Ex Parte Sproles et al

Patent Trial and Appeal Board

Apr 29, 2013

11937896 (P.T.A.B. Apr. 29, 2013)

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.
11/937,896 11/09/2007 Dean I. Sproles 78372/2010 2699
7590 04/29/2013
Iverson Genetic Diagnostics, Inc.
c/o Dean Sproles
19805 North Creek Parkway, Suite 200
Bothell, WA 98011
EXAMINER
BRUSCA, JOHN S
ART UNIT PAPER NUMBER
1631
MAIL DATE DELIVERY MODE
04/29/2013 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 DEAN I. SPROLES and ROY L. SWANK
__________

Appeal 2013-000615
Application 11/937,896
Technology Center 1600
__________

Before JACQUELINE WRIGHT BONILLA, ULRIKE W. JENKS, and
SHERIDAN K. SNEDDEN, Administrative Patent Judges.

SNEDDEN, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
for assessing a genetic expression of multiple sclerosis. The Examiner has
rejected the claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm.

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STATEMENT OF THE CASE
Appellants’ invention relates to “to transcriptional detection of single
nucleotide polymorphisms (SNP) and insertion/deletion (I/D) genetic
polymorphisms through a proportional analysis of RNA sequences detected
through fluorescence hybridization on a custom manufactured microarray
gene expression platform” (Specification 10, ¶ [0029]).
Claims 21-36 are on appeal. Claim 21, the only independent claim on
appeal, is representative and reads as follows (emphasis added):
21. A method for assessing a genetic expression of multiple
sclerosis, comprising:
a) obtaining at least one sample of genetic material from
each of a plurality of people exhibiting a potential for
developing multiple sclerosis;
b) isolating strands of genetic sequences from each
sample from a);
c) for each sample from each person, separating at least
one strand of genetic sequence from the strands from b),
wherein said at least one strand of genetic sequence is
identified by a specific genetic sequence associated with
multiple sclerosis;
d) grouping said at least one strand of genetic sequence
from each sample from c), wherein all strands in each group
are identified by a specific genetic sequence and are grouped
across each sample from each person;
e) determining a first correlation between a first genetic
sample and a first genetic sequence associated with multiple
sclerosis and determining a second correlation between a
second genetic sample and a second genetic sequence
associated with multiple sclerosis;
f) determining a third correlation between the first and
second correlations of e)
g) collecting data about the first, second and third
correlations into a client computer; and
h) transmitting the data from g) to a server computer.
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The claims stand rejected as follows:
I. Claims 21-25 and 27-36 under 35 U.S.C. § 103(a) as being
unpatentable over the combination of Gödde,
1
Ardlie,
2
and Huff
3

as evidenced by Wang.
4

II. Claim 26 under 35 U.S.C. § 103(a) as being unpatentable over the
combination of Gödde, Ardlie, Huff, and Leyva
5
as evidenced by
Wang.
The same issue is dispositive for each rejection.

Issue
The Examiner finds that “Göode et al. shows correlations between
SNPs and multiple sclerosis, and the measurement of the SNPs in genetic
samples, and further shows that three SNPs are likely to be inherited
together as a haplotype, which is a correlation of SNPs that correlate with
multiple sclerosis” (Ans. 9). The Examiner relies on Wang “to show that the
hybridization process of Göode [sic] et al. inherently performs separation of

1
Gödde et al., Association of the HLA region with multiple sclerosis as
confirmed by a genome screen using > 10,000 SNPs on DNA chips, 83 J.
MOL. MED. 486-494 (2005).
2
Ardlie et al., Patterns of Linkage Disequilibrium in the Human Genome, 3
NATURE REVIEWS GENETICS 299-309 (2002).
3
Huff, US 6,760,731 B2, issued Jul. 6, 2004.
4
Wang et al., Large-Scale Identification, Mapping, and Genotyping of
Single-Nucleotide Polymorphisms in the Human Genome, 280 SCIENCE 1077
-1082 (1998).
5
Leyva et al., IFNAR1 and IFNAR2 polymorphisms confer susceptibility to
multiple sclerosis but not to interferon-beta treatment response, 163
JOURNAL OF NEUROIMMUNOLOGY 165-171 (2005).
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strands” as required by claim 21 (id. at 8-9). That is, the “[h]ybridization of
strands to different regions of a microarray by virtue of the presence of
different probes at each microarray region results in separation and grouping
of strands in the sample between the different probes on the microarray
according to their sequence” (id. at 9).
The issue presented is:
Does the evidence of record support the Examiner’s finding that the
combined prior art renders obvious a genetic assessment method involving
separating and grouping strands of genetic sequences according to a specific
genetic sequence as recited in claim 21?
Findings of Fact
The following findings of fact (“FF”) are supported by a
preponderance of the evidence of record.
FF1. Gödde discloses the results of a multiple sclerosis (MS) genome
screen where “[t]wo hundred individual DNA (pop1) were screened, each
using 11,555 SNP markers on DNA chips” (Gödde 489, right column).
FF2. “More than 500 SNPs revealed significant differences between
cases and controls before Bonferroni correction” (id. at Abstract).
FF3. “Highly significant association was evidenced for loci rs23951
66, rs2213584, rs2395182 and rs2227139 located in the immediate vicinity
of the HLA-DRA gene” (id. at 491, left column).
Principles of Law
“[T]he examiner bears the initial burden, on review of the prior art or
on any other ground, of presenting a prima facie case of unpatentability. If
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that burden is met, the burden of coming forward with evidence or argument
shifts to the applicant.” In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992).
“The combination of familiar elements according to known methods
is likely to be obvious when it does no more than yield predictable results.”
KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007).
Analysis
Interpretation of “genetic sequence”
We begin with claim interpretation, since until a claim is properly
interpreted, its scope cannot be compared to the prior art. The method of
claim 21 recites the steps of separating and grouping genetic sequences that
have been isolated from a sample (e.g., blood sample). The phrase “genetic
sequence” is not defined in the Specification, however, the use of “genetic
sequence” in the Specification is informative (see, e.g., Specification 14-16,
¶¶ [38]-[43]).
The method disclosed in the Specification describes the isolation of
genetic material based upon the specific gene sequence of a RNA strand, for
example, “a gene sequence associated with a gene expression indicative of a
specific MS trait” (id. at ¶ [41]). The strands are grouped, where “[s]uch
grouping allows for the assimilation of data on an aggregate level based on
various gene expressions” (id. at ¶ [42]) or “aggregate[ion of] information
associated with each blood sample ... accomplished through the groupings of
similar strands” (id. at ¶ [43]). In light of above disclosure, we find that the
Specification supports a finding that the recitation of “grouping said at least
one strand of genetic sequence from each sample” in claim 21 refers to the
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grouping of the information contained in the genetic sequence obtained from
individual samples.
Obviousness of Claim 21 over Gödde, Ardlie, Huff and Wang
We are not persuaded by Appellants’ contention that the Examiner
fails “to show that the prior art teaches separating and grouping strands of
genetic sequences according to a specific genetic sequence as recited in
claim 21” (App. Br. 18). Rather, we agree with the Examiner that the
isolation of genetic material on a DNA chip for the purpose of performing a
genotyping analysis of a multiple sclerosis patient population, as suggested
by the cited references, inherently involves the separation and grouping of
genetic sequence information as recited in claim 21. We are not persuaded
by Appellants’ arguments to the contrary and we find no evidence of record
that clearly distinguishes the method of the combined references from the
claimed method.
Appellants further contend that “[t]here is no art of record that teaches
or even suggests the concept of establishing a correlation amongst
correlations” (id. at 21). We first note that the Specification does not define
or use the term “correlation.” Rather, Appellants’ rely on the disclosure at
¶¶ [42] – [44] of the Specification for support of this element of the claim
(App. Br. 9-10). Here, we find no meaningful distinction between the
method described in these passages of the Specification and the methods
involved with association mapping disclosed in the cited prior art. For
example, the Specification discloses that “[w]ith any number of associations
in place from the groupings, statistical data from the aggregated blood
samples based on associations of one blood sample with another may be
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extrapolated” (Specification at 16, ¶ [44]). In comparison, Gödde discloses
a highly significant association for loci located in the immediate vicinity of
the HLA-DRA gene (Gödde at 491, left column), suggesting that a marker in
the HLA region may be used to determine susceptibility of MS (see, Ans. 4).
Furthermore, to the extent that the claims encompass the association of
multiple genetic sequences to MS or the association of a genetic sequence to
other genetic sequences, Ardlie discloses the use of genetic patterns as a
mapping tool. Specifically, Ardlie explains the analysis involved with
linkage disequilibrium (LD) mapping, where
LD is the non-random association of alleles at adjacent
loci. When a particular allele at one locus is found together on
the same chromosome with a specific allele at a second locus –
more often than expected if the loci were segregating
independently in a population – the loci are in disequilibrium.

(Ardlie at 300). Ardlie suggests that “association studies offer substantially
greater power for mapping common disease genes than do traditional
linkage studies, and that LD can offer a shortcut to genome-wide association
studies” (id. at 299).
In view of these disclosures of Gödde and Ardlie, we find the prior art
to teach or suggest the recited correlations, as interpreted in view of the
Specification. Appellants have pointed to no evidence of record that clearly
distinguishes the claimed correlations from association mapping techniques
disclosed in the combined cited art.
In view of the above, we find that the Examiner has set forth a prima
facie case of obviousness that has not been adequately rebutted by
Appellants. The Examiner has provided a rational basis for combining the
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cited references, where the proposed modifications address each disputed
element of claim 21 and are supported by the evidence on this record.
Conclusion of Law
The preponderance of evidence on this record supports the
Examiner’s finding that combined prior art renders claim 21 obvious.
Claims 21-25 and 27-36 fall with claim 21. 37 C.F.R. § 41.37(c)(1)(vii).

II.
The Examiner rejected claim 26 under 35 U.S.C. § 103(a) as being
unpatentable over the combination of Gödde, Ardlie, Huff, and Leyva as
evidenced by Wang. Appellants argue that claim 26 is allowable by virtue
of its dependence on claim 21 without providing additional argument or
evidence (App. Br. 24). Thus, for the same reasons discussed above,
Appellants arguments do not persuade us that the Examiner has erred in
concluding that claim 26 is obvious over Gödde, Ardlie, Huff, Leyva and
Wang.

SUMMARY
We affirm all rejections on appeal.

AFFIRMED

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