Ex Parte Mohammed et al

Patent Trial and Appeal Board

Jan 30, 2014

11134133 (P.T.A.B. Jan. 30, 2014)

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.
11/134,133 05/19/2005 Mansoor S. Mohammed 034827-3303 1327
22428 7590 01/31/2014
FOLEY AND LARDNER LLP
SUITE 500
3000 K STREET NW
WASHINGTON, DC 20007
EXAMINER
POHNERT, STEVEN C
ART UNIT PAPER NUMBER
1634
MAIL DATE DELIVERY MODE
01/31/2014 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 MANSOOR S. MOHAMMED,
NATASA DZIDIC, CHRISTOPHER MCCASKILL,
and JAEWEON KIM1
________________

Appeal 2012-007014
Application 11/134,133
Technology Center 1600
________________

Before TONI R. SCHEINER, JOHN G. NEW, and
SUSAN L.C. MITCHELL, Administrative Patent Judges.

NEW, Administrative Patent Judge.

DECISION ON APPEAL

1 The real party-in-interest is Quest Diagnostics Investments Incorporated.
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SUMMARY
Appellants file this appeal under 35 U.S.C. § 134(a) from the
Examiner’s Non-Final Rejection of claims 1-13, 15-29, 33-61, 64-68, and
70-73. Specifically, Claims 1, 2, 19, 34-35, and 60-61 stand rejected under
35 U.S.C. § 102(b) as anticipated by Mark Schena et al., Parallel human
genome analysis: Microarray-based expression monitoring of 1000 genes,
93 PROC. NATL. ACAD. SCI. USA 10614 (1996) (“Schena”).
Claims 1, 2, 19, 37, and 60-61 stand rejected under 35 U.S.C.
§ 102(b) as anticipated by Luo (US 2003/0044808 A1, March 6, 2003)
(“Luo”).
Claims 1-5, 19-29, 33-51, and 57-59 stand rejected under 35 US.C.
§ 103(a) as being obvious over the combination of Luo, Urdea (US
4,775,619, October 4, 1988) (“Urdea”) alone or in further combination with
Brown et al. (U.S. 2002/0115841 A1, August 22, 2002) (“Brown”), Shafer
(US 2004/0053275 A1, March 18, 2004) (“Shafer”), Getts (WO 03/012147
A1, February 13, 2003) (“Getts”), Shah et al. (US 2003/0124542 A1, July
3, 2003) (“Shah”), Singh (US 6,514,700 B1, February 4, 2003) (“Singh”),
and/or Baker et al. (WO 01/87348 A2, November 22, 2001) (“Baker”).
Claims 6-10, 52, and 64-67 stand rejected under 35 U.S.C. § 103(a)
as being obvious over Luo in combination with Urdea alone or in
combination with Shah and/or Shafer.
Claims 11-13 and 15-18 stand rejected under 35 U.S.C. § 103(a) as
being obvious over Luo in combination with Urdea alone or in combination
with Shafer, Shah, Delenstarr et al. (US 2002/0068293 Al, June 6, 2002)
(“Delenstarr”) and/or Getts.
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Claims 53-56 stand rejected under 35 U.S.C. § 103(a) as being
obvious over Luo in combination with Pinkel et al. (WO 93/18186,
September 16, 1993) (“Pinkel”). App. Br. 7.
We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.

NATURE OF THE CLAIMED INVENTION
Appellants’ invention is directed to methods of detecting and
mapping chromosomal or genetic abnormalities associated with various
diseases or with predisposition to various diseases or to detecting the
phenomena of large scale copy number variants. In particular, the present
invention provides advanced methods of performing array-based
comparative hybridization that allow reproducibility between samples and
enhanced sensitivity by using the same detectable label for both test sample
and reference sample nucleic acids. Invention methods are useful for the
detection or diagnosis of particular disease conditions such as cancer, and
detecting predisposition to cancer based on detection of chromosomal or
genetic abnormalities and gene expression level. Invention methods are
also useful for the detection or diagnosis of hereditary genetic disorders or
predisposition thereto, especially in prenatal samples. Moreover, invention
methods are also useful for the detection or diagnosis of de novo genetic
aberrations associated with post-natal developmental abnormalities.
Abstract.

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GROUPING OF CLAIMS

Appellants contend that the same arguments in favor of patentability
apply to independent claims 1, 60, and 70.2 App. Br. 16. We therefore
select claim 1 as representative of this group. Claim 1 recites:
1. A method for performing comparative hybridization, said
method comprising,

(i) simultaneously hybridizing test and reference nucleic acids
to a single nucleic acid array wherein said array
comprises a plurality of individual spots, wherein each
spot comprises a plurality of substantially identical
nucleic acid probes, and

(ii) after step (i), comparing the relative amount of test and
reference nucleic acids at a plurality of individual spots
as an indication of the comparative hybridization,
wherein said test and reference nucleic acids are labeled
with an indistinguishable detectable label and a signal
from said detectable label is used to determine the
amount of hybridization of the test and reference nucleic
acids to an individual spot.

App. Br. 44.

2 Appellants state that claims 68 and 70-73 are on appeal, but make no
separate arguments for them. We consequently affirm the Examiner’s
rejection of these claims.
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ISSUES AND ANALYSES
A. Rejection of claim 1 under 35 U.S.C. § 102(b) as anticipated by Schena

Issue
Appellants argue that the Examiner erred in finding that Schena
anticipates all of the limitations of claim 1. App. Br. 8. We therefore
address the issue of whether the Examiner so erred.
Analysis
Appellants argue that (1) the Examiner erred in interpreting the
disclosures of Schena; and (2) that Schena does not disclose making
comparisons at individual spots on the array. App. Br. 10-11. According to
Appellants, the Examiner erred in finding that the Jurkat cell cDNA and the
Arabidopsis cDNA correspond to the test and reference samples,
respectively, of claim 1. App. Br. 10. Appellants argue that the Examiner
failed to identify where in Schena the hybridization of these two nucleic
acid samples are compared and, furthermore, that any direct comparison of
the Arabidopsis and Jurkat cell cDNAs would be meaningless because they
are drawn from plant and human samples, respectively. Id.
Appellants argue further that claim 1 requires: “after step (i),
comparing the relative amount of test and reference nucleic acids at a
plurality of individual spots as an indication of the comparative
hybridization” and that claim 1 therefore requires comparison on a spot-by-
spot basis; an element which, Appellants claim, Schena does not disclose.
App. Br. 11. Appellants contend that, even if some comparison of the
Arabidopsis and Jurkat cDNA hybridization is performed, Schena would
necessarily make that comparison across different spots on the array; viz.,
spots 1-10 for Arabidopsis cDNA and spots 11-1056 for Jurkat cell cDNA.
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Therefore, argue Appellants, Schena does not disclose the disputed
limitation of claim 1.
The Examiner responds that Schena discloses that Arabidopsis
mRNA was “doped” in the reverse transcriptase reaction, and the reverse
transcriptase reaction was hybridized to the arrays. Ans. 36. The Examiner
finds that Schena further discloses scanning the array and thus determining
the amount of the hybridized test and reference cDNA in the sample. Id.
(citing Schena, p. 10614, 2nd col.; Figure 1). The Examiner finds that
Figure 1 of Schena discloses that the color bar was calibrated in separate
experiments in which known quantities of Arabidopsis control mRNA was
used. Ans. 36. Therefore, finds the Examiner, Schena discloses that
Arabidopsis mRNA was spiked into reverse transcription reactions and then
hybridized to the arrays, and the known quantities of Arabidopsis mRNA
were used to calibrate (or compare) the individual arrays so that a
comparison could be made between the different arrays. Id.
The Examiner further finds that claim 1 requires “simultaneously
hybridizing test and reference nucleic acids to a single nucleic acid array
wherein said array comprises a plurality of individual spots, wherein each
spot comprises a plurality of substantially identical nucleic acid probes.”
Id. The Examiner therefore finds that claim 1 recites no limitation requiring
that the test and reference nucleic acid are hybridized to the same spot. Id.
The Examiner finds that the rejected claims require a comparison of the
relative amounts of test and reference nucleic acids to a plurality of
individual spots. Id. The Examiner finds that the “wherein” clause of
claim 1 merely indicates the indistinguishable label used allows for the
determination of the amount of test and reference nucleic acids at an
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individual spot. Id. The Examiner finds that claim 1 does not require that
the test and reference nucleic acids are hybridized at a single spot. Id.
We are not persuaded by the Examiner’s reasoning. As an initial
matter, we find that a plain reading of Schena discloses that the test samples
recited in claim 1 correspond to the Jurkat cell mRNA (not cDNA) from
either the heat shock- or phorbol ester-treated Jurkat cells and the reference
samples are mRNA from the non-treated (control) Jurkat cells. Schena, p.
10614, col. 2 (“Jurkat mRNA was isolated as described by Schena et al. (4).
…. Arabidopsis control mRNAs were made by in vitro transcription of
cloned HAT4, HAT22, and YesAt-23 cDNAs (4, 8, 9) using an RNA
Transcription Kit (Stratagene)”). The Arabidopsis cDNA in the library and
the Arabidopsis mRNA probes were used as controls. Id. We disagree with
the Examiner’s contention that Jurkat cell or Arabidopsis cDNA was
employed as a test or reference sample; rather, we find that Schena
discloses the hybridization of the Jurkat cell test and reference mRNAs (and
Arabidopsis control mRNA) against a library of 1046 human cDNA clones
made with mRNA from human peripheral blood lymphocytes transformed
with the Epstein-Barr virus, and 10 Arabidopsis cDNA clones (as controls).
Schena, p. 10614, cols. 1-2.
However, we find that Schena explicitly teaches that the test and
reference Jurkat mRNA probes were hybridized to separate arrays, which
were then compared to determine differential gene expression between the
test and reference samples. Schena, p. 10615, col. 2 (“Comparative
expression analysis of heat shocked versus control cells in the two
experiments revealed 17 array elements that displayed altered fluorescence
ratios of ≥2.0-fold (Figs. 1 and 24)”). We are not persuaded by the
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Examiner’s argument that “[t]he claims do not require that the test and
reference nucleic acids are hybridized at a single spot.” Ans. 38. We find,
rather, that the limitation of claim 1 reciting “wherein said test and
reference nucleic acids are labeled with an indistinguishable detectable
label and a signal from said detectable label is used to determine the amount
of hybridization of the test and reference nucleic acids to an individual
spot” (emphasis added) necessarily requires determining the amount of both
test and reference hybridization at an individual spot. The Examiner does
not point to, nor can we find, any disclosure of Schena that teaches this
requirement.
Furthermore, claim 1 expressly requires “wherein said test and
reference nucleic acids are labeled with an indistinguishable detectable
label.” As Appellants stated on page 9 of their Brief and at oral argument,
Schena explicitly teaches that the Jurkat cell test and reference mRNA
probes are labeled with different labels:
Control (37oC) and heat-treated (43°C) cells were harvested and
lysed, and total mRNA from the two cell samples was labeled
by reverse transcriptase incorporation of fluorescein- and Cy5-
dCTP, respectively. In a second set of labeling reactions, the
fluorescent groups were “swapped” such that samples from
control and heat-treated samples were labeled with Cy5- and
fluorescein-dCTP, respectively.

Schena, p. 10615, cols. 1-2. Schena thus teaches that the test and reference
nucleic acids are labeled with distinguishable detectable labels (fluorescein-
and Cy5-dCTP).
Therefore, because we find that Schena does not teach all of the
limitations of claim 1, we cannot affirm the Examiner’s rejection of
claim 1.
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B. Rejection of claim 1 under 35 U.S.C. § 102(b) as anticipated by Luo

Issue
Appellants argue that the Examiner erred in finding that Luo
anticipates all of the limitations of claim 1. App. Br. 12. We therefore
address the issue of whether the Examiner so erred.
Analysis
Appellants argue that the Examiner’s interpretation of “an array” is
inconsistent with the Specification and a common-sense reading of Luo.
App. Br. 13. According to Appellants, the Examiner first ignores the
definitional requirement that an array be confined to “a defined area.”
Appellants contend that, under the correct interpretation, each of Luo’s
microtiter wells contains a single array because the array elements are
contained in a defined area which segregates each sample from the other
samples. Id. Appellants argue that although the arrays printed in each of
Luo’s wells may be substantially identical, each well contains a different
and separate “array” of capture nucleic acids. Id. Appellants argue that
Luo thus discloses a plurality of arrays for the parallel processing of
multiple samples and that Luo specifically distinguishes his multiple-array
microtiter plates from the large-format single arrays typical of those printed,
e.g., on microscope slides. App. Br. 13-14. Appellants argue that Luo
therefore discloses hybridizing test and reference nucleic acids to two
different arrays, each contained in an individual microtiter well, whereas
claim 1 requires that the test and reference nucleic acids are hybridized to a
single array. App. Br. 14.
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Appellants argue that the Examiner erred because Luo hybridizes the
test and reference samples to different nucleic acid arrays, and not to the
same array as required by the present claims. Therefore, argue Appellants,
Luo does not disclose measuring the hybridization of both test and
reference nucleic acids to the same (i.e., an individual) spot on a single
array as required by claim 1. App. Br. 15. Appellants contend that Luo
discloses, at most, comparing test and reference nucleic acid hybridization
to different, but equivalent spots across two different arrays. Id.
The Examiner responds that Luo discloses that the
“KnowledgeWellTM bio grid array” refers to the microtiter plate formatted
microarray platform of Applicant’s prior Application, and to the
microarrays spotted thereon. Ans. 38 (citing Luo, ¶ [0047]). The Examiner
finds that arrays composed of various types of material would be referred to
by the type of material in the array, for example, “Bio Grid Array”
more generally, but also “Gene Grid Array,” “Protein Grid Array,” “PNA
Grid Array,” “Cell Grid Array,” or any other material that would be
contained in an array. Ans. 38. The Examiner finds that Appellants’
microtiter plate formatted microarray platform may be, for example, in the
footprint of a 96-, 384- or 1536-well microtiter plate. Id.
The Examiner finds further that the base of the array, as described in
Appellants’ prior application is a glass material and is overlaid with a
bottomless plastic material in a grid having wells divided therein and being
adhesively bound to the glass base to create wells with plastic walls and
glass bottoms. Ans. 38-39.
The Examiner also finds that limitation (ii) of the claim, as recited
supra, does not specifically require the measuring of both test and reference
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nucleic acids at a specific spot, but rather, the comparison of a plurality of
individual spots, and that Appellants are therefore reading limitations into
the claim that are not explicit in the claim. Ans. 43.
As an initial matter, we cannot agree with Appellants’ interpretation
of Luo as disclosing that each individual well in the disclosed microtiter
microassay plate constitutes an individual array. Appellants’ Specification
describes the claim term “array” thus:
The term “array” or “microarray” or “biochip” or “chip” as
used herein refers to a plurality of elements arranged onto a
defined area of a substrate surface. In practicing the methods of
the invention, any known array and/or method of making and
using arrays can be incorporated in whole or in part, or
variations thereof….

Spec., ¶ [0077]. Luo discloses an embodiment of its invention thus: “The
base … is a glass material and is overlaid with a bottomless plastic material
in a grid having wells divided therein and being adhesively bound to the
glass base to create wells with plastic walls and glass bottoms.” Luo, ¶
[0047]. Luo also discloses that:
The labeled cDNA samples are then deposited 18 in to
the KnowledgeWell™ bio grid array microtiter plate format
assay platform 20, on the bottom inner glass surface of each
well of which is immobilized an array of various known
reagents including genes or portions thereof including DNA or
RNA sequences, PNA, polynucleotides or polypeptide
biopolymers such as known DNA fragments, cDNA or short
oligonucleotides, proteins or polypeptides …. The labeled
samples, once deposited in the wells, are then allowed to
hybridize with the various immobilized reagents, and any
resulting binding is measured by reading the signals from the
label in a reader selected based on the label. Analysis is then
performed from the various signals using software that acquires
and processes the data into information useful for analysis.
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Luo, ¶ [0054]. We agree with the Examiner that the “labeled cDNA
samples” (i.e., nucleic acid probes), that Luo discloses are deposited on the
bottom glass surface of each well, correspond more closely with the “spots”
of claim 1, which are also described as the “multiple elements” of the array
in the definition provided by Appellants’ Specification. Since there is a
plurality of these cDNA spots (one in each well) and a plurality of wells in
Luo’s grid array microtiter plate, we find that the grid array microtiter plate
disclosed by Luo, corresponds to the Specification’s definition of “array.”
Nevertheless, we are not persuaded by the Examiner’s reasoning that
claim 1 does not require that both test and reference nucleic acids be
hybridized to the same individual spot. As we have related supra, we find
that the claim explicitly so requires. The Examiner neither points to, nor
can we find, any disclosure of Luo that requires binding by the test and
reference nucleic acids to a single spot in the array. We therefore cannot
affirm the Examiner’s rejection of claim 1.

C. Rejection of claim 1 under 35 U.S.C. § 103(a)
Issue
Appellants argue that the Examiner erred in finding that Luo together
with prior art reference Urdea alone or in further combination with Shafer,
Getts, Shah, Singh, Baker and/or Brown teach or suggest the limitations of
claim 1. App. Br. 15. We therefore address the issue of whether the
Examiner so erred.

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Analysis
Appellants argue, as they did supra, that Luo neither teaches nor
suggests comparing the relative amount of test and reference nucleic acid
hybridization at a plurality of individual spots on the single array. Ans. 17.
We have related why we agree that Luo neither teaches nor suggests that
the test and reference hybridize to a single spot in the array. The question
therefore before us is whether any of the remaining references cure that
deficiency.

1. Luo and Urdea
Appellants argue that Urdea provides methods for detecting specific
nucleic acid sequences hybridized to capture nucleic acids on a solid
support. App. Br. 18. According to Appellants, Urdea teaches that a
detectable label is present on the distal end of either the capture nucleic acid
or the probe, such that the label is released via cutting by a restriction
enzyme; detection of the “detectable label in the supernatant after treatment
with the restriction enzyme implies hybridization of a soluble nucleic acid
to the immobilized capture nucleic acid.” Id.
Appellants argue that Urdea neither teaches nor suggests hybridizing
two different nucleic acid samples (e.g., test and reference samples) to a
single nucleic acid array, wherein each sample is labeled with the same
detectable label. App. Br. 18-19. Appellants also contend that Urdea
assesses the detectable label associated with only one nucleic acid sample;
there is no indication in Urdea to assess two different samples hybridized to
a single array.
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The Examiner responds that Urdea teaches or suggests the use of
more than one cleavage site. Ans. 47. The Examiner finds that Urdea
teaches that there can be at least one recognition site common to the probe
and the sample polynucleotide, which can be digested with a restriction
enzyme, thus releasing the probe from the support. Id. (citing Urdea, col. 7,
ll. 41-44).
We are persuaded by Appellants’ reasoning that Urdea does not teach
or suggest hybridizing both test and reference nucleic acid samples to a
single spot on the array. As such, it does not overcome the deficiency of
Luo. We therefore decline to affirm the Examiner’s rejection of claim 1 on
this ground.

2. Shafer
Appellants argue that the Examiner relies on Shafer to demonstrate
that detectable labels may be attached to nucleic acids via dendrimers and
that labeling may be done either before or after array hybridization. App.
Br. 19. Appellants contend that nothing in Shafer teaches or suggests a
method in which two different nucleic acid samples (e.g., a test and a
reference sample) are hybridized to a single nucleic acid array and the
comparative hybridization assessed using an indistinguishable detectable
label.
We agree with Appellants that the teachings and suggestions of
Shafer do not cure the deficiencies of Luo cited supra. We therefore
reverse the Examiner’s rejection of claim 1 on this ground.

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3. Getts
Appellants argue that Getts provides a method for probing target
nucleic acids captured on a nucleic acid array by adding two labeled probes
in series rather than simultaneously. App. Br. 20. According to Appellants,
Getts teaches hybridizing target nucleic acids to an array and visualizing the
complex using a detectably-labeled probe; the probe is then stripped from
the array, with a confirmation measurement to ensure complete stripping,
and the array-bound nucleic acids are visualized again using a second
detectably-labeled probe. Id.
Appellants contend that Getts neither teaches nor suggests
hybridizing two different nucleic acid samples (e.g., test and reference
samples) to a single nucleic acid array; nor, Appellants argue, does Getts
suggest determining the comparative hybridization of two different nucleic
acid samples at individual spots on an array using an indistinguishable
detectable label. Id. According to Appellants, Getts merely provides a
serial probe labeling technique as an alternative to the traditional
simultaneous labeling methods. Id.
We agree with Appellants that Getts does not cure the deficiencies of
Luo cited supra. We therefore reverse the Examiner’s rejection of claim 1
on this ground.

4. Shah
Appellants argue that the Examiner relies on Shah to demonstrate the
standard technique of comparative genomic hybridization. App. Br. 20-21.
According to Appellants, the basic technique involves hybridizing two
nucleic acid samples (usually a test and reference sample) to a nucleic acid
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array. App. Br. 21. Each of the samples is detectably labeled to visualize
and measure the amount of hybridization of the respective samples to
individual array spots. Id. Appellants argue that Shah teaches that different
detectable labels must be used in order to distinguish between the two
samples during detection. Id.
We agree with Appellants that the teachings and suggestions of
Brown do not cure the deficiencies of Luo cited supra. We therefore
reverse the Examiner’s rejection of claim 1 on this ground.

5. Singh and Baker
The Examiner finds that the Office Action of January 25, 2011 fails
to disclose a rejection in which Luo is used as a primary reference in a
rejection with Singh and/or Baker and concludes that Appellants’
arguments are therefore moot.
We agree with the Examiner that, lacking a rejection based on these
grounds, Appellants’ argument is moot. However, because the deficiencies
of Luo remain uncured, we do not affirm the Examiner’s rejection of claim
1 on the previously-stated ground.

6. Brown
Appellants argue that the Examiner relies on Brown for teaching pH-
sensitive linkers, and in particular linkers that are cleaved upon exposure to
a hydroxyl radical (i.e., under basic condition). App. Br. 22. According to
Appellants, the teachings of Brown are not materially different than those
of Urdea and/or Baker which also disclose cleavable linkers, and that
nothing in Brown remedies the fundamental deficiencies of Luo.
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We agree with the Examiner that the teachings and suggestions of
Brown do not cure the deficiencies of Luo cited supra. We therefore
reverse the Examiner’s rejection of claim 1 on this ground.

7. Delenstarr
Appellants argue that the Examiner relies on Delenstarr as teaching
that background signals may be subtracted from target signals to determine
the amount of target signal on a nucleic acid array. App. Br. 36.
Appellants argue that Delenstarr is not relevant to the use of a single,
indistinguishable detectable label for assessing hybridization of two
samples to a single spot. Id.
We agree with Appellants that the teachings and suggestions of
Delenstarr do not cure the deficiencies of Luo cited supra. We therefore
reverse the Examiner’s rejection of claim 1 on this ground.

D. Rejection of the remaining claims under 35 U.S.C. §§ 102(b) and 103(a)
Appellants argue that the Examiner erred in rejecting the remaining
claims for the same reasons as with respect to claim 1 argued supra. App.
Br. 16, 24, 32, 40. We agree. With respect to the rejection of independent
claim 60 under 35 U.S.C. § 102 as being anticipated by Luo, we reverse the
Examiner’s rejection for the same reasons that we have related supra with
respect to the rejection of claim 1 on this ground.
With respect to the remaining claims depending on independent
claims 1 and 60 we reverse the Examiner’s rejections for the same reasons
that we have related supra with respect to the rejection of claim 1.

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DECISION
The Examiner’s rejection of claims 1, 2, 19, 34-35, 37, and 60-61
under 35 U.S.C. § 102(b) is reversed.
The Examiner’s rejection of claims 1-13 15-29, 33-59, and 64-67
under 35 U.S.C. § 103(a) is reversed.

REVERSED

cdc