Ex Parte Wang et al

Patent Trial and Appeal Board

Apr 21, 2017

13263426 (P.T.A.B. Apr. 21, 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.
13/263,426 10/07/2011 Edwin Wang 1036-0009 6019
36844 7590 04/25/2017
Pp.rmak Nalcaiima Rr Mofrnwan T T P
EXAMINER
127 S. Peyton Street, Suite 200
ALEXANDRIA, VA 22314
GALISTEO GONZALE, ANTONIO
ART UNIT PAPER NUMBER
1636
NOTIFICATION DATE DELIVERY MODE
04/25/2017 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):
CGOODE@cnmiplaw.COM
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PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte EDWIN WANG, JIE LI, YINGHAI DENG,
ANNE E. G. LENFERINK, MAUREEN D. O’CONNOR-McCOURT,
and ENRICO PURISIMA
Appeal 2016-002484
Application 13/263,426
Technology Center 1600
Before DEMETRA J. MILLS, JEFFREY N. FREDMAN, and
DEVON ZASTROW NEWMAN, Administrative Patent Judges.
FREDMAN, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal1 under 35 U.S.C. § 134 involving claims to a process
for determining predictive gene expression signal sets. The Examiner
rejected the claims as being directed to non-statutory subject matter. We
have jurisdiction under 35 U.S.C. § 6(b). We affirm.
1 Appellants identify the Real Party in Interest as The National Research
Council of Canada (see App. Br. 2).
Appeal 2016-002484
Application 13/263,426
Statement of the Case
Background
“There is not currently a satisfactory approach to determine which
patients with cancer would benefit from extra therapy (such as
chemotherapy) after surgery. The identification of genes and proteins
specific to cancer cells that can be used for prognostic purposes would be
helpful in this regard” (Spec. 1:13—17).
The Claims
Claims 6—17 are on appeal. Claim 6 is representative and reads as
follows:
6. A process for determining predictive gene expression
signal sets comprising the following steps:
1) obtaining gene expression signal information and
patient clinical information for a characteristic of interest for a
known tumour population for a cancer of interest;
2) correlating the gene expression signals with clinical
patient information regarding the characteristic of interest to
identify which genes have predictive power for clinical
outcome;
3) creating at least 30 random training datasets from the
identified gene expression signals;
4) comparing identified gene expression signals of step 1
to a list of known genes active in cancer;
5) selecting identified gene expression signals which
correspond to those on the list of known cancer genes;
6) grouping the selected identified gene expression
signals according to their role in biological processes;
7) generating random gene expression signal sets of at
least 25 genes from a selected gene expression signals group of
step 6;
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8) correlating the random gene expression signal sets to
the random training datasets obtained in step 3;
9) obtaining a P value for a survival screening from the
correlation for each gene expression signal set of step 7;
10) if the P value for a gene expression signal set is less
than 0.05 for more than 90% of the random training datasets,
keeping the gene expression signal set;
11) ranking the random gene expression signal sets kept
in step 10 based on frequency of gene appearances in the set;
12) selecting the top at least 26 genes as potential
candidate markers;
13) repeating steps 7 to 12 and producing another,
independent, rank set of at least 26 genes;
14) comparing the top genes from step 12 and step 13;
15) if more than 25 of the genes are the same, the top
genes are kept as marker sets;
16) twice repeating steps 7 to 15 to obtain three different
marker sets;
17) outputting said three different marker sets.
The Issue
The Examiner rejected claims 6—17 under 35U.S.C. § 101 as being
directed to non-statutory subject matter (Final Act. 4—7).
The Examiner finds that claim 6 is “directed to a method for
determining predictive gene expression signal sets comprising obtaining
gene expression signals, and correlating the gene expression signals with
clinical information to identify which genes are predictive, which is a natural
phenomenon” (Final Act. 4). The Examiner further finds
the steps append well-understood, routine and conventional
activities previously known in the industry (obtaining gene
expression) which is specified at a high level of generality. The
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Application 13/263,426
steps do not impose meaningful limits on the claim scope and
are only insignificant extrasolution activity because obtaining
gene expression signal information and patient clinical
information and correlating the gene expression signal with the
clinical information are steps that are necessary for all practical
applications of the natural principle and everyone practicing the
natural principle would be required to perform these steps.
Furthermore, the additional steps (creating, comparing,
selecting, generating, correlating,...) are mental steps, and
complete absence of a machine-or-transformation in a claim
signals the likelihood that the claim is directed to a natural
principle and has not been instantiated.
(Final Act. 6). The Examiner concludes “the steps do not add ‘significantly
more’ than the judicial exception, and therefore, the claims are not directed
to patent subject eligible matter” (Final Act. 6).
The issue with respect to this rejection is: Does the evidence of
record support the Examiner’s conclusion that claim 6 is directed to non-
statutory subject matter?
Findings of Fact
1. The Specification teaches “it will be desirable to study tumour
tissue for a patient by extracting gene expression signals (e.g. mRNA,
protein) and assaying the presence (and in some cases level) of gene
expression signals of interest using a reporter specific for the gene
expression signal of interest” (Spec. 12:11—14).
2. The Specification teaches prior art screening techniques were
used where “surface and secreted proteins were identified from the
microarray data of JM01 cell line (mouse breast cancer cell line, in-house
cell line and data), to screen a public breast cancer dataset (295 samples,
Chang et al., PNAS 102:3738, 2005)” (Spec. 14:3-6).
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Application 13/263,426
3. The Specification teaches: “Detailed information for making
microarray gene chip, scanning and normalization of array data can be found
at Agilent company website: http://www.chem.agilent.com/enUS/products/
instruments/dnamicroarrays/pages/default.aspx.and [sic] in the publicly
available literature” (Spec. 23:21—25).
4. The Specification teaches: “All message RNA sequences for
each gene in Table 1 are extracted from National Center for Biotechnology
Information (NCBI), a public database” (Spec. 31:4—6) (emphasis original).
5. The Specification teaches that prior art data was used as
training sets, specifically: “In Example 1, two training datasets, defined as
Dataset 1 (78 samples, van’t Veer et al., Nature, 2002), and Dataset 2 (286
samples, Wang et al., Lancet, 365:671, 2005), were used” (Spec. 14:19-21).
6. The Specification teaches prior art software and information
was used to obtain signal lists, specifically:
Using the St-ER+ gene expression signal list, Gene Ontology
(GO) analysis (using GO annotation software, David,
http://david.abcc.ncifcrf.qov/) is performed, only the genes
which belong to GO terms that are known to be associated with
cancer, such as cell cycle, cell death and so on are used for
further marker screening.
(Spec. 15:7-11).
7. The Specification teaches application of known statistical
techniques, specifically that “statistical significance of the correlation
between the expression values of each random-gene-set (30 genes) and
patient survival status (‘good’ or ‘bad’) is examined, for example by
performed Kaplan-Meier analysis by implementing the Cox-Mantel log-rank
test” (Spec. 15:21-24).
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8. The Specification teaches the “prior art discloses five such gene
expression signal sets and these have been developed as biomarkers for
breast cancer samples” (Spec. 2:22—24).
Principles of Law
[W]e 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.
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.”
Alice Corp. Pty. Ltd. v. CLS Bank Inti, 134 S. Ct. 2347, 2355 (2014).
Analysis
We agree with and adopt the Examiner’s findings of fact and
reasoning regarding the conclusion that claim 6 is unpatentable as being
directed to non-statutory subject matter consistent with binding precedent
(Final Act. 4—7; FF 1—8). We address Appellants’ arguments below.
Appellants contend
the subject matter of the rejected claims is not “natural” in the
sense that the data set and the marker set will never be
identified or “naturally occurring” in a single individual. The
presently claimed process is not a test to identify a naturally
occurring gene which directly correlates with a cancer
prognosis.
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(App. Br. 7).
We do not find this argument persuasive because the underlying
information in claim 6 is “gene expression signal information” that is
associated with “a characteristic of interest for a known tumour population”
and is then subjected to further analytical processes as recited in claim 6.
The signals from the microarray represent natural levels of gene expression
in naturally occurring tumors in patients (FF 1, 8). Applying the first step of
the two step test in Mayo and Alice, we agree with the Examiner that the
gene expression signal information is directed to a patent-ineligible concept,
specifically laws of nature regarding expression levels of genes in tumors.
This is factually similar to Mayo itself, where the underlying levels of 6-
thioguanine were “naturally occurring,” like the gene expression signal
information in the instant case, and not medical applications that were “not
sufficient to transform unpatentable natural correlations into patentable
applications of those regularities.” Mayo Collaborative Services v.
Prometheus Laboratories, Inc., 566 U.S. 66, 80 (2012).
Appellants contend
the rejected claims calls for 17 steps to be carried out in a
particular order, with separate numeric requirements for many
of the steps (for example, step 3: “at least 30 random training
datasets;” step 7: “generating random gene expression signal
sets of at least 25 genes.; step 12: selecting “the top at least 26
genes as potential candidate markers.”). While each of these
steps, in isolation, represents practice of a known scientific
technique, when taken together as a whole, they constitute
significantly more than a judicial exception.
(App. Br. 9).
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We do not find Appellants’ argument persuasive. “Mayo demanded
that, when a claim involves ... a law of nature . . . eligibility under section
101 requires that the claim involve ‘enough’ else—applying the idea in the
realm of tangible . . . physical actions (for process claims)—that is beyond
‘well-understood, routine, conventional activity.’” SmartGene, Inc. v.
Advanced Biological Laboratories, SA, 555 F. App’x. 950, 955 (Fed. Cir.
2014).
The claim here does not do so. Under the second step of the two-step
test, we find that claim 6 does not add “significantly more” to the natural law
of gene expression levels in tumors. Each step of claim 6 is based on
routine, prior art, conventional activity as acknowledged by Appellants’ own
Specification. Thus, step (1) of obtaining gene expression signal
information uses known prior art microarray technologies (FF 3). The
correlating steps (2) and (8), obtaining a P value steps (9) and (10) and
ranking step (11) rely on known statistical techniques (FF 7). The creating
training data set step (3) uses prior art datasets (FF 5). The comparison of
signals step (4) and selecting and grouping those associated with known
cancer genes steps (5) and (6) rely on prior art data for the cancer genes (FF
6, 8) and known prior art normalization approaches (FF 3). Repeating
known steps does not add “significantly more.”
Thus, Appellants do not identify any step that is something other than
applying known methods of gathering and processing known types of
information. We note that “[cjlaims directed to the ‘process of gathering
and analyzing information of a specified content, then displaying the
results,’ without ‘any particular assertedly inventive technology for
performing those functions,’ were held ineligible in Electric Power Grp.,
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Application 13/263,426
LLC v. Alstom S.A., 830 F.3d 1350, 1354 (Fed. Cir. 2016).” Trading Techs.
Infl, Inc. v. CQG, INC., 2017 WL 192716 *3 (Fed. Cir. 2017). We find
claim 6 analogous to the claims held patent ineligible in Electric Power.
“Merely requiring the selection and manipulation of information . . .
by itself does not transform the otherwise-abstract processes of information
collection and analysis.” Electric Power, 830 F.3d at 1355. Appellants do
not identify any technological advance to the process of analyzing the data,
but simply select particular known data manipulations. Thus, we agree with
the Examiner that the claim limitations, analyzed alone and in combination,
fail to add “something more” to “transform” the claimed abstract idea of
weighting informative sequence regions to obtain optimal reference
sequences for use in organism classification into “a patent-eligible
application.” See Alice, 134 S. Ct. at 2354, 2357.
Appellants contend that claim 6 “recites a process that includes 17
steps. These steps place meaningful limits on the scope of the rejected
claims, such that the claims do not foreclose all applications of the natural
principle that gene expression is correlated with certain clinically important
characteristics” (App. Br. 9; cf. App. Br. 11).
We find this argument unpersuasive because “[wjhile preemption may
signal patent ineligible subject matter, the absence of complete preemption
does not demonstrate patent eligibility.” Ariosa Diagnostics, Inc. v.
Sequenom, Inc., 788 F.3d 1371, 1379 (Fed. Cir. 2015). Importantly, the
preemption concern is addressed by the two-part test considered above. See
id. After all, every patent “forecloses . . . future invention” to some extent,
Mayo, 566 U.S. at 86, and, conversely, every claim limitation beyond those
that recite the abstract idea limits the scope of the preemption.
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Appellants “submit that the Examiner’s interpretation is not the
broadest reasonable construction of the claim . . . Applicants respectfully
submit that the claims are not reasonably read to encompass ‘mere
inspection’ of the data by an individual” (App. Br. 10).
We find this argument unpersuasive because the issue is not whether
the claims may be performed by an individual, but rather whether the claims
are drawn to a patent ineligible natural concept and whether the claims add
significantly more to that concept. For the reasons given above, we find that
consistent with binding precedent, claim 6 does not satisfy this two-part test
and is drawn to non-statutory subject matter.
We do note that the Examiner finds: “It was well known in the
industry to compare expression signal and patient data to create training sets
and generating gene expression signals to identify predictive gene
expression signal sets” (Ans. 9) and this finding is supported by the
Specification itself which recognizes the prior art of Chang using training
sets for gene expression analysis in 2005, prior to the effective filing date of
the instant application (FF 2).
Appellants contend: “It is indisputable that every step in this claim is
not ‘a familiar part of the conscious process that doctors can and do perform
in their heads.’ For at least this reason, the Smartgene decision is entitled to
no weight in deciding the present case” (Reply Br. 4).
We find this argument unpersuasive. The claims at issue in
SmartGene relied upon “expert rules for ‘evaluating and selecting’ from a
stored ‘plurality of different therapeutic treatment regimens.’” SmartGene,
555 F. App’x. at 951—952, claim 1). The “expert rules” in SmartGene are
analogous to the “correlating” step using “random training datasets” to
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identify top genes in claim 6. In neither SmartGene nor the instant claims is
there any evidence of record that specific rules or factors were required, that
the steps represented something “significantly more” than the prior art, or
that Appellants invented new computer software or analysis techniques not
known in the prior art for the analysis (see, e.g., FF 1—7).
We have considered, but find unpersuasive, Appellants’ reference to
the Federal Circuit decisions SiRF Tech., Inc. v. Int'l Trade Comm’n, 601
F.3d 1319 (Fed. Cir. 2010) and CyberSource Corp. v. Retail Decisions, Inc.,
654 F.3d 1366 (Fed. Cir. 2011), Research Corp. Techs, v. Microsoft Corp.,
627 F.3d 859 (Fed. Cir. 2010) (see Reply Br. 4—5), all decided prior to the
binding precedent of the Supreme Court decisions of Mayo and Alice. We
are constrained by Mayo and Alice, and for the reasons given, find that claim
6 does not satisfy the two-part test for patentable subject matter presented in
Mayo and Alice.
Conclusion of Law
The evidence of record supports the Examiner’s conclusion that claim
6 is directed to non-statutory subject matter.
SUMMARY
We affirm the rejection of claim 6 under 35U.S.C. § 101 as being
directed to non-statutory subject matter. Claims 7—17 fall with claim 6.
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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