Ex Parte Stuelpnagel et alDownload PDFPatent Trial and Appeal BoardSep 20, 201612419218 (P.T.A.B. Sep. 20, 2016) Copy Citation UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. FILING DATE 12/419,218 0410612009 20995 7590 09/22/2016 KNOBBE MARTENS OLSON & BEAR LLP 2040 MAIN STREET FOURTEENTH FLOOR IRVINE, CA 92614 FIRST NAMED INVENTOR John R. Stuelpnagel UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www .uspto.gov ATTORNEY DOCKET NO. CONFIRMATION NO. ILLINC.59CPPC1C 1148 EXAMINER STEELE, AMBER D ART UNIT PAPER NUMBER 1676 NOTIFICATION DATE DELIVERY MODE 09/22/2016 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address( es): j ayna.cartee@knobbe.com efiling@knobbe.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte JOHN R. STUELPGNAGEL, MARKS. CHEE, STEVEN R. AUGER, GAN G. WANG, LAURA S. CASAS, SHAWN CHRISTOPHER BAKER, and ROBERT C. KAIN1 Appeal2014-007798 Application 12/419,218 Technology Center 1600 Before JOHN G. NEW, RICHARD J. SMITH, and DEVON ZASTROW NEWMAN, Administrative Patent Judges. NEWMAN, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134 involving claims to a method of forming a plurality of random arrays of encoded particles on a substrate, which have been rejected as anticipated, obvious, and for non-statutory obviousness-type double patenting. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. 1 Appellants identify the Real Party in Interest as Illumina, Inc. App. Br. 3. Appeal2014-007798 Application 12/419,218 STATEMENT OF THE CASE Background The Specification discloses: The present invention is directed to the formation of very high density arrays that can allow simultaneous analysis, i.e. parallel rather than serial processing, on a number of samples. This is done by forming an "array of arrays", i.e. a composite array comprising a plurality of individual arrays, that is configured to allow processing of multiple samples. For example, each individual array is present within each well of a microtiter plate. Thus, depending on the size of the microtiter plate and the size of the individual array, very high numbers of assays can be run simultaneous! y. Spec. 5:36-6:4. [T]he invention provides composite array compositions comprising a first substrate with a surface comprising a plurality of assay locations and a second substrate comprising a plurality of array locations, each array location comprising discrete sites. The compositions further comprise a population of microspheres comprising at least a first and a second subpopulation, wh rein [sic wherein] each subpopulation comprises a bioactive agent. The microspheres are distributed on each of the array locations. Spec. 2:32-3:6. Claims 51-55 are on appeal. Claim 51 illustrates the subject matter and reads as follows: 51. A process of forming a plurality of random arrays of encoded particles on a substrate, wherein each of the arrays are formed by random placement of encoded particles, wherein differently encoded particles have a different label, compnsmg: 2 Appeal2014-007798 Application 12/419,218 (i) placing and confining a group of differently encoded particles into one or more sites on a substrate having a plurality of sites, so as to form a first confined group of particles occupying particular sites; (ii) recording the positions of the encoded particles within said confined group; (iii) placing and confining an additional group of differently encoded particles into unoccupied sites on the substrate so as to form an additional group of confined particles occupying particular sites; (iv) recording the positions of particles within said additional confined group; and repeating steps (iii) to (iv) several times so as to form a plurality of a random encoded arrays of particles. App. Br., Claims Appendix, p. 15. The following rejections are before us to review (Ans. 2-10): Claims 51-55 are rejected under pre-AIA 35 U.S.C. § 102(e) as being anticipated by Walt.2 Claims 51-55 are rejected under pre-AIA 35 U.S.C. § 103(a) as obvious over Kedar3 and Walt. Claims 51-5 5 are rejected on the ground of nonstatutory obviousness- type double patenting over claims 1-21 of Chee '431. 4 Claims 51-5 5 are rejected on the ground of nonstatutory obviousness- type double patenting over claims 1-11 of Kermani. 5 2 U.S. Pat. No. 6,023,540, issued Feb. 8, 2000 (filed Mar. 14, 1997). 3 U.S. Pat. No. 6,165,778, issued Dec. 26, 2000 (filed July 2, 1998, effective filing date Nov. 2, 1993). 4 U.S. Pat. No. 7,166,431 B2, issued Jan. 23, 2007. 5 U.S. Pat. No. 7,499,806 B2, issued Mar. 3, 2009. 3 Appeal2014-007798 Application 12/419,218 Claims 51-5 5 are rejected on the ground of nonstatutory obviousness- type double patenting over claims 1-31 of Chee '57 6. 6 Claims 51-5 5 are rejected on the ground of nonstatutory obviousness- type double patenting over claims 1-15 of Chee '764. 7 Claims 51-5 5 are rejected on the ground of nonstatutory obviousness- type double patenting over claims 1-21 of Chee '274. 8 Claims 51-5 5 are rejected on the ground of nonstatutory obviousness- type double patenting over claims 1-13 of Chee '584. 9 ANTICIPATION We select claim 51 as representative of the rejected claims. 37 C.F .R. § 41.37(c)(l)(iv). As stated in In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992): [T]he examiner bears the initial burden ... of presenting a prim a facie case of unpatentability .... After evidence or argument is submitted by the applicant in response, patentability is determined on the totality of the record, by a preponderance of evidence with due consideration to persuasiveness of argument. Appellants' arguments do not persuade us that a preponderance of the evidence fails to support the Examiner's prima facie case of anticipation as to claim 51. Claim 51 recites a process of forming a plurality of random arrays of encoded particles on a substrate in which each array is made by randomly 6 U.S. Pat. No. 7,563,576, issued July 21, 2009. 7 U.S. Pat. No. 6,890,764, issued May 10, 2005. 8 U.S. Pat. No. 6,998,274, issued Feb. 14, 2006. 9 U.S. Pat. No. 6,620,584, issued Sep. 17, 2003. 4 Appeal2014-007798 Application 12/419,218 placing encoded particles on the substrate. App. Br., Claims Appendix, p. 15. Each of the encoded particles has a different label that allows the particle location to be "recorded" by detecting the label on the particle. Id. As the Examiner found (Final Action10 4), Walt discloses methods for creating multiple arrays by placing and then affixing microspheres (i.e. particles), which each contain different biological reagents for subsequent detection (i.e. labels), into wells at the ends of a silicon optical fiber bundle. (See Walt, abstract: An optical fiber bundle sensor is also disclosed in which the separate microspheres may be optically coupled to discrete fibers or groups of fibers within the bundle. The functionalies [sic functionalities] are encoded on the separate micro spheres using fluorescent dyes and then affixed to wells etched in the end of the bundle. Thus, a single sensor may carry thousands of chemistries. Only those microspheres exhibiting reactions then need to be decoded to identify the corresponding functionality.) As the Examiner found (Final Action 4), Walt discloses that the microspheres may be randomly placed. See Walt Fig. 7 A and 7B, reflecting random placement of microspheres affixed in an array in which not every well is occupied, and Walt 4:63---67 ("micrographs showing the array of microspheres in their corresponding wells prior and subsequent to physical agitation, tapping and air pulsing, demonstrating the electrostatic binding of the microspheres in the wells.") 10 Office Action mailed July 10, 2013. 5 Appeal2014-007798 Application 12/419,218 As the Examiner found (Final Action 4), Walt discloses that the biological reagents on the microspheres can be detected (i.e. recorded). See Walt 3 :4 3--46 (" ... the chemical functionality on each bead is determined via an optical signature which is encoded with a description of the chemical functionality.") Thus, Walt discloses the steps of random placement and affixing of differently labeled "encoded particles," and "recording" the location of those particles. Claim 51 also recites that the "plurality of random arrays" is created through serial performance of the steps of "placing and confining a group of differently encoded particles" into unoccupied sites on a multi-site substrate, and "recording the positions of the particles within the group." App. Br., Claims Appendix, p. 15. As the Examiner found (Final Action 4), Walt discloses that the microspheres may be serially placed: The microspheres are then placed in the wells 250 in step 276 according to a number of different techniques. The placement of the microspheres may be accomplished by dripping a solution containing the desired randomly mixed subpopulations of the microspheres over the distal end 212, sonicating the bundle to settle the microspheres in the wells, and allowing the microsphere solvent to evaporate. Alternatively, the subpopulations could be added serially to the bundle end. Walt 12:49-57 (emphasis added). 6 Appeal2014-007798 Application 12/419,218 The Examiner also found claims 1 7 and 21 of Walt (dependent on claim 19) teach distributing and monitoring (i.e. recording) the beads and serial addition of subpopulation of beads: 17. A method for constructing and using an analytic chemistry sensor, comprising: forming wells at terminal ends of optical fibers within a bundle; distributing beads carrying chemical functionalities within the wells; and monitoring a status of the chemical functionalities from a proximal end of the bundle. 19. The method described in claim 17, further comprising forming a population of beads in the wells from separate subpopulations, each subpopulation carrying a different chemical functionality and an optically interrogatable code descriptive of the chemical functionality. 21. The method described in claim 19, further comprising serially adding the subpopulations to the \vells. The Examiner concluded that "the presently claimed method is anticipated by the teachings of Walt et al." Final Action 4. Appellants argue that Walt does not disclose any method that includes at least steps "(iii) placing and confining an additional group of differently encoded particles into unoccupied sites on the substrate" and "'repeating steps (iii) to (iv) several times' (emphasis added)" of claim 51. App. Br. 5. Appellants argue that a "subpopulation" of microspheres as used in Walt refers to beads or spheres "all of which have the same functionality." Id. According to Appellants, the teachings within Walt that the Examiner cited for serial addition of subpopulations instead teach serial addition of a group 7 Appeal2014-007798 Application 12/419,218 of uniformly-labeled microspheres and not "a group of differently encoded particles" that contain more than one type of label. Id. at 5-6. Therefore, Appellants argue, Walt's "single step embodiment" does not teach the claimed method because "Applicant's claims require at least three steps of 'placing and confining beads"' (i.e. step (i), step (iii) and the repetition of step (iii)), and the "serial addition embodiment" of Walt does not teach claim 51 because "the beads within each serially added 'subpopulation' of Walt are the same whereas the particles within each serially placed 'group' of the claims are 'differently encoded"'. Id. at 6-7. Appellants argue "the sections of Walt cited by the Examiner disclose neither '(iii) placing and confining an additional group of differently encoded particles into unoccupied sites on the substrate' nor 'repeating step (iii) to (iv)."' Id. In response, the Examiner cites to teachings in Walt that explain "the subpopulations can be randomly mixed together" and therefore "a recitation of 'subpopulations' (i.e. plural) encompasses randomly mixed subpopulations." Ans. 12. We agree with Appellants that "subpopulation" as used in Walt refers to a population of spheres or beads that contains a single type of detectable functionality. Nevertheless, we are not persuaded that a preponderance of the evidence fails to support the Examiner's prima facie case of anticipation as to claim 51. Walt discloses that arrays can be made as follows: The microspheres are then placed in the wells 250 in step 276 according to a number of different techniques. The placement of the microspheres may be accomplished by dripping a solution containing the desired randomly mixed subpopulations of the microspheres over the distal end 212, sonicating the bundle to settle the microspheres in the wells, 8 Appeal2014-007798 Application 12/419,218 and allowing the microsphere solvent to evaporate. Alternatively, the subpopulations could be added serially to the bundle end. 12:49-57 (text emphasis added). When "randomly mixed subpopulations of the microspheres" are placed into wells via a dripped solution, the identity and distribution of the microsphere subpopulations within the wells would necessarily be random. As each well is "unoccupied" at the time the array making process begins, each placement of randomly mixed subpopulations of microspheres comprises "placing and confining an additional group of differently encoded particles into unoccupied sites on the substrate so as to form an additional group of confined particles occupying particular sites" as recited by claim 51. Thus, Walt discloses repeating steps (i) and (iii) multiple times to create "a plurality of a random encoded array of particles" as recited by claim 51. ii.Jthough \Valt does not teach the monitoring/recording step after each addition of randomly distributed microsphere subpopulations to the wells, this does not preclude a finding of anticipation because claim 51 is not so limited. That is, the monitoring/detecting step can be performed subsequent to the distribution of the particles as disclosed in Appellants' Specification: It should be noted that while most of the methods described herein add the beads to the substrate prior to the assay, the order of making, using and decoding 11 the array can vary. For example, the array can be made, decoded, and then the assay done. Alternatively, the array can be made, used in an assay, 11 Although claim 51 recites "recording," the Specification uses the term "decoding." 9 Appeal2014-007798 Application 12/419,218 and then decoded; this may find particular use when only a few beads need be decoded. Spec. 32:37-33:4 In view of this disclosure, we find that the recording step of claim 51 need not be performed subsequent to each step of "placing and confining an additional group of differently encoded particles into unoccupied sites on the substrate so as to form an additional group of confined particles occupying particular sites." See In re Hampel, 162 F.2d 483, 485-86 (CCPA 1947) ("There is nothing in the instant record which indicates that the particular order of steps produces results differing in any way from those which would be brought about if another order of steps were followed.") With this interpretation, the disclosure of Walt, e.g., claims 17, 19 and 21, teaches every step of the claimed invention. Furthermore, in considering the disclosure of a reference for anticipation, it is proper to take into account not only specific teachings of the reference but also the inferences that one skilled in the art would reasonably be expected to draw therefrom. In re Preda, 401 F.2d 825, 826 (CCP A 1968). We find the disclosure of Walt, and in particular, claims 17, 19 and 21, teach the ordinary artisan that the steps of creating an assay for use in the method of claim 51 can be performed in a different sequence as desired. In sum, for the reasons discussed, Appellants' arguments do not persuade us that the Examiner erred in finding that Walt describes a method for forming a plurality of random arrays that has all of the features required by claim 51. Accordingly, we affirm the Examiner's rejections of claim 51 10 Appeal2014-007798 Application 12/419,218 as anticipated by Walt. Because they were not argued separately, claims 52- 55 fall with claim 51. 37 C.F.R. § 41.37(c)(l)(iv). OBVIOUSNESS In rejecting claims 51-55 for obviousness over Kedar and Walt, the Examiner relied on Kedar as a reference that teaches all elements of claim 51 except fixing beads onto a support. Ans. 5-7. The Examiner additionally relied on the teachings of Walt discussed above, including the teaching on "fiber optic supports wherein the beads can be fixed onto wells etched into each fiber of the fiber optic bundle." Id. at 7. We agree with the Examiner's conclusions regarding the scope and content of the prior art and adopt them. Appellants argue that Kedar discloses neither "placing and confining an additional group of differently encoded particles into unoccupied sites on the substrate" nor ordered step "'(ii) recording the positions of the encoded particles within said confined group' of Claim 51." App. Br. 9-11. Appellants reiterate their argument that Walt fails to teach these steps (id. at 11) and further argue one of skill in the art would not modify the process of Kedar to use the methods of Walt because doing so would render the Kedar process "unsuitable for its intended purpose." Id. at 12. As discussed above, Appellants do not persuade us that Walt lacks any of the limitations of claim 51. Accordingly, because Appellants' arguments do not identify any deficiency in the Examiner's obviousness rejection of claims 51-55 for obviousness over Walt, we affirm the rejection. In addition, we find that even if Walt were found not to meet all of the limitations of claim 51 for failure to repeat the claimed steps as argued by Appellants, we find that claim 51 would still have been obvious to one of 11 Appeal2014-007798 Application 12/419,218 ordinary skill in the art. See PerfectWeb Techs., Inc. v. InfoUSA, Inc., 587 F.3d 1324, 1331 (Fed. Cir. 2009) ("performing the recited prior art method of steps [] more than once [as required by the claimed method] was one of the 'inferences and creative steps that a person of ordinary skill would employ" (citing KSR Int'! Co. v. Teleflex Inc., 550 U.S. 398, 418). OBVIOUSNESS-TYPE DOUBLE PATENTING Appellants do not contest or address the obviousness-type double patenting rejections. Therefore, we summarily affirm, and will not further discuss, these rejections. See Manual of Patent Examining Procedure § 1205.02 ("If a ground of rejection stated by the examiner is not addressed in the appellant's brief, appellant has waived any challenge to that ground of rejection and the Board may summarily sustain it."). SUMMARY For the reasons discussed, we affirm the rejection of claim 51 on the ground of anticipation by Walt. Claims 52-55 have not been argued separately and therefore fall with claim 51. 37 C.F.R. § 41.37(c)(l)(iv). For the reasons discussed, we affirm the rejection of claim 51 on the ground of obviousness over Kedar and Walt. Claims 52-55 have not been argued separately and therefore fall with claim 51. 37 C.F.R. § 41.37(c)(l)(iv). We summarily affirm the rejection of claims 51-55 on the ground of nonstatutory obviousness-type double patenting over claims 1-21 of Chee '431. 12 Appeal2014-007798 Application 12/419,218 We summarily affirm the rejection of claims 51-55 on the ground of nonstatutory obviousness-type double patenting over claims 1-11 of Kermani. We summarily affirm the rejection of claims 51-55 on the ground of nonstatutory obviousness-type double patenting over 1-31 of Chee '57 6. We summarily affirm the rejection of claims 51-55 on the ground of nonstatutory obviousness-type double patenting over claims 1-15 of Chee '764. We summarily affirm the rejection of claims 51-55 on the ground of nonstatutory obviousness-type double patenting over claims 1-21 of Chee '274. We summarily affirm the rejection of claims 51-55 on the ground of nonstatutory obviousness-type double patenting over claims 1-13 of Chee '584. 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). AFFIRMED 13 Copy with citationCopy as parenthetical citation