Ex Parte CHEE

Patent Trial and Appeal Board

Apr 22, 2016

13165648 (P.T.A.B. Apr. 22, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/165,648 06/21/2011
20995 7590 04/26/2016
KNOBBE MARTENS OLSON & BEAR LLP
2040 MAIN STREET
FOURTEENTH FLOOR
IRVINE, CA 92614
FIRST NAMED INVENTOR
MarkS. CHEE
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.
ILLINC.212Cl 4273
EXAMINER
STRZELECKA, TERESA E
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
04/26/2016 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):
j ayna.cartee@knobbe.com
efiling@knobbe.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte MARK S. CHEE
Appeal2014-001572
Application 13/165,648
Technology Center 1600
Before ROMULO H. DELMENDO, RICHARD M. LEBOVITZ, and
RICHARD J. SMITH, Administrative Patent Judges.
DELMENDO, Administrative Patent Judge.
DECISION ON APPEAL
The Appellant1 seeks our review under 35 U.S.C. § 134(a) of a
decision of the Primary Examiner to reject claims 1-11 and 14--25. We have
jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.
BACKGROUND
The subject matter on appeal relates to a method for sequencing a
plurality of different target nucleic acids by a DNA pyrosequencing method
that includes using enzymes distributed on a surface of a substrate to detect a
1 The Appellant states that "Illumina, Inc." is the real party in interest
(Appeal Brief filed June 28, 2013, hereinafter "App. Br.," 3).
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Application 13/165,648
pyrophosphate released during the DNA synthesis reaction (Specification,
hereinafter "Spec," Abst.; i-fi-12, 9). Representative claims 1 and 21 are
reproduced from pages 38--40 of the Appeal Brief (Claims App.),2 with the
key limitations at issue indicated in italicized text, as follows:
1. A method of sequencing a plurality of different
target nucleic acids, comprising:
(a) providing a first population of micro spheres
comprising capture probes;
(b) providing target nucleic acids comprising target
sequences;
( c) hybridizing said target nucleic acids to said
capture probes on said micro spheres;
( d) providing a second population of microspheres
comprising at least one bioactive agent selected from
sulfonyltransferase enzymes and luciferase enzymes;
( e) distributing said first and said second
populations of microspheres in wells on a surface of a
substrate,
( f) hybridizing a primer to each of said target
nucleic acids,
(g) providing a polymerase and a uniform
population of nucleotides to said wells, wherein
incorporation of a nucleotide complementary to said
target sequence is accompanied by release of
13165pyrophosphate; and
(h) detecting said pyrophosphate using said
sulfonyltransferase or luciferase enzymes, thereby
sequencing said plurality of target nucleic acids.
2 On March 20, 2013, the Appellant submitted proposed amendments to the
claims after final rejection, but the Examiner denied entry of these
amendments as raising an additional written description (new matter) issue
(Adv. Act. entered Mar. 20, 2013). The Appellant did not file a petition to
seek review of the Examiner's denial.
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21. A method of sequencing a plurality of
different target nucleic acids, comprising:
(a) providing a substrate having a plurality of sites,
wherein said sites comprise covalently bound target
nucleic acids and covalently bound bioactive agents
selected from sulfonyltransferase enzymes and luciferase
enzymes;
(b) binding at least one primer to said target
nucleic acids;
( c) extending said at least one primer in the
presence of a polymerase and a population of uniform
nucleotides wherein incorporation of a nucleotide
complementary to said target sequence is accompanied
by release of pyrophosphate; and
( d) detecting the release of the pyrophosphate
using the covalently bound bioactive agents, thereby
sequencing said target nucleic acids.
THE REJECTIONS
The Examiner has rejected the claims as follows:
I. Claims 1-11 and 14--25 under 35 U.S.C. § 112, i-f 1, as
failing to comply with the written description
requirement;
II. Claims 1---6, 9-11 and 14--25 under 35 U.S.C. § 103(a) as
being unpatentable over Margulies et al. ("Margulies")3
and Margulies et al. ("Supplemental Material");4
III. Claims 7 and 8 under 35 U.S.C. § 103(a) as being
unpatentable over Margulies, Supplemental Material, and
3 Margulies, Marcel et al., Genome Sequencing in Open Microfabricated
High Density Picoliter Reactors, 437 Nature 376-380 (2005).
4 Margulies, Marcel et al., Supplemental Materials 3, 437 Nature 1-34
(2005); referred to by the Appellant and the Examiner as "Supplemental
Material"
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~ , .... ' .. /ll'.~ , ........ ,." .. Kosemna1 et al. ~-·KosemnacJ;J ana
IV. Claims 7 and 8 under 35 U.S.C. § 103(a) as being
unpatentable over Margulies, Supplemental Material, and
Pourmand et al. ("Pourmand"). 6
(Examiner's Answer, entered September 17, 2013, hereafter "Ans.," 2-10;
Final Office Action entered January 7, 2013, hereinafter "Final Act.," 7-
27.)7
DISCUSSION
In arguing for reversal of the rejections, the Appellant argues
independent claims 1 and 21 together, focusing on claim 1. Therefore,
consistent with 37 C.F.R. § 41.37(c)(l)(iv), we confine our discussion to
representative claim 1 and, by rule, our decision on the appeal for claim 1
controls our decision for claims 2-11 and 14--25.
A dispositive issue in this appeal is whether Margulies, which
published on September 15, 2005, is available as prior art against claim 1,
which was amended during examination of the current application
(Amendment filed October 18, 2012). For the reasons discussed in more
detail below, we find claim 1, which was amended to recite
5 Rosenthal, Andre et al., Genomic walking and sequencing by oligo-cassette
mediated polymerase chain reaction, 18 Nucl. Acids Res. 3095-3096 3095-
3096 (1990).
6 Pourmand, Nadar et al., Multiplex Pyrosequencing, 30 Nucl. Acids Res. 1-
5 (2002).
1 In the Answer at page 10, the Examiner withdrew an objection to the
Specification amendment, filed October 18, 2012, and a rejection of claims
1-11 and 14-25 under 35 U.S.C. § 112, i-f 1, as failing to comply with the
enablement requirement.
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"sulfonyltransferase enzymes" and "providing ... a uniform population of
nucleotides," fails to comply with the written description requirement of 35
U.S.C. § 112, i-f 1. As a result, under 35 U.S.C. §§ 119(e) and 120, we find
that claim 1 is not entitled to any of the earlier filing dates or priority
benefits (see Bibliographic Data Sheet) before the publication date of
Margulies. See In re Hogan, 559 F.2d 595, 609 (CCPA 1977) ("There has
to be a continuous chain of copending applications each of which satisfies
requirements of§ 112 with respect to subject matter presently claimed ...
There must be continuing disclosure through the chain of applications,
without hiatus, to ultimately secure benefit of earliest filing date.'") (internal
citations omitted).
The Examiner rejected claims 1-11 and 14--25 under 35 U.S.C. § 112,
i-f 1, "as failing to comply with the written description requirement" because
the Examiner determined that "[t]he claim(s) contains subject matter which
was not described in the specification in such a way as to reasonably convey
to one skilled in the relevant art that . . . the inventor( s ), at the time the
application was filed, had possession of the claimed invention" (Ans. 10).
Specifically, the Examiner determined that claim 1 includes the following
claim limitations, each of which the Examiner determined does not comply
with the written description requirement: "sulfonyltransferase enzymes,"
"least one bioactive agent selected from sulfonyltransferase enzymes and
luciferase enzymes," "distributing said first and said second populations of
microspheres in wells," and "providing ... a uniform population of
nucleotides to said wells" (Final Act., 10). We address each of these
limitations separately below.
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1. "!Slulfonyltransferase enzymes" limitation
With respect to the claim requirement "sulfonyltransferase enzymes,"
the Examiner has determined that claim 1 reciting this limitation does not
comply with the written description because the Specification does not recite
the term "sulfonyltransferase enzymes" and "the term does not even exist in
the official enzyme nomenclature, as shown in the search results of enzyme
database" (Ans. 11-12). In response, the Appellant concedes that "[t]he
specification of the present application does not recite 'sulfonyltransferase',"
but argues "the specification frequently recites 'sulfurylase' activity" (App.
Br. 29) (citing Spec. i-f 5). According to the Appellant, "[t]he terms
'sulfonyl' and 'sulfuryl' each refer to an -S(=0)2- moiety," the Specification
specifically requires "the conversion of PPi to ATP by the enzyme
sulfurylase," and therefore argues"[ o ]ne of ordinary skill in the art would
understand that the moiety being transferred to ATP is the -S(=0)2- moiety
synonymously referred to by both 'Sulfonyl' and 'sulfuryl"' (id.).
Therefore, the Appellant contends "sulfonyltransferase was sufficiently
described by the specification of the pending application" (id.).
We have fully considered the Appellant's arguments; however we
find the arguments do not reveal a reversible error in the Examiner's
conclusion that "sulfonyltransferase enzymes" fails to comply with the
written description requirement. As found by the Examiner (Ans. 11 ), and
conceded by the Appellant (App. Br. 29), the Specification does not recite or
explicitly disclose "sulfonyltransferase enzymes" and therefore the relevant
inquiry is whether there is evidence that one ordinary skill in the art would
consider the description related to "sulfurylase enzymes" in the Specification
sufficient to support "sulfonyltransferase enzymes" See In re Alton 76 F.3d
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1168, 1175 (CCPA 1996) (citing In re Wertheim, 541F.2d257 (CCPA
1976) and In re Oetiker, 977 F.2d 1443 (Fed.Cir.1992), stating "[i]f, on the
other hand, the specification contains a description of the claimed invention,
albeit not in ipsis verb is (in the identical words), then the examiner or Board,
in order to meet the burden of proof, must provide reasons why one of
ordinary skill in the art would not consider the description sufficient. Once
the examiner or Board carries the burden of making out a prima facie case of
unpatentability, 'the burden of coming forward with evidence or argument
shifts to the applicant'").
Here, the Examiner proffered evidence to suggest term
sulfonyltransferase is not recognized in the official enzyme nomenclature.
Additionally, the Appellant concedes that "sulfuryl moieties are associated
with inorganic chemical bonds, while sulfonyl moieties are associated with
organic chemistry" (Reply Brief entered November 18, 2013 hereinafter
"Rep. Br.," 5). From reading the Specification, it would be clear that the
substrate adenosine 5 '-phosphosulphate comprises the sulfuryl moiety
associated with the inorganic chemical bond of the phosphate group. Spec. i-f
38. In view of this distinction and the Examiner's specific findings
discussed supra, we find that the record includes sufficient evidence that the
"sulfurylase" as described in the Specification is not sufficiently descriptive
of the presently claimed "sulfonyltransferase" and thus hold that the claim
reciting "sulfonyltransferase enzymes" does not comply with written
description requirement as required by 35 U.S.C. § 112 i-f 1. In so holding,
we note that Appellant has proffered no factual evidence, besides mere
attorney speculation, that rebuts the Examiner's findings and determinations
or that would suggest that one of ordinary skill in the art would find the term
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"sulfurylase" to be descriptive of "sulfonyltransferase" in compliance with
the written description requirement. See In re Scarborough, 500 F.2d 560,
566 (CCPA 1974).
2. "[C]omprising at least one bioactive agent selected from
sulfonyltransferase enzymes and luciferase enzymes" limitation
With respect to the claim requirement "comprising at least one
bioactive agent selected from sulfonyltransferase enzymes and luciferase
enzymes," the Examiner, after a thorough review of the specification,
determined that the term "bioactive agent" was in the context of "being a
probe which binds a target analyte, and the only instance of the bioactive
agent as a protein contemplated in the disclosure was an antibody protein
target" and there is no connection between "bioactive agent" and
"sulfonyltransferase enzymes and luciferase enzymes" as required by the
claims (Ans. 16-17). Specifically, the Examiner, citing all the instances that
the term "bioactive agent" is used in the disclosure, determined that the
disclosure as a whole provides by a "preponderance of evidence that the
term 'bioactive agent' was used to describe a probe directly detecting a
target molecule" (id. at 16-34). Therefore, the Examiner concluded that the
"designation of sulfonyltransferase enzymes and luciferase enzymes as
bioactive agents does not have support in either the original disclosure of the
instant application or in the material incorporated by reference" (id. at 35).
The Appellant responds that the Specification, as amended, recites
"[b ]y ... 'bioactive agent' ... as used herein describes any molecule, e.g.,
protein, oligopeptide, small organic molecule, polysaccharide,
polynucleotide, etc. which can be attached to the microspheres of the
invention" and then argues the specification additionally discloses "[i]n a
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preferred embodiment, the bioactive agents are proteins" (App. Br. 29-30;
Rep. Br. 6-7). Additionally, Appellant argues "enzymes" as bioactive
agents is fully supported by the specification because that the specification
readily describes "a) bioactive agents can be proteins, b) bioactive agents are
used to detect target analytes, c) PPi is a molecule targeted for detection, and
d) sulfurylase and luciferase can detect PPi" (Rep. Br. 8).
We have thoroughly reviewed the Examiner's review of the
disclosure; however, we agree with Appellant that the concept of a
"bioactive agent" in connection with the disclosed "enzymes" is sufficiently
supported by the disclosure to comply with 35 U.S.C. § 112 i-f 1. As
persuasively argued by the Appellant (Rep. Br. 6), the Specification, when
including the incorporated subject matter, defines the term "bioactive agent"
to describe "any molecule, e.g., protein, oligopeptide, small organic
molecule, polysaccharide, polynucleotide, etc. which can be attached to the
microspheres" (Amendment to Specification, entered October 18, 2012, pg.
2). We find this explicit definition to be sufficient to convey to one of
ordinary skill in the art that the inventor had possession of the claimed
"bioactive agent" including "sulfurylase and luciferase" enzymes (Spec. i-f
5).
Even in the event that the specific definition does not impart a
definition, we find that one having ordinary skill in the art reading the claims
and giving "bioactive agent" its ordinary and customary meaning in the art
would have readily recognized the term to encompass any compound,
molecule, or agent that exhibits bioactivity, which upon a review of the
Specification would encompass "sulfurylase and luciferase" enzymes. See
Phillips v. AWH Corp., 415 F.3d 1303, 1313 (Fed. Cir. 2005) ([t]he ordinary
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and customary meaning of a claim term is the meaning that the term would
have to a person of ordinary skill in the art in question at the time of the
invention, i.e., as of the effective filing date of the patent application). See
also Brookhill-Wilk 1, LLC v. Intuitive Surgical, Inc., 334 F.3d 1294, 1298
(Fed. Cir. 2003) ("In the absence of an express intent to impart a novel
meaning to the claim terms, the words are presumed to take on the ordinary
and customary meanings attributed to them by those of ordinary skill in the
art"). With these understandings, we find the Examiner has not sufficiently
met her burden of providing reasons why one of ordinary skill in the art
would not consider the description sufficient to support the concept of
bioactive agents including the disclosed enzymes. See Alton 76 F.3d 1175.
3. "[D]istributing said first and said second populations of
microspheres in wells" limitation
With respect to the claim requirement "distributing said first and said
second populations of microspheres in wells," the Examiner determined the
Specification does not support a claim reciting "enzymes attached to
microspheres in the same wells" (Final Act. 10). Additionally, in a
clarifying finding, the Examiner maintained that while the claims do not
specifically require "in the same well," the "presence of microspheres
containing both capture probes and detecting enzymes [in the same well] is
the inherent consequence" of the claim requirements (Ans. 14).
Additionally, the Examiner found that "while the disclosure contemplates
detecting enzymes in the 'vicinity' of the sequencing reaction, it does not
describe or suggest that the beads containing detecting enzymes be present
in the same wells as the beads with capture probes to which the target is
bound" (Ans. 14--15). In response, the Appellant argues the claims do not
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require the "in the same wells" as asserted by the Examiner and thus argues
the rejection is in error (App. Br. 30-31 ). The Appellant also argues that,
even under the Examiner's analysis, the disclosure specifically describes
using a secondary enzymes during pyrosequencing and the use of these
secondary enzymes generate a "chemiluminescent signal in the zone around
the bead ... [and] [b]y attaching the secondary enzyme required to generate
the signal, an increased concentration of the required enzymes is obtained in
the immediate vicinity of the reaction" (Rep. Br. 8-9). The Appellant
argues, even if the claims require "in the same wells," one of ordinary skill
in the art would find the specification sufficiently describes the first and
second microspheres are distributed in the same wells as required by the
Examiners interpretation (id.).
Here, again, we find the Examiner has not met her burden of
providing reasons why one of ordinary skill in the art would not consider the
description sufficient to support the claim requirement of "a distributing said
first and said second populations of microspheres in wells." See Alton 7 6
F.3d 1175. As argued by the Appellant, the claims recites that the first and
second microspheres are distributed "in wells on a surface of a substrate,"
rather than the more specific "same well" as argued by the Examiner. The
claim is thus open to the presence of the microspheres in the same or
different wells. The Specification discloses the substrate can include
"discrete, individual sites" that may comprises "physical configurations such
as wells or small depressions in the substrate that can retain the beads, such
that a microsphere can rest in the well" (i-fi-f 103). Additionally, the
Specification discloses "the surface of the substrate may be modified such
that discrete sites are formed that can only have a single associated bead, or
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alternatively, the surface of the substrate is modified and beads may go
down anywhere, but they end up at discrete sites" (i-fi-f 104). In other words,
the microspheres can be at the same or different sites, as long as the sites are
discrete, such as being "wells." Paragraph 54, as argued by the Appellant,
indicates that the secondary enzymes may be "in the immediate vicinity of
the reaction." The "immediate vicinity" provides support for the same well,
or different, but adjacent, wells because in each case the secondary enzyme
attached to the microspheres would be near the location of the reaction.
In view of these disclosures, we find the claim limitation "distributing
said first and said second populations of microspheres in wells" is supported
by the written description.
As persuasively argued by the Appellant (Rep. Br. 9) and conceded by
the Examiner (Ans. 15), the Specification discloses during pyrosequencing
"a chemiluminescent signal in the 'zone' around the bead" is generated by
enzymes attached to the microspheres that are in the vicinity of the
sequencing reaction (i-fi-f 0054). Additionally, the Specification, after
discussing the distribution of microspheres in individual sites such as wells
or small depressions, further discloses "the surface of the substrate is
modified to allow attachment of the microspheres at individual sites,
whether or not those sites are contiguous or non-contiguous with other sites"
(i-fi-f 104). Thus, in view of these disclosures, we find that one of ordinary
skill in the art would find that the Examiner's requirement that the claims
inherently requires "distributing said first and said second populations of
microspheres in the same wells" is supported by the Specification.
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4. "!Plroviding ... a uniform population of nucleotides to said
wells" limitation
With respect to the claim requirement "providing ... a uniform
population of nucleotides to said wells," the Examiner determined that term
"uniform population of nucleotides" was not defined or described in the
original disclosure to comply with the written description requirement (Ans.
13). The Examiner further noted that the term "uniform population" was not
defined by Appellant and noted "the 'uniformity' of having the same base is
only one possibility" (id.). The Examiner further noted "[ fJor example,
'uniform population' could mean that each of the different types of dNTPs
has the same concentration in the reaction mixture, or that the population
includes only pyridines or only pyrimidines, etc" (id. 14). In view of these
alternative meanings, the Examiner determined the limitation "uniform
population of nucleotides" as required by the claims "introduces new matter
into the disclosure" (id.).
In response, the Appellant argues the term "uniform population of
nucleotides' is sufficiently supported by the disclosure "the four
deoxynucleotides (dATP, dGTP, dCTP and dTTP; collectively dNTPs) are
added stepwise" (App. Br. 31 ). From this, the Appellant argues "[ o ]ne of
skill in the art would understand this to mean that the deoxynucleotides are
added in populations sharing a common base one at a time, that is, 'uniform
populations"' (id.). The Appellant, in response to Examiner's articulated
position, argued that"[ o ]ne of skill in the art at the time of filing the
application would not have explored the Examiner's plethora of alternate
definitions of the term 'uniform population' of nucleotides, but instead
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would have assumed, based on the specification and knowledge in the art,
that they were the same nucleotide bases" (Rep. Br. 11 ).
Because the Appellant has proffered insufficient factual evidence to
the contrary, we agree with the Examiner's analysis and find that one
ordinary skill in the art would not find the disclosure of common nucleotide
base to be sufficiently descriptive to support "uniform population of
nucleotides" as required by 35 U.S.C. § 112 i-f 1. Here, as found by the
Examiner (Ans. 13), the requirement of "uniform population of nucleotides"
is not specifically described by the disclosure and thus, again the relevant
inquiry is whether one ordinary skill in the art would consider the disclosure
sufficient to support "uniform population of nucleotides." See In re Alton 7 6
F.3d 1175. The Examiner has proffered evidence that one of ordinary skill
in the art would reasonably interpret "uniform population of nucleotides" to
have alternative interpretations and thus the Examiner found that one
ordinary skill in the art would not find the disclosure of one possible
interpretation to be sufficiently descriptive of all reasonable interpretations
(Ans. 13). In view of this finding, we find that the Examiner has met her
burden and the Appellant has proffered no factual evidence, besides mere
attorney speculation, that refutes Examiner's findings and analysis or that
demonstrates that one of ordinary skill in the art would find the disclosure
that the nucleotides having a common base is sufficiently descriptive of
"uniform population of nucleotides." See Scarborough, 500 F.2d 566.
In sum, we hold that claim 1 violates the written description
requirement of 35 U.S.C. § 112, i-f 1, and, therefore, cannot be entitled to
benefit of priority or an earlier filing date as to any of the earlier-filed
provisional or non-provisional applications.
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The Examiner also determined that claim 21, like claim 1, includes
the following claim limitations "sulfonyltransferase enzymes," "covalently
bound bioactive agents selected from sulfonyltransferase enzymes and
luciferase enzymes" and "uniform population of nucleotides." Our
discussion of these limitations in claim 1 applies equally with respect to
claim 21.
With respect to Rejections II, III, and IV, the Examiner determined
that the claims do not "have support in either the original disclosure of the
instant application or in the material incorporated by reference ... [and] [a]s
a consequence, the priority date of the instant claims is the filing date of the
instant application, June 21, 2011" and thus maintained "the rejection of the
instant claims based on the Margulies et al. reference ... since it is proper
prior art based on the priority date of the instant claims" (Ans. 35). In
response, the Appellant contends that because the instant claims are "fully
supported by the present specification, then they would be supported by the
priority specifications in the family since they all contain virtually the same
language" (Rep. Br. 4).
As conceded by the Appellant (Rep. Br. 4), the earlier applications
and the current application contain virtually the same disclosure language.
Therefore, since we have held supra that the present claims fail to comply
with the written description requirement as required by 35 U.S.C. § 112 i-f 1,
it follows that the other identical, but earlier, disclosures also fail to comply
with the written description requirement. Because there is not a continuous
chain of copending applications that satisfy the requirements of the first
paragraph of 35 U.S.C. § 112, we agree with the Examiner and find the
invention recited in the claims is not entitled to an earlier effective filing
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date that is before the publication date of ivfargulies. See In re Hogan, 559
F.2d 609.
The Appellant has set forth no additional substantive arguments
regarding the merits of the Examiner's factual findings, reasoning and
conclusions of obviousness for Rejections II, III, and IV, stating "[a]ll of the
Examiner's rejections of the pending claims as obvious rely wholly or in part
upon Margulies, published in 2005 ... five years after the effective priority
date of the pending application, it is not prior art, and thus cannot support a
claim under 35 US.C. 103(a)" (App. Br. 32). Because we rejected this
argument supra and found the Appellant's reliance on an earlier effective
filing date misplaced, we summarily affirm Rejections II, III, and IV for
essentially the reasons as set forth in the Final Rejection.
SUMMARY
For these reasons and those set forth in the Examiner's Answer, the
Examiner's final decision to reject claims 1-11 and 14--25 is affirmed.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(l).
AFFIRMED
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