Ex Parte GOELET et al

Board of Patent Appeals and Interferences

Oct 15, 2010

09258132 (B.P.A.I. Oct. 15, 2010)

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.
09/258,132 02/26/1999 PHILIP GOELET 04990.0007.U 3407
7590 10/15/2010
David A. Kalow, Esq.
KALOW, SPRINGUT & BRESSLER, LLP
488 Madison Ave.
19th Floor
New York, NY 10022
EXAMINER
MYERS, CARLA J
ART UNIT PAPER NUMBER
1634
MAIL DATE DELIVERY MODE
10/15/2010 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 PHILIP GOELET, MICHAEL R. KNAPP, and
STEPHEN ANDERSON
__________

Appeal 2009-009122
Application 09/258,132
Technology Center 1600
__________

Before ERIC GRIMES, FRANCISCO C. PRATS, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL1
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of identifying bases in a nucleotide sequence. The Examiner has rejected the

1 The two-month time period for filing an appeal or commencing a civil
action, as recited in 37 C.F.R. § 1.304, or for filing a request for rehearing,
as recited in 37 C.F.R. § 41.52, begins to run from the “MAIL DATE”
(paper delivery mode) or the “NOTIFICATION DATE” (electronic delivery
mode) shown on the PTOL-90A cover letter attached to this decision.
Appeal 2009-009122
Application 09/258,132

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claims as obvious over the prior art. We have jurisdiction under 35 U.S.C.
§ 6(b). We affirm.
STATEMENT OF THE CASE
Claims 64 and 66-71 are on appeal. The claims have not been argued
separately and therefore stand or fall together. 37 C.F.R. § 41.37(c)(1)(vii).
Claim 64 is representative and reads as follows:
64. A method of determining the identity of one or more nucleotide
bases at a plurality of specific positions in one or more nucleic acid
molecules of interest, comprising:
(a) treating a sample comprising the one or more nucleic acid
molecules of interest, if the nucleic acid molecules of interest comprise
double-stranded nucleic acid, so as to obtain unpaired nucleotide bases
spanning the specific positions, or directly employing a sample comprising
the one or more nucleic acid molecules of interest in step (b) if the nucleic
acid is singlestranded;
(b) contacting the sample from step (a) with a plurality of different
oligonucleotide primers, wherein:
(i) each such different oligonucleotide primer hybridizes, under
high stringency hybridization conditions, to a corresponding different stretch
of nucleotide bases present in the nucleic acid molecules of interest which is
immediately adjacent to the specific position of a nucleotide base to be
identified with that oligonucleotide primer, so as to form a duplex such that
the nucleotide base to be identified is the first unpaired base of the nucleic
acid molecule of interest immediately downstream of the 3' end of the
oligonucleotide primer; and
(ii) each different oligonucleotide primer comprises a
corresponding different affinity moiety, the oligonucleotide primer
comprising the affinity moiety being capable of hybridizing with a nucleic-
acid template and undergoing a nucleic acid template-dependent primer
extension reaction with terminators of a terminator reagent, the affinity
moiety permitting affinity separation of the extended oligonucleotide primer
from the terminator reagent;
(c) contacting the duplexes from step (b) with a terminator reagent
free of dATP, dCTP, dGTP, and dTTP and comprising four different
terminators of a nucleic acid template-dependent primer extension reaction,
Appeal 2009-009122
Application 09/258,132

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each terminator comprising a different detectable label corresponding to the
terminator, wherein one of the terminators is complementary to a nucleotide
base to be identified by each of the oligonucleotide primers, wherein the
contacting is carried out in a primer-extension reaction medium under
conditions sufficient to permit a template dependent primer extension
reaction which incorporates the complementary terminator onto the 3' end of
each of the different oligonucleotide primers to thereby extend the 3' end of
each of the oligonucleotide primers by one terminator;
(d) affinity separating the respective extended oligonucleotide primers
from primer-extension reaction medium by causing each of the extended
oligonucleotide primers to contact an affinity group attached to a solid
support, such affinity group being complementary to the affinity moiety
incorporated in the oligonucleotide primer; and
(e) determining the presence and identity of the nucleotide base at
each of the respective specific positions in the one or more nucleic acid
molecules of interest by detecting the detectable label of the terminator
incorporated at the 3' end of each of the affinity separated extended
oligonucleotide primers.

The Examiner has rejected all of the claims under 35 U.S.C. § 103(a)
as follows: claims 64, 66, 67, 69, and 70 based on either Cohen EP2 or
Cohen FR,3 combined with Davis4 (Answer 4); claim 68 based on either
Cohen EP or Cohen FR, combined with Davis and Prober5 (Answer 6); and
claim 71 based on either Cohen EP or Cohen FR, combined with Davis and
Tabor6 (Answer 7). We adopt the Examiner’s findings regarding the
teachings of the prior art (Answer 4-5, 7), and the reasoning supporting her
conclusion that the cited references would have made obvious the claimed

2 Cohen et al., EP 0 412 883 A1, published Feb. 13, 1991.
3 Cohen et al., FR 2,650,840, published Feb. 15, 1991.
4 Davis et al., WO 90/11372, published Oct. 4, 1990.
5 Prober et al., US 5,332,666, issued July 26, 1994.
6 Tabor et al., US 4,962,020, issued Oct. 9, 1990.
Appeal 2009-009122
Application 09/258,132

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method (Answer 6, 7, 8). We also agree with the Examiner’s response to
Appellants’ arguments (Answer 8-26), and add the following remarks only
for emphasis.
Appellants argue that Cohen FR7 teaches that its technique has the
advantage of not requiring immobilization of a nucleic acid on a membrane,
which was required by three previously known techniques for identifying a
mutation in a nucleic acid (Appeal Br. 11). Appellants argue that Davis’
technique,
like the previously known techniques distinguished in the
Cohen et al. patent, involved immobilization of nucleic acid on
a membrane. It is submitted, therefore, that the hypothetical
combination proposed in the Office Action on appeal would
have been understood by persons of ordinary skill in the art as
of the effective filing date of the subject application as running
directly counter to the teachings of the Cohen et al. patent.
(Id. at 11-12.)
As the Examiner pointed out (Answer 9), however, Davis expressly
teaches that its method has the advantage of allowing analysis of multiple
sequences simultaneously (see Davis 26: “It . . . is an advantage of the
invention that by using unique tails, any number of alleles or loci may be
tested for simultaneously.”). Thus, a person of ordinary skill in the art
would have recognized that, although combining the methods of Cohen FR
and Davis would require immobilization of nucleic acid on a membrane,
which Cohen FR characterizes as a disadvantage, it would have the

7 Both Appellants and the Examiner cite only to Cohen FR, although the
Examiner finds that the application to which Cohen EP claims priority is
identical to Cohen FR (Answer 4).
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offsetting advantage of allowing the method of Cohen FR to determine the
identity of multiple nucleic acid positions in a single experiment.
“[A] given course of action often has simultaneous advantages and
disadvantages, and this does not necessarily obviate motivation to combine.”
Medichem, S.A. v. Rolabo S.L., 437 F.3d 1157, 1165 (Fed. Cir. 2006). See
also Winner Int’l Royalty Corp. v. Wang, 202 F.3d 1340, 1349 n.8 (Fed. Cir.
2000) (“The fact that the motivating benefit comes at the expense of another
benefit . . . should not nullify its use as a basis to modify the disclosure of
one reference with the teachings of another. Instead, the benefits, both lost
and gained, should be weighed against one another.”). In this case, we agree
with the Examiner that a worker of ordinary skill would have been led to
combine the methods disclosed by Cohen FR and Davis in order to gain the
advantage of analyzing multiple nucleic acid positions in a single
experiment, notwithstanding the need to immobilize nucleic acids on a
membrane in order to do so.
SUMMARY
We affirm all of the rejections on appeal: claims 64, 66, 67, 69, and
70 as obvious based on either Cohen EP or Cohen FR, combined with Davis;
claim 68 as obvious based on either Cohen EP or Cohen FR, combined with
Davis and Prober; and claim 71 as obvious based on either Cohen EP or
Cohen FR, combined with Davis and Tabor.
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Application 09/258,132

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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

cdc

DAVID A. KALOW, ESQ.
KALOW, SPRINGUT & BRESSLER, LLP
488 MADISON AVE.
19TH FLOOR
NEW YORK, NY 10022