Ex Parte Nolan et al

Patent Trial and Appeal Board

Dec 15, 2017

11338957 (P.T.A.B. Dec. 15, 2017)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
111338,957 01124/2006
77974 7590 12/19/2017
Stanford University Office of Technology Licensing
Bozicevic, Field & Francis LLP
201 REDWOOD SHORES PARKWAY
SUITE 200
REDWOOD CITY, CA 94065
Garry P. Nolan
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
STAN-503 6823
EXAMINER
CLOW, LORIA
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
12/19/2017 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):
docket@bozpat.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte GARRY P. NOLAN, OMAR D. PEREZ, KAREN SACHS, and
DOUGLAS ALAN LAUFFENBURGER1
Appeal2016-000569
Application 11/338,957
Technology Center 1600
Before JOHN G. NEW, RICHARD J. SMITH, and RYAN H. FLAX,
Administrative Patent Judges.
FLAX, Administrative Patent Judge.
DECISION ON APPEAL
This is a decision on appeal under 35 U.S.C. § 134(a) involving
claims directed to a method for characterizing (or diagnosing/prognosing) a
disease state. Claims 13, 14, 43--45, 52, 53, 60, 63, 67, 69, 72, 73, and 78-
87 are on appeal as rejected under 35 U.S.C. § 101. We have jurisdiction
under 35 U.S.C. § 6(b).
We affirm.
1 Appellants identify the Real Parties in Interest as "The Board of Trustees
of The Leland Stanford Junior University" and "Massachusetts Institute of
Technology." App. Br. 3.
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Application 11/338,957
STATEMENT OF THE CASE
The Specification states, as background: "[ e ]xtracellular
and/intracellular cues trigger a cascade of information flow, in which
signaling molecules become chemically, physically or locationally modified,
gain new functional capabilities, and affect subsequent molecules in the
cascade, culminating in a phenotypic cellular response." Spec. ,-i 4. The
Specification further states, "Bayesian networks, a form of graphical models,
have been proffered as a promising framework for modeling complex
systems such as cell signaling cascades by representing probabilistic
dependence relationships among multiple interacting components." Spec.
,-i 5 (citing, inter alia, Friedman, Pe'er, and Sachs, as identified, infra at n.3).
The Specification further states, "[t]he present disclosure discloses
experimental and computational methods for constructing cell signaling
networks." Spec. ,-i 3. To do so, the Specification explains, "[m]ethods of
developing and using models of cellular networks by applying a
probabilistic graphical model are provided," where "cellular components can
be detected using any of a number of techniques. For example, the cellular
components can be detected by flow cytometry or confocal microscopy"
and, upon this detection, "[a ]ny probabilistic graphical model algorithm can
be used. . . . In certain embodiments, the probabilistic graphical model
algorithm is a Bayesian network structure inference algorithm." Spec. ,-i,-i 6,
10.
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Claims 13, 14, and 80 are the independent claims. We find claims 13
and 14 are representative; they are reproduced below:
13. A method of characterizing a disease state comprising:
a) measuring a plurality of cellular components in individual
cells exhibiting said disease state to generate a first data set,
wherein said measuring comprises:
(i) contacting said cells exhibiting said disease state with
a set of distinguishably detectable probes that bind to said
cellular components, and
(ii) detecting the binding of said probes to said cellular
components in each individual cell of said cells exhibiting
said disease state to generate said first data set comprising
a plurality of individual cell data sets from said cells
exhibiting said disease state;
b) providing a first set of arcs for said cellular components in
cells exhibiting said disease state from said first data set, wherein
the arcs are obtained by the probabilistic analysis of causal
connections between said cellular components in each individual
cell in said first data set;
c) measuring a plurality of cellular components in individual
cells not exhibiting said disease state to generate a second data
set, wherein said measuring comprises:
(i) contacting said cells not exhibiting said disease state
with said set of distinguishably detectable probes that bind
to said cellular components, and
(ii) detecting the binding of said probes to said cellular
components in each individual cell of said cells not
exhibiting said disease state to generate a second data set
comprising a plurality of individual cell data sets from said
cells not exhibiting said disease state;
d) providing a second set of arcs for said cellular components in
cells that do not exhibit said disease state from said second data
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set, wherein the arcs are obtained by the probabilistic analysis of
causal connections between said cellular components in each
individual cell in said second data set; and
e) comparing the presence, absence or change of one or more
arcs from said first set of arcs as compared to said second set of
arcs to determine one or more decisional arcs, wherein said
decisional arc is indicative of said disease state.
14. A method of diagnosing or prognosing a disease state in a
subject comprising:
a) providing a set of decisional arcs, wherein said set of
decisional arcs are indicative of causal connections between
cellular components and wherein said decisional arcs are also
indicative of the presence, absence or prognosis of said disease
state;
b) obtaining a first set of cells from said subject;
c) providing a set of probes that bind to said cellular
components in said first set of cells, wherein each probe is
labeled with a distinguishable label;
d) detecting the binding of said probes to said cellular
components in each individual cell of said first set of cells to
generate a first data set associated with cellular components in
each of said first cells, wherein the first data set comprises a
plurality of individual cell data sets from said individual cells;
and
e) applying a probabilistic graphical model algorithm to said
first data set to identify a set of arcs between said cellular
components in each said individual cell, wherein the results of
the detecting of probe binding in each individual cell is treated
as an independent observation in said probabilistic analysis, and
wherein the set of arcs are indicative of causal connections
between said cellular components; and
f) comparing said set of arcs for said cellular components to
said set of decisional arcs for said cellular components, wherein
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the presence, absence or change of one or more arcs as compared
to one or more decisional arcs is used to diagnose or prognose
said disease state in said subject.
App. Br. 25-26 (Claims App'x.).
The following rejection is appealed:
Claims 13, 14, 43--45, 52, 53, 60, 63, 67, 69, 72, 73, and 78-87 stand
rejected under 35 U.S.C. § 101 as patent-ineligible. Final Action 3.
CLAIM INTERPRETATION
When analyzing claims, the Patent Office applies the broadest
reasonable construction standard in proceedings. Cuozzo Speed Tech., LLC
v. Lee, 136 S. Ct. 2131, 2145 (2016). "[T]he words of a claim 'are generally
given their ordinary and customary meaning."' Phillips v. A WH Corp., 415
F.3d 1303, 1312-13 (Fed. Cir. 2005). "[W]hile it is true that claims are to
be interpreted in light of the specification ... , it does not follow that
limitations from the specification may be read into the claims .... [T]he
claims define the invention." Sjolundv. Musland, 847 F.2d 1573, 1581-82
(Fed. Cir. 1988). "When the specification explains and defines a term used
in the claims, without ambiguity or incompleteness, there is no need to
search further for the meaning of the term." Multiform Dessicants, Inc. v.
Medzam, Ltd., 133 F.3d 1473, 1478 (Fed Cir. 1998).
Here, several of the terms recited by the claims are specifically
explained and defined by the Specification. The claim term "arc," as it
relates to cellular components, is explained in the Specification to mean
something, e.g., a graphical representation or recognized link, which
"show[s] statistical dependence of [a] downstream ('second') cellular
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component on [an] upstream ('first') cellular component," or a "causal
influence[] from the upstream cellular component upon the downstream
cellular component." Spec. ii 39. With this understanding of "arc," the
Specification then explains that the claim term "'decisional arcs' refer[ s] to
arcs used for comparison to other arcs. Decisional arcs can have a value
and/or a directionality." Id. ii 47. The Specification explains that "[t]he
[claim] term 'cellular component' refers to a molecule regardless of
molecular weight found within an organism or cell." Id. ii 52. Regarding
the claim term "probe," the Specification states "[ v ]irtually any molecule
can be used as [a] probe to detect one or more of the cellular component
described herein." Id. ii 89. Further, regarding the claim term
"distinguishable," the Specification states "[b]y 'distinguishable' we mean
that the [probe] labels should be spectrally resolvable from one another." Id.
ii 95.
We interpret the relevant claim language consistent with the
Specification, as discussed above.
DISCUSSION
Unless otherwise indicated herein, we adopt the Examiner's findings
of fact, reasoning on scope and content of the claims and prior art, and
conclusions set out in the Final Action and Answer. 2 Only those arguments
made by Appellants in the Appeal Brief and properly presented in the Reply
Brief have been considered in this Decision. Arguments not so presented in
2 Final Office Action, mailed Nov. 12, 2014 ("Final Action"); Examiner's
Answer, mailed Aug. 13, 2015 ("Answer").
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the Briefs are waived. See 37 C.F.R. § 41.37(c)(l)(iv) (2015); see also Ex
parte Borden, 2010 WL 191083 at *2 (BP AI 2010) (informative) ("Any
bases for asserting error, whether factual or legal, that are not raised in the
principal brief are waived.").
Further, while separately argued claims are to be separately
considered when determining patentability, "[a] statement which merely
points out what a claim recites will not be considered an argument for
separate patentability of the claim." 37 C.F.R. § 41.37(c)(l)(vii). "[T]he
Board [has] reasonably interpreted Rule 41.37 to require more substantive
arguments in an appeal brief than a mere recitation of the claim elements and
a naked assertion that the corresponding elements [create points of
patentability]." In re Lovin, 652 F.3d 1349, 1357 (Fed. Cir. 2011).
"Phenomena of nature, though just discovered, mental processes, and
abstract intellectual concepts are not patentable, as they are the basic tools of
scientific and technological work." Mayo Collaborative Servs. v.
Prometheus Labs, Inc., 566 U.S. 66, 71 (2012) (quoting Gottschalkv.
Benson, 409 U.S. 63, 67 (1972)). Claims directed to nothing more than
abstract ideas (such as mathematical algorithms), natural phenomena, and
laws of nature are not eligible for patent protection. Diamond v. Diehr, 450
U.S. 175, 185 (1981); accord MPEP § 2106 (II) (discussing Diehr).
In analyzing patent-eligibility questions under 35 U.S.C. § 101, the
Supreme Court instructs us to "first determine whether the claims at issue
are directed to a patent-ineligible concept." Alice Corp. Pty. Ltd. v. CLS
Bank Int'!, 134 S. Ct. 2347, 2355 (2014). If the initial threshold is met, we
then move to a second step and "consider the elements of each claim both
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individually and 'as an ordered combination' to determine whether the
additional elements 'transform the nature of the claim' into a patent-eligible
application." Id. (quoting Mayo, 566 U.S. at 78-79).
In their brief, Appellants argue the appealed claims under thirteen
separate headings. See generally App. Br. "The Examiner [did] not agree
with said 'Grouping[ s ]' ," but determined "that Independent claims 13 and 80
and those claims dependent therefrom (claims 43, 44, 45, 52, 53, 69, 72, 73,
78, 81, 82, 84, 85 and 87) are drawn to the recitations of claim[ s] 13 and 80
which are 'characterizing a disease state' and Claim 14 and those claims
dependent therefrom (claims 44, 45, 52, 53, 60, 63, 67, 79, 83, and 86) are
drawn to a method of diagnosing or prognosing." Answer 6. However, the
Examiner went on to address the claims in the groupings of Appellants'
brief. Id. at 6-17. Therefore, we address the claims similarly below.
Group I - Claims 13 and 80
Following the two-step patent eligibility analysis dictated by Alice and
Mayo, the Examiner determined that "[t]he claims are directed to the natural
occurring correlation between diseased cells versus normal cells (normal
state versus disease state)" and "[ c ]omparisons of changes in 'arcs' (edges)
which represent cellular components are made to determine a disease state."
Final Action 3--4. The Examiner added "the claims are directed to a natural
phenomenon, as well as an abstract idea," and "it is noted that more than one
judicial exception is present in the instant claims, i.e. abstract idea recited as
providing a first and second set of arcs which entails probabilistic statistical
analyses of causal connections." Answer 7.
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Having determined that this subject matter was directed to a judicial
exception to patent-eligibility, the Examiner moved to step-two of the
analysis to ascertain whether the claims, each as a whole, considering
individual elements and their ordered combination, recited "something
significantly different than the judicial exception," so as to transform the
nature of the claim' into a patent-eligible application. Final Action 3. The
Examiner determined, inter alia, that:
1.
the instant claims do not provide a direct manipulation of the
natural correlation other than assessment of changes between one
cell-type (diseased) versus another (normal/not diseased). This
is a well-known and routine procedure in the art of molecular
biology and statistical analysis (using Bayesian analysis to
represent states). Id. at 5.
2.
the steps of comparing profiles (a cell that is diseased to cell that
is not) is well-understood in the art. Id.
3.
The instant claims recite nothing more than the application of a
statistic to assess differences between cell set A (disease) and cell
set B (not diseased) and add nothing specific to the natural
principle that would render it patent eligible. Id. at 7.
4.
the claims recite well-known steps of detecting probe binding to
generate data sets amongst diseased versus normal cells. Such
steps are well-known in the art of molecular biology and
bioinformatics. Id.
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5.
Generation of "arcs" (edges in a Bayesian network) is routine
procedure for such an analysis, as it is a statistical analysis of the
natural phenomenon, which is conventional. Id. at 8.
6.
The additional elements recited in the claims 13, 14, and 80, as
already established, are:
-measuring a plurality of cellular components in individual
cells exhibiting said disease state . . . by contacting said cells
exhibiting said disease state with a set of distinguishably
detectable probes ... and detecting binding of said probes ...
-measuring a plurality of cellular components in individual
cells not exhibiting said disease state ... by contacting said cells
not exhibiting said disease state with a set of distinguishably
detectable probes ... and detecting binding of said probes ...
Those additional steps, when viewed both individually and
as a whole, do not provide "significantly more". Answer 8.
We conclude the Examiner has established that the claims are not
patent-eligible because they are directed to an abstract idea and natural
phenomenon and do not claim more than routine and conventional additional
elements. We address Appellants' arguments below.
Appellants argue the "claims include a combination of physical and
analytical steps that was in no way routine or conventional at the time of
filing. In addition, the claimed method is not drawn to any natural
correlation itself, but instead to a method of identifYing a correlation." App.
Br. 10. The physical and analytical steps to which Appellants refer include
measuring by contacting cells with detectable probes, which bind to cellular
components, followed by detection of that binding. Id. Appellants contend
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that it is important that these steps are performed on individual cells and that
related probabilistic analysis of causal connections relate to cellular
components in each such individual cell. Id. Appellants argue the Examiner
failed to consider the claimed steps as a combined whole. Id. at 11.
Appellants also contend the Examiner failed to provide evidence that the
claimed steps were routine and conventional, arguing that the Examiner's
withdrawal of an obviousness rejection over a prior art combination is
evidence that these steps are not routine or conventional, but are both novel
and non-obvious.3 Id. Appellants argue the claimed invention does not fall
under the holding of the Supreme Court in Mayo. Id. at 11-12.
These arguments are not persuasive. They amount to little more than
mere attorney argument. Appellants do not reasonably call into question the
Examiner's determination that the claims are directed to patent-ineligible
subject matter (an abstract idea and a natural phenomenon) and do not
establish that any of the additional claim elements amount to anything
3 See Final Office Action dated March 3, 2010, wherein the Examiner
rejected the claims under 35 U.S.C. § 103 (and§ 102) over combinations of:
US 2003/0232364 Al (pub. Dec. 18, 2003) ("Shaughnessy");
Dana Pe'er et al., Inferring Subnetworks from Perturbed Expression
Profiles, 17 BIOINFORMATICS S215-24 (2001) ("Pe' er");
Nir Friedman, Bayesian Network Classifiers, 29 MACHINE LEARNING
131-63 ( 1997) ("Friedman");
Stephen P. Perfetto et al., Seventeen-colour Flow Cytometry:
Unravelling the Immune System, 4 INNOVATION 648-55 (2004) ("Perfetto");
Karen Sachs et al., Bayesian Network Approach to Cell Signaling
Pathway Modeling, SCIENCE'S STKE 1-5 (Sept. 3, 2002) ("Sachs"); and
Amy Norris, University of Waterloo, Thesis: Multivariate Analysis
and Reverse Engineering of Signal Transduction Pathways (2002)
("Norris").
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significantly more than the natural phenomena and abstract idea identified
by the Examiner. Appellants' arguments seeking to distinguish their claims
from those in Mayo are also not persuasive because, whether or not the
appealed claims involve physical and/or analytical steps for identifying a
naturally occurring correlation (or relate to individual cells), they
nevertheless are directed to merely determining the presence of molecules in
samples of normal and diseased cells and applying a mathematical algorithm
to illustrate a biological correlation, which, as the examiner determined, is
not patent-eligible as being directed to both a natural phenomenon and
abstract idea.
Furthermore, having reviewed the prior art references of the
withdrawn obviousness rejection(s) of record in this appeal and identified by
Appellants (see supra, n.3), we note that the prior art evidences that the
claim elements in addition to the patent-ineligible subject matter amount to
mere well-known, routine, and conventional concepts and processes. For
example, the prior art reference Shaughnessy teaches that the use of
molecular probes was known in the prior art for correlating genes with
disease states, that flow cytometry was a known analysis tool for detecting
molecular markers, that it was known that gene expression could be altered
to discriminate between normal and malignant (diseased) cells, that
Bayesian networks and arcs between nodes could be used as a probabilistic
analysis tool to identify genes (cellular components) whose over/under
expression is apparent in the comparison of healthy samples and diseased
samples of cells. Shaughnessy iii! 22, 78, 179, 201-15. Further, Pe' er
teaches that it was known to use Bayesian networking to identify direct
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interactions between genes (cellular components) regulating one another.
Pe' er S2 l 5, S2 l 7, S222. Friedman teaches that Bayesian classifiers were
known as one of the most effective predictive tools, useful in analyzing
biological processes. Friedman 131, 140. Further, Perfetto also teaches that
flow cytometry was a known technique to measure multiple fluorescent
markers/probes in molecular-cell-analysis. Perfetto 648. Sachs teaches that
it was known to use Bayesian networks to analyze cell signaling and model
multivariate probabilistic relationships for cellular component pathways
(e.g., relating to phosphorylated receptors, activated enzymes, and other
biomolecules), and to use flow cytometry in association with such
mathematical processes. Sachs 1, 4. Finally, Norris teaches that it was
known to use Bayesian networks to recreate biological connections between
molecules or genes (cellular components). Norris 59. Thus, the evidence of
record supports the Examiner's determination that the claims do not recite
elements beyond the patent-ineligible concepts that amount to more than
well-known, routine, and conventional steps or techniques.
Claim 1 of U.S. Patent No. 6,355,623, at issue in Mayo, reads as
follows:
A method of optimizing therapeutic efficacy for treatment of an
immune-mediated gastrointestinal disorder, comprising:
(a) administering a drug providing 6-thioguanine to a subject
having said immune-mediated gastrointestinal disorder; and
(b) determining the level of 6-thioguanine in said subject having
said immune-mediated gastrointestinal disorder,
wherein the level of 6-thioguanine less than about 230 pmol per
8x 108 red blood cells indicates a need to increase the amount of
said drug subsequently administered to said subject and
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wherein the level of 6-thioguanine greater than about 400 pmol
per 8x 108 red blood cells indicates a need to decrease the amount
of said drug subsequently administered to said subject.
Mayo, 566 U.S. at 74-75. This is analogous to the claims on appeal, if even
less overtly directed to an abstract idea than the appealed claims, and is
potentially more specific and narrow than the broadest claims on appeal. It
is directed to, but does not expressly claim, the natural phenomenon that an
administered compound correlates to predictable levels of metabolites and
that understanding this allows doctors to determine this correlation in vivo to
better treat patients with the compound. The Supreme Court held that
determining the results of a natural correlation using well-understood,
routine, conventional steps, as per the appealed claims here, amounted to
simply telling doctors to apply the natural law, identifying that "a scientific
truth, or the mathematical expression of it, is not a patentable invention." Id.
at 71 (quoting Mackay Radio & Telegraph Co. v. Radio Corp. of Am., 306
U.S. 86, 188 (1939)), 79.
Also relevant is Parker v. Flook, 437 U.S. 584 (1978), where the
Supreme Court held that a claimed invention amounting to a mathematical
process for setting (or adjusting) alarm limits relating to the chemical
processes involved in catalytic conversion of hydrocarbons was not patent
eligible as directed to an abstract idea. In Flook, the Court found the
claimed method, in essence, consisted of measuring a value of a variable
(e.g., temperature), using an algorithm to calculate an alarm-limit value, and
adjusting the alarm limit to an adjusted value, where the difference between
the conventional methods of changing alarm limits and the invention resided
in the mathematical algorithm. Here, as in Flook, the basic methodologies
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of the claimed invention are well-known, conventional things (e.g., applying
a detectable probe to molecules of separate samples, comparing
measurements of those probes between samples). The manipulation of data
obtained by such conventional techniques using probability mathematics,
which may illustrate a biological correlation between molecules and disease
state, is not patent-eligible.
Further, inAriosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371,
1374 (Fed. Cir. 2015), the Federal Circuit held that the following claim was
not patent-eligible:
25. A method for performing a prenatal diagnosis on a maternal
blood sample, which method comprises obtaining a non-cellular
fraction of the blood sample amplifying a paternally inherited
nucleic acid from the non-cellular fraction and performing
nucleic acid analysis on the amplified nucleic acid to detect
paternally inherited fetal nucleic acid.
The court held that this claim was directed to a natural phenomenon: the
existence of cfIDNA in maternal blood, which could be advantageously used
for genotyping from this blood. Id. at 1376. The court found that the
otherwise claimed methodology, e.g., using PCR to amplify and detect
cfIDNA, was merely well-understood, routine, and conventional, specified
at a high level of generality, and, so, the claims were not patent-eligible.
Here the claims are directed to a natural phenomenon, i.e., a correlation
between cell disease and associated cellular components and the abstract
idea that one may apply a probabilistic mathematical algorithm to illustrate
such a correlation and the steps and processes used to analyze such cells
were well-known, routine, and conventional. The claims on appeal are more
general and broader than those in Ariosa.
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In view of the above-discussed precedent, we must agree with the
Examiner that the claims are directed to the patent-ineligible concepts of
characterizing a disease state based on a correlation between the disease and
cellular components and using a mathematical algorithm to illustrate this
correlation and further agree that the other claimed subject matter amounts
to no more than known, routine, conventional steps and techniques.
Therefore, we affirm the rejection.
Group II - Claim 43
Appellants quote the claim language "applying a probabilistic
graphical model algorithm to said first data set and said second data set to
identify a set of arcs between individual cellular components in each said
cells," and argue the recited step is not routine or conventional and that the
Examiner has not provided evidence to the contrary. App. Br. 12.
This argument amounts to no more than quoting the claim language
and stating that it renders the claim patentable; more is required of an appeal
argument. See 37 C.F.R. § 41.37(c)(l)(vii); and In re Lovin, 652 F.3d at
1357. In any event, as with claim 13, we find that applying a mathematical
algorithm to identify a relationship between analyzed cellular components is
an abstract idea, as well as something that was known, routine, and
conventional in the prior art, as discussed above. The Specification states
that "[a]ny probabilistic graphical model algorithm can be used." Spec.
iJ 10. It also lists several well-known techniques, including Bayesian, factor
graph, Markov, and conditional random field models. Id. Further, the use of
Bayesian networks to illustrate biological relationships were disclosed in
several of the prior art references discussed above and are understood to
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have been routine and conventional. For these reasons, Appellants'
argument is not persuasive.
Group III-Claims 69, 73, and 73
Appellants quote the claim language "contacting said cells exhibiting
said disease state with an agent that modulates one or more of the plurality
of cellular components in said cells prior to contacting said cells exhibiting
said disease state with a set of probes," and argue this step is physical, and
that the Examiner has not provided evidence that this step in combination
with the others claimed is/are routine or conventional. App. Br. 13.
This argument amounts to no more than quoting the claim language
and stating that it renders the claim patentable; more is required of an appeal
argument. See 37 C.F.R. § 41.37(c)(l)(vii); and In re Lovin, 652 F.3d at
1357. In any event, as with claim 13, we find that using a cellular activity
modulator, e.g., altering gene expression, activated enzymes, etc., was
known, routine, and conventional in the prior art, as discussed above. The
Specification identifies that the cellular components analyzed can be any
molecule found in an organism or cell, which expands the universe of things
that are potentially modulated to almost any biological substance. Spec.
ii 52. The Specification further explains that "[b ]y 'modulate' [it means]
that the agent interacts with the cellular component such that the cellular
component switches from one state or form to another," which includes
virtually any change effected on any cellular component. Spec. ii 79. No
inventive concept is added by including these claim elements. For these
reasons, Appellants' argument is not persuasive.
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Group IV- Claims 78 and 81
Appellants quote the claim language "'the cellular components are
activatable elements, and the probes used are activation state-specific
probes"' and argue the claims "represent a way to limit the claimed method
in such a way to further ensure that others are not foreclosed from using any
alleged judicial exception." App. Br. 14.
This argument amounts to no more than quoting the claim language
and stating that it renders the claim patentable; more is required of an appeal
argument. See 37 C.F.R. § 41.37(c)(l)(vii); and In re Lovin, 652 F.3d at
1357. In any event, as with claim 13, we find that analyzing activatable
cellular components, e.g., altering gene expression, activated enzymes, etc.,
was known, routine, and conventional in the prior art, as discussed above.
The Specification explains that a cellular component is not activatable if it
does not switch from one form to another, thus, a cellular component that
can change is activatable. Spec. ii 75. Some common examples of such
activatable cellular components are identified as PKA, calcium, mevalonate,
thymidine, glucose, kinases, proteins, enzymes, and nucleotides. Id. ii 76.
Detecting such cellular components was indisputably routine and
conventional. For these reasons, Appellants' argument is not persuasive.
Group V - Claims 82 and 84
Appellants quote the claim language "'one or more of the activatable
elements is a protein and one or more of the activation state-specific probes
is an antibody,"' and argue the claims "represent a way to limit the claimed
method in such a way to further ensure that others are not foreclosed from
using any alleged judicial exception." App. Br. 14.
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This argument amounts to no more than quoting the claim language
and stating that it renders the claim patentable; more is required of an appeal
argument. See 37 C.F.R. § 41.37(c)(l)(vii); and In re Lovin, 652 F.3d at
1357. In any event, as with claims 13 (and 80), we find that analyzing
activatable protein cellular components, e.g., activated enzymes, etc., was
known, routine, and conventional in the prior art, as discussed above. As to
the argument that the claims are not preemptive, "[ w ]hile preemption may
signal patent ineligible subject matter, the absence of complete preemption
does not demonstrate patent eligibility." Ariosa, 788 F.3d at 1379.
Appellants' argument does not change the conclusion that the claims are
directed to patent-ineligible subject matter. For these reasons, Appellants'
argument is not persuasive.
Group VI-Claims 85 and 87
Appellants quote the claim language "'detecting comprises a detection
technique selected from the group consisting of: flow cytometry and
confocal microscopy,"' and argue the claims "represent a way to limit the
claimed method in such a way to further ensure that others are not foreclosed
from using any alleged judicial exception." App. Br. 15.
This argument amounts to no more than quoting the claim language
and stating that it renders the claim patentable; more is required of an appeal
argument. See 37 C.F.R. § 41.37(c)(l)(vii); and In re Lovin, 652 F.3d at
1357. In any event, as with claim 13, we find that using, e.g., flow
cytometry, was known, routine, and conventional in the prior art, as
discussed above. See supra, discussion of Shaughnessy and Perfetto. As to
the argument that the claims are not preemptive, "[ w ]hile preemption may
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signal patent ineligible subject matter, the absence of complete preemption
does not demonstrate patent eligibility." Ariosa, 788 F.3d at 1379.
Appellants' argument does not change the conclusion that the claims are
directed to patent-ineligible subject matter. For these reasons, Appellants'
argument is not persuasive.
Group VII - Claim 14
Similar to their arguments over claims 13 and 80, Appellants argue
the claim "a combination of physical and analytical steps that was in no way
routine or conventional at the time of filing. In addition, the claimed method
is not drawn to any natural correlation itself, but instead to a useful
application of a correlation." App. Br. 15. Appellants identify the step of
detecting the binding of probes to cellular components as a physical step
and, again, contend that it is relevant that the probabilistic algorithm method
and collected data relate to individual cells. Id. at 16. Again, as with their
arguments in relation to claim 13, Appellants contend the Examiner has not
provided evidence that the claimed combination of steps was routine or
conventional and point to the aforementioned withdrawn obviousness
rejection as evidence that they were novel and non-obvious and, so, not
routine or conventional. Id. Appellants again argue that this claim does not
fall under the holding of Mayo, contending that, here, the wherein clauses
indicating that the method steps are practically applied are integrated into the
claim and that the lack of similar integration in the claims at issue in Mayo
was the cause of their patent-ineligibility. Id. at 17.
Appellants' arguments over claim 14 essentially restate those made
regarding claim 13, which we found unpersuasive, as discussed above.
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While the language of claims 13 and 14 is not identical, we agree with the
Examiner that these claims are directed to the same natural phenomenon and
abstract idea, that is, identifying the natural relationships between cellular
components in diseased cells and illustrating the same using a mathematical
algorithm, and recite additional elements that are merely known, routine, and
conventional, that is, using decisional arcs, using probes, etc., as exemplified
by the prior art of record. Therefore, for the same reasons discussed above
regarding claim 13, we affirm the rejection as to claim 14.
Group VIII - Claims 60, 63, and 67
Appellants quote the claim language "'contacting said first set of cells
with an agent that modulates one or more of the plurality of cellular
components in said cells prior to providing a set of probes that bind to the set
of cellular components,"' and argue that this is an additional physical step
and that the Examiner has not provided evidence that it was routine or
conventional. App. Br. 18.
As was the argument relating to Group III, this argument amounts to
no more than quoting the claim language and stating that it renders the claim
patentable; more is required of an appeal argument. See 37 C.F.R.
§ 41.37(c)(l)(vii); and In re Lovin, 652 F.3d at 1357. In any event, as with
claims 13 and 14, we find that using a cellular activity modulator, e.g.,
altering gene expression, activated enzymes, etc., was known, routine, and
conventional in the prior art, as discussed above. As discussed above, the
Specification identifies that the cellular components can be any molecule
found in an organism or cell, i.e., almost any biomolecule. Spec. ,-i 52. As
also discussed above, the Specification further explains that "[b ]y
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'modulate' [it means] that the agent interacts with the cellular component
such that the cellular component switches from one state or form to
another," which includes virtually any change. Spec. iJ 79. No inventive
concept is added by including these claim elements. For these reasons,
Appellants' argument is not persuasive.
Group IX - Claim 79
Appellants quote the claim language "'the cellular components are
activatable elements, and the probes used are activation state-specific
probes,'" and argue the claim "represents a way to limit the claimed method
in such a way to further ensure that others are not foreclosed from using any
alleged judicial exception." App. Br. 19.
As was the argument relating to Group IV, this argument amounts to
no more than quoting the claim language and stating that it renders the claim
patentable; more is required of an appeal argument. See 37 C.F.R.
§ 41.37(c)(l)(vii); and In re Lovin, 652 F.3d at 1357. In any event, as with
claims 13 and 14, we find that analyzing activatable cellular components,
e.g., altering gene expression, activated enzymes, etc., was known, routine,
and conventional in the prior art, as discussed above. As discussed above,
the Specification explains that a cellular component is not activatable if it
does not switch from one form to another, thus, a cellular component that
can change is activatable, and the Specification also provides a list of several
common examples of activatable components. Spec. iii! 7 5-7 6. Detecting
such cellular components was routine and conventional. For these reasons,
Appellants' argument is not persuasive.
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Group X - Claim 83
Appellants quote the claim language "'one or more of the activatable
elements is a protein and one or more of the activation state-specific probes
is an antibody,"' and argue the claim "represents a way to limit the claimed
method in such a way to further ensure that others are not foreclosed from
using any alleged judicial exception." App. Br. 19.
As was the argument relating to Group V, this argument amounts to
no more than quoting the claim language and stating that it renders the claim
patentable; more is required of an appeal argument. See 37 C.F.R.
§ 41.37(c)(l)(vii); and In re Lovin, 652 F.3d at 1357. In any event, as with
claims 13, 80, and 14, we find that analyzing activatable protein cellular
components, e.g., activated enzymes, etc., was known, routine, and
conventional in the prior art, as discussed above. As to the argument that the
claims are not preemptive, "[ w ]hile preemption may signal patent ineligible
subject matter, the absence of complete preemption does not demonstrate
patent eligibility." Ariosa, 788 F.3d at 1379. Appellants' argument does not
change the conclusion that the claims are directed to patent-ineligible subject
matter. For these reasons, Appellants' argument is not persuasive.
Group XI - Claim 86
Appellants quote the claim language "'detecting comprises a detection
technique selected from the group consisting of: flow cytometry and
confocal microscopy,"' and argue the claim "represents a way to limit the
claimed method in such a way to further ensure that others are not foreclosed
from using any alleged judicial exception." App. Br. 20.
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As with the argument relating to Group VI, this argument amounts to
no more than quoting the claim language and stating that it renders the claim
patentable; more is required of an appeal argument. See 37 C.F.R.
§ 41.37(c)(l)(vii); and In re Lovin, 652 F.3d at 1357. In any event, as with
claims 13 and 14, we find that using, e.g., flow cytometry, was known,
routine, and conventional in the prior art, as discussed above. See supra,
discussion of Shaughnessy and Perfetto. As to the argument that the claims
are not preemptive, "[ w ]hile preemption may signal patent ineligible subject
matter, the absence of complete preemption does not demonstrate patent
eligibility." Ariosa, 788 F.3d at 1379. Appellants' argument does not
change the conclusion that the claims are directed to patent-ineligible subject
matter. For these reasons, Appellants' argument is not persuasive.
Group XII - Claims 44 and 45
Appellants quote the claim language "wherein the probabilistic
graphical model algorithm is selected from the group consisting of a
Bayesian network structure inference algorithm, a factor graph, a Markov
random fields model, and a conditional random fields model," and argue this
is an additional limitation to an analytical step and that the Examiner has not
provided evidence that it was routine or conventional. App. Br. 20.
As with the argument relating to Group II, this argument amounts to
no more than quoting the claim language and stating that it renders the claim
patentable; more is required of an appeal argument. See 37 C.F.R.
§ 41.37(c)(l)(vii); and Jn re Lovin, 652 F.3d at 1357. In any event, as with
claims 13 and 14, we find that applying a mathematical algorithm to
illustrate a relationship between analyzed cellular components is an abstract
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idea as well as something that was known, routine, and conventional in the
prior art, as discussed above. As discussed above, the Specification states
that "[a ]ny probabilistic graphical model algorithm can be used," and lists
several well-known techniques, including those of the claims here. Spec.
iJ 10. Further, the use of Bayesian networks to illustrate biological
relationships was disclosed in several of the prior art references discussed
above and are understood to have been routine and conventional. For these
reasons, Appellants' argument is not persuasive.
Group XIII- Claims 52 and 53
Appellants quote the claim language "wherein one or more of said
arcs is identified between one of said cellular components bound by one of
said probes and a cellular components not bound by one of said probes" and
"wherein one or more of said arcs is identified between at least two of said
cellular components bound by said probes" of claims 52 and 53,
respectively, and argue these are additional limitations to an analytical step
and that the Examiner has not provided evidence they were routine or
conventional. App. Br. 22.
This argument amounts to no more than quoting the claim language
and stating that it renders the claim patentable; more is required of an appeal
argument. See 37 C.F.R. § 41.37(c)(l)(vii); and In re Lovin, 652 F.3d at
1357. In any event, as discussed above, marking molecules of different
samples using probes was routine and conventional. Using a mathematical
algorithm to analyze such samples is not patent-eligible. We are not
persuaded by Appellants' argument.
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SUMMARY
The rejection of the claims as directed to patent-ineligible subject
matter is affirmed.
TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § l .136(a).
AFFIRMED
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