Ex Parte Sampas

Patent Trial and Appeal Board

Jun 25, 2013

11881932 (P.T.A.B. Jun. 25, 2013)

UNITED STATES PATENT AND TRADEMARK OFFICE
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BEFORE THE PATENT TRIAL AND APPEAL BOARD
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Ex parte NICHOLAS MICHAEL SAMPAS1
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Appeal 2012-000980
Application 11/881,932
Technology Center 1600
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Before LORA M. GREEN, ERICA A. FRANKLIN, and
JACQUELINE WRIGHT BONILLA, Administrative Patent Judges.

BONILLA, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims directed to a
method for analyzing a DNA sample for the presence of a single nucleotide
polymorphism (SNP), where the method involves the use of a probe that
comprises a restriction enzyme cleavage site. The Examiner has rejected the
claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We
reverse.

1 Appellants identify the Real Party in Interest as Agilent Technologies, Inc.
(App. Br. 3).
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STATEMENT OF THE CASE
The Specification describes “microarray platforms for the detection of
single nucleotide polymorphisms (SNPs) using restriction enzyme analysis,”
as well as “[m]ethods for determining the presence of an allele comprising at
least one SNP site in a DNA sample” (Spec. 1-2). The Specification
discloses digesting a DNA sample with at least one restriction enzyme (id. at
2). A restriction enzyme is “a protein that recognizes specific, short
nucleotide sequences in a DNA sequence and cleaves [or digests] the DNA
at those sites,” which are “typically 4, 5, 6, or 8 bases long” (id. at 12).
The Specification describes labeling digested and undigested samples
and hybridizing each sample “to a microarray comprising a probe or probes
complementary to sequences comprising SNP sites present in the DNA
sample” (id. at 16-17). “The signal from the labeled digested sample to the
signal from labeled undigested sample is compared,” and a “change in signal
intensity” between the two samples “is indicative of the presence of the SNP
site” (id. at 17). The measured “signal” corresponds to the amount of
labeled DNA bound to the probe on the microarray. If a DNA sequence
comprising a SNP site cleavable by a restriction enzyme is present in the
sample, the digested sample signal will be less than an undigested sample
signal. Specifically, because the probe comprises a sequence complimentary
to the restriction cleavage site, it will exhibit better hybridization to a sample
that is uncut by the restriction enzyme, as compared to a cut sample.
Claims 38-57 are on appeal. Claim 38, the only independent claim, is
representative and reads as follows: (emphasis added):
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38. A method for sample analysis, comprising:
a) contacting a first DNA sample with a first restriction enzyme
to provide a digested sample, wherein:
i) said DNA sample may comprise a target sequence
comprising a SNP site; and
ii) said first restriction enzyme cleaves said target
sequence at a cleavage site only if a first allele of a SNP is
present at said SNP site;
b) hybridizing said digested sample to a surface-bound
polynucleotide comprising a probe sequence that hybridizes to said
target sequence wherein:
i. the surface-bound polynucleotide is up to 200
nucleotides in length,
ii. the probe sequence comprises said cleavage site, and
iii. the probe sequence is designed such that cleavage of
the target sequence at said cleavage site by said first restriction
enzyme results in less hybridization of the digested sample
relative to a sample in which the target sequence is undigested
by the first restriction enzyme;
c) comparing the hybridization signal between the digested
sample and the probe sequence to a reference signal, and
d) determining whether the first allele of the SNP is present in
the DNA sample, wherein the hybridization signal of the digested
sample to the probe sequence as compared to the reference signal
indicates whether the first allele of said SNP is present in the DNA
sample.
The claims on appeal stand rejected under 35 U.S.C. §103(a) as
obvious over cited art.2 Independent claim 38, and dependent claims, 39, 40,

2 The Appeal Brief also discusses rejections under 35 U.S.C. § 112, first ¶,
and second ¶ (App. Br. 5-6). The Examiner discusses obviousness rejections
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42-45, 47-50, and 55-57, stand rejected as obvious over Ausubel3 in view of
Chee.4 Claims 51-54 stand rejected as obvious over Ausubel in view of
Chee and Wenzl.5 Claim 41 stands rejected as obvious over Ausubel in
view of Chee and Bougueleret.6 Claim 46 stands rejected as obvious over
Ausubel in view of Chee and Fodor.7
Analysis
Independent claim 38, and therefore its dependent claims, recite a
method for “sample analysis” that involves contacting, i.e., digesting, a
DNA sample with a restriction enzyme, where the enzyme “cleaves said
target sequence at a cleavage site only if a first allele of a SNP is present at
said SNP site.” The method further comprises hybridizing the digested
sample “to a surface-bound polynucleotide comprising a probe sequence,”
where “the probe sequence comprises said cleavage site” of the restriction
enzyme.”
In the obviousness rejections of all claims on appeal, the Examiner
relies on Ausubel as teaching a relevant method involving hybridization of a
digested sample to a “probe sequence compris[ing] said cleavage site,” as

in the Answer, but not § 112 rejections. Thus, we assume the Examiner has
withdrawn the § 112 rejections, and we do not address them here.
3 Ausubel et al., U.S. Pat. No. 6,110,709, issued Aug. 29, 2000.
4 Chee et al., W0 95/11995 A1, published May 4, 1995.
5 Wenzl et al., Diversity Arrays Technology (DArT) for whole-genome
profiling of barley, 101 PROCEEDINGS NATIONAL ACADEMY OF SCIENCES
9915-9920 (2004).
6 Bougueleret et al., U.S. Pat. No. 6,582,909 B1, issued June 24, 2003.
7 Fodor et al., U.S. Pat. No. 5,925,525, issued July 20, 1999.
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recited in claim 38. Specifically, the Examiner refers to column 13 of
Ausubel as teaching a relevant method involving polymerase chain reaction
(PCR) amplification of a DNA sequence using primers (one primer tagged
and a second primer untagged) (Ausubel, col. 13, ll. 25-29) (Ans. 5-6). In
Ausubel, PCR products are digested (or not), and one contacts those
products with an oligonucleotide (bound to a solid support) that is
“complementary to a sequence in the strand of the PCR product containing
the detectable label, the sequence being between the polymorphic restriction
site and the sequence complementary to the second primer” (Ausubel, col.
13, ll. 25-38 (emphasis added). The Examiner also states that Ausubel
teaches a relevant method that includes “the use of the complement bound
(Y) which has the restriction site to a solid support to detect the presence or
absence of labeled X hybridized to a solid support,” citing Figure 1 Ausubel
(Ans. 6).
The Examiner relies on Chee as teaching other elements of claim 38,
but does not adequately explain how this reference as teaches or suggests a
relevant probe comprising a cleavage site of a restriction enzyme (id. at 7-8).
Nonetheless, the Examiner concludes “it would have been prima facie
obvious to one of ordinary skill in the art at the time the invention was made
to use the probes of Chee with the SNP (restriction site at a central location)
in the SNP detection method of Ausubel” (id. at 8-9).
We find that neither Ausubel nor Chee teaches or suggests the use of
a probe comprising the cleavage site of a restriction enzyme used in a
relevant method, as required in claim 38. Figure 1 of Ausubel presents the
following:
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Figure 1 depicts the use of two PCR primers, i.e., a first primer tagged with
label (x) and a second primer tagged with a member of a binding pair (y), to
amplify a DNA sequence (Ausubel, col. 8, ll. 9-19.) While Figure 1 depicts
detecting x, i.e., a label bound to the first PCR primer, Figure 1 does not
depict an oligonucleotide bound to the solid support used to detect binding
of x.
Figure 3 (and Figures 4-6) in Ausubel, on the other hand, depicts an
oligonucleotide (i.e., probe) that is used to “detect x bound to solid support”
as stated in Figure 1. Figure 3 is depicted below:
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Figure 3 depicts a schematic of a detection method, similar to what is shown
in Figure 1, where the method also comprises contacting (annealing)
digested PCR products “with an oligonucleotide complementary to the P1
[labeled primer] strand and located to the right of the restriction site (R) near
to, but not overlapping primer P2” (see also Ausubel, col. 8, ll. 33-47;
Figures 4-6 (indicating that the probe does not span restriction site R)). A
black rectangle in Figure 3 (and Figures 4-6) corresponds to the
“oligonucleotide,” i.e., a relevant probe, which is located to the right of
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restriction site R in the DNA sample analyzed, i.e., the sequence amplified
by PCR using primers P1 and P2.
Such teachings are consistent with the passage quoted by the
Examiner from column 13 of Ausubel (Ans. 5-6). Column 13 states that the
oligonucleotide is complementary to a sequence in the PCR product that is
“between the polymorphic restriction site and the sequence complementary
to the second primer” (Ausubel, col. 13, ll. 31-39). In other words, the
relevant probe in Ausubel —i.e., the “oligonucleotide” attached to a solid
support, as distinct from PCR primers—does not comprise the cleavage site
of the restriction enzyme, as required in claim 38.
Chee teaches using immobilized probes “for comparing a reference
polynucleotide sequence of known sequence with a target sequence showing
substantial similarity with the reference sequence, but differing in the
presence of e.g., mutations” (Chee, abstract). As noted by the Examiner,
Chee teaches use of probes that are “complementary to a target sequence
[except] for the interrogation position” (Ans. 8, citing Chee, p. 27). As
stated in Chee, “[t]he interrogation position on a column of probes
corresponds to the position in the target sequence whose identity is
determined from analysis of hybridization to the probes in that column”
(Chee, p. 26, ll. 2-5). Chee also refers to “strategies [that] allow detection of
variations, such as mutations or polymorphisms, in the target sequence (id.
at p. 18, ll. 2-10). Thus, Chee suggests the idea of using probes to identify
SNPs, as well as the concept of using a probe that is complementary to a
sequence that comprises a SNP (id. at 29, ll. 8-9). That said, the Examiner
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cites to nothing in Chen that suggests using a probe comprising a restriction
enzyme cleavage site.
In response to Appellant’s argument, the Examiner acknowledges that
“Chee does not teach probes that span a restriction site,” but states that
“Ausubel teaches probes that span the polymorphic site that can be cleaved
by a restriction enzyme” (Ans. 15, 17). We find to the contrary. As
discussed above, Ausubel does not teach use of a relevant probe comprising
a restriction enzyme cleavage site. The Examiner does not establish that
Chee, or any other cited reference, cures the deficiency of Ausubel in this
regard.
Thus, the Examiner does not establish by a preponderance of the
evidence that any cited reference teaches or suggests the use of a probe
comprising a restriction enzyme cleavage site, as recited in claim 38. Thus,
the Examiner does not establish a prima facie case of obviousness of claim
38, nor its dependent claims.
SUMMARY
We conclude that the Examiner does not establish by a preponderance
of the evidence that Ausubel in view of Chee renders independent claim 38
obvious. Thus, we reverse the rejection of claim 38, and therefore
dependent claims, 39, 40, 42-45, 47-50, and 55-57, as obvious over
references cited by the Examiner.

REVERSED
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