Ex Parte Matson

Patent Trial and Appeal Board

May 17, 2018

14828204 (P.T.A.B. May. 17, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
14/828,204 08/17/2015 Wayne R. Matson
27667 7590 05/21/2018
HA YES SOLOWAY P.C.
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
IXC 13.01/03 DIVl 6100
EXAMINER
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ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
05/21/2018 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
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PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte WAYNER. MATSON 1
Appeal2018-004298
Application 14/828,204
Technology Center 1600
Before ERIC B. GRIMES, RYAN H. FLAX, and DAVID COTTA,
Administrative Patent Judges.
GRIMES, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of treating a disease condition, which have been rejected as being obvious
and directed to patent-ineligible subject matter. We have jurisdiction under
35 U.S.C. § 6(b).
We affirm.
STATEMENT OF THE CASE
The Specification discloses
a method for developing a treatment for a disease condition in a
living organism comprising analyzing multiple component data
1 Appellant identifies the Real Party in Interest as Ixcela, Inc. Appeal Br. 2.
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Application 14/828,204
between or among categories of individuals of normal and
diseased individuals to develop therapeutic lead compounds
through analysis of biochemical networks linking two or more
of the genome, transcriptome, proteome, metabolome, gut
microbiome and environmental factors.
Spec. 3:7-12. The "invention employs the analysis procedures using a
multi-electrode LCEC [liquid chromatography/electrochemistry] array ... ,
following the teachings of ... U.S. Patent 6,210,970." Id. at 6:15-16.
Claims 1, 6, and 7 are on appeal. Claim 1 is illustrative and reads as
follows:
Claim 1: A method for treating a disease condition in a living organism
compnsmg:
using LC-EC, obtaining multiple component data of measurements of
electroactive compounds from body samples between or among
pairings of a normal category of individuals and a disease
category of individuals;
using said data, mapping a coordinately bound metabolome in a
periphery of the proteome of a body system or organ of interest
or in the proteome of the body system or organ of interest, or
mapping a coordinately and covalently bound metabolome in
DNA and RNA, or a metabolome of the gut microbiome;
analyzing physical, measurable changes in correlations in biochemical
networks between said pairings, wherein the biochemical
networks link two or more of the genome, transcriptome,
proteome, metabolome, gut microbiome and environmental
factors;
identifying physical, measurable differences in the biochemical
networks between said normal category of individuals and said
disease category of individuals;
selecting at least one therapeutic treatment compound for treating said
disease condition, wherein the at least one therapeutic treatment
compound is selected to adjust a measurement of an
electroactive compound from the diseased category of
individuals towards a measurement of a correlating measured
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electroactive compound obtained from the normal category of
individuals; and
treating said living organism with the at least one therapeutic
treatment compound selected.
The claims stand rejected as follows:
Claims 1 and 7 under 35 U.S.C. § I03(a) as obvious based on Matson
'873, 2 Matson '469, 3 Matson '970,4 and Adourian5 (Ans. 4--5);
Claim 6 under 35 U.S.C. § I03(a) as obvious based on Matson '873,
Matson '469, Matson '970, Adourian, and Williams 6 (Ans. 6); and
Claims 1, 6, and 7 under 35 U.S.C. § 101 as being directed to a
judicial exception (Ans. 3).
I
The Examiner has rejected claims 1 and 7 as obvious based on Matson
'873, Matson '469, Matson '970, and Adourian. The Examiner has rejected
claim 6 as obvious based on Matson '873, Matson '469, Matson '970,
Adourian, and Williams. The same issue is dispositive for both rejections.
The Examiner finds that Matson '873 teaches using LC-EC to detect
small molecules in a
method for treating living organisms by analyzing body fluids
from normal and afflicted individuals to generate chemical
analysis patterns for electrochemically active small molecules,
comparing the patterns and identifying differences in the
2 US 4,863,873, issued Sept. 5, 1989.
3 US 2013/0267469 Al, published Oct. 10, 2013.
4 US 6,210,970 Bl, issued Apr. 3, 2001.
5 US 2011/0010099 Al, published Jan. 13, 2011.
6 Horace R. T. Williams et al., Serum Metabolic Profiling in Inflammatory
Bowel Disease, 57 Dig. Disease Sci. 2157-2165 (2012).
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patterns in metabolic pathways of the individuals, selecting
chemical compounds known to block, potentiate, supply or
retard the compounds identified as abnormal in the patterns and
administering the compounds to the living organism.
Ans. 5.
The Examiner finds that Matson '469 and Matson '970 provide
evidence that the LC-EC detection system of Matson '873 "is able to
measure the coordinately and covalently bound metabolome ... and that
these values are included in the analysis of the metabolic pathway patterns
taught in" Matson '873. Id.
The Examiner finds that Matson '873 "is silent [as] to analyzing
correlations in biochemical networks that link two or more of the genome[,]
transcriptome, proteome, metabolome, gut microbiome, and environmental
factors in claim 1." Id. However, the Examiner finds that this aspect of the
claimed method is taught by Adourian, which
discloses utilizing a systems biology approach to perform a
correlation analysis to identify patterns of correlations between
and among data sets for different biomolecular component
types, i.e. genes, gene transcripts, lipids, proteins, and/or
metabolites, and that comparisons between the correlations in a
test group, which is group of individuals afflicted with a
disease, and a control group, which is a group of healthy
individuals, can be made as part of the method.
Id. The Examiner finds that Adourian discloses that its method can include
measurements made by known measurement techniques or combinations of
them, including liquid chromatography. Id. at 6.
The Examiner concludes that it would have been obvious to combine
the teachings of Matson '873 and Adourian, because Adourian "discloses
that analyzing complex clinical samples at a systems biology level provides
new information about the state of the biological system that was previously
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unobtainable through traditional techniques and creates knowledge that
advances pharmaceutical research." Id.
Id.
Therefore, one of ordinary skill in the art would have been
motivated to utilize the systems biology data analysis method
for assessing profile differences taught by Adourian et al. in the
place of the pattern analysis method taught by Matson ['873], in
order to gain the improvements of providing previously
unobtainable information and advancing pharmaceutical
research.
We agree with, and adopt, the Examiner's fact-findings, and her
conclusion that the claimed method would have been obvious to a person of
ordinary skill in the art based on Matson '873, Matson '469, Matson '970,
and Adourian.
Appellant does not dispute that the Matson references disclose the
teachings relied on by the Examiner. See Appeal Br. 14--15, Reply Br. 4--5.
Appellant, however, argues that "claim 1 recites, in part, analyzing physical,
measurable changes in correlations of biochemical networks between
pairings, wherein the biochemical networks link two or more of the genome,
transcriptome, proteome, metabolome, gut microbiome and environmental
factors" and "Adourian fails to teach or suggest using any measurements (for
example, methods similar to those taught by the Matson references) to
identify physical measurable changes in correlations of the biochemical
network pairings as required by Applicant's claims." Appeal Br. 14.
This argument is not persuasive. As the Examiner has pointed out
(Ans. 9--10), Adourian expressly teaches using measurements to identify
physical, measurable changes in biochemical correlations. Adourian states
that its methods "rely on measurements of constituents of biological
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samples, including metabolites, proteins, genes, gene transcripts, lipids[,]
sugars, etc. to permit a skilled artisan to understand a biological system more
holistically and in greater depth than an approach that examines only one or
a subset of these factors." Adourian ,r 56 (emphasis added). Adourian states
that "[t]he data can include measurements or features (e.g. concentrations or
absolute values) relating to various biological sample types (e.g., blood
serum and saliva), types of measurement techniques (e.g., mass spectrometry
(MS) and nuclear magnetic resonance spectrometry (NMR)), and
biomolecular component types ( e.g. metabolites and transcripts)." Id. ,r 57.
Adourian also states that
[a] "measurement technique" refers to any analytical technique
that generates or provides data that is useful in the analysis of a
state of a biological system. For example, measurement
techniques include, but are not limited to, mass spectrometry
("MS"), nuclear magnetic resonance spectroscopy ("NMR"),
liquid chromatography ("LC"), gas-chromatography ("GC"),
high performance liquid chromatography ("HPLC"), capillary
electrophoresis ("CE"), gel electrophoresis ("GE") and any
known form of hyphenated mass spectrometry in low or high
resolution mode, such as LC-MS, GC-MS, CE-MS, MS-MS,
MSn, and other variants.
Id. ,r 65. Finally, Adourian states that the steps of its process can include
selecting animals, including human subjects, and, in appropriate
cases, test and control subject groups. For each subject, one or
more of various types of samples can be taken and analyzed for
one or more types of biomolecules. These data then can be
preprocessed and normalized so that valid comparisons among
them can be done, and then the correlations, if any, can be
detected. In some embodiments, the method begins with
parallel analyses of mRNA, protein, and metabolite data sets
derived from complex samples extracted from both diseased
and healthy populations. The mean quantities, as well as the
ranges and variances, for all measured compounds can be
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collectively analyzed using methods to identify molecules to
link gene response, protein activity, and metabolite dynamics.
Id. ,I 91.
Thus, Adourian does in fact teach analyzing physical, measurable
changes between normal and diseased individuals (subjects in control and
test groups, respectively) in correlations in biochemical networks linking
two or more of the genome, transcriptome, proteome, metabolome, gut
microbiome, and environmental factors, as required by claim 1. The
rejection of claim 1 under 35 U.S.C. § 103(a) based on Matson '873, Matson
'469, Matson '970, and Adourian is affirmed. Claim 7 was not argued
separately and therefore falls with claim 1. 37 C.F.R. § 4I.37(c)(l)(iv).
With respect to claim 6, Appellant argues only that "[ c ]laim 6
indirectly depends on claim 1 and is allowable over the applied art for the
same reasons above adduced relative to claim 1, as well as its own additional
limitations." Appeal Br. 15. However, Appellant provides no substantive
arguments directed to the additional limitation of claim 6. We therefore
affirm the rejection of claim 6 under 35 U.S.C. § 103(a) based on Matson
'873, Matson '469, Matson '970, Adourian, and Williams. See 37 C.F.R.
§ 4I.37(c)(l)(iv) (The Appeal Brief must contain "[t]he arguments of
appellant with respect to each ground of rejection."); Hyatt v. Dudas, 551
F.3d 1307, 1314 (Fed. Cir. 2008) ("When the appellant fails to contest a
ground of rejection to the Board, ... the Board may treat any argument with
respect to that ground of rejection as waived.").
II
The Examiner has rejected all of the claims on appeal on the basis that
they are "directed to a judicial exception (i.e., a law of nature, a natural
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phenomenon, or an abstract idea) without significantly more." Ans. 3. The
Examiner finds that the claims "recite the judicial exception that is the
abstract idea of data analysis and comparison" and "additional elements that
equate to well-understood, routine and conventional activities," and
"[t]herefore, the claims do not amount to significantly more than the judicial
exception itself." Id. at 3--4.
We agree with the Examiner that, under the two-step test of Alice
Corp. Pty. Ltd. v. CLS Bank Int'!, 134 S. Ct. 2347 (2014), claim 1 is not
directed to patent-eligible subject matter. The Alice Court stated that "[i]n
Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S.-,
132 S.Ct. 1289, 182 L.Ed.2d 321 (2012), we set forth a framework for
distinguishing patents that claim laws of nature, natural phenomena, and
abstract ideas from those that claim patent-eligible applications of those
concepts." Alice Corp., 134 S. Ct. at 2355.
The Alice Court described the Mayo test as follows:
First, we determine whether the claims at issue are directed to
one of those patent-ineligible concepts. If so, we then ask,
"[ w ]hat else is there in the claims before us?" To answer that
question, we consider the elements of each claim both
individually and "as an ordered combination" to determine
whether the additional elements "transform the nature of the
claim" into a patent-eligible application. We have described
step two 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."
Id. (alterations in original, citations omitted).
The Mayo Court applied its test to claims that are similar to those of
the instant application. In Mayo, the claimed invention was a "method of
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optimizing therapeutic efficacy for treatment of an immune-mediated
gastrointestinal disorder" comprising administering a certain class of drug
and then determining the level of 6-thioguanine ( 6-TG) in a patient, where a
level of 6-TG below or above certain amounts indicated a need to increase or
decrease, respectively, the drug dosage. Mayo Collaborative Servs. v.
Prometheus Labs., Inc., 566 U.S. 66, 74--75 (2012).
Claim 1 of the instant application is similar, in that it is directed to a
method of treating a disease condition by looking for differences in
metabolites----components of the metabolome-between normal and
diseased individuals, and then selecting and administering a therapeutic
treatment compound based on its expected effect of changing a metabolite
measurement in a diseased individual so that it is closer to the measurement
seen in normal individuals. Similar to the method at issue in Mayo,
therefore, the method of instant claim 1 is directed to a method of providing
effective therapy based on the levels of a set ofbiomarkers (metabolites) in
patient samples.
The Mayo Court concluded that the claims at issue in that case "set
forth laws of nature-namely, relationships between concentrations of
certain metabolites in the blood and the likelihood that a dosage of a
thiopurine drug will prove ineffective or cause harm." Id. at 77.
Similarly here, claim 1 on appeal sets forth a law of nature-namely,
a relationship between the levels of certain ( albeit unspecified) biomarkers
and the likelihood that treatment with a certain ( albeit unspecified)
therapeutic treatment compound is likely to be effective in treating a certain
(albeit unspecified) disease condition. Under the first step of the Alice/Mayo
test, claim 1 on appeal is directed to a law of nature or natural phenomenon.
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The Mayo Court next turned to the question "[ w ]hat else is there in
the claims before us?" Id. at 78. The claims in Mayo included an
"administering" step, a "determining" step, and a "wherein" clause. Id. The
Court concluded that "[ t ]he upshot is that the three steps simply tell doctors
to gather data from which they may draw an inference in light of the
correlations." Id. at 79. In other words,
the claims inform a relevant audience about certain laws of
nature; any additional steps consist of well-understood, routine,
conventional activity already engaged in by the scientific
community; and those steps, when viewed as a whole, add
nothing significant beyond the sum of their parts taken
separately.
Id. at 79--80. The Court concluded that "the steps are not sufficient to
transform unpatentable natural correlations into patentable applications of
those regularities." Id. at 80.
Like the steps of the claims in Mayo, the manipulative steps of claim 1
on appeal also "consist of well-understood, routine, conventional activity
already engaged in by the scientific community." Id. at 79--80. "Whether
something is well-understood, routine, and conventional to a skilled artisan
at the time of the patent is a factual determination." Berkheimer v. HP Inc.,
881 F.3d 1360, 1369 (Fed. Cir. 2018). The prior art references cited by the
Examiner show that using liquid chromatography and electrochemical
detection to obtain measurements of electroactive compounds was
conventional (Matson '873, col. 3, 11. 35-54), as was using this approach to
provide a small molecule (i.e., metabolite) inventory or metabolic pathway
pattern (id. at col. 4, 11. 14--18) and using differences in such patterns
between normal and diseased individuals to design a treatment protocol (id.
at col. 4, 11. 31-38), including selecting therapeutic compounds (id. at col. 4,
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1. 60 to col. 5, 1. 6) to treat a disease state (id. at col. 5, 11. 7-8). See also id.
at col. 6, 1. 51 to col. 7, 1. 5.
Thus, the steps of measuring and analyzing metabolites in samples
from normal and diseased individuals to identify changes in biochemical
networks in the two groups, then selecting and administering a therapeutic
compound based on the measured and analyzed differences, represent
nothing more than "routine, conventional activity already engaged in by the
scientific community." Mayo, 566 U.S. at 79-80. The active step of
"treating ... with the at least one therapeutic treatment compound" of claim
1 does not add anything other than routine and conventional activity to the
natural correlation based on which the compound is selected. See Matson
'873, col. 6, 1. 52 ("a method for treating a disorder") and col. 7, 11. 6-7 ("a
method of treating a disease state").
Thus, when claim 1 is considered as an ordered combination, it
informs a relevant audience of certain laws of nature: specifically, that
levels of certain biomarkers will differ in diseased patients compared to
normal patients, and that a therapeutic compound that will bring the
biomarker level in the diseased patient closer to those of normal patients can
be selected and administered based on the natural correlation. All of the
additional steps of claim 1 consist of well-understood, routine, conventional
activity already engaged in by the scientific community, as shown by the
references cited by the Examiner. We conclude that, under the Alice/Mayo
test, claim 1 is directed to patent-ineligible subject matter.
Appellant argues that claim 1 is "directed to a method of treating a
living organism with at least one therapeutic treatment compound selected
based on the recited steps and is not directed to an abstract idea." Appeal
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Br. 11. Appellant argues that this position is supported by Classen
Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057 (Fed. Cir. 2011), and
Rapid Litigation Management Ltd. v. CellzDirect, Inc., 827 F.3d 1042 (Fed.
Cir. 2016). Appeal Br. 11-12.
We do not find this argument persuasive. As discussed above,
administering a therapeutic compound that is selected based on the natural
correlations to which claim 1 is directed represents routine and conventional
activity, as shown by the cited references. Therefore, the "treating" step of
claim 1 does not "'transform the nature of the claim' into a patent-eligible
application" of the natural correlations. See Alice Corp., 134 S. Ct. at 2355.
We also find unpersuasive Appellant's reliance on Classen
Immunotherapies, which was decided on the basis of Bilski v. Kappas, 561
U.S. 593 (2010). Classen Immunotherapies, 659 F.3d 1057, 1059 (Fed. Cir.
2011) ("We review the question of eligibility with the Court's guidance in
Bilski v. Kappas."). The Supreme Court has since clarified and expanded on
the standard for patent-eligibility under 35 U.S.C. § 101 in the Mayo and
Alice decisions that are discussed above. Those decisions set out the
applicable standard and, for the reasons discussed above, we conclude that
claim 1 is not eligible for patenting under the Alice/ Mayo standard.
Appellant cites CellzDirect for its statement that "the 'directed to'
analysis of a process claim requires more than 'merely identify[ing] a patent-
ineligible concept underlying the claim' and instead requires an analysis of
whether 'the end result of the process, the essence of the whole, was a
patent-ineligible concept."' Appeal Br. 12 (quoting CellzDirect, 827 F.3d at
1048, 1050). Appellant argues that the claims are "directed to methods of
developing a treatment for a disease condition in a living organism using the
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specified process steps .... Accordingly, the pending claims are not
directed to a law of nature, a natural phenomenon, or an abstract idea." Id.
We do not find Appellant's reliance on CellzDirect to be persuasive.
The invention claimed in CellzDirect was an improved method for
producing hepatocytes, which allowed them to be frozen and thawed more
than once. CellzDirect, 827 F.3d at 1045--46. The court held that "the
claims are simply not directed to the ability of hepatocytes to survive
multiple freeze-thaw cycles. Rather, the claims ... are directed to a new and
useful laboratory technique for preserving hepatocytes." Id. at 1048.
The court distinguished several cases involving "claims ... we have
found patent ineligible in cases since Mayo and Alice." Id. The court found
that, "[ a ]lthough the claims in each of these cases employed method steps,
the end result of the process, the essence of the whole, was a patent-
ineligible concept," whereas the claims at issue in CellzDirect were
"directed to a new and useful method of preserving hepatocyte cells." Id.
We conclude that the claims on appeal are not comparable to those
found eligible for patenting in CellzDirect. Rather, claim 1 recites a method
for determining naturally occurring correlations between levels of certain
metabolites and a patient's status as healthy or diseased, and selecting and
administering a therapeutic compound based on the natural correlation. The
claimed method therefore includes active steps in addition to the natural
phenomenon on which the method is based, but as discussed above, the
evidence shows that selecting and administering a therapeutic compound
based on the natural correlations to which claim 1 is directed represents
routine and conventional activity. "[S]imply appending conventional steps,
specified at a high level of generality, to laws of nature, natural phenomena,
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and abstract ideas cannot make those laws, phenomena, and ideas
patentable." Mayo, 566 U.S. at 82.
Appellant also argues that "even if the pending claims are found to
include some features of judicially recognized exception, ... the pending
claims include additional elements that add significantly more to the
exception." Appeal Br. 12. Specifically, Appellant argues that, "[p ]rior to
the filing of the subject application, it was unconventional to obtain and
identify the specific pairings based on electroactive compounds, and select
specific treatment compounds based on the recited pairings of biochemical
networks, as required by Applicant's claims." Id. at 13.
This argument is also unpersuasive. Matson '873, which issued in
1989, states that "[i]n recent years, LCEC (Liquid Chromatography with
Electrochemical Detection) has become a common tool for the determination
of catecholamines biogenic amines and their metabolites in biological
fluids." Matson '873, col. 2, 11. 30-33. As discussed in detail above, claim
1 recites a method of discovering certain laws of nature----correlations
between patients' metabolite levels and their status as diseased or normal
patients-and "any additional steps consist of well-understood, routine,
conventional activity already engaged in by the scientific community; and
those steps, when viewed as a whole, add nothing significant beyond the
sum of their parts taken separately." Mayo, 566 U.S. at 79-80.
Claims 6 and 7 were not argued separately and therefore fall with
claim 1. 37 C.F.R. § 4I.37(c)(l)(iv).
SUMMARY
We affirm all of the rejections on appeal.
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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).
AFFIRMED
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