GENETIC TECHNOLOGIES LIMITED

Patent Trials and Appeals Board

Jan 7, 2021

2020002775 (P.T.A.B. Jan. 7, 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.
15/169,498 05/31/2016 Nila Patil 5517-74-3 2866
22442 7590 01/07/2021
Sheridan Ross PC
1560 Broadway
Suite 1200
Denver, CO 80202
EXAMINER
LU, FRANK WEI MIN
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
01/07/2021 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):
e-docket@sheridanross.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte NILA PATIL, DAVID R. COX, ANTHONY J. BERNO,
and DAVID A. HINDS1
Appeal 2020-002775
Application 15/169,498
Technology Center 1600
Before ERIC B. GRIMES, JOHN E. SCHNEIDER, and
MICHAEL A. VALEK, 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
system and method of genomic analysis, which have been rejected as
indefinite and being directed to patent ineligible subject matter. We have
jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.

1 Appellant identifies the real party in interest as Genetic Technologies
Limited. Appeal Br. 3. We use the word “Appellant” to refer to “applicant”
as defined in 37 C.F.R. § 1.42.
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STATEMENT OF THE CASE
“[M]ost of the sequence of the DNA of [human] genomes is identical.
However, there are variations in DNA sequence between individuals . . .
called ‘single nucleotide polymorphisms’ (SNPs).” Spec. ¶ 5. “Alleles
(variants) making up blocks of [common] SNPs in close physical proximity
are often correlated, resulting in reduced genetic variability and defining a
limited number of ‘SNP haplotypes.’” Id. ¶ 6. “The present invention relates
to methods for identifying variations that occur in the human genome and
relating these variations to the genetic bases of phenotype such as disease
resistance, disease susceptibility or drug response.” Id. ¶ 9.
Claims 27–34 are on appeal. Claim 27, reproduced below, is
illustrative:
27. A system for genomic analysis to determine
pharmacogenomic-related genetic loci without a priori
knowledge of the location of said loci, the system comprising:
one or more databases that store information obtained
from genotyping genomic DNA of individuals in a case
population which comprises individuals who exhibit a response
to a drug to determine frequency of one or more informative
genetic variations in the case population and information
obtained from genotyping genomic DNA of individuals in a
control population which comprises individuals who do not
exhibit the response to the drug to determine frequency of one
or more informative genetic variations in the control
population, wherein the one or more informative genetic
variations distinguish one haplotype pattern from other
haplotype patterns of a haplotype block;
a server comprising:
one or more processors; and
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a computer memory comprising processor-
executable instructions that, when executed by the one or more
processors, cause the one or more processors to perform the
following:
access the one or more databases;
compare frequencies of the one or more
informative genetic variations between the case population and
the control population;
select the one or more informative genetic
variations which have a frequency in the case population which
is significantly different to the control population as
pharmacogenomic-related genetic loci; and
provide a report to a client device in
communication with the server across a communications
network, wherein the report includes a description of the one or
more informative genetic variations which have a frequency in
the case population which is significantly different to the
frequency in the control population as pharmacogenomic-
related genetic loci.
Claim 30 is the other independent claim, and is directed to a
computer-implemented method that corresponds to the system of claim 27,
with an additional step of “adding, by the one or more processors, the
selected one or more informative genetic variations as pharmacogenomic-
related loci.”
The claims stand rejected as follows:
Claims 27–34 under 35 U.S.C. § 101 as being directed to patent
ineligible subject matter (Ans. 3) and
Claims 27–34 under 35 U.S.C. § 112, second paragraph, as indefinite
(Ans. 6).
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OPINION
Claim Definiteness
All of the claims stand rejected as indefinite because, according to the
Examiner, “it is unclear where a haplotype block comes from or is located.”
Ans. 7.
Appellant argues that “paragraph [0077] of the specification discusses
Figure 2. This section makes it clear, as do other sections of the
specification, that a haplotype block can be found at a specific site of the
genome.” Appeal Br. 30.2 Appellant also points to the statement in the same
paragraph “that polymorphisms (such as SNPs) in variants of a haplotype
block ‘are linked’. The inventors go even further stating ‘SNP haplotype
blocks are chromosomal regions that tend to be inherited as a unit, with a
relatively small number of common patterns’.” Id. Finally, Appellant argues
that “this section is consistent with paragraph [0043] relating to SNP
haplotype blocks defined as a ‘group of variant or SNP locations that do not
appear recombine independently and that can be grouped together in blocks
of variants or SNPs’.” Id.
“Applying the broadest reasonable interpretation of a claim, . . . the
Office establishes a prima facie case of indefiniteness with a rejection
explaining how the metes and bounds of a pending claim are not clear

2 Appellant’s citations appear to be to the published application. The
paragraph numbers in the published application, starting at paragraph 18, are
one greater than the paragraph numbers in the Specification as filed, because
the description of Figure 1 became a separate numbered paragraph in the
published application. Thus, paragraph 77 in the published application
corresponds to paragraph 76 in the application as filed.
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because the claim contains words or phrases whose meaning is unclear. See
In re Packard, 751 F.3d 1307, 1310 (Fed. Cir. 2014).” Ex parte McAward,
2017 WL 3669566, at *2 (PTAB 2017) (precedential).
However, “the definiteness of the language employed must be
analyzed—not in a vacuum, but always in light of the teachings of the prior
art and of the particular application disclosure as it would be interpreted by
one possessing the ordinary level of skill in the pertinent art.” In re Moore,
439 F.2d 1232, 1235 (CCPA 1971).
In this case, the Examiner concludes that “it is unclear where a
haplotype block comes from or is located.” Ans. 7. The Examiner explains
that
it is unclear whether a haplotype block comes from genomic
DNA of individuals in a case population . . . or genomic DNA
of individuals in a control population . . . or it is unclear
whether a haplotype block is located on genomic DNA of
individuals in a case population . . . or genomic DNA of
individuals in a control population.
Ans. 19–20.
The Specification’s discussion of “haplotype blocks,” however, makes
clear that they are not limited to individuals in a case population or
individuals in a control population; they are present in the human genome
generally. The meaning of “haplotype blocks” is clear in view of, at least,
Appellant’s Figure 2 and the Specification’s discussion of it. The
Specification states that “Figure 2 provides one illustration of showing how
variants, usually SNPs, occur in haplotype blocks in a genome.” Spec. ¶ 76.3

3 Our citations are to the Specification as filed.
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“Certain SNP haplotype patterns were observed at a much higher
frequency than would be expected in a non-linkage case. Thus, SNP
haplotype blocks are chromosomal regions that tend to be inherited as a
unit, with a relatively small number of common patterns.” Id. (emphasis
added). Referring to Figure 2, the Specification states that “[v]ariants in
block 261 will tend to occur together. Similarly, the variants in block 262
will tend to occur together, as will those variants in block 263.” Id.
We agree with Appellant that the meaning of “haplotype block” is
reasonably clear when the phrase is read in light of the Specification; it
refers to a group of genetic variations, such as single nucleotide
polymorphisms (SNPs), that tend to be inherited together. We therefore
reverse the rejection of claims 27–34 under 35 U.S.C. § 112, second
paragraph.
Eligibility
All of the claims stand rejected as being “directed to a judicial
exception (i.e., a law of nature, a natural phenomenon, or an abstract idea)
without significantly more.” Ans. 3. The Examiner finds that “[c]laims 27–
34 are directed to abstract ideas comprising a system for genomic analysis
. . . and a computer-implemented method of genomic analysis.” Id.
More specifically, the Examiner finds that “[t]he one or more
databases recited in claims 27–29 are directed to abstract ideas while all
method steps recited in claims 30–34 are directed to a process comprising
performing abstract ideas.” Id. at 4. The Examiner also finds that the claims
recite only generic computer implementation and “do not show that the
claimed invention can improve computer-related technology or computer
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functionality.” Id. Finally, the Examiner finds that “[c]laims 27 and 30 do
not have additional limitations that constitute conventional [sic,
unconventional?] steps appended to the abstract ideas,” and therefore are
patent ineligible. Id. at 6.
Appellant argues that, “[u]nder the Supreme Court’s Alice/Mayo test
and USPTO’s Revised Guidance issued January 7, 2019, independent claims
27 and 30 do not recite a judicial exception” and, “[t]o the extent any
judicial exception is recited in them, these claims recite a practical
application of the judicial exception.” Appeal Br. 12.
Appellant points out that the Revised Guidance defines three
categories of abstract ideas, and argues that the databases of claim 27 “do
not fall under any of these enumerated categories. They are not a
mathematical concept. They are not methods of organizing human activity
. . . . They are also not mental processes.” Id. at 16. Appellant therefore
argues: “Since a database is not included in any of the listed groupings,
claim 27 does not recite an abstract idea.” Id.
Similarly, Appellant argues that
none of the steps recited in claim 30 fall under the USPTO’s
enumerated groupings of abstract ideas. These are neither
mathematical concepts, nor methods of organizing human
activity. . . . Moreover, all of the steps recited in claim 30
require performance by ‘one or more processors’ and as such,
they are not mental processes.
Id. at 17.
Appellant also argues that “the claimed systems and methods provide
a significant improvement in the field of pharmacogenomic studies.” Id. at
20.
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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.
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
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(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
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,
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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”).4 “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 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”).5

4 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
Update”) (available at https://www.uspto.gov/sites/default/files/
documents/peg_oct_2019_update.pdf).
5 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
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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.
Revised Guidance, 84 Fed. Reg. at 52–56.
Revised Guidance Step 2A, Prong 1
Following the Revised Guidance, we first consider whether the claims
recite a judicial exception. The Revised Guidance identifies three groupings
of subject matter included in the abstract idea exception: “Mathematical
concepts,” “Certain methods of organizing human activity,” and “Mental
processes.” 84 Fed. Reg. at 52. The Revised Guidance states that, except in
rare circumstances, “[c]laims that do not recite matter that falls within these
enumerated groupings of abstract ideas should not be treated as reciting
abstract ideas.” Id. at 53.6

practical application. See Revised Guidance - Section III(A)(2), 84 Fed. Reg.
54–55.
6 The Revised Guidance describes the extra measures that an Examiner
should apply in the rare circumstances of an “abstract idea” that does not fall
in one of the enumerated categories. Id. at 56–57. Those measures were not
taken in the present case.
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The Examiner finds that the “databases recited in claims 27–29 are
directed to abstract ideas.” Ans. 4. We agree with Appellant, however, that a
database is not a mathematical concept, a method of organizing human
activity, or a mental process. The Examiner therefore has not shown that
claims 27–29 recite an abstract idea within the categories set out in the
Revised Guidance.
The Examiner also finds that “all method steps recited in claims 30–
34 are directed to a process comprising performing abstract ideas.” Ans. 4.
However, the Examiner has provided no analysis showing that any of the
steps of claim 30 recites a mathematical process, a method of organizing
human activity, or a mental process. The Examiner therefore has not shown
that claims 30–34 recite an abstract idea within the categories set out in the
Revised Guidance.
In summary, the Examiner has not shown that—when analyzed
according to the criteria set out in the Revised Guidance—the claims on
appeal recite, much less are directed to, abstract ideas that constitute patent
ineligible subject matter.
The Examiner points out that the rejection in the Final Office Action
could not have followed the Revised Guidance because that Office Action
was mailed before the Revised Guidance was issued. Ans. 16. While this is
true, it is also true (as Appellant has pointed out, Reply Br. 2) that the
Examiner could have applied the appropriate analysis in the rejection set out
in the Answer, but failed to do so. The Examiner’s conclusory statement that
“rewriting the rejection under 35 U.S.C. 101 according to ‘Revised
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Guidance’ will not change the results” (Ans. 16) does not take the place of a
proper analysis.
For the reasons discussed above, we reverse the rejection of claims
27–34 under 35 U.S.C. § 101.
DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
27–34 101 Eligibility 27–34
27–34 112, second
paragraph
Indefiniteness 27–34
Overall
Outcome
27–34

REVERSED