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 .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 03/24/2026 was filed after the mailing date of the Non-final Rejection on 02/06/2026. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Status of Claims / Response to Amendment
This office action is in response to an amendment filed on April 30, 2026.
Claims 1, 8, 14, 22-24, 27-40 were previously pending. Applicant amended claims 1, 14, 28 and 35; cancelled claims 22-24 and 27; claims 41-44 are newly added.
Claims 1, 8, 14, 28-44 are currently pending, with claims 1, 8, 14, 28-34 and 41-43 withdrawn. Claims 35-40 and 44 are under consideration.
All of the previously presented rejections have been withdrawn as being obviated by the amendment of the claims, which added new limitations to the claims, that were not considered in the previous rejections. Namely, claim 35 has been amended to recite "incorporating an unterminated nucleotide to extend a complementary polynucleotide."
Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
This office action contains new grounds for rejection necessitated by amendment.
Priority
For the instant claims 35-40 and 44, the applicant claims priority of the US provisional application NO. 63/247,155, which has a filling date on September 22, 2021.
Claim Interpretation
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP§ 2111.
For the purpose of applying prior art, the term "variation of a pore current," as recited throughout the claims, is not expressly defined in the application's disclosure. Thus, under BRI, it is interpreted to encompass any change, shift, or variation observable in the pore current of a nanopore. This includes, for example, changes in pore current caused by blockage due to the introduction of a polynucleotide into a previously empty nanopore, temporal changes in pore current between two time points, or changes in pore current resulting from the application of different voltages across the membrane.
For the purpose of applying prior art, claim 35 recites "applied read potential," which is a term not expressly defined in the application's disclosure. The specification in paragraph [0141] provides the following relevant description:
"In another embodiment, since the applied electric potential difference may shift the position of the polynucleotide relative to the nanopore recognition zone, the regions of the polynucleotide sensed by the recognition zone may be shifted/offset when different electric potential differences are applied, and thus different maps may be used when different electric potential differences are applied. For example, at one applied voltage, the regions of the polynucleotide sensed by the recognition zone may include a 5-mer in the template strand and 3 nucleotides in the complementary strand; at another applied voltage, the regions of the polynucleotide sensed by the recognition zone may include a 5-mer in the template strand and 2 nucleotides in the complementary strand."
Thus, under BRI and in light of the specification, the term "applied read potential" is understood as voltage applied to the nanopore system, thereby allowing sensing of polynucleotides.
New Grounds of Rejection: Double Patenting- Obvious Type
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 35, 37-40 and 44 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 6, 9 of copending Application No. 17/947,877 1(reference application, amended claims filed on 01/29/2026), in view of Laszlo (Laszlo et al. Decoding long nanopore sequencing reads of natural DNA. Nat Biotechnol. 2014 Aug;32(8):829-33. doi: 10.1038/nbt.2950. Epub 2014 Jun 25. PMID: 24964173; PMCID: PMC4126851).
Instant claim 35 recites:
A method of sequencing a template polynucleotide using a nanopore, comprising:
incorporating an unterminated nucleotide to extend a complementary polynucleotide (‘877 Application, claim 1);
determining a variation of a pore current when a single-stranded portion of the template polynucleotide and a duplex portion of the template polynucleotide and the complementary polynucleotide are held at an applied read potential in a position within the nanopore such that extension of the complementary polynucleotide cannot occur (‘877 Application, claim 1, 2);
comparing the variation of the pore current to a K-mer map,
the K-mer map comprising a plurality of entries in which each entry includes a K-mer sequence and a pore current variation at the applied read potential,
the K-mer sequence includes at least one position of the template polynucleotide in the single-stranded portion and at least one position of the template polynucleotide in the duplex portion; and
determining a sequence of the template polynucleotide based upon the comparison of the variation of the pore current to the K-mer map.
The ‘877 Application claims nanopore sequencing method comprising incorporating an unterminated nucleotide to extend a complementary polynucleotide and measuring current signal of a duplex portion of the template polynucleotide within the nanopore.
While the ‘877 Application does not expressly claim the use of a k-mer map, Laszlo fills the gap and teaches a method for identifying polynucleotide sequences in nanopore sequencing using a k-mer map (see Abstract, "quadromer map").
Laszlo teaches comparing measured current signals to values in a K-mer map (page 2, para 3; page 3, para 1-2, measured current level sequences were compared to predicted current levels based on the quadromer map.), the K-mer map comprising a plurality of entries in which each entry includes a K-mer sequence and a pore current (Supplementary Table 1), and determining a sequence of the template polynucleotide based upon the comparison of the pore current to the K-mer map (page 5, para 1).
Laszlo further suggests advantages of this k-mer map approach, such as "strong homology between quadromer-based current predictions and nanopore sequencing reads" (page 3, para 3, lines 1-2) and "highly predictive of ion current levels of previously unmeasured, complex, natural DNA sequences." (page 5, para 1, lines 4-5).
Accordingly, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to apply Laszlo's teaching of using a k-mer map to the nanopore sequencing method in the ‘877 Application. Both relate to the same field ꟷ polynucleotide analysis using nanopores. A skilled artisan would have been motivated to generate and apply a k-mer map for duplexes in order to improve base calling for each nucleotide added in ‘877 Application’s nanopore sequencing method, with high predictive confidence as suggested by Laszlo.
Therefore, instant claims 35, 39-40 and 44 are obvious over claims 1-2 of the ‘877 Application , in view of Laszlo. Instant claims 37; 38 are obvious over claims 6; 9 of the ‘877 Application , in view of Laszlo.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Claims 35, 37-40 and 44 are rejected; claim 36 is objected to as being dependent upon a rejected base claim. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TIAN NMN YU whose telephone number is (703)756-4694. The examiner can normally be reached Monday - Friday 8:30 am - 5:30 pm.
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/TIAN NMN YU/Examiner , Art Unit 1681 /AARON A PRIEST/Primary Examiner, Art Unit 1681
1 Both the application under examination and the reference application have the same patent term filing date.
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