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 .
Office Action Outline
Claim Status
Pending:
1-4, 6-10, and 13-23
Withdrawn:
6-7 and 9-10
Canceled:
5 and 11-12
Examined:
1-4, 8, and 13-23
Objected to:
none
Independent:
1
Amended:
1 and 2
New:
18-23
Allowable:
none
Rejections applied
Abbreviations
X
112/b Indefiniteness
PHOSITA
"a Person Having Ordinary Skill In The Art before the effective filing date of the claimed invention"
112/b "Means for"
BRI
Broadest Reasonable Interpretation
X
112/a Enablement,
Written description
CRM
"Computer-Readable Media" and equivalent language
112 Other
IDS
Information Disclosure Statement
102, 103
JE
Judicial Exception
X
101 JE(s)
112/a
35 USC 112(a) and similarly for 112/b, etc.
101 Other
N:N
page:line
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed in the 02/17/2022 filing receipt, this application claims priority to as early as 03/25/2021, the filing date of parent Japanese application JP2021-050981. At this point in examination, all claims have been interpreted as being accorded this priority date.
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. See paper entered 03/17/2022.
Overview of Withdrawal/Revision of Objections/Rejections
In view of the amendment and remarks received 11/17/2025:
• The objection to claim 1 is withdrawn.
• New 112(a) rejections are applied below.
• The 112(b) rejection is withdrawn, and new 112(b) rejections are applied below.
• The 101 rejection is maintained with revision.
• The 103 rejection is withdrawn for the following reasons: The claims are free of the analogous art at least because close art, e.g., Karger, (Nucleic acids research, 19(18), pp.4955-4962 (1991); cited on the 09/07/2023 form PTO-892), in view of Bromba, (Analytical Chemistry, vol. 55(4), pages 648-653 (1983); cited on the 09/07/2023 form PTO-892), in view of Perrin, (Analytical Chemistry, vol. 73(20), pages 4903-4917 (2011); cited on the 05/13/2024 form PTO-892), in view of Stewart, (Systems and computational biology bioinformatics and computational modeling, pages 311-333 (2011); cited on the 09/07/2023 form PTO-892), in view of Zhang, (PLoS One, vol. 8(1): e54510, pages 1-10 (2013); cited on the 05/13/2024 form PTO-892), either individually or in obvious combination, does not teach all limitations of the claimed invention, specifically, e.g., the claim 1 limitations "wherein the correcting results in reducing noise by at least 30% while maintaining peak intensity within the predetermined allowable range," "calculating a minimum cutoff frequency at which a rate of a decrease over time in the peak intensity of the specific wavelength data falls within a predetermined allowable range, wherein the calculating includes using the initial cutoff frequency as a starting value and repeating the filtering processing while lowering the cutoff frequency," and "acquiring, as an initial cutoff frequency, a maximum frequency at which power of the sample-derived component is higher than power of a white noise level in a power spectrum of the specific wavelength data" are not taught in the prior art. Applicant's 11/17/2025 remarks at pp.13-14 support the withdrawal of the 103 rejection..
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 22 and 23 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 22 recites "the method provides an increase in dynamic range of at least 10% for detection of low-abundance nucleic acid sequences compared to unfiltered electrophoresis data." Instant Specification paragraphs [0002-0003] discuss an abundance ratio with regard to a gene mutation, while dynamic range with regards to the abundance ratio is discussed at [0003], however, [0002-0003] do not show specific support for "the method provides an increase in dynamic range of at least 10% for detection of low-abundance nucleic acid sequences compared to unfiltered electrophoresis data" of claim 22. There is no support for "the method provides an increase in dynamic range of at least 10% for detection of low-abundance nucleic acid sequences compared to unfiltered electrophoresis data" within the instant Specification, nor the parent disclosure (JP2021-050981). Therefore the recitations introduce new matter. The rejection may be overcome, e.g., by clarifying on the record where support can be found and how that support relates to the recitations, or by amending claim 22 appropriately such that it does not recite new matter.
Claim 23 recites "a charged-coupled device (CCD) detector or photomultiplier tube (PMT) detector." Instant Specification paragraph [0029] discloses a "photodetector," however, [0029] does not show specific support for "a charged-coupled device (CCD) detector or photomultiplier tube (PMT) detector" of claim 23. There is no support for "a charged-coupled device (CCD) detector or photomultiplier tube (PMT) detector" within the instant Specification, nor the parent (JP2021-050981). Therefore the recitations introduce new matter. The rejection may be overcome, e.g., by clarifying on the record where support can be found and how that support relates to the recitations, or by amending claim 23 appropriately such that it does not recite new matter.
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.
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 1-4, 8, and 13-23 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. Claims depending from rejected claims are rejected similarly, unless otherwise noted, and any amendments in response to the following rejections should be applied throughout the claims, as appropriate.
In the claim 1 "calculating..." step, the relationships are unclear between the variously recited instances of "frequency," i.e. "a minimum cutoff frequency" (beginning of step), "the initial cutoff frequency" (middle) and then simply "lowering the cutoff frequency" (end). It is unclear whether "lowering the cutoff frequency" refers to the "minimum cutoff frequency" or the "first cutoff frequency."
In claim 8, the recited "the first cutoff frequency" requires but lacks clear antecedent. If this recitation refers to a previously instantiated instance, then it is not clear which instance that is. If this recitation instantiates this claim element, this is not clear. This rejection might be overcome by for example amending to recite the article "a" instead of "the."
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, 8, and 13-23 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
MPEP 2106 details the following framework to analyze Subject Matter Eligibility:
• Step 1: Are the claims directed to a category of statutory subject matter (a process, machine, manufacture, or composition of matter)? (see MPEP § 2106.03)
• Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. an abstract idea, a law of nature, or a natural phenomenon? (see MPEP § 2106.04(a)). Note, the MPEP at 2106.04(a)(2) & 2106.04(b) further explains that abstract ideas and laws of nature are defined as:
mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
laws of nature and natural phenomena are naturally occurring principles/ relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature.
• Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application? (see MPEP § 2106.04(d))
• Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept? (see MPEP § 2106.05).
Step 1:
Claims 1-4, 8, and 13-23 are directed to a 101 process, here a method, and therefore to a category of statutory subject matter. (Step 1: Yes.)
Step 2A, Prong One:
The claims are found to recite abstract ideas in the form of mental processes and mathematical concepts as follows:
Independent claim 1 recites mental processes and mathematical processes of: determining whether each peak is a sample-derived peak or a spike; performing the correction of the data; selecting specific wavelength data; performing filtering processing using a low pass filter; acquiring a maximum frequency at which the power of the sample derived component is higher than the power of the noise level; performing smoothing processing on the power spectrum; comparing peak intensities; calculating a minimum cutoff frequency...using the initial cutoff frequency as a starting value of the cutoff frequency and repeating the filtering processing while lowering cutoff frequency; correcting the first data; determining that the specific wavelength is one of data of a measurement wavelength lacking a spike or data of another measurement wavelength in which a peak value of the spike is determined to fall within a same range as a peak value of the sample-derived component; determining a mutation occurrence position; calculating a peak intensity change rate over time for each of the peaks; determining that the peak at which an absolute value of the peak intensity change rate over time is greater than a predetermined threshold at one or more measurement wavelengths is the spike, where the predetermined threshold exceeds an upper limit of the predetermined allowable range; where correcting first data or color call data includes reducing noise by 30% while maintaining peak intensity in the allowable range; improving sensitivity of detection based on the correction.
Claim 2 further limits the predetermined allowable range and how peak intensity is represented. Claims 3 and 4 further limit how peak intensity is represented. Claim 8 further limits the first data and the abstract ideas of correcting by performing filtering processing. Claim 13 further limits the predetermined allowable range. Claim 16 recites a mental process of determining of the specific wavelength data determines that the data of the measurement wavelength lacks the spike. Claim 17 recites a mental process of determining the specific wavelength data determines that the data of the measurement wavelength is the data of the other measurement wavelength. Claims 18-22 further limit the abstract ideas, respectively, of calculating the peak intensity change rate, performing filtering processing, acquiring the initial cutoff frequency, improving sensitivity, and repeating the filtering processing.
Step 2A Prong One Summary: The claims recite mental processes and mathematical concepts. When considering the broadest reasonable interpretation (BRI) of the claims, the mental processes recited in independent claim 1 (e.g., "selecting specific wavelength data"; "performing filtering processing"; "comparing peak intensities", etc.) are directed to processes that may be performed in the human mind, or with pen and paper, as there are no particular limitations recited in claim 1 which would prevent the mental processes from being performed in the human mind or with pen and paper. The claims recite inherent mathematical processes in e.g., performing filtering, calculating rates of peak intensities, and correcting data. Calculations, while details of which are not explicitly shown, are discussed throughout the Specification, e.g., at [0076-0079], [0083-0085], [0125-0127], etc. Such analysis performed mentally, or with paper and pencil, may take considerable time and effort, and although a general-purpose computer can perform these calculations at a rate and accuracy that can far exceed the mental performance of a skilled artisan, the nature of the activity is essentially the same, and therefore constitutes an abstract idea. Therefore, the claims recite elements that constitute a judicial exception in the form of an abstract idea. (Step 2A, Prong One: Yes.)
Step 2A, Prong Two:
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs). Here at Step 2A, Prong Two, any remaining steps and/or elements not identified as JEs are therefore in addition to the identified JE(s), and are considered additional elements. Because the claims have been interpreted as being directed to judicial exceptions (abstract ideas in this instance) then Step 2A, Prong Two provides that the claims be examined further to determine whether the judicial exception is integrated into a practical application [see MPEP § 2106.04(d)]. A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception.
MPEP § 2106.04(d)(I) lists the following five example considerations for evaluating whether a judicial exception is integrated into a practical application:
(1) An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a).
(2) Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2).
(3) Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b).
(4) Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c).
(5) Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
The claims recite additional elements as follows:
Additional elements of data gathering: Independent claim 1 recites the additional element of "acquiring first data by performing electrophoresis of a labeled nucleic acid sample". Claim 23 recites an additional element of capillary electrophoresis with fluorescent detection. Data gathering steps are additional elements which perform functions of inputting, collecting, and outputting the data needed to carry out the abstract idea. These steps are considered insignificant extra-solution activity, and are not sufficient to integrate an abstract idea into a practical application as they do not impose any meaningful limitation on the abstract idea or how it is performed, nor do they provide an improvement to technology (see MPEP § 2106.04(d)(I)).
Additional elements of computer components and detectors: Claim14 recites the additional element of a processor coupled to memory. Claim15 recites the additional element of a non-transitory computer-readable storage medium. Claim 23 recites the additional elements of a charged-coupled device (CCD) detector or photomultiplier tube (PMT) detector. The claims require only generic computer components and detectors, which do not improve computer technology or electrophoresis technology, and do not integrate the recited judicial exception into a practical application (see MPEP § 2106.04(d)(1) and MPEP § 2106.05(f)).
Step 2A Prong Two summary: Claims 1-4, 8, and 13-23 have been further analyzed with respect to Step 2A, Prong Two, and no additional elements have been found, alone or in combination, that would integrate the judicial exception into a practical application. At this point in examination, it is not yet the case that any of the Step 2A Prong Two considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of: 1. an improvement, 2. a treatment, 3. a particular machine, or 4. a transformation is clear in the record. For example, regarding the first consideration for improvement at MPEP 2106.04(d)(1), the record, including the Specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field, and the claims do not yet clearly result in such an improvement. Although claim 1 recites "reducing noise by at least 30% while maintaining peak intensity within the predetermined allowable range," and " improving sensitivity of detection of the mutated gene," and Specification [0002] discloses highly sensitive detection of a gene mutation and also quantification of its abundance ratio is important, this is not yet enough to show an improvement. See discussion in "response to Applicant Arguments" below. (Step 2A, Prong Two: No).
Step 2B analysis: Because the additional claim elements do not integrate the abstract idea into a practical application, the claims are further examined under Step 2B, which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept. An inventive concept is furnished by an element or combination of elements that is recited in the claim in addition to the judicial exception, and is sufficient to ensure that the claim, as a whole, amounts to significantly more than the judicial exception itself (see MPEP § 2106.05).
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exceptions because the claims recite additional elements that are well-understood, routine, and conventional. Those additional elements are as follows:
Additional elements of data gathering: The additional elements of data gathering, i.e., acquiring first data by performing electrophoresis of a labeled nucleic acid sample (claim 1) and the capillary electrophoresis with fluorescent detection (claim 23) do not cause the claims to rise to the level of significantly more than the judicial exception. The courts have recognized receiving or transmitting data over a network; storing and retrieving information in memory; and analyzing DNA to provide sequence information or detect allelic variants, [see MPEP§2106.05(d)(II)], as well-understood, routine, conventional activity when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity. Additionally, the data gathering by capillary electrophoresis with fluorescent detection is shown to be conventional by the following references:
Durney, (Analytical and bioanalytical chemistry, vol. 407, pages 6923-6938 (2015)), presents a review on DNA analysis using capillary electrophoresis (p. 6927, col.2, and entire doc.).
Galievsky, (Analytica Chimica Acta, vol. 935, pages 58-81 (2016)), presents a tutorial of fluorescence detection in capillary electrophoresis (p.59-61, and entire doc.) Galievsky shows photomultiplier tubes (p.74, col.1, section 6.2 titled "Photomultiplier tubes").
Additional elements of computer components and detectors: The additional elements of a processor coupled to memory (claim 14), a non-transitory computer-readable storage medium (claim 15), and charged coupled device/photomultiplier tube (claim 23) do not cause the claims to rise to the level of significantly more than the judicial exception; these are conventional computer components. Additionally, the following references shows charged coupled devices and photomultiplier tubes to be conventional:
Galievsky, (Analytica Chimica Acta, vol. 935, pages 58-81 (2016)), presents a tutorial of fluorescence detection in capillary electrophoresis (p.59-61, and entire doc.) Galievsky shows photomultiplier tubes (p.74, col.1, section 6.2, under "Photomultiplier tubes") and charge-coupled devices (CCDs) (p.75, col.1, section 6.4, under "Multichannel arrays").
Further regarding the conventionality of the conventionality of additional elements, the MPEP at 2106.05(b) and 2106.05(d) presents several points relevant to conventional computers and data gathering steps in regards to Step 2A Prong 2 and Step 2B, including:
• A general purpose computer that applies a judicial exception, such as an abstract idea, by use of conventional computer functions, does not qualify as a particular machine (see 2106.05(b)(I), as in the case of claims 14 and 15, which are interpreted to recite conventional computer components.
• 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 2106.05(b)(II). In claim 14, the processor acts only as a tool to execute the method.
• Use of a machine that contributes only nominally or insignificantly to the execution of the claimed method (e.g., in a data gathering step or in a field-of-use limitation) would not integrate a judicial exception or provide significantly more (see 2106.05(b)(III). Data gathering steps (such as acquiring data by electrophoresis, recited in claim 1) do not impose meaningful limitations on the claims.
• The courts have recognized "receiving or transmitting data over a network", "performing repetitive calculations", and "storing and retrieving information in memory", as well-understood, routine, and conventional functions when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (see MPEP 2106.05(d)(II)). The acquiring of data in claim 1 is recited in a generic manner.
All limitations of claims 1-4, 6-10, and 13-23 have been analyzed with respect to Step 2B, and none provides a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception, and thus do not transform the judicial exception into a patent eligible application of the exceptions. (Step2B: NO.)
Therefore, when the limitations are considered individually and as a whole, claims 1-4, 6-10, and 13-23, are rejected under 35 U.S.C. § 101 as being directed to non patent-eligible subject matter.
Response to Applicant Arguments - 35 USC § 101
The Applicant's arguments filed 11/17/2025 have been fully considered but they are not yet persuasive.
The Applicant asserts (p.10-11): Technological Improvement Through Specific Technical Implementation; Measurable Performance Improvements to Technology Field; Integration into Practical Application Through Signal Processing; Specific Technical Operations Beyond Generic Computer Implementation; and Practical Application in Disease Detection.
The arguments, while helpful, are not yet persuasive because they do not yet persuasively show an improvement to technology, i.e. the first consideration at Step 2A Prong Two of the 101 analysis. Regarding claim 1, more explanation is needed regarding how specifically and persuasively the improvement of detecting mutations is tied to the actual technology field of electrophoresis, mainly in two aspects.
First, there is a lack of specificity as to the source of the incoming data leading to mutation detection. Specifying the source would help to relate the asserted improvement to the technology field. Particularly if the only supported embodiment of the claim is acquiring post-color call data (interpreted as first data) from sequence data obtained from sequencing a nucleic acid sample, as appears to be true, then this may be clearly recited in the claims.
Second, the claim lacks detail showing that the mutation will be detected, and this is important to persuasively demonstrating improvement, especially improvement regarding the real-world application, e.g. better clinical outcomes. Claim 1 recites "determining a mutation occurrence position on a genome in a mutated gene derived from a disease," but the output of the data analysis steps (the JE portion of the claim) for correcting first data / post color call data and improving sensitivity of mutated gene detection would require further comparison which is not recited, e.g., comparison to a reference sequence, in order to detect (or not detect) a mutation. It is important to the explanation of improvement to convey that the improved mutation detection will occur, in order for the real-world effect of, for example, improved clinical outcome to be persuasive.
Amending the claims to focus the two aspects above will help show a practical application through improvement to the technical field of electrophoresis and its clinical applications. It would be more persuasive if the explanation of improvement were continued to discuss the real-world application which would immediately follow the output of the claim. That is, how is the improved data output used and what are its effects in the real-world, e.g. in a clinical setting? How proximate are those effects? What is the nexus between the JE, the improvement and a practical application? In support of Prong Two, arguments and evidence may be extrinsic to the original disclosure, including references available after the priority date, as long as it is clear that an argument applies to all embodiments of a properly supported claim. Also, argument may clearly and adequately explain cause and effect leading to improvement or, for example when such cause-and-effect explanation is not possible, then may include evidence (e.g. experimental data or a declaration) comparing a claimed result to conventional results.
Applicant is encouraged to request an interview if it would be helpful.
Conclusion
No claims are 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.
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/M.A.V./Examiner, Art Unit 1687
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686
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