Ex Parte Bobrow et al

Patent Trial and Appeal Board

Oct 26, 2018

11615739 (P.T.A.B. Oct. 26, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO.
11/615,739
91026 7590
Rhodes IP PLC
3090 Electric Rd
Suite F
Roanoke, VA 24018
FILING DATE FIRST NAMED INVENTOR
12/22/2006 Mark N. Bobrow
10/30/2018
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.
PKI-702110 1378
EXAMINER
SISSON, BRADLEY L
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
10/30/2018 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):
crhodes@rhodesip.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte MARK N. BOBROW, KARL EDWIN ADLER, and
MACK J. SCHERMER1
Appeal2018-005585
Application 11/615, 739
Technology Center 1600
Before JEFFREY N. FRED MAN, JOHN E. SCHNEIDER, and
RY ANH. FLAX Administrative Patent Judges.
SCHNEIDER, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
for determining the number of copies of two or more genomic loci in a
genomic DNA sample which have been rejected as non-enabled and as
obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM. 2
1 Appellants identify the Real Party in Interest as "PerkinElmer Health
Sciences, Inc." Appeal Br. 3.
2 We have considered and herein refer to the Specification of Dec. 22, 2006
("Spec."); Final Office Action of Mar. 20, 2017 ("Final Act."); Appeal Brief
Appeal2018-005585
Application 11/615, 739
STATEMENT OF THE CASE
"Comparative Genomic Hybridization (CGH) is a method that
evaluates genomic content. CGH can be used to analyze congenital
abnormalities, inherited diseases and cancers, for example." Spec. 1. The
Specification describes methods for evaluating genomic content using
encoded particles to evaluate multiple samples in parallel. Id.
Claims 1, 3, 5, 6, 8-12, 14, 16, 18-30, 33, 34, 36-40, and 51-73 are
on appeal. Claim 1 is illustrative and reads as follows:
1. A method of determining the number of copies of two
or more genomic loci in a genomic DNA sample, the method
compnsmg:
providing a genomic DNA sample;
providing a reference DNA sample containing a known
number of copies of each genomic locus to be evaluated;
wherein the genomic DNA sample and the reference
DNA sample are labeled with the same detectable label;
providing a particle mixture, the mixture comprising
particles from different particles sets, wherein each particle set
comprises a plurality of encoded particles attached to nucleic
acid hybridization probes specific for a particular genomic
locus, such that the particle mixture collectively includes probes
for a plurality of different genomic loci, and wherein the
nucleic acid hybridization probe of each particle comprises
cloned nucleic acid produced by sonicating or fragmenting the
cloned nucleic acid;
wherein the encoded particles of each particle set are (i)
encoded with the same code, and (ii) encoded differently from
encoded particles of another particle set, and wherein each
particle set corresponds to a different genomic locus;
of Oct. 20, 2017 ("Appeal Br."); Examiner's Answer of Mar. 9, 2018
("Ans."); and Reply Brief of May 9, 2018 ("Reply Br.").
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contacting the genomic DNA sample to a first portion of
the particle mixture in a first container under hybridization
conditions to permit formation of a genomic particle mixture
comprising labeled, genomic DNA specifically hybridized to
the particle mixture;
contacting the reference DNA sample to a second portion
of the particle mixture in a second container separate from the
first container under hybridization conditions to permit
formation of a reference particle mixture comprising labeled,
reference DNA specifically hybridized to the particle mixture;
wherein the hybridization conditions are selected such
that the nucleic acid hybridization probe of each particle set
specifically hybridizes to a complementary nucleic acid
sequence present in the genomic locus for which the probe is
specific;
isolating the particles of the genomic particle mixture
from unhybridized genomic DNA;
isolating the particles of the reference particle mixture
from unhybridized reference DNA;
evaluating the isolated genomic particle mixture and the
isolated reference particle mixture by monitoring (i) the code of
each particle, wherein the code is indicative of the genomic
locus evaluated, and (ii) a corresponding signal from the
detectable label, wherein the signal from the detectable label
associated with an encoded particle is indicative that a genomic
locus from the reference or genomic DNA sample has
hybridized to the encoded particle; and
determining the number of copies of each genomic locus
in the genomic DNA sample by comparing signals from the
isolated reference particle mixture and the isolated genomic
particle mixture.
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Application 11/615, 739
The claims stand rejected3 as follows:
Claims 1, 3, 5, 6, 8-12, 14, 16, 18-30, 33, 34, 36-40, and 51-73 have
been rejected under 35 U.S.C. § 112, first paragraph, for failure to comply
with the enablement requirement.
Claims 1, 3, 5, 6, 8-12, 14, 16, 18-30, 33, 34, 36-40, and 51-73 have
been rejected under 35 U.S.C. § I03(a) as unpatentable over Beattie,4
Wang, 5 Liu, 6 and Appellants' admissions in the Specification.
ENABLEMENT
Issue
The issue with respect to this rejection is whether the Specification
describes the invention in such "full, clear, concise, and exact terms to
enable any person skilled in the art to which it pertains or with which it is
most nearly connected, to make and use the invention." 35 U.S.C. § 112,
first para.
The Examiner finds that the claims are not enabled because it would
have required one skilled in the art to conduct an undue amount of
experimentation to practice the invention. Final Act. 8-9. The Examiner
finds that the term genomic sample can embrace any known species, thus
constituting an enormous undefined class of samples. Id. The Examiner
3 Claims 45-53 and 55-62 were rejected on the grounds of non-statutory
obviousness-type double patenting over US 9,044,391 B2, issued June 2,
2015. That rejection was withdrawn after Appellants filed a terminal
disclaimer. Advisory Act. mailed Aug. 8, 2016.
4 Beattie et al., US 6,268,147 Bl, issued July 31, 2001 ("Beattie").
5 Wang et al., US 2004/0096892 Al, published May 20, 2004 ("Wang").
6 Liu, US 2003/0082549 Al, published May 1, 2003 ("Liu").
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finds that the Specification does not provide guidance as to any nucleotide
sequence that constitutes the genomic locus recited in the claims. Id. The
Examiner finds that "[ n ]either the as-filed specification nor the state of the
art provides such guidance so that one skilled in the art, without any undue
experimentation, could reasonably generate such a broad scope of probes
and reference systems contemplated by the intended breadth of the claimed
method." Id. at 9--10.
Appellants contend that the Specification provides sufficient guidance
to one skilled in the art to practice the claimed method. Appeal Br. 35.
Appellants argue that while the term genomic sample may encompass any
potential species, the term, as used in the claims, does not render the claims
overly broad with respect to the discosure. Id. Appellants point out the in
the claimed method, the reference DNA is known and it is the reference
DNA that is used (as a starting point) to find the loci sequences in the
genomic sample. Id. at 36-37. Appellants contend that if the loci sequence
of the genomic DNA sample were known, there would be no need to
perform the claimed method. Id. at 3 7. Thus, to summarize, Appellants
argue the invention is generally directed to comparing an unknown DNA
sample to a known DNA reference.
Principles of Law
The enablement requirement is often more indulgent than
the written description requirement. The specification need not
explicitly teach those in the art to make and use the invention;
the requirement is satisfied if, given what they already know,
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the specification teaches those in the art enough that they can
make and use the invention without "undue experimentation."
Amgen, Inc. v. Hoechst Marion Roussel, Inc., 314 F.3d 1313, 1334,
(Fed. Cir. 2003).
Analysis
We have considered the Examiner's determinations and Appellants'
arguments and find that Appellants have the better position. The invention
is directed to a method for determining if a specific loci is present in a
genomic DNA sample and if present, how many copies are present. Appeal
Br. 46 (Claims App'x). The method uses a reference sample containing a
known number of copies of the locus being analyzed. Id. As Appellants
point out, it is not necessary to know whether the locus is present in the
genomic DNA sample because the test itself will determine if the locus is
present. Appeal Br. 3 7.
The Examiner's focus on the fact that the existence of the locus in the
genomic DNA sample and that the claims appear to encompass every
species of organism is not taught by the Specification is misplaced. As
discussed above, the purpose of the claimed method is to determine if a
locus is present in a sample compared to a known reference and, if present,
how often it is repeated within the given sample.
Conclusion of Law
We conclude that the Examiner's determination that the claims are not
enabled is in error.
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OBVIOUSNESS
Issue
The issue with respect to this rejection is whether a preponderance of
the evidence supports the Examiner's conclusion that the subject matter of
the claims would have been obvious over Beattie combined with Wang, Liu
and the admissions by Appellants in the Specification.
The Examiner finds that Beattie discloses a method for detecting
multiple hybridization reactions simultaneously. Final Act. 31. The
Examiner finds that Beattie teaches using a multiplexed assay having probes
bound to distinguishable microspheres; the probes being capable of binding
to one or more regions of a known nucleic acid sequence. Id. The Examiner
finds that Beattie teaches that the method can be used to scan for known or
unknown mutations in a gene of a known nucleotide sequence, genotyping
of organisms, and genome mapping. Id. The Examiner further finds that
Beattie teaches that the method can be used to effect isolation of hybridized
probe particle complexes from unhybridized genomic DNA. Id. at 32.
The Examiner finds that while Beattie does not teach performing a
multiplexed assay with a test and reference sample simultaneously, that
element is taught by Wang as well as being admitted as known in the art in
the present Specification. Final Act. 32-36. The Examiner concludes
In view of the well-developed state of the art and the
detailed guidance provided therein, one of ordinary skill in the
art at the time of the invention would have been amply
motivated to have modified the multiplexed bead-based assay
of Beattie et al., with the reference of Wang et al, and the
detection means of Liu, whereby one employs commercially-
available beads identified by applicant and the flow cytometer
of Liu as such would have allowed for the multiplexed analysis
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of genomic loci of interest, including that of human and non-
human origin.
By using a reference (Wang et al.) in the method of
Beattie et al., one is able to have an immediate and direct
reference by which one can determine the accuracy of the given
assay. Said ordinary artisan would have been motivated to have
minimized any difference between the test and reference
samples as such would have reduced the chance of any
difference in reagents and/ or conditions would impart a
difference in result. Said ordinary artisan would have also been
motivated to have used the commercially-available beads and
detection systems (Liu and applicant's admissions) as such
would have reduced the number of variables in the assay as
well as facilitated the ready performance of the assay.
Id. at 37 (paragraph numbers omitted).
Appellants contend that Beattie does not disclose or suggest the
specific particle sets cited in the claims. Appeal Br. 41. Appellants argue
that Beattie does not teach or suggest that the particles comprise nucleic acid
produced by sonicating or fragmenting the cloned nucleic acid. Rely Br. 5-
6. With respect to Wang, Appellants argue that Wang does not teach or
suggest the use of encoded particles as recited in the claims. Appeal Br. 42.
Finally Appellants argue that Liu does not remedy the deficiencies of
Beattie. Id. at 42--43.
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 ofunpatentability. If that burden is met, the burden of
coming forward with evidence or argument shifts to the
applicant.
After evidence or argument is submitted by the applicant
in response, patentability is determined on the totality of the
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record, by a preponderance of evidence with due consideration
to persuasiveness of argument.
In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992).
"Non-obviousness cannot be established by attacking references
individually where the rejection is based upon the teachings of a
combination of references. . . . [The reference] must be read, not in
isolation, but for what it fairly teaches in combination with the prior art as a
whole." In re Merck & Co., 800 F.2d 1091, 1097 (Fed. Cir. 1986).
Analysis
We adopt the Examiner's findings of fact, reasoning on scope and
content of the prior art, and conclusions set out in the Final Action and
Answer regarding this rejection. Final Act. 27-38, Ans. 31-38. We find the
Examiner has established that the subject matter of the claims would have
been obvious to one of ordinary skill in the art at the time the invention was
made over Beattie in view of Wang, Liu, and the admissions in the
Specification. Appellants have not produced evidence showing, or
persuasively argued, that the Examiner's determinations on obviousness are
incorrect. Only those arguments made by Appellants in the Briefs have been
considered in this Decision. Arguments not presented in the Briefs are
waived. See 37 C.F.R. § 4I.37(c)(l)(iv) (2015). We have identified claim 1
as representative; all claims fall with claim 1. 7 We address Appellants'
arguments below.
7 With respect to claims 18, 21, 26, 27, 62, 67, and 68, Appellants have not
argued the claims separately as required by 37 C.F.R. § 4I.37(c)(iv). ([A]ny
claim( s) argued separately shall be argued under a separate subheading that
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Appellants contend that Beattie does not describe or suggest the
particle mixture recited in the claims. Appellants argue that the particles in
Beattie do not comprise a
mixture comprising particles from different particles sets,
wherein each particle set comprises a plurality of encoded
particles attached to nucleic acid hybridization probes specific
for a particular genomic locus, such that the particle mixture
collectively includes probes for a plurality of different genomic
loci, and wherein the nucleic acid hybridization probe of each
particle comprises cloned nucleic acid produced by sonicating
or fragmenting the cloned nucleic acid.
Appeal Br. 41.
We have considered Appellants' argument and are not persuaded.
Beattie teaches
Simultaneous hybridization of a DNA sample to
numerous oligonucleotide probes attached to a solid support
material ("DNA chip," or "genosensor") has been proposed as a
powerful research tool in various kinds of DNA sequence
analysis, including sequencing by hybridization, scanning for
known or unknown mutations in a gene of known nucleotide
sequence, genotyping of organisms, and genome mapping.
Beattie col. 2, 11. 26-33. Beattie also teaches the use of beads or
microparticles with sequence specific capture probes attached to the beads as
part of a multiplex analysis. Id. at col. 3 8, 11. 31--4 7. Beattie also teaches the
use of sonication to prepare nucleic acid fragments. Id. at col. 33, 11. 49--53.
identifies the claims by number.) Because Appellants have not properly
presented separate arguments for these claims we consider them as a group
with claim 1.
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We agree with the Examiner that Beattie discloses the microparticle
composition recited in the claims. Ans. 32-36.
Appellants contend that Wang does not teach the use of microparticles
as recited in the claims. Appeal Br. 42. Appellants argue that Wang is
limited to a specific karyotyping process wherein a population of sequence
tags is generated from defined portions of the genome of a test eukaryotic
cell. Id. Appellants contend that the tags are then used to determine the
number of individual sequence tags present in the population. Id.
Appellants argue that Wang does not use encoded particles in the process.
Id.
Appellants' arguments are not persuasive as it is an attack on Wang
alone, which fails to consider the combined teachings of the cited prior art
references. The Examiner relies on Beattie, not Wang, to teach the use of
microparticles. Final Act. 31-35. Wang is cited for the specific teaching of
performing an analysis of genomic loci using a reference sample. Final Act.
35-36. It is the combined teachings of Beattie and Wang that renders the
claims obvious.
Appellants next argue that Liu does not add to the teachings of Beattie
and Wang in a way that renders the claims obvious. Again we are not
persuaded. As discussed above, Beattie and Wang teach the claimed
method. Liu has been cited for the use of a florescent label as required by
claims 5, 6, 16, 18, 34, 58, and 59. Final Act. 36-37.
Conclusion of Law
We conclude that a preponderance of the evidence supports the
Examiner's conclusion that the subject matter of claim 1 would have been
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obvious over Beattie combined with Wang, Liu and the admissions made by
Appellants in the Specification.
Claims 3, 5, 6, 8-12, 14, 16, 18-30, 33, 34, 36-40, and 51-73 have
not been argued separately and therefore fall with claim 1. 37 C.F.R.
§ 4I.37(c) (1) (IV).
SUMMARY
We reverse the rejection under 35 U.S.C. § 112, first paragraph.
We affirm the rejection under 35 U.S.C. § 103(a).
TIME PERIOD FOR RESPONSE
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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