Ex Parte Frutos et al

Board of Patent Appeals and Interferences

Feb 1, 2011

11437477 (B.P.A.I. Feb. 1, 2011)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte ANTHONY G. FRUTOS, JACQUES GOLLIER,
JINLIN PENG, GARRETT A PIECH, and MICHAEL B. WEBB
__________

Appeal 2010-011099
Application 11/437,477
Technology Center 1600
__________

Before TONI R. SCHEINER, LORA M. GREEN, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

FREDMAN, Administrative Patent Judge.

DECISION ON APPEAL1
This is an appeal under 35 U.S.C. § 134 involving claims to a method
for using an optical reader system. The Examiner rejected the claims as
anticipated and obvious. We have jurisdiction under 35 U.S.C. § 6(b). We
affirm.

1 The two-month time period for filing an appeal or commencing a
civil action, as recited in 37 C.F.R. § 1.304, or for filing a request
for rehearing, as recited in 37 C.F.R. § 41.52, begins to run from
the “MAIL DATE” (paper delivery mode) or the
“NOTIFICATION DATE” (electronic delivery mode) shown on
the PTOL-90A cover letter attached to this decision.
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Statement of the Case
The Claims
Claims 1, 2, 4, 5, 8, 11-18, and 20-22 are on appeal. Claims 1 and 20
are representative, and the remaining claims have not been argued separately
and therefore stand or fall together with claims 1 and 20. 37 C.F.R.
§ 41.37(c)(1)(vii). Claims 1 and 20 read as follows:
1. A method for using an optical reader system,
said method comprising the steps of:
generating a first optical beam which has a
diameter that is smaller than a biosensor;
scanning the first optical beam across the
biosensor;
collecting a second optical beam which is
out-coupled from the biosensor while the first
optical beam is being scanned across the
biosensor;
processing the second optical beam to obtain
raw spectral/angular data which is a function of a
position on the biosensor; and
recording the raw spectral/angular data.

20. The method of Claim 1, further comprising
steps of performing a 1-dimensional beam scan
across at least one diagonal fiducial marking
associated with said biosensor and estimating both
an x and y location of said biosensor which are
used to determine a position of the biosensor
relative to the optical reader system.

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The issues
A. The Examiner rejected claims 1, 2, 5, 8, 11, 13, and 15-18 under 35
U.S.C. § 102(b) as anticipated by Cunningham2 (Ans. 4-5).
B. The Examiner rejected claim 4 under 35 U.S.C. § 103(a) as obvious
over Cunningham and Dorsel3 (Ans. 6-7).
C. The Examiner rejected claims 12 and 14 under 35 U.S.C. § 103(a) as
obvious over Cunningham and Sigrist4 (Ans. 7-8).
D. The Examiner rejected claim 20 under 35 U.S.C. § 103(a) as obvious
over Cunningham and Grace5 (Ans. 8-10).
E. The Examiner rejected claims 21 and 22 under 35 U.S.C. § 103(a) as
obvious over Cunningham (Ans. 10-11).
A. U.S.C. § 102(b) over Cunningham
The Examiner finds that
Cunningham et al. teach a device and method for
using an optical detection (reader) system, said method
comprising the steps of: generating a first optical beam
which has a diameter smaller than a biosensor; scanning the
first optical beam across the biosensor; collecting a second
optical beam which is reflected (out-coupled) from the
biosensor while the first optical beam is being scanned
across the biosensor; processing the second optical beam to
obtain raw spectral/angular data which is a function of a
position on the biosensor; and recording the raw
spectral/angular data

2 Cunningham et al., US 2003/0059855 A1, published Mar. 27,
2003.
3 Dorsel et al., US 2002/0132261 A1, published Sep. 19, 2002.
4 Sigrist et al., US 6,346,376 B1, issued Feb. 12, 2002.
5 Grace et al., US 2005/0088648 A1, published Apr. 28, 2005.
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(Ans. 4; citations omitted).
Appellants contend that
Cunningham’s first optical reader system does not
collect a second optical beam which is reflected from the
biosensor while the first optical beam is being scanned
across the biosensor. And, Cunningham’s first optical reader
system does not process the collected second optical beam to
obtain raw spectral/angular data that is a function of a
position on the biosensor

(App. Br. 8). Appellants contend that “Cunningham’s second optical reader
system does not teach the claimed limitation where the first optical beam is
smaller than a biosensor and is scanned across the biosensor” (id. at 9).
Appellants contend that “the Examiner combined different parts of
Cunningham’s various optical reader systems to present an anticipation
rejection of claim 1. However, not one of Cunningham’s optical reader
systems disclosed all of the elements of the present invention as they are
‘arranged as in the claim’” (id. at 11).
The issue with respect to this rejection is: Does the evidence of record
support the Examiner’s conclusion that Cunningham anticipates the instant
claim 1?
Findings of Fact
1. Cunningham teaches “a method and system for detecting
biomolecular interactions. Preferably, these biomolecular interactions occur
on a subwavelength structured surface biosensor” (Cunningham 2 ¶ 0048).
2. Cunningham teaches that in
one preferred embodiment of a measuring apparatus, white
light source 205 illuminates a ~1 millimeter (mm) diameter
region of the grating region 215 through a 400 micrometer
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diameter fiber optic and the collimating lens 210 at
nominally normal incidence through the bottom of a
microtiter plate. Such a microtiter plate could have a
standard 96-, 384-, or 1526-well microtiter plate format, but
with a biosensor attached to the bottom.

(Cunningham 13 ¶ 0180.)
3. Cunningham teaches that the
bottom surface 342 of the microarray chip 328 is scanned in
a sequential manner. To accomplish a complete scan of the
bottom surface 342, the microarray chip 328 is transported
along a scan direction “A.” As the microarray chip 328 is
transported along this scan direction, the collimated light
330 traverses along the complete length of the bottom
surface 342 of the microarray chip. In this manner, the
instrument system 319 sequentially illuminates and reads out
all of the spot[s] in a microarray chip 328. For example, as
the chip 328 is moved in the “A” scan direction, chip row
333 is first illuminated and read out, and then chip row 331
is illuminated and then read out. The process continues until
all rows are read.

(Cunningham 15 ¶ 0204.)
4. Cunningham teaches that
if the imaging spectrometer includes a CCD camera that
contains 512×2048 imaging elements, then an illuminating
line is spatially segregated into 512 imaging elements or
points. A wavelength spectra is measured for each of the 512
imaging elements or points along the orthogonal axis of the
CCD camera. Where the CCD camera contains 512×2048
imaging elements, the CCD would have a resolution of 2048
wavelength data points.

(Cunningham 15 ¶ 0207.)
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5. Cunningham teaches an embodiment where “the apparatus 202
scans the detection head 209 of a dual illumination probe across the
biosensor surface. Based on the reflected light, the apparatus measures
certain values, such as the peak wavelength values (PWV’s), of a plurality of
locations within the biosensor embedded microtiter plate.” (Cunningham 13
¶ 0173.)
6. Cunningham teaches that the
instrument collects light reflected from the illuminated
biosensor surface. The instrument may gather this reflected
light from multiple locations on the biosensor surface
simultaneously. The instrument can include a plurality of
illumination probes that direct the light to a discrete number
of positions across the biosensor surface. The instrument
measures the Peak Wavelength Values (PWVs) of separate
locations within the biosensor-embedded microtiter plate
using a spectrometer

(Cunningham 3 ¶ 0053).
7. Cunningham teaches an “imaging spectrometer containing a
two-dimensional Charge Coupled Device (CCD) camera and a diffraction
grating. The reflected light 334 containing the biosensor resonance signal for
each spot is diffracted by the grating in the spectrometer unit. The diffraction
produces a spatially segregated wavelength spectra for each point within the
illuminated area” (Cunningham 15 ¶ 0206).
8. Cunningham teaches that “[m]olecular binding on the surface
of a biosensor is indicated by a shift in the peak wavelength value, while an
increase in the wavelength corresponds to an increase in molecular
absorption” (Cunningham 17 ¶ 0230).
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9. The Specification teaches that in the optical reader, the “light
source outputs an optical beam which is scanned across a moving biosensor
and while this is happening the detector collects the optical beam which is
reflected from the biosensor” (Spec. 2, ll. 18-21).
10. Figures 15A and 15B of the Specification are reproduced
below:

“FIGURES 15A and 15B are two diagrams that show different examples of
patterning techniques that may be used on an intra-well referenced biosensor
102’” (Spec. 18, ll. 12-14).
Principles of Law
“It is axiomatic that, in proceedings before the PTO, claims in an
application are to be given their broadest reasonable interpretation consistent
with the specification.” In re Sneed, 710 F.2d 1544, 1548 (Fed. Cir. 1983).
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“A claim is anticipated only if each and every element as set forth in
the claim is found, either expressly or inherently described, in a single prior
art reference.” Verdegaal Bros., Inc. v. Union Oil Co. of California, 814
F.2d 628, 631 (Fed. Cir. 1987).
Analysis
Claim interpretation is at the heart of patent examination because
before a claim is properly interpreted, its scope cannot be compared to the
prior art. In this case, Appellants challenge the Examiner’s interpretation of
the term “biosensor” as recited in Claim 1, arguing that “Cunningham’s
second optical reader system does not teach the claimed limitation where the
first optical beam is smaller than a biosensor and is scanned across the
biosensor” (App. Br. 9). Appellants contend that “[i]nstead, Cunningham’s
second optical reader system emits light 330 which illuminates a complete
row or a complete column of spots contained on the microarray chip 328”
(id.).
During prosecution, claim terms are given their broadest reasonable
interpretation as they would be understood by persons of ordinary skill in the
art in the light of the Specification. Therefore, we first turn to the
Specification to determine whether the meaning of the phrase “biosensor”
should be limited as argued by Appellants to something less than the entire
microarray or broadly interpreted as argued by the Examiner as “the entire
substrate surface of the biosensor” (Ans. 13). Appellants do not identify any
portion of the Specification which specifically defines the term “biosensor.”
The Specification teaches that “FIGURES 15A and 15B are two
diagrams that show different examples of patterning techniques that may be
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used on an intra-well referenced biosensor 102’” (Spec. 18, ll. 12-14; FF
10). As is evident from Figures 15A and 15B, the Specification
encompasses biosensors with multiple features on a single biosensor.
Thus, when the Specification uses the term “biosensor,” the
Specification is reasonably understood as encompassing substrates with
multiple features or spots on a single substrate (FF 10).
The Examiner finds that Cunningham teaches methods “wherein a
first optical beam is generated, which is always smaller than the entire
substrate surface of the biosensor” (Ans. 13).
We are persuaded that the Examiner has the better position. “[D]uring
patent prosecution when claims can be amended, ambiguities should be
recognized, scope and breadth of language explored, and clarification
imposed.” In re Zletz, 893 F.2d 319, 321 (Fed. Cir. 1989). We agree with
the Examiner that “biosensor” is reasonably interpreted as the entire
microarray substrate on which the different features or spots reside, rather
than the individual features or spots. This is consistent with the usage in the
Specification, which expressly uses biosensor to refer to entire microarrays
(FF 10).
Having interpreted biosensor in claim 1 to encompass the entire
microarray of Cunningham, even Appellants acknowledge that
“Cunningham’s second optical reader system emits light 330 which
illuminates a complete row or a complete column of spots contained on the
microarray chip 328” (App. Br. 9). Thus, the second optical reader system
does not illuminate the entire biosensor or microarray, but rather only a
single row, which satisfies the requirement of claim 1 for “a first optical
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beam which has a diameter that is smaller than a biosensor” since a single
row is a subset of the entire microarray. Cunningham expressly teaches that
the instrument system 319 sequentially illuminates and reads
out all of the spot[s] in a microarray chip 328. For example,
as the chip 328 is moved in the “A” scan direction, chip row
333 is first illuminated and read out, and then chip row 331
is illuminated and then read out. The process continues until
all rows are read.

(Cunningham 15 ¶ 0204; FF 3.)
Appellants argue that “not one of Cunningham’s optical reader
systems disclosed all of the elements of the present invention as they are
‘arranged in the claim’” (App. Br. 11).
We are not persuaded, since the “second” optical reader of
Cunningham generates a first optical beam smaller than the biosensor, as
discussed above (FF 1-3, 10), scans the first optical beam across the
biosensor (FF 3), and “collects light reflected from the illuminated biosensor
surface. The instrument may gather this reflected light from multiple
locations on the biosensor surface simultaneously” (Cunningham 3 ¶ 0053;
FF 6), and Cunningham teaches that “reflected light 334 containing the
biosensor resonance signal for each spot is diffracted by the grating in the
spectrometer unit. The diffraction produces a spatially segregated
wavelength spectra for each point within the illuminated area” (Cunningham
15 ¶ 0206; FF 7).
Conclusion of Law
The evidence of record supports the Examiner’s conclusion that
Cunningham anticipates the instant claim 1.

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B. 35 U.S.C. § 103(a) over Cunningham and Dorsel
The Examiner finds it obvious “to include with the method of
Cunningham et al. the use of a stationary biosensor, wherein the fiber/lens
associated with the light source and detector is movable as taught by Dorsel
et al. because Dorsel et al. teach the benefit of a stationary biosensor” (Ans.
7).
The Examiner provides sound fact-based reasoning for combining
Cunningham and Dorsel. As Appellants do not identify any material defect
in the Examiner's reasoning, and only argue the underlying rejection of
Cunningham which we affirmed above, we affirm this rejection for the
reasons stated by the Examiner.
C. 35 U.S.C. § 103(a) over Cunningham and Sigrist
The Examiner finds it obvious
to include with the method and device of Cunningham et al.
predefined reference regions as taught by Sigrist et al.
because Sigrist et al. teach the benefit of creating
referencing pads or regions of non-specific binding
components along with the analyte-binding pads or regions
on an optical sensor in order to allow for on chip referencing
and calibration of the specific analyte-binding pads

(Ans. 8).
The Examiner provides sound fact-based reasoning for combining
Cunningham and Sigrist. As Appellants do not identify any material defect
in the Examiner's reasoning, and only argue the underlying rejection of
Cunningham which we affirmed above, we affirm this rejection for the
reasons stated by the Examiner.

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D. 35 U.S.C. § 103(a) over Cunningham and Grace
The Examiner finds it obvious
to include with the method and device of Cunningham et al.
a diagonal fiducial marking or diffraction grating . . . as
taught by Grace et al. because Grace et al. teach the benefit
of including an etched diffraction grating on a substrate of a
planar optical waveguide comprising a recognition surface
in order to effectively align the optical waveguide with a
laser in both the x and y direction

(Ans. 9-10).
Appellants contend that Grace’s laser “aligning step is not the same as
the claimed step of determining the position of the biosensor relative to the
optical reader system because Grace’s biosensor can have many different
positions relative to the ‘correctly positioned’ laser 230 and still be properly
aligned with the ‘correctly positioned’ laser 230” (App. Br. 15).
The issue with respect to this rejection is: Does the evidence of record
support the Examiner’s conclusion that Cunningham and Grace render
obvious claim 20?
Findings of Fact
11. Grace teaches that “[p]lanar optical waveguide 210 sits on a
substrate 220 onto which diffraction grating 215 has been etched” (Grace 3
¶0033).
12. Grace teaches, in the aligning laser step, that “the user looks
through viewing window 165 to ensure that laser beam 235 is properly
aligned with diffraction grating 210[.] Using horizontal laser alignment
wheel 140 and vertical laser alignment wheel 145, the user aligns laser 230
to the correct position” (Grace 4 ¶ 0045).
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Principles of Law
“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).
Analysis
The Examiner acknowledges that Cunningham does not teach fiducial
markings on a biosensor and relies upon Grace to teach the alignment of the
laser and microarray by scanning fiducial markings (Ans. 8-9).
Grace teaches, in the aligning laser step, that “the user looks through
viewing window 165 to ensure that laser beam 235 is properly aligned with
diffraction grating 210[.] Using horizontal laser alignment wheel 140 and
vertical laser alignment wheel 145, the user aligns laser 230 to the correct
position” (Grace 4 ¶ 0045; FF 12).
Appellants contend that Grace’s laser “aligning step is not the same as
the claimed step of determining the position of the biosensor relative to the
optical reader system because Grace’s biosensor can have many different
positions relative to the ‘correctly positioned’ laser 230 and still be properly
aligned with the ‘correctly positioned’ laser 230” (App. Br. 15).
We are not persuaded. In Grace’s method, as in claim 20, the
relationship of the optical reader and the biosensor are determined in an x
and y coordinate system using fiducial markings (FF 12). Appellants’
argument implies that in their system, only a single position of the
microarray would be “properly aligned,” unlike in Grace’s biosensor where
there may be many different correct positionings of the biosensor and laser.
However, this argument does not find basis in the claim, which does not
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require that a specific location is found, only that the relative x and y
position is determined relative to the optical reader. Grace’s alignment is
reasonably understood to at least determine and estimate a relative position
of the biosensor and the laser, if not necessarily determining an absolute
position (FF 11-12). “[L]imitations are not to be read into the claims from
the specification.” In re Van Geuns, 988 F.2d 1181, 1184 (Fed. Cir. 1993)
(citing In re Zletz, 893 F.2d at 321).
Conclusion of Law
The evidence of record supports the Examiner’s conclusion that
Cunningham and Grace render obvious claim 20.
E. 35 U.S.C. § 103(a) over Cunningham
The Examiner finds it obvious “to include with the method of
Cunningham et al. a specific angular and/or lateral sensitivity during the
scanning step in order to optimize the signal- to-noise ratio and thereby the
sensitivity of the device and method of scanning and/or detection as taught
by Cunningham” (Ans. 10).
The Examiner provides sound fact-based reasoning for modifying
Cunningham. As Appellants do not identify any material defect in the
Examiner's reasoning, and only argue the underlying rejection of
Cunningham, which we affirmed above, we affirm this rejection for the
reasons stated by the Examiner.
SUMMARY
In summary, we affirm the rejection of claim 1 under 35 U.S.C.
§ 102(b) as anticipated by Cunningham. Pursuant to 37 C.F.R.
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§ 41.37(c)(1)(vii)(2006), we also affirm the rejection of claims 2, 5, 8, 11,
13, and 15-18, as these claims were not argued separately.
We affirm the rejection of claim 4 under 35 U.S.C. § 103(a) as
obvious over Cunningham and Dorsel.
We affirm the rejection of claims 12 and 14 under 35 U.S.C. § 103(a)
as obvious over Cunningham and Sigrist.
We affirm the rejection of claim 20 under 35 U.S.C. § 103(a) as
obvious over Cunningham and Grace.
We affirm the rejection of claims 21 and 22 under 35 U.S.C. § 103(a)
as obvious over Cunningham.

AFFIRMED

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CORNING INCORPORATED
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