DETAILED ACTION
Applicant’s response, filed 02 Feb. 2026 has been fully considered. The following rejections and/or objections are reiterated. They constitute the complete set presently being applied to the instant application.
Any reference to the previous Office action refers to the Office action mailed 10 Nov. 2025.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 02 Feb. 2026 has been entered.
Status of Claims
Claims 1-20 are pending.
Claims 1-20 are rejected.
Priority
The instant application does not claim the benefit of priority under 35 U.S.C 119(e) or under 35 U.S.C. 120, 120, or 365(c) to any prior applications. Accordingly, the effective filing date for the instant application is 14 Jan. 2022.
Claim Objections
The objection to claims 1, 9, and 17 in the previous Office action has been withdrawn in view of claim amendments received 02 Feb. 2026.
Claim Interpretation
Claim 1 recites “a controller” that is configured to perform various steps. Applicant’s specification at para. [0095] discloses dedicated hardware elements are referred to as “processors”, “controllers”, or some similar technology, and the use of the term “processor” or “controller” may include digital signal processor hardware, a network processor, application specific integrated circuit, circuitry, field programmable gate array, read only memory, random access memory, or some other physical hardware component. Accordingly, the term “controller” is interpreted to synonymous to a processor.
Claim Rejections - 35 USC § 101
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. This rejection is previously recited.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 1, 9, and 17 being representative) is directed a system, method, and product. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claims 1, 9, and 17 recite the following steps which fall under the mathematical concepts and/or mental processes groupings of abstract ideas:
identifying qualifying variants within the sequence data, the qualifying variants comprising variants that meet criteria for analysis;
for each qualifying variant, determining a genomic coordinate of said qualifying variant at the portion of the chromosome, as well as a number of the individuals in the population carrying said qualifying variant,
generating a sliding window comprising a selection of a sequential set of variants within the portion of the chromosome, wherein a number of the individuals in the population carrying a qualifying variant at the sliding window is within a predetermined range;
iteratively: performing a statistical analysis that indicates whether qualifying variants at genomic coordinates within a region occupied by the sliding window are correlated with the trait, based on a comparison of trait data for individuals carrying a qualifying variant of the qualifying variants to trait data for individuals in the population, and
moving the sliding window across at least one variant along a chromosomal direction, while dynamically adjusting a number of variants encompassed by the sliding window to maintain a number of the individuals in the population carrying a qualifying variant at the sliding window within the predetermined range; and
selectively categorizing qualifying variants as correlated with the trait, based on the statistical analysis.
The identified claim limitations falls into one of the groups of abstract ideas of mathematical concepts and/or mental processes for the following reasons. In this case, identifying qualifying variants within sequence data and determining a genetic coordinate of the qualifying variant can be performed mentally by performing data comparisons between the variant the criteria for analysis and then analyzing coordinate information of the portion of the chromosome. Determining a number of individuals in the population carrying the variant can be performed mentally by counting each individual with the variant. Furthermore, generating a sliding window covering a selection of sequential variants as claimed can be performed mentally by analyzing a number of individuals in the population with a qualifying variant within a window of the portion of the chromosome and iteratively making adjustments until the number is within the predetermined range, which amounts to a mere analysis of data. The iterative steps of performing a statistical analysis and moving the sliding window recite a mental process because the steps involve performing data comparisons to determine a statistic (e.g. an odds ratio, as recited in dependent claim 5) and then considering a new portion of the chromosome corresponding to a new sliding window that has the number of individuals within the predetermined range. Categorizing qualifying variants as correlated based on the statistical analysis recites a mental process because the step can be performed by simply identifying windows within the chromosomal region with a statistic above some threshold and categorizing the variants within the identified windows as correlated. That is, other than reciting the steps are carried out by a processor or controller, nothing in the claims precludes the steps form being practically performed in the mind. Last, the step of performing a statistical analysis additionally recites a mathematical concept because it requires performing mathematical calculations, as recited at para. [0046]-[0047] of Applicant’s specification. See MPEP 2106.04(a)(2) I.
Dependent claims 2-8, 10-16, and 18-20 further recite an abstract idea and/or are part of the abstract idea identified above. Dependent claims 2, 10, and 18 further limit the mental process of sliding the sliding window by adjusting the rear boarder one variant and the front border a variable number of variants. Dependent claims 3, 11, and 19 further recite the mental process of comparing results of the statistical analysis for different regions and the mental process and mathematical concept of identifying at least one region more highly correlated with the trait than other regions. Dependent claims 4, 12, and 20 further recite the mental process of altering the predetermined range, generating a new sliding window, iteratively performing the statistical analysis and moving the new sliding window using the altered predetermined range. Dependent claims 5 and 13 further limit the mental process and mathematical concept of the statistical analysis to include determining a first and second ratio, and then an odds ratio based on the two ratios, a number of individuals carrying the qualifying variant, a number of individuals in the population, and consideration of covariates. Dependent claims 6 and 14 further limits the mental process of generating a sliding window and also recites a mathematical concept of using a range of a number of individuals carrying a qualifying variant to ensure an odds ratio is calculated to a predetermined margin of error. Dependent claims 7 and 15 further limit the step of moving the sliding window to move in one of two directions and cover multiple variants in the portion of the chromosome. Dependent claims 8 and 16 further limit the mental process of identifying qualifying variants to involve determining that the variants alter a structure of a protein generated by the portion of the chromosome.
The claims additionally recite the law of nature of a natural correlation between the presence of particular variants in a chromosome and a trait in an individual (i.e. a correlation between genotype and phenotype), similar to the natural relationship between a patient’s CYP2D6 metabolizer genotype and the risk that the patient will suffer QTc prolongation after administration of a medication called iloperidone, Vanda Pharmaceuticals Inc. v. West-Ward Pharmaceuticals, 887 F.3d 1117, 1135-36, 126 USPQ2d 1266, 1281 (Fed. Cir. 2018). See MPEP 2106.04(b) I.
Therefore, claims 1-20 recite an abstract idea and law of nature. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Dependent claims 2-3, 5-8, 10-11, 13-16, and 18-19 do not recite any elements in addition to the judicial exception and thus are part of the judicial exception.
The additional elements of claims 1, 9, and 17 include:
a controller (claim 1);
a memory configured to store [data] (claim 1);
a non-transitory computer readable medium (claim 17);
storing sequence data for a portion of a chromosome that indicates, for each individual in a population, variants found in the individual within the portion of the chromosome;
storing trait data indicating, for each of the individuals, an extent that the individual expresses a predefined trait controlled by the portion of the chromosome;
reporting/report qualifying variants correlated with the trait to a user via a display (i.e. outputting data).
Dependent claims 4, 12, and 20 further recite:
reporting/report qualifying variants correlated with the trait for both the predetermined range and the altered predetermined range (i.e. outputting data).
The additional elements of a memory, controller, non-transitory computer readable medium, storing data, and outputting data are generic computer components and processes. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f).
Further regarding the step of reporting the qualifying variants, including for both the predetermined range and altered predetermined range, the limitation only serves to output data generated by the abstract idea, which amounts to insignificant post-solution activity that does not integrate the recited judicial exception into a practical application. See MPEP 2106.05(g).
Therefore, the additionally recited elements amount to insignificant extra-solution activity and/or merely invoke computers as a tool, and as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 1-20 are directed to an abstract idea and law of nature. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception.
Dependent claims 2-3, 5-8, 10-11, 13-16, and 18-19 do not recite any elements in addition to the judicial exception and thus are part of the judicial exception.
The additional elements of claims 1, 9, and 17 include:
a controller (claim 1);
a memory configured to store [data] (claim 1);
a non-transitory computer readable medium (claim 17);
storing sequence data for a portion of a chromosome that indicates, for each individual in a population, variants found in the individual within the portion of the chromosome;
storing trait data indicating, for each of the individuals, an extent that the individual expresses a predefined trait controlled by the portion of the chromosome;
reporting/report qualifying variants correlated with the trait to a user via a display (i.e. outputting data).
Dependent claims 4, 12, and 20 further recite:
reporting/report qualifying variants correlated with the trait for both the predetermined range and the altered predetermined range (i.e. outputting data).
The additional elements of a memory, controller, non-transitory computer readable medium, storing data, and outputting data are conventional computer components and processes. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). Furthermore, the courts have recognized the following computer functions as well‐understood, routine, and conventional functions when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity: storing and retrieving information in memory, Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93;
Therefore, taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea and law of nature without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Response to Arguments
Applicant's arguments filed 02 Feb. 2026 regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Applicant remarks that for the same reasons previously presented, Applicant maintains the claims are not directed to any judicial exception (Applicant’s remarks at pg. 1, para. 6).
This argument is not persuasive for the same reasons set forth in the “Response to Arguments” section of the previous Office action.
Applicant remarks the claims are directed to the improvement of the technology of genome analysis, and thus are integrated into a practical application, pointing to various paragraphs in the specification as disclosing the improvements, and remarks the generation and movement of a sliding window of genome data to be statistically analyzes reduces the volume of data to be analyzed to identify variants associated with a specific trait (Applicant’s remarks at pg. 2, para. 1-2). Applicant remarks that Applicant has explained how additional elements provide the improvement, noting the generating and movement of the sliding window improve the genomic analysis, which the Office dismisses as an abstract idea, and states the claims include additional elements to implement and utilize a sliding window that provides the improvement to the technological field of genomic analysis(Applicant’s remarks at pg. 2, para. 3 to pg. 4, para. 2).
This argument is not persuasive. This argument is not persuasive. Improvements in “genomic analysis” that are provided only by the abstract idea do not reflect an improvement to technology, as set forth in MPEP 2106.05(a). MPEP 2106.05(a) explains an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements, or by the additional element(s) in combination with the judicial exception.
Furthermore, Applicant states that they’ve explained how additional elements provide the improvement, but then immediately discusses how the improvement is provided by the use of a sliding window, which is part of the abstract idea as discussed in the above rejection. While Applicant states that the “Office dismisses as an abstract idea” the sliding window, Applicant does not actually present any arguments regarding the classification of the sliding window as an abstract idea and why this limitation should be considered an additional element, or non-abstract. An explanation regarding why generating a sliding window and using the window to iteratively perform a statistical analysis recite a mental process and mathematical concept are provided in the above rejection, explaining that: (1) generating a sliding window covering a selection of sequential variants as claimed can be performed mentally by analyzing a number of individuals in the population with a qualifying variant within a window of the portion of the chromosome and iteratively making adjustments until the number is within the predetermined range, which amounts to a mere analysis of data; and (2) the iterative steps of performing a statistical analysis and moving the sliding window recite a mental process because the steps involve performing data comparisons to determine a statistic (e.g. an odds ratio, as recited in dependent claim 5, which is a mathematical calculation) and then considering a new portion of the chromosome corresponding to a new sliding window that has the number of individuals within the predetermined range.
Therefore, Applicant still has not provided an explanation regarding how the additional element(s) of the claim, either alone or in combination with the judicial exception, improve technology. Instead, Applicant explains how the abstract idea of using a sliding window and performing statistical analyses within a sliding window improves the abstract idea of genomic analysis, rather than a technology. An improvement in the abstract idea is not an improvement to technology. See MPEP 2106.05(a). For the reasons discussed in the above rejection, the additional elements of the claims do not integrate the recited judicial exception, including the sliding window, into a practical application, and instead amount to insignificant extra-solution activity and/or merely invoke computers as a tool.
Response to Affidavit
The affidavit under 37 CFR 1.132 filed 02 Feb. 2026 is insufficient to overcome the rejection of claims 1-20 based upon 35 U.S.C. 101 as set forth in the last Office action because:
Applicant remarks the invention is directed to an improved genomic analysis through the use of a moving“ sliding window”, which group variants located near each other into one unit and improves statistical power (Affidavit at pg. 1, sections 6-10). Applicant further presents empirical data regarding the improvements to genomic analysis, including more uniform statistical power, improvements in detecting associations with binary traits, and improvements in detecting quantitative traits, and therefore, the claimed invention improves the technological field of genomic analysis (Applicant’s remarks at pg. 2, section 11 to pg. 3, section 13).
This argument is not persuasive. As discussed above in the response to arguments section, improvements in “genomic analysis” that are provided only by the abstract idea do not reflect an improvement to technology, as set forth in MPEP 2106.05(a). MPEP 2106.05(a) explains an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements, or by the additional element(s) in combination with the judicial exception.
The Affidavit discusses improvements in abstract ideas, including statistical power and detecting traits, provided by an improved analysis of genomic data using a sliding window to improve statistical power. However, an improvement in the abstract idea is not an improvement to technology. Nor can one patent "a novel and useful mathematical formula," Parker v. Flook, 437 U.S. 584, 585, 198 USPQ 193, 195 (1978). Therefore, while the claims may reflect an improved analysis of genomic data, the claim fails to recite additional elements beyond the judicial exception that integrate the judicial exception into a practical application.
Conclusion
No claims are allowed.
Claims 1-20 are free of the prior art for the reasons discussed in the Office action mailed 31 July 2025.
All claims are identical to or patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). 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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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685