KONINKLIJKE PHILIPS N.V.

Patent Trials and Appeals Board

Mar 16, 2022

2021003063 (P.T.A.B. Mar. 16, 2022)

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. 15/502,924 02/09/2017 Sitharthan Kamalakaran 2014P00525WOUS 9410 24737 7590 03/16/2022 PHILIPS INTELLECTUAL PROPERTY & STANDARDS 1600 Summer Street 5th Floor Stamford, CT 06905 EXAMINER ARCHER, MARIE ART UNIT PAPER NUMBER 1631 NOTIFICATION DATE DELIVERY MODE 03/16/2022 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): marianne.fox@philips.com patti.demichele@Philips.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE __________ BEFORE THE PATENT TRIAL AND APPEAL BOARD __________ Ex parte SITHARTHAN KAMALAKARAN and JOSEPH N. PAULSON __________ Appeal 2021-003063 Application 15/502,924 Technology Center 1600 __________ Before ERIC B. GRIMES, JEFFREY N. FREDMAN, 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 calculating phylogenetic information for isolate identification. The Examiner rejected claims under 35 U.S.C. § 101 as directed to non-statutory subject matter, under 35 U.S.C. § 102 as anticipated, and under 35 U.S.C. § 103 as obvious. 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 Koninklijke Philips N.V. (see Appeal Br. 3). Appeal 2021-003063 Application 15/502,924 2 Statement of the Case Background “Healthcare-associated infections (HAIs) are patient-acquired infections received during healthcare treatment for conditions unrelated to the infection. . . . HAIs in the medical literature are often referred to as nosocomial infections” (Spec. ¶ 1). “There is a need to be able to track hospital-associated infections and determine the source of transmission to reduce the number of additional infections” (id. ¶ 3). For example, “[w]hen an infection, such as an HAI, is detected, samples may be collected by medical staff from patients, surfaces, food, equipment, or other suspected sources” (Spec. ¶ 21). “[T]he evolutionary distance distribution of infection isolate samples and/or reference sequences may be estimated. A new infection isolate sample’s evolutionary distance may be compared to the evolutionary distances of known reference sequences or previously analyzed infection isolate samples” (id. ¶ 46). “The source of transmission of an infection may then be determined based on which cluster the infection isolate sequence has the highest probability of inclusion” (id. ¶ 48). “The user may then use the determination of the infection source to coordinate efforts by the infection control staff to take measures to isolate and remove the source of infection” (id. ¶ 50). The Claims Claims 1-6, 14-20, 25, and 26 are on appeal. Independent claim 1 is representative and reads as follows with bracketed letters added to identify the elements: 1. A method, comprising: [a] receiving an electronic data representative of an infection isolate sequence; Appeal 2021-003063 Application 15/502,924 3 [b] comparing the electronic data representative of the infection isolate sequence to at least one reference sequence stored in a database; [c] determining variants between the infection isolate sequence and the at least one reference sequence; [d] determining at least a portion of an evolutionary history of the infection isolate based, at least in part, on the variants; [e] calculating, based at least in part on the portion of the evolutionary history, a phylogenetic metric of the infection isolate; [f] comparing the phylogenetic metric of the infection isolate to a phylogenetic metric of the at least one reference sequence; [g] determining, based at least in part, on a difference between the phylogenetic metric of the infection isolate and the phylogenetic metric of the at least one reference sequence, whether the infection isolate was transmitted by a first reservoir or a second reservoir, wherein each at least one reference sequence is associated with one of the first and second reservoirs; and [h] providing an indication of whether the infection isolate was transmitted by the first reservoir or the second reservoir. The Issues A. The Examiner rejected claims 1-4, 14, 17-20, 25, and 26 under 35 U.S.C. § 102(a)(2) as anticipated by Kreiswirth2 (Final Act. 12-15). B. The Examiner rejected claim 5 under 35 U.S.C. § 103 as obvious over Kreiswirth and Huelsenbeck3 (Final Act. 16). 2 Kreiswirth et al., US 2002/0120408 A1, published Aug. 29, 2002. 3 Huelsenbeck et al., Performance of Phylogenetic Methods in Simulation, 44(1) Systemic Biology 17-48 (1995). Appeal 2021-003063 Application 15/502,924 4 C. The Examiner rejected claim 6 under 35 U.S.C. § 103 as obvious over Kreiswirth and Britton4 (Final Act. 16-17). D. The Examiner rejected claims 15 and 16 under 35 U.S.C. § 103 as obvious over Kreiswirth and Dopazo5 (Final Act. 17-18). E. The Examiner rejected claims 1-6, 14-20, 25, and 26 under 35 U.S.C. § 101 as being directed to non-statutory subject matter (Final Act. 4-11). A. 35 U.S.C. § 102(a)(2) over Kreiswirth The issue with respect to this rejection is: Does a preponderance of the evidence of record support the Examiner’s finding that Kreiswirth anticipates the claims? Findings of Fact 1. Kreiswirth teaches “a system and method for performing real- time infection control over a computer network” because when there is a nosocomial infection a hospital may try to combat the outbreak by locating the source of the infection. The source could be a patient in the hospital, a health care worker, an animal, a contaminated object, such as a bronchoscope, a prosthetic device, the plumbing in a dialysis machine, or a myriad of other locations. It is thus very important that the hospital be able to locate the source of the infection. (Kreiswirth ¶¶ 11, 20). 4 Britton et al., Phylogenetic dating with confidence intervals using mean path lengths, 24 Molecular Phylogenetics and Evolution 58-65 (2002). 5 Dopazo, J., Estimating Errors and Confidence Intervals for Branch Lengths in Phylogenetic Trees by a Bootstrap Approach, 38 J. Mol. Evol. 300-04 (1994). Appeal 2021-003063 Application 15/502,924 5 2. Kreiswirth teaches, as to step [a] in claim 1 of receiving electronic infection isolate data, that a “region of the DNA that is sequenced has been predetermined to have desirable characteristics for infection tracking” in order to “distinguish epidemiologically related or clonal isolates, from unrelated isolates. Epidemiologically related isolates can be identified as being descendants from a common precursor cell” (Kreiswirth ¶¶ 73, 75). Kreiswirth teaches: If the DNA was sequenced by a hospital, health care facility or laboratory, then the digital sequence data is transmitted to infection control facility 148 via network 100. Otherwise, the digital sequence data is obtained from sequencer 146. In step 222, server 118 in infection control facility 148 stores the received sequence data and patient’s medical history in centralized database 128. (Kreiswirth ¶¶ 86-87). 3. Kreiswirth teaches, as to step [b] in claim 1 of comparing the isolate sequence to a database sequence, that “server 118 attempts to determine the identity of the species and subspecies of the bacteria by comparing the DNA of the bacterial isolate with other historical DNA data stored in the database” (Kreiswirth ¶ 88). 4. Kreiswirth teaches, as to step [c] in claim 1 of determining variants between the isolate sequence and a reference sequence, that “server 118 determines the relatedness of the bacterial isolate to other isolates stored in the database, by comparing the differences in the digital sequence data” (Kreiswirth ¶ 89). Kreiswirth teaches the bacterial isolate’s relatedness to other species/sub-species of bacteria is determined. The isolate’s sequence data is compared to other sequence data stored in the database taken from other Appeal 2021-003063 Application 15/502,924 6 isolates. When comparing two isolates, the software compares the two isolates, and a relative “cost” is calculated. The relative cost is a measure of the phylogenetic relatedness or phylogenetic distance between the two sequences being compared. A low relative cost would indicate a low number of differences between the two sequences and hence a high degree of relatedness. A high relative cost would indicate a high number of difference between the two sequences, and hence a low degree of relatedness. (Kreiswirth ¶ 105). 5. Kreiswirth teaches, as to step [d] in claim 1 of determining a portion of an evolution history of the infection isolate, that a phylogenetic tree can then be created by determining the relatedness of the bacterial strains to other bacterial isolate DNA data stored in the database. The phylogenetic tree depicts the relatedness of each subspecies of bacteria to other subspecies, and thus reveals the path of transmission. “Phylogenetically closely related” means that the isolates are closely related to each other in an evolutionary sense, and therefore have significant similarities in their DNA. (Kreiswirth ¶ 89). 6. Kreiswirth teaches, as to steps [e] and [f] in claim 1 of calculating a phylogenetic metric by comparison with the metric of a reference sequence, one approach is that an absolute cost could be calculated for each isolate. The absolute cost for an isolate can be calculated for each isolate by determining its phylogenetic distance from some predetermined reference sequence configuration. An absolute cost can be calculated for each individual isolate. The relatedness between isolates can then be determined based on comparison of their absolute costs. Thus, relative costs are generated by comparing sequences with each other, whereas absolute costs are generated by comparing each particular isolate with a reference configuration. Appeal 2021-003063 Application 15/502,924 7 (Kreiswirth ¶ 106). 7. Kreiswirth teaches, as to step [g] in claim 1 of determining the source of the infection isolate, that “[a]fter the costs are determined by comparing the isolate to a wide range of historical bacterial isolate data, in step 314, the position of the isolate in the phylogenetic tree is determined. This will allow for determination of the path of transmission of the bacteria” (Kreiswirth ¶ 125). Kreiswirth explains “the path of transmission of the bacteria can be determined based upon the position in the phylogenetic tree. For example, if a number of bacterial isolates have been emanating from the burn ward of a particular hospital, the hospital can be notified that it might have an outbreak problem” (id. ¶ 127). In another example, Kreiswirth teaches “server 118 could determine that an infection originated in the burn ward of a particular hospital, and then after one month, it spread to a cancer ward” (id. ¶ 91). 8. Kreiswirth teaches, as to step [h] of claim 1 of providing an indication of the infection isolate source that, for example, server 118 can determine that a hospital has had seven patients in the last month who have picked up the same or similar subspecies of S. aureus, and the infection is emanating from the burn ward. Server 118 then notifies the hospital that it may have an incipient outbreak occurring. The hospital can then take measures to correct the outbreak, and stop the infection from spreading. (Kreiswirth ¶ 96). 9. Kreiswirth teaches by sequencing multiple regions of the DNA, the bacteria can be classified into hierarchical levels of subspecies. This process is especially effective when gene 3 has a faster mutation rate than gene 2, which has a faster mutation rate that gene 1. Some Appeal 2021-003063 Application 15/502,924 8 genes may mutate too fast to be an effective tool, by themselves, for tracking infections. However, when sequenced in addition to other more slowly mutating genes, the information can be made useful by organizing the species into hierarchical levels. (Kreiswirth ¶ 137). Kreiswirth teaches “genes with slower rates of mutation are more suitable for long-term tracking of infections, such as tracking the global spread of an infection. Genes with faster rates of mutation are more suitable for short-term tracking of infections, such as tracking and controlling the real-time spread of an infection” (Kreiswirth ¶ 138). Kreiswirth teaches: The more time that passes, the more the bacterial DNA will mutate. These mutations allow a path of infection to be traced. For example, if two patients A and B are both carrying bacteria that have identical DNA sequences in a predetermined region of the DNA, then it is likely that patient A transmitted the bacteria to patient B, or vice versa, or patient A and patient B both obtained the bacteria from the same source within a short time frame. If the predetermined region DNA sequences from the two bacterial isolates are very different then they are probably from different strains and it is unlikely that transmission occurred between the two patients. If the DNA from the two bacteria are somewhat similar, than it can be determined that the two patients may have picked up the infection in the same institution. (Kreiswirth ¶ 74). 10. The Specification teaches: Replication rate, total replication, mutation rate, total nucleotide change and other metrics that represent a measure of phylogenetic relationship, phylogenetic status, reproductive or replication history of samples may be used in addition or as substitute to the metrics described herein. As such, any phylogenetic metric, measure, indicator, or predictor is within Appeal 2021-003063 Application 15/502,924 9 the scope of the present invention, and is hereinafter referred to as a phylogenetic metric. (Spec. ¶ 34). The Specification further teaches that [u]nder the assumption of a similar molecular clock, that is, a rate of evolution . . . [such as] mutation rates may be calculated for the different infection isolates. . . . If the replication rate of a pathogen is known for an environment, it may be determined that an infection isolate originated from that environment based on the calculated mutation rate. (Spec. ¶¶ 33-34). Principles of Law “A claim is anticipated only if each and every element as set forth in the claim is found, either expressly or inherently described, in a single prior art reference.” Verdegaal Bros. v. Union Oil Co. of California, 814 F.2d 628, 631 (Fed. Cir. 1987). Anticipation requires “that the reference describe not only the elements of the claimed invention, but also that it describe those elements ‘arranged as in the claim.’” Net MoneyIN, Inc. v. VeriSign, Inc., 545 F.3d 1359, 1371 (Fed. Cir. 2008). Analysis We adopt the Examiner’s findings of fact and conclusion of law (see Final Act. 12-15; FF 1-10) and agree that Kreiswirth anticipates the rejected claims. We address Appellant’s arguments below. Appellant contends that Kreiswirth fails to disclose, for example, a method for determining a transmission route of an infection isolate sequence where identified variants between the infection isolate sequence and a reference sequence are used to determine the evolutionary history of the infection isolate based [sic] and calculate a phylogenetic metric of the infection isolate relative Appeal 2021-003063 Application 15/502,924 10 to a phylogenetic metric of the reference sequence, and then making a determination based on the phylogenetic metric comparison whether the infection isolate was transmitted by a first reservoir or a second reservoir, where the reference sequence is associated with one of the first and second reservoirs. (Appeal Br. 20). We do not agree with Appellant. Kreiswirth teaches “determination of the path of transmission of the bacteria” “by comparing the isolate to a wide range of historical bacterial isolate data” because “the path of transmission of the bacteria can be determined based upon the position in the phylogenetic tree” (FF 7). Kreiswirth teaches that one way to compare these isolates uses an “absolute cost” metric, which reasonably falls within the broad scope of “phylogenetic metric” as recited in the Specification (FF 10). Specifically, Kreiswirth teaches that an “absolute cost [i.e., phylogenetic metric] for an isolate can be calculated for each isolate by determining its phylogenetic distance from some predetermined reference sequence configuration” (FF 6). This value can be used to generate a “phylogenetic tree [that] depicts the relatedness of each subspecies of bacteria to other subspecies, and thus reveals the path of transmission” (FF 5). And as to determining which reservoir was the source, Kreiswirth teaches an example where two possible reservoirs are discussed, a hospital burn ward and a cancer ward, and “server 118 could determine that an infection originated in the burn ward of a particular hospital, and then after one month, it spread to a cancer ward” (FF 7), thus determining that the infection isolate was initially transmitted in a first reservoir but was later transmitted by a second reservoir. Appeal 2021-003063 Application 15/502,924 11 The evidence therefore demonstrates that Kreiswirth teaches methods for determining transmission routes consistent with the requirements of claim 1. Appellant contends “Kreiswirth does not disclose a determination of a reservoir or transmission medium by comparing a mutation or transmission rate of an infection isolate to a mutation or transmission rate of the reference sequence” (Appeal Br. 20). And Appellant contends in response to the Examiner that “[v]ariants are mutations, and thus the phylogenetic metric is based on mutations. The comparison of mutations from an infection to mutations in a reference sequence is necessarily a determination of a mutation rate” (id. at 21). We are not persuaded and instead agree with the Examiner (see Ans. 20). In claim 1, the term “variant” is not an equivalent of the term “mutation rates.” The terms are not equivalent for identification of a reservoir of infective organisms. A “mutation rate” is a measure of the change in the number of mutations or variants in the nucleic acid sequences in an organism over time while a “variant” simply represents a particular sequence difference between two organisms (see FF 10). A rate of change is not reasonably understood as equivalent and identical to the change itself. Claim 1 does not use the term “mutation rate” but rather the term “variant.” Thus, as the Examiner correctly and sensibly notes, the argument regarding mutation rates and transmission rates lacks specific support in claim 1. Therefore “appellant’s arguments fail from the outset because . . . they are not based on limitations appearing in the claims.” In re Self, 671 F.2d 1344, 1348 (CCPA 1982). Appeal 2021-003063 Application 15/502,924 12 We also agree with the Examiner that Kreiswirth teaches the use of slower mutation rates for long term tracking and faster mutation rates for short term tracking (FF 9). The Examiner points to Kreiswirth’s exemplary teaching that: The more time that passes, the more the bacterial DNA will mutate. These mutations allow a path of infection to be traced. For example, if two patients A and B are both carrying bacteria that have identical DNA sequences in a predetermined region of the DNA, then it is likely that patient A transmitted the bacteria to patient B, or vice versa, or patient A and patient B both obtained the bacteria from the same source within a short time frame. If the predetermined region DNA sequences from the two bacterial isolates are very different then they are probably from different strains and it is unlikely that transmission occurred between the two patients. If the DNA from the two bacteria are somewhat similar, than it can be determined that the two patients may have picked up the infection in the same institution. (FF 9; cf. Ans. 21). This is reasonably understood as comparing the mutation rates of the sequences of two organisms and determining that, if they share the same sequence, they also share an infection source and a short time frame, but if they do not share closely related sequences, they do not share an infection source (see FF 9). Thus, even if the term “mutation rates” were incorrectly read into the claims, Kreiswirth teaches the use of such “mutation rates” for identifying a transmission reservoir. Conclusion of Law A preponderance of the evidence of record supports the Examiner’s finding that Kreiswirth anticipates the claims. Appeal 2021-003063 Application 15/502,924 13 B.-D. 35 U.S.C. § 103 Appellant does not substantively separately argue these obviousness rejections, instead relying upon their arguments to overcome Kreiswirth that we found unpersuasive above. The Examiner provides sound fact-based reasoning for combining Kreiswirth with Huelsenbeck, Britton, and Dopazo (see Final Act. 16-18). Having affirmed the anticipation rejection over Kreiswirth for the reasons given above, we also find that the further combinations render the rejected claims obvious for the reasons given by the Examiner. E. 35 U.S.C. § 101 The Examiner finds that the claims “encompass mental processes” and “encompasses a mathematical concept: calculating, based at least in part on the portion of the evolutionary history, a phylogenetic metric of the infection isolate” (Final Act. 5; emphasis omitted). The Examiner finds the claimed “combination of elements does not integrate the exception into a practical application because it does not impose any meaningful limits on practicing the abstract ideas” (id. at 7). The Examiner also finds the claims “do not recite additional steps or elements that integrate the recited judicial exceptions into a practical application of the exception(s)” (id.). We analyze the Examiner’s findings and Appellant’s arguments below. 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 Appeal 2021-003063 Application 15/502,924 14 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 Subject Matter Eligibility Guidance (“Guidance”).6 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. 6 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019). Appeal 2021-003063 Application 15/502,924 15 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 is 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 54-56. 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 Appeal 2021-003063 Application 15/502,924 16 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, the claims recite at least one judicial exception identified in the Guidance. Claim 1 recites a mental process because the process may be performed by a human (Guidance 53). In this situation, the ordinary artisan would be able to compare several DNA sequences composed of a list of four nucleotides to identify variants, to calculate a relationship between those variants, and use the determined evolutionary history to identify the source of an infection isolate. We do not rely on the Examiner’s mathematical concept reasoning as a judicial exception. Appellant contends the “claims are not directed to an abstract idea or a law of nature, but to a specific novel and non-obvious system and method for more accurately determining the route of transmission of a potentially deadly pathogen” (Appeal Br. 17). We are not persuaded. 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). Claim 1 simply uses performs a mental process using “electronic data” and a “database.” The claims do not require the database to be on a Appeal 2021-003063 Application 15/502,924 17 computer, and the use of such “electronic data” does not convert the ineligible mental process judicial exception into a patent eligible invention. We find the mental process in claim 1 analogous to that in SmartGene, where the Federal Circuit held that claims directed to “comparing new and stored information and using rules to identify medical options” did not satisfy Alice step one. See SmartGene, Inc. v. Advanced Biological Labs., SA, 555 F. App’x 950, 951-52, 955-56 (Fed. Cir. 2014) (nonprecedential). As in Smartgene, the “electronic data” recited in claim 1 does not rely on an inventive device or technique for displaying information or new computer systems or techniques, but rather relies on a mental process that “may allow an infection to be traced back to its source” (Spec. ¶ 20). This mental process is not patent eligible. See SmartGene, 555 F. App’x at 954 (holding claims were patent ineligible because they did “no more than call on a ‘computing device,’ with basic functionality for comparing stored and input data and rules, to do what doctors do routinely”). Appellant contends: “Given the enormous amount of data, this is not something that the human mind could perform in an entire lifetime. Genomic data from a single microorganism comprises thousands or millions of data points” (Appeal Br. 18). Appellant contends that “identifying all the variants between the infection isolate sequence and a reference sequence comprises many billions of calculations that a human mind could not complete in a lifetime, or multiple lifetimes” (id. at 19). Appellant contends “one of skill in the art would know that ‘comparing[’] . . . comprises entire genomes and thus comprises millions of base pairs” (id.). We are not persuaded by Appellant’s argument because it is not commensurate in scope with any of the claims. No claim requires Appeal 2021-003063 Application 15/502,924 18 comparison of even thousands of data points and no claim requires analysis of entire genomes. “[A]ppellant’s arguments fail from the outset because . . . they are not based on limitations appearing in the claims.” Self, 671 F.2d at 1348. We agree with the Examiner (see Ans. 18-19) that the claims are reasonably interpreted as encompassing an analysis of short diverse regions of microorganisms with limited numbers of variants that would be easily analyzed in the mind of an ordinary artisan. See In re Zletz, 893 F.2d 319, 321 (Fed. Cir. 1989) (“[D]uring patent prosecution when claims can be amended, ambiguities should be recognized, scope and breadth of language explored, and clarification imposed.”). As the Examiner has established a prima facie case that the claims recite mental processes, “the burden shifts to the applicant to come forward with rebuttal evidence or argument.” In re Brandt, 886 F.3d 1171, 1176 (Fed. Cir. 2018). No such evidence has been presented. Nor does Appellant provide any evidence that the process cannot practically be performed by pen and paper. We conclude, in agreement with the Examiner, that claim 1 recites the judicial exception of a mental process. Guidance Step 2A Prong 2 Having determined that claim 1 recites a judicial exception, 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 Appeal 2021-003063 Application 15/502,924 19 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 contends: The claimed invention provides a novel and specific solution to the ongoing challenge of tracking and preventing healthcare- or hospital-acquired infections (HAIs). When used in the analysis of pathogenic samples, for example, this is an important practical application of the claimed invention which can potentially save millions of dollars in unnecessary healthcare and can even save lives. (Appeal Br. 17-18). We are not persuaded because “[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). Claim 1 is therefore not eligible as instructing the artisan to use mental processes to identify an infection source by determining the phylogeny of the isolate using the steps of claim 1. Claim 1 does not include additional elements that are sufficient to amount to significantly more than the judicial exception. The Specification expressly relies on generic disclosures of databases, processing units, electronic displays, and computers (see Spec. ¶ 39). The Specification also Appeal 2021-003063 Application 15/502,924 20 relies on known sequencers, teaching the “infection isolate may be processed and sequenced according to a sequencing technology known in the art at Step 310. Examples of companies that provide sequencing technology include 454 Life Sciences, a Roche company and Pacific Biosciences” (Spec. ¶ 35). The Specification lastly recognizes the use of “reference sequences of known pathogens from public or private databases . . . . Variants may be found using existing software tools such as BWA- samstools and Golden Helix” (id.). Claim 1 lacks any physical or structural component that integrates the judicial exception of mental processes into any practical application that improves a computer itself. 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). “[G]enerally 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. Thus, limiting the method of claim 1 by requiring calculation of a phylogenetic metric does not integrate the judicial exception into a practical application. As discussed above, the mental process falls as a judicial exception 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 of any element of the claims. Indeed, our affirmance of the anticipation rejection over Kreiswirth above suggests that every element of the claim was known in the prior art. For the above reasons, Appellant has not shown that the Examiner erred in concluding that claim 1 does not integrate the recited judicial exception into a practical application. Appeal 2021-003063 Application 15/502,924 21 Guidance Step 2B Having concluded that claim 1 recites a judicial exception but does not integrate it into a practical application-i.e., that the claim is “directed to” an exception (Guidance 54)-we finally turn to whether the claim provides an “inventive concept,” i.e., whether the additional elements beyond the exception, individually and in combination, amount to more than the exception itself. 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. Appellant contends that rather than simply recite conventional steps appended to a judicial exception, the claims recite a specific multi-step method using a multi-component device or system that improves the determination of the route of transmission of an infection isolate. The components do not represent a simple generic computer system. Rather, the claims recite a novel, complicated system with much more than a generic computer or a processor. (Appeal Br. 19). We find this argument unpersuasive because, as already discussed above, we and the Examiner note that methods of using isolate sequence information for phylogenetic analysis to identify infection reservoirs was known as shown by the anticipation analysis over Kreiswirth discussed above (see FF 1-9). Appellant provides no evidence rebutting the Appeal 2021-003063 Application 15/502,924 22 Examiner’s findings that features of the claims were well-understood, routine and conventional (see Ans. 19). The use of a generic computer to perform generic computer functions that are “well-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 fails to present an “inventive concept” because the claim does not recite additional elements that provide “significantly more” than the recited judicial exception. 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 2-6, 14-20, 25, and 26 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 1-4, 14, 17-20, 25, 26 102(a)(2) Kreiswirth 1-4, 14, 17- 20, 25, 26 5 103 Kreiswirth, Huelsenbeck 5 6 103 Kreiswirth, Britton 6 15, 16 103 Kreiswirth, Dopazo 15, 16 Appeal 2021-003063 Application 15/502,924 23 Claims Rejected 35 U.S.C. § Reference(s)/Basis Affirmed Reversed 1-6, 14-20, 25, 26 101 Eligibility 1-6, 14-20, 25, 26 Overall Outcome 1-6, 14-20, 25, 26 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