DETAILED CORRESPONDENCE
Application Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 06/12/2026 has been entered.
3. Applicant’s amendment to the claims filed on 05/20/2026 in response to the Final Rejection mailed on 04/03/2026 is acknowledged. This listing of claims replaces all prior listings of claims in the application.
4. Claims 112-126 and 128-132 are pending.
5. Applicant’s remarks filed on 05/20/2026 in response to the Final Rejection mailed on 04/03/2026 have been fully considered and are deemed persuasive to overcome at least one of the rejections and/or objections as previously applied.
The text of those sections of Title 35 U.S. Code not included in the instant action can be found in the prior Office Action.
Examiner Comment
6. Applicants’ request for interview filed on 09/15/2026 is acknowledged. On 09/18/2026, Examiner Holland contacted applicants’ attorney of record, Mr. Donald Prather, Reg. No. 61,160, to indicate that the request was premature as the RCE had been filed, and it would be more beneficial to arrange an interview once action had been taken on the amendment. Applicants’ representative is invited to contact the Examiner to arrange an interview if so desired upon receipt and review of the office action set forth below.
Claim Rejections - 35 USC § 103
7. The rejection of claims 112-114, 116-126, and 128-131 under 35 U.S.C. 103 as being unpatentable over Sealover et al. (WO 2018/148196 A1; cited on PTO-892 mailed on 09/19/2025) in view of Grandela et al. (BioRXiv preprint, 12/09/2021; cited on IDS filed on 01/16/2026) is withdrawn in view of applicants’ amendment to the claims to recite “marker expression only occurs when the insertion is within a transcriptional unit and in a correct direction”.
8. The rejection of claim 115 under 35 U.S.C. 103 as being unpatentable over Sealover et al. (WO 2018/148196 A1; cited on PTO-892 mailed on 09/19/2025) in view of Grandela et al. (BioRXiv preprint, 12/09/2021; cited on IDS filed on 01/16/2026) as applied to claims 112-114, 116-126, and 128-131, above and further in view of Anderson et al. (WO 2020/086627 A1; cited on PTO-892 mailed on 09/19/2025) is withdrawn in view of applicants’ amendment to the claims to recite “marker expression only occurs when the insertion is within a transcriptional unit and in a correct direction”.
9. The rejection of claim 132 under 35 U.S.C. 103 as being unpatentable over Sealover et al. (WO 2018/148196 A1; cited on PTO-892 mailed on 09/19/2025) in view of Grandela et al. (BioRXiv preprint, 12/09/2021; cited on IDS filed on 01/16/2026) as applied to claims 112-114, 116-126, and 128-131, above and further in view of Naso et al. (US Patent Application Publication 2022/0331361 A1, priority to 04/07/2021; cited on PTO-892 mailed on 04/03/2026).
10. Claims 112-114, 116-126, and 128-131 are newly rejected under 35 U.S.C. 103 as being unpatentable over Sealover et al. (WO 2018/148196 A1; cited on PTO-892 mailed on 09/19/2025) in view of Grandela et al. (BioRXiv preprint, 12/09/2021; cited on IDS filed on 01/16/2026) and Friedrich et al. (Genes & Development, 1991; examiner cited). This new grounds of rejection is necessitated by applicants’ amendment to the claims to recite “marker expression only occurs when the insertion is within a transcriptional unit and in a correct direction”.
11. With respect to claim 112, Sealover et al. teach a method of integrating a DNA construct into a genome, the method comprising: a. contacting the genome from a sample with one or more agents, wherein the one or more agents are capable of cleaving the genome at a locus; b. integrating a first nucleic acid sequence into the genome at the locus; and c. integrating one or more second nucleic acid sequences into the first nucleic acid sequence in the genome, thereby integrating the DNA construct into the genome, wherein each of the one or more second nucleic acid sequences comprises a cargo sequence [see Abstract; paragraphs 0013-0022]. Sealover et al. teach the method wherein the one or more vectors comprise a selectable marker comprising an antibiotic marker or fluorescent protein [see paragraphs 0024 and 0060].
With respect to claim 114, Sealover et al. teach the method wherein the locus comprising a human genomic locus comprising AAVS1 [see paragraphs 0005, 0069].
With respect to claim 116, Sealover et al. teach the method wherein the first nucleic acid sequence comprises a landing pad sequence comprising one or more genes, regulatory elements or combinations thereof including recognition sites for FLP and Cre recombinase [see paragraph 0020].
With respect to claim 117, Sealover et al. teach the method wherein the one or more genes comprise a gene encoding a recombinase [see paragraph 0020].
With respect to claim 118, Sealover et al. teach the method wherein the one or more genes comprise a gene encoding a recombinase including fusion proteins thereof [see paragraphs 0017-0020]. The fusion proteins thereof are interpreted as a “variant thereof” as a variant of an ERT2 absent an explicit definition includes any modifications that result into any protein.
With respect to claim 119, Sealover et al. teach the method wherein the expression of the gene encoding the recombinase is induced by a gene expression system [see paragraphs 0017-0021].
With respect to claim 120, Sealover et al. teach the method wherein the fluorescent protein comprises a red fluorescent, green fluorescent, yellow fluorescent, blue fluorescent, or cyan fluorescent proteins [see paragraphs 0024].
With respect to claim 121, Sealover et al. teach the method wherein the one or more regulatory elements comprise a promoter, a terminator, a recombinase recognition site, wherein the promoter comprises a PGK promoter [see paragraph 0059], a SV40, and bGH terminator [see paragraph 0022].
With respect to claim 122, Sealover et al. teach the method wherein the first nucleic acid sequence comprises a landing pad sequence comprising one or more genes, regulatory elements or combinations thereof [see paragraph 0020]. The teachings of Sealover et al. are interpreted as reading on the claims given the recitation in claim 122 of “a sequence comprising…”, which can broadly and reasonably be interpreted as any nucleic acid sequence that shares at least two contiguous nucleotides with the claimed sequences.
With respect to claim 124, Sealover et al. teach the method wherein the one or more vectors comprise a selectable marker comprising an antibiotic marker [see paragraph 0060].
With respect to claim 125, Sealover et al. teach the method wherein the genome in the sample is contained in a cell, wherein the contacting step and integrating step are performed in the cell [see paragraph 0025].
With respect to claim 126, Sealover et al. teach the method wherein the cell comprises a mammalian cell comprising a human cell or a mouse cell [see paragraph 0069].
With respect to claim 128, Sealover et al. teach the method wherein the one or more agents are delivered via a carrier comprising a vector [see paragraph 0028].
With respect to claim 129, Sealover et al. teach the method wherein the sample comprises a biological sample comprising a cell obtained from a human [see paragraph 0069].
With respect to claim 130, Sealover et al. teach the method wherein the integrating steps b) and c) comprises sequential integration [see paragraph 0064].
With respect to claim 131, Sealover et al. teach the method wherein the integrating in steps b) and c) comprises homology-directed recombination and wherein the integrating comprises utilizing a constitutive site-specific recombinase Cre, Flp, or self-excising recombinase [see paragraphs 0020, 0059, 0065].
However, Sealover et al. does not teach the method of claim 112, of excising the marker sequence and wherein the marker sequence is devoid of a promoter and marker expression only occurs when the insertion within a transcriptional unit and in a correct direction; the method of claim 113, wherein the cargo sequence comprises at least 1 kilobase of claim 113 and wherein the nucleic acid sequence comprises approximately 10 kilobases to 1,000 kilobases of claim 123.
Grandela et al. teach methods of inserting large DNA payloads >10 kb in to specific genomic sites of mammalian cells by combining site specific recombinases with CRISPR/Cas mediated homologous recombination for specific replacement of genomic fragments of at least 50 kb in size into human induced pluripotent stem cells targeting an AAVS1 locus using fluorescent reporters followed by excision of the auxiliary sequences by Cre and FLP to prevent silencing of the transgenes leaving only the integrated DNA payload in the locus [see Summary; p. 6-7, p. 9-10 and Figure 3]. Grandela et al. demonstrates that this technique offers a precise approach to generate genetically matched panels of human induced pluripotent stem cell lines efficiently and cost-effectively [see Summary].
Friedrich et al. teach promoter trap systems in mice embryonic stem cells that allow screening and selection for mutations in cell lines that avoid extensive breeding by designing constructs lacking a promoter and including a reporter gene such that activation of the reporter gene depends on its insertion within an active transcription unit [see Abstract; p. 1513, column 2]. Friedrich et al. teach that this approach provides for an efficient genetic screen to identify and mutate genes in the mouse, and allows for selection for mutagenic insertions, and include a means to easily monitor the activity of the tagged promoter once the embryonic stem cell clone has been used to create chimeras and transgenic cell lines [see p. 1517, column 2].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Sealover et al., Grandela et al., and Friedrichs et al. according to the teachings of Grandela et al. and Friedrichs et al. to include excision of the auxiliary/selectable marker sequences and a promoter trap sysemt in the methods of Sealover et al. because Sealover et al. teach a method of integrating a DNA construct into a genome using CRISPR/Cas and recombinase technology. Grandela et al. teach similar methods to Sealover et al. for inserting large payloads in to the genome of a mammalian cell locus coupled with the excision of auxiliary sequences to prevent transgene silencing. Friedrich et al. teach that promoter trap systems embryonic stem cells allow screening and selection for mutations in cell lines that avoid extensive breeding by designing constructs lacking a promoter and including a reporter gene such that activation of the reporter gene depends on its insertion within an active transcription unit. One of ordinary skill in the art would have had a reasonable expectation of success, a reasonable level of predictability and would have been motivated to combine the teachings of Sealover et al., Grandela et al., and Friedrich et al. because Grandela et al. acknowledges the presence of auxiliary sequences in targeted genomic integration can lead to transgene silencing and excision of said sequences leaves only the desired integrated DNA payload and Friedrich et al. acknowledges a promoter trap system approach provides for an efficient genetic screen to identify and mutate genes in embryonic stem cells, and allows for selection for mutagenic insertions, and include a means to easily monitor the activity of the tagged promoter once the embryonic stem cell clone has been used to create chimeras and transgenic cell lines. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
12. Claim 115 is newly rejected under 35 U.S.C. 103 as being unpatentable over Sealover et al. (WO 2018/148196 A1; cited on PTO-892 mailed on 09/19/2025) in view of Grandela et al. (BioRXiv preprint, 12/09/2021; cited on IDS filed on 01/16/2026) and Friedrich et al. (Genes & Development, 1991; examiner cited) as applied to claims 112-114, 116-126, and 128-131 above, and further in view of Anderson et al. (WO 2020/086627 A1; cited on PTO-892 mailed on 09/19/2025). This new grounds of rejection is necessitated by applicants’ amendment to the claims to recite “marker expression only occurs when the insertion is within a transcriptional unit and in a correct direction”.
13. The relevant teachings of Sealover et al., Grandela et al., and Friedrich et al. as applied to claims 112-114, 116-126, and 128-131 are set forth above.
With respect to claim 115, Friedrich et al. teach the targeting of the ROSA locus [see p. 1514, column 2].
However, the combination of Sealover et al., Grandela et al., and Friedrich et al. do not teach the method wherein the locus comprises murine ROSA26.
Anderson et al. is in the same field of Sealover et al., Grandela et al., and Friedrich et al. and teach methods for integrating large DNA payloads into a genomic locus using a retroviral integrase and Cas protein, wherein the locus comprises human and mouse ROSA26 locus [see Abstract; p. 2, p. 10], wherein the donor template is 18kb or more [see p. 70 bottom to top of p. 71].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Sealover et al., Grandela et al., Friedrich et al. and Anderson et al. according to the teachings of Anderson et al. to utilize the integrase and Cas protein methods of Anderson et al. to deliver large DNA payloads for integration into a genome of murine ROSA26 because Sealover et al., Grandela et al., and Friedrich et al. teach stable integration of genes into genomic DNA of a cell using safe harbor sites in the cell. Anderson et al. teach similar methods that permit the integration of large DNA targeting the murine ROSA26 locus. One of ordinary skill in the art would have had a reasonable expectation of success and a reasonable level of predictability to combine the teachings of Sealover et al., Grandela et al., Friedrich et al., and Anderson et al. because Anderson et al. acknowledges that large payloads of DNA can be integrated into the murine ROSA26 locus. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
14. Claim 132 is newly rejected under 35 U.S.C. 103 as being unpatentable over Sealover et al. (WO 2018/148196 A1; cited on PTO-892 mailed on 09/19/2025) in view of Grandela et al. (BioRXiv preprint, 12/09/2021; cited on IDS filed on 01/16/2026) and Friedrich et al. (Genes & Development, 1991; examiner cited) as applied to claims 112-114, 116-126, and 128-131 above, and further in view of Naso et al. (US Patent Application Publication 2022/0331361 A1, priority to 04/07/2021; cited on PTO-892 mailed on 04/03/2026). This new grounds of rejection is necessitated by applicants’ amendment to the claims to recite “marker expression only occurs when the insertion is within a transcriptional unit and in a correct direction”.
15. The relevant teachings of Sealover et al., Grandela et al., and Friedrich et al. as applied to claims 112-114, 116-126 and 128-131 are set forth above.
However, the combination of Sealover et al., Grandela et al., and Friedrich et al. do not teach the methods of claim 132 wherein the one or more agents comprises erCas12a (MAD7).
Naso et al. teach methods for genome engineering of induced pluripotent stems cells using MAD7 CRISPR nuclease based system [see Abstract] for the efficient insertion of genetic elements in human induced pluripotent stem cells [see paragraph 0006].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Sealover et al., Grandela et al., Friedrich et al. and Naso et al. according to the teachings of Naso et al. to use a MAD7 CRISPR nuclease system in the methods of Sealover et al., Grandela et al. and Friedrich et al. because Sealover et al., Grandela et al., and Friedrich et al. teach stable integration of genes into genomic DNA of a human induced pluripotent stem cell using safe harbor sites in the cell and CRISPR/Cas nuclease system. Naso et al. teach that a MAD7 CRISPR nuclease based system provides efficient insertion of genetic elements in human induced pluripotent stem cells. One of ordinary skill in the art would have had a reasonable expectation of success and a reasonable level of predictability to combine the teachings of Sealover et al., Grandela et al., Friedrich et al. and Naso et al. because Naso et al. acknowledges that a MAD7 CRISPR nuclease based system provides efficient insertion of genetic elements in human induced pluripotent stem cells. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Response to Remarks Regarding Prior Art Rejections
16. Applicants’ remarks filed on 05/20/2026 have been fully considered by the examiner; however, they are rendered moot in view of the new rejections set forth above, which were necessitated by applicants’ amendment to the claims.
Conclusion
17. Status of the claims:
Claims 112-126 and 128-132 are pending.
Claims 112-126 and 128-132 are rejected.
No claims are in condition for an allowance.
Applicant's submission of an information disclosure statement under 37 CFR 1.97(c) with the timing fee set forth in 37 CFR 1.17(p) on 01/16/2026 prompted the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 609.04(b). 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 PAUL J HOLLAND whose telephone number is (571)270-3537. The examiner can normally be reached Monday to Friday from 8AM to 5PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath Rao can be reached at 571-272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PAUL J HOLLAND/Primary Examiner, Art Unit 1656
