Ex Parte Wolber et alDownload PDFBoard of Patent Appeals and InterferencesApr 24, 200911008603 (B.P.A.I. Apr. 24, 2009) Copy Citation UNITED STATES PATENT AND TRADEMARK OFFICE ____________________ BEFORE THE BOARD OF PATENT APPEALS AND INTERFERENCES ____________________ Ex parte PAUL K. WOLBER, ROBERT H. KINCAID, DOUGLAS AMORESE, DIANE ILSLEY-TYREE, ANDREW S. ATWELL, MEL N. KRONICK, and ERIC M. LE PROUST, Appellants ____________________ Appeal 2009-2252 Application 11/008,6031 Technology Center 1600 ____________________ Decided:2 April 24, 2009 ____________________ Before CAROL A. SPIEGEL, TONI R. SCHEINER, and MELANIE L. MC COLLUM, Administrative Patent Judges. SPIEGEL, Administrative Patent Judge. DECISION ON APPEAL 1 Application 11/008,603, ("the 603 application"), Chemical Arrays and Methods of Using the Same, filed 8 December 2004, is a continuation-in-part of application 09/628,472, filed 31 July 2000. The real party in interest is AGILENT TECHNOLOGIES, INC. (Appellants' Brief filed 30 May 2008 ("App. Br.") at 3). 2 The two month time period for filing an appeal or commencing a civil action, as recited in 37 C.F.R. § 1.304, begins to run from the decided date shown on this page of the decision. The time period does not run from the Mail Date (paper delivery) or Notification Date (electronic delivery). Appeal 2009-2252 Application 11/008,603 2 I. Statement of the Case Appellants appeal under 35 U.S.C. § 134 from an Examiner's final rejection of claims 1-9. Claims 12-18, the only other pending claims, stand withdrawn from consideration (App. Br. 3; Ans.3 2). We have jurisdiction under 35 U.S.C. § 134. We REVERSE. The subject matter on appeal is directed to a method comprising generating a mixture of desired nucleic acid products and contacting the mixture with an addressable array of nucleic acid probes. Claim 1 is illustrative and reads (App. Br. 12): 1. A method comprising: (a) subjecting an array comprising a plurality of features, each comprising nucleic acids immobilized on a surface of a solid support via a cleavable domain having a cleavable region, to conditions sufficient to generate a solution phase composition of nucleic acids; (b) contacting said solution phase composition of nucleic acids with one or more reactants to produce a mixture of product nucleic acids; and (c) contacting said product nucleic acids with an addressable array of probe nucleic acids. The Examiner has rejected claims 1-9 under 35 U.S.C. § 103(a) as unpatentable over Lipshutz4 and Nallur5 (Ans. 3). 3 Examiner's Answer mailed 21 August 2008 ("Ans."). 4 U.S. Patent 6,013,440, Nucleic Acid Affinity Columns, issued 11 January 2000, to Lipshutz et al. ("Lipshutz"). 5 U.S. Patent 6,692,915 B1, Sequencing a Polynucleotide on a Generic Chip, issued 17 February 2004, based on application 09/619,812, filed 20 July 2000, to Girish N. Nallur ("Nallur"). Appeal 2009-2252 Application 11/008,603 3 According to the Examiner, Lipshutz discloses steps (a) and (b) of claim 1, but fails to disclose immobilizing the product nucleic acids of step (b) by capturing them with an array-addressed nucleic acids (Ans. 3-4). The Examiner found that Lipshutz discloses not only two other methods of immobilizing the product nucleic acids onto an affinity matrix, but also that immobilization techniques are known in the art (Ans. 4). According to the Examiner, Nallur discloses capturing a mixture of product nucleic acids with an addressable array of nucleic acids for high throughput sequence identification of novel sequences without cloning or other sequencing techniques (Ans. 5). The Examiner concluded that it would have been obvious to use an addressable array as disclosed by Nallur to immobilize the product nucleic acids to the affinity matrix of Lipshutz for the expected benefits of high throughput identification of novel sequences without cloning or other sequencing techniques, as taught by Nallur (Ans. 5). Appellants essentially argue that since Lipshutz relies on hybridization between the nucleic acids immobilized on the affinity matrix and target nucleic acids in a sample to specifically bind and remove the target nucleic acids from the sample, immobilizing the product nucleic acids by hybridization to an addressable array of complementary nucleic acids would render the affinity matrix unsuitable for use (App. Br. 7-8; Reply Br.6 3-4). In other words, if the "capture" product nucleic acids were attached to the affinity matrix of Lipshutz via hybridization to an array of complementary nucleic acids, the complementary nucleic acids in the array would compete with the complementary target nucleic acids in the sample 6 Appellants' Reply Brief filed 7 October 2008 ("Reply Br."). Appeal 2009-2252 Application 11/008,603 4 for hybridization to the capture product nucleic acids, thereby rendering the affinity matrix unsuitable for its intended use. Thus, the issue is whether Appellants have shown that the Examiner's proposed modification of the affinity matrix of Lipshutz by Nallur would render the affinity matrix of Lipshutz unsuitable for its intended use. II. Findings of Fact ("FF") [1] Lipshutz discloses a method comprising (a) immobilizing an array of template nucleic acids on a substrate via cleavable linkers, the template nucleic acids having different, known sequences which preferably encode "capture probes" which can be incorporated into an affinity matrix; (b) cleaving the linker to release the template nucleic acids into solution where they are amplified, preferably by a PCR (polymerase chain reaction), to provide a population of capture probes; and (c) attaching the capture probes to a solid matrix to produce an affinity matrix (Lipshutz 2:16-26 and 55-62; 10:39-54). [2] According to Lipshutz, sample is contacted with the affinity matrix such that the incorporated/immobilized capture probe specifically hybridizes to and thereby captures its complementary target nucleic acid (Lipshutz 7:34-38; 26:3-6). [3] Further according to Lipshutz, methods of attaching oligonucleotides to solid supports are well known in the art and the amplified capture probes may be attached to the matrix via covalent coupling or streptavidin-biotin coupling (Lipshutz 23:52- 63). Appeal 2009-2252 Application 11/008,603 5 [4] Nallur discloses a method of analyzing a target sequence in a sample, wherein the target sequence is at least partially single stranded and contains a region of recognizable sequence adjacent to the single stranded terminus (Nallur 2:33-42). [5] The method of Nallur comprises amplifying the target sequence and hybridizing the amplified products with an addressable array of capture probes, thereby analyzing the sample (Nallur 2:43-67; 3:52-53). [6] Nallur exemplifies preparing an addressable array by depositing each capture probe onto a known location on a derivatized glass slide to promote covalent association of probes to the glass surfaces (Nallur 34:51-35:32). III. Discussion A. Legal principles "[R]ejections on obviousness grounds cannot be sustained by mere conclusory statements; instead, there must be some articulated reasoning with some rational underpinning to support the legal conclusion of obviousness." In re Kahn, 441 F.3d 977, 988 (Fed. Cir. 2006). Where a proposed modification would render the prior art invention being modified unsatisfactory for its intended purpose, the proposed modification would not have been obvious. See Tec Air Inc. v. Denso Mfg. Michigan Inc., 192 F.3d 1353, 1360 (Fed. Cir. 1999); In re Gordon, 733 F.2d 900, 902 (Fed. Cir. 1984). B. Analysis A solid phase affinity matrix removes a target moiety from a sample by specifically binding the target moiety to a capture moiety immobilized on Appeal 2009-2252 Application 11/008,603 6 the solid phase matrix, e.g., by specifically hybridizing one nucleic acid sequence to its complementary nucleic acid sequence. Lipshutz is directed to a method of making an affinity matrix which comprises attaching a capture moiety, i.e., capture probes, to an affinity matrix (FF 1). The affinity matrix of Lipshutz specifically hybridizes to and thereby captures its complementary target nucleic acid (FF 2). According to Lipshutz, the capture probes are attached to matrix using covalent coupling, streptavidin- biotin coupling, or other known attachment techniques (FF 3). It stands to reason that if the capture probes were removed from the affinity matrix, the matrix would lose its affinity for target. The Examiner proposes attaching the capture probes of Lipshutz to an addressable array of complementary probes via hybridization as taught by Nallur (FF 5) (Ans. 4-5). Appellants argue that the affinity matrix of Lipshutz requires the capture probes to be covalently attached to the matrix or else the affinity matrix will be unsuitable for its intended use of specifically hybridizing to and removing target from a sample (App. Br. 7-8; Reply Br. 3-4). In other words, the capture moieties of Lipshutz can either hybridize to the array of Nallur or to the target moieties of the sample; and, since Lipshutz teaches that its affinity matrices "'rely on hybridization between the nucleic acids comprising the affinity matrix and any target nucleic acids'", the Examiner's proposed modification would render the affinity matrix unsuitable for its intended use (Reply Br. 3, quoting Lipshutz 24:31-35 (emphasis added)). The Examiner repeatedly responds that Lipshutz does not require the capture probes to the covalently linked to the affinity matrix not only because covalent linkage is taught as an alternative attachment means, but Appeal 2009-2252 Application 11/008,603 7 also because a biotinylated oligonucleotide and a streptavidin coated support linkage is not a covalent linkage (Ans. 6-8; see also FF 3). The Examiner is technically correct that linking a biotinylated oligonucleotide to a streptavidin coated support does not form a covalent linkage. However, the Examiner's response fails to address substantively Appellants' essential argument that the capture probes of Lipshutz will either hybridize to the array of Nallur or to the target moieties of the sample and, thus, render the affinity matrix unsuitable for its intended use. Notably, both Lipshutz and Nallur teach and/or suggest immobilizing the probes to solid matrices in a such manner that the probes will not be released from the solid matrices as a result of the hybridization reaction which captures target (FF 3 (covalent or biotin-streptavidin coupling, e.g.) and 6 (covalent coupling)). Thus, while Lipshutz does not require the capture probes to be covalently linked to the affinity matrix, the Examiner has not explained why one of ordinary skill in the art would have attached the capture probes of Lipshutz to its affinity matrix with a technique which allows for the capture probes to be released from the affinity matrix during use due to competitive hybridization between the complementary nucleic acids in the matrix array and the complementary nucleic acids in the sample. Therefore, based on the foregoing, we are constrained to reverse the rejection of claims 1-9 under § 103 over Lipshutz and Nallur. C. Conclusion Appellants have shown that the Examiner's proposed modification of the affinity matrix of Lipshutz by Nallur would render the affinity matrix of Lipshutz unsuitable for its intended use. Appeal 2009-2252 Application 11/008,603 8 IV. Order Upon consideration of the record, and for the reasons given, it is ORDERED that the decision of the Examiner to reject claims 1-9 under 35 U.S.C. § 103(a) as unpatentable over Lipshutz and Nallur is REVERSED. REVERSED MAT AGILENT TECHNOLOGIES, INC. Intellectual Property Administration, Legal Dept. MS Bldg E P.O. Box 7599 Loveland, CO 80537 Copy with citationCopy as parenthetical citation