Institute for Systems Biology

Patent Trials and Appeals Board

Oct 20, 2020

2020004626 (P.T.A.B. Oct. 20, 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.
15/202,378 07/05/2016 Robert L. MORITZ 65565-20053.00 7027
25225 7590 10/20/2020
MORRISON & FOERSTER LLP
12531 HIGH BLUFF DRIVE
SUITE 100
SAN DIEGO, CA 92130-2040
EXAMINER
DEJONG, ERIC S
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
10/20/2020 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):
EOfficeSD@mofo.com
PatentDocket@mofo.com
pair_mofo@firsttofile.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte ROBERT L. MORITZ, SAMUEL BADER, and
ULRIKE KUSEBAUCH
__________

Appeal 2020-0046261
Application 15/202,378
Technology Center 1600
__________

Before FRANCISCO C. PRATS, TAWEN CHANG, and
CYNTHIA M. HARDMAN, Administrative Patent Judges.

HARDMAN, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
multiplexed method to identify proteins to which a test compound binds,
which have been rejected as being directed to patent-ineligible subject
matter. We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.

1 We use the word “Appellant” to refer to “applicant” as defined in 37
C.F.R. § 1.42. Appellant identifies Institute for Systems Biology as the real
party in interest. Appeal Br. 2.
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CLAIMED SUBJECT MATTER
Claims 1–4 and 13–18 are on appeal. Final Act. 2. Claim 1 is
illustrative and reads as follows:
1. A multiplexed method to identify proteins to which a
test compound binds in a sample containing numerous proteins
or for identifying a compound capable of binding to a target
protein contained in a sample comprising numerous proteins,
including said target protein, which method comprises:
(a) subjecting a first portion of the sample that contains
test compound and a second portion of the sample that does not
contain test compound to at least one temperature at which at
least some of the proteins in said sample are more soluble when
bound to the test compound and less soluble when not bound to
said test compound;
(b) separating each of said first and second portions to
obtain a soluble fraction and an insoluble fraction of each;
(c) determining the concentration of a multiplicity of
proteins in either the soluble fraction or the insoluble fraction of
each portion or both;
wherein said determining is performed in an unbiased
manner by Sequential Windowed data independent Acquisition
of the Total High resolution Mass Spectroscopy (SWATH-MS);
or
wherein said determining is performed in a biased
manner by Selected Reaction Monitoring (SRM-MS);
wherein a protein whose concentration in the soluble
fraction of the first portion is increased at said temperature as
compared to the soluble fraction of the second portion and/or
whose concentration in the insoluble fraction of the first portion
is decreased at said temperature as compared to the insoluble
fraction of the second portion is identified as a protein that
binds said test compound, or
wherein a higher concentration of said target protein in
the soluble fraction of the first portion at said temperature as
compared to the soluble fraction of the second portion and/or a
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lower concentration of target protein in the insoluble fraction in
the first portion at said temperature as compared to the
insoluble fraction of the second portion identifies said test
compound as binding the target protein.
Appeal Br. 8 (Claims Appendix).
REJECTION
Claims 1–4 and 13–18 stand rejected under 35 U.S.C. § 101 as being
directed to patent-ineligible subject matter. Final Act. 3.
DISCUSSION
The Examiner found that the claims are directed to a method for
identifying proteins to which a test compounds binds, where the claims
“recite a series of abstract data analysis . . . steps (concentration
determinations) to be performed on Mass Spectroscopy data so as to
identify[] the binding properties of a test compound to an arbitrary protein of
interest.” Final Act. 3. The Examiner found that a method “directed
essentially to a series of algorithmic/mathematical procedures is not a
statutory process.” Id. at 4. The Examiner additionally found that the
claimed steps of determining whether a protein concentration is increased or
decreased and identifying a test compound as one that binds to a target are
mental steps. Ans. 4.
The Examiner acknowledged that the claims “recite additional
elements beyond the judicial exception,” but found that they “do no indicate
an improvement to either the sample or testing methods themselves,” but
rather “only turn to known SWATH-MS or SRM-MS analysis procedures to
generate the requisite sample data for analysis.” Final Act. 4. The Examiner
also found that the additional steps are “data gathering required to practice
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the judicial exception and thus do not amount to a real-world integration of
the judicial exceptions.” Ans. 5. The Examiner additionally found that
“[t]he information arrived at (whether a protein can bind) is not used in any
practical manner which amount[s to] a meaningful limitation of that
information.” Id.
Appellant argues that claimed steps (a) through (c) describe a prior art
method for determining interaction of a test compound with a single protein,
and that “the invention itself is directed to an improvement which permits
multiplexing” of this prior art method.2 Appeal Br. 4. Appellant asserts the
claimed improvement lies in “requiring that the sample comprise numerous
proteins and requiring that the determining is performed by SWATH-MS or
SRM-MS.” Id. at 3. Appellant argues that this is “a new method for
determining protein/compound interactions,” and thus “improv[es] a
technological process.” Id. at 5, 6; see also Reply Br. 3 (“[T]he claims recite
an improvement to the technical field described, for example, in the ’014
patent.”).
Appellant additionally argues that the Examiner “nowhere considers
the claims as a whole,” but “when considered as a whole, the claims are
directed to an improvement in determining test compound interaction with
proteins and thus integrate the alleged judicial exception into a practical
application.” Reply Br. 4. Appellant further argues that the Specification
“explains the improvement and its benefit.” Id. at 7–8 (citing Spec. ¶¶ 3–6,
8–11, and Example 1).

2 Appellant indicates that the prior art method is claimed in US Patent
8,969,014 (“the ’014 patent”). Appeal Br. 3.
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Principles of Law
1. Section 101
An invention is patent-eligible if it claims a “new and useful process,
machine, manufacture, or composition of matter.” 35 U.S.C. § 101.
However, the U.S. Supreme Court has long interpreted 35 U.S.C. § 101 to
include implicit exceptions: “[l]aws of nature, natural phenomena, and
abstract ideas” are not patentable. E.g., Alice Corp. v. CLS Bank Int’l, 573
U.S. 208, 216 (2014).
In determining whether a claim falls within an excluded category, we
are guided by the Court’s two-part framework, described in Mayo and Alice.
Id. at 217–18; Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566
U.S. 66, 75–77 (2012). In accordance with that framework, we first
determine what concept the claim is “directed to.” Alice, 573 U.S. at 219
(“On their face, the claims before us are drawn to the concept of
intermediated settlement, i.e., the use of a third party to mitigate settlement
risk.”); see also Bilski v. Kappos, 561 U.S. 593, 611 (2010) (“Claims 1 and 4
in petitioners’ application explain the basic concept of hedging, or protecting
against risk.”).
Concepts determined to be abstract ideas, and thus patent ineligible,
include certain methods of organizing human activity, such as fundamental
economic practices (Alice, 573 U.S. at 219–20; Bilski, 561 U.S. at 611);
mathematical formulas (Parker v. Flook, 437 U.S. 584, 594–95 (1978)); and
mental processes (Gottschalk v. Benson, 409 U.S. 63, 67 (1972)). Concepts
determined to be patent eligible include physical and chemical processes,
such as “molding rubber products” (Diamond v. Diehr, 450 U.S. 175, 191
(1981)); “tanning, dyeing, making water-proof cloth, vulcanizing India
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rubber, smelting ores” (id. at 182 n.7 (quoting Corning v. Burden, 56 U.S.
252, 267–68 (1854))); and manufacturing flour (Benson, 409 U.S. at 69
(citing Cochrane v. Deener, 94 U.S. 780, 785 (1876))).
In Diehr, the claim at issue recited a mathematical formula, but the
Court held that “a claim drawn to subject matter otherwise statutory does not
become nonstatutory simply because it uses a mathematical formula.”
Diehr, 450 U.S. at 187; see also id. at 191 (“We view respondents’ claims as
nothing more than a process for molding rubber products and not as an
attempt to patent a mathematical formula.”). Having said that, the Court
also indicated that a claim “seeking patent protection for that formula in the
abstract . . . is not accorded the protection of our patent laws, and this
principle cannot be circumvented by attempting to limit the use of the
formula to a particular technological environment.” Id. (citation omitted)
(citing Benson and Flook); see, e.g., id. at 187 (“It is now commonplace that
an application of a law of nature or mathematical formula to a known
structure or process may well be deserving of patent protection.”).
If a claim is “directed to” an abstract idea, we turn to the second step
of the Alice and Mayo framework, where “we must examine the elements of
the claim to determine whether it contains an ‘inventive concept’ sufficient
to ‘transform’ the claimed abstract idea into a patent-eligible application.”
Alice, 573 U.S. at 221 (internal quotation marks omitted). “A claim that
recites an abstract idea must include ‘additional features’ to ensure ‘that the
[claim] is more than a drafting effort designed to monopolize the [abstract
idea].’” Id. (alterations in original) (quoting Mayo, 566 U.S. at 77).
“[M]erely requir[ing] generic computer implementation[] fail[s] to transform
that abstract idea into a patent-eligible invention.” Id.
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2. USPTO Section 101 Guidance
In January 2019, the U.S. Patent and Trademark Office (“USPTO”)
published revised guidance on the application of § 101. 2019 Revised Patent
Subject Matter Eligibility Guidance, 84 Fed. Reg. 50 (Jan. 7, 2019)
(“Guidance”).3 “All USPTO personnel are, as a matter of internal agency
management, expected to follow the guidance.” Id. at 51; see also October
2019 Update at 1.
Under the Guidance and October 2019 Update, we first look to
whether the claim recites:
(1) any judicial exceptions, including certain groupings
of abstract ideas (i.e., mathematical concepts, certain methods
of organizing human activity such as a fundamental economic
practice, or mental processes) (“Step 2A, Prong One”); and
(2) additional elements that integrate the judicial
exception into a practical application (see MPEP
§§ 2106.05(a)–(c), (e)–(h) (9th ed. Rev. 08.2017, Jan. 2018))
(“Step 2A, Prong Two”).4
Guidance at 51–55.

3 In response to public comments, the Office issued further guidance on
October 17, 2019, clarifying the Guidance. USPTO, October 2019 Update:
Subject Matter Eligibility (“October 2019 Update”) (available at
https://www.uspto.gov/sites/default/files/documents/peg_oct_2019
_update.pdf).
4 This evaluation is performed by (a) identifying whether there are any
additional elements recited in the claim beyond the judicial exception, and
(b) evaluating those additional elements individually and in combination to
determine whether the claim as a whole integrates the exception into a
practical application. See Guidance - Section III(A)(2), 84 Fed. Reg. at 54–
55.
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Only if a claim (1) recites a judicial exception and (2) does not
integrate that exception into a practical application, do we then look, under
Step 2B, to whether the claim:
(3) adds a specific limitation beyond the judicial
exception that is not “well-understood, routine, conventional”
in the field (see MPEP § 2106.05(d)); or
(4) simply appends well-understood, routine,
conventional activities previously known to the industry,
specified at a high level of generality, to the judicial exception.
Id. at 52–56.
Analysis
For the reasons explained below, we agree with Appellant that the
Examiner has not established that the claimed subject matter is patent-
ineligible.
The independent claims on appeal generally relate to methods of
detecting binding between proteins and a test compound. Appeal Br. 8–10
(Claims Appendix). A process (or method) is one of the four categories of
patent-eligible subject matter enumerated in 35 U.S.C. § 101. We thus
proceed to Step 2A, Prong 1 of the Guidance.
Guidance Step 2A, Prong 1
Pursuant to Step 2A, Prong 1, we analyze whether the claims recite
any judicial exception(s) to patent eligibility. Guidance at 54.
The Examiner found that the claims recite “an abstract analysis of
data in order to produce new information on a generic sample under
investigation,” as well as the “mental step[s]” of “determining whether a
protein concentration is increased or decreased (comparison of data which is
a mental step) and identifying that a test compound as one which binds to a
target based on the increase or decrease.” Ans. 7, 4.
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With regard to the three judicially-excepted groupings of abstract
ideas identified in the Guidance, we first note that the Examiner did not
contend that the claims recite any method of organizing human activity such
as fundamental economic practices. See Guidance at 52. Indeed, we
determine that the claims do not recite any such method.
The Examiner contended that the claims recite mental processes. See
Ans. 4. Although the Examiner did not make any factual findings
substantiating the contention that any step in the claims could practicably be
performed in the human mind or with pen and paper, it is arguably
conceivable that at least the claimed steps of identifying a protein that binds
a test compound could be performed in the mind.5 Indeed, Appellant did not
dispute that the claims recite mental processes as proposed by the Examiner.
Accordingly, under the broadest reasonable interpretation standard, we
conclude that the claimed steps relating to “identif[ying]” a protein that
binds a test compound could be viewed as a mental process, such that the
claims recite the judicial exception of mental processes, and, thus, abstract
ideas. Accordingly, we will proceed to analyze the claims under Step 2A,
Prong 2 of the Guidance.

5 The specific language in independent claim 1 reads: “wherein a protein . . .
is identified as a protein that binds said test compound” and “wherein a
higher concentration of said target protein . . . identifies said test compound
as binding the target protein.” The specific language in independent claim
13 reads: “wherein a protein whose concentration [meets the recited
parameters] is identified as a protein that binds said test compound.” The
specific language in independent claim 18 reads: “wherein any protein
whose concentration [meets the recited parameters] is identified as a protein
that binds said test compound.” See Appeal Br. 8–10 (Claims Appendix).
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Before we do so, however, we complete our discussion of the
categories of abstract ideas identified in the Guidance by addressing the third
category, mathematical concepts. See Guidance at 52. We determine that
the claims do not recite any mathematical concept, such as a specific
mathematical algorithm or formula. See Flook, 437 U.S. at 586; Diehr, 450
U.S. at 187. To be sure, the claim limitations “wherein said determining is
performed in an unbiased manner by Sequential Windowed data independent
Acquisition of the Total High resolution Mass spectroscopy (SWATH-MS)”
and “wherein said determining is performed in a biased manner by Selected
Reaction Monitoring (SRM-MS)” undoubtedly employ mathematical
relationships, formulas, or calculations. Nevertheless, those mathematical
relationships, formulas, or calculations are not themselves explicitly recited
in the claims. See, e.g., Ex parte Hannun, Appeal No. 2018-003323, slip op.
at 3, 10 (PTAB April 1, 2019) (informative) (where claims recited
“obtaining predicted character probabilities output” and specification
disclosed an algorithm to obtain the probabilities, finding that the claims did
not themselves recite a mathematical concept). Moreover, as further
discussed below, even if the claims were considered to recite mathematical
concepts, we find that under Step 2A, Prong 2 of the Guidance, the claims
integrate any such concepts into a practical application.
Guidance Step 2A, Prong 2
“[M]ere recitation of a judicial exception does not mean that the claim
is ‘directed to’ that judicial exception under Step 2A Prong Two.” October
2019 Update at 10. Instead, if the claim as a whole integrates the judicial
exception into a practical application, the claim is not “directed to” a judicial
exception. Guidance at 54; October 2019 Update at 10. As in the
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Mayo/Alice framework, we must look at the claim elements individually and
as an ordered combination to determine whether the additional elements
integrate the recited abstract idea(s) into a practical application, such as an
improvement to technology or to a technical field. Guidance at 54–55.
As explained in the October 2019 Update, “first the specification
should be evaluated to determine if the disclosure provides sufficient details
such that one of ordinary skill in the art would recognize the claimed
invention as providing an improvement.” October 2019 Update at 12.
Second, “the claim must be evaluated to ensure that the claim itself reflects
the disclosed improvement.” Id. This analysis is performed “without
reference to what is well-understood, routine, conventional activity.” Id.
Here, the Specification describes the invention as an improvement in
the technical field of assays (such as thermal shift assays) that assess the
interaction of a compound with a protein. Specifically, the claimed steps
recite a method of identifying and quantifying proteins to which a test
compound binds in a sample containing numerous proteins, where the
interaction between the test compound and proteins are determined using
SWATH-MS or SRM-MS. Spec. ¶ 11; Appeal Br. 8–10 (Claims Appendix).
According to the Specification, the claimed application of SWATH-MS or
SRM-MS to prior art thermal shift assays “overcomes the obstacles”
associated with using such assays on “complex protein samples.” Spec. ¶ 6.
In particular, the Specification states:
[a]dapting the SWATH-MS technique to characterizing
the results of proteome thermal shift assays has the highly
desirable result of permitting simultaneous analysis of all of the
proteins to which a compound is (or is not) bound along with a
measure of the affinity of the binding. This enables
identification not only of compounds that are successful in
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interacting with a desired target protein, but also assessing the
possibility of side effects of a drug, for example, by viewing the
interaction of a successful (or unsuccessful) test compound with
alternative proteins where interaction is unknown or is not
desired.
Id. ¶ 7 (emphasis added); see also Reply Br. 7–8 (citing Spec. ¶¶ 3–6, 8–11,
and Example 1).
Accordingly, in light of the Specification, we find that the claimed
subject matter is patent eligible as an improvement in a specific technology,
i.e., assays (such as thermal shift assays) that assess the interaction of a
compound with a protein. See Guidance at 55; see also Finjan, Inc. v. Blue
Coat Sys., Inc., 879 F.3d 1299, 1304 (Fed. Cir. 2018) (finding claims patent
eligible because the claimed virus scanning method newly permitted
protection against unknown computer viruses, whereas prior art methods
recognized only known viruses); Thales Visionix Inc. v. United States, 850
F.3d 1343, 1349 (Fed. Cir. 2017) (finding claims patent eligible where they
“specif[ied] a particular configuration of inertial sensors and a particular
method of using the raw data from the sensors in order to more accurately
calculate the position and orientation of an object on a moving platform”).
The Examiner appears to suggest that the claimed subject matter is not
a patent eligible improvement in a specific technology because “the claims
do not indicate an improvement to either the sample or testing methods
themselves,” and “only turn to known SWATH-MS or SRM-MS analysis
procedures to generate the requisite sample data for analysis.” Ans. 5; see
also id. at 6. The Examiner also appears to suggest that the sample
preparation and separation steps (recited in steps (a)–(c)) are “routine and
conventional data gathering activity.” Final Act. 5.
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The Examiner’s focus on use of existing test methods and known
SWATH-MS and SRM-MS methods runs afoul of the Guidance’s directive
that “Step 2A specifically excludes consideration of whether the additional
elements represent well-understood, routine, conventional activity.”
Guidance at 55. “[A] claim that includes conventional elements may still
integrate an exception into a practical application, thereby satisfying the
subject matter eligibility requirement of Section 101.” Id. Additionally, we
agree with Appellant that Examiner’s analysis improperly “separately
analyzes the inventiveness of the ‘sample preparation’ and ‘multiplexing’
aspects of claim 1,” and “nowhere considers the claim as a whole.” Reply
Br. 4 (footnotes omitted). We agree with Appellant that, “when considered
as a whole, the claims are directed to an improvement in determining test
compound interaction with proteins,” as discussed above. Id.; see also
Guidance at 54 (“In Prong Two, examiners should evaluate whether the
claim as a whole integrates the recited judicial exception into a practical
application of the exception.”).
In sum, based on the record before us, we are persuaded that the
Examiner erred in determining that the claims are directed to a patent-
ineligible abstract idea, rather than to a patent-eligible improvement to a
technological field.
CONCLUSION
We reverse the rejection of claims 1–4 and 13–18 under 35 U.S.C.
§ 101.
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DECISION SUMMARY
Claims
Rejected
35 U.S.C. § Reference(s)/Basis  Affirmed Reversed
1–4, 13–18 101 Eligibility 1–4, 13–18

REVERSED