Ex Parte Chettier et al

Patent Trial and Appeal Board

Aug 23, 2016

13364378 (P.T.A.B. Aug. 23, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/364,378 02/02/2012
52966 7590
Schramm-Personal-ACT
Michael R. Schramm
350 West
2000 South
Perry, UT 84302
08/25/2016
FIRST NAMED INVENTOR
Rakesh N. Chettier
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.
ABI-0038-1 8446
EXAMINER
KAPUSHOC, STEPHEN THOMAS
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
08/25/2016 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):
mikeschramm@besstek.net
mschramm@juneaubiosciences.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte RAKESH N. CHETTIER, LESA M. NELSON,
KENNETH WARD, JAMES W. OGILVIE, and
ROBERTO A. MACINA 1
Appeal2016-003639
Application 13/364,378
Technology Center 1600
Before ERIC B. GRIMES, ULRIKE W. JENKS, and TIMOTHY G.
MAJORS, 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 degenerative disc disease, which have been rejected on several
grounds: reciting an improper Markush group, indefiniteness, including
patent-ineligible subject matter, nonenablement, anticipation, and
obviousness. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm.
1 Appellants identify the Real Party in Interest as Michael R. Schramm.
(Appeal Br. 2.)
Appeal 2016-003639
Application 13/364,378
STATEMENT OF THE CASE
The Specification states that the "invention relates to degenerative
disc disease (DDD) prognosis, diagnosis and therapy. In particular, the
present invention relates to genetic markers such as specific single
nucleotide polymorphisms (SNPs) in the human genome, and their
association with DDD and related pathologies." (Spec. ,-i 2.) "Table 1 lists
133 SNPs associated with DDD." (Id. at ,-i 35.) The Specification states that
"SNP genotyping is useful for numerous practical applications," including
"determining therapeutic strategies based on an individual's genotype." (Id.
at,-i 144.)
Claims 68-87 are on appeal. Claims 68 and 69 are illustrative and
read as follows:
68. A method comprising applying at least one DDD condition
therapeutic to a patient based on at least one DDD altered risk associated
biological marker determined to be present in said patient.
69. The method of claim 68, wherein said DDD altered risk defines at
least one of an increased risk ofDDD existence or development of DDD and
a decreased risk ofDDD existence or development ofDDD, and wherein if
said altered risk defines said increased risk, said at least one biological
marker defines the minor allele of at least one marker disclosed in table 1
having an OR of greater than 1.0, and wherein if said altered risk defines
said decreased risk, said at least one biological marker defines the minor
allele of at least one marker disclosed in table 1 having an OR of less than
1.0.
The claims stand rejected as follows:
Claims 69-71, 76-78, and 82-84 under the nonstatutory doctrine of
improper Markush grouping;
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Claims 68-74, 77, 78, and 82-84 under 35 U.S.C. § 112, second
paragraph, as indefinite;
Claims 68-87 under 35 U.S.C. § 101 as directed to patent-ineligible
subject matter;
Claims 68-87 under 35 U.S.C. § 112, first paragraph, as nonenabled;
Claims 68, 72, 73, 75, 79, 81, and 85 under 35 U.S.C. § 102(b) as
anticipated by Seki;2 and
Claims 68, 72-75, 79-81, and 85-87 under 35 U.S.C. § 103(a) as
obvious based on Seki.
I
The Examiner has rejected claims 69-71, 76-78, and 82-84 on the
basis that they recite an improper Markush group. The Examiner reasons
that, according to MPEP § 803 .02, "[for] members of a proper Markush
group[] there should be (1) a common utility, and (2) a substantial structural
feature essential to that utility." (Final Rej. 3 5.) The Examiner finds that the
rejected claims do not meet this standard because "the various different
SNPs and combinations thereof, recited as 'at least one marker disclosed in
table l ', do not share any common structural element that is essential to the
asserted utility of being associated [with] DDD altered risk" because they
"are composed of different allelic nucleotides in distinct genetic contexts."
2 Seki et al., A functional SNP in CILP, encoding cartilage intermediate
layer protein, is associated with susceptibility to lumbar disc disease, 36
Nature Genetics 607-612 (2005).
3 Office Action mailed March 16, 2015.
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Application 13/364,378
(Id.) The Examiner concludes that "there does not appear to be any common
structure related to the function of the SNPs in the claims." (Id.)
We agree with the Examiner that the SNPs recited in claim 69 are an
improper Markush group. "A Markush claim contains an 'improper
Markush grouping' if: (1) The species of the Markush group do not share a
'single structural similarity,' or (2) the species do not share a common use."
Supplementary Examination Guidelines for Determining Compliance With
35 U.S.C. 112 and for Treatment of Related Issues in Patent Applications,
76 Fed. Reg. 7162, 7166 (2011).
Claim 69 depends from claim 68 and adds the limitation that the
"biological marker defines the minor allele of at least one marker disclosed
in table l." (Appeal Br. 24 (Claims App'x).) Claim 69 thus recites a
Markush group; specifically, the 133 allelic sequences shown in Table 1.
The sequences shown in Table 1 do not share any common sequence,
and therefore do not share a common structure. For example, the first two
sequences shown in Table 1 are ggtgattctgaagacc[A/G]ctgctatatgtcatct and
taaaggatgggaactg[ A/C]aactagaagaccgtca. (Spec. 57. 4) Although both
sequences, like all DNA sequences, are made up of the same four bases, they
do not share any significant similarity in the order in which those bases are
arranged. Thus, the structures of the DNA molecules represented by the
sequences are different. We therefore agree with the Examiner that the 133
DNA sequences shown in the Specification's Table 1 do not make up a
proper Markush group.
4 [A/G] and [A/CJ represent the polymorphic nucleotide, which can be either
of the indicated bases.
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Appellants argue that "every marker disclosed in the instant
application shares the SSS [single structural similarity] of have a single
nucleotide for nucleotide substitution disclosed in the respective nucleotide
sequence, and that it is the substitution that is essential to the association
with DDD." (Appeal Br. 4.)
This argument is not persuasive. The sequences shown in Table 1
share the property of being single nucleotide polymorphisms; i.e., sequences
that include a position where the specific base varies. That property,
however, is not a structural similarity that is shared by the sequences shown
in Table 1.
Appellants also argue that similar rejections for improper Markush
groups were made in two other applications and subsequently withdrawn.
(Appeal Br. 4-5.) What may have happened during prosecution of other
applications, however, has no bearing on whether the Examiner's rejection
in this case is merited.
Finally, Appellants argue that the Examiner erred in rejecting the
claims on the basis that they are found in different loci throughout the
genome. (Id. at 6-7.) This argument is also unpersuasive because the
Examiner correctly found that the sequences shown in the Specification's
Table 1 lack a common structural feature, as required for members of a
proper Markush group. (See Final Rej. 5.)
II
The Examiner has rejected claims 68-74, 77, 78, and 82-84 under 35
U.S.C. § 112, second paragraph, as indefinite, for three reasons. First, the
Examiner concludes that the recitation in claim 68 of applying a therapeutic
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Application 13/364,378
"based on" a biological marker being present is indefinite, because "[i]t is
unclear what relationship is required for any application of a therapy to be
'based' on a present biological marker. It is not clear if the claim is
requiring some sort of mental correlation between the presence of a marker
and the need for a therapy." (Final Rej. 7.)
Appellants argue that the "phrase 'based on' merely conveys a
motivation or reason for performing the prescribed (singular) therapeutic
application step of claim 68." (Appeal Br. 7.) That is, "Claim 68 is a single
step (i.e. as opposed to a multi-step) method that requires application of a
DDD condition therapeutic to a patient determined to have a DDD altered
risk associated biological marker in the patient - nothing more and nothing
less." (Id. at 9.) Appellants argue that the "claim does not impose any
mental correlation between the marker and the therapeutic or a need for a
therapeutic." (Id. at 8.)
We agree with Appellants that claim 68 recites a single active step:
applying a therapeutic for a DDD condition to a patient who has a "DDD
altered risk biological marker." Although claim 68 also recites that the DDD
marker is "determined to be present in said patient," the claim does not
recite any step of actually determining the presence of the marker, and thus
the recitation that the applying step is "based on" a marker that is present
merely represents an intended motivation or reason for carrying out the
"applying" step. Cf KSR Int'! Co. v. Teleflex Inc., 550 U.S. 398, 419 (2007)
("In determining whether the subject matter of a patent claim is obvious,
neither the particular motivation nor the avowed purpose of the patentee
controls."); Pitney Bowes Inc. v. Hewlett Packard Co., 182 F.3d 1298, 1305
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(Fed. Cir. 1999) (Preamble language that merely states "the purpose or
intended use of the invention ... is of no significance to claim
construction."). Thus, the claim's statement that the "applying" is "based
on" a "DDD altered risk associated biological marker determined to be
present" requires only that the patient being treated has a biological (e.g.,
genetic) marker that indicates an altered risk of DD D.
The Examiner also concluded that some of the claims "are unclear
over recitation of the phrase "the minor allele of at least one marker
disclosed in table l." (Final Rej. 9.) "The phrase is unclear because table 1
does not appear to specifically indicate that any particular allele of each
listed SNP is 'the minor allele."' (Id.)
Appellants argue that "the heading supplied in table 1 of 'MA' stands
for 'Minor Allele."' (Appeal Br. 9.) Appellants also argue that "supplying
table 1 with the minor allele (MA) data in the instant CIP application was in
direct response to the rejection for lack of identifying the minor allele (MA)
data in the application of which the instant application is a continuation-in-
part of." (Id.)
We agree with Appellants that the Specification adequately shows that
a skilled artisan would understand the "MA" heading in table 1 to mean
"minor allele." In discussing how the data of table 1 were determined, the
Specification states that "SNPs with a Minor Allele Frequency (MAF) <3%
in cases and/or controls and P <0.001 for deviations from Hardy-Weinberg
equilibrium (HWE) in cases as well as in controls were eliminated." (Spec.
,-i 196, emphasis added.) Since "MAP" is used as an abbreviation for "Minor
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Allele Frequency," a skilled worker would understand that the "MA"
heading in table 1 stands for "Minor Allele."
Finally, the Examiner states that certain claims "are rejected over
recitation of the phrase 'table l."' (Final Rej. 10.) The Examiner cites to a
portion of the MPEP stating that reference to a figure or table is discouraged,
and the Examiner states that Appellants "may recite SEQ ID NOs: 1-133
instead of making reference to 'table 1. "' (Id.)
Appellants argue that "the rejection [is] form over substance." (Reply
Br. 15.)
We agree with Appellants that the Examiner has not shown that any
indefiniteness results from the claims' reference to "table l." The
Examiner's suggestion to substitute reference to SEQ ID NOs 1-133 shows
that the Examiner understands the scope of the claims, and the Examiner has
not shown that a person of ordinary skill in the art would not also understand
what is encompassed by the rejected claims.
III
The Examiner has rejected claims 68-87 under 35 U.S.C. § 101 as
being directed to patent-ineligible subject matter. The Examiner finds that,
under the test set out in Mayo Collaborative Services v. Prometheus
Laboratories, Inc., 132 S. Ct. 1289 (2012), the claims do not recite anything
significantly different from the natural principle of "DDD risk deduced from
the determination of biological markers in a subject." (Final Rej. 13.) The
Examiner reasons that "[ w ]hile the claims include a step of applying a
therapeutic, the step is set forth at a high level of generality" and "a
treatment step is a conventional step for any subject diagnose[ d] with a
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disease or predisposition thereto; and so the addition of such a general
treatment step does not serve to transform the claims into patent eligible
subject matter." (Id.)
We agree with the Examiner that claim 68 is directed to a patent-
ineligible method. In Mayo, the Court considered a claimed method that
required administering a drug to a subject, determining the level of a
metabolite of the drug in the subject, and using certain thresholds of
metabolite level to indicate a need to increase or decrease dosage of the
drug. Id. at 1295.
The Court noted that the claims "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. The Court held that the dispositive question was:
"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?" Id. at 1297.
The Court held that the claim's "administering" step, "determining"
step, and "wherein" clauses did not transform the claim into a patentable
application of a natural law, id. at 1297-98: "The 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.
The Court's analysis in Mayo is directly applicable to claim 68, which
requires applying a DDD therapeutic to a patient having a biological marker
that indicates altered risk of DDD. Applying a therapeutic such as surgery
to a patient having a biological marker indicating susceptibility to DDD was
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a conventional activity engaged in by those in the relevant field, as
demonstrated by Seki, which is discussed in detail below. Thus, the addition
of this conventional step to the natural phenomenon or law of nature (a
genetic marker associated with altered DDD risk) does not "transform
unpatentable natural correlations into patentable applications of those
regularities." Mayo, 132 S. Ct at 1298.
Just as in Mayo, claim 68 informs a relevant audience of a law of
nature (specifically, a correlation between certain genetic markers and
altered DDD risk) and "any additional steps consist of well-understood,
routine, conventional activity already engaged in by the scientific
community." Id. Thus, claim 68 is directed to a patent-ineligible natural
phenomenon or law of nature.
Appellants argue that "it may be that the correlation of a particular
marker and a disease is a natural phenomenon judicial exception," but
"appellants are merely claiming the application of a treatment to a patient
group who happen to have in their bodies a particular genetic sequence(s)."
(Appeal Br. 13.)
This argument is unpersuasive. Claim 68 includes treatment of a
DDD patient using any conventional therapeutic, just as the claim at issue in
Mayo included a standard treatment for autoimmune diseases. Mayo, 132 S.
Ct. at 1294-95. The claimed method in Mayo increased or decreased the
amount of drug administered according to the level of a metabolite in a
patient's blood, id. at 1295, and therefore could be characterized as a method
of applying a treatment (higher or lower drug administration) to a group of
patients who had a particular level of metabolite in their body. The Mayo
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Court nonetheless concluded that the claim was patent-ineligible, because it
added nothing more than "well-understood, routine, conventional activity
already engaged in by the scientific community." Id. at 1298. The same is
true of the step of applying a DDD therapeutic that is recited in claim 68.
Appellants also argue that the claims pass muster under the USPTO's
2014 Interim Eligibility Guidelines. (Appeal Br. 13-16.) However, as
Appellants themselves acknowledge, the Guidelines "are not law." (Id. at
13.) The Supreme Court's interpretation of§ 101, on the other hand, is
controlling case law, and under the standard set out in Mayo, claim 68 is not
a patent-eligible method.
Finally, Appellants cite two Supreme Court cases from the 1800s as
bases for concluding that claim 68 is patentable. (Appeal Br. 16-18.) The
Court's most recent precedent, however, controls and is clearly applicable to
the rejected claims here. Appellants make no attempt to distinguish the facts
of this case from those of Mayo.
Therefore, we affirm the rejection of claim 68 under 35 U.S.C. § 101.
Claims 69-87 fall with claim 68 because they were not argued separately.
37 C.F.R. § 41.37(c)(l)(iv).
IV
The Examiner has rejected claims 68-87 as nonenabled. The
Examiner concludes that "neither the prior art nor the instant specification is
enabling for the claimed methods that generically encompass any markers
with the required functionality of being associated with altered DDD risk."
(Final Rej. 17-18.) The Examiner finds that
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In so far as some of the claims require the elected SNPs of SEQ
ID NO: 1-133 ... the specification does not provide the skilled
artisan with the information regarding which allele of any of the
required biallelic SNPs is asserted to be either a high-risk allele
or protective allele.
(Id. at 18.)
The Examiner concludes that "an undue amount of experimentation
would be required to make and use the invention as claimed. The
specification does not provide the information required for the skilled artisan
to assess DDD risk based on analysis of genetic markers as required by the
rejected claims." (Id. at 22.)
Appellants argue that they "have specifically disclosed a full 133
markers (i.e. the minor allele of SEQ ID NOs: 1-133), each one of which as
having an altered risk association with DDD for the population disclosed."
(Appeal Br. 19.) Appellants also argue that the Specification's Table 1
provides the minor allele (MA) and odds ratio (OR) for the disclosed
markers, and a skilled artisan would interpret the table to mean that if the
OR is greater than 1, the minor allele indicates a higher risk ofDDD, and if
the OR is less than 1, the minor allele indicates a lower risk of DDD. (Id. at
19-20.)
We agree with Appellants that the Examiner has not shown that the
Specification is nonenabling with respect to the specific SNPs disclosed in
Table 1. The Examiner stated that the Specification does not indicate which
allele at each position is associated with increased or decreased risk of DDD
but, as indicated by (for example) dependent claim 69, the data in the table
indicate an increased risk of DDD when the OR is greater than 1.0, and a
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decreased risk ofDDD when the OR is less than 1.0. We therefore reverse
the rejection of claims 69-71, 7 6-78, and 82-84 based on nonenablement.
However, we agree with the Examiner that undue experimentation
would be required to practice the full scope of claim 68, which encompasses
treatment of a patient with any biological marker that is associated with an
altered risk of DDD. The Specification states that"[ c Jase samples and
controls were collected from the same geographical region, were principally
Caucasian and generally of Northern and Western European descent."
(Spec. 54:8-10.) "[A]bout 96 DNA samples from DDD patients and 1504
controls were genotyped using the Affymetrix GeneChip 6.0 SNP
microarray system." (Id. at 54: 12-13.) "This single array interrogates
906600 SNPs." (Id. at 55: 1.) After certain SNPs were excluded,
"approximately 492,892 SNPs were available for analysis." (Id. at 55:26-
27.) "Of the SNPs tested, 133 SNPs were determined to be associated with
the disease (see Table 001)." (Id. at 56:3--4.) The Specification thus
describes 133 SNPs associated with DDD, principally in Caucasians of
Northern and Western European descent, which are shown in Table 1.
However, the Specification does not purport to describe all of the
SNPs associated with DDD, or provide an enabled method to discover SNPs
other than those specifically described, that are associated with either an
increased or decreased risk of DDD. The Specification does not, for
example, provide a reasonable basis for concluding that the disclosed 133
SNPs associated with DDD are common to demographic groups other than
Northern and Western European Caucasians, or that the disclosed SNPs are
the only ones that would be associated with DDD in Northern and Western
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European Caucasians, even if a method other than the Affymetrix GeneChip
6.0 SNP microarray system was used.
In short, the Specification provides a number of specific SNPs that
were found to be associated with increased or decreased risk of DDD, but it
does not provide adequate guidance to discover all such SNPs, as required to
enable a skilled worker to practice the method of claim 68 without undue
experimentation. Like claim 68, claims 72-75, 79-81, and 85-87
encompass treatment of a patient with any DDD-associated biological
marker, and are nonenabled for the same reasons discussed above.
v
The Examiner has rejected claims 68, 72, 73, 75, 79, 81, and 85 as
anticipated by Seki. The Examiner finds that Seki "teaches determining that
biological markers associated with altered risk of lumbar disc disease
(LDD), which is a degenerative disc disease (DDD), are present in subjects."
(Final Rej. 24.) The Examiner also finds that Seki "also teaches that the
subjects were treated with at least one DDD condition therapeutic," and
therefore anticipates claim 68. (Id.) We agree with the Examiner's findings.
Appellants argue that the rejection for anticipation contradicts the
rejection for nonenablement. (Appeal Br. 20.) We disagree. A prior art
reference that enables a single embodiment within the scope of a claim
anticipates that claim, even if the same embodiment would not enable the
full scope of the later-claimed invention. Cf In re Lukach, 442 F.2d 967,
97 0 ( CCP A 1971) (" [T]he description of a single embodiment of broadly
described subject matter constitutes a description of the invention for
anticipation purposes ... , whereas the same information in a specification
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might not alone be enough to provide a description of that invention for
purposes of adequate disclosure."). The rejections are not contradictory.
Appellants also argue that Seki "does not identify a single DDD
associated marker" or indicate which allele is associated with either an
increased or decreased risk ofLDD. (Appeal Br. 21.)
This argument is also unpersuasive. Seki discloses "a functional SNP
(1184T~c, resulting in the amino in the acid substitution I395T) in CILP,
which encodes the cartilage intermediate layer protein, that acts as a
modulator of LDD susceptibility." (Seki 607, abstract.) Seki also refers to
the "susceptibility-associated l l 84C allele." (Id.) A person of ordinary skill
in the art would understand Seki' s description to indicate that the single
nucleotide polymorphism (SNP) in which C (cytosine) is present at position
1184 of the CILP gene is associated with an increased risk of (susceptibility
to) lumbar disc disease.
Finally, Appellants argue that Seki's subjects were selected "based on
such cases having already had at least one DDD condition therapeutic (e.g.
disc surgery) administered to them." (Appeal Br. 22.) Appellants argue that
"Seki couldn't have taught treating patients based on the knowledge of DDD
markers being in the patient's DNA," because their genetic markers had not
been tested when the LDD therapeutic was administered to them. (Id.)
This argument is also unpersuasive. As discussed above in regard to
claim definiteness, and as argued by Appellants, claim 68 requires only a
single active step of applying a DDD condition therapeutic to a patient
having a biological marker that indicates altered risk of DDD. Seki's
subjects had therapy for LDD. (Seki 610, right col.) LDD is a form of
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DDD. (Spec. 2:19-21.) Seki discloses that the l 184T~c in the CILP gene
was associated with susceptibility to LDD, which would be understood to
mean that at least some of the subjects who were treated for LDD had a
biological marker indicating an altered risk of DDD. Seki therefore
discloses a method meeting the limitations of claim 68.
Claims 72, 73, 75, 79, 81, and 85 were not argued separately and
therefore fall with claim 68. 37 C.F.R. § 41.37(c)(l)(iv).
VI
The Examiner has rejected claims 68, 72-75, 79-81, and 85-87 as
obvious based on Seki. (Final Rej. 27.) As discussed above, we agree with
the Examiner that Seki anticipates claim 68, which is therefore also
unpatentable under 35 U.S.C. § 103. See In re McDaniel, 293 F.3d 1379,
1385 (Fed. Cir. 2002) ("It is well settled that 'anticipation is the epitome of
obviousness."').
Appellants reprise their arguments from the anticipation rejection (see
Appeal Br. 22-23) but, for the reasons discussed above, those arguments are
unpersuasive. Claims 72-75, 79-81, and 85-87 fall with claim 68 because
they were not argued separately.
SUMMARY
We affirm the rejection of claims 69-71, 76-78, and 82-84 based on
the doctrine of improper Markush grouping.
We reverse the rejection of claims 68-74, 77, 78, and 82-84 under 35
U.S.C. § 112, second paragraph.
We affirm the rejection of claims 68-87 under 35 U.S.C. § 101.
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We affirm the rejection of claims 68, 72-75, 79-81, and 85-87 under
35 U.S.C. § 112, first paragraph, but reverse the rejection as applied to
claims 69-71, 76-78, and 82-84.
We affirm the rejection of claims 68, 72, 73, 75, 79, 81, and 85 under
35 U.S.C. § 102(b).
We affirm the rejection of claims 68, 72-75, 79-81, and 85-87 under
35 U.S.C. § 103(a).
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. § l.136(a).
AFFIRMED
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