Ex Parte GELFAND et al

Patent Trial and Appeal Board

Aug 2, 2018

12421188 (P.T.A.B. Aug. 2, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
12/421, 188 04/09/2009 DAVID H GELFAND
41504 7590 08/06/2018
ROCHE I KILPATRICK TOWNSEND & STOCKTON LLP
Mailstop: IP Docketing - 22
1100 Peachtree Street
Suite 2800
Atlanta, GA 30309
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
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ATTORNEY DOCKET NO. CONFIRMATION NO.
88883-761270 (007810US) 3964
EXAMINER
SISSON, BRADLEY L
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
08/06/2018 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):
ipefiling@kilpatricktownsend.com
pair_roche@firsttofile.com
KTSDocketing2@kilpatrick.foundationip.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte DAVID H GELFAND, IVO GL YNNE GUT,
KEITH A. BAUER, and FLORENCE MAUGER 1
Appeal2017-001917
Application 12/421,188
Technology Center 1600
Before ERIC B. GRIMES, JOHN G. NEW, and TIMOTHY G. MAJORS,
Administrative Patent Judges.
NEW, Administrative Patent Judge.
DECISION ON APPEAL
SUMMARY
Appellants file this appeal under 35 U.S.C. § 134(a) from the
Examiner's Final Rejection of claims 1-3, 5, 7, 9, 11, 12, 14, 15, 53, and 54
1 Appellants identify Roche Molecular Systems, Inc. and CEA/Institut de
Genomique - Centre National de Genotypage of Batiment G2 as the real
parties-in-interest. App. Br. 3.
Appeal2017-001917
Application 12/421, 188
as unpatentable under 35 U.S.C. § 112, first paragraph, for lack of
enablement.
The claims also stand rejected as unpatentable under 35 U.S.C. § 101
because the claimed invention is not supported by either a specific,
substantial, and credibly-asserted utility or a well-established utility and
under 35 U.S.C. § 112, first paragraph, as lacking enablement. 2
We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.
NATURE OF THE CLAIMED INVENTION
Appellants' invention is directed to polynucleotides comprising 5'-
tails with sequence segments useful for the detection of target nucleic acid
sequences, and methods for their use in detecting target nucleic acids.
Abstract.
REPRESENTATIVE CLAIM
Claim 1 is representative of the claims on appeal and recites:
1. A method of determining if a sample contains a
target nucleic acid, the method comprising:
(a) contacting the sample with a primer polynucleotide, a
nucleotide set and a polymerase to generate an amplification
mixture, wherein;
(i) the primer polynucleotide comprises a 5' portion
and a 3' portion, the 5' portion comprising two or more
contiguous sequence segments, wherein each sequence
segment comprises at least three nucleotide bases, and the
5'-end nucleotide base of each sequence segment is unique
2 The Examiner also rejected the claims under 35 U.S.C. § 101 as
inoperable. Final Act. 12. The Examiner has withdrawn this rejection.
Ans. 2.
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Application 12/421, 188
within one sequence segment and is the same in each
sequence segment;;
(ii) the nucleotide set comprises four different types
of nucleotide bases, wherein three nucleotide bases are
only in the form of deoxyribonucleotides ( dNTPs ), and the
majority of bases of a fourth type is in the form of a
ribonucleotide (rNTP), wherein the base of the
ribonucleotide is complementary to the unique 5'
nucleotide base of each sequence segment of the primer
polynucleotide; and
(iii) the polymerase comprises deoxyribonucleotide
and ribonucleotide incorporating activities;
(b) submitting the amplification mixture to specific
amplification conditions to produce an amplicon, if the target
nucleic acid is present, said amplicon comprising two or more
contiguous amplicon segments complementary to the two or
more contiguous sequence segments in the 5'-portion of the
primer polynucleotide, and comprising the rNTP incorporated as
the 3 '-end nucleotide base of each amplicon segment;
( c) following said submitting, subjecting the amplification
mixture to an alkaline solution not sufficient to degrade DNA but
sufficient to cleave the amplicon, if generated, at the site of the
incorporated rNTP, thereby generating a fragment consisting of
the amplicon segment; and
( d) detecting a mass of the fragment, if generated, by mass
spectrometry wherein the detected mass indicates amplification
of the target nucleic acid sequence, thereby determining if the
sample contains the target nucleic acid sequence.
App. Br. 16.
ISSUES AND ANALYSES
We decline to adopt the Examiner's findings of fact and conclusions
that the appealed claims are non-enabled or lack utility. We address the
arguments raised by Appellants below.
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Application 12/421, 188
A. Rejection under 35 U.S.C. § 112, first paragraph
Issue
Appellants argue that the Examiner erred in concluding that it would
have taken undue experimentation by a person of ordinary skill in the art to
perform the full scope of the claimed invention and, specifically, to
determine if a sample contains a "target nucleic acid." App. Br. 7.
Analysis
The Examiner has construed Appellants' claimed invention as
encompassing the simultaneous detection of an infinite number of different
target nucleic acids in a common solution. Final Act. 5 ( citing Spec. ,r 51 ).
The Examiner finds that Appellants' claims encompass the determination of
the mass of any conceivable "target nucleic acid," regardless of source, type
of sample, or concentration. Id. at 5-6 ( citing Spec. ,r 39).
The Examiner finds that, given the very large variety of sources of
nucleic acids, the quantity of experimentation necessary to enable the full
scope of the claimed invention is great, on the order of many man-years, and
even then with little if any reasonable expectation of successfully enabling
the full scope of the claims. Final Act. 8. In support of this finding, the
Examiner notes that the claimed method requires the pairing of primers with
a template. Id. The Examiner finds that, in order to select the appropriate
probe/primers, which are deemed to be essential, one must have knowledge
of the nucleotide sequence of the template: absent knowledge of the
nucleotide sequence of the template, selection of the correct primer is highly
unpredictable. Id.
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Application 12/421, 188
The Examiner further finds, by way of example, that, because the
nucleotide sequence for the genome of any given species of bacteria is
highly unpredictable, for a person of ordinary skill to practice the full scope
of the invention, one would have to first determine the nucleotide sequence
for each and every organism before one would be able to select appropriate
probe and/or primer sequences that are essential to the claimed invention.
Final Act. 8.
The Examiner therefore concludes that, in view of the breadth of
scope of the claims, the limited guidance provided, the unpredictable nature
of the art to which the claimed invention is directed, and in the absence of
convincing evidence to the contrary, the claims are not enabled by the
disclosures of Appellants' Specification. Final Act. 12.
Appellants argue first that claims that read on some inoperable
embodiments are not necessarily invalid for lack of enablement. App. Br. 7
(citing, e.g., ln re Angstadt, 537 F.2d 498, 502-503 (C.C.P.A. 1976).
According to Appellants, their claimed invention is directed to a specific
method of detecting a target nucleic acid using an allegedly novel and
nonobvious method. Id. at 8. Appellants point out that the Examiner does
not appear to question the fact that there was, at the time of filing, a very
large number of known target nucleic acids that could have been readily
used in the claimed method. Id. Instead, argue Appellants, the Examiner
finds that even though many target nucleic acids were known, a large
number of target nucleic acids were not known and that it would have taken
an undue amount of experimentation to determine them. Id.
Appellants assert that their claimed method of detecting target nucleic
acids could have been applied the day the application was filed in view of
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Application 12/421, 188
the very large database of sequences available, for example in Genbank, as
of April, 2009. App. Br. 8. Appellants further contend that the claimed
method could have been readily applied to such sequences without undue
experimentation. Id. Appellants point out that, as of the date of filing,
approximately 500 complete genomes had been sequenced. Id. at 8-9
(citing http://sulab.org/ 2013 / 06/ sequenced-genomes-per-year/ (last visited
July 26, 2018) ). Furthermore, Appellants argue, this evidence submitted to
the Examiner represents only complete genomes sequenced; many other
gene sequences were available from partially sequenced genomes at the time
of filing. Id. at 9. Furthermore, Appellants add, many gene sequences of
interest, even in genomes not yet completely sequenced, are related to
similar sequences in known genomes. Id. Therefore, Appellants contend,
not only could those of ordinary skill in the art have applied the claimed
method to the numerous nucleic acid sequences known at the time, but with
little or no experimentation, related gene sequences could have been
determined and detected according to the claimed methods. Id.
Appellants therefore assert that for the currently claimed invention, a
person of ordinary skill in the art could have readily identified what
sequences were known in the art (e.g., by searching Genbank) and could
have readily performed simple PCR experiments to test whether primers
based on known sequences would amplify target sequences if desired from
organisms that had not been sequenced. App. Br. 10. Thus, to the extent the
claims read on inoperative embodiments, one of ordinary skill in the art
could have readily determined which embodiments were inoperative. Id.
We agree with Appellants. The Examiner concludes that, because the
claims recite a general method of identifying nucleic acid target sequences,
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and because the number of possible nucleic acid target sequences in all of
nature is astronomically large and that the majority of potential target
sequences in nature are, as of yet, unknown, then the claims are not enabled.
Specifically, the Examiner concludes that it would take an undue amount of
experimentation to determine the possible target sequences of all nucleic
acid sequences in all extant species in nature, and therefore the claims are
not enabled.
We do not think this is a reasonable approach. We agree with
Appellants' evidence-supported argument that, as of the time of filing, the
nucleic acid sequences of many important genes, and even whole genomes
were well known and readily accessible in the art. The number of known
target sequences has only grown since that time. We further agree with
Appellants that, having identified a target nucleic acid sequence of interest, a
person of ordinary skill in the art would have been able to apply the claimed
method to identify the presence of that target nucleic acid sequence without
undue experimentation. Certainly, the Examiner has made no finding of fact
that a person of ordinary skill, having identified a target nucleic acid
sequence of interest, would have been unable to apply Appellants' claimed
method to detect it without undue experimentation.
Appellants' Specification discloses several Examples employing the
claimed methods, and the Examiner makes no finding of fact that these
Examples are not enabling of the claims. Furthermore, given the highly
conservative structure of nucleic acids in nature, i.e., four deoxyribose- or
ribose-based nucleotides arranged in a helical structure, the Examiner has
made no finding of fact supporting the contention that Appellants' claimed
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method would not be enabled for any possible nucleic acid target sequence
determined by a person of ordinary skill in the art.
Both the Examiner and Appellants point to Promega Corp. v. Life
Technologies Corp., 773 F.3d 1338 (Fed. Cir. 2014) (rev'd on other grounds
in Life Technologies Corp. v. Promega Corp., 137 S.Ct. 734 (2017). The
Examiner points to our reviewing court's finding in Promega that:
[T]he claims at issue here similarly cover potentially thousands
of undisclosed embodiments in an unpredictable field. And
similar to Wyeth, the specification of the Promega patents
provides only a starting point. ... As the extensive evidence here
demonstrates, undue experimentation would have been required
in order to enable the full scope of coverage sought by Promega-
the successful co-amplification of potentially thousands of
unrecited STR loci combinations.
Ans. 11-12 (quoting Promega, 773 F.3d at 1347). However, we are not
persuaded that the Examiner's reliance upon Promega is apposite in this
instance. In Pro mega, the language of the claims at issue was construed in
such a manner as to include a possibly infinite number of short tandem
repeat ("STR") loci in a co-amplification method in which it was admitted
by both parties that the addition of each additional locus added a layer of
undue complexity and uncertainty in an unpredictable art. Promega, 773
F.3d at 1347. Because the claim language employing the claim term
"comprising" admitted of the possibility of multiple, unnamed, additional
loci, adding a degree of uncertainty such that it would require an undue
amount of experimentation to practice the claim, the Federal Circuit held
that the claims were not enabled. Id. at 1350.
Appellants' claims, however, are directed to a method of determining
whether a sample contains a target nucleic acid sequence. Unlike the case in
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Promega, the claimed method does not require the co-amplification of
multiple loci, rather the steps of claim 1 are directed to a method of
amplifying a single target sequence. It is true, as the Examiner finds, that
Appellants' Specification discloses that potentially large numbers of sites
can be co-amplified by this method. See, e.g., Spec. ,r 84. But such co-
amplification is not required by claim 1, and
[ e ]ven if some of the claimed combinations were inoperative,
the claims are not necessarily invalid. 'It is not a function of
the claims to specifically exclude * * * possible inoperative
substances * * * *' .... Of course, if the number of inoperative
combinations becomes significant, and in effect forces one of
ordinary skill in the art to experiment unduly in order to
practice the claimed invention, the claims might indeed be
invalid.
Atlas Powder Co. v. E.I. Du Pont De Nemours & Co., 750 F.2d 1569, 1576
(Fed. Cir. 1984) ( citations omitted).
Consequently, because we conclude that a person of ordinary skill in
the art could have practiced Appellants' claimed invention, as supported by
the disclosures of the Specification, to identify a target nucleic acid sequence
without undue experimentation, we reverse the Examiner's rejection of the
claims.
B. Rejection under 35 U.S.C. § 101 as lacking utility and 35 U.S.C.
§ 112, first paragraph, as lacking enablement
Issue
Appellants argue the Examiner erred in finding that the claims are not
supported by a specific, substantial, and credible asserted utility, or a well-
established utility. App. Br. 11.
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Analysis
The Examiner repeats the finding that the claimed method is
construed as encompassing the determination of mass of any conceivable
"target nucleic acid," regardless of source, type of sample, or concentration.
Final Act. 18. The Examiner notes that the claims do not require that the
nucleic acid to ultimately be detected and the mass thereof be determined
even be known at the time of filing, much less require that it be useful under
Section 101. Id. at 19. The Examiner points to MPEP § 2107.01 B(C),
which states that "[a] method of assaying for or identifying a material that
itself has no specific and/or substantial utility" is not considered to have a
substantial utility. Id. The Examiner finds that, although nucleic acids that
satisfy the utility requirements of 3 5 USC § 101, were known at the time of
filing, such narrowing limitations have not been read into the claims. Id.
(citing MPEP § 2111.01). The Examiner urges Appellants to consider
amending the claims such that the claims are drawn to those nucleic acids
that unquestionably do have utility under 35 USC§ 101 and which are
adequately supported by Appellants' Specification. Id.
Finally, because the Examiner concludes that the claimed invention is
not supported by either a specific, substantial, and credible asserted utility,
or a well-established utility, a person of ordinary skill in the art clearly
would not know how to use the claimed invention, and therefore rejects the
claims as lacking enablement under 35 U.S.C. § 112, first paragraph.
Appellants argue that their claims on appeal have a specific and
substantial utility. App. Br. 11. Appellants point to their Specification,
which discloses that: "The present invention relates to the field of nucleic
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acid detection." Id. (quoting Spec. ,r 2). Appellants assert that nucleic acid
detection has numerous uses including diagnostic uses and research uses. Id.
at 11-12. Therefore, Appellants argue, their claimed invention has a
specific utility. Id. at 12.
Furthermore, Appellants contend, the claimed invention was useful to
the public as of the filing date. App. Br. 12. Appellants point to Example 1
of the Specification, which illustrates use of the claimed method for SNP
genotyping. Id. ( citing Spec. ,r,r 101-105). Appellants argue that the
claimed invention is akin to the "research tools such as gas chromatographs,
screening assays, and nucleotide sequencing techniques" cited in MPEP
§ 2107.01 ( c) in that the method can be applied as a research tool. Id.
Appellants contend that such research tools have "unquestionable utility
( e.g., they are useful in analyzing compounds)" and therefore have a specific
and substantial utility. Id.
We agree with Appellants. "Many research tools such as gas
chromatographs, screening assays, and nucleotide sequencing techniques
have a clear, specific and unquestionable utility ( e.g., they are useful in
analyzing compounds)." MPEP §2107.0lC. Appellants' claims are directed
to "A method of determining if a sample contains a target nucleic acid" by
contacting the sample with a primer polynucleotide, a nucleotide set and a
polymerase to generate an amplification mixture, producing an amplicon,
cleaving the amplicon from the incorporated rNTP, and detecting a mass of
the fragment by mass spectrometry. This is a means of detecting the
presence of specific nucleic acid target sequences and, as such, has an
undoubted utility. We acknowledge the Examiner's point that the MPEP
states that: "A method of assaying for or identifying a material that itself has
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no specific and/or substantial utility" and that requires carrying out further
research to identify or reasonably confirm a "real world" context of use does
not define a "substantial utility," but we reject the Examiner's reasoning,
contrary to the Examples in Appellants' Specification, that identifying the
presence of target nucleic acid sequences is a method for assaying "a
material that itself has no specific and/or substantial utility." Examples of
the utility of identifying the presence of a targeted nucleic acid sequence,
e.g., in diagnostic, forensic, and research instances, are so numerous as to be
commonplace. We consequently reverse the Examiner's rejection upon this
ground.
DECISION
TheExaminer'srejectionofclaims 1-3, 5, 7, 9, 11, 12, 14, 15, 53,
and 54 as unpatentable under 35 U.S.C. § 112, first paragraph, is reversed.
TheExaminer'srejectionofclaims 1-3, 5, 7, 9, 11, 12, 14, 15, 53,
and 54 as unpatentable under 35 U.S.C. §§ 101 and 112 is reversed.
REVERSED
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