Ex Parte Son et al

Board of Patent Appeals and Interferences

Jun 29, 2010

10383846 (B.P.A.I. Jun. 29, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
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APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
10/383,846 03/07/2003 Ho-Sun Son 006556.P001 1951
7590 06/30/2010
Stephen M. De Klerk
BLAKELY, SOKOLOFF, TAYLOR & ZAFMAN LLP
Seventh Floor
12400 Wilshire Boulevard
Los Angeles, CA 90025
EXAMINER
HILL, KEVIN KAI
ART UNIT PAPER NUMBER
1633
MAIL DATE DELIVERY MODE
06/30/2010 PAPER
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.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte HO-SUN SON, NEON-C JUNG, EUN-WOOK CHOI,
DONG SEUNG SEEN, KYUNG-JIN KIM, and SUNG-EUN CHO
__________

Appeal 2009-014936
Application 10/383,846
Technology Center 1600
__________

Decided: June 30, 2010
__________

Before ERIC GRIMES, TONI R. SCHEINER, and JEFFREY N.
FREDMAN, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
for preparing a viral vector. The Examiner has rejected the claims as
obvious. We have jurisdiction under 35 U.S.C. § 6(b). We affirm.

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Application 10/383,846

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STATEMENT OF THE CASE
Claims 1, 3-6, 8, 10, 12, and 13 are on appeal. Claim 1 is
representative and reads as follows:
1. A method for preparing a linear recombinant viral vector, wherein
a desired DNA is inserted into a viral genomic DNA by in vitro site-specific
recombination, comprising:
i) cleaving the viral genomic DNA into two cleaved DNA segments,
wherein each of the two cleaved DNA segments has a site-specific
recombinant site at one end of the segment, and wherein each of the two
cleaved DNA segments do not bind to each other directly;
ii) providing a carrier vector comprising at least one desired DNA
flanked with a site-specific recombination site at each end, and wherein the
site-specific recombination sites of the desired DNA react with
corresponding site specific recombinant sites of each of the two cleaved
DNA segments of i); and
iii) reacting the DNA segments of i) and the carrier vectors of ii) in
vitro to produce a recombinant virus including the desired gene.

Issue
The Examiner has rejected claims 1, 3-4, 6, 8, 10 and 13 under 35
U.S.C. § 103(a) as being obvious in view of Hardy1 and Cheo. 2 The
Examiner has also rejected claims 5 and 12 under 35 U.S.C. § 103(a) as
being obvious in view of Hardy, Cheo and Chartier. 3 Since the same issue
is dispositive to both rejections, we will consider them together. The claims

1 Hardy et al., Construction of Adenovirus Vectors through Cre-lox
Recombination, 71 JOURNAL OF VIROLOGY NO. 3, 1842-1849 (1997)
2 Cheo et al., US 2002/0007051A1, Jan. 17, 2002
3 Chartier et al., Efficient Generation of Recombinant Adenovirus Vectors by
Homologous Recombination in Escherichia coli, 70 JOURNAL OF VIROLOGY
NO. 7, 4805-4810 (1996)
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have not been argued separately and therefore stand or fall together. 37
C.F.R. § 41.37(c)(1)(vii).
The Examiner finds that Hardy discloses an in vivo site-specific
recombination method to construct a recombinant adenoviral vector having
an inserted DNA, using cleaved portions of the viral genome (Ans. 4). The
Examiner finds that Cheo discloses joining two or more segments of nucleic
acid by site-specific recombination in vivo or in vitro (id.). The Examiner
also finds that Cheo discloses that the “starting molecules can be any nucleic
acid molecule derived from any source” and that “when multiple
recombination sites are located on a nucleic acid molecule of interest, such
sites do not substantially recombine or do not recombine with each other on
that molecule” (id. at 4-5). The Examiner finds that Cheo discloses “the use
of viral and bacteriophage vectors…, e.g., adenoviral vectors” (id.).
The Examiner concludes that it “would have been obvious to one of
ordinary skill in the art to modify the recombination method of Hardy et al
with the recombination method of Cheo et al … because Cheo et al
demonstrate the broad applicability of their inventive method to use multiple
site-specific recombinases to join multiple nucleic acids to obtain an
artisan’s desired final nucleic acid product, such as a recombinant viral
vector” (id. at 6). The Examiner reasons that it would have been obvious to
practice the method in vitro “because the reaction conditions may be freely
adjusted to optimize enzyme activities, DNA molecules that are
incompatible with the desired biological host cell may be used …, and
recombination proteins from diverse sources can be employed … to
optimize the synthesis of the desired final nucleic acid product” (id. at 6-7).
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Appellants contend that one of skill in the art would not have had a
reasonable expectation of successfully arriving at the claimed method
because Hardy discloses that chromosomes with two loxP sites are unstable
(Reply Br. 2). Appellants also contend that they have shown unexpected
results that overcome any prima facie case of obviousness (Appeal Br. 7;
Reply Br. 2-3).
The issues presented are: Does the evidence of record support the
Examiner’s conclusion that one of ordinary skill in the art would have had a
reasonable expectation of success in combining the teachings of Hardy and
Cheo? and, if so,
Have Appellants shown evidence of unexpected results for the
claimed method that outweighs the evidence supporting the prima facie case
of obviousness?
Findings of Fact
1. Cheo discloses “methods for joining or combining two or more …
segments or molecules of nucleic acid by the recombination reaction
between recombination sites, at least one of which is present on each
molecule or segment” (Cheo 4, ¶ 0043).
2. Cheo discloses that the recombination reactions can be conducted
in vivo or in vitro (id.).
3. Cheo discloses that “[i]n a preferred aspect, the nucleic acid
molecules or segments for use in the invention are linear molecules having
at least one recombination site at or near at least one termini of the molecule
and preferably comprise at least one recombination site at or near both
termini of the molecule” (id. at 4, ¶ 0045).
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4. Cheo discloses that “[i]n another preferred aspect, when multiple
recombination sites are located on a nucleic acid molecule of interest, such
sites do not substantially recombine or do not recombine with each other on
that molecule. In this embodiment, the corresponding binding partner
recombination sites preferably are located on one or more other nucleic acid
molecules to be linked or joined” (id.).
5. Cheo discloses that the recombination proteins can be “selected
from the group consisting of Cre, Int, IHF, Xis, Flp, Fis, Hin, Gin, Cin, Tn3
resolvase, TndX, XerC, XerD, and ΦC31” (id. at 6, ¶ 0055).
6. Cheo discloses that the recombination sites can be “selected from
the group consisting of lox sites; psi sites; dif sites; cer sites; ftt sites; att
sites; and mutants, variants, and derivatives of these recombination sites
which retain the ability to undergo recombination” (id.).
7. Cheo discloses that the starting molecules may be derived from
viral vectors (id. at 5, ¶ 0046).
8. Cheo discloses that the starting molecules may be adenovirus
vectors (id. at 47, ¶ 0418).
9. Cheo discloses that viral vectors that carry target DNA may be
constructed (id. at 47, ¶ 0417).
10. Hardy discloses using in vivo site-specific recombination to
construct adenovirus vectors carrying an exogenous expression cassette
(Hardy, abstract, Fig. 3).
11. Hardy discloses an adenovirus vector having two loxP sites that,
upon recombination with each other, generate an adenovirus vector having
one loxP site and delete the viral packaging sequence (Hardy, abstract, Fig.
3).
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12. Hardy discloses that the packaging sequence-deleted adenovirus
vector is recombined with target DNA via the one loxP site (Hardy, abstract,
Fig. 3).
13. Hardy discloses that “[c]hromosomes with two loxP sites are
unstable, as they can rapidly recombine back to the two starting molecules
by intramolecular recombination. Recombinants with single loxP sites are
more stable, since their reversion occurs by much slower intermolecular
recombination” (id. at 1848).
14. The Specification discloses an embodiment in which “a vector
comprising viral genomic DNAs is cleaved to two or more segments before
being applied to in vitro site-specific recombination, in which both of the
segments are essential for viral replication. A DNA fragment including
desired genomic materials is inserted between the two genomic DNA
segments specifically.” (Spec. 6, ¶ 18.4) The Specification discloses that
“since un-bound viral genomic DNA segments cannot be expressed by
themselves, only the viruses having desired DNA fragment shall be
expressed. Therefore, one can obtain desired recombinant viruses from host
cells directly without further procedures.” (Id.)
Principles of Law
“Although it is well settled that comparative test data showing an
unexpected result will rebut a prima facie case of obviousness, the
comparative testing must be between the claimed invention and the closest
prior art.” In re Fenn, 639 F.2d 762, 765 (CCPA 1981) (emphasis added).

4 Citations are to the substitute Specification filed May 21, 2007.
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Analysis
Claim 1 is directed to an in vitro method of making a linear
recombinant viral vector, by cleaving a viral genomic DNA into two
segments, each with a site-specific recombinant site at one end, and reacting
the fragments with a vector comprising a desired DNA flanked with site-
specific recombination sites that can react with corresponding sites of the
viral genomic DNA segments, to produce a recombinant virus including the
desired gene.
Cheo discloses an in vitro method for joining two, three, or more
nucleic acid segments by site-specific recombination, with at least one site-
specific recombination site on each molecule. Cheo discloses a preferred
embodiment in which the nucleic acid segments are linear molecules having
recombination sites at or near at least one end (FF 3). Cheo discloses that a
variety of recombination sites and recombination proteins can be used in its
method (FFs 5, 6) and that corresponding binding partner recombination
sites are located on the molecules to be joined (FF 4). Cheo also discloses
that the method may be used with adenovirus vectors (FF 8). Hardy
discloses the use of site-specific recombination in vivo to construct an
adenovirus vector that carries an expression cassette.
In view of these disclosures, it would have been obvious to one of
skill in the art to modify Hardy’s method of making a recombinant, linear
adenovirus vector using site-specific recombination by reacting two
adenoviral DNA segments, each with a site-specific recombination site at
one end as taught by Cheo (FF 3), with a carrier vector comprising a desired
DNA flanked by the corresponding site-specific recombination sites, to
produce a recombinant adenovirus including the desired gene. A person of
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ordinary skill in the art would have recognized that modifying Hardy’s
method as suggested by Cheo would allow greater flexibility in inserting
exogenous sequence(s) into recombinant adenoviral vectors, because Cheo
discloses that its method can be used to combine any number of DNAs using
a variety of recombination systems.
Appellants contend that the Examiner has not established a reasonable
expectation of success in combining the cited references because “if
recombinant sites were added to the end of each fragment [of Hardy] and
reacted with recombinant sites at each end of a third DNA fragment as
proposed by the Examiner, the resulting virus would have two loxP sites”
(Appeal Br. 7) and Hardy discloses that chromosomes with two loxP sites
are unstable (Reply Br. 2)
This argument is not persuasive. Cheo discloses that when multiple
recombination sites are located on the same nucleic acid molecule, they are
preferably chosen so that they do not recombine with each other but with a
corresponding site on a different nucleic acid molecule (FF 4); i.e, the same
recombination site is not used twice in the same nucleic acid molecule.
Thus, one of ordinary skill in the art would have considered it obvious to
construct the desired nucleic acid product (i.e. a viral vector with a target
DNA insert) using different recombination sites rather than multiple copies
of the same recombination site, in order to avoid the problem disclosed by
Hardy.
Appellants also contend that they have shown unexpected results that
overcome any prima facie case of obviousness (Appeal Br. 7; Reply Br. 2-
3). Appellants contend that the claimed method provides unexpected
advantages in that an “in vitro mixture of the invention can be applied to
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host cells directly to produce recombinant viruses without a further step of
selection” (Appeal Br. 7).
This argument is not persuasive. The Specification discloses an
embodiment in which both of the viral genomic DNA fragments are
essential for viral replication (FF 14). The Specification discloses that in
this embodiment, “only the viruses having desired DNA fragment shall be
expressed. Therefore, one can obtain desired recombinant viruses from host
cells directly without further procedures.” (FF 14.) However, the claims are
not limited to a method in which both viral genomic DNA fragments are
essential for viral replication. Appellants have not shown unexpected results
for the claimed method because the claims do not include the limitation that
results in the advantage that Appellants rely on.
With respect to the rejection of claims 5 and 12, Appellants argue
only that Chartier does not cure the deficiencies of Hardy and Cheo in
suggesting the invention of claim 1 (Appeal Br. 8). This argument is not
persuasive for the reasons discussed above.
Conclusion of Law
The evidence of record supports the Examiner’s conclusion that one
of ordinary skill in the art would have had a reasonable expectation of
success in combining the teachings of Hardy and Cheo. Appellants have not
shown evidence of unexpected results for the claimed method that outweighs
the evidence supporting the prima facie case of obviousness.
SUMMARY
We affirm the rejection of claims 1, 3-6, 8, 10, 12, and 13 under 35
U.S.C. § 103(a).
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Application 10/383,846

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

AFFIRMED

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STEPHEN M. DE KLERK
BLAKELY, SOKOLOFF, TAYLOR & ZAFMAN LLP
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12400 WILSHIRE BOULEVARD
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