Ex Parte Michael

Board of Patent Appeals and Interferences

Oct 31, 2011

11436718 (B.P.A.I. Oct. 31, 2011)

UNITED STATES PATENT AND TRADEMARKOFFICE
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.
11/436,718 05/17/2006 Seul Michael LEAPS-C11-C1 8815
26158 7590 10/31/2011
WOMBLE CARLYLE SANDRIDGE & RICE, LLP
ATTN: IP DOCKETING
P.O. BOX 7037
ATLANTA, GA 30357-0037
EXAMINER
FORMAN, BETTY J
ART UNIT PAPER NUMBER
1634
MAIL DATE DELIVERY MODE
10/31/2011 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 BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte MICHAEL SEUL
____________

Appeal 2010-004008
Application 11/436,718
Technology Center 1600
______________

Before ERIC B. GRIMES, LORA M. GREEN, and
RICHARD M. LEBOVITZ, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision on the appeal under 35 U.S.C. § 134 by the Patent
Applicant from the Patent Examiner’s rejections in the above-identified U.S.
Patent Application. The Board’s jurisdiction for this appeal is under 35
U.S.C. §§ 6(b) and 134. We affirm-in-part.

Appeal 2010-004008
Application 11/436,718

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BACKGROUND
The claims in this application (“the ‘718 application”) are directed to
a “bead array comprising a planar, random assembly of encoded,
oligonucleotide-bearing beads in a designated area on a substrate.”
According to the ‘718 application, the arrays have “applications in
pharmaceutical and agricultural drug discovery and in in-vitro or genomic
diagnostics.” (P. 1, ll. 9-10.) Claims 114, 116, 117, 143, and 144 are
pending and stand rejected by the Examiner as follows:
1. Claim 114 under 35 U.S.C. § 102(b) as anticipated by Drmanac;1
and
2. Claims 116, 117, 143, and 144 under 35 U.S.C. § 103(a) as
obvious in view of Drmanac combined with Coffer2 or Seul.3
Claim 114 is representative and reads as follows:
114. A bead array comprising a planar, random assembly
of encoded, oligonucleotide-bearing beads in a
designated area on a substrate, wherein different
oligonucleotide-bearing beads are randomly distributed
throughout the array, wherein different oligonucleotides
are attached to different beads and said beads are
encoded with a fluorescent signature which permits
identification of the oligonucleotides attached thereto,
and permits distinguishing of individual beads including

1 EP 0 392 546, published October 17, 1990, inventor Radoje T. Drmanac,
hereinafter referred to as “Drmanac.”
2 Coffer, Jeffery, L., et al. (1992), Characterization of quantum-confined
CdS nanocrystallites stabilized by deoxyribonucleic acid (DNA),
Nanotechnology, 3, 69-75. Hereinafter referred to as “Coffer.”
3 Seul, Michael & Andelman, D. (1995), Domain Shapes and Patterns: The
Phenomenology of Modulated Phases, Science,267(5197), 476-483.
Hereinafter referred to as “Seul.”

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distinguishing different beads from each other, wherein
the beads have a diameter of from 2 microns to 20
microns, and said beads are affixed to the substrate in an
ordered array configuration wherein the beads are in
designated positions, in accordance with a given outline.
(App Br. 7, Claims Appendix)

CLAIM INTERPRETATION
We begin with claim interpretation because a claim must be properly
interpreted before it can be compared to the prior art. During patent
examination, claim terms are given “the broadest reasonable meaning . . . in
their ordinary usage as they would be understood by one of ordinary skill in
the art, taking into account whatever enlightenment by way of definitions or
otherwise that may be afforded by the written description contained in the
applicant’s specification.” In re Morris, 127 F.3d 1048, 1054 (Fed. Cir.
1997).
The claimed bead array is recited to be a “random assembly of
encoded, oligonucleotide-bearing beads in a designated area on a substrate,
wherein different oligonucleotide-bearing beads are randomly distributed
throughout the array.” The beads are “in an ordered array configuration
wherein the beads are in designated positions, in accordance with a given
outline.” The beads are thus in a “random assembly” and “randomly
distributed” in “designated positions.” The Specification uses such terms
but does not define them (e.g., p. 19, ll. 1-2; p. 19, ll. 32-33; p. 20, ll. 6-7; p.
20, ll. 16-19). Thus, we adopt the ordinary meaning of these terms as they
would be understood by a person of skill in the art.
The terms “random assembly” and “randomly distributed” indicate
that each bead has an equal probability of occurring at any position in the
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bead array.4 The beads are also “in a designated area” on the substrate and
“in designated positions, in accordance with a given outline.” The latter
phrases would be interpreted in the context of the claim to mean that the
beads are placed in areas (the “designated area” or “positions . . . in
accordance with a given outline”) of the substrate which were chosen
beforehand (the “designated” area or “given” outline).
The beads “are in designated positions, in accordance with a given
outline.” We interpret the term “outline” to mean that the area in which the
beads are placed has a defined boundary or outer limit, consistent with the
ordinary meaning of such term.5 The Specification refers to “a designated
area of arbitrary outline” (p. 12, l. 10) and forming arrays “with a given
overall outline” (p. 20, ll. 18-19), descriptions which also indicate that
“outline” is a reference to the boundary of the designated area in which the
beads are placed.

1. ANTICIPATION BY DRMANAC
Findings of Fact (“FF”)
Drmanac
[FF1] Drmanac describes sequencing by hybridization (“SBH”) comprising
attaching genomic clones to discrete particles (“DP”) (col. 7, ll. 22-27 & 41-
42).

4 Merriam-Webster, http://www.merriam-
webster.com/dictionary/random?show=1&t=1319301942, accessed October
22, 2011.
5 Merriam-Webster, http://www.merriam-webster.com/dictionary/outline,
accessed October 22, 2011.
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[FF2] “Aliquotes [sic] of DPs from each well are mixed together and spread
in the monolayer of required density. This is followed by the necessary
number of fixations. In this way one can obtain hybridization areas (HA)
similar to filters in a dot blot procedure.” (Col. 7, ll. 27-31.)
[FF3] “One can imagine a simple case in which each HA contains enough
randomly displayed DPs that each clone from the library is represented at
least once. The other HAs are replicas but DPs are present in different
places.” (Col. 7, ll. 33-37.)
[FF4] Drmanac explains that the DPs can be recognized in three principal
ways “which can be combined.”
1) Labeling with physical attributes of DP like size,
shape and color which can be differentiated in a phase of
reading, for instance, during image analysis.
2) Labeling with different combinations of ONs which
can be recognized as such by hybridization with appropriate
ONPs
. . . .

3) Labeling (better recognition) by the use of certain
fraction of ONPs on all HA.
(Col. 7, l. 45 to col. 8, l. 3.)
[FF5] Drmanac describes a method of determining genomic sequences
using oligonucleotide probes (“ONP”) bound to discrete particles (“DP”)
(col. 8, ll. 32-37). The method is called “Inverse DP-SBH” (“ISBH”) (id.).
[FF6] The DPs “are used for forming monolayer HA (OHA
oligohybridization area).” (Col. 9, ll. 13-14.)
[FF7] Drmanac describes methods of making DPs, each carrying a different
ON (oligonucleotide) (col. 15, ll. 14-32).
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[FF8] The hybridization areas into which the DPs are placed are
characterized by Drmanac as a “random monolayer,” where the area has a
defined shape, e.g., 10 cm x 10 cm (col. 17, ll. 28-34).
[FF9] Drmanac teaches that “more or less square submatrices are possible”
in the hybridization areas (HA) comprising DPs (col. 19, ll. 45-46).
[FF10] Drmanac teaches:
Therefore, parallel formation of many submatrices of the type
104 to 105 targets x 10-100 ONPs seems to us as most rational
way to proceed. The parallelism can be of the two kinds: a
formation of all 100-1000 submatrices with the same group of
ONPs on a single HA, and simultaneous hybridization in
separate vessels on HA “replicas” with many different ONP
groups.
(Col. 19, l. 54 to col. 20, l. 3.)
[FF11] Drmanac teaches that “different fluorescent molecules” can be used
as labels for the DPs to discriminate between different DPs (col. 20, ll. 47-
52; col. 21, ll. 9-31).
[FF12]
This functional cassette preparations are independent (and
usable for any) of the individual object of a species given, i.e.
individual genome. The consequence is preparation of ONPs
containing integrated information of type - basic element x
position, usable for any DNA. This also results in DP
preparation integrating the addressing information, so that it
needs not be determined by robotic positioning operations.
(Col. 23, ll. 10-18.)
[FF13] Drmanac describes DPs with a 4 µm diameter (col. 17, l. 26).
[FF14] Drmanac does not describe the material which comprised the DPs.

Legal Principles
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“To anticipate a claim, a prior art reference must disclose every
limitation of the claimed invention, either explicitly or inherently.
Anticipation is an issue of fact, and the question whether a claim limitation
is inherent in a prior art reference is a factual issue. . . .” In re Schreiber,
128 F.3d 1473, 1477 (Fed. Cir. 1997) (citations omitted).
Analysis
The following findings of fact establish that Drmanac describes every
limitation of the claimed “bead array”:
•“A bead array comprising a planar, random assembly of encoded,
oligonucleotide-bearing beads” and “different oligonucleotide-bearing beads
are randomly distributed throughout the array” (App Br. 7, Claims
Appendix).
[FF15] Drmanac describes a “random monolayer” of oligonucleotide-
bearing beads (FF2, FF3, FF6, & FF8) which meets the limitation of
“a planar, random assembly of encoded, oligonucleotide-bearing
beads” and of beads “randomly distributed throughout the array.”
[FF16] Drmanac explicitly teaches that the DPs (“beads”) do not
have to be placed at predetermined positions in the array, but can be
randomly displayed, because Drmanac’s method allows the DPs to be
recognized by imaging once the DPs have been arrayed randomly in
the hybridization area substrate (FF4 & FF6).

•Beads “in a designated area on a substrate” and “wherein the beads
are in designated positions, in accordance with a given outline” (App Br. 7,
Claims Appendix).
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[FF17] Drmanac teaches that the DPs (“beads”) are placed in defined
hybridization areas of the substrate (FF2, FF8, & FF9) and thus are
placed in positions that were designated beforehand to hold the DPs –
meeting the limitation of a “designated area” in “designated positions
. . . in accordance with a given outline” as those phrases would be
understood by a person of skill in the art.

•“wherein different oligonucleotides are attached to different beads” (App
Br. 7, Claims Appendix).
[FF18] Drmanac teaches making DPs (“beads”), each carrying a
different ON (oligonucleotide) (FF7).

•“said beads are encoded with a fluorescent signature which permits
identification of the oligonucleotides attached thereto, and permits
distinguishing of individual beads including distinguishing different beads
from each other” (App Br. 7, Claims Appendix).
[FF19] Drmanac describes labeling the DPs with fluorescent
molecules to discriminate between the different DPs having different
oligonucleotides (FF4, FF7, & FF11), meeting the “fluorescent
signature” limitation of the claim.

•“wherein the beads have a diameter of from 2 microns to 20 microns” (App
Br. 7, Claims Appendix).
[FF20] Drmanac describes using DPs (“beads”) of a 4 µm diameter
(FF13), which falls within the claimed range.

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•“wherein the beads are in designated positions, in accordance with a given
outline.” (App Br. 7, Claims Appendix).
[FF21] Drmanac describes making hybridization areas and
submatrices of square sizes (FF8 (10 cm x 10 cm) & FF9) and thus
describes beads in a “given outline” or outer square boundary –
meeting the corresponding limitation of the claim.

Appellant’s Arguments
Appellant contends that the particles are not “randomly distributed
throughout the array” as recited in the claims (App. Br. 3-4). We do not
agree. Drmanac expressly refers to “randomly displayed DPs” and a
“random monolayer” (FF3 & FF8; FF15 & FF16) – providing explicit
support for the claimed limitation.
Appellant also contends that Drmanac does not describe “beads . . . in
designated positions, in accordance with a given outline.” Appellant states:
[t]he fact that HA regions are replicated across the surface does
not create beads “in accordance with a given outline.” There is
no description in Drmanac that the replicas are placed in a
particular position with respect to every other replica, as would
be necessary to place the beads in particular positions.
(App. Br. 4.)
As summarized above, Drmanac describes placing DPs in an area of a
substrate that was determined beforehand to be for DPs (FF17), and thus
meets the limitation of “designated positions . . . in accordance with a given
outline” as we have interpreted that phrase. The hybridization areas
comprising the DPs can be square and thus have a “given outline” as recited
in the claim (FF21).
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Appellant’s argument about Drmanac not describing beads in “a
particular position with respect to every other replica” is unpersuasive
because the claim does not require this feature. Rather, the beads are
expressly recited to be “randomly distributed” in the arrays. The claim also
does not require there to be more than one replica in the claimed bead array.
The term “designated” as used in the claim means that the area in
which the beads are placed was determined beforehand to be a place for the
beads – not that the beads must be arrayed in specific predetermined
positions within this area. Interpreting claim 114 to require the beads to be
in particular positions chosen before arraying would be contrary to the
recited limitation that the “beads are randomly distributed throughout the
array.” Appellant did not explain how randomly arrayed beads could be
“random” and, at the same time, be “placed in a particular position with
respect to every other replica” (App. Br. 4).
The rejection of claim 114 as anticipated by Drmanac is affirmed.

2. OBVIOUSNESS REJECTION
Legal principles
Where, as here, the claimed and prior art products are
identical or substantially identical, or are produced by identical
or substantially identical processes, the PTO can require an
applicant to prove that the prior art products do not necessarily
or inherently possess the characteristics of his claimed product.
. . .
Whether the rejection is based on “inherency” under 35
U.S.C. § 102, on “prima facie obviousness” under 35 U.S.C. §
103, jointly or alternatively, the burden of proof is the same,
and its fairness is evidenced by the PTO’s inability to
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manufacture products or to obtain and compare prior art
products.
In re Best, 562 F.2d 1252, 1255 (CCPA 1977) (footnote omitted).
Once “the PTO shows sound basis for believing that the products of
the applicant and the prior art are the same, the applicant has the burden of
showing that they are not.” In re Spada, 911 F.2d 705, 708 (Fed. Cir. 1990).
(citation omitted.)
Analysis
Claim 143 is drawn to a “bead array” having substantially the same
limitations as recited in claim 114, but further reciting that the “beads are
affixed to the substrate in an ordered crystalline array configuration.” The
Examiner found that Drmanac did not teach a bead array in a crystalline
array configuration (Answer 5). However, the Examiner found that
“nanoparticles in crystalline arrangement were well known in the art at the
time the claimed invention was made as taught by Coffer and Seul.” (Id.)
Based on Coffer and Seul, the Examiner concluded:
it was well known that aliquots of DNA-containing particles
form DNA stabilized crystalline monolayers and the formation
was ubiquitous. Therefore, it would have been obvious to one
of ordinary skill in the art at the time the claimed invention was
made that at least some of the particles in the HA of Drmanac
would be in crystalline formation.
(Id. at 6.)
The Examiner’s position is that inherently at least some of the
particles in the HA of Drmanac would be in the claimed crystalline array
configuration formation. Thus, the issue is whether the Examiner had a
factual basis upon which to believe that Drmanac’s beads would be arrayed
in a “crystalline array configuration” as recited in claim 143.
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The Examiner based the belief on the teachings in Coffer and Seul.
We thus turn to these publications.
Coffer describes cadmium sulfide crystallites stabilized by DNA
(Coffer, p. 69). Cadmium sulfide (CdS) is a semiconductor (id.). The
Examiner did not provide sufficient evidence that the discrete particles (DP)
disclosed in Drmanac would form lattice planes of crystalline particles as
described by Coffer (id. at 71, col. 2). In particular, Drmanac did not
describe the material which comprised the DPs (FF14). Thus, there is
insufficient information to determine whether Drmanac’s DPs would behave
similarly to the CdS crystallites described in Coffer. Consequently, we
conclude that the Examiner did not have reasonable basis upon which to
believe that Drmanac’s DPs would form a crystalline array.
Seul was cited by the Examiner for its “teaching that crystalline
configurations are ubiquitous in particle formations and as such, suggests
that at least some of the particles of Drmanac would have been in crystalline
formation.” This finding is insufficient evidence that the DPs (particles
bearing oligonucleotides) described in Drmanac would form crystalline
arrays. The Examiner did not show a basis for believing that the DPs of
unknown composition (FF14) of Drmanac would form a crystalline array as
did the specific particles in Seul.
The Examiner also did not provide a reason why a person of ordinary
skill in the art would have utilized the particles in either Coffer or Seul as the
DPs of Drmanac.
In view of the foregoing we reverse the rejection of claim 143, and
claims 116, 117, and 144 which depend on claim 143 and incorporate all the
limitations of claim 143.
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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-IN-PART

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