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 .
It is noted that the Examiner of record has changed herein due to an Application transfer.
Election/Restrictions
The restriction requirement set forth in the Office action mailed 03 Feb. 2026 has been withdrawn because, after further consideration of the claims, the claims do no lack unity of invention.
Applicant’s election without traverse of Group II, claims 9-14 in the reply filed on 30 March 2026 is acknowledged.
Claims 1-8 and 15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 30 March 2026.
Status of Claims
Claims 1-15 are pending.
Claims 1-8 and 15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 9-14 are rejected.
Priority
Applicant’s claim for the benefit of a prior-filed application, PCT/JP2021/018618 filed 17 May 2021, under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Accordingly, the effective filing date of the claimed invention is 17 May 2021.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on 18 Oct. 2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the list of cited references was considered in full by the examiner.
Drawings
The drawings filed 18 Oct. 2023 are objected to because:
FIG. 1-11 are objected to for failing to comply with 37 CFR 1.84(u)(2), which states numbers and letters identifying the views must be simple and clear and must not be used in association with brackets, circles, or inverted commas. The view numbers should be amended to remove the brackets “[…]”; and
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they do not include the following reference sign(s) mentioned in the description:
#S302-1, S302-2, and S302-3 in para. [0100]-[0102] of the specification as published; and
#S403-1, S403-2, and S403-2 in para. [0128]-[0131] of the specification as published.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
References to Applicant’s specification throughout the Office action are made with respect to the published version of the application.
The replacement abstract received 18 Oct. 2023 has been entered.
Claim Interpretation - 35 USC § 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 limitations are:
“A gene analyzer for analyzing a base sequence…” in claim 9, and dependent claims 10-14
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.
In cases involving a special purpose computer-implemented means-plus-function limitation, the Federal Circuit has consistently required that the structure be more than simply a general purpose computer or microprocessor and that the specification must disclose an algorithm for performing the claimed function. See, e.g., Noah Systems Inc. v. Intuit Inc., 675 F.3d 1302, 1312, 102 USPQ2d 1410, 1417 (Fed. Cir. 2012); Aristocrat, 521 F.3d at 1333, 86 USPQ2d at 1239. The structure for the “gene analyzer for analyzing…” is disclosed as the following:
the gene analyzer is described in Applicant’s specification at FIG. 1 and [0035]-[0041], and comprises an electrophoresis device and a data analyzer, wherein the data analyzer includes a control device, connection interface, and storage device. Applicant’s specification at para. [0037]-[0039] discloses that the control device is a central processing unit (CPU) and graphics processing unit (GPU), the storage device is a memory, and the connection interface is an interface connecting an input and output device or an interface connected to an external device via a network. Accordingly, the data analyzer is a computer comprising a CPU, GPU, memory, and interface. Therefore, the structure for the gene analyzer is interpreted to be an electrophoresis device and a computer comprising a CPU, GPU, memory, and interface (and equivalents thereof).
the algorithm for the gene analyzer analyzing a base sequence of sample is recited in the claims, and similarly in Applicant’s specification at para. [0011].
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 Interpretation
Claim 9 recites “the gene analyzer managing an observation environment and mobility correction data for correcting a position…”. The limitation “for correcting a position” is interpreted as an intended use of the gene analyzer managing an observation environment and mobility correction. Furthermore, Applicant’s specification at para. [061]-[0062] discloses characteristic data is managed as a function, and electrophoretic characteristic information manages characteristic data representing a relationship between variables. Accordingly, the term “managing” is interpreted to encompass analyzing or associating information.
Claim Rejections - 35 USC § 112(b)
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.
Claims 9-14 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 9, and claims dependent therefrom, are indefinite for recitation of “A gene analyzer…the gene analyzer managing an observation environment and mobility correction amount data…and executing the following processes including: a first process…; a second process…; and a third process…”.A single claim which claims both an apparatus and the method steps of using the apparatus is indefinite under 35 U.S.C. 112(b) . See In re Katz Interactive Call Processing Patent Litigation, 639 F.3d 1303, 1318, 97 USPQ2d 1737, 1748-49 (Fed. Cir. 2011). See MPEP 2173.05(p). In the instant case, claim 9 recites a system of “A gene analyzer”, and then recites method steps of using the apparatus of “managing” and “executing”, which renders the claim indefinite. Specifically, it is not clear if infringement occurs when one creates a system that is configured to manage and/or execute as claimed, or if infringement occurs when the system actively manages and/or executes. It is further unclear if “the gene analyzer managing an observation environment and mobility correction amount data” is merely expressing the intended use of the gene analyzer (given this limitation appears in the preamble of the claim), or if the gene analyzer is also intended to be configured to execute the managing. Clarification is requested via claim amendment. For purpose of examination, claim 9 is interpreted to meant that the gene analyzer is configured to perform the managing, first, second, and third processes. If Applicant agrees with this interpretation, claim 9 can be amended to recite “A gene analyzer…by electrophoresing the sample, wherein the gene analyzer is configured to: manage an observation environment…, and execute the following processes including: a first process…; a second process….; and a third process…”’ dependent claims should be amended to correct grammar as necessary.
Claim 9, and claims dependent therefrom, are indefinite for recitation of “the observation environment different from a first observation environment” in lines 2-3 of the “a first process” limitation. There is insufficient antecedent basis for this limitation in the claim because claim 9 previously recites “an observation environment”, but does not require that the observation environment is different from a first observation environment. See MPEP 2173.05(e), stating a claim which refers to "said aluminum lever," but recites only "a lever" earlier in the claim, is indefinite because it is uncertain as to the lever to which reference is made. Clarification is requested via claim amendment. “the mobility correction amount data associated with the observation environment different from the first observation environment…” and is indefinite for the same reasons. For purpose of examination, the limitation will be interpreted to refer to “the observation environment”.
Claim 9, and claims dependent therefrom, are indefinite for recitation of “the position in the time direction of the time-series data of the signal intensities of the plurality of bases” in lines 1-3 of the “second process” limitation. Claim 9 previously recites “time-series data of the signal intensities of the plurality of bases” in lines 6-7 of the claim and “receives time-series data of signal intensities of signal intensities of a plurality of bases acquired…in the first observation environment” in lines 4-6 of the “first process” limitation. It is not clear if the “the time-series data of the signal intensities of the plurality” in lines 1-3 of the “second process” limitation is referring to the time-series data in lines 6-7 of the claims or the time-series data in the “second process” limitation. Clarification is requested via claim amendment.
Claim 9, and claims dependent therefrom, are indefinite for recitation of “the signal intensities of the plurality of bases” in the last two lines of the claim. As discussed above, claim 9 previously recites “time-series data of the signal intensities of the plurality of bases” in lines 6-7 of the claim and “receives time-series data of signal intensities of signal intensities of a plurality of bases acquired by electrophoresing the sample in the first observation environment” in lines 4-6 of the “first process” limitation. As a result, it is not clear which signal intensities are being referenced. Clarification is requested via claim amendment.
Claim 10 is indefinite for recitation of “the base” in line 4. Claim 9, from which claim 10 depends, recites a “plurality of bases” in each of “the gene analyzer” limitation and the “first process limitation”, and therefore it is not clear which base is being referenced. For purpose of examination, the limitation is interpreted to mean “a base”.
Claim 10 is indefinite for recitation of “the electrophoretic characteristic data associated with the first observation environment” and “the electrophoretic characteristic data associated with the observation environment different from the first observation environment” in the “a scale is calculated” limitation. There is insufficient antecedent basis for these limitations in the claim, because claim 10 previously recites “electrophoretic characteristic data representing…”, but does not recite electrophoretic characteristic data associated with each of the observation environment and the first environment. As a result, it is further not clear if this is the same “electrophoretic characteristic data” for each environment or if these are two separate electrophoretic characteristic data (one for each environment).
Claim 12 is indefinite for recitation of “when the overall difference…is large”. The term “large” in is a relative term which renders the claim indefinite. The term “large” 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. For purpose of examination, the claim will be interpreted to mean when there is a difference, then the automatic mobility correction amount data is replaced by the default data.
Claims 13 is indefinite for recitation of “where the difference…is large”. The term “large” 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. For purpose of examination, the limitation is interpreted to mean where the difference is identified, the identified portion is replaced by the default mobility data.
Claim 14 is indefinite for recitation of “…where the difference…is large and a variation is large is identified…”. The term “large” 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. For purpose of examination, the claim is interpreted to mean where there is a difference between the automatic mobility data and the default mobility data and a variation is identified, the identified portion is corrected.
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 9-14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claim 9 being representative) is directed to a system. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claim 9 recites the following steps which fall under the mathematical concepts and/or mental processes groupings of abstract ideas:
managing an observation environment and mobility correction amount data for correcting a position in a time direction of the time-series data of the signal intensities of the plurality of bases in association with each other;
a first process of scaling the mobility correction amount data associated with the observation environment different from a first observation environment to generate default mobility correction amount data when the gene analyzer receives time-series data of signal intensities of a plurality of bases acquired by electrophoresing the sample in the first observation environment;
a second process of correcting the position in the time direction of the time-series data of the signal intensities of the plurality of bases using an optimization algorithm of a mobility correction amount and the default mobility correction amount data; and
a third process of identifying the base sequence of the sample using the corrected time-series data of the signal intensities of the plurality of bases.
The identified claim limitations falls the group of abstract ideas of mental processes for the following reasons. In this case, managing an observation environment and mobility correction amount data encompasses analyzing observation environment and mobility correction data and associating or organizing the information (see claim interpretation above), which can be practically performed in the mind. Furthermore, scaling the mobility correction amount data associated with the observation environment to generate default mobility correction amount data encompasses multiplying the mobility correction amount data by a number (e.g. a scaling factor) to calculate the default data, wherein multiplication can be practically performed in the human mind. Correcting a position in the time direction of time-series data of the signal intensities using an optimization algorithm of a mobility correction amount and the default mobility correction amount data can be practically performed in the mind for the following reasons. Using an optimization algorithm to correct a position encompasses inputting the default mobility data as the initial value of optimization, sliding a block over time-series data, searching for a mobility correction amount that minimizes an overlap of waveforms of bases in the block, and repeating the process, as discussed in Applicant’s specification at para. [0107]-[0109] and also discussed in claim 11. The step of identifying the base sequence using the corrected time-series data of the signal intensities of the plurality of bases can be practically performed in the mind by analyzing the time-series data of the electrophoresis to identify a peak corresponding to a base. That is, other than reciting these limitations are carried out by a gene analyzer, nothing in the claims precludes the steps from being practically performed in the mind. See MPEP 2106.04(a)(2) III.
The limitations of scaling the mobility correction amount data associated with the observation environment to generate default mobility correction amount data and using an optimization algorithm of a mobility correction amount and the default mobility correction amount data further recite a mathematical concept. Scaling data to generate default data amounts to a textual equivalent to performing multiplication, as explained above, and thus recites a mathematical calculation. Similarly, using an optimization algorithm in light of Applicant’s specification requires minimizing overlap of waveforms in each block of data, which amounts to a textual equivalent to performing subtraction. See MPEP 2106.04(a)(2) I.
Dependent claims 10-14 further recite an abstract idea. Dependent claim 10 further recites the mathematical concept of a relationship between an observation environment and electrophoretic characteristic data and calculating a scale using the electrophoretic characteristic data associated with two observation environments, and scaling the mobility correction amount data based on the scale. Dependent claim 11 further recites the mental process and mathematical concept of generating automatic mobility correction data based on the optimization algorithm, and correcting the automatic mobility correction data based on a difference between the automatic and default mobility correction amount data. Dependent claim 12 further recites the mathematical concept and mental process of determining an overall difference between the automatic and default mobility correction data, and the mental process replacing/substituting the automatic data with the default data. Dependent claim 13 further recites the mental process and mathematical concept of identifying a difference between the automatic and default mobility correction amount data, and the mental process of replacing the identified portion by the default data. Dependent claim 14 further recites the mental process and mathematical concept of identifying a portion with a large difference between the automatic and default data and a large variation, and correcting the identified portion such that a difference from the default data decreases. Therefore, claims 9-14 recite an abstract idea. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Dependent claims 10-14 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements of claim 9 include.
a gene analyzer (interpreted as an electrophoresis device and a computer comprising a CPU, GPU, memory, and interface (and equivalents thereof) under 35 U.S.C. 112(f) above).
The gene analyzer encompasses a CPU, GPU, memory and interface (i.e. a generic computer), which is only used as a tool to carry out the abstract idea identified above. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit).
The gene analyzer further includes an electrophoresis device. MPEP 2106.05(b) explains that integral use of a machine to achieve performance of a method may integrate the recited judicial exception into a practical application or provide significantly more, in contrast to where the machine is merely an object on which the method operates, which does not integrate the exception into a practical application or provide significantly more. See CyberSource v. Retail Decisions, 654 F.3d 1366, 1370, 99 USPQ2d 1690, 1694 (Fed. Cir. 2011). In the instant case, the electrophoresis device is not relied upon or used by the judicial exception in any way such that the judicial exception identified above (resulting in the identification of a base sequence) is integrated into a practical application. Instead, the electrophoresis device is merely part of the apparatus used to implement the above judicial exception, and thus amounts to mere instructions to apply the exception as discussed above.
Therefore, the additionally recited elements merely invoke a computer as a tool to apply the exception and, as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 9-14 are directed to an abstract idea. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception.
Dependent claims 10-14 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements of claim 9 include.
a gene analyzer (interpreted as an electrophoresis device and a computer comprising a CPU, GPU, memory, and interface (and equivalents thereof) under 35 U.S.C. 112(f) above).
The gene analyzer encompasses a CPU, GPU, memory and interface (i.e. a conventional computer), which is only used as a tool to carry out the abstract idea identified above. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit).
Regarding the electrophoresis device, this additional element is well-understood, routine, and conventional. This position is supported by Meldrum (Automation for Genomics, Part Two: Sequencers, Microarrays, and Future Trends, 2000, Genome Research, 10, pg. 1288-1303). Meldrum reviews automation in genomics, including sequencers (Abstract) and discloses various commercially available electrophoresis systems (pg. 1291, col. 2, para. 4 to pg. 1292, col. 1, para. 7; pg. 1297, col. 2, para. 3). Meldrum discloses various online sequencing systems for electrophoresis (pg. 1921, col. 1, para. 2-3) and that the sequencing instruments are useless if it is not possible to obtain the information we are interested in, and thus various software tools are developed for processing raw data (pg. 1291, col. 2, para. 1).
Therefore, taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
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.
Claims 9-10 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Yokoyama (2020).
Cited reference: Yokoyama et al., WO 2020179405 A1; effectively filed 14 Feb. 2020 and published 10 Sept. 2020
Regarding claim 9, Yokoyama discloses a genotype analyzer, wherein the genotype analyzer comprises a data analyzer including a control unit processor and user interface (i.e. cpu and gpu) and electrophoresis apparatus ([001]; [0020]), and the genotype analyzer is configured to perform the following steps:
Yokoyama discloses the control unit of the genotype analyzer includes a mobility model management unit that includes environment information receiving unit and mobility prediction unit (i.e. managing an observation environment and mobility correction amount data) ([0021]). Yokoyama discloses the mobility management unit is for correcting lengths in time-series data of fluorescence intensity values for base calling in a sequence ([009]; [0046], e.g. result of electrophoresis is waveform; [0055]; [0062]).
Regarding the first process, Yokoyama discloses a mobility prediction model is generated in advanced by the device manufacturer (i.e. mobility correction amount data associated with the observation environment)([0078]), and further that the mobility prediction model can be updated to reflect migration characteristics of a new allele ladder (i.e. in the first environment, different from the original observation environment) in the prediction of the base length of the allele ([00127]; [0078]; [00105]; [00122])). Yokoyama discloses the prediction model can be a linear regression model ([00118]), and updating the model comprises updating learning a new parameter set having the best evaluation index to generate updated correction lengths (i.e. default mobility correction data) ([00122]). Updating parameters of a linear regression model for predicting correction length demonstrates scaling mobility correction amount data associated with the observation environment to generate default mobility correction amount data. Yokoyama further discloses this updating process is performed when electrophoresis data for a new allelic ladder is performed (i.e. when the gene analyzer receives time-series data of signal intensities of bases acquired by electrophoresing the sample in the first environment). ([00125]-[00127], e.g. updating prediction model to reflect migration characteristics of new allele ladder). Yokoyama discloses storing correction lengths (i.e. the default mobility correction amount) output by the updated prediction model with the original correction lengths ([0089]-[0090]; FIG. 16).
Regarding the second process, Yokoyama discloses using the newly updated prediction model for allele calling for the actual sample ([00124]). Yokoyama discloses using the prediction model predicts the correction length for the standard base length of each allele ([0076]-[0077]), and the correction length is added to the standard base length of the allele as output (i.e. correcting the position in the time direction of the time-series data of the signal intensities) ([0098]; [0071] and FIG. 15; e.g. see peak shift in time-series data; FIG. 17). Yokoyama further discloses correcting the position involves re-executing of the length correction value prediction with a prediction model when allele identification fails until a detected allele is within a tolerance range (i.e. the length correction uses an optimization algorithm of a mobility correction amount and the default mobility correction data))([0096]-[0098]).
Regarding the third process, Yokoyama discloses identifying an allele (i.e. base sequence) of the sample using the corrected length data (i.e. the corrected time-series data) ([0094]).
Regarding claim 10, Yokoyama discloses the mobility management model unit manages observed environment information, a prediction model storage unit, and mobility prediction unit ([0021]; [0073]), wherein the prediction model represents a relationship between a set of vector v of a value of environmental information, a base length p (i.e. depending on electrophoresis), and a correction length (i.e. migration time) at the base length p (i.e. a relationship between a position of the base depending on electrophoresis and migration time/length) ([0077]).
Yokoyama further discloses, regarding the first process, the scale (i.e. updated model parameter) is calculated using electrophoretic time-series data when an allelic ladder is newly electrophoresed and data of new conditions may be added to the training data (e.g. the original training data plus additional added training data is used in the model, which shows characteristic data associated with the first observation environment and observation environment) ([00123]; [00125]).
Yokoyama further discloses the correction length prediction for the new ladder (i.e. mobility correction amount data for the first environment) is predicted using the updated model (i.e. based on the scale) ([00125]-[00127]; [0089]-[0090]; FIG. 16, e.g. updated correction lengths stored).
Therefore, Yokoyama anticipates the claimed invention.
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 11-14 are rejected under 35 U.S.C. 103 as being unpatentable over Yokoyama (2020) in view of Kawaguchi (2019).
Cited references:
Yokoyama et al., WO 2020179405 A1; published 10 Sept. 2020; and
Kawaguchi et al., US 2019/0032126 A1; cited on IDS filed 18 Oct. 2023.
Regarding claim 11, Yokoyama discloses a genotype analyzer, wherein the genotype analyzer comprises a data analyzer including a control unit processor and user interface (i.e. cpu and gpu) and electrophoresis apparatus ([001]; [0020]), and the genotype analyzer is configured to perform the following steps:
Yokoyama discloses the control unit of the genotype analyzer includes a mobility model management unit that includes environment information receiving unit and mobility prediction unit (i.e. managing an observation environment and mobility correction amount data) ([0021]). Yokoyama discloses the mobility management unit is for correcting lengths in time-series data of fluorescence intensity values for base calling in a sequence ([009]; [0046], e.g. result of electrophoresis is waveform; [0055]; [0062]).
Regarding the first process, Yokoyama discloses a mobility prediction model is generated in advanced by the device manufacturer (i.e. mobility correction amount data associated with the observation environment)([0078]), and further that the mobility prediction model can be updated to reflect migration characteristics of a new allele ladder (i.e. in the first environment, different from the original observation environment) in the prediction of the base length of the allele ([00127]; [0078]; [00105]; [00122])). Yokoyama discloses the prediction model can be a linear regression model ([00118]), and updating the model comprises updating learning a new parameter set having the best evaluation index to generate updated correction lengths (i.e. default mobility correction data) ([00122]). Updating parameters of a linear regression model for predicting correction length demonstrates scaling mobility correction amount data associated with the observation environment to generate default mobility correction amount data. Yokoyama further discloses this updating process is performed when electrophoresis data for a new allelic ladder is performed (i.e. when the gene analyzer receives time-series data of signal intensities of bases acquired by electrophoresing the sample in the first environment). ([00125]-[00127], e.g. updating prediction model to reflect migration characteristics of new allele ladder). Yokoyama discloses storing correction lengths (i.e. the default mobility correction amount) output by the updated prediction model with the original correction lengths ([0089]-[0090]; FIG. 16).
Regarding the second process, Yokoyama discloses using the newly updated prediction model for allele calling for the actual sample ([00124]). Yokoyama discloses using the prediction model predicts the correction length for the standard base length of each allele ([0076]-[0077]), and the correction length is added to the standard base length of the allele as output (i.e. correcting the position in the time direction of the time-series data of the signal intensities) ([0098]; [0071] and FIG. 15; e.g. see peak shift in time-series data; FIG. 17). Yokoyama further discloses correcting the position involves re-executing of the length correction value prediction with a prediction model when allele identification fails until a detected allele is within a tolerance range (i.e. the length correction uses an optimization algorithm of a mobility correction amount and the default mobility correction data))([0096]-[0098]).
Regarding the third process, Yokoyama discloses identifying an allele (i.e. base sequence) of the sample using the corrected length data (i.e. the corrected time-series data) ([0094]).
Further regarding claim 11, Yokoyama discloses generating additional correction length predictions using a trained candidate predictive model (i.e. automatic mobility correction amount data based on the optimization algorithm) ([0096]).
Yokoyama further discloses that when the default mobility correction amount data (i.e. the original correction length prediction) fails at detecting an allele, the additional correction length is predicted and is applied if allele identification using the additional correction length is successful ([0096]-[0098]).
Further regarding claims 11-14, Yokoyama does not disclose the following:
Regarding claim 11, While Yokoyama does disclose correcting mobility correction amount data (i.e. the predicted correction lengths) by generating a new correction length using the predictive model, Yokoyama does not disclose correcting the automatic mobility correction amount data based on a difference between the automatic mobility correction amount data and the default mobility correction amount data.
Regarding claim 12, Yokoyama does not disclose that when the overall difference between the automatic mobility correction amount data and the default mobility correction amount data is large, the automatic mobility correction amount data is replaced by the default mobility correction amount data.
Regarding claim 13, Yokoyama does not disclose a portion where the difference between the automatic mobility correction amount data and the default mobility correction amount data is large is identified, and the identified portion is replaced by the default mobility correction amount data.
Regarding claim 14, Yokoyama does not disclose a portion where the difference between the automatic mobility correction amount data and the default mobility correction amount data is large and a variation is large is identified, and the identified portion is corrected such that a difference from the default mobility correction amount data decreases.
However, these limitations were prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, as shown by Kawaguchi.
Regarding claim 11, Kawaguchi discloses a method for base sequencing determination from capillary array electrophoresis (Abstract), including a mobility correction unit that outputs a mobility correction signal obtained by mobility correction of a time-series signal of a wavelength spectrum for each base ([0008]). Kawaguchi discloses the mobility correction comprises determining a “mobility correction in-progress signal” (i.e. a default mobility correction amount) and calculating a peak shift d’(G), d’(A), d’(T)’, and d’(C) for each nucleotide G, A, T, and C respectively (i.e. corresponding to the generated automatic mobility correction amounts) ([0049]-[0052]). Kawaguchi then either (a) shifts a channel corresponding to G of the mobility correction in-progress signal rearward by d’(G), and similarly for A, T, and C, or (2) if any of d’(G), d’(A), d’(T), and d’(C) is sufficiently small, then the mobility correction in-progress signal is substituted into the mobility-corrected signal (i.e. the mobility correction is corrected if there is a difference between the automatic mobility correction amount and the default mobility correction amount)([0052]-[0054]).
Regarding claims 12-13, Kawaguchi discloses that if any of d’(G), d’(A), d’(T), and d’(C) is sufficiently small (i.e. a portion where there is a difference between d(G)-d’(G), or for A, T, and C, based on the equations in [0051]), then the mobility correction in-progress signal is substituted into the mobility-corrected signal (i.e. the automatic mobility correction amount data is replaced by the default mobility correction amount data ([0052]-[0054]).
Regarding claim 14, Kawaguchi discloses when identifying d’(G), d’(A), d’(T), and d’(C) is sufficiently small (i.e. a portion where there is a difference between d(G)-d’(G) and a variation between d(A) and d’(A) based on the equations in [0051]), then the mobility correction in-progress signal is substituted into the mobility-corrected signal (i.e. the automatic mobility correction amount data is replaced by the default mobility correction amount data ([0052]-[0054]).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the system of Yokoyama to have corrected the automatic mobility correction by replacing the automatic mobility data with the default mobility data when a difference and variation between the automatic mobility correction amount data and the default mobility correction amount data is identified, as shown by Kawaguchi as applied above, thus arriving at the inventions of claims 11-14. One of ordinary skill in the art would have been motivated to combine the methods of Yokoyama and Kawagachi in order to only correct peak signals where mobility shifts are detected, as shown by Kawagachi ([0052]-[0053]). This modification would have had a reasonable expectation of success given both Yokoyama and Kawagachi correct mobility shifts in time-series signal data, such that the correction process of Kawagachi applies to the method of Yokoyama.
Therefore, the invention is prima facie obvious.
Citation of Pertinent Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Karabiber et al., QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis, 2013, RNA, 19, pg. 63-73.
Karabiber (2013) discloses a normalization process (scaling) in experimentally derived data, which have experimental biases that stem from variations concentrations of chemicals used in experiments, and in order to compare experiments, such biases need to be removed, which is through statistical normalization (pg. 4, para. 1). Karabiber discloses a method for analyzing time-varying signals from capillary electrophoresis for use in base calling (Abstract; Figure 2), Karabiber discloses a graphical user interface that manages electrophoresis result information, including various channel observations (i.e. observation environment) and mobility shifts of time-series data of signal intensities regarding the mobility of nucleic acid (i.e. mobility correction amount data) (pg. 65, col. 1, para. 4; Figure 3A-C, e.g. see Channel types Rx, BG, etc. and “Split Channels”).
Conclusion
No claims are allowed.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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