Ex Parte Wittwer et al

Patent Trial and Appeal Board

Jan 26, 2015

11926775 (P.T.A.B. Jan. 26, 2015)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte CARL T. WITTWER, KIRK M. RIRIE,
and RANDY P. RASMUSSEN
_________

Appeal 2012-008405
Application 11/926,775
Technology Center 1600
__________

Before DEMETRA J. MILLS, JEFFREY N. FREDMAN, and
CHRISTOPHER G. PAULRAJ, Administrative Patent Judges.

PAULRAJ, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal1 under 35 U.S.C. § 134 involving claims to a system
for performing PCR and monitoring the reaction during temperature cycling.
The Examiner rejected the claims on indefiniteness, anticipation,
obviousness, and obviousness-type double patenting grounds. We have
jurisdiction under 35 U.S.C. § 6(b). We affirm.

1 Appellants identify the Real Party in Interest as the University of Utah
Research Foundation (see App. Br. 4).
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STATEMENT OF THE CASE
Background
“This invention relates generally to observing fluorescence signals
resulting from hybridization in conjunction with the polymerase chain
reaction. More specifically, the present invention relates to observing
hybridization with fluorescence during and/or immediately after PCR and
using this information for product identification, sequence alteration
detection, and quantification.” (Spec. 1, ll. 20–24). The Specification states
that “[i]t is an object of the present invention to provide a double-strand-
specific DNA dye for monitoring product hybridization during PCR” (id. at
4, ll. 28–29). “SYBR™ Green I is a preferred double-strand-specific dye for
fluorescence monitoring of PCR, primarily because of superior sensitivity,
arising from greater discrimination between double stranded and single
stranded nucleic acid” (id. at 34, ll. 11–13). “SYBRTM Green I is heat labile,
however, and thus is not useful for fluorescence monitoring of PCR
according to conventional methods where the temperature of the reaction
mixture is maintained at melting temperatures for extended periods of time”
(id. at 32, l. 30–33 l. 2). The Specification states that “it was unexpected to
discover that SYBRTM Green I can be used to monitor PCR reactions when
melting temperatures are not maintained for extended period” (id. at 33, l. 2–
5).
The Claims
Claims 1–3 and 5–17 are under appeal. Independent claim 1 is
representative, and reads as follows:
l. A system for performing PCR and monitoring the
reaction during
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temperature cycling comprising:
a sample container for holding a PCR sample,
a heat exchange component for heating and cooling the
sample, wherein the heat exchange component heats to at least
90°C during at least a portion of the thermal cycling,
a control device programmed for repeatedly operating the
heat exchange component to subject the PCR sample to thermal
cycling,
an excitation source for optically exciting the sample to
cause the sample to fluoresce,
a photodetector configured for detecting fluorescent
emissions from SYBR@ Green I, and a processor for recording
and processing emissions from SYBR Green I.
The Rejections

The Examiner rejected the claims as follows:
I. Claims 1–3 and 5–17 under 35 U.S.C. § 112, second paragraph
as being indefinite.
II. Claims 1, 2, 5–8, 10–13, and 15–17 under 35 U.S.C. § 102(e) as
being anticipated by Fujita,2 as evidenced by Suzuki.3
III. Claim 3 under U.S.C. § 103(a) as being unpatentable over
Fujita, as evidenced by Suzuki, and further in view of
Richardson.4

2 Fujita et al., U.S. Patent No. 6,106,777, issued Aug. 22, 2000.
3 Takeshi Suzuki et al., DNA Staining for Auorescence and Laser Confocal
Microscopy, 45 J. HISTOCHEM. & CYTOCHEM. 49–53 (1997).
4 Richardson et al., US Patent No. 4,257,774, Mar. 24, 1981.
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IV. Claim 9 under 35 U.S.C. § 103(a) as being unpatentable over
Fujita, as evidenced by Suzuki, and further in view of Mullis,5
Latimer,6 and Schneeberger.7
V. Claim 14 under 35 U.S.C. § 103(a) as being unpatentable over
Fujita, as evidenced by Suzuki, and further in view of
Morrison.8
VI. Claims 1–3, 5–8, and 10–17 under 35 U.S.C. § 103(a) as being
unpatentable over Morrison, as evidenced by Suzuki, and
further in view of Kurn9 and Kureshy.10
VII. Claims 1–3 and 5–17 under non-statutory obviousness-type
double patenting grounds over claims 1–14 of Wittwer (U.S.
Patent No. 7,670,832).11
Appellants do not address the obviousness-type double patenting
rejection (Rejection VII) in their Appeal Brief. We, therefore, summarily
affirm that rejection and will not discuss it further in this Decision.
FINDINGS OF FACT
We adopt the Examiner’s findings of fact as set forth in the Answer.
We highlight the following for emphasis.

5 Mullis, US Patent No. 4,683,202, Jul. 28, 1987.
6 Laura J. P. Latimer et al., Ethidium Bromide Does Not Fluoresce when
Intercalated Adjacent to7-Deazaguanine in Duplex DNA, 266 J. BIOL.
CHEM. 13849–51 (1991).
7 Christian Schneeberger et al., Quantitative Detection of Reverse
Transcriptase-PCR Products by Means of a Novel and Sensitive DNA Stain,
4 PCR METHODS ANDAPPL., 234 –38 (1995).
8 Morrison, EP 0,232,967, published Aug. 19, 1987.
9 Kurn et al., US Patent No. 4,868,104, issued Sept. 19, 1989.
10 Kureshy et al., US Patent No. 5,207,987, issued May 4, 1993.
11 Wittwer et al., U.S. Patent No. 7,670,832 B2, issued Mar 2, 2010.
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FF1. Fujita teaches a DNA analysis method and device wherein “[t]he
PCR cycling condition was 27 cycles of 94° C. (1 minute), 57° C.
(1.2 minute) and 72° C. (1 minute) in this order” (Fujita, col. 5, ll.
23–25).
FF2. Fujita teaches fluorescence detection of the sample DNA using an
ethidium bromide dye. Specifically, Fujita teaches “[v]ia the
presence of ethidium bromide intercalated with the sample DNA,
fluorescence of 590 nm is emitted, which is then collimated with
the optical system 807 followed by detection with photoelectric
converter 808” (id., col. 11, ll. 26–30).
FF3. Suzuki teaches that the maximum wavelength of excitation for
SYBR Green I is 519 nm (Suzuki, Table I).
FF4. Schneeberger teaches the quantitative detection of reverse
transcriptase-PCR products by means of a novel and sensitive
DNA stain. Schneeberger teaches:
We encountered the problem of heteroduplex formation
during later stages of PCR, which could be solved by
decreasing the PCR cycle number. This was
accompanied by a significant loss of sensitivity.
Sensitivity could be restored using a novel and extremely
sensitive DNA stain (SYBR Green I) instead of ethidium
bromide.

(Schneeberger, Abstract).
ANALYSIS
I. Indefiniteness Rejection

The Examiner rejected the claims as indefinite, asserting “it is unclear
whether the claimed invention is directed to a method or an apparatus” (Ans.
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6). In particular, the Examiner finds, “with regard to claim 1, the claimed
‘apparatus’ recites the step, ‘wherein the heat exchange component heats
to…,’” and “[w]ith regard to claim 17, the claimed ‘apparatus’ recites the
steps, ‘wherein the control device operates the heat exchange device’”
(id.,emphasis added).
We do not sustain the indefiniteness rejection. The Examiner relies
upon IPXL Holdings, LLC v. Amazon.com, Inc., 430 F.3d 1377, 1384 (Fed.
Cir. 2005), in which the Federal Circuit held that because a claim “recites
both a system and the method for using that system, it does not apprise a
person of ordinary skill in the art of its scope, and it is invalid under section
112, paragraph 2.” We do not find IPXL Holdings to be applicable here.
The claim at issue in IPXL Holdings was directed to a “system,” but
included the limitation that “the user uses the input means to either change
the predicted transaction information or accept the displayed transaction type
and transaction parameters.” Id. Unlike the claim found indefinite in that
decision, where it was it was unclear if infringement would occur when one
created a system (as would be true if the claim were for an apparatus) or if
one would actually have to use it (as required for one to infringe a system),
the functional language relied upon by the Examiner for the present claims
does not require a separate “user” to perform any method steps.
Properly interpreted, we find that the claim language at issue here
only requires a heat exchange component/device with the capability to heat
to at least 90°C during at least a portion of the thermal cycling (Cl. 1) or to
heat the sample at a rate of ≥0.1° C/second (Cl. 17). See Microprocessor
Enhancement Corp. v. Texas Instruments Inc., 520 F.3d 1367, 1375 (Fed.
Cir. 2008) (finding claim to be “clearly limited to a pipelined processor
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possessing the recited structure and capable of performing the recited
functions, and is thus not indefinite under IPXL Holdings”).
II. Anticipation Rejection Based on Fujita, as Evidenced by Suzuki

The Examiner finds that:
Fujita discloses devices for the fluorescent-based analysis of
PCRs (fig. 12-16; col. 5; col. 9-11, for example). Specifically, the
reference teaches a device comprising: a sample container (fig. 12;
col. 5, for example), a heat exchange component and a control
device (fig. 14, temperature controller 302, capable of performing
all recited actions, for example), an excitation source and a
photodetector (fig. 15, 801, 808, source, detector, and filter, for
example), and a processor (fig. 15, 16, 810 signal processor,
capable of performing all recited actions, for example).

(Ans. 7; see also FF1–2).
The Examiner relies upon Suzuki to assert that the “peak emission
fluorescence wavelength [of SYBRTM Green I] is about 520 nm (see Suzuki,
Table I, for example,” and “[t]hus, the photodetector including filter as
taught in Fujita, i.e. filter allowing fluorescent emissions of at least 590 nm
(see col. 11, lines 20-40) is capable of detecting fluorescent emissions from
SYBR® Green I” (Ans. 7–8; see also FF3). The Examiner further points to
the following fluorescent spectra of SYBRTM Green I, obtained from the
Invitrogen website (http://products.invitrogen.com/ivgn/product/S7567,
accessed January 23, 2012):
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(Ans. 19). Based on this, the Examiner asserts that “it is clear SYBR Green
I necessarily emits a detectable amount of photons at 590nm,” which is
within the range of detection by the photoelectric converter of Fujita (id.).
We agree with the Examiner’s conclusion that Fujita anticipates
independent claim 1. We have considered Appellants’ arguments, but are
not persuaded otherwise.
Appellants argue that Fujita’s “disclosure of detecting fluorescent
emissions above 590 nm does not read upon a system for detecting
fluorescent emissions for a dye whose peak emissions are at 520 nm—well
below the disclosed fluorescent emissions” (App. Br. 15). As noted above,
however, the Examiner has presented evidence, i.e., the fluorescent spectra
from the manufacturer of SYBRTM Green I, establishing that the dye emits
detectable photons at 590 nm.12 Appellants have not disputed that

12 We note that the Examiner first identified the SYBRTM Green I fluorescent
spectra in the Answer to support the rejection. Appellants, however, have
not raised any concerns about a new ground of rejection in accordance with
the procedures available under 37 C.F.R. § 41.40. See MPEP § 1207.03(b).
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contention. We, therefore, find sufficient evidence to support the conclusion
that the photodetector taught by Fujita is necessarily “configured for
detecting fluorescent emissions from SYBR® Green I” as required by claim
1.
Appellants further argue that that “[s]ince SYBR Green I was previously
believed to have been heat labile by those of ordinary skill in the art, no
detection system utilizing SYBR Green I would include a heater operable to
heat to at least 90° C, as such a structure would render the detection system
useless with a heat labile dye” (App. Br. 16). We are not convinced by this
argument. Fujita plainly discloses PCR cycling at 94° C, which meets the
structural capability requirements of Appellants’ claims (FF1). At most,
Appellants may have identified a new use for the prior art apparatus of
Fujita, i.e., utilization with SYBR Green I. However, that alone is
insufficient to impart patentability. “[T]he patentability of apparatus or
composition claims depends on the claimed structure, not on the use or
purpose of that structure.” Catalina Mktg. Int’l, Inc. v. Coolsavings.com,
Inc., 289 F. 3d 801, 809 (Fed. Cir. 2002); see also In re Schreiber, 128 F.3d
1473, 1477 (Fed. Cir. 1997) (“It is well settled that the recitation of a new
intended use for an old product does not make a claim to that old product
patentable.”).
We, therefore, affirm the anticipation rejection of claim 1. Appellants
have not separately argued claims 2, 4–8, 10–13, and 15–17, and, therefore,
those claims fall with claim 1. 37 C.F.R. § 41.37(c)(i)(vii).

We, therefore, do not treat the Examiner’s reliance on the SYBRTM Green I
fluorescent spectra as constituting a new ground of rejection.
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III.-VI. Obviousness Rejections
With respect to the obviousness rejections of claims 3, 9, and 14,
Appellants repeat the argument that “[s]ince SYBR Green I was
previously believed to have been heat labile by those of ordinary skill in
the art, no detection system utilizing SYBR Green I would include a
heater operable to heat to at least 90° C, as such a structure would render
the detection system useless with a heat labile dye” (App. Br. 17).
Accordingly, Appellants assert that:
there could be no motivation for combining the prior art
references recited to establish the claimed invention, as the
understanding as of the priority date of the present invention
was that combining a photodetector configured for detecting
fluorescent emissions from SYBR Green I, a processor for
recording and processing emissions from SYBR Green I, and a
heater operable to heat to at least 90° C would result in an
unworkable system that had no utility.

(App. Br. 17–18).
We again are not persuaded by this argument. As discussed above,
we find that Fujita’s device inherently meets the structural requirements for
detecting fluorescent emissions from SYBR Green I, and no further
modification of the prior art device would have been needed to achieve that
capability. Furthermore, Schneeberger specifically teaches that fluorescence
detection using SYBR Green I was superior in restoring sensitivity for PCR
applications compared to ethidium bromide stain (FF4), thus, providing
sufficient motivation to include SYBR Green I in the sample container of the
PCR device, as required by claim 9. Appellants do not address this teaching
in Schneeberger. Nor do Appellants present any evidence to support their
assertion that a skilled artisan would have understood that a heater operable
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to heat to at least 90° C would result in an unworkable system for detecting
SYBR Green I. The Examiner relies upon the additional references
(Richardson, Mullis, Latimer, and/or Morrison) for other aspects of the
dependent claims (Ans. 9–15), but there is no rebuttal evidence to suggest
that one skilled in the art would not have been motivated to modify the
device of Fujita as proposed in view of any asserted heat labile properties of
SYBR Green I.
Appellants do not present any additional arguments for the
obviousness rejection based on Morrison, as evidenced by Suzuki, and
further in view of Kurn and Kureshy (App. Br. 18). We accordingly affirm
each of the obviousness rejections.

SUMMARY
We reverse the rejection of claims 1–3 and 5–17 under 35 U.S.C.
§ 112, second paragraph as being indefinite.
We affirm the rejection of claims 1, 2, 5–8, 10–13, and 15–17 under
35 U.S.C. § 102(e) as being anticipated by Fujita, as evidenced by Suzuki.
We affirm the rejection of claim 3 under U.S.C. § 103(a) as being
unpatentable over Fujita, as evidenced by Suzuki, and further in view of
Richardson.
We affirm the rejection of claim 9 under 35 U.S.C. § 103(a) as being
unpatentable over Fujita, as evidenced by Suzuki, and further in view of
Mullis, Latimer, and Scheenerger.
We affirm the rejection of claim 14 under 35 U.S.C. § 103(a) as being
unpatentable over Fujita, as evidenced by Suzuki, and further in view of
Morrison.
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We affirm the rejection of claims 1–3, 5–8, and 10–17 under 35
U.S.C. § 103(a) as being unpatentable over Morrison, as evidenced by
Suzuki, and further in view of Kurn and Kureshy.
We summarily affirm the rejection of claims 1–3 and 5–17 under non-
statutory obviousness-type double patenting grounds over claims 1–14 of
Wittwer (U.S. Patent No. 7,670,832).
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED

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