STICHTING KATHOLIEKE UNIVERSITEIT, MORE PARTICULA- RLY THE FACULTY OF SCIENCE OF RADBOUD UNIVERSITY

Patent Trials and Appeals Board

Oct 20, 2020

2020000153 (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.
15/106,064 06/17/2016 Jeroen Jansen BHD-5875-25 7913
23117 7590 10/20/2020
NIXON & VANDERHYE, PC
901 NORTH GLEBE ROAD, 11TH FLOOR
ARLINGTON, VA 22203
EXAMINER
NEGIN, RUSSELL SCOTT
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):
PTOMAIL@nixonvan.com
pair_nixon@firsttofile.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte JEROEN JANSEN, LUTGARDE BUYDENS,
LEO KOENDERMAN, BART HILVERING, and
OSCAR VAN DEN BRINK
Appeal 2020-000153
Application 15/106,064
Technology Center 1600
Before ERIC B. GRIMES, FRANCISCO C. PRATS, and LILAN REN,
Administrative Patent Judges.
REN, Administrative Patent Judge.
DECISION ON APPEAL
STATEMENT OF THE CASE
Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from the
Examiner’s decision to reject claims 18–28 and 30–37. See Final Act. 3.
We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.

1 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 applicants
Stichting Katholieke Universiteit and University Medical Center Utrecht te
Utrecht. Appeal Br. 2.
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Application 15/106,064
2
CLAIMED SUBJECT MATTER
The claims are directed to a method of “analysing data from a
cytometer [wherein] the data comprises data from healthy individuals and
challenged individuals.” Spec. 1:8–9. Claim 18, reproduced below, is
illustrative of the claimed subject matter:
18. Computer implemented method of analysing data
comprising measured values of characteristics of objects in
samples, the data stored on a non-transitory computer readable
medium comprising:
- a first set of data (Xireference) with measured values of
characteristics of ten or more reference objects in reference
samples; and
- a test set of data (Xitest) with measured values of the
characteristics of ten or more objects in a test sample;
the method comprising using a computer for,
- reading the first set of data from the computer readable
medium and fitting a control model to the first set of data to
determine control loadings (Pcontrol) each representing an
independent correlation between characteristics;
- projecting the first set of data (Xireference) onto the control
loadings (Pcontrol) for reference determining a first set control
scores (Tcontrol,ireference) and determining one or more confidence
intervals for the first set of control scores (Tcontrol,ireference);
- projecting the test data onto the control loadings (Pcontrol)
for determining test control scores;
- using a comparator to determine if the test control scores
are within the one or more confidence intervals
characterized in that
- a first set of control residuals (Yireference) is determined by
using computation means for projecting the first set of data
(Xireference) onto the control loadings (Pcontrol), and
- wherein a test set of control residuals is determined by
using computation means for projecting the test set of data onto
the control loadings (Pcontrol),
comprising
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- using computation means projecting a second set of
data (Xiperturbed) with measured values of the characteristics of
objects in perturbed samples onto the control loadings (Pcontrol)
for determining a second set of control residuals (Yiperturbed);
- using computation means for fitting a perturbation
model to the second set of control residuals (Yiperturbed) to
determine perturbation loadings (Pperturbation) each representing
an independent correlation between characteristics;
- using computation means for projecting the first set of
control residuals (Yireference) onto the perturbation loadings
(Pperturbation) and determining a first set of perturbation scores
(TCT,ireference)
- determining one or more further confidence intervals
for the first set of perturbation scores (TCT,ireference);
- projecting the test data onto the control loadings
(Pcontrol) to determine test control residuals;
- projecting the test control residuals onto the
perturbation loadings (Pperturbation) and determining test
perturbation scores;
- comparing the test perturbation scores with the one or
more further confidence intervals with a comparator; and
- based on the comparison, identifying objects having the
test perturbation scores outside the one or more further data
confidence intervals and/or identifying presence of an illness.
Claims Appendix (Appeal Br. 27–28).

REJECTION
Claims 18–28 and 30–37 are rejected under 35 U.S.C. § 101. Final
Act. 3.
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OPINION
Legal Framework
In determining whether a claim falls within a category excluded from
eligible subject matter, our inquiry focuses on the Supreme Court’s two-step
framework described in Mayo and Alice, set forth above. Alice, 573 U.S. at
217–18 (citing 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.” See Alice, 573 U.S. at 219. Concepts determined
to be abstract ideas, and thus patent ineligible, include mental processes
(Gottschalk v. Benson, 409 U.S. 63, 67 (1972)) and mathematical formulas
(Parker v. Flook, 437 U.S. 584, 594–95 (1978)). 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 waterproof cloth, vulcanizing India rubber, smelting ores”
(id. at 182 n.7 (quoting Corning v. Burden, 56 U.S. 252, 267–68 (1853)));
and manufacturing flour (Benson, 409 U.S. at 69 (citing Cochrane v.
Deener, 94 U.S. 780, 785 (1876))).
However, not every claim that recites a mathematical formula is
patent ineligible. In Diamond v. Diehr, 450 U.S. 175, 191 (1981), the claim
at issue recited a mathematical formula, but the Supreme 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 176; 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.”). The Supreme Court also indicated that a
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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. (citing Flook and Benson); see also, 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 the 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 (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. (quoting Mayo, 566 U.S. at 77).
In January 2019, the USPTO published revised guidance on the
application of § 101. 2019 Revised Patent Subject Matter Eligibility
Guidance, 84 Fed. Reg. 50 (Jan. 7, 2019) (the “2019 Revised Guidance”).2
Under the 2019 Revised Guidance, 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

2 In response to received public comments, the Office issued further
guidance on October 17, 2019, clarifying the 2019 Revised Guidance.
USPTO, October 2019 Update: Subject Matter Eligibility (the “October
2019 Update”) (available at https://www.uspto.gov/sites/default/files/
documents/peg_oct_2019_update.pdf).
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6
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.
2018)) (“Step 2A, Prong Two”).3
2019 Revised Guidance, 84 Fed. Reg. at 52–55. 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.
See 2019 Revised Guidance, 84 Fed. Reg. at 52, 55–56.
Judicial Exception (Step 2A, Prong One)
Consistent with the Examiner’s analysis, claim 18 recites at least one
judicial exception. Specifically, claim 18 recites a “method of analyzing
data” that requires “using a computer for” an act of “fitting a control model
to the first set of data to determine control loadings (Pcontrol) each
representing an independent correlation between characteristics.” The
portion of the Specification Appellant cites in written description support for
this particular claim limitation provides that “loadings correspond to
components determined in a principal component analysis. Scores refer to

3 We perform this evaluation 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 2019 Revised Guidance - Section III(A)(2),
84 Fed. Reg. at 54–55.
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7
the expression on the components (loadings) and may be seen as coefficients
in the linear model wherein the components are variables.” Spec. 9:8–10
(cited in Appeal Br. 4). The Specification provides equation (1) (an image of
which is reproduced below as Figure 1) for describing such a control model.
Id. at 9:29–31.

Fig. 1. An Image of Equation (1) from the Specification. Spec. 9:31.
The Specification further provides that “Pcontrol is a matrix (J × Rcontrol)
representing the control loadings.” Id. at 10:7. These actions, particularly
the application of equation (1), involve mathematical concepts.
Claim 18 further recites acts of “projecting” certain data for
“determining” various parameters including “confidence intervals” and “a
first set of control scores” followed by “using a comparator to determine if
the test control scores are within the one or more confidence intervals.” The
Specification provides, for example, that “a confidence interval . . . indicates
the variability between objects observed in reference samples” (Spec. 9:14–
15 (cited in Appeal Br. 5)) and that “[t]he matrices Tcontrol,ireference for all
reference samples together form a first set of control scores.” Id. at 10:5–6.
These actions involve mathematical concepts such as matrices.
Claim 18 also recites “a test set of control residuals is determined by
using computation means for projecting the test set of data onto the control
loadings (Pcontrol)” which comprises various additional limitations of “using
computation means for” various functions such as “projecting a second set
of data” and “fitting a perturbation model” followed by “comparing the test
perturbation scores with the one or more further confidence intervals with a
comparator.” The Specification provides equation (2) (an image of which is
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reproduced below as Figure 2) for “the model of perturbed samples in a
second set of data.” Spec. 11:18–19.

Fig. 2. An Image of Equation (2) from the Specification. Spec. 11:20.
The Specification goes on to provide equation (3) (an image of which is
reproduced below as Fig. 3) for a perturbation model. Spec. 13:20–23 (cited
in Appeal Br. 6).

Fig. 3. An Image of Equation (3) from the Specification. Spec. 13:23.
These actions, particularly the application of equations (2) and (3), involve
mathematical concepts.
The Specification goes on to provide equation (4) (an image of which
is reproduced below as Fig. 4) for the calculation of Yireference. Spec. 14:23.

Fig. 4. An Image of Equation (4) from the Specification. Spec. 14:23.
The action involving the application of equation (4), involves mathematical
concepts.
Claim 18 additionally recites “based on the comparison, identifying
objects having the test perturbation scores outside the one or more further
data confidence intervals and/or identifying presence of an illness.” Such
identification is based on the application of the mathematical concepts and
thus cannot be separated therefrom. Moreover, comparing and identifying a
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9
difference which could be indicative of an anomaly and an illness is well
within a human’s mental activity.4
The Examiner finds that claim 18 is directed to an abstract idea of a
mathematical formula. Final Act. 3; Ans. 3. Appellant acknowledges that
“some of the limitations in the claims are based on mathematical
concepts[.]” Appeal Br. 19. The Specification provides a table of a specific
“[a]lgorithm” which “comprises some steps of the method” and states, for
example, that the “[t]he perturbation scores, the perturbation loadings and
the perturbation residuals are computed using computation means.” Spec.
15–16, 13:29–30. Appellant’s citation to certain examples in the 2019
Revised Guidance does not provide an elaborated argument with any
explanation as to why these examples are similar to the claims at issue here.
See Appeal Br. 19. Given that claim 18 recites an abstract idea, we proceed
with the next step in the analysis. Appellant does not raise separate
arguments for other pending claims under prong 1. Appeal Br. 18–19.
Integration into a Practical Application (Step 2A, Prong 2)
Turning to Step 2A, Prong 2 of the 2019 Revised Guidance, we
determine that claim 18, as a whole, does not integrate the judicial exception
into a practical application. Integration into a practical application requires
an additional element or a combination of additional elements in the claim to
“apply, rely on, or use the judicial exception in a manner that imposes a
meaningful limit on the judicial exception, such that the claim is more than a
drafting effort designed to monopolize the exception.” 2019 Revised

4 The Examiner finds that “diagnosing an illness is a mental step” and falls
under the judicial exception. Ans. 3. Appellant does not respond to this
finding. Reply Br. 3.
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Guidance, 84 Fed. Reg. at 53–54; see also id. at 55 (setting forth exemplary
considerations indicative that an additional element or combination of
elements may have integrated the judicial exception into a practical
application).
Consistent with the Examiner’s determination that claim 18 recites
limitations that are no more than “data manipulations” (Final Act. 3),
Appellant acknowledges that the method is “better suited to describe the data
of reference samples than” the prior art. Appeal Br. 18. Appellant argues
that “the claimed features provide methods and systems that are better suited
to describe the data of reference samples for determining the presence of an
illness automatically while avoiding subjective influence and differences
between operators or laboratories” but does not explain how the limitations
of claim 18 are integrated into such a purported application. Id. at 19. In
any event, identifying the presence of an illness is not required by claim 18
as it recites “and/or identifying the presence of an illness.” Appeal Br. 28.
Appellant argues that claim 18 “sets forth features for identifying
objects having the test perturbation scores outside the one or more further
data confidence intervals and/or identifying presence of an illness” and thus
integrates the mathematical concept into a practical application. Appeal Br.
20; see also id. at 23, 24.
As the October 2019 Update to the 2019 Revised Guidance explains,
“[a]n important consideration to evaluate when determining whether the
claim as a whole integrates a judicial exception into a practical application is
whether the claimed invention improves the functioning of a computer or
other technology.” October 2019 Update, 12. To do so, we consider
whether Appellant’s Specification “provides sufficient details such that one
of ordinary skill in the art would recognize the claimed invention as
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providing an improvement.” Id. If the Specification sets forth an
improvement in technology, we then evaluate claim 18 “to ensure that the
claim itself reflects the disclosed improvement.” Id.
Here, the Specification provides: “Objects (here cells) having scores
outside the confidence interval may be identified using a comparator of the
computer and separated from the other objects in a sample by a sorter.
Sorters are well known for flow cytometers.” Spec. 13:7–9 (cited in Appeal
Br. 6 as written description support for claim 18). Not only are such
comparator and sorters well known in the art as acknowledged by the
Specification (id.), but the Specification also does not support Appellant’s
argument that there is any “improvement” sufficient to integrate the judicial
exception into a practical application.
Moreover, the Specification provides that the recited method for
“analyzing data” seeks to address “the complexity of the calculations”
because “performing the principal component analysis by hand is only
possible for around 2 objects.” Spec. 1:9, 27–28. Thus the recited “method
may be executed using a computer running software.” Id. at 17:3. Any
purported improvement accomplished by claim 18 (such as the avoidance of
subjective influences (Appeal Br. 24)) is therefore a result of addressing “the
complexity of the calculations” which is a generic function of a general
purpose computer. See id. at 1:27; see also 2019 Guidance (identifying
“add[ing] insignificant extra-solution activity to the” abstract idea as an
example of when an abstract idea has not been integrated into a practical
application). Likewise, comparing results of a calculation using a computer
is insignificant post-solution activity. See Elec. Power Grp. LLC v. Alstom,
830 F.3d 1350, 1353 (Fed. Cir. 2016) (pointing out “that merely presenting
the results of abstract processes of collecting and analyzing information,
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without more (such as identifying a particular tool for presentation), is
abstract as an ancillary part of such collection and analysis”).
Appellant’s preemption argument (Appeal Br. 19) is also
unpersuasive. In particular, preemption is not a stand-alone test for patent
eligibility. Although preemption “‘might tend to impede innovation more
than it would tend to promote it,’ thereby thwarting the primary object of the
patent laws” (Alice, 573 U.S. at 216 (quoting Mayo, 566 U.S. at 71)), “the
absence of complete preemption does not demonstrate patent eligibility”
(Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1379 (Fed. Cir.
2015)); see also OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359,
1362–63 (Fed. Cir. 2015) (“[T]hat the claims do not preempt all price
optimization or may be limited to price optimization in the e-commerce
setting do not make them any less abstract.”).
Appellant additionally argues that claim 19 “is directed to a specific
device,” more specifically, a cytometer, which integrates claim 19 into a
practical solution. Appeal Br. 20. Claim 19 does not recite a cytometer. In
any event, the Specification provides that the recited method is for
“analyzing data from a cytometer” (Spec. 1:9–10) and receiving data from a
cytometer does not integrate the mathematical concept involved in analyzing
such data into a practical application.
In sum, neither the Specification nor Appellant’s unelaborated
arguments show that the combination of elements improves the functioning
of a computer or improves any other technology. Their collective functions
merely provide conventional computer implementation. Accordingly, we
determine the additional elements do not integrate the abstract concept of
judicial exception into a practical application. CLS Bank Int'l v. Alice Corp.
Pty. Ltd., 717 F.3d 1269, 1286 (Fed. Cir. 2013) (en banc) (“[S]imply
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appending generic computer functionality to lend speed or efficiency to the
performance of an otherwise abstract concept does not meaningfully limit
claim scope for purposes of patent eligibility.”), aff’d, 573 U.S. 208 (2014).
Inventive Concept (Step 2B)
Turning to Step 2B, we next analyze whether claim 18 adds any
specific limitation beyond the judicial exception that is not “well-
understood, routine, conventional” in the field. 2019 Revised Guidance,
84 Fed. Reg. at 56; MPEP § 2106.05(d). In so doing, we analyze the claim
elements individually and as an ordered combination. See Alice, 573 U.S. at
217–18, 221–22 (“[W]e consider the elements of each claim both
individually and ‘as an ordered combination’” to determine whether the
claim includes “significantly more” than the ineligible concept)
(quoting Mayo, 566 U.S. at 78–79); see also BASCOM Glob. Internet Servs.,
Inc. v. AT&T Mobility LLC, 827 F.3d 1341, 1350 (Fed. Cir. 2016) (“[A]n
inventive concept can be found in the non-conventional and non-generic
arrangement of known, conventional pieces.”).
Here, claim 18 recites no more than a generic “non-transitory
computer readable medium” and the operations are recited as performing
generic computer functions routinely used in computer applications.
Generic computer components recited as performing generic computer
functions that are well-understood, routine and conventional activities
amount to no more than implementing the abstract idea with a computerized
system. The use of generic computer components in this manner does not
impose any meaningful limit on the computer implementation of the abstract
idea. As the Examiner points out, “the combination of computer programs
and flow cytometry is routine and conventional in the art.” Ans. 4.
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Court decisions have recognized that generic computer-system
components operating to communicate, manipulate, and display data are
well understood, routine, and conventional to a skilled artisan. See, e.g.,
Alice, 573 U.S. at 226–27; SAP Am., Inc. v. InvestPic, LLC, 898 F.3d 1161,
1164–65 & n.1, 1170 (Fed. Cir. 2018); Apple, Inc. v. Ameranth, Inc., 842
F.3d 1229, 1234, 1241–42 (Fed. Cir. 2016); Symantec, 838 F.3d at 1316–20;
Versata Dev. Group Inc. v. SAP Am. Inc., 793 F.3d 1306, 1334 (Fed. Cir.
2015); Ultramercial, Inc. v. Hulu, LLC, 772 F.3d 709, 715–716 (Fed. Cir.
2014); buySAFE, 765 F.3d at 1355.
Appellant argues, without elaboration, that “there is no evidence that
the computer performing or configured to perform the operations recited in
the claims is well understood, routine, or conventional.” Appeal Br. 24.
Appellant, however, does not identify any particular limitation in claim 18
showing that the computer used to carry out the algorithm as exemplified in
the Specification (Spec. 15–16) is anything other than a general purpose
computer. Moreover, contrary to Appellant’s assertion that the Examiner
“fails to address the argument that the requirement to provide evidence
under guidance per Berkheimer” (Reply Br. 4), the Examiner, in the Final
Office Action, states that “the prior art review article of Laerum et al. teach
that the flow cytometry limitations recited outside the claims are routine and
conventional in the prior art.” Final Act. 4 (addressing Appellant’s
argument with regard to Berkheimer). Appellant does not dispute the
Examiner’s finding with regard to the prior art reference Laerum in the
opening brief. See, e.g., Appeal Br. 15–25.5

5 We decline to address the belatedly raised argument with regard to Laerum
in the Reply Brief. See Reply Br. 4. An argument raised for the first time in
a Reply Brief can be considered waived if Appellant does not explain why it
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Accordingly, in the absence of evidence or argument to the contrary,
we determine claim 18 fails to add any specific limitation beyond the
judicial exception that is not “well-understood, routine, conventional” in the
field.
Because the Examiner correctly concluded claim 18 is directed to a
judicial exception, and because Appellant does not identify any error in the
Examiner’s determination under the 2019 Revised Guidance, we sustain the
rejection of claim 18 under 35 U.S.C. § 101. The rejection of all other
pending claims is sustained for the same reason.

CONCLUSION
The Examiner’s rejection is affirmed.
More specifically,

could not have been raised previously. See Ex parte Nakashima, 93
USPQ2d 1834 (BPAI 2010) (informative) (explaining that arguments and
evidence not timely presented in the principal Brief will not be considered
when filed in a Reply Brief, absent a showing of good cause explaining why
the argument could not have been presented in the Principal Brief); Ex parte
Borden, 93 USPQ2d 1473, 1477 (BPAI 2010) (informative) (“Properly
interpreted, the Rules do not require the Board to take up a belated argument
that has not been addressed by the Examiner, absent a showing of good
cause.”). Appellant has not explained why the argument could not have
been raised in the opening brief to afford the Examiner an opportunity to
respond. We therefore decline to address the belatedly raised argument. See
Ex Parte Hindersinn, 177 USPQ 78, 80 (Bd. App. 1971).
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DECISION SUMMARY
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
18–28, 30–
37
101 Eligibility 18–28, 30–
37

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. § 1.136(a). See 37 C.F.R.
§ 1.136(a)(1)(iv).
AFFIRMED