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 status
Applicants reply filed 4/15/2026 is acknowledged.
Claims 11, 13 is/are cancelled and claims 65, 66 is/are newly added. Claims 1, 4, 5, 8, 12, 15, 17, 22-25, 43, 45, 52, 54-57, 65, 66 is/are currently pending with claims 22-25, 43, 45, 52, 54-57 is/are withdrawn. Claims 1, 4, 5, 8, 12, 15, 17, 65, 66 is/are under examination.
Claim Objections - Withdrawn
Objection to Claim 1 is withdrawn in light of claim amendment.
Claim Rejections - 35 USC § 112(b) – New, necessitated by claim amendment
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.
Previous rejection of Claims 1, 4, 5, 8, 11-13, 15 and 17 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention is withdrawn in light of claim amendments or cancellation.
Claim 12 is 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 12 recites a “The method of claim 11” however there is no claim 11 rendering claim 12 indefinite. For the purpose of compact prosecution, the claim(s) 12 is/are interpreted as “The method of claim 1[[1]]”.
Claim Interpretation
Claim 65 recites probes of length “about 100bp to about 140bp”. The specification defines “about” as “The term "about" or "approximately" as used herein as applied to one or more values of interest, refers to a value that is similar to a stated reference value, or within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, such as the limitations of the measurement system.” [0046]. Thus, the term “about” in claim 65 is broadly interpreted such that the probe length is within an acceptable range of 100-140bp for one of ordinary skill in the art. Since a probe that performs the required function in the claim (i.e. bind target genomic DNA) would be acceptable to an ordinary artisan, it is further interpreted that a probe that performs the required function in the claim is within an acceptable range of 100-140bp for an ordinary artisan.
Claim Rejections - 35 USC § 102 - Withdrawn
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.
Rejection of Claim(s) 1, 4, 5, 8, 11, 15, 17 under 35 U.S.C. 102(a)(1) as being anticipated by Moretti et al (Somatic gene editing ameliorates skeletal and cardiac muscle failure in pig and human models of Duchenne muscular dystrophy. Nature Medicine, Vol. 26, February 2020, 207–214) is withdrawn in light of amendment to claim 1.
Claim Rejections - 35 USC § 103 – New, necessitated by claim amendments
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.
Rejection of Claim(s) 11-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Moretti as applied to claim 1 above, and further in view of Burns et al (US 2019/0142972 A1, May 16, 2019) is withdrawn due to the withdrawal of rejection of claim 1 above.
Claim(s) 1, 8, 12, 65 and 66 is/are rejected under 35 U.S.C. 103 as being unpatentable over Burns et al (US 2019/0142972 A1, May 16, 2019; ref of record) and Zhang et al (dCATCH-Seq: improved sequencing of large continuous genomic targets with double hybridization; BMC Genomics (2017) 18:811) as evidenced by Day et al (Targeted Sequencing of Large Genomic Regions with CATCH-Seq. PLOS ONE, Oct 2014, Vol. 9, Issue 10)
Regarding claim 1, Burns teaches a method for screening gRNA pairs for editing a genomic nucleic acid in a subject (Figure 1). The method comprises generating a plurality of pairs of gRNA comprising a first gRNA that targets a first nucleic acid sequence in the genomic nucleic acid and a second gRNA that targets a second nucleic acid sequence in the genomic nucleic acid (=claimed (a); [0242], Table 7). The Cas9 protein and the plurality of pairs of gRNAs are expressed in cells comprising the genomic nucleic acid such that at least one pair is expressed per cell such that the region of the genomic nucleic acid between the first nucleic acid sequence and the second nucleic acid sequence is excised resulting formation of new junction by joining of the two cut sites (=claimed (b); [0242, 243]). Next, after this gene editing step, genomic DNA is extracted from the cells (=claimed (c); [242-243]).
To identify the gRNA pairs with greater efficiency, Burns uses sequencing method wherein Burns uses PCR-based amplification of the region targeted for gene editing and then processing the amplified region for sequencing.
Burns teaches sequencing the isolated genomic nucleic acid, aligning the sequenced genomic nucleic acids to reference genome to identify the cut sites for each gRNA pair tested and identify the gRNA pairs with higher excision rate based on higher number of sequences with cut cites (=new junctions, =claimed (h)-(k); [0239, 243], Table 7)
Regarding claim 8, Burns teaches use of vectors for expression of CRISPR reagents wherein the Cas9 and gRNA encoding sequences are on separate vectors (= claimed first and second vector; [194, 204]. Burns also teaches cells transfected with different gRNA pairs [0242-243] which when present on a first vector would implicitly result in different cells being transfected with different first vector.
Regarding claim 12, Burns teaches aligning sequences to BAM files [239, 243], thus teaching computational means for sequence alignment.
Although, Burns uses PCR-based target enrichment strategy to identify cut sites and thus gRNA pairs with greater efficiency, other methods such as hybridization-capture, as claimed, were known in the art for target enrichment.
Zhang teaches hybridization-based target enrichment strategy comprising two rounds of hybridization capture (Abstract).
Zhang’s method also comprises isolating genomic DNA from cells (=claimed (c); Cell culture and DNA extraction) but in comparison to Burns, in Zhang’s’ method the isolated genomic DNA is fragmented and contacted with a first pool of probes (=claimed (d) in part) then isolating the bound fragments (=claimed (e), followed by contacting the bound fragments with a second pool of probes (=claimed (f) in part) then isolating the fragments that are now bound to the first and second pool of probes (=claimed (g)) (Enrichment of targets by two rounds of hybridization). Finally, Zhang teaches sequencing the isolated fragments (=claimed (h); Enrichment of targets by two rounds of hybridization).
Regarding the hybridization probes, Zhang uses biotinylated probes that are about 200-400bp that span the entire target genomic DNA of interest such that they bind and pull-down targeted genomic DNA fragments, as evidenced by Day (Figure 1, Biotinylated probe synthesis, page 4, col. 1) (as required by claims 65, 66; see claim interpretation above). Zhang references Day in the section “Enrichment of targets by two rounds of hybridization” as a prior publication where the probe design was discussed.
Zhang teaches that their method is useful for improving target capture efficiency for large genomic regions, such as spanning several Mbs (Introduction, para 3).
Therefore, it would be obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use Zhang teaches double hybridization-based target enrichment strategy in place of Burns PCR-based target enrichment strategy when the genomic region of interest targeted for excision in Burns’ method is a large genomic region. An ordinary artisan would be motivated to use Zhang double hybridization-based target enrichment strategy in place of Burns PCR-based target enrichment strategy when the genomic region of interest targeted for excision in Burns’ method is a large because Zhang teaches the improved efficiency of their method for such sequences. Burns PCR-based target enrichment strategy that requires first amplifying the genomic region of interest and then sequencing the entire amplified region would be unsuitable for enriching and sequencing large genomic region of interest. An ordinary artisan would reasonably expect to use Zhang double hybridization-based target enrichment strategy in place of Burns PCR-based target enrichment strategy because Zhang teaches method for design of hybridization probes required for targeting a genomic sequence of interest and the method for target enrichment. An ordinary artisan would use Zhang’s teachings regarding design of hybridization probes to generate a pool of probes that span the entire target genomic DNA of interest where cut sites are expected to be created by the gRNAs. Such pool of probes would comprise probes that specifically bind the cut sites and portion of first or second nucleic acid sequence that flanks the cut cite (=claimed first and second pool of probes in (d) and (f). Furthermore, such first and second pools of probes could be used together or separately in the two rounds of hybridization capture, taught by Zhang, with the probes binding their complementary sequences in either configuration.
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in
the art at the effective time of filing of the invention, especially in the absence of evidence to the
contrary.
Claim(s) 4, 5, 15 and 17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Burns and Zhang, as evidenced by Day, as applied to claim 1 above, and further in view of Moretti et al (Nature Medicine, Vol. 26, February 2020, 207–214; ref of record).
The teachings of Burns, Zhang and evidence from Day detailed in the rejection above are relied upon for the instant rejection.
Claim 4, 5, 15 and 17 apply the gRNA screening method of claim 1 to a specific genomic sequence within the dystrophin gene.
Burns applies their gRNA screening method to intron 3 of the TCF4 gene that comprises triple nucleotide repeats (Figure 1, [242-243]) .
Burn and Zhang do not teach applying their gRNA screening method to identify gRNA pairs for the excision of exon 50, which is flanked by intron 50 and 51, of the dystrophin gene, as recited in claims 4, 5, 15, 17.
Moretti teaches a method for excision of exon 50 of dystrophin gene for the treatment of DMD (Abstract). Moretti teaches that the genomic nucleic acid comprises exon 51 of the DMD gene, the first gRNA target a first nucleic acid that is a sequence in intron 50, the second gRNA target a second nucleic acid that is a sequence in intron 51, and introns 50 and 51 flank exon 51 such that the excised nucleic acid comprises exon 51 (as required for claims 4, 5, 15, 17; Methods: gRNA design, gRNA design and off-target analysis; Extended data Figure 1, Supplementary Figure 5).
In comparison to Burns that tests 190 gRNAs and then 96 pairs of gRNAs, Moretti’s tests only 16 pairs (Supplementary Figure 5). This is because Moretti does not use a high-throughput method such as next-generation sequencing used by Burns. Moretti uses a PCR primer set to amplify the portion of the DMD gene targeted by the gRNA pairs and the cut/uncut DMD gene product is then detected by southern blot (pairs of forward and reverse primers listed in Table 7, southern blot shown in Extended data Figure 1 and Supplementary Figure 5).
Therefore, it would be obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use Burns and Zhang’s method to screen gRNA pairs for excision of exon 50 in dystrophin gene, as taught by Moretti. An ordinary artisan would be motivated to use Burns and Zhang’s method to screen gRNA pairs for excision of exon 50 in dystrophin gene because of the high-throughput nature of Burns and Zhang’s method allowing for testing of additional gRNA pairs to identify a more efficient gRNA pair. An ordinary artisan would reasonably expect to use Burns and Zhang’s method to screen gRNA pairs for excision of exon 50 in dystrophin gene because Burns and Zhang’s provide the requisite teachings for design of gRNA pairs and hybridization probes for a target sequence.
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in
the art at the effective time of filing of the invention, especially in the absence of evidence to the
contrary.
Response to Arguments
Applicant’s arguments with respect to the U.S.C. 102 rejection of claim(s) 1, 4-5, 8, 11, 15 and 17 and U.S.C. 103 rejection of claim 11-13 have been considered but are moot because the new ground of rejection necessitated by claim amendments.
The Applicant' s amendments limiting claims to include new steps and new claims necessitated the withdrawal of the previous rejections. Applicant' s arguments are drawn to Moretti and Burns failing to teach the new limitations (page 8-9, bridging para; page 9, para 2). However, the new limitations are addressed in the new rejections.
Conclusion
No claim is allowed.
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 MATASHA DHAR whose telephone number is (571)272-1680. The examiner can normally be reached M-F 8am-4pm (EST).
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, Peter Paras Jr. can be reached at (571)272-4517. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/MATASHA DHAR/Examiner, Art Unit 1632
/EMILY A CORDAS/Primary Examiner, Art Unit 1632
Prosecution Insights