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 .
Priority
This application 18/036,392 filed on 05/10/2023 is a 371 national phase of PCT//US2021/058809 filed on 11/10/2021, and claims the benefit of provisional U.S. Patent Application No. 63/111,951, filed on 11/10/2020.
The priority date of claims 1 and 24 and their respective dependent claims is determined to be 11/10/2020, the filing date of provisional U.S. Patent Application No. 63/111,951.
Status of Claims
Applicant’s amendments to claims filed 03/17/2026 in response to the Non-Final Rejection mailed 12/17/2025 are acknowledged.
Claim 1 is amended.
Claims 10-14, 23-25, and 48-51 have been canceled.
Claims 1 and 3-9 are pending and under examination.
Response to Remarks filed 03/17/2026
The amendments and arguments presented in the papers filed 03/17/2026 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 12/17/2025 listed below have been reconsidered as indicated.
Clarity in the record has been made to correct the typographical error in the previous Office Action. The U.S. Provisional Patent Application No. 63/111,951 is acknowledged in the priority section included in this Office Action.
The objections to the drawings are withdrawn in view of replacement drawings provided 03/17/2026.
The objections to the specification regarding the use of trade names or marks are withdrawn in view of the amendments to the specification.
The 35 USC 112(b) indefiniteness rejections of claims 1, 3-14 and 23 have been withdrawn in view of the amendments to claim 1 and cancellation of dependent claims.
The 35 USC 112(b) indefiniteness rejection of claim 8 for indefiniteness has been withdrawn in view of the amendments to claim 8.
The 35 USC 112(b) indefiniteness rejections of claims 13, 23, and 24 are moot in view of the cancellation of the claims.
The rejection of claims 11-13 under 35 U.S.C. 101 are moot in view of the cancellation of the claims.
The rejection of claims 1 and 3-14 under 35 U.S.C. 103 as being unpatentable over Buenrostro et al. (US 20200248255) in view of Ku et al. (Single- cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification. 2019. Nature Methods.16 (4): p. 1-6, on IDS dated 11/01/2023) are withdrawn in view of amendments and cancellation of the claims.
The rejection of claims 23-25 and 48-51 under 35 U.S.C. 103 as being unpatentable over Buenrostro et al. (US 20200248255) in view of Ku et al. (Single- cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification. 2019. Nature Methods.16 (4): p. 1-6, on IDS dated 11/01/2023) as applied to claims 1 and 3-14 above, and further in view of Kennedy et al. (US 20190390253) are withdrawn as being moot in view of the cancellation of the claims.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Drawings - New
The drawings are objected to because: Figure 8, parts A and B contain multiple typographical errors in the figure labels, including, for example, in 8A: “clearage”, “per wet” and in 8B: “inacinang”, “crossrie”, among others. Please replace Figure 8 with corrected labels.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claim 1 is objected to because of the following informalities: The amended claim recites “--providing fixed cell comprising--”. The intended language is interpreted to be “providing a fixed cell comprising”. Appropriate correction is required.
Claim 7 is objected to because of the following informalities: The amended claim recites “-- contacting the RNA with a reverse transcriptase primer--”. The intended language is interpreted to be “contacting the RNA with a reverse transcription primer”. Appropriate correction is required.
Claim 8 is objected to because of the following informalities: The amended claim recites “The method of claim 8, the first oligonucleotide adaptor --”. The intended language is interpreted to be “The method of claim 8, wherein the first oligonucleotide adaptor”. Appropriate correction is required.
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.
Claims 1 and 3-9 are rejected under 35 U.S.C. 103 as being unpatentable over Buenrostro et al. (US 20200248255) in view of Ku et al. (Single- cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification. 2019. Nature Methods.16 (4): p. 1-6, on IDS dated 11/01/2023) and Zhu et al. (An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. 2019. Nat. Struct. Mol. Biol. 26: 1-22 with supplemental).
The following are new rejections necessitated by amendments
Buenrostro teaches a method for analyzing genomic DNA and RNA from single cells, the method comprising crosslinking cells using a fixative (para 59), fragmenting DNA by contacting chromatin within individual cells with a transposase to generate fragmented cellular genomic DNA (para 11); reverse transcribing the mRNA to generate cDNA (para 11); attaching oligonucleotides to the fragmented genomic DNA with the transposase (para 54 and Fig. 1A) and attaching barcoded tags to the DNA during tagmentation (para 80); ligating adapters to cDNA using a oligonucleotide comprising a poly(dT) sequence and a unique molecular identifier (UMI) (i.e. barcode) (para 13); using split and pool strategies (para 11) and amplifying the genomic DNA and cDNA (para 7); generating a library for sequencing (para 56), and profiling chromatin accessibility and mRNA expression (paras 144-149), including joint profiling of chromatin accessibility and transcription (para 34 and Fig. 18).
Buenrostro does not teach (i) profiling chromatin occupancy or (ii) that the attaching of oligonucleotides comprises contacting the chromatin-cleaved end and the cDNA with a terminal deoxynucleotidyl transferase (TdT) in the presence of an oligonucleotide adaptor thereby generating a plurality of tailed nucleic acid molecules.
Regarding (i), Ku teaches a method of single-cell chromatin immuno-cleavage sequencing comprising cleaving chromatin, ligating adapters to cleaved DNA fragments to prepare sequencing libraries (p. 1, col. 1) and profiling genome-wide transcription factor binding sites and histone modification (i.e. chromatin occupancy) (p.1, col 1).
Ku states that their method of profiling chromatin occupancy may find broad applications in elucidating chromatin states in rare primary and patient samples (p. 3, col. 2) and that there is a potential association of cellular heterogeneity in gene expression with that in the chromatin state of individual cells in the population (p. 1, col. 1).
Ku teaches ligating adapters by end repair and does not teach attaching adapters by terminal deoxynucleotidyl transferase (TdT).
Zhu teaches a method for single-cell joint analysis of chromatin and transcriptome, the method comprising simultaneously tagging both chromatin fragments and cDNA molecules generated from reverse transcription (RT) (p. 1, col. 2). Zhu teaches adding DNA barcode tags (oligos) to genomic DNA and cDNA by TdT-assisted DNA tailing (Fig. 1a) to prepare libraries for sequencing.
Zhu states that the TdT tailing methods were adopted from TELP, a previously reported sequencing library construction method.
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 combine the teachings of Buenrostro with Ku and Zhu to arrive at the instantly claimed invention. The modification would have entailed substituting the chromatin cleavage steps of Ku for the fragmenting DNA steps in the method of Buenrostro. One would have been motivated to make the substitution in order to have a method capable of profiling chromatin occupancy instead of accessibility and applying the findings to patient samples. The modification would further have entailed using the TdT-assisted DNA tailing method of Zhu to add the oligonucleotide adapters of Buenrostro. One would have been motivated to choose a known method for adapter addition and sequence library preparation. One would have been additionally motivated by the teachings of Zhu that TdT tailing could simultaneously label both DNA and cDNA in the same sample. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 3, Ku teaches chromatin cleavage with pA-MNase (p. 323, col. 1).
Regarding claim 4, Ku teaches chromatin cleavage with MNase, an endo-exonuclease (p. 323, col. 1).
Regarding claim 5, Buenrostro teaches reverse transcription is performed in a single cell (i.e. in situ) (paras 54, 160).
Regarding claim 6, Buenrostro teaches reverse transcription using an oligonucleotide comprising a poly(dT) sequence (para 13) and gene-specific primers (i.e. primers that do not anneal to rRNA) (para 88).
Regarding claim 7, Buenrostro teaches a barcode may identify the type of nucleic acids molecules. For example, all DNA molecules may comprise a first common barcode sequence and all RNA molecules or cDNA molecules generated from RNA molecules may comprise a second common barcode sequence (para 93).
Regarding claim 8, Buenrostro teaches cell barcodes were simultaneously ligated to cDNA and chromatin fragments (i.e. chromatin cleaved ends) (para 226).
Regarding claim 9, Buenrostro teaches DNA molecules may comprise a first common barcode (para 93), which reads on barcode adaptors that allow identification of cleaved chromatin.
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.
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/JESSICA GRAY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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