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 .
The amendment filed on 04/13/2026 has been entered.
Claims 1 and 14 were amended in the claim set filed on 04/13/2026.
Applicant’s election without traverse of Group I (Claims 1-21), drawn to a method for paired-end sequencing in the reply filed on 11/18/2025 is acknowledged.
Claims 36 (previously withdrawn) and 18 are canceled.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Claims 1-17 and 19-21 in the claim set filed on 04/13/2026 are currently under examination.
Response to the Arguments
The submitted Information Disclosure Statements on file are dated May 8, 2023 and February 16, 2024. The Information Disclosure Statements (IDS) filed were marked as being considered and initialed by the Examiner were filed December 17, 2025. Please see, all references considered notation at the bottom of each page with the examiners initials and signed on the last page of the lists.
Applicant’s arguments regarding previous rejection(s) of claim(s) 14 and 21 under 35 U.S.C. 112 have been fully considered and are persuasive. The 35 U.S.C. 112 rejections documented in the previously mailed non-final have been withdrawn in light of applicants claim amendments and arguments on Pg. 6-8.
As necessitated by amendment, new grounds of 35 U.S.C. 112 rejections of claims 1-17 and 19-20 are documented below in the 35 U.S.C. 112 rejection in this office action on Pg. 4.
Applicant’s arguments regarding previous rejection(s) of claim(s) 1-5, 8-11 and 15 under 35 U.S.C. 102 have been fully considered and are not persuasive. As necessitated by amendment, the 35 U.S.C. 102 rejections of claim(s) 1-5, 8-11 and 15 documented in the previously mailed non-final have been maintained and revised in light of applicants claim amendments and arguments. Applicant' s argument on Pg. 8, states that “claim 1 is amended to include the subject matter of claim 18. Because claim 18 is novel over the cited art, claim 1 as amended herein is novel over the cited art.” The maintained and revised rejection are made as documented below in the 35 U.S.C. 103 rejection in this office action on Pg. 4-11.
Applicant’s arguments regarding previous rejection(s) of claim(s) 12-14, 16-17 and 19-20 under 35 U.S.C. 103 have been fully considered and are not persuasive. As necessitated by amendment, the 35 U.S.C. 103 rejections of claim(s) 12-14, 16-17 and 19-20 documented in the previously mailed non-final have been maintained and revised in light of applicants claim amendments and arguments on Pg. 9, as documented below in the 35 U.S.C. 103 rejection in this office action on Pg. 4-11.
Applicant’s arguments regarding previous rejection(s) of claim(s) 6-7 under 35 U.S.C. 103 have been fully considered and are not persuasive. As necessitated by amendment, the 35 U.S.C. 103 rejections of claim(s) 6-7 documented in the previously mailed non-final have been maintained and revised in light of applicants claim amendments, as documented below in the 35 U.S.C. 103 rejection in this office action on Pg. 13-14.
Applicant’s arguments regarding previous rejection(s) of claim(s) 21 under 35 U.S.C. 103 have been fully considered and are not persuasive. The 35 U.S.C. 103 rejections of claim(s) 21 documented in the previously mailed non-final have been maintained and revised in light of applicants clarification, claim amendments and arguments, as documented below in the 35 U.S.C. 103 rejection in this office action on Pg. 14.
The revised rejections for claims 1-17 and 19-21 are documented below in this Final Office Action are necessitated by claim amendments filed on 04/13/2026.
Priority
This application claims priority to U.S. Provisional Patent Application No. 63/246,188, filed September 20, 2021, which claims priority to U.S. Provisional Patent Application No. US 63/219,738, filed July 8, 2021.The priority date of claim set filed on Sept. 27, 2022, is determined to be July 8, 2021.
Claim Rejections - 35 USC § 112
Claim 1 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01. The omitted steps are: hybridizing a primer to a region from which to synthesize a first or second masking strand complementary to the forward or reverse strand.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-5, 8-17 and 19-20 are rejected under 35 U.S.C. 103 as being unpatentable over Hosono et al. (“Hosono”; Patent App. Pub. WO 2019209946 A1, Oct. 31, 2019).
Hosono discloses “methods for determining the nucleotide sequence of sequences of interest using paired-end sequencing. Dumbell circular templates can be generated and used in a rolling circle amplification reaction by ligating two hairpin adaptors on a double-stranded amplicon. Disclosed also are methods using double-stranded DNA, including both sense and antisense strands in a single circle to sequence, sequentially from the same concatemers.” (Abstract).
Regarding claim 1 step (a), Hosono teaches a method comprising “a target nucleic acid molecule for sequencing. The method can comprise forming a first partially double stranded circular DNA wherein the partially double stranded circular DNA contains (i) a sequence of interest having a first strand and a second strand, (ii) a first hairpin adapter, and (iii) a second hairpin adapter, wherein the first and second strands of the sequence of interest are complementary to each other… wherein the amplification of the first partially double stranded circular DNA results in a plurality of concatemers” (Pg 43. ln 1-7). Hosono teaches a method comprising “methods involving concatemer RCA-based NGS pair-end sequencing using a circular template that can be in the shape of a dumbbell” (Pg. 43, ln 8-9). Hosono teaches a method comprising “the first hairpin adapter and the second hairpin adapter are different.” (Pg 43. ln 15).
Regarding claim 1 step (b), Hosono teaches a method comprising “a concatamer or plurality of concatamers disclosed herein can be used as a template for sequencing” (Pg. 40 ln 18-19). Hosono teaches a method comprising “any other oligonucleotides can be synthesized” (Pg. 59 ln 9-10). “any other oligonucleotides” reads on a first masking strand complementary to the forward strand and a second masking strand complementary to the reverse strand. Hosono teaches a method comprising “Hairpin adapters can vary widely in length, and can depend in part on the number and type of functional elements desired. Examples of functional elements include, but are not limited to, anchor sequences, sequences complementary to capture probe sequences (e.g. for attachment to surfaces), tagging sequences, secondary structure sequences, sequences for attachment/hybridization of label probes, functionalization sequences, primer binding sites, recognition sites for nucleases, such as nicking enzymes, restriction endonucleases, and the like” (Pg. 20 ln 28-33- Pg. 21 ln 1). It would be obvious to the ordinary artisan to use one or more the functional elements of the first or second hairpin adapter to hybridize a primer for synthesis of a oligonucleotide strand (masking strand) at least partially complementary to the forward or reverse strand, respectively. Hosono also teaches a method comprising “wherein the amplification of the first partially double stranded circular DNA results in a plurality of partially double stranded concatamers, (c) contacting at least one of the partially double stranded concatamers with a first primer, wherein the first primer hybridizes to the first primer binding site, (d) extending the first primer in the presence of one or more dideoxynucleotides thereby generating a first primer elongation product, (e) contacting at least one of the partially double stranded concatamers with a second primer, wherein the second primer hybridizes to the second primer binding site; (f) extending the second primer, thereby generating a second primer elongation product; and (g) identifying at least one nucleotide of the sequence of interest adjacent or close to the first primer binding site and at least one nucleotide of the sequence of interest adjacent or close to the second primer binding site. In some aspects, the extension steps of (d) and (f) can be carried out using the well-known sequencing method referred to as the sequencing-by-synthesis (SBS) method.” (Pg. 40 ln 29-33 and Pg.41 ln 1-9).
Thus, Hosono suggests a method for paired-end sequencing comprising: a) providing a nucleic acid concatemer comprising multiple sequential copies of: a first adapter region, a forward strand of a target nucleic acid sequence, a second adapter region different from the first adapter region, and a reverse strand of the target nucleic acid sequence that is complementary to the forward strand; and b) performing a sequencing process to produce paired-end reads of the target nucleic acid sequence by: i) synthesizing a first masking strand complementary to the forward strand, hybridizing a first sequencing primer to the first adapter regions, and obtaining a first read of a first portion of the target nucleic acid sequence by sequencing from the first sequencing primer; and ii) synthesizing a second masking strand complementary to the reverse strand, hybridizing a second sequencing primer to the second adapter regions, and obtaining a second read of a second portion of the target nucleic acid sequence by sequencing from the second sequencing primer; wherein the first read and the second read comprise paired-end reads of the target nucleic acid sequence.
Therefore, the invention as recited in claims 1 is prima facie obvious over the prior art Hosono et al. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of the method for paired-end sequencing as recited in claim 1 in view of Hosono et al. It would have been obvious to perform paired-ended sequencing with a concatamer of a target nucleic acid sequence according to the limitations of the instant application claim 1 based on Hosono et al. (Patent App. Pub. No. WO 2019209946 A1).
The teachings of Hosono are documented above in the rejection of claim 1 under 35 U.S.C. 103. Claims 2, 5 and 10, 16-17 and 19-20 depend on claim 1. Claims 3 and 4 depend on claim 2, which depends on claim 1. Claim 9 depends on claim 8, which depends on claim 5, which depends on claim 1. Claims 1-14 depend on claim 11. Claims 11 and 15 depend on claim 10, which depends on claim 1.
Regarding claim 2, Hosono teaches a method wherein the nucleic acid concatemer is produced providing a circular nucleic acid as depicted in Figure 3. (See Figure 3 below). Thus, Hosono suggests a method wherein the nucleic acid concatemer is produced by: providing a circular nucleic acid molecule comprising: a central region comprising the forward strand and the complementary reverse strand; the central region having two ends, the forward strand connected to the reverse strand at one end with a first connecting region, and the forward strand connected to the reverse strand at the other end with a second connecting region; and performing rolling circle amplification using the circular nucleic acid molecule as a template to produce the nucleic acid concatemer.
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Regarding claim 3, Hosono teaches a method wherein “RCA can be performed in solution” (Pg. 34 ln 27). Thus, Hosono suggests a method wherein the rolling circle amplification step is performed in solution.
Regarding claim 4, Hosono teaches a method wherein “concatemers generated via RCA seeded onto a single flow cell” (Pg. 43 ln 15) and “crosslinking rolonies (e.g., concatemers) onto a flow cell” (Pg. 77 ln 22). Thus, Hosono suggests a method wherein the rolling circle amplification step is performed on the surface of a solid support.
Regarding claim 5, Hosono teaches a method wherein “sequential sequencing using two primer strands” (Pg.7 Ln 8; Example 11-12 pg ). Thus, Hosono suggests a method wherein step ii) is performed after step i).
Regarding claim 8, Hosono teaches a method wherein “In other words the two strands of a concatamer can be sequenced sequentially without removing the first primer elongated during the extension of the first primer” (Pg. 43 ln 5-7). Thus, Hosono suggests a method wherein the nascent strands formed by sequencing from the first primer are not removed.
Regarding claim 9, Hosono teaches a method wherein “The concatemers can be seeded onto the flow cell and NGS reaction can be performed using two different primers sequentially, initially with a sequencing primer from, for example, Adapter A and performing 50 cycles followed by a one base addition-blocking step using dideoxynucleotides to block the sequencing fragments from elongating any further. Adapter B, for example, can then be used to perform another 50 cycles. This allows sequencing from both (+) and (-) strands from the same concatemer attached to the flow cell in the same position on a flow cell.” (Pg. 43 ln 17-22). Thus, Hosono suggests a method wherein the 3' ends of the nascent strands formed by sequencing from the first primer are blocked before hybridizing the second sequencing primer to the second adapter regions.
Regarding claim 10-11, Hosono teaches a method wherein “amount of reads that were mapped to one strand (red) or to both strands (blue) at the same time” (Pg. 70 ln 5-6; Fig. 12). Thus, Hosono suggests a method wherein steps i) and ii) are performed at the same time.
Regarding claim 11, Hosono further teaches a method wherein “Each coordinate was color coded based on the lambda clone mapped sequence” and “To aid in detection and quantitation of nucleic acids amplified using the disclosed methods, detection labels can be directly incorporated into amplified nucleic acids or can be coupled to detection molecules. As used herein, a detection label is any molecule that can be associated with amplified nucleic acid, directly or indirectly, and which results in a measurable, detectable signal, either directly or indirectly.” (Pg. 29 ln 5-9). “Preferred fluorescent labels for combinatorial multicolor coding are FITC and the cyanine dyes Cy3, Cy3.5, Cy5, Cy5.5 and Cy7. The absorption and emission maxima, respectively, for these fluors are: FITC (490 nm; 520 nm), Cy3 (554 nm; 568 nm), Cy3.5 (581 nm; 588 nm), Cy5 (652 nm: 672 nm), Cy5.5 (682 nm; 703 nm) and Cy7 (755 nm; 778 nm), thus allowing their simultaneous detection” Thus, Hosono suggests a method wherein sequencing from the first and second sequencing primers to obtain the first and second reads comprises detecting signals, wherein signals that contribute to obtaining the first read are distinguishable on the basis of their intensity from signals that contribute to obtaining the second read.
Regarding claim 12, Hosono teaches a method wherein “particular reagents unless otherwise specified, as such may, of course, vary.” (Pg 7 ln 30-31). Thus, Hosono suggests a method wherein the first and second sequencing primers are provided at different concentrations.
Regarding claim 13, Hosono teaches a method wherein “In some aspects, the extension step of steps (d) and/or (f) can be carried out in the presence of one or more dideoxynucleotides. In some aspects, the extension step of steps ( d) and/or (f) can be carried out in the presence of one or more nucleotide analogues that comprise a reversible 3 'OH-protecting group.” (Pg. 41 ln 9-13). Thus, Hosono suggests a method wherein the second sequencing primer is provided as a mixture of extendable and non-extendable oligonucleotides.
Regarding claim 14, Hosono teaches Table 3 indicating the amount of reads that can be mapped by three different primers to a location differ. (Pg 69 ln 18; Table 3). Thus, Hosono suggests a method wherein the first sequencing primer and the second sequencing primer anneal to their respective adapter regions with significantly different efficiencies.
Regarding claim 15, Hosono teaches a method wherein “It is preferred that nucleic acid samples known or identified for use in amplification or detection methods” (Pg. 13 ln 15-17). Thus, Hosono suggests a method wherein sequencing from the first and second sequencing primers to obtain the first and second reads comprises mapping to a known reference sequence.
Regarding claim 16, Hosono teaches a method wherein “Strand displacement can be accomplished by using a strand displacing DNA polymerase or a DNA polymerase in combination with a compatible strand displacement factor” (Pg. 54 ln 17-19; Examples 11-12). Thus, Hosono suggests a method wherein sequencing from the first and second sequencing primers comprises extending the first and second sequencing primers with a strand-displacing polymerase.
Regarding claim 17, Hosono teaches a method wherein “Strand displacement factors useful…single-stranded DNA binding proteins” (Pg. 25 ln 12-17). Thus, Hosono suggests a method wherein sequencing from the first and second sequencing primers is performed in the presence of a single-stranded binding protein.
Regarding claim 19, Hosono teaches a method wherein “a sequencing reaction can be carried out using first a sequencing primer that can hybridize to a sequence within one of the hairpin adapters (e.g. a first or second primer binding site)” (Pg. 38 ln 19-21). Thus, Hosono suggests a method wherein sequencing from the first and second sequencing primers comprises performing a sequencing by binding technique.
Regarding claim 20, Hosono teaches a method wherein “The continuous strand extension creates long, single-stranded DNA consisting of hundreds of concatemers comprising multiple copies of sequences complementary to the circle” (Pg. 55 ln 26-28). Thus, Hosono suggests a method wherein the nucleic acid concatemer comprises at least 100 sequential copies of the first adapter region, the forward strand, the second adapter region, and the reverse strand.
Therefore, the invention as recited in claims 2-5, 8-17 and 19-20 are prima facie obvious over the prior art Hosono et al. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of the claims in view of Hosono et al. It would have been obvious to perform paired-ended sequencing with a concatamer of a target nucleic acid sequence according to the limitations of the instant application claims 2-5, 8-17 and 19-20 based on Hosono et al. (Patent App. Pub. No. WO 2019209946 A1).
Response to Arguments
Applicant's arguments filed 04/13/2026 (Pg. 6-7) with respect to claims 1-19 have been fully considered but they are not persuasive. To clarify some instances argued in the response filed 04/13/2026 see responses to each argument made by Applicant below:
Applicants’ argument: “claim 1 is amended to include the subject matter of claim 18. Because claim 18 is novel over the cited art, claim 1 as amended herein is novel over the cited art” (Pg. 8)
Response: Applicant’s arguments have been fully considered and found unpersuasive because as stated in the revised 103 rejection above, Hosono does suggest the subject matter of the previously claimed 18. The 35 U.S.C. 102 rejection is revised and documented as a 35 U.S.C. 103 rejection in the Final action above as claim 18.
Applicants’ argument: “The Office's position is supported only by conclusory assertions, rather than by articulated reasoning with a rational underpinning sufficient to support a conclusion of obviousness.” (Pg. 9)
Response: Applicant’s arguments have been fully considered and found unpersuasive because as stated in the revised 103 rejection above, “Therefore, the invention as recited in claim 1 is prima facie obvious over the prior art Hosono et al. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of the method for paired-end sequencing as recited in claim 1 in view of Hosono et al. It would have been obvious to perform paired-ended sequencing with a concatamer of a target nucleic acid sequence according to the limitations of the instant application claim 1 based on Hosono et al. (Patent App. Pub. No. WO 2019209946 A1)” and “Therefore, the invention as recited in claims 2-5, 8-17 and 19-20 are prima facie obvious over the prior art Hosono et al. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of the claims in view of Hosono et al. It would have been obvious to perform paired-ended sequencing with a concatamer of a target nucleic acid sequence according to the limitations of the instant application claims 2-5, 8-17 and 19-20 based on Hosono et al. (Patent App. Pub. No. WO 2019209946 A1).”
Claims 6 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Hosono et al. (“Hosono”; Patent App. Pub. WO 2019209946 A1, Oct. 31, 2019) in view of Li et al. (“Li”; Patent App. Pub. EP 3260554 A1, Dec. 27, 2017).
The teachings of Hosono are documented above in the rejection of claims 1-5, 8-17 and 19-20 under 35 U.S.C. 103.
Regarding claim 6 and 7, Hosono teaches a method wherein “using uracil-containing primers” (Pg. 7 ln 3). Hosono teaches a method wherein “after a first primer elongation product is generated, at least one of the partially double stranded concatamers can be contacted with a second primer and the second primer can be extended” (Pg. 42 ln 28-30).
Hosono does not explicitly teach the limitations of claims 6 and 7.
Li discloses “In some embodiments, the present teachings provide methods for paired end sequencing. In some embodiment, a polynucleotide template to be subjected to paired end sequencing comprises at least one cross linking moiety and at least one scissile moiety. In some embodiments, a paired end sequencing reaction comprises (a) a forward sequencing step, (b) a cleavage step, and (c) a reverse sequencing step. In some embodiments, a paired end sequencing reaction comprises (a) a forward sequencing step, (b) a cross-linking step, (c) a cleavage step, and (d) a reverse sequencing step.” (Abstract)
Regarding claims 6 and 7, Li teaches a method wherein “In some embodiments, a paired end sequencing reaction comprises: (a) a forward sequencing step; (b) a cleavage step, and (c) a reverse sequencing step.” (Para.173). It would be obvious to one skilled in the art that the cleavage step would be performed to remove the first primer in pair end sequencing after the obtaining the first read and include a washing step for separation of the cleavage product. Thus, Hosono and Li suggest a method wherein, after obtaining the first read, nascent strands formed by sequencing from the first primer are removed before hybridizing the second sequencing primer to the second adapter regions; wherein the nascent strands formed by sequencing from the first primer are removed by cleavage and washing, exonuclease digestion, or denaturation.
Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of paired-end sequencing as taught by Hosono to incorporate the method with the cleavage step as taught by Li and provide a method wherein, after obtaining the first read, nascent strands formed by sequencing from the first primer are removed before hybridizing the second sequencing primer to the second adapter regions; wherein the nascent strands formed by sequencing from the first primer are removed by cleavage and washing, exonuclease digestion, or denaturation. Doing so would aid in removal of the first nascent after the read has been obtained to aid in an accuracy of target sequence reads using paired-end sequencing method.
Response to Arguments
Applicant's arguments filed 04/13/2026 have been fully considered but they are not
persuasive. Arguments against Hosono on Pg. 10 are not persuasive as discussed above.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Hosono et al. (“Hosono”; Patent App. Pub. WO 2019209946 A1, Oct. 31, 2019).
Regarding claim 21, Hosono teaches a method comprising “a target nucleic acid molecule for sequencing. The method can comprise forming a first partially double stranded circular DNA wherein the partially double stranded circular DNA contains (i) a sequence of interest having a first strand and a second strand, (ii) a first hairpin adapter, and (iii) a second hairpin adapter, wherein the first and second strands of the sequence of interest are complementary to each other… wherein the amplification of the first partially double stranded circular DNA results in a plurality of concatemers” (Pg 43. ln 1-7). Hosono teaches a method comprising “methods involving concatemer RCA-based NGS pair-end sequencing using a circular template that can be in the shape of a dumbbell” (Pg. 43, ln 8-9). Hosono teaches a method comprising “the first hairpin adapter and the second hairpin adapter are different.” (Pg 43. ln 15).
Regarding claim 21, Hosono teaches a method comprising “The method further involves immobilizing multiple concatemers on a surface of a substrate, where the surface is functionalized. The method involves immobilizing the concatemers on the surface using capture probes.” (Pg. 24 ln 20-24). The “capture probes” reads on a masking primer with the capability to hybridize to the second adapter region and be extended to form a masking strand complementary to the forward strand prior to hybridizing the first sequencing primer to the first adapter regions. Hosono teaches a method comprising “Hairpin adapters can vary widely in length, and can depend in part on the number and type of functional elements desired. Examples of functional elements include, but are not limited to, anchor sequences, sequences complementary to capture probe sequences (e.g. for attachment to surfaces), tagging sequences, secondary structure sequences, sequences for attachment/hybridization of label probes, functionalization sequences, primer binding sites, recognition sites for nucleases, such as nicking enzymes, restriction endonucleases, and the like” (Pg. 20 ln 28-33- Pg. 21 ln 1). Hosono teaches a method comprising “any other oligonucleotides can be synthesized” (Pg. 59 ln 9-10). “any other oligonucleotides can be synthesized” reads on extending the masking primer to produce a first masking strand complementary to the forward strand. Hosono also teaches a method comprising “extending the first primer in the presence of one or more dideoxynucleotides thereby generating a first primer elongation product can be performed in the presence of a dideoxynucleotides that once incorporated would irreversibly terminate the extension reaction” (Pg. 42 ln 14-16). Hence, suggesting that an extended sequence can be blocked from further extending the oligonucleotide with dideoxynucleotides prior to elongating the entirety of the first adapter.
Regarding claim 21, Hosono teaches a method comprising “ “amplifying the first partially double stranded circular DNA via rolling circle amplification, wherein amplification of the first partially double stranded circular DNA results in replicated strands, wherein during amplification 5 at least one of the replicated strands is displaced from the first partially double stranded circular DNA by strand displacement replication, wherein the amplification of the first partially double stranded circular DNA results in a plurality of partially double stranded concatamers; (c) contacting at least one of the partially double stranded concatamers with a first primer, wherein the first primer hybridizes to the first or second primer binding, 10 and (d) identifying at least one nucleotide of the sequence of interest adjacent or close to the first primer binding site”
Thus, Hosono suggests a method for nucleic acid sequencing comprising: providing a nucleic acid concatemer comprising multiple sequential copies of: a first adapter region, a forward strand of a target nucleic acid sequence, a second adapter region different from the first adapter region, and a reverse strand of the target nucleic acid sequence that is complementary to the forward strand; hybridizing a masking primer to the second adapter regions, and extending the masking primer to produce a first masking strand complementary to the forward strand, wherein the first masking strand is not also complementary to the entirety of the first adapter region; and hybridizing a first sequencing primer to the first adapter regions, and sequencing from the first sequencing primer to obtain a first read of a first portion of the target nucleic acid sequence.
Therefore, the invention as recited in claims 21 is prima facie obvious over the prior art Hosono et al. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of the claims in view of Hosono et al. It would have been obvious to perform paired-ended sequencing with a concatamer of a target nucleic acid sequence according to the limitations of the instant application claim 21 based on Hosono et al. (Patent App. Pub. No. WO 2019209946 A1).
Response to Arguments
Applicant's arguments filed 04/13/2026 have been fully considered but they are not persuasive. Furthermore, to clarify some instances argued in the response filed 04/13/2026 see responses to each argument made by Applicant below:
Applicants’ argument: “The Office Action alleges that the capture probes of Hosono read on a ''masking strand complementary to the forward strand prior to hybridizing the first sequencing primer to the first adapter regions." Office Action at page 13. Applicant respectfully disagrees. Hosono's capture probes are sequences complementary to sequences present in adapters (Hosono at page 20, lines 28-33). Thus, a capture probe of Hosono is annealed to adapter sequences. Claim 21 recites ''hybridizing a masking primer to the second adapter regions, and extending the masking primer to produce a first masking strand complementary to the forward strand." The masking primer of claim 21 may be analogous to Hosono's capture probe, but Hosono's capture probe is not the ''masking strand complementary to the forward strand'' of claim 21. ” (Pg. 11).
Response: In response to applicants’ arguments stated above, I admit that the interpretation was stated inappropriately, the purpose of the interpretation was to show that the capture probes taught by Hosono suggest utilization as a masking primer to the second adapter region. The rejection is maintained and revised as the capture probe does read on masking primer and Hosono suggests synthesis of any nucleotide synthesis which reads on extending the masking primer to produce a first masking strand. Thus, Hosono does suggest every element of claim 21.
Conclusion of Response to Arguments
In view of the amendments, the previous rejections under 35 U.S.C. 102(a)(1) are maintained and transferred to 35 U.S.C. 103, the other 35 U.S.C. 103 rejections are maintained and revised, and the above responses to arguments are documented in this Final Office Action . No claims are in condition for allowance.
Conclusion
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENDRA R VANN-OJUEKAIYE whose telephone number is (571)270-7529. The examiner can normally be reached M-F 9:00 AM- 5:00 PM.
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/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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