DETAILED ACTION
Applicant's response, filed 06/18/2025, 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 10/22/2021 is a National Stage entry of PCT/JP2020/017795, with an International Filing Date of 04/24/2020, and claims foreign priority to Japanese Application 2019-085839, filed 04/26/2019. The claims are therefore examined as filed on 04/26/2019, 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).
Election/Restrictions
Claims 4-9 and 41-43 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected inventions, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 6/18/2025.
Applicant’s election without traverse of claims 1-3 and 10 in the reply filed on 6/18/2025 is acknowledged.
Claim Status
Claims 1-10 and 41-43 are pending.
Claim 1 is objected to.
Claims 4-9 and 41-43 are withdrawn.
Claims 1-3 and 10 are directed to the elected invention.
Claims 1-3 and 10 are examined.
Claims 1-3 and 10 are rejected.
Information Disclosure Statement
The Information Disclosure Statements are in compliance with the provisions of 37 CFR 1.97. Accordingly, all references have been considered.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see pg 77 of the disclosure). 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 Objections
Claim 1 is objected to because of the following informalities:
In claim 1, the phrase “using the partial sequence information of sequence information on a single biological units” in step (C) should be corrected to “using the partial sequence information of sequence information on [[a]]the single biological units”
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.
Claim 2 is 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 2 recites the limitation "a step of adding, to the cluster, partial sequence information…corresponding to the cluster in a database" in line 2 of the claim. There is insufficient antecedent basis for this limitation in the claim, as there is no mention of a specific cluster, or specifically a cluster in a database, in claim 1, from which claim 2 depends. Claim 1 refers to a step of clustering, and using the partial sequence information in a database created independently from the clustering; so it is unclear what is meant by the cluster in a database. The claim is therefore indefinite due to lack of clarity.
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 1-3 and 10 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental processes and mathematical concepts, 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 1-3 and 10 are directed to a process (computer implemented method).software, which does not fall under one of the statutory classes.
With regard to step (2A)(1) (Do the claims recite a judicially recognized exception?): Yes. The claims recite the abstract ideas of processing data using mental steps and mathematical concepts. 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:
Clustering partial sequence information based on an organism lineage identification sequence (mental process/mathematical concept; the human mind is capable of matching partial sequences and clustering based on similarity; clustering is an algorithm using measures of similarity to group data; claim 1)
Creating a sequence information draft for single biological units by using partial sequence information and sequence information in a database (mental process; the human mind is capable of combining sequence data to create an information draft; claim 1)
Adding partial sequence information to a cluster based on information corresponding to the cluster in a database (mental process; the human mind is capable of adding data to a cluster based on a database; arranging data is a mental process, claim 2)
Removing partial sequence information comprising a sequence site found to have a large number of duplications (mental process; the human mind is capable of removing data based on a characteristic; arranging data is a mental process; claim 3)
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. The claims recite the additional element of “giving an instruction to a computer to execute processing” for performing the method of the claims. Claim 10 further recites the additional element of performing long-read sequencing to determine partial sequence information.
While claim 10 recites the additional element of acquiring data using long-read sequencing, a data gathering step without any technical details of how the data is obtained, in a way that is impacted by the judicial exception, is an insignificant extrasolution activity that does 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. Similarly, while the claims recite additional elements related to the use of computers, they do not provide any specific details by which the computer or processor performs or carries out the judicial exception listed in step (2A)(1), nor do they provide any details of how specific structures of the computer 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 produce data for analysis do not provide an inventive concept. Non-particular instructions to gather or output data using computer elements 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, and “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 are recognized as conventional activities). Further, gathering data using known sequencing techniques are also considered well-understood, routine and conventional activities (see MPEP 2106.05(d), which indicates that limitations such as “Analyzing DNA to provide sequence information or detect allelic variants”, Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546 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 also recognized as routine and 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.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim Rejection
Claims 1-2 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by HEDLUND 2014 “Impact of single-cell genomics and metagenomics on the emerging view of extremophile microbial dark matter” (provided on the IDS filed 07/18/2023).
Claim Interpretation and Scope and Contents of Prior Art
Claim 1 recites a method to execute processing of sequence information on a single biological unit, with a step of clustering partial sequence information of sequence information on a plurality of single biological units for each of the same lineages based on an organism lineage identification sequence; and a step of creating a sequence information draft for the single biological units by using the partial sequence information of sequence information on a single biological units and sequence information on the single biological units in a database created independently from the clustering.
With respect to these limitations, HEDLUND teaches a computer-based method of processing sequence information for single cells by clustering contigs by nucleotide composition into bins based on identification of phylogenetic anchor genes within a given bin (pg 867 par 1-2, Fig 1), and creating draft genomes from the clustered sequence information and from sequence information from metagenome datasets and reference genomes (Fig 1, pg 867 col 2).
Claim 2 recites the limitation wherein claim 1 also contains a step of adding, to the cluster, partial sequence information on the single biological units corresponding to the cluster in a database. With respect to this limitation, HEDLUND teaches adding sequencing information to clustered sequence data that correspond to a cluster in the metagenome contigs and reads (Fig 1).
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.
Claim Rejection
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over HEDLUND as applied to claims 1-2 above, and further in view of EBBERT 2016 “Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches.”
Claim Interpretation and Scope and Contents of Prior Art
Claim 3 recites the limitation wherein step (C) comprises removing a certain amount of partial sequence information comprising a sequence site found to have a large number of duplications to correct a bias in sequence reads.
With respect to this limitation, HEDLUND teaches overcoming amplification bias (pg 867 col 2), but does not specifically teach removing a certain amount of partial sequence information comprising a sequence site found to have a large number of duplications. However, EBBERT teaches different approaches for removing duplicates from sequencing data (Abstract).
Resolving Ordinary Skill in the Art and Obviousness Rationale
A teaching, suggestion, or motivation in the prior art would have led one of ordinary skill in the art to modify or combine the prior art to arrive at the claimed invention. Specifically, a person of ordinary skill in processing sequencing data would have been motivated to combine the teachings of HEDLUND with the teachings of EBBERT, in order to achieve the claimed invention, because duplicates are a common result of the target nucleotides being sequenced multiple times, and because numerous bioinformatic algorithms have been developed to
account for this (Abstract). A person of ordinary skill would reasonably expect success from combining these teachings, as both HEDLUND and teach EBBERT teach methods of analyzing sequencing data to minimize errors and bias. Therefore, the claims at issue would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention as there is both a reason to modify or combine the prior art, and a reasonable expectation of success (see MPEP 2143.02 (I)).
Claim Rejection
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over HEDLUND as applied to claims 1-2 above, and further in view of POLLARD 2018 “Long reads: their purpose and place.”
Claim Interpretation and Scope and Contents of Prior Art
Claim 10 recites the limitation wherein the partial sequence information is determined by long-read sequencing. HEDLUND does not specifically teach using long-read sequencing to gather their sequencing information. However, POLLARD teaches long-read sequencing technologies (Abstract) and further teaches that this technology has useful applications in single-cell sequencing (pg 239 col 1 par 3).
Resolving Ordinary Skill in the Art and Obviousness Rationale
A teaching, suggestion, or motivation in the prior art would have led one of ordinary skill in the art to modify or combine the prior art to arrive at the claimed invention. Specifically, a person of ordinary skill in sequencing would have been motivated to combine the teachings of HEDLUND with the teachings of POLLARD, in order to achieve the claimed invention, because long-read sequencing technology has useful applications in single-cell sequencing (pg 239 col 1 par 3) and can be used in sequencing large numbers of individuals and characterizing genomes at high resolution (Abstract). A person of ordinary skill would reasonably expect success from combining these teachings, as both HEDLUND and POLLARD teach sequencing methods and applications. Therefore, the claims at issue would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention as there is both a reason to modify or combine the prior art, and a reasonable expectation of success (see MPEP 2143.02 (I)).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY C LEVERETT whose telephone number is (571)272-5494. The examiner can normally be reached 8:00am - 5:00pm M-Th.
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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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/M.C.L./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687