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 .
Office Action: Notice
Any objection or rejection of record in the previous Office Action, mailed 1/13/2025, which is not addressed in this action has been withdrawn in light of Applicants' amendments and/or arguments. This action is FINAL.
Claim Status
Claims 1, 8, 11, 15, 21, 22, 28, 40, 42, 43 and 77 have been amended (7/14/2025). Claim 2 is cancelled (7/14/2025). No new matter was added. Thus, claims 1, 5, 7, 8, 11-15, 21, 22, 28, 29, 36, 40-43 and 77 are under examination.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of 35 U.S.C. (pre-AIA ). See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosures of the prior-filed application, Application No: 62/850,449, fail to provide adequate support or enablement in the manner provided by 35 U.S.C. 112 (pre-AIA ), first paragraph for one or more claims of this application. The application fails to provide support for the claims under examination, since there is no disclosure of specific enzyme numbers and/or types, sequential and simultaneous digestion and timing of ligase digestion related to preparing spatially-proximate DNA molecules; the specifications considered in preparing these molecules (i.e., enzyme and digestion type) is first disclosed in the PCT patent application, filed May 19, 2020. In addition, there is no disclosure for the application of specific high-throughput genomic and epigenomic techniques to capture chromatin conformation; the incorporation of a series of chromosome conformation capture technologies is first disclosed in the PCT patent application, filed May 19, 2020. In addition, there is no disclosure of library preparation methods and details for proximity-ligated DNA molecules; the library preparations steps are first disclosed in the PCT patent application, filed May 19, 2020. Therefore, claims 1-2 and 29 are deemed to have an effective filing date of May 20, 2019, the filing date of the earliest U.S. Provisional Patent Application No. 62/850,449. Claims 5, 7-8, 11-15, 21-22, 28, 36, 40-43 and 77 are deemed to have an effective filing date of May 19, 2020, the filing date of the PCT Patent Application No. PCT/US2020/033666.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Information Disclosure Statement from 7/14/2025 is considered.
Objections Withdrawn
Specification:
The objections to the specification due to the use of a trademark is withdrawn in view of Applicant’s amendments.
The objection to the specification due to the use of an embedded hyperlink is withdrawn in view of Applicant’s amendments.
Claims:
The objections to correct minor clerical issues to claims 8, 11, 15, 28 and 77 are withdrawn due to Applicant’s amendments.
Rejections Withdrawn
Claim Rejections - 35 USC § 112(b)
The rejections of claims 1-2, 5, 7-8, 11-15, 21-22, 28-29, 36, 40-43 and 77 under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, 2nd paragraph, are withdrawn in view of Applicant’s amendments of claims 1, 11, 21-22 and 40-43.
Rejections Maintained
Claim Rejections - 35 USC § 103
Claims 1, 5, 7-8, 11-15, 21-22, 28-29, 36, 40-43 and 77 are rejected under 35 U.S.C. 103 as being unpatentable over Ren et al., (WO 2018/045137 Al, published 3/8/2018), in view of Dubey et al. (“Rapid NMR Assignments of Proteins by Using Optimized Combinatorial Selective Unlabeling”, ChemBioChem: Full Papers, published 2/2016). This rejection is modified, as necessitated by Applicants' amendments.
Regarding claims 1, 5, 7, 8, 11-13, and 77 Ren teaches methods and kits for genome-wide identification of chromatin interactions in a cell (Abstract). Specifically, Ren teaches a method focusing on a set of chromosomes within a cell containing genomic DNA, followed by incubating the cell with one or more fixation agents, affinity tags, or a restriction endonucleases (i.e., Nlalll, Mbol, Msel, Hinfl, Bfal) (p. 7, lines 15-25; p. 12, lines 25-35), to create a fixed cell comprising a complex having genomic DNA crosslinked with a protein or DNA molecule by using an antibody that is specific to such a DNA-binding protein (Figure 1A; p. 5, lines 10-15; p. 9, lines 10-15), via fixation of chromatin to cement spatial relationships or spatially-proximal DNA molecules (p. 5, lines 20-30). Ren teaches that the produced overhanging sequences or overhands can be the same or vary in size or comprise single-stranded overhands at the 5' or 3' end (p. 7, lines 25-35). Further, Ren teaches that these fixed cells are permeabilized and digested with 4-bp cutter enzymes (i.e., Mbol) followed by in situ proximity ligation, lysing of chromatins and shearing via sonication (Figure 1a; p. 3, lines 1-8; p. 8, lines 10-15) to create enriched ligation junctions enriched before paired-end sequencing and processing of the products to recover a matrix of proximate associations among genomic regions (p. 2, lines 25-35).
Regarding claims 14-15, 21-22 and 28-29, Ren teaches that utilizing a 4-base cutting enzyme or a mixture of different enzymes leads to greater coverage with less sequencing read depth; however, one restriction enzyme can be used, followed by digestion, even though using multiple enzymes, followed by digestion, can generate more uniform distribution of data and a higher-resolution map (p. 7, lines 1-10). Specifically, Ren teaches that proximity ligation is performed in situ through permeabilizing the fixed cells, fragmenting the DNA by restriction enzyme or endonuclease digestion, carried out with one or more enzymes, either 4-cutter or a 6-cutter (Figure 1A; p. 2, lines 15-25). Further, Ren teaches that any single 6-base cutting restriction enzyme or endonuclease can generate proximity-ligation data that covers 5-10% of the genome, but by using multiple such enzymes in the same experiment, one can cover >80% of the genome (p. 6, lines 20-30). Ren teaches, that following ligation, the next step is to separate genomic DNA that has been immunoprecipitated for library construction via in situ Hi-C protocol (i.e., chromatin immunoprecipitation (ChIP)) (Figure 3D; p. 23, lines 1-5; p. 26, lines 20-26). Additionally, Ren teaches that through the utilization of such techniques, including Hi-C comparisons with PLAC-seq signals (p. 23, lines 1-10), generated maps may include chromatin interactions across the entire genome (p. 15, lines 30-35).
Regarding claims 36 and 40-43, Ren teaches that resultant maps, generated from a library of polynucleotide fragments or template molecules, generated via previously described, contain chromatin interaction sites and can include interactions across the entire genome (Figure 1A; p. 15, lines 25-35). Further, Ren teaches that mapping of these interactions helps to define target genes for cis regulatory elements, including long-range molecules (p. 4, lines 25-35). Ren teaches that long-range intra-chromosomal pairs or cis molecules make up 67% of the fragments or template molecules analyzed, representing significantly more usable reads for interaction detection using PLAC-seq vs ChIA-PET (Fig. lB; p. 21, lines 25-35).
However, Ren does not teach or suggest the use of unmarked or unlabeled ligation junctions to create the previously described spatially-proximal DNA molecules later used for library preparation.
Dubey teaches methods for selective unlabeling of molecules in genomic analysis techniques via a set of multiple amino acid types for selective unlabeling and identifying specific tripeptides surrounding the labeled residues from specific 2D NMR spectra in a combinatorial manner (Abstract). Specifically, Dubey teaches the benefits of using unlabeled molecules to generate sequence data, highlighting that selective unlabeling can improve detection sensitivity (Introduction: Paragraph 1). Additionally, Dubey teaches that the combination of amino acids distinguished using unlabeling techniques include; different chemical-shift categories, abundance and distribution in the sequence and baseline instrumental controls (i.e., misincorporation (scrambling) of 14N or 12C (Table S2; Optimal Choice of Amino Acids for Selective Unlabeling).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Ren’s method to use unmarked ligation junctions, as taught by Dubey. Dubey demonstrates that unlabeled molecules provide cleaner data with less interference from labeling artifacts (Introduction: Paragraphs 1-3). Further, using unmarked junctions would simplify the protocol by eliminating labeling steps, thus reducing cost and complexity—a simple substitution that would be expected to yield predictable results. A person of ordinary skill in the art would have had a reasonable expectation of success in making this modification because both Ren and Dubey present experimental goals aligning with genomic DNA analysis methods using molecular biology approaches. Further, Dubey showcases that unlabeled molecules work effectively for sequence analysis and the modification only requires routine molecular biology techniques that are well-established in the field.
Applicant’s Response: The Applicant argues that the combination of references, Ren and Dubey, does not render the claims obvious. Specifically, Ren does not teach that ligation junctions are unmarked, and Dubey does not teach unmarked ligation junctions either. Instead, Dubey relates to actively unlabeling amino acids in NMR spectra during protein analysis and does not address nucleic acids at all. Thus, Dubey cannot compensate for Ren’s deficiencies, and therefore no case of prima facie obviousness has been established.
Examiner’s Response to Traversal: Applicant’s arguments have been fully considered but are not found persuasive, as discussed below.
Specifically, Ren teaches contacting crosslinked genomic DNA with one or more restriction endonucleases, thereby digesting DNA to generate spatially proximal ends followed by ligation to create proximity-ligated molecules for downstream sequencing (Figure 1A; p. 7, lines 15-25; p. 8, lines 10-15). Thus, Ren teaches the overall method of generating ligated junctions from digested, crosslinked DNA molecules. While Ren does not explicitly recite whether the ligation junctions are “marked” or “unmarked”, the characterization of the junctions is a matter of routine choice, as the resulting ligated molecules inherently contain unmarked ligation junctions absent an express labeling step.
Further, Dubey, while focused on protein NMR, provides clear motivation to use unlabeled rather than labeled molecules to avoid interference and improve detection sensitivity (Abstract; Introduction, Paragraphs 1-3). Dubey teaches that selective unlabeling simplifies protocols by eliminating labeling steps and provides cleaner data (Dubey, Table S2). The rationale applies equally to nucleic acid analysis because both references are directed to biomolecular analysis techniques where label interference can reduce resolution. As established in MPEP 2143, it is not necessary that the prior art references teach the claimed invention in ipissimis verbis, only that there be some teaching, suggestion, or motivation to combine known elements with a reasonable expectation of success. Here, a person of ordinary skill in the art would have recognized that unmarked ligation junctions in Ren’s system would provide the same benefits discussed by Dubey (i.e., clearer downstream sequencing results and reduced artifacts) using routine molecular biology techniques.
More so, the Applicant argues that Dubey’s unlabeling of amino acids is not relevant to nucleic acids. However, MPEP 2141 makes clear that analogous art is not limited to the same field of endeavor, but also includes references reasonably pertinent to the problem faced by the inventor. Specifically, Dubey addresses interference from labeling on downstream sequence analysis through teaching that removing labels improves sensitivity and reduces noise, and thus is reasonably pertinent. As a result, a person of ordinary skill in the art would have applied this teaching to Ren’s nucleic acid ligation junctions with predictable results.
Therefore, when Ren’s proximity-ligation method is combined with Dubey’s motivation to use unmarked molecules, the result is the claimed method wherein the ligation junctions are unmarked. Such modification constitutes an obvious optimization of known techniques, requiring only routine skill in the art (see MPEP 2144).
For these reasons, the Applicant’s arguments do not overcome the rejection and the 35 USC 103 rejection of claims 1, 5, 7-8, 11-15, 21-22, 28-29, 36, 40-43 and 77 is maintained.
Conclusions
No claim is 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 extension fee 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 date of this final action.
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/ELIZABETH ROSE LAFAVE/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684