Ex Parte Fredrick

Board of Patent Appeals and Interferences

Dec 3, 2009

10868330 (B.P.A.I. Dec. 3, 2009)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte JOSEPH P. FREDRICK
__________

Appeal 2009-004048
Application 10/868,330
Technology Center 1600
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Decided: December 3, 2009
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Before TONI R. SCHEINER, RICHARD M. LEBOVITZ, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

SCHEINER, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 from the rejection of claims
16-27 and 31-33, directed to methods of contacting a defined region of a
chemical array with a fluid. The claims have been rejected on the grounds
of anticipation and indefiniteness. We have jurisdiction under 35 U.S.C.
§ 6(b).
Appeal 2009-004048
Application 10/868,330

STATEMENT OF THE CASE
Chemical arrays such as biopolymer arrays . . . include
regions of usually different sequence polynucleotides arranged
in a predetermined configuration on a substrate. . . . The arrays,
when exposed to a sample, will exhibit an observed binding
pattern . . . indicative of the presence and/or concentration of
one or more polynucleotide components of the sample

(Spec. ¶ 1).
The invention is directed to a method of delivering sample and
reagent fluids to defined regions of the array (Spec. ¶¶ 4, 5).
Claims 16 and 31 are representative of the subject matter on appeal:
16. A method of contacting a first fluid with a defined region of a surface
of an array assembly comprising at least one chemical array, said method
comprising:
(a) positioning a reservoir plate comprising a support comprising a
plurality of holes through said plate relative to said surface of said array
assembly such that a capillary space is provided between said reservoir plate
and said surface of said array assembly; and
(b) introducing said first fluid through at least one hole of said
reservoir plate such that said first fluid contacts a defined region of said
array assembly surface.

31. A method of contacting a fluid with a defined region of a surface of an
array assembly, said method comprising:
(a) operatively positioning a reservoir plate, comprising a support
comprising a plurality of holes through said plate, relative to said surface of
said array assembly;
(b) introducing said fluid through at least one hole of said reservoir
plate such that said fluid contacts a defined region of said array assembly
surface;
(c) removing said reservoir plate a distance from said array assembly
to flood a surface of said array assembly with a liquid; and
(d) flooding a surface of said array assembly with a liquid.

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The Examiner rejected claims 16-27 and 31-33 under 35 U.S.C.
§ 102(b) as anticipated by Pfost et al. (US Patent 6,485,690 B1, issued
November 26, 2002).
The Examiner also rejected claims 22 and 23 under 35 U.S.C. § 112,
second paragraph, as indefinite.
We affirm-in-part.
ANTICIPATION
The Examiner finds that Pfost discloses all of the steps of the claimed
methods.
Appellant contends that Pfost doesn’t disclose positioning the
reservoir plate and array assembly such that “a capillary space [is] located
between the reservoir plate and the surface of the array assembly” (App. Br.
8). In addition, Appellant contends that Pfost doesn’t disclose “flushing the
surface of the array assembly, wherein said flushing step does not comprise
a reservoir plate” (id. at 18), or “removing the reservoir plate a distance from
the array assembly, and flooding the surface of the array assembly with a
liquid” (id. at 22).
The principal issues raised by this rejection are as follows:
Has Appellant shown that the Examiner erred in finding that Pfost
discloses the step of positioning a reservoir plate relative to the surface of an
array assembly such that a capillary space is provided between them?
Has Appellant shown that the Examiner erred in finding that Pfost
discloses flushing the surface of the array assembly, where the flushing step
does not comprise a reservoir plate?
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Has Appellant shown that the Examiner erred in finding that Pfost
discloses the step of removing the reservoir plate a distance from the array
assembly to flood a surface of the array assembly with a liquid?
FINDINGS OF FACT
The Invention
FF1 The claimed invention is directed to methods for contacting a
fluid with (i.e., depositing a fluid on) a defined region of a surface of a
chemical array comprising “positioning a reservoir plate comprising a
support comprising a plurality of holes through said plate relative to said
surface of said array assembly” and introducing a fluid through the reservoir
plate such that the fluid “contacts a defined region of said array assembly
surface” (claims 16 and 31).
FF2 In one embodiment, the method includes positioning the
reservoir plate relative to the surface of an array assembly “such that a
capillary space is provided between said reservoir plate and said surface of
said array assembly” (claim 16).
FF3 The Specification doesn’t define “capillary space,” but defines
“capillary distance” as follows:
By capillary distance is meant a gap small enough to hold
capillary. In this manner, the capillary distance enables fluid to
be maintained between the reservoir plate and a surface of the
array assembly at a defined region by capillary forces, where
the capillary distance is any suitable distance that provides a
capillary. . . . In this manner, fluid may be retained at defined
regions of the array assembly . . . due at least in part to the
capillary forces provided by the capillary distance of the
spaced-part [sic] reservoir plate.

(Spec. ¶ 111.)
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FF4 “In use, a reservoir plate is positioned in opposition and relative
to an array assembly as shown in FIG. 11” of the Specification (Spec ¶ 103),
reproduced immediately below:

Figure 11 of the Specification shows an embodiment of the invention in
which “a reservoir plate is positioned in opposition and relative to an array
assembly . . . spaced-apart from the array substrate a distance [D] such as a
capillary distance” (id.).
FF5 Another embodiment of the invention includes positioning the
reservoir plate “relative to a surface of an array assembly such that the
reservoir plate or a portion thereon is directly contacted with a surface of the
array assembly” (e.g., claim 33) (id. at ¶ 107).
FF6 In certain embodiments, after positioning the reservoir plate
relative to the array assembly, and introducing a fluid through the reservoir
plate to contact a defined region of the array assembly, the method includes
removing the reservoir plate a distance from the array assembly and flooding
a surface of the array assembly with a liquid (e.g., claims 31-33).

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Application 10/868,330

Pfost
FF7 Pfost discloses a method of synthesizing a chemical array using
a “multiple fluid sample processor” 10, also called a fluid array layered
device, or a fluidic array (Pfost, col. 5, ll. 50-56), shown in Figures 2, 6, 7,
and 8 reproduced immediately below:

Figure 2 illustrates Pfost’s layered processor 10, which includes top reagent
reservoir layer 12, middle fluidic delivery or distribution layer 14, and
bottom layer or well plate layer 16 (id. at col. 5, ll. 57-61). Figures 6, 7, and
8 show cross sections of layers 12, 14, and 16, respectively.

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FF8 Layer 12 of Pfost’s processor
contains a number of apertures 20 which are selectively
positioned immediately above channels 22 in the middle or
fluidic layer 14 and in communication with fluidic inlets in
layer 14. . . . A series of micro-sized channels . . . [in] plate 12
convey the materials (e.g. liquids) from the apertures 20 to
positions above selected openings 22 and/or 24 in the middle
layer. The openings 22 and 24 are connected in the middle
layer 14 by an elongated microchannel 26 which in turn has a
plurality of small passage channels 28. . . .

(Pfost, col. 5, l. 64 to col. 6, l. 8.)
Layer 16 has a plurality of reaction wells 30 and “[e]ach of the
reaction wells 30 has one or more entrance channels 32 and one or more
exhaust or drain channels 34” (id. at col. 6, ll. 16-17).
FF9 Pfost teaches that a liquid reagent is inserted into openings 20'
(or 20) and “[t]hen, by capillary forces . . . the reagent fills the row or
column channel 26', as shown in FIG. 12” (Pfost, col. 7, l. 67 to col. 8, l. 2).
Pfost’s Figure 12 is reproduced immediately below:

Figure 12 is a cross section of Pfost’s processor. In addition to channel 26',
(also called an elongated microchannel), which runs through middle layer
14, Figure 12 shows a “capillary forming structure (also called a microvalve)
37 . . . in channel 32' at the entrance to the reaction well 30'” (id. at col. 8, ll.
5-7). “A second smaller capillary valve 39 is formed at the outlet . . . to the
well 30'” (id. at col. 8, ll. 40-41).
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FF10 “The microvalves can be capillary forming structures which
form capillary barriers and prevent further movement of liquid materials”
(Pfost, col. 7, ll. 3-5).
FF11 Pfost teaches that “layer 16 . . . is preferably detachably coupled
to layer 14 or a combination of layers 12 and 14, although layer 16 could
also be permanently bonded to them” (Pfost, col. 6, ll. 29-31).
FF12 The Examiner finds that Pfost discloses “forming capillary
spaces between the upper and bottom plates (e.g., Figures 7-10; col.6, lines
5+; cols. 7-8, bridging para), which reads on the providing capillary space of
clms 16, 32 and 33” (Ans. 3). Specifically, the Examiner finds that “the
feature 26 or 26' are formed between two layers of substrates and form
microchannels (i.e., capillary space) that have dimensions in various ranges
such as 5-300 microns (e.g. col.6, lines 5+; col.7, lines 40+) and the spaces
indicated as 26 or 26' can be filled by capillary forces (e.g. col.8, lines 1+)”
(id. at 8).
FF13 During the chemical synthesis process, the processor is
contacted with various reaction reagents, and “washing fluid is then
delivered to openings 20' and pressure is applied to the chip member 10'
through the microchannels. This results in waste materials being exhausted
from the chip” (Pfost, col. 8, ll. 45-48). Once the “chemical synthesis
process is completed[,] [t]he final products in each of the wells are then
removed from the member 10' by being independently ejected into arrays of
wells in a product layer (a/k/a “mother”) plate 41 where they are available
for analysis or biological assays” (id. at col. 8, ll. 61-65).
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PRINCIPLES OF LAW
“To anticipate a claim, a prior art reference must disclose every
limitation of the claimed invention, either explicitly or inherently.” In re
Schreiber, 128 F.3d 1473, 1477 (Fed. Cir. 1997).
During examination, the PTO must interpret terms in a claim using
“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 (Fed. Cir. 1997).
Nevertheless, “courts must not ‘import[ ] limitations from the
specification into the claim.’ . . . [I]t is improper to ‘confin[e] the claims to
th[e] embodiments’ found in the specification . . . .” In re Trans Texas
Holdings Corp., 498 F.3d 1290, 1299 (Fed. Cir. 2007) (citations omitted,
bracketed text in internal quotes in original).
ANALYSIS
Claims 16, 18-20, and 24-27
Appellant does not provide separate arguments for claims 18-20 and
24-27, therefore, we select claim 16 as representative of this group of claims.
37 C.F.R. § 41.37(c)(1)(vii) (2006).
Appellant contends that the Examiner erred in “equating . . . ‘forming
capillary spaces between the upper and bottom plates’ in Pfost with the
‘capillary space’ between the reservoir plate and the surface of the array
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assembly as in Claim 16” (App. Br. 7).1 Appellant contends “in contrast to
the ‘capillary space’ between the reservoir plate and the surface of the array
assembly . . . as shown by ‘D’ in the . . . embodiment of the invention
depicted in Fig. 11” (id. at 8),
microchannel [26] disclosed in Pfost does not provide a
capillary space between the reservoir plate and the surface of
the array assembly as in the current claims, because the
microchannel “space” is located between two walls of
microchannel 26 in the middle of layer 14 . . . [and] do[es] not
provide a gap small enough to retain fluid between the reservoir
plate and the surface of the array assembly

(id. at 11).
If we understand Appellant’s argument, it is that the claimed method
requires positioning the reservoir plate (analogous to Pfost’s layer 12) over
the array assembly (analogous to Pfost’s layer 16) so that a capillary space
“small enough to retain fluid between the reservoir plate and the surface of
the array assembly” is maintained between them, with no intervening
structures. (Id.) Pfost, on the other hand, positions layer 14 in between and
in contact with layers 12 and 16, with microchannels running through layer
14 to connect openings in layer 12 with corresponding reaction wells in
layer 16.
Appellant’s argument is not persuasive. Claim 16 may encompass the
embodiment depicted in Figure 11 of the Specification (FF4), but it is not

1 Appellant also contends that the Examiner erred in equating Pfost’s
“capillary forming structures” (element 37) with the “capillary space”
between the reservoir plate and the surface of the array assembly required by
claim 16 (App. Br. 7). We agree with Appellant that capillary forming
structure 37 is a “microsized valve” (FF10, FF11) rather than a “space.”
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limited to that embodiment. Claim 16 merely requires positioning a
reservoir plate relative to the surface of an array assembly “such that a
capillary space is provided between said reservoir plate and said surface of
said array assembly” and “introducing said first fluid through . . . said
reservoir plate such that said first fluid contacts a defined region of said
array assembly surface.” Pfost teaches that microchannel 26 is filled by
“capillary forces” (FF9). Moreover, microchannel 26 “in turn has a plurality
of small passage channels 28” each of which connects to an entrance
channel 32 on the array and feeds directly into a reaction well 30 of the array
- a defined region of the array assembly surface (FF8). It’s true that the
capillary space formed by Pfost’s microchannel 26 is provided in a layer
interposed between layers 12 and 16, but nothing in claim 16 precludes a
layer between the reservoir plate and the array assembly.
Appellant has not shown that the Examiner erred in finding that Pfost
discloses the step of positioning a reservoir plate relative to the surface of an
array assembly such that a capillary space is provided between them.
Claim 17
Claim 17 depends from claim 16 and further requires “maintaining
said fluid at said defined region by . . . capillary forces.” Appellant contends
that “Pfost does not disclose the element of maintaining fluid at a defined
region of a surface of an array assembly by at least one of capillary forces,
because there is no surface of the array assembly that is a capillary space
from the reservoir plate in Pfost” (App. Br. 15).
This argument is not persuasive. Pfost teaches that microvalves or
capillary forming structures (i.e., elements 37 and 39) “form capillary
barriers and prevent further movement of liquid materials” (FF9, FF10).
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Claim 21
Claim 21 depends indirectly from claim 16 and requires “flushing said
surface of said array assembly” with a fluid. Appellant contends that “the
washing step of Pfost comprises fluid that flows through microchannels 26
in middle layer 14, before reaching well 30” and “the surface of [Pfost’s]
layer 16 is not even exposed, but rather abuts the bottom of layer 14” (App.
Br. 18). If we understand Appellant’s argument, it is that claim 21 requires
flushing every surface of the array, not just the surface of a well.
This argument is not persuasive. While the present Specification does
disclose several illustrative embodiments where every surface of a planar
array is exposed and flushed with a washing fluid, claim 21 is not limited to
those embodiments and does not recite language that would reasonably be
interpreted to require washing or flushing every surface of the array. Pfost’s
washing step flushes reagents from the wells of the array (FF13), and Pfost’s
wells are defined regions of the surface of an array - the regions on which
the synthesis reaction occurs.
Claim 23
Claim 23 requires flushing the surface of the array assembly,
“wherein said flushing step does not comprise a reservoir plate.”
Appellant contends that Pfost “does not disclose the element of
removing the reservoir plate” to flush the surface of the array (App. Br. 21).
We agree with Appellant on this point. While Pfost teaches that layer
16 (the array) can be removed from layers 12 and 14 once synthesis is
complete (FF11), the Examiner has not shown that Pfost discloses
introducing fluids to the array without introducing them through the
reservoir plate and microchannels (FF13).
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Claims 31-33
Claims 31-33 require “positioning a reservoir plate . . . relative to said
surface of said array assembly;” introducing a fluid to the array through the
reservoir plate; and “removing said reservoir plate a distance from said array
assembly to flood a surface of said array assembly with a liquid;” and
“flooding a surface of said array assembly with a liquid.”
Appellant contends that “Pfost fails to teach . . . removing the
reservoir plate a distance from the array assembly, and flooding the surface
of the array assembly with a liquid” (App. Br. 22).
Appellant’s argument is persuasive. “Removing” is an active step
which requires moving the reservoir plate from its initial position relative to
the array assembly to a new position before flooding the array with a liquid.
As discussed above, Pfost teaches that layer 16 (the array) can be removed
from layers 12 and 14 once synthesis is complete (FF11), but the Examiner
has not shown that Pfost discloses introducing fluids to the array without
introducing them through the reservoir plate and microchannels (FF13).
CONCLUSIONS OF LAW
Appellant has not shown that the Examiner erred in finding that Pfost
discloses the step of positioning a reservoir plate relative to the surface of an
array assembly such that a capillary space is provided between them.
The Examiner erred in finding that Pfost discloses flushing the surface
of the array assembly, where the flushing step does not comprise a reservoir
plate.
The Examiner erred in finding that Pfost discloses the step of
removing the reservoir plate a distance from the array assembly to flood a
surface of the array assembly with a liquid.
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The rejection of claims 16-27 and 31-33 as anticipated by Pfost is
affirmed with respect to claims 16-22 and 24-27 and reversed with respect to
claims 23 and 31-33.
INDEFINITENESS
The Examiner rejected claims 22 and 23 as indefinite in reciting
“wherein said second fluid comprising said flushing step comprises a
reservoir plate,” and “said flushing does not comprise a reservoir plate,”
respectively, because “[i]t is not clear how the reaction reagent can comprise
a method step, or how a method step can comprise an apparatus part.” (Ans.
12.)
We will reverse this rejection. We agree with Appellant that one of
skill in the art would understand that the flushing step in claim 22 involves
introducing a fluid through the reservoir plate, while the flushing step in
claim 23 does not (App. Br. 30).
SUMMARY
The rejection of claims 16-27 and 31-33 under 35 U.S.C. § 102(b) as
anticipated by Pfost is affirmed with respect to claims 16-22 and 24-27 and
reversed with respect to claims 23 and 31-33.
The rejection of claims 22 and 23 under 35 U.S.C. § 112, second
paragraph, is reversed.
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Application 10/868,330

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)(1)(iv)(2006).

AFFIRMED-IN-PART

cdc

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