Debra Wawro et al.

Patent Trials and Appeals Board

Oct 30, 2020

2020000958 (P.T.A.B. Oct. 30, 2020)

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.
13/470,250 05/11/2012 Debra Wawro OPTIC 4404003 5031
100772 7590 10/30/2020
Shiells Law Firm P.C
1910 Pacific Avenue Suite 14000
Dallas, TX 75201
EXAMINER
FOSTER, CHRISTINE E
ART UNIT PAPER NUMBER
1699
NOTIFICATION DATE DELIVERY MODE
10/30/2020 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):
admin@shiellslaw.com
docket@blackhillsip.com
tfshiells@shiellslaw.com
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte DEBRA WAWRO, SHELBY ZIMMERMAN,
YIWU DING, ROBERT MAGNUSSON, and PETER KOULEN
____________

Appeal 2020-000958
Application 13/470,250
Technology Center 1600
____________

Before ANTON W. FETTING, ULRIKE W. JENKS, and
RACHEL H. TOWNSEND, Administrative Patent Judges.

FETTING, Administrative Patent Judge.

DECISION ON APPEAL

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STATEMENT OF THE CASE1
Debra Wawro, Shelby Zimmerman, Yiwu Ding, Robert Magnusson,
and Peter Koulen (Appellant2) seeks review under 35 U.S.C. § 134 of a final
rejection of claims 1–13, 15–17, 20, 21, and 23–28, the only claims pending
in the application on appeal. We have jurisdiction over the appeal pursuant
to 35 U.S.C. § 6(b).
Appellant invented a GMR sensor that can be used to simultaneously
detect an array of analytes in guided-mode resonance (GMR) sensor
systems. Specification para. 3. Basically, the claims recite an apparatus that
can detect the presence of certain substances and interactions based on
optical properties. These substances and interactions are made susceptible to
such optical detection by binding to appropriate biologically selective
agents.
An understanding of the invention can be derived from a reading of
exemplary claim 1, which is reproduced below (bracketed matter and some
paragraphing added).
1. A biomarker sensor measurement system, comprising
[1] a guided mode resonance (GMR) sensor assembly,
comprising:

1 Our decision will make reference to Appellant’s Appeal Brief (“App. Br.,”
filed January 17, 2019) and Reply Brief (“Reply Br.,” filed November 18,
2019), and the Examiner’s Answer (“Ans.,” mailed September 16, 2019),
and Final Action (“Final Act.,” mailed April 17, 2018).
2 We use the word “Appellant” to refer to “applicant” as defined in
37 C.F.R. § 1.42. Appellant identifies the real party in interest as Resonant
Optics Incorporated (Appeal Br. 7).

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[1a] said GMR sensor assembly having a waveguide
structure configured for operation at or operably near one
or more leaky modes,
[1b] said waveguide structure having disposed thereon an
array of biologically selective agents
[1c] for binding to at least three biomarkers
having at least a first, second and third
biomarker that may be present in media in
contact with said waveguide structure
and,
when at least said first, second and third
biomarker are detected in predetermined
combinations in media in contact with said
waveguide structure,
are indicative of at least a first, or
second disease state,
wherein said first and second disease
states are states of primary and or
metastatic ovarian serous papillary
carcinoma, respectively;
[2] a beam shaper for receiving input light from a source of
light
wherein said beam shaper includes one or more line
focusing elements to focus input light onto the
waveguide structure
to cause one or more leaky transverse electrical
light (TE) and transverse magnetic light (TM)
resonant modes;
[3] a light sensitive detector for detecting presence of an array
of said at least first, second and third biomarkers,
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[4] wherein the light sensitive detector is disposed with respect
to said waveguide structure
to detect changes in one or more of the angle, phase,
waveshape and/or magnitude of each of a TE resonance
and[[/or]] a TM resonance
to permit distinguishing between first and second
physical states of said waveguide structure or its
immediate environment,
said immediate environment including said
media,
said light-sensitive detector having an output
for permitting determination of which
combination of said first, second and third
biomarkers are present to permit
determination of said first or second disease
state;
[5] at least said first and second biomarkers having an at least
two-fold up- or down- regulation
indicative of said first disease state,
[6] said third biomarker having an at least two-fold up- or
down- regulation indicative of said second disease state,
said up- or down- regulation of said third biomarker
being opposite in up- or down- regulation sense from the
up- or down- regulation of at least one of said first and
second biomarkers
in the presence of at least one of said first and
second disease states,
whereby said first and second disease states may
be distinguished from each other.
Claims Amendment filed March 21, 2018.
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PRIOR ART
The Examiner relies upon the following prior art:
Name Reference Date
Jazaeri US 2005/0095592 A1 May 5, 2005
D. Wawro et al., "Guided-mode resonance sensors for rapid medical
diagnostic testing applications" 2009 Proc. SPIE 7173, Optical Fibers
and Sensors for Medical Diagnostics and Treatment Applications IX: p.
717303-1 to 717303-9 (“Wawro”).
D. Wawro et al., "Guided-mode resonance sensor system for early
detection of ovarian cancer" 25 February 2010 Proc. SPIE 7572,
Optical Diagnostics and Sensing X: Toward Point-of-Care Diagnostics,
pages 75720D-1 to 75720D-6 (“Wawro2”).
Z. Zhang et al., "Three Biomarkers Identified from Serum Proteomic
Analysis for the Detection of Early Stage Ovarian Cancer" CANCER
RESEARCH 64, 5882-5890, August 15, 2004 (“Zhang”).

REJECTIONS
Claims 1–13, 15–17, 20, 21, and 23–28 stand rejected under 35 U.S.C.
§ 101 as directed to a judicial exception without significantly more.
Claims 1–13, 15–17, 20, 21, and 23–28 stand rejected under 35 U.S.C.
§ 112(a) as lacking a supporting written description within the original
disclosure.
Claims 1–13, 15–17, 20, 21, and 23–28 stand rejected under 35 U.S.C.
§ 112(b) as failing to particularly point out and distinctly claim the
invention.
Claims 1–13, 15–17, 20, 21, 23, 24, 26 and 27 stand rejected under 35
U.S.C. § 103(a) as unpatentable over Wawro, Wawro2, and Zhang.
Claims 25 and 28 stand rejected under 35 U.S.C. § 103(a) as
unpatentable over Wawro, Wawro2, Zhang, and Jazaeri.
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ISSUES
The issues of eligible subject matter turn primarily on whether the
claims recite more than the natural correlation between biomarkers and
disease states.
The issues of written description matter turn primarily on whether the
disclosure shows possession of the genus claimed.
The issues of indefiniteness matter turn primarily on whether one of
ordinary skill can understand the metes and bounds of the claims.
The issues of obviousness turn primarily on whether the applied art
describes detecting and differentiating primary and metastatic ovarian
cancer.
FACTS PERTINENT TO THE ISSUES
The following enumerated Findings of Fact (FF) are believed to be
supported by a preponderance of the evidence.
Facts Related to the Prior Art
Wawro
01. Wawro is directed to a tag-free photonic resonance concept
occurring on subwavelength waveguide gratings that is applied for
rapid medical testing applications. Wawro Abstract.
02. Wawro describes high-resolution sensors operating in real
time while being sensitive to a wide variety of analytes, including
microbials. A sensor system uses a single, fixed wavelength
source with a shaped input wave from which to auto-scan in angle.
As binding events occur at the sensor surface, shifts in a resonance
reflection peak (or a corresponding transmission minimum) are
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tracked as a function of incident angle. The amount of angular
shift is correlated to the quantity of analyte in the test sample. Due
to inherent polarization diversity, two narrow peaks shift their
positions on the sensor surface when a bio reaction occurs, thereby
providing cross-referenced data. The sensor system connects to
portable interfaces for data acquisition and analysis. Wawro
Abstract.
Wawro2
03. Wawro2 is directed to a high-accuracy sensor system that
provides near-instantaneous detection of biomarker proteins as
indicators of ovarian serous papillary carcinoma. Based upon
photonic guided-mode resonance technology, these high-
resolution sensors employ multiple resonance peaks to rapidly test
for relevant proteins in complex biological samples. Wawro2
Abstract.
04. Wawro2 describes a label-free sensor approach that requires
minimal sample processing and has the capability to measure
multiple agents simultaneously and in real time. It describes a
detection system having identification and quantification of
protein biomarkers that are up- or down- regulated in blood and
serum as indicators of ovarian cancer. Wawro2 Abstract.
05. Wawro2 describes using diagnostic tools to detect biomarker
proteins including calreticulin and ryanodine receptor 3. Wawro2
75750D-3.
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Zhang
06. Zhang is directed to describing a form of early detection, which
remains the most promising approach to improve long-term
survival of patients with ovarian cancer. Zhang Abstract.
07. In a five-center case-control study, data from patients with
early stage ovarian cancer and healthy women at two centers were
analyzed independently and the results cross-validated to discover
potential biomarkers. Three biomarkers were identified as follows:
(a) apolipoprotein Al (down-regulated in cancer); (b) a truncated
form of transthyretin (down-regulated); and (c) a cleavage
fragment of inter-α-trypsin inhibitor heavy chain H4 (up-
regulated). These biomarkers demonstrated the potential to
improve the detection of early stage ovarian cancer. Zhang
Abstract.
08. Zhang describes discovering three potential biomarkers for
early stage ovarian cancer. Two of them were down-regulated in
the cancer group, and the third was up-regulated in the cancer
group. Zhang 5883-84, 5886.
ANALYSIS
Claims Objections
We agree with the Examiner that the “arguments are acknowledged
but are moot as objections are not subject to review by the Patent Trial and
Appeal Board.” Ans. 45.
Claims Construction
All claims are drawn to apparatuses. There are no process or
composition of matter claims, and no computer software on media claims.
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All of the claims, however, recite both the structure of the claimed
apparatus, and what the apparatus operates upon, that is, what the apparatus
detects. Thus, we construe the claims to delineate the claimed structure.
As to independent claim 1, it recites a system having as component
parts (1) GMR sensor, (2) beam shaper, and (3) light sensitive detector. The
GMR sensor, in turn has a waveguide structure that includes “disposed
thereon” an array of biologically selective agents. Limitations 1a and 1b.
Limitation 1c, however, describes biomarkers that the agents in the
array of biologically selective agents have the capacity to bind to, and is not
part of the recited structure of the GMR sensor. Rather, it provides for
further characterization of the agents in limitation 1b in that the array of
biologically selective agents must include ones that are able to bind at least
three such biomarkers. However, the biomarkers do not form part of the
structure of the claimed GMR sensor.
Limitations 2–4 describe the structure and relative juxtaposition of the
beam shaper and detector with respect to the waveguide structure. For
example, the beam shaper must be able to focus input light onto the
waveguide structure. The light sensitive detector has to be able to detect
certain changes of either or both of a transverse electric light (TE) resonance
and a transverse-magnetic light (TM) resonance “of the waveguide structure
or its immediate environment.”
Limitations 5 and 6 further characterize the biomarkers the
biologically selective agents of the array may bind with. As with limitation
1c, these limitations do not describe the structure of the apparatus per se, but
instead characterize capacity of the particular agents. They describe the
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attributes of biomarkers that the agents are chosen to have the capacity to
bind with.
Limitations 1c, 5, and 6 then recite the criteria for selecting the
particular agents that form part of the structure in limitation 1b. Thus claim
1 is construed as a system having a GMR sensor, a beam shaper, and a
detector, each having its recited attributes. The sensor in turn has a
waveguide structure, in turn having an array of agents. The particular agents
so forming part of the structure are selected based on the criteria recited in
limitations 1c, 5, and 6.
The primary implication of this construction is that, although much of
the Examiner’s findings and Appellant’s arguments refer to the biomarkers,
which are not actually part of the recited structure, those findings and
arguments pertain indirectly to the agents that actually form part of the
structure, because the biomarkers are the selection criteria for the agents, and
those findings and arguments are understood as such.
Claims 1–13, 15–17, 20, 21, and 23–28 rejected under 35 U.S.C. § 101 as
directed to a judicial exception without significantly more
The Examiner determines that the “claims are directed to naturally
occurring correlations and to abstract ideas, namely the naturally occurring
correlations between the presence/ levels of biomarkers and the presence of
disease states.” Final Act. 24. Although the independent claims include a
natural product as part of the device, i.e., “an array of biologically selective
agents for binding to at least three biomarkers,” all independent claims recite
several other specific structural elements that are arranged in a particular
way that forma biomarker sensor measurement system or GMR biosensor.
The claims do not even recite the detection of a disease state itself, even if
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that is what the Specification identifies as the capability of the biomarker
sensor measurement system claimed. This is a specific device whose
technological implementation details are explicitly recited and thus
integrates the recited natural product into a practical application. The
Examiner answers that such devices were known. Ans. 59–61. Whether or
not such devices were known is not relevant to the patent-eligible subject
matter question. See, e.g., Two-Way Media Ltd. v. Comcast Cable
Commc’ns, LLC, 874 F.3d 1329, 1340 (Fed. Cir. 2017 (“Eligibility and
novelty are separate inquiries.”).

Claims 1–13, 15–17, 20, 21, and 23–28 rejected under 35 U.S.C. § 112(a) as
lacking a supporting written description within the original disclosure
The Examiner posits five theories for lack of written description. First,
The Examiner determines that the Specification does not enable the scope of
the genus recited in the claims. Second, the Examiner determines that some
of the disclosed proteins do not perform as disclosed. Third, the Examiner
determines the Specification does not adequately describe any detector or
output having the claimed functional capability. Fourth, the Examiner
determines that there can be no possession of the recited output. Fifth, the
Examiner determines that several limitations across multiple claims are new
matter.
The first rejection theory is that Appellant has not shown it possessed
the entire genus of what is claimed. Final Act. 7–10. We agree with the
Examiner’s answer to this rejection. Ans. 46–48. In particular, we
determine the following.
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Appellant claims an apparatus that includes agents that may bind to all
biomarkers, known or unknown, that exhibit the recited characteristics.
Appellant exemplifies eight example biomarkers, but does not disclose how
to extrapolate to other biomarkers exhibiting similar characteristics.
Appellants claim a potentially vast genus in functional terms without
providing sufficient examples or structural features to show possession of
the entire genus.
[A] generic claim may define the boundaries of a vast genus of
chemical compounds, and yet the question may still remain
whether the specification, including original claim language,
demonstrates that the applicant has invented species sufficient
to support a claim to a genus. The problem is especially acute
with genus claims that use functional language to define the
boundaries of a claimed genus. In such a case, the functional
claim may simply claim a desired result, and may do so without
describing species that achieve that result. But the specification
must demonstrate that the applicant has made a generic
invention that achieves the claimed result and do so by showing
that the applicant has invented species sufficient to support a
claim to the functionally‐defined genus.
Ariad Pharmaceuticals v. Eli Lilly and Co., 598 F.3d 1336, 1349 (Fed. Cir.
2010)
[A] sufficient description of a genus instead requires the
disclosure of either a representative number of species falling
within the scope of the genus or structural features common to
the members of the genus so that one of skill in the art can
“visualize or recognize” the members of the genus. We
explained that an adequate written description requires a precise
definition, such as by structure, formula, chemical name,
physical properties, or other properties, of species falling within
the genus sufficient to distinguish the genus from other
materials. We have also held that functional claim language can
meet the written description requirement when the art has
established a correlation between structure and function. But
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merely drawing a fence around the outer limits of a purported
genus is not an adequate substitute for describing a variety of
materials constituting the genus and showing that one has
invented a genus and not just a species.
Id. at 1350; see also LizardTech, Inc. v. Earth Resource Mapping, Inc., 424
F.3d 1336, 1345 (Fed. Cir. 2005) (holding such written description
requirements in other technology claims).
Appellant argues
[t]hat the Claims use specifically defined biomarkers does not
mean that the claims are as a whole directed towards
biomarkers. Instead, the claims as a whole are directed to a
system. Moreover, the test results do not produce the
biomarkers - they are detecting the biomarkers that are already
there. . . .
In the claims, this possession is shown by both the example
biochemicals and markers to be tested, and also a description of
the GMR sensor that identifies biomarkers with specific
characteristics. Appellant is not claiming as a whole a genus;
instead, Appellant is claiming a system that identifies specified
biomarkers, or biomarkers that are defined as having identified
characteristics
Appeal Br. 17–18. This mischaracterizes the rejection. The claims include
an array of agents included in the structure, not the biomarkers. The claims
as a whole are indeed directed to a system, but the structure of that system
may be any of an unknown number of species defined by the attributes of
biologically selective agents being able to ascertain two-fold up-regulation
or down-regulation of three biomarkers being indicative of primary or
metastatic ovarian serous papillary carcinoma disease. The Specification
does not set forth any established correlation between biologically selective
agents and biomarkers having such a relationship. The Specification does
not even describe a correlation between structure of biomarkers for
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identification of primary and or metastatic ovarian serous papillary
carcinoma, much less that differentiate between the two by virtue of two
biomarkers that are either up or down regulated and a third biomarker being
regulated in the opposite direction. There is even less disclosure of
biologically selective agents for detecting such unknown biomarkers.
“One needs to show that one has truly invented the genus, i.e., that
one has conceived and described sufficient representative species
encompassing the breadth of the genus. Otherwise, one has only a research
plan, leaving it to others to explore the unknown contours of the claimed
genus.” AbbVie Deutschland GmbH & Co. v. Janssen Biotech, Inc., 759
F.3d 1285, 1300 (Fed. Cir. 2014). There is insufficient disclosure to show
Appellant had possession of the entire genus of such species. Although
eight example agents detecting the recited biomarkers are disclosed, there is
nothing in the record to suggest that this is a sufficient number to show
possession of the entire genus. Eight is not a particularly large number. The
genus breadth arises from the number of potential biomarkers, known and
unknown, that may be used to detect and distinguish primary and metastatic
ovarian serous papillary carcinoma by exhibiting two-fold or more up or
down regulation. Appellant’s argument does not respond to this issue.
Appellant next argues that
[w]hat is claimed, however, is a system that evaluates the
various biomarkers levels to generate a read-out as to the
primary vs. metastatic nature of the ovarian cancer.
Undoubtedly, the status of certain "mutations" would play a
role in the primary versus metastatic stage, however, those
factors are already accounted for in the claimed system.
Appeal Br. 18. This is simply not responsive to the rejection. The claims
are indeed system claims, but whether factors such as mutations which
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might expand the size of the genus are in some sense “accounted for” does
not show that one of ordinary skill knew how to extrapolate from eight
disclosed examples to the entire genus.
We agree with Appellant that the Specification discloses sufficient
structure for the detector and output limitations. Appeal Br. 18 and 22. But
this is not pertinent to the genus problem of the array of agents limitation.
We are not persuaded by Appellant's argument that “[t]he inventors
are testing for quantitative levels and testing for those quantitative levels.
Further, it is proper to extrapolate [to the large genera being claimed] since
the disclosed cell lines are biological derivatives of the claimed diseased
states that the system seeks to distinguish.” Appeal Br. 19. This is simply
not responsive to the issue of the breadth of the genus of agents able to bind
to biomarkers exhibiting the recited characteristics. Further, only five cell
lines are disclosed. Spec. para. 110; Table 2.
We are not persuaded by Appellant's argument that “there is no
evidence on the record that the biomarkers cannot be extrapolated into a
larger universe, especially as what is being tested for is the relative
quantitative levels of the marker as a predictive factor of tumor cell
behavior.” Appeal Br. 19. Appellant must show that it is in possession of
the genus. The fact that only eight biomarkers are disclosed and there is no
disclosure of how to extrapolate from agents, now known or not, that bind to
those eight disclosed biomarkers and are indicative of primary or metastatic
ovarian serous papillary carcinoma is sufficient for the Examiner to present a
prima facie case that Appellant is not in such possession. That what is being
tested for is the relative quantitative levels of the marker as a predictive
factor of tumor cell behavior does not shed any light on this issue.
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We are not persuaded by Appellant's argument that “[w]hat is being
tested is the relative quantitative levels of the marker as a predictive factor of
tumor cell behavior. This is an apparatus that allows for a test of chemicals.
The claimed GMR sensor provides the structure.” Id. Again, simply relating
what is being tested sheds no light on the genus of testing device agents (i.e.
Species). As Appellant argues, the claimed GMR sensor provides the
structure, and that structure includes an array of agents that may bind to
biomarkers that have the recited characteristics. The genus of such agents is
what creates the genus of such sensors and therefore systems.
In response to Examiner’s citation to AbbVie Deutschland GmbH &
Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1346 (Fed. Cir. 2014)
(“One needs to show that one has truly invented the genus”), (Final Act. 10),
Appellant argues “Abbvie is directed to a biochemical as claimed, whereas
the present system can detect biomarkers as claimed. These are different
statutory classes.” Appeal Br. 20. This is not pertinent to the analysis. It is
the breadth of the genus of biochemical agents forming part of the claimed
system that Appellant must show it was in possession of. Appellant’s
argument that “what is claimed by the Appellant is NOT a chemical
invention. What is claimed is a system that detects biomarkers. The
Examiner again is applying analysis perhaps pertinent to claiming a
biochemical itself to a system that employs biomarkers for detection,”
(Appeal Brief 21), is similar and similarly answered.
The remaining independent claims 12 and 28 have similar scope of
genus issues. Although claims 12 and 28 recite that three of the biomarkers
to be detected must be biomarkers from a group including the eight
disclosed examples, no specific agents are recited or disclosed. The
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Specification only describes the agents as selected from a group of
antibodies, aptamers, peptides, DNA/RNA, or other agents designed to be
selective for biomarker proteins. Spec. para. 20. So the genus of agents is
open ended both for being somehow related to the identified biomarkers, and
for the open ended nature of that relationship to any particular biomarker
recited.
The dependent claims retain these issues from their parent claims 1
and 12. Claim 28 has no dependent claims.
Examiner also determines that two of the disclosed eight biomarkers
are not workable examples. Final Act. 12. Mitogen activated protein kinase
(MAPK) “was detected in reagent diluent, but no protein was detected in any
of the cell supernatants or media, including the spike and recovery samples.
This could be due to the cell media/supernatant interfering with the
antibodies on the sensor surface, thus preventing MAPK 13 detection.”
Spec. para. 132. “The detected TIMP-3 [Metalloproteinase inhibitor 3] level
in SK-OV-3 supernatant is 472 ng/ml and media is 427.5 ng/ml, showing
only a slight secretion of protein in the ovarian cancer cell supernatant.”
Spec. para. 62. Appellant argues
[d]ue to the ‘opposite’ requirement of the claimed detection
states (two-fold up or down regulated), a non-detection of an
up-regulation is still information regarding a disease state and
its presence or absence of the biomarkers. Therefore, the above
argument of the Examiner is not directed to this claimed
language, and is therefore inapposite.
Appeal Br. 21–22. This argument misses the point. The Specification does
not describe the context as one in which the biomarkers would not be
expected to be detected. Unless a biomarker is known to be capable of being
detected, it does not meet the criteria recited in the claim for selecting an
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agent. Thus, Examiner is actually determining that only six of the eight
examples are workable examples.
Examiner’s rejection as to claims 9 and 18 are similar, and are
similarly persuasive, although we note that claim 18 stands cancelled and so
is no longer at issue. Final Act. 13–14.
Examiner’s rejection of claim 27 is summarily affirmed because
Appellant does not argue the rejection. Final Act. 15.
We are persuaded by Appellant's argument that the rejections under
New Matter (Final Action 15–18) are improper for the reasons Appellant
argues. Appeal Br. 28–31. Appellant points to adequate support for each
rejection.
Claims 1–13, 15–17, 20, 21, and 23–28 rejected under 35 U.S.C. § 112(b) as
failing to particularly point out and distinctly claim the invention
As to claim 5, reciting “[t]he measurement system of claim 3, further
comprising other biomarker proteins that are up- or down- regulated at least
two-fold in ovarian cancer disease states.” The Examiner finds this further
comprising other biomarker proteins to be logically inconsistent with the
parent claims, because the measurement system structure has no biomarker
proteins. Final Act. 19. This is correct, as we determine in the claim
construction above. Appellant argues that “Appellant amended Claim 5 to
clarify that the system is capable of detecting such other biomarker
proteins.” Appeal Br. 28. This simply does not respond to the finding that
the structure itself does not comprise any biomarkers.
As to claim 12, we agree with and adopt the various rejections the
Examiner enters. Final Act. 19–21. The rejections are generally for
antecedent basis and ambiguities issues, some of which Appellant does not
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even argue. All are reasonable issues of one of ordinary skill having
difficulty seeing the metes and bounds. All are easily fixed. Appellant’s
arguments are generally not pertinent. Appeal Br. 31.
The rejection to claim 24 is summarily affirmed because Appellant
does not argue it.
We are persuaded by Appellant's argument that claims 1, 26, 27, and
28 are not indefinite for the reasons argued. Appeal Br. 31.

Claims 1–13, 15–17, 20, 21, 23, 24, 26 and 27 rejected under 35 U.S.C. §
103(a) as unpatentable over Wawro, Wawro2, and Zhang
The Examiner determines that Wawro describes claim 1 limitations
[1a], [2], [3], and [4]. Final Act. 28 and 29. This is uncontested. The issues
surrounding obviousness arise from the characteristics of the biologically
selective agents recited in limitation [1b] as being disposed on the recited
but uncontested waveguide structure in limitation [1a]. More specifically,
the issues surround the attributes recited in limitations [1c], [5], and [6] of
biomarkers that bind to these recited agents. It is the array of agents, not the
biomarkers, that form part of the recited structures. Those agents, however,
must be able to bind to biomarkers that meet the claim limitations. Thus, the
agents are selected based on the criteria recited in limitations [1c], [5], and
[6].
In particular, the agents must be such, that they bind to biomarkers
that
when at least said first, second and third biomarker are detected
in predetermined combinations in media in contact with said
waveguide structure, are indicative of at least a first, or second
disease state, wherein said first and second disease states are
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states of primary and or metastatic ovarian serous papillary
carcinoma, respectively
Claim 1, limitation 1c. This indication occurs from
at least said first and second biomarkers having an at least two-
fold up- or down- regulation indicative of said first disease
state, said third biomarker having an at least two-fold up- or
down- regulation indicative of said second disease state, said
up- or down- regulation of said third biomarker being opposite
in up- or down- regulation sense from the up- or down-
regulation of at least one of said first and second biomarkers in
the presence of at least one of said first and second disease
states, whereby said first and second disease states may be
distinguished from each other.
Claim 1, limitations 5 and 6. We are persuaded by Appellant's argument
that the applied references do not describe this combination.
[T]he claims of the present Application are directed towards
both determining a degree of cancer, which Zhang is not, but
moreover, the bioindicators have a differing up-regulated or
down-regulated pattern as to whether the cancer is primary
versus metastatic ovarian serous papillary carcinoma.
Moreover, this is accomplished using the upregulated and
downregulated for specificity of rejection, which is not found in
the prior art.
Appeal B. 44. The Examiner answers that the
limitations would at best reflect the intended use of the claimed
system, and because the prior art detects the exact same
biomarkers, it meets the claim as it would be capable of
performing this intended use.
Similarly, arguments that Zhang is comparing stage zero to
stage four cancers whereas the "assays of the present invention"
compares stages one to three vs. stage 4 are unpersuasive
because the claims are to a device and not to assays.
Furthermore, the claim language that the biomarkers are up- or
down-regulated in disease states reflects inherent characteristics
Appeal 2020-000958
Application 13/470,250

21

of the claimed biomarkers and the prior art suggests the same
biomarkers.
Ans. 67–68 (citations omitted). The Examiner fails to account for the
recitation that agents that are present in the sensor must be able to
distinguish, by quantitative detection, between primary and metastatic
ovarian serous papillary carcinoma
That the references describe certain biomarkers as up or down
regulated in cancer does not describe the capacity to distinguish primary
from metastatic carcinoma. Such capacity to distinguish necessarily requires
knowledge about the relationship between the biomarkers and their
increased or decreased expression level in primary and or metastatic ovarian
serous papillary carcinoma. Examiner has not explained why one would
select a particular combination of agents to detect biomarkers that have a
two-fold up or downregulation while the third agent detecting yet another
biomarker has an expression level that is opposite of the first two agents.
Any inherent characteristics the Examiner refers to would extend only
to how the biomarkers interact with the agents in the references. Even if the
references disclose two-fold up or down regulation for a biomarker,
Examiner provides no explanation for making the particular selection
required to meet elements [5] and [6] of claim 1.
The remaining independent claims have similar limitations, and the
remaining dependent claims inherit this limitation from their parent claims.
Claims 25 and 28 rejected under 35 U.S.C. § 103(a) as unpatentable over
Wawro, Wawro2, Zhang, and Jazaeri
These rejections are improper for similar reasons.
Appeal 2020-000958
Application 13/470,250

22

CONCLUSIONS OF LAW
The rejection of claims 1–13, 15–17, 20, 21, and 23–28 under 35
U.S.C. § 101 as directed to a judicial exception without significantly more is
improper.
The rejection of claims 1–13, 15–17, 20, 21, and 23–28 under 35
U.S.C. § 112(a) as lacking a supporting written description within the
original disclosure is proper.
The rejection of claims 5, 12, 13, 15–17, 20, 24, 27 under 35 U.S.C. §
112(b) as failing to particularly point out and distinctly claim the invention
is proper.
The rejection of claims 1–4, 6–11, 21, 23, 25, 26, 28 under 35 U.S.C.
§ 112(b) as failing to particularly point out and distinctly claim the invention
is improper.
The rejection of claims 1–13, 15–17, 20, 21, 23, 24, 26 and 27 under
35 U.S.C. § 103(a) as unpatentable over Wawro, Wawro2, and Zhang is
improper.
The rejection of claims 25 and 28 under 35 U.S.C. § 103(a) as
unpatentable over Wawro, Wawro2, Zhang, and Jazaeri is improper.
Appeal 2020-000958
Application 13/470,250

23

CONCLUSION
The rejection of claims 1–13, 15–17, 20, 21, and 23–28 is affirmed.
In summary:
Claims
Rejected
35 U.S.C. § Basis Affirmed Reversed
1–13, 15–17,
20, 21, 23–28
101 Eligibility 1–13, 15–17,
20, 21, 23–28
1–13, 15–17,
20, 21, 23–28
112(a) Written
Description
1–13, 15–17, 20,
21, 23–28

1–13, 15–17,
20, 21, 23–28
112(b) Indefiniteness 5, 12, 13, 15–17,
20, 24, 27
1–4, 6–11, 21,
23, 25, 26, 28
1–13, 15–17,
20, 21, 23, 24,
26, 27
103 Wawro,
Wawro2,
Zhang
1–13, 15–17,
20, 21, 23, 24,
26, 27
25, 28 103 Wawro,
Wawro2,
Zhang,
Jazaeri
25, 28
Overall Outcome 1–13, 15–17, 20,
21, 23–28

No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a). See 37 C.F.R.
§ 1.136(a)(1)(iv) (2011).

AFFIRMED