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 .
Claim Status
Claims 1-21 are currently pending and under exam herein.
Claims 1-21 are rejected.
Claim 17 is objected to.
Priority
The instant application does not claim the benefit of priority to any earlier filed applications. Therefore, the effective filing date of claims 1-21 is April 28, 2023.
Information Disclosure Statement
The information disclosure statements (IDS) submitted June 2, 2023 and June 21, 2023 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Claim Objections
Claim 17 is objected to because of the following informalities:
The claim limitations wherein the processor further: subdivides an interacting phenotype by: determines a mean…; defines a first…; and defines a second… are grammatically incorrect because they are double-predicate errors. It is suggested to amend determines to determining and both defines to defining. Appropriate correction is required.
Claim Interpretation
The following definition will be used to interpret the meaning of probands from the National Human Genome Research Institute: An individual who is affected by a genetic condition or who is concerned they are at risk.
Claim Rejections - 35 USC § 112
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 3, 10, and 17 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.
Regarding claims 3, 10, and 17, the claims are rendered indefinite because it is not clear if subdividing an interacting phenotype is done before selecting the interacting phenotype based on the odds ratio difference or if the subdivision is done only on the selected interacting phenotypes.
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 1-21 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
Step 1:
The first part of the eligibility analysis evaluates whether a claim falls within any statutory category (MPEP 2106.03). Claims 1-7 are a series of steps to determine the risk of developing a primary phenotype when a subject has an interacting phenotype. The claims are directed to a method and fall within one of the statutory categories of invention.
Claims 8-14 recite a non-transitory computer readable medium that causes a processor to execute a method to determine the risk of developing a primary phenotype when a subject has an interacting phenotype. The claims are directed to a machine and fall within one of the statutory categories of invention.
Claims 15-21 recite a computer system that performs a method to determine the risk of developing a primary phenotype when a subject has an interacting phenotype. The claims are directed to a machine and fall within one of the statutory categories of invention (Step 1: YES).
Step 2A, prong 1:
In accordance with MPEP 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature, or natural phenomenon (Step 2A, prong 1). In the instant application, the claims recite the following limitations that equate to those concepts:
Claim 1 recites: identifying, from a larger population of gene sequences, a first plurality of gene sequences of probands having a genetic variant that is susceptible to contracting a primary phenotype; … identifying, from the first plurality of gene sequences, a second plurality of gene sequences of probands having the interacting phenotype; determining a difference between an odds ratio indicating a likelihood of probands having the primary phenotype for the second plurality of gene sequences and an odds ratio indicating a likelihood of probands having the primary phenotype for the first plurality of gene sequences; and selecting the interacting phenotype based on the difference; and identifying a risk of contracting the primary phenotype for each of the selected interacting phenotypes.
Claim 2 recites: processing a gene sequence of a patient to determine that the gene sequence of the patient has the genetic variant that is susceptible to contracting the primary phenotype; and determining a risk of the patient contracting the primary phenotype based on whether the patient has a selected interacting phenotype.
Claim 3 recites: … determining a mean of a probability distribution of the interacting phenotype for the first plurality of gene sequences; defining a first interacting phenotype comprising values outside one standard deviation higher than the mean; and defining a second interacting phenotype comprising values outside one standard deviation lower than the mean.
Claim 4 recites: selecting the interacting phenotype if a positive predictive value of the interacting phenotype contributing to the primary phenotype breaches a pre-determined threshold; and selecting the interacting phenotype if a negative predictive value of the interacting phenotype contributing to the primary phenotype breaches another pre-determined threshold.
Claim 5 recites: including an additional interacting phenotype to identify the second plurality of gene sequences for selection.
Claim 6 recites: computing an odds ratio for the additional interacting phenotype.
Claim 7 recites: performing a regression analysis to compute the odds ratios.
Claim 8 recites: identifying, from a larger population of gene sequences, a first plurality of gene sequences of probands having a genetic variant that is susceptible to contracting a primary phenotype; … identifying, from the first plurality of gene sequences, a second plurality of gene sequences of probands having the interacting phenotype; determining a difference between an odds ratio indicating a likelihood of probands having the primary phenotype for the second plurality of gene sequences and an odds ratio indicating a likelihood of probands having the primary phenotype for the first plurality of gene sequences; and selecting the interacting phenotype based on the difference; and identifying a risk of contracting the primary phenotype for each of the selected interacting phenotypes.
Claim 9 recites: processing a gene sequence of a patient to determine that the gene sequence of the patient has the genetic variant that is susceptible to contracting the primary phenotype; and determining a risk of the patient contracting the primary phenotype based on whether the patient has a selected interacting phenotype.
Claim 10 recites: … determining a mean of a probability distribution of the interacting phenotype for the first plurality of gene sequences; defining a first interacting phenotype comprising values outside one standard deviation higher than the mean; and defining a second interacting phenotype comprising values outside one standard deviation lower than the mean.
Claim 11 recites: selecting the interacting phenotype if a positive predictive value of the interacting phenotype contributing to the primary phenotype breaches a pre-determined threshold; and selecting the interacting phenotype if a negative predictive value of the interacting phenotype contributing to the primary phenotype breaches another pre-determined threshold.
Claim 12 recites: including an additional interacting phenotype to identify the second plurality of gene sequences for selection.
Claim 13 recites: computing an odds ratio for the additional interacting phenotype.
Claim 14 recites: performing a regression analysis to compute the odds ratios.
Claim 15 recites: … identifies, from a larger population of the gene sequences, a first plurality of gene sequences of probands having a genetic variant that is susceptible to contracting a primary phenotype; … identifies, from the first plurality of gene sequences, a second plurality of gene sequences of probands having the interacting phenotype; determines a difference between an odds ratio indicating a likelihood of probands having the primary phenotype for the second plurality of gene sequences and an odds ratio indicating a likelihood of probands having the primary phenotype for the first plurality of gene sequences; and selects the interacting phenotype based on the difference; and identifies a risk of contracting the primary phenotype for each of the selected interacting phenotypes.
Claim 16 recites: … processes a gene sequence of a patient to determine that the gene sequence of the patient has the genetic variant that is susceptible to contracting the primary phenotype; and determines a risk of the patient contracting the primary phenotype based on whether the patient has a selected interacting phenotype.
Claim 17 recites: … determines a mean of a probability distribution of the interacting phenotype for the first plurality of gene sequences; defines a first interacting phenotype comprising values outside one standard deviation higher than the mean; and defines a second interacting phenotype comprising values outside one standard deviation lower than the mean.
Claim 18 recites: … selects the interacting phenotype if a positive predictive value of the interacting phenotype contributing to the primary phenotype breaches a pre-determined threshold; and selects the interacting phenotype if a negative predictive value of the interacting phenotype contributing to the primary phenotype breaches another pre-determined threshold.
Claim 19 recites: includes an additional interacting phenotype to identify the second plurality of gene sequences for selection.
Claim 20 recites: … computes an odds ratio for the additional interacting phenotype.
Claim 21 recites: … performs a regression analysis to compute the odds ratios.
The limitations in claims 1, 8, and 15 of identifying a first plurality of gene sequences, identifying a second plurality of gene sequences, selecting interacting phenotypes based on a difference, and identifying a risk of contracting the primary phenotype encompass mental process of observation and evaluation of data to identify groupings, selecting desired data, and pointing out risk of contracting the primary phenotype. The limitations of determining a difference between odds ratios are verbal equivalents of mathematical calculations. The limitations in claims 5, 12, and 19 further limit the mental processes and mathematical calculations in claims 1, 8, and 15, respectively, by adding another interacting phenotype for consideration.
The limitations in claims 2, 9, and 16 of processing a gene sequence of a patient to determine presence of a genetic variant and determining risk of contracting the primary phenotype encompass mental processes of observing and evaluating data to detect a genetic variant and assign risk to the patient.
The limitations in claims 3, 10, and 17 of determining a mean of a probability distribution is a verbal recitation of mathematical calculations. The limitations of defining a first interacting phenotype and a second interacting phenotype encompass mental processes to observed and classify data.
The limitations in claims 4, 11, and 18 of selecting the interacting phenotype based on a positive predictive value or a negative predictive value breaching a threshold encompass the mental process of observing and evaluating data to choose desired interacting phenotypes.
The limitations in claims 6-7, 13-14, and 20-21 of computing an odds ratio for the additional interacting phenotype and performing a regression analysis to compute odds ratios are recitations of mathematical calculations.
Therefore, these limitations fall under the “Mathematical concepts” and “Mental processes” groupings of abstract ideas (Step 2A, prong 1: YES).
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 (Step 2A, prong 2). The claims recite the following additional elements:
Claim 8 recites: A non-transitory computer readable medium embodying programmed instructions which, when executed by a processor, are operable for performing a method…
Claim 15 recites: a database of gene sequences of probands; and a processor…
The additional element in claim 8 of a non-transitory computer readable medium embodying programmed instructions is an invocation of using a computer to perform the judicial exception and amount instructions to apply the judicial exception in a generic computer environment (MPEP 2106.05(f)). Similarly, the additional elements in claim 15 of a database of gene sequences and a processor are instructions to apply the judicial exception in a generic computer.
Therefore, the judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies/uses the recited judicial exception in some other meaningful way and the claims are directed to the judicial exception (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). The claims recite additional elements in claims 8 and 15 that equate to mere instructions to apply the recited judicial exception in a generic computing environment. Claims that amount to nothing more than instructions to apply the judicial exception using a generic computer do not render an abstract idea eligible. Alice Corp., 576 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984.
As such, the combination of additional elements recited in the claims is well-understood, routine, and conventional. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transform the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: NO) and claims 1-21 are not patent eligible.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-2, 5-7, 8-9, 12-14, 15-16, and 19-21 are rejected under 35 U.S.C. 103 as being unpatentable over Andreassen et al. (US20150356243A1) in view of Genome Toolbox (Online blog, retrieved July 30, 2026). The italicized text corresponds to the instant claim limitations.
Regarding claims 1, 8, and 15, Andreassen et al. teach a method of providing knowledge about genotype-phenotype associations by first obtaining genome wide association studies (GWAS) data of a particular trait or disease from at least two subjects (paragraph 0090) and, in some embodiments from all available GWAS studies (paragraph 0099) then combining data into one set as shown in Figure 20 (paragraphs 0091-0093) which discloses identifying, from a larger population of gene sequences, a first plurality of gene sequences of probands having a genetic variant that is susceptible to contracting a primary phenotype… Andreassen et al. teach annotating each single nucleotide polymorphism (SNP) and then obtaining enrichment factor information for each SNP; which can be an associated or co-morbid phenotype (paragraphs 0094-0095) which discloses …for each of a plurality of interacting phenotypes: identifying, from the first plurality of gene sequences, a second plurality of gene sequences of probands having the interacting phenotype because after identifying SNPs associated with a first condition/disease, they identified a subset of SNPs that are implicated in an associated/co-morbid phenotype (e.g., SNPs associated with bipolar disorder greatly increase the signal in schizophrenia). Andreassen et al. teach employing statistical tools to obtain true discovery rate (TDR) values and false discovery rate (FDR) values and improving technical calculations of the GWAS by combing enrichment factors including pleiotropic enrichment (i.e., genes involved in a trait and an associated/co-morbid phenotype) which can be utilized to provide an estimated risk for specific phenotypes (paragraphs 0096-0099) which discloses identifying a risk of contracting the primary phenotype for each of the selected interacting phenotypes.
Regarding claims 8 and 15, Andreassen et al. teach a variety of computer-related embodiments, including computer programming for analyzing and comparing polymorphisms embodied on a program storage device (paragraphs 0100-0101, 0107) which discloses the claim 8 limitation of a non-transitory computer readable medium embodying programmed instructions which, when executed by a processor, are operable for performing a method… Andreassen et al. teach the computer system can have a processor and database (paragraphs 0103-0104) which discloses the claim 15 limitations of a database of gene sequences of probands; and a processor…
Regarding claims 2, 9, and 16, Andreassen et al. teach one utility for their invention is providing an estimate of risk for specific phenotypes using GWAS from an individual person (paragraph 0099) which discloses processing a gene sequence of a patient to determine that the gene sequence of the patient has the genetic variant that is susceptible to contracting the primary phenotype; and determines a risk of the patient contracting the primary phenotype based on whether the patient has a selected interacting phenotype.
Regarding claims 5, 12, and 19, Andreassen et al. teach in some embodiments, updates are provided on gene function such as enrichment factors (which can be associated or co-morbid phenotypes) when new information is available (paragraphs 0095, 0099) which discloses including an additional interacting phenotype to identify the second plurality of gene sequences for selection.
Regarding claims 6, 13, and 20, Andreassen et al. teach when using pleiotropy-informed conditional and conjunction analyses, excess pleiotropy is predicted when a log-odds ratio is greater than zero (paragraphs 0153-0158) which discloses computing an odds ratio for the additional interacting phenotype.
Andreassen et al. teach using other phenotypes determined to be pleiotropic to increase prediction power in their methods (paragraphs 0153-0160), but appear to be silent on the claims 1, 8, and 15 limitations of determining a difference between an odds ratio indicating a likelihood of probands having the primary phenotype for the second plurality of gene sequences and an odds ratio indicating a likelihood of probands having the primary phenotype for the first plurality of gene sequences; and selecting the interacting phenotype based on the difference… and the claims 7, 14, and 21 limitations of performing a regression analysis to compute the odds ratios. However, these limitations were known in the art prior to the effective filing date of the invention as taught by Genome Toolbox.
Regarding claims 1, 8, and 15, Genome Toolbox teaches testing for statistical difference between two odds ratios is useful in determining if an association has statistically different effects in different groups or strata of a variable (Test for a Difference in Two Odds Ratios, paragraphs 1-4) which discloses determining a difference between an odds ratio indicating a likelihood of probands having the primary phenotype for the second plurality of gene sequences and an odds ratio indicating a likelihood of probands having the primary phenotype for the first plurality of gene sequences; and selecting the interacting phenotype based on the difference… The two different strata of a variable are the second plurality of gene sequences and the first plurality of gene sequences which are both associated with the primary phenotype (i.e., the variable). Differences deemed statistically significant would be selected (e.g., associations stronger in older individuals than in younger individuals) (Id.).
Regarding claims 7, 14, and 21, Genome Toolbox teaches to test a difference between two odds ratios, the beta estimate from a logistic regression is needed as an odds ratio estimate (Test for a Difference in Two Odds Ratios, paragraph 1) which discloses performing a regression analysis to compute the odds ratios.
An invention would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the invention if some motivation in the prior art would have led that person to combine or modify the prior art teachings to arrive at the claimed invention. Genome Toolbox teaches an odds ratio difference is useful to determine if an association has statistically different effects in different groups or strata of a variable (Test for a Difference in Two Odds Ratios, paragraph 1) and Andreassen et al. teach due to the polygenic architecture of most complex traits and disorders, a large number of SNPs are likely to have associations too weak to be identified with the currently available sample size and new analytical methods are needed since recruitment and genotyping new samples are expensive (paragraph 0003-0004). Therefore, one of ordinary skill in the art would have been motivated to utilize the odds ratio difference taught by Genome Toolbox in the methods to diagnose, characterize, and predict diseases and trait of Andreassen et al. in order to improve the prediction power and identify true SNP associations. Furthermore, an ordinary artisan would predict the odds ratio difference of Genome Toolbox could be readily added to the methods of Andreassen et al. because both are statistical analyses in bioinformatics used to determine associations. The invention of claims 1-2, 5-7, 8-9, 12-14, 15-16, and 19-21 is therefore prima facie obvious.
Claims 3-4, 10-11, and 17-18 are rejected under 35 U.S.C. 103 as being unpatentable over Andreassen et al. (US20150356243A1) in view of Genome Toolbox (Online blog, retrieved July 30, 2026), as applied to claims 1, 8, and 15 above, and further in view of Halford et al. (Nature Communications, vol. 13, no. 1, p. 5106). The italicized text corresponds to the instant claim limitations.
The limitations of claims 1, 8, and 15 have been taught by Andreassen et al. and Genome Toolbox.
Andreassen et al. and Genome Toolbox appear to be silent on the limitations of claims 3-4, 10-11, and 17-18. However, those limitations were known in the art prior to the effective filing date of the invention as taught by Halford et al.
Regarding claims 3, 10, and 17, Halford et al. teach investigating the ability to determine the pathogenicity of gene variants by analyzing their effect size on an endophenotype (e.g., low-density-lipoprotein concentration for variants associated with familial hypercholesterolemia) (p. 2-3, Variant-level effect sizes and pathogenicity category; Figure 1A-C). Halford et al. also teach applying an effect size threshold to identify variants having a large effect size of 0.5 standard deviation of the endophenotype distribution and other threshold ranges; including a standard deviation of one (p. 4-5, Application of an effect size threshold to provide evidence of pathogenicity, paragraphs 1, 6) which discloses the limitations of subdividing an interacting phenotype by: determining a mean of a probability distribution of the interacting phenotype for the first plurality of gene sequences; defining a first interacting phenotype comprising values outside one standard deviation higher than the mean; and defining a second interacting phenotype comprising values outside one standard deviation lower than the mean.
Regarding claims 4, 11, and 18, Halford et al. teach tabulating positive predictive values and negative predictive values (p. 4, Application of an effect size threshold to provide evidence of pathogenicity, paragraphs 1) which discloses selecting the interacting phenotype if a positive predictive value of the interacting phenotype contributing to the primary phenotype breaches a pre-determined threshold; and selecting the interacting phenotype if a negative predictive value of the interacting phenotype contributing to the primary phenotype breaches another pre-determined threshold.
An invention would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the invention if some motivation in the prior art would have led that person to combine or modify the prior art teachings to arrive at the claimed invention. Andreassen et al. teach that due to the polygenic architecture of most complex traits and disorders, a large number of SNPs are likely to have associations too weak to be identified with the currently available sample size and new analytical methods are needed since recruitment and genotyping new samples are expensive (paragraph 0003-0004). Halford et al. teach determining clinical significance of a rare genetic variation has critical implications for optimal care for patients and their families and incorrect classification of genetic variation increases risk for adverse consequences (p. 1, Introduction, paragraph 1). However, it is common to lack sufficient evidence for pathogenicity which leads to the inability to discriminate variants of uncertain significance (Id.).
Therefore, one of ordinary skill in the art would have been motivated to utilize the standard deviation thresholds, positive predictive values, and negative predictive values to assess whether an endophenotype could determine pathogenicity of genetic variants for a disease as taught by Halford in the methods to diagnose, characterize, and predict diseases and trait of Andreassen et al. because Halford et al. demonstrated that variant effect size on endophenotypes discriminated between pathogenic and benign variants (p. 5, Discussion, paragraph 1). Furthermore, an ordinary artisan would predict the statistical analyses in Halford et al. could be readily added to the methods of Andreassen et al. because both are analyzing overlapping or pleiotropic phenotypes to determine associations between genetic variation and a phenotype of interest such as a disease. The invention of claims 3-4, 10-11, and 17-18 is therefore prima facie obvious.
Conclusion
No claims are allowed.
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/T.Y.O./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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