Ex Parte Beutler et al

Board of Patent Appeals and Interferences

Jun 30, 2006

10121264 (B.P.A.I. Jun. 30, 2006)

The opinion in support of the decision being entered today was not written
for publication and is not binding precedent of the Board.

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte ERNEST BEUTLER, RICHARD BRUCE,
SCOTT A. ELROD, JOHN STUART FITCH, HUANGPIN BEN HSIEH
ERIC PEETERS and RICHARD A. LERNER
__________

Appeal No. 2006-0227
Application No. 10/121,264
__________

ON BRIEF
__________

Before ADAMS, GRIMES, and GREEN, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL

This appeal involves claims to a device comprising genomic DNA. The examiner
has rejected the claims as anticipated by or obvious in view of the prior art. We have
jurisdiction under 35 U.S.C. § 134. Because we agree with the examiner that the claims
are broad enough to read on devices in the prior art, we affirm.
Discussion
1. Claim construction
Claims 23-28, 31-34, and 40 are on appeal. Claims 14-22 and 35-39 are also
pending but have been withdrawn from consideration by the examiner.
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The claims subject to each rejection stand or fall together, because Appellants
have not argued them separately. See 37 CFR § 41.37(c)(1)(vii). Claims 23, 24, and
40 are representative and read as follows:
23. A device comprising
a) a substrate comprising
1) a matrix;
2) one or more separate transfer agent spaces; and
3) one or more transfer agent layers contained in one or more of
the separate transfer agent spaces; and
b) genetic material deposited on or in one or more of the transfer agent
layers, wherein the genetic material on each of a majority of the transfer agent
layers comprises purified genomic DNA comprising more than one chromosome
of the genomic DNA from at least one cell of an individual within a defined
population.

24. The substrate of claim 23, wherein at least one of the transfer agent layers
comprises a saccharide selected from at least one of sucrose and
glucose.

40. A device comprising:
a) a substrate;
b) a transfer agent layer; and
c) a first genetic material position and a second genetic material position
on or in the transfer agent layer that each comprise genetic material,
wherein the genetic material of the first genetic material position
comprises purified genomic DNA comprising more than one
chromosome of the genomic DNA from at least one cell of an individual
within a defined population and the genetic material of the second
genetic material position comprises purified genomic DNA comprising
more than one chromosome of the genomic DNA from at least one cell
of an individual within a defined population, and wherein the genetic
material of the first genetic material position is separate from the
genetic material of the second genetic material position.

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“[T]he PTO applies to the verbiage of the proposed claims the broadest
reasonable meaning of the words 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, 44 USPQ2d 1023, 1027
(Fed. Cir. 1997).
The specification expressly defines most of the terms of the claims:
• a “substrate” is defined as “an object onto which genetic material may be
deposited” (specification, page 16);

• a “matrix” is defined as “a material that includes transfer agent spaces” (id.,
page 14);

• a “transfer agent space” is defined as “a region capable of containing at least
one transfer agent” (id.);

• a “transfer agent” is defined as “a substance onto or into which genetic material
may be deposited, which can transport the genetic material when the transfer agent is
moved” (id., page 13);

• a “transfer agent layer” is defined as “a layer comprising a transfer agent” (id.);

• “purified” is defined as “substantially separated from at least one other material
with which it had been intermingled” (id., page 16);

• an “individual” is defined to include “vertebrate, invertebrate, plant, and
prokaryotic sources” (id., page 19); and

• a “defined population” is defined as “any group of individuals . . . In certain
embodiments, a defined population may include a random group of individuals that may
or may not share at least one common characteristic” (id., page 11).

Thus, when we interpret claim 23 in light of the definitions in the specification, we
conclude that it is directed to a device comprising “an object onto which genetic material
may be deposited,” that object comprising “a material that includes” “a region capable of

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containing” “a substance onto or into which genetic material may be deposited, which
can transport the genetic material when the [substance] is moved,” where the region
also contains a “layer comprising” “a substance onto or into which genetic material may
be deposited, which can transport the genetic material when the [substance] is moved.”
In addition, the layer comprising a substance that can transport the genetic
material when the substance is moved has deposited on or in it genomic DNA
comprising more than one chromosome from a “vertebrate, invertebrate, plant, and
prokaryotic” individual that belongs to “any group of individuals.”
When we give the terms of claim 23 their broadest reasonable interpretation
consistent with the definitions in the specification, we interpret claim 23 to be directed to
a device comprising an object that includes a region having a layer of a substance that
can transport genetic material when the substance is moved, and that has deposited on
or in it at least two chromosomes from the genomic DNA of any organism.
Claim 24 is directed to the same device, wherein the layer of a substance that
can transport genetic material when the substance is moved comprises “a saccharide
selected from at least one of sucrose and glucose.” (Although the preamble of claim 24
recites the “substrate of claim 23,” we interpret the claim as being directed to the device
defined by claim 23; a dependent claim must incorporate all of the limitations of the
claim from which it depends. 35 U.S.C. § 112, fourth paragraph.)
Claim 40 is directed to a device comprising “an object onto which genetic
material may be deposited,” and a “layer comprising” “a substance onto or into which
genetic material may be deposited, which can transport the genetic material when the
[substance] is moved,” where the layer comprises two separate positions at which there

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is deposited genomic DNA comprising more than one chromosome from a “vertebrate,
invertebrate, plant, and prokaryotic” individual that belongs to “any group of individuals.”
When we give claim 40 its broadest reasonable interpretation consistent with the
specification, we interpret it to be directed to a device comprising an object onto which
genetic material can be deposited and a layer of a substance that can transport genetic
material when the substance is moved, where the layer has deposited on or in it, at two
separate positions, at least two chromosomes from the genomic DNA of any organism.
2. Anticipation
The examiner rejected claim 40 under 35 U.S.C. § 102(b) as anticipated by
Chu.1 (Since the present application was filed in 2002 and Chu issued in 2004, the
examiner’s citation of 35 U.S.C. § 102(b) appears to be a mistake. However, the
application that issued as the Chu patent was filed in 1998, so Chu appears to qualify
as prior art under 35 U.S.C. § 102(e). Appellants have not disputed that Chu is prior
art.)
The examiner reasoned that
Chu discloses a device comprising a substrate (tray)[,] a transfer agent
layer (slide) and a first genetic material position and a second genetic
material position . . . comprising more than one chromosome from at least
one individual within a defined population (chromosome spread whereby
the chromosomes are removed from the cells[;] i.e.[,] purified) and wherein
the first material position is separate from the second material position
(i.e.[,] different wells) (Column 32, line 35-Column 34, line 14).

Examiner’s Answer, pages 5-6.
We agree with the examiner that Chu’s Example 9 anticipates instant claim 40.
Chu states that “[c]hromosomes can be examined for gross abnormalities such as

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1 Chu, U.S. Patent 6,703,247, issued March 9, 2004 (application filed Dec. 23, 1998).

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translocations by a technique known as whole chromosome painting.” Col. 32, lines 37-
39. Chu states that the method typically involves staining multiple chromosomes at a
time, with dyes that fluoresce in different colors: “For example, chromosomes 1, 2 and
3 can be stained simultaneously by using probes which fluoresce orange for one
chromosome, probes which fluoresce green for a second chromosome, and probes
which fluoresce red for a third chromosome.” Col. 32, lines 47-51.
Since human cells have a total of 24 chromosomes, “one test would typically use
8 slides of cells to examine the complete nuclear genome of a human. This test would
include . . . placing the 8 slides onto 8 wells of a tray.” Col. 32, lines 52-54. That is, the
same three (orange, green, and red) labels would be attached to different probes and
used to label three different chromosomes on each slide, allowing all twenty-four
chromosomes to be examined using eight slides.
Chu discloses an apparatus designed to allow all twenty-four chromosomes to be
examined on a single slide. Chu’s Figure 16A and Figure 16B are reproduced below:

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As described by Chu, these figures show:
A chip or tray 400 designed to allow the analysis of all 24 chromosomes
on a single slide 70 . . . . The tray 400 is one which can snap on to or
otherwise be attached to a microscope slide 70. The chip or tray 400
contains 8 wells 410 with each well 410 separated from neighboring wells
410 by a gap or a trough 420. Such a tray 400 is illustrated in FIG. 16A.

Col. 32, lines 57-63. “FIG. 16B is a side view of the 8 well tray 400 shown in FIG. 16A.”
Col. 10, lines 14-15. “In a preferred embodiment, the probes are predried onto the 8
wells 410 of the tray 400 with probes for 3 different chromosomes in each well 410. . . .
Metaphase or interphase cells are fixed across a slide 70 and the slide 70 is placed in
contact with the tray 400. Then buffer is added to the openings 430 to each well 410.”
Col. 33, lines 18-24.
Chu also describes a “more preferred embodiment [in which] the slide 70
includes positive and negative controls in the regions 440 which are those which are in
contact with the hybridization fluid in each of the 8 wells 410. Using microarray
technology . . . , nucleic acids which are complementary to the probes being used to
paint the chromosomes are coated and immobilized onto the slide 70 . . . . One example
of an array is shown in FIG. 16E in which all 24 nucleic acids are arrayed around the
edges of each region 440 which will contact each of the 8 wells 410.” Col. 33, lines 46-
60.

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Chu’s Figure 16E is reproduced below:

The figure shows one of the regions 440 having twenty-four smaller regions
around its perimeter; the smaller regions are labeled with the numbers 1 through 22, x,
and y, corresponding to the twenty-four chromosomes in the human genome. Chu
describes the function of the smaller regions as follows: “If[,] for example, a first region
440 is one which will contact a well 410 containing probes for chromosomes 1, 2 and 3,
then the control nucleic acids for these chromosomes should light up after staining
(each showing only a single color) while the remaining 21 controls should not hybridize
and should not fluoresce. In this manner there are both positive and negative controls
and labels for each of the 8 wells 410.” Col. 33, lines 60-67.
Thus, as we interpret the reference disclosure, Chu teaches a microscope slide
to allow chromosome painting of all twenty-four human chromosomes on a single slide.
In a preferred embodiment, each of eight regions on the slide has samples of each of
the twenty-four human chromosomes (1-22, X, and Y) arrayed around its edge; the

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chromosomes serve as positive and negative controls for hybridization of the
chromosome-specific probes to the target chromosomes in the sample.
We agree with the examiner that Chu’s disclosure anticipates claim 40. The
device disclosed by Chu comprises a substrate (i.e., “an object onto which genetic
material may be deposited”). Specifically, Chu teaches that the eight wells of the tray
can have probes predried in them (col. 33, lines 18-20). Thus, the tray is an object into
which genetic material may be deposited – a substrate.
Chu’s device also comprises a transfer agent layer (i.e., a “layer comprising” “a
substance onto or into which genetic material may be deposited, which can transport
the genetic material when the [substance] is moved”). Specifically, Chu teaches a
microscope slide having samples of all twenty-four human chromosomes immobilized at
each of eight regions. The chromosomes would be transported when the microscope
slide is moved. Thus, the microscope slide meets the definition of a transfer agent
layer.
Finally, Chu teaches that the microscope slide (transfer agent layer) has all
twenty-four human chromosomes immobilized on it at each of eight separate locations.
Thus, the microscope slide comprises eight genetic material positions, each of them
comprising more than one chromosome of genomic DNA. Genomic DNA by definition
comes from a cell, and all cells are ultimately derived from an individual. According to
the specification, a “defined population” is any group of individuals; thus, all individuals
belong to some defined population.
Claim 40, in its broadest reasonable interpretation, reads on the device disclosed
by Chu. Therefore, claim 40 is anticipated by Chu.

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Appellants argue that Chu’s microscope slide is not a transfer agent layer:
At best, the slide is a substrate. In fact, Appellants’ specification defines
the term “substrate” as “an object onto which genetic material may be
deposited. . . . [I]n certain embodiments, the substrate may be, but is not
limited to, a multiwell plate, a glass slide, a filter membrane. . . .”
Specification at page 16, paragraph [047] (emphasis added). Therefore,
the slide of Chu does not serve as a transfer agent layer.

Appeal Brief, page 22 (emphasis and alterations in original).
We disagree with Appellants’ proposed claim construction. The specification
defines a “transfer agent layer” as a “layer comprising” “a substance onto or into which
genetic material may be deposited, which can transport the genetic material when the
[substance] is moved.” A microscope slide is a layer of glass, and glass is a substance
onto which genetic material may be deposited, which can transport the genetic material
when the glass is moved. Therefore, a microscope slide is a “transfer agent layer”
when that term is given its broadest reasonable interpretation consistent with the
specification. While it is true, as Appellants argue, that the specification states that a
glass slide can be a substrate in certain embodiments (Appeal Brief, page 22), that
does not mean that a microscope slide cannot also be a transfer agent layer in other
embodiments.
Appellants also argue that “the tray of Chu is not a substrate. . . . The
specification defines a substrate as ‘an object onto which genetic material may be
deposited. . . . The genetic material of Chu is . . . always directly adhered to the slide,
and is never deposited onto the tray. Thus, the tray of Chu is not a substrate as defined
by Appellants’ specification.” Appeal Brief, page 23 (emphasis in original).

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We also disagree with this proposed interpretation of the claim. As Appellants
note, the specification defines a substrate as “an object onto which genetic material may
be deposited.” Chu states that probes (genetic material) can be predried on the wells of
the tray. See col. 33, lines 18-20: “In a preferred embodiment, the probes are predried
onto the 8 wells 410 of the tray 400 with probes for 3 different chromosomes in each
well 410.” Thus, the tray is an object onto which genetic material may be deposited,
and the tray meets the specification’s definition of a substrate.
We affirm the rejection of claim 40 as anticipated by Chu. The examiner also
rejected claim 40 under 35 U.S.C. § 102(b) as anticipated by Kausch.2 However, since
we have already found that the claim is anticipated by Chu, we need not consider
whether it is also anticipated by Kausch.
3. Obviousness based on Chu and Sabatini
The examiner rejected claims 23, 25-28, and 31-34 under 35 U.S.C. § 103 as
obvious in view of Chu and Sabatini.3 We agree with the examiner that claim 23 is
unpatentable in view of the cited references. In fact, we find that Chu anticipates claim
23.
Given its broadest reasonable interpretation, claim 23 is directed to a device
comprising an object that includes a region having a layer of a substance that can
transport genetic material when the substance is moved, and that has deposited on it or
in it at least two chromosomes. Such a device is shown in Chu’s Figures 16B and 16C:

2 Kausch et al., U.S. Patent 5,665,582, issued September 9, 1997.
3 Sabatini, U.S. Patent 6,544,790, issued April 8, 2003 (application filed Sept. 18, 2000).

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Chu describes the figures as follows:
FIG. 16B is a side view of the 8 well tray 400 shown in FIG. 16A. A slide
70 is shown on the tray 400. . . . FIG. 16C is an end-on view of the slide
and tray of FIGS. 16A and 16B. . . . Slide 70 is shown resting above sides
of tray 400 showing optional clips 402 to hold slide 70 to tray 400.

Col. 10, lines 14-22.
As discussed above with respect to claim 40, Chu’s microscope slide meets the
instant specification’s definition of a transfer agent layer that has deposited on it at least
two chromosomes. Supra, pages 9-10. The device disclosed by Chu also comprises a
transfer agent space; i.e., “a region capable of containing” “a substance onto or into
which genetic material may be deposited, which can transport the genetic material when
the [substance] is moved.” Such a space is shown in Chu’s Figure 16C: the space
between the two clips 402 is a region capable of containing a microscope slide, which is
a substance onto which genetic material can be deposited, which can transport the
genetic material when the slide is moved. Thus, Chu’s device comprises a transfer
agent space.

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The device also comprises a matrix; i.e., “a material that includes transfer agent
spaces.” The tray onto which the microscope slide is fitted includes transfer agent
spaces, and therefore the tray (or more properly, perhaps, the material the tray is made
of) meets the definition of a matrix.
Finally, the device comprises a substrate that comprises all of the above
elements. The specification defines a substrate as “an object onto which genetic
material may be deposited.” The assembled device shown in Chu’s Figure 16B
includes all of the above elements and can have genetic material deposited on it
(specifically, probes can be deposited on the tray part of the device and chromosomal
DNA controls can be deposited on the microscope slide; see Chu at col. 33, lines 18-20
and lines 46-67).
As with the rejection of claim 40, Appellants argue that Chu’s slide is not a
transfer agent layer as defined in the instant specification. See the Appeal Brief, page
26. We have already addressed this argument. Supra, page 10.
We find that Chu discloses a device meeting all the limitations of claim 23. We
therefore affirm the examiner’s rejection based on obviousness in view of Chu and
Sabatini: “[A]nticipation is the epitome of obviousness.” Connell v. Sears, Roebuck &
Co., 722 F.2d 1542, 1548, 220 USPQ 193, 198 (Fed. Cir. 1983). Appellants have not
separately argued claims 25-28 and 31-34. Therefore, those claims fall with claim 23.
See 37 CFR § 41.37(c)(1)(vii).
We affirm the rejection of claims 23, 25-28, and 31-34 under 35 U.S.C. § 103 as
obvious in view of Chu and Sabatini. Our reasoning, however, differs from that of the
examiner. Therefore, we will designate our affirmance a new ground of rejection in

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order to give Appellants a fair opportunity to respond. See In re Kronig, 539 F.2d 1300,
1302-03, 190 USPQ 425, 426-27 (CCPA 1976).
4. Obviousness based on Chu, Sabatini, and Kausch
The examiner also rejected claim 24 under 35 U.S.C. § 103 as obvious in view of
Chu, Sabatini, and Kausch. We will affirm this rejection as well, although our reasoning
differs from that of the examiner.
Claim 24 depends on claim 23 and adds the limitation that the transfer agent
layer comprises either sucrose or glucose. Thus, claim 24 is directed to a device
comprising an object that includes a region having a layer of a substance (comprising
either sucrose or glucose) that can transport genetic material when the substance is
moved, and that has deposited on it or in it at least two chromosomes.
Kausch discloses such a device in Example 1C (Chromosome Preparation):
[T]he microcentrifugation chambers were set up. The transparent cap of a
15 ml Falcon tube was filled with 1M sucrose at a pH of about 8.5 to a
depth of about 1 cm. The coverslip was dipped in the sucrose with the
prefixed side up and should rest on the raised central portion of the
chamber. There should be a few mm of sucrose above the coverslip. . . .

Cells were lysed in about 1% Nonidet P-40 (a detergent). . . . The lysate
was layered over the sucrose cushion in the chamber, and centrifuged.

Column 26, line 62, to column 27, line 9.
The device described by Kausch meets all the limitations of claim 24. The 1M
sucrose solution forms a pool that meets the specification’s definition of a “transfer
agent layer,” since it is a layer of “a substance onto or into which genetic material may
be deposited, which can transport the genetic material when the [substance] is moved.”
For example, if the 1M sucrose with chromosomal DNA layered on it were poured into a

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different container or taken up in a pipette, it would transport the chromosomal DNA
along with it.
The upturned Falcon tube cap meets the specification’s definition of a substrate
(“an object onto which genetic material may be deposited”) that comprises a matrix (“a
material that includes transfer agent spaces”; specifically, the plastic that the cap is
made of) and a transfer agent space (“a region capable of containing at least one
transfer agent”; specifically, the concave area inside the upturned cap, which is capable
of containing the sucrose solution). Thus, claim 24 reads on the microcentrifugation
chamber disclosed by Kausch.
Appellants argue that “the sucrose in Kausch that the Examiner alleges is a
transfer agent layer does not meet the definition of a transfer agent layer presented in
Appellants’ specification. Kausch uses sucrose as a physical cushion for a coverslip, to
prevent the coverslip from breaking during centrifugation. The sucrose itself never
moves independent of the coverslip, and does not transport genetic material anywhere.”
Appeal Brief, page 28.
We disagree with Appellants’ interpretation of the claim. The specification
defines a transfer agent layer as a layer comprising “a substance onto or into which
genetic material may be deposited, which can transport the genetic material when the
[substance] is moved.” Specification, page 13. A solution of 1M sucrose (or any other
liquid, for that matter) is capable of having genetic material deposited into it, and of
transporting the genetic material when the solution is moved. Thus, a one centimeter
deep layer of 1M sucrose meets the specification’s definition of a transfer agent layer.
The fact that the solution was not actually used to transport chromosomes from one

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place to another is immaterial – the specification’s definition merely requires that the
transfer agent be capable of transporting genetic material, not that it actually be used to
do so.
We affirm the rejection of claim 24 as obvious in view of Chu, Sabatini, and
Kausch. Since our reasoning again differs from that of the examiner, however, we
designate our affirmance a new ground of rejection in order to give Appellants a fair
opportunity to respond.
Summary
We affirm the rejection of claim 40 as anticipated by Chu. We also affirm the
rejections based on obviousness but we designate those affirmances as new grounds of
rejection because our reasoning differs from that of the examiner.
Time Period for Response
Regarding the affirmed rejection, 37 CFR § 41.52(a)(1) provides "[a]ppellant may
file a single request for rehearing within two months from the date of the original
decision of the Board."
In addition to affirming the examiner's rejection(s) of one or more claims, this
decision contains a new ground of rejection pursuant to 37 CFR § 41.50(b) (effective
September 13, 2004, 69 Fed. Reg. 49960 (August 12, 2004), 1286 Off. Gaz. Pat. Office
21 (September 7, 2004)). 37 CFR § 41.50(b) provides "[a] new ground of rejection
pursuant to this paragraph shall not be considered final for judicial review."
37 CFR § 41.50(b) also provides that the appellant, WITHIN TWO MONTHS
FROM THE DATE OF THE DECISION, must exercise one of the following two options

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with respect to the new ground of rejection to avoid termination of the appeal as to the
rejected claims:
(1) Reopen prosecution. Submit an appropriate amendment of the
claims so rejected or new evidence relating to the claims so rejected, or
both, and have the matter reconsidered by the examiner, in which event
the proceeding will be remanded to the examiner. . . .

(2) Request rehearing. Request that the proceeding be reheard
under § 41.52 by the Board upon the same record. . . .

Should the appellant elect to prosecute further before the examiner pursuant to
37 CFR § 41.50(b)(1), in order to preserve the right to seek review under 35 U.S.C. §§
141 or 145 with respect to the affirmed rejection, the effective date of the affirmance is
deferred until conclusion of the prosecution before the examiner unless, as a mere
incident to the limited prosecution, the affirmed rejection is overcome.

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If the appellant elects prosecution before the examiner and this does not result in
allowance of the application, abandonment or a second appeal, this case should be
returned to the Board of Patent Appeals and Interferences for final action on the
affirmed rejection, including any timely request for rehearing thereof.

AFFIRMED, 37 CFR § 41.50(b)

Donald E. Adams )
Administrative Patent Judge )
)
)
) BOARD OF PATENT
Eric Grimes )
Administrative Patent Judge ) APPEALS AND
)
) INTERFERENCES
)
Lora M. Green )
Administrative Patent Judge )

EG/dym

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