Ex Parte Blanche et al

Board of Patent Appeals and Interferences

Jun 1, 2011

11582427 (B.P.A.I. Jun. 1, 2011)

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.
11/582,427 10/18/2006 Francis Blanche FR2006/073-A-80911.0036 9628
29693 7590 06/01/2011
WILEY REIN LLP
1776 K. STREET N.W.
WASHINGTON, DC 20006
EXAMINER
KAUSHAL, SUMESH
ART UNIT PAPER NUMBER
1633
MAIL DATE DELIVERY MODE
06/01/2011 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 FRANCIS BLANCHE, MICHEL COUDER,
NICOLAS MAESTRALI, THIERRY GUILLEMIN,
and DAVID GAILLAC
__________

Appeal 2011-002495
Application 11/582,427
Technology Center 1600
__________

Before FRANCISCO C. PRATS, MELANIE L. McCOLLUM, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

FREDMAN, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to methods
of preparing pharmaceutical grade plasmid DNA. The Examiner rejected
the claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We
affirm.

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Statement of the Case
“The invention is based on the discovery of a method for producing
and isolating highly purified plasmid DNA. The plasmid DNA produced and
isolated by the method of the invention contains very low levels of
contaminating chromosomal DNA, RNA, protein, and endotoxins.” (Spec. 6,
ll. 15-17.)
The Claims
Claims 1-18, 24-29, 42, 45, 46, 48, and 49 are on appeal. Claim 1 is
representative, claim 1 reads as follows:
1. A method of preparing a
pharmaceutical grade plasmid DNA composition
comprising:
(a) providing a cell solution, the cells in the
cell solution containing cell membranes, genomic
DNA and plasmid DNA;
(b) contacting the cell solution with a lysis
solution to lyse the cells;
(c) performing an extraction or filtration step
to remove the cell membranes and the genomic
DNA;
(d) performing anion exchange
chromatography;
(e) after step (d), performing triplex affinity
chromatography; and
(f) after step (e) performing either gel
permeation chromatography or hydrophobic
interaction chromatography, wherein the resulting
plasmid DNA composition has less than about
0.0001% host cell genomic DNA contamination.

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The issue
The Examiner rejected claims 1-18, 24-29, 42, 45, 46, 48, and 49
under 35 U.S.C. § 103(a) as obvious over Schluep1 and Nochumson2 (Ans.
3-6).
The Examiner finds that
Schluep et al. describe a method for producing
pharmaceutical grade plasmid DNA from a clarified
Escherichia coli lysate by triplex affinity or triple helix
interaction chromatography, to produce plasmid that showed
no RNA or cell DNA contamination in HPLC analysis. The
authors further state that the support could be used in a
continuous affinity purification process, with a high
potential for scale up[.]

(Ans. 3.) The Examiner finds that “Nochumson et al. state their invention
relies, in part on the use of anion exchange chromatography, preferably with
a Fractogel EMD 650S TMAE(S) resin (column 4, lines 35-38), used in
conjunction with hydrophobic interaction chromatography” (id. at 4).
The Examiner finds that
a person of ordinary skill in the art would have been
motivated to combine their respective teachings to increase
the purity of plasmid DNA yield, as Schluep et al.
specifically teach the combination of the triplex affinity
purification with classical purification steps for downstream
processing and production of pharmaceutical grade plasmid
DNA[.]

1 Thomas Schluep and Charles L. Cooney, Purification of plasmids
by triplex affinity interaction, 26 NUCLEIC ACIDS RESEARCH 4524-
4528 (1998).
2 Nochumson et al., US 7,026,468 B2, issued Apr. 11, 2006.
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(Ans. 5 (citation omitted).)
Appellants contend that “the specific combination was nowhere
present in the cited art, the results achieved are unexpected, and the art of
record shows that the claimed combination of steps solves the problem of
preparing pharmaceutical grade plasmid DNA in a non-obvious way.” (App.
Br. 9.)
Appellants contend that
a) the rejection relies upon an incorrect legal analysis, which
leads to an incomplete analysis of the art of record; b) the
rejection improperly assumes a reasonable expectation for
success when numerous possible combinations have not
even been analyzed; c) the rejection relies on improper legal
analysis to find a motivation to arrive at the claimed
invention; d) the rejection fails to accord proper evidentiary
weight to two documents cited as teaching away; and e) the
rejection inappropriately dismisses Applicants significant
evidence of unexpected results.

(Id.)
Appellants contend that the “results in Figure 3 show an exponential
decrease in each of the impurities tested. Levels of gDNA contaminant are
0.00008% for the claimed invention compared to 0.2 to 0.6% in other
methods, and the levels of RNA contamination are 0.00002% in the claimed
invention compared to 0.01%” (App. Br. 22).
The issues with respect to this rejection are:
(i) Does the evidence of record support the Examiner’s conclusion
that Schluep and Nochumson render obvious the method of claim 1?
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(ii) If so, have Appellants presented evidence of secondary
considerations, that when weighed with the evidence of obviousness, are
sufficient to support a conclusion of non-obviousness?
Findings of Fact
1. Schluep teaches that “[p]roduction of pharmaceutical grade
plasmid DNA is an important issue in gene therapy” (Schluep, abstract).
2. Schluep teaches a first step of providing a cell solution,
specifically “Escherichia coli DH5 cultures transformed with pTS2 were
grown in 100 ml LB (100 µg/ml ampicillin) overnight at 37°C in a 500 ml
shaker flask. Cells were harvested by centrifugation at 6000 g and 4°C for
15 min and resuspended in 4 ml 50 mM Tris, pH 8, 1 mM EDTA” (Schluep
4525, col. 2).
3. Schluep teaches a second step of lysing the cells, where cells
“were lysed by addition of 4 ml 200 mM NaOH, 1% SDS and incubation for
5 min at room temperature. Then 4 ml chilled 3 M potassium acetate, pH
5.5, was added” (Schluep 4525, col. 2).
4. Schluep teaches a third step of performing an extraction to
remove genomic DNA, where the “lysate was centrifuged for 30 min at 20
000 g and 4°C. The supernatant was recentrifuged for 10 min under the same
conditions to give 12 ml clarified lysate” (Schluep 4525, col. 2).
5. Schluep teaches a fourth step of purification with triplex
affinity beads where the “plasmid was then allowed to bind to the affinity
beads for 2 h at room temperature with moderate shaking on a spinning
wheel” (Schluep 4525, col. 2).
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6. Schluep teaches that “[f]uture work will focus on integration of
the triplex affinity principle into a continuous affinity purification process
which can be easily scaled up. Combination of such a process with classical
purification steps will hopefully result in a large scale production process for
pharmaceutical grade plasmid DNA” (Schluep 4528, col. 2).
7. Schluep teaches that in “gel electrophoresis, triplex affinity-
purified plasmid appeared predominantly as supercoiled plasmid DNA and
no RNA or cell DNA contamination was detectable” (Schluep 4527, col. 2).
8. Nochumson teaches “a scalable alkaline lysis process, including
procedures and devices for the isolation of large quantities (grams and
kilograms) of plasmid DNA from recombinant E. coli cells.” (Nochumson,
col. 3, ll. 64-67).
9. Nochumson teaches alkaline lysis followed by “the use of anion
exchange chromatography, preferably with a Fractogel EMD 650S
TMAE(S) resin with a 20-40 micron” (Nochumson, col. 4, ll. 23-37).
10. Nochumson teaches that
the use of hydrophobic interaction chromatography, which is
used to separate plasmid DNA from E. coli chromosomal
DNA and RNA and may also be used to separate open
circular plasmid DNA from supercoiled DNA. Overall, HIC
is a powerful technique for plasmid DNA purification. This
disclosure reveals the surprising and unexpected value that
hydrophobic interaction chromatography (HIC) has,
especially when used in conjunction with anion-exchange
chromatography, for large-scale plasmid DNA purification.

(Nochumson, col. 4, ll. 56-65.)
11. Nochumson teaches that “[p]articularly surprising is the ability
of HIC to resolve the supercoil form of a plasmid from the relaxed open
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circle form. Supercoiled DNA may be easier to formulate and with certain
formulations supercoiled plasmid may have higher expression levels in
vivo” (Nochumson, col. 4, l. 65 to col. 5, l. 3).
12. Nochumson teaches that “[a]nalysis of the final product, 1-
antitrypsin plasmid, indicated the preparation 95% plasmid DNA”
(Nochumson, col. 15, ll. 5-6).
Principles of Law
“The combination of familiar elements according to known methods
is likely to be obvious when it does no more than yield predictable results.”
KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007).
Analysis
Schluep teaches a method of preparing pharmaceutical grade plasmid
DNA (FF 1) by providing a cell solution, lysing the cell solution, and
extracting the solution to remove membranes and genomic DNA (FF 2-4).
Schluep then teaches performing triplex affinity chromatography (FF 5).
Schluep teaches that “[f]uture work will focus on integration of the triplex
affinity principle into a continuous affinity purification process which can be
easily scaled up. Combination of such a process with classical purification
steps will hopefully result in a large scale production process for
pharmaceutical grade plasmid DNA” (Schluep 4528, col. 2; FF 6).
Nochumson teaches alkaline lysis process for isolation of large
amounts of plasmid DNA (FF 8) employing classical purification steps such
as anion exchange chromatography (FF 9) and hydrophobic interaction
chromatography (FF 10).
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Applying the KSR standard of obviousness to the findings of fact, we
conclude that an ordinary artisan would have reasonably found it obvious to
incorporate steps of anion exchange chromatography and hydrophobic
interaction chromatography, since Schluep suggests that such a combination
of steps will result in large scale production of pharmaceutical grade DNA
(FF 6). Such a combination is merely a “predictable use of prior art
elements according to their established functions.” KSR, 550 U.S. at 417.
Appellants “submit that when the actual facts of what one of skill in
the art would have considered an equivalent purification step or which
chromatography steps would likely to lead to success, there is no prima facie
case established here” (App. Br. 13).
We are not persuaded. We agree with the Examiner that it would
have been predictable that incorporation of multiple different purification
methods would have resulted in superior purification than the application of
a single purification method alone. This is the essence of the teaching in
KSR that the “combination of familiar elements according to known methods
is likely to be obvious when it does no more than yield predictable results.”
KSR, 550 U.S. at 416.
Appellants contend that it “is unclear why the Examiner insists that
the future work and ‘hope’ presented from the actual contents of Schluep
would be translated into a reasonable expectation of success by one of
ordinary skill in the art” (App. Br. 15). Appellants contend that “it is
practically inconceivable that even a large group of researchers would ever
endeavor to try and compare the results from even 100 different
chromatographic step combinations for purifying plasmid DNA” (id. at 16).
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We are not persuaded. Kubin stated that “[r]esponding to concerns
about uncertainty in the prior art influencing the purported success of the
claimed combination, this court [in O’Farrell] stated: ‘[o]bviousness does
not require absolute predictability of success … all that is required is a
reasonable expectation of success.”’ In re Kubin, 561 F.3d 1351, 1360 (Fed.
Cir. 2009) (citing In re O’Farrell, 853 F.2d 894, 903-904 (Fed. Cir. 1988)).
Here, there is virtually an absolute expectation of success in purifying
DNA by combining the methods of Schluep and Nochumson. While
Appellants note a “goal of using plasmid DNA in gene therapy” (App. Br.
14), this goal is not reflected in claim 1. Claim 1 simply requires
“pharmaceutical grade” DNA, which the Specification defines as “a DNA
preparation that contains no more than about 5% . . . of cellular components”
(Spec. 10, ll. 23-24). Both Schluep and Nochumson achieve this quality.
Schluep teaches that in “gel electrophoresis, triplex affinity-purified plasmid
appeared predominantly as supercoiled plasmid DNA and no RNA or cell
DNA contamination was detectable” (Schluep 4527, col. 2; FF 7).
Nochumson teaches that “[a]nalysis of the final product, 1-antitrypsin
plasmid, indicated the preparation 95% plasmid DNA” (Nochumson, col. 15,
ll. 5-6; FF 12).
We are also not persuaded by the asserted “large number of
combinations.” That the prior art “discloses a multitude of effective
combinations does not render any particular formulation less obvious. This
is especially true because the claimed composition is used for the identical
purpose taught by the prior art.” Merck & Co. v. Biocraft Labs., Inc., 874
F.2d 804, 807 (Fed. Cir. 1989). In the instant case, Appellants have
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provided no evidence that the order of performance of the purification steps
is of any consequence, so the ordinary artisan would reasonably expect that
performance of the three different purification columns in any order would
result in improved purification relative to performance of each column
alone.
Appellants contend that “[c]ombining the one chromatography step
discussed in Schluep with the two steps from Nochumson has nothing to do
with equivalency” (App. Br. 17).
While we appreciate Appellants’ point, the issue is whether it would
have been obvious to an ordinary artisan of ordinary creativity to improve
purification methods by using multiple different types of purification
columns, a concept directly suggested by Schleup (FF 6). Schluep’s direct
suggestion to combine triple affinity chromatography with other purification
methods strongly supports the Examiner’s prima facie case of obviousness.
Appellants contend that “[e]ach of Ferreira and Stadler teach away
from a combination of steps from Schluep and Nochumson as presented
here” (App. Br. 17). Appellants contend that Ferreira3 teaches that “triple-
helix chromatography is described as being ridden with technical limitations,
especially since it is inefficient for separating plasmid DNA from
endotoxins” (id. at 18). Appellants contend that Stadler4 teaches that “triple-

3 Ferreira et al., Downstream processing of plasmid DNA for gene
therapy and DNA vaccine applications, 18 TIBTECH 380-388
(2000).
4 Stadler et al., Plasmid DNA purification, 6 J. GENE MEDICINE
S54-S66 (2004).
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helix chromatography has serious limitations, which makes it undesirable for
use in pharmaceutical-grade plasmid DNA preparation” (id. at 19).
We are not persuaded. While Appellants correctly note that Ferreira
teaches that triple helix chromatography did not reduce endotoxin levels,
Ferreira also specifically teaches that “[u]p to 62% recovery yields were
achieved with a simultaneous reduction of the RNA and gDNA content to
undetectable levels” (Ferreira 386, col. 1). The ordinary artisan of ordinary
creativity would have recognized that while triple helix chromatography
alone was insufficient to purify DNA for gene therapy, it would reliably
remove significant amounts of contaminating RNA and gDNA, which
provide a reason to use the method.
We also disagree with Appellants dismissal of Ferreira’s teaching that
the reason triple helix affinity chromatography is not used is that it is “still
economically unfeasible” (Ferreira 386, col. 2). Appellants’ claims do not
require “economic feasibility,” nor does even claim 18 require anything
other than “large-scale manufacture.” No specific amounts are required by
any claim, and “large-scale manufacture” is not defined by the Specification.
Similarly, we are not persuaded that Stadler teaches away from the
use of triple helix chromatography. Stadler states that by “choosing the
proper pH and salt conditions for binding, washing and elution, highly pure
supercoiled pDNA can be obtained in a single step” (Stadler s60, col. 1).
Stadler’s has the same concern as Ferreira, which is that the “approach is
still not available as a product for process scale” (Stadler s60, col. 1).
Stadler does not teach away from the use of the method, but recognizes that
triple helix affinity chromatography operates highly effectively.
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Appellants contend that the “results in Figure 3 show an exponential
decrease in each of the impurities tested. Levels of gDNA contaminant are
0.00008% for the claimed invention compared to 0.2 to 0.6% in other
methods, and the levels of RNA contamination are 0.00002% in the claimed
invention compared to 0.01%” (App. Br. 22). Appellants contend that there
“is nothing in any of the art of record in this appeal that even suggests such
levels can be achieved or that a reduction to these levels is possible when a
third chromatography step is added to a two-step process” (id.).
We are not persuaded. Schluep teaches that in “gel electrophoresis,
triplex affinity-purified plasmid appeared predominantly as supercoiled
plasmid DNA and no RNA or cell DNA contamination was detectable”
(Schluep 4527, col. 2; FF 7). Thus, Schluep would have expected
undetectable levels of RNA and genomic DNA (see also Ferreira 386, col. 1,
describing “reduction of the RNA and gDNA content to undetectable
levels”).
More significantly, given the significant reduction in contaminating
nucleic acid species expected, we also conclude that even if we treated the
results in Figure 3 as slightly “unexpected,” that showing is insufficient to
overcome the strong showing of obviousness in this case, where Schluep and
Nochumson provide reasoned guidance suggesting the claimed method (FF
1-12). See Pfizer, Inc. v. Apotex, Inc., 480 F.3d 1348, 1372 (Fed. Cir. 2007)
(“[W]e hold that even if Pfizer showed that amlodipine besylate exhibits
unexpectedly superior results, this secondary consideration does not
overcome the strong showing of obviousness in this case. Although
secondary considerations must be taken into account, they do not necessarily
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control the obviousness conclusion. Newell Cos., Inc. v. Kenney Mfg. Co.,
864 F.2d 757, 768 (Fed.Cir.1988)”).
Appellants contend that “claims 5-17 do not stand together with claim
1 as the reduction in genomic DNA content recited in claim 1 is further
limited by the reduction in additional contaminants in claims 5-17” (App.
Br. 22). Appellants also contend that claim 18 requires a method “amenable
to scale-up” (id. at 23). Appellants also contend that claims 24-26 stand
apart.
We have separately considered the limitations of claims 5-17 and 24-
26, but note, as discussed above, that Schluep teaches that only undetectable
levels of RNA and genomic DNA as contaminants remained (FF 7), and
Appellants have provided no evidence that the claimed levels would have
been unobvious over this teaching. Nochumson teaches that less than 0.2
EU/mg of plasmid DNA for endotoxins was present in his purified plasmid
(see Nochumson, col. 15, l. 7) which reasonably renders obvious the “about
0.1 EU/mg endotoxin” claims, particularly in light of the further purification
suggested by Schluep by combining purification methods. See In re
Peterson, 315 F.3d 1325, 1329 (Fed. Cir. 2003) (“We have also held that a
prima facie case of obviousness exists when the claimed range and the prior
art range do not overlap but are close enough such that one skilled in the art
would have expected them to have the same properties”).
As we already discussed, no parameters are required for “large-scale
manufacture” in claims 18 and 24.
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Conclusions of Law
(i) The evidence of record supports the Examiner’s conclusion that
Schluep and Nochumson render obvious the method of claim 1.
(ii) Appellants have not presented evidence of secondary
considerations, that when weighed with the evidence of obviousness, are
sufficient to support a conclusion of non-obviousness.
SUMMARY
In summary, we affirm the rejection of claims 1-18, 24-29, 42, 45, 46,
48, and 49 under 35 U.S.C. § 103(a) as obvious over Schluep and
Nochumson.

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

JNF
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