Ex Parte Wheeler et al

Board of Patent Appeals and Interferences

Sep 7, 2010

11405128 (B.P.A.I. Sep. 7, 2010)

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.
11/405,128 04/13/2006 Elizabeth K. Wheeler IL-11384 1883
24981 7590 09/08/2010
Lawrence Livermore National Security, LLC
LAWRENCE LIVERMORE NATIONAL LABORATORY
PO BOX 808, L-703
LIVERMORE, CA 94551-0808
EXAMINER
STAPLES, MARK
ART UNIT PAPER NUMBER
1637
MAIL DATE DELIVERY MODE
09/08/2010 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 BOARD OF PATENT APPEALS
AND INTERFERENCES
____________________

Ex parte ELIZABETH K. WHEELER,
CHRISTOPHER G. BAILEY,
and
ALLEN T. CHRISTIAN,
Appellants1
____________________

Appeal 2010-000368
Application 11/405,128
Technology Center 1600
____________________

Before CAROL A. SPIEGEL, TONI R. SCHEINER, and
FRANCISCO C. PRATS, Administrative Patent Judges.

SPIEGEL, Administrative Patent Judge.

DECISION ON APPEAL2

1 The real party in interest is LAWRENCE LIVERMORE NATIONAL
SECURITY, LLC and the UNITED STATES OF AMERICA as represented
by the UNITED STATES DEPARTMENT OF ENERGY (Appellants' Brief
(37 C.F.R. § 1.192) filed 7 January 2009 ("App. Br.") at 2). This decision
also cites the Replacement Examiner's Answer mailed 9 July 2009 ("Ans.")
and Appellants' Reply Brief (37 C.F.R. § 1.192) filed 22 July 2009 ("Reply
Br.").
2 The two-month period for filing an appeal or commencing a civil action, as
recited in 37 C.F.R. § 1.304, or for filing a request for rehearing, as recited
in 37 C.F.R. § 41.52, begins to run from the "MAIL DATE" (paper delivery
mode) or the "NOTIFICATION DATE" (electronic delivery mode) shown
on the PTOL-90A cover letter attached to this decision.
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Appellants appeal under 35 U.S.C. § 134(a) from an Examiner's final
rejection of claims 1-3 and 7-9. Claims 11-20, the only other pending
claims, stand withdrawn from consideration as directed to a nonelected
invention. (App. Br. 3; Ans. 4; Reply Br. 1.) We have jurisdiction under 35
U.S.C. § 134. We REVERSE.
I. Statement of the Case
The subject matter on appeal is directed to methods of capturing and
amplifying nucleic acid on a packed column matrix, e.g., a packed silica bed,
followed by eluting and detecting amplification markers and amplified
nucleic acid. Claims 1-3 and 7 are illustrative and read (App. Br. 34-35,
bold step numbers added):
1. A method of nucleic acid capture,
amplification, and detection, comprising the
following steps in the following order:
[1] providing a packed bed,
[2] introducing a sample potentially
containing the nucleic acid into said packed bed,
wherein said sample contains contaminants and
wherein the nucleic acid adheres to said packed
bed,
[3] introducing a wash solution into said
packed bed and washing away said contaminants,
[4] introducing an amplification mix and
amplification markers into said packed bed,
[5] thermal cycling said packed bed and
said sample potentially containing the nucleic acid
between denaturation, annealing, and extension
temperatures for polymerase chain reaction
amplification, wherein said step of thermal cycling
said packed bed and said sample potentially
containing the nucleic acid being accomplished
while said sample potentially containing the
nucleic acid is in said packed bed and said step of
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thermal cycling said packed bed and said sample
producing amplified DNA in said packed bed,
[6] releasing said amplification markers
for detection,
[7] eluting said amplified DNA from said
packed bed, and
[8] detecting the nucleic acid in said
amplified DNA.

2. The method of nucleic capture,
amplification, and detection of claim 1 wherein
said step of detecting nucleic acid in said amplified
DNA includes thermal cycling said amplified
DNA.

3. The method of nucleic acid capture,
amplification, and detection of claim 1 wherein
said step of introducing an amplification mix and
amplification markers into said packed bed
comprises introducing an amplification mix and e-
tags or taqman probes amplification markers into
said packed bed and wherein said step of releasing
said amplification markers for detection comprises
releasing e-tags or taqman probes amplification
markers for detection.

7. A method of DNA capture, amplification,
and detection, comprising the following steps in
the following order:
[1] packing bed media into a tubing or
housing to form a packed bed,
[2] connecting a heater in operative
position to said tubing or housing,
[3] introducing a sample potentially
containing the DNA into said packed bed, wherein
said sample contains contaminants and wherein the
DNA adheres to said bed media,
[4] introducing a wash solution into said
packed bed and washing away said contaminants,
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[5] introducing an amplification mix into
said packed bed,
[6] introducing amplification markers into
said packed bed,
[7] using said heater for thermal cycling
said packed bed and said sample potentially
containing the DNA between denaturation,
annealing, and extension temperatures for PCR
amplification producing amplified DNA in said
packed bed,
[8] releasing said amplification markers
for detection,
[9] eluting said amplified DNA from said
packed bed,
[10] thermal cycling said amplified DNA
between denaturation, annealing, and extension
temperatures for PCR amplification, and
[11] detecting the nucleic acid in said
amplified DNA.

The Examiner has rejected various claims as indefinite, anticipated,
and/or obvious. We address the various rejections in that order.
II. Indefiniteness
The Examiner has rejected claims 3, 8, and 9 as indefinite under 35
U.S.C. § 112, second paragraph, in reciting "the trademark/trade names E-
TAG™ and/or TAQMAN®" (Ans. 13) because reciting "a trademark or
trade name does not identify or describe the goods associated with the
trademark or trade name" (id. at 14).
"The legal standard for definiteness is whether a claim reasonably
apprises those of skill in the art of its scope." In re Warmerdam, 33 F.3d
1354, 1361 (Fed. Cir. 1994).
The issue is whether the Examiner has shown that the terms "e-tags or
taqman probes" fail to reasonably apprise those of skill in the art of the
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scope of claims 3, 8, and 9. In our opinion, the applied prior art suggests
that those skilled in the art would be reasonably apprised of the scope of
claims 3, 8, and 9 as evident from the prior art of record. Virgos,3 e.g.,
generically defines electrophoretic- or "e"-tags as
probes [that] have the form (D, Mj)-N-Tj, which
are cleaved to an electrophoretic tag reporter of the
form (D, Mj)-N', where
(i) D is a detection group comprising a
detectable label or a catalytic group capable of
catalyzing a detectable reaction;
(ii) Tj is an oligonucleotide target-binding
moiety for binding an e-tag probe recognition
sequence;
(iii) N is [a] linker joined to the 5'-end
nucleotide in Tj through a cleavable bond;
(iv) N' is the residue of N remaining after
cleavage;
(v) Mj is a mobility modifier having a
charge/mass ratio that imparts to the corresponding
electrophoretic tag, an electrophoretic mobility
that is unique to a given extension sequence; and
(vi) (D, Mj)-includes both D-Mj- and Mj-D-
[Virgos ¶¶ 23-29].

Therefore, we reverse the rejection of claims 3, 8, and 9 under 35
U.S.C. § 112, second paragraph, as indefinite. The Examiner has failed to
show that the terms "e-tags or taqman probes" fail to reasonably apprise
those of skill in the art of the scope of claims 3, 8, and 9.

3 U.S. Patent Application Publication US 2004/0191823 A1, Universal E-
Tag Primer and Probe Compositions and Methods, published 30 September
2004, by Carmen Virgos and Maureen Cronin ("Virgos").
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III. Anticipation
The Examiner rejected claims 1 and 2 under 35 U.S.C. § 102(b) as
anticipated by Utermohlen4 (Ans. 11-13 and 14-15) and claims 1, 2, 7, and 8
under 35 U.S.C. § 102(b) as anticipated by Gerdes5 (id. at 7-9) or Petersen6
(id. at 9-11).7
Anticipation requires that each and every element as set forth in the
claim is found, either expressly or inherently described, in a single prior art
reference. In re Robertson, 169 F.3d 743, 745 (Fed. Cir. 1999). Inherency,
however, may not be established by probabilities. Id., citing In re Oelrich,
666 F.2d 578, 581 (CCPA 1981). It is also well settled that "the reference
must be enabling and describe the applicant's claimed invention sufficiently

4 U.S. Patent 5,595,879, Multi-Domain DNA Ligands for Protein and Nucleic
Acid Affinity Chromatography and Processing of Solid-Phase DNA, issued
21 January 1997, to Joseph G. Utermohlen ("Utermohlen").
5 International Patent Application Publication WO 98/46797, Nucleic Acid
Archiving, published 22 October 1998, by Gerdes et al. ("Gerdes").
6 U.S. Patent Application Publication US 2001/0012612 A1, Method for
Analyzing a Fluid Sample, published 9 August 2001, by Petersen et al.
("Petersen").
7 The Examiner withdrew the final rejection of claim 7 under 35 U.S.C. §
102(b) as anticipated by Utermohlen (Ans. 4). In addition, in the Final
Rejection mailed 16 October 2008 ("FR"), the Examiner rejected claim 8
under 35 U.S.C. § 103(a) over Gerdes or Petersen each further in view of
Virgos (FR 9-10). Thus, the Appeal Brief argued the rejection of claims 1,
2, and 7 under 35 U.S.C. § 102(b) over Gerdes or Petersen and the rejection
of claim 8 under 35 U.S.C. § 103(a) over Gerdes or Petersen each in view of
Virgos (App. Br. 12-13). However, the Examiner rejected claims 1, 2, 7,
and 8 under 35 U.S.C. § 102(b) over Gerdes or Petersen in his Answer (Ans.
7, 9). Since Appellants responded to the "modified" anticipation rejections
under § 102(b) over Gerdes or Petersen in their Reply Brief (Reply Br. 3-
12), Appellants' due process rights have not been violated. Therefore, we
decide this appeal on the briefings before us.
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to have placed it in possession of a person of ordinary skill in the field of the
invention." In re Paulsen, 30 F.3d 1475, 1478-79 (Fed. Cir. 1994). "One
shows that one is 'in possession' of the invention by describing the invention,
with all its claimed limitations, not that which makes it obvious." Lockwood
v. American Airlines Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966
(Fed. Cir. 1997).
A. Rejection based on Utermohlen
The Examiner rejected claims 1 and 2 under 35 U.S.C. § 102(b) as
anticipated by Utermohlen (Ans. 11-13 and 14-15). The Examiner found
that Utermohlen expressly discloses steps [1]-[5] and [8] and inherently
discloses steps [6] and [7] of claim 1 in the recited order (id. at 38-41).
Appellants disagree (App. Br. 22-24; Reply Br. 13-16). Appellants
particularly argue that the "flat solid phase matrix" of Utermohlen is not a
"packed bed" as claimed (Reply Br. 13, 15-16).
The dispositive issue is whether Utermohlen expressly or inherently
describes each step of claim 1 in the recited order.
The following findings of fact ("FF") are based on a preponderance of
the evidence of record.
1. According to Utermohlen, mRNA affinity column chromatography
has some important disadvantages, e.g., packed columns often do not
permit large RNA to move freely through the matrix resulting in
exclusion and trapping of non-ligand bound RNA (Utermohlen 2:66-
3:8), disadvantages which "have been addressed by attempts to alter
the geometry of the packed column by flattening the three
dimensional nature of the matrix" (id. at 3:9-11).
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2. A conventional mRNA affinity column, e.g., comprises "[a] slurry of
… oligo-dT substituted cellulose powder was packed as a column
matrix …" (id. at 3:57-59).
3. Utermohlen discloses binding mRNA or viral RNA to a solid phase
binding matrix, e.g., diazotized arylamine-substitute[d] cellulose
papers or bead-type matrices coated with an arylamine, via an
oligonucleotide ligand (id. at 4:19-31; 5:21-39; claim 3).
4. An exemplary oligonucleotide ligand has a 3' terminal domain of
deoxythymidylate residues (oligo-dT) which binds to a diazotized
solid phase and a 5' terminal domain of deoxyguanidylate residues
(oligo-dG) which binds to 3' polyadenylated terminal residues of
bound RNAs, thereby orienting the bound RNA for priming cDNA
synthesis (id. at 6:1-14).
5. In an exemplary process, Utermohlen discloses preparing an oligo-dT
diazotized affinity paper ("oligo-dT paper") and extracting RNA from
HIV-RF infected cells (id. at 6:65-7:13; 9:1-5).
6. The RNA extract was annealed to the oligo-dT paper, which was
subsequently washed (id. at 6:21-26; 9:6-7).
7. After forming a cDNA complement of the oligo-dT paper bound RNA
by adding reverse transcriptase and deoxynucleotides, the paper
bound RNA was removed with an alkaline solution that left the cDNA
bound to the paper (id. at 9:7-11).
8. A polymerase chain reaction ("PCR") was run for 30 cycles of
denaturation, annealing, and primer extension using the oligo-dT
paper bound cDNA as template, primers SK38 and SK39, and Taq I
polymerase (id. at 1:67-2:16; 9:11-19).
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9. The PCR amplification products (199 bp product, lane 3) were
detected by ethidium bromide electrophoresis using a 123 bp marker
(lane 6) (id. at 9:20-22; Figure 2).
10. According to Utermohlen, since "the [cDNA] template for the
amplification reaction is bound to an insoluble matrix, it can be
removed from the [PCR] reaction without altering the template and
[be] re-used at a later time" (id. at 10:4-7).
Other findings of fact follow below.
The Examiner found that Utermohlen discloses step [1] of claim 1,
i.e., providing a packed bed, by teaching that oligo-dt substituted cellulose
mRNA affinity chromatography columns are known (see FF 1-2) and that its
solid phase matrix can also contain cellulose (FF 3). However, in our
opinion, the Examiner is picking and choosing disparate portions of
Utermohlen in order to find anticipation of step [1]. In NetMoney, Inc. v.
Verisign, Inc., 545 F.3d 1359, 1371 (Fed. Cir. 2008), the Federal Circuit
stated:
The district court was also wrong to combine parts
of the separate protocols shown in the iKP reference in
concluding that claim 23 was anticipated. Granted, there
may be only slight differences between the protocols
disclosed in the iKP reference and the system of claim
23. But differences between the prior art reference and a
claimed invention, however slight, invoke the question
of obviousness, not anticipation….see also In re Arkley,
59 C.C.P.A. 804, 455 F.2d 586, 587 (1972)
("[R]ejections under 35 U.S.C. § 102 are proper only
when the claimed subject matter is identically disclosed
or described in the prior art." (emphasis and internal
quotation marks omitted)). Thus, it is not enough that
the prior art reference discloses part of the claimed
invention, which an ordinary artisan might supplement to
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make the whole, or that it includes multiple, distinct
teachings that the artisan might somehow combine to
achieve the claimed invention. See Arkley, 455 F.2d at
587 ("[T]he [prior art] reference must clearly and
unequivocally disclose the claimed [invention] or direct
those skilled in the art to the [invention] without any
need for picking, choosing, and combining various
disclosures not directly related to each other by the
teachings of the cited reference.").

That is the case here. The Examiner has failed to explain where
Utermohlen, either explicitly or implicitly, describes packing its solid phase
matrix into a chromatography column/bed. It may well be that a slurry of
arylamine-substituted cellulose was used to form a diazotized arylamine-
substitute[d] cellulose paper (see e.g., FF 3) rather than a packed bed.
Inherency may not be established by probabilities. Roberston, 169 F.3d at
745.
In addition, step [5] of claim 1 recites amplifying the nucleic acid in
the sample. Utermohlen, however, extracts the nucleic acid (RNA) from the
sample (FF 5) and converts it to cDNA (FF 6), i.e., Utermohlen does not
amplify the RNA (nucleic acid) in the sample. Utermohlen amplifies its
cDNA (FF 8-9). The nucleic acid (RNA) from the sample was discarded,
i.e., removed from the solid phase, prior to cDNA amplification (FF 7).
Furthermore, steps [6] and [7] of claim 1 require two separate,
sequential steps of "releasing said amplification markers for detection" and
"eluting said amplified DNA from said packed bed", respectively.
According to the Examiner, the amplification markers, i.e., primers, are
released "from being annealed from the solid phase" by the denaturation step
of the PCR "for detection [of the nucleic acid of step 7]" (Ans. 40).
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However, Utermohlen detects the PCR amplification products, not the
primers (FF 9).
Based on the foregoing, we agree with Appellants that Utermohlen
does not expressly or inherently describe each step of claim 1 in the recited
order. Therefore, we reverse the rejection of claims 1 and 2 under 35 U.S.C.
§ 102(b) as anticipated by Utermohlen.
B. Rejection based on Gerdes
The Examiner rejected claims 1, 2, 7, and 8 under 35 U.S.C. § 102(b)
as anticipated by Gerdes (Ans. 7-9). The Examiner found that Gerdes
teaches the methods of claims 1 and 7 (id. at 20-28).
Appellants argue that Gerdes does not show Appellants' specific set of
steps in the specific order claimed in claims 1 and 7 (App. Br. 15).
Specifically, Appellants argue that Gerdes does not teach the preamble, steps
[5] to [8] of claim 1 or the preamble, steps [2], [6], [7], [8], [10], or [11] of
claim 7 (App. Br. 15; Reply Br. 3-4, 7-8).
The dispositive issue is whether Gerdes expressly or inherently
describes each step of claim 1 and claim 7 in their respective recited order.
Additional findings of fact:
11. Gerdes discloses
methods of using solid phases to irreversibly
capture RNA, DNA or other nucleic acids as a
means for: aqueous washes, buffer changes and
volume reductions during procedural
manipulations; rapid and immediate capture of
nucleic acid as a method of automating extraction;
integrating nucleic acid capture and purification
with oligonucleotide or probe hybridization or
target or signal amplification for direct analysis of
nucleic acid bound to the solid phase as either
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single or double strands; repeat and/or expanded
analysis of the bound nucleic acid following its
capture onto the solid phase matrix (nucleic acid
archiving); and, gravity or high flow rate solid
phase chromatography as a means of either
concentrating nucleic acid from large volume
specimens or removing contaminant nucleic acid
from aqueous buffers or solutions. [Gerdes 5:12-
23.]

12. Example 1 of Gerdes measures binding of P32-labeled DNA to by
gravity flow filtration through an aluminum oxide bead packed
chromatography column (id. at 11:29-12:18).
13. In Example 4 of Gerdes, a mixture of 106 copies of HIV DNA and 1
µl of mycobacterium DNA are simultaneously bound to aluminum
oxide in water. The bound HIV DNA is amplified using PCR,
followed by amplification of the bound mycobacterium DNA using
strand displacement amplification. The amplification products were
detected using ethidium bromide stained agar electrophoresis. [Id. at
14:26-15:10.]
14. Example 4 also illustrates capturing RNA from HIV virions in plasma
via high volume gravity filtration onto aluminum oxide in an
amplifiable state (id. at 15:22-16:1).
15. In Example 5, DNA is bound to aluminum and sequentially amplified
by PCR using five short tandem repeat markers to demonstrate
repeated solid phase aluminum amplification of the bound DNA as
detected by silver stained gel electrophoresis (id. at 16:2-13).
16. Example 7 teaches a nucleic acid extraction protocol comprising 1)
adding binding buffer to an aluminum oxide PCR tube, 2) adding
specimen to each tube, 3) washing by repeat pipetting wash buffer,
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then aspirating wash buffer to waste, 4) adding PCR amplification
master mix, and 5) amplifying in a thermal cycler (id. at 18:4-10).
17. Claims 1, 12, and 13 of Gerdes read as follows:
1. A method for archiving nucleic acid,
comprising:
a) irreversibly binding single- or
multiple-stranded nucleic acid contained in an
aqueous specimen to a solid phase matrix;
b) manipulating said solid phase bound
nucleic acid; and
c) storing said bound nucleic acid on said
solid phase matrix.

12. The method as defined in claim 1 wherein
direct manipulation methodology is selected from
the group consisting of enzyme reactions,
oligonucleotide hybridization, probe hybridization,
signal amplification and target amplification.

13. The manipulation as defined in claim 12
wherein said amplification methodology is
selected from the group consisting of PCR, SDA,
NASBA, IsoCR, CRCA, Q beta replicase and
branched chain DNA. (Id. at 28-29.)

Other findings of fact follow below.
In essence, the Examiner combines parts of various Examples in
Gerdes to find "methods" which anticipate the methods of claims 1 and 7.
As to claim 1, the Examiner found claim 1, steps [4] and [5],
"introducing an amplification mix and amplification markers into said
packed bed" and "thermal cycling …", respectively, disclosed in Gerdes'
Example 7 and claim 13 (Ans. 21-22) (see FF 16-17). The Examiner further
found claim 1, steps [6] and [7], i.e., "releasing said amplification markers
for detection" and "eluting said amplified DNA from said packed bed",
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inherent in Gerdes' Examples 4 and 5 (Ans. 22-23) (see FF 13-15). In other
words, the Examiner found that following PCR amplification in Gerdes'
Example 7, a short tandem repeat marker from Example 5 is released for
detection by silver stained gel electrophoresis which, according to Example
5 is used to detect PCR amplification products and/or a PCR "marker" from
Example 4 is released for detection by ethidium bromide stained gel
electrophoresis, which according to Example 4 is used to detect PCR
amplification products (Ans. 22-23). Furthermore, the Examiner relies on
the same disclosure in Gerdes to anticipate each of claim 1, steps [6] to [8],
i.e., page 16, lines 11-13, and Figure 7, and page 15, lines 18-30, and Figure
6 (id.). Either Gerdes teaches that the PCR amplification step in its Example
7 necessarily requires claim 1, steps [6] and [7], prior to detection of PCR
amplification products, i.e., claim 1, step [8] or not. It may very well be that
the PCR amplification products of Gerdes' Example 7 are detected in real-
time. Here, Gerdes' Example 7 is silent both regarding what reactants are
present in the PCR amplification "master mix" and how and when the
resulting PCR amplification products are detected.
Therefore, we agree with Appellants that Gerdes does not expressly or
inherently describe each of steps [1] to [8] of claim 1 in the recited order.
Claim 7, steps [7] to [9], parallel claim 1, steps [5] to [7]. Indeed, the
Examiner finds that the same disclosure in Gerdes said to anticipate the
latter also anticipates the former (compare Ans. 21-23 with Ans. 26-27).
Therefore, we also agree with Appellants that Gerdes does not expressly or
inherently describe each of steps [1] to [11] of claim 7 in the recited order.
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Since claims 2 and 8 contain all of the limitations of independent
claims 1 and 7, respectively, from which they depend, we also agree with
Appellants that claims 2 and 8 are not anticipated by Gerdes.
In summary, we reverse the rejection of claims 1, 2, 7, and 8 under §
102(b) as anticipated by Gerdes because Gerdes does not expressly or
inherently describes each step of claim 1 and claim 7 in their respective
recited order.
C. Rejection based on Petersen
The Examiner rejected claims 1, 2, 7, and 8 under 35 U.S.C. § 102(b)
as anticipated by Petersen (Ans. 9-11). The Examiner found that Petersen
teaches the methods of claims 1 and 7 (id. at 29-37).
Appellants argue that Petersen does not show Appellants' specific set
of steps in the specific order claimed in claims 1 and 7 (App. Br. 18; Reply
Br. 9). Specifically, Appellants argue that Petersen does not describe the
preamble and steps [5] to [7] of claim 1 or the preamble and steps [2], [6],
[7], [8], [10], or [11] of claim 7 (App. Br. 19-20). Appellants further argue
that Petersen does not disclose the claimed "packed bed" (Reply Br. 9, 12).
The dispositive issue is whether Petersen expressly or inherently
describes each step of claim 1 and claim 7 in their respective recited order,
including step [1], i.e., "providing a packed bed" and/or "packing bed media
into a tubing or housing to form a packed bed."
Additional findings of fact:
18. Petersen discloses an apparatus for separating a desired analyte, such
as a nucleic acid, from a fluid sample and for holding the analyte for a
chemical reaction, such as for amplification, e.g., using PCR, and
optical detection (Petersen ¶¶ 4, 53-55).
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19. Preferably, the analyte is separated from the sample by introducing
the sample into a cartridge containing a lysing chamber having at least
one filter for separating cells or viruses from the sample and two sets
of beads. The sample is forced to flow through the chamber,
capturing the cells or viruses with the filter. The captured cells or
viruses bind to a first set of beads in the lysing chamber and are
mechanically lysed by agitating the second set of beads. (Id. at ¶¶ 5-
6.)
20. In one embodiment, cartridge 20 includes a reaction vessel 40 which
has a reaction chamber 42 for holding a reaction mixture (e.g., nucleic
acid mixed with amplification reagents and fluorescent probes) for
chemical reaction and optical detection. The vessel 40 may be
inserted between a pair of opposing thermal plates for heating and
cooling the chamber 42 without decoupling the vessel 40 from the rest
of the cartridge 20. (Id. at ¶ 57; Figure 2).
21. Petersen describes an exemplary protocol as follows:
(i) the cartridge is preferably primed with wash solution before the
fluid sample is forced to flow from the sample chamber (id. at ¶ 144),
(ii) sample liquid flows through the filter stack to capture target cells
or viruses in the sample (id. at ¶ 145),
(iii) wash solution is forced to flow into the lysing chamber to wash
away PCR inhibitors and contaminants from the lysing chamber (id. at ¶
147),
(iv) the lysing chamber is filled with lysing reagent and a transducer is
used to impart a velocity to the liquid in the lysing chamber (id. at ¶¶
148-151),
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(v) the beads in the filter stack are agitated by the pressure waves in
the lysing chamber and the beads mechanically rupture the cells or
viruses to release the material, e.g., nucleic acid, therefrom (id. at ¶ 151),
(vi) following cellular/viral disruption, pressure is used to force the
lysis reagent to elute the nucleic acid from the filter stack and to flow the
nucleic acid into an optional neutralization chamber (id. at ¶ 152),
(vii) pressure is used to force neutralizing lysing reagent and nucleic
acid into a reaction chamber containing PCR reagents and fluorescent
probes to form a reaction mixture (id. at ¶ 153),
(viii) pressure is used to move the reaction mixture into a reaction
vessel (id. at ¶ 154),
(ix) the walls of the reaction chamber are pressurized to contact and
conform to the inner surfaces of opposing thermal plates to ensure
optimal thermal conductance between the plates and the reaction mixture
in the chamber (id. at ¶ 155), and
(x) the reaction mixture in the vessel is thermally processed and
optically interrogated, preferably at the lowest temperature point in each
cycle, to determine the presence or absence of a target analyte in the
mixture (id. at ¶¶ 155, 157).
Other findings of fact follow below.
Again, we agree with Appellants that Petersen does not expressly or
inherently describe each step of claim 1 and/or claim 7 in their respective
recited order, including step [1], i.e., "providing a packed bed" and/or
"packing bed media into a tubing or housing to form a packed bed."
Assuming arguendo that the beads in the lysing chamber (FF 19) correspond
to the "packed bed" recited in step [1] of both claims 1 and 7, it is clear that
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the PCR reagents, i.e., the amplification mix and amplification markers of
claim 1, step [4], and claim 7, step [6], are not added to the "packed bed" but
rather are contained in a separate reaction chamber to which lysed sample
eluted from the lysing chamber is added (FF 20-21). It is not enough that
Petersen includes multiple distinct teachings that the artisan might somehow
combine to achieve the claimed invention. NetMoney, Inc., 545 F.3d at
1371. "[R]ejections under 35 U.S.C. § 102 are proper only when the
claimed subject matter is identically disclosed or described in 'the prior art.'"
Arkley, 455 F.2d at 587.
Since claims 2 and 8 contain all of the limitations of independent
claims 1 and 7, respectively, from which they depend, we also agree with
Appellants that claims 2 and 8 are not anticipated by Petersen.
In summary, we reverse the rejection of claims 1, 2, 7, and 8 under §
102(b) as anticipated by Petersen because Petersen does not expressly or
inherently describe each step of claim 1 and claim 7 in their respective
recited order.
IV. Obviousness
The Examiner rejected claim 3 under 35 U.S.C. § 103(a) as obvious
over any of Utermohlen, Gerdes or Petersen as applied to claim 1 and further
in view of Virgos (Ans. 15-16). The Examiner also rejected claims 8 and 9
under 35 U.S.C. § 103(a) as obvious over Gerdes or Petersen as applied to
claim 7 and further in view of Virgos (id. at 16-18).
Claims 3, 8, and 9 all require introducing e-tags or taqman probes
amplification markers into the packed bed in claim 1, step [4], and claim 7,
steps [5] and [6].
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The Examiner relies on Virgos to teach methods of nucleic acid
amplification using e-tags and taqman probes (Ans. 16-17). According to
the Examiner, it would have been obvious to modify the methods of
Utermohlen, Gerdes, and Petersen by using e-tags because Virgos teaches
that e-tag primers are useful in e-tag probe-mediated analysis of target
nucleic acids and taqman probes allow genotyping to be done is a singe tube
(id. at 16-18, 43-45).
Appellants argue that Virgos does not remedy the deficiencies of
Utermohlen, Gerdes or Petersen (App. Br. 29-31; Reply Br. 19-22).
Appellants further argue that the Examiner has not explained how or why
Virgos and Gerdes, Petersen, or Utermohlen would be combined (App. Br.
32; Reply Br. 22).
"The test of obviousness vel non is statutory. It requires that one
compare the claim's 'subject matter as a whole' with the prior art 'to which
said subject matter pertains.' 35 U.S.C. § 103. The inquiry is thus highly
fact-specific by design. This is so 'whether the invention be a process for
making or a process of using, or some other process.'" In re Brouwer, 77
F.3d 422, 425 (Fed. Cir. 1996). In KSR Int'l Co. v. Teleflex, Inc., 550 U.S.
398, 418 (2007) (citing In re Kahn, 441 F.3d 997, 988 (Fed. Cir. 2006)), the
Supreme Court noted that "[t]o facilitate review, this [obviousness] analysis
should be made explicit."
Furthermore, obviousness requires a suggestion of all limitations in a
claim. In re Royka, 490 F.2d 981, 985 (CCPA 1974).
The dispositive issues are whether the combination of Virgos and any
of Utermohlen, Gerdes or Petersen teach or suggest all the limitations of
claim 1 incorporated into claim 3 and whether the combination of Virgos
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and Gerdes or Petersen teach or suggest all the limitations of claim 7
incorporated into claims 8 and 9.
Additional findings of fact:
22. According to Virgos, Whitcombe teaches "a homogeneous
fluorescence assay for PCR amplicons where a 5'-exonuclease assay
of amplicon annealed fluorogenic TaqMan® probes is carried out in
conjunction with the Amplification Refractory Mutagenesis System
(ARMS). The assay is used for the single-tube genotype analysis of
human DNA polymorphisms and mutations" (Virgos ¶ 12).
23. Virgos discloses using a single set of e-tag probes to identify samples
containing any group of different target sequences (id. at ¶ 91).
24. According to Virgos, "target sequences with bound probes are treated
under the selected conditions, to release an e-tag reporter from each e-
tag probe bound to a target sequence, the released reporters are
separated electrophoretically, and the separated reporters are detected,
to identify and, optionally, quantitate, target sequences that hybridized
to the probes" (id. at ¶ 93).
Again we agree with Appellants that the combined teachings of the
applied prior art fail to teach or suggest all the limitations present in claims
3, 8, and 9. In short, the Examiner relies on Utermohlen, Gerdes, and
Petersen to teach all the limitations of independent claims 1 and 7
incorporated into dependent claim 3 and claims 8 and 9, respectively. This
reliance is misplaced for the reasons set forth in the anticipation analyses
above. Therefore, we reverse the rejections of claim 3 under 35 § 103(a) as
obvious over any of Utermohlen, Gerdes or Petersen as applied to claim 1
and further in view of Virgos and of claims 8 and 9 under § 103(a) as
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obvious over Gerdes or Petersen as applied to claim 7 and further in view of
Virgos. The combination of Virgos and any of Utermohlen, Gerdes or
Petersen teach or suggest all the limitations of claim 1 incorporated into
claim 3 and whether the combination of Virgos and Gerdes or Petersen teach
or suggest all the limitations of claim 7 incorporated into claims 8 and 9.
V. Order
Upon consideration of the record, and for the reasons given, it is
ORDERED that the decision of the Examiner to reject claims 3, 8, and
9 as unpatentable under 35 U.S.C. § 112, second paragraph, as indefinite is
REVERSED;
FURTHER ORDERED that the decision of the Examiner to reject
claims 1 and 2 as unpatentable under 35 U.S.C. § 102(b) as anticipated by
Utermohlen is REVERSED;
FURTHER ORDERED that the decision of the Examiner to reject
claims 1, 2, 7, and 8 as unpatentable under 35 U.S.C. § 102(b) as anticipated
by Gerdes is REVERSED;
FURTHER ORDERED that the decision of the Examiner to reject
claims 1, 2, 7, and 8 as unpatentable under 35 U.S.C. § 102(b) as anticipated
by Petersen is REVERSED;
FURTHER ORDERED that the decision of the Examiner to reject
claim 3 as unpatentable under 35 U.S.C. § 103(a) as obvious over any of
Gerdes, Petersen or Utermohlen, as applied to claim 1, and further in view of
Virgos is REVERSED; and,

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FURTHER ORDERED that the decision of the Examiner to reject
claims 8 and 9 as unpatentable under 35 U.S.C. § 103(a) as obvious over
Gerdes or Petersen, as applied to claim 7, and further in view of Virgos is
REVERSED.

REVERSED

alw

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