DETAILED ACTION
Response to Amendment
Applicant’s response to the office action filed on December 12, 2025 has been entered. The claims pending in this application are claims 44-65 wherein claims 48-51, 56, and 57 have been withdrawn due to the restriction requirement in the office action mailed on June 25, 2025. Claims 44-47, 52-55, and 58-65 will be examined.
Specification
The disclosure is objected to because of the following informalities: pages 24, 26-29, 31-34, 36-39, and 49 contain nucleotide sequences having more than 10 nucleotides. However, there is no SEQ ID Nos for these nucleotide sequences in pages 24, 26-29, 31-34, 36-39, and 49. Note that applicant has not addressed this issue in the response filed on December 12, 2025.
Appropriate correction is required.
Claim Objections
Claim 44 is objected to because of the following informalities: (1) “the rephasing” in line 5 should be “the method”; (2) “corresponding to” in steps (i) and (iii) should be “is complementary to”; (3) “the sequencing primers from step (ii)” should be “extended sequencing primers without the first blocking group from step (ii)”; and (4) “said first and second blocking groups are each” in the last “wherein” phrase should be “said first blocking group and said second blocking group are”.
Claim 45 is objected to because of the following informality: “the only nucleotide triphosphate” should be “the single nucleotide triphosphate”.
Claim 46 is objected to because of the following informality: this claim should be deleted since claims 44 and 45 have all limitations recited in the claim.
Claim 47 is objected to because of the following informality: “one of the first and second blocking groups is an O-azidomethyl group, and one of the first and second blocking groups is an O-NH₂ group” should be “one of the first blocking group and the second blocking group is an O-azidomethyl group, and another of the first blocking group and the second blocking group is an O-NH₂ group”.
Claim 52 is objected to because of the following informality: “five to fifteen of said cycles are performed in step (a)” should be “the multiple cycles are five to fifteen cycles”.
Claim 55 is objected to because of the following informality: “the cleaving in step (ii)” should be “step (ii)”.
Claim 58 is objected to because of the following informality: “resuming cycles of
the sequencing of the clonal population of DNA templates after the rephasing” should be
“sequencing the clonal population of DNA templates after said rephasing the sequencing primers in the clonal population of DNA templates”.
Claim 59 is objected to because of the following informality: “performing multiple cycles of sequencing of a plurality of clonal populations of DNA templates in which a sequencing primer hybridized to each DNA template is extended by one nucleotide per cycle, thereby identifying a complementary nucleotide in the DNA template; after a number of such sequencing cycles, rephasing the sequencing primers according to the method of claim 44; then resuming cycles of the sequencing to identify further nucleotides in the DNA template” should be “performing multiple cycles of sequencing a plurality of clonal populations of DNA templates in which a sequencing primer hybridized to each of the DNA templates is extended by one nucleotide in each of the multiple cycles, thereby identifying a complementary nucleotide in each of the DNA templates; after a number of the multiple cycles, rephasing the sequencing primers according to the method of claim 44; then sequencing the plurality of clonal populations of DNA templates to identify further nucleotides in each of the DNA templates”.
Claim 60 or 61 or 62 or 65 is objected to because of the following informality: “the rephasing” should be “said rephasing the sequencing primers”.
Claim 60 is objected to because of the following informality: the phrase “within the first 800 of said multiple cycles” should be deleted.
Claim 61 is objected to because of the following informality: “extends the number of
clonal populations of DNA templates in the plurality having a discordance percentage of less than 2% by at least 1.5-fold” should be “increases at least 1.5-fold of clonal populations of DNA templates having a discordance percentage of less than 2% in the plurality clonal populations of DNA templates”.
Claim 62 is objected to because of the following informality: “extends the number of
clonal populations of DNA templates in the plurality having a discordance percentage of less than 2% by at least 200 cycles” should be “extends clonal populations of DNA templates having a discordance percentage of less than 2% in the plurality clonal populations of DNA templates for at least 200 cycles”.
Claim 65 is objected to because of the following informality: “during the sequencing” should be deleted.
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.
Claims 44-47, 52-55, and 58-65 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.
Claim 44 is rejected as vague and indefinite in view of the preamble of the claim because it is unclear that a method of dinucleotide frequency rephasing (DFR) what is used to restore phase at a selected dinucleotide XY from where during a process of sequencing-by-synthesis. Please clarify.
Claim 44 is rejected as vague and indefinite because the phrase “the extending being continued until substantially all of the extended sequencing primers are blocked with the first blocking group” in step (i) does not make sense. Does this phrase mean that “said extending the sequencing primers being stopped until 3’ ends of extended sequencing primers are blocked with the first blocking group”? Please clarify.
Claim 44 is rejected as vague and indefinite in view of step (ii) because it is unclear that the first blocking group located in where is unblocked. Please clarify.
Claim 44 is rejected as vague and indefinite in view of step (b). Since, after step (b), extending sequencing primers can be blocked with a second blocking group, without unblocking the second blocking group from extended sequencing primers from step (iii) in step (b), it is unclear why step (a) can be repeated. Please clarify.
Claim 54 is rejected as vague and indefinite because the claim does not make sense. Does this claim mean that “wherein said readjusting the 3’ end of the sequencing primers to an upstream position comprises cleaving uracil bases from the sequencing primers and the uracil bases are the analogs which are incorporated to the sequencing primers before readjusting step”? Please clarify.
Claim 65 is rejected as vague and indefinite because it is unclear that a read length of at least 800 bases is obtained from where. Please clarify.
Response to Arguments
Applicant’s arguments with respect to claims 41, 43-47, 52-55, and 59-65 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
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.
No claim is allowed.
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/FRANK W LU/
Primary Examiner, Art Unit 1683
December 31, 2025