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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on April 7, 2026 has been entered.
Claim Status/Action Summary
This action is in response to the papers filed on April 7, 2026.
Claims 1-13 are under examination. No other claims are currently pending in the present application.
Applicant is reminded that no new matter may be added.
Priority
The present application, filed on March 24, 2023, is a 371 of PCT/US2021/044011, filed on July 30, 2021, which claims the benefit of U.S. Provisional Application No. 63/085,319, filed on September 30, 2020.
Drawings
The drawings filed on March 24, 2023 are acceptable.
Claim Rejections - 35 USC § 112
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.
Claims 1-13 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Regarding claim 1:
Claim 1, as presently amended, reads:
“A method of preparing a sample for in situ hybridization, the method comprising:
applying an electric field to a sample comprising a target polynucleotide; and contacting the sample with one or more detectable nucleic acid probes which specifically bind to the target polynucleotide while the electric field is being applied,
wherein the electric field is also being applied during each of the steps of deparaffinization, antigen retrieval, and nucleic acid exposure, and optionally wherein the electric field is also applied during removal of trapped liquid or solvent and/or coverslip mounting.”
Claim 1 positively recites only the method steps: i) “applying an electric field to a sample comprising a target polynucleotide” and ii) “contacting the sample with one or more detectable nucleic acid probes which specifically bind…while the electric field is being applied”. Claim 1 further recites “each of the steps of deparaffinization, antigen retrieval… nucleic acid exposure… removal of trapped liquid or solvent… or coverslip mounting”. There is insufficient antecedent basis for these limitations in the claim because the claim does not positively recite any of these steps as required by the claim. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See MPEP 2111.01 and In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
Furthermore, it is unclear what method(s) applicant intends to cover in this claim, as “in situ hybridization” methods do not comprise a step of “antigen retrieval”, as this term is known in the art (and as it is used in the specification; see, for example, paragraph 0030). Rather “antigen retrieval” and equivalent terms in the art refer to steps directed to rendering antigens (i.e. molecules to which antibodies bind) available for binding by antibodies.
Additionally, the claim recites “preparing a sample for in situ hybridization”. The specification provides a special, limiting definition for the term “sample” at paragraph 0062: “As used herein, the term “sample” means a biological, chemical, industrial or sample for which analysis is desired, such as a tissue sample, blood sample, or cellular sample.” Therefore, this claim term, given its broadest reasonable interpretation, encompasses samples that are not embedded in paraffin such as: fresh, frozen tissues or slices thereof, cultured cells, chromosome spreads (i.e. wherein the nucleic acids are not within a cell), or blood plasma comprising cell-free DNA. However, claim 1 recites “…the steps of deparaffinization…” without reciting any particular limitation on the type of samples provided or any particular step(s) of embedding a sample in paraffin.
Because “in situ hybridization” methods do not all comprise a step of “deparaffinization”, and in situ hybridization methods are known in the art which do not require paraffin-embedded samples it cannot be said that this step is inherent to all “method(s) of preparing a sample for in situ hybridization”. (see, for instance Jin et al., “In Situ Hybridization: Methods and Applications” Journal of Clinical Laboratory Analysis 11:2-2 (1997) at page 4, column 1, paragraph 2 “Tissue Preparations” or Alamri et al., “Fluorescence In Situ Hybridization of Cells, Chromosomes, and Formalin-Fixed Paraffin-Embedded Tissues” Virginia Espina (ed.) Molecular Profiling: Methods and Protocols, Methods in Molecular Biology, vol. 1606. (2017)”).
It is therefore unclear whether applicant intends to cover methods wherein any sample type is prepared for in situ hybridization, or whether the claim is intended to be limited to methods wherein the sample is embedded in paraffin.
Where applicant acts as his or her own lexicographer to specifically define a term of a claim contrary to its ordinary meaning, the written description must clearly redefine the claim term and set forth the uncommon definition so as to put one reasonably skilled in the art on notice that the applicant intended to so redefine that claim term. Process Control Corp. v. HydReclaim Corp., 190 F.3d 1350, 1357, 52 USPQ2d 1029, 1033 (Fed. Cir. 1999). Claim 1 as amended recites the term “the step of… nucleic-acid exposure”. Neither the claims nor the specification provide any limiting definition of this claim term, and it does not appear that this term has any special definition known in the art beyond its plain meaning. As such, the term “a step of nucleic acid exposure” could reasonably be interpreted as either: a step of exposing a nucleic acid to some unspecified condition (e.g. temperature), reagent (e.g. nuclease, NaOH, H2SO4), light, or any other incident particle or wave (e.g. sound) and it is unclear what is actually required of the process user by the language of the claim. While the specification provides, “In some embodiments, the present methods comprise exposing the DNA in a sample. In some embodiments, this is done without proteolytic digestion… In some embodiments, DNA exposure can be accomplished by exposing the tissue to an electrical field…” (Specification, paragraph 0087), these exemplary embodiments do not constitute a specific, limiting definition contrary to the ordinary meaning of a term and although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See MPEP 2111.01 and In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Therefore, the term is indefinite because the specification does not clearly redefine the term.
While the response (dated April 7, 2026) asserts: ““nucleic-acid exposure,” as required by the claims, is a preparatory step that renders chromatin-bound nucleic acids accessible for probe binding within the sample, for example by reversing crosslinks or reducing steric hindrance that would otherwise prevent hybridization.” (Response page 2, paragraph 1), this proffered definition is not present in the specification and does not appear to be defined in the prior art in this manner. Even more, because the claim is generic to “a sample” as defined by the specification, which does not require that the nucleic acids in the sample are “chromatin-bound” or are not “accessible for probe binding”, it is unclear whether this step is intended to limit the claim to a particular set of samples wherein the nucleic acids are not accessible to probe binding.
Claim 8 recites the limitation “the electric field is applied for at least 1 minute to expose target polynucleotide.” This claim limitation is indefinite for the following reasons.
First, it is unclear whether “expose target polynucleotide” is intended to refer to the target polynucleotide established by claim 1, or a target polynucleotide that is different from the target polynucleotide established by claim 1.
Second, as discussed at length for claim 1 above, “nucleic acid exposure” is not defined by the claims, the specification, and does not have a special meaning established in the prior art. Given its broadest reasonable interpretation according to the plain meaning of the words of the claim, it is unclear what the electric field application for at least 1 minute accomplishes, be it rendering chromatin-bound nucleic acids accessible for probe binding within the sample… (as espoused by the response), exposing target polynucleotide(s) to: the electric field, a particular temperature, an unspecified reagent, light, or some other unspecified condition, particle, wave (e.g. sound), or form of energy, or something else entirely. Even more, the claim may be interpreted as “sufficient to release DNA [from the nucleus or from the cell]” or alternatively, “sufficient to expose the DNA to the one or more detectable nucleic acid probes”.
Claim 10 recites the limitation "the nucleic acid probe". There is insufficient antecedent basis for this limitation in the claim because claim 1, upon which claim 10 depends, recites “one or more detectable nucleic acid probes” and it is unclear whether “the nucleic acid probe” referred to by claim 10 limits claim 10 to embodiments wherein only one detectable nucleic acid probe is contacted with the sample, or whether it is intended to refer to a particular one of the “one or more detectable nucleic acid probes”.
Claims 11 and 12 recite the limitation "the labeled probes". There is insufficient antecedent basis for this limitation in the claim because claim 1 recites “one or more detectable nucleic acid probes” and does not require that the nucleic acid probes are “labeled”. A “labeled probe” is not inherent to “detectable nucleic acid probe” because the latter term does not, in all embodiments, require a label (for example, where a secondary, labeled probe is used to detect the first probe or a product thereof (e.g. amplification of signal by rolling circle amplification)).
Claims 12 and 13 recite the limitations "removing substantially all paraffin" and “the paraffin is removed”, respectively. There is insufficient antecedent basis for this limitation in the claim because claim 1, upon which these claims depend, does not require that the sample comprises paraffin.
Claims 2-13 are additionally indefinite because of their dependence from the claim(s) identified as indefinite above.
Applicant is reminded that no new matter may be added.
Claim Interpretation
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art.
As described in the 112(b) rejections above, claim 1 as amended, positively recites (requires) only the steps: “applying an electric field to a sample comprising a target polynucleotide” and “contacting the sample with one or more detectable nucleic acid probes which specifically bind to the target polynucleotide while the electric field is being applied”. In the interest of compact prosecution, for the purposes of prior art rejections, the claims have been treated under both the broadest reasonable interpretation (above) and according to the preferred embodiments espoused by the April 7, 2026 remarks.
The claims recite the term “nucleic-acid exposure”, identified as indefinite in the 112(b) rejections above. In the interest of compact prosecution, for the purposes of prior art rejections, the claims have been treated under both the broadest reasonable interpretation (wherein “nucleic-acid exposure” is interpreted as exposing a/the nucleic acid(s) to some unspecified condition or reagent) and according to the preferred embodiments espoused by the April 7, 2026 remarks wherein “nucleic-acid exposure” is asserted to have a special definition not found in the specification or the prior art: ““nucleic acid exposure”… is a preparatory step that renders chromatin-bound nucleic acids accessible for probe binding within the sample, for example by reversing crosslinks or reducing steric hindrance that would otherwise prevent hybridization.”
Prior art rejections
Claim rejections below address the broadest reasonable interpretation of the claims according to the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art.
The broadest reasonable interpretation of the claims as presently written is: “A method of preparing a sample for in situ hybridization, the method comprising applying an electric field to a sample comprising a target polynucleotide; and contacting the sample with one or more detectable nucleic acid probes which specifically bind to the target polynucleotide while the electric field is being applied” wherein: a) the sample encompasses any sample comprising any polynucleotide, b) the sample encompasses samples that are not embedded in paraffin, and c) “nucleic-acid exposure” is interpreted as a step of “exposing” a “nucleic acid” to an unspecified reagent or force (e.g. “contacting” a nucleic acid with a probe); furthermore, “the steps of deparaffinization [and] antigen retrieval” are not required by the claim language as presently written because they: i) lack antecedent basis, and ii) “antigen retrieval” is specific to methods not encompassed by the claim, and iii) “deparaffinization” is specific to a subset of “samples” that are paraffin-embedded.
Claim rejections below additionally address the preferred embodiments espoused by the April 7, 2026 response in the interest of compact prosecution wherein the claims require the steps: a) deparaffinization (i.e. the sample is a paraffin-embedded sample) and b) “nucleic-acid exposure” that is asserted to mean “a preparatory step that renders chromatin-bound nucleic acids accessible for probe binding within the sample”. It is noted that this preferred embodiment further requires that the “sample comprising a target polynucleotide” is a “sample comprising a target polynucleotide that is a chromatin-bound nucleic acid”.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-8, 10, and 12 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Frenz, US 2020/0277664 A1, published September 3, 2020.
Regarding claim 1, Frenz teaches methods for analyzing the spatial distribution of nucleic acid molecules in a cell (i.e. a sample comprising a target polynucleotide), wherein the introduction of a detectable nucleic acid probe is facilitated by electroporation (i.e. applying an electric field to the sample while contacting the sample with detectable nucleic acid probes) (Frenz, paragraph 1128) (i.e. the electric field is applied during nucleic-acid exposure (i.e. permeabilization of the cell), during which the nucleic acid probes bind to the target polynucleotide) (i.e. the target polynucleotide is rendered accessible to the probes by the method).
Regarding claims 2-6, Frenz teaches the sample is a paraffin-embedded tissue specimen, wherein the specimen comprises whole tissue samples, slices of tissue samples, cultured cell pellets, or touch imprints (i.e. cell smears) (Frenz, paragraphs 0209, 0215-0217, and 0221)
Regarding claim 7, Frenz teaches the sample comprises cells and the target polynucleotide is within a nucleus of the cells (Frenz, paragraphs 0119 and 0194-0195).
Regarding claim 8, Frenz teaches “With electroporation, a biological analyte by a molecule (e.g., a nucleic acid molecule) having a barcode (e.g., a spatial barcode) and a capture domain can enter a cell through one or more pores in the cellular membrane formed by applied electricity. The pore of the membrane can be reversible based on the applied field strength and pulse duration.” (i.e. the target nucleic acid is exposed (by the generation of pores) to the environment containing detectable probes (i.e. is exposed to a detectable probe)) (Frenz, paragraph 1128).
Regarding claim 10, Frenz teaches the method can be performed without subjecting the biological sample to enzymatic and/or chemical degradation of the cells (i.e. without contacting the cell with a proteolytic enzyme) (Frenz, paragraph 1005).
Regarding claim 12, Frenz teaches removing the paraffin prior to analysis (i.e. before contacting the sample with the labeled probes (Frenz, paragraph 0221).
Response to arguments
The response argues that the claims as presently amended overcome the rejection over Frenz because Frenz allegedly does not teach “applying an electric field during deparaffinization or antigen retrieval, both of which are expressly required by claim 1.” This assertion has been thoroughly reviewed and is not persuasive. As discussed at length in the rejections under 35 USC 112 above, the claim does not positively recite antecedent basis for these steps, and are not required by all embodiments of the claim as presently written. Therefore, these arguments are not commensurate in scope with the claimed invention.
The response further argues that the characterization of electroporation as “nucleic acid exposure” improperly conflates cell membrane permeabilization for probe delivery with tissue-level nucleic-acid exposure within a histological preparation workflow. This assertion has been thoroughly reviewed and is not persuasive. It is noted that the claims as presently written do not require “tissue-level nucleic acid exposure within a histological preparation workflow”. Even more, given the broadest reasonable interpretation of the claim term “nucleic acid exposure” (or even the preferred definition asserted by the response), the methods taught by Frenz result in successful hybridization of labeled probes to target polynucleotides in the sample (i.e. the target polynucleotides are rendered accessible by the methods of Frenz). Therefore, these arguments are i) not commensurate in scope with the claimed invention and ii) are not persuasive given the asserted preferred definition of “nucleic acid exposure” (that is not present in the claims, specification, or prior art).
Claims 1-7 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by West et al., US 2019/0262831 A1, published August 29, 2019.
Regarding claim 1, West et al. teach methods for capturing template (i.e. target) nucleic acids in a spatially specific manner (West et al., abstract) comprising applying an electric field to a sample comprising the target nucleic acids while the target nucleic acids specifically bind to a high density array of primers (i.e. detectable probes) (West et al., paragraph 0226 and figure 6). West et al. teach that the nucleic acids are exposed to the array and bind to the array while the electric field is applied (West et al., paragraph 0223-0228).
Regarding claim 2, West et al. teach that the sample is a paraffin-embedded tissue specimen (West et al., paragraphs 0223-0228).
Regarding claims 3-6, West et al. teach suitable samples comprise cell aggregates, cell smears, tissue samples, (West et al., paragraph 0062) and a tissue sample sectioned from an FFPE sample in a thickness of about 4-20 microns (i.e. a slice of whole tissue) West et al., paragraph 0074).
Regarding claim 7, West et al. teach the sample comprises cells and the image map of the tissue with which the probe array is correlated is of sufficient resolution to determine subcellular structures such as the nucleus (i.e. the target polynucleotide is within the nucleus) (West et al., paragraph 0076).
Response to arguments
The response argues that the claims as presently amended overcome the rejection over West because West allegedly does not teach “any step of deparaffinization or antigen retrieval, nor does it disclose exposing nucleic acids through any preparatory process.” This assertion has been thoroughly reviewed and is not persuasive. As discussed at length in the rejections under 35 USC 112 above, the claim does not positively recite antecedent basis for these steps, and are not required by all embodiments of the claim as presently written. Therefore, these arguments are not commensurate in scope with the claimed invention.
The response further argues that the interpretation of the claim term “nucleic acid exposure” applied previously (and herein) “improperly collapses distinct steps” (i.e. conflates cell membrane permeabilization for probe delivery with tissue-level nucleic-acid exposure within a histological preparation workflow). This assertion has been thoroughly reviewed and is not persuasive. It is noted that the claims as presently written do not require “tissue-level nucleic acid exposure within a histological preparation workflow”. Even more, given the broadest reasonable interpretation of the claim term “nucleic acid exposure” (or even the preferred definition asserted by the response), the methods taught by West result in successful hybridization of labeled probes to target polynucleotides in the sample (i.e. the target polynucleotides are rendered accessible by the methods of West). Therefore, these arguments are i) not commensurate in scope with the claimed invention and ii) are not persuasive given the asserted preferred definition of “nucleic acid exposure” (that is not present in the claims, specification, or prior art).
Claims 1-6 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Barker et al., US 2013/0309688 A1, published November 21, 2013.
This rejection has been updated as necessitated by the amendments to the claims.
Regarding claim 1, Barker et al. teach methods for processing samples for in situ hybridization (Barker et al., paragraph 0002) wherein an electric field is applied to the sample while in contact with detectable nucleic acid probes. Barker et al. teach the electric filed reduces the required reaction time and improves the quality of tissue staining (Barker et al., paragraphs 78-81).
Barker et al. further teach that wash buffers are pulled across a slide by attracting nanoparticles (i.e. removal of a liquid) (Barker et al., paragraph 0089).
Regarding claim 2, Barker et al. teach the sample is a paraffin-embedded tissue sample (Barker et al., paragraph 0002).
Regarding claims 3-6, Barker et al. teach the sample may be a variety of biological samples comprising tissues, histological samples (i.e. whole tissues), thin-layer preparations, a slice of tissue, blood smears, cell preparations, cells, and isolated cells (i.e. cell pellets) (Barker et al., paragraph 0060).
Response to arguments
The response argues that the claims as presently amended overcome the rejection over Barker because Barker allegedly does not teach “deparaffinization, antigen retrieval, or nucleic acid exposure as claimed. The cited passages related to reagent transport and staining efficiency, not to the specific preparatory steps required by claim 1” This assertion has been thoroughly reviewed and is not persuasive. As discussed at length in the rejections under 35 USC 112 above, the claim does not positively recite antecedent basis for these steps, and are not required by all embodiments of the claim as presently written. Therefore, these arguments are not commensurate in scope with the claimed invention.
The response further argues that the interpretation of the claim term “nucleic acid exposure” applied previously (and herein) “improperly collapses distinct steps” (i.e. conflates cell membrane permeabilization for probe delivery with tissue-level nucleic-acid exposure within a histological preparation workflow) and “the action… effectively treats any electric field assisted manipulation of a sample as equivalent to the claimed workflow”. This assertion has been thoroughly reviewed and is not persuasive. It is noted that the claims as presently written do not require “tissue-level nucleic acid exposure within a histological preparation workflow”. Even more, given the broadest reasonable interpretation of the claim term “nucleic acid exposure” (or even the preferred definition asserted by the response), the methods taught by Barker result in successful hybridization of labeled probes to target polynucleotides in the sample (i.e. the target polynucleotides are rendered accessible by the methods of Barker). It is reiterated that claim 1, as presently written, requires only “applying an electric field to a sample…” and “contacting the sample with one or more detectable nucleic acid probes which specifically bind to the target polynucleotide while the electric field is being applied”. Therefore, these arguments are i) not commensurate in scope with the claimed invention and ii) are not persuasive given the asserted preferred definition of “nucleic acid exposure” (that is not present in the claims, specification, or prior art).
Claims 1 and 7-9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Pilarski et al., US 2012/0082978 A1, Published April 5, 2012.
Regarding claim 1, Pilarski et al. teach applying an electric field to a sample during hybridization with detectable probes (Pilarski et al., paragraph 0151) (i.e. during nucleic-acid exposure).
Regarding claim 7, Pilarski et al. teach the sample is a population of cells of interest (i.e. comprises one or more cells) (Pilarski et al., paragraph 0026) and that target polynucleotides are within the nucleus of the cells (Pilarski et al., paragraphs 0008 or 0100).
Regarding claim 8, Pilarski et al. teach applying the electric field for at least two minutes (i.e. at least one minute) (Pilarski et al., paragraph 0151).
Regarding claim 9, Pilarski et al. teach the electric field is applied at a strength of 10 V/cm across channel (712) which is shorter than 75mm in length (i.e. 7.5 cm) (see figure 7). Because field strength=V/m, the total voltage applied across the channel is less than 10V/cm * 7.5 cm (i.e. is less than 75 V) (i.e. the applied potential is less than 500V) (Pilarski et al., paragraph 0151). Furthermore, 10V/cm is equivalent to 1V/mm (i.e. less than 500V/mm).
Response to arguments
The response asserts that Pilarski’s disclosure “presupposes that nucleic acids are already accessible and does not constitute a preparatory exposure step. Pilarski does not disclose applying an electric field during deparaffinization or antigen retrieval, nor does it disclose any process for rendering nucleic acids accessible within a tissue sample… [and] improperly equates hybridization conditions with preparatory exposure.”
This assertion has been thoroughly reviewed and is not persuasive. As discussed at length in the rejections under 35 USC 112 above, the claim does not positively recite antecedent basis for these steps, and are not required by all embodiments of the claim as presently written. Therefore, these arguments are not commensurate in scope with the claimed invention.
The response further argues that the interpretation of the claim term “nucleic acid exposure” applied previously (and herein) “improperly collapses distinct steps” (i.e. conflates cell membrane permeabilization for probe delivery with tissue-level nucleic-acid exposure within a histological preparation workflow). This assertion has been thoroughly reviewed and is not persuasive. It is noted that the claims as presently written do not require “tissue-level nucleic acid exposure within a histological preparation workflow”. Even more, given the broadest reasonable interpretation of the claim term “nucleic acid exposure” (or even the preferred definition asserted by the response), the methods taught by Pilarski result in successful hybridization of labeled probes to target polynucleotides in the sample (i.e. the target polynucleotides are rendered accessible by the methods of Pilarski). Therefore, these arguments are i) not commensurate in scope with the claimed invention and ii) are not persuasive given the asserted preferred definition of “nucleic acid exposure” (that is not present in the claims, specification, or prior art).
Claims 1 and 10-11 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kang et al., “Nanofountain Probe Electroporation (NFP-E) of Single Cells” Nano Letters 2013, 13, pages 2448-2457.
Regarding claim 1, Kang et al. teach applying an electric field to single cells (i.e. a sample comprising target polynucleotides while contacting the sample with a detectable nucleic acid probe (a 30 bp GAPDH-target beacon) (Kang et al., figure 2 and 9e) (i.e. exposing the nucleic acid and hybridization during application of the electric field).
Regarding claim 7, Kang et al. teach the sample comprises one or more cells and the target polynucleotide is in the nucleus (Kang et al., figure 9e).
Regarding claim 10, Kang et al. teach electroporating the nucleic acid probe into live cells attached to a solid substrate (i.e. not treated with a proteolytic enzyme).
Regarding claim 11, Kang et al. teaches the sample is rinsed with media without phenol red to avoid autofluorescence (Kang et al., page 2453, column 1, paragraph 1).
Response to arguments
The response asserts that the claims as presently amended overcome the rejection over Kang et al. because “Kang is directed to single-cell electroporation and does not disclose deparaffinization or antigen retrieval… [and] the electroporation process described in Kang is fundamentally different from the claimed tissue-preparation steps and does not correspond to nucleic-acid exposure within a histological workflow”.
This assertion has been thoroughly reviewed and is not persuasive. As discussed at length in the rejections under 35 USC 112 above, the claim does not positively recite antecedent basis for these steps, and are not required by all embodiments of the claim as presently written. Therefore, these arguments are not commensurate in scope with the claimed invention.
The response further argues that the interpretation of the claim term “nucleic acid exposure” applied previously (and herein) “improperly collapses distinct steps” (i.e. conflates cell membrane permeabilization for probe delivery with tissue-level nucleic-acid exposure within a histological preparation workflow). This assertion has been thoroughly reviewed and is not persuasive. It is noted that the claims as presently written do not require “tissue-preparation steps” nor “a histological workflow” nor “tissue-level nucleic acid exposure within a histological preparation workflow”. Even more, given the broadest reasonable interpretation of the claim term “nucleic acid exposure” (or even the preferred definition asserted by the response), the methods taught by Kang result in successful hybridization of labeled probes to target polynucleotides in the sample (i.e. the target polynucleotides are rendered accessible by the methods of Kang). Therefore, these arguments are i) not commensurate in scope with the claimed invention and ii) are not persuasive given the asserted preferred definition of “nucleic acid exposure” (that is not present in the claims, specification, or prior art).
Claims 1-9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tomoo et al., JP 2018-139504 A (published September 13, 2018).
This rejection under 35 U.S.C. 102(a)(1) is made under the broadest reasonable interpretation of the claims (described above) wherein “a sample” has the generic scope identified in the instant specification (i.e. does not require that the sample is embedded in paraffin) and “nucleic-acid exposure” is given its plain meaning in view of the specification.
Regarding claim 1, Tomoo et al. teach methods of in situ hybridization comprising steps of: i) applying an electric field to a sample comprising a target polynucleotide and ii) contacting the sample with detectable nucleic acid probes while the electric field is being applied, wherein the application of the electric field “efficiently modifies” complementary nucleic acids to a preferable state for hybridization, and the time of hybridization can be shortened (relative to conventional hybridization methods) (Tomoo et al, Figure 1, Figure 3 (reproduced below) and paragraph 0011).
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Tomoo et al. further teach that the “modification” to the double stranded target polynucleotide renders the target polynucleotide accessible to hybridization with a labeled probe (Tomoo et al., paragraph 0019) (also see paragraphs 0057-0064).
Regarding claim 2, Tomoo et al. teach the sample comprises paraffin-embedded tissue (Tomoo et al., paragraph 0064).
Regarding claim 3, Tomoo et al. teach the sample comprises “an organ of a living organism” (i.e. a whole tissue) (Tomoo et al., paragraph 0061).
Regarding claim 4, Tomoo et al. teach the sample comprises a slice of whole tissue (Tomoo et al., paragraph 0061).
Regarding claim 5, Tomoo et al. teach the sample comprises cell pellets (paragraph 0061).
Regarding claim 6, Tomoo et al. teach the sample comprises cell smears (paragraph 0061).
Regarding claim 7, Tomoo et al. teach the sample comprises cells and the target polynucleotide is within a nucleus of the cells (Tomoo et al., paragraph 0066).
Regarding claim 8, Tomoo et al. teach applying the electric field for 1 to 5 minutes (Tomoo et al., paragraph 0035).
Regarding claim 9, Tomoo et al. teach the electric field has a voltage as low as 0.35 kV/mm (i.e. 340 V/mm; less than 500 V/mm) (Tomoo et al., paragraph 0034).
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.
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 1-4 and 7-8 are rejected under 35 U.S.C. 103 as being unpatentable over Lim et al., US 2018/0120207 A1 (Published May 3, 2018) in view of Fujishima et al., “Novel method for rapid fluorescence in-situ hybridization of ALK rearrangement using non-contact alternating current electric field mixing”, Scientific Reports 7:15116 (Published November 8, 2017).
Regarding claim 1, Lim et al. teaches methods of deparaffinization of tissues comprising applying an electric field to a sample comprising target polynucleotides (Lim et al., paragraph 0015). Lim et al. teach removing paraffin from tissue samples comprising applying an electric field allows for minimization/removal of the necessity for contacting target nucleic acids with aromatic hydrocarbon solvents such as xylene that are known to cause oxidation of DNA and RNA nucleotides that can negatively impact sequencing or hybridization-based detection of the target nucleic acids (Lim et al., paragraph 0015). Lim specifically contemplates that nucleic acid assays such as fluorescence in situ hybridization of DNA or RNA probes to target nucleic acids in deparaffinized tissue could benefit from methods of electrical, rather than purely chemical (i.e. by treatment with xylene) deparaffinization (Lim et al., paragraph 0015).
Lim et al. do not teach contacting the sample with one or more detectable nucleic acid probes which specifically bind to the target polynucleotide while the electric field is being applied.
However, Fujishima et al. teach methods for “rapid fluorescence in-situ hybridization” designed to facilitate hybridization between fluorescent nucleic acid probes and target nucleic acids (Fujishima et al., page 1, paragraph 1). Fujishima et al. teach that the rapid FISH technique produces results in 4.5 hours rather than 20 hours with equivalently accurate results (Fujishima et al., page 1, paragraph 1). The rapid FISH method adapts a method originally developed for rapid immunohistochemistry wherein an electric field is applied to deparaffinized tissue samples while an antibody (or nucleic acid probes) are in contact with the sample (Fujishima et al., page2, paragraph 2).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the method of electric field-mediated paraffin removal from tissue samples and subsequent staining by conventional FISH, taught by Lim et al. with the teachings of Fujishima et al. that applying an electric field during the hybridization process significantly increases the speed with which a clinician may obtain FISH results (Fujishima et al., page 2, paragraph 2). The ordinary artisan would have been motivated to have combined the electric field-assisted deparaffinization step, taught by Lim et al., with the electric field-assisted denaturation and hybridization steps, taught by Fujishima et al. because of the teaching of Fujishima et al. that rapid processing by rapid FISH allows for faster determination of informative genetic signals in cancer samples (Fujishima et al., page 4, paragraph 4) and by the teaching of Lim et al. that fluorescence in-situ hybridization techniques would be expected to benefit from better-quality nucleic acid removal from paraffin (i.e. without or with reduced exposure to DNA damaging chemicals such as xylene) (Lim et al., paragraph 0015).
Regarding claim 2, Lim et al. (paragraph 0015) and Fujishima et al. (page 4, paragraph 7) teach the samples are paraffin-embedded tissues.
Regarding claims 3-4 Lim et al. teach the tissues are embedded in paraffin and may be sectioned (i.e. sliced) prior to mounting on a slide (Lim et al., paragraph 0007-0008).
Regarding claim 7, Fujishima et al. teach the sample comprises one or more cells and the target nucleic acids are within the nuclei of the cells (Fujishima et al., Figure 1).
Regarding claim 8, Fujishima et al. teach the application of the electric field during steps of “denaturation and hybridization” for 3 hours (i.e. at least 1 minute) (Fujishima et al., Figure 1 and table 2).
Response to arguments
The response asserts that the claims as presently amended requires applying an electric field during “each of the steps of deparaffinization, antigen retrieval, nucleic-acid exposure, and optionally during removal of trapped liquid or solvent and/or coverslip mounting.
As discussed at length in the rejections under 35 USC 112 above, the claim does not positively recite antecedent basis for these steps, and are not required by all embodiments of the claim as presently written. Therefore, these arguments are not commensurate in scope with the claimed invention.
Furthermore, even if the claim were amended to properly positively recite the definite method steps asserted in the response, the combination of Lim and Fujishima teach each of these elements and clearly motivate their combination (as described in the 103 rejection above).
The assertion in the response that Lim teach only electric-field-assisted deparaffinization and does not suggest extending the electric field to downstream preparation steps such as antigen retrieval or nucleic-acid exposure appears to acknowledge the cited teachings of Lim in the context of piecemeal analysis.
The assertion in the response that Fujishima “assumes that nucleic acids are already accessible and does not disclose or suggest using an electric field to perform upstream preparation steps, including antigen retrieval or nucleic-acid exposure” is i) not commensurate in scope with the claimed invention as discussed at length above, and ii) not persuasive even in the context of a piecemeal analysis of the teachings considering the preferred definition of “nucleic-acid exposure” (not clearly supported by the specification nor used in the art) espoused in the response wherein “antigen retrieval or nucleic-acid exposure” is a preparatory step that renders chromatin-bound nucleic acids accessible for probe binding within the sample (i.e. the preparatory step is defined by its function of rendering nucleic acids accessible for probe binding). Fujishima et al. teach applying an electric field during steps of “denaturation” (i.e. opening the DNA duplex for accessibility of nucleic acids to probes) “and hybridization” (Fujishima et al., figure 1 and table 2, reproduced below with added highlight for clarity of the record).
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Furthermore, Fujishima applies this electric field to these steps in the context of samples that are whole cells and detects probe binding within nuclei. Therefore, Fujishima clearly and definitively demonstrates denaturing chromatin-bound nucleic acids (i.e. “rendering… accessible”) while applying an electric field and successfully hybridizing nucleic acids to the denatured, chromatin-bound nucleic acids much faster than in a standard FISH comparison (3 hours vs 16-18 hours).
Finally, the response asserts that there is no teaching, suggestion, or motivation in the cited art to use an electric field as a unified mechanism across multiple distinct preparation steps. This assertion has been thoroughly considered and is not persuasive.
As described above, Fujishima teaches applying an electric field to “denaturation and hybridization” steps (i.e. “distinct preparation steps”). Furthermore, Lim specifically contemplates that nucleic acid assays such as fluorescence in situ hybridization of DNA or RNA probes to target nucleic acids in deparaffinized tissue could benefit from methods of electrical, rather than purely chemical (i.e. by treatment with xylene) deparaffinization (Lim et al., paragraph 0015) and Fujishima teach applying an electric field during the hybridization process significantly increases the speed with which a clinician may obtain FISH results (Fujishima et al., page 2, paragraph 2).
Therefore, both Lim and Fujishima teach methods for improved fluorescence in situ hybridization (FISH) comprising applying electric fields to different steps in the FISH workflow. As described above, it would have been obvious to the ordinary artisan to have combined the electric field-assisted deparaffinization step, taught by Lim et al., with the electric field-assisted “denaturation and hybridization” steps, taught by Fujishima et al. because of the teaching of Fujishima et al. that rapid processing by rapid FISH allows for faster determination of informative genetic signals in cancer samples (Fujishima et al., page 4, paragraph 4) and by the teaching of Lim et al. that fluorescence in-situ hybridization techniques would be expected to benefit from better-quality nucleic acid removal from paraffin (i.e. without or with reduced exposure to DNA damaging chemicals such as xylene) (Lim et al., paragraph 0015). The ordinary artisan would further have had a reasonable expectation that the combination of these electric-field aided steps would have resulted in a method that combines the advantages taught by the two references (e.g. less DNA damage during deparaffinization taught by Lim and faster denaturation and hybridization taught by Fujishima).
Claims 1, 5-6, 10, and 12-13 are rejected under 35 U.S.C. 103 as being unpatentable over Lim et al. in view of Fujishima et al. as applied to claims 1-4 and 7-8 above, and further in view of Frenz, US 2020/0277664 A1 (Published September 3, 2020).
Regarding claim 1, as described in the preceding 103 rejection, Lim et al. in view of Fujishima et al. teach methods comprising applying an electric field to a sample comprising a target polynucleotide and contacting the sample with detectable nucleic acid probes while the electric field is being applied.
Lim et al. in view of Fujishima et al. teach electric field-assisted methods for paraffin removal comprising minimal contact with mutagenic solvents such as xylene (Lim et al., paragraphs 0015 or 0049) and electric field assisted methods for rapid hybridization of detectable nucleic acid probes to target nucleic acids (Fujishima et al., Figure 1 and page 4, paragraph 7).
Regarding claims 5-6, Lim et al. in view of Fujishima et al. do not teach that a sample may be “cell pellets” or “cell smears”
However, Frenz teaches methods for analyzing the spatial distribution of nucleic acid molecules in a cell (i.e. a sample comprising a target polynucleotide), wherein the introduction of a detectable nucleic acid probe is facilitated by electroporation (i.e. applying an electric field to the sample while contacting the sample with detectable nucleic acid probes) (Frenz, paragraph 1128).
Frenz teaches the sample is a paraffin-embedded tissue specimen, wherein the specimen comprises whole tissue samples, slices of tissue samples, cultured cell pellets, or touch imprints (i.e. cell smears) (Frenz, paragraphs 0209, 0215-0217, and 0221).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods taught by Lim et al. in view of Fujishima et al. comprising electric field-assisted removal of paraffin from tissue samples and hybridization of detectable nucleic acid probes to target nucleic acids in the deparaffinized tissue samples to further apply the techniques disclosed by Lim et al. in view of Fujishima et al. to other frequently used clinical sample types (i.e. cell pellets as in fractionated blood samples (for example, buffy coats or peripheral blood mononuclear cells, etc.) or cell smears (for example, whole blood smears used in, among other applications, parasitology).
Regarding claim 10, Frenz teaches the method can be performed without subjecting the biological sample to enzymatic and/or chemical degradation of the cells (i.e. without contacting the cell with a proteolytic enzyme) (Frenz, paragraph 1005).
Regarding claim 12, Frenz teaches removing the paraffin prior to analysis (i.e. before contacting the sample with the labeled probes (Frenz, paragraph 0221). Alternatively, Lim et al. teach removing substantially all of the paraffin prior to genomic analysis (i.e. hybridizing probes) (Lim et al., paragraph 0049-0051).
Regarding claim 13, Lim et al. teach that removal of paraffin is conventionally performed by dipping the tissue slide in xylene. Lim et al. further teach electric field-based deparaffinization removes most or substantially all of the paraffin, which minimizes or eliminates the use of xylene… which is highly desirable given that xylene is a toxic chemical (Lim et al., paragraph 0049).
Therefore, Lim et al. teach embodiments wherein the use of xylene is “minimized” in the deparaffinization process (i.e. the paraffin is removed by a combination of applying an electric field and rinsing the sample with a deparaffinization solvent) (Lim et al., paragraph 0049). Alternatively, Lim et al. teach other solvents such as isopropyl alcohol are also used to remove paraffin (Lim et al., paragraph 0011).
Response to arguments
The response asserts that Frenz does not cure the deficiencies in Lim and Fujishima. This assertion is not persuasive for the reasons of record and all of the reasons discussed at length above in the response to the arguments regarding the 103 rejection over Lim and Fujishima.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,525,759 B2 (herein referred to as ‘759) (issued December 13, 2022) in view of Fujishima et al.
Claim 1 of ‘759 recites a method for preparing a tissue comprising applying an electric field to a tissue sample (i.e. comprising a target polynucleotide). The claims of ‘759 do not recite contacting the sample with detectable nucleic acid probes while the electric field is being applied.
However, Fujishima et al. teach methods for “rapid fluorescence in-situ hybridization” designed to facilitate hybridization between fluorescent nucleic acid probes and target nucleic acids (Fujishima et al., page 1, paragraph 1). Fujishima et al. teach that the rapid FISH technique produces results in 4.5 hours rather than 20 hours with equivalently accurate results (Fujishima et al., page 1, paragraph 1). The rapid FISH method adapts a method originally developed for rapid immunohistochemistry wherein an electric field is applied to deparaffinized tissue samples while an antibody (or nucleic acid probes) are in contact with the sample (Fujishima et al., page2, paragraph 2).
Therefore, it would have been prima facie obvious for one of ordinary skill in the art to have modified the method claimed by ‘759 to further comprise contacting FISH probes with the sample while the electric field is applied, after removal of substantially all of the paraffin. The ordinary artisan would have been motivated to detect nucleic acids in a tissue prepared (i.e. deparaffinized) by the method claimed by ‘759 because of the teaching of Fujishima et al. that that rapid processing (i.e. hybridization) by rapid FISH in deparaffinized clinical samples allows for faster determination of informative genetic signals in cancer samples (Fujishima et al., page 4, paragraph 4).
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 17, and 18 of U.S. Patent No. 10,613,005 B2 (herein referred to as ‘005) in view of Fujishima et al.
Claims 1 and 17 of ‘005 recite a method for deparaffinizing a tissue comprising applying an electric field to the tissue (i.e. a sample comprising a target polynucleotide) (‘005, claim 1) and staining the tissue after removing the paraffin (‘005, claim 17).
The claims of ‘005 do not recite that the stain is a detectable nucleic acid probe or probes or that the electric field is applied to the tissue while the sample is contacted with detectable nucleic acid probes.
However, Fujishima et al. teach methods for “rapid fluorescence in-situ hybridization” designed to facilitate hybridization between fluorescent nucleic acid probes and target nucleic acids (Fujishima et al., page 1, paragraph 1). Fujishima et al. teach that the rapid FISH technique produces results in 4.5 hours rather than 20 hours with equivalently accurate results (Fujishima et al., page 1, paragraph 1). The rapid FISH method adapts a method originally developed for rapid immunohistochemistry wherein an electric field is applied to deparaffinized tissue samples while an antibody (or nucleic acid probes) are in contact with the sample (Fujishima et al., page2, paragraph 2).
Therefore, it would have been prima facie obvious for one of ordinary skill in the art to have modified the method claimed by ‘005 to further comprise contacting FISH probes with the sample while the electric field is applied, after removal of substantially all of the paraffin. The ordinary artisan would have been motivated to detect nucleic acids in a tissue prepared (i.e. deparaffinized) by the method claimed by ‘005 because of the teaching of Fujishima et al. that that rapid processing (i.e. hybridization) by rapid FISH in deparaffinized clinical samples allows for faster determination of informative genetic signals in cancer samples (Fujishima et al., page 4, paragraph 4).
Response to arguments
The response asserts that the amendment of claim 1 to recite that “the electric field is also being applied during the step of deparaffinization, antigen retrieval, nucleic-acid exposure, removal of trapped liquid or solvent, and/or coverslip mounting” renders the double patenting rejections of record moot because “this is not taught in the cited prior art”.
As is addressed in the double patenting rejections of record, these broadly claimed limitations are, in fact, present in the cited prior art.
Furthermore, the arguments in the response fail to comply with 37 CFR 1.111(b) because they amount to a general allegation that the claims define a patentable invention without specifically pointing out how the language of the claims patentably distinguishes them from the references.
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5, and 10 of U.S. Patent No. 12,050,163 (herein referred to as ‘163) in view of Fujishima et al.
The claims of ‘163 recite a method for deparaffinizing a tissue (i.e. preparing for in situ hybridization) comprising applying an electric field to a sample comprising a target polynucleotide (‘163, claims 1 and 5), and further staining the tissue (‘163, claim 10).
The claims of ‘163 do not teach that the “staining the tissue” comprises contacting the sample with one or more detectable nucleic acid probes which specifically bind to the target polynucleotide while the electric field is being applied.
However, Fujishima et al. teach methods for “rapid fluorescence in-situ hybridization” designed to facilitate hybridization between fluorescent nucleic acid probes and target nucleic acids (Fujishima et al., page 1, paragraph 1). Fujishima et al. teach that the rapid FISH technique produces results in 4.5 hours rather than 20 hours with equivalently accurate results (Fujishima et al., page 1, paragraph 1). The rapid FISH method adapts a method originally developed for rapid immunohistochemistry wherein an electric field is applied to deparaffinized tissue samples while an antibody (or nucleic acid probes) are in contact with the sample (Fujishima et al., page 2, paragraph 2).
Therefore, it would have been prima facie obvious for one of ordinary skill in the art to have modified the method claimed by ‘163 to further comprise contacting FISH probes with the sample while the electric field is applied, after removal of substantially all of the paraffin. The ordinary artisan would have been motivated to detect nucleic acids in a tissue prepared (i.e. deparaffinized) by the method claimed by ‘163 because of the teaching of Fujishima et al. that that rapid processing (i.e. hybridization) by rapid FISH in deparaffinized clinical samples allows for faster determination of informative genetic signals in cancer samples (Fujishima et al., page 4, paragraph 4).
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 10 of U.S. Patent No. 12,326,387 (herein referred to as ‘367) in view of Fujishima et al.
The claims of ‘387 recite a method for deparaffinizing a tissue (i.e. preparing for in situ hybridization) comprising applying an electric field to a sample comprising a target polynucleotide (‘387, claim 1), and further staining the tissue (‘387, claim 10).
The claims of ‘387 do not teach that the “staining the tissue” comprises contacting the sample with one or more detectable nucleic acid probes which specifically bind to the target polynucleotide while the electric field is being applied.
However, Fujishima et al. teach methods for “rapid fluorescence in-situ hybridization” designed to facilitate hybridization between fluorescent nucleic acid probes and target nucleic acids (Fujishima et al., page 1, paragraph 1). Fujishima et al. teach that the rapid FISH technique produces results in 4.5 hours rather than 20 hours with equivalently accurate results (Fujishima et al., page 1, paragraph 1). The rapid FISH method adapts a method originally developed for rapid immunohistochemistry wherein an electric field is applied to deparaffinized tissue samples while an antibody (or nucleic acid probes) are in contact with the sample (Fujishima et al., page 2, paragraph 2).
Therefore, it would have been prima facie obvious for one of ordinary skill in the art to have modified the method claimed by ‘387 to further comprise contacting FISH probes with the sample while the electric field is applied, after removal of substantially all of the paraffin. The ordinary artisan would have been motivated to detect nucleic acids in a tissue prepared (i.e. deparaffinized) by the method claimed by ‘387 because of the teaching of Fujishima et al. that that rapid processing (i.e. hybridization) by rapid FISH in deparaffinized clinical samples allows for faster determination of informative genetic signals in cancer samples (Fujishima et al., page 4, paragraph 4).
Claim 1 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 12 and 15 of copending Application No. 18/747,240 (herein referred to as ‘240) in view of Fujishima et al.
The claims of ‘240 recite a method for preparing a tissue comprising providing a tissue embedded with paraffin, applying an electric field to the tissue, wherein the electric field removes the paraffin from the tissue (‘240, claim 12), and further staining the tissue after applying the electric field (‘240, claim 12).
The claims of ‘240 do not teach that the “staining the tissue” comprises contacting the sample with one or more detectable nucleic acid probes which specifically bind to the target polynucleotide while the electric field is being applied.
However, Fujishima et al. teach methods for “rapid fluorescence in-situ hybridization” designed to facilitate hybridization between fluorescent nucleic acid probes and target nucleic acids (Fujishima et al., page 1, paragraph 1). Fujishima et al. teach that the rapid FISH technique produces results in 4.5 hours rather than 20 hours with equivalently accurate results (Fujishima et al., page 1, paragraph 1). The rapid FISH method adapts a method originally developed for rapid immunohistochemistry wherein an electric field is applied to deparaffinized tissue samples while an antibody (or nucleic acid probes) are in contact with the sample (Fujishima et al., page 2, paragraph 2).
Therefore, it would have been prima facie obvious for one of ordinary skill in the art to have modified the method claimed by ‘240 to further comprise contacting FISH probes with the sample while the electric field is applied, after removal of substantially all of the paraffin. The ordinary artisan would have been motivated to detect nucleic acids in a tissue prepared (i.e. deparaffinized) by the method claimed by ‘240 because of the teaching of Fujishima et al. that that rapid processing (i.e. hybridization) by rapid FISH in deparaffinized clinical samples allows for faster determination of informative genetic signals in cancer samples (Fujishima et al., page 4, paragraph 4).
This is a provisional nonstatutory double patenting rejection.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Tanino et al., "Rapid immunohistochemistry based on alternating current electric field for intraoperative diagnosis of brain tumors" Brain Tumor Pathol (2015) 32:12-19 (published May 8 2014) (Year: 2014)
Toda et al., "A Novel Immunohistochemical Staining Method Allows Ultrarapid Detection of Lymph Node Micrometastases While Conserving Antibody" Acta Histochem. Cytochem. 44(3): 133-139, 2011 (Year: 2011)
Tanino et al. and Toda et al. each teach methods for rapid immunohistochemical staining achieved by treatment of fresh, frozen (Toda et al.) or both fresh frozen and FFPE tissues (Tanino et al.) with an electric field.
No claim is allowed.
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/Z.M.T./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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