Ex Parte Eshoo et al

Patent Trials and Appeals Board

Jan 29, 2019

13233913 - (D) (P.T.A.B. Jan. 29, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/233,913 09/15/2011
58057 7590 01/31/2019
Casimir Jones, S.C.
2275 Deming Way, Suite 310
Madison, WI 53562
FIRST NAMED INVENTOR
Mark W. Eshoo
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
10424US01/31464US20RD 8418
EXAMINER
KOSTURKO, GEORGE W
ART UNIT PAPER NUMBER
1628
NOTIFICATION DATE DELIVERY MODE
01/31/2019 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):
docketing@casimirjones.com
pto .correspondence@casimirjones.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte MARK W. ESHOO and JOHN PICURI 1
Appeal2018-000127
Application 13/233,913
Technology Center 1600
Before ERIC B. GRIMES, RICHARD M. LEBOVITZ, and
TA WEN CHANG, Administrative Patent Judges.
LEBOVITZ, Administrative Patent Judge.
DECISION ON APPEAL
This appeal involves claims to a method for labeling a nucleic acid
with an ozone labile dye and a buffer comprising a thiourea. The Examiner
rejected the claims under 35 U.S.C § 103 as obvious. Appellants appeal
under 35 U.S.C. § 134(a) the Examiner's determination that the claims are
unpatentable. We have jurisdiction under 35 U.S.C. § 6(b ). The rejection is
reversed.
1 According to Appellants, the real party in interest is Ibis Biosciences, Inc.
Appeal Br. 3.
Appeal2018-000127
Application 13/233,913
STATEMENT OF THE CASE
The claims stand finally rejected by the Examiner as follows:
Claim 15, 17, 18, 31-34, 36, 38--40, and 42 under pre-AIA 35 U.S.C.
§ 103(a) as obvious in view of William Branham et al. (Elimination of
Laboratory Ozone Leads to a Dramatic Improvement in the Reproducibility
of Microarray Gene Expression Measurements, BMC Biotechnology,
7(8):1-8 (2007)) ("Branham"), Lofquist et al. (US 3,822,996, issued July 9,
1974) ("Lofquist"), and McConnell (US 5,180,500, issued Jan. 19, 1993).
Ans. 2; Pre-Appeal Conference Decision (noting that the Examiner
inadvertently omitted claims 18 and 40 from the rejection).
Claims 29 and 41 under pre-AIA 35 U.S.C. § 103(a) as obvious in
view of Branham, Lofquist, McConnell, and Somdeb Mitra et al. (High-
Throughput Single-Nucleotide Structural Mapping by Capillary Automated
Footprinting Analysis, Nucleic Acids Research 36(11):1-10 (2008))
("Mitra"). Ans. 5.
Claims 37 and 43 under pre-AIA 35 U.S.C. § 103(a) as obvious in
view of Branham, Lofquist, McConnell, and LV Wei et al. (Single Molecule
Fluorescence Fluctuations of the Cyanine Dyes Linked Covalently to DNA,
Science in China Series B: Chemistry, 52(8): 1148-53 (2009) ("Wei"). Ans.
7.
Independent claim 15 and dependent claim 1 7 are representative of
the appealed claims and read as follows:
15. A method for labeling a nucleic acid comprising placing an
ozone-labile fluorescent dye in a buffer comprising one or more
thioureas, and then contacting said fluorescent dye in said
buffer comprising said one or more thioureas with said nucleic
acid.
2
Appeal2018-000127
Application 13/233,913
17. The method of claim 15, wherein said fluorescent dye
comprises Cy5.
REJECTIONS BASED ON BRANHAM, LOFQUIST, & McCONNELL
All the rejections are based on the combination of Branham, Lofquist,
and McConnell. The Examiner found that Branham teaches that "it is
critical to remove ozone when performing DNA microarrays comprising the
ozone-labile fluorescent dye Cy5 dye and cDNA" to improve
"reproducibility of the elected ozone-labile fluorescent dye Cy5 as well as its
fluorescent intensity." Ans. 2-3. The Examiner acknowledged that
Branham does not teach the addition of thiourea to labeling buffer as
required by the claims, but found that Lofquist teaches "that it is
advantageous to add thiourea to ozone-sensitive dyes that comprise a series
of carbon-carbon double bonds" and that it was art-recognized "that ozone
attacks the double bond chemical moiety ( ozonolysis) and quenches the
intensity of the dye by disrupting the conjugated framework." Ans. 3--4.
The Examiner further cited McConnell as teaching that "thiourea behaves as
a scavenger in the presence of ozone," in which "it is oxidized by ozone
from thiourea to urea while ozone is reduced to molecular oxygen, thus
destroying its capacity to react on the double-bonds of the fluorescent dye."
Ans. 4. Based on these findings, the Examiner found one of ordinary skill in
the art would have had reason to utilize thiourea in a labeling buff er as
claimed when using an ozone-labile Cy5 dye as claimed. Id.
Appellants contend that the Examiner provided "no evidence of fact
or law in support of its speculation that the Office's combination of
Branham (i.e., nucleic acid labeling) with Lofquist (i.e., carpet fading) and
McConnell (i.e., scale removal from the interior surfaces of industrial
3
Appeal2018-000127
Application 13/233,913
equipment) was within the level of ordinary skill in the art at the time the
claimed invention was made." Appeal Br. 16. Appellants also argue that
one of ordinary skill in the art would not have had reason to combine
Branham's method of protecting Cy5 dye from ozone using a filter system
of Lofquist which describes different dyes and substrates for the different
purpose of improving "dyefastness" in carpets. Id. at 19. Appellants also
argue that McConnell utilizes a pH of 12 which would hydrolyze DNA and
thus one of ordinary skill in the art would not have turned to it to combine
with Branham. Id. at 19--20.
The Examiner responded to Appellants' arguments by stating that
both Lofquist and McConnell are reasonably pertinent to Branham and the
subject matter of the claims because Lofquist addresses "the problem of
combating ozone degradation on ozone-susceptible fluorescent dyes that
comprise a series of carbon-carbon double bonds with the addition of
thiourea to the fluorescent dye composition" and McConnell explains the
mechanism. Ans. 20-21.
We reverse the rejection.
It is well-established that there are two criteria to be applied when
determining whether a reference is analogous prior art: ( 1) whether the
reference is from the "same field of endeavor" as the claimed invention, and
(2) if the reference is not within the same field of endeavor, "whether the
reference still is reasonably pertinent to the particular problem with which
the inventor is involved." In re Clay, 966 F.2d 656, 658-59 (Fed. Cir.
1992). In this case, the Examiner does not find that Lofquist and McConnell
are in the same field of endeavor as the claimed subject matter, but finds that
4
Appeal2018-000127
Application 13/233,913
they are reasonably pertinent to the problem addressed by the claims. We do
not agree that the evidence supports this conclusion.
Branham teaches that "Environmental ozone can rapidly degrade
cyanine 5 (Cy5), a fluorescent dye commonly used in microarray gene
expression studies." Branham 1 (Abstract). Branham discloses that
microarrays utilize "cyanine dye-labeled cDNAs or cRNAs to DNA probes
covalently attached to microscope slides." Id. at 2. Branham teaches that
"each dye must remain intact from the completion of the hybridization
process through the duration of the scanning process." Id. Branham teaches
that the ozone oxidation "occurs primarily after the hybridization washing
procedures have been completed and the microarray becomes exposed to air
containing environmental ozone." Id. Branham solved the problem of
ozone oxidation by using a carbon filter in its laboratory handling system.
Id. at 1 (Abstract). The problem identified by Branham is therefore
preventing ozone oxidation of Cy5 dye-labeled nucleic acids hybridized to
DNA on microscope slides.
Lofquist is directed to solving a different problem.
Lofquist describes the object of its invention as "to reduce or prevent
the fading of dyed nylon fabrics, such as nylon carpets, caused by ozone."
Lofquist 1 :20-22.
Lofquist states that "Dyes have a multiplicity of double bonds, and
perhaps for this reason are very sensitive to ozone." Id. at 1 :37-38.
Lofquist discloses several different dyes which are used in carpets and
fabrics, none of which are Cy5 as disclosed in Branham. Id. at 1 :40-65; see
also Ans. 3 (structure of Cy5).
5
Appeal2018-000127
Application 13/233,913
Lofquist also teaches that "High humidity is necessary to cause
noticeable ozone fading. Apparently moisture permits the dye to have
sufficient mobility to diffuse to the surface of the yam where the destruction
of the dye occurs." Id. at 1:66-69.
Lofquist discloses that "[a] method and composition have been found
for improving the fastness of dyes when exposed to ozone in
polycarbonamide fibers. The method consists of exposing the fibers to ozone
in the presence of a water-soluble thiourea coated on the fiber." Id. at 2:7-
11. The method of Lofquist involves coating the fiber with the thiourea
compound. Id. at 4:27-37 (claim 1).
Thus, the problem identified and solved by Lofquist is of reducing or
preventing the fading of dyed nylon fabrics cause by ozone (Lofquist
1: 19-21 ). One reason for the problem, as explained by Lofquist, is because
in high humidity the dye diffuses "to the surface of the yam where the
destruction of the dye occurs." Id. at 1 :66-69. Lofquist solved the problem
by coating the fabric fibers with thiourea. Id. at 2:7-11; 4:27-37 ( claim 1 ).
Lofquist is not merely protecting a dye with double-bonds from oxidation,
but is protecting specific dyes utilized to dye fabric from ozone destruction
in high humidity in which noticeable ozone fading occurs. The Examiner
did not establish that a solution to this different problem, using different
dyes than those utilized by Branham, would have been considered by one of
ordinary skill in the art to be reasonably pertinent to labeling nucleic acids as
claimed and hybridizing such labeled nucleic acids to DNA arrays on
microscope slides as described by Branham. The Examiner focused on the
mechanism for ozone oxidation as described in McConnell, but knowing the
6
Appeal2018-000127
Application 13/233,913
mechanism does not provide a solution to it or a reason to apply Lofquist's
solution to a very different problem to Branham and the claims.
For the foregoing reason, the obviousness rejection of claim 15 is
reversed. Independent claim 38, and dependent claims 17, 18, 29, 31-34,
and 36-43, also require thiourea in a labeling buffer and the rejection of
these claims is reversed for the same reason.
REVERSED
7