DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Applicant's amendments and remarks, filed 07/21/2026, are acknowledged. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Status of Claims
Claims 1-7, 10-17, 20 are under examination.
Claims 8, 9, 18, 19 are cancelled.
Priority
This application is a continuation of U.S. Patent Application Serial No. 14/209,703, filed March 13, 2014, which claims the benefit of U.S. Provisional Application Serial No. 61/799,813, filed March 15, 2013. Accordingly, the effective filing date is March 15, 2013.
Withdrawn Rejections
The rejection of claims 1-7, 10-17, 20 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement is withdrawn in view of applicant’s amendment and supporting arguments.
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 1-7, 10-17, 20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The United States Patent and Trademark Office published revised guidance on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”). Under the Guidance, in determining what concept the claim is “directed to,” we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes) (Guidance Step 2A, Prong 1); and
(2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an “‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not “well-understood, routine and conventional in the field” (see MPEP § 2106.05(d)); or 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019).
(4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception.(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54-56.
Step 1
This part of the eligibility analysis evaluates whether the claim falls within any statutory category. See MPEP 2106.03. In this case, the claimed invention (claims 1 and 11 being representative) requires performing a series of process steps. As such, the claims fall into one of the four statutory categories. (Step 1: YES).
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. In this case, the following claim limitations constitute the abstract idea:
based on a respective variant of the BRCA gene and the familial disease data of each individual, classify each individual into one of a plurality of predefined classifications of the BRCA gene arranged from most likely pathogenic to least likely pathogenic, wherein the plurality of classifications include a deleterious variant, a suspected deleterious variant, a variant of uncertain clinical significance (VUS), a genetic variant-favor polymorphism which is likely to be non-pathogenic, and a genetic variant polymorphism;
generate a probability table based on genetic information selected from the set of individuals that have a respective variant of the BRCA gene, the probability table comprising probability data for the set of individuals representing a likelihood that a particular individual carries a respective mutation in the BRCA gene, the probability table constructed by identifying, for each individual, an empirically-observed probability of having a deleterious mutation based on frequencies with which other individuals in the set of individuals having the same respective variant are diagnosed with a disease associated with the BRCA gene;
determine that the first genetic data identifies a variant of the BRCA gene for the first individual and classifies the first individual as having a VUS with respect to the variant of the BRCA gene; generate a score for the first individual based on the probability table and the first genetic data indicating the likelihood that the first individual carries a mutation in the BRCA gene, wherein the score is generated by computing a likelihood ratio for each individual in the set of individuals having the same variant as the first individual, the likelihood ratio relating posterior odds to prior odds of the individual not carrying a deleterious mutation, and cumulatively multiplying the likelihood ratios to obtain the score;
responsive to determining the first genetic data indicates the first individual as having the VUS classification, reclassify the first individual based on the score and the probability table by comparing the score to scores of a composite deleterious control population and a composite benign control population to determine whether the VUS is more likely deleterious or benign;
Mental Processes
With regards to the classify, determine, and reclassify steps, these are recited at a high level of generality and are not limited to any particular techniques or operations. Accordingly, under the BRI, these steps set forth or describe observing and/or analyzing data, which scientists can perform using their brains or a pencil and paper. As such, these steps encompass a mental process of observing data and/or manipulating data. MPEP 2106.04(a)(2), section III.
With regards to the generate steps, these are also recited at a high level of generality. Accordingly, under the BRI, this step sets forth or describes analyzing and/or manipulating data, which scientists can perform using their brains or a pencil and paper. As such, these steps encompass a mental process of observing data and/or manipulating data. MPEP 2106.04(a)(2), section III.
It is important to note that “Claims that recite performing information analysis as well as the collection and manipulation of information related to such analysis, have been determined by our reviewing court to be an abstract concept that is not patent eligible. See SAP, 898 F.3d, 1165, 1167, 1168 (Claims reciting "[a] method for providing statistical analysis" (id. at 1165) were determined to be "directed to an abstract idea" (id. at 1168)); see also Content Extraction & Transmission LLC v. Wells Fargo Bank, Nat'l Ass 'n, 776 F.3d 1343, 1345, 1347 (Fed. Cir. 2014) [Step 2A, Prong 1: YES].
Mathematical Concept
With regards to the generate steps, both of these steps result in generating numerical values (e.g. a probability table representing likelihood and a score). Accordingly, under the BRI, this steps set forth or describe performing mathematical calculations. This position is further supported by applicant’s own specification, which teaches mathematical techniques for achieving the claimed functions [0013, 0014]. While no specific equation is being claimed, Applicant is reminded that there is no particular word or set of words that indicates a claim recites a mathematical calculation. See MPEP 2106.04(a)(2). As such, this step encompasses a mathematical concept of manipulating information through mathematical correlations or calculations. MPEP 2106.04(a)(2) Section I [Step 2A, Prong 1: YES].
Natural Correlation
Additionally, the above claims are also directed to a natural correlation for the following reasons. In particular, the instant claims require obtaining genetic sequence data and correlating this information mutations in the BRCA gene (i.e. a particular disease or phenotype). Therefore, the discriminating step further recites a law of nature because it describes the naturally occurring relationship between a subject’s DNA and a particular phenotype. See MPEP 2106.04(b). It is noted that even if a claim does recite a law of nature or natural phenomenon, it may still be eligible. For example, claims reciting a naturally occurring relationship between a patient’s genotype and the risk of QTc prolongation (a law of nature) were held eligible as not “directed to” that relationship because they also recited a step of treating the patient with an amount of a particular medication that was tailored to the patient’s genotype. Vanda Pharms., 887 F.3d at 1134-36, 126 USPQ2d at 1279-81. This particular treatment step applied the natural relationship in a manner that integrated it into a practical application. The court’s analysis in Vanda is equivalent to a finding of eligibility at Step 2A Prong Two (Pathway B).
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim includes any additional steps/elements that integrate the recited judicial exception into a practical application of the exception. In this case, the additional steps/elements that are not part of the abstract idea are as follows:
store a genetic sequencing data for a set of individuals, the genetic sequencing data comprising a variant of a breast cancer (BRCA) gene for each individual of the set of individuals;
receive and store familial disease data for the set of individuals, the familial disease data comprising information about diseases diagnosed in relatives of individuals in the set of individuals and ages at which the diagnoses were made;
receive, via a web-based frontend, first genetic data of a first individual not included in the set of individuals;
provide, via the web-based interface, the reclassification of the first individual and…update, via the one or more processors, a treatment plan stored in an electronic medical record system associated with the first individual to initiate at least one of an imaging procedure, a biopsy, a physical examination, or enrollment in an enhanced surveillance program with increased frequency of checkups
With regards to the storing and receiving steps, these steps are recited at a high level of generality and amount to obtaining data for use by the abstract idea. As such, these steps amount to insignificant extra-solution activity and are not indicative of an integration into a practical application. See MPEP 2106.05(g).
With regards to the step of providing reclassification, this step recited at a high level of generality and amounts to outputting data (via a web-based interface) and updating a treatment plan (i.e. information) stored in an electronic medical records system. In other words, this step amounts to providing information which is insignificant extra-solution activity. In addition, it is noted that the phrase “to initiate at least one of an imaging procedure, biopsy, examination, or enrollment…” is an intended use recitation that does not impose any limiting effect on the method as claimed, i.e. it is not a positively recited treatment step and does not result in administering any particular treatment. Therefore, the claimed “provide” step amounts to insignificant extra-solution activity (e.g. outputting information or advice), as discussed in MPEP § 2106.05(g), and/or generally linking the use of a judicial exception to a particular technological environment or field of use, as discussed in MPEP § 2106.05(h). Consequently, the claimed invention does not integrate the abstract idea into a “practical application.”
With regards to the processor, “web-based interface” (which is broadly interpreted as a GUI), and medical records system, applicant is reminded that generic computer components such as a computer and database do not satisfy the inventive concept requirement. See MPEP 2106.05(f) and 2106.05(h). Accordingly, the claims as a whole do not integrate the recited judicial exception into a practical application and the claims are directed to the judicial exception. [Step 2A, Prong 2: NO]
C. Guidance Step 2B:
Under the 2019 PEG, a conclusion that an additional element is insignificant extra-solution activity in Step 2A should be re-evaluated in Step 2B. In this case, the claims do not include additional steps and/or elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons:
As discussed above, the non-abstract steps/elements amount to nothing more than insignificant extra-solution activity. Applicant’s own specification teaches that general purpose client-server systems and interfaces for obtaining, receiving, and displaying information were routine and conventional in the art [0043, 0074, 0081, 0086]. Moreover, Vallee et al. (Human Mutation, 2012, Vol. 33, No. 1, 22–28) teaches methods that include using databases for obtaining/storing BRCA genetic sequencing data, as well as functionality for displaying data [pages 24-26]. In addition, the following are examples of activities that the courts have found to be insignificant extra-solution activity:
Presenting offers to potential customers and gathering statistics generated based on the testing about how potential customers responded to the offers; the statistics are then used to calculate an optimized price, OIP Technologies, 788 F.3d at 1363, 115 USPQ2d at 1092-93;
Obtaining information about transactions using the Internet to verify credit card transactions, CyberSource v. Retail Decisions, Inc., 654 F.3d 1366, 1375, 99 USPQ2d 1690, 1694 (Fed. Cir. 2011);
Consulting and updating an activity log, Ultramercial, 772 F.3d at 715, 112 USPQ2d at 1754; and
Selecting information, based on types of information and availability of information in a power-grid environment, for collection, analysis and display, Electric Power Group, LLC v. Alstom S.A., 830 F.3d 1350, 1354-55, 119 USPQ2d 1739, 1742 (Fed. Cir. 2016);
Accordingly, it is the examiner’s position that the additionally recited steps/elements appending to the judicial exception were well understood, routine, and conventional in the art. See MPEP 2106.05(d)(Part II). Thus, the independent claims as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible.
Dependent Claims
Dependent claims 2-7, 10, 12-17, 20 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. Regarding claim(s) claims 2-7, 10, 12-17, 20, these claims recite limitations that further limit the abstract idea or the nature of the data being used by the abstract idea. As such, these claims are not patent eligible for reasons set forth above (Step 2A, prong 1). Therefore, based on the two-part analysis, the instantly rejected claims as a whole are not drawn to eligible subject matter as they are directed to an abstract idea (and/or natural correlation) without significantly more.
Response to Arguments
Applicant’s arguments, filed 07/21/2026, have been fully considered but are not persuasive for the following reasons.
Applicant argues that the claims are not directed to an abstract idea because they now recite that the system updates a treatment plan stored in a database to initiate at list one of several procedures. In response, with regards to the step of providing reclassification, this step recited at a high level of generality and amounts to outputting data (via a web-based interface) and updating a treatment plan stored in an electronic medical records system. In other words, this step amounts to providing information which is insignificant extra-solution activity. In addition, it is noted that the phrase “to initiate at least one of an imaging procedure, biopsy, examination, or enrollment…” is an intended use recitation that does not impose any limiting effect on the method as claimed, i.e. it is not a positively recited treatment step and does not result in administering any particular treatment. Therefore, the claimed “provide” step amounts to insignificant extra-solution activity (e.g. outputting information or advice), as discussed in MPEP § 2106.05(g), and/or generally linking the use of a judicial exception to a particular technological environment or field of use, as discussed in MPEP § 2106.05(h). In other words, updating a database does not amount to the integration of the judicial exception into a practical application. For at least these reasons, the examiner maintains that the claimed invention does not integrate the abstract idea into a “practical application.”
Applicant argues that the amended claims do not recite a mental process or mathematical concept because none of the claimed steps can be reasonably performed by the human mind. In response, the examiner has provided explicit reasoning as to why the classifying, determining, and generating steps recite a mental process (Step 2A, prong 1) and applicant has not provided any evidence to the contrary. Moreover, applicant is reminded that the Office's eligibility guidance does not set limit on the number of calculations that can or cannot be performed mentally. MPEP § 2106.04(a)(2)III. For reasons of record, the examiner maintains that the claimed classifying, determining, and generating steps amount to a mental process for reasons set forth above (Step 2A, prong 1). Secondly, the examiner has also provided explicit reasoning as to why the generating steps recite a mathematical concept. Notably, “mathematical calculations” are specifically included as an exemplar of a mathematical concept. See 2019 PEG Section I, 84 Fed. Reg. at 52. As such, these steps are not simply “based on” mathematical calculations but require performing mathematical calculations. As such, the examiner maintains that the claims are directed to a mathematical concept when read in light of the specification.
Applicant argues that the claims are not directed to a natural correlation because they go “well beyond” merely recognizing or describing a naturally occurring relationship, e.g. they operationalize complex data through defined statistical methods to produce actionable clinical classifications. In response, the examiner maintains that the claims require obtaining genetic sequence data and correlating this information mutations in the BRCA gene (i.e. a particular disease or phenotype). This relationship recites a law of nature because it describes the naturally occurring relationship between a subject’s DNA and a particular phenotype. See MPEP 2106.04(b).
Applicant again argues at length that the claims are integrated into a practical application of the alleged abstract idea. In response to aggregate arguments, the totality of these arguments are not persuasive for reasons discussed above (and as set forth in the Step 2A, prong 2 analysis). Notably, the claimed invention manipulates existing information to generate additional information, which, without more, is not patent eligible. See Digitech Image Techs., LLC v. Elecs. For Imaging, Inc., 758 F.3d 1344, 1351 (Fed. Cir. 2014). Moreover, applicant has not provided any objective evidence of an improvement to the technology, nor does the specification explain the details of an unconventional technical solution expressed in the claim, or identify technical improvements realized by the claim over the prior art. See MPEP 2106.04(d)(1) and MPEP 2106.05(a). Therefore, even when viewed in combination, these additional steps/elements do not integrate the recited judicial exception into a practical application. [Step 2A, Prong 2: NO].
Applicant additionally argues that the claimed abstract idea is integrated into a practical application, namely a particular “data engineering-pipeline” that operationalizes genetic and familial information through processor-executed structures, computations, and outputs. In response, to the extent that applicant is arguing that the practical application is administering a particular treatment, this argument is not persuasive for reasons set forth above. On the other hand, if applicant is arguing that the claimed processor structures (tables), computations, and outputs (data) provide an improvement to the technology, this argument is also not persuasive for the following reasons. In response, the “improvements” analysis in Step 2A determines whether the claim pertains to an improvement to the functioning of a computer or to another technology without reference to what is well-understood, routine, conventional activity. As set forth above, the claimed hardware elements (processor, interface) are recited at a high level of generality and can be viewed as nothing more than generic elements for obtaining data for use by the abstract idea. MPEP 2106.05(g). Applicant also does not contend that it invented any of the processor, GUI, or storage elements or that there were unknown in the art as of time of the invention. Moreover, to the extent that applicant is asserting that “generating” and “determining” steps provide the abstract idea, applicant is reminded that an improvement in the abstract idea itself is not an improvement in technology. See Trading Techs. Int’l v IBG, 921 F.3d 1084, 1093-94 (Fed. Cir. 2019). The claimed invention’s use of the ineligible concept to which it is directed (i.e. the abstract idea) cannot supply the inventive concept that renders the invention ‘significantly more’ than that ineligible concept.” BSG Tech LLC v. BuySeasons, Inc., 899 F.3d 1281, 1290 (Fed. Cir. 2018). Moreover, the courts have instructed that “[t]he different use of a mathematical calculation, even one that yields different or better results, does not render patent eligible subject matter.” Board Of Trustees Of Leland Stanford Junior University, 991 F.3d 1245, 1251 (Fed. Cir. 2021). In summary, the claimed invention is directed to obtaining data, scoring and classifying the data, and outputting the data and does not integrate the abstract idea into a practical application for reasons discussed above.
Applicant argues that the claimed invention recites an inventive concept (i.e. significantly more than any alleged abstract idea) because the claim recites non-conventional domain-specific architecture that: (i) ingests electronic genetic sequence files via a web front end, (ii) constructs and uses probability tables that incorporate familial weighting and population data, (iii) computes a score using the table and the first individual's genetic data, (iv) reclassifies a VUS based on that computed score, and (v) updates a treatment plan stored in an electronic medical record system associated. In response, this argument is not persuasive because at least some of the above steps (or their equivalents) were interpreted as part of the abstract idea and analyzed under the Step 2A (prong 1) analysis, e.g. constructing, computing, reclassifying. As such, Applicant’s inclusion of both abstract steps and non-abstract steps in their arguments regarding Step 2B analysis is confusing. See MPEP § 2106, subsection III. In particular, the Step 2B analysis requires evaluating additional steps/elements appended to the judicial exception to determine whether they amount to an inventive concept requires considering them both individually and in combination to ensure that they amount to significantly more than the judicial exception itself. In this case, the examiner has provided clear and sufficient reasons as to why the non-abstract steps and additional elements do not amount to significantly more than the judicial exception (Step 2B analysis). In addition, Applicant’s own specification teaches that general purpose client-server systems for obtaining, receiving, and displaying information were routine and conventional in the art [see at least page 13, 14]. Moreover, Vallee et al. (Human Mutation, 2012, Vol. 33, No. 1, 22–28) teaches obtaining/storing BRCA genetic sequencing data [pages 25-26]. Accordingly, it is the examiner’s position that the additionally recited steps/elements appending to the judicial exception were well understood, routine, and conventional in the art. See MPEP 2106.05(d)(Part II). In other words, absent any evidence to the contrary, there is nothing unconventional with regards to how the BRCA data is being stored or displayed.
Applicant additionally argues that the claimed invention recites an unconventional combination of steps/elements that conventional approaches could not achieve. In response, applicant has not provided any evidence to support this position. In addition, there is no recitation of elements that are not the abstract idea that when considered alone or in combination are unconventional and implement the abstract idea in a way that improves the performance of a computer. Accordingly, the examiner maintains that the claims do not recite any steps/elements that amount to sufficient to amount to significantly more than the judicial exception. For at least these reasons, and absent any evidence to the contrary, the rejection is maintained.
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 1-7, 10-17, 20 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 pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 1 and 11 is/are also rejected due to said dependency.
Claims 1 and 11 recite “update, via the one or more processors, a treatment plan stored in an electronic medical record system associated with the first individual to initiate at least one of an imaging procedure, a biopsy, a physical examination, or enrollment in an enhanced surveillance program with increased frequency of checkups.” In this case, the term “enhanced” is a relative term and the specification does not provide any limiting definitions, specific properties, or scoring criteria indicating the scope of this term, i.e. in what way is the surveillance ‘enhanced’. As a result, it is unclear as to the metes and bounds of an “enhanced surveillance program” as the result is subjective and imperceptible. Clarification is requested via amendment.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619
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