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 amendment filed on July 23, 2025 is acknowledged and has been entered. Claims 1-12 and 18 have been canceled. Claims 13, 19-21 and 23. Claim 24 has been added. Claims 13-17 and 19-24 are pending.
Claims 13-17 and 19-24 are discussed in this Office action.
All of the amendments and arguments have been thoroughly reviewed and considered but are not found persuasive for the reasons discussed below. Any rejection not reiterated in this action has been withdrawn as being obviated by the amendment of the claims. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
This action is made NON-FINAL.
Previous Grounds of Rejection
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 13-17 and 19-24 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-9, 11-21 of U.S. Patent No. 11,142,788 (Patent ‘788 herein). Although the claims at issue are not identical, they are not patentably distinct from each other because while the claims are very similar, they are not identical. Claim 1 of the instant application and claim 1 of the ‘788 Patent are very similar but not the same. The second step of the ‘788 Patent recites “extending the primer using a polymerase and modified nucleotides that are resistant to nuclease degradation to create a modified polynucleotide that protects the target nucleic acid from nuclease degradation” while the same step in the instant application recites “extending the primer using a polymerase and modified nucleotides that are resistant to nuclease degradation to create a modified polynucleotide”. Further, the dependent claims, are almost identical, as well. For example, compare claim 2 of ‘788 Patent to claim 2 of the instant claims which are directed to modified nucleotide triphosphates. Further, compare claim 3 of ‘788 Patent to claim 3 of the instant application which are directed to specific modified nucleotides including alpha-phosphorothioate nucleotide triphosphates, morpholino triphosphates, peptide nucleic acids, peptide nucleic acid analogs, or sugar modified nucleotide triphosphates. There are multiple claims such as these that are overlapping between the two applications and therefore the claims are not patent eligble.
New Grounds of Rejection
Claim Rejections - 35 USC § 102
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.
Claim(s) 13-17 and 20-23 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tsai et al. (WO2016028887; February 2016).
With regard to claim 13, Tsai teaches a method for isolating a target nucleic acid, the method comprising:
hybridizing at least one primer to a first end of a target nucleic acid in a sample (paragraph 50 and 62, where PNA modifications are included within primer/adapter sequences; see also where paragraph 50 describes primer extension);
extending the primer using a polymerase and modified nucleotides that are resistant to nuclease degradation to create a modified polynucleotide (paragraph 50 and 62, where PNA modifications are included within primer/adapter sequences; see also where paragraph 50 describes primer extension);
binding at least one Cas endonuclease complexed with a guide RNA that targets the Cas
endonuclease to a second end of the target nucleic acid in a sequence- specific manner to create protected target nucleic acid resistant to nuclease degradation (paragraph 70, 72-73, 77, 83, where Cas9 exonuclease cleavage steps are included in the method; see Figures 8 and 10, where one method and approach is depicted that includes polymerase binding at a primer site at one end and Cas9 binding sites on the other; see also paragraph 120, where the method of Fig 8 is described in detail for enriching for DnaE target sequence; see paragraph 122-123, where the method of Fig 10 is described; see also Figure 7, which depicts an example of target, Cas9 binding with guide RNAs, plus the cleavage followed by sequencing which necessarily includes primer binding at one end);
exposing the sample to a nuclease (paragraph 70, 72-73, 77, 83, where Cas9 exonuclease cleavage steps are included in the method; see Figures 8 and 10, where one method and approach is depicted that includes polymerase binding at a primer site at one end and Cas9 binding sites on the other; see also paragraph 120, where the method of Fig 8 is described in detail for enriching for DnaE target sequence; see paragraph 122-123, where the method of Fig 10 is described; see also Figure 7, which depicts an example of target, Cas9 binding with guide RNAs, plus the cleavage followed by sequencing which necessarily includes primer binding at one end);
and isolating the modified polynucleotides and protected target nucleic acid (paragraph 26 and 30 where the nucleic acid can include modified nucleotides that protect from degradation and also where a method is focused on enriching sample for target nucleic acids).
With regard to claim 14, Tsai teaches the method of claim 13, wherein the modified nucleotides comprise modified nucleotide triphosphates (paragraph 50 and 62, where PNA modifications are included within primer/adapter sequences).
With regard to claim 15, Tsai teaches the method of claim 13, wherein natural nucleotides are used in combination with modified nucleotides (paragraph 50 and 62, where PNA modifications are included within primer/adapter sequences).
With regard to claim 16, Tsai teaches the method of claim 14, wherein the modified nucleotide triphosphates comprise alpha-phosphorothioate nucleotide triphosphates, morpholino triphosphates, peptide nucleic acids, peptide nucleic acid analogs, or sugar modified nucleotide triphosphates (paragraph 50 and 62, where PNA modifications are included within primer/adapter sequences).
With regard to claim 17, Tsai teaches the method of claim 16, wherein the modified nucleotide triphosphates are selected from the group consisting of 2'-Deoxycytidine-5'-O-(1-Thiotriphosphate), 2'-O-methyl modified nucleotide triphosphate, 2'-fluoro modified nucleotide, 2'-O-Methyladenosine-5'-Triphosphate, 2'-O-Methylcytidine-5'-Triphosphate, 2'-O-Methylguanosine-5'-Triphosphate, 2'-0- Methyluridine-5'-Triphosphate, 2'-O-Methylinosine-5'-Triphosphate, 2'-O-Methyl-2- aminoadenosine-5'-Triphosphate, 2'-O-Methylpseudouridine-5'-Triphosphate, 2'-O-Methyl-5- methyluridine-5'-Triphosphate, 2'-O-Methyl-N6-Methyladenosine-5'-Triphosphate, 2'-Fluoro-2'- deoxyadenosine-5'-Triphosphate, 2'-Fluoro-2'-deoxycytidine-5'-Triphosphate, 2'-Fluoro-2'- deoxyguanosine-5'-Triphosphate, 2'-Fluoro-2'-deoxyuridine-5'-Triphosphate, and 2'-Fluoro- thymidine- 5'-Triphosphate (paragraph 75, where the modification can include 2’-O-Methyl modifications).
With regard to claim 20, Tsai teaches the method of claim 13, wherein the nuclease comprises an exonuclease (paragraph 70, 72-73, 77, 83, where Cas9 exonuclease cleavage steps are included in the method; see Figures 8 and 10, where one method and approach is depicted that includes polymerase binding at one end and Cas9 binding sites on the other).
With regard to claim 21, Tsai teaches the method of claim 13, further comprising detecting the target nucleic acid (paragraph 29, where samples can be detected using sequencing; paragraph 31, where the sample can be detected through optical label; paragraph 86, 94 and 101, where sequencing steps are included).
With regard to claim 22, Tsai teaches the method of claim 21, wherein the detecting step comprises using hybridization, spectrophotometry, sequencing, electrophoresis, amplification, fluorescence detection, chromatography, DNA staining, or microscopy (paragraph 29, where samples can be detected using sequencing; paragraph 31, where the sample can be detected through optical label; paragraph 86, 94 and 101, where sequencing steps are included).
With regard to claim 23, Tsai teaches the method of claim 14, wherein the sample is a blood sample, serum sample, plasma sample, urine sample, saliva sample, semen sample, feces sample, phlegm sample, or liquid biopsy (paragraph 26, where genomic nucleic acids are collected from cells, whole blood, semen, saliva, tears, urine, fecal material, sweat, buccal cells and skin, for example).
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.
Claim(s) 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Tsai et al. (WO2016028887; February 2016) as applied over claims 13-17 and 20-23 above and further in view of Wang et al. (Science, 2014, 343, p 80-84).
With regard to claim 19, Wang teaches the method of claim 13, wherein the Cas endonuclease is catalytically inactive (Abstract).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have adjusted the teachings of Tsai to include the Cas nuclease as taught by Wang to arrive at the claimed invention with a reasonable expectation for success. Wang teaches “The bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system for genome editing has greatly expanded the toolbox for mammalian genetics, enabling the rapid generation of isogenic cell lines and mice with modified alleles. Here, we describe a pooled, loss-of-function genetic screening approach suitable for both positive and negative selection that uses a genome-scale lentiviral single-guide RNA (sgRNA) library” (Abstract). Therefore, one of ordinary skill in the art at the time the invention was made would have adjusted the teachings of Tsai to include the Cas nuclease as taught by Wang to arrive at the claimed invention with a reasonable expectation for success.
Response to Arguments
Applicant’s arguments with respect to claim(s) 13-17 and 19-24 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Applicant requested the double patenting rejection to be held in abeyance. That request is denied, as the rejection is not the last remaining issue in the case. The rejection is maintained.
Conclusion
No claims are allowed. All pending claims have been rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHANIE KANE MUMMERT whose telephone number is (571)272-8503. The examiner can normally be reached M-F 9:00-5:30.
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/STEPHANIE K MUMMERT/Primary Examiner, Art Unit 1681