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 .
Status of the Application
Claims 37-41 are pending and under examination.
Claims 42-45 are withdrawn.
The following Office Action is in response to Applicant's communication dated 05/19/2026.
Applicant's election with traverse of claims 37-41 in the reply filed on 05/19/2026 is acknowledged. The traversal is on the ground(s) that the groups can be examined together without undue prosecutorial burden. This is not found persuasive because search burden is not an issue herein, since the instant case is a 371 national stage entry of a PCT case, and search burden is only applicable in restriction practice for applications which enter under, for example, 35 U.S.C. 111. See also, MPEP §801, which explicitly states that, “applications entering the National Stage under 35 U.S.C. 371 as a Designated or Elected Office in the U.S. Patent and Trademark Office is covered in Chapter 1800.” Wherein Chapter 1800, and specifically, 1893.03 (d), clearly states that, “Examiners are reminded that unity of invention (not [US] restriction practice pursuant to 37 CFR 1.141 -1.146)) practice is applicable …in national stage applications submitted under 35 U.S.C. 371.” (Emphasis added). Therefore, an argument for rejoining groups on an alleged lack of undue search burden is not persuasive.
The requirement is still deemed proper and is therefore made FINAL.
Drawings
The drawings are objected to because:
Specific deficiency - Sequences appearing in the drawings for Figs.3 is not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Claim Interpretation
Under BRI, the claimed “flap adapter”, “3’ adapter” and “universal oligonucleotide sequence” are not limited to applicant’s specific FENGC Oligo 1-N/U1-N, Oligo 2-N/U1-N, or Oligo 3-N/U2 structures because claim 37 does not recite those specific oligonucleotides. The claim broadly encompasses an adapter/probe arrangement having single strand portion complementary to a region of source sequence, arranged to make a flap structure, and cooperating with a common/universal sequence for ligation and amplification. Under this interpretation, an oligonucleotide/probe system that form 5’ flap, 3’ flap, or double flap structures that ligates common sequence to target sequence is interpreted as satisfying the claimed adapter and universal sequence limitation.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
Claim(s) 37-41 is/are rejected under 35 U.S.C. 103 as being unpatentable over Zheng et al. (US10119162B2, published March 2017) in view of Kladde et al. (US10435740B2, published April 2016, disclosed in IDSS).
Regarding claim 37. Zheng discloses a method for enriching one or more sequences of interest from a source sequence comprising: I. obtaining a source DNA; (e.g. method of simple multiplex targeted amplification of genomic DNA [column 14, lines 66-67])
II denaturing the source DNA; III. annealing one or more first and second flap adapters to first and second regions, respectively, of the denatured source sequence, each of the first and second flap adapters comprising a single-stranded sequence complementary to the first and second regions, respectively, such that annealing of the first and second flap adapters to the denatured source sequence creates corresponding first and second flap structures in the denatured source sequence, each of the first and second flap structures comprising a portion that hybridizes to a universal oligonucleotide sequence wherein the first flap structure comprises a portion of the sequence of interest and the second flap structure is downstream of the sequence of interest; (e.g. target specific probe may be hybridize to the target nucleic acid to generate 5′ flap, 3′ flap, and double flap structure at target ssDNA ends [column 15, lines 1-13]. FIG. 3 (shown below) shows a target specific probe hybridize to target DNA 302 and positions common sequence 304 and 305 adjacent to the target sequence. Fig 3D shows when the source DNA 301 contain extra/flap sequences on both ends of the target sequence, the hybridized probe/common sequence arrangement form double flap structure at 5’ and 3’ ends. Thus, under BRI, Zheng’s probe 303 with common sequence 304 and 305 corresponds to the claimed flap adapter architecture because structure comprises target compliment single strand portions that hybridize to target sequence and portion that hybridize to common sequences 304 and 305. After flap removal, common sequences 304 and 305 ligated to DNA 302, leading to sing strand 306 in which the target ssDNA flanked by common/universal sequences [column 22, line 18-column 24, line 57].)
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IV. cleaving the denatured source DNA using a structure-specific endonuclease to produce a cleaved sequence of interest comprising 5' and 3' cut ends; (e.g. in FIG. 3D the DNA can have both a 5′ flap and a 3′ flap, wherein restriction enzyme may be used to cut both ends [column 22, line 64-column 23, line 2])
V. ligating the 5' cut end to a 3' end of a first universal oligonucleotide sequence of the first flap adapter; (e.g. FIG. 3D, oligo 309 is there to assist the 5′ flap nuclease such as human FEN1 cut target DNA efficiently and precisely to create a nick for ligation in step 321. In step 321, the common sequences 304 3’ end is ligated to target DNA 302 5’ end, resulting in the single strand 306 that includes the target flanked by the common sequences 304 and 305 [column 22, line 18-column 24, line 57])
VI. ligating the 3' cut end to a 5' end of a sequence of a 3' adapter, the 3' adapter
comprising an adapter oligonucleotide sequence comprising a single-stranded portion that
hybridizes to a portion of the sequence of interest and another portion that hybridizes to a second
universal oligonucleotide sequence, wherein the 5' end of the sequence of the 3' adapter is the 5'
end of the second universal sequence, (e.g. the reference’s “3’ adapter” is the combination of both probe 303 and common sequence 305. FIG. 3D, step 321, the common sequences 305 5’ end is ligated to target DNA 302 3’ end, resulting in the single strand 306 that includes the target flanked by the common sequences 304 and 305. The adapter sequence 303 comprising a single-stranded portion that hybridizes to a portion of the sequence of interest [column 22, line 18-column 24, line 57].)
VII. subjecting the sequence of interest from step (V), step (VI), or both, to one or more
exonucleases to produce an enriched single strand of DNA comprising an arrangement of first
universal oligonucleotide sequence-Sequence of interest-second universal oligonucleotide
sequence. (e.g. 3′ to 5′ ssDNA exonucleases shorten the unwanted 3’ flap of ssDNA, so the 5’ flap of common oligo can be cleaved and the nicked can be ligated [column 24, lines 45-56]).
Zheng does not disclose that the 3' end of the second universal sequence is protected from exonuclease digestion.
Kladde discloses a target selection method in which fragmented genomic ssDNA is enriched using oligonucleotide patches, wherein complimentary universal priming sequences U1 and U2 hybridize to their respective oligonucleotide patches and are ligated to target ssDNA at both ends. Kladde further discloses that the U2 primer contains phosphorothioates and a 3-carbon spacer at its 3′ end, prevent unwanted ligation and protect the strand from nuclease degradation. Kladde also discloses amplifying the selected ssDNA using universal primers complimentary to U2 and having same sequence as U1.[Fig 1 (below) and column 3 line 45-column 4 line 10].
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As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to modify Zheng’s second common sequence using the protected U2 structure taught by Kladde because Zheng uses exonuclease during processing of double flap structures and protecting the 3’ end of the second common/universal sequence would predictably prevent unwanted exonuclease digestion of the desired ligated adapter-ssDNA product [column 13, lines 34-56]. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 — 97 (2007) (MPEP § 2143).
Regarding claim 38, Zheng does not disclose subjecting a source sequence to a DNA methyltransferase. However, Kladde discloses treating nuclei/chromatin with M.CviP DNA methyltransferase under conditions that maintain chromatin integrity, hence methylating accessible DNA. It would have been obvious to one of ordinary skill in the art to apply methyltransferase treatment in order to mark assessable DNA regions and permit targeted analysis of methylation and chromatin accessibility.
Regarding claim 39, Zheng further discloses endonuclease comprises one or more enzymes having flap endonuclease activity [Fig 1].
Regarding claim 40, Zheng further discloses purifying the first universal oligonucleotide sequence-Sequence of interest-second universal oligonucleotide sequence (e.g. the final ligation product is purified [column 30, lines 21-23]), and optionally amplifying by PCR [column 30, lines 53-54].
Regarding claim 41, Zheng further discloses sequencing the sequence of interest after step VII [column 10, lines 15-17].
Conclusion
No claims are allowed
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Khai Quynh Tien Pham whose telephone number is (571)272-6998. The examiner can normally be reached M-T, 9-4 ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at (571) 272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KHAI QUYNH TIEN PHAM/ Examiner, Art Unit 1684
/JEREMY C FLINDERS/ Primary Examiner, Art Unit 1684
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