Ex Parte Andersen et al

Patent Trial and Appeal Board

Jun 13, 2016

13323554 (P.T.A.B. Jun. 13, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/323,554 12/12/2011
93599 7590
Eric P, Mirabel, JD, LLM
3783 Darcus Street
Houston, TX 77005
06/15/2016
FIRST NAMED INVENTOR
Lars Dyrskjot Andersen
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.
SRG-321-MBNL2 6997
EXAMINER
HIBBERT, CATHERINE S
ART UNIT PAPER NUMBER
1636
NOTIFICATION DATE DELIVERY MODE
06/15/2016 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):
emirabel@comcast.net
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte LARS DYRSKJOT ANDERSEN and
TORBEN FALCK ORNTOFT 1
Appeal2013-008130
Application 13/323,554
Technology Center 1600
Before ERIC B. GRIMES, ROBERT A. POLLOCK, and
JACQUELINE T. HARLOW, Administrative Patent Judges.
GRIMES, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
method of determining the likelihood of bladder cancer progression, which
have been rejected as directed to patent-ineligible subject matter, indefinite,
nonenabled, and anticipated. We have jurisdiction under 35 U.S.C. § 6(b ).
We affirm
STATEMENT OF THE CASE
The Specification states that bladder cancer can take the form of either
recurring superficial tumors (stages Ta and T 1 ), or it can progress to a
1 Appellants identify the Real Party in Interest as Catalyst Assets LLC and
Aros Applied Biotechnology A/S. (Appeal Br. 3.)
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muscle invasive form (stages T2 and up). (Spec. 1.) "The ability to predict
which tumors are likely to recur or progress would have great impact on the
clinical management of patients with superficial disease, as it would be
possible to treat high-risk patients more aggressively (e.g. with radical
cystectomy or adjuvant therapy)." (Id. at 2.)
"The invention relates to determining expression levels of certain
markers associated with progression or death from bladder cancer. More
particularly, expression levels of markers MBNL2, F ABP4, UBE2C, and
BIRC5 have been associated with progression or death from bladder
cancer." (Id. at 3.)
Claims 14 and 15 are on appeal. Claim 14 is illustrative and reads as
follows:
14. A method of using a quantitative PCR ("QPCR") machine to determine
gene expression levels of the protective bladder cancer progression marker
MBNL2 to generate a record of the likelihood of an individual's bladder
cancer progression, said method comprising:
a. Using QPCR to assay, nucleic acids in a bladder cancer tumor
sample from an individual to obtain a MBNL2 Ct value representing
the gene expression level of the protective marker MBNL2;
b. Comparing said MBNL2 Ct value to a MBNL2 Ct value associated
with a control; and
c. Recording an increased likelihood of bladder cancer progression
for said individual if the comparison indicates decreased expression of
MBNL2 in the sample from said individual relative to expression of
MBNL2 in said control, or recording a decreased likelihood of
bladder cancer progression for said individual if the comparison
indicates increased expression of MBNL2 in the sample from said
individual relative to expression of MBNL2 in said control.
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The claims stand rejected as follows:
Claims 14 and 15 under 35 U.S.C. § 101 on the basis that they are
directed to a law of nature/natural principle (Ans. 2);
Claims 14 and 15 under 35 U.S.C. § 112, second paragraph, as
indefinite (Ans. 7);
Claims 14 and 15 under 35 U.S.C. § 112, first paragraph, for
nonenablement (Ans. 8); and
Claims 14 and 15 under 35 U.S.C. § 102(e) as anticipated by Mack2
(Ans. 15).
I
The Examiner has rejected both of the claims on appeal under 35
U.S.C. § 101 as being directed to patent-ineligible subject matter. The
Examiner finds that "claim(s) 14 and 15 are determined to be directed to a
law of nature/natural principle." (Ans. 2.) The Examiner reached this
conclusion by applying the test set out in Mayo Collaborative Services v.
Prometheus Laboratories, Inc., 132 S. Ct. 1289 (2012), as directed in a 2012
guidance memo. (Ans. 2-7.)
Appellants argue that the claims require the use of QPCR, which is an
additional element that is significantly more than the natural principle of
correlating MBNL2 gene expression levels with the likelihood of bladder
cancer progression. (Appeal Br. 10-11.) Appellants also argue that the
claims do not preempt the natural principle, because "[ n Jo one is foreclosed
from correlating gene expression with bladder cancer progression by other
2 US 2004/0076955 Al, published April 22, 2004.
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processes or means." (Id. at 11.) Finally, Appellants argue that "[i]t was not
known to compare MBNL2 Ct values obtained from a QPCR assay to
determine the likelihood of bladder cancer progression and then record it, as
in all the claims." (Id. at 12.)
We agree with the Examiner that, under the two-step test of Mayo, the
claims are not directed to patent-eligible subject matter. 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 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, 122 S. Ct. at 1295.
Claim 14 of the instant application is similar, in that it is directed to a
method of predicting whether a given patient's bladder cancer is or is not
likely to progress from an early, superficial stage to a muscle-invasive stage
by measuring the expression of the MBNL2 gene and comparing the result
to a control.
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 1296.
Similarly here, claim 14 on appeal sets forth a law of nature-namely,
a relationship between the level of expression of MBNL2 and the likelihood
that a bladder cancer will progress to a more invasive form. Under the first
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step of the Mayo test, claim 14 on appeal is directed to a law of nature or
natural phenomenon.
The Mayo Court next turned to the question "[ w ]hat else is there in
the claims before us?" Id. at 1297. 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 1298. 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. The Court concluded that "the steps are not sufficient to transform
unpatentable natural correlations into patentable applications of those
regularities." Id.
Like the steps of the claims in Mayo, the manipulative steps of claim
14 on appeal also "consist of well-understood, routine, conventional activity
already engaged in by the scientific community." Id. "Using QPCR" to
measure the expression level of a given gene is conventional, as shown by
Mack: "Often, amplification-based assays are performed to measure the
expression level of bladder cancer-associated sequences .... Methods of
quantitative amplification are well known to those of skill in the art." (Mack
ii 153.)
The step of comparing gene expression levels is also routine, as also
shown by Mack, which states that its "invention provides nucleic acid and
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protein sequences that are differentially expressed in bladder disease or
cancer relative to normal tissues." (Id. at i-f 104.) The final step of claim 14,
recording the result, simply preserves and informs others of the correlation.
Thus, when claim 14 is considered as an ordered combination, it
informs a relevant audience of certain laws of nature: specifically, that the
expression level of MBNL2 can be used to distinguish between bladder
cancer patients whose cancer is more likely or less likely to progress. All of
the additional steps of claim 14 consist of well-understood, routine,
conventional activity already engaged in by the scientific community such as
Mack.
We conclude that, under the Mayo test, claim 14 is directed to patent-
ineligible subject matter. The rejection of claim 14 under 35 U.S.C. § 101 is
affirmed. Claim 15 was not argued separately and therefore falls with claim
14. 37 C.F.R. § 41.37(c)(l)(iv).
II
The Examiner has rejected claims 14 and 15 as indefinite, for two
reasons. (Ans. 7-8.) First, the Examiner concludes that claim 14 "provides
for the 'using' of QPCR but since the claim does not set forth any steps
involved in the method/process of 'using' QPCR it is unclear what
method/process applicant is intending to encompass." (Id. at 7.)
Appellants argue that "[t]he claim actually provides using QPCR 'to
assay, nucleic acids in a bladder cancer tumor sample from an individual to
obtain a MBNL2 Ct value representing the gene expression level of the
protective marker MBNL2,' which clearly are active steps." (Appeal Br.
12-13.)
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On this point, we agree with Appellants. The Examiner has not
pointed to evidence showing that those skilled in the relevant art would not
understand what process is referred to as quantitative PCR (QPCR) and in
fact argues, in the context of the § 101 rejection, that QPCR is a routine,
conventional activity engaged in by the scientific community. (See Ans. 5.)
The Examiner notes that "the Mack et al reference discloses the use of
QPCR for performing differential gene expression analysis is routine and
conventional activity." (Id. at 6.) Thus, the evidence supports Appellants'
position that those skilled in the art would know the scope of a step of "using
QPCR" to determine the expression level of a particular gene.
The Examiner also rejected the claims as indefinite because "[i]t is
unclear what is required for the MBNL2 marker, to be considered 'the
protective bladder cancer progression marker MBNL2' or 'the protective
marker MBNL2' because the MBNL2 marker is a defined sequence and it is
not clear whether adjectives such as protective are meant to further limit the
structure of the MBNL2 marker sequence." (Ans. 7-8.)
Appellants argue that MBNL2 is defined in the Specification as a
preferred protective marker, as opposed to a harmful marker. (Appeal Br.
13.)
We will reverse this basis of the rejection as well. As Appellants
point out, the Specification expressly states that MBNL2 is a protective
marker and that increased expression of MBNL2 is associated with a
decreased likelihood of cancer progression. See Spec. 9 ("'Protective
markers' are indicator genes ... for which ... increased expression levels
correlate with non-progression."); id. at 11 ("preferred protective markers,
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for example MBNL2"). Thus, claim 14's reference to MBNL2 as a
protective marker simply recites the characterization of MBNL2 that is set
out in the Specification. It does not imply that a "protective marker
MBNL2" differs structurally from some other MBNL2 marker.
III
The Examiner has rejected both of the claims on appeal for
nonenablement. The Examiner finds that the claims are broad, in that they
only require assaying one marker gene. (Ans. 8.) The Examiner cites three
references as evidence that MBNL2 is actually associated with increased,
not decreased, likelihood of cancer progression. (Id. at 10-12 (citing Mack3,
Clarke,4 and Bignotti5).) The Examiner cites Sanchez-Carbayo6 as evidence
of unpredictability (id. at 12), and notes that the Specification does not
include a working example of the claimed method (id. at 13). The Examiner
concludes that a "skilled artisan could not make and use the claimed
invention from the disclosures in the application coupled with information
known in the art without undue experimentation." (Id. at 14.)
Appellants argue that they have provided evidence showing that the
correlation between MBNL2 expression levels and either progression or
non-progression of bladder cancer is statistically significant. (Appeal Br.
3 US 2004/0076955 Al published April 22, 2004.
4 US 2006/0019256 Al published January 26, 2006.
5 Bignotti et al., Gene expression profile of ovarian serous papillary
carcinomas: identification of metastasis-associated genes, 196 AM. J.
OBSTET. & GYNECOL. 245.e1-245.e11 (2007).
6 Sanchez-Carbayo, Use of High-Throughput DNA Microarrays to Identify
Bio markers for Bladder Cancer, 49 CLINICAL CHEM. 23-31 (2003).
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13-14.) Appellants also argue that the references cited by the Examiner as
evidence that MBNL2 expression is associated with increased likelihood of
progression are either unreliable or not on point. (Id. at 14--16.) Finally,
Appellants argue that the evidence does not show the claimed method to be
unpredictable, and that a "decreased expression level of MBNL2 has been
validated as a progression marker for bladder cancer." (Id. at 16.)
We agree with Appellants that the Examiner has not shown, by a
preponderance of the evidence, that undue experimentation would be
required to practice the claimed method.
[T]he PTO bears an initial burden of setting forth a reasonable
explanation as to why it believes that the scope of protection
provided by that claim is not adequately enabled by the
description of the invention provided in the specification of the
application; this includes, of course, providing sufficient reasons
for doubting any assertions in the specification as to the scope of
enablement.
In re Wright, 999 F.2d 1557, 1561---62 (Fed. Cir. 1993). "After evidence or
argument is submitted by the applicant in response, patentability is
determined on the totality of the record, by a preponderance of evidence
with due consideration to persuasiveness of argument." In re Oetiker, 977
F.2d 1443, 1445 (Fed. Cir. 1992).
In this case, the Examiner has cited several references as evidence that
practicing the claimed method would require undue experimentation because
(a) MBNL2 expression has been associated by others with an increased,
rather than decreased, likelihood of cancer progression, and (b) using gene
expression data for cancer prognosis was unpredictable at the time of the
invention. (Ans. 10-12.)
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In response, Appellants cite evidence that they submitted in
application 13/316,765, which was published as US 2012/0082994. (Appeal
Br. 14.) The evidence describes the methodology used to determine whether
increased expression of certain genes was correlated with increased or
decreased likelihood of bladder cancer progression, and shows that the
results indicated that MBNL2 was a "protective marker" that correlated with
non-progression. (Appeal Br. 19-22, Evidence Appendix.)
The Examiner cites Sanchez-Carbayo as evidence of the
unpredictability of using gene expression data in prognosis of bladder
cancer. (Ans. 12.) Sanchez-Carbayo, however, states that "[n]umerous
markers have been described to correlate to some extent with tumor stage
and prognosis of patients with bladder cancer." (Sanchez-Carbayo 23,
Background.) The Examiner has not explained how Sanchez-Carbayo
indicates unpredictability in using known biomarkers, such as MBNL2, in
the claimed method.
The Examiner also cites Mack, Clarke, and Bignotti as evidence that
others have found increased MBNL2 expression to be associated with an
increased, not decreased, likelihood of cancer progression. (Ans. 10-12.)
We conclude that, while the Examiner's evidence shows some
unpredictability, it is insufficient to outweigh the evidence submitted by
Appellants. Clarke addresses "gene expression profiles associated with solid
tumor stem cells." (Clarke, i-f 8.) Clarke also discloses "providing a
prognosis to [a] subject" based on "at least one stem cell cancer marker ...
from Table 8" (id. at i-f 11 ), but Table 8 does not include MBNL2 (or
MBLL39, which the Examiner states is synonymous (Ans. 11)).
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Bignotti lists MBNL2 as among the genes that are up-regulated at
least two-fold in metastatic, as compared to primary, OSPC. (Bignotti
245.e5.) However, "OSPC" is short for "ovarian serous papillary
carcinoma." (Id. at 245.el .) The Examiner has not provided evidence that a
gene that is overexpressed in metastatic ovarian carcinoma would be
expected to be predictive of cancer progression for bladder cancer.
Finally, the Examiner cites Mack as evidence that MBNL2 expression
shows a higher, not lower, likelihood of bladder cancer progression. (Ans.
10.) The Examiner points out that Mack includes MBNL27 in its list of
"Genes predictive of bladder cancer progression." (Id. at 10.)
Mack, unlike Bignotti and Clark, directly addresses the prognostic
value of MBNL2 in bladder cancer progression. Mack discloses that
increased expression of MBNL2 leads to the opposite prognosis than is
recited in the claims on appeal. However, the Examiner has not persuasively
explained why Mack's conclusion should be considered more likely to be
accurate than Appellants'.
As Appellants point out (Appeal Br. 15), Mack provides little detail in
how the genes that are up-regulated in tumors that later progressed were
identified. Appellants argue that the only relevant description is provided in
Mack's paragraph 347. (Id.) The Examiner does not point to any additional
disclosure regarding methodology in Mack. (See Ans. 10, 27.)
7 There is no dispute that MBNL2 is the same as the gene referred to by
Mack as PR02032. (Ans. 10 and Appeal Br. 16 (acknowledging that
Mack's Table 8A includes MBNL2).)
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Mack states that "[ m ]olecular profiles of various normal and
cancerous tissues were determined and analyzed using gene chips. RNA
was isolated and gene chip analysis was performed as described" in prior art
references. (Mack i-f 347.) As Appellants point out, "Mack et al. do not
describe how many patients were studied, how long the study extended,
when samples were taken, and there is no statistical analysis of the
correlation between up or down regulation and progression." (Appeal Br.
15.)
By contrast, Appellants' evidence (or the published application from
which it came), states that RNA ('994 publ., i-f 94) from 205 patients with
stage Ta or Tl bladder cancer (id. at i-f 91) was converted to cDNA (id. at
i-f 94) and analyzed by QPCR (id. at i-f 95). The '994 published application
also states that "[a ]nalysis of these results led to selection of markers of
interest, which appeared to have high or low expression levels that
correlated well with the clinical determinations of either progression
(including death from bladder cancer) or non-progression." (Id. at i-f 97 .)
Appellants' evidence states that sets of markers of interest were then
identified, and statistical analysis was carried out for each marker: "the
Pearson correlation coefficient ... was calculated" (id. at i-f 101) and "a
t-test, Wilcoxon signed rank test P<0.01, Kolmogorov-Smimov (KS) test,
P<0.01, and Chi-squared test, P<0.01, were run" (id. at i-f 102). Appellants'
evidence states that "the markers that performed the best in all or most of the
above criteria" were separated into groups based on whether higher
expression correlated with progression or non-progression. (Id. at i-f 104.)
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Appellants' evidence is specific to the expression of MBNL2 in
bladder cancer cells and its correlation with progression or non-progression
of the cancer. And Appellants provided a detailed explanation of how the
data were derived and the statistical methods that were used to correlate
changes in expression with progression or non-progression of the cancer.
We conclude that Appellants' evidence is entitled to greater weight than the
evidence cited by the Examiner.
The Examiner responded that Appellants' evidence "is not a study of
the MBNL2 and F ABP4 markers (i.e., called a two-gene signature) but is a
study of a twelve-gene signature, specifically the twelve marker genes listed
in Table 4 of the accompanying Evidence Appendix." (Ans. 26.)
Appellants' evidence, however, states that calculation of the Pearson
correlation coefficient and statistical analyses were performed "for each
marker." (Appeal Br. 19.) We therefore agree with Appellants (Reply Br.
4--5) that the Examiner's position is not consistent with the evidence
presented.
IV
The Examiner has rejected the claims on appeal as anticipated by
Mack. The Examiner finds that Mack discloses assessing the likelihood of
bladder cancer progression based on gene expression levels. (Ans. 15.) The
Examiner finds that Mack includes MBNL2 (which Mack calls PR02032) in
a table of genes predictive of bladder cancer. (Id. at 15-16.) The Examiner
concludes that the recording step and the specific interpretation of the gene
expression data do not change the active steps of claim 14, and are not
entitled to patentable weight. (Id. at 16.)
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Appellants contend that "the listing of MBNL2 in [Mack's] Table 8A
was based on such preliminary data that its mere listing there does not
indicate if it is or is not associated with bladder cancer progression."
(Appeal Br. 16.) Appellants also contend that "Mack et al. is not
anticipatory because if Mack et al. imply anything about MBNL2, it is that
MBNL2 is a harmful marker, and the claims are to the 'protective bladder
cancer progression marker MBNL2. "' (Id. at 17.)
We agree with the Examiner that the broadest reasonable
interpretation of claim 14 reads on Mack's disclosure. Mack discloses
"genes that are up- and down-regulated in bladder cancer cells." (Mack i-f 8.)
Mack states that "[t]he identification of sequences that are differentially
expressed in bladder cancer versus non-bladder cancer tissue allows the use
of this information in a number of ways." (Id. at i-f 103.) Mack states that its
invention relates to "the use of such expression profiles and compositions in
the diagnosis, prognosis, and therapy of bladder cancer." (Id. at i-f 2.) Mack
discloses that differential expression can be determined using quantitative
reverse transcriptase PCR. (Id. at i-f 208.)
Mack states that its "Table 8A shows about 1440 genes up regulated
in Ta or Ti [sic] bladder tumors from patients who later presented with
muscle-invasive bladder tumors (stage T2-T4)." (Id. at i-f 355.) Table 8A is
headed "Genes predictive of bladder cancer progression." (Id. at i-f 382)
Table 8A includes MBNL2. 8 (Id. at page 133, seventh entry.)
8 Mack refers to MBNL2 as "PR02032" but Appellants acknowledge that
Table 8A includes MBNL2. (Appeal Br. 16; cf Spec. 25, gene number
295.)
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Thus, Mack discloses using QPCR to determine MBNL2 expression
levels in bladder cancer cells and comparing them with expression in non-
bladder cancer cells to determine genes that are up- or down-regulated.
Mack discloses that MBNL2 is a gene that is useful in determining a
patient's prognosis because it is predictive of bladder cancer progression.
Mack does not expressly disclose recording a prognosis based on a
particular interpretation of MBNL2 gene expression data. However, as the
Examiner pointed out, an "informing" step does not distinguish a claimed
method from an otherwise anticipating prior art method. See In re Kao, 639
F.3d 1057 (Fed. Cir. 2011). One of the claims in Kao recited "providing
information" that the bioavailability of oxymorphone was increased in
subjects with renal impairment. Id. at 1064. The court held that "[t]hough
the correlation between the renal impairment and bioavailability was not
known, informing someone of the correlation cannot confer patentability
absent a functional relationship between the informing and administering
steps." Id. at 1072. The same is true here: absent a functional relationship
between the prognosis recited in claim 14 and some active step, recording a
particular prognosis does not confer patentability on the claimed method.
Mack also does not disclose the specific interpretation given to
MBNL2 expression levels that is recited in claim 14. That is, Mack
discloses that MBNL2 expression indicates increased likelihood of bladder
cancer progression, while claim 14 states that increased MBNL2 expression
indicates decreased likelihood of progression.
However, the interpretation of data is a purely mental step; whether a
user interprets data in a particular way does not change the actual steps of
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generating those data. See, e.g., In re Kao, discussed above: If a step of
informing someone of a specific prognosis does not confer patentability,
then neither does a step of interpreting data to determine the prognosis. That
is, even if Mack does not disclose the meaning ascribed to MBNL2
expression levels recited in claim 14, interpreting the meaning of an increase
or decrease in MBNL2 expression does not confer patentability absent a
functional relationship between the interpretation of the data and some
active step carried out as a consequence of the interpretation.
Thus, Appellants' argument that "'Mack et al. is not anticipatory
because if Mack et al. imply anything about MBNL2, it is that MBNL2 is a
harmful marker"' (Appeal Br. 17) does not persuade us that the claimed
method differs in any of its active steps from the method disclosed by Mack.
Claim 15 has not been argued separately and therefore falls with claim
14. 37 C.F.R. § 41.37(c)(l)(iv).
SUMMARY
We affirm the rejection of claims 14 and 15 under 35 U.S.C. § 101 as
being directed to patent-ineligible subject matter.
We affirm the rejection of claims 14 and 15 under 35 U.S.C. § 102(e)
as anticipated by Mack.
We reverse the rejection of claims 14 and 15 under 35 U.S.C. § 112,
second paragraph, as indefinite.
We reverse the rejection of claims 14 and 15 under 35 U.S.C. § 112,
first paragraph, for nonenablement.
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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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