Ex Parte Mahant et al

Board of Patent Appeals and Interferences

Mar 19, 2010

10495554 (B.P.A.I. Mar. 19, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte VIJAY K. MAHANT, FAREED KURESHY, and
SHAILENDRA SINGH
____________

Appeal 2009-0038831
Application 10/495,554
Technology Center 1600
____________

Decided: March 22, 2010
____________

Before DONALD E. ADAMS, LORA M. GREEN, and
STEPHEN WALSH, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims 1, 2, 4, 6-8, 12-22,
and 24, the only claims pending in this application. We have jurisdiction
under 35 U.S.C. § 6(b).

1 The Examiner states that Application No. 10/346,879, Appeal No. 2009-
014545 is related to the present Appeal. Accordingly, we have considered
the merits of these two Appeals together.

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STATEMENT OF THE CASE
The claims are directed to an analytical device (claims 1, 2, 4, 6-8,
and 12-22) and a magazine comprising a plurality of analytical devices
(claim 24). Claim 1 is illustrative:
1. An analytical device comprising:
a housing at least partially enclosing a multi-substrate chip, wherein
the multi-substrate chip includes a gel matrix that comprises a light-blocking
material, wherein at least two positional markers and a plurality of substrates
are coupled to the gel matrix, and wherein the gel matrix comprises a
material selected from the group consisting of agarose, gelatin, and
polyacrylamide;
wherein the housing is configured to allow illumination of the at least
two positional markers from a first position above the gel matrix by a first
light source at a first angle such that two reference signals are produced;
wherein the housing is further configured to allow illumination of a
labeled analyte bound to at least one of the plurality of substrates from a
second position above the matrix by a second light source at a second angle
such that an analyte signal is produced, wherein the first angle and the
second angle are not identical;
wherein the positional markers are configured to produce first
fluorescence signals and wherein the labeled analyte is configured to
produce a second fluorescence signal;
wherein the at least two reference markers and each of the plurality of
substrates are disposed on the multi-substrate chip in predetermined spatial
relationships to each other to allow determination of a correct focal plane for
each of the plurality of substrates;
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wherein the housing is still further configured to allow acquisition of
the reference signals and the analyte signal when the multi-substrate chip is
in a substantially horizontal position;
wherein the multi-substrate chip is disposed within an open cavity that
is at least partially formed by the housing, and wherein the cavity has a
predetermined volume of between 0.01 ml and 10 ml; and
wherein the open cavity is configured to allow reagent addition and
illumination of at least one of the plurality of substrates from a point outside
the housing without passing through a wall of the housing or without passing
through a channel that connects the open cavity with an outside of the
housing.

The Examiner relies on the following evidence:
Jolley US 4,704,255 Nov. 3, 1987
Lindholm et al. US 5,250,443 Oct. 5, 1993
Trulson et al. US 5,578,832 Nov. 26, 1996
Tamura et al. WO 00/73504 A2 Dec. 7, 2000
Zeleny et al. US 6,215,894 B1 Apr. 10, 2001
Kris et al. US 6,238,869 B1 May 29, 2001
Nagle et al. US 6,337,212 B1 Jan. 8, 2002

The rejections presented by the Examiner follow:
1. Claims 1, 2, 4, 6-8, 14-18, 21, and 22 stand rejected under 35 U.S.C
§ 103(a) as unpatentable over the combination of Kris, Lindholm, and either
Tamura, Zeleny, or Trulson.
2. Claim 13 stands rejected under 35 U.S.C § 103(a) as unpatentable over
the combination of Kris, Lindholm, Nagle, and either Tamura, Zeleny, or
Trulson.
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3. Claims 12, 19, 20, and 24 stand rejected under 35 U.S.C § 103(a) as
unpatentable over the combination of Kris, Lindholm, Jolley, and either
Tamura, Zeleny, or Trulson.
We reverse.

ISSUE

Has the Examiner met the burden of establishing that Appellants’
claimed invention is prima facie obvious over the combination of Kris,
Lindholm, and either Tamura, Zeleny, or Trulson?

FINDINGS OF FACT
FF 1. The Examiner finds that Kris fails to teach, inter alia, “positional
makers for focal plane determination” (Ans. 5).
FF 2. The Examiner does not rely on Lindholm to teach positional markers
for focal plane determination. Instead the Examiner relies on Lindholm to
teach that “gels having light blocking additives were well known and
routinely” used in the art (Ans. 4).
FF 3. The Examiner finds that Tamura, Zeleny, and/or Trulson teach
“fluorescent positional markers were well known and routinely practiced in
the art at the time the claimed invention was made” (Ans. 5).
FF 4. The Examiner finds that Tamura “teaches positional markers provide
numerous advantages e.g. alignment so as to avoid spot detection error”
(id.). In support of this finding the Examiner directs attention to page 5
through page 6, first full paragraph of Tamura’s disclosure (id.).
FF 5. Tamura is aimed “at providing a method for indexing a microarray
chip for specifying element information to be used for the microarray chip
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without requiring a special-purpose device for reading the element
information such as a letter or barcode reader” (Tamura 3: 9-14).
FF 6. The section of Tamura relied upon by the Examiner teaches “a
microarray chip [that] compris[es] a plurality of spots arranged in a
predetermined positional relationship, wherein some of the plurality of spots
are used as index spots for maintaining index information” (Tamura 5: 12-
16).
FF 7. Tamura teaches that information detected at the index spots can by
used as parity information to avoid spot detection error (Tamura 6: 6-11).
FF 8. Zeleny teaches “[a] system for scanning biochip arrays” (Zeleny,
Abstract).
FF 9. The Examiner finds that Zeleny “teaches and illustrates positional
markers for focusing the substrate (focus targets, Column 3, lines 19-24 and
Fig. 2)” (Ans. 5).
FF 10. For clarity, we reproduce Zeleny’s Figure 2 below:

Zeleny teaches that “[a] typical array region is depicted in . . . FIG. 2. The
region comprises an array of test spots 20, and optionally, a series of control
spots 22 and focus targets 24. The control spots 22 and the targets 24 are
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used at the beginning of the scanning process to calibrate and/or adjust the
scanner” (Zeleny, col. 3, ll. 19-24).
FF 11. The Examiner finds that Trulson “defines an apparatus for imagining
a sample using auto-focusing techniques” (Ans. 5).
FF 12. Trulson teaches “methods and systems for detecting a labeled marker
on a sample located on a support” (Trulson, Abstract). In this regard,
Trulson teaches that labeled material on the sample emits radiation, in
response to the application of excitation radiation, which is collected by
collection optics and imaged onto a detector which generates an image of the
sample (id.).
FF 13. According to Trulson:
Emission from surface-bound and solution-free targets is
distinguished through the employment of confocal and auto-
focusing techniques, enabling the system to image substantially
only emission originating from the surface of the sample.
Generally, the excitation radiation and response emission have
different wavelengths. Filters having high transmissibility in
the label’s emission band and low transmissibility in the
excitation wavelength may be utilized to virtually eliminate the
detection of undesirable emission. These generally include
emission from out-of-focus planes or scattered excitation
illumination as potential sources of background noise.

(Trulson, col. 5, l. 67 - col. 6, l. 11.)
FF 14. More simply, Trulson teaches a device, wherein emission originating
from out-of- focus planes is displaced sideways in relationship to the
collection optics’ optical axis. Therefore, nearly all of the emission from
any plane that is more than slightly out-of-focus is not detected (Trulson,
col. 8, ll. 61-67).
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FF 15. The Examiner relies on Nagle to teach “a gel matrix on a base
element wherein the base element is configured for transfer of thermal
energy” and a “thermal energy transfer device [that] provides individual
control of reactions with increased throughput and decreased reagent
requirements” (Ans. 11).
FF 16. The Examiner relies on Jolley to teach an “analytical device
comprising a base and body wherein the base is wider so as to provide a
guide element for stable stacking of a plurality of the devices forming a
magazine (i.e. stack) of devices” (Ans. 12).

PRINCIPLES OF LAW
“[T]he [E]xaminer bears the initial burden, on review of the prior art
or on any other ground, of presenting a prima facie case of unpatentability.”
In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992). “The combination of
familiar elements according to known methods is likely to be obvious when
it does no more than yield predictable results.” KSR Int’l Co. v. Teleflex
Inc., 550 U.S. 398, 416 (2007). Nevertheless, an invention “composed of
several elements is not proved obvious merely by demonstrating that each of
its elements was, independently, known in the prior art. . . . [I]t can be
important to identify a reason that would have prompted a person of
ordinary skill in the relevant field to combine the elements in the way the
claimed new invention does.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398,
418 (2007).

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ANALYSIS
Appellants’ claimed device comprises, inter alia, positional markers
and substrates that are arranged in predetermined spatial relationships to
each other to allow determination of a correct focal plane for each of the
plurality of substrates (see e.g., claims 1 and 15).
Based on the combined teachings of Kris, Lindholm, and either
Tamura, Zeleny, or Trulson the Examiner concludes that:
It would have been obvious to one of ordinary skill in the
art at the time the claimed invention was made to apply the
multiple positioning and focusing elements of Tamara [sic]
and/or Zeleny and/or Trulson comprising differentially labeled
fluorophores to the device of Kris. One of ordinary skill in the
art would have been motivated to do so to thereby provide for
automated calibration and focusing of the substrate before
and/or during scanning as desired in the art.

(Ans. 5.)
Appellants contend that Tamura teaches the “use of spots to form a
code readable by [an] analyzer wherein that code is used to identify the
type of assay” and therefore “fails to teach reference markers suitable for
determination of a focal plane” (App. Br. 11). We agree.
While Tamura may teach “markers used for positioning” (Ans. 15),
e.g., for managing element information on a microarray chip (FF 5-7); the
Examiner failed to identify an evidentiary basis in Tamura to support the
conclusion that these markers are arranged in predetermined spatial
relationship relative to substrates to allow determination of a correct focal
plane for each of the plurality of substrates as is required by Appellants’
claimed invention (see Reply Br. 3).
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Appellants contend that Trulson teaches “[d]ifferentiation between
focal planes is achieved by lateral angled illumination to so eliminate
incorrect signal by optically shifting such signal away from the detection
optics. Consequently, no determination of the focal plane is required”
(Reply Br. 3-4). We agree (see FF 13 and FF 14 (“nearly all of the emission
from any plane that is more than slightly out-of-focus is not detected”)).
The Examiner failed to identify an evidentiary basis in Trulson to support
the conclusion that positional markers are arranged in predetermined spatial
relationship relative to substrates to allow determination of a correct focal
plane for each of the plurality of substrates as is required by Appellants’
claimed invention (see Reply Br. 3).
Appellants contend that “Zeleny teaches focus targets on the
microscope slide . . . to adjust a scanner to the substrate (i.e., glass slide on
the scanner), but fails to teach positioning of targets such as to allow
determination of a focal plane of the plurality of analytes” (App. Br. 12).
The Examiner is not persuaded. Instead, the Examiner asserts that
Appellants’
claim merely defines reference markers ‘to allow determination
of a correct focal plane’[.] The focal plane determination as
recited in the claim is a recitation of intended use. . . .
[Therefore, the Examiner] maintain[s] that Zeleny teaches all
the structural requirements of the reference markers and
substrate of the claim.

(Ans. 16-17.) We disagree.
Even if the focal plane determination of Appellants’ claimed
invention is a recitation of intended use, the device suggested by the
combination of references must be capable of performing this determination.
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Stated differently, the device suggested by the combination of references
must have positional markers that are arranged in predetermined spatial
relationship relative to substrates to allow determination of a correct focal
plane for each of the plurality of substrates as is required by Appellants’
claimed invention. Beyond identifying that Zeleny teaches a device that
comprises focus targets the Examiner failed to identify an evidentiary basis
in Zeleny to support the conclusion that positional markers are arranged in
predetermined spatial relationship relative to substrates to allow
determination of a correct focal plane for each of the plurality of substrates
as is required by Appellants’ claimed invention.
The Examiner’s reliance on Nagle and Jolley (FF 14 and 15) fail to
make up for the deficiency in the combination of Kris, Lindholm, and either
Tamura, Zeleny, or Trulson.

CONCLUSION OF LAW
Appellants established that the combination of references relied upon
by the Examiner fails to teach or suggest a device wherein at least two
reference markers and each of a plurality of substrates are disposed on a
multi-substrate chip in predetermined spatial relationships to each other to
allow determination of a correct focal plane for each of the plurality of
substrates.
The rejection of claims 1, 2, 4, 6-8, 14-18, 21, and 22 under 35 U.S.C
§ 103(a) as unpatentable over the combination of Kris, Lindholm, and either
Tamura, Zeleny, or Trulson is reversed.
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The rejection of claim 13 under 35 U.S.C § 103(a) as unpatentable
over the combination of Kris, Lindholm, Nagle, and either Tamura, Zeleny,
or Trulson is reversed.
The rejection of claims 12, 19, 20, and 24 under 35 U.S.C § 103(a) as
unpatentable over the combination of Kris, Lindholm, Jolley, and either
Tamura, Zeleny, or Trulson is reversed.

REVERSED

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