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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-14 in the reply filed on 9 March 2026 is acknowledged. Applicant also elects without traverse of Species Group 1, claims 5 and 12, drawn to identifying one or more genetic pathways potentially associated with one or more phenotypic characteristics of the individual, and of Species Group 2, claim 7, drawn to identifying one or more genes potentially associated with one or more phenotypic characteristics of the individual, which are acknowledged in the reply filed on 9 March 2026.
Claim Status
Claims 1-15 are pending.
Claims 6, 8, 13, and 15 are withdrawn.
Claims 1-5, 7, 9-12, and 14 are examined on the merits.
Priority
The instant application is a 371 of PCT/EP2020/082792 filed on 20 November 2020. At this point in examination, the effective filing date of claims 1-5, 9-12, and 14 is 20 November 2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 25 May 2022 in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
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 1, 3-4, 9, and 11 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.
The term “similar” in claim 1, line 7, claim 3, line 2, claim 4, line 2, claim 9, line 7, and claim 11, line 2 is a relative term which renders the claim indefinite. The term “similar” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear what makes phenotype profiles "similar" to each other. The specification is also silent as to how phenotype profiles are "similar". One skilled in the art would not recognize what "similar" means between phenotype profiles because it is not clearly defined in the claim or specification. Therefore, claims 1, 3-4, 9, and 11 are rendered indefinite and rejected under 35 U.S.C. 112(b).
The term “similarity” in claim 1, lines 9 and 12, claim 3, line 2, claim 4, line 3, claim 9, lines 9 and 12, and claim 11, line 2 is a relative term which renders the claim indefinite. The term “similarity” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear what a "similarity" is in a comparison between phenotype profiles. The specification is also silent as to what a "similarity" means. One skilled in the art would not recognize what is considered a "similarity" between a genetic pathway or gene's disease/phenotype associations and a phenotype profile because it is not clearly defined in the claim or specification. Therefore, claims 1, 3-4, 9, and 11 are rendered indefinite and rejected under 35 U.S.C. 112(b).
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 1-5, 7, 9-12, and 14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion).
Subject matter eligibility evaluation in accordance with MPEP 2106:
Eligibility Step 1: Claims 1-5 and 7 are directed to a method (process) for characterizing a relevance of one or more genes or pathways to a disease of an individual using a relevance analysis system. Claims 9-12 and 14 are directed to a system (machine). Therefore, these claims are encompassed by the categories of statutory subject matter, and thus satisfy the subject matter eligibility requirements under Step 1.
[Step 1: YES]
Eligibility Step 2A: First, it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A, Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth described in the claim.
Claims 1-5, 7, 9, 11-12, and 14 recite the following steps which fall within the mental processes and/or mathematical concepts groups of abstract ideas, as noted below.
Independent claim 1 further recites:
identifying, using a database of stored phenotype profiles, one or more database of stored phenotype profiles similar to the individual phenotype profile (i.e., mental processes);
determining a relevance of one or more genetic pathways to the individual phenotype profile, based at least in part on a similarity between the genetic pathway’s known disease/phenotype associations and a phenotype profile of the individual (i.e., mental processes);
determining a relevance of one or more genes to the individual phenotype profile, based at least in part on a similarity between the gene’s known disease/phenotype associations and a phenotype profile of the individual (i.e., mental processes).
Dependent claims 5 and 12 further recite:
wherein determining a relevance of one or more genetic pathways to the individual phenotype profile comprises identifying one or more genetic pathways potentially associated with one or more phenotypic characteristics of the individual (i.e., mental processes).
Dependent claim 7 and 14 further recite:
wherein determining a relevance of one or more genes to the individual phenotype profile comprises identifying one or more genes potentially associated with one or more phenotypic characteristics of the individual (i.e., mental processes).
Independent claim 9 further recites:
(i) identify, using a database of stored phenotype profiles, one or more database of stored phenotype profiles similar to the individual phenotype profile (i.e., mental processes);
(ii) determine a relevance of one or more genetic pathways to the individual phenotype profile, based at least in part on a similarity between the genetic pathway’s known disease/phenotype associations and a phenotype profile of the individual (i.e., mental processes);
(iii) determine a relevance of one or more genes to the individual phenotype profile, based at least in part on a similarity between the gene’s known disease/phenotype associations and a phenotype profile of the individual (i.e., mental processes).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pencil and paper, and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Therefore, claims 1-5, 7, 9, 11-12, and 14 recite an abstract idea.
[Step 2A, Prong One: YES]
Eligibility Step 2A, Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that, when examined as a whole, integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A, Prong One are not integrated into a practical application because of the reasons noted below.
Claims 1 and 9-10 recite the additional non-abstract elements of data gathering:
obtaining a phenotype profile for the individual, comprising one or more phenotypic characteristics of the target individual, differential gene expression information from the target individual, and differential protein expression information from the target individual (claim 1);
reporting one or more genetic pathways and/or one or more genes most relevant to the individual phenotype profile (claim 1);
(iv) report one or more genetic pathways and/or one or more genes most relevant to the individual phenotype profile (claim 9);
provide the report of one or more genetic pathways and/or one or more genes most relevant to the individual phenotype profile (claim 10).
Data gathering steps are not an abstract idea, they are extra-solution activity, as they collect the data needed to carry out the JE. The data gathering does not impose any meaningful limitation on the JE, or how the JE is performed. The additional limitation (data gathering) must have more than a nominal or insignificant relationship to the identified judicial exception. (MPEP 2106.04/.05, citing Intellectual Ventures LLC v. Symantee Corp, McRO, TLI communications, OIP Techs. Inc. v. Amason.com Inc., Electric Power Group LLC v. Alstrom S.A.).
Claims 9-10 recite the additional non-abstract element (EIA) of a general-purpose computer system or parts thereof:
a system comprising a processor (claim 9);
a user interface (claim 10).
The EIA do not provide any details of how specific structures of the computer elements are used to implement the JE. The claims require nothing more than a general-purpose computer to perform the functions that constitute the judicial exceptions. The computer elements of the claims do not provide improvements to the functioning of the computer itself (as in DDR Holdings, LLC v. Hotels.com LP); they do not provide improvements to any other technology or technical field (as in Diamond v. Diehr); nor do they utilize a particular machine (as in Eibel Process Co. v. Minn. & Ont. Paper Co.). Hence, these are mere instructions to apply the JE using a computer, and therefore the claim does not recite integrate that JE into a practical application.
Thus, the additionally recited elements merely invoke a computer as a tool, and/or amount to insignificant extra-solution data gathering activity, and as such, when all limitations in claims 1-5, 7, 9-12, and 14 have been considered as a whole, the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application. Claims 1 and 9-10 contain additional elements that would not integrate a judicial exception into a practical application and are further probed for inventive concept in Step 2B.
[Step 2A, Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
With respect to claims 1 and 9-10: The limitations identified above as non-abstract elements (EIA) related to data gathering do not rise to the level of significantly more than the judicial exception. Activities such as data gathering do not improve the functioning of a computer, or comprise an improvement to any other technical field. The limitations do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide an unconventional step (citing McRO and Trading Technologies Int’l v. IBG). Data gathering steps constitute a general link to a technological environment. Simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception are insufficient to provide significantly more (as discussed in Alice Corp.,).
With respect to claims 9-10: The limitations identified above as non-abstract elements (EIA) related to general-purpose computer systems do not rise to the level of significantly more than the judicial exception. These elements do not improve the functioning of the computer itself, or comprise an improvement to any other technical field (Trading Technologies Int’l v. IBG, TLI Communications). They do not require or set forth a particular machine (Ultramercial v. Hulu, LLC., Alice Corp. Pty. Ltd v. CLS Bank Int’l), they do not affect a transformation of matter, nor do they provide an unconventional step. Simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception are insufficient to provide significantly more (as discussed in Alice Corp., CyberSource v. Retail Decisions, Parker v. Flook, Versata Development Group v. SAP America).
[Step 2B: NO]
Therefore, claims 1-5, 7, 9-12, and 14 are patent ineligible under 35 U.S.C. § 101.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-5, 7, 9-12, and 14 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Buzdin et al. [US20170262578A1].
Regarding claim 1:
Regarding the recited obtaining a phenotype profile for the individual, comprising one or more phenotypic characteristics of the target individual, differential gene expression information from the target individual, and differential protein expression information from the target individual, Buzdin et al. teaches collecting transcriptome data from sick patients, which comprises of differential gene expression data (para. [0173]-[0174], Fig. 3).
Regarding the recited identifying, using a database of stored phenotype profiles, one or more database of stored phenotype profiles similar to the individual phenotype profile, Buzdin et al. teaches a database of stored transcriptome data of healthy patients, which comprises of differential gene expression data similar to that of sick patients (para. [0173]-[0174], Fig. 3). Both sick and healthy phenotype profiles contain similar information, including the same genes and biological pathways.
Regarding the recited determining a relevance of one or more genetic pathways to the individual phenotype profile, based at least in part on a similarity between the genetic pathway’s known disease/phenotype associations and a phenotype profile of the individual, Buzdin et al. teaches comparing pathway activation strength (PAS) scores between a sick patient and a healthy patient to determine an intracellular signaling pathway activation (SPA) associated with a disease or disorder in the sick patient (para. [0033]). This means comparing genetic pathway information between a sick subject and a healthy subject to determine a relevant pathway associated with the sick subject’s disease.
Regarding the recited determining a relevance of one or more genes to the individual phenotype profile, based at least in part on a similarity between the gene’s known disease/phenotype associations and a phenotype profile of the individual, Buzdin et al. teaches comparing transcribed genes between sick patients and healthy patients to define a set of genes which are more strongly expressed or activated in sick people relative to healthy people, and another set of genes which are less strongly expressed or repressed in sick people relative to healthy people (para. [0017]). Also, further teaches analyzing differentially regulated genes revealed differentially activated pathways in tumor tissue (para. [0648]). This means comparing genes between sick subjects and healthy subjects to determine relevant genes in cancer progression.
Regarding the recited reporting one or more genetic pathways and/or one or more genes most relevant to the individual phenotype profile, Buzdin et al. teaches a report on genetic pathways or genes relevant to Patient X (para. [0278]-[0292], [0647]-[0650]).
Regarding claim 2:
Regarding the recited wherein the phenotype profile for the individual further comprises a weight for one or more of the phenotypic characteristics of the target individual, Buzdin et al. teaches applying weighting factors on pathway activation strength (PAS) scores for gene expression data (para. [0151]). This means there is a weight for genetic pathways of an individual.
Regarding claims 3 and 11:
Regarding the recited wherein identifying one or more database of stored phenotype profiles similar to the individual phenotype profile comprises a similarity score for each pairwise comparison between the individual phenotype profile and the stored phenotype profiles, Buzdin et al. teaches a database of stored transcriptome data of healthy patients, which comprises of differential gene expression data similar to that of sick patients (para. [0173]-[0174], Fig. 3). Also, further teaches comparing pathway activation strength (PAS) scores between a sick patient and a healthy patient to determine an intracellular signaling pathway activation (SPA) associated with a disease or disorder in the sick patient (para. [0033]). Buzdin et al. teaches calculating the pathway activation strength (PAS) score by dividing the expression levels for a gene in the sick patient by the expression levels of a healthy patient (para. [0054]). This teaches a score for a comparison between a sick subject’s profile and a healthy subject’s profile.
Regarding claim 4:
Regarding the recited wherein identifying one or more database of stored phenotype profiles similar to the individual phenotype profile comprises selecting one or more stored phenotype profiles with a highest similarity score, Buzdin et al. teaches a database of stored transcriptome data of healthy patients, which comprises of differential gene expression data similar to that of sick patients (para. [0173]-[0174], Fig. 3). Also, further teaches genetic pathways with highest pathway manifestation strength (PMS) scores, which are selected pathways compared between the sick patient and healthy patients (para. [0291]-[0292]). This teaches selecting genetic pathways from similar transcriptome data with a highest comparison score.
Regarding claims 5 and 12:
Regarding the recited wherein determining a relevance of one or more genetic pathways to the individual phenotype profile comprises identifying one or more genetic pathways potentially associated with one or more phenotypic characteristics of the individual, Buzdin et al. teaches comparing pathway activation strength (PAS) scores between a sick patient and a healthy patient to determine an intracellular signaling pathway activation (SPA) associated with a disease or disorder in the sick patient (para. [0033]). Also, further teaches genetic pathways associated with phenotypic characteristics of the sick patient (para. [0291]-[0292]). This means comparing genetic pathway information between a sick subject and a healthy subject to determine a relevant pathway associated with the sick subject’s disease.
Regarding claims 7 and 14:
Regarding the recited wherein determining a relevance of one or more genes to the individual phenotype profile comprises identifying one or more genes potentially associated with one or more phenotypic characteristics of the individual, Buzdin et al. teaches comparing transcribed genes between sick patients and healthy patients to define a set of genes which are more strongly expressed or activated in sick people relative to healthy people, and another set of genes which are less strongly expressed or repressed in sick people relative to healthy people (para. [0017]). Also, further teaches analyzing differentially regulated genes revealed differentially activated pathways in tumor tissue (para. [0648]). This means comparing genes between sick subjects and healthy subjects to determine relevant genes in cancer progression.
Regarding claim 9:
Regarding the recited system and processor, Buzdin et al. teaches a system for analysis of the intracellular signaling pathway activation (SPA), which includes a processor (para. [0036]).
Regarding the recited a phenotype profile for the individual, comprising one or more phenotypic characteristics of the target individual, differential gene expression information from the target individual, and differential protein expression information from the target individual, Buzdin et al. teaches collecting transcriptome data from sick patients, which comprises of differential gene expression data (para. [0173]-[0174], Fig. 3).
Regarding the recited (i) identify, using a database of stored phenotype profiles, one or more database of stored phenotype profiles similar to the individual phenotype profile, Buzdin et al. teaches a database of stored transcriptome data of healthy patients, which comprises of differential gene expression data similar to that of sick patients (para. [0173]-[0174], Fig. 3). Both sick and healthy phenotype profiles contain similar information, including the same genes and biological pathways.
Regarding the recited (ii) determine a relevance of one or more genetic pathways to the individual phenotype profile, based at least in part on a similarity between the genetic pathway’s known disease/phenotype associations and a phenotype profile of the individual, Buzdin et al. teaches comparing pathway activation strength (PAS) scores between a sick patient and a healthy patient to determine an intracellular signaling pathway activation (SPA) associated with a disease or disorder in the sick patient (para. [0033]). This means comparing genetic pathway information between a sick subject and a healthy subject to determine a relevant pathway associated with the sick subject’s disease.
Regarding the recited (iii) determine a relevance of one or more genes to the individual phenotype profile, based at least in part on a similarity between the gene’s known disease/phenotype associations and a phenotype profile of the individual, Buzdin et al. teaches comparing transcribed genes between sick patients and healthy patients to define a set of genes which are more strongly expressed or activated in sick people relative to healthy people, and another set of genes which are less strongly expressed or repressed in sick people relative to healthy people (para. [0017]). Also, further teaches analyzing differentially regulated genes revealed differentially activated pathways in tumor tissue (para. [0648]). This means comparing genes between sick subjects and healthy subjects to determine relevant genes in cancer progression.
Regarding the recited (iv) report one or more genetic pathways and/or one or more genes most relevant to the individual phenotype profile, Buzdin et al. teaches a report on genetic pathways or genes relevant to Patient X (para. [0278]-[0292], [0647]-[0650]).
Regarding claim 10:
Regarding the recited a user interface configured to provide the report of one or more genetic pathways and/or one or more genes most relevant to the individual phenotype profile, Buzdin et al. teaches a display for displaying at least the gene expression data and the pathway cloud map (para. [0101]). Also, further teaches a report on genetic pathways or genes relevant to Patient X (para. [0278]-[0292], [0647]-[0650]). This teaches a display for outputting relevant genetic pathways.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jammy Luo whose telephone number is (571)272-2358. The examiner can normally be reached Monday - Friday, 9:00 AM - 5:00 PM EST.
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/J.N.L./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686
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