DETAILED ACTION
Applicant’s response filed 04/07/2026 has been fully considered. The following rejections and/or objections are either reiterated or newly applied.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 04/07/2026 has been entered.
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 .
Claim Status
Claim 9 is cancelled by Applicant.
Claims 1-8 and 10-15 are currently pending and are herein under examination.
Claims 1-8 and 10-15 are rejected.
Priority
The instant application claims domestic benefit to US Provisional Application 63/166,048 filed 03/25/2021. The claim to domestic benefit is acknowledged. As such, the effective filing date for claims 1-8 and 10-15 is 03/25/2021.
Withdrawn Rejections
35 USC 112(b)
The rejection of claims 1-8 and 10-15 under 35 USC 112(b) is withdrawn in view of claim amendments.
35 USC 103
The rejection of claims 1-8 and 10-15 under 35 U.S.C. 103 as being unpatentable over Conley et al. in view of Choi et al. and Damask et al. is withdrawn in view of Applicant’s arguments. Applicant’s argument regarding Conley suggesting construction of vPGS but not describing how to construct them, especially not in the same way described in the instant claims, is persuasive (pg. 12, sec. A, para. 1) (pg. 16, sec. E, para. 3). Additionally, Applicant’s argument regarding not being able to apply a classical PGS formula of Choi to get the vPGS of Conley, considering different statistical architecture to derive the different scores, is also persuasive (pg. 13, para. 1).
Claim Rejections - 35 USC § 112
35 USC 112(b)
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 7-8 and 10-15 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.
This rejection is newly recited as necessitated by claim amendment and in view of further consideration of the claims.
Claims dependent on a rejected claim are also rejected, unless otherwise noted.
Claim 7, last line, recites “the additional regression” which renders the claim indefinite. It is unclear which additional regression is being referenced because claim 7, line 2, performs an additional regression for each outcome. Clarify which additional regression for which outcome is being referenced.
Claim 10, line 7, recites “the phenotypic information”, which lacks antecedent basis. Provide antecedent basis.
Claim 14, last line, recites “the additional regression” which renders the claim indefinite. It is unclear which additional regression is being referenced because claim 14, lines 2-4, generates an additional regression for each outcome. Clarify which additional regression for which outcome is being referenced.
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 1-8 and 10-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea and a natural phenomenon without significantly more.
Any newly recited portions herein are necessitated by claim amendment.
Step 1:
Step 1 asks whether the claims recite statutory subject matter. In the instant application, claims 1-8 recite a method and claims 10-15 recite a system. As such, these claims recite statutory subject matter (Step 1: YES).
Step 2A, Prong 1:
Claims that recite statutory subject matter are analyzed under Step 2A, Prong 1 to determine if they recite any concepts that equate to an abstract idea, law of nature or natural phenomena. The instant claims recite the following limitations that equate to one or more categories of judicial exception:
Claim 1 recites “generating at least one variance polygenic score (vPGS) of phenotypic information by: performing a regression to predict a squared Z-score for each outcome of the phenotypic information, and summing weights from prediction of the squared Z-score for each outcome into a single index for scoring individuals' DNA variants into the at least one variance polygenic score; performing a regression to predict a statistical measure of spread within a familial relationship of the phenotypic information, for each outcome, and summing weights from prediction of the statistical measure of spread into a single index for scoring individuals' DNA variants into the at least one variance polygenic score; performing a mean-variance quantitative trait loci (vQTL) analysis for variance heterogeneity of the phenotypic information, for each outcome, and summing weights of regressions of the vQTL analysis into a single index for scoring individuals' DNA variants into the at least one variance polygenic score; performing a vQTL analysis for variance effects of phenotypic information, and summing weights of regressions of the vQTL analysis into a single index for scoring individuals' DNA variants into the at least one variance polygenic score; or a combination thereof; and selecting at least one participant for a clinical trial based on a comparison of one or more of the at least one vPGS scores to a threshold vPGS.”
Claim 2 recites “further comprising selecting or defining the one or more outcomes, the one or more outcomes being present in the phenotypic information.”
Claim 3 recites “wherein the one or more outcomes comprise height, body mass index, systolic blood pressure, diastolic blood pressure, number of alcoholic drinks consumed per a given time period, number of cigarettes consumed per a given time period, depression symptomology score, cognitive test score, educational attainment, and/or number of children born.”
Claims 4 and 12 recite “wherein generating the at least one vPGS comprises calculating a statistical measure of spread within a familial relationship of phenotypic information, and wherein the statistical measure of spread comprises one of standard deviation, Levene's distance, and range.”
Claims 5 and 13 recite “further comprising determining whether the at least one vPGS can capture genetic contributions to variability in an outcome, distinct from genetic contributions to levels of an outcome.”
Claim 6 recites “applying the weights determined from performing the regression to predict a squared Z-score for each outcome or the regression to predict a statistical measure of spread within a familial relationship of the phenotypic information to a different data set.”
Claims 7 and 14 recite “further comprising generating a mean polygenic score (mPGS) by running an additional regression using the phenotypic information to predict an inverse normal transformation for each outcome of one or more outcomes, such that weights of the additional regression reflect a contribution of each genetic locus of a plurality of genetic loci to the mean level of the outcome, and summing the weights of the additional regression into the mPGS.”
Claims 8 and 15 recite “further comprising comparing the mPGS and vPGS scores.”
Claim 10 recites “generate at least one variance polygenic score (vPGS) by: performing a regression to predict a squared Z-score for each outcome of the phenotypic information, and summing the weights of the regressions into a single index for scoring individuals' DNA variants into the at least one variation polygenic score; performing a regression to predict a statistical measure of spread within a familial relationship of the phenotypic information, and summing the weights of the regressions into a single index for scoring individuals' DNA variants into the at least one variation polygenic score; performing a mean-variance quantitative trait loci (vQTL) analysis for variance heterogeneity of the phenotypic information, and summing weights of regressions of the vQTL analysis into a single index for scoring individuals' DNA variants into the at least one variation polygenic score; performing a vQTL analysis for variance effects of phenotypic information, and summing weights of regressions of the vQTL analysis into a single index for scoring individuals' DNA variants into the at least one variation polygenic score; or a combination thereof; and select at least one participant for a clinical trial based on a comparison of one or more of the at least one vPGS scores to a threshold vPGS.”
Limitations reciting a mental process.
Claims 1-2, 4-8, 10 and 12-15 contain limitations recited at such a high level of generality that they equate to a mental process because they are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), which the courts identified as concepts practically performed in the human mind. The paragraphs below discuss the limitations in these claims that recite a mental process under their broadest reasonable interpretation (BRI).
Regarding claims 1 and 10, the BRI of performing a regression to predict a squared Z-score includes performing mathematical calculations which could be performed by pen and paper. The BRI of performing a regression to predict a statistical measure of spread includes performing calculations using a linear regression and a standard deviation. The BRI of performing a mean-variance vQTL analysis for variance heterogeneity includes performing a median-based Levene’s test. The BRI of performing a mean-variance vQTL analysis for variance effects includes performing the calculations of a heteroskedastic linear mixed model. The BRI of summing weight into an index score includes performing mathematical calculations. The BRI of generating a mean polygenic score includes performing the equation recited in specification para. [107]. The BRI of selecting at least one participant for a clinical trial based on vPGS scores includes analyzing data and making a determination, wherein the clinical trial itself is an intended use but is not required to be performed by the claim.
The BRI of selecting or defining an outcome includes determining an outcome as representing height and selecting it. The BRI of determining that the vPGS captures genetic contributions to variability in an outcome requires making a determination through analyzing data. The BRI of applying the weights from the regressions to a different data set includes using the same models but with different data. The BRI of comparing mPGS and vPGS scores includes comparing values.
Limitations reciting a mathematical concept.
The above cited limitations in claims 1, 4, 7-8, 10, 12 and 14-15 equate to a mathematical concept because they are similar to the concepts of organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)), which the courts have identified as mathematical concepts. The BRI of performing the limitations recited in claims 1, 4, 7, 10, 12 and 14 includes using the functions/equations listed in specification para. [65-69] and [107] as well as the equations for linear regressions, standard deviations, Levene’s distance, and a range. The BRI of claim 6 includes using the same models with summed weights on a different dataset, which necessitates performing calculations. The BRI of claims 8 and 15 includes mathematical relationships of comparing numerical scores.
Limitations reciting a natural phenomenon.
The above cited limitations in claims 1, 4-7, 10, and 12-14 equate a natural phenomenon because these limitations are similar to the concept of a correlation between the presence of myeloperoxidase in a bodily sample (such as blood or plasma) and cardiovascular disease risk, Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1361, 123 USPQ2d 1081, 1087 (Fed. Cir. 2017), which the courts have established as a natural phenomenon. These claims predict variance in phenotypic outcomes such as height and body mass index based on DNA variants. The natural phenomenon is correlation between genetic variants and phenotype.
Limitations included in the judicial exception.
The above cited limitations in claim 3 are included in the judicial exception because they limit the one or more outcomes but do not change the fact the outcomes are part of the judicial exception. As such, claims 1-8 and 10-15 recite an abstract idea and a natural phenomenon (Step 2A, Prong 1: YES).
Additional Elements:
Once limitations have been identified that recite a judicial exception, the claims are evaluated for additional elements. The additional elements are then analyzed under Step 2A, Prong 2 then Step 2B. The instant claims recite the following additional elements:
Claim 10 recites “A system, comprising: a processor; and a non-transitory computer readable storage medium containing instructions that, when executed, cause the processor to:”
Claim 11 recites “wherein the processor is further configured to receive information selecting or defining the one or more outcomes, the one or more outcomes being present in the phenotypic information.”Claims 11-15 recite the phrase “The system according to claim 10”.
Claims 13-15 recite “wherein the processor is further configured to”.
These above recited additional elements are analyzed below under both Step 2A, Prong 2 and Step 2B:
Step 2A, Prong 2:
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exception is not integrated into a practical application because the claims do not recite additional elements that reflect an improvement to a computer, technology, or technical field (MPEP § 2106.04(d)(1) and 2106.5(a)), require a particular treatment or prophylaxis for a disease or medical condition (MPEP § 2106.04(d)(2)), implement the recited judicial exception with a particular machine that is integral to the claim (MPEP § 2106.05(b)), effect a transformation or reduction of a particular article to a different state or thing (MPEP § 2106.05(c)), nor provide some other meaningful limitation (MPEP § 2106.05(e)). Rather, the claims include limitations that equate to an equivalent of the words “apply it” and/or to instructions to implement an abstract idea on a computer (MPEP § 2106.05(f)). The paragraphs below discuss the additional elements recited above in the instant claims.
Claims 1-8 do not recite any additional elements because all their limitations recite a judicial exception. Thus, claims 1-8 cannot be integrated into a practical application (MPEP § 2106(d).III).
Regarding the above cited limitations in claims 10-15 of the system comprising a processor and non-transitory computer readable storage medium, there are no limitations that the system requires anything other than a generic computer. Therefore, these limitations equate to instructions to implement an abstract idea on a generic computer, which the courts have established does not render an abstract idea eligible in Alice Corp. 573 U.S. at 223, 110 USPQ2d at 1983.
Regarding the above cited limitation in claim 11 of receiving information, this limitation equates to insignificant, extra-solution activity of necessary data gathering because it acquires data necessary to perform to perform the judicial exceptions in claim 10.
As such, claims 1-8 and 10-15 are directed to an abstract idea and a natural phenomenon (Step 2A, Prong 2: NO).
Step 2B:
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because these claims recite additional elements that equate to instructions to apply the recited exception in a generic way and/or in a generic computing environment (MPEP § 2106.05(f)) and to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The paragraphs below discuss the additional elements recited above in the instant claims.
Claims 1-8 do not recite any additional elements because all their limitations recite a judicial exception. Thus, claims 1-8 cannot amount to significantly more than the judicial exception itself (MPEP § 2106.05.I).
Regarding the above cited limitation in claims 10-15 of the system comprising a processor and non-transitory computer readable storage medium, there are no limitations that the system requires anything other than a generic computer. Therefore, these limitations equate to instructions to implement an abstract idea on a generic computing environment, which the courts have established does not provide an inventive concept in Intellectual Ventures I LLC v. Capital One Bank (USA), 792 F.3d 1363, 1367, 115 USPQ2d 1636, 1639 (Fed. Cir. 2015).
Regarding the above cited limitation in claim 10 of a non-transitory computer readable storage medium containing instructions, this limitation equates to storing information in memory, which the courts have established as a WURC function of a generic computer in Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015).
Regarding the above cited limitation in claim 11 of receiving information, this limitation equates to receiving/transmitting data over a network because it is performed by a processor, which the courts have established as WURC limitation of a generic computer in buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014).
When these additional elements are considered individually and in combination, they do not provide an inventive concept because they all equate to WURC functions/components of a generic computer. Therefore, these additional elements do not transform the claimed judicial exception into a patent-eligible application of the judicial exception and do not amount to significantly more than the judicial exception itself (Step 2B: No).
As such, claims 1-8 and 10-15 are not patent eligible.
Response to Arguments under 35 USC 101
Applicant's arguments filed 04/07/2026 have been fully considered but they are not persuasive.
Applicant argues that claims do not recite a natural phenomenon (pg. 6, sec. 1) and are distinct from Mayo (pg. 11, sec. D, para. 2). Applicant’s argument is not persuasive because:
Even though the vPGS requires specific calculations, the vPGS still represents a correlation between genetic variants and phenotypes. A correlation between genetic variants and phenotypes is a natural phenomenon.
Applicant argues that claims do not recite math because the math is not recited at a high level and is used for a particular application (pg. 7, sec. 2, para. 1-2). Applicant’s argument is not persuasive because:
As stated by Applicant, the claims require mathematical operations such as regression analysis and summation of weights. Thus, the claims are not just based on math but rather recite math. MPEP 2106.04(a)(2).I.C recites “A claim that recites a mathematical calculation, when the claim is given its broadest reasonable interpretation in light of the specification, will be considered as falling within the ‘mathematical concepts’ grouping … a step of ‘determining’ a variable or number using mathematical methods or ‘performing’ a mathematical operation may also be considered mathematical calculations when the broadest reasonable interpretation of the claim in light of the specification encompasses a mathematical calculation.”
Regarding practical application, selecting a participant recites a mental process. MPEP 2106.05(a) recites “the judicial exception alone cannot provide the improvement.”
Applicant argues claims involving mathematical operations are not abstract when directed to improvements in technology or when applied to concrete problems (pg. 7, sec. 2, para. 2). Applicant also argues the claims are tied to analysis of genomic data necessarily generated by a physical instrument, and the claims produce a novel, technologically useful output (pg. 7, sec. 2, last para.) Applicant’s argument is not persuasive because:
Claim 1 does not recite producing genetic data. Rather, the BRI includes analyzing previously produced data. Even if the claims required producing genetic data, MPEP recites "It is well-settled that mere recitation of concrete, tangible components is insufficient to confer patent eligibility to an otherwise abstract idea.” See also TLI Communications LLC v. AV Automotive LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016).
The output is being interpreted to mean vPGS scores. vPGS scores recite a judicial exception and thus do not confer a practical application. A practical application must be provided by one or more additional elements or based on how the additional element(s) interacts with the judicial exception. As of record, the only additional elements are generic computer components/functions that apply the abstract idea, which does not equate to a practical application (MPEP 2106.05(f)).
Applicant argues that a human cannot practically perform the math recited in claims (pg. 7, sec. 2, last para.). Applicant’s argument is not persuasive because:
The claims do not require millions of SNPs. The claims do not require performing multiple regressions and vQTL analyses, but rather require just one of the four different “performing” limitations. A human can practically perform on pen and paper a regression to predict a squared Z-score for a couple variants and sum weights into a single score. Even if these calculations could not be performed by a human, they would still recite math.
Applicant argues a practical application conferred by “selecting at least one participant for a clinical trial based on a comparison of one or more of the at least one vPGS scores to a threshold vPGS” (pg. 8, sec. B, para. 1-2). Applicant also argues that this limitation is analogous to a particular treatment similar to Vanda (pg. 8, sec. B, last para – pg. 9, para. 2) (pg. 11, last para.). Applicant’s argument is not persuasive because:
This limitation recites a mental process. A human can make a selection as it requires analysis and determinations. The limitation “for a clinical trial” is an intended use, and the claim does not require performing a clinical trial.
This limitation does not recite a particular treatment. A particular treatment requires an affirmative recitation of an action that effects a particular treatment or prophylaxis such as administrating a specific drug that treats a specific disease or condition (MPEP 2106.02(d)(2)). The instant claims do not recite these requirements.
Applicant argues for an improvement in the field of genetic analysis conferred by the vPGS (pg. 9, para. 3). Applicant’s argument is not persuasive because:
The vPGS is part of the recited judicial exception. MPEP 2106.05(a)(II) recites “it is important to keep in mind that an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology.”
An improvement can be provided by one or more additional elements, or the additional element(s) in combination with the recited judicial exception. However, claims 1-8 do not recite additional elements, and claims 10-15 merely recite generic computer components/functions that equate to mere instructions to implement an abstract idea on a generic computer.
Applicant argues that vPGS is not conventional (pg. 9, sec. 1) and that a combination of vPGS and selecting participants for clinical trials provides an inventive concept (pg. 11, sec. 3). Applicant’s argument is not persuasive because:
The vPGSs and selecting participants for clinical trials are part of the recited judicial exception. Only additional elements are evaluated for whether they recite an inventive concept or well-understood, routine, and conventional (MPEP 2106.05(d)).
Applicant’s argument regarding selecting a participant for a clinical trial not being mere post-solution activity is not persuasive because it recites a mental process, not an additional element (pg. 10, sec. 2).
Applicant’s argument regarding vPGS being distinct from and Mayo and Association for Molecular Pathology v. Myriad Genetics is persuasive because the vPGS does not recite a substance or sequence (pg. 11, sec. D). However, the vPGS still recites a natural phenomenon, a mental process, and a mathematical concept as discussed in the response above.
Applicant’s argument regarding Rapid Litigation Management Ltd. v. CellzDirect, Inc. is not persuasive because the vPGS and selecting participants for clinical trials recite a judicial exception (pg. 12, para. 1). MPEP 2106.05(a) recites “the judicial exception alone cannot provide the improvement.”
Conclusion
No claims are allowed.
Claims 1-8 and 10-15 are free from the prior art because the prior art does not fairly teach or suggest the following limitations in claims 1 and 10: “generating at least one variance polygenic score (vPGS) of phenotypic information by: performing a regression to predict a squared Z-score for each outcome of the phenotypic information, and summing weights from prediction of the squared Z-score for each outcome into a single index for scoring individuals' DNA variants into the at least one variance polygenic score; performing a regression to predict a statistical measure of spread within a familial relationship of the phenotypic information, for each outcome, and summing weights from prediction of the statistical measure of spread for each outcome into a single index for scoring individuals' DNA variants into the at least one variance-polygenic score; performing a mean-variance quantitative trait loci (vQTL) analysis for variance heterogeneity of the phenotypic information, for each outcome, and summing weights of regressions of the vQTL analysis for each outcome into a single index for scoring individuals' DNA variants into the at least one variance polygenic score; performing a vQTL analysis for variance effects of phenotypic information, and summing weights of regressions of the vQTL analysis into a single index for scoring individuals' DNA variants into the at least one variance polygenic score; or a combination thereof.”
The closest prior art is Conley et al. (“Conley”; NPL ref. 16 on IDS filed 03/20/2023; PloS one 13, no. 4 (2018): e0194541; previously cited) who discloses a sibling method for identifying variance quantitative trait loci (vQTL) (abstract). Conley recites “We can extend the polygenic score approach to develop scores that predict variance in a trait (vPGS). Coefficients for a vPGS construction in a prediction sample would be obtained from a vGWAS” (pg. 17, last para.). The sibling method generates “weights for polygenic scores to predict trait variance” (pg. 17, para. 2). “Coefficients for a vPGS construction in a prediction sample would be obtained from a vGWAS done within families with sibling sets” (pg. 17, last para.). However, Conley does not describe how to calculate the vPGS scores as recited in the instant claims.
Furthermore, one of ordinary skill would not have modified Conley using either Choi et al. (“Choi”; Nature protocols 15, no. 9 (2020): 2759-2772; previously cited on PTO892 mailed 10/08/2025) or Damask et al. (“Damask”; Circulation 141, no. 8 (2020): 624-636; previously cited on PTO892 mailed 02/09/2026) to arrive at the claimed vPGSs. As argued by Applicant in Remarks filed 04/07/2026, Conley suggests construction of vPGS but does not teach how to construct them (pg. 12, sec. A, para. 1) (pg. 16, sec. E, para. 3), and one of ordinary skill in the art would not have applied a classical PGS formula of Choi to get the vPGS of Conley, considering different statistical architecture to derive the different scores (pg. 13, para. 1). Similarly, Damask does not discuss how to construct a vPGS.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Noah A. Auger whose telephone number is (703)756-4518. The examiner can normally be reached M-F 7:30-4:30 EST.
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/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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