Ex Parte Simons

Patent Trial and Appeal Board

Dec 13, 2017

12663197 (P.T.A.B. Dec. 13, 2017)

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.
12/663,197 02/05/2010 Malcolm James Simons 400376-20003 1890
25570 7590 12/15/2017
Roberts Mlotkowski Safran Cole & Calderon, P.C.
7918 Jones Branch Drive
Suite 500
McLean, VA 22102
EXAMINER
CHUNDURU, SURYAPRABHA
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
12/15/2017 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
lgallaugher@rmsc2.com
docketing@rmsc2.com
dbeltran @ rmsc2. com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte MALCOLM JAMES SIMONS
Appeal 2016-002684
Application 12/663,1971
Technology Center 1600
Before JOHN G. NEW, TIMOTHY G. MAJORS, and DAVID COTTA,
Administrative Patent Judges.
NEW, Administrative Patent Judge.
DECISION ON APPEAL
1 Appellant states that the real party-in-interest is Haplomic Technologies
Pty, Ltd. App. Br. 2.
Appeal 2016-002684
Application 12/663,197
SUMMARY
Appellant files this appeal under 35 U.S.C. § 134(a) from the
Examiner’s Final Rejection of claims 16, 20, 22, and 24—27. Specifically,
claims 16, 20, 22 and 24—25 stand rejected as unpatentable under 35 U.S.C.
§ 102(b) as being anticipated by X. Liu et al., Preparation of Single Rice
Chromosome for Construction of a DNA Library Using a Laser Microbeam
Trap, 109 J. Biotech. 217—26 (2004). Claims 16, 20, 22 and 24—27 also
stand rejected under 35 U.S.C.
§ 101 as being directed to nonstatutory subject matter.
We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.
NATURE OF THE CLAIMED INVENTION
Appellant’s invention is directed to methods for obtaining epigenetic
information for a polyploid subject; specifically, determining whether any
two modifications are present in cis on one chromosome, or in trans across
two sister chromosomes. Abstract.
REPRESENTATIVE CLAIM
Claim 16 is representative of the claims on appeal and recites:
16. A method for improving methylation mapping,
comprising,
substantially isolating a DNA molecule from the
biological sample, wherein the DNA molecule is an individual
metaphase chromosome or a chromatid, or a fragment obtained
therefrom;
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analyzing the DNA molecule to determine the presence or
absence of one or more methylated bases in the DNA molecule
and determining whether any two methylated bases are present
in cis on the DNA molecule.
App. Br. 17.
ISSUES AND ANALYSES
We decline to adopt the Examiner’s findings and conclusions that the
appealed claims are anticipated by the prior art. However, we adopt the
Examiner’s findings and conclusions that the claims are unpatentable as
being directed to nonstatutory subject matter. We address the arguments
raised by Appellant below.
A. Rejection of claims 16, 20, 22 and 24—25 under 35 U.S.C. $ 102(b)
Issue
Appellant argues that the Examiner erred in finding that Liu discloses
the limitations of claim 16 reciting: “determin[ing] the presence or absence
of one or more methylated bases in the DNA molecule” and “determin[ing]
whether any two methylated bases are present in cis on the DNA molecule.”
App. Br. 4.
Analysis
The Examiner finds that Liu discloses isolation of a single
chromosome, or a fragment thereof, and analyzing the DNA molecule for
methylated bases. Final Act. 4. The Examiner finds that the polymerase
chain reaction (“PCR”) disclosed by Liu would not prevent the analysis of
methylation because the claims as presented only require isolation of a
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Application 12/663,197
single chromosome, or a chromatid or a fragment thereof, and analyzing any
two methylated bases on the DNA molecule. Id. The Examiner further
finds that the method disclosed by Liu is within the scope of the claims as
presented because Liu discloses isolating a single chromosome, or fragments
thereof, and analyzing methylation of any two bases on the DNA molecule.
Id.
Appellant argues that the only disclosure in Liu with respect to
methylation of genomic DNA is at page 225, as cited by the Examiner, and
which discloses:
Mao constructed a rice chromosome 4 library by microdissection
of a pair of chromosome 4 in a metaphase spread and by
amplification using adaptor PCR on Sau3AI digested DNA. It
was demonstrated that 58% single or low copy sequences and
42% repeat sequences were presented in their library. Sau3 AI is
cytosine methylation sensitive. In plants, methylation islands are
clustered in regions of repeat sequences. The methylation islands
were not digested by Sau3AI. Therefore using Sau3AI digested
fragments of rice DNA might give rise to more unique sequences
in the constructed library. The difference in the ratio of unique to
repeated sequences between the two gene libraries reflects the
differences in methodology.
App. Br. 4 (citing Y.W. Mao et al., Construction of a DNA Library from
Chromosome 4 of Rice (Oryza sativa) by Microdissection, 8 Cell Res. 285—
93 (1998) (“Mao”)).
Appellant contends that the library disclosed by Liu was made using
sonicated, T4 polymerase-filled and -trimmed DNA, and not by Sau3AI-
digested DNA as the starting material. App. Br, 4. According to Appellant,
Liu’s reference to Mao’s library is only made to compare the relative
proportions of unique and repeat sequences. Id. at 4—5. Appellant contends
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that, in the disclosure quoted supra, Liu suggests that Mao’s library contains
a higher percentage of unique sequences because clusters of methylation
islands in portions of the genome that are enriched in repeat sequences in the
genome are not fragmented by Sau3AI. Id. at 5. Therefore, Appellant
asserts, despite the use of the methylation-sensitive restriction enzyme
Sau3AI, a person of ordinary skill would not look to Mao’s methodology or
library in order to determine the methylation of genomic DNA according to
the claimed method. Id. Rather, Appellant maintains, nothing in Liu
discloses the additional steps of mapping which bases within the cloned
Sau3 AI fragment are methylated in the original chromosomal fragment, as
recited in claim 16. Id.
The Examiner responds that Liu discloses obtaining a DNA molecule
from an individual metaphase chromosome and characterizing the DNA
molecule by analyzing the percentage of repeat sequences. Ans. 8. The
Examiner finds that Liu infers from the high percentage of repeat sequences
found in the DNA in their data that the repeat sequences have clustered
methylated sequences, and that this anticipates the step of analyzing the
DNA to determine the presence or absence of one or more methylated bases
in the DNA molecule. Id. The Examiner finds that the high percentage of
repeat sequences disclosed by Liu inherently comprises one or more
methylated bases. Id. The Examiner further finds that the step of
determining whether any two methylated bases are present in cis on the
DNA molecule reads on a random distribution of a plurality methylated
bases on a DNA sample and does not necessarily require the presence of two
adjacent methylated bases. Id.
We are not persuaded by the Examiner’s findings. Liu discloses that:
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Application 12/663,197
The 200 inserts from the library established from rice
chromosome 4 were blast to rice repeat database in TIGR in
order to find the ratio of the repeat sequences in our library. A
similarity of >70% was used as a match cutoff. One hundred and
sixty-four (82%) inserts were homologous to rice repeat
sequences. The repeats were unknown retrotransposon or gypsy
retrotransposon elements. In general, there were 50% repetitive
sequences in rice, but the repetitive sequences in our library were
much higher than 50%....
Repeat sequences in a genome are expected to be cloned
at a higher frequency than unique sequences after PCR due to
their relative abundance. This explains the high percentage of
repeat sequences in our single chromosome library.
Liu 224—225. Liu then continues with the paragraph quoted by Appellant
supra.
In comparing their results with those of Mao, Liu attempts to account
for the differences between the high repeat: unique genomic sequence ratio
reported in Liu, compared with those disclosed by Mao. Liu 225. Liu
suggests that the difference may be a result of the fact that Mao sequenced
DNA fragments after digestion with the Sau3AI enzyme, which does not
digest “methylation islands,” i.e., regions of the DNA that are heavily
methylated and which contain many repeat sequences. Id. (“In plants,
methylation islands are clustered in regions of repeat sequences. The
methylation islands were not digested by Sau3AI. Therefore using Sau3 AI
digested fragments of rice DNA might give rise to more unique sequences in
the constructed library”). Consequently, we find that the passages of Liu
cited by the Examiner are directed to accounting for why Liu’s PCR results
demonstrate a higher repeat: unique genomic sequence ratio than Mao, viz.,
because many of the repeat sequences of Mao were contained in the
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undigested “methylation islands” left undigested by the Sau3 AI enzyme and
consequently not analyzed by Mao. However, we do not discern any
disclosure of Liu that is directed to the claimed limitations of claim 16
reciting: “determin[ing] the presence or absence of one or more methylated
bases in the DNA molecule” and “determining] whether any two
methylated bases are present in cis on the DNA molecule.”
“For a claim to be anticipated, each claim element must be disclosed,
either expressly or inherently, in a single prior art reference, and the claimed
arrangement or combination of those elements must also be disclosed, either
expressly or inherently, in that same prior art reference.” Therasense, Inc. v.
Becton, Dickinson and Co., 593 F.3d 1325, 1332—33 (Fed. Cir, 2010). The
Examiner does not point us to, nor do we discern, any passage of Liu that
discloses “determining] the presence or absence of one or more methylated
bases in the DNA molecule” and “determining] whether any two
methylated bases are present in cis on the DNA molecule,” as required by
claim 16. We consequently reverse the Examiner’s rejection of claims 16,
20, 22 and 24—25 on this ground.
B. Rejection of claims 16, 20, 22 and 24—27 under 35 U.S.C. $ 101
Issue
Appellant argues that the Examiner erred in concluding that the claims
on appeal are directed to an “abstract idea” and are therefore directed to a
judicial exception to the subject matter eligible for patenting under 35
U.S.C. § 101. App. Br. 9.
Analysis
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The Examiner finds that, as recited in the claims, correlating
epigenetic information to the presence of any two methylated bases on a
chromosome is considered a law of nature. Final Act. 2. The Examiner also
finds that the additional recited steps of isolating a DNA molecule from a
single metaphase chromosome in a biological sample and treating the
genomic DNA with bisulfite constitute routine conventional activity and do
not significantly transform the naturally existing methylated bases. Id. at 2—
3. The Examiner further finds that the prior art of record discloses the use of
microdissection or laser-mediated dissection to isolate single chromosomes
— techniques used routinely in the field of molecular biology. Id. at 3.
The Examiner concludes that application of routine conventional activity
does not add anything significant to the naturally-existing methylated
chromosome and does not modify the arrangement of nucleotide bases on a
chromosome. Id.
Appellant argues that isolating a DNA molecule is a step that can only
occur in the real, physical world and, as such, is not merely “an abstract
idea.” App. Br. 11. Appellant asserts that, although one might argue that
“analyzing” data represents merely abstract thought, in the claims, the
“analyzing” step is one that requires identification of specific methylated
sites on a DNA molecule, and that such identification requires real-world
manipulation of the DNA. Id. Therefore, Appellant argues that, reviewed as
a whole, the claims are not directed to an abstract idea (or any other judicial
exception). Id.
Appellant argues further that if, arguendo, the claims are determined
to be directed to a judicially-created exception, then the claims also provide
“significantly more” than the judicial exception, so as to render the claim
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eligible for patenting. App. Br. 11. Appellant asserts that the method
recited in claim 16 improves the art of DNA methylation mapping. Id. at 12.
Pointing to the Specification, Appellant contends that it discloses that a
significant improvement over the prior art is achieved by using isolated
haploid genetic material, i.e., an isolated single chromosome as recited in the
claim, as the starting material for analysis of methylation sites along the
DNA molecule. Id. According to Appellant, this technical improvement
resolves ambiguity with respect to the phasing of methylation tags among
the two copies of any one chromosome in a diploid cell — a perceived
problem of techniques disclosed in the prior art. Id. Therefore, Appellant
contends, the claims on appeal recite “significantly more” than the judicial
exception and are therefore directed to patent-eligible subject matter. Id.
Appellant further points to our reviewing court’s holding in DDR
Holdings, LLC v. Hotels.com et al., 773 F.3d 1245, 1258—59 (Fed. Cir.
2014) as supporting their argument. App. Br. 14. According to Appellant,
the field of DNA methylation analysis at the time of the claimed invention
was burdened by a problem of unambiguously determining the phase of any
two methylation marks identified in a DNA methylation analysis, i.e.,
whether said two marks resided on the same chromosome or whether one
was present on a paternal copy of the chromosome and the other was present
on a maternal copy of the chromosome. Id. (citing, e.g., Spec. 5). Appellant
asserts that the claims on appeal recite a solution to this problem, i.e., first
isolating a DNA molecule and then studying it for its methylated bases. Id.
Therefore, Appellant argues, the claims recite “a concept for resolving this
particular DNA methylation analysis-centric problem,” rendering the claims
patent-eligible. Id. (citing DDR Holdings, 773 F.3d at 1266; also citing
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Messaging Gateway Solutions, LLC v. Amdocs, Inc., Civil Action No. 14—
732—RGA, 2015 WL 1744343, at *4 (D. Del. Apr. 15, 2015) (holding that a
claim may be patent eligible if it provides a solution “tethered to the
technology that created the problem” and specifies how claim elements
interact to achieve a “desired result which overrides conventional
practice”)). Appellant concludes that the claims on appeal are not directed
to any isolated DNA molecule itself, and so do not include any natural
product as a judicial exception. App. Br. 14. Furthermore, Appellant
concludes, even if the claims are directed to a judicial exception, the
presently claimed invention adds “significantly more” to the judicial
exception, insofar as it constitutes an improvement in the technical art of
chromosomal methylation mapping. Id.
The Examiner responds that the claims recite a method and are
therefore directed to a statutory category, i.e., a process. Ans. 9. The
Examiner finds, however, that the claims are directed to determining the
presence or absence of one or more methylated bases on the DNA and
determining whether any two methylated bases are present in cis on the
DNA molecule, and, as such, are directed towards a phenomenon of nature.
Id. (see Final Act. 2). The Examiner finds that the claims, when analyzed as
a whole, do not particularly point out any non-naturally occurring
differences between the claimed method and an abstract idea, and that the
additional steps recited (obtaining a DNA molecule or obtaining the DNA
molecule by laser mediated dissection) do not transform or modify the DNA
molecule. Id. at 9—10. Therefore, the Examiner concludes, the claimed
method does not recite “significantly more” than a judicial exception to
Section 101. Id. at 10.
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We are not persuaded by Appellant’s arguments. Section 101 states
that: “Whoever invents or discovers any new and useful process, machine,
manufacture, or composition of matter, or any new and useful improvement
thereof, may obtain a patent therefor, subject to the conditions and
requirements of this title.” 35 U.S.C. § 101. However, the Supreme Court
has long held that there are exceptions to this statute, viz., laws of nature,
natural phenomena, and abstract ideas. Alice Corp. v. CLS Bank Int 7, 134
S.Ct. 2347, 2354 (2014) (collecting cases).
The analytical framework under Section 101 set forth by the Supreme
Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., 132
S.Ct. 1289 (2012) has been summarized by our reviewing court in Ariosa
Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015):
First, we determine whether the claims at issue are directed to a
patent-ineligible concept. If the answer is yes, then we next
consider the elements of each claim both individually and “as an
ordered combination” to determine whether additional elements
“transform the nature of the claim” into a patent-eligible
application....
The Supreme Court has described the second step of this analysis
as a search for an “inventive concept”—i.e., an element or
combination of elements that is “sufficient to ensure that the
patent in practice amounts to significantly more than a patent
upon the [ineligible concept] itself.”
Ariosa, 788 F.3d at 1375 (citing Mayo, 132 S.Ct. at 1297—98, 1294).
Appellant’s independent claim 16 recites a method of “substantially
isolating a DNA molecule from the biological sample... [and] analyzing the
DNA molecule to determine the presence or absence of one or more
methylated bases in the DNA molecule and determining whether any two
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methylated bases are present in cis on the DNA molecule.” Appellant’s
claim recites a method of isolating and describing the location of methylated
sites on DNA isolated from an individual chromosome or chromatid and
determining whether any two of the methylated sites are present in cis, i.e.,
both located on the maternal or paternal chromosome from which it was
isolated. See Spec. 5. As such, Appellant’s claims are directed to a method
of describing the location of methylated sites that are already present in the
chromosomal DNA within the cell. Appellant’s claims do not, explicitly or
inherently, require any alteration of the methylation sites in the isolated
DNA, merely a description of whether two methylated sites are cis (i.e.,
located on the same chromosome) or trans (located on sister chromosomes).
See Spec. 5. Nor are Appellant’s claims of detecting methylation sites
linked to any particular location on a particular chromosome, chromatid, of
fragment thereof.
Appellant’s Specification further shows that the invention is for the
purpose of detecting whether methylated sites are cis or trans without
significantly altering the nature or location of the site:
[T]he present invention provides a method for obtaining
epigenetic information for a polyploid subject, the method
including the steps of obtaining a biological sample from the
subject, the sample containing: (i) at least one paternally-derived
DNA molecule and/or associated protein and/or, (ii) at least one
maternally-derived DNA molecule and/or associated protein,
analyzing any one or more of the paternally- or maternally-
derived DNA molecules or associated proteins for the presence
or absence of modifications [i.e., methylation], wherein the step
of analyzing determines whether any two modifications are
present in cis on one chromosome, or in trans across two sister
chromosomes
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Spec. 5; see also Spec. 3—5; 12—13. Finally, Appellant’s claims do not
unconventional method for isolating sample material or detecting methylated
bases.
We agree with the Examiner that claim 1 is directed to one of the
judicially-created exceptions to Section 101, viz., a phenomenon of nature.
This finding is consonant with the holdings of our reviewing court. See,
e.g., Ariosa, 788 F.3d at 1376 (holding that claims directed to a method for
detecting a naturally-occurring, paternally inherited nucleic acid in a
maternal blood sample were patent ineligible because they were directed to
“detecting the presence of a naturally occurring thing or a natural
phenomenon”); Genetic Techs. Ltd. v. Merial L.L.C., 818 F.3d 1369, 1376
(2016) (holding that claims directed to a method of detecting a coding region
of a genome by amplifying and analyzing a linked non-coding region of that
person’s genome were directed to a natural phenomenon); RapidLitig. Mgmt
Ltd. v. CellzDirect, Inc., 827 F.3d 1042, 1048 (Fed. Cir. 2016) (“In recent
cases, we found claims ‘directed to’ a patent-ineligible concept when they
amounted to nothing more than observing or identifying the ineligible
concept itself.”).
We therefore proceed to the second step of the Mayo analysis, which
requires that “we must examine the elements of the claim to determine
whether it contains an inventive concept sufficient to transform the claimed
abstract idea [or law of nature] into a patent-eligible application.” Alice, 134
S.Ct. at 2357 (internal quotation marks omitted) (citing Mayo, 132 S.Ct. at
1294, 1298). “The question ... is whether the claims do significantly more
than simply describe [a] natural relation[ ].” Mayo, 132 S.Ct. at 1297. The
inventive concept necessary at step two of the Mayo/Alice analysis must not
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be furnished by the unpatentable law of nature (or natural phenomenon or
abstract idea) itself. That is, under the Mayo/Alice analytical framework:
[A] claim directed to a newly discovered law of nature (or natural
phenomenon or abstract idea) cannot rely on the novelty of that
discovery for the inventive concept necessary for patent
eligibility; instead, the application must provide something
inventive, beyond mere “well-understood, routine, conventional
activity.” Mayo, 132 S.Ct. at 1294; see also Association for
Molecular Pathology v. Myriad Genetics, Inc., 133 S.Ct. 2107,
2117 (2013); Ariosa, 788 F.3d at 1379. “[SJimply appending
conventional steps, specified at a high level of generality, to laws
of nature, natural phenomena, and abstract ideas cannot make
those laws, phenomena, and ideas patentable.” Mayo, 132 S.Ct.
at 1300. Claims directed to laws of nature are ineligible for
patent protection when, “(apart from the natural laws
themselves) [they] involve well-understood, routine,
conventional activity previously engaged in by researchers in the
field.” Mayo, 132 S.Ct. at 1294.
Genetic Techs., 818 F.3d at 1376.
Claim 16 broadly claims any and all methods of determining the
location (cis or trans) of methylated sites on isolated cellular DNA. The
claim does not require any particular method of analysis, not does Appellant
argue that the actual localization and identification of the sites relies on a
novel, heretofore undescribed (and unrecited by the claim) method. Indeed,
Appellant contends that their claims are directed to “a concept for resolving
this particular DNA methylation analysis-centric problem.” See App. Br.
14.
Claim 26 depends upon claim 16 and recites:
The method according to claim 16, wherein the analyzing
includes a method selected from the group consisting of DNA
sequencing using bisulfite treatment, restriction landmark
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genomic scanning, methylation-sensitive arbitrarily primed
PCR, Southern analysis using a methylation-sensitive restriction
enzyme, methylation-specific PCR, restriction enzyme digestion
of PCR products amplified from bisulfite-converted DNA, and
combinations thereof.
Claim 26, which similarly depends from claim 16, is more specific:
The method according to claim 16, wherein where the
analyzing includes DNA sequencing using bisulphite treatment,
the analyzing includes:
(a) reacting the DNA with sodium bisulfite to convert unmethylated
cytosine residues to uracil residues while leaving any 5-
methylcytosine residues unchanged to create an exposed
bisulfite-converted DNA sample having binding sites for primers
specific for the bisulfite-converted DNA sample;
(b) performing a PCR amplification procedure using top strand or
bottom strand specific primers;
(c) isolating the PCR amplification products;
(d) performing a primer extension reaction using a methylation-
sensitive single nucleotide primer extension (Ms-SNuPE)
primer, dNTPs and Taq polymerase, wherein the Ms-SNuPE
primer comprises from about a 15-mer to about a 22-mer length
primer sequence that is complementary to the bisulfite-converted
DNA sample and terminates immediately 5' of the cytosine
residue of the one or more CpG dinucleotide sequences to be
assayed; and
(e) determining the methylation state of the one or more CpG
dinucleotide sequences by determining the identity of the first
primer-extended base.
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Appellant contends that these more particularized methods of analysis
further remove the subject matter claimed in claims 25—27 from the realm of
“abstract ideas.” App. Br. 15. Nevertheless, the Examiner finds, and
Appellant does not dispute, that these methods were all well-understood,
routine, conventional activity, and well-known in the prior art. Ans. 10.
We conclude, with the guidance provided by our reviewing court in,
for example, Genetic Techs., that the additional steps of Appellant’s claims
fail to recite an inventive concept beyond “well-understood, routine,
conventional activity previously engaged in by researchers in the field.”
Genetic Techs., 818 F.3d at 1376 (quoting Mayo, 132 S.Ct. at 1294). Rather,
Appellant’s claims “simply append[ ] conventional steps, specified at a high
level of generality, to [...] natural phenomena [...] [which] cannot make
those laws, phenomena, and ideas patentable.” Id. (quoting Mayo, 132 S.Ct.
at 1300). We therefore conclude that the claims fail to add “significantly
more” to the isolation and identification of naturally-occurring methylated
DNA sites as being either cis or tram. Consequently, the claims are
unpatentable under 35 U.S.C. § 101. See Mayo, 132 S.Ct. at 1294.
In this instance, however, Appellant’s claim 16 is directed to no
specific or new laboratory technique, but rather claims any and all
techniques extant for the determination of localizing methylation sites on
isolated cellular DNA. The Examiner finds, and Appellant does not dispute,
that the methods recited in claims 25—27 are well-known in the art.
Appellant does not claim any new technique for the localization of
methylated sites, but only the employment of well-known techniques to
describe a phenomenon of nature already present in the cells. As such, we
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determine that the claims fall within the judicial exception to Section 101 as
impermissibly being directed to a phenomenon of nature.
Alternatively, we find that the claims are directed to another
judicially-created exception to Section 101. Appellant disputes the
Examiner’s finding that the claims require a “correlation step. See App. Br.
12—13. However, claim 16 (and by incorporation its dependent claims)
requires localizing methylated sites on the isolated cellular DNA and
“determining whether any two methylated bases are present in cis [or
inferentially trans\ on the DNA molecule.” In other words, claim 16 is
directed to isolating and localizing, by any and all methods, methylated sites
naturally occurring in cellular DNA and then making a mental assessment as
to whether the localized methylated sites are cis or trans. This latter step
require only a mental comparison step, viz., a comparison of the attained
results, to determine whether two methylated sites are either cis or trans. As
such, we conclude that this step is directed to a patent-ineligible abstract
idea. In this regard, we find the Federal Circuit’s holding in In re BRCA1-
and BRCA2-Based Hereditary Cancer Test Patent Litigation, 11A F.3d 755
(Fed. Cir. 2014) instructive. In BRCA, the Federal Circuit held that method
claims directed to the comparison of wild-type genetic sequences with a
subject’s genetic sequence were directed to the patent-ineligible abstract idea
of comparing BRCA sequences and determining the existence of alterations.
BRCA, 11A F.3d at 763. The Federal Circuit found, in this regard, that:
The methods, directed to identification of alterations of the
gene, require merely comparing the patient’s gene with the wild-
type and identifying any differences that arise. The number of
covered comparisons is unlimited. The covered comparisons are
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not restricted by the purpose of the comparison or the alteration
being detected.
Id. (internal reference omitted); see also Myriad, 133 S.Ct. at 2116.
In the appeal before us, the claims require comparing identified and
naturally-occurring methylation sites on isolated DNA and mentally
determining whether the methylated sites are either cis or trans. The
methods of identification and localization are acknowledged as
encompassing any method (claim 16) or methods that were well known in
the art at the time of invention (claims 26—27) and, in the required second
step of the Mayo analysis, do not add, as we have explained supra,
“significantly more” to the claims. The mental step of making a
determination of whether two methylated sites are cis or trans therefore
constitutes an abstract idea, another judicially-created exception to Section
101, and is an additional reason why Appellant’s claims are not patent
eligible. We consequently find that Appellant’s claims are unpatentable
under 35 U.S.C. § 101 on this basis.
We have already explained why we find that the claims are directed to
a phenomenon of nature or, alternatively, an abstract idea. Appellant’s
claim 16 permits the user to employ any and all methods of analysis to
describe this phenomenon and/or idea. As such, they also preempt any
possibility of determining the cis or trans location of methylated sites by any
method, extant or yet to be invented. The prohibition of such preemption is
a central concern of the judicially-created exceptions to Section 101. See
Alice, 134 S.Ct. at 2354. Similarly, dependent claims 25—27 encompass the
use of technologies well known in the art to similarly achieve this end.
“Where a patent’s claims are deemed only to disclose patent ineligible
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subject matter under the Mayo framework, as they are in this case,
preemption concerns are fully addressed and made moot.” Ariosa, 788 F.3d
at 1379.
We therefore affirm the Examiner’s rejection of claims 16, 20,
22 and 24—27 as being directed to non-statutory subject matter under
35U.S.C. § 101.
DECISION
The Examiner’s rejection of claims 16, 20, 22 and 24—25 as
unpatentable under 35 U.S.C. § 102(b) is reversed.
The Examiner’s rejection of claims 16, 20, 22 and 24—27 as
unpatentable under 35 U.S.C. § 101 is affirmed.
AFFIRMED
19