Ex Parte Schaefer et al

Patent Trial and Appeal Board

Mar 29, 2013

10147322 (P.T.A.B. Mar. 29, 2013)

UNITED STATES PATENT AND TRADEMARKOFFICE
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.
10/147,322 05/17/2002 Frank Schaefer SCHAEFER=1 8851
1444 7590 04/01/2013
Browdy and Neimark, PLLC
1625 K Street, N.W.
Suite 1100
Washington, DC 20006
EXAMINER
SWITZER, JULIET CAROLINE
ART UNIT PAPER NUMBER
1634
MAIL DATE DELIVERY MODE
04/01/2013 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 PATENT TRIAL AND APPEAL BOARD
__________

Ex parte FRANK SCHAEFER, H.D. ALAN LINDQUIST,
JEFFERY DEAN HESTER, and MANJU VARMA
__________

Appeal 2011-006569
Application 10/147,322
Technology Center 1600
__________

Before TONI R. SCHEINER, LORA M. GREEN, and ULRIKE W. JENKS,
Administrative Patent Judges.

SCHEINER, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 from the final rejection of a
claim directed to a multiplex assay for genus-specific and species-specific
detection of species within the genus Encephalitozoon. The claims have
been rejected as obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm.
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STATEMENT OF THE CASE
Claims 14, 18, and 21-25 are pending and on appeal. Claims 26 and
27 have been objected to; claims 7-12 have been withdrawn from
consideration; and claims 1-6, 13, 15-17, 19, and 20 have been canceled
(App. Br. 2).
The claims have not been argued separately. Therefore, we select
claim 21, the only independent claim, as representative, and the remaining
claims will stand or fall accordingly. 37 C.F.R . § 41.37(c)(i)(vii).
Claim 21 is as follows:
21. A multiplex method for genus-specific and species-specific
detection of species within the genus Encephalitozoon spp. and a genus
within the phylum Microsporidia, in a sample suspected of containing
microsporidia spores, the method comprising:
a. contacting the sample with a reaction mixture containing a plurality
of different species specific primer sets, wherein each primer set is
composed of a unique forward primer and a unique reverse primer, DNA
primers for species-level detection and DNA probes for genus-level
detection, DNA of the microsporidia spores (target species), and DNA
polymerase with a 5'-nuclease activity, wherein the primers and probe bind
specifically to DNA of the target species or genus during a PCR annealing
extension step or to DNA amplicons bearing subsequent rounds of
amplification;
b. wherein the DNA probe is labeled with a first fluorescent moiety
and a second fluorescent moiety, wherein the first fluorescent moiety
quenches the fluorescence signature of the second fluorescent moiety;
c. conducting an annealing and extension reaction, wherein during the
extension reaction of the DNA primers, the probe molecules bound to the
DNA target or previously generated amplicons are cleaved by the DNA
polymerase, whereby cleaving of the bound probes stops the quenching of
the fluorescence, causing an increase in fluorescence;
d. measuring the increase in fluorescence to quantify the fluorescence
output to quantify the amount of target DNA in the sample; and
e. wherein, if target DNA is present in the sample, conducting parallel
species identification PCR reaction to detect which species are present.
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Claims 14, 18 and 21-25 stand rejected under 35 U.S.C. § 103(a) as
unpatentable over Hester,1 Bassam,2 Stauffer,3 and Orlandi.4
FINDINGS OF FACT
1. Hester discloses the development of a real-time 5'-nuclease
PCR-based assay for the quantitative detection of three pathogenic
Encephalitozoon species, E. hellem, E. cuniculi, and E. intestinalis, using
three “[s]pecies-specific oligonucleotide primer sets and a genus-specific,
fluorescent-labeled Taqman probe . . . designed to amplify the rDNA gene
for all three Encephalitozoon species” (Hester Abstract ¶ 2).
2. The present Specification teaches that “[t]he principles of
fluorogenic 5' nuclease PCR assays ha[ve] been described extensively”
(Spec. 7).
3. In addition, Bassam discloses specific protocols for real-time
fluorogenic 5' nuclease PCR assays, and teaches that the assays are ideal for
rapid detection of microbial pathogens in food and environmental samples
(Bassam 286-293).

1 J.D. Hester et al., Quantitative Detection of Three Human-Pathogenic
Species from the Microsporidial Genus Encephalitozoon via the 5’-Nuclease
Assay, 101 ABSTRACTS OF THE GENERAL MEETING OF THE AMERICAN
SOCIETY FOR MICROBIOLOGY 631 abs, Q-237 (2001).
2 Brant J. Bassam et al., Nucleic Acid Sequence Detection Systems:
Revolutionary Automation for Monitoring and Reporting PCR Products, 6
NUCLEIC ACID TECHNOLOGIES 285-294 (1996).
3 Fritz Stauffer et al., Genus Level Identification of Mycobacteria from
Clinical Specimens by Using an Easy-To-Handle Mycobacterium-Specific
PCR Assay, 36 JOURNAL OF CLINICAL MICROBIOLOGY 614-617 (1998).
4 Palmer A. Orlandi & Keith Lampel, Extraction-Free, Filter-Based
Template Preparation for Rapid and Sensitive PCR Detection of Pathogenic
Parasitic Protozoa, 38 JOURNAL OF CLINICAL MICROBIOLOGY 2271-2277
(2000).
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4. Stauffer teaches that
[P]retesting of clinical specimens for mycobacteria to the genus
level with a Mycobacterium-specific probe [and pan-genus
primers] offers the routine clinical laboratory the possibility of
detecting tuberculous and nontuberculous mycobacteria with
one test. Specimens that are positive with the Mycobacterium-
specific probe can then be identified by hybridizing the
products from the same amplification reaction to species-
specific probes.
(Stauffer 617.)
5. Orlandi discloses species-specific primer pairs for identification
of several Encephalitozoon species, including E. hellem and E, cuniculi, by
multiplex PCR (Orlandi 2272, col. 2).
DISCUSSION
The Examiner finds that Hester discloses “detecting three human-
pathogenic species from the microsporidial genus Encephalitozoon using a
real-time PCR -based assay, specifically a quantitative 5'-nuclease assay”
(Ans. 4). The Examiner further finds that Hester used three “‘species-
specific oligonucleotide primer sets and a genus specific fluorescent-labeled
Taqman probe’ . . . to amplify the rDNA gene of E. hellem, E. cuniculi, and
E. intestinalis” (id.), i.e, “three sets of primers that amplify products
detectable with the same probe” (id. at 9).
The Examiner cites Bassam for its “detailed discussion of the 5'
nuclease PCR assay which uses a fluorogenic reporter probe system” (id. at
5).
The Examiner finds that “the component steps of the claimed methods
are provided in the combined teachings of Hester et al. and Bassam et al.”
(id.), except that the references “do not teach a single reaction mixture that
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contains [a genus specific probe] and a plurality of different species specific
primer sets” (id. at 6).
However, the Examiner cites Stauffer for the general concept of “a
first pretesting step of determining if any member of the genus [of interest]
is present and, if so, then using a follow up assay to determine which species
is present” (id.). The Examiner notes that Stauffer, in “first testing for the
genus and then testing for the species” is consistent with “what is claimed,
wherein in steps (a)-(d), only a genus level determination would be made,
and in step (e) if it had been determined that the genus is present, species
level identification occurs” (id. at 8).
Finally, the Examiner finds that Orlandi discloses a multiplex PCR
assay for the detection of multiple Encephalitozoon species (id. at 6), using
several “unique, species specific primer pairs” (id. at 8).
The Examiner acknowledges that none of the references “teaches a
method in which a genus-specific probe is used in a multiplex reaction along
with . . . species-specific primers as claimed” (id. at 9). Nevertheless, the
Examiner concludes that it would have been obvious for one of ordinary
skill in the art to “first complete[] a PCR step using all three sets of specific
primers in the assay, and then, if a positive result was obtained resolv[e] the
species . . . present using serial assays” (id. at 6). That is, the Examiner
concludes that the claimed parallel multiplex assay would have been obvious
“[g]iven the teachings of Stauffer et al. regarding the benefits of a
prescreening step, and given the exemplification of multiplex PCR of
Encephalitozoon species, and the teaching of three sets of primers that
amplify products detectable with the same probe” (id. at 9), i.e., the genus-
level specific probe . . . provided by the primary reference of Hester” (id. at
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8). Essentially, the Examiner’s position is that, given the availability of a
genus level probe, as well as multiple species-specific primer pairs that that
amplify products detectable with the same probe, one of ordinary skill in this
art “would have been motivated to carry out . . . multiplex pretesting . . . to
provide a single tube assay to determine if any of the three pathogenic
Encephalitozoon species are present in a sample” (id. at 6).
Appellants contend that the claimed method is “a real-time, multiplex
PCR assay that includes specific primer sets for species along with a genus-
specific probe such that the species identification is conducted in parallel
with the genus identification” (App. Br. 11). “That is, if the reaction for the
genus is positive, individual real-time PCR reactions are conducted in
parallel to determine which species are present” (id.).
Appellants contend that “Hester is not an enabling reference” (id. at
12), as it “merely teaches detecting three human pathogenic species from the
genus Encep[h]alitozoon using real-time PCR” (id.), and “only generally
describes the assay, and is completely silent with respect to multiplex
assays” (id. at 12-13). In any case, Appellants contend that “[t]his is not the
method claimed herein” (id. at 12), as “there is no disclosure or suggestion
. . . of conducting a single assay for both genus and species in a sample”
(id.).
Appellants contend that “[t]he secondary references do not supply
what is missing from Hester” (id. at 13). In particular, Appellants contend
that Bassam “merely describes a nuclease PCR assay that uses a fluorogenic
reporter probe system” which “does not add anything to Hester in teaching
or suggesting a real-time multiplex assay as claimed herein” (id. at 12).
Similarly, Appellants contend that “there is nothing in Stauffer regarding
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parallel species identified as claimed herein, as Stauffer specifically teaches
first testing for the genus and then testing for the species” (id.). Finally,
Appellants contend that “Orlandi merely teaches a template preparation that
can be used in PCR detection of pathogenic parasitic protozoa” and again,
“there is no teaching or suggestion of using unique, species[-]specific primer
sets along with a genus-specific DNA probe” (id.).
Appellants’ arguments are not persuasive. Appellants do not dispute
the Examiner’s finding that multiple sets of species-specific primers capable
of amplifying products detectable with the same genus-level probe were
known (Ans. 9), or that multiplex assays for Encephalitozoon species were
known. Appellants have criticized the references individually, but have not
explained why the Examiner’s rationale for combining the available species-
specific primers with the genus-level probe in a single reaction mixture is
unsound. As noted by the Examiner, one of ordinary skill in this art would
have recognized that performing “a single tube assay” (id. at 6), i.e., a
multiplex assay, using a genus-level probe and multiple pathogenic species-
specific primer sets capable of amplifying products detectable with the
genus-level probe, would not simply reveal that a member of the genus
Encephalitozoon is present in the sample, but would also reveal that at least
one human-pathogenic species is present (id.).
Appellants’ arguments are not sufficient to persuade us that the
Examiner’s rationale for combining the teachings of the references in the
manner required by the claims is unsound.
SUMMARY
The rejection of claims 14, 18, and 21-25 as unpatentable over Hester,
Bassam, Stauffer, and Orlandi is affirmed.
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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

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