Ex Parte Gyllensten et al

Board of Patent Appeals and Interferences

Oct 17, 2011

10529447 (B.P.A.I. Oct. 17, 2011)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte ULF GYLLENSTEN and MARTIN MOBERG

Appeal 2010-006853
Application 10/529,447
Technology Center 1600
__________

Before TONI R. SCHEINER, LORA M. GREEN, and STEPHEN WALSH,
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
claims 9-14 and 18-26, directed to a kit for detection and quantification of
oncogenic human papillomaviruses. The claims have been rejected as
obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We reverse.
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STATEMENT OF THE CASE
“Infection by certain types of human papillomavirus (HPV) is the
single most important risk factor for the development of cervical cancer”
(Spec. 1: 19-20). “More than 95% of cervical cancer biopsies have been
found to contain DNA of high-risk HPV types, most commonly HPV 16,
followed by HPV 18, 45, 31 and 33” (id. at 1: 20-22). In addition, “HPV
titer may represent a powerful means of determining whether an infection
will progress into cervical cancer” (id. at 2: 12-13).
“Many of the PCR systems developed for HPV detection involve an
amplification step followed by a separate step for identification of individual
HPV types” (id. at 1: 30-31). The present Specification, on the other hand,
discloses “an assay and kit for . . . detecting and quantifying the HPV types
most commonly detected in cervical tumors, while minimizing the number
of parallel reactions performed for each sample” (id. at 2: 22-25).
The disclosed assay involves dividing a patient sample into sub-
samples, detecting the presence of two or more HPV types in a single sub-
sample “using a specific primer for amplification of each virus . . . , whereby
the primers are designed not to compete during the amplification-reaction,
and a specific probe for each virus . . . , whereby the probes are designed not
to compete during the amplification-reaction and the detection phase” (id. at
3: 5-9), and calculating the amount of each virus “by analysis of a nuclear
gene in a given amount of another of said sub-samples in a separate
amplification reaction” (id. at 3: 10-11).
The present invention is directed to a kit “for quantitative and
qualitative determination of oncogenic HPV to predict the risk of HPV
infection resulting in cervical carcinoma” (Spec. 1: 5-7).
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Claims 9, 10, 13, and 21 are representative of the subject matter on
appeal:
9. A kit for detection and quantification of human papillomavirus,
comprising a) the amplification primers SEQ ID NO: 1, SEQ ID NO: 2, SEQ
ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5/ SEQ ID NO: 6, SEQ ID NO: 7
and SEQ ID NO: 8, and the probes SEQ ID NO: 21, SEQ ID NO: 22 and
SEQ ID NO: 23/SEQ ID NO: 24, for HPV 16, 31, 18, 45; and optionally b)
the amplification primers SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11,
SEQ ID NO: 12, SEQ ID NO: 13/SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID
NO: 16 and SEQ ID NO: 17/SEQ ID NO: 18 and the probes SEQ ID NO:
25, SEQ ID NO: 26 and SEQ ID NO: 27/SEQ ID NO: 28/SEQ ID NO: 29
for HPV 33, 35, 39, 52, and 58.
10. A kit according to claim 9, further comprising c) the amplification
primers SEQ ID NO: 19 and SEQ ID NO: 20 and the probe SEQ ID NO: 30,
for detection and quantification of the amount of a human single copy gene.
13. A kit according to claim 10, further comprising d) three different
fluorophores.
21. A kit for detection and quantification of human papillomavirus,
comprising a) forward and reverse E7 amplification primers for HPV 16,
forward and reverse E1 amplification primers for HPV 18 and 45, and
forward and reverse E6 amplification primers for HPV 31, and probes
therefore; and optionally b) forward and reverse L1 amplification primers
for HPV 33, 52 and 58, forward and reverse E7 amplification primers for
HPV 39, and forward and reverse E4 amplification primers for HPV 35, and
probes therefore.
The Examiner relies on the following evidence:
Gissmann et al. US 6,228,368 B1 May 8, 2001
Kroeger et al. US 2002/0137021 A1 Sep. 26, 2002

K. Seedorf et al., Identification of early proteins of the human papilloma
viruses type 16 (HPV 16) and type 18 (HPV 18) in cervical carcinoma cells,
6 THE EMBO JOURNAL 139-144 (1987).

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Han-Wook Yoo et al., Hydroxymethylbilane Synthase: Complete Genomic
Sequence and Amplifiable Polymorphisms in the Human Gene, 15
GENOMICS 21-29 (1993).
David C. Swan et al., A Sensitive, Type-Specific, Fluorogenic Probe Assay
for Detection of Human Papillomavirus DNA, 35 JOURNAL OF CLINICAL
MICROBIOLOGY 886-891 (1997).
G.A. Buck et al., Design Strategies and Performance of Custom DNA
Sequencing Primers, 27 BIOTECHNIQUES 528-536 (1999).
Xavier Sastre-Garau et al., Distinct patterns of alteration of myc genes
associated with integration of human papillomavirus type 16 or type 45 in
two genital tumours, 81 JOURNAL OF GENERAL VIROLOGY 198-199 (2000).
M.D. Goldsborough et al., GenBank Accession No. J04353 (1989).
H.W. Yoo et al., GenBank Accession No. M95623 (1993).
X. Sastre-Garau et al., GenBank Accession No. AJ242956 (2000).
The Examiner rejected claims 9 and 21 under 35 U.S.C. § 103(a) as
unpatentable over Kroeger, Gissmann, Goldsborough (with GenBank
Accession No. J04353), Seedorf, Sastre-Garau (with GenBank Accession
No. AJ242956), and Buck;
claims 10, 11, 22, and 23 as unpatentable over the same references
applied to claims 9 and 21, and further in view of Yoo (with GenBank
Accession No. M95623);
claims 12, 14, 24, and 26 as unpatentable over the same references
applied to claims 9 and 21, and further in view of Swan; and
claims 13, 18-20, and 25 as unpatentable over the same references
applied to claims 9 and 21, and further in view of Yoo and Swan.
We reverse.
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OBVIOUSNESS
There are four separate rejections of the claims, but the dispositive
issue is the same for each of them, so we will discuss the rejections together.
The Examiner finds that Kroeger discloses “a kit for detecting
oncogenic HPV, including HVP 16, 18, 31 and 45 . . . comprising primers
and probes that can be used in a cocktail for amplification and detection of
multiple HPV types at once” (Ans. 5). The Examiner acknowledges that
Kroeger’s kit doesn’t include primers and probes specific for the E7 open
reading frame of HPV 16, the E1 open reading frame of HPV 18 and 45, or
the E6 open reading frame of HPV 31 (id. at 6). Nevertheless, the Examiner
cites Buck as “evidence of the equivalence of primers” (id. at 9), and
concludes that it would have been obvious for one of ordinary skill in the art
“to utilize the sequences [of HPV 16, 18, 31, and 45] taught by Gissmann,
Goldsborough, Seedorf and Sastre-Garau in order to design amplification
primers and probes for a kit to detect and quantify HPV in a type-specific
manner, as taught by Kroeger” (id. at 7).
Appellants contend that the claimed kit includes primers and probes
which “provide amplification in different HPV reading frames” for different
HPV types (App. Br. 10), which “allows a primer pair to amplify a specific
HPV nucleic acid while, at the same time, not amplifying a different but
very similar HPV nucleic acid” (id.). Thus, the kit can be used to “detect
and quantitatively analyze multiple types of HPV, or groups of HPV, in one
reaction vessel, without competition among the primers [for templates]
during amplification” (id.), and “minimizing the number of parallel reactions
performed for each sample” (id.). Appellants contend that “all of
[Kroeger’s] probes hybridize within an approximately 140 bp region of the
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L1 gene” (id. at 8), and therefore don’t provide the same “functionality” as
the claimed kits (id. at 10). Moreover, Appellants contend that there is no
“apparent reason to select from the various teachings of each secondary
reference the portions of sequences asserted as relevant by the Examiner”
(id. at 15).
The issue raised by this appeal is whether the evidence of record
supports the Examiner’s conclusion that it would have been obvious for one
of ordinary skill in the art to select sequences from different open reading
frames specific for different HPV types and combine them in a kit in the
manner required by the claims.
Findings of Fact
1. The present Specification discloses an assay “intended for large
scale screening purposes and clinical typing” (Spec. 10: 1), “based on three
parallel real-time PCRs from each patient sample” (id. at 10: 3-4), which can
be performed in three reaction tubes (id. at 10: 3). In one embodiment that
uses a combination of primers and probes encompassed by the claims:
a) Reaction 1 detects and quantifies HPV types 16, 31, 18, and
45 (HPV 18 and 45 detected and quantified together) using
three different fluorophores, b) Reaction 2 detects and
quantifies HPV types 33, 35, 39, 52, 58, and 67 (HPV 33, 52,
58, and 67 detected and quantified together), again using three
different fluorophores, and c) Reaction 3 detects and quantifies
the amount of a human single copy gene . . . Reaction 1
includes a total of seven PCR primers and three probes,
Reaction 2 a total of seven PCR primers and three probes and
Reaction 3, two PCR primers and a single probe[.]
(Id. at 10: 4-11.)
The primers and probes used in the assay and included in the claimed
kits “were designed to optimize the ability for balanced co-amplification of
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different HPV types in mixed samples” (id. at 10: 14-15). In order to find
the most suitable priming sites for co-amplification, and avoid hindrances to
an efficient PCR . . . the amplicons were located in different HPV reading
frames” (id. at 10: 14-17). For example, “the amplicon for HPV 16 is
located in E7, that for HPV 18/45 in E1 and the amplicon for HPV 3 in E6”
(id. at 10: 18-19).
2. Kroeger discloses
[Twenty-six] oligonucleotides (. . .“oligos” or “probes”),
methods for using the probes and kits containing the probes, all
of which can be employed to specifically detect oncogenic HPV
types (i.e., HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58,
59, and 68). The probes . . . can be employed as primers in an
amplification reaction but preferably are employed as
hybridization probes because each of the probes is specific for
at least one HPV type . . . Advantageously, all [26] of the
probes hybridize within an approximately 140 bp region of the
L1 gene found in the HPV genome. Thus, while the probes
individually can be used to detect the oncogenic HPV type(s)
for which they are specific, a cocktail comprising two or more
of the oligos can be employed to detect several HPV types at
once. This is particularly advantageous in an amplification
reaction setting where all, more or part of the approximately
140 bp region can be amplified and the amplified product can
be contacted with a cocktail of probes to determine the presence
of at least one of the oncogenic HPV types in the test sample.
Accordingly, a single amplification reaction can be the basis for
detecting multiple HPV types.
(Kroeger ¶ 7; Table 1.)
3. Gissmann discloses prophylactic vaccines against HPV 16
“which incorporate the structural proteins L1 and L2 of the papilloma virus”
(Gissmann, col. 2, ll. 56-59), and therapeutic vaccines comprising “early
papilloma virus proteins, principally E6 or E7, which are expressed in the
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persistently infected cells” (id. at col. 3, ll. 18-24). Gissmann discloses the
sequence of the HPV 16 E7 gene (id., SEQ ID NO: 3), among other HPV 16
genes. In addition, Gissmann discloses amplification primers for HPV 16
L1 and E7, but the Examiner has not established that any of the primers
correspond to those recited in claim 9 (id. at cols. 8-11).
4. Goldsborough discloses the complete genome of HPV 31,
including the open reading frame of HPV 31 E6 (GenBank Accession No.
J04353).
5. Seedorf discloses the open reading frames of the HPV 18 E6,
E7, E1, E4, E5, L2, and L1 genes (Seedorf Abstract; Fig. 1 (a), (b)).
6. Sastre-Garau discloses the sequences of the HPV 45 L1, L2,
E1, E6, and E7 genes (Sastre-Garau Abstract; GenBank Accession No.
AJ242956).
7. The Examiner has not established that any of the secondary
references relied on for the sequences of HPV types 16, 31, 18, and 45
(Gissmann, Goldsborough, Seedorf, and Sastre-Garau) expressly identifies
any particular region, in any gene, that can differentiate between HPV types.
8. Swan discloses “”fluorogenic probe assays for HPV DNAs . . .
[that] are type specific, quantitative, sensitive, and useful for testing large
numbers of specimens” (Swan 886). Swan’s assays are similar to Kroeger’s
in that “[t]hey are based on the PCR amplification of a portion of the L1
open reading frames of HPV-16, -18, -31, -33, and -35 DNAs by using
genotype-specific primers in the presence of fluorescent, genotype-specific
probes that bind to the amplified DNA” (id.). According to Swan, the assays
exhibit some cross-reactivity, for example, “[t]he HPV-33 assay showed the
greatest degree of cross-reactivity, a signal equivalent to between 30 and 100
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copies of HPV-33 was seen with 2,000 copies of HPV-16 or HPV-51” (id. at
888).
9. Buck discusses various strategies for selecting primer
sequences and concludes that “under optimal sequencing conditions with
highly pure template and primer, many of the commonly applied primer
design parameters are dispensible” (Buck, Abstract).
Principles of Law
A rejection on the ground of obviousness must include “articulated
reasoning with some rational underpinning to support the legal conclusion of
obviousness.” In re Kahn, 441 F.3d 977, 988 (Fed. Cir. 2006). “[T]his
analysis should be made explicit” and it “can be important to identify a
reason that would have prompted a person of ordinary skill in the relevant
field to combine the elements in the way the claimed new invention does.”
KSR Int’l Co., v. Teleflex Inc., 550 U.S. 398, 418 (2007).
Discussion
While we agree with the Examiner that virtually any primer based on
the various oncogenic HPV genomes disclosed in the prior art could be used
to detect the presence of oncogenic HPV in a sample, what is missing from
the prior art relied on by the Examiner is any teaching or suggestion of a
strategy that would have led one of ordinary skill in the art to select the
particular combination of primers and probes required by the claims.
All of Kroeger’s primers and probes hybridize within a 140 base pair
region of the L1 gene. When used in combination, they can detect the
presence of one or more of the target HPV types , but cannot identify or
quantify individual types without further analysis (FF2). Swan also
discusses primers and probes specific for the L1 gene of various oncogenic
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HPV types, and notes that they exhibit some cross-reactivity between HPV
types (FF8). The remaining references disclose the sequences of various
oncogenic HPV types, but the Examiner has not pointed to anything in the
references that expressly identifies any particular region, in any gene, that
can differentiate between HPV types (FFs 3-7).
What the prior art does not teach or suggest is selecting primers and
probes from regions of different genes (e.g., E6, E7, E1) specific for
different HPV types, “whereby the primers are designed not to compete
during the amplification reaction . . . [and] the probes are designed not to
compete during the amplification-reaction and the detection phase” (Spec. 3:
7-9), in order to provide “balanced co-amplification of different HPV types
in mixed samples” (id. at 10: 14-15). The combination of primers and
probes required by the claimed kits allows individual oncogenic HPV types
in a mixed sample to be identified and quantified (FF1). Thus, the claimed
combination of primers and probes has a property not exhibited by a more
random combination of primers and probes derived from the genomes of
various oncogenic HPVs.
CONCLUSION
The evidence of record is not sufficient to support the Examiner’s
conclusion that it would have been obvious for one of ordinary skill in the
art to select sequences from different open reading frames specific for
different HPV types and combine them in a kit in the manner required by the
claims.
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SUMMARY
The rejection of claims 9 and 21 under 35 U.S.C. § 103(a) as
unpatentable over Kroeger, Gissmann, Goldsborough (with GenBank
Accession No. J04353), Seedorf, Sastre-Garau (with GenBank Accession
No. AJ242956), and Buck is reversed;
The rejection of claims 10, 11, 22, and 23 as unpatentable over the
same references applied to claims 9 and 21, and further in view of Yoo (with
GenBank Accession No. M95623) is reversed;
The rejection of claims 12, 14, 24, and 26 as unpatentable over the
same references applied to claims 9 and 21, and further in view of Swan is
reversed; and
The rejection of claims 13, 18-20, and 25 as unpatentable over the
same references applied to claims 9 and 21, and further in view of Yoo and
Swan is reversed.

REVERSED

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