Prosecution Insights
Last updated: October 25, 2026
Application No. 17/006,360

PATHOGENICITY SCORING SYSTEM FOR HUMAN CLINICAL GENETICS

Non-Final OA §101§112
Filed
Aug 28, 2020
Priority
Oct 22, 2013 — provisional 61/894,380 +3 more
Examiner
HAYES, JONATHAN EDWARD
Art Unit
1685
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
Athena Diagnostics, Inc.
OA Round
7 (Non-Final)
36%
Grant Probability
At Risk
7-8
OA Rounds
0m
Est. Remaining
60%
With Interview

Examiner Intelligence

Grants only 36% of cases
36%
Career Allowance Rate
29 granted / 80 resolved
-23.7% vs TC avg
Strong +24% interview lift
Without
With
+23.5%
Interview Lift
resolved cases with interview
Typical timeline
4y 8m
Avg Prosecution
35 currently pending
Career history
125
Total Applications
across all art units

Statute-Specific Performance

§101
40.5%
+0.5% vs TC avg
§103
23.9%
-16.1% vs TC avg
§102
6.4%
-33.6% vs TC avg
§112
24.7%
-15.3% vs TC avg
Black line = Tech Center average estimate • Based on career data from 80 resolved cases

Office Action

§101 §112
DETAILED ACTION Applicant' s response, filed 11 August 2026, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application. Notice of Pre-AIA or AIA Status The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . Continued Examination Under 37 CFR 1.114 A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 11 August 2026 has been entered. Claim Status Claims 24, 27-31, 33, 34, 37-41, and 43-45 are pending and examined herein. Claims 24, 27-31, 33, 34, 37-41, and 43-45 are rejected. Priority Claims 24, 27-31, 33, 34, 37-41, and 43-45 are granted the claim to the benefit of priority to U.S. patent application 15/028190 which is a 371 of PCT/US2014/061730 filed 22 October 2014 which claims the benefit of priority to U.S. Provisional application 61/894380 filed 22 October 2013. Thus, the effective filling date of claims 24, 27-31, 33, 34, 37-41, and 43-45 is 20 March 22 October 2013. Claim Objections The objection to claims 34 in Office action mailed 13 May 2026 is withdrawn in view of the amendment of “determining whether each generated clinical significance score for each genetic variant…” received 11 August 2026. Claim Interpretation Claim 24 recites “identifying, in response to determining that a genetic variant of the plurality of genetic variants is equal to or above a threshold, one or more pharmaceutical agents to target the genetic variant in pharmaceutical research” which is a contingent limitation. The MPEP states at 2111.04(II) “The broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met.” The BRI of the claimed method does not require performing this step of identifying one or more pharmaceutical agents to target the genetic variant in pharmaceutical research because there exists an embodiment of the claim where the condition of “a genetic variant of the plurality of genetic variants is equal to or above a threshold”. Claim 34 recites “testing, in response to determining that a genetic variant of the plurality of genetic variants is equal to or above a threshold, an individual identified as having the genetic variant or immediate blood relative of the individual identified as having the genetic variant for a condition associated with the biological function of the cell or protein” which is a contingent limitation. The MPEP states at 2111.04(II) “The broadest reasonable interpretation of a system (or apparatus or product) claim having structure that performs a function, which only needs to occur if a condition precedent is met, requires structure for performing the function should the condition occur. The system claim interpretation differs from a method claim interpretation because the claimed structure must be present in the system regardless of whether the condition is met and the function is actually performed.” The BRI of the claimed system requires the structure that performs the function of testing should the condition a genetic variant of the plurality of genetic variants is equal to or above a threshold. Claim Rejections - 35 USC § 112 It is noted that the rejection on the ground of 112/a of claims 24, 27-31, 33, 34, 37-41, and 43-45 for claims 24 and 34 reciting “assigning points, which range from positive to negative points, respectively to different edges from a node indicating outcomes of the node” and “computing a value for each node being a sum of points associated with edges in a path from the root to the node” in Office action mailed 13 May 2026 was withdrawn in the advisory action mailed 03 August 2026. It is noted that the rejection on the ground of 112/b of claims 24, 27-31, 33, 34, 37-41, and 43-45 for claims 24 and 34 reciting “computing a value for each node being a sum of points associated with edges in a path from the root to the node” in Office action mailed 13 May 2026 was withdrawn in in the advisory action mailed 03 August 2026. The rejection on the ground of 112/b of claims 24, 27-31, 33, 34, 37-41, and 43-45 for reciting “the genetic variant”, “the variant” and “the plurality of scores” in Office action mailed 13 May 2026 is withdrawn in view of the amendment received 11 August 2026. The rejection on the ground of 112/b of claims 27, 28, 37, and 38 for claims 27 and 37 reciting “the internal node” in Office action mailed 13 May 2026 is withdrawn in view of the amendment of “a first edge from an internal node of the tree…” received 11 August 2026. The rejection on the ground of 112/b of claims 27-29 and 37-39 for reciting “the decision tree” in Office action mailed 13 May 2026 is withdrawn in view of the amendment of “a decision tree” received 11 August 2026. The rejection on the ground of 112/b of claims 34, 37-41, 43, and 45 for claim 34 reciting “generate a report of the clinical significance of the genetic variant based on the determining”, “wherein…the system generates a report…”, and “wherein the generating the report…” in Office action mailed 13 May 2026 is withdrawn in view of the amendment which removes this limitation received 11 August 2026. 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. The rejection below is newly recited necessitated by amendment. Claim 34, 37-41, 43, and 45 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. Claim 34 recites “a computing device comprising a processor configured to… testing, in response to determining that a genetic variant of the plurality of genetic variants is equal to or above a threshold, an individual identified as have the genetic variant or an immediate blood relative of the individual identified as having the genetic… the testing being performed for only a subset of the plurality of genetic variants… wherein in the testing is not performed by the system” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear if the processor is configured to perform this step of testing or if this limitation is meant to be an intended use of the system because the claim recites “a processor configured to… testing…” but also recites “wherein the testing is not performed by the system”. Dependent claims 37-41, 43, and 45 are rejected by virtue of their dependency on a rejected claim without alleviating indefiniteness. For the sake of furthering examination, this limitation will be interpreted as “determining a recommendation to perform a test, in response… on an individual or an immediate blood relative of the individual…”. 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. The rejection below has been modified necessitated by amendment. Claims 24, 27-31, 33, 34, 37-41, and 43-45 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. (Step 1) Claims 24, 27-31, 33, and 44 fall under the statutory category of a process and claims 34, 37-41, 43, and 45 fall under the statutory category of a machine. (Step 2A prong 1) Under the BRI, the instant claims recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mental process”, such as procedures for evaluating, analyzing or organizing information, and forming judgement or an opinion. The instant claims further recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mathematical concept”, such as mathematical relationships and mathematical equations. Independent claim 24 recites a mental process of “building at least one tree depending on at least whether a genetic variant changes a corresponding amino acid, comprising, for each tree of the at least one tree: including leaves corresponding to different levels of clinical significance, assigning points, which range from positive to negative points, respectively to different edges from a node indicating outcomes of the node, assigning a value to a root”, “aggregating the plurality of scores to generate a clinical significance score indicating a clinical significance of the genetic variant”, “determining whether the generated clinical significance score for the variant is above, below, or equal to a threshold”, “identifying, in response to determining that a genetic variant of the plurality of genetic variants is equal to or above a threshold, one or more pharmaceutical agents to target the genetic variant in pharmaceutical research, the identifying being performed for only a subset of the plurality of genetic variants to reduce testing and expedite therapeutic efforts”, and “wherein the aggregating comprises traversing one tree of the at least one tree to reach a leaf using the plurality of scores and taking the value of the leaf as the clinical significance score for the genetic variant” Independent claim 34 recites a mental process of “build at least one tree depending on at least whether a genetic variant changes a corresponding amino acid, comprising, for each tree of the at least one tree: including leaves corresponding to different levels of clinical significance, assigning points, which range from positive to negative points, respectively to different edges from a node indicating outcomes of the node, assigning a value to a root”, “aggregate the plurality of scores to generate a clinical significance score indicating a clinical significance of each genetic variant of the plurality of genetic variants”, “determine whether each generated clinical significance score for each genetic variant of the plurality of genetic variants is above, below, or equal to a threshold”, “determining a recommendation to perform a test, in response to determining that a genetic variant of the plurality of genetic variants is equal to or above a threshold, on an individual…”, and “wherein the aggregating comprises traversing one tree of the at least one tree to reach a leaf using the plurality of scores and taking the value of the leaf as the clinical significance score for the genetic variant”. Independent claims 24 and 34 recite mathematical concepts of “computing a value at each node being a sum of points associated with edges in a path from the root to the node” and “computing a plurality of scores associated with each genetic variant of a plurality of genetic variants in a database, using hypothesis testing for at least one score of the plurality of scores, wherein the plurality of scores comprises (a) a function score…, a frequency score…, a co-occurrence score, and a family segregation score…”. Dependent claims 30 and 40 recite a mental process of “aggregating a second plurality of scores to generate a second clinical significance score…”. Dependent claims 31 and 41 recite a mental process of “excluding a second variant from an output report, responsive to a generated clinical significance score of the second variant being below a threshold”. The claims recite mental processes or analyzing/evaluating data and making a judgment based on the analysis of data as building at least one tree, including leaves corresponding to different levels of clinical significance, assigning points, which range from positive to negative points, respectively to different edges from a node, assigning a value to a root, aggregating the plurality of scores to generate a clinical significance score indicating a clinical significance of the genetic variant, comparing the generated clinical significance score for the variant to a threshold, identifying, in response to determining, one or more pharmaceutical agents to target the genetic variant as a potential therapeutic target, traversing one tree of the at least one tree to reach a leaf using the plurality of scores and taking the value of the leaf as the clinical significance score for the genetic variant, determining a recommendation to perform a test on an individual, aggregating a second plurality of scores to generate a second clinical significance score. The claims recite mental processes of organizing data as excluding a second variant from an output report, responsive to a generated clinical significance score of the second variant being below a threshold. The human mind is capable of performing these steps because the building at least one tree is a series of abstract steps for analyzing genetic data in a specified manner, comparing a combined score to a threshold to see if the score is below, equal to, or above a threshold is a judgment, identifying a pharmaceutical that targets a specific genetic variant, determining a recommendation for testing an individual are mental processes of a judgment, and traversing abstract analysis to produce an aggregated score is a mental process of analyzing/evaluating data. The claims recite mathematical concepts of a mathematical calculations as computing a value for each node being a sum of points associated with edges in a path from the root to the node is a mathematical operation of summing numerical values and computing a plurality of scores associated with each genetic variant of a database of genetic variants using hypothesis testing which is a series of mathematical calculations to produce a numerical value representing whether observed patterns are true or if the observed patterns are due to chance. Dependent claims 27-29, 37-39, 44, and 45 further limit the mental process/mathematical concept recited in the independent claim but do not change their nature as a mental process/mathematical concept. Thus, 24, 27-31, 33, 34, 37-41, and 43-45 recite abstract ideas. (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). Integration into a practical application is evaluated by identifying whether there are any additional elements recited in the claim and evaluating those additional elements to determine whether they integrate the exception into a practical application. The additional element in claims 24 and 34 of using a generic computer to perform judicial exceptions does not integrate the judicial exception into a practical application because this is applying the exception to a generic computer without improvement to computer technology (see MPEP 2106.04(d)(1)). This additional element only interacts with the judicial exceptions in a manner of invoking a generic computer as a tool to perform the judicial exceptions. The additional element in claims 33 and 43 of receiving data does not integrate the judicial exception into a practical application because this is insignificant extra solution activity of data gathering (see MPEP 2106.05(g)). This additional element and the judicial exceptions only interact by providing data to be processed by the judicial exceptions. It is noted that the content of the data falls under the abstract idea itself and does not change the active step receiving/retrieving information in a computer environment. Thus, the additional elements do not integrate the judicial exceptions into a practical application and claims 24, 27-31, 33, 34, 37-41, and 43-45 are directed to the abstract idea. (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 do not include additional elements that are sufficient to amount to significantly more than the judicial exception because: The additional element in claims 24 and 34 of using a generic computer to perform judicial exceptions is conventional as shown by MPEP 2106.05(b) and MPEP 2106.05(d)(II). The additional element in claims 33 and 43 of receiving data into a computer environment is conventional as shown by MPEP 2106.05(b) and MPEP 2106.05(d)(II). It is noted that the content of the data falls under the abstract idea itself and does not change the active step receiving/retrieving information in a computer environment. Thus, the additional elements are not sufficient to amount to significantly more than the judicial exception because they are conventional. Response to Arguments Applicant’s arguments filed 11 August 2026 have been fully considered but they are not persuasive. Argument 1: Applicant argues that similar to Claim 1 in example 40, the present claims recite limiting performance of specific tasks (recommending biological testing). The Office Action asserts that "claim 24 (or it's dependents) does not recite "recommending biological testing" ". Claims 24 and 34 have been amended to clearly recite performing lab work of testing humans or pharmaceutical agents (Reply p. 11). This argument has been fully considered but found to be not persuasive. The BRI of the limitation of “identifying, in response to determining that a genetic variant of the plurality of genetic variants is equal to or above a threshold, one or more pharmaceutical agents to target the genetic variant in pharmaceutical research” in claim 24 encompasses a mental process of evaluating information about one or more pharmaceutical agents to make a judgement, based on this information, that certain pharmaceutical agents target the genetic variant. The BRI of the limitation of determining a recommendation to perform a test, in response to determining that a genetic variant of the plurality of genetic variants is equal to or above a threshold, on an individual identified as having the genetic variant or an immediate blood relative of the individual identified as having the genetic variant for a condition associated with the biological function of the cell or protein” in claim 34 encompasses a mental process of making a judgment of a recommendation to perform a test on an individual, based on if the clinical score of a genetic variant passes a threshold. Thus, these steps fall under the abstract idea/judicial exception and is not limited to performing physical wet lab work or performing a physical test on an individual. As described in further detail below, the claims have a different fact pattern than claim 1 Example 40 due to this step encompassing a mental process and falling under the judicial exception. Argument 2: Applicant argues that the Office Action asserts that in Claim 1, "a computer collecting specific traffic data is a computer processing of receiving data [, is an additional element,] and is not an abstract idea". That is unheard of and incorrect. It has been repeatedly held that data gathering alone is insignificant extra-solution activity. MPEP 2106.05(g); Example 40 itself also states precisely that. That step alone does not cause any improvement and does not take the claim out of the abstractness. In comparison, the present Claim 24 recites extensive details of obtaining the clinical significance score that is entirely lacking in Claim 1. Once again, the claims need to be considered as whole. Given the close analogy between Claim 1 and Claim 24, including causing the same type of improvement to avoid the excessive consumption of useful resources by applying a threshold (to the collected traffic data in Claim 1 and the clinical significance score in Claim 24), the Office Action has continuously failed to tell the two claims apart while arguing for superficial or nonexistent differences (Reply p. 12). This argument has been fully considered but found to be not persuasive. In example 40, the improvement is provided by the combination of the judicial exception of comparing at least one of the collected traffic data to a predefined threshold and the additional element of collecting additional traffic data relating to the network traffic when the collected traffic data is greater than the predefined threshold, the additional traffic data comprising Netflow protocol data. The collection of additional traffic is not an abstract idea because the human mind cannot collect network traffic data and example 40 provides that the collection of network traffic data is collected by a network appliance. Further, the analysis provided for claim 1 of Example 40 provides “Although each of the collecting steps analyzed individually may be view as mere pre- or post-solution activity, the claim as a whole is directed to a particular improvement in collecting traffic data” which shows that the collection of this data is not insignificant extra solution activity when viewed as a whole (i.e., the combination of the additional elements, which are the steps of collecting network traffic data, and the judicial exception of comparing at least one collected traffic data to a predefined threshold). The MPEP provides that “The analysis under Step 2A Prong Two is the same for all claims reciting a judicial exception, whether the exception is an abstract idea, a law of nature, or a natural phenomenon (including products of nature). Examiners evaluate integration into a practical application by: (1) identifying whether there are any additional elements recited in the claim beyond the judicial exception(s); and (2) evaluating those additional elements individually and in combination to determine whether they integrate the exception into a practical application” (see MPEP 2106.04(d)). Unlike claim 1 of example 40, the instant claims do not provide additional elements (i.e., limitations that do not fall under the judicial exception) when considered alone or in combination with the judicial exception that cause the same type of improvement of avoiding the excess consumption of resources. It is noted that the newly amended limitation in claim 24 of “identifying, in response to determining that a genetic variant of the plurality of genetic variants is equal to or above a threshold, one or more pharmaceutical agents to target the genetic variant in pharmaceutical research” encompasses a mental process of evaluating information about one or more pharmaceutical agents to make a judgement, based on this information, that certain pharmaceutical agents target the genetic variant which passed a threshold. It is further noted that the newly amended limitation in claim 34 of “determining a recommendation to perform a test, in response to determining that a genetic variant of the plurality of genetic variants is equal to or above a threshold, on an individual identified as having the genetic variant or an immediate blood relative of the individual identified as having the genetic variant for a condition associated with the biological function of the cell or protein” encompasses a mental process of making a judgment of a recommendation to perform a test on an individual, based on if the clinical score of a genetic variant passes a threshold. Although these analyses are performed on a genetic variant that passes a threshold potentially reducing the number of genetic variants that undergo these analyses, these analyses themselves fall under the abstract idea/judicial exception. This argued improvement is provided by the collection of steps that all fall under the judicial exception (e.g., an improvement to the abstract data analysis being performed on a collection of genetic variant information). As stated in the MPEP “It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements… In addition, the improvement can be provided by the additional element(s) in combination with the recited judicial exception” (see MPEP 2106.05(a)). Thus, the claims are not integrated into a practical application in a similar manner provided by claim 1 of Example 40 because the instant claims do not recite additional elements alone or in combination with judicial exceptions that provide this improvement in avoiding the excess consumption of resources. Argument 3: Applicant argues the Office Action asserts that the claims CardioNet, LLC v. InfoBionic, Inc., 955 F.3d 1358 (Fed. Cir. 2020) are “directed to a particular device” that is not generic but instead but instead includes a computer that is “not a general purpose computer” (Reply p. 12). Applicant argues the cardiac monitoring technology in CardioNet leading to the improvement that is found eligible depends entirely on the steps in Claim 1 to be performed by the computer, exactly the same as the present Claim 24 and the beat detector and ventricular beat detector operating as normal simply provide input data to be processed by the computer and contribute nothing to the improvement (Reply p. 13). Applicant further argues that the software in CardioNet provides the improvement and that is why the court cites cases like McRO and Diamond v. Diehr directed to computing methods to demonstrate the subject matter eligibility of the "logic" recited in Claim 1. Claim 1 if written into a method claim would still be eligible. While Claim 1 leads to better cardiac monitoring, Claim 24 leads to better genetic monitoring, and those are the reasons why these claims are eligible. Neither requires special machinery, even if Claim 1 recites beat data produced by physical components from human bodies, while Claim 24 recites genetic data that were not born online or out of vacuum but produced by sequencing machines also from human bodies (Reply p. 13). This argument has been fully considered but found to not be persuasive. The MPEP provides “It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements… In addition, the improvement can be provided by the additional element(s) in combination with the recited judicial exception” (see MPEP 2106.05(a)). It is noted that the difference in fact patterns between CardioNet, LLC v. InfoBionic, Inc., 955 F.3d 1358 (Fed. Cir. 2020) (herein after CardioNet) and the instant claims is due to the recited additional elements in the respective claims (e.g., although the device in CardioNet recites additional elements as particular detectors present in the system, the difference is not solely due to the system in CardioNet being a “particular device”). The claims in CardioNet recite judicial exceptions of “logic” and recite limitations beyond the judicial exceptions (i.e., additional elements) which include a beat detector, a ventricular beat detector, and a computer implementing the logic. The claims were found to provide an improvement in Cardiac monitoring technology when viewed as a whole (i.e., the combination of the recited logic and all additional elements which include the beat detector, a ventricular beat detector and a computer that implements the logic). Although the individual beat detectors may be operating as normal when viewed in isolation, the analysis for improvement in technology requires the analysis of the claim as a whole. Unlike the claims in CardioNet, when the instant claims are viewed as a whole they provide a series of analysis steps, which all fall under the abstract idea, to process genetic information that invokes a generic computer as tool to perform (e.g., the computer itself is not functioning in a different/improved manner). The instant claims do not provide an improvement to technology in a similar manner provided by the claims in CardioNet because when viewed as a whole, the instant independent claims only provide a generic computer used to perform a collection of steps to analyze genetic information, which all fall under the abstract idea, which does not constitute as an improvement to computer functionality (see MPEP 2106.05(a)). It is noted that dependent claims 33 and 43 recite an additional element of retrieving information from a database which does not integrate the judicial exceptions into a practical application because this step constitutes as insignificant extra solution activity of data gathering. This additional element constitutes as data gathering because it only interacts with the recited judicial exceptions by providing data to the judicial exceptions to analyze. Thus, the instant claims, when viewed as a whole, do not provide an improvement to technology because the claims do not recite additional elements alone or in combination with the judicial exceptions that provide this argued improvement. Although the claims may provide an improvement to analyzing genetic information, this argued improvement in genetic monitoring is provided by the collection of abstract data analysis steps alone which cannot provide the improvement to technology (see MPEP 2106.05(a)). It is noted that the claims at issue in McRO and Diamond v Diehr also recite additional elements (i.e., recited limitations beyond the judicial exceptions recited in the claims) that, when the analyzed as a whole, provide an improvement to technology. It is noted that the claims at issue in McRO recite the additional element of applying morph weight sets to animated characters to produce lip synchronization and facial expression control of animated characters which, when the claim was viewed as a whole, provided an improvement to computer animation technology. Further, the claims at issue in Diamond v Diehr recite additional elements such as constantly collecting temperature data, constantly providing this data to the computer, and opening the press automatically which, when the claims are viewed as a whole, provide an improvement to a manufacturing process. As set out above, the instant claims do not provide an improvement to technology because when viewed as a whole, the instant claims the additional element of a genetic computer only interacts with the recited judicial exceptions by being invoked as tool to perform the judicial exceptions. Conclusion No claims are allowed. Claims 24, 27-31, 33, 34, 37-41, and 43-45 are free of the prior art of record. Goldgar et al. (American Journal of Human Genetics, 2004, 75: 535-544; previously cited) is the closest art of record which shows the usefulness of functional studies of a genetic variant, frequency information of a genetic variant, co-occurrence information of a genetic variant, and family history information of a genetic variant in the classification of variants of unknown clinical significance (Goldgar et al. page 536 Table 1). Goldgar et al. further shows producing likelihood ratios using data from each of these categories and combining these likelihood ratios through multiplying these independent likelihood ratios (Goldgar et al. page 539). Goldgar et al. shows comparing the combined likelihood ratios to a threshold to classify these variants of unknown clinical significance (Goldgar et al. 538 Figure 1). However, the prior art of record does not show building at least one tree which includes leaves corresponding to different levels of clinical significance, assigning points, which range from positive to negative points, respectively to different edges from a node indicating outcomes of the node, assigning a value to a root, and computing a value at each node being a sum of points associated with edges in a path from the root to the node, aggregating the plurality of scores to generate a clinical significance score by traversing one tree of the at least one tree to reach a leaf using the plurality of scores and taking the value of the leaf as the clinical significance score for the genetic variant. Thus, the claims are free of the prior art of record. This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this action. Any inquiry concerning this communication or earlier communications from the examiner should be directed to JONATHAN EDWARD HAYES whose telephone number is (571)272-6165. The examiner can normally be reached M-F 9am-5pm. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached at 571-272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /JONATHAN EDWARD HAYES/Examiner, Art Unit 1685
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Prosecution Timeline

Show 15 earlier events
Dec 23, 2025
Non-Final Rejection mailed — §101, §112
Mar 20, 2026
Response Filed
May 13, 2026
Final Rejection mailed — §101, §112
Jul 08, 2026
Examiner Interview Summary
Jul 10, 2026
Response after Non-Final Action
Aug 11, 2026
Request for Continued Examination
Aug 12, 2026
Response after Non-Final Action
Sep 22, 2026
Non-Final Rejection mailed — §101, §112 (current)

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Prosecution Projections

7-8
Expected OA Rounds
36%
Grant Probability
60%
With Interview (+23.5%)
4y 8m (~0m remaining)
Median Time to Grant
High
PTA Risk
Based on 80 resolved cases by this examiner. Grant probability derived from career allowance rate.

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