DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Request for Continued Examination
2. A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 09 October 2025 has been entered.
Claim Rejections - 35 USC § 112
3. 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.
4. Claims 1-20 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
A. Claim 1 recites the limitation “sequencing the first portion and the second portion of the plurality of template strands concurrently” in ¶ 4 of the claim, however in ¶ 5 the claim states that “wherein a polymerase incorporates one or more types of labeled nucleotides complementary to at least the first portion or the second portion of the plurality of template strands.” It is unclear how the polymerase could only add a labeled nucleotide to the first portion or the second portion if the strands are intended to be sequenced concurrently, therefore the claim is indefinite.
B. Claim 4 recites the limitation “…, and wherein the first base-paired region and the second base-paired region are separated by the non-complementary region.” This claim is structured such that it is unclear whether the wherein clause is intended to limit both (a) or (b) (i.e., either ‘(a) and wherein…’ or ‘(b) and wherein…’), or if the wherein clause is only intended to limit (b) which appears to have proper antecedent basis. The intention of this limitation is unclear, and therefore the claim is indefinite. For the purpose of prosecution, this claim is being interpreted as though the wherein clause only applies to (b), where it appears to have appropriate antecedent basis.
C. Any other claim list above but not specifically rejected here is rejected due to being dependent on a previously rejected claim.
Claim Rejections - 35 USC § 102
5. 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.
6. Claims 1, 3-6, 8-13, 16 and 18 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by King et al (United States Patent Application No. US 20230227905, with valid priority to 20 January 2022).
Regarding claim 1, King teaches a method of determining a polynucleotide sequence (abstract) comprising: preparing a polynucleotide library comprising a double-stranded polynucleotide fragment and adaptor, the double-stranded polynucleotide fragment comprising a first strand and a second strand that is complementary to the first strand (forward and reverse strands; FIG 1A). King teaches amplifying the polynucleotide library to generate a plurality of template strands on a solid support (FIG 6A and 6B), the plurality of template strands comprising a first plurality of template strands comprising a first portion that includes the first sequence of nucleotides (e.g., the forward strand; P3’ in FIG 6B) and a second plurality of template strand comprising a second portion that includes a complement of the second sequence of nucleotides (e.g., the complement of the reverse strand; P3 in FIG 6B). King teaches sequencing the first portion and the second portion of the plurality of template strands concurrently (FIG 7C, sequencing primers 1 and 2, [0013] and [0016]). King teaches contacting the plurality of template strands with a plurality of labeled nucleotides, wherein a polymerase incorporates one or more labeled nucleotides into the first portion or the second portion of the template strands (FIG 7C, [0250] and [0251]). King teaches acquiring intensity data comprising a combined intensity of signal emitted by the labeled nucleotides in response to illumination by a light source, and processing the intensity data to determine sequence information associated with the double-stranded polynucleotide fragment ([0016] and [0250]). King teaches that the intensity data is used to generate a consensus sequence between read 1 and read 2 (i.e., corrected read 1, [0019], [0020], and [0360]). King further teaches that this method of sequencing enables the distinguishing between true somatic variants (i.e., template duplexes that originated with a sequence variant) and sequencing errors (i.e., errors generated during library preparation/amplification; i.e., the intensity data is used to identify a match or a mismatch; [0342]).
Regarding claim 3, King teaches a sequencing solution that comprising different types of labeled nucleotides (i.e., when the sequencing solution is added, the labeled nucleotides are delivered to the solid support simultaneously; [0251]).
Regarding claim 4, King teaches an adaptor comprising two adaptor strands having a base-paired region and a non-complementary region (FIG 1A, Y-adapter).
Regarding claims 5 and 6, King teaches that the combined intensity signals are additive (i.e., co-localized and not spatially resolved on the solid support; [0016]).
Regarding claims 8-11, King teaches an embodiment wherein fluorescently labeled nucleotides are labeled with “at least two unique fluorescent dyes” (i.e., spectrally distinct and configured to emit optical signals for detection by an optical system having two optical channels) and an embodiment wherein fluorescently labeled nucleotides are labeled with 4 unique fluorescent labels (i.e., configured to emit optical signals for detection by an optical system having four optical channels; [0242]). King additionally teaches intensity data acquired from optical signals detected in at least one optical channel ([0016]).
Regarding claims 12 and 13, King teaches that the first and second sequencing primers are extended simultaneously, and that this results in a significant increase in the detected signal resulting in higher base calling accuracy ([0342]). This inherently means that the same nucleotide is incorporated at sequencing primer 1 and sequencing primer 2, indicating a “match” between sequences as the detected signal is “approximately doubled” during simultaneous reading.
Regarding claim 16, King teaches that the first portion and the second portion are sequenced in the same direction (FIG 7C).
Regarding claim 18, King teaches that when sequencing read 1 and sequencing read 2 are detected simultaneously, the signal intensity is approximately doubled (i.e., the nucleotides are matched; [0016] and [0342]).
Claim Rejections - 35 USC § 103
7. 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.
8. This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
9. Claims 2 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over King et al (United States Patent Application No. US 20230227905, with valid priority to 20 January 2022) in view of Fabani et al (International Patent Application No. WO 2015002789, published 08 January 2015).
Regarding claim 2, King teaches the limitations of claim 1 as discussed fully above and incorporated here. King does not teach labeled nucleotides comprising different types of labels that are delivered to the solid support sequentially, nor does King teach that the plurality of nucleotides are configured to emit optical signals for detection by an optical system having one optical channel.
However, Fabani teaches a method wherein labeled nucleotides are delivered to a solid support sequentially (pg. 26 ¶ 1 and pg. 27 ¶ 1).
Regarding claim 7, Fabani further teaches a method wherein the plurality of labeled nucleotides are configured to emit optical signals for detection by an optical system having one optical channel, wherein the intensity data is acquired from optical signals detected in the one optical channel (pg. 32 ¶ 1 and Table 1).
It would have been obvious to one having ordinary skill in the art to have modified the sequencing method taught by King with the sequential delivery of nucleotides and to have those nucleotides labeled with a fluorophore configured for detection in one optical channel as taught by Fabani to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification in order make King’s method more broadly applicable to other sequencing/optical systems and/or chemistry (e.g., 1-channel, 2-channel, 4-channel sequencing chemistries). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in methods to improve the sequencing of nucleic acids.
10. Claims 14, 15, 17, 19-21, 23-25 and 27-30 are rejected under 35 U.S.C. 103 as being unpatentable over King et al (United States Patent Application No. US 20230227905, with valid priority to 20 January 2022) in view of Pel et al (United States Patent Application No. US 20190264273, published 29 August 2019).
Regarding claim 14, the method of claim 1 is discussed fully above and incorporated here. Briefly, King teaches the concurrent sequencing of two nucleic acid strands, teaches that sequencing these two strands simultaneously increases the detected signal of the incorporated nucleotide (i.e., the intensity) approximately two-fold, and teaches that this concurrent sequencing method increases base-calling accuracy and allows an ordinary artisan to distinguish somatic variants from sequencing errors.
However, King does not specifically teach that the polymerase does not incorporate the same type of labeled nucleotide complementary to the first portion of the plurality of template strand and the second portion of the plurality of template strands, wherein the intensity data is used to identify a mismatch between the first portion of the plurality of template strands and the second portion of the plurality of template strands.
Pel teaches a method wherein the polymerase does not incorporate the same type of labeled nucleotides complementary to the first portion of the plurality of template strands and the second portion of the plurality of template strands, and wherein the intensity data is used to identify a mismatch between the first portion of the plurality of template strands and the second portion of the plurality of template strands (FIG 5 and [0153]).
It would have been obvious to one having ordinary skill in the art to have modified the method taught by King with the specific sequencing error identification method taught by Pel to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because King specifically teaches a method of concurrent strand sequencing with improved base calling accuracy and the ability to differentiate sequencing errors and true variants ([0342]), and Pel teaches a method of intensity analysis and signal comparison that provides a direct analysis advantage over the generic disclosure of King. In addition, one having ordinary skill in the art would have recognized that the known techniques of the cited references could have been combined with predictable results because the known techniques of the cited references predictably result in methods for the improvement of nucleic acid sequencing and error correction/identification.
Regarding claim 15, Pel teaches a method wherein the intensity data is not used to determine a base call ([0177]).
Regarding claims 17 and 19, Pel teaches the extraction of intensity data from sequencing images ([0171]) and a method to identify true variants (i.e., matches) and sequencing errors (i.e., mismatches) by comparing results from two different but related sequencing reads ([0177] and FIG 5). Pel doesn’t specifically teach ‘mapping the signals emitted by the one or more labeled nucleotides to a distribution of intensity data representing the match/mismatch,’ however this process is inherent to extracting intensity data and comparing the results between two strands.
Regarding claim 20, Pel teaches a method wherein a sequencing error (i.e., a mismatch) is identified when the combined signal intensities from the first portion and the second portion indicate the base present in the first portion is different than the base present in the second portion (FIG 5).
Regarding claim 21, King teaches a method of determining a polynucleotide sequence (abstract) comprising providing an amplified polynucleotide library comprising a plurality of template strands on a solid support (FIG 6B), hybridizing sequencing primers to the plurality of template strands on the solid support wherein the sequencing primers hybridize to a first strand and the reverse complement of a second strand to sequencing in the same direction on the template strands (FIG 7C), sequencing the plurality of template strands on the solid support using a polymerase to incorporate a plurality of labeled nucleotides comprising one or more types of labeled nucleotides (FIG 7C, [0242] and [0243]), acquiring intensity data comprising a combined intensity of the signals emitted by the one or more types of labeled nucleotides incorporated ([0016] and [0242]), and processing the intensity data to determine sequence information associated with the template strands ([0242] and [0245]). King further teaches that this concurrent sequencing method improves base calling and allows one to distinguish rare variants from sequencing errors (i.e., identifies sequencing errors; [0342]), but King does not specifically teach that sequencing errors are removed from the sequence information.
However, Pel teaches that sequencing errors are removed after comparing the sequences of two copy strands ([0153] and [0188]).
It would have been obvious to one of ordinary skill in the art to have modified the method taught by Kind with the sequencing error analysis taught by Pel to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification in order to improve base-calling and correctly represent true variants compared to errors accumulated during the sequencing method. In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the sequencing and analysis of nucleic acids.
Regarding claim 23, King teaches that the plurality of labeled nucleotides are delivered to the solid support simultaneously ([0251]).
Regarding claim 24, King teaches that the detected signal (i.e., the intensity) from sequencing read 1 and read 2 simultaneously (i.e., the signal from both the first strand and the complement of the second strand) generates a higher signal than either sequencing read individually and translates to higher base-calling accuracy ([0016] and [0017]). King teaches that this sequencing method identifies true variant nucleotides ([0342]).
Regarding claim 25, Pel teaches that intensity data is used to identify a sequencing error (i.e., a mismatch) between the first strand and the second strand ([0006] and [0177]).
Regarding claim 27, King teaches that the plurality of labeled nucleotides comprise at least two unique (i.e., spectrally distinct) labels ([0242] and [0250]).
Regarding claim 28, King teaches that when sequencing read 1 and sequencing read 2 are performed simultaneously the signal intensity is approximately double (i.e., the two incorporated nucleotides generate signal in the same detection channel, therefore the two nucleotides are matched; [0016] and [0017]).
Regarding claim 29, King teaches that the plurality of template strands are produced by ligating adapters to a double stranded DNA (i.e., a first and second strand of a target polynucleotide; FIG 1) and that the polynucleotides are amplified on the surface to produce an amplified library comprising a plurality of template strands (FIG 6B and [0093]).
Regarding claim 30, King teaches a method of determining a polynucleotide sequence (abstract) comprising providing an amplified polynucleotide library comprising a plurality of template strands on a solid support (FIG 6B) wherein the support is a flow cell ([0069]), hybridizing sequencing primers to the plurality of template strands on the solid support wherein the sequencing primers hybridize to a first strand and the reverse complement of a second strand to sequencing in the same direction on the template strands (FIG 7C), sequencing the plurality of template strands on the solid support using a polymerase to incorporate a plurality of labeled nucleotides comprising one or more types of labeled nucleotides (FIG 7C, [0242] and [0243]), acquiring intensity data comprising a combined intensity of the signals emitted by the one or more types of labeled nucleotides incorporated ([0016] and [0242]), and processing the intensity data to determine sequence information associated with the template strands ([0242] and [0245]). King teaches that the intensity of the signals emitted from both the first and second reads (i.e., the first strand and the complement of the second strand) identifies a base call at a position in a DNA sequence ([0016] and [0017]). King further teaches that this concurrent sequencing method improves base calling and allows one to distinguish rare variants from sequencing errors (i.e., identifies sequencing errors; [0342]), but King does not specifically teach that sequencing errors are removed from the sequence information.
However, Pel teaches that sequencing errors are removed after comparing the sequences of two copy strands ([0153] and [0188]).
It would have been obvious to one of ordinary skill in the art to have modified the method taught by Kind with the sequencing error analysis taught by Pel to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification in order to improve base-calling and correctly represent true variants compared to errors accumulated during the sequencing method. In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the sequencing and analysis of nucleic acids.
11. Claims 22 and 26 are rejected under 35 U.S.C. 103 as being unpatentable over King et al (United States Patent Application No. US 20230227905, with valid priority to 20 January 2022) in view of Pel et al (United States Patent Application No. US 20190264273, published 29 August 2019) as applied to claim 21 above, and further in view of Fabani et al (International Patent Application No. WO 2015002789, published 08 January 2015).
Regarding claim 22, the method of claim 21 is discussed fully above and incorporated here.
The combination of King in view of Pel does not teach that the plurality of different types of labeled nucleotides are delivered to the solid support sequentially.
However, Fabani teaches a method wherein labeled nucleotides are delivered to a solid support sequentially (pg. 26 ¶ 1 and pg. 27 ¶ 1).
Regarding claim 27, Fabani further teaches a method wherein the plurality of labeled nucleotides are configured to emit optical signals for detection by an optical system having one optical channel, wherein the intensity data is acquired from optical signals detected in the one optical channel (pg. 32 ¶ 1 and Table 1).
It would have been obvious to one having ordinary skill in the art to have modified the sequencing method taught by King in view of Pel with the sequential delivery of nucleotides and to have those nucleotides labeled with a fluorophore configured for detection in one optical channel as taught by Fabani to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification in order make King’s method more broadly applicable to other sequencing/optical systems and/or chemistry (e.g., 1-channel, 2-channel, 4-channel sequencing chemistries). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in methods to improve the sequencing of nucleic acids.
Response to Arguments
12. Applicant’s arguments with respect to claims 1-30 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Conclusion
13. No claims are allowed.
14. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN ELLIS YOUNG whose telephone number is (703)756-5397. The examiner can normally be reached M-F 0730 - 1700.
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/BRIAN ELLIS YOUNG/Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682