Ex Parte Espy et al

Board of Patent Appeals and Interferences

Aug 6, 2010

11459789 (B.P.A.I. Aug. 6, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________________

Ex parte MARK J. ESPY
and
THOMAS F. SMITH,
Appellants1
____________________

Appeal 2010-003551
Application 11/459,789
Technology Center 1600
____________________

Before CAROL A. SPIEGEL, FRANCISCO C. PRATS, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

SPIEGEL, Administrative Patent Judge.

DECISION ON APPEAL2
Appellants appeal under 35 U.S.C. § 134(a) from an Examiner's final
rejection of all pending claims, claims 23, 26, and 27 (Br. 4; Ans.3 2). We
have jurisdiction under 35 U.S.C. § 134. We AFFIRM.

1 The real parties in interest are MAYO FOUNDATION FOR MEDICAL
EDUCATION AND RESEARCH and ROCHE MOLECULAR SYSTEMS,
INC. (Brief On Appeal filed 6 July 2009 ("Br.") at 2).
2 The two-month 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.
3 Examiner's Answer mailed 19 October 2009 ("Ans.").
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The subject matter on appeal is directed to articles of manufacture
containing specified pairs of probes and primers suitable for use in a real-
time polymerase chain reaction ("PCR") for detecting influenza A virus.
Claim 23 is illustrative and reads (Br. 15):
An article of manufacture, comprising:
a pair of influenza A primers, wherein said pair of
influenza A primers comprise a first influenza A primer and a
second influenza A primer, wherein said first influenza A
primer consists of the sequence 5'-TAA CCG AGG TCG AAA
CGT ATG TTC T-3' (SEQ ID NO:1) and wherein said second
influenza A primer consists of the sequence 5'-GGC ATT TTG
GAC AAA GCG TCT A-3' (SEQ ID NO:2);
a pair of influenza A probes, wherein said pair of
influenza A probes comprises a first influenza A probe and a
second influenza A probe, wherein said first influenza A probe
consists of the sequence 5'-CGA AAT CGC GCA GAG ACT
TGA AGA TGT-3' (SEQ ID NO:3) and wherein said second
influenza A probe consists of the sequence 5'-TTG CTG GGA
AAA ACA CAG ATC TTG AGG C-3' (SEQ ID NO:4); and
a donor fluorescent moiety and a corresponding acceptor
fluorescent moiety.

The Examiner rejected claims 23, 26, and 27 as unpatentable under 35
U.S.C. § 103(a) over Smith4 in view of Hall,5 Boivin,6 and Buck7 (Ans. 4-8).

4 Smith et al., Rapid detection of influenza A and B viruses in clinical
specimens by Light Cycler real time RT-PCR, 28 JOURNAL OF CLINICAL
VIROLOGY 51-58 (2003) ("Smith").
5 Hall et al., Variation in Nucleotide Sequences Coding for the N-Terminal
Regions of the Matrix and Nonstructural Proteins of Influenza A Viruses, 38
JOURNAL OF VIROLOGY 1-7 (April 1981) ("Hall").
6 WO 2004/057021 A2, Molecular Methods and Compositions for Detecting
and Quantifying Respiratory Viruses, published 8 July 2004, for Guy Boivin
("Boivin").
7 Buck et al., Design Strategies and Performance of Custom DNA
Sequencing Primers, 27 BIOTECHNIQUES 528-536 (1999) ("Buck").
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The Examiner found that Smith teaches a pair of primers and a pair of
probes, each probe labeled with either a donor or an acceptor fluorescent
moiety, for detecting influenza A virus by real time PCR, albeit not the
specifically claimed pairs of probes defined by SEQ ID NOs: 1 and 2 and
primers defined by SEQ ID NOs: 3 and 4 (Ans. 4). The Examiner relies on
Hall and Boivin for teaching sequences similar (88%) or substantially
identical to the sequences of the claimed primers and probes (id. 4-5). The
Examiner also relies on Buck as evidence of a reasonable expectation of
success when using primers selected according to ordinary criteria (id. 7-8).
The Examiner concluded that the claimed primers and probes would have
been prima facie obvious over the cited references in the absence of
secondary considerations of patentability (id. 6).
Appellants argue that primer and probe design for real-time PCR
amplification is not always predictable, citing Guidelines,8 Csordas,9
Elnifro,10 Tichopad,11 and Abd-Elsalam12 in support of their position (Br. 9-
10). According to Appellants, DNA sequencing requires only forward

8 University of Chicago Cancer Research Center DNA Sequencing Facility,
Choosing Primers for Sequencing, downloaded from http://cancer-
seqbase.uchicago.edu/primers.html ("Guidelines").
9 Csordas et al., Comparison of primers for the detection of Salmonella
enterica serovars using real-time PCR, 39 LETTERS IN APPLIED
MICROBIOLOGY 187-193 (2004) ("Csordas").
10 Elnifro et al., Multiplex PCR: Optimization and Application in Diagnostic
Virology, 13 CLINICAL MICROBIOLOGY REVIEWS 559-570 (2000).
11 Tichopad et al., Inhibition of real-time RT-PCR quantification due to
tissue-specific contaminants, 18 MOLECULAR AND CELLULAR PROBES 45-50
(2004) ("Tichopad").
12 Kamel A. Abd-Elsalam, Minireview: Bioinformatic tools and guideline for
PCR primer design, 2 AFRICAN JOURNAL OF BIOTECHNOLOGY 91-95 (2003)
("Abd-Elsalam").
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primers, whereas PCR amplification requires both forward and reverse
primers. Thus, insofar as Buck relates to DNA sequencing, Buck is not
representative of primers for PCR amplification (id. 9). Appellants further
argue that the claimed sequences provide "an extremely high sensitivity and
specificity toward their targets" and that the probes can be used to further
increase the accuracy of detecting influenza A as shown by Examples 2 and
4 of their specification (id. 12). Further according to Appellants, there is no
motivation to select the particularly claimed primer and probe pairings from
a very large genus of oligonucleotides complementary to the full-length gene
sequence of influenza A (id. 10-13). In particular, Appellants maintain that
there is no case law holding that "a longer sequence makes per se obvious
specific primer and probe sequences from within that longer sequence", i.e.,
"that two oligonucleotides that have different sequences but are
complementary to the same target sequence are 'structural homologs'" (id.
11).
According to Appellants, claims 23, 26, and 27 stand or fall together
(Br. 9). Therefore, we decide this appeal on the basis of claim 23. 37 C.F.R.
§ 41.37(c)(1)(vii).
At issue is whether the claimed primers and probes defined by SEQ
ID NOs: 1-4 would have been obvious based on standard criteria used to
design primers for real-time PCR use and, if so, whether Appellants have
provided objective evidence of nonobviousness.
II. Findings of Fact
The following findings of fact ("FF") are supported by a
preponderance of the evidence of record.
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[1] Respiratory tract infection caused by influenza viruses is a
significant cause of morbidity and mortality and, thus, there is a need
for rapid detection and diagnosis of influenza (Spec.13 1:13-30;
Smith abstract; Boivin 1:17-24 and 9:25-28).
[2] Smith teaches detecting influenza A virus by real-time PCR analysis
with primer/probe sets designed to recognize an N-terminal 300 bp
region of the matrix gene (M1) as the viral target sequence based on
criteria of Roche Light Cycler probe design software, version 1.0,
available from Roche Diagnostics (Smith abstract; p. 53, col. 2, ¶ 2;
p. 54, col. 1, ¶ 1).
[3] Smith does not disclose the consensus sequence of the M1 gene
region used to design its probes and primers for the real-time PCR
(Smith p. 53, col. 2, ¶ 2).
[4] Hall discloses the N-terminal sequence of a human influenza virus A
M1 (Hall Figure 1).
[5] Smith does disclose the sequences of its probes and primers, which
are not identical to SEQ ID NOs: 1-4 of the claimed probes and
primers.
[6] Boivin describes known PCR primer sequences for amplifying
influenza A virus useful in a multiplex PCR for detecting respiratory
viruses, i.e., SEQ. ID. Nos. 139 and 140 (hereinafter "primers 139
and 140") (Boivin abstract; 24:23-24; 35:29-30).
[7] According to Tables 10 and 12 of Boivin, forward and reverse
primers 139 and 140 were used to amplify a 245 bp region of the
matrix gene of influenza A virus (Boivin 72, 74).

13 Specification of Application 11/459,789 ("Spec.").
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[8] The Examiner found that Boivin primer 140 was substantially
identical to the claimed primer defined by SEQ ID NO:2 (Ans. 4-5).
[9] Boivin also provides DNA sequences of human influenza virus A
strains Hong Kong and Charlottesville, i.e., SEQ. ID. NOs. 130 and
131 (Boivin Figures 42-43/52), and viral probe SEQ. ID. NO. 162
(id. Table 11, p. 73).
[10] The Examiner found that the claimed probes defined by SEQ ID
NOs: 3 and 4 were substantially identical to nucleotides 9-117 [sic,
9-17] and 120-147, respectively, within Boivin SEQ ID NO. 130,
while the claimed primer defined by SEQ ID NO:1 was 88%
identical to nucleotides 39-60 within Boivin SEQ ID NO. 130 (Ans.
4-5).
[11] Table 1 of Buck enumerates optimal and observed characteristics of
primers for DNA sequencing or PCR, i.e.,

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[12] According to the Guidelines, DNA sequencing primers should have a
melting temperature in the range of 50o-60oC; lack dimerization
capability, hairpin formation capability, and secondary priming sites;
will be about 18 to 30 nucleotides long; and, have a GC content of
40 to 60% (Guidelines 1-2).
[13] The Guidelines "strongly recommend the use of computer software
to design primers with these characteristics", e.g., LaserGene, Oligo,
MacVector, and the GCG suite, but note that "no set of guidelines
will always accurately predict the success of a primer" (Guidelines
2).
[14] Csordas teaches that primers originally designed for end-point PCR
may yield poor sensitivity in real-time PCR because of their
tendency to form primer dimers (Csordas p. 187, col. 1, ¶ 1; p. 191,
col. 2, ¶ 5).
[15] Csordas uses software (Primer Premier 5.0) to design a primer set for
real-time PCR which, given a particular target sequence and primer
set, searches for potential primer dimers as well as for locations
outside the target sequence where primers have a tendency to anneal,
leading to nonspecific product formation (Csordas p. 189, ¶ bridging
cols. 1-2).
[16] Csordas uses software (Primer Premier 5.0, PREMIER Biosoft
International) to design a primer set given a particular target
sequence (Csordas p. 189, col. 1, ¶ 4).
[17] Elnifro explains that in multiplex PCR more than one target
sequence can be amplified by using more than one pair of primers in
the reaction (Elnifro, p. 559, col. 1, ¶ 1), however the presence of
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more than one primer pair increases the chances of nonspecific
amplification products, primarily because of primer dimer formation
(id., col. 2, ¶ 4).
[18] Elnifro states that
[e]mpirical testing and a trial-and-error approach
may have to be used when testing several primer
pairs, because there are no means to predict the
performance characteristics of a selected primer
pair even among those that satisfy the general
parameters of primer design. However, special
attention to primer design parameters such as
homology of primers with their target nucleic acid
sequences, their length, the GC content, and their
concentration have to be considered. Ideally, all
the primer pairs in a multiplex PCR should enable
similar amplification efficiencies for their
respective target. This may be achieved through
the utilization of primers with nearly identical
optimum annealing temperatures (primer length of
18 to 30 bp or more and a GC content of 35 to
60% may prove satisfactory) and should not
display significant homology either internally or to
one another. [Elnifro p. 560, col. 1, ¶ 1, endnotes
omitted.]
[19] Tichopad discusses inhibition of real-time reverse transcription-PCR
due to tissue-specific contaminants, observing that this affect can be
ameliorated in part by appropriate primer selection (Tichopad
abstract).
[20] According to Abd-Elsalam, "[m]aybe the most critical parameter for
successful PCR is the design of Primers" (Abd-Elsalam p. 94, col. 1,
¶ 2).
[21] Abd-Elsalam
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provide[s] a guide to choosing the most efficient
way to design a new specific-primer by applying
current publicly available links and Web services.
Also … general recommendations for the design
and use of PCR primers. [Abd-Elsalam abstract.]
[22] Tables 1, 2, and 3 of Abd-Elsalam describe twenty online primer
design sites, six PCR oligonucleotide resources for predicting primer
parameters such as melting temperature, and eighteen PCR primer
design software programs for personal computers, respectively (Abd-
Elsalam pp. 92-93).
[23] Abd-Elsalam provides express guidelines for choosing two PCR
amplification primers, including primer length, melting temperature,
GC content, 3'-end sequence, avoidance of primer sequences leading
to self-dimerization or primer-dimer formation (Abd-Elsalam pp. 94-
95).
[24] According to the Specification, primers that amplify an influenza A
molecule can be designed using a computer program, e.g.,. OLIGO,
taking into account important features including similar melting
temperatures for the members of each pair of primers and primer
length, typically 15 to 30 nucleotides (Spec. 7:23-8:2).
[25] Further according to the Specification, probes can be designed in a
manner similar to primers, e.g., with similar melting temperatures
and lengths also generally from 15 to 30 nucleotides (Spec. 8:3-21).
[26] The Specification states that "the PCR test method compared with
standard cell culture [resulted in]: sensitivity, 96%, specificity, 92%;
positive predictive value, 53%; and negative predictive value, 100%"
based on the results of Example 2 (Spec. 24:23-25:2).
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[27] According to Example 2 of the Specification, of 557 tested clinical
samples, 49 were positive by both PCR and cell culture methods,
463 were negative by both PCR and cell culture methods, 43 were
positive by PCR but not cell culture, and 2 were positive by cell
culture but not PCR (Spec. 24:19-22).
[28] According to Example 4 of the Specification,
[i]nfluenza A virus infections were detected
by sensitive real-time PCR technology in 10 of 50
(20%) study patients after 7 days of hospitalization
(Table 3). In contrast, only 5 of 50 (10%) patients
were positive by the shell-vial [cell culture] assay
after 7 days and none [were] positive using
conventional tube cell culture methods (Table 3).
These data suggest that patients can shed influenza
A virus beyond the CDC recommended 5 day
droplet isolation period. Importantly, PCR results
may not equate with active virus; however, a
positive molecular result may indeed indirectly
indicate infectious or active virus since cell culture
techniques have reduced sensitivity compared to
PCR. [Spec. 26:9-16.]
III. Discussion
A. Legal principles
"One of the ways in which a patent's subject matter can be proved
obvious is by noting that there existed at the time of invention a known
problem for which there was an obvious solution encompassed by the
patent's claims." KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 419-20
(2007). "When there is a design need or market pressure to solve a problem
and there are a finite number of identified, predictable solutions, a person of
ordinary skill has good reason to pursue the known options within his or her
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technical grasp." Id. Furthermore, "[o]bviousness does not require absolute
predictability of success.… For obviousness under § 103, all that is required
is a reasonable expectation of success." In re O’Farrell, 853 F.2d 894, 903-
04 (Fed. Cir. 1988).
B. Analysis
There is a recognized need to detect and diagnose respiratory tract
infection caused by influenza A virus (FF 1). Smith teaches detecting
influenza A virus by real-time PCR analysis using primer/probe sets
designed to target the M1 (matrix) gene region of influenza A virus (FF 2).
The DNA sequence of the M1 gene is known (FF 4). It is not only
conventional, but also strongly recommended (FF 13), in the art to use
primer design software to design primers for use in real-time PCR based on
defined criteria, such as nucleotide length, melting temperature in the range
of about 50o-60oC, about 40-60% GC content, and avoiding significant
homology within a primer or between primers (FF 3, 11, 12, 15, 16, 18, 21-
23). Indeed, as noted by the Examiner (Ans. 10-11), the instant
Specification describes using primer design software, taking into account
nucleotide length and melting temperatures, etc. to obtain primers and
probes (FF 24-25). Thus, given a known influenza A detection target
sequence in the prior art (the M1 gene), we agree with the Examiner that one
of ordinary skill in the art would have had every motivation to use
conventional primer design software and every reasonable expectation of
success in obtaining the primers and probes of claim 23.
Notably, the Guidelines state that no set of guidelines for primer
design will always accurately predict the success of a primer (FF 13), but
obviousness does not require absolute predictability of success, only a
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reasonable expectation of success. In re O’Farrell, 853 F.2d at 903-04.
Here, the prior art cited by the Examiner, particularly Buck, as well as the
rebuttal prior art cited by Appellants consistently teach using the same or
substantially the same criteria to design primers and provide a reasonable
expectation of success of detecting a target DNA sequence (FF 3, 11, 12, 15,
16, 18, 21-23). Unlike in In re Deuel, 51 F.3d 1552 (Fed. Cir. 1995), one of
ordinary skill in the art is not selecting a particular DNA sequence from
among a large number of degenerate variants, but rather selecting particular
DNA sequences (primers and probes) having particular art-recognized
parameters, e.g., nucleotide length, GC content, melting temperature, and
homology both within and without the particular DNA sequence. Similarly,
unlike in In re Bell, 991 F.2d 781, 784 (Fed. Cir. 1993), here the prior art is
not suggesting a nearly infinite number of primer and/or probe possibilities
without any suggestion of which of those possibilities to select. Therefore,
we agree with the Examiner that the subject matter of claim 23 is prima
facie obvious over the applied prior art.
Appellants argue that Examples 2 and 4 of their Specification
demonstrate that the claimed probes and primers exhibit "extremely high
sensitivity and specificity toward their targets" (Br. 12). However,
Examples 2 and 4 compare the results of a real-time PCR method to the
results of cell culture methods (FF 26-29), not to the closes prior art, the
real-time PCR method of Smith. However, to establish that claimed subject
matter yields an unexpected result, the claimed subject matter must be
compared to the closest prior art. In re Baxter-Travenol Labs., 952 F.2d
388, 392 (Fed. Cir. 1991) ("[W]hen unexpected results are used as evidence
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of nonobviousness, the results must be shown to be unexpected compared
with the closest prior art."). This Examples 2 and 4 fail to do.
C. Conclusion
Therefore, we will sustain the rejection of claims 23, 27, and 28 under
35 U.S.C. § 103(a) over Smith in view of Hall, Boivin, and Buck. Based on
the evidence of record, the claimed primers and probes defined by SEQ ID
NOs: 1-4 would have been obvious based on standard criteria used to design
primers for real-time PCR use and Appellants have not provide evidence
secondary considerations of patentability sufficient to overcome that
conclusion of obviousness.
IV. Order
Upon consideration of the record, and for the reasons given, it is
ORDERED that the decision of the Examiner to reject claims 23, 27,
and 28 as unpatentable under 35 U.S.C. § 103(a) over Smith in view of Hall,
Boivin, and Buck is AFFIRMED; and,
FURTHER ORDERED that no period for taking any subsequent
action in connection with this appeal may be extended under 37 C.F.R. §
1.136(a)(1)(iv).
AFFIRMED

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