least one other claim of Broad’s involved2

patents and anticipated or obvious over the disclosure of at least one other involved Broad patent.3

It is expected that the default page limit will not be sufficient to address all of Broad’s involved4

claims. See Standing Order ¶ 121.2. Accordingly, Senior Party requests that increasing default5

page limits, waiving statements of fact, and excluding claim charts from page limits be discussed6

during the initial teleconference.7

10. Motion 10 for Judgment That All of Broad’s Involved Claims Are8

Unpatentable for Lacking Proper Inventorship9

The Board should find that all claims of each of Broad’s involved patents are10

unpatentable for lack of proper inventorship. Each of Broad’s involved patents names either11

Feng Zhang as the sole inventor or Feng Zhang in combination with one or more of Fei Ran, Le12

Cong, Patrick Hsu, Randall Platt, and Neville Sanjana as the inventive entity.13


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26

U.S. Patent Nos. Listed Inventor(s)

8,697,359

8,771,9458,795,965

8,889,356

8,945,839

Feng Zhang

8,865,4068,895,308

Feng Zhang

Fei Ran

8,871,445

8,932,814

Feng Zhang

Le Cong

8,906,616Feng Zhang

Le Cong

Patrick Hsu

Fei Ran

8,993,233

Feng Zhang

Le CongFei Ran

Randall Platt

Neville Sanjana

8,999,641

Feng Zhang

Le Cong

Randall Platt

Neville Sanjana

During the same time period in which Broad filed its earliest provisional applications1

(e.g., U.S. Provisional Application Nos. 61/736,527 and 61/748,427) to which the involved2

patents claim benefit, Feng Zhang’s research group published a journal article that is3

substantially similar to, and likely derived from or the basis for, Broad’s provisional applications.4

See Cong et al., Multiplex Genome Engineering Using CRISPR/Cas Systems, 339(6121) SCIENCE 5

819-823 (2013) (“Cong”).6


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Broad’s earliest provisional applications list the following inventors:1

U.S. Provisional

Application

Listed Inventors U.S. Provisional

Application

Listed Inventors

61/736,527

Feng Zhang

61/748,427

Feng Zhang

Le Cong Le Cong Naomi Habib Naomi Habib

David Cox David Cox

Patrick Hsu Patrick Hsu

Shuailiang Lin Shuailiang Lin

Fei Ran Fei Ran

Luciano Marraffini Luciano Marraffini

The Cong publication lists many co-authors, including Robert Barretto, Xuebing Wu, and2

Wenyan Jiang, who are not listed as inventors on any of Broad’s earliest provisionals.3

Cong et al., 339(6121) SCIENCE 819-823 (2013)

Feng Zhang

Le Cong

Fei Ran

Patrick Hsu

David Cox

Shuailiang Lin

Naomi Habib

Luciano Marraffini

Robert Barretto

Xuebing WuWenyan Jiang

Individuals who are listed as co-authors of the Cong publication and co-inventors of Broad’s4

earliest provisionals (i.e., David Cox, Shuailiang Lin, Naomi Habib, and Luciano A. Marraffini)5

are not listed as co-inventors on any of Broad’s involved patents. See In re Katz, 687 F.2d 450,6

453 (C.C.P.A. 1982) (“Even though authorship may not conclusively establish inventorship, it is7

reasonable to infer that such a relationship exists . . . . In our view, disclaiming affidavits or8

declarations by the other authors are required in order to support appellant’s contention that he is9

the sole inventor of the subject matter described in the Chiorazzi article and claimed here.”).10


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28

Furthermore, Broad itself has taken inconsistent positions that some of these co-authors1

are indeed inventors on the involved patents. For example, Le Cong and Fei Ran are named as2

inventors on one or more of Broad’s ‘406, ‘445, ‘308, ‘616, ‘814, ‘233, and ‘641 Patents, and3

Neville Sanjana is listed as an inventor of Broad’s ‘233 and ‘641 patents. Thus, Broad has taken4

the position that these individuals made inventive contributions despite having filed sworn5

testimonial statements with the USPTO, stating that these individuals worked “under the6

direction, supervision and control of Feng Zhang.” See Declarations of Fei Ran and Le Cong,7

filed in the ‘406; ‘445; ‘308; ‘616; ‘814; ‘233; and ‘641 Patents on January 5, 2016 and8

Declaration of Neville Sanjana, filed in the ‘233 and ‘641 Patents on January 5, 2016.9

No declarations from other co-authors named in the Cong publication, e.g., Shuailiang10

Lin, Robert Barretto, Naomi Habib, Patrick D. Hsu, Xuebing Wu, Wenyan Jiang, and Luciano A.11

Marraffini, regarding their contributions to the claimed subject matter in Broad’s involved12

patents have been submitted to the USPTO. All of Broad’s involved patents, however, claim13

benefit to U.S. Provisional Application Nos. 61/736,527 and 61/748,427, which name some of14

the above-listed co-authors as co-inventors, i.e., Shuailiang Lin and Luciano A. Marraffini.15

Thus, absent testimonial evidence to the contrary, for at least these additional reasons, it appears16

that each of Broad’s involved patents fails to provide proper inventorship and, therefore, the17

claims of each of Broad’s involved patents are unpatentable. See 35 U.S.C. § 102(f); see also18

AIA 35 U.S.C. § 115(a). 19

Further, Broad previously submitted and attempted to rely on the laboratory notebook20

and presentation slides of Shuailiang Lin in relation to the claimed subject matter, but Broad21

failed to provide a corresponding declaration from Shuailiang Lin explaining why he is not a co-22

inventor. Despite relying on Neville Sanjana’s testimony as to the authenticity of Shuailiang23


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29

Lin’s documents and to Shuailiang Lin’s role in the Zhang lab, Broad’s submissions are nothing1

more than hearsay. Due to declarations of several co-inventors asserting their lack of inventive2

contribution and the absence of a declaration from Shuailiang Lin confirming or denying his3

contribution to the subject matter claimed in Broad’s involved patents, it appears that each of4

Broad’s involved patents fails to provide proper inventorship and, therefore, the claims of each5

of Broad’s involved patents are unpatentable. See 35 U.S.C. § 102(f); see also AIA 35 U.S.C.6

§ 115(a).7

Finally, Dr. Marraffini, a co-author named in the Cong publication and listed co-inventor8

on Broad’s ‘527 and ‘427 provisional applications, disputes the inventorship of at least Broad’s9

involved ‘359 and ‘945 Patents. Specifically, Dr. Marraffini filed U.S. Patent Application No.10

14/324,960 and copied the claims of Broad’s ‘359 and ‘945 Patents. Dr. Marraffini alleges that11

he should have been named as an inventor, and Rockefeller University named as an assignee, on12

Broad’s ‘359 and ‘945 Patents. See U.S. Patent Application 14/324,960. An excerpt from13

Marraffini/Rockefeller’s USPTO communications is provided below.14


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30

12

Miscellaneous Communication filed on July 28, 2014, in U.S. Patent Application No.3

14/324,960.4

Accordingly, each of Broad’s involved patents fails to provide proper inventorship and5

therefore the claims of each of Broad’s involved patents are unpatentable. See 35 U.S.C.6

§ 102(f); see also AIA 35 U.S.C. § 115(a).7

11. Motion 11 for Judgment That All of Broad’s Involved Patents Were8

Obtained Through Inequitable Conduct9

Proposed Motion 11 is a motion for judgment under Standing Order ¶ 208.7 that Broad’s10

involved patents were obtained through inequitable conduct. See 37 C.F.R. § 10.23(b)(4).11

During prosecution of all of Broad’s involved patents and in response to applied or potential12

rejections, Broad submitted sworn testimony from Dr. Feng Zhang, an inventor common to all of13

Broad’s involved patents, alleging that all elements of the claimed subject matter were present in14


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the experimental data and results of supporting documents submitted therewith. See, e.g., the1

‘359 Patent, Prosecution History, Declaration Under 37 C.F.R. §§ 1.132 and 1.131, filed January2

30, 2014. However, upon review of the supporting documents, it is clear that, for example, Dr.3

Feng Zhang never had or made use of tracrRNA—an essential element of the claimed subject4

matter—in any of the submitted experimental data and results.4 Accordingly, Dr. Feng Zhang5

never demonstrated in his supporting documents that he was in possession of any claimed6

methods that made use of tracrRNA. Because the omission of essential subject matter in Dr.7

Feng Zhang’s supporting documents would have been readily evident to a person of ordinary8

skill in the art, it is believed that Broad withheld or misrepresented material information with the9

intent to deceive the USPTO, contributing to the issuance of Broad’s involved patents. See 3710

C.F.R. § 10.23(c)(2)(ii), see also Therasense, Inc. v. Becton, Dickinson & Co., 649 F.3d 1276,11

1287 (Fed. Cir. 2011).12

E. PRIORITY OF INVENTION13

12. Motion 12 for Priority of Invention 14

Should a priority phase be reached, Motion 12 will be a motion for judgment awarding15

Senior Party priority of invention.16

F. MISCELLANEOUS ISSUES17

When Senior Party requested an interference with Broad, Senior Party’s Suggestions of18

Interference requested an interference not only with Broad’s twelve involved patents, but also19

with five Broad patent applications as well. It is believed that the Patent Office did not include20

those additional patent applications in this interference because the claims of those applications21

4 Dr. Zhang’s own publication (Cong, et al., published online on January 3, 2013, i.e., before the

Zhang Declaration was submitted) demonstrates the criticality of tracrRNA.


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32

were not yet in condition for allowance. Subsequent to this interference being declared, the1

USPTO allowed Broad’s U.S. Application No. 14/704,551 (“the ‘551 Application), which claims2

interfering subject matter and was included in Senior Party’s Suggestion of Interference. Senior3

Party requests that the status and treatment of Broad’s ‘551 Application and other pending4

applications directed to interfering subject matter be discussed during the initial teleconference.5

Senior Party wishes to preserve its ability to request that the ‘551 Application and any6

subsequently-allowed Broad application(s) with an interfering claim be added to this7

interference.8

Senior Party may request additional discovery at a later date. As an example, Senior9

Party may request permission to depose and serve narrowly-tailored document requests upon Dr.10

Luciano Marraffini, whose activities are relevant to the inventorship and/or ODP issues. Senior11

Party is exploring whether Dr. Marraffini and others will cooperate in providing the requested12

information, which would obviate the need for a miscellaneous motion seeking additional13

discovery. Should agreement not be reached on these issues, Senior Party wishes to preserve its14

right to request additional discovery.15

Finally, Senior Party requests that waiving statements of fact and excluding claim charts16

from page limits in the proposed motions be discussed during the initial teleconference.17


36/37


33

Respectfully submitted,1

Date: March 3, 2016 By: /Todd R. Walters/2

Todd R. Walters, Esq.3

Registration No. 34,0404

BUCHANAN I NGERSOLL & R OONEY PC5 1737 King Street, Suite 5006

Alexandria, VA 223147

Telephone (703) 836-66208Facsimile (703) 836-20219

[email protected] 10

Counsel for UC and Vienna11

Date: March 3, 2016 By: /Brian A. Fairchild/12

Brian A. Fairchild, Ph.D., Esq.13

Registration No. 48,64514GOODWIN PROCTER LLP 15

Exchange Place, 53 State Street16

Boston, Massachusetts 0210917Telephone (617) 570-100018

Facsimile (617) 523-123119

[email protected] 20

Counsel for EC21


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CERTIFICATE OF FILING AND SERVICE

I hereby certify that on this 3rd

day of March, 2016, the foregoing SENIOR PARTY

LIST OF PROPOSED MOTIONS is being filed, via the Interference Web Portal, by 5:00 PM

Eastern Time. Pursuant to agreement by the parties, service copies are being sent, via electronic

mail by 8:00 PM Eastern Time today, to Junior Party’s counsel as follows:

Thomas J. Kowalski, Esq.Deborah L. Lu, Esq.

VEDDER PRICE PC

1633 Broadway, 47th

Floor New York, NY 10019

(212) 407-7640

[email protected]

[email protected]

A courtesy service copy is being sent, via email by 8:00 PM Eastern Time today, to

Junior Party’s anticipated substitute counsel as follows:

Steven R. Trybus, Esq.Harry J. Roper, Esq.

JENNER & BLOCK LLP

353 North Clark StreetChicago, Ililnois 60654

(312) [email protected]

[email protected]

(substitution of counsel pending)

Date: March 3, 2016 /Todd R. Walters/

Todd R. Walters, Esq.

Registration No. 34,040

BUCHANAN I NGERSOLL & R OONEY PC1737 King Street, Suite 500

Alexandria, VA 22314Telephone (703) 836-6620Facsimile (703) 836-2021

[email protected]

Counsel for UC and Vienna

uc's motions

Documents