Ex Parte Densham

Patent Trial and Appeal Board

Sep 11, 2018

12651824 (P.T.A.B. Sep. 11, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/651,824 01/04/2010
148184 7590
Hologic/McNeill Baur
125 Cambridge Park Drive
Suite 301
Cambridge, MA 02140
09/13/2018
FIRST NAMED INVENTOR
Daniel Henry Densham
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.
Ol 159-0001-03US 9961
EXAMINER
SISSON, BRADLEY L
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
09/13/2018 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@mcneillbaur.com
PatentDept@hologic.com
eofficeaction@appcoll.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte DANIEL HENRY DENSHAM
Appeal2017-009327
Application 12/651,824 1
Technology Center 1600
Before ERIC B. GRIMES, ELIZABETH A. LA VIER, and DAVID COTT A,
Administrative Patent Judges.
LA VIER, Administrative Patent Judge.
DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellant seeks review of the
Examiner's rejection of claims 50-53. We have jurisdiction under 35 U.S.C.
§ 6(b ). For the reasons set forth below, we REVERSE.
BACKGROUND
The Specification relates to improved methods for determining the
sequence of a polynucleotide. See Spec. 1 :3--4, 2: 18-23. More particularly,
the Specification seeks to increase sequencing speed and automation, while
decreasing complexity and cost, as compared with prior art methods. See id.
1 Appellant states the real parties in interest are Gen-Probe Inc. and Hologic,
Inc. Appeal Br. 4.
Appeal2017-009327
Application 12/651,824
at 2: 18-23. The Specification explains that "[ t ]he present invention is based
on the realisation that the measurement of electromagnetic or other radiation
can be used to detect a conformational and/or mass change in a polymerase
enzyme which occurs when a nucleotide is incorporated into a nascent
polynucleotide strand." Id. at 2:25-29.
Claim 50, the only independent claim on appeal, is illustrative:
50. A method for sequencing a polynucleotide, comprising:
(i) introducing a target-primer complex comprising a target
DNA and a primer to a polymerase that is immobilised on a
solid support positioned in a fluidic cell to form a primed
complex, wherein the fluidic cell is suitable for use in total
internal reflection fluorescence spectroscopy (TIRF) and
wherein the polymerase is maintained within an area of the field
of measurement for total internal reflection fluorescence
spectroscopy;
(ii) introducing one or more nucleotides to the primed complex
under conditions sufficient for a polymerase reaction, wherein
a. each of the one or more nucleotides comprises a
blocking group comprising a fluorescent label, and the
blocking group prevents a polymerase reaction involving
the 3' end of the nucleotide, and
b. if the one or more nucleotides comprise different types
of nucleotides, the different types of nucleotides are
selected from the group consisting of dCTP, dTTP,
dGTP, and dATP, and the label on each type of
nucleotide is detectably distinguishable from the
fluorescent label on each other different type of
nucleotide;
(iii) removing unincorporated nucleotides from the fluidic cell;
and
(iv) detecting each incorporated nucleotide complementary to
the target polynucleotide to the primer, or an extended primer,
after the polymerase reaction, wherein detection is carried out
through the use of TIRF, wherein, after detection, the blocking
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Application 12/651,824
group comprising the fluorescent label is removed from each
incorporated nucleotide and the fluidic cell, and wherein steps
(ii) through (iv) are repeated one or more times, thereby
determining the sequence of the target polynucleotide.
Appeal Br. 38-39 (Claims Appendix) (emphasis added).
REJECTION MAINTAINED ON APPEAL
Claims 50-53 stand rejected under pre-AIA 35 U.S.C. § 103(a) as
unpatentable over Cheeseman, 2 Squirrell, 3 Melamede, 4 and Appellant's
admissions. Ans. 4.
DISCUSSION
The Examiner finds that Cheeseman discloses a method of DNA
sequencing, utilizing fluorescently-labeled 3'-blocked nucleotide
triphosphates. Final Action 29 (discussing Cheeseman Abstract). The
Examiner acknowledges that although Cheeseman uses fluorescent
spectroscopy, Cheeseman does not use TIRF specifically; furthermore,
Cheeseman does not teach immobilizing the polymerase. Id. at 30. The
Examiner cites Melamede as teaching an automated sequencing system
(including a flow cell the Examiner equates to the claimed fluidic cell) in
which, as in Cheeseman, unincorporated reactants are removed "prior to any
detection step," and fluorescent spectroscopy can be used for detection. Id.
at 31 (discussing Melamede cols. 7 (first paragraph), 9 (first paragraph)).
The Examiner cites Squirrell as teaching using TIRF to detect fluorescent
2 Cheeseman, US 5,302,509, issued Apr. 12, 1994.
3 Squirrell, WO 93/06241, published Apr. 1, 1993.
4 Melamede, US 4,863,849, issued Sept. 5, 1989.
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Application 12/651,824
labels incorporated into nucleotides hybridized to a target nucleic acid. Id.
at 32. As for the immobilization of the polymerase as claimed, the Examiner
finds that Appellant "admits the procedure for immobilizing the polymerase
has been known for years" (id. at 31 ), based on the following statement in
the Specification:
Immobilisation of the Polymerase
Immobilisation of the polymerase to the sensor chip surface
was carried out according to (Jonsson et al., Biotechniques
(1991); ll:620-627[5]).
Spec. 11 :4---6; see also Final Action 31 ( quoting the same).
Appellant argues, inter alia, that the Specification's citation to
Jonsson does not amount to an admission that immobilization of
polymerases was known in the art, much less as applied in a sequencing
method. See Appeal Br. 28-29; see also Reply Br. 3---6. Appellant contends
that Jonsson "described a method for attaching proteins to solid surfaces,
specifically demonstrating attaching an antibody to a surface." Appeal Br.
29 ( citing Jonsson 625).
There is a difference between stating that a polymerase could be
immobilized using known, generally-applicable methods (which the
Specification does) and admitting that polymerases were in fact immobilized
according to that method in the prior art (which the Specification does not).
In our view, the Examiner's analysis fails to account adequately for this
difference, or to respond to Appellant's point that, at best, nothing in
Jonsson's "general discussion of other applications involving protein
attachment" (Appeal Br. 29 (citing Jonsson 624--25)) suggests the use of
5 Hereinafter "Jonsson."
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Application 12/651,824
Jonsson's method for sequencing. Cf In re Kerkhoven, 626 F.2d 846, 852
(CCPA 1980) (finding "[m]ere knowledge" of usefulness of prior art
technique insufficient to render obvious specific, different application of that
technique).
Because the Specification ( either directly or via citation to Jonsson)
does not admit that polymerase immobilization was known in the art, and
because none of Cheeseman, Squirrell, or Melamede is relied upon for such
a teaching, we conclude that the Examiner has not carried the burden of
establishing a prima facie case of obviousness. On the record before us, we
cannot sustain the rejection.
CONCLUSION
The rejection of claims 50-53 under 35 U.S.C. § 103(a) is reversed.
REVERSED
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