Ex Parte Murphy et alDownload PDFPatent Trial and Appeal BoardDec 8, 201612466663 (P.T.A.B. Dec. 8, 2016) Copy Citation United States Patent and Trademark Office 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 APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 12/466,663 05/15/2009 Patricia D. Murphy 1120-02-4C 6317 108981 7590 12/09/2016 Fish & RirharHsnn PF EXAMINER P.O. Box 1022 MYERS, CARLA J Minneapolis, MN 55440-1022 ART UNIT PAPER NUMBER 1634 MAIL DATE DELIVERY MODE 12/09/2016 PAPER 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. PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte PATRICIA D. MURPHY, MARGA B. WHITE, MARK B. RABIN, SHERI J. OLSON, MATTHEW YOSHIKAWA, GEOFFREY M. JACKSON, TARA ESKANDARI, BRENDA SCHRYER, and MICHAEL PARK Appeal 2015-005591 Application 12/466,6631 Technology Center 1600 Before ERIC B. GRIMES, RICHARD J. SMITH, and DAVID COTTA, Administrative Patent Judges. COTTA, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134 involving claims to a method of analyzing exon 16 of a BRCA2 gene in a human patient. The Examiner rejected the claims on appeal as directed to patent-ineligible subject matter, as obvious under 35 U.S.C. § 103(a), and for failing to meet the enablement requirement. We affirm. 1 According to Appellants, the real party in interest is Myriad Genetics, Inc. App. Br. 1. Appeal 2015-005591 Application 12/466,663 STATEMENT OF THE CASE The Specification teaches that “[ljocating one or more mutations in the BRCA2 region of chromosome 13 provides a promising approach to reducing the high incidence and mortality associated with breast cancer through the early detection of women and men at high risk.” Specification 1. The Specification further teaches that the genomic sequence information for BRCA2 in GenBank and through the Breast Information Core (BIC) database was, at the time of the invention, inaccurate. Id. at 2—3. The inventors claim to have solved this problem, teaching “[t]he present invention is based on the discovery of the correct genomic BRCA2 sequence and five novel sequence haplotypes found in normal human subjects of the BRCA2 gene.” Id. at 3. Claims 64, 66, 81 and 83 are on appeal. Claim 64 is illustrative and reads as follows: 64. A method of analyzing exon 16 of a BRCA2 gene in a human patient comprising: obtaining nucleic acid from a sample from said patient; analyzing, using an automatic computerized sequencer, said nucleic acid to determine its nucleotide sequence; and comparing, with software programmed to perform a base-by-base comparison, the nucleotide sequence of said nucleic acid to the sequence of SEQ ID NO:3; and providing, for display on a computer, data representing the differences between the nucleotide sequence of said nucleic acid and the sequence of SEQ ID NO:3. 2 Appeal 2015-005591 Application 12/466,663 The claims stand rejected as follows: Claims 64, 66, 81, and 83 under 35 U.S.C. § 101 as directed to patent- ineligible subject matter; Claims 64, 66, 81, and 83 under 35 U.S.C. § 103(a) as unpatentable over Tavtigian.2 Claims 64, 66, 81, and 83 under 35 U.S.C. § 103(a) as unpatentable over Futreal.3 Claims 64 and 66 under 35 U.S.C. § 112, first paragraph, as failing to comply with the enablement requirement. In the Examiner's Answer, the Examiner withdrew the pending rejection of claims 64, 66, and 83 under 35 U.S.C. § 112, second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the applicant regards as the invention. Ans. 21. This issue is thus no longer a part of this appeal. PATENT-INELIGIBLE SUBJECT MATTER The Examiner rejected claims 64, 66, 81, and 83 as directed to patent- ineligible subject matter. The Examiner first determined that the claims were directed to the abstract idea of: [A] computer mediated process to analyze a nucleotide sequence of a patient and compare the nucleotide sequence to SEQ ID NO: 3 to thereby accomplish the objectives of analyzing exon 16 of a BRCA2 gene (claims 64 and 66) and sequencing a BRCA2 gene of a patient (claims 81 and 83). 2 Tavtigian et al., US Patent No. 5,837,492, issued Nov. 17, 1998 (“Tavtigian”). 3 Futreal et al., US Patent No. 6,045,997, issued Apr. 4, 2000 (“Futreal”). 3 Appeal 2015-005591 Application 12/466,663 Ans. 3. The Examiner then determined that the additional steps recited in the claims other than the abstract idea consisted of “well-understood, routine, conventional activity” amounting to “no more than mere instructions to implement the idea on a computer and/or recitation of generic computer structure that serves to perform generic computer functions . . . Id. at 6. We agree with the Examiner that the claims are directed to patent- ineligible subject matter. Determination of subject matter eligibility involves a two-step test. First one must determine if the claimed subject matter is directed to a judicially recognized exception such as a product of nature. Mayo Collaborative Serves, v. Prometheus Lab., Inc. 132 S. Ct. 1289, 1297 (2012). If the claims address a judicially recognized exception, the next step is to determine if the claims recite additional elements that transform the nature of the claim. Id. The Federal Circuit addressed the patentability of method claims similar to those at issue here in University of Utah Res. Foundation v. Ambry Genetics Corp., 11A F.3d 755 (Fed. Cir. 2014). The method claims at issue in Ambry involved methods of comparing the sequence of a wild-type BRCA1 gene with the sequence obtained from a human subject. Claims 7 and 8 of U.S. Patent No. 5,753,441 (“the ’411 Patent”), the patent at issue in Ambry, read as follows: 7. A method for screening germline of a human subject for an alteration of a BRCAl gene which comprises comparing germline sequence of a BRCAl gene or BRCAl RNA from a tissue sample from said subject or a sequence of BRCAl cDNA made from mRNA from said sample with germline sequences of wild-type BRCAl gene, wild-type BRCAl RNA or wild- type BRCAl cDNA, wherein a difference in the 4 Appeal 2015-005591 Application 12/466,663 sequence of the BRCAl gene, BRCA1 RNA or BRCAl cDNA of the subject from wild-type indicates an alteration in the BRCAl gene in said suhject[,] wherein a germline nucleic acid sequence is compared by hybridizing a BRCAl gene probe which specifically hybridizes to a BRCAl allele to genomic DNA isolated from said sample and detecting the presence of a hybridization product wherein a presence of said product indicates the presence of said allele in the subject. 8. A method for screening germline of a human subject for an alteration of a BRCAl gene which comprises comparing germl ine sequence of a BRCAl gene or BRCAl 'RNA from a tissue sample from said subject or a sequence of BRCAl cDNA made from mRNA from said sample with germline sequences of wild-tvpe BRCAl gene, wild-type BRCAl RNA or wild- type BRCAl cDNA, wherein a difference in the sequence of the BRCAl gene, BRCAl RNA or BRCAl cDNA of the subject from wild-type indicates an alteration in the BRCAl gene in said subject[,] wherein a germline nucleic acid sequence is compared by amplifying all or part of a BRCAl gene from said sample using a set of primers to produce amplified nucleic acids and sequencing the ampli fied nucleic acids. Id. at 761-62. With respect to the first step of the subject matter eligibility test, the Ambry court held that “the comparisons described in the first paragraphs of claims 7 and 8 are directed to the patent-ineligible abstract idea of comparing BRCA sequences and determining the existence of alterations.” Id. at 763. With respect to the second step, the Court found that the additional limitations recited in the claims — which require hybridizing and detecting a hybridization product (claim 7) or amplifying and sequencing 5 Appeal 2015-005591 Application 12/466,663 (claim 8) — “do not add ‘enough’ to make the claims as a whole patent- eligible.” Id. at 764. The court explained “[njothing is added by identifying the techniques to be used in making the comparison because those comparison techniques were the well-understood, routine, and conventional techniques that a scientist would have thought of when instructed to compare two gene sequences.” Id. at 764. The court’s analysis in Ambry is directly applicable to the claims at issue here. As in Ambry, the claims at issue recite the abstract idea of “comparing BRCA sequences and determining the existence of alterations.” In the claims at issue here, the additional limitations beyond the comparison of BRCA sequences involve: • “using an automatic computerized sequencer” (claims 64, 66, 81 and 83); • “comparing, with software programed to perform a base-by- base comparison” (claims 64 and 66); • “providing, for display on a computer, data representing the differences between the nucleotide sequence[s]” (claims 64 and 66); • “synthesizing in vitro a nucleic acid comprising the sequence of SEQ ID NO:3 . . . determining] its nucleotide sequence” (claims 66 and 83); and • “reporting that the nucleotide sequence of BRCA2 . . . comprises the sequence of SEQ ID NO:3” (claims 81 and 83). We find that these additional limitations simply recite “well-understood, routine, and conventional techniques that a scientist would have thought of 6 Appeal 2015-005591 Application 12/466,663 when instructed to compare two gene sequences.” Ambry, 774 F.3d at 764. Accordingly, like the additional limitations in Ambry, the additional limitations at issue here do not add enough to make the claims patent eligible. Appellants argue that “[t]he pending claims simply do not prevent others from currently, or in the future, using the BRCA2 gene and comparison with the BRCA2 gene in other ways.” Reply Br. 5. Accordingly, Appellants contend that the claims are patent eligible because they do not preempt all uses of the BRCA2 sequence. Id. at 5—6. But even assuming that one can find other meaningful uses of the BRCA2 sequence, “the absence of complete preemption does not demonstrate patent eligibility.” Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1379 (Fed. Cir. 2015). Appellants argue that, like the claims in Diamond v. Diehr, the claims at issue here modify and improve a real-world process — the process of BRCA2 sequencing. Reply Br. 2—3. Appellants further argue that their claims “include[] features that are plainly not abstract, such as computer implementation, actual sequencing of the BRCA2 gene, and actual analysis of a nucleotide sequence to analyze exon 16 of a BRCA2 gene.” Id. at 6—7. We are not persuaded at least because we cannot distinguish the improvements and claim features at issue here from those at issue in Ambry. Accordingly, we affirm the Examiner’s rejection of claims 64, 66, 81, and 83 as drawn to patent-ineligible subject matter. OBVIOUSNESS OVER TAVTIGIAN AND OVER FUTREAL The Examiner rejected claims 64, 66, 81, and 83 as obvious over Tavtigian and, separately, as obvious over Futreal. The Examiner found that 7 Appeal 2015-005591 Application 12/466,663 both Tavtigian and Futreal taught “a method for analyzing the BRCA2 gene and methods of sequencing exon 16 of the BRCA2 gene comprising obtaining a nucleic acid from a sample from a patient, [and] analyzing the nucleic acid to determine its nucleotide sequence using an automated DNA sequencer.” Ans. 9, 14—15. The Examiner recognized that neither Tavtigian nor Futreal disclosed the particular sequence of SEQ ID NO:3, but found that SEQ ID NO:3 constituted nonfunctional descriptive material that “cannot render nonobvious an invention that would otherwise have been obvious.” Id. at 10-11, 15—16. Appellants argue that “the fundamental problem with such rejections [is] that there is no disclosure in either reference of SEQ ID NO:3, let alone a method utilizing the sequence of SEQ ID NO:3.” Reply Br. 9. Appellants contend that SEQ ID NO:3 is “integral to the claimed methods, and substantively affect[s] the way the operations of the claims occur.” Id. at 10. Appellants assert that the Examiner’s conclusion that SEQ ID NO:3 is “nonfunctional descriptive information” applies only in the context of printed material and thus has no application here. Id. We find that the Examiner has the better position. The facts of this case are similar to those in Ex parte Nehls, 88 USPQ2d 1883 (BPAI 2008) (precedential). The claims in Nehls were directed to a computer based system that required SEQ ID NOs corresponding to specific nucleotide sequences. The Board concluded that “the particular sequence data recited in claim 13 is nonfunctional descriptive material and does not distinguish the claimed computer-based system from the prior art system that is the same except for its sequence data.” Nehls, 88 USPQ2d at 1888. The Board explained: 8 Appeal 2015-005591 Application 12/466,663 There is no evidence that SEQ ID NOs 9-1008 functionally affect the process of comparing a target sequence to a database by changing the efficiency or accuracy or any other characteristic of the comparison. Rather, the SEQ ID NOs are merely information being manipulated by a computer; the SEQ ID NOs are inputs used by a computer program that calculates the degree of similarity between a target sequence and each of the sequences in a database. The specific SEQ ID NOs recited in the claims do not affect how the method of the prior art is performed — the method is carried out the same way regardless of which specific sequences are included in the database. Id. at 1889. Having found that the SEQ ID NOs were nonfunctional, the Board found the claims obvious, holding that “the nature of the information being manipulated does not lend patentability to an otherwise unpatentable computer-implemented product or process.” Id. Here, as in Nehls, the claims differ from the prior art only in that they recite different nucleic acid sequences. As in Nehls, the SEQ ID NOs are merely information being manipulated by a computer; they do not functionally affect the process by changing the efficiency or accuracy or any other characteristic of the comparison. Accordingly we affirm the Examiner’s decision to reject claims 64, 66, 81, and 83 as obvious over Tavtigian. We similarly affirm the Examiner’s decision to reject claims 64, 66, 81, and 83 as obvious over Futreal. ENABLEMENT The Examiner rejected claims 64 and 66 for failing to meet the enablement requirement. In the Final Office Action, the Examiner made detailed findings of fact with regard to the factors enumerated in In re Wands, 858 F.2d 731 (Fed. Cir. 1988). We adopt the Examiner’s findings of 9 Appeal 2015-005591 Application 12/466,663 fact and reasoning (Final Act. 15—25) and agree with the Examiner that claims 64 and 66 are not enabled. We address Appellants’ arguments below. Appellants argue that the Examiner erred by looking “not to whether the area of the claimed subject matter was unpredictable, but instead to whether chemistry and biology generally are unpredictable arts.” Reply Br. 10. We disagree. In finding that claims 64 and 66 were not enabled, the Examiner found that the claims were directed to a method of comparing nucleotide sequences of a human BRCA2 gene. Final Act. 15. The Examiner then found that the purpose of doing so, as taught in the Specification, was to “determine whether the patient has a variation in the sequence of exon 16 that is correlated with an increased risk of breast or ovarian cancer.” Id. at 16. In analyzing the degree of unpredictability in the art, the Examiner found that “[kjnowledge of the sequence of the wildtype BRCA2 gene does not allow one to predict the identity of mutations in the BRCA2 gene and ascertain which of those mutations may be correlated with breast or ovarian cancer.” Id. at 21—22. The Examiner then determined that there was “no predictable means for distinguishing between polymorphisms and mutations that result in a BRCA2 DNA coding for a non-functional protein or a protein with substantially reduced or altered function, and which are thereby correlated with the phenotype of susceptibility to breast or ovarian cancer.” Id. These findings are specific to the claimed subject matter and not based on the general unpredictability of chemistry and biology. Appellants also argue that the Examiner erred in determining that the only purpose of the recited methods was to determine “whether a patient has 10 Appeal 2015-005591 Application 12/466,663 a variation in exon 16 ‘that is correlated with an increased risk of breast or ovarian cancer. Reply Br. 10. Appellants argue that the claims have other uses. Id. Specifically, Appellants assert that claim 64: [I]s directed to a particular way of analyzing a nucleic acid to determine whether it has a nucleotide sequence that varies from SEQ ID NO:3 at a position corresponding to a nucleotide in exon 16 of a BRCA2 gene. . . . Thus, the claims at no point require determining whether a patient has a variation in exon 16 that is correlated with an increased risk of breast or ovarian cancer. App. Br. 15. While it is true that the claims do not require determining whether a patient has an increased risk of cancer, the claims must have some utility. And the only utility described in the Specification is identifying an increased cancer risk. That a person of ordinary skill in the art may be able to carry out a claimed method is irrelevant if the applicant does not establish that the method provides a useful result. See, In re Fisher, 421 F.3d 1365, 1378—79 (Fed. Cir. 2005); In re Kirk, 376 F.2d 936, 942 (CCPA 1967) (“ Necessarily, compliance with § 112 requires a description of how to use presently useful inventions, otherwise an applicant would anomalously be required to teach how to use a useless invention.”). Here, Appellants have not identified any specific teachings in the Specification that explain how comparing the claimed nucleotide sequence to the sequence found in a patient provides a useful result, other than by indicating increased cancer risk. Accordingly, we affirm the Examiner’s decision to reject claims 64 and 66 for lack of enablement. 11 Appeal 2015-005591 Application 12/466,663 SUMMARY For these reasons and those set forth in the Examiner’s Answer, and the Final Office Action, the Examiner’s final decision to reject claims 64, 66, 81, and 83 is affirmed. No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a)(1). AFFIRMED 12 Copy with citationCopy as parenthetical citation