Ex Parte Adey et al

Patent Trial and Appeal Board

Sep 22, 2016

12562543 (P.T.A.B. Sep. 22, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/562,543 09/18/2009
20551 7590 09/26/2016
THORPE NORTH & WESTERN, LLP.
P.O. Box 1219
SANDY, UT 84091-1219
FIRST NAMED INVENTOR
Nils Adey
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.
2323-35639.NP 4447
EXAMINER
WHISENANT, ETHAN C
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
09/26/2016 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):
patentdocket@tnw.com
rich@tnw.com
annette.fields@tnw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte NILS ADEY, ARNOLD OLIPHANT, and W ANYUAN A0 1
Appeal2014-004043
Application 12/562,543
Technology Center 1600
Before DONALD E. ADAMS, MELANIE L. McCOLLUM, and
JEFFREY N. FREDMAN, Administrative Patent Judges.
McCOLLUM, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims directed to
recovering, labeling, or amplifying biological material. The Examiner has
rejected the claims as anticipated or obvious. We have jurisdiction under
35 U.S.C. § 6(b).
We affirm.
1 Appellants identify the real party in interest as Roche Diagnostics GmbH
(App. Br. 3).
Appeal2014-004043
Application 12/562,543
STATEMENT OF THE CASE
Claims 1-8 and 13-37 are on appeal (App. Br. 5).2'3 Claim 1 is
representative and reads as follows:
1. A method for recovering biological material coupled to a
microarray slide, comprising:
selecting a biological material to be recovered from the microarray
slide;
finding the biological material within a distinct spatial region on the
microarray slide surface as a result of a diagnostic utility of the microarray
slide; and
eluting at least a portion of the selected biological material from the
distinct spatial region without eluting substantial amounts of non-selected
biological material from regions of the microarray slide that are not within
the distinct spatial region.
Claims 1, 5, 17, 22, 23, and 29-37 stand rejected under 35 U.S.C.
§ 102(e) as anticipated by Petersdorf! (Final Act. 3).
Claims 2--4 stand rejected under 35 U.S.C. § 103(a) as obvious over
Petersdorf in view ofUematsu5 (id.).
Claims 6-8 stand rejected under 35 U.S.C. § 103(a) as obvious over
Petersdorf in view of Uematsu and Albert6 (id.).
2 Claims 9-12 are also pending but have been withdrawn from consideration
(App. Br. 5).
3 We note that the Claims Appendix to Appellants' Appeal Brief does not
include claims 35-37 (App. Br. 29-35), although they were included in the
Response filed September 10, 2012. We have not, however, reviewed the
Claims Appendix for any other inconsistencies.
4 Petersdorf et al., US 2008/0125324 Al, published May 29, 2008.
5 Uematsu et al., US 5,945,525, issued Aug. 31, 1999.
6 Albert et al., US 2008/0194414 Al, published Aug. 14, 2008. We note that
the Examiner identifies this patent document by the Patent Number for
Uematsu (Final Act. 3). However, a proper citation for Albert was provided
by Appellants (App. Br. 10).
2
Appeal2014-004043
Application 12/562,543
Claims 13-16 stand rejected under 35 U.S.C. § 103(a) as obvious over
Petersdorf in view of Wei7 (id.).
Claims 18-20 stand rejected under 35 U.S.C. § 103(a) as obvious over
Petersdorf in view of Olejnik8 or LeProust9 (id. at 4).
Claim 21 stands rejected under 35 U.S.C. § 103(a) as obvious over
Petersdorf in view of Chow10 (id.).
Claims 24-26 stand rejected under 35 U.S.C. § 103(a) as obvious over
Petersdorf in view of Olejnik or LeProust (id.).
Claim 27 stands rejected under 35 U.S.C. § 103(a) as obvious over
Petersdorf in view of Atwood11 (id.).
Claim 28 stands rejected under 35 U.S.C. § 103(a) as obvious over
Petersdorf in view ofNotomi 12 (id.).
ANTICIPATION
The Examiner finds: "Petersdorf et al. teach a method for recovering
biological material coupled to a microarray slide which comprises the three
steps recited in Claim 1, see ,-is 9-105 noting especially Examples 1-3. See
especially, ,-i 89." (Non-Final Act. 3 (dated May 8, 2012).)
7 Wei, US 2009/0029380 Al, published Jan. 29, 2009.
8 Jerzy Olejnik et al., Photocleavable Biotin Derivatives: A Versatile
Approach for the Isolation of Biomolecules, 92 PROC. NATL. ACAD. SCI.
7590-94 (1995).
9 Eric LeProust et al., Characterization of Oligodeoxyribonucleotide
Synthesis on Glass Plates, 29 NUCLEIC ACIDS RESEARCH 2171-80 (2001).
10 Chow et al., US 2003/0165884 Al, published Sept. 4, 2003.
11 Atwood et al., US 5,364,790, issued Nov. 15, 1994.
12 Tsugunori Notomi et al., Loop-Mediated Isothermal Amplification of
DNA, 28 NUCLEIC ACIDS RESEARCH e63 (2000).
3
Appeal2014-004043
Application 12/562,543
Findings of Fact
1. Petersdorf discloses:
The present invention provides a novel method for specifically
isolating and separating large segments of genomic DNA that
can be subsequently used to determine genomic haplotypes.
The method relies on using a solid phase, such as a flat glass
slide, arrayed with oligonucleotides designed to specifically
hybridize to a specific haplotype of an individual sample. The
genomic DNA is exposed and hybridized to the arrayed
oligonucleotides and the genomic DNA is separately released
from the surface of the array.
(Petersdorfii 3.)
2. Petersdorf also discloses:
The probes are arrayed to allow separate manipulation of each
spot on the solid phase surface. Genomic DNA is allowed to
hybridize to the probe on the surface of the solid phase ....
Excess genomic DNA is eliminated with a buffer wash. The
haplotyped DNA from each probe can be separately released by
denaturing the hybridized probe/DNA complex and removing
the DNA.
(Id. ii 14.)
3. In addition, Petersdorf discloses: "In an array format a large
number of different hybridization reactions can be run essentially 'in
parallel.' This provides rapid, essentially simultaneous, evaluation of a large
number of loci." (Id. ii 56.)
4. As an example, Petersdorf discloses:
Oligonucleotide probes were selected to encode a sequence of
nucleotides that unequivocally distinguish the two HLA-B
alleles in the samples. HLA-B oligonucleotide arrays were
constructed on treated microscopic slides by attaching pre-
synthesized oligonucleotide probes. The two probes were
arrayed onto the slide to allow separate manipulation on each
4
Appeal2014-004043
Application 12/562,543
spot. Genomic DNA was allowed to hybridize to the glass slide
. . . . Excess genomic DNA was eliminated with a buffer wash
and the bound genomic DNA released from each of the probes
and collected separately.
(Id. ii 82.)
5. In addition, Petersdorf discloses:
Human genomic DNA samples encoding various HLA-B
genotypes were studied. 20 µl of a selected genomic DNA
sample (100 ng/µl) were boiled for 2 min and immediately
dropped into ice and cooled for about 2 to 5 min. The sample
was removed from the ice and 5 µl of 20xSSPE was added with
gentle pipetting to mix. A drop of 4 µl of the DNA/SSPE
solution was placed into the center of each spot/ probe, which
had been previously marked with a circle on the glass slide.
The slide was incubated in at room temperature in the
hybridization chamber for 3 hr in the presence of double
distilled H20 ( ddH20). After the incubation period, the slide
was removed and washed twice with 200 ml of 2xSSPE for
5 min. The slides were removed from the wash and allowed to
air dry until the SSPE was gone. The slide was replaced in the
hybridization chamber at 50° C. and denatured by the addition
of 10 µl of 50° C. ddH20 to each spot. The denaturation was
allowed to proceed for 1 min, and the denatured DNA and
ddH20 removed from the slide with a pipette and put into tubes
according to the labeled spot. If the samples were arrayed in
duplicate, both samples were placed into the same tube to
increase the yield.
(Id. ii 89.)
Analysis
In view of the above findings of fact (FF), we conclude that the
Examiner has set forth a prima facie case that claim 1 is anticipated.
5
Appeal2014-004043
Application 12/562,543
Appellants argue, however, that "Petersdorf does not teach the use of
a microarray in its first separation step" (App. Br. 15). We are not
persuaded.
As noted by the Examiner (Ans. 2), Petersdorf teaches "a solid phase,
such as a flat glass slide, arrayed with oligonucleotides" (FF 1 ). Petersdorf
also discloses: "In an array format a large number of different hybridization
reactions can be run essentially 'in parallel.' This provides rapid, essentially
simultaneous, evaluation of a large number of loci." (FF 3.) Appellants
have not adequately explained why Petersdorf fails to teach the claimed
microarray slide.
We note Appellants' reliance on a Wikipedia entry to define the term
"'microarray' ... as 'a 2D array on a solid substrate (usually a glass slide or
silicon thin-film cell) that assays large amounts of biological material using
high-throughput screening methods"' (App. Br. 16). However, we conclude
that Appellants have not adequately explained how this definition
distinguishes Petersdorf' s "solid phase ... arrayed with oligonucleotides"
(FF 1) from the claimed microarray.
Appellants also argue that "[t]here does not appear to be a teaching in
Petersdorf of the elution of a distinct region of an actual microarray" and
that "Petersdorf does not provide enabling disclosure for the extraction of
biological material from such small distinct spatial locations on a
microarray" (App. Br. 15). We are not persuaded.
As noted by the Examiner (Ans. 3), Petersdorf discloses: "The probes
are arrayed to allow separate manipulation of each spot on the solid phase
surface. . . . The haplotyped DNA from each probe can be separately
released by denaturing the hybridized probe/DNA complex and removing
6
Appeal2014-004043
Application 12/562,543
the DNA." (FF 2; see also FF 4.) In particular, Petersdorf discloses that
"the denatured DNA and ddH20 [was] removed from the slide with a pipette
and put into tubes according to the labeled spot" (FF 5). Appellants do not
adequately explain why Petersdorf fails to teach and enable elution of a
distinct region of a microarray.
We note Appellants' argument that Petersdorf" does not enable or
even contemplate extracting biological material from a distinct spot on a
microarray that has, for example, 100,000 spots of biological material"
(Reply Br. 10). However, claim 1 does not require a microarray having
100,000 spots of biological material.
In addition, Appellants argue "that Petersdorf does not teach the step
of 'finding the biological material within a distinct spatial region on the
microarray slide surface as a result of a diagnostic utility of the microarray
slide"' (App. Br. 18). We are not persuaded.
The Examiner finds "that the initial hybridization step of Petersdorf et
al. has diagnostic utility because it informs the experimenter of the presence
and identity of one or more alleles in the sample under examination"
(Ans. 3--4; see also FF 4 ("probes were arrayed onto the slide to allow
separate manipulation on each spot")). We conclude that Appellants have
not adequately explained why the Examiner's position is in error.
Conclusion
The evidence supports the Examiner conclusion that Petersdorf
anticipates claim 1. Claims 5, 17, 22, 23, and 29-3 7 have not been argued
separately and, therefore, fall with claim 1. 37 C.F.R. § 41.37( c )(1 )(iv).
7
Appeal2014-004043
Application 12/562,543
OBVIOUSNESS
In the obviousness rejections, the Examiner relies on Petersdorf as
discussed above (Non-Final Act. 9-23 (dated May 8, 2012)). In addition,
the Examiner relies on additional references to teach various features of the
claims (id.).
Analysis
As in the anticipation rejection, Appellants argue that "Petersdorf does
not teach finding and subsequently eluting the biological material within a
distinct spatial region on the microarray slide surface" and "finding the
biological material in a microarray as a result of a diagnostic utility of the
microarray" (App. Br. 21-27). In addition, Appellants argue that the
additional references do not cure the deficiencies of Petersdorf (id.).
However, having found no deficiencies in Petersdorf, we are not persuaded
by these arguments.
Conclusion
The evidence supports the Examiner's conclusion that the applied
references suggest the methods of claims 2--4, 6-8, 13-16, 18-21, and 24-
28. We, therefore, affirm the obviousness rejections of these claims.
DECISION
We affirm the rejections of claims 1-8 and 13-3 7.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § l.136(a).
AFFIRMED
8