DETAILED ACTION
Applicant’s response, filed 26 March 2025, 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 .
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 34, 37-41, 43, and 45 are granted the claim to the benefit of priority to PCT/US2014/061730 filed 22 October 2014. Thus, the effective filling date of claims 34, 37-41, 43, and 45 is 22 October 2014. Claims 34, 37-41, 43, and 45 are not granted benefit to provisional application 61/894380 because there is no disclosure of providing recommendations for further testing.
Claims 24, 27-31, 33, and 44 are not granted the benefit of any priority claims because there is no disclosure of “testing an individual identified as having the variant or an immediate blood relative…”. Thus, the effective filling date of claims 24, 27-31, 33, and 44 is the date of the reply in which this amendment was added (i.e. 26 March 2025).
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code in paragraph [0063]. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Rejections - 35 USC § 112
The rejection on the ground of 112/b of claim 45 in Office action mailed 30 December 2024 is withdrawn in view of the amendment of “The system of claim 34” received 26 March 2025.
The rejection on the ground of 112/d of claim 32 and 42 in Office action mailed 30 December 2024 is withdrawn in view of the amendment of the cancelation claims 32 and 42 received 26 March 2025.
112/a New Matter
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 24, 27-31, 33, and 44 are rejected 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. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 24 recites “testing an individual identified as having the variant or an immediate blood relative…”. There is not an adequate written description for testing an individual. The instant disclosure provides “the report contains recommendations for the end user regarding the information displayed therein. In some embodiments, said recommendations can be chosen from recommendations for further testing of the individual, or the individual’s immediate blood relatives” (in [093] of the disclosure). There is no disclosure for performing testing of an individual. Thus, this limitation constitutes as new matter. Dependent claims 27-31, 33, and 44 are further rejected by virtue of their dependency on the rejected claim.
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 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 claims 24 and 34 recite mental processes of “aggregate the plurality of scores to generate a clinical significance score…”, “determining that the generated clinical significance score for the variant is above a threshold”, and “wherein aggregating the plurality of scores further comprises summing up the plurality of scores with pre-determined weights or retrieving a value for the clinical significance score from a leaf node of a decision tree, wherein each score of the plurality of scores is associated with an internal node of the decision tree”.
Independent claim 34 recites a mental process of “generating a report containing a recommendation…”.
Independent claims 24 and 34 recite mathematical concepts of “aggregating the plurality of scores to generate a clinical significance score…” and “wherein aggregating the plurality of scores further comprises summing up the plurality of scores with pre-determined weights”.
Dependent claims 30 and 40 recite a mental process and a mathematical concept 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 analyzing/evaluating data as “aggregate the plurality of scores to generate a clinical significance score…”, “determining that the generated clinical significance score for the variant is above a threshold”, and “wherein aggregating the plurality of scores further comprises summing up the plurality of scores with pre-determined weights or retrieving a value for the clinical significance score from a leaf node of a decision tree, wherein each score of the plurality of scores is associated with an internal node of the decision tree”. The claims recite 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 analyzing/evaluating data and organizing data. The claims recite mathematical concepts of a calculation of “aggregating the plurality of scores to generate a clinical significance score…” and “wherein aggregating the plurality of scores further comprises summing up the plurality of scores with pre-determined weights”. Summing up numbers is a mathematical calculation. Thus, 24, 27-31, 33, 34, 37-41, and 43-45 recite abstract ideas.
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.
(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 claim 24 of testing an individual identified as having the variant or an immediate blood relative of the individual identified as having the variant for a condition does not integrate the judicial exception into a practical application because this additional element only generally links the use of a judicial exception to a particular technological environment of field of use (see MPEP 2106.05(h)).
The additional element in claims 24 and 34 of using a generic computer does not integrate the judicial exception into a practical application because this is simply applying the exception to a generic computer without improvement to computer technology.
The additional element in claims 34 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)).
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)
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, 33, 34, and 43 of receiving data into a computer environment is conventional as shown by MPEP 2106.05(b) and MPEP 2106.05(d)(II).
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 24 of testing for a condition associated with a function of the cell or protein when a variant is present with clinical significance is conventional as shown on pages 95 right col. and 99 left col. Sardanelli et al. (Investigative radiology 46.2 (2011): 94-105; previously cited) which shows that women with high genetic risk for breast cancer where further screened using mammography and pages 428 right col., page 431 table 2, and page 432 table 3 that shows women with genetic predispositions being in the study population for further cancer screening methods of mammography and MRI of Kriege et al. (New England Journal of Medicine 351.5 (2004): 427-437; previously cited).
The combination of additional elements in claim 24 of inputting data, using a generic computer, and testing for a condition when a variant is present is conventional as shown by Kriege et al. (New England Journal of Medicine 351.5 (2004): 427-437; previously cited) which shows on pages 428 right col., page 431 table 2, page 432 table 3, and page 429 right col. second paragraph that women with genetic predispositions being in the study population for further cancer screening methods of mammography and MRI, inputting data from a database, and using statistical software (SPSS). The combination of additional elements in claim 24 of inputting data, using a generic computer, and testing for a condition when a variant is present is conventional as shown on pages 95 right col. and 99 left col. Sardanelli et al. (Investigative radiology 46.2 (2011): 94-105; previously cited) which shows that women with high genetic risk for breast cancer where further screened using mammography and shows using statistical software (SPSS).
Thus, the additional elements (alone and in combination) do not amount to significantly more than the judicial exceptions because they are conventional.
Response to Arguments
Applicant's arguments filed 26 March 2025 have been fully considered but they are not persuasive.
Applicant argues when considered as a whole the judicial exceptions are integrated into a practical application because the claims explicitly recite testing an individual identified as having the variant or an immediate blood relative of the individual identified as having the variant for a condition associated with the biological function of a cell or protein. Applicant further argues affirmative testing of an individual is not “mere instructions to apply an exception” in the claims, the “receiving” step concerns receiving, by a computing device, a plurality of scores associated with a genetic variant, whereas the testing step concerns testing an individual (or relative thereof) for a condition associated with a biological function of a cell or protein. In other words, the alleged exceptions in the receiving step is not applied to the individual in testing step (Reply p. 10).
This argument has been fully considered but found to be not persuasive. The MPEP 2106.04(d)(III) states “The Prong Two analysis considers the claim as a whole. That is, the limitations containing the judicial exception as well as the additional elements in the claim besides the judicial exception need to be evaluated together to determine whether the claim integrates the judicial exception into a practical application… However, the way in which the additional elements use or interact with the exception may integrate it into a practical application”. The judicial exceptions are practiced to determine that a generated clinical significance score for a variant is above a threshold while the test is performed for an individual having this variant for a condition associated with the biological function of the cell or protein. The interaction between the judicial exceptions and the additional element of testing is a general link of testing an individual that has been identified. The testing step is generic and encompasses all known tests for conditions that are associated with all variants that are identified as being clinically significant. Thus, the testing step is an additional element that only generally links the use of a judicial exception to a particular technological environment of field of use (see MPEP 210.05(h)).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 24, 27-31, 33, and 44 are rejected under 35 U.S.C. 103 as being unpatentable over Karbassi et al. (U.S. Patent No. 10,762,981; previously cited) in view of Ali, Jehad, et al. (International Journal of Computer Science Issues (IJCSI) 9.5 (2012): 272; previously cited).
Claim 24 is directed to receiving, by a computing device, a plurality of scores associated with a genetic variant, wherein the plurality of scores comprises (a) a function score based on known or projected impact of the variant on a biological function of a cell or protein
Karbassi et al. shows determining this function score (Karbassi et al. page 11 col. 1-2, page 13 col. 5, and claim 1 lines 3-4).
(b) a frequency score based on the frequency of the variant in a population
Karbassi et al. shows determining this frequency score (Karbassi et al. page 11 col. 1-2, page 13 col. 5, claim 1 line 5).
(c) a co-occurrence score based on how the variant co-occurs with a reference variant having known clinical significance relating to a clinical disease or condition
Karbassi et al. shows determining this co-occurrence score (Karbassi et al. col. 1-2, col. 5, claim 1 lines 6-7).
And (d) a family segregation score based on how the variant segregates with a disease or condition in a family
Karbassi et al. shows determining this family segregation score (Karbassi et al. col. 1-2, col. 5, claim 1 lines 8-9).
aggregating, by the computing device, the plurality of scores to generate a clinical significance score indicating a clinical significance of the genetic variant
Karbassi et al. shows aggregating these scores to indicate a clinical significance of the genetic variant (Karbassi et al. col. 1-2, col. 6, and claim 1 lines 15-17)
and determining that the generated clinical significance score for the variant is above a threshold
Karbassi et al. shows determining that the significance score is above a threshold (Karbassi et al. claim 1 lines 25 and 26).
testing an individual identified as having the variant or an immediate blood relative of the individual identified as having the variant for a condition associated with the biological function of the cell or protein, responsive to the determination that the generated clinical significance score for the variant is above the threshold,
Karbassi et al. shows wherein an individual (or an immediate blood relative) identified as having a variant is tested for a condition associated with the biological function of the cell or protein, responsive to the determination that the generated clinical significance score for the variant is above the threshold (Karbassi et al. claim 1 lines 27-30). It would have been obvious to one of ordinary skill in the art to perform this testing on an individual or an immediate blood relative.
wherein aggregating the plurality of scores further comprises (1) summing up, by the computing device, the plurality of scores with pre-determined weights,
Karbassi et al. shows this aggregation by summation with predetermined weights (Karbassi et al. col. 1-2, col. 6, and claim 1 lines 18-20).
or (2) retrieving, by the computing device, a value for the clinical significance score from a leaf node of a decision tree,
Karbassi et al. shows aggregation by the use of a decision tree which each leaf of the decision tree comprises a value for the clinical significance score (Karbassi et al. col. 1-2, col. 6, and claim 1 lines 18-20).
Karbassi et al. does not show wherein each score of the plurality of scores is associated with an internal node of the decision tree.
Like Karbassi et al., Ali et al. shows a decision tree where the output of the decision tree is retrieved from the leaf node of the model. Ali et al. shows that two or more branches can be extended from each internal node with a node representing a certain characteristic while the branch represents a range of values (Ali et al. page 273 right col). Ali et al. further shows the range of values are the partition points for the set of values of the given characteristics (Ali et al. page 273 right col).
Claim 27 is directed to wherein a first value of a first score of the plurality of scores is associated with a first branch of the internal node of the decision tree corresponding to the first score. Claim 28 is directed to the internal node of the decision tree corresponding to the first score has at least three branches corresponding to distinct values of the first score.
Ali et al. shows that two or more branches can be extended from each internal node with a node representing a certain characteristic while the branch represents a range of values (Ali et al. page 273 right col). Ali et al. further shows the range of values are the partition points for the set of values of the given characteristics (Ali et al. page 273 right col).
Claim 29 is directed to wherein the decision tree comprises at least one leaf node at a first layer of the decision tree, and at least one leaf node at a second, higher layer of the decision tree.
Ali et al. shows that a decision tree may be built with at least one leaf node in different layers of the tree structure (Ali et al. page 273 right col.)
Claim 30 is directed to responsive to the generated clinical significance score being above a first threshold and below a second threshold, aggregating a second plurality of scores to generate a second clinical significance score, wherein at least one of the second plurality of scores is based on new data accumulated after generating the clinical significance score.
Karbassi et al. shows this step of aggregating a second plurality of scores when the generated clinical significance score is above a first threshold and below a second threshold (Karbassi et al. claim 25).
Claim 31 is directed to excluding a second variant from an output report, responsive to a generated clinical significance score of the second variant being below the threshold.
Karbassi et al. shows this step of excluding a second variant from an output report (Karbassi et al. claim 26).
Claim 33 is directed to retrieving, by the computing device from a database comprising a plurality of variants and associated patients, co-occurrence or family segregation data for the variant.
Karbassi et al. shows the retrieval from a database of a plurality of variants and associated patients, co-occurrence or family segregation data for the variant (Karbassi et al. claim 27).
Claim 44 is directed to wherein the plurality of scores further comprises a minor evidence score based on information from at least one functional impact prediction algorithm, whether the variant occurs within a critical protein domain, whether the variant would alter a post-translational modification, whether other known pathogenic variants occur within the same codon, and whether the variant is known to occur in at least one patient of a disease or condition.
Karbassi et al. shows an embodiment of determining this minor evidence score (Karbassi et al. page 11 col. 1-2, page 13 col. 5, claim 1 lines 10-14).
It would have been obvious to one of ordinary skill in the art before the effective filling date to have modified the decision tree structure of Karbassi et al. with the structure of the decision tree model set out in Ali et al. because this gives a method of using a decision tree where the plurality of scores (which are the characteristics of the dataset) are internal nodes with the branches representing different ranges of values for each characteristic which can partition the data (Ali et al. page 273 right col). One would have a reasonable expectation of success because decision tree models are known to have the structure that comprises different variations of a root node, internal nodes, branches, and leaf nodes depending on the application with internal nodes and branches acting as the partition points of the model as shown in Ali et al. so the decision tree of Karbassi et al. may be built in a manner that uses the plurality of scores as internal nodes because the scores are the characteristics of the dataset.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 24, 27-31, 33, and 44 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 25-27 of Karbassi et al. (U.S. Patent No. 10,762,981; previously cited) in view of Ali, Jehad, et al. (International Journal of Computer Science Issues (IJCSI) 9.5 (2012): 272; previously cited).
Claim 24 is directed to receiving, by a computing device, (a) a function score, (b) a frequency score, (c) a co-occurrence score and (d) a family segregation score
Karbassi et al. shows determining this function score (Karbassi et al. claim 1 lines 3-4). Karbassi et al. shows determining this frequency score (Karbassi et al. claim 1 line 5). Karbassi et al. shows determining this co-occurrence score (Karbassi et al. claim 1 lines 6-7). Karbassi et al. shows determining this family segregation score (Karbassi et al. claim 1 lines 8-9).
aggregating, by the computing device, the plurality of scores to generate a clinical significance score indicating a clinical significance of the genetic variant
Karbassi et al. shows aggregating these scores to indicate a clinical significance of the genetic variant (Karbassi et al. claim 1 lines 15-17)
and determining that the generated clinical significance score for the variant is above a threshold
Karbassi et al. shows determining that the significance score is above a threshold (Karbassi et al. claim 1 lines 25 and 26).
testing an individual identified as having the variant or an immediate blood relative of the individual identified as having the variant for a condition associated with the biological function of the cell or protein, responsive to the determination that the generated clinical significance score for the variant is above the threshold,
Karbassi et al. shows wherein an individual (or an immediate blood relative) identified as having a variant is tested for a condition associated with the biological function of the cell or protein, responsive to the determination that the generated clinical significance score for the variant is above the threshold (Karbassi et al. claim 1 lines 27-30). It would have been obvious to one of ordinary skill in the art to perform this testing on an individual or an immediate blood relative.
wherein aggregating the plurality of scores further comprises (1) summing up, by the computing device, the plurality of scores with pre-determined weights,
Karbassi et al. shows this aggregation by summation with predetermined weights (Karbassi et al. claim 1 lines 18-20).
or (2) retrieving, by the computing device, a value for the clinical significance score from a leaf node of a decision tree,
Karbassi et al. shows aggregation by the use of a decision tree which each leaf of the decision tree comprises a value for the clinical significance score (Karbassi et al. claim 1 lines 18-20).
Karbassi et al. does not show wherein each score of the plurality of scores is associated with an internal node of the decision tree.
Like Karbassi et al., Ali et al. shows a decision tree where the output of the decision tree is retrieved from the leaf node of the model. Ali et al. shows that two or more branches can be extended from each internal node with a node representing a certain characteristic while the branch represents a range of values (Ali et al. page 273 right col). Ali et al. further shows the range of values are the partition points for the set of values of the given characteristics (Ali et al. page 273 right col).
Claim 27 is directed to wherein a first value of a first score of the plurality of scores is associated with a first branch of the internal node of the decision tree corresponding to the first score. Claim 28 is directed to the internal node of the decision tree corresponding to the first score has at least three branches corresponding to distinct values of the first score.
Ali et al. shows that two or more branches can be extended from each internal node with a node representing a certain characteristic while the branch represents a range of values (Ali et al. page 273 right col). Ali et al. further shows the range of values are the partition points for the set of values of the given characteristics (Ali et al. page 273 right col).
Claim 29 is directed to wherein the decision tree comprises at least one leaf node at a first layer of the decision tree, and at least one leaf node at a second, higher layer of the decision tree.
Ali et al. shows that a decision tree may be built with at least one leaf node in different layers of the tree structure (Ali et al. page 273 right col.)
Claim 30 is directed to responsive to the generated clinical significance score being above a first threshold and below a second threshold, aggregating a second plurality of scores to generate a second clinical significance score, wherein at least one of the second plurality of scores is based on new data accumulated after generating the clinical significance score.
Karbassi et al. shows this step of aggregating a second plurality of scores when the generated clinical significance score is above a first threshold and below a second threshold (Karbassi et al. claim 25).
Claim 31 is directed to excluding a second variant from an output report, responsive to a generated clinical significance score of the second variant being below the threshold.
Karbassi et al. shows this step of excluding a second variant from an output report (Karbassi et al. claim 26).
Claim 33 is directed to retrieving, by the computing device from a database comprising a plurality of variants and associated patients, co-occurrence or family segregation data for the variant.
Karbassi et al. shows the retrieval from a database of a plurality of variants and associated patients, co-occurrence or family segregation data for the variant (Karbassi et al. claim 27).
Claim 44 is directed to wherein the plurality of scores further comprises a minor evidence score
Karbassi et al. shows an embodiment of determining this minor evidence score (Karbassi et al. claim 1 lines 10-14).
It would have been obvious to one of ordinary skill in the art before the effective filling date to have modified the decision tree structure of Karbassi et al. with the structure of the decision tree model set out in Ali et al. because this gives a method of using a decision tree where the plurality of scores (which are the characteristics of the dataset) are internal nodes with the branches representing different ranges of values for each characteristic which can partition the data (Ali et al. page 273 right col). One would have a reasonable expectation of success because decision tree models are known to have the structure that comprises different variations of a root node, internal nodes, branches, and leaf nodes depending on the application with internal nodes and branches acting as the partition points of the model as shown in Ali et al. so the decision tree of Karbassi et al. may be built in a manner that uses the plurality of scores as internal nodes because the scores are the characteristics of the dataset.
Claims 34, 37-43, and 45 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 15 and 25-27 of Karbassi et al. U.S. Patent No. 10,762,981 (referred herein as Karbassi et al.; previously cited) in view of Burke et al. (Jama 277.12 (1997): 997-1003; previously cited) in view of Ali, Jehad, et al. (International Journal of Computer Science Issues (IJCSI) 9.5 (2012): 272; previously cited).
Claim 34 is directed to receive a function score, a frequency score, a co-occurrence score, and a family segregation score
Karbassi et al. shows a system that generates this function score (Karbassi et al. claim 15 lines 5 and 6), Karbassi et al. shows a system that generates this frequency score (Karbassi et al. claim 15 lines 7 and 8), Karbassi et al. shows a system that generates this co-occurrence score (Karbassi et al. claim 15 lines 9-11), Karbassi et al. shows a system that generates this family segregation score (Karbassi et al. claim 15 lines 12 and 13)
(ii) aggregate the plurality of scores to generate a clinical significance score indicating a clinical significance of the genetic variant,
Karbassi et al. shows a system that aggregates these scores (Karbassi et al. claim 15 lines 19-24)
and (iii) determine that the generated clinical significance score for the variant is above a threshold
Karbassi et al. shows a system that determines that the generated clinical significance score for the variant is above a threshold (Karbassi et al. claim 15 lines 25 and 26)
wherein the processor is further configured to (1) sum up the plurality of scores with pre-determined weights, or (2) retrieve a value for the clinical significance score from a leaf node of a decision tree
Karbassi et al. shows a system that aggregates these scores by way of a weighted sum or decision tree (Karbassi et al. claim 15 lines 19-24)
Karbassi et al. does not show and wherein, responsive to the determination by the system that the generated clinical significance score for the variant is above the threshold, the system generates a report containing a recommendation that an individual identified as having the variant or an immediate blood relative of the individual identified as having the variant is further tested for a condition associated with the biological function of the cell or protein, wherein the testing is not performed by the system
When combined with Karbassi et al., Burke et al. shows giving testing recommendations for a condition associated with the biological function of the cell or protein of an individual associated with variants in a gene with a connection to a disease. Burke et al. shows providing testing recommendations for cancer surveillance when genetic variants are present (Burke et al. page 1287 and table 4).
Karbassi et al. in view of Burke et al. does not show wherein each score of the plurality of scores is associated with an internal node of the decision tree.
Like Karbassi et al. in view of Burke et al., Ali et al. shows a decision tree where the output of the decision tree is retrieved from the leaf node of the model. Ali et al. shows that two or more branches can be extended from each internal node with a node representing a certain characteristic while the branch represents a range of values (Ali et al. page 273 right col). Ali et al. further shows the range of values are the partition points for the set of values of the given characteristics (Ali et al. page 273 right col).
Claim 37 is directed to wherein a first value of a first score of the plurality of scores is associated with a first branch of the internal node of the decision tree corresponding to the first score. Claim 38 is directed to the internal node of the decision tree corresponding to the first score has at least three branches corresponding to distinct values of the first score.
Ali et al. shows that two or more branches can be extended from each internal node with a node representing a certain characteristic while the branch represents a range of values (Ali et al. page 273 right col). Ali et al. further shows the range of values are the partition points for the set of values of the given characteristics (Ali et al. page 273 right col).
Claim 39 is directed to wherein the decision tree comprises at least one leaf node at a first layer of the decision tree, and at least one leaf node at a second, higher layer of the decision tree.
Ali et al. shows that a decision tree may be built with at least one leaf node in different layers of the tree structure (Ali et al. page 273 right col.)
Claim 40 is directed to responsive to the generated clinical significance score being above a first threshold and below a second threshold, aggregating a second plurality of scores to generate a second clinical significance score, wherein at least one of the second plurality of scores is based on new data accumulated after generating the clinical significance score.
Karbassi et al. shows this step of aggregating a second plurality of scores when the generated clinical significance score is above a first threshold and below a second threshold (Karbassi et al. claim 25).
Claim 41 is directed to excluding a second variant from an output report, responsive to a generated clinical significance score of the second variant being below the threshold.
Karbassi et al. shows this step of excluding a second variant from an output report (Karbassi et al. claim 26).
Claim 43 is directed to retrieving, by the computing device from a database comprising a plurality of variants and associated patients, co-occurrence or family segregation data for the variant.
Karbassi et al. shows the retrieval from a database of a plurality of variants and associated patients, co-occurrence or family segregation data for the variant (Karbassi et al. claim 27).
Claim 45 is directed to wherein the plurality of scores further comprises a minor evidence score
Karbassi et al. shows an embodiment of determining this minor evidence score (Karbassi et al. claim 15 lines 14-18).
It would have been obvious to one of ordinary skill in the art before the effective filling date to have combined the determination of clinical significance of a variant of Karbassi et al. with the recommendation of testing based on a classified variant of Burke et al. because this would allow for a compressive method that recommends actions to take for surveillance of a disease if a variant is deemed to be of clinical significance and would allow individuals with clinical significant variants to screen for the condition earlier than the general population (Burke et al. page 999 left col.). One would be motivated to make this combination because Burke et al. shows as with self-examination, the contribution of clinician examination in cancer detection may be particularly important for women at risk for early breast cancer (Burke et al page 999 left col.). It would have been further obvious to one of ordinary skill in the art before the effective filling date to have modified the decision tree structure of Karbassi et al. in view of Burke et al. with the structure of the decision tree model set out in Ali et al. because this gives a method of using a decision tree where the plurality of scores (which are the characteristics of the dataset) are internal nodes with the branches representing different ranges of values for each characteristic which can partition the data (Ali et al. page 273 right col). One would have a reasonable expectation of success because Karbassi et al. can identify clinically significant variants while Burke et al. can give recommendations for further testing when variants are present and decision tree models are known to have the structure that comprises different variations of a root node, internal nodes, branches, and leaf nodes depending on the application with internal nodes and branches acting as the partition points of the model as shown in Ali et al. so the decision tree of Karbassi et al. on view of Burke et al. may be built in a manner that uses the plurality of scores as internal nodes because the scores are the characteristics of the dataset.
Claims 24, 27-29, 33, and 44 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 24-28 of copending Application No. 19022034 in view of Sardanelli et al. (Investigative radiology 46.2 (2011): 94-105; previously cited).
Claim 24 is directed to receiving a function score, a frequency score, a co-occurrence score, and a family segregation score
Karbassi et al. shows querying a database to receive a function score, a frequency score, co-occurrence score, and a family segregation score (Karbassi et al. claim 24 lines 3-10).
aggregating, by the computing device, the plurality of scores to generate a clinical significance score indicating a clinical significance of the genetic variant
Karbassi et al. shows determining a clinical significance score through aggregation (Karbassi et al. claim 25).
wherein aggregating the plurality of scores further comprises (1) summing up, by the computing device, the plurality of scores with pre-determined weights,
Karbassi et al. shows this aggregation by summation with predetermined weights (Karbassi et al. claim 27).
or (2) retrieving, by the computing device, a value for the clinical significance score from a leaf node of a decision tree,
Karbassi et al. shows aggregation by the use of a decision tree to determine a clinical significance score (Karbassi et al. claim 28).
Karbassi et al. does not show determining that the generated clinical significance score for the variant is above a threshold, testing an individual identified as having the variant or an immediate blood relative of the individual identified as having the variant for a condition associated with the biological function of the cell or protein.
When combined with Karbassi et al., Sardanelli et al. shows testing for breast cancer when a genetic risk has been established. Sardanelli et al. shows that women with high genetic risk for breast cancer where further screened using mammography (Sardanelli et al. pages 95 right col. and 99 left col.).
Karbassi et al. in view of Sardanelli et al. does not show wherein each score of the plurality of scores is associated with an internal node of the decision tree.
Like Karbassi et al. in view of Sardanelli et al., Ali et al. shows a decision tree where the output of the decision tree is retrieved from the leaf node of the model. Ali et al. shows that two or more branches can be extended from each internal node with a node representing a certain characteristic while the branch represents a range of values (Ali et al. page 273 right col). Ali et al. further shows the range of values are the partition points for the set of values of the given characteristics (Ali et al. page 273 right col).
Claim 27 is directed to wherein a first value of a first score of the plurality of scores is associated with a first branch of the internal node of the decision tree corresponding to the first score. Claim 28 is directed to the internal node of the decision tree corresponding to the first score has at least three branches corresponding to distinct values of the first score.
Ali et al. shows that two or more branches can be extended from each internal node with a node representing a certain characteristic while the branch represents a range of values (Ali et al. page 273 right col). Ali et al. further shows the range of values are the partition points for the set of values of the given characteristics (Ali et al. page 273 right col).
Claim 29 is directed to wherein the decision tree comprises at least one leaf node at a first layer of the decision tree, and at least one leaf node at a second, higher layer of the decision tree.
Ali et al. shows that a decision tree may be built with at least one leaf node in different layers of the tree structure (Ali et al. page 273 right col.)
Claim 33 is directed to retrieving, by the computing device from a database comprising a plurality of variants and associated patients, co-occurrence or family segregation data for the variant.
Karbassi et al. shows the retrieval from a database of a plurality of variants and associated patients, co-occurrence or family segregation data for the variant (Karbassi et al. claim 26).
Claim 44 is directed to wherein the plurality of scores further comprises a minor evidence score.
Karbassi et al. shows an embodiment of receiving this minor evidence score (Karbassi et al. claim 25).
It would have been obvious to one of ordinary skill in the art before the effective filling date to have combined the method of determining the clinical significance of a variant of Karbassi et al. with the testing of patients for cancer that have been identified with a variant of high risk of Sardanelli et al. because this would give a comprehensive method of testing patients for cancer that have been identified as having clinically significant variants. One would have a reasonable expectation of success because Karbassi et al. shows determining clinically significant variants while Sardanelli et al. shows testing patients with high-risk variants. It would have been further obvious to one of ordinary skill in the art before the effective filling date to have modified the decision tree structure of Karbassi et al. in view of Sardanelli et al. with the structure of the decision tree model set out in Ali et al. because this gives a method of using a decision tree where the plurality of scores (which are the characteristics of the dataset) are internal nodes with the branches representing different ranges of values for each characteristic which can partition the data (Ali et al. page 273 right col). One would have a reasonable expectation of success because decision tree models are known to have the structure that comprises different variations of a root node, internal nodes, branches, and leaf nodes depending on the application with internal nodes and branches acting as the partition points of the model as shown in Ali et al. so the decision tree of Karbassi et al. may be built in a manner that uses the plurality of scores as internal nodes because the scores are the characteristics of the dataset.
This is a provisional nonstatutory double patenting rejection.
Response to Arguments
Applicant's arguments filed 26 March 2025 have been fully considered but they are not persuasive.
Applicant argues the amendment of “testing an individual…” overcomes the non-statutory double patenting rejection (Reply p. 11).
This argument has been fully considered but found to be not persuasive. Karbassi et al. U.S. Patent No. 10,762,981 (referred herein as Karbassi et al.; previously cited) shows wherein an individual (or an immediate blood relative) identified as having a variant is tested for a condition associated with the biological function of the cell or protein, responsive to the determination that the generated clinical significance score for the variant is above the threshold (Karbassi et al. claim 1 lines 27-30) which renders performing the testing obvious. Thus, the amendment does not overcome the non-statutory double patenting rejection.
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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
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/J.E.H./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685