Ex Parte 6,814,934 et al

Patent Trial and Appeal Board

Apr 26, 2013

90010131 (P.T.A.B. Apr. 26, 2013)

UNITED STATES PATENT AND TRADEMARK OFFICE
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
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
90/010,131 03/31/2008 6,814,934 4380-RX US 6014
52059 7590 04/26/2013
LIFE TECHNOLOGIES CORPORATION
Attn: IP Department
5791 Van Allen Way
Carlsbad, CA 92008
EXAMINER
TURNER, SHARON L
ART UNIT PAPER NUMBER
3991
MAIL DATE DELIVERY MODE
04/26/2013 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 APPLIED BIOSYSTEMS, LLC,
Patent Owner and Appellant
____________________

Appeal 2012-012210
Merged reexamination control 90/010,131 & 90/010,905
Patent 6,814,934 B1
Technology Center 3900
____________________

Before RICHARD M. LEBOVITZ, JEFFREY B. ROBERTSON, and
RAE LYNN P. GUEST, Administrative Patent Judges.

GUEST, Administrative Patent Judge.

DECISION ON APPEAL
I. STATEMENT OF CASE
Applied Biosystems, LLC (hereinafter “Appellant”), the real party in
interest1 of Patent 6,814,934 B1 (hereinafter the “’934 patent”), appeals under 35
U.S.C. §§ 134(b) and 306 from the Examiner’s decision to reject claims 1-12.
Final Office Action, mailed November 28, 2011, pages 7-17. We have jurisdiction
under 35 U.S.C. §§ 134(b) and 306. An oral hearing took place on April 4, 2013.
A transcript of the oral hearing will be made of record in due course.

1 See Appellant’s Appeal Brief filed March 27, 2012 (hereinafter “App. Br.”) at 2.
Appeal 2012-012210
Application 90/010,131 & 90/010,905

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We REVERSE.
This appeal is from two merged reexamination proceedings. The first was
filed by Troll Busters, LLC and assigned reexamination control number
90/010,131. Request for Ex Parte Reexamination, filed March 31, 2008. The
second was filed by Novak Druce + Quigg LLP and assigned reexamination
control number 90/010,905. Request for Ex Parte Reexamination, filed March 10,
2010. The reexamination proceedings were merged in a Decision before the
Director of the Central Reexamination Unit on August 4, 2010.
The ’934 patent relates to a method for monitoring the accumulation of the
product of a nucleic acid amplification reaction while the reaction is in progress,
namely by simultaneous amplification and detection of signaling agent, such as a
fluorescent dye, that is capable of binding double-stranded DNA. ’934 patent, col.
5, l. 33-col. 6, l. 8.
Representative claim 1 on appeal reads as follows:
1. An instrument for use in monitoring a nucleic acid
amplification reaction comprising multiple thermal cycles,
comprising:
(a) an automated thermal cycler capable of alternately heating
and cooling, and adapted to receive, at least one reaction vessel
containing an amplification reaction mixture comprising a target
nucleic acid, reagents for nucleic acid amplification, and a detectable
nucleic acid binding agent; and
(b) a detector operable to detect a fluorescence optical signal
while the amplification reaction is in progress and without opening the
at least one reaction vessel, which fluorescence optical signal is
related to the amount of amplified nucleic acid in the reaction vessel.
Claims App’x, App. Br. 41. Claim 7, the only other independent claim on appeal,
includes identical requirements for an “automated thermal cycler” and a “detector.”
Id. at 42.
Appeal 2012-012210
Application 90/010,131 & 90/010,905

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II. REJECTIONS
The Examiner maintains the following rejections on appeal:
1. Claims 1, 3, 4, 6, 7, 9, and 12 rejected under 35 U.S.C. § 102(b) as
anticipated by, or in the alternative under 35 U.S.C. § 103(a) as obvious
over, either the Morrison article2 or the Morrison patent3 (collectively
referred to herein as “Morrison4”), as evidenced by the Stirling
Declaration.5 Examiner’s Answer, dated June 21, 2012 (hereinafter
“Ans.”) at 2-6.
2. Claims 1, 3, 4, 6, 7, 9, and 12 rejected under 35 U.S.C. § 103(a) as
obvious over, Garner6 in view of Morrison, as evidenced by the Stirling
Declaration. Ans. 6-9.
The Examiner further rejects dependent claims 2, 5, 8, 10, and 11 under 35
U.S.C. § 103(a) as obvious over Morrison, as evidenced by Stirling, and further in
view of additional prior art. Ans. 9-12. As discussed in detail below, we reverse
all the Examiner’s rejections.

2 Morrison et al., "Solution-Phase Detection of Polynucleotides Using Interacting
Fluorescent Labels and Competitive Hybridization,” Anal. Biochem. 183:231-244
(1989).

3 U.S. Patent 5,928,862, issued July, 27, 1999 to Larry E. Morrison.

4 The Examiner and Appellant acknowledge that the Morrison article and the
Morrison patent are essentially cumulative, i.e., they include substantially identical
disclosures. Ans. 5; App. Br. 28. Accordingly, we refer to them collectively as
“Morrison.” All citations herein are to the Morrison article.

5 The Declaration under 37 C.F.R. § 1.132 of Dr. Colin Stirling, dated March 1,
2010 (hereinafter the “Stirling Declaration” or “Stirling Decl.”).

6 U.S. Patent 5,092,674, issued March 3, 1992 to Harold R. Garner.
Appeal 2012-012210
Application 90/010,131 & 90/010,905

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III. ISSUE ON APPEAL
Central to this appeal is the interpretation of the term “automated thermal
cycler” as recited in the independent claims on appeal. In finding that Morrison
discloses an “automated thermal cycler,” the Examiner stated that the term
“automated thermal cycler” is not sufficiently defined in the ‘934 Patent to
distinguish the Haake Model A81 water bath with external temperature control
disclosed in Morrison and the automatically temperature controlled micropipette
adaptor for a spectrophotometer disclosed in Garner. Ans. 2-3, 7, 15-28; Morrison,
¶ spanning p. 234, col. 2 to p. 235, col. 1, last ¶, p. 237, col. 2 to first full ¶, p. 238,
col. 1 and p. 238, col. 2, Figure 3; Garner, col. 8, ll. 6-50.
Appellant argues that the term “automated thermal cycler” has a specific
meaning in the art that is distinguishable from the water bath of Morrison or the
micropipette adaptor of Garner in that it is a specialty instrument capable of very
rapid temperature cycling specifically for use with polymerase chain reaction
(PCR) amplification of nucleic acids. App. Br. 7.
In support of its claim interpretation, Appellant relies on the testimony
provided by the Second Batt Declaration7 and the Third Batt Declaration.8 Dr. Batt
testifies to “have made practical use of PCR and realtime PCR in my research and

7 The Second Declaration under 37 C.F.R. § 1.132 of Dr. Carl A. Batt, dated
November 10, 2010, and entered into the record on November 10, 2010
(hereinafter “2nd Batt Declaration” or “2nd Batt Decl.”). App. Br., Evidence
Appendix, Exhibit L.

8 The Third Declaration under 37 C.F.R. § 1.132 of Dr. Carl A. Batt, dated July 5,
2010, and entered into the record on July 5, 2011 (hereinafter “3rd Batt
Declaration” or “3rd Batt Decl.”). App. Br., Evidence Appendix, Exhibit FF.

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teaching since their discovery.” First Batt Declaration,9 ¶ 4. Upon review of Dr.
Batt’s stated credentials and attached CV, 1st Batt Decl., ¶ 3 and Exhibit A, we find
that Dr. Batt is qualified to testify as to the general history of temperature
management for PCR reactions and the use of the term “automated thermal cycler”
to one of ordinary skill in the art at the time of the filing of the application that
became the ’934 patent, i.e., May of 1991.
Accordingly, the dispositive issue before us is: Did the term “automated
thermal cycler” have a special meaning to one of ordinary skill in the art at the
time of filing the application that became the ’934 patent that distinguishes the
claimed device over the water bath relied upon in the teachings of Morrison and
the micropipette adaptor relied upon in the teachings of Garner? We answer this
question in the affirmative.
III. ANALYSIS
The ’934 patent is expired and as a result, “the Board's review of the claims
of an expired patent is similar to that of a district court's review.” In re Rambus
Inc., 694 F.3d 42, 45 (Fed. Cir. 2012); Ex Parte Papst-Motoren, 1 U.S.P.Q.2d 1655,
1655-56 (B.P.A.I. Dec. 23, 1986).
An expanded panel of the Board has pointed out that the language in Papst-
Motoren regarding the construction of a patent claim “that will render it valid” can
be misleading. Ex parte Katz, 2010 WL 1259722 at *7 (BPAI 2010). The maxim
that claims are construed, if possible, to sustain their validity is limited “to cases in
which ‘the court concludes, after applying all the available tools of claim
construction, that the claim is still ambiguous.’ [quoting] Phillips v. AWH Corp.,

9 The First Declaration under 37 C.F.R. § 1.132 of Dr. Carl A. Batt, dated January
30, 2006, and entered into the record on January 29, 2010 (hereinafter “1st Batt
Declaration” or “1st Batt Decl.”). App. Br., Evidence Appendix, Exhibit K.
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415 F.3d 1303, 1327 (Fed. Cir. 2005) (en banc) (citing Liebel-Flarsheim Co. v.
Medrad, Inc., 358 F.3d 898, 911 (Fed. Cir. 2004)).” Id.
We consistently follow the proposition that a claim term is accorded its
“ordinary and customary meaning” which 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.” Phillips v. AWH
Corp., 415 F.3d 1303, 1313 (Fed. Cir. 2005).
We note that the District Court of Connecticut interpreted the term
“automated thermal cycler” in a Markman proceeding. See Memorandum Opinion
on Claim Construction, Applera Corp. v. Stratagene Corp., No. 3:04–CV–1881,
2007 WL 776329, *7-8 (Dist. Conn. March 12, 2007). In doing so, the District
Court, crediting the testimony of Dr. Batt, interpreted the phrase “automated
thermal cycler” to mean “an instrument for use in a nucleic acid amplification
reaction comprising multiple thermal cycles for alternately heating or cooling
samples.” Id.
We agree with Appellant that the term “automated thermal cycler” has a
special meaning in the art and that one of ordinary skill in the art would have
understood the term distinguishable from the water bath of Morrison and the
micropipette adaptor of Garner.
The term “automated thermal cycler” is not found in the Specification of the
’934 patent. However, “thermal cycler” is recited in the Specification, and the
entire process of performing amplification is described as an automated process
and format. ‘934 patent, col. 5, ll. 23-30 and 41-42; col. 9, ll. 35-44; col. 11, ll. 49-
52; Figures 6A, 6B and 8.
The Specification is primarily directed to methods for nucleic acid detection
during amplification. ’934 patent, col. 5, ll. 33-42. While the methods described
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therein are not limited to any particular type of nucleic acid amplification, see ’934
patent, col. 7, ll. 27-32, we find that the tools and devices that are described therein
are used only with respect to the amplification method known as polymerase chain
reaction (PCR) using thermostable enzymes. See col. 9, ll. 41-44 (“A machine
specifically adapted for use with a thermostable enzyme is disclosed more
completely in EP No. 236,069, which is incorporated herein by reference, and is
commercially available from PECI.”) and col. 10, ll. 42-45 (“The embodiments of
the invention exemplified herein disclose the process for detecting amplified
nucleic acids in conjunction with PCR.”). The Specification further states:
In preferred methods for PCR, the amplification reaction is
carried out as an automated process. A thermocycler 15 currently
available from Perkin Elmer Cetus Instruments uses a heat block
capable of holding up to 48 reaction tubes. Consequently, 48
amplification reactions can be carried out simultaneously. . . .
Alternatively, it will be obvious to one skilled in the art that such a
detection system is not necessarily limited to a particular thermocycler
machine or number of reaction vessels. However, the description of
the 48 well PECI thermocycler serves to demonstrate this aspect of
the present invention.
’934 patent, col. 11, l. 49-col. 12, l. 2. Devices are not described for any other type
of nucleic acid amplification reaction other than a PCR reaction using thermostable
enzymes.
We find this consistent with Dr. Batt’s description of how the term “thermal
cycler” was understood in the art. Dr. Batt testifies that “[a]n automated thermal
cycler has a clear and specific meaning as it pertains to real time PCR. The term
“automated thermal cycler” is universally understood by people who practice
PCR.” 3rd Batt Decl. ¶ 5. According to Dr. Batt, a thermal cycler, as the term is
used in the context of PCR, is “a new class of instruments for rapidly and precisely
heating and cooling” that was “was made newly and singularly important by the
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invention of PCR.” 2nd Batt Decl. ¶¶ 33 and 35. According to Dr. Batt, the phrase
“thermal cycler” “grew out of the PCR revolution.” Id. at ¶ 35. Dr. Batt
emphasized the need for thermal cyclers to perform both precise and rapid heating
and cooling to avoid exposure of the sample to excessive exposure of heat,
particularly the latent heat present with slow cooling times, as such additional heat
exposure would more rapidly inactivate the thermostable DNA polymerase and
alter the binding kinetics of the primer for its target sequence. Id. at ¶¶ 36-38, 40
and 43. Dr. Batt thus emphasizes “the critical needs for both active heating and
cooling” that is reproducible. 3rd Batt Decl. ¶¶ 8 and 10. Dr. Batt cites to what
appears to be the preeminent “thermal cycler” patent, also cited to in the ’934
patent, namely European Patent Publication 0236069. 3rd Batt Decl. ¶ 21; ’934
Patent, col. 9, ll. 41-44. Dr. Batt testified that, while PCR amplification was done
prior to the invention of the thermal cycler, the discovery of thermostable DNA
polymerases created an additional need in the art not met by conventional heating
devices. 3rd Batt Decl. ¶¶ 19-23. We find no evidence of record that contradicts
Dr. Batt’s statements as to the features the skilled artisan would understand to be
consistent with an “automated thermal cycler.”
The Stirling Declaration is relied upon as evidence that the Haake Model
A81 water bath described in Morrison is capable of performing PCR amplification,
and functions as an automated thermal cycler . Ans. 4 and 24-25. Dr. Stirling
performs a PCR amplification using a “Neslab Endocal refrigerated circulating
bath” which he alleges is “comparable to and available at the same time as the
Haake Model A81 [refrigerated water bath].” Stirling Decl. ¶ 36. The testimony
of Dr. Stirling is not persuasive. In particular, the Stirling Declaration
acknowledges that the two refrigerated circulating baths are not the same, in
particular that the Neslab Endocal recirculating water bath “was found to be
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capable of substantially faster ramp rates than those used in the study by
Morrison.” Stirling Decl. ¶ 37.
Moreover, the statements of Dr. Stirling and Morrison appear to
acknowledge that a “thermal cycler” is a specific device in the prior art for PCR
amplification. Dr. Stirling performs certain operations on a “modern thermal
cycler . . . to reduce the time taken to complete these studies.” Stirling Decl. ¶ 39.
Dr. Stirling also recognizes that “[t]he cycle time [of the Neslab Endocal water
bath] was 50 minutes (compared with 3 minutes in a modern thermal cycler)” or
even longer if the lid to the Neslab Endocal recirculating water bath was
permanently closed. Id. at ¶ 40. Accordingly, Dr. Stirling appreciates the
significant increase in efficiency in performing PCR amplification on a thermal
cycler. Similarly, Morrison describes the use of a “Perkin Elmer Cetus DNA
Thermal Cycler” for the PCR amplification reaction performed therein. Morrison,
p.235, col. 1, first full ¶. Accordingly, Morrison appears to acknowledge the
special use of a “thermal cycler” for efficient PCR amplification reactions.
The Specification of the ’934 patent describes a PCR process in which the
temperature cycles between about 50°C and about 94°C but is held at these
temperatures for no longer than 1 minute. See e.g., col. 23, ll. 21-25. While the
Specification does not expressly recite the rates of cooling and rates of heating for
the thermal cycler, Figures 5A and 5B illustrate that in 2000 seconds
(approximately 33 minutes), what appears to be 8 cycles have occurred. See ’934
patent, Figures 5A and 5B. This finding is also consistent with Dr. Batt’s
testimony that an “automated thermal cycler” is characterized by its performing
accurate and very rapid temperature cycling. In fact, we find Dr. Batt’s
comparison of cycling speeds, see 2nd Batt Decl. ¶ 39, persuasive that it is the
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efficiency and rapidity of an “automated thermal cycler” which defines the device
as a specialty instrument for efficient PCR amplification.
The Examiner has relied exclusively on a position that the ’934 patent and
claims lacks a clear description of the scope of the term “automated thermal
cycler,” particularly with respect to any particular rate of cooling or rate of cycling.
See Ans. 15-20. Yet an express description of the scope would be unnecessary if a
skilled artisan would have understood that the phrase referred to a special device in
the art.
We credit the testimony of Dr. Batt, which is not contradicted by any
evidence of record, that the skilled artisan would have understood the term
“automated thermal cycler” to have a special meaning in the art. Accordingly,
based on the testimony of Dr. Batt, we conclude that an “automated thermal
cycler” is limited to a special machine which includes both a heating source and a
cooling source capable of being used with thermostable enzymes in rapid and
efficient PCR nucleic acid amplification processes. Such a special definition
renders the Stirling Declaration irrelevant, for even if the skilled artisan recognizes
that the water bath of Morrison is capable of PCR amplification, the skilled artisan
would not find Morrison’s water bath meets the recognized meaning of an
“automated thermal cycler” as it is understood in the art.
Morrison describes a DNA melting apparatus including a Teflon stoppered
cuvette provided in a Haake Model A81 water bath with external temperature
control. The DNA melting procedure includes the continuous monitoring of a
DNA sample via cuvette spectroscopy of a fluorescing agent while the temperature
of the DNA sample is only disclosed as being linearly increased and decreased at a
rate of 10°C per hour. Ans. 2-3; Morrison, ¶ spanning p. 234, col. 2 to p. 235, col.
1, last ¶, p. 237, col. 2 to first full ¶, p. 238, col. 1 and p. 238, col. 2, Figure 3.
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Similarly, Garner discloses an automatically temperature controlled
micropipette adaptor for a spectrophotometer. Ans. 7; Garner, col. 8, ll. 6-50.
Garner discloses controlling the temperature of a resistive heater wire by a
temperature feedback control system. Garner, col. 4, ll. 24-50. The adaptor is only
disclosed as heating a sample at a rate of about 5.7°C per minute. Garner, col. 8, ll.
65-68.
In light of the above discussion, we agree with Appellant that Morrison and
Garner fail to disclose an instrument having a detector and an “automated thermal
cycler” as the term is understood in the art. Neither Morrison nor Garner discloses
a machine which includes both a heating source and a cooling source that is
capable of the rapid heating and cooling necessary in order to be used with
thermostable enzymes in rapid and efficient PCR nucleic acid amplification
processes.
The Examiner applied the teachings of Morrison in the same manner in
rejecting the dependent claims on appeal. Ans. 9-12. Thus we reverse all of the
Examiner’s rejections for the reasons discussed above.
IV. CONCLUSION
On the record before us, we reverse the rejections maintained by the
Examiner.
V. TIME PERIOD FOR RESPONSE
Requests for extensions of time in this ex parte reexamination proceeding
are governed by 37 C.F.R. § 1.550(c). See 37 C.F.R. § 41.50(f).

Appeal 2012-012210
Application 90/010,131 & 90/010,905

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REVERSED

FOR PATENT OWNER:

LIFE TECHNOLOGIES CORPORATION
Attn: IP Department
5791 Van Allen Way
Carlsbad, CA 92008

FOR THIRD-PARTY REQUESTER:

JEFFREY B. OSTER
8339 SE 57th St.
Mercer Island, WA 98040