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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 24 November 2025 has been entered.
Application Status
The Amendments and Remarks filed 24 November 2025 in response to the Office Action dated 30 June 2025 are acknowledged and have been entered. Claims 1, 3-31 and 34 are pending and being examined on the merits.
Priority
The instant application is a continuation of application 14/319,693 filed 06/30/2014 which claims priority to application 61/906,188 filed 11/19/2013.
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 1, 3-14, 17-21, 24-29 and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Gratz (Gratz et al. Genetics, 2013, 194:1029-1035; published August 2013, of record) in view of Giles (Giles et al. Fly, 7:4, 249-255. 2013).
Regarding claim 1, 4-6, 17, 19-21, and 28-29, Gratz teaches the ability to replace a gene with a sequence that enables site-specific integration of engineered genes into the targeted locus [pg. 1030, col. 2, para 5). Gratz teaches a method comprised of introducing to a drosophila cell (1) nucleic acids encoding for two guide RNA sequences that are complementary to two different target sequences and (2) nucleic acids encoding for Cas9 (i.e., RNA guided DNA binding protein), wherein the Cas9 protein interacts with the guide RNA sequences to induce two double stranded breaks to excise a 4.6kb intervening nucleic acid sequences [pg. 1030, see “Engineered defined deletions”; pg.1032, left column, para2; Table S1] and (3) exogenous single stranded nucleic acid sequence comprising a attP docking site that is inserted into the break sites through homologous recombination [page 1030, see "Cas9-mediated homologous recombination"; Figure 1-2]. Gratz further demonstrates in drosophila cells that the expressions of two guide RNAs and Cas9 are effective at excising unwanted nucleic acid sequences, follow by insertion of an exogenous nucleic acid sequence via homologous recombination into the cleaved DNA, and transmitting the gene modification to progenies [page 1033, right column, last paragraph; table 1].
Gratz does not teach that the exogenous sequence to be inserted is greater that 1000 base pairs in length.
Regarding claims 1, 3, 12 and 17-18 Giles teaches that while ssODN donors such as the one we utilized to integrate an attP docking site are useful for small modifications, larger insertions and the incorporation of visible markers for screening will require double-stranded DNA (dsDNA) donors [pg. 252, col. 1, para 2]. Giles teaches that injected dsDNA donor templates have been successfully utilized in Drosophila to incorporate up to 13 kb of exogenous sequence in both P element and ZFN-induced HR [pg. 252, col. 1, para 2]. Giles teaches that based on a comprehensive analysis of ZFN-induced HR, dsDNA donors containing flanking homology arms of at least 1 kb in length serve as effective donors [pg. 252, col. 1, para 2]. Giles teaches that dsDNA donors have been employed in mammalian cells as templates for CRISPR/Cas9-induced HR and there is every reason to expect they will work as effectively in flies [pg. 252, col. 1, para 2]. Giles teaches that while this strategy requires generating a donor template, it will facilitate simple screening while enabling a broad range of modifications, from gene deletion and replacement to the incorporation of fluorescent tags [pg. 252, col. 1, para 2].
It would have been obvious to one ordinary skilled in the art before the effective filing date of the claimed invention to modify the method of Gratz by using an dsDNA donor exogenous sequence of 1kb or more which is flanked by homology arms of at least 1 kb in length. One of ordinary skill would be motivated to make the modification for the advantage of facilitating simple screening while enabling a broad range of modifications, to include the incorporation of fluorescent tags. One of ordinary skill would have a reasonable expectation of success since Giles teaches that dsDNA donors greater than 1kb in length have been successfully incorporated into DNA using ZFN induced HR and that dsDNA donors have been employed in mammalian cells as templates for CRISPR/Cas9-induced HR.
Regarding claims 7-8, Gratz teaches that efficient target recognition by the CRISPR RNA/Cas9 system requires 20 nucleotides (nt) of homology between the chiRNA and its genomic target, thereby teaches wherein the chiRNA has at least 20 nucleotides [pg. 1030, col. 1, para 2].
Regarding claims 9-10, 24-25 and 34, Gratz teaches that the chimeric RNA (chiRNA) comprises the crRNA and tracrRNA (i.e., a sgRNA) from Streptococcus pyogenes [pg. 1029, col. 2, para 2].
Regarding claims 11 and 26, Gratz teaches that the genome editing occurred on the X chromosome of Drosophila [pg. 1030, col. 1, para 2].
Regarding claim 13, Gratz teaches Cas9-generated DSBs are repaired by NHEJ and HR [Fig. 1].
Regarding claim 27, Gratz teaches cells comprising the CRISPR system with targeted deletion [pg. 1030, col. 2, para 1-4].
Claims 15-16, 22-23, and 30-31 are rejected under 35 U.S.C. 103 as being unpatentable over Gratz (Gratz et al. Genetics, 2013, 194:1029-1035; published August 2013, of record) in view of Giles (Giles et al. Fly, 7:4, 249-255. 2013), as applied to claims 1, 17, and 27 and further in view of Frendewey (US 2013/0309670 A1).
The teachings of Gratz and Giles are discussed above as applied to claims 1, 17, and 27 and similarly apply to claims 15-16, 22-23, and 30-31.
Gratz and Giles do not teach wherein the cell is a human induced pluripotent stem cell.
Frendewey teaches a method of modifying human pluripotent stem cell comprised of cleaving genomic DNA to cause a double stranded break using a nuclease and providing a large targeting vector comprising exogenous nucleic acid sequences that is inserted into the cleaved genomic DNA [entire document, specifically 0005 and 0022; Fig. 1].
It would have been obvious to one ordinary skilled in the art before the effective filing date of the claimed invention to substitute the eukaryotic cell of Gratz for the pluripotent stem cell of Frendewey. This modification would amount to a simple substitution of one cell for another, wherein both cells are known to be modified using CRISPR Cas systems. Additionally, the combination of prior art elements according to known methods to yield predictable results supports can support a conclusion of obviousness. See MPEP 2143(I). One of ordinary skill in the art would have a reasonable expectation of success since both Gratz, Giles and Frendewey each teach the use of CRISPR Cas Systems to modify cells comprised using a nuclease to cleave genomic DNA to cause a double stranded break and providing a large targeting vector comprising exogenous nucleic acid sequences that is inserted into the cleaved genomic DNA.
Response to Arguments
Applicant's arguments filed 06/11/2026 have been fully considered and were persuasive.
Applicant argues that Gratz does not teach the claimed invention because Gratz inserts only a short 50-nt attP docking site into a deleted locus and does not teach insertion of an exogenous nucleic acid sequence greater than 1000 base pairs between two Cas9-generated double-stranded breaks.
This argument has been fully considered but is not persuasive.
The rejection does not rely upon Gratz alone for teaching every limitation of the claims. Rather, the rejection relies upon Gratz in view of Giles. As set forth in the Office Action, Gratz teaches introducing two guide RNAs together with Cas9 to generate two double-stranded breaks that excise an intervening genomic sequence approximately 4.6 kb in length and further teaches insertion of an exogenous nucleic acid into the cleaved locus by homologous recombination. The Office Action expressly acknowledged that Gratz does not teach the claimed size of the inserted exogenous nucleic acid sequence and relied upon Giles for that teaching.
Applicant further argues that Giles is no more relevant than Zhang because Giles allegedly teaches insertion of large donor sequences only into a single cut site. This argument is likewise unpersuasive. Giles teaches that CRISPR/Cas9-mediated homologous recombination is suitable for gene replacement using exogenous donor templates and specifically explains that larger insertions require double-stranded donor DNA templates. Giles further teaches that injected double-stranded donor templates had already been successfully used to incorporate large exogenous DNA sequences and states that there is every reason to expect such donor templates to function effectively with CRISPR/Cas9-mediated homologous recombination. Thus, Giles teaches the use of large donor templates for CRISPR-mediated gene replacement and provides the motivation relied upon in the rejection.
Applicant additionally argues that one of ordinary skill in the art would not have had a reasonable expectation of successfully inserting an exogenous sequence greater than 1000 bp into a genomic region excised by two guide RNAs.
This argument is not persuasive because the rejection is based upon the combined teachings of the references rather than any individual reference in isolation. Gratz teaches that following generation of two Cas9-mediated double-stranded breaks, the intervening genomic sequence is removed and an exogenous nucleic acid is incorporated into the cleaved locus through homologous recombination. Giles teaches that larger exogenous sequences are appropriately introduced using double-stranded donor templates during CRISPR-mediated homologous recombination. A person of ordinary skill in the art would therefore have recognized that the donor template taught by Giles represents a predictable variation of the donor template used by Gratz for accomplishing homologous recombination-mediated replacement at the targeted locus. Merely increasing the size of the donor sequence while employing the same homologous recombination repair mechanism would have constituted the application of a known technique to a known CRISPR-mediated genome editing method.
Applicant also contends that the Office Action provides no evidence establishing predictability for the proposed combination.
The argument is not persuasive because obviousness under 35 U.S.C. §103 does not require that the prior art disclose the identical working example recited in the claims. Rather, the issue is whether the combined teachings of the prior art would have suggested the claimed subject matter to one of ordinary skill in the art with a reasonable expectation of success. Here, Gratz teaches the use of two guide RNAs and Cas9 to excise a genomic region followed by homologous recombination-mediated insertion of exogenous DNA, while Giles teaches that larger exogenous DNA sequences are introduced using double-stranded donor templates in CRISPR-mediated homologous recombination. The combination therefore represents the predictable use of known CRISPR genome engineering techniques to obtain the claimed method.
Accordingly, applicant has not identified reversible error in the rejection, and the rejection of claims under 35 U.S.C. §103(a) over Gratz in view of Giles is maintained.
Conclusion
No claims allowed.
THIS ACTION IS MADE FINAL. 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 TIFFANY N GROOMS whose telephone number is (571)272-3771. The examiner can normally be reached M-F 830-530.
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/TIFFANY NICOLE GROOMS/Examiner, Art Unit 1637
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