Lexogen GMBHDownload PDFPatent Trials and Appeals BoardOct 20, 20212021000753 (P.T.A.B. Oct. 20, 2021) 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. 14/903,425 01/07/2016 Andreas Turk 011984-00001 5645 28827 7590 10/20/2021 GABLEGOTWALS 110 North Elgin Avenue, Suite 200 TULSA, OK 74120-1495 EXAMINER NEGIN, RUSSELL SCOTT ART UNIT PAPER NUMBER 1631 NOTIFICATION DATE DELIVERY MODE 10/20/2021 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): iplaw@gablelaw.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE __________ BEFORE THE PATENT TRIAL AND APPEAL BOARD __________ Ex parte ANDREAS TURK __________ Appeal 2021-000753 Application 14/903,425 Technology Center 1600 __________ Before JEFFREY N. FREDMAN, ULRIKE W. JENKS, and JOHN G. NEW, Administrative Patent Judges. FREDMAN, Administrative Patent Judge. DECISION ON APPEAL This is an appeal1 under 35 U.S.C. § 134 involving claims to a method of estimating transcript abundances using data generated from a sample sequenced by a sequencer. The Examiner rejected the claims under 35 U.S.C § 101 as directed to non-statutory subject matter. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. 1 We use the word “Appellant” to refer to “applicant” as defined in 37 C.F.R. § 1.42. Appellant identifies the Real Party in Interest as LEXOGEN GMBH (see Appeal Br. 3). Appeal 2021-000753 Application 14/903,425 3 Statement of the Case Background “An essential step in next generation sequencing is the library preparation or library prep for short. This process takes mRNA or cDNA as input and produces a library of short cDNA fragments, each corresponding to a section of an mRNA molecule” (Spec. 1) The Specification teaches “[t]hese fragments are then sequenced by an NGS [next generation sequencer] . . . This results in short sequences of nucleotides which are called reads” (id.). The Specification teaches that a prior art method called cufflinks “constructs a parsimonious set of transcripts that ‘explain’ the reads observed” and can use this information to “estimate the abundances of the transcript isoforms present in the sample” (id. at 1–2). The Specification teaches “to provide improved methods that allow a more accurate assessment of transcript abundances” (Spec. 2). The Claims Claims 1–20 are on appeal. Independent claim 1 is representative and reads as follows: 1. Method of estimating transcript abundances using data generated from a sample sequenced by a sequencer, the data including transcript fragment sequencing data from a potential mixture of fragments of a genetic locus of interest; the method being executed by a computer containing a computer program, the computer program including machine code for: a) assigning by the computer said transcript fragment sequencing data to genetic coordinates of said locus of interest thereby obtaining a data set of fragment genetic coordinate coverage, said coverage for each genetic coordinate combined forming a coverage envelope curve, b) setting by the computer a number of transcripts of said rnixture, Appeal 2021-000753 Application 14/903,425 4 c) pre-setting by the computer a probability distribution function of modelled genetic coverage for each transcript i, with i denoting the numerical identifier for a transcript, wherein said probability distribution function is defined by a weight factor i of said transcript i multiplied with the sum of at least 2 probability subfunctions j, with j denoting the numerical identifier for a probability subfunction, each probability subfunction j being independently weighted by a weight factor i,j, d) by the computer adding the probability distribution functions of each transcript to obtain a sum function, e) by the computer fitting the sum function to the coverage envelope curve thereby optimizing the values for i and i,j to increase the fit, f) by the computer repeating steps e) and f) until a pre-set convergence criterion has been fulfilled, g) obtaining the estimated transcript abundance for each transcript of the mixture given by the weight factor i as optimized after the pre-set convergence criterion has been fulfilled; and h) displaying the estimated transcript abundance for each transcript. The Issue The Examiner rejected claims 1–20 under 35 U.S.C. § 101 as being directed to non-statutory subject matter (Final Act. 2–3). The Examiner finds that the claims are “directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more” (Final Act. 2). The Examiner also finds the claims do “not include additional elements that are sufficient to amount to significantly more than the judicial exception (MPEP Section 2106.05) because the review article of Metzker [Genome Research, volume 15, 2005, Appeal 2021-000753 Application 14/903,425 5 pages 1767–1776] teaches that using sequencers to sequence genetic data is routine and conventional in the prior art” (id. at 3). The Alice Test 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. See, 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 if there is a judicial exception. “If a claim is directed essentially to a method of calculating, using a mathematical formula, even if the solution is for a specific purpose, the claimed method is nonstatutory.” Digitech Image Techs., LLC v. Elecs. for Imaging, Inc., 758 F.3d 1344, 1351 (Fed. Cir. 2014). If the claim is “directed to” a judicial exception, 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). Guidance The United States Patent and Trademark Office published guidance on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent Appeal 2021-000753 Application 14/903,425 6 Subject Matter Eligibility Guidance (“Guidance”).2 Under the Guidance, in determining what concept the claim is “directed to,” we first look to whether the claim recites: (1) any judicial exceptions, including “[l]aws of nature, natural phenomena, and abstract ideas,” (quoting Alice, 573 U.S. at 216) and/or 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) (Guidance Step 2A, Prong 1); and (2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)– (c), (e)–(h)) (Guidance Step 2A, Prong 2). 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 contains an “‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim: (3) adds a specific limitation beyond the judicial exception that are not “well-understood, routine and 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. (Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54–56. 2 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50–57 (January 7, 2019). Appeal 2021-000753 Application 14/903,425 7 Guidance Step 1 First, under “Step 1,” we consider whether the claimed subject matter falls within the four statutory categories set forth in § 101, namely “[p]rocess, machine, manufacture, or composition of matter.” Guidance 53– 54; see 35 U.S.C. § 101. Claim 1 recites a “method” and, thus, falls within the “process” category. Consequently, we proceed to the next step of the analysis. Guidance Step 2A Prong 1 Second, under “Step 2A Prong 1,” we evaluate “whether the claim recites a judicial exception, i.e., an abstract idea, a law of nature, or a natural phenomenon.” Guidance 54. In this case, claim 1 recites at least three judicial exceptions identified in the Guidance. Claim 1 relies upon mathematical concepts, specifically “a probability distribution function” that is “executed by a computer” (Guidance 52). Claim 1 also recites a mental process because the process can be performed by a human (id. at 53). The Federal Circuit has explained that the courts “continue to ‘treat[] analyzing information by steps people [could] go through in their minds, or by mathematical algorithms, without more, as essentially mental processes within the abstract-idea category.’” Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1146–47 (Fed. Cir. 2016). Lastly, claim 1 recites a natural correlation of transcript abundances in order “to infer which mRNA molecules were present in the original sample” (Spec. 18). In Claim 1, steps incorporating these the judicial exceptions are combined with data gathering and analysis steps that are “executed by a computer.” Steps (a) “assigning by the computer said transcript Appeal 2021-000753 Application 14/903,425 8 sequencing data” to obtain a data set (b) “setting by the computer a number of transcripts,” and (h) “displaying the estimated transcript abundance” gather or display data. Steps (c) pre-setting by the computer a particular probability distribution function, (d) summing the probability distribution functions of each transcript, (e) optimizing the values for i and i,j to increase fit, (f) repeating steps e) and f) to obtain convergence, (g) obtaining the estimated transcript abundance, and are directly drawn to the judicial exception of mathematical algorithms and mental processes. These steps also rely on the natural correlation between amount of transcript sequence data for particular mRNA transcripts generated from a sample and the amount of the physical transcript that is found in a particular sample. The Specification expressly states that the claim depends on a mathematical algorithm, stating the “invention provides a statistical model that is capable of learning simultaneously the bias of the read distribution along a transcript and the transcript abundances” (Spec. 4). The Specification provides a series of specific equations that are used to perform the analytical method (see Spec. 19, equation 1 to Spec. 26, equation 14). The Specification further recites “Mathematical foundations of the Mix2 model” (Spec. 26) and recites a series of equations from pages 27 to 39 of the Specification. And the courts have explained that, “if a claim is directed essentially to a method of calculating, using a mathematical formula, even if the solution is for a specific purpose, the claimed method is nonstatutory.” Parker v. Flook, 437 U.S. 584, 595 (1978). Appeal 2021-000753 Application 14/903,425 9 Claim 1 obtains specific information, analyzes that information using mathematical algorithms, and then displays the information. Claim 1 may obtain useful information, but claim 1 does not improve the computer itself or any other device. See Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1355 (Fed. Cir. 2016) (“[M]erely selecting information, by content or source, for collection, analysis, and display does nothing significant to differentiate a process from ordinary mental processes.”). Appellant does not identify any teaching in the Specification that actually improves either the computer or the physical components of the system. Appellant contends Appellant quantitatively demonstrates how the claimed method is “far superior” in terms of its accuracy relative to the Cufflinks model, “most common method" for estimating transcript abundances – see id. at page l, line 35–36; page 48, lines 1– 11 & Tbl. 9 – as well as more accurate than other prior art methods. (Appeal Br. 12). We find this argument unpersuasive because “it is not enough, however, to merely improve a fundamental practice or abstract process.” Customedia Techs., LLC v. Dish Network Corp., 951 F.3d 1359, 1364 (Fed. Cir. 2020). Instead, to “be a patent-eligible improvement to computer functionality, we have required the claims to be directed to an improvement in the functionality of the computer or network platform itself.” Id. As in the situation in claim 1, the Federal Circuit “held patent ineligible claims directed to ‘selecting certain information, analyzing it using mathematical techniques, and reporting or displaying the results of the analysis.’” SAP Am., Inc. v. InvestPic, LLC, 898 F.3d 1161, 1167–68 (Fed. Cir. 2018). Appeal 2021-000753 Application 14/903,425 10 Therefore, we find that claim 1 recites the judicial exceptions drawn to abstract ideas including mathematical concepts, mental processes and to a law of nature. 3. Guidance Step 2A Prong 2 Having determined that claim 1 recites judicial exceptions, we proceed to “Step 2A Prong 2” of the Guidance, which requires that we evaluate whether “the claim as a whole integrates the recited judicial exception into a practical application of the exception.” Id. at 54. “A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that the claim is more than a drafting effort designed to monopolize the judicial exception.” Id.; see Mayo, 566 U.S. at 78. The Guidance specifies that this evaluation is conducted by first “[i]dentifying whether there are any additional elements recited in the claim beyond the judicial exception(s), [then] ‘evaluating those additional elements individually and in combination to determine whether they integrate the exception into a practical application.’” Guidance 54–55. Appellant cites to three board decisions, Ex Parte Chan, Appeal 2018- 009183 (drawn to a method of measuring an analyte using mass spectrometry), Ex Parte Olsen, Appeal 2017-006489 (drawn to registering a catheter navigation system with fiducials), and Ex parte Smith, Appeal 2018- 000064 (drawn to a method of trading derivatives on an exchange) (see Appeal Br. 14–15). Appellant asserts “there is no requirement that a judicial exception that is integrated into a practical application save computational Appeal 2021-000753 Application 14/903,425 11 time, reduce cost, or use less computational resources than conventional techniques” (id. at 15). We first note that none of these decisions is precedential, nor do any of these decisions involve the use of mathematical algorithms as clearly as in the instant case, which expressly recites the use of a “probability distribution function” as the central inventive element of claim 1. We also recognize that the method uses DNA sequencing (see, e.g., Appeal Brief 17) but the method of claim 1 is not drawn to an improvement in DNA sequencing itself, but rather to analysis of data obtained from DNA sequencing by any method whatsoever. Indeed, claim 1 encompasses the use of any sequencing device, and even data already generated, and after performing the mathematical analysis, displays the results of the analysis. Even if we agree that integration need not necessarily improve the operation of a computer, depending on the type and nature of the judicial exception and the technology at issue, “[a]n inventive concept that transforms the abstract idea into a patent-eligible invention must be significantly more than the abstract idea itself, and cannot simply be an instruction to implement or apply the abstract idea on a computer.” BASCOM Glob. Internet Servs., Inc. v. AT&T Mobility LLC, 827 F.3d 1341, 1349 (Fed. Cir. 2016). Here, the claim simply instructs the artisan to apply the mathematical algorithm as “executed by a computer” that analyzes data to obtain and display analyzed data as a result. Claim 1 does “not include additional elements that are sufficient to amount to significantly more than the judicial exception. The Specification expressly relies upon known prior art next generation sequencing methods (Spec. 1 and teaches “a computer program product employing said method, Appeal 2021-000753 Application 14/903,425 12 e.g. containing machine code to perform or assist in said methods and steps on a computer. The computer program product can be provided on any kind of memory device” (Spec. 3). The Specification teaches the “abundance information can be displayed on an output device, such as a video screen, a printer or a computer readable medium” (Spec. 13). Claim 1 lacks any physical or structural component that integrates the judicial exceptions of the mathematical algorithms into any practical application that improves the computer system itself, the sequencer itself, or any particular device. The only improvement recited, if any, is to the judicial exception of the mathematical algorithm itself and the application of the mathematical algorithm on data gathered by known means. Appellant contends “a claim cannot recite significantly more if an examiner is permitted to remove the significantly more from the claim language. Had the Diehr Court followed this same approach, the rubber curing mold would have been removed from the claim along with other limitations leaving only the Arrhenius equation” (Appeal Br. 19). We find this argument unpersuasive because it is exactly backward. The approach, whether in Diehr or here, looks to see whether the mathematical equation used directs physical steps into something “significantly more”. In Diehr, that was properly cured rubber from the mold. Here, the method takes one type of data and transforms it into another type of data without any improvement in the sequencing device, the computer display, or anything structural or physical at all. Step 2A Prong 2 requires that only “any additional elements recited in the claim beyond the judicial exception(s)” be considered. Guidance 54–55 (emphasis added). As discussed above, the algorithm and mathematical Appeal 2021-000753 Application 14/903,425 13 analysis of RNA abundances fall under the judicial exceptions to § 101. Appellant does not provide any rebuttal evidence, whether in the form of references, a Declaration, or other disclosure, demonstrating that the ordinary artisan was unaware that nucleic acid sequences could be analyzed for their abundance levels. Indeed, the Specification supports our understanding by teaching prior art methods include a method called Cufflinks (Spec. 1) and that this prior art Cufflinks method “can estimate the abundances of the transcript isoforms present in the sample, either using a known reference annotation, or after an ab-initio assembly of the transcripts using only the reference genome” (Spec. 2). We note that “add[ing] insignificant extra-solution activity to the judicial exception” is insufficient to integrate the exception into a practical application (Guidance 55). Data gathering steps typically constitute such insignificant extra-solution activity. See Mayo, 566 U.S. at 79 (concluding that additional element of measuring metabolites of a drug administered to a patient was insignificant extra-solution activity); OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363 (Fed. Cir. 2015) (holding that mere data gathering is insufficient to confer patent eligibility). Moreover, “generally link[ing] the use of a judicial exception to a particular technological environment or field of use” is insufficient to integrate a judicial exception into a practical application. Guidance 55. See Parker, 437 U.S. at 595 (determining that limiting an ineligible alarm limit calculation to specific process variables in a chemical process was insufficient for patent eligibility). Thus, limiting the method of claim 1 by Appeal 2021-000753 Application 14/903,425 14 requiring a preliminary known and routine sequencing process does not integrate the judicial exception into a practical application. For the above reasons, Appellant has not shown that the Examiner erred in concluding that claim 1 does not integrate the recited judicial exceptions into a practical application. 4. Guidance Step 2B Having concluded that claim 1 recites judicial exceptions but does not integrate them into a practical application—i.e., that the claim is “directed to” those exceptions (Guidance 54)—we finally turn to whether the claim provides an “inventive concept,” i.e., whether the additional elements beyond the exceptions, individually and in combination, amount to “significantly more” than the exceptions themselves. Id. at 56. According to the Guidance, “[a]dd[ing] a specific limitation or combination of limitations that are not well-understood, routine, conventional activity in the field” may indicate an inventive concept is present. Id. Conversely, “simply append[ing] well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality,” typically indicates an inventive concept is absent. Id. As already discussed above, we note that the Specification itself demonstrates that the use of sequencing to obtain RNA abundance information not novel, referencing “Cufflink can estimate the abundances of transcript isoforms” (Spec. 2) As discussed above, we find that the only “additional” elements recited in claim 1 is the mathematical algorithm and law of nature associated with the particular optimized RNA abundance algorithm. The use of a generic computer to perform generic computer functions that are “well- Appeal 2021-000753 Application 14/903,425 15 understood, routine, conventional activit[ies]” previously known in the industry is not enough to transform the abstract idea into a patent-eligible invention. See Alice, 573 U.S. at 225–26. Thus, for the reasons explained above, we agree with the Examiner that claim 1 “simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality,” and, thus, fails to present an “inventive concept” because the claim does not recite additional elements that provide “significantly more” than the recited judicial exceptions. See Guidance 56. Therefore, we sustain the Examiner’s rejection of claim 1 as ineligible subject matter under § 101. As a result, we also sustain the rejection of claims 2–20 under § 101. See 37 C.F.R. § 41.37(c)(1)(iv). DECISION SUMMARY In summary: Claims Rejected 35 U.S.C. § Reference(s)/Basis Affirmed Reversed 1–20 101 Eligibility 1–20 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