DETAILED ACTION Notice of Pre-AIA or AIA Status The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Status of the Claims Claims 1-13 are pending and examined herein. No claims are canceled. Priority As detailed on the 08 April 2022 filing receipt, the application claims priority as early a s 08 October 2019 to foreign patent JP 2019-185444 . At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date. Information Disclosure Statement The information disclosure statement s (IDS) were submitted on 13 November 2022 and 01 April 2022 . The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the references are being considered by the examiner. Specification The disclosure is objected to because the paragraph numbering does not include the first paragraph. The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (pg. 1, paragraph [2]). 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 Interpretation Claim 9 recites an “external apparatus” which is not disclosed in the specification. The specification discloses “an external server” (pg. 29, paragraph [102]). Therefore, the apparatus is interpreted as a server and thus a computer. Claim Interpretation under 35 U.S.C. 112(f) The following is a quotation of 35 U.S.C. 112(f): (f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof. The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph: An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof. The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked. As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph: (A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function; (B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and (C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function. Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function. Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function. Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) is/are: “a filter processing unit that outputs a score” (claim 1), “an output unit that creates rank information” (claim 1), “a database filter” (claim 9), and “a function prediction filter” (claim 9). Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. The corresponding structure in the instant specification and independent claims is a computer which executes the steps (pg. 3, paragraph [7]) or a “general computer apparatus” including a control unit (interpreted as a processor), storage, operation, input/output, and display (pg. 5, paragraph [11]), and thus the steps are interpreted as computer-implemented. The specification must disclose an algorithm for performing the claimed specific computer function, or else the claim is indefinite under 35 U.S.C. 112(b) (MPEP 2181 (II)(B)). The recited “filter processing unit that outputs a score.” The processing unit includes “a database filter” and “function prediction filter.” The outputting of a score by the filter processing unit is disclosed in the specification as a “judgmental result as to whether or not each condition is satisfied for each mutation state while applying the filters corresponding to a plurality of conditions in a predetermined order” (pg. 1 5-16 , paragraph [ 53] ) . However, it is unclear what the specific algorithmic steps are that allow said judgment. The database filter is disclosed as checking “whether or not the mutation state to be analyzed is registered in a predetermined database” and “sets a score” based on its presence, but how this set score relates to the filter processing unit’s output score is unclear. Furthermore, the function prediction filter sets a score based on pathogenicity of mutations (pg. 14, paragraph [46]) but is also unclear how this set score is combined or evaluated with the previous score or final outputted score. The recited “output unit that creates rank information” and said rank information is disclosed as “the degree of possibility that the mutation state is pathologic based on the determined score” (pg. 3, paragraph [7]), but the calculation of the degree and metric of possibility is not disclosed. If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. Claim Rejections - 35 USC § 112(b) from 35 USC § 112( f) 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. Claim s 1-11 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. Claim limitation s of the “output unit”, “filter processing unit”, “database filter”, and “function prediction filter” invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function as explained in the claim interpretation above. Specifically, the algorithmic steps for the recited retention are unclear. Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. Applicant may: (a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph; (b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or (c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)). If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either: (a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or (b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181. Claim Rejections - 35 USC § 112(b) Claims 4-5 recite sequences being similar to other sequences. The term “ similar ” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. As t he threshold of similarity is not recited in the claims, and so what is considered similar is unclear. Claim 5 recites “a fusion gene” and is dependent on claim 4, which also recites “a fusion gene.” Therefore, it is unclear whether the fusion gene in claim 5 refers to the fusion gene of claim 4 or a different fusion gene. Claims 9 and 11 recite “possibility” being “high” when a predetermined condition is satisfied. The term “ high ” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Therefore, the claims are unclear. Appropriate amendment is required. Claim Rejections - 35 USC § 112(a) from 35 USC § 112( f) 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. Claim 1-11 a re rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, because the claim purports to invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, but fails to recite a combination of elements as required by that statutory provision and thus cannot rely on the specification to provide the structure, material or acts to support the claimed function , where said elements are the “output unit”, “filter processing unit”, “database filter”, and “function prediction filter” . As such, the claim recites a function that has no limits and covers every conceivable means for achieving the stated function, while the specification discloses at most only those means known to the inventor. Specifically, the steps for retaining the information by the retention unit is not described. Accordingly, the disclosure is not commensurate with the scope of the claim. 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 1-13 are rejected under 35 USC § 101 because the claimed inventions are directed to an abstract idea without significantly more. "Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I). Abstract ideas include mathematical concepts, and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2 )). The claims as a whole, considering all claim elements individually and in combination, are directed to a judicial exception at Step 2A, Prong 2, and the additional elements of the claims, considered individually and in combination, do not provide significantly more at Step 2B than the abstract idea of ranking possibility a mutation is pathologic. MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below. Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)? Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e ., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))? Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))? Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)? Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter ( MPEP 2106.03)? The claims are directed to a computer system (claims 1 -11), a method (claim 12), and a non-transitory computer-readable medium (claim 1 3 ), each of which falls within one of the categories of statutory subject matter. [Step 1: Yes] Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. , a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))? With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as: • mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations) (MPEP 2106.04(a)(2)(I)); • certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or • mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)). Mathematical concepts recited in the independent claims include determining a score and ranking a degree of possibility (claims 1 and 12-13). These steps are interpreted as numerical determinations and represent probability, which are mathematical concepts. A mathematical relationship may be expressed in words and there is no particular word or set of words that indicates a claim recites a mathematical calculation (MPEP 2106.04(a)(2)). Claim 2 recites generating a record and outputting information , where generating a record can be performed by hand and thus is a mental process . Claims 3-8 recite additional information about determining the score, which is a mathematical concept as explained above. Mental processes, defined as concepts practically performed in the human mind such as steps of observing, evaluating, or judging information, recited are evaluating information, determining mutation state, and comparing information (claim 9); evaluating whether pathogenicity is present (claim 10); and evaluating quality of sequencing (claim 11). These steps are interpreted as data evaluation and thus practically performed by the human mind. Hence, the claims explicitly recite numerous elements that, individually and in combination, constitute abstract ideas. The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). [Step 2A: Yes] Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))? The independent claims recite additional elements that are not abstract idea including receiving sequence information and outputting the created rank information (claims 1 and 12-13) and a storage medium (claim 13). Claim 9 recites an external apparatus , interpreted as a computer . The claims recite use of at least one general purpose computer including memory and receiving/storing information. The claims comprising computer components do not describe any specific computational steps by which the computer performs or carries out the abstract idea, nor do they provide any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than that a generic computer performs the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; and MPEP 2106.05(f)). The specification discloses the output is to the control unit, which is interpreted as a computer or processor (pg. 6, paragraph [17]). The claim elements comprising storing records are mere instructions to apply an exception using a computer (MPEP 2106.05(f)) and insignificant extra solution activity (MPEP 2106.05(g)) , and necessary data input and output do not integrate the abstract ideas into a practical application . None of the dependent claims recite any additional non-abstract elements; they are all directed to further aspects of the information being analyzed, the manner in which that analysis is performed, or the mathematical operations performed on the information. [Step 2A Prong Two: No] Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)? 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 of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05). The claims recite receiving sequence information and outputting the created rank information (claims 1 and 12-13) and a storage medium (claim 13); generating a record in the computer (claim 2); and an external apparatus, interpreted as a computer (claim 9). The claims recite a t least one computer, interpreted as instructions to apply the abstract idea using a computer, where the computer does not impose meaningful limitations on the judicial exceptions, which can be performed without the use of a computer (MPEP 2106.04(d) § I; and MPEP 2106.05(f)). Receiving information , including over a network to/from an external computer, is a conventional computer function ( buySAFE , Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network). Finally, storage of sequence information in databases is disclosed as widely used (pg. 1, paragraph [2]). Therefore, the recited additional elements, alone or in combination with the judicial exceptions, do not appear to provide an inventive concept. [Step 2B: No] Conclusion: Claims are Directed to Non-statutory Subject Matter For these reasons, the claims, when the limitations are considered individually and as a whole, are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as being directed to non-statutory subject matter. Claim Rejections - 35 USC § 103 In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status. The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action: A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made. The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows: 1. Determining the scope and contents of the prior art. 2. Ascertaining the differences between the prior art and the claims at issue. 3. Resolving the level of ordinary skill in the pertinent art. 4. Considering objective evidence present in the application indicating obviousness or nonobviousness. This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention. Claims 1 - 3 and 6 -13 Claims 1-3 and 6-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Velculescu (US 20160273049 A1; previously cited on the 01 April 2022 IDS form) in view of Ganel (Bioinformatics 33(7): 1083-1085, 2017; newly cited) and Yarham ( Human Mutation 32(11): 1319-1325, 2011; newly cited ). Claim 1 recites a receiving unit that receives mutant base sequence information representing the mutation state, where the mutation state includes a mutation location in a base sequence and the content of the mutation, extracted from genetic information of a sample to be analyzed by sequence alignment. Velculescu teaches obtaining sequence reads from a patient (paragraph 7]) and alignment (paragraph [144]), where alignment would reveal location and content of a mutation. Claim 1 recites a filter processing unit that outputs a score determined depending on whether or not the mutation state represented by the mutant base sequence information received by the receiving unit is a structural mutation across multiple genes. Velculescu teaches structural variations tending to indicate disease (paragraph [77]) and filtering the data by screening for structural variant cancer genes (Fig. 3), but not a score based on the presence of a structural variant. Claim 1 recites an output unit that creates rank information representing the degree of possibility that the mutation state is pathologic based on the score output by the filter processing unit and outputs the created rank information. Velculescu teaches performing said steps can be performed using a computer system including processors and memory in communication (pg. 13, col. 1, paragraph [133]). Velculescu does not teach possibility of pathology by the score represented as a rank. Ganel teaches predicting deleterious structural variants (pg. 1084, col. 2, third paragraph), where a pathologic mutation state reads on a deleterious variant , resulting in pathogenicity scores (abstract). Yarham teaches scoring mutations into ranked categories, where the categories are (in order of increasing possibility of pathogenicity: neutral polymorphisms, possibly pathogenic, probably pathogenic, and definitely pathogenic (pg. 1320, Table 1). Claim 12 recites a method performing the steps recited in claim 1. The previously combined art Velculescu , Ganel , and Yarham teach these steps as explained above. Claim 13 recites a non-transitory medium storing the instructions for performing the steps recited in claim 1. The previously combined art Velculescu , Ganel , and Yarham teach these steps as explained above. Velculescu (paragraph [135 ] ) teaches storing instructions on a non-transitory medium. Claim 2 recites the filter processing unit further generates record information representing whether or not each of a plurality of the mutation states is the structural mutation, and the output unit outputs the record information in association with the rank information. Ganel teaches different variant types including SNPs and structural variants (pg. 1083, second and third paragraphs) and Velculescu teaches saving mutations (paragraph [165]). Claim 3 recites a retaining unit that retains the mutant base sequence information received by the receiving unit, wherein the filter processing unit determines the score depending on whether or not the mutant base sequence information that is extracted from genetic information of an individual common to the mutant base sequence information currently received by the receiving unit and that is previously received by the receiving unit represents the same mutation state as that in the currently-received mutant base sequence information. Velculescu teaches classification as a mutation when the candidate mutation is present in a database of variants (paragraph [144]). Claim 6 recites the filter processing unit determines the score depending on whether or not a position of a conserved sequence, the conserved sequence being a base sequence conserved between genomes of different organism species, is included in the mutation location of the mutation state. Yarham teaches a method of ranking pathogenicity including evolutionary conservation (pg. 1320, Table 1), where conservation across different organisms is interpreted as evolutionary conservation. Claim 7 recites the filter processing unit determines the score depending on whether or not the mutation state is a chromosome translocation. Velculescu teaches translocation as a variant type (paragraph [41]). Claim 8 recites the filter processing unit determines the score depending on whether or not the mutation state is a deletion of a registered gene that is registered in advance. Velculescu teaches at least a deletion detected in comparison to a known gene (paragraph [172]). Claim 9 recites the filter processing unit includes a database filter that determines whether or not the mutation state is registered in an external apparatus as a mutation with pathogenicity; and a function prediction filter that evaluates whether or not pathogenicity is present in the mutation state, if the database filter determines that the mutation state is not registered in the external apparatus as a mutation with pathogenicity, wherein the database filter and the function prediction filter determine, as the score, a value indicating that the possibility of the mutation state being pathologic is high in the case where the database filter determines that the mutation state is registered in the external apparatus as a mutation with pathogenicity and in the case where the database filter determines that the mutation state is not registered in the external apparatus as a mutation state with pathogenicity and where the function prediction filter evaluates that pathogenicity is present in the mutation state, as compared to the case where the database filter determines that the mutation state is not registered in the external apparatus as a mutation state with pathogenicity and where the function prediction filter evaluates that pathogenicity is not present in the mutation state. Velculescu teaches classification as a mutation when the candidate mutation is present in a database of variants (paragraph [144]) and Yarham teaches comparison to a database of known pathogenic and polymorphic changes to determine pathogenicity, where the mutation state registered as pathogenic reads on its presence in a database as pathogenic. Yarham also teaches evaluation of novel mutations, where mutations not registered as pathogenic reads on novel . Claim 10 recites t he function prediction filter evaluates whether or not pathogenicity is present in the mutation state by predicting whether or not the mutation states affects protein function. Ganel teaches “functional consequences” of a mutation state (pg. 1083, col. 2, second paragraph) , where protein function is interpreted as reading on functional consequences. Claim 11 recites the filter processing unit evaluates quality of sequencing of the mutation state and determines, as the score, a value indicating that the possibility of the mutation state being pathologic is high in the case where the quality of sequencing of the mutation state is determined to satisfy a predetermined condition, as compared to the case where the quality of sequencing of the mutation state has failed to be determined to satisfy a predetermined condition. Velculescu teaches filtering low quality reads, where the threshold is a phred score of less than 30 for a tumor and 20 for normal tissue (paragraph [144]). Combining Velculescu , Ganel , and Yarham An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have been motivated to combine the work of Ganel , which teaches a method of evaluating the impact of structural variation based on SNP pathogenicity (abstract) , with the work of Velculescu bec a use Ganel teaches detecting deleteriousness (or pathogenicity) of mutations by generating a score. Generating a score is a desirable trait to qualify or quantify the deleteriousness suggested by Velculescu . Both Velculescu and Ganel teach screening structural variants to characterize mutations as disease-causing or pathogenic, and their combination would be expected to succeed. One would have been further motivated to combine the work of Yarham , which teaches a method of scoring pathogenicity of mutations (abstract) , with the work of Velculescu because Yarham teaches categories of pathogenicity of the analyzed novel mutations, where the categories are taught as increasing the use of reporting mutations and improving data available to clinicians and researchers (pg. 1324, col. 2, first paragraph). Yarham is also directed to the shared field of endeavor of the determining pathogenicity or deleteriousness of mutations, and implementation of the categorical coding system would be expected to succeed. Therefore, the invention is prima facie obvious. Claim 4 Claim 4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Velculescu in view of Ganel and Yarham as applied to claims 1-3 and 6-13 above, and further in view of Nik-Zainal (US 20190130997 A1; newly cited). Claim 4 recites the filter processing unit determines the score depending on whether or not a fusion gene, in which a gene having a base sequence similar to a base sequence of a candidate gene is fused with another gene, is included in a base sequence corresponding to the mutation state, the candidate gene serving as a driver mutation candidate in a fusion gene fused with another gene. Velculescu teaches classification as a mutation when the candidate mutation is present in a database of variants (paragraph [144]) but not specifically a driver mutation related to gene fusion. Nik-Zainal teaches characterizing sequence data including identifying driver mutations related to gene fusions (paragraph [153]). Combining Velculescu , Ganel , Yarham , and Nik-Zainal An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have been motivated to combine the work of Nik-Zainal, which teaches testing a tumor for signatures of mutations (abstract) with the previously combined art because Nik-Zainal teaches driver mutations forming fusions of genes (pg. 1, paragraph [4]). Nik-Zainal teaches that fusions can create activated, dominant cancer genes (pg. 9, paragraph [153]), and so their detection would be of interest in scoring pathogenic mutations as described by the previously combined art. The detection of gene fusions appears to be related to the alignment methods of mutation previously taught and so such a combination would be expected to succeed. Therefore, the invention is prima facie obvious. Claim 5 Claim 5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Velculescu in view of Ganel , Yarham , and Nik-Zainal as applied to claims 1-4 and 6-13 above, and further in view of Burke (US 20180300451 A1; newly cited). Claim 5 recites the filter processing unit determines the score depending on whether or not a fusion gene, in which two genes respectively similar to two candidate genes are fused, is included in the base sequence corresponding to the mutation state, the two candidate genes serving as driver mutation candidates in a fusion gene in which the candidate genes of a specific combination are fused. Velculescu teaches classification as a mutation when the candidate mutation is present in a database of variants (paragraph [144]) but not specifically a driver mutation related to gene fusion. Nik-Zainal teaches characterizing sequence data including identifying driver mutations related to gene fusions (paragraph [153]) but not alignment to different regions of the genome. Burke teaches alignment to more than a single location in the genome as evidence of a gene fusion event ( pg. 13, paragraph [115]) . Combining Velculescu , Ganel , Yarham , Nik-Zainal, and Burke An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have been motivated to combine the work of Burke , which teaches determination of signal suggesting fusions by alignment to different locations in the genome (pg. 13, paragraph [115]) with the work of Nik-Zainal in particular because while Nik-Zainal teaches detection of f usion event, it does not teach detection evidenced by alignment in different regions, which would be reasonably expected to comport with gene fusion. Burke and the previously combined prior art are directed to the shared field of detecting sequence variations that may indicate a pathologic state and their combination would be expected to succeed. Therefore, the invention is prima facie obvious. 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 . Claim s 1- 3, 7-8, and 11-1 3 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim s 1-2 of copending Application No. 18846165 in view of Velculescu . Claim 4 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of copending Application No. 18846165 in view of Velculescu as applied to claims 1-3, 7-8, and 11-13 above and further in view of Nik-Zainal. Claim 5 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of copending Application No. 18846165 in view of Velculescu as applied to claims 1-4, 7-8, and 11-13 above and further in view of Nik-Zainal. Claims 6 and 9 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of copending Application No. 18846165 in view of Velculescu as applied to claims 1-3, 7-8, and 11-13 above and further in view of Yarham . Claim 10 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of copending Application No. 18846165 in view of Velculescu as applied to claims 1-3, 6-9, and 11-13 above and further in view of Nik-Zainal. This is a provisional nonstatutory double patenting rejection. Regarding instant claim 1 , reference claim 1 discloses the limitations of instant claim 1 of filtering sequence variations and classifying as harmful/pathologic except for receiving mutant base sequence information . Velculescu teaches obtaining sequence reads from a patient (paragraph 7]) and alignment (paragraph [144]), where alignment would reveal location and content of a mutation , and structural variations indicative of disease ( pg. 2, col. 1 , paragraph [17]). Regarding instant claims 12 and 13, Velculescu teaches storing instructions on a non-transitory medium (paragraph [135 ] ) and performing said steps can be performed using a computer system including processors and memory in communication (pg. 13, col. 1, paragraph [133]). Regarding instant claim 2, Velculescu teaches saving mutations (paragraph [165]). Regarding instant claim 3 which recites determining if the mutation state is the same , reference claim 3 teaches variations being different from each other. Regarding instant claim 4 which recites determination of a fusion gene is included and the candidate gene serving as a mutation driver in a fusion, Velculescu teaches classification as a mutation when the candidate mutation is present in a database of variants (paragraph [144]) but not specifically a driver mutation related to gene fusion , and Nik-Zainal teaches characterizing sequence data including identifying driver mutations related to gene fusions (paragraph [153]). Regarding instant claim 5 which recites additional information about the scoring of fused candidate genes, Velculescu teaches classification as a mutation when the candidate mutation is present in a database of variants (paragraph [144]) but not specifically a driver mutation related to gene fusion , N ik-Zainal teaches characterizing sequence data including identifying driver mutations related to gene fusions (paragraph [153]) but not alignment to different regions of the genome , and Burke teaches alignment to more than a single location in the genome as evidence of a gene fusion event (pg. 13, paragraph [115]). Regarding instant claim 6 which recites determining if a state is conserved based on a different organism, Yarham teaches a method of ranking pathogenicity including evolutionary conservation (pg. 1320, Table 1), where conservation across different organisms is interpreted as evolutionary conservation. Regarding instant claim 7 which recites determining a score based on the mutation being a chromosome translocation, Velculescu teaches translocation as a variant type (paragraph [41]). Regarding instant claim 8 which recites determining a score based on the mutation being a deletion of a pre-registered gene, Velculescu teaches at least a deletion detected in comparison to a known gene (paragraph [172]). Regarding instant claim 9 which recites determining a mutation is pathogenic based on an external database, Velculescu teaches classification as a mutation when the candidate mutation is present in a database of variants (paragraph [144]) and Yarham teaches comparison to a database of known pathogenic and polymorphic changes to determine pathogenicity, where the mutation state registered as pathogenic reads on its presence in a database as pathogenic. Yarham also teaches evaluation of novel mutations, where mutations not registered as pathogenic reads on novel. Regarding instant claim 10 which recites evaluating pathogenicity based on whether a mutation affects protein function, Ganel teaches “functional consequences” of a mutation state (pg. 1083, col. 2, second paragraph) , where protein function is interpreted as reading on functional consequences. Regarding instant claim 11 which recites indicating that the possibility of the mutation state being pathologic is high in the case where the quality of sequencing of the mutation state is determined to satisfy a predetermined condition , Velculescu teaches filtering low quality reads, where the threshold is a phred score of less than 30 for a tumor and 20 for normal tissue (paragraph [144]). An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have been motivated to combine the reference application, which teaches a method of filtering sequences and classifying them as harmful, with the work of Velculescu because Velculescu teaches characterizing patient - specific variations as mutations that are indicative of a disease (abstract) where the variations may be structural (pg. 2, col. 1, paragraph [17]) and based on specific criteria (pg. 16, paragraph [164]). One would have been motivated to combine the work of Nik-Zainal, which teaches testing a tumor for signatures of mutations (abstract) with the previously combined art because Nik-Zainal teaches driver mutations forming fusions of genes (pg. 1, paragraph [4]). Nik-Zainal teaches that fusions can create activated, dominant cancer genes (pg. 9, paragraph [153]), and so their detection would be of interest in scoring pathogenic mutations as described by the previously combined art. The detection of gene fusions appears to be related to the alignment methods of mutation previously taught and so such a combination would be expected to succeed. One would have been motivated to combine the work of Burke, which teaches determination of signal suggesting fusions by alignment to different locations in the genome (pg. 13, paragraph [115]) with the work of Nik-Zainal in particular because while Nik-Zainal teaches detection of f usion event, it does not teach detection evidenced by alignment in different regions, which would be reasonably expected to comport with gene fusion. Burke and the previously combined prior art are directed to the shared field of detecting sequence variations that may indicate a pathologic state and their combination would be expected to succeed. One would have been motivated to combine the work of Yarham , which teaches a method of scoring pathogenicity of mutations (abstract), with the work of Velculescu because Yarham teaches categories of pathogenicity of the analyzed novel mutations, where the categories are taught as increasing the use of reporting mutations and improving data available to clinicians and researchers (pg. 1324, col. 2, first paragraph). Yarham is also directed to the shared field of endeavor of the determining pathogenicity or deleteriousness of mutations, and implementation of the categorical coding system would be expected to succeed. One would be further motivated to combined with Ganel , which teaches a method of evaluating the impact of structural variation based on SNP pathogenicity (abstract), with the work of Velculescu because Ganel teaches detecting deleteriousness (or pathogenicity) of mutations by generating a score. Generating a score is a desirable trait to qualify or quantify the deleteriousness suggested by Velculescu . Both Velcu