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or rejection of record in the previous Office Action, mailed 1/14/2026, which is not addressed in this action has been withdrawn in light of Applicants' amendments and/or arguments.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 1-2, 5, 13, 15-16, 20-22, 28, 33-35, 37, 56 and 62-63 are under examination (3/30/2026). Applicant amended claims 1, 5, 22, and 25 (3/30/2026). Claims 6, 11, 25, 45, and 50 are cancelled (3/30/2026). Claims 62-63 are new (3/30/2026). No new matter was added.
Priority
Claims 1-2, 5, 13, 15-16, 20-22, 28, 33-35, 37, 56 and 62-63 receive a priority date of 12/22/2019, the effective filing date of US Provisional Patent 62952357.
Objections Withdrawn
Specification:
The objections to the specification due to the use of a trademark or tradenames are withdrawn in view of Applicant’s amendments.
Claims:
The objections to claims 22 and 25 are withdrawn in view of Applicant’s amendments to claim 22 and cancellation of claim 25.
Rejections Withdrawn
Claim Rejections - 35 USC § 101
The rejection of claims 33-37 under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more is withdrawn due to Applicant’s amendments, arguments and affidavit. Specifically, as amended, the claims recite a specific technological process for detecting epigenetic modifications, including covalent labeling of the epigenetic modification of interest, single-molecule imaging, analysis in the absence of bisulfite conversion, and detection from low-concentration DNA samples without amplification. These limitations integrate any alleged judicial exception into a practical application and amount to significantly more than a mere observation of a natural correlation because they improve the technological process for identifying epigenetic signatures in DNA samples.
Claim Rejections – 35 USC § 102
The 102 (a) (1) and 102 (a) (2) rejections of claims 1-2, 5-6, 11, 13, 15-16, 20-22, 25, 28, 33-35, 37, 45, 50, and 56 are withdrawn in view of Applicant’s arguments and amendments (3/30/2026). Specifically, amended independent claim 1 now recites, inter alia, covalent labeling of the epigenetic modification of interest, detection using single-molecule imaging, and analysis of DNA samples having concentrations more than 10/g/uL in the absence of bisulfite conversion and DNA amplification, limitations that are not expressly or inherently disclosed by Spetzler in the claimed arrangement.
New Rejections
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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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 1-2, 5, 13, 15-16, 20-22, 28, 33-35, 37, 56 and 62-63 are rejected under 35 U.S.C. 103 as being unpatentable over Spetzler et al. (WO 2016/141169 A1; published 9/9/2016), in view of Hori et al. (“Synthetic-Molecule/Protein Hybrid Probe with Fluorogenic Switch for Live-Cell Imaging of DNA Methylation”, Journal of the American Chemical Society, published 1/30/2018) and Schueder et al. (“Multiplexed 3D super-resolution imaging of whole cells using spinning disk confocal microscopy and DNA-PAINT”, Nature Communications, published 12/12/2017).
Regarding claims 1-2, Spetzler teaches methods and systems of molecular profiling of diseases, such as cancer and in some embodiments, the molecular profiling can be used to identify treatments for the disease, such as treatments that provide likely benefit or likely lack of benefit for the disease, where the molecular profiling can include analysis of a sequence of a nucleic acid via identifying at least one treatment associated with a cancer in a subject (Abstract). Further, Spetzler teaches that one method to detect epigenetic silencing is to determine that a gene which is expressed in normal cells is less expressed or not expressed in tumor cells, where the invention provides for a method of molecular profiling comprising detecting epigenetic silencing (Paragraph 203, lines 1-5). Spetzler also teaches that the method comprises isolating DNA from disease tissues (e.g., tumors) and reference tissues (e.g., healthy tissue) and labeling each with a different "color" or fluor (Paragraph 267, lines 1-5). Specifically, Spetzler teaches that the previously described samples are mixed and hybridized to normal metaphase chromosomes and in the case of array or matrix CGH, the hybridization mixing is done on a slide with thousands of DNA probes (Paragraph 267, lines 5-10). Spetzler teaches that the previously described method can be further analyzed via nucleic acid analysis techniques include, by way of non-limiting examples, amplification, polymerase chain amplification, hybridization, microarrays, in situ hybridization, sequencing, dye-terminator sequencing, next generation sequencing, pyrosequencing, and restriction fragment analysis (Paragraph 268, lines 20-30).
Spetzler teaches that the fluorophores generally are within 10 nanometers of each for energy transfer to occur successfully (Paragraph 223, lines 30-40).
Spetzler teaches that the reagent can be any useful reagent for performing molecular profiling and for example, the reagent may comprise at least one of a reagent for extracting nucleic acid from a sample, a reagent for performing ISH, a reagent for performing IHC, a reagent for performing PCR, a reagent for performing Sanger sequencing, a reagent for performing next generation sequencing, a reagent for a DNA microarray, a reagent for performing pyrosequencing, a nucleic acid probe, a nucleic acid primer, an antibody, a reagent for performing bisulfite treatment of nucleic acid, and a combination thereof (Paragraph 60, lines 10-20).
Regarding claim 5, Spetzler teaches methods and systems of molecular profiling of diseases, such as cancer and in some embodiments, the molecular profiling can be used to identify treatments for the disease, such as treatments that provide likely benefit or likely lack of benefit for the disease, where the molecular profiling can include analysis of a sequence of a nucleic acid via identifying at least one treatment associated with a cancer in a subject (Abstract). Further, Spetzler teaches that one method to detect epigenetic silencing is to determine that a gene which is expressed in normal cells is less expressed or not expressed in tumor cells. Accordingly, the invention provides for a method of molecular profiling comprising detecting epigenetic silencing (Paragraph 203, lines 1-5). Spetzler also teaches that the method comprises isolating DNA from disease tissues (e.g., tumors) and reference tissues (e.g., healthy tissue) and labeling each with a different "color" or fluor (Paragraph 267, lines 1-5). Specifically, Spetzler teaches that the previously described samples are mixed and hybridized to normal metaphase chromosomes and in the case of array or matrix CGH, the hybridization mixing is done on a slide with thousands of DNA probes (Paragraph 267, lines 5-10). Spetzler teaches that the previously described method can be further analyzed via nucleic acid analysis techniques include, by way of non-limiting examples, amplification, polymerase chain amplification, hybridization, microarrays, in situ hybridization, sequencing, dye-terminator sequencing, next generation sequencing, pyrosequencing, and restriction fragment analysis (Paragraph 268, lines 20-30).
Further, Spetzler teaches that for each nucleotide variant, two linear, allele- specific probes are designed and that the two allele-specific probes are identical with the exception of the 3'-base, which is varied to complement the variant site and in the first stage of the assay, target DNA is denatured and then hybridized with a pair of single, allele-specific, open-circle oligonucleotide probes (Paragraph 253, lines 1-10).
Spetzler also teaches that the presence or absence of one or more genes nucleotide variant or amino acid variant in an individual can be determined using any of the detection methods described above (Paragraph 256, lines 1-2).
Regarding claim 13, Spetzler teaches that the fluorophores generally are within 10 nanometers of each for energy transfer to occur successfully (Paragraph 223, lines 30-40).
Regarding claims 15-16, Spetzler teaches that, in microchips, a large number of different oligonucleotide probes are immobilized in an array on a substrate or carrier, e.g., a silicon chip or glass slide (Paragraph 250, lines 1-5). Further, Spetzler teaches that formalin-fixed paraffin-embedded patient tissue blocks were sectioned (4 µm thick) and mounted onto glass slides (Paragraph 273, lines 1-2).
Regarding claim 20, Spetzler teaches that in a common embodiment, a probe that recognizes the sequence of interest is contacted with a sample, where an antibody or other binding agent that recognizes the probe, e.g., via a label carried by the probe, can be used to target an enzymatic detection system to the site of the probe (Paragraph 263, lines 1-10).
Regarding claim 21, Spetzler teaches that modification of surfaces of array substrates can be accomplished by many techniques and for example, siliceous or metal oxide surfaces can be derivatized with bifunctional silanes, i.e., silanes having a first functional group enabling covalent binding to the surface (e.g., Si-halogen or Si-alkoxy group, as in— S1CI3 or ~Si(OCH.sub.3) .sub.3, respectively) and a second functional group that can impart the desired chemical and/or physical modifications to the surface to covalently or non-covalently attach ligands and/or the polymers or monomers for the biological probe array (Paragraph 184, lines 15-25).
Regarding claim 22, Spetzler teaches that pyrosequencing is a nucleic acid sequencing method based on sequencing by synthesis, which relies on detection of a pyrophosphate released on nucleotide incorporation, where specifically an illustrative system for pyrosequencing involves the following steps: ligating an adaptor nucleic acid to a nucleic acid under investigation and hybridizing the resulting nucleic acid to a bead; amplifying a nucleotide sequence in an emulsion; sorting beads using a picoliter multiwell solid support; and sequencing amplified nucleotide sequences by pyrosequencing methodology (e.g., Nakano et al., "Single-molecule PCR using water-in-oil emulsion;" Journal of Biotechnology 102: 117-124 (2003)) (Paragraph 222, lines 1-30).
Regarding claim 28, Spetzler teaches that the previously described method can be used interchangeably with gene, cDNA, mRNA, oligonucleotide, and polynucleotide (Paragraph 96, lines 15-20).
Regarding claims 33-35, Spetzler teaches that a gene or gene product can be considered up or down-regulated if the differential expression meets a statistical threshold, a fold-change threshold, or both and for example, the criteria for identifying differential expression can comprise both a p-value of 0.001 and fold change of at least 1.5-fold (up or down) where one of skill will understand that such statistical and threshold measures can be adapted to determine differential expression by any molecular profiling technique disclosed herein (Paragraph 171, lines 40-50). Further, Spetzler teaches various methods of the invention make use of many types of microarrays that detect the presence and potentially the amount of biological entities in a sample and arrays typically contain addressable moieties that can detect the presence of the entity in the sample, e.g., via a binding event. Microarrays include without limitation DNA microarrays, such as cDNA microarrays, oligonucleotide microarrays and SNP microarrays, microRNA arrays, protein microarrays, antibody microarrays, tissue microarrays, cellular microarrays (also called transfection microarrays), chemical compound microarrays, and carbohydrate arrays (glycoarrays) (Paragraph 172, lines 1-10).
Specifically, Spetzler teaches that for example, antibody arrays can be used to detect biomarkers from bodily fluids, e.g., serum or urine, for diagnostic applications where tissue microarrays comprise separate tissue cores assembled in array fashion to allow multiplex histological analysis and cellular microarrays, also called transfection microarrays, comprise various capture agents, such as antibodies, proteins, or lipids, which can interact with cells to facilitate their capture on addressable locations, and chemical compound microarrays comprise arrays of chemical compounds and can be used to detect protein or other biological materials that bind the compounds (Paragraph 172, lines 10-20).
Further, Spetzler teaches that the systems and methods allow identification of one or more therapeutic targets whose projected efficacy can be linked to therapeutic efficacy, ultimately based on the molecular profiling (FIGs. 2, 49A-B and 50), where the invention comprises use of molecular profiling results to suggest associations with treatment responses (Paragraph 283, lines 1-10).
Regarding claim 37, Spetzler also teaches that the previously described method can be applied to characterization of a number of miRNAs indicates that they influence a variety of processes, including early development, cell proliferation and cell death, apoptosis and fat metabolism (Paragraph 141, lines 1-5).
Regarding claim 56, Spetzler teaches that aberrant methylation, which may be referred to as hypermethylation, of the gene or genes can be detected and, the methylation status is determined in suitable CpG islands which are often found in the promoter region of the gene(s) and may refer to the presence or absence of 5-methylcytosine at one or a plurality of CpG dinucleotides within a DNA sequence (Paragraph 202, lines 10-15).
Spetzler does not teach or suggest a fluorescent label or a specified single imaging tool, specifically epi-fluorescence microscopy. Further, Spetzler does not teach or suggest covalent labeling of the epigenetic modification of interest, single-molecule imaging, and analysis of low-concentration DNA samples in the absence of both bisulfite conversion and DNA amplification.
Hori teaches detecting an epigenetic modification, specifically DNA methylation, using a labeled hybrid probe for detection of DNA methylation, an epigenetic modification, wherein a DNA-binding fluoregen is associated with a methylated-DNA-binding domain and produces enhanced fluorescence upon binding methylated DNA (Abstract, Introduction: Paragraphs 1-5, Figure 1). Further, Hori teaches imaging methylated DNA in living cells by fluorescence microscopy and quantifying methylated DNA based on the resulting fluorescence signals (Figure 4; Live-Cell Imaging of Methylated DNA).
Schueder teaches detection and imaging using single-molecule localization microscopy (SMLM), including DNA-PAINT super-resolution imaging, wherein labeled probes are used to image biological targets at the single-molecule level with localization precisions on the order of nanometers (Abstract; Introduction: Paragraphs 1-3; Whole-cell 2D imaging of protein targets; Results: Paragraph 1).
It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the epigenetic profiling methods of Spetzler to employ the fluorescence-based detection techniques of Hori and the single-molecule imaging techniques of Schueder. One of ordinary skill the art would have been motivated to do so because Spetzler expressly contemplates the use of alternative molecular detection methodologies for analyzing epigenetic biomarkers, while Hori demonstrates that DNA methylation can be detected through fluorescent labeling strategies and Schueder teaches that single-molecule localization microscopy provides enhanced sensitivity and spatial resolution for imaging biological targets. The combination would have predictably improved the ability to detect and visualize epigenetic modifications while retaining the molecular profiling objectives of Spetzler. Accordingly, one of ordinary skill in the art would have had a reasonable expectation of success incorporating the fluorescent methylation-detection techniques of Hori and the single-molecule imaging techniques of Schueder into the epigenetic analysis methods of Spetzler to obtain the predictable result of single-molecule imaging of fluorescently labeled epigenetic modifications.
More so, Hori teaches fluorescence-based detection of epigenetic modifications using hybrid probes created through protein-labeling technology, wherein proteins are specifically modified with fluorophore-conjugated ligands and used to detect methylated DNA in cells. Schueder further teaches single-molecule imaging of biological targets and teaches covalently coupling DNA-PAINT docking strands to antibodies for subsequent single-molecule localization microscopy. Accordingly, it would have been obvious to one of ordinary skill in the art to employ fluorescently labeled epigenetic detection probes from Hori, with the single-molecule imaging techniques of Schueder to obtain the predictable result of detecting covalently labeled epigenetic modifications using single-molecule imaging, with a reasonable expectation of success.
Applicant’s Response: The Applicant argues that Spetzler does not teach or suggest covalently labeling an epigenetic modification of interest in a DNA sample with a label and further fails to disclose detecting hybridization using single-molecule imaging. The Applicant further contends that Spetzler’s epigenetic profiling methods do not teach the claimed fluorescence-based labeling and single-molecule imaging limitations, particularly in the absence of amplification and bisulfite conversion.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully and fully considered and are found partially persuasive, as discussed below.
While Applicant correctly notes that Spetzler does not anticipate the newly amended limitations in independent claim 1, specifically covalently labeling an epigenetic modification of interest with a fluorescent label or detecting hybridization using single-molecule imaging, the rejection has been modified from anticipation under 35 USC 102 to obviousness under 35 USC 103 to account for these distinctions.
As set forth above, Hori teaches fluorescence-based detection of epigenetic modifications using labeled hybrid probes, while Schueder teaches single-molecule imaging techniques and the use of covalently coupled imaging probes for detecting biological targets. It would have been obvious to one of ordinary skill in the art to incorporate the fluorescence-based labeling strategies of Hori and the single-molecule imaging methods of Schueder into the epigenetic profiling methods of Spetzler to improve sensitivity, spatial resolution, and detection of epigenetic biomarkers, yielding the predictable result of detecting labeled epigenetic modifications using single-molecule imaging with a reasonable expectation of success. See MPEP 2143 and KSR Int’l Co. v. Teleflex Inc., 550 US 398, 417 (2007) (a combination of familiar elements according to known methods is likely to be obvious when it yields predictable results).
Furthermore, the claim does not require any particular covalent labeling chemistry, imaging modality beyond single-molecule imaging, or direct covalent attachment of a label to a modified nucleotide, and such limitations cannot be imported into the claims, even if set forth in the Applicant’s arguments or attached affidavit. See MPEP 2111.01.
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 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 ELIZABETH ROSE LAFAVE whose telephone number is (703)756-4747. The examiner can normally be reached Compressed Bi-Week: M-F 7:30-4:30.
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/ELIZABETH ROSE LAFAVE/Examiner, Art Unit 1684 /HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
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