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 .
Applicant’s reply to the June 25, 2025 Office Action, filed December 24, 2025, is acknowledged. Applicant cancels claims 2, 13, 18, 25, and 33-35. Claims 1, 3-12, 14-17, 19-24, and 26-32 are currently pending and under examination.
Any objection or rejection of record in the previous Office Action, which is not addressed in this action has been withdrawn in light of Applicant’s amendments and/or arguments. This action is Final.
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.
Claims 1, 3-12, 14-17, 19-24, 26-32 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. This is a new rejection as necessitated by amendments.
Claim 1 is considered vague and indefinite for the following reasons:
Claim 1 recites the limitation "the at least one barcode" in lines 13 and 14. There is insufficient antecedent basis for this limitation in the claim.
Claim 1 recites the limitation "the barcodes" in lines 13 and 14. There is insufficient antecedent basis for this limitation in the claim.
Claim 1 recites the limitation "the resulting barcoded genomic DNA or RNA" in line 16. There is insufficient antecedent basis for this limitation in the claim.
Claim 1 recites the limitation "the resulting cells" in line 16. There is insufficient antecedent basis for this limitation in the claim.
Claims 3-12, 14-17, 19-24 and 31-32 depend from claim 1 and are therefore included in this rejection.
Claim 26 is considered vague and indefinite for the following reasons:
Claim 26 recites the limitation "the at least one barcode" in lines 14 and 15. There is insufficient antecedent basis for this limitation in the claim.
Claim 26 recites the limitation "the barcodes" in lines 14 and 15. There is insufficient antecedent basis for this limitation in the claim.
Claim 26 recites the limitation "the resulting barcoded genomic DNA or RNA" in line 17. There is insufficient antecedent basis for this limitation in the claim.
Claim 26 recites the limitation "the resulting cells" in lines 17 and 18. There is insufficient antecedent basis for this limitation in the claim.
Claim 27 is considered vague and indefinite for the following reasons:
Claim 27 recites the limitation "the genomic DNA" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 27 recites the limitation "the at least one barcode" in lines 14 and 15. There is insufficient antecedent basis for this limitation in the claim.
Claim 27 recites the limitation "the barcodes" in lines 14 and 15. There is insufficient antecedent basis for this limitation in the claim.
Claim 27 recites the limitation "the resulting barcoded genomic DNA or RNA" in line 17. There is insufficient antecedent basis for this limitation in the claim.
Claim 27 recites the limitation "the resulting cells" in lines 17 and 18. There is insufficient antecedent basis for this limitation in the claim.
Claim 28 is considered vague and indefinite for the following reasons:
Claim 28 recites the limitation "the at least one barcode" in lines 12 and 13. There is insufficient antecedent basis for this limitation in the claim.
Claim 28 recites the limitation "the barcodes" in lines 12 and 13. There is insufficient antecedent basis for this limitation in the claim.
Claim 28 recites the limitation "the resulting barcoded genomic DNA or RNA" in line 17. There is insufficient antecedent basis for this limitation in the claim.
Claim 28 recites the limitation "the resulting cells" in lines 17 and 18. There is insufficient antecedent basis for this limitation in the claim.
Claims 29-30 depend from claim 28 and are therefore included in this rejection.
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 1, 3-12, 14-17, 19-20, 22-24, 27-29 and 31-32 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Hendel et al. (“Quantifying Genome Editing Outcomes at Endogenous Loci using SMRT Sequencing”, Cell Rep. 7(1) :293-305, published April 10, 2014). This is a new rejection as necessitated by amendments.
Regarding claim 1, Hendel teaches a method of identifying how different homologous sequences affect the frequency of donor molecule integration into genomic DNA in cells (Abstract, Page 3, First Paragraph, Page 7, Third Paragraph, Page 10, Fourth Paragraph and Fig. 5). Hendel teaches exposing the cells to a plurality of donor molecules and a rare-cutting endonuclease (Abstract and Page 3, First Paragraph). Hendel teaches each donor molecule comprises a different homology sequence, and at least one different barcode (Page 3, First Paragraph, Page 12, First Paragraph and Figs. 1-5). Hendel teaches each different homology sequence comprises a sequence that is homologous to a target locus within the genomic DNA and the homology sequence for each donor molecule is different from the homology sequences of other donor molecules (Page 7, Second Paragraph and Figs. 1-5). Hendel teaches the plurality of donor molecules comprises homologous sequences with homology to a target locus within the same gene (Figs. 1-5). Hendel teaches the at least one barcode for each donor molecule is different from the barcodes for other donor molecules (Page 12, First Paragraph). Hendel teaches the at least one barcode is integrated into the target locus (Page 12, First Paragraph and Supplemental Text, Page 7, First Paragraph). Hendel teaches sequencing the resulting barcoded genomic DNA or RNA of the resulting cells (Page 12, First Paragraph). Hendel teaches quantifying the frequency of each barcode thereby identifying the frequency of donor molecule integration into the genomic DNA of the resulting cells (Abstract, Page 3, First Paragraph, Page 7, Third Paragraph, Page 10, Fourth Paragraph, Fig. 5 and Supplemental Text, Page 1, First Paragraph, Page 7, First Paragraph—Page 8, Third Paragraph, Page 11, Last Paragraph).
Regarding claim 3, Hendel teaches homology sequence for each donor molecule comprises at least one homology arm (Page 3, First Paragraph and Fig. 5).
Regarding claim 4, Hendel teaches the homology sequence for each donor molecule comprises two homology arms (Page 3, First—Second Paragraph and Fig. 5).
Regarding claim 5, Hendel teaches the donors additionally comprise a cargo sequence (Page 7, Last Paragraph)
Regarding claim 6, Hendel teaches the cargo sequences are the same (Page 7, Last Paragraph and Supplemental Text, Page 7, First and Second Paragraph).
Regarding claim 7, Hendel teaches the cells are exposed to an equal molar ratio or equal concentration of each of the donor molecules within the plurality of donor molecules (Page 6, Last Paragraph and Fig. 5).
Regarding claim 8, Hendel teaches the plurality of donor molecules comprises at least two donor molecules (Page 7, Second Paragraph, Page 11, Second Paragraph and Figs. 5).
Regarding claim 9, Hendel teaches the plurality of donor molecules comprises at least ten donor molecules (Page 7, Second Paragraph, Page 11, Second Paragraph and Figs. 5).
Regarding claim 10, Hendel teaches the plurality of donor molecules comprises at least one hundred donor molecules (Page 7, Second Paragraph, Page 11, Second Paragraph and Figs. 5).
Regarding claim 11, Hendel teaches the plurality of donor molecules comprises at least one thousand donor molecules (Page 7, Second Paragraph, Page 11, Second Paragraph and Figs. 5).
Regarding claim 12, Hendel teaches the plurality of donor molecules comprises at least ten thousand donor molecules (Page 7, Second Paragraph, Page 11, Second Paragraph and Figs. 5).
Regarding claim 14, Hendel teaches the rare-cutting endonuclease is selected from a CRISPR nuclease or a zinc-finger nuclease (Abstract, Page 10, Third Paragraph, Page 9, Last Paragraph and Page 3, First Paragraph).
Regarding claim 15, Hendel teaches the rare-cutting endonuclease is delivered as protein, RNA, DNA, or an RNA/protein mixture (Abstract and Page 10, Third Paragraph).
Regarding claim 16, Hendel teaches the rare-cutting endonuclease is a nuclease or nickase (Abstract and Page 10, Second Paragraph).
Regarding claim 17, Hendel teaches the genomic DNA is from a eukaryotic cell (Page 9, Second Paragraph and Page 10, Paragraph 4).
Regarding claim 19, Hendel teaches the donor molecule format is selected from single-stranded oligonucleotides, double-stranded oligonucleotides, single-stranded linear DNA, double-stranded linear DNA, single-stranded circular DNA, double-stranded circular DNA (Page 12, First Paragraph, Page 2, First-Second Paragraph and Fig. 1).
Regarding claim 20, Hendel teaches the donor molecules are harbored on viral vectors (Page 9, Second Paragraph).
Regarding claim 22, Hendel teaches the donors are harbored on non-viral vectors (i.e., Plasmid, Page 10, Third-Fourth Paragraph).
Regarding claim 23, Hendel teaches that the non-viral vectors are delivered to cells using lipids, calcium phosphate, cationic polymers, DEAE-dextran, dendrimers, polyethylene glycol (PEG) cell penetrating peptides, gas-encapsulated microbubbles, electroporation or magnetic beads (Page 8, Second Paragraph).
Regarding claim 24, Hendel teaches the donor molecules further comprise single-nucleotide polymorphisms to prevent binding or cleavage by a rare cutting endonuclease (Page 10, Fourth Paragraph and Page 3, Second Paragraph).
Regarding claim 27, Hendel teaches a method of identifying optimal donor molecule structure for integration into the genomic DNA of cells of patient (Leukemia patient, Abstract, Page 3, First Paragraph, Page 7, Second-Third Paragraph, Page 10, Fourth Paragraph and Fig. 5). Hendel teaches identifying the patient (K562 cells, Page 7, Second Paragraph and Page 8, Second Paragraph—Page 9, Second Paragraph). Hendel teaches exposing the cells to a plurality of donor molecules and a rare-cutting endonuclease (Abstract and Page 3, First Paragraph). Hendel teaches each donor molecule comprises a different homology sequence, and at least one different barcode (Page 3, First Paragraph, Page 12, First Paragraph and Figs. 1-5). Hendel teaches each different homology sequence comprises a sequence that is homologous to a target locus within the genomic DNA and the homology sequence for each donor molecule is different from the homology sequences of other donor molecules (Page 7, Second Paragraph and Figs. 1-5). Hendel teaches the plurality of donor molecules comprises homologous sequences with homology to a target locus within the same gene (Figs. 1-5). Hendel teaches the at least one barcode for each donor molecule is different from the barcodes for other donor molecules (Page 12, First Paragraph). Hendel teaches the at least one barcode is integrated into the target locus (Page 12, First Paragraph and Supplemental Text, Page 7, First Paragraph). Hendel teaches sequencing the resulting barcoded genomic DNA or RNA of the resulting cells (Page 12, First Paragraph). Hendel teaches determining the frequency of each barcode, thereby identifying how the different homologous sequences affect the frequency of donor molecule integration into the genomic DNA of the resulting cells (Abstract, Page 3, First Paragraph, Page 7, Third Paragraph, Page 10, Fourth Paragraph, Fig. 5 and Supplemental Text, Page 1, First Paragraph, Page 7, First Paragraph—Page 8, Third Paragraph, Page 11, Last Paragraph).
Regarding claim 28, Hendel teaches a method of identifying the frequency of donor molecule integration into genomic DNA in cells (Abstract, Page 3, First Paragraph, Page 7, Third Paragraph, Page 10, Fourth Paragraph and Fig. 5). Hendel teaches exposing the cells to a plurality of donor molecules with a different homology sequence and at least one different barcode (Page 3, First Paragraph, Page 12, First Paragraph and Figs. 1-5). Hendel teaches each different homology sequence comprises a sequence that is homologous to a target locus within the genomic DNA and the homology sequence for each donor molecule is different from the homology sequences of other donor molecules (Page 7, Second Paragraph and Figs. 1-5). Hendel teaches the plurality of donor molecules comprises different homologous sequences with homology to a target locus within the same gene (Figs. 1-5). Hendel teaches the at least one barcode for each donor molecule is different from the barcodes for other donor molecules (Page 12, First Paragraph). Hendel teaches the at least one barcode is integrated into the target locus (Page 12, First Paragraph and Supplemental Text, Page 7, First Paragraph). Hendel teaches each donor molecule is harbored on a different format of DNA or vectors (Page 9, Second Paragraph, Page 10, Third-Fourth Paragraph, Page 12, First Paragraph, Page 2, First-Second Paragraph and Fig. 1). Hendel teaches sequencing the resulting barcoded genomic DNA or RNA of the resulting cells (Page 12, First Paragraph). Hendel teaches determining the frequency of each barcode, thereby identifying how the different homologous sequences affect the frequency of donor molecule integration into the genomic DNA of the resulting cells (Abstract, Page 3, First Paragraph, Page 7, Third Paragraph, Page 10, Fourth Paragraph, Fig. 5 and Supplemental Text, Page 1, First Paragraph, Page 7, First Paragraph—Page 8, Third Paragraph, Page 11, Last Paragraph).
Regarding claim 29, Hendel teaches the format of DNA or vectors is selected from the group consisting of linear double-stranded DNA, circular double- stranded DNA, linear single-stranded DNA, circular, double-stranded DNA, and viral vectors (Page 12, First Paragraph, Page 2, First-Second Paragraph and Fig. 1).
Regarding claim 31, Hendel teaches identification of the frequency of donor molecule integration into genomic DNA in cells for the identification of optimal donor molecule structure for the integration (Abstract, Page 3, First Paragraph, Page 7, Third Paragraph, Page 10, Fourth Paragraph and Fig. 5).
Regarding claim 32, Hendel teaches the barcodes are flanked by two different homology arms (Page 3, Second Paragraph and Fig. 1).
Hendel discloses each and every limitation of claims 1, 3-12, 14-17, 19-20, 22-24, 27-29 and 31-32 and therefore Hendel anticipates claims 1, 3-12, 14-17, 19-20, 22-24, 27-29 and 31-32.
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 21, 26 and 30 are rejected under 35 U.S.C. 103 as being unpatentable over Hendel et al. (“Quantifying Genome Editing Outcomes at Endogenous Loci using SMRT Sequencing”, Cell Rep. 7(1) :293-305, published April 10, 2014), as applied to claims 1, 3-12, 14-17, 19-20, 22-24, 28-29 and 31-32 above, in view of Schiller et al. (WIPO International Application Publication WO 2018/017419 A1, published January 25, 2018), previously cited in the June 25, 2025 Office Action. This is a new rejection as necessitated by amendments.
Regarding claims 21 and 30, Hendel teaches the viral vector as discussed above.
Regarding claim 26, Hendel teaches a method of identifying optimal donor molecule structure for integration into the genomic DNA of cells (Abstract, Page 3, First Paragraph, Page 7, Third Paragraph, Page 10, Fourth Paragraph and Fig. 5). Hendel teaches exposing the cells to a plurality of donor molecules and a rare-cutting endonuclease (Abstract and Page 3, First Paragraph). Hendel teaches each donor molecule comprises a different homology sequence, and at least one different barcode (Page 3, First Paragraph, Page 12, First Paragraph and Figs. 1-5). Hendel teaches each different homology sequence comprises a sequence that is homologous to a target locus within the genomic DNA and the homology sequence for each donor molecule is different from the homology sequences of other donor molecules (Page 7, Second Paragraph and Figs. 1-5). Hendel teaches the plurality of donor molecules comprises homologous sequences with homology to a target locus within the same gene (Figs. 1-5). Hendel teaches the at least one barcode for each donor molecule is different from the barcodes for other donor molecules (Page 12, First Paragraph). Hendel teaches the at least one barcode is integrated into the target locus (Page 12, First Paragraph and Supplemental Text, Page 7, First Paragraph). Hendel teaches sequencing the resulting barcoded genomic DNA or RNA of the resulting cells (Page 12, First Paragraph). Hendel teaches determining the frequency of each barcode, thereby identifying how the different homologous sequences affect the frequency of donor molecule integration into the genomic DNA of the resulting cells (Abstract, Page 3, First Paragraph, Page 7, Third Paragraph, Page 10, Fourth Paragraph, Fig. 5 and Supplemental Text, Page 1, First Paragraph, Page 7, First Paragraph—Page 8, Third Paragraph, Page 11, Last Paragraph).
Hendel does not explicitly teach or suggest the viral vectors are selected from the group consisting of retroviral, adenoviral, adeno-associated vectors (AAV), herpes simplex, pox virus, hybrid adenoviral vector, Epstein-Barr virus, lentivirus, or herpes simplex virus. Hendel does not teach or suggest the genomic DNA of cells are of an organ. Hendel does not teach or suggest identifying the organ.
Schiller teaches a method of identifying optimal donor molecule structure for integration into the genomic DNA of cells of an organ (Page 3, [0013] and Page 8, [0030]). Schiller teaches identifying the organ (Page 8, [0030] and Page 20, [0079]). Schiller teaches genomic DNA of cells of a patient and identifying the patient (Page 3, [0013], Page 15, [0060], Page 8, [0030]-[0031] and Page 34, [0121]). Schiller teaches exposing the cells from the patient to a plurality of donor molecules and a rare-cutting endonuclease (Pages 22-23, [0085] and Page 46, [0149]). Schiller teaches each donor molecule comprises a homology sequence, and at least one barcode (Page 15, [0060], Page 22, [0084]-[0085]). Schiller teaches a method of identifying optimal donor molecule structure for the integration into the genomic DNA of cells of a patient and identifying the patient (Page 3, [0013], Page 15, [0060], Page 8, [0030]-[0031] and Page 34, [0121]). Schiller teaches exposing the cells from the patient to a plurality of donor molecules and a rare-cutting endonuclease (Pages 22-23, [0085] and Page 46, [0149]). Schiller teaches each donor molecule comprises a homology sequence, and at least one barcode (Page 15, [0060], Page 22, [0084]-[0085]). Schiller teaches a target flanked by two different homology arms (Page 24, [0092]). Schiller teaches the donor molecules are harbored on viral vectors and the viral vectors are selected from the group consisting of retroviral, adenoviral, adeno-associated vectors (AAV), herpes simplex, pox virus, hybrid adenoviral vector, Epstein-Barr virus, lentivirus, or herpes simplex virus (Page 18, [0072] and Page 22, [0085]). Schiller teaches the at least one barcode for each donor molecule is different from the barcodes for other donor molecules (Pages 32-33, [0113]-[0116] and Pages 40-41, [0129]-[0130]). Schiller teaches the at least one barcode is integrated into the target locus (Page 13, [0054]). Schiller teaches using these methods allows for advantages over existing technologies including measuring a functional readout, measuring single cells in a population separately and exploring several variables simultaneously (Page 42, [0134]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the invention to modify the teachings of Hendel with the teachings of Schiller to use a donor molecule on a viral vector selected from the group consisting of retroviral, adenoviral, adeno-associated vectors (AAV), herpes simplex, pox virus, hybrid adenoviral vector, Epstein-Barr virus, lentivirus, or herpes simplex virus. This would allow for advantages over existing technologies including measuring a functional readout, measuring single cells in a population separately and exploring several variables simultaneously as taught by Schiller (Page 42, [0134]). Additionally, 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 Hendel by substituting the viral vectors of Schiller (specifically the adeno-associated viral vector 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 viral vector of Hendel with viral vector of Schiller would obtain predictable results because both Hendel and Schiller teach methods using viral vectors with two different homology arms. Additionally the viral vectors of Schiller are well suited for the system of Hendel because Hendel teaches that the disclosed technique may be used to directly compare gene editing outcomes with different donor architectures including plasmids and viral vectors (Pages 9, Second Paragraph).
Response to Arguments
Applicant’s arguments and amendments filed December 24, 2025, with respect to the rejections under U.S.C. § 102 and 103 have been fully considered are deemed to be persuasive. Therefore, these rejections are withdrawn.
However, upon further consideration, new grounds of rejection under 35 U.S.C. § 102, 103 and 112 are made in view of Applicant’s amendments.
As discussed above, newly cited Hendel discloses a plurality of donor molecules that comprise different homology arms flanking a barcode integrated at the target locus. Hendel further discloses sequencing the resulting barcoded genomic DNA or RNA of the resulting cells and determining the frequency of integration of each barcode into the genomic DNA of the resulting cells thereby identifying how different homologous sequences affect the frequency of donor molecule integration into the genomic DNA of the resulting cells.
Therefore, for all these reasons, and those listed above, Hendel and Hendel in view of Schiller are deemed to anticipate and/or render the instant invention obvious.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
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