DETAILED ACTION
The Applicant’s filing, received 29 May 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 .
Status of the Claims
Claims 1-3, 5, 7-12, and 18-20 are pending.
Claims 1-3, 5, 7-12, and 18-20 are rejected.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
This application is a 371 of PCT/EP2020/082303, filed 16 November 2020.
Foreign applications for which benefit of priority are claimed:
EPO 19383010.6, filed 15 November 2019; and
EPO 20164353.3, filed 19 March 2020.
Unless otherwise noted, the effective filing date of the claimed invention is 15 November 2019.
Claim Objections
The warning of duplicate claims (11 and 18) in the Office action mailed 29 December 2025 is withdrawn in view the Applicant’s arguments/remarks in the amendment received 29 May 2026.
Response to Arguments
The Applicant’s arguments/remarks received 29 May 2026 have been fully considered and are persuasive.
The Applicant states on page 11 (as filed) of the Remarks that the features covered by amended claim 11 and 18 are sufficiently distinct that they should not be considered duplicative, because, in particular, claim 11 proceeds from a therapeutic gene-expression profile, while claim 18 proceeds from target profile data of a therapeutic and human protein interaction data indicating a group of genes in a network of genes regulated in response to the therapeutic, and further states that these are distinct therapeutic profile construction pathways and correspond to different disclosed embodiments.
These arguments/remarks are persuasive.
Claim Rejections - 35 USC § 112
The rejection of claims 8, 16, 17, and 20 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, in the Office action mailed 29 December 2025 has been withdrawn in view of the amendment received 29 May 2026.
Claim Rejections - 35 USC § 101
The amendment received 29 May 2026 has been fully considered, however after further consideration, the rejection of claims 1-20 under 35 U.S.C. 101 in the Office action mailed 29 December 2025 has been maintained with modification in view of the amendment received 29 May 2026, as noted below.
The rejection of claims 4, 6, and 13-17 has been withdrawn in view of these claims having been cancelled in the amendment.
The rejection has been modified as necessary in view of the newly added limitations presented in 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 1-3, 5, 7-12, and 18-20 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) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion); (b) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (c) a law of nature (e.g., naturally occurring relationships).
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 1-3, 5, and 7-10 recite a method (i.e., a process); claims 11-12 recite a system (i.e., a machine and/or a manufacture); and claims 18-20 recite a system (i.e., a machine and/or a manufacture).
Therefore, these claims are encompassed by the categories of statutory subject matter, 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:
analyzing, using one or more machine learning techniques, the gene expression profile in relation to the genetic data obtained from the at least one data source to determine one or more genes included in the gene expression profile that have at least a threshold amount of representation in at least one of the co-occurring condition genetic data, the phenotype classification genetic data, or the biological pathway genetic data (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculations);
determining a therapeutic responders profile that includes a plurality of features, at least a portion of the plurality of features corresponding to the one or more genes (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data), wherein determining the therapeutic responders profile comprises:
determining a first ranking of a gene included in the gene expression profile based on an amount of up-regulation of the gene in response to the therapeutic or an amount of down-regulation of the gene in response to the therapeutic;
determining that the gene is present in at least one of the co-occurring condition genetic data, phenotype classification genetic data, or biological pathway genetic data; and
generating an additional gene expression profile that includes the gene with the gene having a second ranking in the additional gene expression profile, the second ranking being based on the first ranking and the additional gene expression profile being included in the therapeutic responders profile;
analyzing, using one or more additional machine learning techniques, information corresponding to a plurality of subgroups of individuals in which a neurodevelopmental condition is present to determine respective profiles corresponding to each of the subgroups, the respective subgroup profiles each indicating features of individuals included in the respective subgroups (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculations), the respective subgroup profiles each indicating features of individuals included in the respective subgroups, wherein analyzing the information corresponding to the plurality of subgroups comprises
generating a further gene expression profile for the subgroup of the plurality of subgroups, the further gene expression profile indicating a third group of genes that are up-regulated in individuals included in the subgroup and a fourth group of genes that are down-regulated in individuals included in the subgroup;
determining an amount of overlap between the plurality of features included in the therapeutic responders profile and the features of individuals included in the respective subgroup profiles (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data) wherein determining the amount of overlap comprises
determining a measure of similarity between the additional gene expression profile included in the therapeutic responders profile and the further gene expression profile for the subgroup, the measure of similarity corresponding to at least a portion of the amount of overlap between the plurality of features included in the therapeutic responders profile and a number of features corresponding to the individuals included in the subgroup;
determining a subgroup of the plurality of subgroups that has at least a threshold amount of overlap between the plurality of features included in the therapeutic responders profile and a number of features corresponding to individuals included in the subgroup profile (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data); and
determining a probability that the therapeutic is a candidate treatment for the neurodevelopmental condition with respect to the subgroup (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculating a probability).
Independent claim 11 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
analyzing, using one or more machine learning techniques, the gene expression profile in relation to the genetic data obtained from the at least one data source to determine one or more genes included in the gene expression profile that have at least a threshold amount of representation in at least one of the co-occurring condition genetic data, the phenotype classification genetic data, or the biological pathway genetic data (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculations);
determining a therapeutic responders profile that includes a plurality of features, at least a portion of the plurality of features corresponding to the one or more genes (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data), wherein determining the therapeutic responders profile comprises
determining a first ranking of a gene included in the gene expression profile based on an amount of up-regulation of the gene in response to the therapeutic or an amount of down-regulation of the gene in response to the therapeutic;
determining that the gene is present in at least one of the co-occurring condition genetic data, phenotype classification genetic data, or biological pathway genetic data; and
generating an additional gene expression profile that includes the gene with the gene having a second ranking in the additional gene expression profile, wherein the second ranking is based on the first ranking, the additional gene expression profile is included in the therapeutic responders profile, and the additional gene expression profile indicates up-regulation of a third group of genes that includes at least a portion of the first group of genes and down-regulation of a fourth group of genes that includes at least a portion of the second group of genes;
analyzing, using one or more additional machine learning techniques, information corresponding to a plurality of subgroups of individuals in which a neurodevelopmental condition is present to determine respective subgroup profiles corresponding to each of the subgroups, the respective subgroup profiles each indicating features of individuals included in the respective subgroups (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculations), wherein the information corresponding to the plurality of subgroups of individuals in which the neurodevelopmental condition is present includes genetic information of a plurality of individuals included in the plurality of subgroups; and
analyzing the information corresponding to the plurality of subgroups of individuals in which the neurodevelopmental condition is present to determine the respective subgroup profiles corresponding to each of the subgroups comprises determining, based on the genetic information, up-regulation of a fifth group of genes in the plurality of individuals and down-regulation of a sixth group of genes in the plurality of individuals; and
generating a subgroup gene expression profile that includes the fifth group of genes and the sixth group of genes, the subgroup gene expression profile being included in the subgroup profile;
determining an amount of overlap between the plurality of features included in the therapeutic responders profile and the features of individuals included in the respective subgroup profiles (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data), wherein determining the amount of overlap comprises comparing individual genes selected from the third group of genes with individual genes included in the sixth group of genes;
determining a number of first pairs of shared genes between the individual genes included in the third group of genes and the individual genes included in the sixth group of genes with each first pair of shared genes including one gene included in the third group of genes and an additional gene included in the sixth group of genes;
determining a number of first pairs of differing genes between the individual genes included in the third group of genes and the individual genes included in the sixth group of genes with each first pair of differing genes including a gene included in the third group of genes and another gene included in the sixth group of genes;
increasing a value of a first measure of similarity based on the number of first pairs of shared genes;
decreasing the value of the first measure of similarity based on the number of first pairs of differing genes;
comparing individual genes selected from the fourth group of genes with individual genes included in the fifth group of genes;
determining a number of second pairs of shared genes between the individual genes included in the fourth group of genes and the individual genes included in the fifth group of genes with each second pair of shared genes including one gene included in the fourth group of genes and an additional gene included in the fifth group of genes;
determining a number of second pairs of differing genes between the individual genes included in the fourth group of genes and the individual genes included in the fifth group of genes with each second pair of differing genes including a gene included in the fourth group of genes and another gene included in the fifth group of genes;
increasing a value of a second measure of similarity based on the number of second pairs of shared genes;
decreasing the value of the second measure of similarity based on the number of second pairs of differing genes; and
combining the first measure of similarity and the second measure of similarity to generate an overall measure of similarity between the additional gene expression profile and the subgroup gene expression profile, wherein a probability that the therapeutic is a candidate treatment for the neurodevelopmental condition with respect to the subgroup is based at least partly on the overall measure of similarity;
determining a subgroup of the plurality of subgroups that has at least a threshold amount of overlap between the plurality of features included in the therapeutic responders profile and a number of features corresponding to individuals included in the subgroup profile (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data); and
determining the probability that the therapeutic is a candidate treatment for the neurodevelopmental condition with respect to the subgroup (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculating a probability).
Independent claim 18 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
analyzing the target profile data and protein interaction data in relation to the genetic data obtained from the at least one data source to determine one or more genes included in the network of genes that have at least a threshold amount of representation in at least one of the co-occurring condition genetic data, the phenotype classification genetic data, or the biological pathway genetic data (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data);
determining a therapeutic responders profile that includes a plurality of features, at least a portion of the plurality of features corresponding to the one or more genes (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data);
analyzing, using one or more machine learning techniques, information corresponding to a plurality of subgroups of individuals in which a neurodevelopmental condition is present to determine respective subgroup profiles corresponding to each of the subgroups, the respective subgroup profiles each indicating features of individuals included in the respective subgroups (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculations);
determining an amount of overlap between the plurality of features included in the therapeutic responders profile and the features of individuals included in the respective subgroup profiles (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data);
determining a subgroup of the plurality of subgroups that has at least a threshold amount of overlap between the plurality of features included in the therapeutic responders profile and a number of features corresponding to individuals included in the subgroup profile (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data); and
determining a probability that the therapeutic is a candidate treatment for the neurodevelopmental condition with respect to the subgroup (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculating a probability).
Independent claims 1, 11, and 18, and those claims dependent therefrom, further recite a law of nature by associating genomic data (e.g., at least one of co-occurring condition genetic data, phenotype classification genetic data, or biological pathway genetic data) with phenotypes (e.g., a therapeutic responders profile), i.e., a genotype-phenotype correlation (MPEP 2106.04(b)).
Dependent claims 2-10, 12-17, 19, and 20 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 2 further recites:
the co-occurring condition genetic data is related to a first number of genes that are over-expressed in a group of first individuals in which the neurodevelopmental condition and an additional biological condition are present and a second number of genes that are under-expressed in the group of first individuals in which the neurodevelopmental condition and the additional biological condition are present (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data);
the phenotype classification genetic data indicates one or more genes that correspond to at least one phenotype of a group of second individuals in which the neurodevelopmental condition is present (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data); and
the biological pathway genetic data indicates one or more genes that are expressed in relation to disruption of at least one biological pathway in a group of third individuals in which the neurodevelopmental condition is present (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data).
Dependent claim 3 further recites:
at least one first individual included in the group of first individuals is different from at least one second individual included in the group of second individuals and from at least one third individual included in the group of third individuals (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data); and
at least one additional second individual included in the group of second individuals is different from at least one additional third individual included in the group of third individuals (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data).
Dependent claim 5 further recites:
determining that an additional gene included in the gene expression profile is not present in at least one of the co-occurring condition genetic data, phenotype classification genetic data, or biological pathway genetic data (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data); and
determining that the additional gene is to be excluded from the additional gene expression profile (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data).
Dependent claim 7 further recites:
the therapeutic responders profile includes at least one of a biological pathway that is disrupted in individuals in which the neurodevelopmental condition is present, a co-occurring biological condition that is present in individuals in which the neurodevelopmental condition is present, a phenotype that is related to individuals in which the neurodevelopmental condition is present, levels of analytes present in individuals in which the neurodevelopmental condition is present, or a morphological condition that is present in individuals in which the neurodevelopmental condition is present (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data).
Dependent claim 8 further recites:
the probability that the therapeutic is a candidate treatment for the neurodevelopmental condition with respect to the subgroup corresponds to a probability that the therapeutic alleviates at least a portion of one or more symptoms of the neurodevelopmental condition present in individuals included in the subgroup (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculating a probability).
Dependent claim 9 further recites:
determining a first number of genes of individuals included in a subgroup of the plurality of subgroups that are up-regulated (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculating a number);
determining a second number of genes that are up-regulated by the therapeutic (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculating a number); and
analyzing the first number of genes with respect to the second number of genes to determine a probability that the subgroup of the plurality of subgroups are adverse responders to the therapeutic (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculating a probability).
Dependent claim 10 further recites:
determining a first number of genes of individuals included in a subgroup of the plurality of subgroups that are down-regulated (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculating a number);
determining a second number of genes that are down-regulated by the therapeutic (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculating a number); and
analyzing the first number of genes with respect to the second number of genes to determine a probability that the subgroup of the plurality of subgroups are adverse responders to the therapeutic (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data; and mathematical concepts, e.g., calculating a probability).
Dependent claim 12 further recites:
generating a ranked list of genes based on respective amounts of up-regulation and respective amounts of down-regulation of a plurality of genes in response to the therapeutic (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data);
determining a first number of genes of the ranked list that have at least a threshold amount of up-regulation (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data); and
determining a second number of genes of the ranked list that have at least a threshold amount of down-regulation (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data); and
the first group of genes included in the gene expression profile includes the first number of genes and the second group of genes included in the gene expression profile includes the second number of genes (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data).
Dependent claim 19 further recites:
the neurodevelopmental condition is autism spectrum disorder (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data).
Dependent claim 20 further recites:
analyzing at least one of deoxyribonucleic acid (DNA) sequencing information or ribonucleic acid (RNA) sequencing information of individuals included in the subgroup to determine the one or more genes included in the plurality of features (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data); and
analyzing at least one of DNA sequencing information, RNA sequencing information, or metabolomic information of the subgroup to determine one or more biological pathways modified in response to the neurodevelopmental condition (i.e., mental processes, e.g., assessing and evaluating data, and/or organizing/formatting data).
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., determining a therapeutic responders profile that includes a plurality of features, at least a portion of the plurality of features corresponding to the one or more genes; and determining an amount of overlap between the plurality of features included in the therapeutic responders profile and the features of individuals included in the respective subgroup profiles), 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., using one or more additional machine learning techniques; and determining a probability that the therapeutic is a candidate treatment for the neurodevelopmental condition with respect to the subgroup) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind. Furthermore, a law of nature correlating a genotype-phenotype relationship is identified at Eligibility Step 2A Prong One.
Therefore, claims 1-3, 5, 7-12, and 18-20 recite an abstract idea and a law of nature.
[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 2, 3, 5, 7, 8, and 19 do not further 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:
a computing system including one or more hardware processors and memory;
obtaining genetic data from at least one data source including at least one of co-occurring condition genetic data, phenotype classification genetic data, or biological pathway genetic data; and
obtaining a gene expression profile corresponding to a therapeutic, the gene expression profile indicating a first group of genes that are up-regulated in response to the therapeutic and a second group of genes that are down-regulated in response to the therapeutic.
The additional elements in independent claim 11 include:
one or more hardware processors;
one or more non-transitory computer-readable storage media storing computer readable instructions;
obtaining genetic data from at least one data source including at least one of co-occurring condition genetic data, phenotype classification genetic data, or biological pathway genetic data; and
obtaining a gene expression profile corresponding to a therapeutic, the gene expression profile indicating a first group of genes that are up-regulated in response to the therapeutic and a second group of genes that are down-regulated in response to the therapeutic.
The additional elements in independent claim 18 include:
one or more hardware processors;
one or more non-transitory computer-readable storage media storing computer readable instructions;
obtaining genetic data from at least one data source including at least one of co-occurring condition genetic data, phenotype classification genetic data, or biological pathway genetic data; and
obtaining target profile data of a therapeutic and human protein interaction data indicating a group of genes in a network of genes that are regulated in response to the therapeutic and interactions between the group of genes with proteins in a population of humans.
The additional elements in dependent claims 9, 10, 12, and 20 include:
a computing system (claims 9 and10);
one or more non-transitory computer-readable storage media store additional computer readable instructions (claims 12 and 20); and
one or more hardware processors (claims 12 and 20).
The additional elements of a computing system (claims 1, 9, and 10); one or more hardware processors (claims 1, 11, 12, 18, and 20); memory (claim 1); and one or more non-transitory computer-readable storage media store additional computer readable instructions (claims 11, 12, 18, and 20); invoke a computer merely as a tool 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, does not integrate the judicial exceptions into a practical application (see MPEP 2106.04(d)(1)).
The additional element of obtaining data (claims 1, 11, and 18) is merely a pre-solution activity of gathering data for use in the claimed process – a nominal addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
Thus, the additionally recited elements merely invoke a computer and/or computer related components as tools; and/or amount to insignificant extra-solution activity; and as such, when all limitations in claims 1-3, 5, 7-12, and 18-20 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, and therefore claims 1-3, 5, 7-12, and 18-20 are directed to an abstract idea (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 2, 3, 5, 7, 8, and 19 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claims 1, 11, and 18 and dependent claims 9, 10, 12, and 20 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 a computing system (claims 1, 9, and 10); one or more hardware processors (claims 1, 11, 12, 18, and 20); memory (claim 1); and one or more non-transitory computer-readable storage media store additional computer readable instructions (claims 11, 12, 18, and 20); and obtaining data (claims 1, 11, and 18); 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).
Therefore, when taken alone (i.e., individually), all additional elements in claims 1-3, 5, 7-12, and 18-20 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as an ordered combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1-3, 5, 7-12, and 18-20 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
[Step 2B: NO]
Response to Arguments
The Applicant’s arguments/remarks received 29 May 2026 have been fully considered, but are not persuasive.
The Applicant states on page 11 (as filed) of the Remarks that the amended claims are not directed merely to generalized ‘analysis’ of biological information, and that as amended, claim 1 requires a specific computational workflow in which the system obtains a therapeutic gene-expression profile including up-regulated and down-regulated genes, identifies genes in that therapeutic profile that have threshold representation in defined categories of genetic data, generates an additional gene-expression profile included in a therapeutic responders profile, generates a subgroup gene-expression profile including subgroup up-regulated and down-regulated genes, and determines a similarity measure between the therapeutic-side and subgroup-side gene-expression profiles as part of determining whether the therapeutic is a candidate treatment for the subgroup. The Applicant further states that claim 11 relates to a system with the same type of workflow, including first and second similarity measures and an overall measure of similarity between the additional gene expression profile and the subgroup gene expression profile. The Applicant further states on page 12 (para. 2) that the amended claims do not merely contain high-level ‘analyzing,’ ‘determining,’ and ‘probability,’ nor merely state a desired result, but rather, they recite how the therapeutic responders profile is constructed, how the subgroup gene-expression profile is generated, and how overlap is quantified through profile comparison. The Applicant further states that the application as filed describes the invention as a computational biology system for identifying one or more therapeutics that can be prescribed as treatment for a neurodevelopmental condition, and further states that the system can determine one or more therapeutics that have at least a threshold probability of relieving symptoms of a group of individuals and that grouping individuals according to characteristics that are not merely behavioral characteristics can increase the probability of identifying therapeutics that can effectively treat the condition. The Applicant further states (para. 3) that the amended claims are directed to a specific machine-implemented workflow for therapeutic-to-subgroup matching based on gene-expression profiles and defined similarity logic, and they produce a subgroup-specific treatment-candidacy output rather than merely reporting a natural correlation at a high level of abstraction, and the Applicant further states that the claims are also materially different from a generic instruction to apply machine learning to data, and that the recited profile-generation and similarity-computation steps impose meaningful limits on claim scope and define the manner in which the result is obtained, and therefore, the claims integrate any alleged judicial exception into a practical application. The Applicant further states (para. 4) that the features are not limited to generic processors or storage media, and are not limited to mere data gathering, and further states that the amended claims require construction of a therapeutic responders profile from genes in a therapeutic gene-expression profile that satisfy threshold representation criteria in defined genetic-data categories, construction of subgroup gene-expression profiles, and profile-to-profile similarity analysis that drives determination of the subgroup-specific treatment candidacy, and further states that these ordered combinations are sufficient to satisfy the eligibility requirements.
These arguments/remarks are not persuasive, because first, the MPEP at 2106.04(a) states that examiners should determine whether a claim recites an abstract idea by (1) identifying the specific limitation(s) in the claim under examination that the examiners believes recites an abstract idea, and (2) determining whether the identified limitation(s) fall within at last one of the groupings of abstract ideas. If the identified limitation(s) falls within at least one of the groupings of abstract ideas, it is reasonable to conclude that the claim recites an abstract idea in Step 2A Prong One. As noted in the rejection above at Eligibility Step 2A Prong One, claim limitations are identified that recite abstract ideas from one or both of the judicial exception groupings of mathematical concepts and mental processes, e.g., claim 1 recites the limitation “analyzing, by the computing system and using one or more machine learning techniques, the gene expression profile in relation to the genetic data obtained from the at least one data source to determine one or more genes included in the gene expression profile that have at least a threshold amount of representation in at least one of the co-occurring condition genetic data, the phenotype classification genetic data, or the biological pathway genetic data.” Using this limitation for illustrative purpose, claims can recite a judicial exception even if they are claimed as being performed on a computer (MPEP 2106.04(a)(2)(III)(C)) (“by the computing system”); “using one or more machine learning techniques” at least recites mathematical concepts because the primary objective of any machine learning algorithm is to approximate a function, often a high-order non-linear function. This approximation seeks to establish a mapping, assuming its existence, between input and output data within a given training dataset. The acquired approximated function, commonly referred to as a model, is then utilized to predict the most probable output for unseen data. Additionally, a machine learning model can also be calculated manually (i.e., in the human mind with the aid of pen and paper) depending on the type of model, e.g., the simplest type of machine learning model could be a linear regression, which predicts a continuous numerical output by fitting a straight line (y = mx + b) to data, by using an input variable (x) and an output variable (y), making its mathematical relationship easy to calculate and interpret. Further regarding the foregoing illustrative claim 1 limitation, “analyzing the gene expression profile in relation to the genetic data obtained from the at least one data source to determine one or more genes included in the gene expression profile that have at least a threshold amount of representation in at least one of the co-occurring condition genetic data, the phenotype classification genetic data, or the biological pathway genetic data,” this limitation is identified as a mental process because the fundamental nature of analyzing genomic data can be practically performed in the human mind, particularly with the aid of pen and paper, and the amount of data (e.g., file size and/or gigabytes of data processing) does not change the fundamental nature of the process of analyzing genomic data, and therefore does not take the process out of the realm of the human mind. Second, regarding the Applicant’s argument that “that the claims are also materially different from a generic instruction to apply machine learning to data,” it is noted that the machine learning limitations in the instant claims are identified as judicial exceptions at Step 2A Prong One in the above rejection, as opposed to, for example, an additional element that might be characterized in such a way as merely “a generic instruction to apply machine learning to data.” Third, regarding the Applicant’s argument that “the recited profile-generation and similarity-computation steps impose meaningful limits on claim scope and define the manner in which the result is obtained, and therefore, the claims integrate any alleged judicial exception into a practical application,” it is noted that the MPEP at 2106.04(d) states that 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” and “Examiners evaluate integration into a practical application by: (1) identifying whether there are any additional elements recited in the claim beyond the judicial exception(s); and (2) evaluating those additional elements individually and in combination to determine whether they integrate the exception into a practical application, using one or more of the considerations introduced in subsection I at 2106.04(d) of the MPEP, and discussed in more detail in MPEP §§ 2106.04(d)(1), 2106.04(d)(2), 2106.05(a) through (c) and 2106.05(e) through (h).” However, as noted in the above rejection, when all limitations in claims 1-3, 5, 7-12, and 18-20 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, and therefore claims 1-3, 5, 7-12, and 18-20 are directed to an abstract idea. Fourth, regarding the Applicant’s argument that “the features are not limited to generic processors or storage media, and are not limited to mere data gathering,” it is noted that a limitation such as “one or more hardware processors” and/or “one or more non-transitory computer-readable storage media” are limitations that are in fact generic to the possible species of hardware processors and storage media, and further noted that a step of obtaining data (i.e., receiving data) at a computer for a purpose of performing analysis using the data, is a limitation that is a mere data gathering steps, i.e., insignificant extra-solution activity, as noted and discussed in the above rejection. Fifth, regarding the Applicant’s argument that “these ordered combinations are sufficient to satisfy the eligibility requirements,” it is noted that the evaluation of ‘an ordered combination’ is conducted at Step 2B of the eligibility analysis, where only the additional elements identified at Step 2A Prong Two are carried over for further evaluation at Step 2B. Accordingly, it is further noted that several of the limitations in the Applicant’s foregoing argument (i.e., “these ordered combinations…”) are identified as judicial exceptions at Step 2A Prong One in the above rejection, and therefore are not carried over to Step 2B for further evaluation.
The Applicant states on page 12 (para. 5) of the Remarks that the Applicant requests that the pending claims be examined according to the framework and analysis set forth in Enfish and in McRO, and the Applicant further states that the analysis in both Enfish and McRO takes place with the first step of the patent eligibility analysis set forth in the Alice decision, which corresponds to the MPEP, Step 2A, Prong One analysis. The Applicant further states (page 13, para. 1) that in Alice, the Supreme Court identified a framework for determining whether claimed subject matter is directed to an abstract idea, and that according to the Alice decision, the Court must first determine whether the claims at issue are directed to a patent-ineligible concept. The Applicant further states that the analysis in Alice at step one focused on determining whether the claims purport to improve the functioning of the computer itself or effect an improvement in any other technology or technical field. The Applicant further states that this analysis is performed before the additional elements analysis performed under step 2 of the Alice patent eligibility framework/MPEP, Step 2A, Prong Two and Step 2B analysis. The Applicant sets forth the Enfish framework for evaluating subject matter eligibility on pages 13-14 of the Remarks, and further sets forth an analysis of the pending claims under the Enfish patent eligibility framework on pages 15-18 of the Remarks. In particular, the Applicant states on page 15 (para. 3) that claim 1 is directed to patent eligible subject matter because the specific process enumerated in claim 1 provides improvements in the field of identifying treatments for patients having neurodevelopmental conditions, and further states that the specification of the present application (e.g., at paras. [0027], [0030], and [0035]) details the problems with existing technologies in relation to identifying effective treatments for individuals having neurodevelopmental conditions and how the claimed features provide solutions to these problems. The Applicant further states on page 18 (paras. 2-3) these features of claim 1 as well as the corresponding features of claims 11 and 18 are also directed to providing an improvement in the field of identifying candidate treatments for various groups of patients in which a neurodevelopmental condition is present, and further states that as a result of providing the technical improvements to the technical problems described in the specification related to identifying treatments for individuals having a neurodevelopmental condition, that similar to the claim in Enfish, claims 1, 11, and 18 are directed to patent eligible subject matter under the Alice Step One / MPEP Step 2A, Prong One analysis.
These arguments/remarks are not persuasive, because first, the framework and analysis set forth in both Enfish and in McRO is incorporated into the eligibility analysis at MPEP 2106, and in particular, with regard to the Applicant’s foregoing arguments, incorporated at 2106.04(d)(1), where it states a “claim reciting a judicial exception is not directed to the judicial exception if it also recites additional elements demonstrating that the claim as a whole integrates the exception into a practical application. One way to demonstrate such integration is when the claimed invention improves the functioning of a computer or improves another technology or technical field.” Second, regarding the Applicant’s attempt at analogizing the instant claims to Enfish, the instant claims are not analogous to the claims in Enfish, because the instant claims broadly encompass a data analysis workflow comprising steps of identifying profiles for subgroups of individuals and then analyzing the profiles of these subgroups with respect to additional profiles of therapeutic responders in order to determine a probability that the therapeutic is a candidate treatment for the neurodevelopmental condition with respect to the subgroup, whereas in contrast, the improvement recited in Enfish is found in a data structure (i.e., a data structure as a programmatic mechanism used within computer memory to store and manipulate data efficiently) that corresponds to a storage and retrieval structure configured in a computer memory comprising a self-referential table that is designed to improve the way a computer stores and retrieves data in memory, and thus is an improvement to computer functionality itself. Stated a different way, the improvement was found in the structure of the table itself (e.g., relationships between rows and columns) as arranged (i.e., configured) in a physical memory device, irrespective of any particular data being stored or searched (or analyzed). Third, with regard to the Applicant’s attempt at analogizing the instant claims with the eligibility determination in McRO, it is noted that in McRO, when looked at as a whole, claim 1 is directed to a patentable, technological improvement over the existing, manual 3-D animation techniques, i.e., the claim recited “a specific asserted improvement in computer animation” that was directed to the creation of something physical – namely, the display of lip synchronization and facial expressions of animated characters on screens for viewing by human eyes, and therefore was determined to not be directed to an unpatentable abstract idea at Eligibility Step 2A (i.e., Alice step one). Unlike the technological improvement found in McRO, the instant claimed improvement of more effectively determining treatments for different groups of patients having a neurodevelopmental condition by analyzing profiles of individual subgroups of patients with respect to therapeutics responder’s profiles, is a purported improvement to the abstract idea (i.e., data analysis), and not an improvement to computer functionality itself, or an improvement to another technology or technical field.
The Applicant states on page 18 (para. 4) of the Remarks that under the Alice Step Two / MPEP Step 2A, Prong 2 and Step 2B, elements of the claims are not directed to a mental process or recite a mathematical concept, and further states (para. 5) that the Office action (mailed 29 December 2025) summarily categorized many elements of the independent and dependent claims as being included in the mental steps and mathematical concepts grouping of abstract ideas, however, the Office action provides no explanations as to why these claim elements are directed to mathematical concepts or how the operations related to the claim elements can be reasonably performed in the human mind, and thus, the Applicant requests that the Office provide an explanation as to why the features of claim 1 and the corresponding features of claims 11 and 18 (Remarks, pages 18-19) are included in the mental process and mathematical concepts grouping of abstract ideas. The Applicant points to the MPEP at 2106.04(a)(2)(I) and further states on page 19 (bottom) that several features of claim 1 and the corresponding features of claims 11 and 18 do not fall under the mathematical concepts or mental steps grouping of abstract ideas, and further states on page 20 (top & middle) that more generally, the MPEP at 2106.04 provides additional guidance with regard to the difference between claimed features that recite an abstract idea and claimed features that involve an abstract idea. The Applicant further states on page 20 (bottom) that the features of claim 1 provided in the arguments and corresponding features of claims 11 and 18 do not actually recite mathematical relationships, mathematical formulas, or mathematical calculations, but are based on or involve a mathematical concept, and that support for the assertion that these features do not recite mathematical concepts, but are based on or involve mathematical concepts can be found in the reasoning applied to the finding of features in subject matter eligibility examples 38 and 39. The Applicant points to the MPEP at 2106.04(a)(2)(III), and further states on page 21 (para. 3) that additionally, with regard to the mental steps characterization of the claims in the Office action, the Applicant notes that mental processes are concepts performed with the human mind, such as observation, evaluation, judgement, and opinion, and further states that a claim directed to operations that cannot practically be performed in the human mind does not recite a mental process, and further states that the analysis as to whether a claim can practically be performed in the human mind is based on an interpretation of the claim in view of the specification as interpreted by one of ordinary skill in the art, and in particular, the scope of a claim is based on the broadest reasonable interpretation in light of the specification as it would be interpreted by one of ordinary skill in the art. The Applicant further states that one of ordinary skill in the art would recognize that the claims recite features that cannot be practically performed in the human mind. The Applicant further states (para. 4) that the features of claim 1 and the corresponding features of claims 11 and 18 directed to the generating of therapeutic responders profiles, the subgroup profiles, and the analysis of these profiles with respect to one another also cannot practically be performed in the human mind, and that for example, determining an amount of overlap between the plurality of features included in the therapeutic responders profile and the features of individuals included in the respective subgroup profiles, is a complex process, as described at least at paragraph [00236] of the present application, and that one skilled in the art would recognize cannot reasonable be performed in the human mind. The Applicant further states (para. 5) that accordingly, any interpretation of the pending claims as including features that could reasonable be performed by the human mind is based on an unreasonably broad interpretation of the claims and is limited to consideration of only select portions of the claim language, without consideration of the Applicant’s specification or the understanding of a person of ordinary skill in the art, and that for these reasons, claims 1, 11, and 18 include features, as properly interpreted, that are not capable of being practically performed in the human mind, and therefore, claims 1, 11, and 18 are not directed to a mental process and are not directed to an abstract idea.
These arguments/remarks are not persuasive, because, first, for the reasons already provided in the foregoing responses to arguments. Second, with regard to the Applicant’s assertion that “the features of claim 1 provided in the arguments and corresponding features of claims 11 and 18 do not actually recite mathematical relationships, mathematical formulas, or mathematical calculations, but are based on or involve a mathematical concept” (emphasis added), it is noted that the MPEP at 2106.04(a)(2)(I) that a mathematical concept need not be expressed in mathematical symbols, because words used in a claim operating on data to solve a problem can serve the same purpose as a formula, and still further, there is no particular word or set of words that indicates a claim recites a mathematical concept, that is, a claim does not have to recite the word “calculating” in order to be considered a mathematical calculation. Accordingly, at least the instant claimed limitation reciting “using one or more machine learning techniques” is determined to recite a mathematical concept at Step 2A Prong One, as discussed in more detail in the foregoing responses to arguments. Third, with regard to the Applicant’s attempt to analogize the instant claims to Examples 38 and 39 of the 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG), it is noted that the instant claims are not analogous to Example 38 because the instant claims do not recite a method for providing a digital computer simulation of an analog audio mixer, and the instant claims are not analogous to Example 39 because the instant claims do not recite a method for training a neural network for facial detection. Furthermore, Examples 38 and 39 consider hypothetical methods and are only intended to be illustrative of the claim analysis process performed using MPEP 2106, and of the particular issues noted in the particular Example. Each Example should be interpreted based on the fact patterns set forth in the Example's claim, as other fact patterns may have different eligibility outcomes, as evidenced in the rejection of the instant claims above. While the exemplified analyses of Examples 38 & 39 conclude that each claim does not recite any judicial exceptions (e.g., mental processes or mathematical concepts), these conclusions are determined from the particular fact pattern of the hypothetical claimed processes, and should not be generalized as an axiom that claim limitations reciting training a neural network and/or providing a digital computer simulation do not recite judicial exceptions. The Applicant is directed to the July 2024 Subject Matter Eligibility Examples (examples 47, 48, and 49) for updated guidance on the eligibility analysis of claims that recite limitations specific to artificial intelligence, particularly the use of machine learning models.
Claim Rejections - 35 USC § 103
The rejection of claims 1-20 under 35 U.S.C. 103 as being unpatentable over Zhao et al. and Narain et al. and Athey et al. in the Office action mailed 29 December 2025 has been withdrawn in view of the amendment received 29 May 2026.
Response to Arguments
The Applicant’s arguments/remarks received 29 May 2026 have been fully considered, and are persuasive.
The Applicant states on page 22 (bottom) of the Remarks that Zhao is directed to genotype/phenotype subgrouping and discriminant genotype markers in autism spectrum disorder, not to therapeutic matching, and further states that Narain and Athey do not cure the deficiencies of Zhao. The Applicant further states on page 23 (top) that neither reference teaches the amended claim structure in which a therapeutic gene-expression profile is filtered into an additional gene-expression profile included in a therapeutic responders profile and then compared with a subgroup gene-expression profile to determine similarity and subgroup-specific treatment candidacy. The Applicant further states (para. 2) that amended claim 1 requires, among others, generation of an additional gene-expression profile included in the therapeutic responders profile and a further gene-expression profile for the subgroup, followed by determination of a measure of similarity between those two profiles, and that these features are not disclosed by the cited prior art. The Applicant further states (para. 3) that amended claim 11 goes further and requires third/fourth therapeutic gene groups, fifth/sixth subgroup gene groups, first and second similarity measures, and an overall measure of similarity that is tied to treatment candidacy, and that particularly, Zhao does not disclose these features. The Applicant further states that the claims as amended are not directed merely to using machine learning in a biomedical context, but are directed to a particular therapeutic-to-subgroup matching architecture that proceeds through therapeutic gene-expression profiling, biologically filtered therapeutic responders profiling, subgroup gene-expression profiling, and similarity-based treatment-candidacy determination, and further states that the cited art does not teach or suggest that sequence of operations as a whole. The Applicant further states on page 24 (para. 2) that neither Narain, Athey, nor the combination of Narain and Athey provide any teaching or suggestion of “determining, by the computing system, an amount of overlap between the plurality of features included in the therapeutic responders profile and the features of individuals included in the respective subgroup profiles … [by] determining a measure of similarity … corresponding to at least a portion of the amount of overlap between the plurality of features included in the therapeutic responders profile and the number of features corresponding to the individuals included in the subgroup,” as recited in amended claim 1. The Applicant further states (page 24, para. 3, and page 25, para. 1) that Narain does not provide any teaching or suggestion directed to generating two sets of profiles that include respective sets of genes that have been determined using different data sets and then analyzing these two profiles to determine an amount of overlap between them, as in amended claim 1, and further states on page 25 (para. 2) that similarly, Athey also provides not teaching or suggestion directed to generating two sets of profiles that include respective sets of genes that have been determined using different data sets and then analyzing these two profiles to determine an amount of overlap between them, as in amended claim 1. The Applicant further states (para. 4) that claim 11 provides additional details about how the therapeutic responders profile is determined and how that amount of overlap is determined between the therapeutic responders profile and the subgroup profiles, and further states that neither the teaching of Narain nor the teaching of Athey correspond to the specific features of amended claim 11 directed to how the therapeutic responders profile is determined and do not correspond to the specific features of amended claim 11 directed to determining the amount of overlap between the therapeutic responders profile and the subgroup profiles.
These arguments/remarks are persuasive.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/
Primary Examiner, Art Unit 1687
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