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 .
Claims 1 and 4-18 are pending. Claims 1, 5, and 7-18 are amended. Claims 2-3 are canceled. Claims 1 and 4-18 are under review.
Response to Amendment
The Amendment filed 11/7/25 has been entered. Claims 1 and 4-18 are pending. Applicant’s amendments to claims 5, 8, 10, 12, 14, and 16-18, and cancellations of claims 2-3, have overcome the objections and 112(b) rejections previously set forth in the Non-Final Office Action mailed 5/7/25.
Response to Arguments
Applicant’s arguments, see pages 6-10, filed 11/7/25, with respect to the rejections of claims 1 and 4-18 under 35 USC 103 have been fully considered and are found unpersuasive, and the 103 rejections documented in the Non-Final mailed 5/7/25 have been revised to address claim amendments filed 11/7/25 in this Final Office Action. More detailed responses to Applicant’s arguments are provided at the end of each maintained rejection. Additionally, upon further consideration, new grounds of 112(b) rejections necessitated by claim amendments are made in this Final Office Action.
Claim Rejections - 35 USC § 112 – Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1 and 4-18 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites “GC-rich sequences, and AT-rich sequences” in lines 5-6. These limitations are indefinite because the Specification does not provide a limiting definition for these limitations. Although the Applicant argues that “GC-rich” and “AT-rich” are art-recognized terms – and provides textbook definition examples which are absent from the Specification – these limitations are not present within the instant disclosure. Absent a limiting definition, the broadest reasonable interpretation of these indefinite limitations allows application of any prior art that would read on nucleotide sequences with more GC than AT, and vice versa. These limitations are further indefinite because the metes and bounds encompassed by “rich” can be affected by the length of the nucleotide. For example, a nucleotide sequence with a length of 30 nucleotides with 15 GC-nucleotides: would this 50% cutoff be considered GC-rich? Furthermore, for the same nucleotide sequence, would 16 GC-nucleotides be considered GC-rich? For purposes of compact prosecution, these limitations are interpreted as sequences containing ≥70% GC or AT content.
Claims 6-18 directly and/or indirectly depend upon claim 1 and are similarly indefinite.
Claims 4-5 are written as dependent upon cancelled claim 2. For purposes of compact prosecution, claims 4-5 are interpreted as dependent upon claim 1. Claims 4-5 are thus similarly indefinite in regards to the “GC-rich” and “AT-rich” limitations.
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.
Claims 1, 4-8, 10-12, and 14-18 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Russell et al. (2016; WO 2016/077426 A1; FOR citation N in PTO-892 filed 5/7/25) in view of Chang et al. (2017; WO 2017/156336 A1; FOR citation O in PTO-892 filed 5/7/25).
This rejection is revised/updated in response to claim amendments filed 11/7/25.
(i) Russell et al. teaches “Hybridization Probes and Methods” (Title).
Relevant to claim 1, Russell et al. teaches “compositions and methods for generating and using hybridization probes” (Abstract). Russell et al. teaches “a method of generating a probe to a nucleic acid of interest, comprising: a) identifying regions of the nucleic acid target of interest” (page 4, lines 4-6). This teaching reads on claim 1 A method for preparing probes for targets on nucleic acids of interest comprising the steps of: a) obtaining a target DNA sequence of interest.
Relevant to claims 1 and 4, Russell et al. teaches “d) further amplifying a subset of the probes to generate probes substantially free of undesired sequences (e.g., ISH probes lacking, for example, undesired repeat sequences)” (page 3, lines 17-19). This teaching reads on claim 1 a) excluding a region containing an undesired sequence from an initial sequence, wherein the undesired sequence is selected from the group consisting of repetitive sequences; and claim 4 the method of exclusion is to amplify the target DNA sequence of interest.
Relevant to claim 5, Russell et al. teaches “the undesired region is… at least 100 bp in length” (page 4, lines 19-22). This teaching reads on claim 5 the region containing the undesired sequence comprises at least 100 bp.
Relevant to claim 7, Russell et al. teaches “the probes are labeled (e.g., with a fluorescent label)” (page 11, line 10). This teaching reads on claim 7 the probe further comprises a label.
Relevant to claim 8, Russell et al. teaches their definition of “label” to include “any atom or molecule that can be used to provide a detectable (preferably quantifiable) effect, and that can be attached to a nucleic acid or protein” (page 6, lines 29-31). Russell et al. includes “biotin,… luminogenic, phosphorescent or fluorogenic moieties; and fluorescent dyes…” amongst others (page 6, lines 29-34; page 7, lines 1-6). This teaching reads on claim 8 the label is selected from the group consisting of…
Relevant to claims 10-11, Russell et al. teaches “In some embodiments, the probes are attached to nucleic acid adaptors. In some embodiments, the adaptors are amplification primers. In some embodiments, the amplification primers are functionalized for downstream applications (e.g., by the addition of labels, binding sites, or restriction sites). In some embodiments, the probes are separated and a subset of the probes [is] isolated” (page 3, lines 24-28). This teaching reads on claim 10 wherein in step d), generating the probe further comprises amplifying the modified DNA sequence using a primer configured to bind to the first or second adapter sequence; and claim 11 wherein the primer further comprises a label.
Relevant to claim 12, Russell et al. teaches their definition of “label” to include “any atom or molecule that can be used to provide a detectable (preferably quantifiable) effect, and that can be attached to a nucleic acid or protein” (page 6, lines 29-31). Russell et al. includes “biotin,… luminogenic, phosphorescent or fluorogenic moieties; and fluorescent dyes…” amongst others (page 6, lines 29-34; page 7, lines 1-6). This teaching reads on claim 12 the label is selected from the group consisting of…
Relevant to claim 14, Russell et al. teaches “compositions and methods for generating and using hybridization probes” (Abstract). This teaching reads on claim 14 A method for performing a hybridization assay comprising: generating a probe according to the method of claim 1; and contacting the target nucleic acids with the probe.
Relevant to claim 15, Russell et al. teaches “e) performing a hybridization assay (e.g., ISH [in situ hybridization] assay such as FISH) with the probe set” (page 13, lines 7-8). This teaching reads on claim 15 the hybridization assay is an in situ hybridization.
Relevant to claim 16, Russell et al. teaches Example 2, wherein “Designs were carried out using model targets p53, HER2 and p16 based on available BAC probes for comparison” (page 46, lines 5-7). The three Russell et al. model targets read on claim 16 generating a plurality of probes according to the method of claim 1.
Relevant to claim 17, Russell et al. teaches within Example 2 that the HER2 probes were “ready for labeling with any desired fluorophore” (page 48, line 17). As the Russell et al. labels for the different target probes are amenable to labeling with “any desired fluorophore”, it would be obvious to the skilled artisan to ensure different color fluorophores for distinctions between labeled probes. This teaching reads on claim 17 wherein, when a plurality of labeled probes is present, each of the labeled probes are configured to display a different color under examination.
(ii) Russell et al. is silent to specifics regarding transposase-mediated fragmentation and adding adapters (claim 1 steps b)-d); claim 14), transposases (claim 6), and 3D FISH of fixed target cells (claim 18). However, these limitations were known in the prior art and taught by Chang et al.
Chang et al. teaches “Transposase-mediated Imaging of the Accessible Genome” (Title).
Relevant to claim 1, Chang et al. teaches “In these embodiments, the transposase complex comprises a transposase loaded with either a single adaptor molecule that contains a recognition sequence for the transposase at both ends, or two adaptor molecule[s] that each contain a recognition sequence for the transposase at one end. The latter type can be used of the chromatin is going to be sequenced by ATAC-seq… Such complexes can be combined with chromatin to add the adaptor molecule to the chromatin at accessible sites. If a transposase complex contains a single adaptor molecule that contains a transposon recognition sequence at both ends, the adaptor molecule will be inserted into the chromatin. If a transposase complex contains a two adaptor molecules that contains a transposon recognition sequence at one end, the transposase catalyzes simultaneous fragmentation of the chromatin and tagging of the fragments with sequences that are adjacent to the transposon recognition sequence (i.e., by ‘tagmentation’)” (page 10, lines 26-31 continued to page 11, line 1).
This teaching reads on claim 1 steps b)-d) b) using a transposase to fragment the target DNA sequence to produce a fragmented DNA sequence; c) adding a first adapter sequence to a first end of the fragmented DNA sequence and adding a second adapter sequence to a second end of the fragmented DNA sequence to obtain a modified DNA sequence; and d) using the modified DNA sequence for generating a probe.
Relevant to claim 6, Chang et al. teaches “Examples of transposases include, but are not limited to, Tn transposase (e.g. Tn3, Tn5, Tn7, Tn10, Tn552, Tn903), a MuA transposase, a Vibhar transposase (e.g. from Vibrio harveyi), Ac-Ds, Ascot-I, Bsl, Cin4, Copia, En/Spm, F element, hobo, Hsmarl, Hsmar2, IN (HIV), ISl, IS2, IS3, IS4, IS5, IS6, ISIO, IS21, IS30, IS50, IS51, IS150, IS256, IS407, IS427, IS630, IS903, IS911, IS982, IS1031, ISL2, Ll, Mariner, P element, Tam3, Tel, Tc3, Tel, THE-1, Tn/O, TnA, Tn3, Tn5, Tn7, TnlO, Tn552, Tn903, Toll, Tol2, TnlO, Tyl, any prokaryotic transposase, or any transposase related to and/or derived from those listed above” (page 14, lines 8-15). This teaching reads on claim 6 the transposase is selected from one of or any combination of…
Relevant to claim 18, Chang et al. teaches “DNA FISH in human neutrophil” example on page 35, wherein “3D DNA FISH images were taken” (page 36, line 6) of formaldehyde-fixed human neutrophils (page 35, line 25). This teaching reads on claim 18 the in situ hybridization is 3D FISH labeling the probes to fixed target cells.
Although Russell et al. does not include transposases within their methodologies, it would have been prima facie obvious to the skilled artisan to include the transposase-mediated fragmentation and addition of adapters, transposases, and 3D FISH of fixed target cells taught by Chang et al.
Russell et al. and Chang et al. are analogous disclosures to the instant preparation and use of hybridization probes. The methodology of Russell et al. can include “c) fragmenting the probe-containing nucleic acids to generate probes” (page 3, lines 16-17). Russell et al. further teaches that their “probes are attached to nucleic acid adaptors” (page 3, line 24). Although these processes of fragmentation and adapter addition are not performed by transposases, the skilled artisan would be motivated to perform these functions via transposase because Chang et al. teaches that “the transposase enzyme can insert the nucleic acid sequence into the polynucleotide in a substantially sequence-independent manner… Methods for tagmenting, as well as transposon end sequences, are well known in the art” (page 11, lines 3-6). Thus, the skilled artisan would be motivated to take advantage of well-known and customizable, sequence-independent tagmentation methodologies to perform simultaneous fragmentation and adapter addition. The skilled artisan would be further motivated to include the methodologies rendered obvious by Russell et al. in view of Chang et al. to perform 3D FISH because Chang et al. teaches that the methodologies of “Labeling DNA in this manner can be used to provide spatial information regarding the positioning of regulatory DNA in the genome and makes possible the imaging… of cells” (Abstract).
Taken together, Russell et al. in view of Chang et al. renders obvious A method for preparing probes for targets on nucleic acids of interest… (claim 1) and A method for performing a hybridization assay… (claim 14). The skilled artisan would have a reasonable expectation of success based on the disclosures of Russell et al. in view of Chang et al.
Applicant’s Arguments
“Applicant contends that Chang does not cure the noted deficiencies of Russell. Applicant notes that while Chang disclosed the cleavage and linker features related to transposase, Chang fails to disclose that:
1) adding detectable labeling groups, including but not limited to dyes, radioactive labels, etc., into the cleavaged product to form probes; and
2) applying the probes as generated above to FISH detection, to achieve the advantages of species independent Cot-1 DNA for blocking repetitive fragments, low required DNA template quantity, and high detection accuracy.
Applicant contends that Chang, therefore, fails to teach or suggest to one of ordinary skill in the art two operations that contribute substantially to achieving the noted benefits of the recited methods. Applicant further contends that the transposase complex disclosed by Chang is only one tool utilized in the recited methods and does not obviate the recited method” (Remarks 11/7/25, last four paragraphs of page 9; emphasis added).
Response to Applicant’s Arguments
Applicant is reminded that the cited prior art reference must be read in its entirety, not
merely selective portions. As set forth in MPEP 2141.02:
Ascertaining the differences between the prior art and the claims at issue requires
interpreting the claim language, and considering both the invention and the prior art references
as a whole… A prior art reference must be considered in its entirety, i.e., as a whole,
including portions that would lead away from the claimed invention… However, ‘the prior art’s
mere disclosure of more than one alternative does not constitute a teaching away from any
of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage
the solution claimed….’ In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir.
2004) (emphasis added)
The Examiner respectfully disagrees with the assertion that Chang et al. “does not cure the noted deficiencies of Russell” et al.
Relevant to Applicant’s point 1): Russell et al. teaches adding detectable labeling groups to form probes (see rejections of claims 7-8 and 10-12) and “c) fragmenting the probe-containing nucleic acids to generate probes; d) attaching adaptors to the probes” (page 4, lines 8-9), and Chang et al. additionally teaches detectable labels (Abstract and pages 4, 12-13). Taken together, these disclosures (expanded in further detail above) obviate “1) adding detectable labeling groups… into the cleavage product to form probes”.
Relevant to Applicant’s point 2), Russell et al. teaches application of the generated probes to FISH detection (see rejection of claim 15), and Chang et al. teaches 3D FISH labeling of probes (see rejection of claim 18).
The skilled artisan would recognize that the combination of the analogous disclosures of Russell et al. and Chang et al. obviate the instant invention. As discussed above in the revised rejection, and reproduced below for clarity:
The methodology of Russell et al. can include “c) fragmenting the probe-containing nucleic acids to generate probes” (page 3, lines 16-17). Russell et al. further teaches that their “probes are attached to nucleic acid adaptors” (page 3, line 24). Although these processes of fragmentation and adapter addition are not performed by transposases, the skilled artisan would be motivated to perform these functions via transposase because Chang et al. teaches that “the transposase enzyme can insert the nucleic acid sequence into the polynucleotide in a substantially sequence-independent manner… Methods for tagmenting, as well as transposon end sequences, are well known in the art” (page 11, lines 3-6). Thus, the skilled artisan would be motivated to take advantage of well-known and customizable, sequence-independent tagmentation methodologies to perform simultaneous fragmentation and adapter addition. (emphasis added)
Additionally, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
Claims 9 and 13 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Russell et al. (2016; WO 2016/077426 A1; FOR citation N in PTO-892 filed 5/7/25) in view of Chang et al. (2017; WO 2017/156336 A1; FOR citation O in PTO-892 filed 5/7/25) as applied to claims 1, 4-8, 10-12, and 14-18 above, and further in view of Han et al. (2017; NPL citation U in PTO-892 filed 5/7/25; “Inorganic Nanoparticles as Donors in Resonance Energy Transfer for Solid-Phase Bioassays and Biosensors”. Langmuir 2017 33 (45), 12839-12858 DOI: 10.1021/acs.langmuir.7b01483).
The teachings of Russell et al. in view of Chang et al. are applied to instantly rejected claims 9 and 13 as they were previously applied to claims 1, 4-8, 10-12, and 14-18 as rendering obvious a method for preparing probes and performing a hybridization assay.
Russell et al. in view of Chang et al. is silent to using specific nanostructures for probe labels (claim 9) and primer labels (claim 13). However, these limitations were known in the prior art and taught by Han et al.
Han et al. teaches “Bioassays for the rapid detection and quantification of specific nucleic acids… are fundamental tools in many clinical settings. Traditional optical emission methods have focused on the use of molecular dyes as labels to track selective binding interactions and as probes… Such dyes can offer good detection limits based on brightness but typically have broad emission bands and suffer from time-dependent photobleaching. Inorganic nanoparticles such as quantum dots and upconversion nanoparticles are photostable over prolonged exposure to excitation radiation and tend to offer narrow emission bands, providing a greater opportunity for multiwavelength multiplexing” (Abstract).
Relevant to claims 9 and 13, Han et al. teaches “QDs [quantum dots] can serve as FRET [fluorescence resonance energy transfer] donors for the development of solution-phase bioassays, and CdSe/ZnS QDs have been used to develop multiplexed assay strategies for the detection of nucleic acids. Typically, QDs were conjugated to multiple probe oligonucleotide, and FRET-sensitized emission from molecular dyes that were associated with a complementary target was determined as a quantitative measure of hybridization” (page 12840, column 2, paragraph 2). The inorganic nanoparticle quantum dots of Han et al. read on claims 9 and 13 the nanostructures are selected from the group consisting of inorganic nanoparticles.
Although Russell et al. and Chang et al. are silent to nanostructure labels, it would have been prima facie obvious to the skilled artisan to include the Han et al. nanostructure labels within the methodology rendered obvious by Russell et al. in view of Chang et al.
Russell et al., Chang et al., and Han et al. are all analogous methods within nucleic acid probe hybridization. The skilled artisan would be motivated to use the Han et al. nanostructure labels in order to optimize on the improved photostability and multiwavelength multiplexing benefits that Han et al. discloses within their Abstract. Han et al. further provides the motivation that the nanostructure labels have been previously used in nucleic acid hybridization assays (page 12840, column 2, paragraph 2).
The skilled artisan would have a reasonable expectation of success based on the disclosures of Russell et al. in view of Chang et al., and further in view of Han et al.
Applicant’s Arguments
“Applicant contends that Han does not teach or suggest to one of one of ordinary skill in the art the addition of detectable markers to the fragments generated by DNA fragmentation using transposase to form probes for in situ hybridization” (Remarks 11/7/25, first paragraph of page 10).
Response to Applicant’s Arguments
Han et al. is not relied upon to teach “addition of detectable markers to the fragments generated by DNA fragmentation using transposase to form probes for in situ hybridization”. As discussed in the preceding rejections of claims 1, 4-8, 10-12, and 14-18, Russell et al. in view of Chang et al. obviates the aforementioned limitation.
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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/SARAH JANE KENNEDY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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