CTNF 18/564,478 CTNF 100667 DETAILED ACTION Notice of Pre-AIA or AIA Status 07-03-aia AIA 15-10-aia The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Claim Status Applicant’s preliminary amendment to the claims submitted on 11/27/2023 is acknowledged. Claims 1-13 are pending and being examined on the merits. Information Disclosure Statement 06-49-06 AIA The listing of references in the specification is not a proper information disclosure statement (paragraphs [0063-0064, 0066, 0077-0083]). 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered. Specification 07-29 AIA The disclosure is objected to because of the following informalities: Paragraph [0009] reads “An alkyne-single stranded DNA (ssDNA) probe generated through the described method, yield fluorescent FISH dots.” This should read “An alkyne-single stranded DNA (ssDNA) probe generated through the described method, [[yield]] yields fluorescent FISH dots.” Paragraph [0010] reads “Non-EDC treatment results in loss of signals after harsh.” This should read “Non-EDC treatment results in loss of signals after harsh treatment. ” or “Non-EDC treatment results in loss of signals after harsh wash. ” Paragraph [0017] reads “For example, a protein probe may be connected with one or more nucleic acid molecules to for a probe that is a chimera.” This should read “For example, a protein probe may be connected with one or more nucleic acid molecules to [[for]] form a probe that is a chimera.” Appropriate correction is required. The use of the term “MetaPhor” (paragraph [0008]), which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term. Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks. Claim Objections 07-29-01 AIA Claim s 1, 3, and 10-12 are objected to because of the following informalities: Claim 1 , line 8, read “one or more reactive groups, at the 3’ end of the primer”. This should read “one or more reactive groups, at the 3’ end of the hybrid- primer” to maintain consistent terminology throughout the claim. Claim 3 reads “wherein the reactive group is” and should read “wherein the one or more reactive group s are [[is]]” to maintain consistency between claim 3 and claim 1. Claim 10 reads “wherein the hybrid-primer comprises a sequence complementarity to a region of the RNA template” and should read “wherein the one or more hybrid-primer s [[comprises]] comprise a sequence complementarity to a region of the one or more RNA template s ”. Claim 11 reads “wherein the probes” and should read “wherein the one or more single stranded DNA probes”. Claim 12 reads “wherein the probes” and should read “wherein the one or more single stranded DNA probes” . Appropriate correction is required. Claim Rejections - 35 USC § 112b - Indefiniteness 07-30-02 AIA 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. 07-34-01 Claims 1-13 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 is directed to a method to generate probes. However, there is no active step of generating a single stranded DNA probe via reverse transcription described. The hybrid-primers are contacted with RNA templates in conditions that are suitable for reverse transcription but the very next step is degradation of the RNA template and the hybrid-primer. As written, it is unclear if the one or more single stranded DNA probes are derived from the RNA template or are a completely separate part of the reaction. For the purposes of examination, the claim is being interpreted to mean that the resulting single stranded DNA probes are reverse transcribed from the RNA template, however clarification is required. It is also unclear if the one or more 5’ reactive groups at the 5’ ends of the single stranded DNA probes are the same reactive group as at the 3’ end of the hybrid-primer or if they’re different reactive groups. The claim currently lacks definition as to how the single stranded DNA probes are generated and as a result is unclear as to whether or not the 3’ reactive group at the end of the hybrid-primer is said reactive group at the 5’ end of the single stranded DNA probe. Clarification is required. Claims 2-13 depend from claim 1, inherit this deficiency, and are rejected on the same basis. Claim 3 is directed to the method of claim 1 “wherein the reactive group is selected from”. It is unclear if this is referring to the one or more reactive groups at the 3’ end of the primer or if it’s referring to the one or more reactive groups at the 5’ end of the single stranded DNA probes (or both). Clarification is required. Claim 11 is directed to the method of claim 1 “wherein the probes are washed after each step”. However, the single-stranded DNA probes are not generated/isolated until the end of claim 1 and there are no further steps beyond that. It is unclear if this would be a wash step after the probe has been generated, or if this is a wash step that is supposed to occur between when reverse transcription is implied to occur and when the degradation of the RNA template and hybrid primer occurs. For purposes of examination, the probes are fully made by the end of step (ii), after the RNA template and hybrid-primer have been degraded. Therefore, “the probes are washed after each step” can only occur after step (ii) and after step (iii). However, clarification is required. Claims 12-13 depend from claim 11, inherit this deficiency, and are rejected on the same basis. Claim 12 is directed to the method of claim 11 “wherein the probes are washed with a buffer that removes non-specific interactions”. It is unclear what interactions are being referred to here. Is the wash meant to prevent the probes from interacting with non-specific targets within a tissue? If this is the case, there is no preceding step in which probes are introduced to a sample to enable these interactions to occur. If this is not the case, it is unclear what other non-specific interactions may be being referred to. Clarification is required. Claim 13 depends from claim 12, inherits this deficiency, and is rejected on the same basis. Claim Rejections - 35 USC § 112d – Failure to Further Limit 07-36 AIA The following is a quotation of 35 U.S.C. 112(d): (d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers. The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph: Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers. 07-36-01 AIA Claim 8 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. In the instant case, claim 8 depends from claim 1, which contains the limitation “contacting one or more RNA templates with a reverse transcriptase and one or more hybrid-primers under conditions suitable for reverse transcription”. Conditions suitable for reverse transcription necessarily include buffers, dNTPs, and proper temperatures for the transcriptase to function. Without these conditions, the single stranded DNA probes would not have been generated by the method of claim 1. Therefore, claim 8 does not further limit claim 1 . Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements. Claim Rejections - 35 USC § 103 07-06 AIA 15-10-15 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. 07-20-aia AIA 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. It is noted that claims 12 and 13 are not being rejected under 35 USC 103, not because they are free of the prior art but because the indefiniteness, as outlined in the 112b rejection above, makes it unclear how these claims should be interpreted in light of the prior art. It is unclear what non-specific interactions are being prevented by the buffer wash and therefore unclear what types of stringent buffers would be employable in this instance. Amendments to the claims to address the 112b may require further consideration in view of the prior art. 07-21-aia AIA Claim s 1-11 are rejected under 35 U.S.C. 103 as being unpatentable over Murgha (Murgha et al., Biotechniques 2016) in view of Monforte (Monforte et al., US 5,830,655 A) . Regarding claim 1: Murgha teaches a method of generating probes in which one or more RNA templates are contacted with a reverse transcriptase and a hybrid-primer under conditions suitable for reverse transcription and the hybrid-primer hybridizes to an RNA template (Figure 3 Step 3, Table 1 (P3)). The hybrid-primer comprises one or more deoxyribonucleotides and one or more ribonucleotides. Murgha teaches degrading the RNA template and hybrid primer (Figure 3 Step 4). Murgha teaches isolating one or more single stranded DNA probes following degradation of the RNA template and hybrid primer (Figure 3, Materials and Methods - RNA-DNA chimeric primer for cDNA synthesis). Murgha does not teach that the hybrid-primer has one or more reactive groups at the 3’ end or that the one or more single stranded DNA probes comprise one or more reactive groups at their 5’ ends. However, 3’ modifications of hybrid-primers for introductions of a 5’ modification to a resulting amplicon is known in the art, as taught by Monforte. Monforte teaches a method of using cleavable primers in which a cleavable moiety is placed at the 3’ end of a primer (Abstract). Upon generation of an extension product, this moiety can be selectively cleaved and a size selected fragment is released (Abstract). Relevant to the instantly rejected claims, Monforte teaches incorporation of modified bases such as a 5-allyl amino that allows for immobilization of the primer to a functionalized support through an amide linkage (col 16, ln 32-47). Importantly, Monforte teaches incorporation of this immobilization attachment site downstream of the 3’ cleavable moiety, ensuring that this reactive group is then attached to the 5’ end of the generated extension product (col 18, ln 5-16). It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Murgha in which hybrid-primers are used to generate single stranded DNA probes through reverse transcription of an RNA template, to incorporate the 3’ reactive groups and subsequent 5’ reactive groups on said primers and resultant products as taught by Monforte. One would be motivated to employ these modifications given the assertion by Monforte that this enables “immobilization of the extension segment” following by subsequent washing to “remove reaction products (salts, enzymes, nucleotide fragments, reagents) prior to release and subsequent size and/or sequence analysis” (col 18, ln 13-16). One would have a reasonable expectation of success given that Monforte teaches that incorporation of these moieties does not interfere with primer extension (col 18, ln 10-12) and can also be performed using primers that contain ribonucleotides (in which ribose can be employed as a cleavable site to remove the primer through the use of ammonium hydroxide; col 23, ln 11-17). Regarding claim 2: Murgha teaches generating an RNA template from synthetic DNA (Materials and Methods – In vitro transcription). Regarding claim 3: Monforte teaches that the reactive group is an amide (col 16, ln 32-47). Regarding claim 4: Murgha teaches that the degradation of the RNA template and hybrid-primer is accomplished by alkaline hydrolysis (“Upon completion of the reaction, the RNA was degraded using the Alkaline hydrolysis of RNA protocol”, Materials and Methods - RNA-DNA chimeric primer for cDNA synthesis). Regarding claim 5-7: Monforte teaches that degradation of RNA template can be accomplished through enzymatic degradation, specifically by RNase A (col 24, ln 29-32). Regarding claim 8: Murgha teaches buffer conditions, a suitable temperature, and dNTPs used for reverse transcription (Materials and Methods - Reverse transcription and Materials and Methods - RNA-DNA chimeric primer for cDNA synthesis). Regarding claim 9: Murgha teaches that the hybrid-primer is 24 nucleotides long, which reads on at least 17 nucleotides in length (Table 1, P3). Regarding claim 10: Murgha teaches that the hybrid-primer is 100% complementarity to a region of the RNA template (Figure 3). Regarding claim 11: Monforte teaches that the extension product (probes) are washed after they are created (col 18, ln 13-16). Conclusion No claims are allowed. Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAILEY E CASH whose telephone number is (571)272-0971. 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If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /KAILEY ELIZABETH CASH/Examiner, Art Unit 1683 /STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683 Application/Control Number: 18/564,478 Page 2 Art Unit: 1683 Application/Control Number: 18/564,478 Page 3 Art Unit: 1683 Application/Control Number: 18/564,478 Page 4 Art Unit: 1683 Application/Control Number: 18/564,478 Page 5 Art Unit: 1683 Application/Control Number: 18/564,478 Page 6 Art Unit: 1683 Application/Control Number: 18/564,478 Page 7 Art Unit: 1683 Application/Control Number: 18/564,478 Page 8 Art Unit: 1683 Application/Control Number: 18/564,478 Page 9 Art Unit: 1683 Application/Control Number: 18/564,478 Page 10 Art Unit: 1683 Application/Control Number: 18/564,478 Page 11 Art Unit: 1683