PIONEER HI-BRED INTERNATIONAL, INC.

Patent Trials and Appeals Board

Sep 23, 2020

14913177 - (D) (P.T.A.B. Sep. 23, 2020)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
14/913,177 02/19/2016 Andrew Cigan BB2344-US-PCT 8869
27310 7590 09/23/2020
PIONEER HI-BRED INTERNATIONAL, INC.
7250 NW 62ND AVENUE
PO BOX 552
JOHNSTON, IA 50131-0552
EXAMINER
COLLINS, CYNTHIA E
ART UNIT PAPER NUMBER
1662
NOTIFICATION DATE DELIVERY MODE
09/23/2020 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
IPsupport@corteva.com
sue.smith@corteva.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte ANDREW MARK CIGAN, PHILLIP P. PATTEN, and
JOSHUA K. YOUNG

____________

Appeal 2020-001237
Application 14/913,177
Technology Center 1600
____________

Before ERIC B. GRIMES, TIMOTHY G. MAJORS, and
MICHAEL A. VALEK, Administrative Patent Judges.

VALEK, Administrative Patent Judge.

DECISION ON APPEAL
Appellant1 submits this appeal2 under 35 U.S.C. § 134(a) involving
claims to a method for modifying a target site in the genome of a cell that

1 We use the word “Appellant” to refer to “applicant” as defined in
37 C.F.R. § 1.42(a). Appellant identifies Pioneer Hi-Bred International, Inc.
and E.I. DuPont de Nemours & Company as the real parties in interest.
Appeal Br. 3. Herein, we refer to the Final Action mailed October 18, 2018
(“Final Act.”); Appellant’s Appeal Brief filed May 10, 2019 (“Appeal Br.”);
Examiner’s Answer mailed October 4, 2019 (“Ans.”); and Appellant’s Reply
Brief filed December 3, 2019 (“Reply Br.”).
2 This Appeal is related to Appeal 2019-003067 (Application 14/463,687)
and Appeal 2020-001230 (14/913,614), Decisions affirming the rejections of
record entered June 24, 2020 and September 10, 2020 respectively.
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have been rejected for anticipation under 35 U.S.C. § 102 and obviousness
under 35 U.S.C. § 103. We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.
STATEMENT OF THE CASE
“Recombinant DNA technology has made it possible to insert foreign
DNA sequences into the genome of an organism, thus, altering the
organism’s phenotype.” Spec. 1. According to the Specification,
[a]lthough several approaches have been developed to target a
specific site for modification in the genome of a cell, there still
remains a need for more efficient and effective methods for
producing an organism, such as but not limited to yeast and
fertile plants, having an altered genome comprising specific
modifications in a defined region of the genome of the cell.
Id. at 2.
Appellant’s Specification describes “compositions and methods for
genome modification of a target sequence in the genome of a cell” that
“employ a guide polynucleotide/Cas endonuclease system to provide an
effective system for modifying target sites within the genome of a cell.”
Spec. 19. A Cas endonuclease is a protein encoded by a “CRISPR-
associated (Cas)” gene such as Cas9. Id. at 20–21. “Once a genomic target
site is identified, a variety of methods can be employed to further modify the
target sites such that they contain a variety of polynucleotides.” Id. at 2, 19–
20.
Claims 16–18, 25, 26, and 28 are on appeal and can be found in the
Claims Appendix of the Appeal Brief. Claim 16 is illustrative of the claims
on appeal. It reads as follows:
16. A method for modifying a target site in the genome of a
cell, the method comprising providing a guide polynucleotide
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and a Cas endonuclease to a cell, wherein said guide
polynucleotide comprises at least one deoxyribonucleotide,
wherein said guide polynucleotide and Cas endonuclease form a
guide polynucleotide Cas endonuclease complex, wherein the
Cas endonuclease introduces a double strand break at said
target site.
Appeal Br. 17.
Appellant seeks review of the following rejections:
I. Claims 16, 18, 25, and 26 under 35 U.S.C. § 102(a)(2) as anticipated
by Joung;3 and
II. Claims 17 and 28 under 35 U.S.C. § 103 as unpatentable over Joung
in view of Zhang.4
Appeal Br. 6.
I. ANTICIPATION REJECTION OVER JOUNG
Issue
Appellant does not argue the rejection of dependent claims 18, 25, and
26 separately from the rejection of independent claim 16. Accordingly, we
focus our analysis on claim 16, and the other claims stand or fall with claim
16. See 37 C.F.R. § 41.37(c)(iv).

3 US 2016/0024524 A1, published Jan. 28, 2016 (“Joung”). Joung claims
priority to a number of applications, including provisional application no.
61/838,178, filed on June 21, 2013 (“’178 Provisional”).
4 US 2014/0186919 A1, published July 3, 2014 (“Zhang”). Zhang claims
priority to a number of provisional applications filed prior to the earliest
possible effective filing date of Appellant’s present application. Appellant
does not address the disclosure in any of Zhang’s provisional applications in
its briefing, nor does Appellant otherwise dispute that Zhang is prior art to
the present application.
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The issue for this rejection is whether a preponderance of the evidence
supports Examiner’s conclusion that Joung anticipates the method recited in
claim 16.
Findings of Fact
FF1. Joung discloses “methods [for increasing specificity] of genome
editing using the CRISPR/Cas system, e.g., using Cas9 or Cas9-based fusion
proteins.” Joung ¶¶ 3, 5; ’178 Provisional 1.5
FF2. One such method disclosed in Joung involves the use of “a synthetic
guide ribonucleic acid . . . wherein one or more of the nucleotides is a
deoxyribonucleic acid.” Joung ¶ 6; ’178 Provisional 3. In particular, Joung
discloses “methods for inducing a single or double-stranded break in a target
region of a double-stranded DNA molecule, e.g., in a genomic sequence in a
cell” comprising the step of:
expressing in or introducing into the cell: a Cas9 nuclease or
nickase; and (a) a guide RNA that includes one or more
deoxyribonuclotides (e.g., where the sequence may also be
partially or wholly DNA but with thymine in place or [sic]
uracil), e.g., a guide RNA that includes a sequence of 17-20
nucleotides that are complementary to the complementary
strand of a target sequence, preferably a target sequence
immediately 5' of a protospacer adjacent motif (PAM), e.g.,
NGG, NAG, or NNGG, wherein the guide RNA includes one or
more deoxyribonuclotides (e.g., where the defined sequence
may also be partially or wholly DNA but with thymine in place
or [sic] uracil), e.g., a hybrid nucleic acid as described herein.

5 We include parallel citations to supporting disclosure in the ’178
Provisional. The ’178 Provisional was filed prior to the earliest possible
effective filing date of Appellant’s present application. Appellant does not
dispute that the ’178 Provisional provides written description support for one
or more claims in Joung.
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Joung ¶¶ 22, 36–37, 72; ’178 Provisional 3–4.
FF3. Joung discloses that the synthetic guide RNA in its method forms
“complexes” with Cas9 “to improve the genome-wide specificity of the
CRISPR/Cas9 nuclease system.” Joung ¶ 77; ’178 Provisional 18; see also
Joung Fig. 1; ’178 Provisional Fig. 1 (depicting a guide polynucleotide/Cas9
complex bound to a target DNA site).
FF4. Joung explains the rationale for its method of using “DNA-Based
Guide Molecules” as follows:
Existing Cas9-based RGNs [RNA-guided nucleases] use
gRNA-DNA heteroduplex formation to guide targeting to
genomic sites of interest. However, RNA-DNA heteroduplexes
can form a more promiscuous range of structures than their
DNA-DNA counterparts. In effect, DNA-DNA duplexes are
more sensitive to mismatches, suggesting that a DNA-guided
nuclease may not bind as readily to off-target sequences,
making them comparatively more specific than RNA-guided
nucleases. To this end, we propose an engineered Cas9-based
RGN wherein a short DNA oligonucleotide replaces all or part
of the complementarity region of a gRNA (for example, see
FIG. 4). This DNA-based molecule could replace either all or
part of the gRNA in a single gRNA system or alternatively
might replace all of part of the crRNA in a dual
crRNA/tracrRNA system. Such a system that incorporates
DNA into the complementarity region should more reliably
target the intended genomic DNA sequences due to the general
intolerance of DNA-DNA duplexes to mismatching compared
to RNA-DNA duplexes.
Joung ¶¶ 85–86; ’178 Provisional 19–20. Joung further discloses that
“[m]ethods for making such duplexes are known in the art.” Id. (citing
references).
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FF5. At least claim 7 of Joung is supported by the written description in
the ’178 Provisional. See ’178 Provisional 3–4, 8, 10, 19–20 (referring to
“Strategy 2B: DNA-based guide molecules”).
Analysis
Examiner finds that Joung discloses “a method comprising providing
a guide polynucleotide and a Cas endonuclease to a cell” wherein the guide
polynucleotide comprises “a crNucleotide and a tracrRNA” that is “a
deoxyribonucleotide sequence or a combination of a deoxyribonucleotide
and ribonucleotide sequence” and “wherein the guide polynucleotide and
Cas endonuclease are capable of forming a complex that enables the Cas
endonuclease to introduce a double strand break at a target site.” Final Act.
4–5. Examiner further determines these disclosures are supported by the
’178 Provisional and, therefore, Joung is entitled to the date of the ’178
Provisional for purposes of assessing Joung as prior art. Id. at 6; see also
Ans. 9 (explaining that Joung is “now issued as a patent, U.S. Patent No.
9,885,033” and finding that claim 1 of that ’033 patent is supported by the
disclosure in the ’178 Provisional).
We agree with, and adopt, Examiner’s findings of fact and reasoning
supporting the determination that Appellant’s claims are anticipated by
Joung. See Final Act. 3–7; Ans. 3–5, 8–21; FF1–FF5. We are not
persuaded by Appellant’s arguments, as explained below.
We are not persuaded by Appellant’s argument that “Joung was at
best ‘ambiguous’ in merely mentioning DNA” in the guide RNA of the
method it discloses. Appeal Br. 7–8 (citing Wasica Finance GmbH v.
Continental Automotive Systems Inc., 853 F.3d 1272 (Fed. Cir. 2017)).
Unlike the prior art reference considered in Wasica, Joung specifically and
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sufficiently describes the method of claim 16, including the limitation
requiring “at least one deoxyribonucleotide” in the guide polynucleotide.
FF2–FF3. Moreover, Joung explains that the rationale for including one or
more deoxyribonucleotides in its guide RNA is that “DNA-DNA duplexes
are more sensitive to mismatches” and, therefore, a guide RNA comprising
at least some DNA will be “comparatively more specific” and “more reliably
target the intended genomic DNA sequences.” FF4. Given these
disclosures, there is no ambiguity in Joung’s disclosure of a method
comprising providing a Cas endonuclease and a DNA-containing guide
polynucleotide to a cell, as recited in claim 16.
Appellant further asserts that Joung “does not qualify as an enabling
prior art” because “every example related to methods and results for guide
RNA polynucleotides only.” Appeal Br. 7. In other words, Appellant
contends that the method disclosed in Joung is not enabled because Joung
does not provide a working example demonstrating that method with a guide
RNA that “included any DNA.” Id. We are not persuaded.
As Examiner correctly points out, Joung need not provide a working
example demonstrating the claimed method to anticipate. Ans. 10; see
Bristol-Myers Squibb Co. v. Ben Venue Labs., Inc., 246 F.3d 1368, 1379
(Fed. Cir. 2001) (holding that “anticipation does not require actual
performance of suggestions in a disclosure”). What is required is that the
prior art reference disclose a method comprising all of the steps “arranged or
combined in the same way as in the claim.” See In re Gleave, 560 F.3d
1331, 1334 (Fed. Cir. 2009) (quotations omitted). We agree with Examiner
that Joung discloses such a method. See FF1–FF4. That disclosure is
“presumptively enabling.” See In re Antor Media Corp., 689 F.3d 1282,
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1287 (Fed. Cir. 2012). It is the patent applicant who bears the burden to
“submit rebuttal evidence” to show these teachings are not enabled. Id. at
1289.
Appellant, however, has not persuasively explained why, much less
provided the rebuttal evidence required to show, the anticipating disclosure
in Joung (see FF1–FF5) is not enabled. Appellant’s argument that Joung
does “not demonstrate a guide polynucleotide comprising anything other
than RNA” (Appeal Br. 8) is not persuasive because Appellant has not
offered evidence-backed argument explaining why Joung’s detailed
description of the claimed method is insufficient to enable a skilled artisan to
practice that method. The only specific argument Appellant advances is that
“Joung only contemplates methods for the introduction of only DNA
molecules into a cell that must necessarily be capable of expressing a
protein,” i.e., “DNA-only expression plasmids,” in which all of the
components “including the guide polynucleotide – are transcribed into all
RNA within the target cell after transformation.” Appeal Br. 10–11.
According to Appellant, the “DNA component of a guide polynucleotide
cannot be provided to the recipient cell via a DNA expression plasmid” and,
therefore, Joung is not enabled. Id. at 11. We are not persuaded because, as
Examiner points out, “Joung repeatedly refers to providing the required
components indirectly (expressing) or directly (introducing into)” the cell.
Ans. 14 (citing Joung ¶¶ 22, 36, 37). Thus, Appellant’s argument that Joung
only discloses transformation with DNA-only expression plasmids is
rebutted by Joung’s express teaching that the DNA-containing guide RNA it
discloses may also be directly “introduced” into the cell. FF2.
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The record also supports Examiner’s finding that “a person of
ordinary skill in the biotechnological arts would recognize that a guide RNA
that includes one or more deoxyribonucleotides (DNA) could be provided to
the recipient cell directly, since the direct introduction of nucleic acids into
cells was known and practiced in the [prior] art.” Ans. 14. In particular,
Examiner also cites Beetham,6 which describes techniques for the direct
introduction of chimeric RNA/DNA oligonucleotides into plant cells. Id.;
see Beetham 8776 (describing the introduction of such molecules by
“microparticle bombardment”). Appellant responds,7 urging that Beetham
“does not mention any method of delivering both an endonuclease and a
guide polynucleotide to a cell.” Reply Br. 7. But that argument misses the
point. It is Joung that discloses the introduction of both a Cas endonuclease
and a guide RNA to form a Cas endonuclease complex that induces targeted
double-strand breaks in the genome of a cell. FF1–FF5. Examiner points to
Beetham merely as further evidence that techniques for directly introducing
polynucleotides into cells were known in the art. Appellant has not
presented persuasive argument, much less offered rebuttal evidence, on this

6 Peter R. Beetham et al., A Tool for Functional Plant Genomics: Chimeric
RNA/DNA Oligonucleotides Cause In Vivo Gene-Specific Mutations, 96
Plant Biology 8774–78 (1999) (“Beetham”).
7 Inasmuch as Appellant contends it was prejudiced by not having an
“opportunity to address allegations related to [Beetham] in any previous
response,” (Reply Br. 7) it could have petitioned to re-open prosecution (i.e.,
to have the alleged new rationale from Examiner be designated a new
ground). See 37 C.F.R. § 41.40. Appellant did not, but instead elected to
respond in its Reply Brief, thus maintaining the appeal. 37 C.F.R.
§ 41.39(b)(2).
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point. Accordingly, we agree with Examiner that Beetham further
demonstrates that the anticipatory disclosure in Joung is enabled.
For these reasons, Examiner’s rejection of claim 16 as anticipated by
Joung is supported by the preponderance of the evidence. We, therefore,
affirm the rejection. We affirm the anticipation rejection of claims 18, 25,
and 26 for the same reasons.
II. OBVIOUSNESS REJECTION OVER JOUNG AND ZHANG
Issue
The issue for this rejection is whether a preponderance of the evidence
supports Examiner’s conclusion that Joung in combination with Zhang
renders the method of claims 17 and 28 obvious.
Additional Findings of Fact
FF6. Zhang teaches that in the context of a CRISPR system “formation of a
CRISPR complex (comprising a guide sequence hybridized to a target
sequence and complexed with one or more Cas proteins) results in cleavage
of one or both strands in or near . . . the target sequence.” Zhang ¶ 158; see
also id. ¶ 152 (teaching that a CRISPR system comprising “Cas9 generates
double stranded breaks at target site sequences”). Zhang explains that the
various “elements of a CRISPR system” may be introduced into a host cell
on one or more vectors. Id. ¶ 158. Zhang further teaches that “[a] variety of
delivery systems can be introduced [sic] to introduce Cas9 (DNA or RNA)
and guide RNA (DNA or RNA) into the host cell.” Id. ¶ 171; see also id.
¶ 239 (listing techniques).
FF7. Zhang teaches that, along with the other elements of a CRISPR
system, a “recombination template” may be provided “to serve as a template
in homologous recombination, such as within or near a target sequence
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nicked or cleaved by a CRISPR enzyme as part of a CRISPR complex.”
Zhang ¶ 174; see also id. ¶ 210 (teaching that “[t]he break created by the
CRISPR complex can be repaired by . . . high fidelity homology-directed
repair” in which “an exogenous polynucleotide template can be introduced”
and “used to modify a genome sequence”). Zhang ¶ 210; see also ¶ 174
(teaching that “a recombination template is designed to serve as a template
in homologous recombination, such as within or near a target sequence
nicked or cleaved by a CRISPR enzyme as part of a CRISPR complex”).
Zhang explains that this “exogenous polynucleotide template comprises a
sequence to be integrated (e.g., a mutated gene)” such as “polynucleotides
encoding a protein.” Id. ¶ 212. Zhang further teaches that the
“recombination template may be . . . contained in a separate vector, or
provided as a separate polynucleotide” from the other elements of the
CRISPR system introduced into the cell. Id. ¶ 174.
Analysis
Examiner relies upon the same findings regarding the teachings in
Joung discussed for the anticipation rejection above. Final Act. 8. Examiner
acknowledges that Joung does “not teach a method further comprising
providing a donor DNA to the cell or a method further comprising
introducing a polynucleotide modification template into the cell,” as recited
in claims 17 and 28. Id. Examiner finds that the additional limitations of
claims 17 and 28 are taught by Zhang. Id. Moreover, Examiner determines
it would have been obvious to combine these teachings with Joung’s
method:
[g]iven the teachings of Joung . . . that the target site in the
genome of a cell may be modified by providing a guide
polynucleotide and a Cas endonuclease to the cell, given the
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teachings of Zhang . . . that the target site in the genome of a
cell may also be modified by providing a guide polynucleotide,
a Cas endonuclease and a donor DNA or a modification
template to the cell, and given the further teachings of Joung . .
. that the guide polynucleotide may comprise at least one
deoxyribonucleotide which may reduce off-target effects, it
would have been prima facie obvious . . . to modify a target site
in the genome of a cell by providing a guide polynucleotide
comprising at least one deoxyribonucleotide, a Cas
endonuclease and a donor DNA or a modification template to
the cell. One skilled in the art would have been motivated to do
so in order to modify a target site in the genome of a cell and
potentially reduce off-target effects as well. One skilled in the
art would have had a reasonable expectation of success, given
the success of both Joung . . . and Zhang . . . in modifying a
target site in the genome of a cell.
Id. at 9.
We agree with, and adopt, Examiner’s findings and reasoning as well
as Examiner’s conclusion of obviousness. See Final Act. 7–9; Ans. 6–8, 22–
32; FF1–FF7. We are not persuaded by Appellant’s arguments, as explained
below.
Appellant’s argument that the prior art provides “no guidance for the
usage of a guide polynucleotide comprising DNA” is not persuasive.
Appeal Br. 11–13 (emphasis omitted). As explained above, Joung
specifically discloses the use of a guide polynucleotide comprising at least
one deoxyribonucleotide in a CRISPR-Cas system for the purpose of
inducing targeted double-strand breaks in the genome of a cell. FF1–FF3.
Moreover, Joung evidences that one of ordinary skill in the art would be
motivated to do so because the inclusion of DNA in the guide RNA
promotes specificity and potentially reduces off-target effects. FF4.
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Notwithstanding these teachings, Appellant argues “[t]here can be no
expectation of success in the absence of demonstrable evidence in Joung
and/or Zhang.” Appeal Br. 13–15. Specifically, Appellant contends
Examiner’s finding that there would have been a reasonable expectation of
success is too “conclusory” and “speculative” to support the rejection
“because neither [reference] demonstrated success of modifying a target site
in the genome of a cell with a Cas endonuclease and a guide polynucleotide
comprising DNA” and Examiner has “erroneously equat[ed] the alleged
success of Zhang in modifying a target site with a guide polynucleotide
made of only RNA to one of skill in the art achieving reasonable success
with a guide polynucleotide made of both RNA and DNA.” Id. at 13–14.
Appellant’s argument is unpersuasive for several reasons. First, it is
well-settled that “[t]he reasonable expectation of success requirement for
obviousness does not necessitate an absolute certainty for success.” Par
Pharm., Inc. v. TWI Pharms., Inc., 773 F.3d 1186, 1198 (Fed. Cir. 2014).
Thus, obviousness is not avoided merely because the cited references do not
provide a working example or other data to demonstrate Joung’s teachings
and rationale for using a guide polynucleotide comprising at least one
deoxyribonucleotide.
Second, Examiner found, and Appellant does not dispute, that Joung
provides examples successfully demonstrating the use of a Cas endonuclease
and guide RNA to induce targeted double-strand breaks in the genome of a
cell. See Ans. 28–29. Appellant has failed to persuasively explain why a
skilled artisan would not reasonably expect that results successfully
demonstrated using a purely RNA guide polynucleotide could also be
obtained when one or more of the nucleotides in that guide RNA was
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replaced with a deoxyribonucleotide, as taught in Joung. See, e.g., Joung
¶ 36 (teaching that the same polynucleotide guide sequences can be used
“wherein the guide RNA includes one or more deoxyribonucleotides (e.g.,
where the defined sequence may also be partially or wholly DNA but with
thymine in place or [sic] uracil)”).8
For these reasons, we determine that Examiner’s rejection is
supported by the preponderance of the evidence and, therefore, affirm the
rejection of claims 17 and 28 as obvious over the combination of Joung and
Zhang, as articulated by Examiner.
CONCLUSION
In summary:
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
16, 18, 25,
26
102 Joung 16, 18, 25,
26

17, 28 103 Joung, Zhang 17, 28
Overall
Outcome
16–18, 25,
26, 28

No time period for taking any subsequent action in connection with this
appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv).

8 Appellant asserts that “[t]he demonstration in the instant application, that a
functional Cas9 complex can be formed with a guide comprising both
RNA and DNA, was surprising and unexpected.” Appeal Br. 9. This
argument is unpersuasive because Appellant has not offered evidence to
show that the results in the Specification would have been surprising or
unexpected to a skilled artisan in light of the teachings in Joung. See FF2–
FF4; see also In re De Blauwe, 736 F.2d 699, 705 (Fed. Cir. 1984)
(explaining that arguments and conclusions unsupported by factual evidence
carry no evidentiary weight).
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AFFIRMED