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 .
Priority
The instant application 17/742,173 filed 05/11/2022 is a continuation of U.S. Patent Application 16/637,586 filed on February 7, 2020, which is the U.S. National Stage of International Application PCT/EP2018/071557, filed August 8, 2018, which claims the benefit of European Application 17306055.9 filed August 8, 2017.
The priority date of claim 16 and its dependents except for claim 25 is determined to be August 8, 2017.
The priority date for claim 25 (directed to cfDNA) is not supported by the European Application 17306055.9 filed August 8, 2017 and is instead given the priority date of the National Stage Application PCT/EP2018/071557, filed August 8, 2018.
Status of Claims
Applicant’s amendments to claims filed 06/19/2025 in response to the Non-Final Rejection mailed 04/22/2025 are acknowledged.
Claims 16,19, 23, 29-32 are amended.
Claim 18 has been canceled.
Claims 16,17, and 19-35 are pending and under examination.
Response to Remarks filed 06/19/2025
The amendments and arguments presented in the papers filed 06/19/2025 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 04/22/2025 listed below have been reconsidered as indicated.
a) Deficiencies in the sequence disclosures have been remedied and objections are withdrawn in view of amendments to the specification.
b) Objections to the specification for improper language of the abstract are withdrawn in view of amendments to the abstract.
c) Objections to claim 16 for informalities are withdrawn in view of amendments to the claims.
d) The 35 USC 112(b) indefiniteness rejections of claims 19, 23, and 29-32 have been withdrawn in view of the amendments to claims.
c) The nonstatutory double patenting rejections of (1) claims 16, 17, 19-23, 26-29, 31, and 33-34 over claims 1-20 of U.S. Patent No. 11,384,383, and claims 18, 24-25, 30, 32, and 35 over claims 1-20 of U.S. Patent No. 11,384,383 in view of Tsai et al. (US PGPub 20160208241); and (2) claims 16, 17, 19-23, 26, 28-29, and 34-35 over claims 1-23 of U.S. Patent No. 11,473,124, claims 18, 24-25, and 30-33 over claims 1-23 of U.S. Patent No. 11,473,124 in view of Tsai et al. (US PGPub 20160208241), and claim 27 over claims 1-23 of U.S. Patent No. 11,473,124 in view of Carpenter et al (WO 2016100955) are withdrawn in view of the filed Terminal Disclaimers.
d) The provisional nonstatutory double patenting rejections of claims 16-21, 26, 28-29, 31, 34 over claims 1-6, 8-12, and 14-33 of copending Application No. 17/282,683, claims 22-25, 30, 32-33, and 35 over claims 1-6, 8-12, and 14-33 of copending Application No. 17/282,683 in view of Tsai et al. (US PG Pub 20160208241), and claim 27 over claims 1-6,8-12, and 14-33 of copending Application No. 17/282,683 in view of Carpenter et al. (WO 2016100955) are withdrawn in view of the filed Terminal Disclaimer. It is noted that since the Office Action dated 04/22/2025, copending Application No. 17/282,683 has been patented and assigned patent number 12,305,218.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
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 16, 17, 19, 20, 22, 24-26, 28, and 33-35 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Carpenter et al. (WO 2016100955 on IDS filed 05/11/2022).
These are new rejections necessitated by claim amendments filed on 06/19/2025.
Regarding claim 16, Carpenter teaches methods for depleting targeted nucleic acid sequences from a sample, enriching for sequences of interest from a sample, and/or partitioning of sequences from a sample, a method comprising: contacting a sample comprising sequences of interest with a plurality of CRISPR/Cas system protein-gRNA complexes, wherein the gRNAs are complementary to targeted sequences (para 10). A sample comprises nucleic acid sequences (para 10).
Carpenter teaches the CRISPR/Cas system protein can be catalytically dead, for example the catalytically dead CRISPR/Cas system protein is dCas9 (para 10) and that such a protein can bind to a target site in any nucleic acid (where the target site is determined by the guide RNA), but the protein is unable to cleave or nick the double- stranded DNA (para 162 and Fig 2), thereby generating dCas9-bound fragments.
Carpenter teaches the method further comprises treating the product (dCas9-bound fragments) with an enzyme that has exonuclease activity (para 10).
Regarding claim 17, Carpenter teaches the catalytically dead Cas protein is dCas9 (paras 10,163-164).
Regarding claim 19, Carpenter teaches using lambda exonuclease to deplete or degrade DNA (paras 188 and 250).
Regarding claim 20, Carpenter teaches ligating adapters to fragmented extracted sequences (para 10), and further teaches the adapters are hairpin adapters (paras 122-123).
Regarding claim 22, Carpenter teaches extracting DNA from a specimen and fragmenting (para 184).
Regarding claim 24, Carpenter teaches gRNAs from 50-250 bp, that are complementary to a site in a target nucleic acid that can be 45 or 50 base pairs (para 133), which reads on target regions of at least 44 nucleotides.
Regarding claim 25, Carpenter teaches the sample maybe blood (i.e. circulating or cell-free nucleic acids) (para 106).
Regarding claim 26, Carpenter teaches gRNAs are complementary to sequences including repeat regions (para 10).
Regarding claim 28, Carpenter teaches bound nucleic acid sequences can be eluted from the Cas9/gRNA (para 164).
Regarding claim 33, Carpenter teaches sequences of interest comprise less than 10% of the extracted nucleic acids (para 10).
Regarding claim 34, Carpenter teaches contacting the sample with at least 10 unique CRISPR/Cas system protein-gRNA complexes (para 10), and eluting bound nucleic acid sequences from the Cas9/gRNA complex (para 164).
Regarding claim 35, Carpenter teaches making an epigenetic map of a region of the genome of said cells by mapping information obtained from the sequence reads from selected targets to the region (para 18), which reads on modified bases that are epigenetic modifications.
Claim Rejections - 35 USC § 103
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 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.
Claims 21, 23, and 29-32 are rejected under 35 U.S.C. 103 as being unpatentable over Carpenter et al. (WO 2016100955 on IDS filed 05/11/2022) in view of Tsai et al. (US PGPub 20160208241, on IDS dated 05/11/2022).
These are new rejections necessitated by claim amendments filed on 06/19/2025.
The relevant teachings of Carpenter et al. as applied to claims 16, 17, 19, 20, 22, 24-26, 28, and 33-35 are set forth above.
Tsai teaches methods for enriching for a target region in a nucleic acid sample using the CRISPR-Cas9 system,
Regarding claim 21, Carpenter does not teach a site-specific endonuclease.
Tsai teaches site-specific cleavage by TALENs and zinc-finger nucleases, or mutant Cas9 nuclease (para 64).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Carpenter and Tsai to arrive at the instantly claimed invention. The modification would have entailed adding the step of a site-specific endonuclease from Tsai to the method of Carpenter. Choosing a site-specific endonuclease as a protector instead of a hairpin as in the original method of Carpenter would have been merely a matter of judicious selection and routine optimization. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claim 23, Carpenter teaches fragmentation of the nucleic acid sample but is silent as to the method of fragmentation.
Tsai teaches generating a nucleic acid sample by fragmentation with restriction enzymes (site-specific endonucleases) (para 26).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Carpenter and Tsai to arrive at the instantly claimed invention. The modification would have entailed using the restriction enzymes of Tsai as the mechanism of fragmentation in the method of Carpenter. Determining an appropriate method for fragmentation would have been merely a matter of judicious selection and routine optimization. One would have been motivated by the convenience of restriction enzymes that can be purchased, and by the predictability of known cutting sites for restriction enzymes. On would have been motivated There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Regarding claims 29-32, Carpenter teaches removing the bound nucleic acid sequences from the Cas9/gRNA complex for amplification and sequencing (para 164). However, Carpenter is silent regarding additional methods after the step of isolating the target region.
Carpenter does not teach a method further comprising at least one single-stranded nucleic acid molecule is hybridized to a single-stranded region of the target region of step c) (claim 29); wherein the at least one single- stranded nucleic acid molecule is hybridized to a 3' overhang of the target region of step c) (claim 30); wherein the at least one single- stranded nucleic acid molecule hybridizes at least 50 nucleotides from a Type II Cas protein protospacer adjacent motif (PAM) (claim 31); or wherein the isolated target region is used as a substrate for detecting protein binding to nucleic acid (claim 32).
Regarding claim 29, Tsai teaches hybridizing an oligonucleotide (which can be single-stranded) to a single-stranded region (para 50).
Regarding claim 30, Tsai teaches that fragmentation can produce 3’ overhangs (para 26) and that an overhang sequence can be used for ligation of an adapter having a complementary overhang (i.e. a single-stranded sequence) (para 64).
Regarding claim 31, Tsai teaches that target regions can be 5, 10, 15, 20, 50, or 100 kb or more in length (para 68) and that two gRNA-Cas9 complexes can be used to cleave the target region at each end (para 38). Tsai teaches that the protospacer adjacent motif (PAM) for a sgRNA-Cas9 endonuclease complex can be 3 nucleotides in length (para37 and Figs. 2 and 3). Tsai also teaches that target regions can be excised by Cas9 cleavage at two PAM sites on either end of the target region (para 67 and Fig. 7) thus placing the two ends of the target region more than 50 nucleotides away from each other. Tsai further teaches that the end of the target region can be modified by the addition of adapters (i.e. single-stranded nucleic acid molecule) (para 38). Adapters on either end are thus 5, 10, 15, 20, 50, or 100 kb or more away from the Type II Cas protein protospacer adjacent motif on the other end, as required by the limitation of claim 31.
Regarding claim 32, Tsai teaches proteins that bind to specific sequences in nucleic acids (para 89), which reads on using the isolated target region as a substrate for detecting protein binding to nucleic acid.
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Carpenter and Tsai to arrive at the instantly claimed invention. The modification would have entailed incorporating the downstream steps of Tsai in the method of Carpenter for analysis of the isolated target regions. One would have been motivated by ability to use the added known analytical tools taught by Tsai to analyze the bound regions of interest in Carpenter. There would have been a reasonable expectation of success given the underlying materials and methods are widely known, successfully demonstrated, and commonly used as evidenced by the prior art.
Claim 27 is rejected under 35 U.S.C. 103 as being unpatentable over Carpenter et al. (WO 2016100955 on IDS filed 05/11/2022).
Regarding claim 27, Carpenter teaches that the ratio of gRNA:targeted nucleic acids can be at least 10:1 (i.e. nucleic acids: gRNA ratio of 1:10) (paras 142 and 143). Carpenter also teaches contacting nucleic acid sample with a plurality of CRISPR/Cas system protein-gRNA complexes (para 139), and contacting the nucleic acid sample with at least 102 unique complexes, where the unique nature of the complex is determined by the unique nature of the gRNA itself (para 140) and the unique gRNA may be 1 unique gRNA (para 138).
Carpenter further teaches large amounts (e.g. >30 pmoles) of CRISPR/Cas System proteins and guide RNAs may be needed, usually >100 fold excess amount over target DNA (paras 170,263).
Carpenter does not explicitly teach the specific ratio of target nucleic acid:Type II Cas protein:gRNA is at least 1:10:10. However, it would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the claimed invention to have determined varying ratios of the nucleic acid:Type II Cas protein:gRNA utilizing the teachings of Carpenter based on the desired results. Such manipulations are within the artisan’s capabilities and would have been conventional and routine within the technological field. In addition, as set forth above, Carpenter teaches the need for >100 fold amounts of gRNA and Cas protein relative to target nucleic acids, which is encompassed by a ratio of target nucleic acid:Type II Cas protein:gRNA is at least 1:10:10. One of ordinary skill in the art would have been motivated to modify the primary reference in the manner of the claims to achieve the expected benefits, optimizations and/or expanded applications.
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.
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/JESSICA GRAY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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