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 .
Applicants Amendment
Applicants’ amendment filed 1/22/2026 has been received and entered. Claims 2-6, 8-12, 14-18 have been cancelled, claims 1, 7 and 13 have been amended.
Claims 1, 7 and 13 are pending.
Election/Restriction
Applicant’s election without traverse of Group I in the reply filed on 7/17/2025 was acknowledged. During the initial search and review of the claims the restriction requirement is withdrawn.
Claims 1, 7 and 13 drawn to an evaluation method comprising providing sequencing data and evaluating partial sequences for possible mutations by positional relationship evaluation, a medium with instructions to compare two sequence data sources that evaluate whether a difference is a genetic mutation and an evaluation device are currently under examination.
Priority
This application filed 11/10/2021 is a continuation of PCT/JP2019/018965 filed 5/13/2019.
No comment regarding the summary of priority was made in the instant application.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 12/18/2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
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 1, 7 and 13 stand provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6, 8-10, 12 of copending Application No 18/149768.
Response to Applicants arguments
Applicants note the claims have been amended and state that the claims are subject to change and that it is premature to file a terminal disclaimer.
In response, no specific difference is noted by applicants. In evaluating the amendments, it appears that both claims now specifically use an ‘inverted index’ and provide for evaluation of mutations effect on codons and provides for segmented analysis for the product of the gene mutation based on type and position of the altering mutation. Both appear to encompass in silico analysis and the same type of possible mutations and possible codon changes among the plurality of bases. In each, the method steps require analyzing each consecutive base for the assessment of codons and for possible effect on the resulting amino acid sequence and possible assessment of effects of mutants on the basic structure. In each case the sequences are segmented and evaluated. ‘768 does not require that each base be evaluated, but it would be obvious to assess all the three bases in a given potential codon to establish the resulting amino acid.
A copy of pending claim 1 of ‘768 is provided for the record (not amended as of 6/8/2026):
A non-transitory computer-readable storage medium storing an information processing program for causing a computer to perform processing comprising:
obtaining a plurality of pieces of segmented genome data, which is genome information of a specific individual;
generating a plurality of pieces of segmented codon data obtained by encoding each of the plurality of pieces of segmented genome data in a codon unit on the basis of a codon conversion table in which a codon and a code are associated with each other;
identifying, on the basis of reference codon data obtained by encoding reference genome data to be a reference in the codon unit and each of the plurality of pieces of segmented codon data, a type and a position of an appearance of gene mutation different from the code that appears in the reference codon data among a plurality of the codes that appears in the plurality of pieces of segmented codon data; and
generating a gene mutation inverted index in which the gene mutation and the type and position of the appearance of the gene mutation are associated with each other.
This is a provisional nonstatutory double patenting rejection.
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.
It is noted that application with the same Applicant and shared inventors provides methods which are complimentary to the instantly claimed method. The present claims are directed to evaluating the nucleic acid, and the claims of 18/502405 comprise evaluating an amino acid and the codon sequences with a focus on amino acid transposition not necessarily the coding sequence per se.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 7 and 13 stand 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.
Claim analysis
Claim 1 has been amended and still is generally directed to evaluating a nucleic acid sequence on base at a time according to rules associated with amino acid sequences as set forth in dependent claims. More specifically, the claim is amended to provide data of statistical frequency of a mutation occurrence put into a bitmap inverted index associated with the position, and the evaluating using the index alterations using bitwise logical operations. The claims provide a computer implemented method where a sequence is represented as a sequence which is analyzed base by base in the form of an index file, either in frame or with possible alterations, and assessing alterations on the amino acid sequence and its basis structure.
Response to Applicants arguments
Applicants assert as amended the claim provide a specific technical improvement using an bitmap inverted index and a combination of unconventional combination of operations, and the ordered combination is an improvement to how the computer operates to solve a specific problem and provides a practical application.
In response, the amendments are acknowledged but inverted indexes are not new, nor is the use of logical operations generically provided. What appears to be provided are instructions to implement the comparison of altered sequences, and affects on the codons it produces. The use of logic statements or the use of a known index form does not appear to be an improvement, and there does not appear to be a technical problem addressed, but rather the claims as a whole provide a series of computer implemented instructions to compare two altered sequences based on possible codon changes.
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a method and a product.
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of accessing sequence data for coding sequences or the codon rules that provide for a specific amino acid. The step of aligning and comparing sequence to arrive at the identification or evaluation are instructional steps. The claim requires generic evaluation of sequences base by base. The judicial exception is a set of instructions for analysis of sequence data and appear to fall into the category of a Mental Processes, that is concepts performed in the human mind including an observation, evaluation, judgment, opinion. The breadth of “generating”, “specifying”, and “evaluating” encompasses non-transformative visual assessment of an individual sequence, in part coupled with prior knowledge, for example a codon chart for certain rules, and possible correlation of any change in amino acid to some basic structure of the protein. This breadth does not impose a meaningful limit on the claim scope, such that all others are not precluded from using the natural principle of translating a nucleic acid into a corresponding amino acid sequence. Although the claims recite the method for a computer to execute, the courts have also identified limitations that did not integrate a judicial exception into a practical application; for example, merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea, as discussed in MPEP § 2106.05(f). Computing, constructing datasets and using statistical models was well understood, conventional, and routinely performed in the art at the time the application was filed.
Recent guidance from the office requires that the judicial exception be evaluated under a second prong to determine whether the judicial exception is practically applied. In the instant case, the claims do not have an additional element to which the analysis is applied. For the products of a medium and device for implementing the method, this judicial exception requires steps recited at high level of generality and are only stored on a non-transitory, and is not found to be a practical application of the judicial exception as broadly set forth.
For step 2B of the 101 analysis, to the extent the method would be practiced on a computer, each of the independent claims recites additional elements and are found to be the steps of obtaining sequence data for the evaluation. As such, the claims do not provide for any additional element to consider under step 2B which appears to be significantly more or an improvement when the claim is viewed as a whole. For the the method, it is noted that in explaining the Alice framework, the Court wrote that "[i]n cases involving software innovations, [the step one] inquiry often turns on whether the claims focus on the specific asserted improvement in computer capabilities or, instead, on a process that qualifies as an abstract idea for which computers are invoked merely as a tool." The Court further noted that "[s]ince Alice, we have found software inventions to be patent-eligible where they have made non-abstract improvements to existing technological processes and computer technology." Moreover, these improvements must be specific -- "[a]n improved result, without more stated in the claim, is not enough to confer eligibility to an otherwise abstract idea . . . [t]o be patent-eligible, the claims must recite a specific means or method that solves a problem in an existing technological process." As indicated in the summary of the judicial exception above and in view of the teachings of the specification, the steps are drawn to analysis of sequence data. While the instruction are stored on a medium and could be implemented on a computer, together the steps do not appear to result in significantly more than a means to compare sequences. The judicial exception of the method as claimed can be performed by hand and in light of the previous claims to a computer medium and in light of the teaching of the specification on a computer. In review of the instant specification the methods do not appear to require a special type of processor and can be performed on a general purpose computer. Dependent claims set forth additional steps which are more specifically define the considerations and steps of calculating, and comparing, and do not add additional elements which result in significantly more to the claimed method for the analysis. No additional steps are recited in the instantly claimed invention that would amount to significantly more than the judicial exception. Without additional limitations, a process that employs mathematical algorithms (aligning sequences) to manipulate existing information (identify a mutants or variant amino acid sequences) to generate additional information is not patent eligible. In other words, patenting abstract idea (designing probes to a target sequence) cannot be circumvented by attempting to limit the use to a particular technological environment or purpose and desired result.
One way to overcome a rejection for non-patent-eligible subject matter is to persuasively argue that the claimed subject matter is not directed to a judicial exception. Another way for the applicants to overcome the rejection is to persuasively argue that the claims contain elements in addition to the judicial exception that either individually or as an ordered combination are not well understood, routine, or conventional. Another way for the applicants to overcome the rejection is to persuasively argue that the claims as a whole result in an improvement to a technology. Persuasive evidence for an improvement to a technology could be a comparison of results of the claimed subject matter with results of the prior art, or arguments based on scientific reasoning that the claimed subject matter inherently results an improvement over the prior art. The applicants should show why the claims require the improvement in all embodiments.
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.
Claims 1, 7 and 13 rejected under 35 U.S.C. 103 as being unpatentable over Sunthornwat et al (2011) and Peterlongo et al (2009) (both of record) is withdrawn.
The art of record fails to provide for using a bitmap inverted index to compare sequences.
Conclusion
No claim is 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R Skowronek can be reached at 571 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Joseph Woitach/ Primary Examiner, Art Unit 1687
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