STANLEY LAPIDUS et al.

Patent Trials and Appeals Board

May 11, 2021

2019006224 (P.T.A.B. May. 11, 2021)

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.
12/727,824 03/19/2010 STANLEY LAPIDUS PLA-3201-CP 4054
47328 7590 05/11/2021
SEQUENOM, INC. - GRANT IP, INC.
2385 CAMINO VIDA ROBLE
SUITE 102
CARLSBAD, CA 92011
EXAMINER
POHNERT, STEVEN C
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
05/11/2021 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):
BGRANT@GRANTIP.COM
KDICKINSON@GRANTIP.COM
PDOCS@CPAGLOBAL.COM
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte STANLEY LAPIDUS, JOHN F. THOMPSON,
DORON LIPSON, PATRICE MILOS, J. WILLIAM EFCAVITCH, and
STANLEY LETOVSKY1

Appeal 2019-006224
Application 12/727,824
Technology Center 1600
Before ERIC B. GRIMES, JEFFREY N. FREDMAN, and
RACHEL H. TOWNSEND, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
method for detecting a fetal chromosomal imbalance, which have been
rejected as lacking adequate written description and being directed to patent
ineligible subject matter. We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM the rejection for patent ineligibility.

1 Appellant identifies the real parties in interest as Sequenom, Inc. and
Illumina, Inc. Appeal Br. 3. We use the word “Appellant” to refer to
“applicant” as defined in 37 C.F.R. § 1.42.
Appeal 2019-006224
Application 12/727,824

2
STATEMENT OF THE CASE
Chromosomal imbalance (aneuploidy) causes Down syndrome,
Edward syndrome, and Patau syndrome. Spec. 1. “Chromosomal
abnormalities are generally diagnosed by karyotyping of fetal cells obtained
by invasive procedures such as chorionic villus sampling or amniocentesis.
Those procedures are associated with potentially significant risks to both the
fetus and the mother.” Id. “The invention generally relates to methods for
detecting fetal nucleic acids and for diagnosing fetal abnormalities.” Id. at 2.
The Specification states that “[c]ertain steps in the sample preparation
or sequencing process may result in a GC bias, where the relative
representation of each chromosome is influenced not only by the relative
quantity (copy number) of that chromosome, but also by its GC content.”
Id. at 32. “Methods of the invention . . . allow for correction of the GC bias
in the sequence information.” Id. “In certain embodiments, a subset of
genomic bins is selected within a given range such that the average GC
content per chromosome is equalized (or less skewed). Chromosomal
counting is then performed on the selected subset.” Id.
Claims 90, 93, 94, 115, and 126 are on appeal. Claim 90, reproduced
below, is illustrative:
90. A method for detection of the presence or absence of a fetal
chromosome imbalance comprising:
(a) sequencing DNA from a sample of blood, blood plasma, or
serum from a pregnant human female by a nucleotide
sequencing process that generates sequence reads with GC bias;
(b) mapping the sequence reads to bins of a reference genome,
wherein: (i) the bins represent a human reference genome that
has been partitioned into genomic bins, (ii) the bins represent
Appeal 2019-006224
Application 12/727,824

3
different sections of the human reference genome and (iii) the
GC content of the bins has been determined;
(c) determining counts of sequence reads mapped to each bin;
(d) selecting a subset of bins with a GC content of 0.42 to 0.48,
wherein the sequence reads in the selected subset of bins exhibit
reduced or no GC bias;
(e) determining chromosome counts for at least one
chromosome, from counts of sequence reads of bins of the
selected subset that correspond to the at least one chromosome,
wherein the counts of sequence reads of the bins of the selected
subset are the same as the counts for the bins determined in
step c; and
(f) determining the presence or absence of a fetal chromosome
imbalance based on comparing the determined chromosome
counts for the at least one chromosome to a standard measured
across one or more normal samples, wherein a deviation from
chromosome counts of the standard indicates a fetal
chromosome imbalance.

Appeal Br. 31 (Claims Appendix).

The claims stand rejected as follows:
Claims 90, 93, 94, 115, and 126 under 35 U.S.C. § 112, first
paragraph, for lack of adequate written description (Ans. 3), and
Claims 90, 93, 94, 115, and 126 under 35 U.S.C. § 101 as being
directed to patent ineligible subject matter (Ans. 4)
OPINION
Written Description
The Examiner finds that the Specification does not adequately
describe step (a) of the claims: “sequencing DNA from a sample of blood,
blood plasma, or serum from a pregnant human female by a nucleotide
Appeal 2019-006224
Application 12/727,824

4
sequencing process that generates sequence reads with GC bias.” Ans. 4.
The Examiner reasons that “[t]he amendment requires results with GC bias,
however the claim is not limited to any specific method of sequencing DNA.
The claims and specification do not support that all methods of sequencing
DNA provide sequences with a GC bias. Thus it is unclear how step (a) is
performed.” Id.
Appellant argues, among other things, that “[t]he Examiner appears to
apply an artificially constructed and unnecessary requirement to § 112
instead of applying the proper written description requirement.” Appeal Br.
27. “Simply put, one of ordinary skill in the art in light of the disclosure in
the specification would have understood how sequencing samples in step (a)
result[s] in sequencing reads with GC bias. Hence, at the time of filing the
instant application, Appellant had possession of the invention as recited in
claim 90.” Id.
We agree with Appellant that the Examiner has not persuasively
shown that the Specification fails to adequately describe the disputed
limitation. The examiner
“bears the initial burden . . . of presenting a prima facie case of
unpatentability.” In re Oetiker, 977 F.2d 1443, 1445, 24
USPQ2d 1443, 1444 (Fed. Cir. 1992). Insofar as the written
description requirement is concerned, that burden is discharged
by “presenting evidence or reasons why persons skilled in the
art would not recognize in the disclosure a description of the
invention defined by the claims.”
In re Alton, 76 F.3d 1168, 1175 (Fed. Cir. 1996). “[T]he test . . . is whether
the disclosure of the application relied upon reasonably conveys to those
skilled in the art that the inventor had possession of the claimed subject
Appeal 2019-006224
Application 12/727,824

5
matter as of the filing date.” Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d
1336, 1351 (Fed. Cir. 2010).
Here, the Specification describes sequencing methods. Spec. 2 (“The
sequencing reaction may be any sequencing reaction. In particular
embodiments, the sequencing reaction is a single molecule sequencing
reaction.”); see also id. at 2–3 (listing references describing single-molecule
sequencing and summarizing the technique), 31 (“The samples were loaded
into HELISCOPE Sequencer channels (Single molecule sequencing
instrument, Helicos BioSciences Corporation) according to the
manufacturer’s instructions.”).
The Specification also describes the potential problem of GC bias that
can result from sequencing chromosomes with extreme GC content. Id. at 32
(“Certain steps in the sample preparation or sequencing process may result
in a GC bias, where the relative representation of each chromosome is
influenced not only by the relative quantity (copy number) of that
chromosome, but also by its GC content.”).
In view of these descriptions, the Examiner has not persuasively
shown that a skilled artisan would not have recognized that Appellant was in
possession, as of the filing date, of a method that included a generic step of
“sequencing DNA from a sample of blood, blood plasma, or serum from a
pregnant human female by a nucleotide sequencing process that generates
sequence reads with GC bias,” as recited in claim 90. The rejection under
35 U.S.C. § 112, first paragraph, for lack of adequate written description is
therefore reversed.
Appeal 2019-006224
Application 12/727,824

6
Patent Eligibility
Claims 90, 93, 94, 115, and 126 stand rejected under 35 U.S.C. § 101
on the basis that “the claimed invention is directed to abstract ideas or
mental step without significantly more.” Ans. 4. Specifically, the Examiner
finds that:
Step (b) of mapping is a mental step equivalent.
Step (c) of determining counts is a mental step equivalent
and/or mathematical step.
Step (d) of selecting a subset of bins in a mental step
equivalent.
Step (e) of determining chromosome counts in a mental step
equivalent and/or a mathematical step.
Step (f) is a mental step equivalent and/or a decision process
which requires a mental step of comparing.
Id. at 6. The Examiner therefore finds that claim 90 recites the “abstract idea
of mental steps, mathematical steps and decision making step.” Id.
The Examiner also finds that the only other step in claim 90 is “a data
gathering step of sequencing” (id.), and “there are no steps which depend
upon the judicial exception” (id. at 5). The Examiner concludes that the
“judicial exception is not integrated into a practical application.” Id. at 4–5.
Finally, the Examiner finds that claim 90 does not include additional
elements that are significantly more than the judicial exception because “the
claim requires a single active step of sequencing . . . , which is the only
element ‘in addition’ to the judicial exceptions. The specification supplies
evidence that such sequencing is routine, conventional and well understood,”
particularly because the Specification states that “[t]he sequencing reaction
may be any sequencing reaction.” Id. at 7 (quoting Spec. ¶ 11).
Appeal 2019-006224
Application 12/727,824

7
Appellant argues that claim 90
does not recite a mental process, as steps (b) – (f) individually
or in combination could not be practically performed in the
human mind . . . due to the complexity of the required operation
of mapping the tremendous amount of data of sequence reads to
bins of a reference genome (tens to hundreds of thousands of
sequence reads per chromosome).
Appeal Br. 9. “Hence, the claim is not directed to an abstract idea.” Id. at 10.
Appellant also argues that, even if claim 90 is found to recite an
abstract idea, “it is directed to a practical application” because it recites a
technological improvement and it uses any judicial exception in a particular
technological environment. Id. at 10–17. “Simply put, the claim is not just a
drafting effort designed to monopolize all fetal chromosome imbalance
determinations.” Id. at 17.
Finally, Appellant argues that claim 90 “recites an inventive concept
from the combination of claim elements that were not routine, conventional
or well-understood.” Id. at 21.
Principles of Law
A. 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.
Appeal 2019-006224
Application 12/727,824

8
Id. 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
(“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
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
Appeal 2019-006224
Application 12/727,824

9
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 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 (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.
B. USPTO Section 101 Guidance
In January 2019, the U.S. Patent and Trademark Office (USPTO)
published revised guidance on the application of § 101. See 2019 Revised
Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50 (Jan. 7, 2019)
(“Revised Guidance”).2 “All USPTO personnel are, as a matter of internal

2 In response to received public comments, the Office issued further
guidance on October 17, 2019, clarifying the Revised Guidance. USPTO,
October 2019 Update: Subject Matter Eligibility (the “October 2019
Appeal 2019-006224
Application 12/727,824

10
agency management, expected to follow the guidance.” Id. at 51; see also
October 2019 Update at 1.
Under the Revised Guidance and the 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”).3
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

Update”) (available at https://www.uspto.gov/sites/default/files/
documents/peg_oct_2019_update.pdf).
3 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 Revised Guidance - Section III(A)(2), 84 Fed. Reg.
54–55.
Appeal 2019-006224
Application 12/727,824

11
(4) simply appends well-understood, routine, conventional
activities previously known to the industry, specified at a high
level of generality, to the judicial exception.
Revised Guidance, 84 Fed. Reg. at 52–56.
Revised Guidance Step 2A, Prong 1
Following the Revised Guidance, we first consider whether claim 90
recites a judicial exception. The Revised Guidance identifies three groupings
of subject matter included in the abstract idea exception, including “[m]ental
processes—concepts performed in the human mind (including an observation,
evaluation, judgment, opinion).” 84 Fed. Reg. at 52.
Claim 90 recites
(b) mapping the sequence reads to bins of a reference genome,
wherein: (i) the bins represent a human reference genome that
has been partitioned into genomic bins, (ii) the bins represent
different sections of the human reference genome and (iii) the
GC content of the bins has been determined.
The claim language itself defines the recited “bins” as subsequences
of a reference genome; the “sequence reads” are partial sequences of the
DNA in the sample from the subject female. Thus, the “mapping” step of
claim 90 simply requires matching the determined partial sequences to the
part of the genome that they correspond to.
Claim 90 also recites “(c) determining counts of sequence reads
mapped to each bin”; i.e., counting the number of sequence reads that
correspond to each subsequence of the reference genome.
Claim 90 recites “(d) selecting a subset of bins with a GC content of
0.42 to 0.48”; in other words, selecting those bins with a GC content in the
range of 42–48%.
Appeal 2019-006224
Application 12/727,824

12
Claim 90 also recites “(e) determining chromosome counts for at least
one chromosome, from counts of sequence reads of bins of the selected
subset that correspond to the at least one chromosome.” This step requires
counting the sequence reads that correspond to bins having a GC content in
the range of 42–48% for a specific chromosome.
Finally, claim 90 recites “(f) determining the presence or absence of a
fetal chromosome imbalance based on comparing the determined
chromosome counts for the at least one chromosome to a standard measured
across one or more normal samples.” This step requires comparing the
counts determined in step (e) with those of a normal sample to determine
whether the counts of the subject sample deviate in a way that would
indicate fetal chromosomal imbalance.
All of these steps consist of observation and evaluation, which can
practically be performed in the human mind. Claim 90 therefore recites a
mental process, which is an abstract idea and a judicial exception to
patentability.
Revised Guidance Step 2A, Prong 2
Although claim 90 recites an abstract idea, it would still be patent-
eligible if “the claim as a whole integrates the recited judicial exception into
a practical application of the exception.” Revised Guidance, 84 Fed. Reg. at
54. “A claim that integrates a judicial exception into a practical application
will apply, rely on, or use the judicial exception in a manner that imposes a
meaningful limit on the judicial exception.” Id. The analysis of whether a
claim integrates a judicial exception into a practical application includes
“[i]dentifying whether there are any additional elements recited in the claim
Appeal 2019-006224
Application 12/727,824

13
beyond the judicial exception(s)” and “evaluating those additional elements
individually and in combination to determine whether they integrate the
exception into a practical application.” Id. at 54–55.
The exemplary considerations indicating that an additional element
may integrate an exception into a practical application include “[a]n
additional element [that] reflects an improvement in the functioning of a
computer, or an improvement to other technology or technical field.” Id. at
55. However, “an additional element [that] adds insignificant extra-solution
activity to the judicial exception” is an indication that “a judicial exception
has not been integrated into a practical application.” Id. Such insignificant
extra-solution activity includes “mere data gathering such as a step of
obtaining information about credit card transactions so that the information
can be analyzed in order to detect whether the transactions were fraudulent.”
Id. at 55, n.31.
Here, in addition to the steps that are equivalent to mental processes,
claim 90 recites “(a) sequencing DNA from a sample of blood, blood
plasma, or serum from a pregnant human female by a nucleotide sequencing
process that generates sequence reads with GC bias.”
The recited “sequencing” step, however, is the step required to gather
the data for the mental processes subsequently recited in claim 90. The
“sequencing” data-gathering step is therefore merely insignificant extra-
solution activity, and is not an indication that the recited judicial exception
has been integrated into a practical application.
The Specification makes clear that the sequencing step recited in
claim 90 does not represent an improvement in technology, because the
Appeal 2019-006224
Application 12/727,824

14
Specification states that “[t]he sequencing reaction may be any sequencing
reaction.” Spec. 2.
In summary, we conclude that claim 90 is directed to the process of
gathering sequence data (i.e., a set of “sequence reads”), then mentally
matching the sequence reads to their corresponding genomic locations and,
after excluding a certain part of the data, counting the sequence reads
corresponding to a particular chromosome and comparing that count to the
count for a normal sample in order to identify the presence of fetal
chromosomal imbalance. Because all of the claimed steps except the data
gathering can be carried out mentally, we conclude that claim 90 is directed
to a judicial exception.
Revised Guidance Step 2B
The Revised Guidance directs us to consider whether claim 90
includes “additional elements . . . [that] provide[] ‘significantly more’ than
the recited judicial exception.” 84 Fed. Reg. at 56. The Revised Guidance
states that an additional element that “simply appends well-understood,
routine, conventional activities previously known to the industry, specified
at a high level of generality, to the judicial exception, . . . is indicative that
an inventive concept may not be present.” Id.
As discussed above, and aside from the elements that are directed to
mental processes, claim 90 recites “(a) sequencing DNA from a sample of
blood, blood plasma, or serum from a pregnant human female by a
nucleotide sequencing process that generates sequence reads with GC bias.”
As also noted above, the Specification states that “[t]he sequencing
reaction may be any sequencing reaction.” Spec. 2. Thus, this step represents
Appeal 2019-006224
Application 12/727,824

15
“well-understood, routine, conventional activities previously known to the
industry, specified at a high level of generality, [added] to the judicial
exception,” and is indicative that an inventive concept is not present.
In summary, the combination of elements recited in claim 90 does not
amount to significantly more than the recited judicial exception itself, and
under 35 U.S.C. § 101 the claimed method is not eligible for patenting.
Appellant’s Arguments
Appellant argues that claim 90
does not recite a mental process, as steps (b) – (f) individually
or in combination could not be practically performed in the
human mind. That is, these steps could not practically be
mentally performed due to the complexity of the required
operation of mapping the tremendous amount of data of
sequence reads to bins of a reference genome (tens to hundreds
of thousands of sequence reads per chromosome).
Appeal Br. 10.
We are not persuaded by this argument, because claim 90 does not
require generating any specific number of sequence reads in step (a), and
does not require mapping or counting any minimum number of sequence
reads in steps (b), (c), and (e). Thus, a process meeting the claim
requirements could practically be carried out in the human mind. We also
note that not only does claim 90 not require any particular computer
implementation, it does not recite computer implementation at all. The claim
language itself thus encompasses a process carried out entirely in the human
mind, except for the sequence-gathering step. See Cybersource Corp. v.
Retail Decisions, Inc., 654 F.3d 1366, 1373 (Fed. Cir. 2011) (“Such a
Appeal 2019-006224
Application 12/727,824

16
method that can be performed by human thought alone is merely an abstract
idea and is not patent-eligible under § 101.”).
Appellant also argues that, even if claim 90 is found to recite an
abstract idea, it is patent eligible because it recites a technological
improvement in the technical field of sequence-based, non-invasive prenatal
testing. Appeal Br. 10–11. Specifically, Appellant argues that previous
methods corrected for GC bias by use of a mathematical formula, which
changes the original counts of sequence reads and may introduce errors.
Id. at 11. By contrast, Appellant argues,
the claimed method allows use of the raw sequencing data
(sequence reads) to detect a fetal chromosome imbalance. It
does so by utilizing sequence reads obtained from bins selected
based on bin GC content. Use of counts of sequence reads with
reduced or no GC bias obtained by the claimed method results
in more accurate chromosome counts which enables a more
accurate detection of a fetal chromosome imbalance.
Id. at 12.
This argument is unpersuasive, because Appellant has not pointed to
any technical aspect of claim 90 that represents an improvement over the
prior art. Rather, the advance recited in claim 90 appears to be excluding
part of the data—counts of sequence reads that map to bins with a GC
content outside the range of 42–48%—from consideration when determining
chromosome counts. However, thinking differently about a particular data
set does not represent the type of technical improvement that integrates an
abstract idea into a practical application. Rather, the improvement (if any) is
in the abstract idea—the mental process—itself. Cf. SAP America, Inc. v.
InvestPic, LLC, 898 F.3d 1161, 1163 (Fed. Cir. 2018) (“[T]he advance lies
entirely in the realm of abstract ideas, with no plausibly alleged innovation
Appeal 2019-006224
Application 12/727,824

17
in the nonabstract application realm. An advance of that nature is ineligible
for patenting.”).
Appellant argues that the claimed process is similar to those found
patent eligible in Diamond v. Diehr, 450 U.S. 175 (1981), McRO, Inc. v.
Bandai Namco Games Amer., Inc., 837 F.3d 1299 (Fed. Cir. 2016), and
Enfish, LLC v. Microsoft Corp., 822 F.3d 1327 (Fed. Cir. 2016). Appeal Br.
15–16. We disagree. In each of the cases cited by Appellant, the process at
issue produced something concrete: cured rubber in Diamond, lip synched
animations in McRO, or a particular data structure in Enfish. Diamond, 450
U.S. at 185; McRO, 837 F.3d at 1313; Enfish, 822 F.3d at 1337. Here, by
contrast, the result of the claimed process is simply data—a decision
regarding the presence or absence of fetal chromosome imbalance—that
might be entirely within a human mind, since the claim includes no
requirement to act upon or even to communicate the result determined in the
claimed process.
Appellant also argues that claim 90 is a practical application because
it limits use of any judicial exception to the technical field of sequence-
based non-invasive prenatal testing (NIPT). Appeal Br. 16. Appellant notes
that step (a) of claim 90 requires sequencing DNA from a pregnant human
female using a process that generates sequence reads with GC bias and “step
(b) requires mapping the sequence reads to bins of a reference genome in a
particular way.” Id. at 17. Appellant also points out that steps (c)–(e) recite
additional steps of counting sequence reads corresponding to bins, and step
(f) states that the result is detection of fetal chromosome imbalance (if
present). Id. Appellant argues that
Appeal 2019-006224
Application 12/727,824

18
[i]n sum, the elements of claim 90 when viewed as a whole
integrate any alleged abstract idea into a practical application
by sufficiently limiting the use of the alleged abstract idea to
determining the presence or absence of a fetal chromosome
imbalance as specifically claimed. Simply put, the claim is not
just a drafting effort designed to monopolize all fetal
chromosome imbalance determinations.
Id.
This argument is unpersuasive because the “practical application”
asserted by Appellant is the mental process of interpreting the chromosome
counts (which can also be in the human mind) of the claimed method as
indicating the presence or absence of fetal chromosome imbalance. The
issue is not whether claim 90 is designed to monopolize all fetal
chromosomal imbalance determinations, but whether the claim includes
elements in addition to the recited mental processes, which are judicial
exceptions to patentability, so as to result in a practical application of those
mental processes. We conclude that it does not. In addition, “pre-emption is
not the test for determining patent-eligibility.” Rapid Litig. Mgmt. v.
CellzDirect, Inc., 827 F.3d 1042, 1052 (Fed. Cir. 2016). “[C]laims that are
otherwise directed to patent-ineligible subject matter cannot be saved by
arguing the absence of complete preemption.” Return Mail, Inc. v. United
States Postal Service, 868 F.3d 1350, 1370 (Fed. Cir. 2017).
Appellant argues that the patent eligibility of the claimed process is
supported by the Board’s decision in Ex parte Smith, Appeal 2018-000064
(Feb. 1, 2019) (informative), and Example 41 of the 2019 Subject Matter
Eligibility Guidance. Appeal Br. 18–21. As Appellant notes (id. at 18),
however, the invention in Ex parte Smith was “a hybrid trading system for
concurrently trading securities or derivatives through both electronic and
Appeal 2019-006224
Application 12/727,824

19
open-outcry trading mechanisms” and the invention described in Example
41 of the 2019 Guidance was a method of establishing cryptographic
communications. We do not agree that the patentability of these inventions
supports the patent eligibility of claim 90.
Instead, the claims are more similar to those of In re Bd. of Trustees of
Leland Stanford Junior Univ., 989 F.3d 1367, 1374 (Fed. Cir. 2021) where
claims to a method of using nucleic acid allele data to resolve haplotype
phase were found ineligible based on a failure “to explain how that
combination of elements moves the claimed subject matter beyond the
abstract and into the practical.” That is, the claim “recite[d] no steps that
practically apply” the invention and “[s]imply storing information and
providing it upon request does not alone transform the abstract idea into
patent eligible subject matter.” Id. at 1374. Here, there is also no step that
practically applies the determined fetal chromosome imbalance.
Finally, Appellant argues that claim 90 is patent eligible “because it
recites an inventive concept from the combination of claim elements that
were not routine, conventional or well-understood.” Appeal Br. 21.
Specifically, Appellant argues that
the claim features include an inventive concept of determining
the presence or absence of a fetal chromosome imbalance
through a novel combination of elements. It achieves this
inventive concept as claimed by determining chromosome
counts for at least one chromosome, from counts of sequence
reads of bins of the selected subset (the subset of bins with a
GC content of 0.42 to 0.48 exhibiting reduced or no GC bias).
The claim then recites determining the presence or absence of a
fetal chromosome imbalance specifically based on comparing
the determined chromosome counts for the at least one
chromosome to a standard measured across one or more normal
Appeal 2019-006224
Application 12/727,824

20
samples. Assuming that the Examiner’s asserted abstract idea is
maintained . . . , the claimed features recite sufficiently more
than this asserted abstract idea to qualify as an inventive
concept.
Id. at 22–23.
This argument is also unpersuasive. As the Examiner has pointed out
(Ans. 7), the only active step required by claim 90 is step (a): sequencing
DNA from a pregnant human female. All of steps (b) through (e) are steps of
manipulating the data generated in step (a), which can be carried out as a
mental process, and step (f) is the mental step of drawing a conclusion from
the data manipulation. To the extent that claim 90 requires mentally
manipulating the data in a novel manner, any novelty is in the patent
ineligible aspects of claim 90. See SAP America, Inc. v. InvestPic, LLC, 898
F.3d 1161, 1163 (Fed. Cir. 2018) (“The claims here are ineligible because
their innovation is an innovation in ineligible subject matter. . . . [T]he
advance lies entirely in the realm of abstract ideas, with no plausibly alleged
innovation in the nonabstract application realm. An advance of that nature is
ineligible for patenting.”).
DECISION SUMMARY
In summary:
Claim(s)
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
90, 93, 94,
115, 126
112, first
paragraph
Written Description 90, 93, 94,
115, 126
90, 93, 94,
115, 126
101 Eligibility 90, 93, 94,
115, 126

Overall
Outcome
90, 93, 94,
115, 126

Appeal 2019-006224
Application 12/727,824

21
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