DETAILED ACTION
Notice of Pre-AIA or AIA 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 .
Election/Restrictions
2. Applicant’s election without traverse of Group I (claims 1, 2, 4-7, 9, 11-12, 14-15, 17, and 21-24) in the reply filed on May 5, 2026 is acknowledged.
Applicant’s election without traverse of the following species for examination in the reply of May 5, 2026 is also acknowledged: (i) Cas9 and (ii) gRNA.
As noted by Applicant, claims 1, 2, 4-6, 9, 11-12, 14-15, 17, and 21-24 read on the elected invention and species.
Claims 7, 45, 50, 58, and 64 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention (claims 45, 50, 58, and 64) or a nonelected species (claim 7), there being no allowable generic or linking claim. Election was made without traverse in the reply filed on May 5, 2026.
Drawings
3. The drawings filed on February 1, 2023 are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: 207, 602, and 607.
Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Substitute Specification
4. The substitute specification filed on November 17, 2023 is objected to because para. 3 states that web links are incorporated by reference. This is not proper per MPEP 608.01 VII. See also 37 CFR 1.75(e) and MPEP 608.01(p).
Claim Objections
5. Claim 11 is objected to because “double stranded” should be hyphenated.
Claim Rejections - 35 USC § 112
6. 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.
Claims 1, 2, 4-6, 9, 11, 12, 14, 15, 17, and 21-24 are 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 1 is indefinite because it is not clear as to how the recited steps accomplish the goal stated in the preamble. More specifically, the preamble states that the method is for “capturing target nucleic acid sequences,” but the steps recited in the body of the claim do not appear to result in target nucleic acid capture since they only recite nuclease-mediated digestion followed by adapter ligation. In other words, there is no step of isolating or separating the adapter-ligated fragments generated in step (c) from other nucleic acids in the sample. As a result, it is not clear as to how the method functions to capture target nucleic acids as stated in the preamble.
Claim 1 is also indefinite because step (c) in the claim is missing an apparent essential element or step. This step recites “contacting the plurality of nucleic acid fragments with third adapters, thereby generating a plurality of fragments ligated to either the first or second adapter at one end and the third adapter at the other end.” Step (c) does not require the presence of a ligase, nor does it require chemical ligation of the third adapters. As well, merely contacting adapters with nucleic acid fragments will not result in ligation. Therefore, step (c) in claim 1 is missing an essential element or step.
Claims 2, 4-6, 9, 11, 12, 14, 15, 17, and 21-24 are also indefinite since they depend from claim 1 and do not correct its indefiniteness issues.
Claim 14 is also indefinite because it is not entirely clear whether the recited length limitation applies to the adapter-ligated nucleic acids in step (a), the adapter-ligated nucleic acids in step (c), or both types of adapter-ligated nucleic acids. If the claim is intended to limit the nucleic acids in step (a), Applicant could address the issue by amending the claim to recite “wherein the adapter-ligated nucleic acids in step (a) are from 20 bp to 5000 bp in length.”
Claim 17 is also indefinite because it is not clear whether “the adapters” refers to: (i) the first adapter, (ii) the second adapter, (iii) the third adapter, (iv) two of the aforementioned three types of adapters, or (v) all three types of adapters recited in claim 1. See also the discussion in MPEP 2173.05(e), where it is noted that a claim referring to “said lever” or “the lever” could be indefinite if the previous portion of the claim recited two different levers. In this case, claim 1 recites three different adapters, and it is not clear whether “the adapters” in claim 17 refers to all, some, or just one of the three different adapters in claim 1. Accordingly, claim 17 is indefinite.
Claim Rejections - 35 USC § 103
7. 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.
8. 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.
9. Claims 1, 2, 4-6, 9, 11, 12, 14, 15, 17, 21, 22, and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Pinter et al. (US 2004/0209299 A1) in view of Zeiner et al. (US 2014/0357523 A1).
The claims are drawn to a method for using a nucleic acid-guided nuclease to capture target nucleic acid sequences. More specifically, the method comprises using nucleic acid-guided nuclease-gNA complexes to cleave nucleic acids having a first adapter ligated at one end and a second adapter ligated at the other end at targeted sites of interest. The resulting fragments contain the first or second adapter at one end and no adapter at the other end. The fragments are then ligated to a third adapter such that the resulting ligation products contain the first or second adapter at one end and the third adapter at the other end.
As noted above, Applicant has elected the combination of Cas9 nuclease and gRNAs for examination.
Regarding claims 1, 9, 11, 12, and 22, Pinter discloses a method that includes the following steps (see Example 20 on page 40; see also Fig. 42 and its description in para. 162):
(a) providing a sample comprising a plurality of adapter-ligated nucleic acids (genomic DNA), wherein the nucleic acids are ligated to a first adapter at one end and a second adapter at the other end, and wherein the first and second adapters are identical;
(b) contacting the sample with a nuclease that targets specific sites to generate fragments containing either the first or second adapter at one end and no adapter at the other end;
(c) ligating a third adapter to the fragments generated in step (b) to generate ligation products containing the first or second adapter at one end and the third adapter at the other end; and
(d) amplifying the resulting ligation products using a first or second and third adapter-specific PCR method.
Further regarding claim 11, which requires the adapter-ligated nucleic acids to be double-stranded DNA, the teachings of Pinter in Example 20 suggest double-stranded DNA by teaching genomic DNA. The reference also teaches that the disclosed methods may be practiced with double-stranded DNA, including double-stranded genomic DNA (see, e.g., paras. 185 and 219-220).
Pinter does not teach all of the elements of the rejected claims because the reference fails to teach using a Cas9-gRNA complex(es) to conduct the nuclease-mediated fragmentation step as required by the claims in view of the species elections.
Zeiner, however, discloses a method for fragmenting a genome (abstract). Regarding claims 1, 2, and 4-6, the method of Zeiner comprises using a plurality of different Cas9-gRNA complexes to cleave double-stranded DNA (e.g., genomic DNA from any organism, including a human) at targeted sites of interest, thereby fragmenting the genome (see, e.g., the abstract and paras. 3, 27, 34, and 46-50 and 52). Zeiner teaches that the gRNA component of the Cas9-gRNA complexes can be designed to target different, predefined sites of interest in the genome such that the fragments generated by the method contain a particular sequence of interest (e.g., a SNP, insertion, deletion, or mutation, or structural variation as recited in claim 15) and/or have a length within a particular length range (abstract and paras. 49-50).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for the ordinary artisan to use a Cas9-gRNA complex(es) to conduct the nuclease-mediated digestion step in the method of Pinter. Zeiner provides motivation to do so by teaching that Cas9-gRNA complexes can be designed to cleave double-stranded DNA, such as the adapter-ligated double-stranded nucleic acids of Pinter, at any desired predetermined site (paras. 49-50). The ordinary artisan would have recognized that digestion using the Cas9-gRNA complexes described in Zeiner would offer more options for the digestion step in Pinter since the potential cleavage sites need not be limited to those of restriction endonucleases or methylation-sensitive restriction endonuclease. The ordinary artisan would have had a reasonable expectation of success in view of the guidance provided by Zeiner (see, e.g., paras. 33-34 and 49-50) and also since Pinter imposes no particular limitations on the nuclease used for the fragmentation step. Thus, the methods of claims 1, 2, 4-6, 9, 11, 12, and 22 are prima facie obvious.
Further regarding claim 14, which depends from claim 1, since Pinter does not disclose the lengths of the adapter-ligated nucleic acids in Example 20, the reference fails to teach that the adapter-ligated nucleic acids have a length within the claimed range of 20-5,000 bp. The reference does teach, though, that adapter-ligated nucleic acids, in general, may have a size of 200-2,000 bp (para. 285). This range lies inside the claimed range. As well, Zeiner teaches that the disclosed method may be used to generate fragments with a variety of lengths (see, e.g., para. 50, where length ranges of 30-50 bp, 1-10 kb, and 10-100 kb are disclosed). The first of these length ranges lies inside the claimed range, and the second of these length ranges overlaps with the claimed range. Further, no evidence of unexpected results has been presented with respect to the claimed range. This is sufficient to establish a prima facie case of obviousness with respect to the claimed range. See MPEP 2144.05 I, where prior art that discloses an overlapping range and/or a range that lies within a claimed range renders the claimed range obvious in the absence of unexpected results. Thus, the method of claim 14 is also prima facie obvious.
Further regarding claim 15, which depends from claim 1, as noted above, Zeiner teaches that the disclosed fragmentation method may be used to obtain fragments containing a SNP, insertion, deletion, structural variation, or other mutation (para. 49). The reference also discusses the desirability of analyzing SNPs, e.g., in the human genome (paras. 143-145) and further notes that exons and regulatory regions may be analyzed (para. 88). Pinter also teaches that adapter-ligated nucleic acids, in general, can be used for SNP genotyping or analysis of deletions, insertions, repeats, or structural variations (para. 102; see also para. 374). These teachings would have provided the ordinary artisan practicing the method suggested by Pinter in view of Zeiner with a motivation and reasonable expectation of success in designing the Cas9-gRNA complexes such that the targeted sites of interest include any of the following: exons, regulatory regions, SNPs, repeats, insertions, deletions, genetic mutations, and structural variations. Thus, the method of claim 15 is also prima facie obvious.
Further regarding claim 17, which depends from claim 1, Pinter teaches that the homopolymeric C-tail that forms part of the adapter is ten nucleotides in length (para. 406 & Fig. 36). The reference does not clearly teach the length of the U portion of the adapter used in Example 20, but it does teach that suitable universal adapters may have a long strand that is 18-100 nucleotides in length and a complementary short strand that is 7-20 nucleotides in length (para. 205). The resulting adapters have a length that lies within or close to the claimed range of 20-100 bp. Pinter also teaches a specific example in which the long and short strands are 20 and 11 nucleotides in length, respectively (para. 205). When filled in, this adapter also has a length within the claimed range. As well, no evidence of unexpected results has been presented with respect to the claimed length range. This is sufficient to establish a prima facie case of obviousness per MPEP 2144.05 I. Thus, the method of claim 17 is also prima facie obvious.
Further regarding claim 21, Pinter does not specify the type of sample from which the genomic DNA used in Example 20 was obtained. The reference does teach, though, that the disclosed methods may be applied to clinical samples, which are also biological samples (para. 218) as well as DNA from any source (paras. 219-220). This, in combination with the teaching of Zeiner that biological samples, clinical samples, and environmental samples are suitable for use with the disclosed method (paras. 47-48 and 145), would have provided the ordinary artisan with motivation and a reasonable expectation of success in practicing the method suggested by Pinter in view of Zeiner using any of the recited samples. Thus, the method of claim 21 is also prima facie obvious.
Further regarding claim 24, the adapter-ligated nucleic acids in Example 20 of Pinter are a sequencing library. This term only requires that the library be suitable for sequencing, and the library disclosed in Example 20 of Pinter meets this requirement. Thus, the method of claim 24 is also prima facie obvious.
10. Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Pinter et al. (US 2004/0209299 A1) in view of Zeiner et al. (US 2014/0357523 A1) and further in view of Amorese et al. (US 2013/0231253 A1).
As discussed above, the teachings of Pinter in view of Zeiner render obvious the methods of claims 1, 2, 4-6, 9, 11, 12, 14, 15, 17, 21, 22, and 24.
Regarding claim 23, the teachings of Pinter in view of Zeiner do not teach or suggest that the first and second adapters are different.
Prior to the effective filing date of the claimed invention, though, it would have been prima facie obvious for the ordinary artisan to practice the method suggested by Pinter in view of Zeiner using a first adapter that is not identical to the second adapter. Amorese provides motivation to do so by teaching that it can be desirable to include a barcode in one adapter used in a method that produces nucleic acids containing an adapter at each end (see, e.g., paras. 9-12 and 60; see also Figs. 1 and 3 for a general description of the method). The ordinary artisan would have had a reasonable expectation of success since modifying an adapter to include a barcode was routine prior to the effective filing date of the claimed invention. Thus, the method of claim 23 is prima facie obvious.
Conclusion
11. No claims are currently allowable.
Cann et al. (US 2016/0017396 A1) is cited as a reference of interest. More specifically, Cann teaches a method that comprises the use of Cas9-gNA complex for nucleic acid capture and enrichment (abstract and pages 1-3).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Angela Bertagna whose telephone number is (571)272-8291. The examiner can normally be reached on 8-5, M-F.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached on 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ANGELA M. BERTAGNA/
Primary Examiner, Art Unit 1681
Prosecution Insights