DETAILED ACTION
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 29 June 2026 has been entered.
Status of the Claims
Claim set received 26 May 2026 has been entered into the application.
Claims 1, 12, and 25 are amended.
Claim 5 is cancelled.
Claims 2, 6-10, 13, and 15-17 are previously cancelled.
Claims 26-30 are new.
Claim 30 is withdrawn.
Claims 1, 3-4, 11-12, 14, and 18-29 are pending.
Priority
This Application is 371 of PCT/US2019/033845 filed 23 May 2019 which claims benefit to U.S Provisional Applicant 62/793,793 filed 17 January 2019 and U.S Provisional Application 62/675,486 filed 23 May 2018.
Examiner’s Note
Newly submitted claim 30 is directed to an invention that is independent or distinct from the invention originally claimed for the following reasons:
Claim 30 is drawn to identifying at least one de-novo or inherited structural variation in genomes of a population of subjects having or at risk of developing a disorder or condition having a genetic component as compared to claims 1 and 28 reciting identifying at least one de-novo or inherited structural variation in a genome of a subject having or at risk of developing autism.
Claim 30 involves analyzing populations of subjects (i.e., family trios: mother-father-child) for identifying structural variations across the population of subjects using CCC analysis and combining the identified NMI and the conserved regions identified by the CCC analysis.
Claims 1, 28, and 30 recite:
Claims 1 and 28 recite assembling single nucleotide polymorphism (SNP) data from the subject and the subject's biological mother and the subject's biological father.
Claim 30 recites assembling single nucleotide polymorphism (SNP) data from each of a plurality of parent- child trios.
Claims 1 and 28 recite comparing, using a processor, the subject's SNP data, the father's SNP data, and the mother's SNP data.
Claim 30 recites comparing, using a processor, the SNP data of each trio to identify SNP loci that do not conform to Mendelian inheritance.
Claims 1, 28, and 30 recite similar language for the identifying specific SNPs in the subject's SNP data that display non-Mendelian inheritance pattern (NMI) step.
Claims 1, 28, and 30 recite similar language for the filtering out specific SNPs in the subject's SNP data that display NMI and correspond to known structural variations by cross-referencing each NMI locus against a database.
Claim 30 recites identifying conserved regions of the genomes by applying a custom correlation coefficient (CCC) analysis to the genotypes of the parent-child trios to identify evolutionary conserved blocs disrupted by structural variation.
Claim 30 recites identifying structural variations across the population of subjects by combining the identified NMI and the conserved regions identified by the CCC analysis, wherein each identified structural variation resides in a gene having an identified CCC bloc.
Claims 1, 28, and 30 recite wherein the structural variation is within or near a gene associated with the subject's disorder or condition.
Here, although claims 1 and 28 and claim 30 recite similar limitations, claim 30 is drawn to distinct method for analyzing populations of families for non-Mendelian loci for identifying NMI and conserved regions using CCC analysis and combining the NMI and conserved regions for identifying structural variations across the population of subjects.
Since applicant has received an action on the merits for the originally presented invention, this invention has been constructively elected by original presentation for prosecution on the merits.
Accordingly, claim 30 is withdrawn from consideration as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP § 821.03.
Claim Rejections - 35 USC § 112
35 USC § 112(b)
It is noted the amendments received 26 May 2026 are necessitated by new ground(s) of rejection.
The rejection of claim 1, 3-4, 11-12, 14, and 18-25 under 35 U.S.C § 112(b) in the Office Action mailed 027 March 2026 is withdrawn in view of the amendments received 26 May 2026.
The rejection of claim 5 under 35 U.S.C § 112(b) in the Office Action mailed 027 March 2026 is withdrawn in view of the amendments received 26 May 2026 because the claim was cancelled.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 3-4, 11-12, 14, and 18-29 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1 identifying at least one de-novo step and 28 step (a) recite “identifying at least one de-novo or inherited structural variation in the genome of the subject from the candidate large structural variations, wherein the structural variation is within or near a gene associated with the subject's disorder or condition (claim 1)/ASD (claim 28).” However, the claim 1 is rendered indefinite because there are no steps for determining a disease or condition which can be treated. Here, claim 1 recites identifying de novo or inherited structural variation within or near a gene associated, but it is not clear what is being utilized to determine a therapy, for example, the gene or the structural variation SNPs. Thus, it is not clear if the basis for treating a disease/condition (claim 1) or treating ASD (claim 28) relies on the identified de novo or inherited structural variation of the large candidate structural variation or if claim relies on the gene/ASD gene for treating the disease/ASD with a therapy: stimulus, gene editing, or CAR T cells. Here, while claim 1 does recite “determining a therapy targeting the gene…”, there are no steps of using the identified gene with identified large de novo or inherited structural variations for determining a therapy. Claim 28 does not recite a determining therapy step. It is recommended to amend the claimed steps to recite steps of determining a treatment based on structural variation upstream or downstream (i.e., within or near) of said gene (i.e., gene/ASD) to clarify how treatment is determined and clarify the determined conditions that will be required for treating ASD with either gene therapy or CAR T cells.
Claims 3-4, 11-12, 14, 18-28, and 29 are rejected because they fail to provide limitations to overcome the deficiencies of the base claim(s).
Claim 28 recites “(a) a gene editing technology, wherein sequence is removed back to the SNPs on either side of the structural variation that demonstrate normal Mendelian inheritance, and wherein the homologous chromosomal sequence serves as a guide for replacement of the structural-variation altered sequence”. The claimed step has multiple antecedent basis issues that renders claim 28 indefinite.
First, claim 28 step (a) [line 1] recites “wherein sequence…”. The claimed step lacks antecedent for the “sequence…”. There is insufficient antecedent basis for this limitation in the claim. It is not clear what sequence the “sequence” is referring. It is not clear if the sequence is referring to a sequence (i.e., gene) containing least one de-novo or inherited structural variation, not clear if the sequence is referring to “the structural variation that demonstrate normal Mendelian inheritance”, not clear if the sequence is referring to “the homologous chromosomal sequence”, and/or not clear if the sequence is referring to “the structural-variation altered sequence”. It is recommended to amend the claim to provide antecedent basis for the sequence and amend the claim to clarify what sequence is the “sequence” represent or encompass.
Secondly, claim 28 step (a) [lines 1] recites “the SNP’s on either side…”. There is insufficient antecedent basis for this limitation in the claim. The claimed step lacks antecedent basis for the limitations “the SNPs on either side...”. It is not clear what SNP’s the Applicant is referring. It is not clear if the “SNP’s” are referring to non-Mendelian Inherited (NMI) SNP’s, identified specific SNPs, or subject’s SNP’s because the previous and subsequent claimed steps do not provide as to which SNPs the “SNPs” are referring.
Thirdly, claim 28 step (a) [lines 1-2] recites “the structural variation that demonstrate normal Mendelian inheritance”. There is insufficient antecedent basis for this limitation in the claim. The claimed step lacks antecedent basis for the claimed limitation. It is not clear what sequence “the structural variation that demonstrate normal Mendelian inheritance” is referring to. The previous step does not contain “a structural variation that demonstrate normal Mendelian inheritance”. It is not clear what sequence/structural variation is to be represented as the “structural variation that demonstrate normal Mendelian inheritance”. It is not clear if the “structural variation that demonstrate normal Mendelian inheritance” is referring to the “identified at least one de-novo or inherited structural variation” or the “sequence” of step (a). It is recommended to amend the claim to provide antecedent basis for “the structural variation that demonstrate normal Mendelian inheritance” and amend the claim to clarify what sequence or variation the “the structural variation that demonstrate normal Mendelian inheritance” is to represent or encompass.
Fourthly, claim 28 [lines 2-3] recites “wherein the homologous chromosomal sequence serves as a guide for replacement”. There is insufficient antecedent basis for this limitation in the claim. The claimed step lacks antecedent basis for the claimed limitation. It is not clear what sequence “the homologous chromosomal sequence serves as a guide for replacement” is referring to. The previous step does not contain “the homologous chromosomal sequence serves as a guide for replacement”. It is not clear what sequence is to be represented as the “the homologous chromosomal sequence serves as a guide for replacement”. It is not clear if the “the homologous chromosomal sequence serves as a guide for replacement” is referring to the “sequence containing least one de-novo or inherited structural variation”, not clear if the sequence is referring to “the structural variation that demonstrate normal Mendelian inheritance”, not clear if the sequence is referring to “the homologous chromosomal sequence”, and/or not clear if the sequence is referring to “the structural-variation altered sequence”. It is recommended to amend the claim to provide antecedent basis for the “the structural variation that demonstrate normal Mendelian inheritance” and amend the claim to clarify what sequence or variation the “the structural variation that demonstrate normal Mendelian inheritance” is represent or encompass.
Fifthly, claim 28 [lines 3-4] recites “the structural-variation altered sequence”. The claimed step lacks antecedent basis for the claimed limitation. It is not clear what sequence “” is referring to. There is insufficient antecedent basis for this limitation in the claim. The previous steps do not contain antecedent basis for the claimed limitation. It is not clear what sequence the “the structural-variation altered sequence” is referring because the previous steps do not contain “a structural-variation altered sequence” to which the “the structural-variation altered sequence” is to refer. It is not clear if “the structural-variation altered sequence” is referring to the “sequence [line 1]” or “identified de novo or inherited structural variation”. It is recommended to amend the claim to provide antecedent basis for the “the structural-variation altered sequence” and amend the claim to clarify what sequence the “the structural-variation altered sequence” is represent or encompass.
Moreover, claim 28 step (a) recites “the structural variation that demonstrate normal Mendelian inheritance”. The claimed limitation renders the claim indefinite because it is not clear how “the structural variation that demonstrates normal Mendelian inheritance” is to limit the claim when claim 28 is drawn to identifying and filtering non-Mendelian structural variation. It is further unclear how a non-Mendelian gene (i.e., ASD) can exhibit normal Mendelian structure variation when ASD results from non-Mendelian inheritance because the previous and subsequent claimed steps do not recite any steps for determining whether structural variation on either side of the SNP demonstrate normal Mendelian inheritance. It is not clear how “…SNPs on either side of the structural variation that demonstrate normal Mendelian inheritance” when normal Mendelian inheritance describes how single-gene traits are passed from parents to offspring based on dominant and recessive allele. It is not clear how SNPs of an ASD can demonstrate with a gene is “dominant or recessive” when ASD is not the result of “recessive or dominant” genes (Mendel’s law of segregation and independent assortment), but the result of non-Mendelian methods resulting from traits that can blend, show equal expression, involve multiple genes, or pass down through non-nuclear DNA.
It is further not clear what sequence is to be utilized for/as the guide so that gene therapy can be performed on said subject with ASD because the claimed step recites “the homologous chromosomal sequence serves as a guide for replacement of the structural-variation altered sequence”, and the previous and subsequent claimed steps do not provide “the homologous chromosomal sequence” or provide “the structural-variation altered sequence” that can serve as a guide or act as a sequence being replaced so that gene therapy can be performed on a subject with ASD. Here, it is recommended to amend the claim to provide as to what sequence is to act or serve as the guide.
Next, claim 28 step (b) recites “treating the subject's ASD with at least one of gene therapy...or administering CAR T cells…”. However, the claim is rendered indefinite because there are no steps for determining which therapy to utilize based on the previous identified large candidate de novo and inherit structural variation. For example, it is not clear how CAR T cell therapy limits the claim because the previous and subsequent claimed steps do not provide steps of analyzing large de novo or inherited structural variations of an ASD gene in response to immune responses and/or as a result of immunological dysfunction/pathologies of ASD so that CAR T cell can be used to treat immune responses of ASD patients. Thus, the relationship between identifying large de novo or inherited structural variation within or near the ASD gene and treating ASD with CAT T cells is not clear.
Furthermore, with respect to gene editing, it is not clear how gene therapy limits the claim because the previous and subsequent claimed steps do not provide steps analyzing large de novo or inherited structural variations of an ASD gene so that large candidate de novo or inherited or other sequence can be put back into the original sequence and/or be utilize as a guidance.
Moreover, the claimed step renders the claim indefinite because it is not clear how a sequence is “removed back” to the SNPs on either side of the structural variation that demonstrate normal Mendelian inheritance. It is not clear if the Applicant intend to mean “removed back” or “added/placed back” to the SNPs. It is recommended to amended the claim to provide clarity as to what the Applicant intends to mean by “removed back”.
Claims 29 is rejected because it fails to provide limitations to overcome the deficiencies of the base claim(s).
Claim Rejections - 35 USC § 101
The instant rejection is maintained for reason for record in the Office Action mailed 27 March 2026 and modified in view of the amendments filed 26 May 2026. It is noted the amendments received 26 May 2026 are necessitated by new ground(s) of rejection.
The rejection of claim 5 under 35 U.S.C § 101 in the Office Action mailed 027 March 2026 is withdrawn in view of the amendments received 26 May 2026 because the claim was cancelled.
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, 11-12, 14, and 18-29 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Following the flowchart of the MPEP 2106
Step I - Process, Machine, Manufacture or Composition
Claims 1, 3-5, 11-12, 14, and 18-27 are drawn to a method, so a process.
Claims 28-29 are drawn to a method, so a process.
2A Prong I - Identification of an Abstract Idea
Claim 1 recites:
assembling single nucleotide polymorphism (SNP) data from the subject and the subject's biological mother and the subject's biological father
This step can be performed in the human mind by organizing data to assemble single polymorphism (SNP) from a subject’s biological mother and father and is therefore an abstract idea.
Comparing, using a processor, the subject's SNP data, the father's SNP data, and the mother's SNP data
This step can be performed in the human mind by observing and comparing subject’s, father’s, and mother’s SNP data and is therefore an abstract idea.
identifying specific SNPs in the subject's SNP data that display non-Mendelian inheritance pattern (NMI), wherein each identified specific SNP is scored as an NMI locus and classified as a paternal NMI locus, a maternal NMI locus, or a de novo NMI locus
This step can be performed in the human mind by observing and evaluating the subjects SNP data that displays (NMI) to identify specific SNPs in a subject SNPs and is therefore an abstract idea. The step can be performed in the human mind by observing and evaluating the subjects SNP data that displays (NMI) to score and classify each identified specific SNP and is therefore an abstract idea.
filtering out specific SNPs in the subject's SNP data that display NMI and correspond to known structural variation by cross-referencing each NMI locus against a database of known insertions, deletions, inversions, mobile element insertions, and INDELs, thereby producing filtered NMI loci
This step can be performed in the human mind by observing, comparing (i.e., cross-referencing), and evaluating information (i.e., nucleic acid data) each NMI locus against a database for filtering data (i.e., SNP’s) to produce filtered NMI loci data and is therefore an abstract idea. This step encompasses performing mathematical comparison (i.e., using equalities and inequalities) for filtering information (i.e., SNP data) which reads on abstract ideas.
sorting the filtered NMI loci by chromosomal position and computing a running sum of the position-sorted filtered NMI loci using a sliding window, thereby identifying candidate large structural variations comprising runs of consecutive NMI loci
This step can be performed in the human mind observing and evaluating information (i.e., filtering NMI loci data and organizing information (i.e., filtered NMI loci) by chromosomal position and is therefore an abstract idea. This step encompasses performing mathematical comparison (i.e., using equalities and inequalities) for sorting information (i.e., filtered NMI loci by chromosomal position) which reads on abstract ideas.
This step can be performed in the human mind by mind by organizing information (i.e., position-sorted filtered NMI loci from a sliding window) for identifying candidate large structural variations and is therefore an abstract idea. This step encompasses “computing” a running sum which encompasses performing mathematical concepts (i.e., summing information) which reads on abstract ideas. Here, the term “computing” is interpreted as an alternative term for “calculating”. See MPEP 2106.04(a)(2)(I)(C).
identifying at least one de-novo or inherited structural variation in the genome of the subject from the candidate large structural variation
This step can be performed in the human mind by observing and evaluating the structural variation in the genome of the subject to determine at least one de novo or inherited structural variation and is therefore an abstract idea.
wherein the structural variation is within or near a gene associated with the subject's disorder or condition
This step describes the location of the structural variation that is analyzed by the abstract idea/mental process.
determining a therapy targeting the gene and treating the subject's disorder or condition
This step can be performed in the human mind by following instructions to determine a therapy and is therefore an abstract idea. This step can be further performed in the human mind by following instructions to treat a subject and is therefore an abstract idea. Here, under broadest reasonable interpretation (BRI), the limitation “treating the subject’s disorder or condition” is broad and reads on abstract ideas.
Claims 5, 12, and 14, and 20-27 are further drawn to further abstract ideas and limitations that describe the abstract ideas of claim 1 and are therefore also abstract ideas.
Claim 28 recites:
assembling single nucleotide polymorphism (SNP) data from the subject and the subject's biological mother and the subject's biological father
This step can be performed in the human mind by organizing data to assemble single polymorphism (SNP) from a subject’s biological mother and father and is therefore an abstract idea.
comparing, using a processor, the subject's SNP data, the father's SNP data, and the mother's SNP data
This step can be performed in the human mind by observing and comparing subject’s, father’s, and mother’s SNP data and is therefore an abstract idea.
identifying specific SNPs in the subject's SNP data that display non-Mendelian inheritance pattern (NMI), wherein each identified specific SNP is scored as an NMI locus and classified as a paternal NMI locus, a maternal NMI locus, or a de novo NMI locus
This step can be performed in the human mind by observing and evaluating the subjects SNP data that displays (NMI) to identify specific SNPs in a subject SNPs and is therefore an abstract idea. The step can be performed in the human mind by observing and evaluating the subjects SNP data that displays (NMI) to score and classify each identified specific SNP and is therefore an abstract idea.
filtering out specific SNPs in the subject's SNP data that display NMI and correspond to known structural variations by cross-referencing each NMI locus against a database of known insertions, deletions, inversions, mobile element insertions, and INDELs, thereby producing filtered NMI loci
This step can be performed in the human mind by observing, comparing (i.e., cross-referencing), and evaluating information (i.e., nucleic acid data) each NMI locus against a database for filtering data (i.e., SNP’s) to produce filtered NMI loci data and is therefore an abstract idea. This step encompasses performing mathematical comparison (i.e., using equalities and inequalities) for filtering information (i.e., SNP data) which reads on abstract ideas.
sorting the filtered NMI loci by chromosomal position and computing a running sum of the position-sorted filtered NMI loci using a sliding window, thereby identifying candidate large structural variations comprising runs of consecutive NMI loci
This step can be performed in the human mind observing and evaluating information (i.e., filtering NMI loci data and organizing information (i.e., filtered NMI loci) by chromosomal position and is therefore an abstract idea. This step encompasses performing mathematical comparison (i.e., using equalities and inequalities) for sorting information (i.e., filtered NMI loci by chromosomal position) which reads on abstract ideas.
This step can be performed in the human mind by mind by organizing information (i.e., position-sorted filtered NMI loci from a sliding window) for identifying candidate large structural variations and is therefore an abstract idea. This step encompasses “computing” a running sum which encompasses performing mathematical concepts (i.e., summing information) which reads on abstract ideas. Here, the term “computing” is interpreted as an alternative term for “calculating”. See MPEP 2106.04(a)(2)(I)(C).
identifying at least one de-novo or inherited structural variation in the genome of the subject from the candidate large structural variations, wherein the structural variation is within or near a gene associated with ASD
This step can be performed in the human mind by observing and evaluating the structural variation in the genome of the subject to determine at least one de novo or inherited structural variation within or near a gene associated with ASD and is therefore an abstract idea.
Claims 29 is further drawn to further abstract ideas and limitations that describe the abstract ideas of claim 28 and are therefore also abstract ideas.
2A Prong II - Consideration of Practical Application
Claim 1 does not recite any additional element which integrates the recited judicial exception into a practical application because treating the subject’s disorder or condition using the treatments of claims 11 and 18 does not apply or use a particular treatment or prophylaxis for a disease or medical condition. The treatment or prophylaxis limitation must have more than a nominal or insignificant relationship to the exception(s). Furthermore, claim 1 does not integrate the recited judicial exception because claim 1 does not encompass any steps for determining a condition such that a therapy can be determined to treat. Additionally, claim 1 does not integrate the recited judicial exception because claim 1 does not provide any steps for determining a condition or disease and relating/associating the condition or disease to either at least one de-novo structural variation or inherited structural variation such that a therapy can be determined for treatment. Here, the claim limitation must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. As such, this treating step is not particular, and is instead merely instructions to "apply" the exception in a generic way. Therefore, the administration step does not integrate the mental analysis step into a practical application. See MPEP 2106.04(d)(2).
Claim 11 does not recite an additional element which integrates the recited judicial exception into a practical application because broadly treating the subject’s disorder or condition does not apply or use a particular treatment or prophylaxis for a disorder or medical condition. The treatment or prophylaxis limitation must have more than a nominal or insignificant relationship to the exception(s). The claim limitation must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. Thus, this treating step is not particular, and is instead merely instructions to "apply" the exception in a generic way. Therefore, the administration step does not integrate the mental analysis step into a practical application. See MPEP 2106.04(d)(2). Moreover, claim 11 does not integrate the recite judicial exception because claim 11 depends on claim 1 also not integrated into a practical application.
Claims 18-19 and 28 do not recite any additional element which integrate the recited judicial exception into a practical application because the particular treatments or prophylaxis (i.e., gene editing of claims 18 and 28 and gene editing technology of CRSPR of claim 19) are not correlated and/or associated with any ASD genes so that ASD can be treated, and the analysis steps of claims 1 and 28 are not specific to ASD and does not utilize and/or correlate any mutations (i.e., NMI SNPs) or specific NMI SNPs to any ASD biomarkers/genes so ASD can be treated using the treatments (i.e., gene editing) of claims 18-19 and 28 which only provides a nominal and/or insignificant relationship to the exception. See MPEP 2106.04(d)(2). Moreover, claim 11 does not integrate the recite judicial exception because claim 11 depends on claim 1 which is also not integrated into a practical application.
Claim 20 does not recite an additional element which integrates the recited judicial exception into a practical application because the abstract ideas are not integrated with the subject’s disorder (i.e., autism) and treating the subject’s disorder (i.e., using the Car T cells). Here, the claim 20 recites administering Car T to treat autism spectrum disorder, but the claims do not utilize and/or correlate any mutations (i.e., NMI SNP’s) or specific NMI SNPs and associated gene to autism such that Car T cells can be used to treat autism or treat underlying conditions associated with autism. Additionally, claim 1 is not specific to analyzing/determining/identifying autism and associating and correlating genes with de novo and/or inherited structural variations to autism such that a subject with autism can be treated with Car T cells (claim 20). Therefore, claim 20 is not integrate into a practical application because there are no data analysis steps correlating any NMI SNPs (i.e., genes with SNPs de novo and/or inherited structural variations) to autism, and there is no autism specific data analysis steps (claim 1) using genes with identified SNPs from de novo and/or inherited structural variations such that to integrate said disease or condition (i.e., autism) with administration of a treatment (i.e., Car T cells). Therefore, the administration step does not integrate the mental analysis step into a practical application. See MPEP 2106.04(d)(2).
Moreover, claim 20 does not integrate the recited judicial exception because claim 20 depends on claim 1 which is also not integrated into a practical application.
Claims 23-24 do not recite an additional element which integrates the recited judicial exception of claim 1 into a practical application because reciting generically “treating” the subject’s disorder does not apply or use a particular treatment or prophylaxis (i.e., pharmaceutical or non-pharmaceutical treatment) for a disease or medical condition. See MPEP 2106.04(d)(2).
Moreover, claims 23-24 does not integrate the recite judicial exception because claims 23-24 depends on claim 1 which is also not integrated into a practical application.
Claim 25 does not recite an additional element which integrates the recited judicial exception of claim 1 into a practical application because the abstract ideas are not integrated with the subject’s disorder (i.e., autism) and treating the subject’s disorder (i.e., reducing stimuli) and reducing said stimuli. Here, claim 25 recites a non-pharmaceutical treatment (i.e., reducing stimuli) for treating autism spectrum disorder, but the analysis of claim 1 is not specific to autism, and the claims do not utilize and/or correlate any mutations (i.e., NMI SNPs) associated with autism such that to treat autism by reducing stimuli which only provides a nominal and/or insignificant relationship to the exception. Furthermore, “reducing stimuli” is not a particular treatment. For example, it is known “reducing stimuli” can encompass sensory integration therapy, environmental modifications, and behavioral techniques (i.e., sensory diets, noise-canceling headphones, dimmed lighting, weighted blankets, and occupational therapy) to manage sensory overload. Here, the claim does not provide as to what stimuli is being reduced (i.e., light, social settings, noise, cognitive) and/or what method/treatment (i.e., sensory integration therapy, environmental modifications) is reducing the stimuli which provides only a nominal and/or insignificant relationship to the exception. See MPEP 2106.04(d)(2).
Moreover, claim 25 does not integrate the recite judicial exception because claim 25 depends on claim 1 which is also not integrated into a practical application.
Claims 28 does not recite an additional element which integrates the recited judicial exception into a practical application because the abstract ideas are not integrated with the subject’s disorder (i.e., autism) and treating the subject’s disorder (i.e., gene editing or Car T cells).
Claim 28 does not integrate the recited judicial exception because claim 28 step (a) recites “wherein sequence is removed back to the SNPs on either side of the structural variation that demonstrate normal Mendelian inheritance”. Here, the previous and subsequent steps do not provide steps of removing the sequence and/or adding the edited sequence back into the other sides of SNPs which provides disconnected/disjointed which does not integrate the judicial exception into a practical application.
Claim 28 step (a) does not utilize any gene/gene elements with any identified de-novo or inherited structural variation SNPs associated with ASD for acting as a guide with respect to using said gene in editing technology to target cells or tissues that are indicative of the symptoms or other conditions originated from or induced by ASD. Furthermore, claim 28 is not integrated into a practical application because claim 28 step (a) is disjointed from the previous and subsequent steps. For example, claim 28 recites “wherein sequence is removed”, “the structural variation that demonstrate normal Mendelian inheritance”, and “the structural-variation altered sequence”, but the previous and subsequent steps do not provide as to what “sequence” is removed, does not provide steps for analyzing structural variation so that normal Mendelian inheritance can be demonstrated, does not provide a homologous chromosomal sequence that serves as a guide when gene editing is commenced, and does not provide structural-variation altered sequence that is replaced. Thus, the steps are further disjointed and disconnected from the claim.
Here, claim 28 (b) recites administering Car T to treat ASD, but the claims do not utilize and/or correlate any mutations (i.e., NMI SNP’s) or specific NMI SNPs (i.e., genes with SNPs de novo and/or inherited structural variations) so that Car T cells can be used to treat ASD. Furthermore, claim 28 does not integrate the recited judicial exception because claim 28 does not encompass any data analysis steps for determining when to utilize gene editing or CAR T cell based on the genes/gene elements (i.e., coding/noncoding elements, regulatory elements (i.e., promoters) upstream or downstream or within the gene) with SNPs resulting from de novo and/or inherited structural variations. Here, although claim 28 is drawn to a method for risk of developing ASD and treating ASD, there are no data analysis steps (i.e., identified at least one de-novo or inherited structural variation within or near a gene) for correlating and/or associating at least one de-novo or inherited structural variation (i.e., SNPs) of gene/gene elements of an ASD in the genome of the subject with ASD. Additionally, the claim is disjointed because there are no data analysis for determining if a subject that has gene/gene elements with de novo mutated SNPs is to be treated with gene editing or CAR T cells or if a subject that has gene/gene elements with inherited mutated SNPs is to be treated with gene editing or CAR T cells.
Therefore, the combination of ASD, CAR T cells, and gene editing does not integrate the recited judicial exception because there is no correlation between any ASD genes with de novo or inherited NMI SNPs and no specific SNPs with ASD association, there is also no analysis steps for determining whether to use gene editing or CAR T based on association/correlation of genetic structural variation SNPs present on ASD gene/gene elements (i.e., promoters, coding and noncoding regions) so that to integrate and link said disease or condition (i.e., ASD) with administration of a treatment (i.e., Car T cells/gene editing), and step (a) is disjointed/disconnected from the subsequent and previous analysis. Therefore, the administration steps do not integrate the mental analysis step into a practical application. See MPEP 2106.04(d)(2).
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception.
2B Analysis - Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea.
The recited additional element of data gathering by obtaining SNP data of claim 1 does not add more than the recited judicial exception because using a SNP chip assay to obtain/gather nucleic acid data is deemed well-known and conventional extra-solution activity. See MPEP See MPEP 2106.05(d)(II) and 2106.05(g). To provide evidence of conventionality, Sherer et al. (Sherer) discloses using SNP array data for 10,246 control individuals (4,829 male: 5,417 female), for CNVs at PTCHD1 and the upstream region [Sherer, page 9 para 0059]. Sherer discloses analyzing ASD-linked mutations using arrays such as Affymetrix 500k SNP arrays and Illumina 550x arrays [Sherer, page 3 para 0033] (US Patent Pub No.: US 2012/0100995, Patent Pub Date: 26 April 2012).
The recited additional element of using SNP chip array of claims 1, 3-4, 28, and 30 does not add more than the recited judicial exception because using bead chip assays to gather nucleic sequence data that is subsequently analyzed by the abstract ideas is deemed well-known and conventional. See MPEP 2106.05(d)(II). To provide evidence of conventionality, Chakravarti et al. (Chakravarti) discloses methods for determining a genetic predisposition to or the presence of autism or an autism spectrum disorder which uses 5.0 arrays for obtaining array data for a dataset consisting of 1,031 nuclear families (856 with two parents) and a total of 1,553 affected offspring [Chakravarti, page 10 para 0096]. Chakravarti discloses using Illumina 550K array (i.e., array of at least 400,000 SNPs) [Chakravarti, page 10 para 0096]. Chakravarti discloses genotype calling for the 5.0 arrays was performed by Birdseed (26.27) and for the 500K arrays BRLMM was performed [Chakravarti, page 10 para 0140, claim 14]. (US Patent Publication: US 2014/0127685, Patent Pub Date: 08 May 2014).
The recited additional element of using computer processes and equipment of claims 1, 28, and 30 does not add more than the recited judicial exception because using computer to store data and abstract ideas is deemed well-known and conventional. See MPEP 2106.05(b).
The recited additional element of using the gene editing technology (claims 18 and 28) by using CRISPR (claim 19) does not add more than the recited judicial exception because using gene editing technologies such as CRISPR is deemed well-known and conventional.
The recited additional element of administering CAR T cells as a treatment of claims 20 and 28 does not add more than the recited judicial exception because using CAR T cell is deemed well-known and conventional. To provide evidence of conventionality, Greenfield et al. (Greenfield) teach gene editing with respect to bioethics, teach using CRISPR [pages 81-82 box 6.2]. Greenfield teaches using modified T-cell form donors, known as UCART 19 cell, to treat a one-year-old with aggressive lymphoblastic leukemia (ALL) [page 41 box 4.2] (Cited in the Office Action mailed 26 November 2024).
The recited additional element of using pharmaceutical and non-pharmaceutical of claim 23-24 does not add more than the recited judicial exception because treating a subject using pharmaceuticals and non-pharmaceuticals is deemed well-known and conventional.
The recited additional element of reducing stimuli for treating autism spectrum disorder (ASD) of claim 25 does not add more than the recited judicial exception because reducing stimuli is deemed well-known and conventional. To provide evidence of conventionality, Nunez eta l. (Nunez) teach all the experiments were held at the therapy playground, a simple environment with reduced stimuli where children usually attend to train with the therapist [page 839 section III evaluation] (2016 25th IEEE International Symposium on Robot and Human Interactive Communication (RO-MAN), 2016, p.837-842).
In conclusion, and when viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Arguments
Applicant's arguments filed 26 May 2026 have been fully considered but the rejection is maintained.
The Applicant states claim 1 does not recite mental processes. The Applicant points to MPEP 2106.04(a) and 2106.04(a)(2)(1Il)(A) for guidance [remarks, pages 9-10]. The Applicant states the claims cannot be performed in the human mind because the claims require assembling at least 400,000 SNP data points and subsequently storing the data. The Applicant points to the amending of the computer into the claims for comparing not to avoid scrutiny under 35 U.S.C § 101, but to show the processor is required for scoring and classifying at least 400,000 SNP trios, filtering by chromosomal position, and performing running sum to identify structural variation.
In response, it is noted that using a computer to process large data sets does not preclude the claims from being performed mentally because claims that require computer may still recite metal processes. See MPEP 2106.04(2)(III)(C) (1-3). Here, for example, it is acknowledged that such computations performed mentally (i.e., processing 400,000 SNPS from family members, scoring and classifying data), or with paper and pencil, would take considerable time and effort, but that is, of course, the singular purpose of computers and computer networks, to perform large numbers of calculations, via algorithms, rapidly, and without error (assuming no error in user input). Although a general-purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea. See SiRF Tech: "In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations" and Bancorp: "the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter. … Using a computer to accelerate an ineligible mental process does not make that process patent-eligible". Thus, using a computer to produce quantitative data for scoring and to perform comparisons for data classification therefore reads on abstract ideas.
The Applicant states the claims are analogous to the claims of SRL Int’l. The Applicant states the human mind is not equipped to assemble data point and compare 1.2 million data points [remarks, page 10]. The Applicant points to the amendments to the claims and new claims for guidance. The Applicant states the claims require precisely the kind of computational tools and systematic processing that the Federal Circuit has consistently recognized as beyond human cognitive capacity, and amended steps of claim 1 cannot be performed in the human mind [remarks, page 10]. The Applicant points to a declaration submitted by Dr. Alana R. Templeton filed 26 May 2026 for guidance regarding the amended claimed method being performed mentally [remarks, page 10].
In response, the argument is not persuasive because the Applicant is arguing the amended limitations that are not recited in the claims. For example, the claims do not recite utilizing 1.2 million but merely require at least 400,000 SNPs from the subjects and subject’s mother and father, not a combined 1.2 million data points. It is not further persuasive because, with respect to SRI International's cybersecurity patents containing abstract ideas, their claimed automated network monitoring and packet analysis system was patent-eligible as it solved a technical problem by analyzing live network packets across massive distributed systems to catch coordinated multi-node hacks. Here, one cannot look at raw network traffic data in real time to spot hidden threats. Thus, the invention improved computer network functionality itself rather than automating a routine mental task. Therefore, even with the declaration from Dr. Templeton, the argument is not persuasive because the claims do not recite analyzing 1.2 million data points and using computers to process abstract ideas (i.e., comparing 400,000 data points) more efficiently still reads on abstract ideas. See MPEP 2106.04(2)(III)(C)(1-3).
Moreover, and for example, regarding the data points, the argument is not persuasive because it is acknowledged that such computations performed mentally, or with paper and pencil, would take considerable time and effort, but that is, of course, the singular purpose of computers and computer networks, to perform large numbers of calculations, via algorithms, rapidly, and without error (assuming no error in user input). Although a general-purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea. See SiRF Tech: "In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations" and Bancorp: "the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter. … Using a computer to accelerate an ineligible mental process does not make that process patent-eligible".
The Applicant states new claims 28 and 30 include the same systematic, multi-step, computationally-intensive operations applied across several hundreds of thousands of data points that can only be accomplished using a processor and database as recited in claim 1. Claim 30 extends the analysis to a population to identify conserved regions. The Applicant points to new claim 30 for guidance [remarks, pages 10-11]. The Applicant compares the analysis steps of new claim 30 to amended claim 1. The Applicant points to the specification [para 0068] for guidance. The Applicant further points to the analysis steps of claims 1 and new claim 30 and points to new claim 28 for clarification. The Applicant states amended limitations and new claims do not present simple observations and judgments that fall with abstract ideas [remarks, pages 10-12].
It is noted the specification does not contain these paragraphs [0068] and/or does not contain numbered paragraphs.
In response, and regarding claim 30, the argument is not persuasive because claim 30 has been withdrawn from consideration. Regarding the analysis steps of claim 28, like claim 1, they contain abstract ideas and abstract ideas processed in a computing environment. See MPEP 2106.04(2)(III)(C) (1-3). Here, it is noted that, like claim 1, the assembling, comparing, identifying, filtering, sorting, and identifying steps read on abstract ideas.
With respect to processing 400,000 SNP data points, using a computer to observe, compare, and evaluate data, does not preclude the claims from containing abstract ideas. As further noted above, regarding computationally-intensive operations applied across several hundreds of thousands of data points that can only be accomplished using a processor and database, the argument is not persuasive because it is acknowledged that such computations performed mentally (i.e., assembling, comparing, identifying, filtering, sorting, and identifying data points), or with paper and pencil, would take considerable time and effort, but that is, of course, the singular purpose of computers and computer networks, to perform large numbers of calculations, via algorithms, rapidly, and without error (assuming no error in user input). Although a general-purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea. See SiRF Tech: "In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations" and Bancorp: "the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter. … Using a computer to accelerate an ineligible mental process does not make that process patent-eligible". Thus, the amended limitations of claim 1 and new limitations of claim 28 present abstract ideas that that are performed using a computer as a tool and performed in a computer environment for computational efficiency.
Therefore, under Step 2A Prong I of the 35 U.S.C 101 analysis, claims 1 and 28 encompass abstract ideas and are patent ineligible.
The Applicant states the claims are integrated into a practical application [remarks, page 12]. The Applicant states the claims provide 1) an improvement to technology, 2) provide a particular treatment or prophylaxis for a disease or medical condition, 3) integrate the judicial exception with a particular machine, and 5) integrates the judicial exception in a meaningful way such that the claim as a whole is more than a drafting effort designed to monopolize the exception [remarks, page 12]. The Applicant states the claims recite an improvement to technology of SNP array analysis. The Applicant points to MPEP § 2106.05(a) for guidance. The Applicant points to the specification [0024 and 0027] for clarification. The Applicant states amended claim 1 and new claims 28 and 30 reflect the improvement identified in the specification. The Applicant points to McRo for guidance [remarks, pages 13-14]. The Applicant states, like McRo, claim 1, 28, and 30, the claimed method achieves a specific improvement to genomic analysis of SNP array technology through a defined sequence of computational steps (NMI scoring, database cross-referencing, chromosomal sorting, and sliding-window running sums) [remarks, pages 13-14]. The Applicant states new claim 30 reinforces the claimed improvement by using CCC analysis. The Applicant states “This ordered combination of additional elements (SNP chip assay, processor-based comparison, NMI scoring, database cross-referencing, chromosomal sorting, sliding-window computation, and CCC analysis) works in combination with the analytical steps to provide an improvement to genomic structural variation detection technology that enables identification of variations that short-read sequencing and hybridization arrays physically cannot resolve.” [remarks, pages 13-14].
In response, the argument, regarding claim 30, is not persuasive because claim 30 has been withdrawn from consideration. Regarding paragraphs [0024 and 0027] of the specification, it is noted that the specification does not provide paragraph numbering or contain paragraphs with numbers. Here, the Applicant is invited to point out where the specification (pages or paragraphs) provides embodiments which supports that claims 1 and 28 recite a practical application and/or an improvement to technology.
With respect to claim 1 providing a practical application/improvement of the judicial exception, as noted in Step 2A Prong II of the 101 analyses above, claim 1 does not recite any additional element which integrates the recited judicial exception into a practical application because the treating the subject’s disorder or condition using the treatments of claims 11 and 18 does not apply or use a particular treatment or prophylaxis for a disease or medical condition. The treatment or prophylaxis limitation of claim 1 merely provides a nominal/insignificant relationship to the exception(s), does not encompass any steps for determining a condition such that a therapy can be determined to treat, and does not provide any steps for determining a condition or disease and relating/associating the condition or disease to either at least one de-novo structural variation or inherited structural variation such that a therapy can be determined for treatment. Thus, as above in Step 2A Prong II, treating step of claim 1 is not particular, and is instead merely instructions to "apply" the exception in a generic way. Therefore, the administration step does not integrate the mental analysis step into a practical application. See MPEP 2106.04(d)(2).
On the other hand, and as noted in Step 2A Prong II above, the combination of ASD, CAR T cells, and gene editing of claim 28 does not integrate the recited judicial exception because there is no correlation between any ASD genes with the de novo or inherited NMI SNPs and no specific SNPs with ASD association, there are also no analysis steps for determining whether to use gene editing or CAR T based on association/correlation of genetic structural variation SNPs present on ASD gene/gene elements (i.e., promoters, coding and noncoding regions) so that to integrate and link said disease or condition (i.e., ASD) with the administration of a treatment (i.e., Car T cells/gene editing), and step (a) is disjointed/disconnected from the subsequent and previous analysis. Therefore, the administration steps of claim 28 do not integrate the mental analysis step into a practical application. See MPEP 2106.04(d)(2).
Therefore, under Step 2A Prong II of the 35 U.S.C 101 analysis, the claims remain patent ineligible.
Regarding McRo, the claimed method focused on a specific technological method—using specific, limited rules that relate phoneme sequences and time to set morph weights—rather than just claiming the general result of a talking 3D character. Here, the claims of McRo were limited to a particular way of doing automated lip-syncing using said specific automated 3D animation rules as compared the nucleic acid data (i.e., A, T, C, G) analysis and subsequent treatment steps of claims 1 and 28. As noted above, claims 1 and 28 do not provide an improvement similar to McRo because McRo provided an improvement to the actual rules of computer-aided animation design, rather than just using a general-purpose computer as a generic tool to run conventional activities as claim 1 is drawn to applying the exception while claim 28 merely provides a nominal/insignificant relationship with the judicial exception because the analysis steps of claim 28 are disjointed/disconnected from its additional elements (i.e., gene editing and Car T-cells).
Regarding the ordered combination of additional elements, ordered combination of additional elements are evaluated under Step 2B of the 101 analyses.
The Applicant states claim 1 and 28 provide a particular treatment for a disease [remarks, page 14 B]. The Application points to MPEP 2106.04(d)(2) for guidance. The Applicant states amended Claim 1 falls squarely within the former category: the therapy must target the specific gene identified through the NMI analysis, just as the beta blocker must be dosed to account for the identified genotype. Dependent Claims 11, 18, 19, and 20 further narrow the treatment to gene editing technology (Claim 18), CRISPR (Claim 19), and CAR T cells for ASD (Claim 20). The Applicant states claims 20, 28, and 29 integrate the judicial exception into a practical application. The Applicant states new claims 28 addresses issues and now provides specific gene such as IL-6, for example [remarks, pages 14-17].
As noted in Step 2A Prong II of the 101 analyses above, regarding claims 1, 11, 18-19, 20, and 28:
As noted above, claim 1 does not integrate the recited judicial exception because claim 1 does not encompass any steps for determining a condition such that a therapy can be determined to treat, does not provide any steps for determining a condition or disease and relating/associating the condition or disease to either at least one de-novo structural variation or inherited structural variation such that a therapy can be determined for treatment. Thus, the treating step is not particular and is instead merely instructions to "apply" the exception in a generic way. See MPEP 2106.04(d)(2).
Claim 11 does not recite an additional element which integrates the recited judicial exception into a practical application because treating the subject’s disorder or condition of claim 11 is broadly recited which does not apply or use a particular treatment or prophylaxis for treating a disorder or medical condition and reads on mere instructions to "apply" the exception in a generic way.
Regarding claims 18-19, claims 18-19 do not recite any additional element which integrate the recited judicial exception into a practical application because the particular treatments or prophylaxis (i.e., gene editing of claim 18 and gene editing technology of CRSPR of claim 19) are not correlated and/or associated with any de novo or inherited structural variation near or with an ASD genes so that ASD can be treated, and the analysis steps of claims 1 are not specific to ASD and does not utilize and/or correlate any mutations (i.e., NMI SNPs) or specific NMI SNPs to any ASD biomarkers/genes so ASD can be treated using the treatments (i.e., gene editing) of claims 18-19 which only provides a nominal and/or insignificant relationship to the exception. See MPEP 2106.04(d)(2).
Regarding claim 20, claim 20 does not recite an additional element which integrates the recited judicial exception into a practical application because the abstract ideas are not integrated with the subject’s disorder (i.e., autism) and treating the subject’s disorder (i.e., using the Car T cells) as claim 1 is not specific to analyzing/determining/identifying autism and associating and correlating genes with de novo and/or inherited structural variations to autism such that a subject with autism can be treated with Car T cells (claim 20), there are no data analysis steps correlating any NMI SNPs (i.e., genes with SNPs de novo and/or inherited structural variations) to autism, and there is no autism specific data analysis steps (claim 1) using genes with identified SNPs e novo and/or inherited structural variations so that to integrate said disease or condition (i.e., autism) with administration of a treatment (i.e., Car T cells).
Regarding claim 28, claim 28 (b) recites administering the particular treatments of Car T and gene editing to treat ASD, but the claims do not utilize and/or correlate any mutations (i.e., NMI SNP’s) or specific NMI SNPs (i.e., genes with SNPs de novo and/or inherited structural variations) so that Car T cells or gene editing can be used to treat ASD, does not encompass any data analysis steps for determining when to utilize gene editing or CAR T cell based on the genes/gene elements (i.e., coding/noncoding elements, regulatory elements (i.e., promoters) upstream or downstream or within the gene) with SNPs resulting from de novo and/or inherited structural variations, and the analysis steps are disjointed because there are no data analysis steps for determining if a subject that has gene/gene elements (i.e., noncoding elements, promoters, introns, exons) with de novo mutated SNPs is to be treated with gene editing or CAR T cells or if a subject that has gene/gene elements with inherited mutated SNPs is to be treated with gene editing or CAR T cells.
Regarding the applicants’ arguments that new claims 28 now provide specific genes such as IL-6, for example [remarks, pages 14-17], it is not persuasive because, as noted in Sewp 2A Prong I above, the inflammatory cytokines (i.e., IL-6) of claim 29, for example, merely describe the cytokines the target T cells or cells of claim 28.
Therefore, the claims, under Step 2A Prong II, do not utilize any additional elements outside of extra-solution activities (i.e., data gathering elements) and tangential computer elements to construct a practical application or an improvement to technology.
The Applicant states the claims recites significantly more than the recited abstract idea [remarks, page 16 Step 2B]. The Applicant points to specification [0025-0027, 0229-0234]. The Applicant states amended claim 1 treats NMI, not as erroneous information, but as meaningful data indicative of a genetic variation, and then applies a specific multi-step computational pipeline including NMI scoring, parent-of-origin classification, database cross-referencing, and a sliding-window running sum - to transform raw NMI data, that the cited art discarded, into actionable structural variation calls [remarks, page 17]. The Applicant further points to the declaration filed by Dr. Templeton for guidance [remarks, page 17]. The Applicant states moreover, and even if the elements are well understood, the combination of additional elements may amount to an inventive concept. The Applicant points to the MPEP § 2106.05(d) for guidance. The Applicant states the ordered combination recited in the amended claims represents precisely such a non-conventional and non-generic arrangement that amounts to significantly more than any alleged abstract idea. Accordingly, even under Step 2B, the claims are patent eligible [remarks, pages 17-18]. The Applicant further points to the MPEP 2106.05(d) for guidance. The Applicant states the Examiner's conclusory assertions that individual elements are "well-known and conventional" do not satisfy the evidentiary standard required by Berkheimer for the ordered combination as a whole [remarks, pages 17-18].
It is noted the specification does not contain these paragraphs [0025-0027, 0229-0234] and/or does not contain numbered paragraphs.
As noted in the arguments above, and with respect to Dr. Templetons’ declaration, the argument is not persuasive because even though Dr. Templeton argues the data analysis steps provide different analysis than the instant claimed method, under Step 2B, the recited additional elements are conventional, and the ordered combination of said amended and new claim do not provide unconventional methods, and the claimed method steps are drawn to abstract ideas such as filtering data, for example.
Furthermore, under Step 2A Prong II, the additional elements of the claims do not integrate the recited judicial exceptions into practical applications/improvements to technology.
For example, claim 1 is drawn to applying the exception while the particular treatments of claim 28 are only nominally/insignificantly related to the exception(s) (i.e., ASD/treatment correlation).
With respect to an order combination of additional elements, the ordered combination, in light of the specification, is drawn to merely gathering information (i.e., sequence data) for analyzing DNA to provide sequence information/detect allelic variants using conventional methods (i.e., tangential computer elements, molecular assays) for determining and treating a disease(s) using different therapies which does not provide unconventional data analysis and treatment steps. See MPEP 2106.05(d)(II) (i-v and vii-viii).
Therefore, the claims contain conventional and routine additional elements.
Regarding the evidentiary standard required by Berkheimer for the ordered combination as a whole, it is noted that MPEP 2106.05(d)(I)(2) states “examiners should rely on what the courts have recognized, or those in the art would recognize, as elements that are well-understood, routine, conventional activity in the relevant field when making the required determination.” Here, it is noted the above under Step 2B, the analysis relies on both court cases citing by the MPEP 2106.05(d)(II)(i-v and vii-viii) and the prior art (i.e., Illumina® chips and Greenfield CAR T-cells, Sherer, Chakravarti). As such, and as recognized by the court and provided by the prior art, conventionality of the claimed elements has been established as outline by the MPEP 2106.05(d)(I)(2).
Therefore, under Step 2B of the 35 U.S.C § 101, the claims remain patent ineligible.
Claim Rejections - 35 USC § 103
The rejection of claim 1, 3-5, 11-12, and 21-22 under 35 U.S.C. 103 as being unpatentable over Belouchi et al. (U.S Patent Pub: US 2009/0081658, Patent Pub Date: 26 March 2009) in view of Iossifov et al. ((Cambridge, Mass.), 2012-04, Vol.74 (2), p.285-299) of view Illumina® (Infinium Exome-24 v1.1 BeadChip (2017)) in the Office Action mailed 27 March 2026 is withdrawn in view of the amendments filed 26 May 2026.
The rejection of claim(s) 18-19 under 35 U.S.C. 103 as being unpatentable over Belouchi in view of Iossifov in view Illumina®, as applied to claims 1, 3-5, 11-12, and 21-22, and in further view of Greenfield (Cited in the Office Action mailed 29 May 2024) in the Office Action mailed 27 March 2026 is withdrawn in view of the amendments filed 26 May 2026.
The rejection of claim 23-24 are rejected under 35 U.S.C. 103 as being unpatentable over Belouchi in view of Iossifov in view Illumina®, as applied to claims 1, 3-5, 11-12, and 21-22, and in further view of Sahin et al. (Science American Association for the Advancement of Science, 2015-11, Vol.350 (6263)) in the Office Action mailed 27 March 2026 is withdrawn in view of the amendments filed 26 May 2026.
The rejection of claim(s) 25 under 35 U.S.C. 103 as being unpatentable over Belouchi in view of Iossifov in view Illumina® in view of Sahin, as applied to claims 1, 2-5, 11, and 21-24, and in further view of Nunez et al. (2016 25th IEEE International Symposium on Robot and Human Interactive Communication (RO-MAN), 2016, p.837-842) in the Office Action mailed 27 March 2026 is withdrawn in view of the amendments filed 26 May 2026.
Conclusion
Claims 1, 3-5, 11-12, 14, and 18-29 are rejected.
No claims are allowed.
Finality
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 action.
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/J.C.P./Examiner, Art Unit 1687
/Anna Skibinsky/
Primary Examiner, AU 1635
Prosecution Insights