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 1-27 are currently pending. Claims 1-4, 6-7, 9-11, 13-15, 17-18 and 20-27 are withdrawn as being drawn to a nonelected invention. Claims 5, 8, 12, 16 and 19 are under examination.
Election/Restrictions
Applicant’s election without traverse of Group III: claims 5, 8, 12, 16 and 19, drawn to a method of targeted generation of 5’ tagged fragments, in the reply filed March 16, 2026 is acknowledged.
Claims 1-4, 6-7, 9-11, 13-15, 17-18 and 20-27 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on March 16, 2026.
Information Disclosure Statement
The Information Disclosure Statements filed February 16, 2023; February 16, 2023; May 22, 2025; and November 12, 2025 have been considered.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see Page 57, [00406] and 59, [00409]). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
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.
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.
Claim 5, 8, 12, 16 and 19 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 5 is vague and indefinite for the following reasons:
Claim 5 recites the limitation “the 5’ ends" in line 4. There is insufficient antecedent basis for this limitation in the claim.
Claim 8 depend from claim 5 and is therefore included in this rejection.
Claim 12 is vague and indefinite for the following reasons:
Claim 12 recites the limitation “the 5’ ends" in line 7. There is insufficient antecedent basis for this limitation in the claim.
Claim 16 is vague and indefinite for the following reasons:
Claim 16 recites the limitation “the temperature" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 16 recites the limitation “the optimum temperature" in line 2. There is insufficient antecedent basis for this limitation in the claim.
In claim 16, line 2, the terms “the optimum temperature" are unclear and confusing. It is unclear as what an “optimum” temperature is to be? Is there a specific temperature that makes it optimal?
Claim 19 is vague and indefinite for the following reasons:
Claim 19 recites the limitation “the 5’ ends" in line 14. There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 5 and 8 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Cann et al. (WIPO International Application Publication WO 2016/014409 A1, published January 28, 2016), cited on the IDS filed February 16, 2023.
Regarding claim 5, Cann teaches a method of targeted generation of 5' tagged fragments of a target nucleic acid (Page 25, [00104] and [00102], Pages 26-27, [00106]-[00107] and Pages 40-41, [00149]). Cann teaches a transposome complex with a transposase comprising a first transposon comprising a 3’ transposon end sequence and a 5’ adaptor sequence (Pages 24-28, [00101]—[00108], Pages 40-41, [0149] and Figs. 4B-D). Cann teaches a catalytically inactive endonuclease associated with a guide RNA that can direct endonuclease binding to one or more nucleic acid sequences of interest (Abstract, Pages 6-7, [0026], Pages 8-9, [0033], Page 75, [00257] and Figs. 4A-D). Cann teaches a second transposon comprising the complement of the transposon end sequence (Pages 26-27, [00106]-[00107] and Pages 40-41, [00149]). Cann teaches combining a sample comprising a double-stranded nucleic acid and a transposome complexes of claim 1, that is a targeted transposome complex (Pages 24-28, [00101]—[00108], Pages 40-41, [0149] and Figs. 4B-D). Cann teaches fragmenting the nucleic acid into a plurality of fragments by the transposase, by joining the 3' end of the first transposon to the 5' ends of the fragments to produce a plurality of 5' tagged fragments (Page 24, [00101], Page 25, [00104], Page 26-27, [00106]-[00107], Pages 40-41, [00149] and Figs. 4B-D).
Regarding claim 8, Cann teaches the combining a sample comprising a double- stranded nucleic acid with one or more transposome complex that is targeted (Pages 24-28, [00101]—[00108], Pages 40-41, [0149] and Figs. 4B-D). Cann teaches combining the sample with a catalytically inactive endonuclease, wherein the catalytically inactive endonuclease is bound to a first binding partner (Pages 3-4, [0015], Page 5, [0020], Pages 6-7, [0025]-[0026], Pages 8-9, [0033], Pages 30-31, [00114], Page 47, [00165] and Page 75, [00258]). Cann teaches adding the transposase and first and second transposons and the transposase is bound to a second binding partner (Pages 24-28, [00101]—[00108], Pages 40-41, [0149], Pages 30-31, [00114], Page 47, [00165] and Page 75, [00258] and Figs. 4B-D). Cann teaches the transposase can bind to catalytically inactive endonuclease by pairing of the first and second binding partners (Pages 24-28, [00101]—[00108], Pages 40-41, [0149], Pages 30-31, [00114], Page 47, [00165] and Page 75, [00258] and Figs. 4B-D).
Regarding claim 19, Can teaches a method of targeted generation of 5' tagged fragments of nucleic acid (Page 25, [00104] and [00102], Pages 26-27, [00106]-[00107] and Pages 40-41, [00149]). Cann teaches hybridizing one or more targeting oligonucleotides to a sample comprising single-stranded nucleic acid (Page 1, [0003], Page 11, [0045], Page 19, [0088], Page 24 [00101], and page 56, [00193]). Cann teaches the one or more targeting oligonucleotides can each bind to a sequence of interest in the nucleic acid (Page 3, [0014] Page 24, [00101], Pages 31-32, [00119]). Cann teaches applying a transposome complex comprising a transposase and a first transposon comprising a 3' transposon end sequence and a 5' adaptor sequence (Pages 24-28, [00101]—[00108], Pages 40-41, [0149] and Figs. 4B-D). Can teaches a second transposon comprising a 5' transposon end sequence and the 5' transposon end sequence is complementary to the 3' transposon end sequence (Pages 26-27, [00106]-[00107] and Pages 40-41, [00149]). Cann teaches fragmenting the nucleic acid into a plurality of fragments by the transposase, by joining the 3' end of the first transposon to the 5' ends of the fragments to produce a plurality of 5' tagged fragments (Page 24, [00101], Page 25, [00104], Page 26-27, [00106]-[00107], Pages 40-41, [00149] and Figs. 4B-D).
Cann teaches each and every limitation of claims 5, 8 and 19, and therefore Cann anticipates claims 5, 8 and 19.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 12 and 16 are rejected under 35 U.S.C. 103 as being unpatentable over Cann et al. (WIPO International Application Publication WO 2016/014409 A1, published January 28, 2016), cited on the IDS filed February 16, 2023, as applied to claims 5, 8 and 19 above, in view of Mir et al. (U.S. Patent Application Publication US 2022/0073980 A1, published March 10, 2022, effectively filed November 27, 2019).
Regarding claim 12, Cann teaches a method of targeted generation of 5' tagged fragments of a target nucleic acid (Page 25, [00104] and [00102], Pages 26-27, [00106]-[00107] and Pages 40-41, [00149]). Cann teach the targeted transposome complex of claim 9, in that Cann teaches a transposase, a first transposon comprising a 3' transposon end sequence and a 5' adaptor sequence (Pages 24-28, [00101]—[00108], Pages 40-41, [0149] and Figs. 4B-D). Cann teaches the targeting oligonucleotide can bind to one or more nucleic acid sequences of interest (Page 3, [0014] Page 24, [00101], Pages 31-32, [00119]). Cann teaches a second transposon comprising a 5' transposon end sequence, wherein the 5' transposon end sequence is complementary to the 3' transposon end sequence (Pages 26-27, [00106]-[00107] and Pages 40-41, [00149]). Cann teaches combining a sample comprising a double-stranded nucleic acid and a transposome complex, that is a targeted transposome complex (Pages 24-28, [00101]—[00108], Pages 40-41, [0149] and Figs. 4B-D). Cann teaches fragmenting the nucleic acid into a plurality of fragments by the transposase, by joining the 3' end of the first transposon to the 5' ends of the fragments to produce a plurality of 5' tagged fragments (Page 24, [00101], Page 25, [00104], Page 26-27, [00106]-[00107], Pages 40-41, [00149] and Figs. 4B-D). Cann teaches the content of Grunenwald et al. United States Patent Application Publication 2010/0120098 A1, published May 13, 2010, (cited on the instant IDS filed 02/16/2023) is incorporated in its entirety by reference, and exemplifies the transposome complexes used in the invention (Page 26, [00106]).
Regarding claim 16, Cann teaches the fragmenting is performed at 45 °C to 65 °C (Page 79, [00269] and Example 3).
Cann does not teach or suggest a targeting oligonucleotide coated with a recombinase. Cann does not teach or suggest initiating strand invasion of the nucleic acid by the recombinase. Cann does not teach or suggest a temperature used for initiating strand invasion is below the optimum temperature for fragmenting by the transposase.
Mir teaches identifying and storing the identity and positions of differently labelled nucleotides incorporated into each of a plurality of sequence fragments (Abstract and Page 3, [0019]). Mir teaches using CRISPR cas9-guide RNA complexes to target sequences (Page 14, [0162]). Mir teaches target transposome complexes comprising a transposase and a transposon end (Pages 14-15, [0162]—[0169]). Mir teaches a targeting oligonucleotide coated with a recombinase (Page 14, [0159]). Mir teaches initiating strand invasion of the nucleic acid by the recombinase (Page 14, [0159]). Mir teaches a temperature used for initiating strand invasion is below the optimum temperature for fragmenting by the transposase (Pages 40-41, [0610], Pages 42, [0628] and Page 16, [0187]). Mir teaches the content of Grunenwald et al. United States Patent Application Publication 2010/0120098 A1, published May 13, 2010, (cited on the instant IDS filed 02/16/2023) is incorporated in its entirety by reference, and exemplifies the transposome complexes used in the invention (Page 14, [0162]).
It would have been prima facie obvious to one having ordinary skill in the art at the time of the invention to modify the method of Cann by substituting the transposome complexes that use strand invasion and a recombinase, of Mir because it has been held that the simple substitution of one known element for another to obtain predictable results is obvious. In re Fout, 213 USPQ 532 (CCPA 1982), In re O'Farrell, 7 USPQ2d 1673 (Fed. Cir. 1988). Simply substituting the transposome complexes that use strand invasion and a recombinase of Mir with the transposome complex of Cann would obtain predictable results because both Mir and Cann disclose methods using transposome complexes. Additionally, the transposome complexes of Mir are well suited for the system of Cann because both Mir and Cam disclose that the transposome complexes may be exemplified by Grunewald.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA DANIELLE PARISI whose telephone number is (571)272-8025. The examiner can normally be reached Mon - Friday 7:30-5:00 Eastern with alternate Fridays off.
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/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684