Ex Parte Kavusi et al

Patent Trial and Appeal Board

Mar 28, 2018

12688193 (P.T.A.B. Mar. 28, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/688, 193 01115/2010
28078 7590 03/28/2018
MAGINOT, MOORE & BECK, LLP
One Indiana Square, Suite 2200
INDIANAPOLIS, IN 46204
FIRST NAMED INVENTOR
SamKavusi
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.
1576-0265 3073
EXAMINER
GROSS, CHRISTOPHER M
ART UNIT PAPER NUMBER
1639
MAILDATE DELIVERY MODE
03/28/2018 PAPER
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.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte SAM KA YUSI, DANIEL ROSER,
CHRISTOPH LANG, and
AMIRALI HAJ HOSSEIN TALASAZ 1
Appeal2016-000284
Application 12/688, 193
Technology Center 1600
Before JOHN G. NEW, RICHARD J. SMITH, and
RACHEL H. TOWNSEND, Administrative Patent Judges.
NEW, Administrative Patent Judge.
DECISION ON APPEAL
1 Appellants state that the real party-in-interest is Robert Bosch GmbH.
App. Br. 2.
Appeal2016-000284
Application 12/688,193
SUMMARY
Appellants file this appeal under 35 U.S.C. § 134(a) from the
Examiner's Final Rejection of claims 1---6, 10, 11, and 19-27 as unpatentable
under 35 U.S.C. § 102(b) as being anticipated by Sosnowski et al. (US
2007/0178516 Al, August 2, 2007) ("Sosnowski").
Claims 20-27 also stand rejected as unpatentable under 35 U.S.C.
§ 112, second paragraph, as indefinite.
We have jurisdiction under 35 U.S.C. § 6(b ).
We AFFIRM.
NATURE OF THE CLAIMED INVENTION
Appellants' invention is directed to a method of determining a number
of a solution constituent. Abstract.
REPRESENTATIVE CLAIM
Claim 1 is representative of the claims on appeal and recites:
1. A method of determining a number of a solution
constituent comprising:
introducing a first number of solution constituents to a first
test location;
creating a first residual number of solution constituents by
binding a first plurality of solution constituents at the first test
location wherein the first plurality of solution constituents
includes a first portion of a first solution constituent of interest
and a first portion of a second solution constituent;
creating a second residual number of solution constituents
by binding a second plurality of solution constituents from the
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first residual number of solution constituents wherein the second
plurality of solution constituents includes a second portion of the
first solution constituent of interest and a second portion of the
second solution constituent;
obtaining a first signal associated with the bound first
plurality of solution constituents;
obtaining a second signal associated with the bound
second plurality of solution constituents; and
determining a second number of the first solution
constituent of interest based upon the obtained first signal and
the obtained second signal, wherein the obtained first signal and
the obtained second signal are used to compensate for the second
solution constituent.
App. Br. 25.
ISSUES AND ANALYSES
We are persuaded by, and expressly adopt, the Examiner's findings
and conclusions establishing that Appellants' claims are prima facie
anticipated by the cited prior art and that claims 20-27 are indefinite. We
address the arguments raised by Appellants below.
A. Rejection of claims 1-6, 10, 11, and 19-27 as unpatentable under 35
U.S.C. § 102(b)
Issue 1
Appellants argue the Examiner erred in finding that Sosnowski
discloses binding portions of two constituents at a first test site. App. Br. 7.
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Analysis
The Examiner finds that Sosnowski discloses a method and an array
device for specific binding of nucleic acids, featuring electronic voltage
biasing in an effort to delineate between hybridization of perfect versus
base-mismatched nucleic acids. Final Act. 3. Specifically, the Examiner
finds, Sosnowski discloses: (1) introducing a first number of solution
constituents to a first test location; (2) creating a first residual number of
solution constituents by binding a first plurality of solution constituents at
the first test location wherein the first plurality of solution constituents
includes a first portion of a first solution constituent of interest and a first
portion of a second solution constituent; (3) creating a second residual
number of solution constituents by binding a second plurality of solution
constituents from the first residual number of solution constituents wherein
the second plurality of solution constituents includes a second portion of the
first solution constituent of interest and a second portion of the second
solution constituent; ( 4) obtaining a first signal associated with the bound
first plurality of solution constituents; and ( 5) obtaining a second signal
associated with the bound second plurality of solution constituents. Id. at 3-
4 (citing Sosnowski i-fi-139, 188, Figs. 10-12). The Examiner points to
Example 7 of Sosnowski which, the Examiner finds, discloses a second
number of a first solution constituent of interest based upon the obtained
first signal and the obtained second signal, in which the obtained first signal
and the obtained second signal are used to compensate for second solution
constituent. Id. at 4 (also citing Sosnowski Fig. 15).
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Application 12/688,193
Appellants argue that paragraph [0039], cited by the Examiner,
discloses only that the disclosed invention relates to various reactions and
does not disclose binding two constituents at a first test site. App. Br. 7.
Appellants also point to paragraph [0188] of Sosnowski, which, Appellants
assert, notes only that some processes can include "multiple or multiplexed
hybridization reactions in both serial and parallel fashion," but also allegedly
fails to disclose binding two constituents at a first test site. Id.
Appellants next contend that Figures 1 Oa-b of Sosnowski, which are
described at paragraph [0208], discloses that each of the micro locations
(ML-1 through ML-7) bind only a single target DNA: only OLIGO 1 binds
at ML-3 and only OLIGO 2 binds at ML-5. App. Br. 7-8. According to
Appellants, binding two different constituents at two different test sites is
not the same as binding two different constituents at the same test site and,
therefore Sosnowski does not disclose binding two constituents at a first test
site. Id. at 8.
With respect to Figures 1 la-c of Sosnowski, Appellants argue that
these figures illustrate how the device of Sosnowski ensures only a single
target molecule is present by denaturing or removing any mismatched DNA
hybrids which happen to be bound; a condition described by Sosnowski as
"electronic stringency control." App. Br. 8 (citing Sosnowski i-f 209).
Appellants assert that Sosnowski's Figures 12a-b disclose only the manner
in which electronic stringency is achieved when a dye is attached to both
single strand and double strand DNA. Id. (citing Sosnowski i-f 214).
The Examiner responds that, in Example 7 of Sosnowski, a first
measurement is taken which includes both matched and mismatched
hybrids. Ans. 7. As such, the Examiner finds, it is not clear how Sosnowski
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does not describe a test site where two constituents from a solution are
bound, as Appellants argue. Id.
The Examiner further finds that Figure 10 of Sosnowski discloses
parallel DNA electronic hybridization starting with a solution containing
five molecules each of oligonucleotides 1 and 2 added to location ML-1 of
the APEX chip in which the probes are a mismatch and no binding occurs.
Ans. 7. The Examiner finds that the next step depicted in Figure 10 depicts
moving the oligonucleotides by voltage biasing testing with different probes
at subsequent locations, with binding of oligonucleotide 1 at site ML-3. Id.
at 7-8. The Examiner finds Figure 10 illustrates three oligonucleotides of
oligonucleotide 1 binding to the probe at ML-3, leaving a residual two
molecules excess of oligonucleotide 1 and five molecules of oligonucleotide
2. Id. at 8. The Examiner finds that the subsequent steps of Figure 10
illustrate the residual oligonucleotides transported to subsequent sites until,
at site ML-5, which bears probes for hybridizing oligonucleotide 2, again
leaving excess oligonucleotides 1 and 2 in solution. Id. The Examiner finds
Figure 10, and its accompanying text, correspond to the recited limitations of
the claims. Id.
We think the Examiner has the better position. Figure 1 Oa of
Sosnowski illustrates moving a plurality of oligonucleotides having the same
DNA sequence across a series of sites (i.e., micro locations) bearing different
target DNA strands and binding to a single complementary site on the test
array (ML-3), with the excess, unbound oligonucleotide removed. Figure
1 Ob illustrates subsequently moving a second plurality of oligonucleotides
having a different DNA sequence across the microlocation array, the second
plurality of oligonucleotides binding to a different microlocation (ML-5) that
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is complementary to the second oligonucleotide's DNA sequence, with the
excess of unbound oligonucleotides removed. Sosnowski, in explaining
Figures 1 Oa and 1 Ob, describes this sequential pairing of successive
oligonucleotide sequences as a "serial hybridization format." Sosnowski i-f
208. However, Sosnowski also expressly discloses that the binding
sequences at the probe site locations can be the same or different. In
particular, Sosnowski discloses:
Another common format for DNA hybridization assays involves
having target DNAs immobilized on a surface, and then
hybridizing specific probes to these target DNAs. This format
can involve either the same target DNAs at multiple locations, or
different target DNAs at specific locations.
Sosnowski i-f 208 (emphasis added). Sosnowski thus expressly discloses that
multiples of the same DNAs can be tested across the various locations of the
array and that different DNAs can be tested at multiple (but different) sites
together. See id. at i-f 56 ("This unique feature allows relatively dilute
charged analytes or reactant molecules free in solution to be rapidly
transported, concentrated, and reacted in a serial or parallel manner at any
specific microlocations which are maintained at the opposite charge to the
analyte or reactant molecules") (emphasis added).
Figure 9 of Sosonowski is illustrative of the parallel testing principle,
where the different target DNAs are located at distinct microlocations, but
each micro location is present at a "first test location" (as required by claim
1) because the sample is added to the entire micro location array area.
Describing Figure 9, Sosnowski discloses:
[E]ach addressable micro location has a specific capture sequence
(90). A sample solution containing target DNA (92) is applied
to the device. All the micro locations are activated and the sample
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DNA is concentrated at the microlocations (FIG. 9(B)). Target
DNA molecules from the dilute solution become highly
concentrated at the microlocations, allowing very rapid
hybridization to the specific complementary DNA sequences on
the surface.
Sosonowski i-f 206. While Figure 9 depicts different target DNAs being
located at distinct microlocations, as noted above, Sosnowski also
contemplates, though does not depict, a single microlocation having multiple
different capture sequences. Id. at i-f56 (reactants in solution "can be reacted
in a serial or parallel manner at any specific microlocations").
In summary, Sosnowski expressly teaches that its disclosed methods
include: "DNA and RNA hybridizations procedures and analysis in
conventional formats; e.g., attached target DNA/probe DNA, attached probe
DNA/target DNA, attached capture DNA/target DNA/probe DNA [and]
multiple or multiplexed hybridization reactions in both serial and parallel
fashion." Sosonowski i-fi-1186-87 (emphasis added).
We therefore agree with the Examiner that Sosnowski discloses that:
multiple, different oligonucleotide sequences can be tested at various sites
together, with excess nucleotide subsequently removed. We further agree
with the Examiner that a person of ordinary skill in the art would recognize
that these disclosures of Sosnowski teach the limitation of claim 1 reciting:
"creating a first residual number of solution constituents by binding a first
plurality of solution constituents at the first test location wherein the first
plurality of solution constituents includes a first portion of a first solution
constituent of interest and a first portion of a second solution constituent."
Issue 2
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Appellants argue that the Examiner erred in finding that Sosnowski
discloses binding a second plurality of solution constituents at a second test
location. App. Br. 9.
Analysis
Appellants contend that the Examiner has failed to identify any
specific disclosure of Sosnowski wherein the sample, after binding portions
of two constituents at the first test site, is exposed to a second test site at
which portions of both of the constituents are again bound. App. Br. 9.
Moreover, Appellants argue, Sosnowski does not disclose that any of the
target molecules of a given probe remain in solution as required by claim 1
after being bound at a given probe location. Id. (citing, e.g., Sosnowski
i-fi-1208-214). According to Appellants, there is therefore no disclosure in
Sosnowski that any of the target molecules of a first probe are not bound by
the first probe and then passed to a second probe at which the target
molecules are bound. Id.
We disagree. As we have explained supra, Figures 1 Oa and 1 Ob of
Sosnowski explicitly illustrate that not all of an oligonucleotide sequence
binds to a specific probe and is subsequently moved to the ensuing sites.
Moreover, and as we have also explained, Figure 11 of Sosnowski shows
that, at any given site, different nucleotides may bind to a probe with varying
degrees of specificity (i.e., "perfect matches" versus "mismatches"). See
Sosnowski i1 210 ("In effect each hybridization is an independent reaction.
With a conventional or passive array format, it is impossible to achieve
optimal stringency for all the hybridization events which are occurring in the
same hybridization solution").
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Consequently, we agree with the Examiner that a person of ordinary
skill in the art would understand that Sosnowski discloses that, when testing
a solution of different oligonucleotides, some of the first and second
oligonucleotides will bind at a first probe site, either specifically or through
a mismatch, and both can also bind at a second probe site, for the same
reasons.
Issue 3
Appellants argue the Examiner erred in finding that Sosnowski
discloses compensating for a second constituent using two signals. App. Br.
10.
Analysis
Appellants argue that the Examiner erroneously relies upon Example
7 and Figure 15 of Sosnowski as disclosing eliminating the effect of an
interfering molecule (the second solution constituent) by using signals
obtained from two bound constituents at a first and second test sites. App.
Br. 10 (citing Final Act. 4 ). According to Appellants, the principle of
operation of Sosnowski is based upon performing electronic stringency
control to ensure that only a single molecule of interest is bound at any given
site and that, once a single molecule is present, a signal indicative of the
amount of bound molecules is obtained. Id.
Appellants assert that, because the interfering molecules are removed
by electronic stringency control, there is no portion of the signal that is
effected by a second molecule at the site. App. Br. 10-11. Appellants
contend that Example 7 is therefore simply a proof of concept, which is
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provided to show that all of the molecules of interest remains at a target site
after the site is subjected to electronic stringency control. Id. at 11. In
Example 7, a first measurement is taken which includes both matched and
mismatched hybrids. Id. (citing Sosnowski i-f 314). Then, Appellants argue,
electronic stringency control is used to unbind the mismatched hybrids and a
second signal is obtained. Id. Therefore, Appellants contend, in this
Example, the second signal is obtained from the same test site and not from
two signals obtained from different test sites. Id. Furthermore, Appellants
argue, the second signal of Sosnowski has no contribution from the second
constituent, since the mismatched oligonucleotides have all been washed
away. Id.
The Examiner responds that, as an initial matter, the features upon
which Appellants rely (i.e., two signals from two different test sites) are not
recited in claim 1. Ans. 9.
The Examiner also notes that Appellants admit that Sosnowski
discloses: "that all of the molecules of interest remain[ ] at a target site after
the site is subjected to electronic stringency control. In Example 7, a first
measurement is taken which includes both matched and mismatched
hybrids." Ans. 9--10 (quoting App. Br. 11). The Examiner points to Figure
15, which the Examiner finds depicts the corresponding measurements of
Example 7 described in Sosnowski paragraphs [0307]-[0313] and [0324],
and which shows approximately 6 relative units may be attributed to
interfering 1 and 2 base pair mismatches out of 100 relative units of signal
under electronic stringency control, as well as the superior signal-to-noise
over conventional hybridization. Id.
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that:
We are not persuaded by Appellants' arguments. Sosnowski discloses
Another common format for DNA hybridization assays
involves having target DNAs immobilized on a surface, and then
hybridizing specific probes to these target DNAs. This format
can involve either the same target DNAs at multiple locations, or
different target DNAs at specific locations. FIGS. lOa and lOb
show an improved version of this serial hybridization format. In
this case micro locations (101-107) are addressed with different
capture DNAs. These are hybridized in a serial fashion[ 2J with
different sequence specific oligonucleotides (108, 109). The
microlocations are sequentially biased positive to transport
molecules to itself and then biased negative to transport
molecules to the next microlocation. At the proper electrode
potential, the specifically hybridized DNA probes will remain at
that microlocation, while un-hybridized probes are transported to
the next microlocation. The sequence specific oligonucleotides
probes can be labeled with a suitable reporter group such as a
fluorophore.
Sosnowski i-f 208; see also Fig. lOa-b (emphasis added). We conclude that a
person of ordinary skill in the art, apprehending this passage of Sosnowski
would understand that a given oligonucleotide probe, labeled with a
fluorophore and hybridized in parallel across successive locations with
different attached DNAs, either unlabeled or labeled with a different
fluorophore, as illustrated in Figures 9 and 10. For example, as illustrated in
Figure 10, parallel hybridization across multiple sites (as depicted in Figure
9), would produce at least two different signals: in Figure 1 Ob these would
be at sites ML-3 and ML-5. By comparing these sequences, a person of
2 Note, however, that paragraph [0056] discloses that such hybridization can
be serial or parallel.
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ordinary skill would be able to determine "a second number of the first
solution constituent of interest based upon the obtained first signal and the
obtained second signal, wherein the obtained first signal and the obtained
second signal are used to compensate for the second solution constituent."
We consequently affirm the Examiner's rejection of the claims.
B. Rejection of claims 20-27 as indefinite under 35 U.S.C. § 112, second
paragraph
Independent claim 20 is exemplary of these claims and recites, in
relevant part: "A method of determining a number of a solution constituent
comprising: providing a first test location with a probe molecule of a first
type; providing a second test location with a probe molecule of the first
type .... " App. Br. 28 (emphasis added).
The Examiner finds that the term "type" in claim 20 is a relative term
which renders the claim indefinite. Final Act. 6. Specifically, the Examiner
finds the term "type" is not defined by the claim, and Appellants'
Specification does not provide a standard for ascertaining the requisite
degree. Id. at 6-7. The Examiner finds that a person of ordinary skill in the
art would therefore not be reasonably apprised of the scope of the invention
because the claim term "probe molecule of a first type" is ill-defined insofar
as the addition of the word "type" to an otherwise definite expression (e.g., a
probe molecule) extends the scope of the expression so as to render it
indefinite. Id. (citing Ex parte Copenhaver, 109 USPQ 118, 118 (Pt. & Tr.
Office Bd. App. 1955)).
Appellants argue that only by addition of the word "type" can the
claim actually make sense. App. Br. 5. According to Appellants, if the
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word "type" is omitted, the claim would require a first test site "with a probe
molecule." Id. Appellants argue that the language of the claim would
further require a second test site with the same probe molecule and that
requiring a single molecule to be at two different locations is a physical
impossibility. Id. Therefore, Appellants contend, without the word "type"
the claim would be rendered indefinite; inclusion of the word "type" clearly
indicates that the probe molecules at both test sites have the same features.
Id.
The Examiner responds that the problem with the claim term "type"
arises from the multitude of ways that a skilled person could interpret the
claim. Ans. 5. The Examiner finds that one possible construction of the
claim language could be that the probe molecule at each location each has
the function of binding the same analyte; whereas the language can also be
construed to mean that "type" refers to the class of compound of the probe
(e.g., DNA versus RNA). Id. at 5---6. The Examiner finds that an alternate
construction could be that each location bears acidic species or other
different chemical properties. Id. at 6. The Examiner therefore finds that,
because neither the claim language nor Appellants' Specification defines "a
probe molecule of a first type," the claim term fails to define the metes and
bounds of the claimed invention. Id.
We agree with the Examiner. The use of the word "type" to modify a
more concrete claim term was addressed by a predecessor of our reviewing
court in Copenhaver. The court held, with respect to the claim term "Friedel
Crafts type compounds and strong organic sulfonic acids," that: "We are of
the view that the word 'type' when appended to an otherwise definite
expression so extends the scope of such expression as to render it
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objectionably indefinite from the standpoint of patent law and procedure."
Copenhaver, 109 USPQ at 118.
Similarly, we agree with the Examiner that the use of the language
reciting: "a probe molecule of a first type," in the absence of any definition
in the claims or in Appellants' Specification, so extends the meaning of "a
probe molecule" as to render the scope of the claim indefinite. We
consequently affirm the Examiner's rejection of the claims.
DECISION
The Examiner's rejection of claims 1-6, 10, 11, and 19-27 under 35
U.S.C. § 102(b) is affirmed.
The Examiner's rejection of claims 20-27 under 35 U.S.C. § 112,
second paragraph, 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 )(iv).
AFFIRMED
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