DETAILED ACTION
The Applicant’s response, received 09 April 2026, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.
Applicant's submission filed on 09 April 2026 has been entered.
Status of the Claims
Claims 1-17, 21-30, 32, and 33 are pending.
Claims 12-14 are withdrawn.
Claims 1-11, 15-17, 21-30, 32, and 33 are rejected.
Priority
This application is a CIP of PCT/US2019/056713, filed 17 October 2019, which claims benefit of 62/746,997, filed 17 October 2018.
This application claims benefit of 62/902,950, filed 19 September 2019, and claims benefit of 62/873,693, filed 12 July 2019, and claims benefit of 62/804,458, filed 12 February 2019.
Claims 1-11, 15-17, 21-30, 32, and 33 are not given the benefit of priority to 62/746,997, filed 17 October 2018, because there is not support for the specific limitations regarding quality control (QC) testing on sequencing results and generating QC scores as recited in independent claim 1.
Claims 1-11, 15-17, 21-30, 32, and 33 are not given the benefit of priority to 62/804,458, filed 12 February 2019, because there is not support for the specific limitations regarding quality control (QC) testing on sequencing results and generating QC scores as recited in independent claim 1.
Claims 1-11, 15-17, 21-30, 32, and 33 are given the benefit of priority to 62/873,693, filed 12 July 2019.
Therefore, the effective filing date of the claimed invention is 12 July 2019.
Claim Rejections - 35 USC § 112
The Applicant’s amendment and arguments/remarks received 09 April 2026 have been fully considered, however after further consideration, the rejection of claim 10 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, in the Office action mailed 09 January 2026 is maintained in view of the amendment and arguments/remarks.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-11, 15-17, 21-30, 32, and 33 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Specifically, claim 1 was amended (claim set received 29 September 2025) to recite a six microservice configured to provide a “match between the subject and one or more therapies, the match being based on at least the subject’s TMB status,” which appears to be a new limitation not supported by the specification. More specifically, the specification and the art of record fails to provide any support or guidance to therapies associated with TMB status. In review of the specification, support is not found for matching any particular TMB statuses with any appropriate particular therapy. While the specification and the art of record supports that there are specific informative mutants which can be treated in particular or specific ways, there is no evidence nor guidance for a generic TMB status (i.e., not a particular status, e.g. TMB-H (high)), and any of “one or more therapies” as amended. While it is acknowledged the assessing TMB is not new and that the art in general supports that it is a process that can be observed in some cancer states or progressions (i.e., not all), neither the instant specification nor the art of record provides for specific therapies that are matched with particular TMB statuses (e.g., TMB-high (TMB-H)).
Providing evidence not present that this is known or amending the claims to be consistent with the art and generic guidance of the specification for known correlations could address the basis of the rejection.
Claims 2-11, 15-17, 21-30, 32, and 33 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, for depending from claim 1 and for failing to remedy the failure of claim 1 to comply with the written description requirement.
Response to Arguments
The Applicant’s arguments/remarks received 09 April 2026 have been fully considered, but are not persuasive.
The Applicant points to Moba B.V. v. Diamond Automation, Inc., on page 10 (para. 4) of the Remarks and states that the written description requirement merely requires that an applicant “convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention” and further points to Union Oil Co. of Cal. v. Atlantic Richfield Co., and further states that the “written description does not require the applicant to ‘describe exactly the subject matter claimed, [instead] the description must clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed.” The Applicant further states (para. 5) that the Office action does not dispute that the specification supports the report providing a match between the subject and one or more therapies, and further states that FIG. 17a shows “an exemplary first page of a report screenshot indicating the results of one RNA sequencing process” and this exemplary report lists “treatment implications” and their relationship to gene expression, and further points to FIGS. 18, 18a, 18b; and para. [0280] (numbering as published). The Applicant further states on page 11 (para. 1) of the Remarks that the Applicant’s disclosure as filed includes a description of “a therapy matching engine 1358 [that] may match therapies based on the information stored in database 160, and one example, the therapy matching engine 1358 matches therapies at the gene level and uses variant-level information to rank the therapies within a case (para. [0259]) and information from the therapy matching engine 1358 is used to generate “pdf or other format reports 1468… for consumption” (para. [0261]; FIG. 11c). The Applicant further states (para. 2) that the disclosure shows that therapy matching may be performed based on “the broad molecular profiling done in the xT gene panel” using information such as CNVs, SNVs, indels, gene expression calls, fusion detection, and immunotherapy biomarker assays (paras. [0353], [0360]), and further states that immunotherapy response itself is based on TMB, e.g., RNA expression based TMB (“xTMB”) is disclosed as having predictive power for immunotherapy response in view of its representation of “what mutations are visible to the responding immune cells” (para. [0371]). The Applicant further states that because the disclosure states that therapy matching may be based on immunotherapy assays and that immunotherapy assays may be based on TMB, the disclosure provides support for the claim feature in question.
These arguments are not persuasive, at least because claim 1 recite the limitation “a match between the subject and one or more therapies, the match being based on at least the subject’s TMB status” but in review of the specification, support is not found for matching any particular TMB statuses with any appropriate particular therapy, i.e., TMB is not a reliable predictor for all cancer types, and immunotherapy broadly stated is not a particular therapy for a cancer, because the term “immunotherapy” is a broad, general class of cancer treatments, within which are different categories of immunotherapies each with particular therapies that are not broadly applicable to all cancers and tissue types. Furthermore, claim 1 does not even limit the “one or more therapies” to an immunotherapy. Therefore, the Applicant’s assertion that “because the disclosure states that therapy matching may be based on immunotherapy assays and that immunotherapy assays may be based on TMB, the disclosure provides support for the claim feature in question” is not persuasive.
The Applicant states on page 11 (para. 3) of the Remarks that in addition to the general description summarized above, the disclosure provides particular examples in which a report is generated including the TMB status and a matched therapy based on the TMB status, and in one illustrative example of the claimed invention, a report is presented to the physician that “includes an approved therapies list 1802 and a pertinent genes list 1804” (paras. [0281]-[0282], FIGS. 18-18a), and that this provides a matching between the subject’s TMB and treatments consistent with guidelines (para. [0284], describing “an indication that an immunotherapy, such as an FDA approved immunotherapy, may be appropriate to prescribe the patient”).
This argument is not persuasive, for the reasons provided in the foregoing response to arguments, and further because the immunotherapies described at the referenced paragraphs in the disclosure are broad categories of therapies (e.g., anti-CD47) and not particular therapies (i.e., drugs and/or agents), and as discussed above, support is not found in the disclosure for matching any particular TMB statuses with any appropriate particular therapy. Furthermore, claim 1 does not even limit the “one or more therapies” to an immunotherapy. Therefore, the Applicant’s previously discussed assertion that “because the disclosure states that therapy matching may be based on immunotherapy assays and that immunotherapy assays may be based on TMB, the disclosure provides support for the claim feature in question” is not persuasive.
The Applicant states on page 11 (para. 4) of the Remarks that in another illustrative example, a report is generated “summarizing the results from the bioinformatics pipeline, including the designation as TMB-high, and what clinical trials and therapies may be most relevant to the patient’s particular genome including those that are effective for TMB-high patients” (para. [0448]), wherein one particular patient, for example, is disclosed as the subject of a report that includes both “the patient’s TMB status” and a matched therapy of “immunotherapy based upon the finding of a TMB-high status” (paras. [0452]-[0453]). The Applicant further states (para. 5) that the disclosure further provides an example in which a microservice (in this example, referred to as the “fourth” microservice) reports curated information that includes both “the generated TMB status and the implications of any curated information to the physician to complete the order (para. [0445]), and that these implications are elsewhere referred to as “treatment implications” and are thus indicative of a match to a therapy (para. [0280]). The Applicant further states on page 12 (para. 2) that in addition to the above-noted figures and written description, the claims themselves as originally filed expressly recite an example in which the report itself presents a matched treatment recommendation that is based on the subject’s TMB status (i.e., claim 30, claim set received 12 December 2020).
These arguments are not persuasive, at least for the reasons provided above in the foregoing responses to arguments, and further because the originally filed claim 30 limitation reciting “the at least one clinical report comprises listing immune checkpoint blockade inhibitors as a treatment when the TMB status is TMB-high” does not provide support for matching any TMB status with any particular therapy.
Claim Rejections - 35 USC § 101
The amendment received 09 April 2026 has been fully considered, however after further consideration, the rejection of claims 1-11, 15-17, 21-30, 32, and 33 in the Office action mailed 09 January 2026 is maintained with modification in view of the amendment.
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-11, 15-17, 21-30, 32, and 33 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion).
Claim Interpretations
Claim 1 recites the limitation “structured databases.” This limitation is interpreted to refer to how data is organized, i.e., structured (e.g., for purposes of manipulation and/or storage (e.g., substitute specification at para. [00171]); and structured querying of tabular data entities, e.g., disease type and level of evidence (e.g., substitute specification at para. [00332])).
Claims 1, 9, 28, 29, and 33 recite the term “microservice.” This term is interpreted to describe a program (i.e., a software program) that manipulates (i.e., processes) data to condition or shape the data to generate new interim data or to structure data in different structured formats for consumption by user application programs (substitute specification, page 27, ¶ [00159]). The limitations reciting “microservice configured to [action]” (e.g., receive, execute, generate, provide) are further interpreted as programming of the microservice, wherein one or more such microservices may be part of an order management system that orchestrates the sequence of events as needed at the appropriate time and in the appropriate order (e.g., substitute specification, page 98, para. [00452]). Additional support for the interpretation of the term “microservice” can be found in Dragoni et al. (arXiv:1606.04036v4 [cs.SE], 2017, https://doi.org/10.48550/arXiv.1606.04036, pp. 1-17, as cited in the Office action mailed 27 May 2025).
Claim 15 recites the term “actionable oncology mutations.” This term is interpreted to mean gene variants that, if detected, would be expected to affect patients’ response to treatment, and therefore can influence treatment decisions (substitute specification, pages 47-48, ¶ [00231]). This term is interpreted to be synonymous with the term “tier 1 genes.”
Claim 16 recites the term “Tier 1 genes.” This term is interpreted to mean genes that can influence treatment decisions (substitute specification, pages 47-48, ¶ [00231]) and that are linked with response or resistance to targeted therapies, resistance to standard care, or toxicities associated with treatment (substitute specification, pages 47-48, ¶ [00231]). This term is interpreted to be synonymous with the term “actionable oncology mutations.”
Claim 1 recites the term “data consume.” This term is interpreted to mean a process of transforming raw data into processed information that is suitable for use in a subsequent process step (substitute specification, page 2, ¶¶ [0006] & [0009]; page 10, ¶ [0010]; page 12, ¶ [0042]; page 14, ¶¶ [0048] - [0051]; page 32, ¶ [00173]; page 33, ¶ [00179]; page 35, ¶ [00183]; and page 57, ¶ [00269]).
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Step 1 of the eligibility analysis asks: Is the claim to a process, machine, manufacture or composition of matter?
Claims 1-11, 15-17, 21-30, 32, and 33 are directed to a system (i.e., a machine or manufacture) for conducting genomic sequencing.
Therefore, these claims are encompassed by the categories of statutory subject matter, i.e., each claim as a whole falls within one or more statutory categories, and thus satisfy the subject matter eligibility requirements under step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim.
Independent claim 1 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
a plurality of differently structured databases (i.e., data and/or software for managing/operating the database) (i.e., mental processes);
a first microservice (i.e., a software program) configured to receive… (i.e., generate a data product) (i.e., mental processes);
a second microservice (i.e., a software program) configured to execute… (i.e., generate a data product) (i.e., mental processes);
a third microservice (i.e., a software program) configured to execute… (i.e., generate a data product) (i.e., mental processes);
a fourth microservice (i.e., a software program) configured to execute (i.e., generate a data product) (i.e., mental processes) quality control (QC) testing on the germline sequencing results to generate a germline QC score and on the somatic sequencing results to generate a somatic QC score (i.e., mental processes and mathematical concepts);
a fifth microservice (i.e., a software program) configured to generate (i.e., generate a data product) (i.e., mental processes) at least one clinical report, wherein the clinical report comprises a tumor mutational burden (TMB) status associated with the subject, wherein the TMB status is based at least in part on the identified sequences of nucleotides in the germline specimen and identified sequences of nucleotides in the somatic specimen (i.e., mental processes and mathematical concepts), and wherein the TMB status is determined based on:
(i) mutations in the germline sequencing results and a panel size of the targeted-panel when the germline QC score is above a passing threshold and the somatic QC score is below a passing threshold (i.e., mental processes and mathematical concepts);
(ii) mutations in the somatic sequencing results and the panel size of the targeted-panel when the somatic QC score is above the passing threshold and the germline QC score is below the passing threshold (i.e., mental processes and mathematical concepts); and
(iii) mutations in the somatic sequencing results, mutations in the germline sequencing results, and the panel size of the targeted-panel when the somatic QC score is above the passing threshold and the germline QC score is above the passing threshold (i.e., mental processes and mathematical concepts); and
a sixth microservice (i.e., a software program) configured to provide (i.e., generate a data product) (i.e., mental processes) at least one clinical report to the physician, the at least one clinical report comprising the subject's TMB status and a match between the subject and one or more therapies, the match being based on at least the subject’s TMB status (i.e., mental processes);
each microservice includes a data consume definition (i.e., mental processes); and
each microservice generates a data product (i.e., mental processes).
Dependent claims 9-11, 21-30, and 33 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below:
Dependent claim 9 further recites:
a seventh microservice (i.e., a software program) configured to execute (i.e., generate a data product) (i.e., mental processes);
Dependent claim 10 further recites:
the second microservice and the third microservice are respectively configured to identify mutations by aligning each respective sequence read in the respective pluralities of sequence reads to a reference genome (i.e., mental processes).
Dependent claim 11 further recites:
wherein the TMB status is calculated from mutations identified in the subject's DNA (i.e., mental processes and mathematical concepts).
Dependent claim 21 further recites:
wherein the TMB status is determined as TMB-high when the subject's TMB is greater than 9 mutations per megabase (i.e., mental processes and mathematical concepts).
Dependent claim 22 further recites:
wherein the TMB status is determined as TMB-low when the subject's TMB is less than 9 mutations per megabase (i.e., mental processes and mathematical concepts).
Dependent claim 23 further recites:
wherein the mutations are identified from only non-synonymous mutations comprising fusions, non-silent somatic coding mutations, missense, insertions, deletions, and stop-loss variants (i.e., mental processes).
Dependent claim 24 further recites:
wherein the somatic QC score passing threshold is based at least in part on mutations having coverage greater than 100x and an allelic fraction greater than 5% (i.e., mental processes and mathematical concepts).
Dependent claim 25 further recites:
wherein the germline QC score passing threshold is based at least in part on mutations having coverage greater than 100x and an allelic fraction greater than 5% (i.e., mental processes and mathematical concepts).
Dependent claim 26 further recites:
wherein the germline QC score passing threshold is not met when a germline specimen is not available to the system (i.e., mental processes).
Dependent claim 27 further recites:
wherein the somatic QC score passing threshold is not met when a somatic specimen is not available to the system (i.e., mental processes).
Dependent claim 28 further recites:
wherein the first microservice is initiated when the system receives the order from the physician (i.e., mental processes);
the second microservice is initiated when the first microservice terminates (i.e., mental processes);
the third microservice is initiated when the first microservice terminates (i.e., mental processes);
the fourth microservice is initiated when both the second and third microservices terminate (i.e., mental processes);
the fifth microservice is initiated when the fourth microservice terminates (i.e., mental processes); and
the sixth microservice is initiated when the fifth microservice terminates (i.e., mental processes).
Dependent claim 29 further recites:
wherein the first microservice is initiated when the system receives the order from the physician (i.e., mental processes);
the second microservice is initiated when the first microservice terminates (i.e., mental processes);
the third microservice is initiated when the first microservice terminates (i.e., mental processes);
the fourth microservice is initiated when both the second and third microservices terminate (i.e., mental processes);
the seventh microservice is initiated when the fourth microservice terminates (i.e., mental processes);
the fifth microservice is initiated when the seventh microservice terminates (i.e., mental processes);
the sixth microservice is initiated when the fifth microservice terminates (i.e., mental processes).
Dependent claim 30 further recites:
wherein the at least one clinical report comprises listing immune checkpoint blockade inhibitors as a treatment when the TMB status is TMB-high (i.e., mental processes).
Dependent claim 33 further recites:
wherein the second microservice (i.e., a software program) is configured to output… (i.e., generate a data product) (i.e., mental processes); and
wherein the third microservice (i.e., a software program) is configured to output… (i.e., generate a data product) (i.e., mental processes).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper (e.g., configuring microservices) and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., determining a TMB status based on QC scores and passing thresholds) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Generating data products for use by other applications comprises processing information that can be practically be performed in the human mind with or without a physical aid and/or operated on mathematically (see MPEP 2106.04(a)(2)).
Therefore, claims 1-11, 15-17, 21-30, 32, and 33 recite an abstract idea.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). 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. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
Dependent claims 10, 11, 21-27, and 30 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements in independent claim 1 include:
one or more computers in communication;
receive data;
output data;
a germline specimen and a somatic specimen;
next generation sequencing (NGS) of a subject’s germline and somatic specimen; and
a targeted panel (i.e., to identify sequences of nucleotides in the germline specimen and in the somatic specimen);
operate independent of the other system resources (i.e., computer and/or computer related components allowing for different software programs to run independently); and
the system is configured to store the germline sequencing results, the somatic sequencing results, the germline QC score, the somatic QC score, and the at least one clinical report as purpose-specific data structures in the respective ones of the plurality of differently structured databases based on at least one of a format, a processing status, or an associated application (i.e., store data).
The additional elements in dependent claims 2-9, 15-17, 28, 29, 32, and 33 include:
wherein the germline sequencing results and the somatic sequencing results include respective pluralities of sequence reads generated from short-read, paired-end NGS (claim 2);
wherein the targeted-panel comprises a plurality of probes; wherein each probe in the plurality of probes uniquely targets a respective portion of a reference genome; and wherein each sequence read in the respective pluralities of sequence reads corresponds to at least one probe in the plurality of probes (claim 3);
wherein the respective pluralities of sequence reads have an average depth of at least 50X across the plurality of probes (claim 4);
wherein the respective pluralities of sequence reads have an average depth of at least 400X across the plurality of probes (claim 5);
wherein the plurality of probes includes probes for at least three hundred different genes selected from a predetermined group of genes (claim 6);
wherein the somatic specimen comprises macro dissected formalin fixed paraffin embedded (FFPE) tissue sections, surgical biopsy, skin biopsy, punch biopsy, prostate biopsy, bone biopsy, bone marrow biopsy, needle biopsy, CT-guided biopsy, ultrasound-guided biopsy, fine needle aspiration, aspiration biopsy, fresh tissue or blood samples, and the germline specimen comprises blood or saliva from the subject (claim 7);
wherein the somatic specimen is of a breast tumor, a glioblastoma, a prostate tumor, a pancreatic tumor, a kidney tumor, a colorectal tumor, an ovarian tumor, an endometrial tumor, a breast tumor, or a combination thereof (claim 8);
a germline specimen and a targeted gene panel (i.e., to identify somatic sequences of nucleotides to generate somatic sequencing results) (claim 9);
cell-free next generation sequencing of a subject’s germline specimen (claim 9);
wherein the NGS is conducted using a gene panel focused on actionable oncology mutations as the targeted panel (claim 15); 1
wherein the NGS is conducted using a gene panel targeting Tier 1 genes as the targeted panel (claim 16);
wherein the NGS is conducted on at least one of the PIK3CA gene, the CDKN2A gene, the PTEN gene, or the EGFR gene (claim 17);
wherein the targeted-panel includes a plurality of probes configured to target specific genes (claim 32);
receive data (claims 28 and 29); and
output data (claims 9, 28, 29, and 33).
The additional elements of one or more computers in communication (claim 1); and operate independent of the other system resources (i.e., computer and/or computer related components allowing for different software programs to run independently) (claim 1); invoke a computer and/or computer-related components merely as tools for use in the claimed process, and therefore are not an improvement to computer functionality itself, or an improvement to any other technology or technical field, and thus, do not integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(1)).
The additional elements of receive data (claims 28 and 29) and/or output data (claims 9, 28, 29, and 33) and/or store data (claim 1) are merely pre-solution or post-solution activities for use in the claimed process – tangential additions to the claims that does not meaningfully limit the claims, and therefore do not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
The additional elements of a germline specimen and a somatic specimen (claims 1, 7, 8, and 9); next generation sequencing (NGS) of a subject’s germline and somatic specimen (claim 1); short-read, paired-end NGS sequencing (claim 2); cell-free next generation sequencing of a subject’s germline specimen (claim 9); a targeted panel (claims 1, 3, and 9); a gene panel as the targeted-panel (claims 15, 16, 17, and 32); and probes (claims 3, 4, 5, 6, and 32); are steps and/or components of the steps of gathering the data for use in the claimed process, and thus amount to insignificant extra-solution activities (MPEP 2106.05(g)), and also do not amount to more than generally linking the use of a judicial exception(s) to a particular technological environment (MPEP 2106.05(h)).
Thus, the additionally recited elements merely invoke a computer as a tool, and/or amount to insignificant extra-solution activities, and/or amount to merely indicating a field of use or technological environment in which to apply a judicial exception, and as such, when all limitations in claims 1-11, 15-17, 21-30, 32, and 33 have been considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
Dependent claims 10, 11, 21-27, and 30 do not recite any elements in addition to the judicial exception(s). The additional elements recited in independent claim 1 and dependent claims 2-9, 15-17, 28, 29, 32, and 33 are identified above, and carried over from Step 2A: Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A: Prong Two was re-evaluated at Step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d).
The additional elements of one or more computers in communication (claim 1), and/or receive data (claims 28 and 29) and/or output data (claims 9, 28, 29, and 33) and/or store data (claim 1) are conventional computer components and/or functions (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
The additional element of operate independent of the other system resources (i.e., computer and/or computer related components allowing for different software programs to run independently) (claim 1); is conventional. Evidence for the conventionality is shown by:
Vandikas et al. ("Microservices in IoT clouds," 2016 Cloudification of the Internet of Things (CIoT), Paris, France, pp. 1-6, newly cited).
Vandikas et al. reviews microservices in IoT clouds generally (Title), and specifically addresses the issue of selecting the technologies to implement a modern microservice type of architecture (page 1, col. 2, para. 1). Vandikas et al. shows that the concept of microservices is not entirely new (page 1, col. 2, para. 4) and shows that there are more than one type of microservice related technologies such as containers and other virtualization/deployment techniques (page 2, col. 1, para. 2). While Vandikas et al. discusses microservice technology in the context of Internet of Things (IoT) technology, the reference nonetheless shows that a typical client/server pattern consists of the following building blocks (Fig. 1): a) a number of assets A, which need to be monitored or controlled, examples being a building room or a vending machine, b) a number of (instrumentation) devices D which are attached to the assets to enable asset monitor and control, c) a fixed or wireless connectivity infrastructure with a core network Internet Gateway for enabling the devices to communicate with local or remote monitoring and control functionality (emphasis added) and d) private and/or public cloud infrastructure for hosting capable services to serve devices or users (page 1, col. 1, para. 1). Vandikas et al. further shows that an integral part of each microservice application server (MAS) is a client/server framework that manages the interaction between the microservice logic and the low-level network (TCP/IP) sockets used for connecting the different microservices (page 2, col. 2, para. 2).
The additional elements of next generation sequencing (NGS) of a subject’s germline and somatic specimen (claim 1); short-read, paired-end sequencing (claim 2); and using gene probes (claims 3, 4, 5, 6, and 32); are conventional. Evidence for the conventionality is shown by Shendure et al. (Nature Biotechnology, 2008, Vol. 26, No. 10, pp. 1135-1145, as cited in the Office action mailed 12 October 2023). Shendure et al. reviews DNA sequencing technologies, paired ends, and short read lengths (page 1140, Table 1). Shendure et al. further shows that probes can be used to precisely identify variant positions (page 1137, Box 2, para. 1); and sequencing for somatic or germline variation discovery in individuals (page 1143, Box 4).
The additional element of cell-free next generation sequencing (claim 9) is conventional. Evidence for the conventionality is shown by Bennett et al. (Oncotarget, 2016, Vol. 7, No. 43, pp. 71013-71035, as cited in the Office action mailed 12 October 2023). Bennett et al. reviews the use of cell-free DNA and next-generation sequencing in personalized medicine for cancer (Title; and Abstract).
The additional element of using a targeted gene panel for genomic sequencing (claims 1, 3, 9, 15, 16, 17, and 32), is conventional. Evidence for the conventionality is shown by Buttner et al. (European Society for Medical Oncology, 2019 (Published online 24 January 2019), Vol 4:e000442, doi:10.1136/esmoopen-2018-000442, pp. 1-12, as cited in the Office action mailed 12 October 2023). Buttner et al. shows that a quantitative measure of the total number of mutations in tumor tissue of patients can be assessed by large targeted gene panel sequencing (Abstract; and page 1, column 2, para. 3). Buttner et al. further shows examples of next-generation sequencing gene panels in development of currently available to assess tumor mutational burden (page 5, Table 2).
Therefore, when taken alone, all additional elements in claims 1-11, 15-17, 21-30, 32, and 33 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1-11, 15-17, 21-30, 32, and 33 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exceptions (MPEP 2106.05(II)).
[Step 2B: NO]
Response to Arguments
The Applicant’s arguments received 09 April 2026 have been fully considered, but are not persuasive.
The Applicant provides a summary overview of the eligibility analysis on pages 12-13 of the Remarks, and further provides a summary overview of recent developments in Office examination policy with regard to Ex parte Desjardins and the December 5, 2025, Memorandum – Advance notice of change to the MPEP in light of Ex parte Desjardins on pages 13-14. The Applicant states on page 14 (para. 3) that while Desjardins itself was directed to an artificial intelligence algorithm, the PTAB has applied its holding to other technological improvements, including data processing, e.g., the PTAB recently reversed a rejection that was based on an Examiner’s conclusion that the claim was “directed to performing operations on a data structure, now a new or improved structure (see Ex parte Kwon) and the Applicant further states that there (i.e., Kwon) the Board noted that “the specification explains similar storage and reduced computational complexity benefits of the invention [], and the claim reflects this improvement at least by the claimed determining, selecting, comparing, and selecting steps based on the generated [data] slices.” The Applicant further states (para. 4) that even instances where the PTAB has applied Desjardins to artificial intelligence are illustrative here, where in one example, the PTAB reversed a rejection of claims that included “modular plug-and-play tactic-specific models[.]” (see Ex parte Carmody) where the Board found that the claims effected an improvement sufficient to integrate the judicial exception into a practical application, in that “modular plug-and-play tactic-specific models allow the models to be modified separately and independently without affecting other models.” The Applicant further notes that quoting Desjardins, the Board (in Carmody) noted that improvements to software can be considered “non-abstract improvements to computer technology, just as hardware improvements can. Finally, the Applicant states (para. 5) that in view of the above, it is clear that (1) Desjardins is applicable to non-AI technologies as well as AI technologies, and (2) improvements to modularize software such that they can be modified separately and independently without affecting other models can render claims so directed patent-eligible.
These arguments are not persuasive, because first, each application is considered on its own merit and fact pattern, and second, with regard to the Applicant’s attempt to analogize the instant claims to the claims and/or decision in Desjardins, these arguments are not persuasive at least because the fact patterns differ between the claims at issue in Desjardins and the instant claims, not least in that the “ARP” in Desjardins notes that the Federal Circuit held that the eligibility determination should turn on whether “the claims are directed to an improvement to computer functionality versus being directed to an abstract idea” (citing Enfish), prior to the “ARP” finding that the improvement to how the machine learning model operates allows artificial intelligence (AI) systems to use less of their storage capacity and enables reduced system complexity, as supported by the Specification – i.e., the improvement to the model provided an improvement to computer functionality itself. This fact pattern contrasts with the fact pattern of the instant claim 1 method of using one or more computers in communication with a plurality of microservices and a plurality of databases to manage a workflow starting with a physician ordering a genetic test and ending with the physician being provided a clinical report with results determined from the genetic testing. Third, with regard to Kwon and Carmody, it is noted that neither are precedential, and to the extent that the Applicant intends to compare the claim sets and adopt the logic of the PTAB, it appears that the cited Kwon and Carmody are just general examples and do not necessarily represent all sides or fact patterns presented to the PTAB and their decisions related to 35 U.S.C. 101. Importantly, the claims at issue in the Kwon and Carmody decisions are significantly different from the instant claims, and given the limitations recited by the instant claims, do not appear to be material to the analysis and examination of the instant claims. Furthermore, the eligibility analysis under 35 U.S.C. 101 relies on the MPEP and the relevant case law cited therein.
The Applicant states on page 14 (bottom) of the Remarks that before discussion of the claims under the Alice/Mayo test, the Applicant here discusses the Office’s construction of certain claim terms, e.g., the Office provides an express claim construction of the term “microservice” and that the Applicant disagrees that this construction is consistent with the broadest reasonable interpretation, and instead, the Applicant submits that one of ordinary skill in the art would have interpreted the term microservice according to its ordinary and customary meaning as an architectural arrangement and not as a mere software program. The Applicant further states on page 15 (para. 2) that the evidence of record, including the evidence cited by the Office itself, supports the Applicant’s claim construction and does not support the Office’s construction. The Applicant further states that the Office has previously cited a 2017 article titled “Microservices: yesterday, today, and tomorrow” (“Dragoni”) at Step 2B of the Alice/Mayo test, and that this document makes clear that a microservice is not a mere software program, but is instead an architectural arrangement, and that even at the early state of microservice development present in 2017, the term microservices was understood as “an architectural style inspired by service-oriented computing[.]” (Dragoni at Abstract). The Applicant further states that Dragoni expressly defines a microservice as “a cohesive, independent process interacting via messages. …[M]icroservices should be independent components conceptually deployed in isolation and equipped with dedicated memory persistence tools (e.g., databases).” The Applicant further states (para. 3) that this is consistent with the term’s usage today, after microservice technology has developed, and that Microsoft, for example, describes microservices as a “popular architectural style for building applications that are resilient, highly scalable, independently deployable, and able to evolve quickly” and notes that “[a] microservices architecture consists of a collection of small, autonomous services.” Finally, the Applicant states that accordingly, the broadest reasonable interpretation of the term “microservice” is not, as proposed by the Office, a mere software program, but instead, the term microservice should be construed as an architectural arrangement in which the microservice itself is independent of other microservices and interacts with the other microservices via messages.
These arguments are not persuasive, because first, the term “microservice” is given the broadest reasonable interpretation in light of the specification in the above rejection (see the Claim Interpretations section in the above rejection). Second, the Dragoni reference was applied at Step 2B in the Office action mailed 27 May 2025 to show conventionality of the ability of a plurality of microservices to “operate independently of the other system resources,” i.e., not to show conventionality of microservices themselves (identified as judicial exceptions at Step 2A Prong One), but rather of non-abstract additional features necessarily required in order for the microservices to operate independently. It would appear that this was not made clear in the record, given the nature of the Applicant’s arguments, and therefore the above rejection has been modified in an attempt to clarify the record to show that at Step 2A Prong One, microservices are identified as judicial exceptions; at Step 2A Prong Two, the claim 1 limitation “operate independently of the other system resources” (i.e., necessary computer and/or computer related non-abstract features) is identified as an additional element; and at Step 2B the additional element of “operate independently of the other system resources” is further evaluated to determine whether this additional element amounts to significantly more than the judicial exceptions (i.e., whether the additional element contributes an “inventive concept”). To further clarify the record, the Dragoni reference has been removed from Step 2B (but retained to add clarity and context to the claim interpretation of “microservice” in the Claim Interpretations section) and a new reference applied at Step 2B to show conventionality of necessary hardware/infrastructure (i.e., non-abstract elements) in order for a plurality of microservices to operate independently of other system resources. Third, with regard to the Applicant’s argument that the term “microservice” should be construed as an architectural arrangement in which the microservice itself is independent of other microservices and interacts with the other microservices via message,” it is noted that one of skill in the art would recognize that there is a distinction between merely stating the term “microservice” and stating the term “microservice architecture,” not least in that the term “microservice” (i.e., software) refers to the individual, small, and independent functional components (i.e., services) themselves, whereas the term “microservice architecture” is the overall design pattern, structure, and organizational approach used to connect, deploy, and manage these services to build a complete application.
Regarding Step 2A Prong One, the Applicant states on page 16 (para. 2) that the Office identifies the following claim features of claim 1 as allegedly being mental processes or mathematical concepts: each of the microservices themselves (under the Office’s construction in which a microservice is “a software program”), which the Office alleges to be mental processes; the operations performed by the fourth through sixth microservices, which the Office alleges to be mental processes and mathematical concepts; and the microservices including a data consume definition and generating a data product, which the Office alleges to be mental processes. The Applicant further states (para. 3), that the Applicant disagrees, and submits that the Office’s interpretation of various features as judicial exceptions is overinclusive and expressly contradicted by legal precedent and Office policy. On page 16 of the Remarks (para. 5), the Applicant points to the MPEP at 2106.04(a), and states (Remarks, page 16, para. 4) that the Office’s finding that microservices (“i.e., a software program”) are mental processes is inconsistent with several Federal Circuit decisions and with the MPEP, and that while the Applicant disagrees with the Office’s construction in which the term microservice is interchangeable with a software program (as set forth above), the Applicant notes that even under the Office’s construction the Office’s reasoning is erroneous. Finally, the Applicant states on page 17 (para. 1) that accordingly, even under the Office’s claim construction of the term microservices, the claimed microservices themselves – separate and distinct from any of the recited tasks that those microservices perform – should not be considered judicial exceptions at Step 2A, Prong One of the Alice/Mayo test.
These arguments are not persuasive, because first, the above rejection does not state or suggest that the term “microservice” is interchangeable with a software program, as alleged by the Applicant, but rather, the above rejection clearly identifies the term “microservice” to actually be a software program, i.e., independent, deployable software that handles a specific function. Second, with regard to the Applicant’s assertion that the Office’s finding that microservices (“i.e., a software program”) are mental processes is inconsistent with several Federal Circuit decisions and with the MPEP, it is noted that the eligibility analysis under 35 U.S.C. 101 in the above rejection relies on the MPEP and the relevant case law cited therein. Third, the microservices identified as judicial exceptions in the above rejection are not automatically identified as an abstract idea on the basis that they are software, as seemingly alleged by the Applicant, but rather, the microservices are identified as judicial exceptions because they are software programs performing functions that could practically be performed in the human mind with or without the aid of pen and paper.
The Applicant states on page 17 (para. 2) of the Remarks that in the previous response, the Applicant presented arguments that certain operations recited in the claims (e.g., operations performed by the fourth and fifth microservices) are not mathematical concepts as clarified by a recently issued Office memorandum (the “August 4 Memo”), which expressly cautions Examiners to be careful to distinguish claims that recite an exception (which require further eligibility analysis) from claims that merely involve an exception (which are eligible and do not require further eligibility analysis). The Applicant further states (para. 3) that among these arguments, the Applicant noted that, with regard to mathematical concepts, the memorandum refers to a claim feature that “involves a broad array of techniques and/or activities that may involve or rely upon mathematical concepts but does not set forth or describe any mathematical relationships, calculations, formulas, or equations using words or mathematical symbols. The Applicant further states that situations where a claim may at some broad level involve mathematical concepts are contrasted with a claim feature that “requires specific mathematical calculations by referring to the mathematical calculations by name, i.e., a backpropagation algorithm and a gradient descent algorithm, [which] therefore recites a judicial exception, namely an abstract idea. The Applicant further states (para. 4) that here, the features that the Office identifies as mathematical concepts are analogous to features that the memorandum indicates do not recite a judicial exception, and they are distinct from features that the memorandum indicates do recite a judicial exception, i.e., the claims do not require any specific mathematical calculations and do not refer to any mathematical calculations by name.
These arguments are not persuasive because first, Prong One of the eligibility analysis asks: Does the claim recite an abstract idea, law of nature, or natural phenomenon? In Prong One examiners evaluate whether the claim recites a judicial exception, i.e. whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim. While the terms "set forth" and "described" are thus both equated with "recite", their different language is intended to indicate that there are two ways in which an exception can be recited in a claim. For instance, the claims in Diehr, 450 U.S. at 178 n. 2, 179 n.5, 191-92, 209 USPQ at 4-5 (1981), clearly stated a mathematical equation in the repetitively calculating step, and the claims in Mayo, 566 U.S. 66, 75-77, 101 USPQ2d 1961, 1967-68 (2012), clearly stated laws of nature in the wherein clause, such that the claims "set forth" an identifiable judicial exception. Alternatively, the claims in Alice Corp., 573 U.S. at 218, 110 USPQ2d at 1982, described the concept of intermediated settlement without ever explicitly using the words "intermediated" or "settlement." Second, with regard to “The Memo” it is noted that each claim (i.e., each claim of the invention being examined) should be interpreted based on the fact patterns set forth in a particular claim, as other fact patterns may have different eligibility outcomes, as evidenced in the rejection of instant claim 1 above.
With regard to the operations of the fourth microservice (and mathematical concepts), the Applicant states on page 17 (para. 5) and page 18 (para. 1) of the Remarks that the claimed fourth microservice, e.g., is configured to execute QC testing on the germline sequencing results to generate a germline QC score and on the somatic sequencing results to generate a somatic QC score, and that nowhere does the claim recite any specific mathematical calculations that the fourth microservice implements to generate the QC score, and the claim does not refer to any mathematical calculations by name. The Applicant further states on page 18 (para. 2) that the Office responds by alleging that the fourth microservice is directed to a mathematical concept “not least because determining a quality control score involves converting a quality predictor value (that is generated using a statistical model) for each base into a score reflecting the probability of an incorrect base call (which requires using a mathematical equation). The Applicant further states that the Office’s use of the term “involves” is evidence of the Office’s error, and that (para. 3) the MPEP expressly distinguishes between “claims reciting abstract ideas from those that are merely based on or involve and abstract idea (pointing to MPEP 2106.04(a)(1)). The Applicant further states (para. 4) that the Office further responds by stating that the August 4 Memo is not intended to announce any new practice or procedure, however the Applicant further states that the August 4 Memo is not evidence that the Office examined the claims correctly under some superseded policy; the August 4 Memo is instead evidence that the Office examined the claims incorrectly under existing policy. The Applicant further states that the very first paragraph of the August 4 Memo evidences the Office’s error described above with regard to the Office’s first reply point: the August 4 Memo “provides guidance on… distinguishing claims that recite a judicial exception from claims that merely involve a judicial exception[.]”. The Applicant further states (para. 5) that thus, the Office’s ultimate conclusion that the “existing USPTO guidance… was adhered to during the examination of the instant claims” is neither correct not a substantive response to the Applicant’s position, and that (page 9, para. 1) the August 4 Memo is evidence that the Office did not adhere to existing USPTO guidance. The Applicant further states that the Applicant’s arguments, which cite to both controlling authority in the form of Federal Circuit and precedential PTAB decisions and to persuasive authority in the form of the MPEP, are further evidence that the Office did not adhere to existing USPTO guidance, and even if the Office’s statement (unsupported by any analysis) that the guidelines were “adhered to during the examination” were considered evidence, this evidence is greatly outweighed by the Memo and the Applicant’s arguments. The Applicant further states (para. 2) that because the appropriate standard is “preponderance of the evidence” and because the evidence that the Office’s interpretations of certain claim features as judicial exceptions is incorrect greatly outweighs the evidence to the contrary, the above-described claim features should not be considered as judicial exceptions. The Applicant further states (para. 3) that by relying on a finding that the claimed operations of the fourth microservice are directed to a mathematical concept merely because they involve mathematical operations, the Office’s conclusion is inconsistent with the MPEP and is thus erroneous, and accordingly, the operations of the fourth microservice should not be considered as judicial exceptions.
These arguments are not persuasive, because first, with regard to the Applicant’s allegation that the Office’s conclusion that the fourth microservice recites a mathematical concept is inconsistent with the MPEP and is thus erroneous, and accordingly, the operations of the fourth microservice should not be considered as judicial exceptions, it is noted that the Applicant’s cherry picking of the word “involves” from a response to arguments does not render the validity of the rejection itself as erroneous, nor does said cherry picking from the explanation in the response to arguments change the basis of the rejection, which clearly states “Independent claim 1 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas” (emphasis added). Second, claim 1 recites “a fourth microservice configured to execute quality control (QC) testing on the germline sequencing results to generate a germline QC score and on the somatic sequencing results to generate a somatic QC score” (emphasis added). It is noted that quality control (QC) scores in sequencing data (known as Phred quality scores (Q)) are generated by base-calling algorithms that calculate the probability (P) of an incorrect base call for every single nucleotide, using the formula Q = -10log10P. A higher Q-score indicates higher accuracy, with Q30 (99.9% accuracy) being the standard benchmark for high-quality NGS data. Therefore, the claim 1 limitation reciting a fourth microservice recites a judicial exception because it describes a mathematical concept.
With regard to the operations of the fifth microservice (and mathematical concepts), the Applicant states on page 19 (para. 4) of the Remarks that the claimed fifth microservice is configured to generate a clinical report that includes a TMB status based at least in part on identified sequences, and that the claim sets forth three inputs from which the TMB status is determined depending on the relationship between the QC scores and thresholds (numbered (i) to (iii) in the claim), but it does not specify any particular algorithm or identify any particular mathematical calculations that must be performed to generate the TMB status. The Applicant further states (para. 5) that the Office responds by alleging that the fifth microservice is directed to a mathematical concept because the claim recite that the TMB status is calculated and recites that the calculation uses threshold values. The Applicant further states that the mere fact that the claim states that the TMB status “is calculated” is not sufficient to conclude that the claims recite mathematical calculations. The Applicant further states (para. 6) that again, the August 4 Memo is instructive, and further states that even if a claim feature involves or relies upon a mathematical calculation, the feature does not recite the calculation if it does not set forth or describe any mathematical calculations using words or mathematical symbols, and that claim features may recite a calculation if the require specific mathematical calculations by referring to the calculations by name. The Applicant further states that the Applicant’s claims here do not refer to any specific mathematical calculation using words or mathematical symbols, and they do not refer to any calculations by name. The Applicant further states on page 20 (para. 2) that the Office’s additional response stating that the August 4 Memo is not intended to announce any new practice or procedure is also applied to the operations of the fifth microservice, however, for the same or similar reasons to those discussed in the preceding subsection, The Memo is evidence that the Office did not adhere to existing USPTO guidance. The Applicant further states that the Applicant’s arguments, which cite to both controlling authority in the form of Federal Circuit and precedential PTAB decisions and to persuasive authority in the form of the MPEP, are further evidence that the Office did not adhere to existing USPTO guidance, and even if the Office’s statement (unsupported by any analysis) that the guidelines were “adhered to during examination” were considered as evidence, this evidence is greatly outweighed by the Memo and the Applicant’s arguments. The Applicant further states (para. 3) that because the appropriate standard is “preponderance of the evidence” and because the evidence that the Office’s interpretation of certain claim features as judicial exceptions is incorrect greatly outweighs the evidence to the contrary, the above-described claim features should not be considered as judicial exceptions. The Applicant further states (para. 4) that solely to advance prosecution, the Applicant has amended the claims to clarify that the TMB status is “determined based on” factors (i) to (iii) recited in the claim, and thus, the Office’s reasoning for maintaining the rejection with regard to the operations of the microservice is moot. Finally, the Applicant states (para. 5) that by relying on a finding that the claimed operations of the fifth microservice are directed to a mathematical concept merely because they recite that a calculation is performed, the Office’s conclusion is inconsistent with the MPEP and is thus erroneous, and accordingly, the operations of the fifth microservice should not be considered as judicial exceptions.
These arguments are not persuasive, because first, with regard to the Applicant’s assertion that the Office’s conclusion is inconsistent with the MPEP and is thus erroneous, it is noted that the broadest reasonable interpretation of the claim 1 limitation reciting “the TMB status is determined based on” steps (i), (ii), and (ii) (i.e., reciting “thresholds”) is that the limitation recites a judicial exception because it describes a mathematical concept. One of skill in the art would understand that a TMB status is generated by measuring the total number of somatic mutations within a tumor’s DNA coding region, typically reported as mutations per megabase of DNA, and is calculated by counting the non-synonymous somatic mutations and dividing that number by the size of the genome region sequenced (i.e., megabases).
With regard to Step 2A Prong Two, the Applicant summarizes MPEP 2106.04(d) on page 20 (bottom) and page 21 (top) and states on page 21 (para. 2) that at Prong Two, the Office identifies seven features of claim 1 as being additional elements that are not part of the judicial exceptions, and that these elements are (1) one or more computers in communication; (2) receive data; (3) output data; (4) a germline specimen and a somatic specimen; (5) next generation sequencing (NGS) of a subject’s germline and somatic specimen; (6) a targeted panel; and (7) the plurality of microservices operating independently of the other system resources. The Applicant further states (para. 3) that in addition to these elements, and as noted in the preceding section, several further features of claim 1 should be considered as additional elements: (8) first through sixth microservices; (9) execute QC testing on germline and somatic sequencing result to generate QC scores; and (10) generate at least one clinical report comprising a TMB status associated with the subject. The Applicant further states that finally, the features added by this amendment are also additional elements: (11) a plurality of differently structured databases; and (12) storing items as purpose-specific data structures in respective ones of the plurality of differently structured databases.
These arguments are not persuasive, at least because of the reasons provided in the foregoing responses to arguments with regard to numbers (8), (9), and (10) in the foregoing argument. With regard to number (11) in the above argument, the limitation “differently structured databases” is identified as a judicial exception because databases with different schemas for how data is organized are still data that is organized according to a particular schema (i.e., a predefined set of rules that outlines how data is organized in a database). With regard to number (12) in the above argument, the limitation “storing items as purpose-specific data structures in respective ones of the plurality of differently structured databases” is identified as an additional element (i.e., storing data) at Step 2A Prong Two in the above rejection.
The Applicant states on page 21 (para. 4) of the Remarks that the claimed first through sixth microservices (feature 8 above), as well as the arrangement and interaction of the various microservices (feature 7 above), integrate the alleged judicial exceptions into a practical application thereof. The Applicant further states that as noted above, an arrangement of or interaction between additional features may integrate a judicial exception into a practical application if the specification sets forth an improvement in technology and the claims themselves reflect the disclosed improvement in technology. The Applicant further states (para. 5) that the Applicant’s disclosure as filed sets forth an improvement that results from the use of multiple distinct microservices that interact with one another (pointing to paras. [0042] & [0043]) and further states on page 22 (para. 2) that disclosure at paras. [0042] & [0043] set forth improvements; specifically, (1) increased system adaptability, (2) increased ability to accommodate new data types as well as treatment and research insights, and (3) improved ability to develop microservices to achieve a specific goal. The Applicant further states (para. 3) that claim 1 reflects the disclosed improvements, and that the above sections of the disclosure notes that benefits (1) and (2) are achieved by compartmentalizing system processes into loosely coupled and distinct microservices, and further notes that benefit (3) is achieved when the interaction between microservices is independent of other system processes. The Applicant further states that claim 1 recites six different microservices, each being distinct from one another, and further recites that each microservice “includes a data consume definition,” “generates a data product,” and “operate[s] independently of the other system resources[.]” The Applicant further states that these are the features disclosed to give rise to the benefits, and further states (para. 4) that thus, considering the claims as a whole and in particular considering the microservices as distinct and independent, it can be seen that the claims effect an improvement in the functioning of a computer or in another technology or technical area, and therefore claim is patent-eligible at Step 2A Prong Two for at least this reason.
These arguments are not persuasive, because first, 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 (MPEP 2106.04(d)). The phrase "meaningful limitations" has been used by the courts even before Alice and Mayo in various contexts to describe additional elements (MPEP 2106.05(e)). The eligibility analysis of claim 1 in the above rejection determined that the claim does not recite any additional elements that apply, rely on, or use the judicial exceptions in a manner that imposes a meaningful limit on the judicial exceptions, because the recited additional elements are merely tools used in the claimed process either to gather data or to execute abstract ideas, or to store data, as discussed in more detail in the above rejection. Second, with regard to the Applicant’s assertion that “the claims effect an improvement in the functioning of a computer or in another technology or technical area, and therefore claim is patent-eligible at Step 2A Prong Two for at least this reason” it is noted that the eligibility analysis in the above rejection does not determine that claim 1 recites any limitation or combination of limitations that could be considered to be an improvement to computer functionality itself (e.g., an improvement to computer memory configuration), or to another technology or technical area.
The Applicant states on page 22 (bottom) of the Remarks that the Applicant’s claimed differently structured databases (features 11 and 12 above) also integrate the alleged judicial exception into a practical application thereof, at least because they reflect an improvement in technology that is set forth in the disclosure. The Applicant further states on page 23 (para. 1) that paragraphs [0044] & [0045] of the disclosure as filed sets forth an improvement that results from the use of differently structured databases, and further states (para. 2) that this portion of the disclosure sets forth improvements of (1) simpler and quicker deployment, (2) faster analytics, and (3) more rapid user application program operations. The Applicant further states (para. 3) that claim 1 reflects the disclosed improvements, and that the above referenced sections of the disclosure note that benefits (1) to (3) are achieved by storing system data in purpose-specific data structures. The Applicant further states that claim 1 as amended recites the plurality of differently structured databases and that various results, scores, and reports are stored as purpose-specific data structures in respective ones of the differently structured databases, and that these are the features disclosed to give rise to the benefits. Finally, the Applicant states (para. 4) that thus, considering the claim as a whole and in particular considering the use of differently structured databases to store data as purpose-specific data structures, it can be seen that the claims effect an improvement in the functioning of a computer or in another technology or technical area, and therefore, claim 1 is patent eligible at Step 2A Prong Two for at least this reason.
These arguments are not persuasive, because first, 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 (MPEP 2106.04(d)). The phrase "meaningful limitations" has been used by the courts even before Alice and Mayo in various contexts to describe additional elements (MPEP 2106.05(e)). The eligibility analysis of claim 1 in the above rejection determined that the claim does not recite any additional elements that apply, rely on, or use the judicial exceptions in a manner that imposes a meaningful limit on the judicial exceptions, because the recited additional elements are merely tools used in the claimed process either to gather data or to execute abstract ideas, or to store data, as discussed in more detail in the above rejection. Second, with regard to the Applicant’s assertion that “considering the claim as a whole and in particular considering the use of differently structured databases to store data as purpose-specific data structures, it can be seen that the claims effect an improvement in the functioning of a computer or in another technology or technical area, and therefore, claim 1 is patent eligible at Step 2A Prong Two for at least this reason” it is noted that the eligibility analysis in the above rejection does not determine that claim 1 recites any limitation or combination of limitations that could be considered to be an improvement to computer functionality itself (e.g., an improvement to computer memory configuration), or to another technology or technical area.
The Applicant states on page 23 (para. 5) that the Applicant’s claimed germline and somatic specimens as well as the use of NGS for sequencing of the specimen and the use of a targeted panel (features 4 to 6 above) also integrate the alleged judicial exceptions into a practical application thereof. The Applicant further states that, for example, these features, considered in the context of the claim as a whole, provide a technological solution to a problem arising from technology. The Applicant points para. [0028] of the disclosure on page 23 of the Remarks (bottom) and page 24 (top) and states on page 24 (para. 2) of the Remarks that as a result of the problems in comparative techniques described in paragraph [0028] in the disclosure, the present disclosure is directed to a system as described at paragraph [0041] in the disclosure, i.e., “a system that is capable of efficiently capturing all treatment relevant data including cancer state factors, treatment decision, treatment efficacy and exploratory factors (e.g., factors that may have a causal relationship to treatment efficacy) and structuring that data to optimally drive different system activities including memorialization of data and treatment decisions, database analytics and user applications and interfaces” and that is ”highly and rapidly adaptable so that it can be modified to absorb new data types and new treatment and research insights as well as to enable development of new user applications and interfaces optimized to specific user activities.” The Applicant further states (para. 3) that in this manner, the disclosure describes a technological problem arising from the use of NGS technology as particularly claimed: lack of standardization and normalization renders it difficult or impossible to obtain treatment efficacy, and that the claims reflect a solution: the use of microservices to perform NGS on somatic and germline specimens, and performing quality control thereon, implements standardization and normalization such that clinical insights can be obtained. The Applicant further states (para. 4) that in the Office’s response to the Applicant’s previous arguments regarding NGS, the Office treats the claimed specimens and NGS thereof individually and finds that they are insignificant extra-solution activities, and further states that it is not enough for the Office to consider the claim features individually; the Alice/Mayo test requires that the additional features be considered in the context of the claim, and thus be considered for how they interact with one another and even with the alleged judicial exception, in other words, even if the use of NGS are “steps of data gathering” they must still be considered in combination with each and every other features of the claim. Finally, the Applicant states (para. 5) that thus, considering the claims as a whole, it can be seen that the claims provide a technological solution to a problem arising from technology, and therefore the Applicant’s claim 1 is patent-eligible at Step 2A Prong Two for at least this reason.
These arguments are not persuasive, because first, 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 (MPEP 2106.04(d)). The phrase "meaningful limitations" has been used by the courts even before Alice and Mayo in various contexts to describe additional elements (MPEP 2106.05(e)). The eligibility analysis of claim 1 in the above rejection determined that the claim does not recite any additional elements that apply, rely on, or use the judicial exceptions in a manner that imposes a meaningful limit on the judicial exceptions, because the recited additional elements are merely tools used in the claimed process either to gather data or to execute abstract ideas, or to store data, as discussed in more detail in the above rejection. Second, with regard to the Applicant’s assertion that “the Office treats the claimed specimens and NGS thereof individually and finds that they are insignificant extra-solution activities” it is noted that the above rejection at Step 2A Prong Two that all limitations in claims 1-11, 15-17, 21-30, 32, and 33 have been considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), and are deemed to not recite any additional elements that would integrate a judicial exception into a practical application (MPEP 2106.04(d)). Third, with regard to the Applicant’s assertion that “it can be seen that the claims provide a technological solution to a problem arising from technology, and therefore the Applicant’s claim 1 is patent-eligible at Step 2A Prong Two for at least this reason” it is noted that claim 1 recites using NGS technology to gather data for use in the claimed process, and further noted that the eligibility analysis in the above rejection does not determine that claim 1 recites any limitation or combination of limitations that could be considered to be an improvement to computer functionality itself (e.g., an improvement to computer memory configuration), or to another technology (i.e., next generation sequencing (NGS) technology) or technical area.
The Applicant states on page 24 (para. 1) of the Remarks that the claims further recite the clinical report comprising a match between the subject and a therapy, the match being based on at least the subject’s TMB status (feature 10 above), and that these additional features provide for improvements in the technological fields of genomic sequencing and cancer treatment. The Applicant points to the disclosure as filed at paragraphs [0259], [0353], [0327], [0354], and [0359] - [0360] for descriptions of improvements, and further states (Remarks, para. 3) that the claims reflect these disclosed improvements, and that the particularly claimed clinical report, comprising the subject’s TMB status which in turn is based on the results of NGS and QC testing, permitted clinically relevant molecular insights to be obtained in the vast majority of cases. The Applicant further states (para. 4) that considering the clinical report generation in conjunction with the claim as a whole, it can be seen that the claims effect an improvement in the functioning of a computer or in another technology or technical area, and therefore claim 1 is patent-eligible at Step 2A Prong Two for at least this reason. Finally, the Applicant states (para. 5) that as set forth above, the claims recite several additional features that, when considered in the context of the claim as a whole, integrate the alleged judicial exception into a practical application thereof.
These arguments are not persuasive, because first, 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 (MPEP 2106.04(d)). The phrase "meaningful limitations" has been used by the courts even before Alice and Mayo in various contexts to describe additional elements (MPEP 2106.05(e)). The eligibility analysis of claim 1 in the above rejection determined that the claim does not recite any additional elements (i.e., the limitation “to generate at least one clinical report” is a judicial exception) that apply, rely on, or use the judicial exceptions in a manner that imposes a meaningful limit on the judicial exceptions, because the recited additional elements are merely tools used in the claimed process either to gather data or to execute abstract ideas, or to store data, as discussed in more detail in the above rejection. Second, with regard to the Applicant’s assertion that “considering the clinical report generation in conjunction with the claim as a whole, it can be seen that the claims effect an improvement in the functioning of a computer or in another technology or technical area, and therefore claim 1 is patent-eligible at Step 2A Prong Two for at least this reason” it is noted that the eligibility analysis in the above rejection does not determine that claim 1 recites any limitation or combination of limitations that could be considered to be an improvement to computer functionality itself (e.g., an improvement to computer memory configuration), or to another technology or technical area.
With regard to Step 2B, the Applicant summarizes aspects of the eligibility analysis on page 26 (para. 1) of the Remarks and states (para. 2) that each of the Applicant’s arguments in the preceding section regarding Step 2A Prong Two are equally applicable to the corresponding claim features at Step 2B of the Alice/Mayo test, and further states that each of the foregoing argued claim features amount to significantly more than the judicial exception itself for at least the same or similar reasons that they integrate the judicial exception into a practical application thereof. Regarding microservices, the Applicant states (para. 3) that considering the additional features of the claims in light of what is well-understood, routine, and conventional, the Applicant notes that the claimed first through sixth microservices render the claims patent eligible for additional reasons under Step 2B. The Applicant further states (para. 4) that in support of the Office’s conclusion that “a plurality of microservices operat[ing] independent if the other system resources… is conventional,” the Office refers to Dragoni, and thus, the Office is attempting to use evidence from category (c) (i.e., a citation to a publication that demonstrated the well-understood, routine, conventional nature of the additional elements). The Applicant further states that the Dragoni reference does not actually support the Office’s conclusion, and further states (para. 5) that Dragoni states that microservices “are a new trend in software architecture” and that microservice architecture “can be considered to be in its infancy since there is still a lack of consensus on what microservices actually are” and that Dragoni further states that microservices “are so recent that we can consider their exploration to have just begun.” The Applicant further states on page 27 (para. 2) of the Remarks that Dragoni was published on April 20, 2017, and that the Office has accorded this application an effective filing date of July 12 2019. The Applicant further states that thus, Dragoni’s statement that microservices “are a new trend in software architecture” supports the opposite conclusion than the one drawn by the Office, and if microservices in general were a “new trend” around the effective filing date of this application, then it does not follow that a plurality of microservices operating independent of other systems was well-understood, routine, or conventional. The Applicant further states that the Office in particular relies on Dragoni’s definition of a microservice, however Dragoni expressly notes that there is a lack of consensus as to how to define a microservice. The Applicant further states (para. 3) that the Office responds to the above arguments by first saying that “the microservices (i.e., software programs) limitations are identified as judicial exceptions from the mental processes grouping of abstract ideas… and therefore are not limitations that are reevaluated at Step 2B” and that this conclusion is flawed for at least two reasons: first, as discussed above, microservices are not synonymous with software programs, and second, even if they were, software programs are not themselves per se judicial exceptions. The Applicant points to the MPEP at 2106.07(a)(III) and states (para. 4) that evidence under category (C) must “demonstrate that the additional elements are widely prevalent or in common use in the relevant field, comparable to the types of activity or elements that are so well-known that they do not deed to be described in detail in a patent application to satisfy 35 U.S.C. 112(a).” The Applicant further states that Dragoni, which describes microservices as new, in their infancy, and lacking a consensus description, does not demonstrate this. The Applicant further states (para. 5) that at least because the MPEP and Federal Circuit both affirmatively state that software is not an abstract idea, the Office is required to consider the claimed microservices at Step 2B. Finally, the Applicant states (para. 6) that as set forth above, the claims recite several additional features that, when considered in the context of the claim as a whole, amount to significantly more than the judicial exception itself, and thus the claims are patent-eligible.
These arguments are not persuasive, because first, and as discussed above in a foregoing response to arguments, the Dragoni reference was applied at Step 2B in the Office action mailed 27 May 2025 to show conventionality of the ability of a plurality of microservices to “operate independently of the other system resources,” i.e., not to show conventionality of microservices themselves (identified as judicial exceptions at Step 2A Prong One), but rather of non-abstract additional features necessarily required in order for the microservices to operate independently. It would appear that this was not made clear in the record, given the nature of the Applicant’s arguments, and therefore the above rejection has been modified in an attempt to clarify the record to show that at Step 2A Prong One, microservices are identified as judicial exceptions; at Step 2A Prong Two, the claim 1 limitation “operate independently of the other system resources” (i.e., necessary computer and/or computer related non-abstract features) is identified as an additional element; and at Step 2B the additional element of “operate independently of the other system resources” is further evaluated to determine whether this additional element amounts to significantly more than the judicial exceptions (i.e., whether the additional element contributes an “inventive concept”). To further clarify the record, the Dragoni reference has been removed from Step 2B (but retained to add clarity and context to the claim interpretation of “microservice” in the Claim Interpretations section) and a new reference applied at Step 2B to show conventionality of necessary hardware/infrastructure (i.e., non-abstract elements) in order for a plurality of microservices to operate independently of other system resources. Second, with regard to the Applicant’s assertion that “at least because the MPEP and Federal Circuit both affirmatively state that software is not an abstract idea, the Office is required to consider the claimed microservices at Step 2B” it is noted that MPEP 2106.04(a) clearly states that the abstract idea exception has deep roots in the Supreme Court’s jurisprudence. See Bilski v. Kappos, 561 U.S. 593, 601-602, 95 USPQ2d 1001, 1006 (2010) (citing Le Roy v. Tatham, 55 U.S. (14 How.) 156, 174–175 (1853)). Despite this long history, the courts have declined to define abstract ideas. However, it is clear from the body of judicial precedent that software and business methods are not excluded categories of subject matter. For example, the Supreme Court concluded that business methods are not "categorically outside of § 101's scope," stating that "a business method is simply one kind of ‘method’ that is, at least in some circumstances, eligible for patenting under § 101." Bilski, 561 U.S. at 607, 95 USPQ2d at 1008 (2010). See also Content Extraction and Transmission, LLC v. Wells Fargo Bank, 776 F.3d 1343, 1347, 113 USPQ2d 1354, 1357 (Fed. Cir. 2014) ("there is no categorical business-method exception"). Likewise, software is not automatically an abstract idea, even if performance of a software task involves an underlying mathematical calculation or relationship. See, e.g., Thales Visionix, Inc. v. United States, 850 F.3d 1343, 121 USPQ2d 1898, 1902 (Fed. Cir. 2017) ("That a mathematical equation is required to complete the claimed method and system does not doom the claims to abstraction."); McRO, Inc. v. Bandai Namco Games Am. Inc., 837 F.3d 1299, 1316, 120 USPQ2d 1091, 1103 (Fed. Cir. 2016) (methods of automatic lip synchronization and facial expression animation using computer-implemented rules were not directed to an abstract idea); Enfish, 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016) (claims to self-referential table for a computer database were not directed to an abstract idea). Third, in the above rejection, the claim 1 limitation reciting “microservice” was not automatically determined to be an abstract idea, but rather, given the broadest reasonable interpretation in light of the specification, and then evaluated in accordance with the eligibility framework provided at section 2106 in the MPEP, and only then having been determined to recite a judicial exception at Step 2A Prong One, thereby excluding the limitation from further evaluation at Step 2B of the eligibility analysis.
Conclusion
No claims are allowed. I
This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this application.
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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687
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