Ex Parte Wilcox et al

Patent Trial and Appeal Board

Mar 29, 2018

13808751 (P.T.A.B. Mar. 29, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/808,751 01107/2013
125354 7590 04/02/2018
Swanson & Bratschun, L.L.C.- SomaLogic, Inc.
8210 SouthPark Terrace
Littleton, CO 80120
FIRST NAMED INVENTOR
Sheri Wilcox
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.
0057.33PCT-US 1096
EXAMINER
DINES, KARLA A
ART UNIT PAPER NUMBER
1639
NOTIFICATION DATE DELIVERY MODE
04/02/2018 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
following e-mail address( es):
efspatents@sbiplaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte SHERI WILCOX, DEBORAH AYERS, NEBOJSA JANJIC,
LARRY GOLD, MICHAEL RIEL-MEHAN, and THALE JARVIS 1
Appeal2017-005853
Application 13/808, 7 51
Technology Center 1600
Before JEFFREY N. FREDMAN, JOHN G. NEW, and
DAVID COTT A, Administrative Patent Judges.
NEW, Administrative Patent Judge.
DECISION ON APPEAL
1 Appellants identify SomaLogic, Inc., as the real party-in-interest is. App.
Br. 3.
Appeal2017-005853
Application 13/808,751
SUMMARY
Appellants file this appeal under 35 U.S.C. § 134(a) from the
Examiner's Final Rejection of claims 1, 6-7, 10, 17, 24, 29-30, 33-38, 40-
41, and 47. Specifically, the claims stand rejected as unpatentable under 35
U.S.C. § 101 as being directed to non-statutory subject matter.
Claims 1, 6, 7, 10, and 17 stand rejected as unpatentable under 35
U.S.C. § 103(a) as being obvious over the combination of Gold et al. (US
2010/0070191 Al, March 18, 2010) ("Gold"), R.S. Stearman et al., A
Macrophage Gene Expression Signature Defines a Field Effect in the Lung
Tumor Microenvironment, 68(1) CANCER RESEARCH 34--43 (2008)
("Stearman"), H.W. Chen et al., Molecular Recognition of Small-Cell Lung
Cancer Cells Using Aptamers, 3 CHEM. MED. CHEM. 991-1001 (2008)
("Chen"), and R.M. Ostroff et al., Unlocking Biomarker Discovery: Large
Scale Application of Aptamer Proteomic Technology for Early Detection of
Lung Cancer, 5(12) JOURNAL OF PROTEOMICS 649---66 (2010) ("Ostroff').
Claims 24, 29, 30, 33-38, and 40 stand rejected as unpatentable under
35 U.S.C. § 103(a) as being obvious over the combination of Gold,
Stearman, C.W. Seder et al., Upregulated INHBA expression may promote
cell proliferation and is associated with poor survival, 11(4) NEOPLASIA
388-96 (2009) ("Seder").
Claim 47 stands rejected as unpatentable under 35 U.S.C. § 103(a) as
being obvious over the combination of Gold, Stearman, Seder, and
E. Kettunen et al., Differentially Expressed Genes in Nonsmall Cell Lung
Cancer: Expression Profiling of Cancer-Related Genes in Squamous Cell
Lung Cancer, 149 CANCER GENETICS AND CYTOGENETICS 98-106 (2004)
("Kettunen").
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Application 13/808,751
We have jurisdiction under 35 U.S.C. § 6(b ).
We AFFIRM.
NATURE OF THE CLAIMED INVENTION
Appellants' invention is directed to biomarkers, methods, devices,
reagents, systems, and kits for the detection and diagnosis of lung cancer.
Abstract.
REPRESENTATIVE CLAIM
Claim 1 is representative of the claims on appeal and recites:
1. A method for diagnosing lung cancer in an individual, the
method comprising:
contacting a tissue test sample from the individual with a
capture reagent having specific affinity for the protein biomarker
TrATPase, wherein the capture reagent is selected from the
group consisting of an aptamer and an antibody, measuring the
level of the protein biomarker TrATPase in the tissue test sample
with a capture reagent-based assay; and wherein a decreased
expression level of the protein biomarker TrATPase in the tissue
test sample compared to the expression level of the protein
biomarker TrATPase in a control non-tumor tissue, indicates a
likelihood that the individual has lung cancer.
App. Br. 25.
ISSUES AND ANALYSES
We agree with, and adopt, the Examiner's findings and conclusion
that the appealed claims are (1) directed to nonstatutory subject matter; and
(2) obvious over the combined cited prior art. We address the arguments
raised by Appellants below.
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Application 13/808,751
A. Rejection of claims 1, 6-7, 10, 17, 24, 29--30, 33-38, 40-41, and 47
under 35 U.S.C. § 101
Issue 1
Appellants argue that the Examiner erred in concluding that the claims
are directed to a judicially-created exception to 35 U.S.C. § 101 and that the
remaining claims do not add significantly more to the claim so as to render it
patentable. App. Br. 8.
Analysis
The Examiner finds that the claims are directed to a judicial
exception, viz., a law of nature, and specifically the correlation between
altered biomarker expression in an individual and the likelihood that the
individual has lung cancer. Final Act. 4. The Examiner also finds that the
claims do not recite something significantly more than the judicial
exception, because the steps of measuring the claimed proteins in a test
sample using aptamers or antibodies are known, routine procedures typically
undertaken to perform testing of a sample. Id. at 4---6 (citing, e.g., Ostroff,
Table 1).
Appellants argue that the claims are directed to a patent-eligible
statutory category, viz., a process. App. Br. 8. However, Appellants assert,
the claims do not seek to monopolize the correlation between lung cancer
and the specified biomarkers, because the claims are limited to a capture
reagent-based assay. Id. Therefore, Appellants argue, other applications of
the correlation are not tied up by the instant claims because there are non-
infringing, alternative methods available to apply the correlation that are
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beyond the scope of Appellants' claims, e.g., assays based on mass
spectrometry. Id.
Appellants argue further that the limitation requiring measuring the
decreased expression of TrATPase protein with a capture reagent having
specific affinity for TrATPase protein, as indicative of lung cancer, is not
"well-understood, routine and conventional in the field" for at least the
reason that the cited references do not teach or suggest this limitation. App.
Br. 8-9 (citing 2014 Interim Guidance on Patent Subject Matter Eligibility,
79(241) Fed. Reg. 74618, 74624 (December 16, 2014)). Appellants point to
the Examiner's finding that Stearman teaches that the Acp5 gene, which
encodes for the TrATPase protein, is up-regulated in lung tissue adjacent to
tumor tissue when compared to that in normal tissue. Id. at 9. Appellants
assert that Stearman therefore does not teach that decreased expression of
TrATPase protein is indicative of lung cancer. Id. Consequently, argue
Appellants, their claims on appeal do not seek to tie up a judicial exception
and also include at least one limitation which adds significantly more to the
claims than a judicial exception. Id.
We are not persuaded by Appellants' arguments. Appellants' claims
are directed to the relationship between decreased expression of the
biochemical marker TrATPase, when compared to a control, and a
likelihood of lung cancer. See claim 1. As an initial matter, although the
avoidance of preempting a judicially-created exception to Section 101 may
be part of the purpose of the judicially-created exceptions to the statute,
whether a claim actually preempts such an exception is not part of the two-
part analysis that the Supreme Court has instructed us, in Mayo
Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66 (2012) and Alice
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Corp. v. CLS Bank Int'!, 134 S.Ct. 2347 (2014), to perform in determining
patentability in such cases. Rather, the analysis requires us to determine,
first, whether the claims are directed to one of the judicially-created
exceptions and, second, if the answer is yes, to determine whether the
elements of each claim both individually and "as an ordered combination,"
possess additional elements that "transform the nature of the claim" into a
patent-eligible application. Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788
F.3d 1371, 1375 (2015) (citing Mayo, 566 U.S. at 78-79). The Supreme
Court has likened this second step of the 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. (citing Mayo, 566 U.S.
at 72-73; also citing Digitech Image Techs., LLC v. Elecs.for Imaging, Inc.,
758 F.3d 1344, 1351 (Fed. Cir. 2014) ("Without additional limitations, a
process that employs mathematical algorithms [an exception] to manipulate
existing information to generate additional information is not patent
eligible").
We find that the steps recited in Appellants' claims are directly
analogous to those at issue in Mayo. In Mayo, the claim at issue similarly
recited: (1) obtaining a sample; (2) analyzing the sample; and (3)
determining a diagnosis and a plan of treatment based upon the results of
that analysis. 2 Mayo, 566 U.S. at 74--75. The Supreme Court first found
2 The claims of the patent-in-suit of Mayo additionally recited the
administration of a thiopurine compound prior to obtaining the sample. By
way of example, claim 1 of Mayo recited:
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that the Mayo claims were directed to a judicially-created exception to
Section 101, viz., a phenomenon of nature. Id. at 77. Specifically, the Court
found that the claims recited 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.
In the appeal presently before us, we conclude that Appellants' claims
are similarly directed to a phenomenon of nature: viz., the relationship
between decreased levels of expression of TrATPase in an individual and an
increased likelihood of lung cancer. We conclude that this is a phenomenon
of nature because the relationship occurs naturally in such an individual
whether or not it is measure or observed.
A method of optimizing therapeutic efficacy for treatment of an
immune-mediated gastrointestinal disorder, comprising:
(a) administering a drug providing 6-thioguanine to a subject
having said immune-mediated gastrointestinal disorder; and
(b) determining the level of 6-thioguanine in said subject
having said immune-mediated gastrointestinal disorder,
wherein the level of 6-thioguanine less than about 230
pmol per 8 x 108 red blood cells indicates a need to increase the
amount of said drug subsequently administered to said subject
and
wherein the level of 6-thioguanine greater than about 400
pmol per 8 x 108 red blood cells indicates a need to decrease the
amount of said drug subsequently administered to said subject.
Mayo, 566 U.S. at 74--75.
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Having so concluded, and continuing to follow the analysis set forth
by the Court in Mayo, we are next required to determine whether the claims
"do significantly more than simply describe these natural relations. To put
the matter more precisely, do the patent claims add enough to their
statements of the correlations to allow the processes they describe to qualify
as patent-eligible processes that apply natural laws?" Mayo, 566 U.S. at 77
(emphasis in original).
We conclude that they do not. We find that the additional recited
steps of Appellants' claims are directly analogous to the steps of the claims
at issue in Mayo which:
[S]imply tell doctors to gather data from which they may
draw an inference in light of the correlations. To put the matter
more succinctly, 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. For these reasons we believe that the steps are
not sufficient to transform unpatentable natural correlations into
patentable applications of those regularities.
Mayo, 566 U.S. at 79--80.
Neither Appellants' claims nor their Specification recite a novel
manner of obtaining or analyzing the collected samples; instead, the scope of
the claim encompasses any and all methods of obtaining and analyzing the
collected sample for TrATPase expression using antibodies or aptamers,
including those commonly known in the art, and as taught by Gold and
Stearman. See, e.g., Gold i-f 21, claims 1--4; Stearman 34--35, Table 1. And,
having made such an analysis of the sample, the person performing it is
required to do no more than understand the phenomenon of nature to which
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the claim is directed, viz., that an abnormally decreased level of TrATPase
expression in the sample is a likely diagnostic indicator of lung cancer. As
such, we conclude that the claims are not directed to significantly more than
the natural phenomenon itself and are, consequently, unpatentable.
Issue
B. Rejection of claims 1, 6-7, 10, 17, 24, 29-30, 33-38, 40, and
47 under 35 U.S.C. § 103(a)
Appellants argue the Examiner erred because, in contrast to the
teaching of Stearman with respect to up-regulation of the Acp5 gene in lung
tissue adjacent to tumor tissue as compared to normal tissue, Appellants
have found decreased expression of the TrATPase protein as indicative of
lung cancer. App. Br. 12.
Analysis
The Examiner finds Gold teaches a method for diagnosing an
individual as having an increased likelihood of lung cancer by employing an
in vitro assay using aptamers as capture reagents. Final Act. 10 (citing, e.g.,
Gold claims 2, 3, and 4).
The Examiner finds that, whereas Gold does not teach the biomarker
TrATPase, Stearman teaches that the level of Acp5 gene expression is a
biomarker for a diagnosis of lung cancer. Final Act. 10 (citing Stearman 34--
35, Table 1). The Examiner also notes that it was known in the art that Acp5
is the gene for the TrATPase protein biomarker. Id. at 10-11 (citing Spec.
Table 18).
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The Examiner concludes that it would have been obvious to one of
ordinary skill in the art to modify the method and system of Gold with the
use of Acp5, as taught by Stearman. Final Act. 11. The Examiner finds that
a skilled artisan would have been motivated to employ Acp5 as a biomarker
because Stearman teaches that the altered expression levels of Acp5 suggest
that the gene expression information is informative for predicting tumor
status. Id. The Examiner acknowledges that Stearman teaches that the Acp5
gene is up-regulated in lung cancer cases, whereas Appellants claim that the
expression level of the TrATPase, which is synthesized by the Acp5 gene,
states that decreased expression of the protein is diagnostic of possible lung
cancer. Id. Nevertheless, the Examiner finds that Chen teaches that genetic
changes do not always correlate with changes at the protein level and that it
would have been obvious to one of ordinary skill in the art to include the use
of a known biomarker in the diagnosis of lung cancer. Id. (citing KSR
International Co. v. Teleflex Inc., 550 U.S. 398, 418 (2007).
Appellants agree with the Examiner that, in contrast to the teaching of
Stearman with respect to relative up-regulation of the Acp5 gene in lung
tissue adjacent to tumor tissue, Appellants have found decreased expression
of the TrATPase protein is indicative of lung cancer. App. Br. 13.
Appellants argue the Examiner's reliance on Chen as teaching that genetic
changes do not always correlate with changes at the protein level is
misplaced, because this teaching of Chen demonstrates that the teachings of
Stearman with respect to the Acp5 gene do not provide any reasonably
reliable information with respect to the TrATPase protein. Id.
Appellants emphasize that they have determined the lack of
correlation between gene expression and protein expression in its own
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research and that, consequently, Stearman in combination with Chen would
not provide one of ordinary skill in the art any reasonably reliable teaching
or suggestion that decreased expression of TrATPase protein is indicative of
lung cancer. App. Br. 13.
We are not persuaded by Appellants' arguments. Stearman expressly
teaches that altered regulation of the Acp5 gene is consistent with a
diagnosis of lung cancer. See, e.g., Stearman 39. We agree with the
Examiner that a person of ordinary skill in the art, understanding the
teachings of Stearman, would look to the expression of the TrATPase
protein expressed by the Acp5 gene teaching as a diagnostic indicator of
lung cancer with a reasonable expectation of success. Such an expectation
would be reasonable because the direct link between Acp5 expression and
TrATPase synthesis was well known in the contemporary art. See Spec.
Table 18. The fact, discovered by Appellants, that TrATPase expression is
decreased, rather than increased, in individuals likely to have lung cancer,
may well have been unexpected, even though Chen expressly teaches that:
"[g]enetic changes can be detected reproducibly by PCR and genomic
hybridization, but they do not always correlate with changes at the protein
level." Chen 991. Nevertheless, Chen also teaches that: "multiple aptamers
can be readily developed for any cancer cells of interest without prior
knowledge of cell-surface marker proteins, and are more predictive of cancer
progression than single probes used in previous studies." Id. at 992. We
find that these combined teachings would have motivated the skilled artisan
to arrive at the claimed invention.
We consequently conclude that a person of ordinary skill in the art
would, knowing that the gene responsible for transcribing TrATPase is a
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useful marker for lung cancer, would have found it obvious to use TrATPase
as a marker for a lung cancer diagnosis based upon the combined teachings
of Gold and Stearman. We consequently affirm the Examiner's rejection of
claims 1, 6, 7, 10, and 17, which Appellants argue together. See App. Br.
12.
Furthermore, Appellants argue claims 24, 29, 30, 33-38, and 40 and
claim 4 7 separately, but rely upon the same arguments presented with
respect to claims 1, 6, 7, 10, and 17. See App. Br. 13-14. For the same
reasons, we affirm the Examiner's rejection of these claims.
DECISION
The Examiner's rejection of claims 1, 6-7, 10, 17, 24, 29-30, 33-38,
40-41, and 47 as unpatentable under 35 U.S.C. § 101 is affirmed.
The Examiner's rejection of claims 1, 6-7, 10, 17, 24, 29-30, 33-38,
40, and 47 as unpatentable under 35 U.S.C. § 103(a) is affirmed.
The Examiner's rejection of claims as unpatentable under the
judicially-created doctrine of obviousness-type double patenting is affirmed.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(l). See 37 C.F.R.
§ 1.136(a)(l )(iv).
AFFIRMED
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