Ex Parte Laitala et al

Patent Trial and Appeal Board

Feb 16, 2017

11252851 (P.T.A.B. Feb. 16, 2017)

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.
11/252,851 10/19/2005 Ville Laitala 1014975-000106.001 9348
21839 7590 02/21/2017
BUCHANAN, INGERSOLL & ROONEY PC
POST OFFICE BOX 1404
ALEXANDRIA, VA 22313-1404
EXAMINER
CHUNDURU, SURYAPRABHA
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
02/21/2017 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):
ADIPDOCl@BIPC.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte VILLE L AIT ALA and ALICE YLIKOSKI
Appeal 2015-000072
Application 11/252,8511
Technology Center 1600
Before DEMETRA J. MILLS, JEFFREY N. FREDMAN and DAVID
COTTA, Administrative Patent Judges.
COTTA, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a
homogeneous bioaffinity assay. The Examiner rejected the claims on appeal
as obvious under 35 U.S.C. § 103(a).
We affirm.
1 According to Appellants, the real party in interest is the Wallac OY. App.
Br. 1
Appeal 2015-000072
Application 11/252,851
STATEMENT OF THE CASE
“This present invention relates to a labeled probe for use in bioaffinity
assays based on time-resolved fluorescence resonance energy transfer [“TR
FRET”] wherein said probe comprises an energy donor as well as an energy
acceptor, and the energy transfer signal of the acceptor is aimed to be
measured.” Specification 11.
Claims 1—10 and 19 are on appeal. Claim 1 is illustrative and reads as
follows:
1. A homogeneous bioaffinity assay for quantitative
or qualitative determination of an analyte comprising the
steps of:
a) providing a labeled probe molecule consisting of:
(i) a TR-FRET label pair consisting of a
luminescent energy donor that is a lanthanide
chelate having an excited state lifetime of at least 1
microsecond and a luminescent energy acceptor
having an excited state lifetime of 1 microsecond
or less; and
(ii) a reactive region, capable of reacting with
an analyte to be determined;
b) contacting said labeled probe molecule with a
sample, expected to comprise said analyte
dissolved in a solvent;
c) allowing said labeled probe molecule and said
analyte to undergo an analyte-specific binding
reaction; said labeled probe molecule having
different energy transfer efficiency between the
donor and the acceptor after said binding reaction
with said analyte as compared to a non-reacted
labeled probe molecule; wherein the donor and the
acceptor are contained in said labeled probe
molecule before and after said analyte specific
binding reaction; and
d) measuring the change in the energy transfer based
acceptor emission using a time-resolved
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Application 11/252,851
measurement on a microsecond time scale;
wherein the amount of acceptor emission is
proportional to the amount of analyte present in the
sample.
The Examiner rejected claims 1—10 and 19 under pre AIA 35 U.S.C.
103(a) as unpatentable over the combination of Hemmila,2 Latva,3 Nurmi4
and Phillips.5
FINDINGS OF FACT
1. Hemmila discloses:
The invention relates to improvements of energy-transfer
based homogeneous assays, which use time-resolved
fluorometry in detection. The specific improvements
relate to the type of lanthanide chelate labels used as
energy donors, optimized energy acceptors for defined
assays, the way energy transfer is measured using
optimized filters and time windows, ways to correct all
possible interferences derived from samples, use the assay
for multi-component analysis and development of
simplified assay protocols.
Hemmila Abstract.
2. Hemmila discloses:
An object of the present invention is to provide a
luminescence energy transfer assay comprising a first
group labelled with an energy donor and a second group
labelled with an energy acceptor, wherein the acceptor is
either a short excited state lifetime luminescent label or a
non-luminescent label. The increase or decrease,
2 Hemmila et al., WO 98/15830, published April 16, 1998 (“Hemmilla”)
3 Fatva et al., US Patent No. 5,998,146, issued Dec. 7, 1999 (“Fatva”).
4 Nurmi et al., WO 01/61034 Al, published Aug. 23, 2001 (“Nurmi”).
5 Phillips et al., US Patent Publication No. 2002/0115082 Al, published
Aug. 22, 2002 (“Phillips”).
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Application 11/252,851
respectively, in energy transfer from the donor label to
the acceptor label resulting from shortening or
lengthening, respectively, of the distance between said
labels, is measured. According to the invention, the donor
is a luminescent lanthanide chelate.
Id. atp. 10,11. 20-30.
3. Latva discloses:
The present invention relates to the field of luminescence
energy transfer assay comprising a first group labeled
with an energy donor and a second group labeled with an
energy acceptor, wherein the acceptor is either a short
excited state lifetime luminescent label or a
nonluminescent label. The increase or decrease,
respectively, in energy transfer from the donor label to
the acceptor label resulting from shortening or
lengthening, respectively, of the distance between said
labels, is measured.
Latva col. 6,11. 8—16.
4. Latva discloses: “According to the invention the
nonoverlapping principle allows one to extend the assortment of acceptor
molecules, wavelength range, improved sensitivity and applications of
multilabel systems.” Id. at col. 1,11. 20—24.
5. Nurmi discloses:
The method can be carried out in the real-time
monitoring of nucleic acid synthesis reactions by
measuring the signal intensity of the label at regular
intervals during a nucleic acid synthesis reaction and
comparing the signal intensities of a reaction containing a
sample of nucleic acids and of a negative control reaction
that does not contain said target polynucleotide
Nurmi p. 8,11. 9-14.
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Application 11/252,851
6. Nurmi discloses:
The Hybridization Probe format (Morrison 1995) used in
the LightCycler system (Wittwer et al, 1997a: Wittwer et
al, 1997b) uses two adjacent probes that are labeled such
that when both probes are hybridized to a target, the
labels are brought close to each other and a FRET occurs
between them. The sensitized acceptor emission is
measured instead of the donor fluorescence.
Nurmi p. 2,11. 18—24.
7. Figure 4 of Phillips is reproduced below:
Probe Fety'nud^oiida
QoSn^eci Reporter
:5kXi
Figure 4 “depicts the method by which the amplification product is detected
using a probe polynucleotide.” Phillips 120.
8. Phillips discloses:
A fluorophore can be attached to one end of the MB and
a quencher can be attached to the other end. In the
absence of a complement to the loop structure, the stem
keeps the two moieties in close proximity to each other,
causing the fluorescence to be quenched by energy
transfer. When a complement to the loop is present, the
loop sequence will form a hybrid with the target nucleic
acid that is longer and more stable than the stem. The
MB is thus linearized, causing the fluorophore and the
quencher to move away from each other, leading to the
restoration of fluorescence.
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Appeal 2015-000072
Application 11/252,851
Phillips 1 85.
9. Phillips discloses: “Methods of the invention can
optionally be implemented in a homogeneous format. This allows for
higher assay throughput due to fewer manipulations of the sample,
and decreased cross-contamination resulting in more reliable assays
and less downtime from cross-contamination.” Id. 116.
ANALYSIS
Claim 1
The Examiner found that both Hemmila and Latva disclosed TR-
FRET assays including all of the elements of claim 1 with the exception that
they did not disclose: 1) “comparing the difference between the energy
transfer-based signal from the acceptor in the sample and that from the
acceptor of a non-reacted labeled probe molecule,” and 2) “that the donor
and acceptor are contained within the labeled probe molecule before and
after binding with an analyte.” Ans. 4—8.
With respect to the claimed comparison, the Examiner found that
Nurmi disclosed a method for detecting a target polynucleotide in a sample
using time-resolved fluorometry. Id. at 8. The Examiner further found that
Nurmi taught that “acceptor emission of a donor/acceptor FRET pair could
be measured as an alternative to measurement of the fluorescence of solely a
lanthanide chelate donor and that comparison of this signal with that of a
non-reacted label probe would indicate the presence or absence of the target
in the sample.” Id. at 9—10. The Examiner thus concluded that it would
have been obvious to use a negative control like that described by Nurmi in
connection with the FRET assays disclosed in Hemmila and Latva. Id. at 9.
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Application 11/252,851
With respect to the requirement that the donor and acceptor be
contained within the labeled probe before and after binding with an analyte,
the Examiner found that Phillips taught a dual-labeled probe “containing a
lanthanide chelate donor and luminescent acceptor” in which the labels are
“contained within the labeled probe molecule before and after binding with
an analyte.” Id. The Examiner concluded that that it would have been
obvious to use a dual labeled probe in connection with the time-resolved
energy transfer assay of Hemmila and Latva because Phillips “expressly
taught that such a probe could be used in homogeneous bioassays, resulting
in higher assay throughput, fewer sample manipulations, decreased cross­
contamination, and more reliable monitoring.” Id. at 10.
We adopt the Examiner’s findings of fact and reasoning regarding the
scope and content of the prior art (Ans. 3—20; Final Act. 3—15) and agree
that the claims are obvious over Hemmila, Latva, Nurmi and Phillips. We
address Appellants’ arguments below.
Appellants acknowledge that Hemmila and Latva disclose TR-FRET
assays, but argue that “[i]n both Hemmila and Latva the two parts of a TR-
FRET pair are on separate probes.” Reply Br. 2. Appellants argue that:
The method of Hemmila depends upon the fact that that
the two probe labels are separate in solution and are
brought together only in the presence of analyte. A
person of ordinary skill reading such a description would
not have contemplated placing both parts of the TR-
FRET pair onto the same probe as this would go against
the principle under which the assay operates.
The same principle is evidenced in Examples 1-4 of
Latva (cols. 11-12). There, separate labeled molecules of
biotin and streptavidin are reacted. While the binding of
biotin to streptavidin brings the probes into proximity to
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Application 11/252,851
permit energy transfer, the fluorphores are never on the
same molecule. In Examples 5-8, antibodies are
separately labeled with donor and acceptor fluorophores
that are again brought together only after a binding
reaction to a target analyte. In Examples 9-11 (cols. 14-
15), separately labeled oligonucleotide probes, one with a
fluorophore and one with a quencher are brought into
proximity. In all of these, the fluorophores are attached to
separate molecules throughout the assay. Again, the
principle relies upon separate probes being brought
together to form a FRET pair, or to cause or relieve
quenching, not a single probe comprising a FRET pair.
App. Br. 12-13.
Appellants assert that the claimed method “differs from the state of
the art approach to FRET assays in that the TR-FRET label pair (i.e. two
fluorescent chemical labels capable [of] time resolved fluorescence energy
transfer) are comprised together on a single probe with a reactive region that
is capable of reacting with an analyte.” App. Br. 7. In addition, “the donor
and the acceptor are contained in the labeled probe molecule before and after
said analyte specific binding reaction” such that the analyte binding reaction
“does not add, or remove, either the acceptor or donor, both of which are
present on the probe at all times.” Id. Appellants contend that “[t]he
principle of operation of Hemmila and Latva is so different from the present
invention that it would not have been obvious, or predictable from Hemmila
and Latva that the present invention could be made to work.” App. Br. 13.
We are not persuaded.
In the TR-FRET assays of Hemmila and Latva, as in the claimed
invention, a change in the distance between the two labels causes a
measurable change in signal. FF2 and FF3. That the distance changes are
likely smaller when the two labels are on the same probe than when they are
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Application 11/252,851
on separate probes does not change this basic principle of operation.
Moreover, Phillips teaches an assay that measures signal change caused by a
change in the distance between the two labels that are both contained on the
same probe. FF7 and FF8.
Appellants have not directed us to any teaching in Hemmila or Latva
suggesting that a minimum distance change is required for TR-FRET or that
the labels must be on separate probes.6 Nor have Appellants identified
persuasive evidence that the person of ordinary skill would not reasonably
have expected to be able to meaningfully discern changes in signal in a TR-
FRET assay, like that of Hemmila and Latva, where the change in distance
between the two labels is relatively small, as when the two labels are on the
same probe. See Johnston v. IVAC Corp., 885 F.2d 1574, 1581 (Fed. Cir.
1989) (“Attorneys’ argument is no substitute for evidence.”); In re Pearson,
494 F.2d 1399, 1405 (CCPA 1974).
We find that a preponderance of the evidence supports the Examiner’s
finding that a person of ordinary skill would have had a reasonable
expectation of success in performing a TR-FRET assay, like that disclosed
in Hemmila or Latva, using a dual-labeled probe, like that disclosed in
Phillips. Doing so would have provided the advantages of TR-FRET and the
advantages of a dual-labeled probe. See, FF1, FF4 and FF9.
6 Hemmila discloses that it was well known at the time of the invention that
“energy transfer between lanthanides attached to different sites of a calcium
binding protein, or DNA [single molecule], have been used as spectroscopic
ruler to measure the locations of ion-binding sites, e.g. with calmodulin
using energy transfer between Eu and Nd.” Hemmila p. 6,11. 17-22
(emphasis added).
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Appellants argue that Phillips “contemplates the use of a fluorophore
and a quencher, which is not an acceptor who’s emission [is] observed as in
the present invention.” App. Br. 15. This, Appellants assert, is “quite
different from a method which relies on the use of an acceptor where the
emission of the acceptor is observed.” Id. Appellants thus contend that “[a]t
best, combining Phillips with Hemmila results in an assay using a quencher,
where the unquenching of a fluorophore is measured to observe a reaction.”
Id. We are not persuaded.
Phillips teaches an assay in which the binding of the analyte to the
dual-labeled probe changes the conformation of the probe such that the
distance between the two labels changes and is accompanied by energy
changes in the molecule. FF7 and FF8. Appellants have not established that
the mere fact that the energy acceptor in the Phillips assay is non-
luminescent7 would have rendered the basic teaching that distance changes
within a single molecule or dual labeled single probe can be associated with
energy changes and used to detect and determine the presence of an analyte
(Phillips), inapplicable to an assay using a luminescent energy acceptor. See
Johnston, 885 F.2d at 1581; In re Pearson, 494 F.2d at 1405. Accordingly,
we disagree with Appellants that the combined teaching of Phillips and
Hemmila (or Latva) is limited to an assay using a quencher. We find that a
person of ordinary skill in the art would have expected that a single
molecule, dual-labeled probe, like that taught in Phillips, could be used
successfully in an assay that replaces Phillips’ non-luminescent energy
acceptor with a luminescent energy acceptor.
7 A quencher is a non-luminescent energy acceptor. Hemmila p. 7,11. 23—
25.
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Appellants contend that Nurmi “does not teach a TR-FRET pair,
rather Nurmi only references the possibility of using a non-time resolved
measurement of a FRET interaction in the TaqMan type experiment
performed in parallel with their own method.” App. Br. 16. Appellants thus
argue that “Nurmi would not lead one to use a TR-FRET pair, and there
would have been no reason to look to Nurmi for guidance [] as to how to
determine the change in emission of [a] TR-FRET pair in response to
reacting a labeled probe with an analyte.” Id. We are not persuaded.
The Examiner did not rely on Nurmi for its teaching of a TR-FRET
pair. Rather, the Examiner relied upon Nurmi for its teaching of a
comparison of the difference between the signal in reacted and non-reacted
labeled probes. Ans. 12; see also, FF5. Appellants do not identify any
reason why this teaching would be inapplicable to TR-FRET assays. Indeed,
Appellants appear to acknowledge that the use of such a control is routine.
Se, Reply Br. 3 (“A person skilled in the art is well aware that every assay
aimed for the measurement of an amount of an analyte needs to have a
reference measurement or value to which the result of unknown sample is
compared to be able to calculate the actual result.”); id. at 4 (“The use of a
reference is naturally included in all of the presented prior art because the
references describe assays”). Moreover, Nurmi discloses FRET (although
not TR-FRET) and teaches that FRET assays can be performed where “the
sensitized acceptor emission is measured instead of the donor fluorescence.”
FF6.
Accordingly we affirm the Examiner’s rejection of claim 1 as obvious
over the combination of Hemmila, Latva, Nurmi and Phillips.
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Claim 19
Claim 19 depends from Claim 1 and further requires that step
(d), the measuring step, comprises:
(i) measuring an energy transfer based acceptor signal
from a reacted sample;
(ii) measuring an energy transfer based acceptor signal
from a non-reacted sample in a reference assay;
(iii) comparing the signals obtained in steps i) and ii);
and
(iv) determining the presence or absence of the analyte
in the sample based on a difference in acceptor
signals obtained in step (iii).
Appellants’ arguments with respect to claim 19 are substantially the
same as their arguments with respect to claim 1. App. Br. 16—17.
Accordingly, we affirm the Examiner’s decision to reject claim 19 for the
reasons discussed above with respect to claim 1.
Claims 2-10
Appellants’ arguments with respect to claims 2—10 are substantially
the same as their arguments with respect to claim 1. App. Br. 18.
Accordingly, we affirm the Examiner’s decision to reject claim 2—10 for the
reasons discussed above with respect to claim 1.
SUMMARY
For these reasons and those set forth in the Examiner's Answer, and
the Final Office Action, we affirm the Examiner’s final decision to reject
claims 1—10 and 19 as unpatentable under 35 U.S.C. § 103(a) over the
combination of Hemmila, Latva, Nurmi and Phillips.
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No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(1).
AFFIRMED
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