DETAILED CORRESPONDENCE
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 .
This action is in response to the papers filed June 17, 2026. Currently, claims 1-12, 16-18, 22-26 are pending. Claims 22-26 have been withdrawn as drawn to non-elected subject matter.
Although the claims filed June 17, 2026 were amended to include dependencies for numerous claims previously lacking in the April 15, 2026 amendment, the set of claims are not properly marked up. Applicant is reminded, the amendment under consideration herein fails to comply with 37 CFR 1.121 because the claim listing does not contain the appropriate markings indicating matter added to the amended claims. Thus, the amendment could be considered non-responsive. In the interest of compact prosecution the amendment at issue will not be considered non-responsive. However, any future responses failing to comply with 37 CFR 1.121 will be held non-responsive, and will not be considered.
Election/Restrictions
Applicant's election without traverse of Group I, Claims 1-12, 16-18 in the paper filed June 17, 2026 is acknowledged.
The requirement is still deemed proper and is therefore made FINAL.
Priority
This application claims priority to
PNG
media_image1.png
66
596
media_image1.png
Greyscale
Drawings
MPEP 608.02, part VIII states:
Color drawings and color photographs are not accepted in utility applications filed under 35 U.S.C. 111 unless a petition filed under 37 CFR 1.84(a)(2) or (b)(2) is granted. Color drawings and color photographs are not permitted in international applications (see PCT Rule 11.13 ).
Unless a petition is filed and granted, color drawings or color photographs will not be accepted in a utility patent application filed under 35 U.S.C. 111. The examiner must object to the color drawings or color photographs as being improper and require applicant either to cancel the drawings or to provide substitute black and white drawings.
The drawings are in color. No petition for color drawings has been filed; therefore, the color drawings or color photographs are being objected to as being improper. The specification is also objected to for not reciting the requisite color petition language as the first paragraph of the brief description of the drawings.
Claim Objections
Claims 1-12, 16-18 are objected to because the claim contains more than one period (see 609.01(m)). Periods may not be used elsewhere in the claims except for abbreviations. For example, a. b. i. ii. Iii. Iv. contains a period and the end of the claim contains a period. This objection may be overcome by amending a. to read a) (see MPEP 608.01(m)).
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.
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.
Claims 1-12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Seitz et al. (US 2015/0152409, June 4, 2015) in view of Pachuk et al. (US 6,143,527, November 7, 2000).
Seitz teaches nucleic acid transcription methods for generating an amplified nucleic acid portion of a template nucleic acid by annealing at least one oligonucleotide primer to a temple, annealing a stopper to the template and elongating the primer in a template specific manner until the elongating product reaches the position of an annealed stopper.
PNG
media_image2.png
122
652
media_image2.png
Greyscale
Seitz teaches many different configurations for the L1 and stopper, including a hairpin loop region with a first and second hybridization sequence.
PNG
media_image3.png
194
156
media_image3.png
Greyscale
With respect to Claims 8-9, the interposing oligonucleotides are required to have a barcode. A barcode is merely a nucleic acid sequence. The loop/linker is considered a barcode. Even more, Seitz teaches the oligonucleotide primers may share similar sequence portions, such as barcodes, that may be used for amplification or identification of products (para 46).
With respect to Claims 11 and 12, Seitz teaches the use of barcodes enable the mixing libraries from different samples and sequence them together in a flow cell (para 147). Seitz teaches analysis of gene expression and identification of differentially expressed genes and identification of genes of importance to disease (para 116).
Seitz does not teach hybridizing a bridge oligonucleotide to a first polynucleotide and a second nucleotide and then amplifying the integrated strand by amplification to product a tagged complement of two independent single stranded polynucleotides.
However, Pachuk teaches using bridge sequences to ligate DNA molecules together to join two molecules into a single, larger, composite nucleic acid molecule. Pachuk teaches bridging oligonucleotide comprises, from 5' to 3', a 10-40 nucleotide sequence which is complementary to a nucleotide sequence on the 5' end of the first strand of said first nucleic acid molecule and a 10-40 nucleotide sequence which is complementary to a nucleotide sequence on the 3' end of the first strand of said second nucleic acid molecule (Claims 2 and 6-7). The resulting composite sequence is then amplified. Pachuk teaches the bridge oligonucleotide allows the joining of fragments in a precise order (col 14, lines 60-67).
With respect to Claim 3, Pachuk teaches amplifying with primers. The primers have a hybridization sequence complementary to a sequence of the first/second polynucleotide. Further the primers are themselves are primer binding sequences.
With respect to Claim 4 and 5, Pachuk teaches amplifying the sequence which involves polymerases.
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention to have modified the method of Seitz with the bridge cloning method of Pachuk. Seitz teaches generating a sequencing library by inserting sequence tags in a longer nucleotide sequence and using varying input lengths. The varying input lengths may product distortion. Pachuk teaches creating longer polynucleotide sequences from two shorter sequences by hybridizing a bridge oligonucleotides. It would have been prima facie obvious to one of ordinary skill in the art to hybridize two shorter sequences using a bridge oligonucleotide since this would allow the creation of composite strands prior to or during the introduction of sequence tags and allow improvement in accurate and precise nucleotides in the amplified array.
Double Patenting
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 1-12 and 16-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 11,155,858 in view of Pachuk et al. (US 6,143,527, November 7, 2000).
Claims 1-12 and 16-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 12,139,754 in view of Pachuk et al. (US 6,143,527, November 7, 2000).
Claims 1-12 and 16-18 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-23 of copending Application No. 18/889/834 in view of Pachuk et al. (US 6,143,527, November 7, 2000).
Glezer ‘754 teaches a method of amplifying a tagged complement with interposing oligonucleotide barcode probes and extending and ligating the extension products (Claim 1). Claim 14 further claims computationally reconstructing sequences of a plurality of individual strands of the sample polynucleotide by joining sequences for adjacent portions of the sample polynucleotide.
Glezer ‘858 teaches a method of amplifying a tagged complement with interposing oligonucleotide barcode probes and extending and ligating the extension products (Claim 1). Claim 23 further claims computationally reconstructing sequences of a plurality of individual strands of the sample polynucleotide by joining sequences for adjacent portions of the sample polynucleotide.
Glezer ‘834 teaches a method of amplifying a tagged complement with interposing oligonucleotide barcode probes and extending and ligating the extension products (Claims 1 and 3).
Glezer ‘754 and Glezer ‘858 and Glezer ‘834 each teach joining portions of oligonucleotides but do not teach hybridizing a bridge oligonucleotide to join a first polynucleotide and a second nucleotide.
However, Pachuk teaches using bridge sequences to ligate DNA molecules together to join two molecules into a single, larger, composite nucleic acid molecule. Pachuk teaches bridging oligonucleotide comprises, from 5' to 3', a 10-40 nucleotide sequence which is complementary to a nucleotide sequence on the 5' end of the first strand of said first nucleic acid molecule and a 10-40 nucleotide sequence which is complementary to a nucleotide sequence on the 3' end of the first strand of said second nucleic acid molecule (Claims 2 and 6-7). The resulting composite sequence is then amplified. Pachuk teaches the bridge oligonucleotide allows the joining of fragments in a precise order (col 14, lines 60-67).
With respect to Claim 3, Pachuk teaches amplifying with primers. The primers have a hybridization sequence complementary to a sequence of the first/second polynucleotide. Further the primers are themselves are primer binding sequences.
With respect to Claim 4 and 5, Pachuk teaches amplifying the sequence which involves polymerases.
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention to have modified the method of Glezer ‘754 and Glezer ‘858 and Glezer ‘834 with the bridge cloning method of Pachuk. Glezer ‘754 and Glezer ‘858 and Glezer ‘834 each teach joining portions of oligonucleotides. The prior art, namely Pachuk teaches creating longer polynucleotide sequences from two shorter sequences by hybridizing a bridge oligonucleotides to join two sequences. It would have been prima facie obvious to one of ordinary skill in the art to join two shorter sequences using a bridge oligonucleotide.
Conclusion
No claims allowable over the art.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Dramanac et al. (US 2016/0046985, February 18, 2016) teaches methods for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting information (abstract, para 14) wherein multiple hairpin oligonucleotides comprising stem/loop structures are annealed onto a plurality of long DNA initial fragments (para 28, 151 and Figure 2A). Drmanac does not teach amplifying the integrated strand by an amplification reaction to produce a tagged complement of two independent single-stranded polynucleotides.
PNG
media_image4.png
448
654
media_image4.png
Greyscale
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEANINE ANNE GOLDBERG whose telephone number is (571)272-0743. The examiner can normally be reached Monday-Friday 6am-3:30pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached on (571)272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JEANINE A GOLDBERG/Primary Examiner, Art Unit 1682
June 19, 2026
Prosecution Insights