Ex Parte Hofstadler

Patent Trial and Appeal Board

Mar 21, 2017

13255064 (P.T.A.B. Mar. 21, 2017)

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.
13/255,064 09/06/2011 Steven A. Hofstadler 9926USO1/30855US2PCT 3283
58057 7590 03/23/2017
Pasimir Tones; P
EXAMINER
2275 Deming Way, Suite 310
Madison, WI 53562
BOWERS, NATHAN ANDREW
ART UNIT PAPER NUMBER
1799
NOTIFICATION DATE DELIVERY MODE
03/23/2017 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 @ c asimirj ones .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 STEVEN A. HOFSTADLER
Appeal 2016-001906
Application 13/255,0641
Technology Center 1700
Before: LINDA M. GAUDETTE, DONNA M. PRAISS, and
DEBRA L. DENNETT, Administrative Patent Judges.
DENNETT, Administrative Patent Judge.
DECISION ON APPEAL2
STATEMENT OF THE CASE
Appellant3 appeals under 35 U.S.C. § 134(a) from a rejection of
claims 1—7, 9, and 10. We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.
1 Appellant identifies Ibis Biosciences, Inc. as the real party in interest.
Appeal Br. 3.
2 In our Opinion, we refer to: the published version of the Specification filed
September 6, 2011 (“Spec.”); the Final Action mailed October 23, 2014
(“Final Act.”); the Appeal Brief filed May 12, 2015 (“Appeal Br.”); the
Examiner’s Answer mailed September 25, 2015 (“Ans.”); and the Reply
Brief filed November 25, 2011 (“Reply Br.”).
Appeal 2016-001906
Application 13/255,064
The claims are directed to methods and systems or kits for selectively
concentrating target nucleic acids and identifying unknown bioagents using
broad range survey primers. Claims 1, 9. Claims 1 and 9, reproduced below
with disputed limitations highlighted, are illustrative of the claimed subject
matter:
1. A method of selectively concentrating target nucleic
acids from a sample comprising;
a) providing;
i) a device for performing SCODA
purification, wherein said device comprises a gel,
ii) a sample comprising non-target nucleic acid,
contaminants, and a target nucleic acid comprising
conserved and variable regions, and
iii) a plurality of broad range survey primers
complementary to a region of said target nucleic
acid, wherein said broad range survey primers
are immobilized in said gel,
b) introducing said sample into said device under
conditions such that said target nucleic acid in said
sample is separated from said contaminants and is
captured by said at least a portion of said broad range
survey primers', and
c) amplifying at least one region of said target
nucleic acid with primer pairs complementary to
conserved regions of said target nucleic acid that flank
a variable region of said nucleic acid.
9. A system or kit comprising:
a) a gel suitable for use in SCODA purification;
b) a plurality of broad range survey primers, said
broad range survey primers being complementary to a
portion of a target nucleic acid', and
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Appeal 2016-001906
Application 13/255,064
c) one or more primer pairs, said primer being
complementary to conserved regions of the target
nucleic acid that flank a variable region of said target
nucleic acid.
Appeal Br. 23, 24.
REFERENCES
The Examiner relies on the following prior art in rejecting the claims
on appeal:
US 5,314,809Erlich et al.
(“Erlich”)
Jensen et al.
(“Jensen”)
Lipkin et al.
(“Lipkin”)
Marziali et al.
(“Marziali”)
US 5,753,467
US 2006/0003352 Al
US 2009/0139867 Al
May 24, 1994
May 19, 1998
Jan. 5, 2006
June 4, 2009
REJECTIONS
The Examiner maintains the following rejections of claims 1—7, 9, and
10 under 35 U.S.C. § 103(a): (1) over Marziali in view of Jensen and/or
Erlich; and (2) over Marziali in view of Lipkin and further in view of Jensen
and/or Erlich. Final Act. 2, 4.
OPINION
The Examiner rejects claims 1—7, 9, and 10 over Marziali (1) in view
of Jensen and/or Erlich, and (2) in view of Lipkin and further in view of
Jensen and/or Erlich. Id. at 2, 4. The Examiner finds that Marziali discloses
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Appeal 2016-001906
Application 13/255,064
a method and apparatus for performing SCODA4 purification using a gel,
and the sample in Marziali comprises non-target nucleic acid, contaminants,
and target nucleic acid, as required by Appellant’s claim 1. Id. at 2—3.
Marziali further discloses covalently bonded complementary DNA
oligonucleotides, which the Examiner finds are “understood to be broad
range survey primers.” Final Act. 3 (citing Marziali 173—176). The
Examiner acknowledges that, if the covalently bonded complementary DNA
oligonucleotides described in Marziali are not “broad range survey primers,”
then Marziali differs from Appellant’s claimed method. Final Act. 4.
“Broad range survey primers” are defined in the Specification as
“primers designed to identify an unknown bioagent as a member of a
particular biological division (e.g., an order, family, class, clade, or genus).”
Spec. 133. “Primer” is defined in the Specification as referring to an
oligonucleotide, whether occurring naturally or produced synthetically,
which is capable of acting as a point of initiation of synthesis when placed
under conditions in which synthesis of a primer extension product that is
complementary to a nucleic acid strand is induced. Id. 144. Appellant
points out that oligonucleotide sequences capable of acting as point of
initiation for synthesis are known to have a 3 ’ OH group. Appeal Br. 11.
Appellant therefore argues that, although Marziali discloses DNA
oligonucleotides, the reference fails to disclose primers. Id. at 7. Appellant
argues that Marziali also fails to disclose the specific “broad range survey
primers” required by each of the claims. Id. at 8. In addition, Appellant
4 SCODA stands for Synchronous Coefficient of Drag Alteration. Spec. 12.
The present invention relates to the use of broad range nucleic acid primers
immobilized in a SCODA method gel to allow for selective concentration of
target nucleic acids. Id.
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Appeal 2016-001906
Application 13/255,064
argues that Marziali fails to disclose the “primer pairs” required by the
claims. Id. at 12.
In the Answer, the Examiner states that:
Marziali teaches that PCR [polymerase chain reaction] is
used to detect pathogens by amplifying analyte DNA. PCR
requires the use of amplification primers, so it is a safe
assumption that the “complementary DNA oligonucleotides”
taught by Marziali must be amplification primers when the
Marziali device is used for PCR. Ans. 2 (emphasis added).
Because Marziali already teaches that “complementary
DNA oligonucleotides” are immobilized within the gel to bind
to nucleic acid analytes, one of ordinary skill would naturally
have found it obvious to put the necessary amplification
primers, which are “complementary DNA oligonucleotides,” in
the gel bind as well. Id. at 3 (emphasis added).
Marziali teaches . . . that “a piece of the gel including the
concentrated DNA may be subjected to PCR”, which strongly
suggests that all components necessary for PCR, including
primers, are provided within the gel. Id. at 5 (emphasis added).
[NJowhere does Marziali state that primers are added to
the gel from an external source . . . [I]t is more reasonable to
assume that the “complementary DNA oligonucleotides . . .
function as the primers required for PCR. Id. at 6 (emphasis
added).
Appellant argues that the Examiner’s conclusions regarding the
teachings of Marziali are incorrect, and lack evidence of fact or law. See
Reply Br. 2—3.
Marziali discloses that PCR can be used to amplify DNA that is
concentrated by scodaphoresis taught in the reference, either by extracting
the DNA from the gel before performing PCR amplification or, in the
alternative, subjecting a piece of the gel including the concentrated DNA to
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Appeal 2016-001906
Application 13/255,064
PCR. Marziali 1207. Marziali does not teach or suggest that PCR is part of
the “moving and concentrating” method and apparatus taught by the
reference. See id. at Abstract. Rather, PCR is a step that may be taken after
the moving and concentrating process has taken place. See id. 1207. There
is no requirement in Marziali that primers be present in the gel.
For the reasons above, the Examiner’s conclusions that Marziali
suggests its complementary DNA oligonucleotides are primers is not
persuasive. Moreover, the Examiner provides no evidence that Marziali,
alone or in combination with secondary references, discloses “broad range
survey primers,” as defined in the Specification. Finally, the Examiner
provides no reason to combine the cited secondary references with Marziali,
other than hindsight.
Because Appellant has identified harmful error in the findings relied
upon by the Examiner in concluding the claimed invention would have been
obvious, we do not sustain the rejection of claims 1—7, 9, and 10 under 35
U.S.C. § 103(a).
DECISION
For the above reasons, the Examiner’s rejection of claims 1—7, 9, and
10 is reversed.
REVERSED
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