Ex Parte Kelso et al

Patent Trial and Appeal Board

Jul 23, 2018

13645447 (P.T.A.B. Jul. 23, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/645,447 10/04/2012
108547 7590 07/25/2018
McDermott Will & Emery LLP
500 North Capitol Street NW
Washington, DC 20001
FIRST NAMED INVENTOR
David M. Kelso
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.
041896-0717 7056
EXAMINER
FORMAN, BETTY J
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
07/25/2018 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
mweipdocket@mwe.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte DAVID M. KELSO, KUN AL SUR, and ZAHEER P ARPIA
Appeal2017-007438 1
Application 13/645,447
Technology Center 1600
Before FRANCISCO C. PRATS, JAMES A. WORTH, and
TIMOTHY G. MAJORS, Administrative Patent Judges.
PRATS, Administrative Patent Judge.
DECISION ON APPEAL
This appeal under 35 U.S.C. § 134(a) involves claims to methods of
processing biological samples to extract analytes, such as nucleic acid, from
the samples. The Examiner entered two rejections for obviousness, and one
provisional rejection for obviousness-type double patenting.
We have jurisdiction under 35 U.S.C. § 6(b)(l).
We reverse one of the obviousness rejections, but affirm the other.
We dismiss the provisional double patenting rejection as moot,
because the copending application forming the basis of the rejection has
been abandoned.
1 Appellants state that the "real party in interest is Northwestern University."
Br. 1.
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Application 13/645,447
STATEMENT OF THE CASE
The following rejections are before us for review:
(1) Claims 1 and 3-12, under 35 U.S.C. § I03(a) for obviousness over
Collier2 (Ans. 2-3);
(2) Claims 1 and 3-18, under 35 U.S.C. § I03(a) for obviousness over
Vinayagamoorthy3 and Collier (Ans. 3---6); and
(3) Claims 1 and 3-18, provisionally rejected on the ground of
nonstatutory obviousness-type double patenting over claims 1-18 of
copending Application No. 13/421,742 ("the '742 application) (Ans. 6-7).
Claim 1, the only independent claim on appeal, is representative and
reads as follows:
1. A method of processing a sample, comprising:
providing a device comprising a first chamber and a
second chamber, wherein the first and second chambers are
operatively connected and, wherein each of said first and
second chambers is configured to contain a solution;
loading the first chamber with a first solution and the
second chamber with a second solution;
after loading, overlaying at least one of the first and
second solutions with a substance that is immiscible with water;
placing a sample into the device;
applying a force to a solid phase carrier in the device, the
solid phase carrier capable of associating with an analyte in the
sample; and
transferring, by relative movement of the applied force
with respect to the device, the solid phase carrier and associated
analyte into and through the substance and into the second
chamber,
2 US 2010/0291666 Al (published Nov. 18, 2010).
3 US 5,912,129, issued June 15, 1999).
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wherein the first and second solutions in the first and
second chambers remain stationary after said loading.
Appeal Br. 10.
OBVIOUSNESS-COLLIER
The Examiner's Prima Facie Case
The Examiner finds that Collier describes a process having all of the
steps and features required by claim 1, but concedes that Collier's process
differs from the process recited in claim 1 in that Collier does not
"specifically teach placing the buffer into the tube prior to overlaying the
wax medium." Ans. 2.
The Examiner concludes, however, that an ordinary artisan would
have considered it obvious to "add the wax medium following addition of
the buffer because Collier specifically teaches the wax above the buffer
whereby the beads are pulled from the buffer, through the wax and out of the
tube." Id. at 3.
Analysis
As stated inJn re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992):
[T]he examiner bears the initial burden ... of presenting a
prima facie case of unpatentability ....
After evidence or argument is submitted by the applicant
in response, patentability is determined on the totality of the
record, by a preponderance of evidence with due consideration
to persuasiveness of argument.
In the present case, having carefully considered the arguments and
evidence advanced by Appellants and the Examiner, Appellants persuade us
that the preponderance of the evidence does not support the Examiner's
conclusion of obviousness. In particular, Appellants persuade us that,
contrary to the Examiner's finding, Collier does not teach or suggest a
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device having two operatively connected chambers encompassed by
Appellants' claim 1.
It is well settled that, during examination, the PTO must interpret
terms in a claim using "the broadest reasonable meaning of the words in
their ordinary usage as they would be understood by one of ordinary skill in
the art, taking into account whatever enlightenment by way of definitions or
otherwise that may be afforded by the written description contained in the
applicant's specification." In re Morris, 127 F.3d 1048, 1054 (Fed. Cir.
1997) ( emphasis added).
Appellants' claim 1 recites the step of "providing a device comprising
a first chamber and a second chamber, wherein the first and second
chambers are operatively connected." Br. 10 (emphasis added).
In finding that Collier teaches claim 1 's step of providing a device
having operatively connected first and second chambers, the Examiner cites
,r 88 of Collier. Ans. 2. Paragraph 88 of Collier discloses of a process in
which a nucleic acid-containing blood sample is introduced into a first tube
containing magnetic beads and a lysis buffer, resulting in lysis of cells in the
blood, release of nucleic acid from the lysed cells, and adsorption of the
released nucleic acid onto the magnetic beads. See Collier ,r 88.
Paragraph 88 of Collier discloses that a magnet is used to transport the
magnetic beads, and the nucleic acids adsorbed thereto, to "a new tube with
the PCR cocktail present." Id.
In reasoning that the second, "new tube," described in Collier (see id.)
is operatively connected to Collier's lysis buffer-containing first tube, as
required by Appellants' claim 1, the Examiner states as follows:
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Collier clearly and specifically teaches applying
magnetic force to the tube to move the support-bound nucleic
acids through the wax and then placing the support-bound
nucleic acids into a second tube. Therefore the first and second
tube are encompassed by the broadly claimed "operatively
connected" because the tubes operate together (i.e. operatively
connected) for transporting the support-bound nucleic acids
from the first and into the second tube.
Ans. 5.
In this instance, we are not persuaded that the Examiner's
interpretation of claim 1 is reasonable. As we understand the Examiner's
contention, the Examiner considers the two tubes of Collier to be operatively
connected because both tubes are involved in the same operation of
transporting support-bound nucleic acids.
As seen above, however, the language at issue in claim 1 recites
"providing a device comprising a first chamber and a second chamber,
wherein the first and second chambers are operatively connected." Br. 10
( emphasis added). Thus, as Appellants contend (id. at 2), claim 1 requires
the operatively connected first and second chambers to be components of a
single device.
The Examiner, however, does not identify, nor do we discern, any
disclosure in Collier teaching or suggesting a single device that includes the
two tubes cited as corresponding to the two chambers of Appellants' claim
1. Accordingly, we are not persuaded that the Examiner has shown
sufficiently that, when claim 1 is given its broadest reasonable interpretation
consistent with the Specification, Collier teaches or suggests a process
having all of the steps and features the claim requires. We, therefore,
reverse the Examiner's rejection of claim 1, and its dependent claims 3-12,
for obviousness over Collier.
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OBVIOUSNESS-
VINA Y AGAMOORTHY AND COLLIER
The Examiner's Prima Facie Case
In rejecting claims 1 and 3-18 over Vinayagamoorthy and Collier, the
Examiner cites Vinayagamoorthy as describing a process having all of the
steps and features of representative claim 1, including the operatively
connected first and second chambers discussed above, but acknowledges
that Vinayagamoorthy differs from claim 1 in that "Vinayagamoorthy does
not teach an immiscible substance." Ans. 4.
The Examiner finds, however, that "immiscible layers were well-
known and routinely practiced in the art at the time the invention was made
as taught by Collier." Id.
In particular, the Examiner cites Collier as disclosing a method similar
to Vinayagamoorthy' s method, "for processing a sample for PCR as
illustrated in Fig. 1, the method comprising providing a device comprising a
first chamber comprising a sample solution, magnetic bead and an
immiscible substance and applying a magnetic field to transfer the bead from
the chamber into PCR chambers." Id. ( citing Collier ,r,r 87-90).
More particularly, the Examiner notes that "Collier teaches the
immiscible substance filters the sample to exclude non-target substances
whereby the target-immobilized beads can be used directly in PCR
reactions." Id. (citing Collier ,r,r 88-90).
Based on the references' combined teachings, the Examiner reasons
that an ordinary artisan would have considered it obvious to "modify the
method of Vinayagamoorthy by providing at least one of the chambers with
the immiscible substance of Collier to thereby filter and exclude non-target
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substances from transfer into subsequent chambers as desired in the art." Id.
( citing Collier ,r,r 88-90).
Analysis
In this instance, having carefully considered the arguments and
evidence advanced by Appellants and the Examiner, Appellants do not
persuade us that the preponderance of the evidence fails to support the
Examiner's conclusion of obviousness. In particular, we agree with the
Examiner that the combination of Vinayagamoorthy and Collier would have
suggested the process recited in Appellants' claim 1 to an ordinary artisan.
Vinayagamoorthy describes a process "for the polymerization and
amplification of sequences of nucleic acids of prokaryotic and eukaryotic
origin involving the polymerase chain reaction or the ligase chain reaction."
Vinayagamoorthy 1: 7-10.
To process the nucleic acid-containing samples, Vinayagamoorthy
provides an "apparatus [which] comprises a housing 20 enclosing four
chambers 21, 22, 23 and 24 forming reaction containers capable of enclosing
reaction zones. Id. at 10:65---67; see also id. at Fig. 6a.
Vinayagamoorthy explains that the "lower parts of the chambers are
not in fluid communication with each other, although the containers share a
common head space 25 above the normal upper level of contained liquids
forming a passage that allows the access to each chamber .... " Id. at
10:67-11: 1. Thus, unlike Collier discussed above, Vinayagamoorthy
describes providing a single device with two operatively connected
chambers, as Appellants' claim 1 requires.
Vinayagamoorthy explains further:
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Each chamber contains a liquid 21a, 22a, 23a and 24a suitable
for carrying out a step in the process. Chamber 21 is for the
step of denaturing double stranded DNA in alkaline conditions.
Chamber 22 is a neutralising chamber containing an aqueous
liquid for neutralizing alkali carried over from chamber 21. ...
Chamber 23 is an annealing chamber containing a solution of
primers. . . . Chamber 24 is provided for the polymerization
reaction and holds a liquid containing a nucleic acid polymerase
that is preferably alkali-tolerant.
Id. at 11 :5-20; see also id. at Fig. 6a. Thus, as Appellants' claim 1 requires,
Vinayagamoorthy's process includes loading first and second solutions into
the chambers.
Vinayagamoorthy explains that processing is performed by placing
the sample in the solution in the first chamber 21, in the presence of
magnetic beads to which the nucleic acids become adsorbed, and then using
an external magnetic to move the beads ( and adsorbed nucleic acids) over
the barriers between the chambers, sequentially from chamber 21, to
chamber 22, to chamber 23, and finally to chamber 24, where
polymerization occurs. Id. at 11 :26-50; see also Figs. 6a-6d (showing
sequential movement of beads ( and adsorbed nucleic acid) through chambers
21-24 ). Thus, as required by Appellants' claim 1, Vinayagamoorthy
discloses applying a force (magnetism) to the solid phase carrier (magnetic
beads), and using that force to move the solid phase carrier from a first
solution in a first chamber into a second solution in a second chamber.
As the Examiner finds, Vinayagamoorthy's process thus differs from
the process of Appellants' claim 1 in that Vinayagamoorthy does not
disclose claim 1 's step of overlaying a water-immiscible substance over at
least one of its processing solutions.
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As noted above, however, and as the Examiner finds (Ans. 4), Collier
discloses a process similar to Vinayagamoorthy's process, in which a nucleic
acid-containing blood sample is introduced into a first tube containing
magnetic beads, resulting in adsorption of the nucleic acids to the beads,
after which a magnet is used to transport the magnetic beads ( and the nucleic
acids adsorbed thereto), to "a new tube with the PCR cocktail present."
Collier ,r 88.
As required by Appellants' claim 1, Collier discloses overlaying a
water-immiscible liquid wax over the lysis solution, through which the beads
( and adsorbed nucleic acids) pass when moved by the magnet. See id.
Collier explains that "[i]t has surprisingly been found that this effectively
filters the pellet, as excess aqueous fluid is excluded by the greater surface
tension of the wax." Id.
In addition to the advantage of removing excess fluid from the nucleic
acid pellet, Collier discloses that the wax overlay provides benefits with
respect to moving the pellet from the lysis tube to the tube used for
performing amplification:
Id.
Optionally, after this step, the wax may be re-hardened
by removing the heat. The resulting bead-nucleic acid pellet
remains trapped in a thin layer of wax easily accessible at the
side of the tube, while the lytic buffer and blood remains
trapped below the wax. The bead-nucleic acid pellet can then
be removed from the side of the tube and introduced to a new
tube with the PCR cocktail present.
Given Collier's teachings that overlaying a water-immiscible wax
over a lysis solution used in a nucleic acid polymerization process not only
provides the advantage of removing excess fluid from the nucleic acid pellet,
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but also provides benefits with respect to moving the pellet from the lysis
tube to the tube used for polymerization, we agree with the Examiner that an
ordinary artisan had adequate reason for, and a reasonable expectation of
success in, overlaying Collier's water-immiscible wax over the solutions in
at least one, if not all, of the tubes used in Vinayagamoorthy' s process. As
the Supreme Court has explained, "if a technique has been used to improve
one device, and a person of ordinary skill in the art would recognize that it
would improve similar devices in the same way, using the technique is
obvious unless its actual application is beyond his or her skill." KSR Int 'l
Co. v. Teleflex Inc., 550 U.S. 398,417 (2007).
Because the Examiner's rejection was based on the teachings
discussed above in Vinayagamoorthy and Collier (see Ans. 4), Appellants do
not persuade us (Br. 7-8) that the rejection failed to provide a sufficient
rationale for concluding that the process recited in claim 1 would have been
obvious to an ordinary artisan.
We acknowledge, as Appellants contend (see id. at 6-7), that claim 1
includes the final recitation "wherein the first and second solutions in the
first and second chambers remain stationary after said loading." Id. at 10.
Claim 1, however, does not recite any specific step, other than those
discussed above, for achieving the result recited in the final wherein clause.
The final wherein clause in claim 1, therefore, simply states the result of
performing the previously recited steps.
This interpretation of the final wherein clause of claim 1 is supported
by ,r,r 216 and 240 of Appellants' Specification, which Appellants cite as
support for the solutions remaining stationary. See Br. 2. Both ,r,r 216 and
240 describe, essentially, the process recited in Appellants' claim 1, in
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which liquid wax is overlaid over a lysis buffer and elution buffer. See
Spec. ,r,r 216, 240.
As the Federal Circuit has explained, "[a] 'whereby' clause that
merely states the result of the limitations in the claim adds nothing to the
patentability or substance of the claim." Texas Instruments, Inc. v.
International Trade Comm., 988 F.2d 1165, 1172 (Fed. Cir. 1993). Thus,
because the cited references, as discussed above, suggest a process having
all of the steps positively recited in claim 1, and because the final wherein
clause of claim 1 simply recites the result of the process suggested by the
prior art, we are not persuaded that claim 1 's process may be considered
unobvious based on the final wherein clause in claim 1, absent some
evidence that the recited result would have been unexpected.
We are also unpersuaded by Appellants' contention (Br. 6) that
Vinayagamoorthy fails to suggest that its solutions remain stationary after
loading, as claim 1 requires, particularly when combined with Collier. We
acknowledge, as noted above, that Vinayagamoorthy's device includes "a
neutralising chamber containing an aqueous liquid for neutralizing alkali
carried over from chamber 21." Vinayagamoorthy 11:8-10.
As seen in Figures 6a---6d of Vinayagamoorthy, however, the beads
are transferred from the neutralizing chamber 22 to the annealing chamber
23, and then the polymerizing chamber 24. Appellants identify no specific
disclosure in Vinayagamoorthy suggesting that the solutions in those
chambers are transferred to the other chambers. Moreover, as discussed
above, given the combined teachings of the references, an ordinary artisan
had adequate reason to overlay Collier's water-immiscible wax onto the
solutions in Vinayagamoorthy's device. As explained in Appellants'
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Specification at ,r,r 216 and 240, performing that overlaying step achieves
the stationary solutions recited in Appellants' claim 1.
We are also unpersuaded by Appellants' contention (Br. 6-7) that
Collier suggests that solutions overlaid with its water-immiscible wax would
not remain stationary after loading, as claim 1 requires. We acknowledge
Collier's disclosure, in certain embodiments, of an optional step of washing
the nucleic acid/bead complex after moving the pellet through the wax layer.
See Collier ,r 169. We acknowledge also Collier's disclosure that passing
the nucleic acid/bead complex through the filtering wax layer "selectively
separat[es] the complex from the bulk of solution." Id. ,r 87.
Although these disclosures might not expressly describe the entirety
of Collier's lysis solution as remaining in its original tube, those disclosures
do not negate Collier's teaching, noted above, that moving the nucleic
acid/bead pellet through the wax overlay "effectively filters the pellet, as
excess aqueous fluid is excluded by the greater surface tension of the wax."
Id. ,I 88.
As explained above, given Collier's disclosure that the wax overlay
filters the pellet and excludes excess aqueous fluid from the nucleic
acid/bead complex, and further given Collier's disclosure of the additional
benefit of the wax overlay with respect to moving the pellet from the lysis
tube to the tube used for polymerization (see id.), we are persuaded that an
ordinary artisan had reasons for, and a reasonable expectation of success in,
overlaying Collier's water-immiscible wax over the solutions in at least one,
if not all, of the tubes used in Vinayagamoorthy's process. As also
explained above, Appellants' own Specification acknowledges that
performing that process results in the stationary first and second solutions
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recited in Appellants' claim 1. See Spec. ,r,r 216 and 240. Thus, the fact that
certain disclosures in Collier, when considered alone, might suggest a result
different than the result recited in Appellants' claim 1, does not demonstrate
that the combined teachings of the cited references fail to suggest a process
having all of the claimed steps, which, as acknowledged by Appellants'
Specification, produces the claimed result.
In sum, for the reasons discussed, Appellants do not persuade us that
the preponderance of the evidence fails to support the Examiner's
conclusion of obviousness as to claim 1. We, therefore, affirm the
Examiner's rejection of claim 1 over Vinayagamoorthy and Collier.
Because they were not argued separately, claims 3-18 fall with claim 1. See
37 C.F.R. § 4I.37(c)(l)(iv).
OBVIOUSNESS-TYPE DOUBLE PATENTING
The '742 application, which forms the basis of the Examiner's
provisional obviousness-type double patenting rejection, has been
abandoned. See '742 application (Notice of Abandonment entered April 5,
2018). We therefore dismiss the Examiner's provisional double patenting
rejection (Ans. 6-7) as moot.
SUMMARY
We reverse the Examiner's rejection of claims 1 and 3-12, under
35 U.S.C. § 103(a) for obviousness over Collier.
We affirm the Examiner's rejection of claims 1 and 3-18, under
35 U.S.C. § 103(a) for obviousness over Vinayagamoorthy and Collier.
We dismiss as moot the Examiner's provisional rejection of claims 1
and 3-18 on the ground of nonstatutory obviousness-type double patenting.
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TIME PERIOD
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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