Ex Parte Knapp et al

Patent Trial and Appeal Board

Jan 22, 2019

14252755 (P.T.A.B. Jan. 22, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
14/252,755 04/14/2014
29540 7590
DAY PITNEY LLP
One Canterbury Green
201 Broad Street
Stamford, CT 06901
01/24/2019
FIRST NAMED INVENTOR
Michael R. Knapp
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.
170865.005990 1010
EXAMINER
PRIEST, AARON A
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
01/24/2019 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):
Patents@daypitney.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte MICHAEL R. KNAPP, JILL M. BAKER, ANDREA W. CHOW,
ANNE R. KOPF-SILL, and MICHAEL SP AID
Appeal 2017-011016
Application 14/252,755 1
Technology Center 1600
Before JEFFREY N. FREDMAN, TIMOTHY G. MAJORS, and
RACHEL H. TOWNSEND, Administrative Patent Judges.
TOWNSEND, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to
methods of detecting a nucleic acid of interest, which have been rejected as
obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We reverse.
STATEMENT OF THE CASE
"One of the most powerful and basic technologies for nucleic acid
detection is nucleic acid amplification." (Spec. ,r 4.) Using the polymerase
chain reaction ("PCR") one can amplify a nucleic acid of interest prior to its
1 Appellants identify the real party in interest as Caliper Life Sciences, Inc.,
which is a PerkinElmer Company. (Appeal Br. 3.)
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Application 14/252,755
detection, which is helpful "because it is easier to detect many copies of a
nucleic acid than it is to detect a single copy." (Id.) "[A] number of high
throughput approaches to performing PCR and other amplification reactions
have been developed, e.g., involving amplification reactions in microfluidic
devices, as well as methods for detecting and analyzing amplified nucleic
acids in or on the devices." (Id. at ,r 6.) However, "certain technical
difficulties persist in amplifying and detecting nucleic acids, particularly rare
copy nucleic acids. This is particularly true where the amplification reagents
amplify a high copy nucleic acid in a given sample in addition to the rare
nucleic acid and the two nucleic acids differ by only one or a few
nucleotides in the same sample." (Id. at ,r 7.) The invention is directed to a
high throughput method of single molecule amplification. (Id. at ,r 11.)
Claims 1, 3-9, and 11-1 7 are on appeal. Claim 1 is representative and
reads as follows:
1. A method of detecting a nucleic acid of interest, the method
compnsmg:
aliquotting a sample comprising the nucleic acid of
interest and one or more additional nucleic acids into a plurality
of reaction mixtures, wherein at least one of the plurality of
reaction mixtures is a single copy reaction mixture comprising a
single copy of the nucleic acid of interest, wherein the plurality
of reaction mixtures additionally comprise at least one additional
reaction mixture comprising at least one copy of the additional
nucleic acid;
simultaneously subjecting the plurality of reaction
mixtures in parallel to one or more amplification reactions while
flowing each of the plurality of reaction mixtures through one of
a plurality of channels of a microfluidic device; and,
detecting the nucleic acid of interest in the at least one
single copy reaction mixture;
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Application 14/252,755
wherein at least one of the plurality of reaction mixtures is
formulated in an aqueous phase of an emulsion comprising
aqueous droplets suspended in and surrounded by an immiscible
liquid.
(Appeal Br. 17 .)
The following ground of rejection by the Examiner is before us on
review:
Claims 1, 3-9, and 11-17 under 35 U.S.C. § 103 as unpatentable over
Curcio, 2 Vogelstein, 3 Lagally, 4 Ghadessy, 5 Nisisako, 6 Dower, 7 Tawfik, 8
Katsura, 9 Fouillet, 10 and Obeid. 11
2 Curcio et al., Continuous Segmented-Flow Polymerase Chain
Reaction for High-Throughput Miniaturized DNA Amplification, 75(1) Anal.
Chem., 1-7, 2003.
3 Vogelstein et al., US 6,440,706, issued Aug. 27, 2002.
4 Lagally et al., Single-molecule DNA amplification and analysis in an
integrated microfluidic device, 73(3) Anal. Chem., 565-70, 2001.
5 Ghadessy et al., Directed evolution of polymerase function by
compartmentalized self-replication, 98(a) PNAS, 4552--4557, 2001.
6 Nisisako et al., Formation of Droplets Using Branch Channels in a
Microfluidic Circuit, SICE 2002, 957-959, 2002.
7 Dower et al., In vitro selection as a powerful tool for the applied evolution
of proteins and peptides, 6(3) Curr. Opin. Chem. Biol., 390-398, 2002.
8 Tawfik et al., Man-made cell-like compartments for molecular evolution,
16(7) Nat. Biotechnol., 652---656, 1998.
9 Katsura et al., Indirect micromanipulation of single molecules in water-in-
oil emulsion, 22(2) Electrophoresis, 289-293, 2001.
1° Fouillet et al., US 2001/0041357 Al, published Nov. 15, 2001.
11 Obeid et al., Microfabricated Device for DNA and RNA Amplification by
Continuous-Flow Polymerase Chain Reaction and Reverse Transcription-
Polymerase Chain Reaction with Cycle Number Selection, 75(2) Anal.
Chem., 288-295, 2003.
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Appeal 2017-011016
Application 14/252,755
DISCUSSION
The Examiner finds that Curcio teaches a method of detecting a
nucleic acid of interest in a sample using amplification in which the sample
is aliquotted into a plurality of reaction mixtures in a channel of a
microfluidic device, each reaction mixture separated from one another by
immiscible filler fluid, resulting in segmented flow. (Final Action 4--5;
Advisory Action 2.) The Examiner acknowledges that Curcio does not
expressly teach the reaction mixture is a single copy reaction mixture. (Final
Action 7.) And, the Examiner also acknowledges that Curcio's segmented
flow does not involve the reaction mixture being formulated in an aqueous
phase of an emulsion or as an aqueous droplet therein. (Advisory Action 2.)
The Examiner contends that "Lagally provides motivation and a
reasonable expectation of success to apply single-molecule dilutions, used in
PCR, to integrated microfluidic devices like Curcio's, which uses sub-
microliter sample volumes." (Final Action 7.) The Examiner points to the
following statements in Lagally as the motivation and reasonable
expectation of success:
"[t]he capability of amplifying single-copy templates combined
with microfluidic integration will facilitate the development of
enhanced microfluidic diagnostic devices" (pg. 566, col. 2)
"[a]n integrated microdevice utilizing sub-microliter sample
volumes with sensitivity to the single-molecule limit would
avoid [amplification time and sensitivity] shortcomings and
could serve as a platform for high-throughput parallelization"
(pg. 566, col. 1)
"[t]he detection of single DNA molecules will also facilitate
single-cell and single-molecule studies to expose the genetic
variation underlying ensemble sequence and expression
averages" (Abs.).
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(Final Action 7-8; see also Advisory Action 2.)
The Examiner contends that "a skilled artisan of ordinary creativity at
the time of the invention would have been motivated to apply the single-
molecule dilution principle of VOGELSTEIN to ... Curcio, in view of the
motivation to apply single-molecule PCR on microfluidic devices from
Lagally, in order to 'accurately and quantitatively detect[] [single-copy or
rare] genetic sequences in mixed populations of sequences."' (Final Action
10-11.) According to the Examiner "VOGELSTEIN teaches the benefits of
single-molecule amplifications to detect low concentration targets among
high background non-targets with ratio-based concentration-determination
techniques, which benefits would have immediately been recognized by a
skilled artisan of ordinary creativity as applicable to microfluidic techniques
which yield high-throughput .... " (Ans. 6).
The Examiner recognizes that Vogelstein's compartments are wells,
but asserts that it would have been obvious to one having ordinary skill in
the art to apply the single-molecule dilution scheme in other single
compartments, citing Ghadessy. (Final Action 10-12.) According to the
Examiner, Ghadessy suggests that the wells of Vogelstein can be replaced
with water-in-oil emulsion compartmentalization as an equivalent alternative
to those wells, where the individual self-replication reaction takes place in
the compartment and there can be between 108 to 109 such compartments per
milliliter. (Id. at 11-12.)
The Examiner further contends that "[a]ll ofNisisaki, Dower, Tawfik
and Katsura provide further evidence as to the motivation to apply emulsions
to single-molecule PCR with a reasonable expectation of success." (Id. at
12.) According to the Examiner "Nisisako teaches that 'a PCR method
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using micro droplets as DNA containers has recently been proposed' such as
w/o emulsions, which 'is under intensive study' and 'will become
increasingly important,' including as applied to 'microfabricated devices."'
(Id.) The Examiner finds "Dower teaches emulsion compartmentalization
(via a 'DNA concentration [that] is selected to insert, on average, a single
DNA molecule in each droplet') of single nucleic acids for PCR (Fig. 3a;
citing Tawfik, ref. 44)." (Id.) The Examiner finds that "Katsura
demonstrates that w/o emulsions can be formed to compartmentalize a single
nucleic acid for PCR." (Id. at 13.)
Regarding the reaction mixture being formulated as an aqueous
droplet in an emulsion therein, the Examiner contends that emulsion droplets
"were known substitutes for well-based droplets" in amplification, citing
Nisisako, Dower, Tawfik, and Katsura. (Ans. 5.)
Finally, regarding the claim requirement of parallel PCR analysis on a
continuous-flow device, the Examiner contends that Curcio itself provides
motivation for such a modification "[t Jo increase the total sample capacity."
(Final Action 14.) The Examiner contends that Curcio "explicitly suggests
to combine smaller-droplet single-molecule amplification systems with
familiar highly-parallelized microfludic systems." (Ans. 6.) The Examiner
bases that contention on a finding that
Curcio specifically suggests that "[t]he use of miniaturized
fluidics on a chip-based format is particularly attractive["] (pg.
7, col. 1, para. 1), and "[t]o increase the total sample capacity,
many flow channels could be operated in parallel" (pg. 7, col. 1,
para. 2). Such suggestions are also repeated in the "Conclusion"
section on page seven.
(Advisory Action 2.) The Examiner, citing to Fouillet and Obeid, notes that
such processing was routinely applied to continuous-flow PCR devices at
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the time of the invention. (Final Action 14.) Thus, the Examiner concludes,
one of ordinary skill in the art would have had a reasonable expectation of
success in carrying out parallel PCR analysis.
We disagree with the Examiner's conclusion that the claimed
invention would have been obvious from the teachings of the various
references cited. Our reviewing Court has "outlined two classes of
situations where 'obvious to try' is erroneously equated with obviousness
under§ 103." In re Kubin, 561 F.3d 1351, 1359 (Fed. Cir. 2009.) One of
those "impermissible 'obvious to try' situations occurs where 'what was
"obvious to try" was to explore a new technology or general approach that
seemed to be a promising field of experimentation, where the prior art gave
only general guidance as to the particular form of the claimed invention or
how to achieve it."' Id.
Emulsion droplet containers were a known alternative that seemed
promising for PCR at the time of the invention. (See Nisisako at 1264 (
To exploit the resulting droplets as small reaction/analysis
chambers, cooperation with a manipulation method will be
required. As a further project in our laboratory, we are working
on the manipulation of micro droplets inside liquid layer by
electric fields.);
(Ghadeesy at 4552 ("We foresee many applications of this
[compartmentalized self-replication] technology.").) We agree with
Appellants that the Examiner has failed to provide any teaching that would
reasonably provide a suggestion with an expectation of success of using
emulsion droplets as reaction chambers for PCR in a continuous flow
system.
As Appellants note, not one of the references suggests use of emulsion
droplets in flow systems. (Reply Br. 4.) Appellants explain that Curcio and
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Obeid (the Group A references) are directed to slug flow PCR. (Appeal Br.
13.)
In the Final Action, the Examiner was of the opinion that Curcio's
slug flow was reasonably considered an emulsion system. (Final Action 5-
6.) However, the Examiner conceded in the Advisory Action dated January
19, 2017 that Curcio's slug flow was not an emulsion system. (See Ans. 3-
4.) Nevertheless, the Examiner maintained the position of a reasonable
expectation of success of using emulsion droplets in continuous flow
systems like Curcio on the basis of the position that ( 1) "emulsion droplets
(Applicants' "Group C") were known substitutes for well-based droplets
used in digital amplification (Applicants' "Group B")" (Ans. 5) and (2)
"Curcio specifically suggests that ' [ t ]he use of miniaturized fluidics on a
chip-based format is particularly attractive (pg. 7, col. 1, para. 1), and '[t]o
increase the total sample capacity, many flow channels could be operated in
parallel' (pg. 7, col. 1, para. 2)" (id. at 6). However, as Appellants note,
Curcio teaches a slug flow system and "merely states that the physical
design of their [ slug flow] system could be further optimized and that the use
of miniaturized fluidics on a chip-based format is particularly attractive."
(Appeal Br. 11-13; Reply Br. 4--5.) In the absence of a teaching or
suggestion by Curcio of an emulsion system, or some other teaching or
evidence that systems such as Curcio's would remain functional when in
emulsion systems, we disagree with the Examiner's finding that Curcio
provides a reasonable expectation of success that an emulsion be used in a
continuous flow system, much less a single droplet compartment within an
emulsion.
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Appellants explain that Lagally and Vogelstein ( the Group B
references) disclose single drop amplification on micro well plates, and that
Ghadessy, Nisisako, Dower, Tawfik, and Katsura (the Group C references)
taken together simply disclose PCR methods using emulsion droplets as
reaction compartments. (Appeal Br. 13-15; Reply Br. 4.) We agree.
Lacking in the Examiner's obviousness rejection is evidence that one skilled
in the art would have had a reason to combine the single drop amplification
methods on micro well plates of Group B and the emulsion droplets of Group
C, neither of which have anything to do with fluid flow systems, with the
slug flow continuous PCR systems of Group A with a reasonable
expectation of success where none of the references "disclose use of
emulsions in continuous flow systems." (Reply Br. 4.) At most, the
Examiner has simply cited references which suggest a promising field of
experimentation which is not sufficient on the record before us to establish
obviousness under 35 U.S.C. § 103.
Consequently, we do not sustain the Examiner's rejection of claims 1,
3-9, and 11-17 as being obvious over Curcio, Vogelstein, Lagally,
Ghadessy, Nisisako, Dower, Tawfik, Katsura, Fouillet, and Obeid.
SUMMARY
We reverse the rejection of claims 1, 3-9, and 11-17 under 35 U.S.C.
§ 103 as unpatentable over Curcio, Vogelstein, Lagally, Ghadessy, Nisisako,
Dower, Tawfik, Katsura, Fouillet, and Obeid.
REVERSED
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