Ashutosh et al.Download PDFPatent Trials and Appeals BoardAug 2, 201914288299 - (D) (P.T.A.B. Aug. 2, 2019) 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. 14/288,299 05/27/2014 Ashutosh 20130278-02 2376 22878 7590 08/02/2019 Agilent Technologies, Inc. Global IP Operations 5301 Stevens Creek Blvd Santa Clara, CA 95051 EXAMINER WOITACH, JOSEPH T ART UNIT PAPER NUMBER 1631 NOTIFICATION DATE DELIVERY MODE 08/02/2019 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): Agilentdocketing@cpaglobal.com ipopsadmin@agilent.foundationip.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE ____________ BEFORE THE PATENT TRIAL AND APPEAL BOARD ____________ Ex parte ASHUTOSH, DEVENDRA JOSHI, and CHRISTIAN A. LE COCQ (APPLICANT: AGILENT TECHNOLOGIES, INC.) ____________ Appeal 2019-002083 Application 14/288,2991 Technology Center 1600 ____________ Before DONALD E. ADAMS, ERIC B. GRIMES, and RICHARD M. LEBOVITZ, Administrative Patent Judges. ADAMS, Administrative Patent Judge. DECISION ON APPEAL This Appeal under 35 U.S.C. § 134(a) involves claims 1–19 (Final Act.2 2). Examiner entered a rejection under 35 U.S.C. § 101. We have jurisdiction under 35 U.S.C. § 6(b). We AFFIRM. 1 Appellants identify “Agilent Technologies, Inc.” as the real party in interest (Appellants’ August 7, 2018 Appeal Brief (App. Br.) 2). 2 Examiner’s January 16, 2018 Final Office Action. Appeal 2019-002083 Application 14/288,299 2 STATEMENT OF THE CASE Appellants’ disclosure relates to a method for identifying a sequence variant in an enriched sample. In certain embodiments, this method may comprise: (a) obtaining: (i) a plurality of sequence reads from a sample that has been enriched for a genomic region and (ii) a reference sequence for the genomic region; (b) assembling the sequence reads to obtain a plurality of discrete sequence assemblies that correspond to potential variants; (c) determining which of the potential variants are true and which are artifacts by examining the sequence reads that make up each of the discrete sequence assemblies; (d) optionally determining whether each of the true potential variants contains a mutation that is known to be associated with the reference sequence; and (e) outputting a report indicating whether the sample comprises a sequence variant[;] . . . a computer system comprising a memory comprising: a) a database of sequences; and b) an executable program for performing the present method[;] . . . a computer- readable storage medium comprising instructions for performing the present method[; and] . . . a method of identifying a variant sequence. In certain embodiments, this method may comprise: a) inputting sequence information into a computer system comprising a program comprising instructions for performing the present method; b) executing the program; and c) receiving an output from the computer system. (Spec. 2–3.) Appellants’ claims 1 and 10–12 are representative and reproduced below: 1. A method for identifying a sequence variant comprising: (a) generating a plurality of at least 100 sequence reads from a sample that has been enriched for a genomic region and Appeal 2019-002083 Application 14/288,299 3 obtaining a reference sequence for the genomic region, wherein the sequence reads are generated by: i. enriching for the genomic region; and ii. sequencing the enriched genomic region; (b) assembling the sequence reads to obtain a plurality of discrete sequence assemblies each of which corresponding to a potential variant; (c) examining, using a computer, the sequence reads that make up each of the discrete sequence assemblies to determine which of the potential variants are true and which are artifacts; (d) optionally determining whether each of the true potential variants contains a mutation that is known to be associated with the reference sequence; and (e) identifying a true sequence variant in the sample based on the determination of which variants are true and which variants are artifacts. (App. Br. 11.) 10. The method of claim 1, wherein said assembling uses graph theory. (Id. at 12.) 11. The method of claim 10, wherein said assembling is done using a minimal de-Bruijn sequence. (Id.) 12. The method of claim 10, wherein said assembling is done using a BEST theorem. (Id.) Ground of rejection before this Panel for review: Claims 1–19 stand rejected under 35 U.S.C. § 101. Appeal 2019-002083 Application 14/288,299 4 ISSUE Does the preponderance of evidence of record support Examiner’s finding that Appellants’ claimed invention is directed to patent ineligible subject matter? PRINCIPLES OF LAW An invention is patent-eligible if it claims a “new and useful process, machine, manufacture, or composition of matter.” 35 U.S.C. § 101. However, the Supreme Court has long interpreted 35 U.S.C. § 101 to include implicit exceptions: “‘[l]aws of nature, natural phenomena, and abstract ideas’” are not patentable. E.g., Alice Corp. v. CLS Bank Int’l, 573 U.S. 208, 216 (2014). In determining whether a claim falls within an excluded category, we are guided by the Supreme Court’s two-step framework, described in Mayo and Alice. Id. at 217–18 (citing Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66, 75–77 (2012)). In accordance with that framework, we first determine what concept the claim is “directed to.” See Alice, 573 U.S. at 219 (“On their face, the claims before us are drawn to the concept of intermediated settlement, i.e., the use of a third party to mitigate settlement risk.”); see also Bilski v. Kappos, 561 U.S. 593, 611 (2010) (“Claims 1 and 4 in petitioners’ application explain the basic concept of hedging, or protecting against risk.”). Concepts determined to be abstract ideas, and thus patent ineligible, include certain methods of organizing human activity, such as fundamental economic practices (Alice, 573 U.S. at 219–20; Bilski, 561 U.S. at 611); mathematical formulas (Parker v. Flook, 437 U.S. 584, 594–95 (1978)); and mental processes (Gottschalk v. Benson, 409 U.S. 63, 69 (1972)). Concepts Appeal 2019-002083 Application 14/288,299 5 determined to be patent eligible include physical and chemical processes, such as “molding rubber products” (Diamond v. Diehr, 450 U.S. 175, 191 (1981)); “tanning, dyeing, making water-proof cloth, vulcanizing India rubber, smelting ores” (id. at 182 n.7 (quoting Corning v. Burden, 56 U.S. 252, 267–68 (1853))); and manufacturing flour (Gottschalk, 409 U.S. at 69 (citing Cochrane v. Deener, 94 U.S. 780, 785 (1876))). In Diehr, the claim at issue recited a mathematical formula, but the Supreme Court held that “[a] claim drawn to subject matter otherwise statutory does not become nonstatutory simply because it uses a mathematical formula.” Diehr, 450 U.S. at 176; see also id. at 191 (“We view respondents’ claims as nothing more than a process for molding rubber products and not as an attempt to patent a mathematical formula.”). Having said that, the Supreme Court also indicated that a claim “seeking patent protection for that formula in the abstract . . . is not accorded the protection of our patent laws, . . . and this principle cannot be circumvented by attempting to limit the use of the formula to a particular technological environment.” Id. (citing Gottschalk and Parker); see, e.g., id. at 187 (“It is now commonplace that an application of a law of nature or mathematical formula to a known structure or process may well be deserving of patent protection.”). If the claim is “directed to” an abstract idea, we turn to the second step of the Alice and Mayo framework, where “we must examine the elements of the claim to determine whether it contains an ‘inventive concept’ sufficient to ‘transform’ the claimed abstract idea into a patent- eligible application.” Alice, 573 U.S. at 221 (quotation marks omitted). “A claim that recites an abstract idea must include ‘additional features’ to Appeal 2019-002083 Application 14/288,299 6 ensure ‘that the [claim] is more than a drafting effort designed to monopolize the [abstract idea].’” Id. (quoting Mayo, 566 U.S. at 77). “[M]erely requir[ing] generic computer implementation[] fail[s] to transform that abstract idea into a patent-eligible invention.” Id. The PTO recently published revised guidance on the application of § 101. USPTO, 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50 (January 7, 2019) (“Revised Guidance”). Under that guidance, we first look to whether the claim recites: (1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes); and (2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)–(c), (e)–(h)). See 84 Fed. Reg. 54–55. Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim: (3) adds a specific limitation beyond the judicial exception that is not “well-understood, routine, conventional” in the field (see MPEP § 2106.05(d)); or (4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception. See 84 Fed. Reg. 51. ANALYSIS The method for identifying a sequence variant, set forth in Appellants’ claim 1 requires, as step (a), the generation of “a plurality of at least 100 sequence reads from a sample that has been enriched for a genomic region and obtaining a reference sequence for the genomic region” (App. Br. 11). Appeal 2019-002083 Application 14/288,299 7 Step (a) of Appellants’ claim 1 further requires that “the sequence reads are generated by: i. enriching for the genomic regions; and ii. sequencing the enriched genomic region” (id.). Step (b) of Appellants’ claim 1 requires that “the sequence reads [are assembled] to obtain a plurality of discrete sequence assemblies each of which correspond[] to a potential variant” (id.; see Ans. 4 (citing Spec. 5) (Examiner finds that Appellants’ Specification defines the term “‘assembling’ . . . as ‘aligning sequences that represent fragments of a longer nucleic acid’”)). Step (c) of Appellants’ claim 1 requires that “the sequence reads that make up each of the discrete sequence assemblies [are examined, using a computer,] to determine which of the potential variants are true and which are artifacts” (id.; see Ans. 4 (Examiner finds that the term “‘examining’ [is] not specifically defined [in Appellants’ Specification] and . . . [that the term] is general and broad on how it is to be performed to establish [a] ‘potential’ variant”)). Step (d) of Appellants’ claim 1 provides an optional requirement, wherein “each of the true potential variants [are evaluated to determine whether they] contain[] a mutation that is known to be associated with the reference sequence” (id.; see Ans. 4–5 (Examiner finds that this optional step is “not required nor specifically defined, but could be performed by search of [a] commercial database”)). Step (e) of Appellants’ claim 1 requires that “a true sequence variant in the sample [is identified] based on the determination of which variants are true and which variants are artifacts” (id.; see Ans. 5 (Examiner finds that the requirement of “‘identifying a true sequence variant in the sample based on the determination . . .’ [is] not defined and [represents a] broad general self- referring step that a true or artifact variant is identified”)). Appeal 2019-002083 Application 14/288,299 8 The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. Examiner finds that a judicial exception is found in method steps (b)– (e) of Appellants’ claim 1 (Ans.3 4; see also id. at 7–9). More specifically, Examiner finds that method steps (b)–(e) represent a mental process under the Revised Guidance. We agree with the Examiner’s finding because the steps comprise “examining,” “determining,” and “identifying,” which can be performed in the mind of the user. See Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1354 (Fed. Cir. 2016) (“analyzing information by steps people go through in their minds, or by mathematical algorithms, without more, [are] essentially mental processes falling within the abstract idea category”). Having determined that Appellants’ claim 1 recites a judicial exception, the Revised Guidance directs us to next consider whether the claims integrate the judicial exception into a practical application. On this record, we find tht Appellants’ claim 1 does not integrate the abstract idea, i.e., the mental process, into a practical application. To the contrary, Appellants’ claimed method directs a person of ordinary skill in this art to generate data, i.e., “a plurality of at least 100 sequence reads from a sample,” manipulate this data, and produce additional data, i.e., the identification of “a true sequence variant in the sample based on the 3 Examiner’s November 29, 2018 Answer. Appeal 2019-002083 Application 14/288,299 9 determination of which variants are true and which variants are artifacts” (see generally App. Br. 11). The claim identifies a “true sequence,” but does not do anything practical with the sequence, other than observe it. See Digitech Image Techs., LLC. v. Elecs. For Imaging, Inc., 758 F.3d 1344, 1351 (Fed. Cir. 2014) (“Without additional limitations, a process that employs mathematical algorithms to manipulate existing information to generate additional information is not patent eligible”); see also Gottschalk, 409 U.S. at 71–72 (holding that a computer based algorithm that merely transforms data from one form to another is not patent-eligible); cf. Diehr, 450 U.S. at 179 n.5 (the claims in Diehr recited a method for operating a rubber-molding press including the step of “opening the press automatically when a said comparison [of calculated cure time vs. elapsed time] indicates equivalence.” Thus, the recited mathematical equation in Diehr had the practical application of automatically operating a press). Therefore, on this record, we conclude that the ineligible subject matter in Appellants’ claim 1 is not integrated into a practical application. Having determined that the judicial exception is not integrated into a practical application, the Revised Guidance requires us to evaluate the additional elements of Appellants’ claimed invention, individually and in combination, to determine whether they provide an inventive concept, such as a specific limitation beyond the judicial exception that is not well- understood, routine, and conventional in the field, or instead simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception. See 84 Fed. Reg. 51. “Whether something is well-understood, routine, and conventional to a skilled artisan at the time of the patent, however, is a Appeal 2019-002083 Application 14/288,299 10 factual determination.” Berkheimer v. HP Inc., 881 F.3d 1360, 1369 (Fed. Cir. 2018). On this record, Examiner finds that Van Eijk4 discloses obtain[ing] enriched forms of DNA from the whole genome and the sequence information from multiple human biopsy samples and . . . methodology [to analyze the samples] for specific cancer associated sequences with a normal . . . reference sequence and provide a report of sensitivity as well as false positives/negatives as verification of the variants within a sample. (Ans. 6.) In addition, Examiner finds that Dahl5 discloses “a method of using massive parallel sequencing (MPS) for analysis and discovery of cancer mutations, more specifically for enriched genomic sequences by using purified DNA from cell lines and clinical blood samples, and provide enrichment through PCR for a variety of cancer associated genes” (id. at 5– 6). Examiner further finds that Boisvert6 provides for methods of assembly and analysis of sequence reads using de Bruijn graphs and the analysis of genomic sequences. In the comparison of assemblers and sequence data analysis, Boisvert . . . teaches that different methods and data for various depths are important in determining sequence variants and artifacts. (Id. at 6.) In addition, Appellants disclose: 4 R. Van Eijk et al., Sensitive and Specific KRAS Somatic Mutation Analysis on Whole-Genome Amplified DNA from Archival Tissues, 12 JOURNAL OF MOLECULAR DIAGNOSTICS 27–34 (2010). 5 F. Dahl et al., Multigene amplification and massively parallel sequencing for cancer mutation discovery, 104 PNAS 9387–9392 (2007). 6 S. Boisvert et al., Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies, 17 JOURNAL OF COMPUTATIONAL BIOLOGY 1519–1533 (2010). Appeal 2019-002083 Application 14/288,299 11 The sequence reads can be assembled to obtain a plurality of discrete sequence assemblies that each corresponds to a potential variant using a variety of different methods. Sequence reads may be assembled using any suitable method, basic steps of which are described in a variety of publications such as Myers et al. (Science 200 287: 2196–204), Batzoglou et al (Genome Research 2002 12: 177–89), Dohm et al (Genome Research 2007 17 : 1697–706) and Boisvert et al (Journal of Computational Biology 2010 17: 1519–33), which are al incorporated by reference for disclosure of those methods. (Spec. 10: 14–20.) Appellants further disclose that “[t]he use of de-Bruijn graphs to assemble reads is described in US Pat 8,209,130; U.S. Pub. 2011/0004413, U.S. Pub. 2011/0015863, and U.S. Pub. 2010/0063742” and a minimum de-Bruin [sic] sequence may be defined by a spanning subgraph, or tree of the directed weighted graph, using the BEST (de Bruijn, Ehrenfest, Smith and Tutte) theorem (which provides a product formula for the number of Eulerian circuits in directed (oriented) graphs, and relates the number of Eulerian circuits to the number of rooted spanning trees at a given vertex). Determining spanning trees of a directed graph may be achieved by any convenient method (see, e.g., Tarjan et al. Proc FOCS 1984 12-20). (Spec. 11: 7–9 and 21–27.) Based on Examiner’s findings and the evidence cited in Appellants’ Specification, we find that when elements of Appellants’ claimed invention are evaluated, individually and in combination, they simply append well- understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (see id. at 7–10; see also Spec. 10: 14–20, 11: 7–9, and 11: 21–27). For the foregoing reasons, we are not persuaded by Appellants’ contention that step (a) of Appellants’ claimed method “recites more than just generating or obtaining sequence data,” because step (a) requires that “a Appeal 2019-002083 Application 14/288,299 12 sample . . . has been enriched for a genomic region” and that “[t]he sequence reads are generated by: i. enriching for the genomic region; and ii. sequencing the enriched genomic region” and that Examiner failed to consider: “the combination of elements in claim 1” or “the claim as a whole” (App. Br. 4–5; see also Reply Br. 2–4). For the same reasons, we are not persuaded by Appellants’ contention that “the recitations of claim 1 include the physical step of generating sequencing reads from an enriched genomic region, specific steps that add meaningful limits, particularly with regard to the assembly of a plurality of discrete sequence assemblies, each of which corresponds to a potential variant” (id. at 6; see also id. at 10 (“Appellant[s] submit[] that the Office has failed to show that the additional elements recited in the dependent claims are well-understood, routine, or conventional”)). As discussed above, Appellants’ claimed method directs a person of ordinary skill in this art to generate data, i.e., “a plurality of at least 100 sequence reads from a sample,” manipulate this data, and produce additional data, i.e., the identification of “a true sequence variant in the sample based on the determination of which variants are true and which variants are artifacts” (see generally App. Br. 11). When considered as a whole, Appellants’ claimed invention is not directed to a practical application, and the additional elements of Appellants’ claim, when considered individually and in combination, simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception. Therefore, we are not persuaded by Appellants’ contention that their claimed method provides an improved technological result over the prior art (see App. Br. 6–8; see also Reply Br. Appeal 2019-002083 Application 14/288,299 13 4–6). Cf. McRO, Inc. v. Bandai Namco Games America Inc., 837 F.3d 1299, 1316 (Fed. Cir. 2016) (holding that the claim in that case is directed to a technological improvement over existing 3-D animation techniques and, therefore, not directed to an abstract idea); BASCOM Global Internet Servs., Inc. v. AT&T Mobility LLC, 827 F.3d 1341, 1351 (Fed. Cir. 2016) (holding that the ‘606 patent is claiming a technology-based solution (not an abstract idea based solution) to filter content on the Internet that overcomes existing problems with other Internet filtering systems); see generally Ans. 11–12. Further, the method of Appellants’ claim 1 does not transform matter; to the contrary, Appellants’ method, at best, transforms information, i.e., data. See Gottschalk, 409 U.S. at 71–72 (holding that a computer based algorithm that merely transforms data from one form to another is not patent-eligible). We are not persuaded by Appellants’ contention that Dahl fails to disclose step (b) of Appellants’ claimed invention, which is disclosed by Boisvert (App. Br. 8; cf. Ans. 6–7; see also Spec. 10: 14–20, 11: 7–9, and 11: 21–27). We are also not persuaded by Appellants’ contention that Examiner “does not identify anything in Boisvest [sic] . . . to show that assembling sequence reads from an enriched genomic region was conventional” (Reply Br. 6). On this record, notwithstanding Appellants’ unsupported assertion to the contrary, the weight of the evidence as cited by Examiner, and disclosed in Appellants’ Specification, weighs in favor of a finding that graph theory, a minimal de-Bruijn sequence, or a BEST theorem were well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality in Appellants’ claimed invention (see Ans. 6–7; see also Spec. 10: 14–20, 11: 7–9, and 11: 21–27). Appeal 2019-002083 Application 14/288,299 14 We are not persuaded by Appellants’ contention that “the combination of elements must not be well-understood, routine and conventional to a skilled artisan,” because Appellants’ claimed invention is free of a prior art rejection (see App. Br. 9). Initially, we note that the additional elements of Appellants’ claims, such as assembling the sequence reads using processes such as graph theory and using a computer to examine sequence reads, are computer based algorithms. “[T]he novelty of the mathematical algorithm is not a determining factor at all,” but is “treated as though it were a familiar part of the prior art.” Flook, 437 U.S. at 591–92. Appellants have given us no reason to depart from this guiding principle. As the Court in Flook explained, “[v]ery simply, our holding today is that a claim for an improved method of calculation, even when tied to a specific end use, is unpatentable subject matter under § 101.” Flook, 437 U.S. at 595 (fn. 18). Thus, Appellants’ additional elements, even if novel when combined, do not make the claim eligible for a patent under § 101. Further, we note that the Supreme Court cautioned that even though the § 101 patent-eligibility inquiry and prior art inquiries might sometimes overlap, “to shift the patent-eligibility inquiry entirely to these later sections risks creating significantly greater legal uncertainty, while assuming that those sections can do work that they are not equipped to do.” Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66, 90 (2012). See also Diamond v. Diehr, 450 U.S. 175, 188–89 (1981) (“[t]he ‘novelty’ of any element or steps in a process, or even of the process itself, is of no relevance in determining whether the subject matter of a claim falls within the § 101 categories of possibly patentable subject matter.”). Putting this into practice, the Federal Circuit has held that “a claim for a new abstract Appeal 2019-002083 Application 14/288,299 15 idea is still an abstract idea. The search for a § 101 inventive concept is thus distinct from demonstrating § 102 novelty.” Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1151 (Fed. Cir. 2016) (holding claims to a method for converting a hardware-independent user description of a logic circuit are ineligible because the use of assignment conditions as an intermediate step in the translation process is an aid to a mental process and does not change the nature of the claims to being directed to more than an abstract idea). Claims 10–12: Appellants contend that “claims 10 to 12 recite[] various techniques for assembling the sequence reads, such as using graph theory, a minimal de-Bruijn sequence, or a BEST theorem. These elements in combination with the elements recited in claim 1 are not well-understood, routine, or conventional” (App. Br. 10; see Reply Br. 7). We are not persuaded. For the reasons set forth above, we find that the weight of the evidence on this record weighs in favor of a finding that graph theory, a minimal de-Bruijn sequence, or a BEST theorem were well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality in Appellants’ claimed invention (see Ans. 6–7; see also Spec. 10: 14–20, 11: 7–9, and 11: 21–27). CONCLUSION OF LAW The preponderance of evidence of record fails to support Examiner’s finding that Appellants’ claimed invention is directed to patent ineligible subject matter. The rejection of claims 1 and 10–12 under 35 U.S.C. § 101 Appeal 2019-002083 Application 14/288,299 16 is affirmed. Claims 2–9 and 13–19 are not separately argued and fall with claim 1. 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 Copy with citationCopy as parenthetical citation