Ex Parte Kostrikis

Board of Patent Appeals and Interferences

Jul 2, 2010

10917421 (B.P.A.I. Jul. 2, 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.
10/917,421 08/13/2004 Leondios G. Kostrikis 42392.206066-old c/m no. 4018
441 7590 07/02/2010
SMITH, GAMBRELL & RUSSELL
1130 CONNECTICUT AVENUE, N.W., SUITE 1130
WASHINGTON, DC 20036
EXAMINER
HUMPHREY, LOUISE WANG ZHIYING
ART UNIT PAPER NUMBER
1648
MAIL DATE DELIVERY MODE
07/02/2010 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 LEONDIOS G. KOSTRIKIS
__________

Appeal 2010-001111
Application 10/917,421
Technology Center 1600
__________

Before DEMETRA J. MILLS, FRANCISCO C. PRATS, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

MILLS, Administrative Patent Judge.

DECISION ON APPEAL1

This is an appeal under 35 U.S.C. § 134. The Examiner has rejected
the claims for obviousness. We have jurisdiction under 35 U.S.C. § 6(b).

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 2010-001111
Application 10/917,421

STATEMENT OF CASE
The following claim is representative.
1. A molecular-beacon-based multi-allelic RT-real-time- PCR multiplex
assay for a SARS virus comprising,
a) obtaining a sample;
b) isolating RNA from the sample;
c) placing the isolated RNA in a tube along with primer pairs specific
for S, E, M, and N genes of the SARS virus wherein the S primer pair
includes 5'-AGGCTGTAAGAA-3' (SEQ ID NO: 18), the E primer pair
includes 5'-TATTGCAGCAGCAGTAC-3' (SEQ ID NO: 38), the M primer
pair includes 5'-AAGCAAGTAG-3' (SEQ ID NO: 59), and the N primer
pair includes 5'-TATTGCAGCAGTAC-3' SEQ ID NO: 80),
d) reverse transcribing the isolated RNA in the presence of a RT
transcriptase to form a cDNA unique for each of the S, E, M and N SARS
viral genes,
e) real-time amplifying the SARS cDNA in the presence of four
distinct types of molecular beacons, each labeled with the same fluorophore
and specific for a different SARSCoV gene selected from S, E, M and or N
viral genes, wherein the molecular beacons are selected from the group
consisting of:

S Gene
LK249 5'-FAM-
CCCACGCCAGAAGGTAGATCACGAACTACACGTGGG-3’-
Dubcyl (SEQ ID NO: 14);

E Gene
LK253 5'-FAM-
CCTCCGCACGAAAGCAAGAAAAAGAAGTACGCCGGAGG-3'-
Dubcyl (SEQ ID NO: 34);

M Gene
LK257 5'-FAM-
CCTCCGACCCMTTMTPTCTGTAGACAGCAGCCGGAGG-3’-
Dubcyl (SEQ ID NO: 55), and

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N Gene
LK261 5'-FAM-
CCTCCGTACCATCTGGGGCTGAGCTCTTTCATCGGAGG-3'-
Dubcyl (SEQ ID NO: 76); and
wherein the S, E, M and N gene specific primer pairs are selected
from the group consisting of,

S Gene
LK251 5'-CTCTATGTTTATMGGGCTATCAACC-3' (SEQ ID NO:
16)
LK252 5'-CCAAGAGGCAACTTAAAAATAGGTTTC- 3' (SEQ ID
NO: 17);

E Gene
LK255 5'- CGGAAGAAACAGGTACGTTAATAG -3' (SEQ ID NO:
36)
LK256 5'- AAGCGCAGTMGGATGGCTA - 3' (SEQ ID NO: 37);

M Gene
LK259 5'- CTTGTTTTCCTCTGGCTCTTG -3' (SEQ ID NO: 57)
LK260 5'- CAAGCCATTGCAATCGCAATC- 3' (SEQ ID NO: 58);
and

N Gene
LK263 5'- ACGAGTTCGTGGTGGTGAC -3' (SEQ ID NO: 78)
LK264 5'- CGTAGGGAAGTGAAGCTTC- 3' (SEQ ID NO: 79); and

f ) measuring fluorescence, which is a collective measure of the presence of
the SARS virus.

Additional Appealed claims may be found in the Claims Appendix to the
Brief.

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Cited References
Peiris et al., Clinical progression and viral load in a community outbreak of
coronavirus-associated SARS pneumonia: a prospective study, 361 LANCET
1767-1772 (2003).

Wu et al., Gene detection of severe acute respiratory syndrome-related
coronavirus, 32 CHINESE JOURNAL OF PATHOLOGY 212-214 (2003).

Cook et al., Development of a multiplex real-time reverse transcriptase-
polymerase chain reaction for equine infectious anemia virus (EIAV), 105 J.
VIROL. METH. 171-179 (2002).

GenBank Accession No. AY274119.3, submitted 13 April 2003, and
AY278741, submitted 17 April 2003.

Buck et al., Design Strategies and Performance of Custom DNA Sequencing
Primers, 27 BIOTECHNIQUES 528-536 (1999).

Grounds of Rejection
1. Claims 1, 3, 12, 14, 27 and 32 are rejected under 35 U.S.C. § 103(a) as
being unpatentable over Peiris in view of Wu, Cook, Buck, GenBank
GI:30027617 and GenBank GI:30248028.

Discussion
ISSUE
The Examiner concludes
it would have been prima facie obvious to one of ordinary skill in
the art at the time the invention was made to have modified the
SARS CoV detection system of Peiris to include any other
primers and probes based on the SARS genome sequences
provided by GenBank G1:30027617 and G1:30248128 and the
consensus sequences of the genes encoding the S, E, M, and N
proteins.
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(Ans. 9.)
Appellant contends that Peiris does not mention molecular beacons,
and Wu does not describe a multi-gene target (App. Br. 6). Appellant argues
that none of the Buck sequences is the same as those claimed (id. at 7) and
that there is no motivation to modify the primary reference and the
references do not teach Appellant’s assay (id. at 8).
The issue is: Do the cited references support the Examiner’s
conclusion of obviousness of the pending claims. Is there a reason to
combine the cited references?

FINDINGS OF FACT
1. The instant claims are directed to a molecular-beacon-based multi-allelic
RT real- time-PCR assay for a SARS virus, comprising:
a) obtaining a sample;
b) isolating RNA from the sample;
c) reverse transcribing the isolated RNA in the presence of the following
gene specific primers:
S-RT 5'-AGGCTGTAAGAA-3' (SEQ ID NO: 18),
E-RT 5'-TATTGCAGCAGCAGTAC-3' (SEQ ID NO: 38),
M-RT 5'-AAGCAACGAAGTAG-3' (SEQ ID NO: 59), and
N-RT 5'-TATTGCAGCAGTAC-3' SEQ ID NO: 80);
d) real-time amplifying SARS cDNA in the presence of S-, E-, M-, and N-
gene specific primer pairs and four distinct molecular beacons specific for S,
E,M and N vial genes and selected from LK 249, LK253, LK257, and LK
261 or functional equivalents thereof; and
e) measuring fluorescence.
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2. The Examiner finds that
Peiris disclose the claimed method of reverse transcriptase
polymerase chain reaction (RT-PCR) for SARS coronavirus done
directly on all clinical samples. Total RNA from clinical samples
was reverse transcribed with random hexamers and cDNA was
amplified with primers. For real-time quantitative PCR assays,
cDNA was amplified in an SYBR Green I (label for the
molecular beacon) fluorescence reaction. See page
1768, right column, lines 7-19.

(Ans. 6.)
3. “Peiris do not disclose multiple gene-specific primer and molecular
beacon (fluorescently labeled probe) sequences directed to S, E, M and N
genes of the SARS CoV genome.” (Id.)
4. The Examiner finds that
Wu disclose a real-time RT-PCR assay for SARS-related
coronavirus in human whole blood using a pair of primers and a
probe (molecular beacon) (Figure 1) that had been designed to be
specific for the recognition of a highly conserved region between
position 15121 and 15661 of the SARS-related coronavirus
(SARS CoV) sequences obtained from GenBank (G1:
130027616), which is the genome sequence of SARS CoV
Urbani strain. In the real-time RT-PCR assay, the extent of
SARS related coronavirus amplification was measured in terms
of the increase in fluorescence during the amplification process.
See Abstract.

(Id. at 7.)
5. “Neither Peiris or Wu disclose a multiplex RT-PCR.” (Id.)
6. “Cook disclose a multiplex real-time RT-PCR for detecting equine
infectious anemia virus (EIAV) and expressly suggest a multiplex system to
compensate for variations inherent in sample preparation, so that the EIAV
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RNA copy number and the nucleic acid recovery rate could be calculated
simultaneously. See Abstract.” (Ans. 7.)
7. The Examiner finds that
GenBank G1:30027617 teaches the complete genome of
the SARS CoV Urbani strain. The reference specifically teaches
the positions of the coding regions for SARS CoV proteins S, E,
M, and N, in the genome at positions 21492-25259, 26117-
26347, 26398-27063, and 28120-29388 of the sequence.
Relevant to the requirements of claims 1 and 33, the sequence
provided in GenBank G1: 30027617 comprises sequences that
are complementary to the claimed molecular probe sequences
(omitting the stem-loop forming sequences) of SEQ ID NO:14
(positions 22103-22126 of G1 :30027617 are complementary to
SEQ ID NO:14), SEQ ID NO:34 (positions 26164- 26187), SEQ
ID NO:55 (positions 26596-26621), and SEQ ID NO:76
(positions 28423- 28447).

(Id. at 7-8.)
8. “Relevant to the requirements of claim 28, the sequence provided in
GenBank GI: 30027617 comprises sequences identical to the primer
sequences of SEQ ID NO:16 (positions 22071 -22096 of G1 :30027617 are
identical to SEQ ID NO:16), SEQ ID NO:17 (positions 22139-22165), and
SEQ ID NO:36 (positions 26133-26156).” (Id. at 8.)
9. The Examiner finds that
GenBank GI:30248028 teaches the complete genome of
the SARS CoV TOR2 strain. The reference specifically teaches
the positions of the coding regions for SARS CoV proteins S, E,
M, and N, in the genome at positions 21492-25259, 26117-
26347, 26398-27063, and 28120-29388 of the sequence.
Relevant to the requirements of instant claims, the sequence
provided in GenBank GI: 30248028 comprises a sequence
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identical to the primer sequence of SEQ ID NO:37 (positions
26227-26208).

(Ans. 8.)
10. The Examiner finds that
Buck expressly provides evidence of the functional
equivalence of primers. Specifically, Buck discloses primer
submissions from a number of labs (39) (page 532, column 3),
with 69 different primers being submitted (see page 530, column
1). Buck also tested 95 primers spaced at 3 nucleotide intervals
along the entire sequence at issue, thereby testing more than 1/3
of all possible 18-mer primers on the 300 base pair sequence
(see page 530, column 1).

(Id.)
11. The Examiner finds that
When Buck tested each of the primers selected by the methods of
the different labs, Buck found that every single primer worked
(see page 533, column 1). Only one primer ever failed and that
primer functioned when repeated. Further, every single control
primer functioned as well (see page 533, column 1). Buck
expressly states: "The results of the empirical sequencing
analysis were surprising in that nearly all of the primers yielded
data of extremely high quality (page 535, column 2)".

(Id.)
12. The Examiner finds that
Therefore, Buck provides direct evidence that all primers would
be expected to function, and in particular, all primers are selected
according to the ordinary criteria, however different, and used by
39 different laboratories. It is particularly striking that all 95
control primers functioned, which represent 1/3 of all possible
primers in the target region. This clearly shows that every primer
would have a reasonable expectation of success.

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Application 10/917,421

(Id. at 8-9.)

13. The Examiner concludes that
It would have been prima facie obvious to one of ordinary
skill in the art at the time the invention was made to have
modified the SARS CoV detection system of Peiris to include
any other primers and probes based on the SARS genome
sequences provided by GenBank G1 :30027617 and GI
:30248128 and the consensus sequences of the genes encoding
the S, E, M, and N proteins. Such primers and probes would
include the claimed gene-specific primers and molecular probes.

(Ans. 9.)

14. The Examiner concludes that one “would have been motivated to create
a system containing the different primers in order to have additional target-
specific reagents in a multiplex for the detection of SARS variants in patient
samples.” (Id.)
15. The Examiner concludes that “[o]ne would have a reasonable
expectation of success in using any primers or probes based on the teachings
of Buck regarding the functional equivalency of primers in primer extension
based reactions. Thus, the invention as a whole was clearly prima facie
obvious to one of ordinary skill in the art at the time the invention was
made.” (Id.)
16. Cook teaches design of PCR primers and probes “using OLIGO
version 3.4 software . . . based on nucleotide sequence . . . plus information
from GenBank accession numbers” (Cook 172, col. 2).

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PRINCIPLES OF LAW
The question of obviousness is resolved on the basis of underlying
factual determinations including: (1) the scope and content of the prior art;
(2) the level of ordinary skill in the art; (3) the differences between the
claimed invention and the prior art; and (4) secondary considerations of
nonobviousness, if any. Graham v. John Deere Co., 383 U.S. 1, 17 (1966).
The Supreme Court has emphasized that “the [obviousness] analysis need
not seek out precise teachings directed to the specific subject matter of the
challenged claim, for a court can take account of the inferences and creative
steps that a person of ordinary skill in the art would employ.” KSR Int'l Co.
v. Teleflex Inc., 550 U.S. 398, 418 (2007).
“[W]hen the question is whether a patent claiming the combination of
elements of prior art is obvious,” KSR directs that “a court must ask whether
the improvement is more than the predictable use of prior art elements
according to their established functions.” Id. at 417.
The Supreme Court has recently emphasized that “the [obviousness]
analysis need not seek out precise teachings directed to the specific subject
matter of the challenged claim, for a court can take account of the inferences
and creative steps that a person of ordinary skill in the art would employ.”
Id. at 418. “The combination of familiar elements according to known
methods is likely to be obvious when it does no more than yield predictable
results.” Id. at 416. Moreover, an “[e]xpress suggestion to substitute one
equivalent for another need not be present to render such substitution
obvious.” In re Fout, 675 F.2d 297, 301 (CCPA 1982).
Kubin commented that, “[r]esponding to concerns about uncertainty in
the prior art influencing the purported success of the claimed combination,
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this court [in O'Farrell] stated: ‘[o]bviousness does not require absolute
predictability of success … all that is required is a reasonable expectation
of success.”’ In re Kubin, 561 F.3d 1351, 1360 (Fed. Cir. 2009).

ANALYSIS
We essentially agree with the Examiner’s fact finding, statement of
the rejection and responses to Appellant’s arguments and adopt them as our
own. We provide the following additional comments.
The Examiner concludes that one would have been motivated to
create a system containing the different primers in order to have additional
target-specific reagents in a multiplex for the detection of SARS variants in
patient samples.
Appellant contends that
The teachings of the references included in the statement of
rejection, taken alone or in combination, are incomplete and do not
provide the requisite evidentiary, basis that would establish a proper
prima facie case of obviousness. None of the references teach or
suggest the simultaneous use of multiple targets, in particular, the
SARS S, E, M and N genes, nor their simultaneous measurement in a
single tube. None of the references teach the primer or beacon
sequences. [Emphasis removed.]

(App. Br. 5-6.)
We conclude that the Examiner has established a prima facie case of
obviousness on the evidence before us. Applying the KSR standard of
obviousness to the findings of fact, we agree with the Examiner that it would
have been obvious to one of ordinary skill in the art at the time the invention
was made to have modified the SARS CoV detection system of Peiris to
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include any other primers and probes based on the SARS genome sequences
provided by GenBank G1:30027617 and GI:30248128 and the consensus
sequences of the genes encoding the S, E, M, and N proteins. Such primers
and probes would include the claimed gene-specific primers and molecular
probes. (Ans. 9.) We conclude, as did the Examiner, that one “would have
been motivated to create a system containing the different primers in order
to have additional target-specific reagents in a multiplex for the detection of
SARS variants in patient samples.” (Id.) We conclude that one of ordinary
skill in the art would have had a reasonable expectation of success because
Buck teaches the functional equivalence of primers and their usefulness and
effectiveness in DNA sequencing while Cook teaches the usefulness of
multiplex RT-PCR in diagnostic assays. Such a combination is merely a
“predictable use of prior art elements according to their established
functions.” KSR, 550 U.S. at 417.
Mechanistically, the Peiris primers, the Wu PCR primers, the Buck
sequencing primers, the Cook primers and Appellants’ claimed primers, all
operate using the same principles. The methods require that the single
stranded oligonucleotide primers hybridize to their single stranded
complement in a target DNA, where a thermostable DNA polymerase then
binds the primer/target DNA complex and extends the primer along the
target to form a double-stranded DNA with fully complementary sequence.
Supporting a finding of a reasonable expectation of success, Buck provides
evidence that virtually all primers selected from a target sequence are
capable of undergoing hybridization and extension by a polymerase.
Therefore, one of ordinary skill in the art would have expected primers to
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the GenBank SARS genomic sequences would have been useful in a
diagnostic assay for SARS variants.
In comparing the obviousness of the instant primers to the
obviousness issue in Kubin, we note that unlike in Kubin where the NAIL
sequence was unknown, the complete sequence from which the instant
primers were selected was disclosed in Genbank (FF 7-9). Additionally,
Cook teaches that computer software to aid in selection of the primers for
the specific multiplex real-time reverse transcriptase PCR assay was
commercially available and was successfully used to select multiple primer
pairs for a different virus (FF 16).
Thus, if Kubin finds that cloning an unknown gene sequence had a
“reasonable expectation of success,” we conclude that it is more than
reasonable to find that selection of particular real-time primer sequences
from a known sequence using commercially available software “would have
had a resoundingly ‘reasonable expectation of success’ in deriving the
claimed invention in light of the teachings of the prior art.” Kubin, 561 F.3d
at 1360.
We do not find any indication of secondary considerations by
Appellant in rebuttal to the Examiner’s prima facie case of obviousness.
Furthermore, Appellants provide no evidence why there would not have
been a reasonable expectation of success in view of the teachings of the cited
references.

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CONCLUSION OF LAW
The cited references support the Examiner’s obviousness rejection and
the Examiner has provided a sufficient reason or motivation to combine the
cited references.
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

SMITH, GAMBRELL & RUSSELL
1130 CONNECTICUT AVENUE, N.W., SUITE 1130
WASHINGTON, DC 20036
14