Ex Parte Frutos et alDownload PDFBoard of Patent Appeals and InterferencesFeb 1, 201111437477 (B.P.A.I. Feb. 1, 2011) Copy Citation 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. Appeal 2010-011099 Application 11/437,477 2 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. Appeal 2010-011099 Application 11/437,477 3 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. Appeal 2010-011099 Application 11/437,477 4 (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 Appeal 2010-011099 Application 11/437,477 5 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.) Appeal 2010-011099 Application 11/437,477 6 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). Appeal 2010-011099 Application 11/437,477 7 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). Appeal 2010-011099 Application 11/437,477 8 “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 Appeal 2010-011099 Application 11/437,477 9 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 Appeal 2010-011099 Application 11/437,477 10 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. Appeal 2010-011099 Application 11/437,477 11 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. Appeal 2010-011099 Application 11/437,477 12 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). Appeal 2010-011099 Application 11/437,477 13 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 Appeal 2010-011099 Application 11/437,477 14 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. Appeal 2010-011099 Application 11/437,477 15 § 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 cdc CORNING INCORPORATED SP-TI-3-1 CORNING, NY 14831 Copy with citationCopy as parenthetical citation