Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Remarks
This Office Action fully acknowledges Applicant’s remarks filed on February 12th, 2026. Claims 19-22, 24, 25, and 27-30 are pending. Claims 1-18, 23, and 26 are canceled.
Priority
As seen below, the present claims introduce new matter to the disclosure and as a result, the priority date is now reflected as the filing date of the present Continuation application itself as in July 28th, 2023.
Specification
The specification is objected to as failing to provide proper antecedent basis for the claimed subject matter. See 37 CFR 1.75(d)(1) and MPEP § 608.01(o). Correction of the following is required: The specification lacks proper antecedent basis for the recitations of claims 19-22, 24, 25, and 27-30.
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 19-22, 24,25, and 27-30 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract idea without significantly more. The claim(s) recite(s) individually and as an ordered combination are drawn to mathematical concepts (Step 2A, Prong 1). This judicial exception is not integrated into a practical application because the “compensating” to correct lead/lag effect by applying a lead or lag compensation is drawn to mathematical concepts to remove noise/background from a component. (See general disclosure to “a lead-lag compensation equation” and its determination as in pars.[0009-0010]+, [0041-0049]+, [0064]+ in Applicant’s pre-grant publication US 2024/0060128, and pars. [0008-0010]+ with respect to “ratio contribution” and its application with the lead-lag compensation equation)
Further, as in Step 2A, Prong 2, this judicial exception is not integrated within a practical application, wherein the final step of “identifying a plurality of labeled nucleotide analogues” is drawn to insignificant extra-solution activity. This output is not unique to Applicant’s mathematical concepts in the sequencing application as general sequencing itself is a diagnostic tool to inform the kind of genetic information in a DNA segment, as in identifying the sequence of nucleotides in a DNA molecule.
As in Step 2B, the claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the step “performing a plurality of cycles of incorporation…” is generically recited and a known process (e.g. Solexa/Illumina’s sequencing-by-synthesis (SBS) such as in USPNs 6,833,246, 7,057,026). Further, the step of “obtaining a dataset comprising…” is drawn to mere data gathering that do not add meaningful limitations to the method of claim 1 wherein such steps fail to provide significantly more than the judicial exception, and thus fail Step 2B.
This is likewise seen in the dependent claims 20-22, 24,25, and 27-30, which further provide mathematical concepts delineated from the initial mathematical concepts (i.e. the various “ratio contributions”), offer additional insignificant extra-solution activity in repetition of steps, as well as assignment of quality scores that amount to another abstract idea in a correlation-mental step without particular application.
Claim Rejections - 35 USC § 112
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 19-22, 24, 25, and 27-30 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.
The amended recitation in claim 19 to “compensating the first fluorescence intensity based on…” is drawn to new matter and not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor/join inventor, at the time the application was filed, had possession of the claimed invention.
Applicant’s disclosure does not support this general “compensating the first fluorescence intensity…so as to correct at least one of a lead and lag effect…” as recited herein.
As best-correlated herein to above recitation at-hand, Applicant provides general disclosure to “a lead-lag compensation equation,” while also never particularly providing such a lead-lag compensation equation. This is likewise seen with the discussion to “ratio contribution” that is dependent upon the “lead-lag compensation equation” (see pars.[0008-0010]+, [0064]+.
Applicant postulates that the lead/lag compensation equation “is determined by applying equation” as seen in pars.[0010]+, [0041-0049]+, [0064]+ which both does not set forth an actual lead-lag compensation equation, nor are the purported “applying equations” drawn to equations themselves, wherein they are drawn to mere multiplication factors.
Paragraph [0064]+ of Applicant’s pre-grant publication US 2024/0060128 speaks to “an algorithm for processing data for nucleic acids in a nucleotide sequence…” and generally describes aspects of the algorithm as in items a) and b), but does not suffice to set forth an actual algorithm for correcting lead/lag, let alone for the more broadly claimed “compensating the first fluorescence intensity…” provided herein. Further, and as discussed above, Applicant speaks to the “sequence lead-lag compensation equation” being determined by applying equation, wherein such disclosure fails to provide an actual lead-lag compensation equation or “algorithm”, and further, such “equation” as in pars.[0064]+ are not equations and are drawn to multiplication factors.
Returning to the presently claimed “compensating the first fluorescence intensity…” step it can be seen that this is wholly undefined and unsupported in the disclosure. This step is an even broader constitution than they already insufficiently-supported “sequence lead-lag compensation equation” and its means of determination (i.e. species relative to the presently claimed genus-type characterization in a general “compensating”).
Applicant’s disclosure is absent any particular discussion as to support and 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 with respect to such a step.
Further, as discussed above, it can be seen that as the species-type application is insufficiently supported and described herein, it follows that the presently-claimed genus-type application is insufficiently supported.
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 21 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.
The metes and bounds of the sought “determining” step are indefinitely provided herein.
Herein, the correlation of a ratio to “measuring a rate at which a lag and/or lead occurs…” is indefinitely provided. A ratio is a static value, while “measuring a rate at which…” involves time-dependent monitoring from a relative standpoint, which has no particular basis herein and does not correlate or coincide with a general “ratio contribution” that has been provided herein and in prior claims 19/20.
Examiner asserts that the amended recitation to “said rate corresponds to a fraction of labeled…” does not obviate the rejection and remains to fail to provide a “rate.” This discussion is drawn to what this supposed “rate” corresponds to, and a fraction, and as recited herein, is not a “rate” that involves a time-dependent value.
Clarification is required.
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 pre-AIA 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) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
Claim(s) 19-20, 22, 24, 25, 27, 29, and 30 is/are rejected under pre-AIA 35 U.S.C. 102a1 as being anticipated by Erlich et al. (“Alta-Cyclic: a self-optimizing…” Nature Methods Vol. 5, No. 8, pp. 679-682, August 2008), hereafter Erlich.
With regard to claim 19, Erlich discloses a method for correcting lead or lag effects comprising performing a plurality of cycles of incorporation […] as recited therein, and (i) obtaining a dataset comprising first, second, and third fluorescence intensities are cited therein (see discussion of Next-generation sequencing and the various synthesis cycles, including signals from the interrogation position and signals from adjacent nucleotides thereto, pg. 679, for example). Erlich further discloses (ii) applying an adjustment […] as recited therein, and repeating steps (i)-(ii) as recited therein (see pgs. 680-681, figs. 2,3). Erlich further discloses identifying a plurality of labeled nucleotides […] as recited herein (see abstract, wherein confident identification is achieved). With regard to claim 20, Erlich discloses determining ratio contributions […] and applying the ratio contribution […] as recited herein (see discussion of phasing noise wherein the purity of the signal at the interrogated position (i.e. first fluorescence) is contaminated by signals from adjacent nucleotides (i.e. second, third fluorescence), and wherein Alta-Cyclic applies deconvolution to correct for phasing noise in which an iterative grid search is utilized in base calling and optimal correction factors (i.e. ratio) are applied to deconvolute and remove such neighboring contamination (pg. 679, 680, fig. 2, for example). With regards to claims 22 and 27, Erlich discloses repetition of steps (i)-(ii) at least three times and at least fifty times (pg. 681, fig. 3C, page 682, 1st par. to ‘read length to 78 bases,’ for example). With regard to claim 24, Erlich discloses assigning a quality score as claimed (see first full paragraph, pg. 680, fig. 2E, for example). With regard to claim 25, the data set can be obtained in one or more color channels. With regard to claim 26, as best understood herein, Erlich discloses applying an adjustment as recited therein comprising determining Klead/lag and in a matrix in as much as understood and recited herein (see pg. 679, 680 with respect to the model accounting phasing noise as it influences lead and lag across the entire sequence read and an iterative two-dimensional grid search to describe the phasing noise). With regards to claims 29 and 30, Erlich discloses repeating steps (i)-(ii) for at least a majority as in cl. 29, and for substantially all as recited in claim 30 (Alta-Cyclic calculates phasing parameters based on a parametric model using data from the latest cycles and Alta-Cyclic calculates phasing parameters based on parametric model as a function of cycle for sequence reads and full sequencing run; pg. 680,681, fig. 3C).
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claim 28 is/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Erlich in view of Rothberg et al. (US 2004/0248161), hereafter Rothberg.
Erlich has been discussed above.
Erlich does not specifically disclose repeating steps (i)-(ii) at least one hundred times.
Rothberg discloses methods of sequencing a nucleic acid, such as in sequencing by synthesis and discloses providing read length as desired until the desired amount of sequence of the sequence product is obtained and discloses at least one hundred cycles (abstract; par.[0123], for example).
It would have been obvious to one of ordinary skill in the art to modify Erlich to repeat steps (i)-(ii) at least one hundred times such as suggested by the analogous art of Rothberg to sequencing a nucleic acid by synthesis in which utilizing at least one hundred cycles provides for an ability to achieve a desired amount of sequence of the product to be obtained and also thus provide improved resolution and better detection of structural variations by way of further cycles.
Response to Arguments
Applicant's arguments filed February 12th, 2026 have been fully considered but they are not persuasive.
With regard to the rejection of claims 19-22 and 24-30 under 35 USC 112 a/1st paragraph, Applicant traverses the rejection.
Applicant asserts that that the claims have been amended to recite “compensating the first fluorescence intensity…” and the disclosure (see pars.[0008-0010,0309-0323] clearly and expressly provides support for such limitations as claimed.
Examiner asserts that the amendment does not obviate the prior rejection of the claims under 35 USC 112 a/1st and maintains that the claims, as amended, are likewise insufficient supported by the disclosure for the reasons discussed above in the body of the action and herein repeated below.
The amended recitation in claim 19 to “compensating the first fluorescence intensity based on…” is drawn to new matter and not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor/join inventor, at the time the application was filed, had possession of the claimed invention.
Applicant’s disclosure does not support this general “compensating the first fluorescence intensity…so as to correct at least one of a lead and lag effect…” as recited herein.
As best-correlated herein to above recitation at-hand, Applicant provides general disclosure to “a lead-lag compensation equation,” while also never particularly providing such a lead-lag compensation equation. This is likewise seen with the discussion to “ratio contribution” that is dependent upon the “lead-lag compensation equation” (see pars.[0008-0010]+, [0064]+).
Applicant postulates that the lead/lag compensation equation “is determined by applying equation” as seen in pars.[0010]+, [0041-0049]+, [0064]+ which both does not set forth an actual lead-lag compensation equation, nor are the purported “applying equations” drawn to equations themselves, wherein they are drawn to mere multiplication factors.
Paragraph [0064]+ of Applicant’s pre-grant publication US 2024/0060128 speaks to “an algorithm for processing data for nucleic acids in a nucleotide sequence…” and generally describes aspects of the algorithm as in items a) and b), but does not suffice to set forth an actual algorithm for correcting lead/lag, let alone for the more broadly claimed “compensating the first fluorescence intensity…” provided herein. Further, and as discussed above, Applicant speaks to the “sequence lead-lag compensation equation” being determined by applying equation, wherein such disclosure fails to provide an actual lead-lag compensation equation or “algorithm”, and further, such “equation” as in pars.[0064]+ are not equations and are drawn to multiplication factors.
Returning to the presently claimed “compensating the first fluorescence intensity…” step it can be seen that this is wholly undefined and unsupported in the disclosure. This step is an even broader constitution than they already insufficiently-supported “sequence lead-lag compensation equation” and its means of determination (i.e. species relative to the presently claimed genus-type characterization in a general “compensating”).
Applicant’s disclosure is absent any particular discussion as to support and 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 with respect to such a step.
Further, as discussed above, it can be seen that as the species-type application is insufficiently supported and described herein, it follows that the presently-claimed genus-type application is insufficiently supported.
Examiner further notes that Applicant has not provided any substantive remarks or rebuttals to the prior rejection of the claims under 35 USC 112 a/1st and the particular issues raised therein the action mailed January 12th, 2026 outside of a general traversal thereof.
With respect to the cited Priority date being drawn to the filing date of the present continuation as in July 28th, 2023, Applicant provides similar discussion to the amended language of “compensating the first fluorescence intensity…”
As discussed above, this recitation is drawn to new matter in the specification and that is not sufficiently supported herein. Likewise to the above discussion as in 35 USC 112 a/1st, this is unpersuasive and thus the priority date is found as July 28th, 2023.
The specification likewise remains objected to for the reasons discussed above in the body of the action.
With regard to claim 21 rejected under 35 USC 112 b/2nd, Applicant traverses the rejection.
Examiner asserts that the amended recitation to “said rate corresponds to a fraction of labeled…” does not obviate the rejection and remains to fail to provide a “rate.” This discussion is drawn to what this supposed “rate” corresponds to, and a fraction, and as recited herein the claims, is not a “rate” that involves a time-dependent value.
With regards to the claims 19-20, 22, 24-27, 39, and 30 rejected under 35 USC 102 anticipated by Erlich and claim 28 rejected under 35 USC 103 as being unpatentable over Erlich in view of Rothberg, Applicant traverses the rejection.
Applicant asserts that, as discussed above, the claims are entitled to a March 19th, 2008 priority date and such Erlich is not available prior art, and concordantly therewith Erlich in view of Rothberg.
Examiner maintains, as discussed above, that the claims are afforded the priority date of the present application filing of July 28th, 2023, and the claims thus remain rejected under 35 USC 102 and 103 as discussed above in the body of the action.
With regards to claims 19-22 and 24-30 rejected under 35 USC 101, Applicant traverses the rejection.
Applicant references prior Office Actions including those of Feb. 8th, 2024 and June 3rd, 2024. Applicant further asserts that Applicant successfully argued that the claimed subject matter is directed to patentable subject matter leading to a prior allowance (see Applicant’s responses Oct. 3rd, 2024 and November 4th, 2024).
Applicant asserts that the claimed embodiments as captured by at least independent claim 19 amounts to significantly more than just the concept of sequencing using fluorescence intensities and is not an abstract idea.
Examiner asserts that Applicant has failed to provide substantive arguments to the above-discussed rejection of the claims under 35 USC 101, and the claims remain rejected under 35 USC 101 for the reasons discussed therein.
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NEIL N TURK whose telephone number is (571)272-8914. The examiner can normally be reached M-F 930-630.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Charles Capozzi can be reached at 571-270-3638. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/NEIL N TURK/ Primary Examiner, Art Unit 1798
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