DETAILED ACTION
Applicant's response, filed 3/23/2026, has been fully considered.
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 .
Priority
This application filed 12/01/2022 is a National Stage entry of PCT/JP2021/014475, with an International Filing Date of 04/05/2021, and claims foreign priority to 2020-096551, filed 06/03/2020. The claims are therefore examined as filed on 06/03/2020, the effective filing date. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further review of the priority application(s).
Claim Status
Claims 1-9 are pending.
Claims 5-8 are withdrawn.
Claims 1, 3-4, and 9 are directed to the elected invention.
Claim 9 is newly added.
Claim 2 is cancelled.
Claim 1 is objected to.
Claims 1, 3-4 and 9 are examined.
Claims 1, 3-4, and 9 are rejected.
Withdrawn Specification Objections
The objection of the disclosure in the Office action mailed 12/23/2025 is withdrawn in view of the amendments filed 2/23/2026.
Withdrawn Claim Objections
The objection to claims 1 and 3, in the Office action mailed 12/23/2025 is withdrawn in view of the amendments filed 2/23/2026.
Withdrawn Claim Rejections
The rejection of claims 1-4 under 35 U.S.C. 103 over KIM in view of FEDRIZZI, in the Office action mailed 12/23/2025, is withdrawn in view of the amendments filed 2/23/2026, and persuasive argument that the cited references do not teach the limitation of comparing multiple genes that include, specifically, at least “30S ribosome S1 to S21 (rpsA to rpsU), 50S ribosome L1 to L36 (rplA to rplF, rplI to rplU, rpmA to rpmJ), 5S ribosome RNA (rrf), 16S ribosome RNA (rrs), 23S ribosome RNA (rrl), rpoB, groEL2, gyrB, inhA, tlyA, katG, pncA, erm, eis, and embB” to identify the species or subspecies of NTM using MLST (remarks pg 17). However, this withdrawal is dependent on the interpretation of the claim as explained in the 112(b) rejection below.
Claim Objections
Claim 1 is objected to because of the following informalities:
The phrase “Komonogorov-Smimov” in claim 1 should be corrected to “Komonogorov-Smirnov” (spelling correction).
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 3-4 and 9 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.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 1 recites the broad recitation “wherein the multiple genes are selected from the group consisting of 184 genes of the listed genes”, and the claim also recites, in the next section, “wherein the multiple genes include at least 30S ribosome S1 to S21 (rpsA to rpsU), 50S ribosome L1 to L36 (rplA to rplF, rplI to rplU, rpmA to rpmJ), 5S ribosome RNA (rrf), 16S ribosome RNA (rrs), 23S ribosome RNA (rrl), rpoB, groEL2, gyrB, inhA, tlyA, katG, pncA, erm, eis, and embB”, which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. The genes in the first clause are a closed selection (the multiple genes are selected from this group, multiple implying at least 2) while the second clause lists the genes as an open selection (the genes include at least those listed, and may include more). As such, it is unclear what genes are actually required by the claim limitation.
Similarly, it is unclear whether the genes listed in parentheses are meant to provide an example of what genes encode each listed ribosome subunit , or if they are meant to list out all of the genes required by the claim limitation. This claim is therefore indefinite due to lack of clarity.
Claims 3-4 and 9 are also indefinite as they depend from claim 1, and do not resolve the issue of indefiniteness.
To resolve the above issues, it is recommended that the genes required to satisfy claim 1 are written out as a single list of genes (for example, “wherein the multiple genes include at least rpsA, rpsB, rpsC…” etc), with no parentheses/ribosome names or separate clause of other genes, so it is clear which genes are required. For the current office action, the claim is interpreted as requiring all of the genes listed in the final clause of claim 1 (instead of 2 or more out of the list in the previous clause), as this appears to be what the Applicant intends, given the remarks filed 03/23/2026 in response to the previous 103 rejection.
Claims 3-4 are further indefinite because a URL is used to define the metes and bounds of the claims, and the content within them is not recited in the claim.
Claim 9 is further indefinite as the terms of the recited formula are undefined, and it is similarly unclear how the “length of a loci” is defined.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 3-4 are also rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. For claims 3-4, specifying the URL locations where the database and software can be found does not further limit the structure of the system (comprising the database and software) of claim 1. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 1-4 and 9 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental processes, without significantly more.
The MPEP at MPEP 2106 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of matter?
(2A)(1) Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea?
(2A)(2) Do the claims recite additional elements that integrate the judicial exception into a practical application?
(2B) If the claims recite a judicial exception and do not integrate the judicial exception, do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?
With regard to step (1) (Are the claims directed to a process, machine, manufacture or composition of matter?): Yes. The claims are directed to one of the statutory classes. Claims 1-4 are directed to a machine product (a system comprising a sequencing device, database and software).
With regard to step (2A)(1) (Do the claims recite a judicially recognized exception?): Yes. Claims 1-4 recite the abstract ideas of processing data using mental steps and mathematical concepts, and observing the processed data. Claims that recite nothing more than abstract ideas, natural phenomena, or laws of nature are not eligible for patent protection (see MPEP 2106.04).
Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include but are not limited to:
Comparing sequence information of multiple genes with sequence information stored in a database (mental process; the human mind is capable of comparing sequencing data to data stored in a database; claim 1)
Selecting from known NTM stored in a database, species or subspecies of NTM having the most similar sequence information to the sequence information of NTM in a specimen (mental process; the human mind is capable of making a selection of data based on a similarity, and comparing data to determine a similarity; claim 1)
Mapping sequence reads from a specimen against the sequences of multiple genes (mental process; the human mind is capable of aligning reads of sequence data; claim 1)
Trimming mapped regions (mental process; the human mind is capable of trimming sequence data; claim 1)
Calculating an MLST score (mental process/mathematical concept; the human mind is capable of calculating a score using the formula of claim 9, performing a calculation is a mathematical process; claims 1, 9)
Filtering results by statistical significance in a Komonogoro-Smirnov test (mental process/mathematical concept; the human mind is capable of calculating statistical significance using a test such as Komonogoro-Smirnov, and performing a calculation is a mathematical process; claim 1)
Therefore, the claims recite elements that constitute one or more judicial exceptions.
With regard to step (2A)(2) (Do the claims recite additional elements that integrate the judicial exception into a practical application?): No. Claim 1 and its dependents recite the additional elements of a system comprising a sequencing device for acquiring information, a database for storing information, and a computing device comprising software for performing the abstract idea, and claims 3-4 further provide a location where the database and software can be accessed.
While the claims recite the additional element of acquiring data using a sequencer, and storing that data in a database, such steps that only amount to necessary data gathering without any technical details of how the data is obtained or stored that integrate the judicial exception, are insignificant extrasolution activities that do not add a meaningful limitation to the claims (see MPEP 2106.05(g)). As a result, the judicial exception is not integrated into a practical application. In addition, while claims recite elements related to the use of computers, they do not provide any specific details by which the system or computer performs or carries out the judicial exception listed in step (2A)(1), nor do they provide any details of how specific structures of the system are used to implement these functions. The judicial exception is therefore not integrated into a practical application because the generically recited computer elements do not add a meaningful limitation to the abstract idea, as they amount to simply implementing the abstract idea on a computer (see MPEP 2106.05(f)). Because the claims do not recite any additional elements that integrate the judicial exception into a practical application, the claims as a whole are directed to an abstract idea.
With regard to step (2B) (Do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?): No.
The claims recite an abstract idea with additional elements; however, these additional elements are general computer elements added to abstract ideas, and non-particular instructions to apply the abstract idea by linking it to a field of use or extrasolution activity (see MPEP 2106.05(f-h)). General computer elements used to perform an abstract idea do not provide an inventive concept, and similarly, non-particular instructions to gather or store data do not provide an inventive concept. Non-particular instructions to gather data using non-specific sequencing methods and store data are also considered well-understood, routine and conventional activities (see MPEP 2106.05(d), which indicates that limitations such as “Receiving or transmitting data over a network” from Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362, “Storing and retrieving information in memory” from Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, and “amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014) are recognized as conventional activities). The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As a result, the claims as a whole do not provide an inventive concept.
Response to Arguments – Rejections Under 35 USC § 101
In the remarks filed 03/23/2026, Applicant asserts that the claims are not directed to abstract ideas as the claims cannot be performed by the human mind (pg 13). However, according to MPEP 2106.04(a)(2) section III, the courts do not distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. The limitations outlined in the claims, despite requiring a computer, are still reciting mental processes, because the human mind, with or without a physical aid (such as computer elements) can still perform the claimed steps of comparing data, aligning sequences, trimming regions, calculating a score from a formula, and filtering results. Therefore the claims are still directed to abstract ideas.
Conclusion
No claim is allowable.
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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/M.C.L./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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