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 .
Applicant previously canceled claims 1-58. Claims 59-90 are currently pending and under examination.
Information Disclosure Statement
The Information Disclosure Statement filed November 14, 2025 has been considered.
Drawings
The drawings 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: Reference characters 301-310 in Figure 3, 401-405 in Figure 4A, 405-408 in Figure 4B, 501-505 in Figure 5A, 505-508 in Figure 5B, 601-605 in Figure 6, 701-706 in Figure 7A, 705-708 in Figure 7B, 801-806 in Figure 8A, 801-806 in Figure 8B, 806-811 in Figure 8C, 901-905 in Figure 9A, 905-908 in Figure 9B, 1001-1006 in Figure 10A, 1001-1002, 1007-1010 in Figure 10B, 1001, 1011-1015 in Figure 10C, 1006, 1010, 1015-1017 in Figure 10D, 1101-1106 in Figure 11A, 1101-1106 in Figure 11B, 1106-1111 in Figure 11C and 1201-1207 in Figure 7. 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.
Claim Objections
Claims 60, 80 and 86 are objected to because of the following informalities:
In claim 60, line 1, the terms “The method of claim 60”, should read, “The method of claim 59”.
In claim 80, line 3, the terms “the gNAs are configured to hybridize to at least one sequence”, should read “the gNAs hybridize to at least one sequence”.
In claim 86, lines 1-2, the terms “the gNAs are deoxyribonucleic acids (gDNAs) or ribonucleic acids (gRNAs)”, should read “the gNAs are guide deoxyribonucleic acids (gDNAs) or guide ribonucleic acids (gRNAs)”.
Applicant is advised that should claim 62 be found allowable, claim 77 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 59-90 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 59 recites the limitation "the 3’" in line 4. There is insufficient antecedent basis for this limitation in the claim.
Claim 59 recites the limitation "the 5 and 3’ ends’" in line 13. There is insufficient antecedent basis for this limitation in the claim.
Claims 60-90 depend from claim 59 and are therefore included in this rejection.
Claim 80 recites the limitation “the mixture” in line 9. There is insufficient antecedent basis for this limitation in the claim.
Claims 81-89 depend from claim 80 and are therefore included in this rejection.
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.
Claim 59-71, 74, 76-79 and 90 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Betts et al. (U.S. Patent Application Publication 2017/0327882 A1, published November 16, 2017), cited on the IDS filed November 14, 2025.
Regarding claim 59, Betts teaches a method of preparing a library of nucleic acids (Page 8, [0059] and Page 12, [0084]). Betts teaches providing a sample of nucleic acids comprising at least one sequence of interest (Page 2, [0019]). Betts teaches contacting the sample of nucleic acids with a terminal transferase and NTPs under conditions sufficient to transfer NTPs to the 3' end of the nucleic acids thereby generating a plurality of nucleic acids comprising 3' tails (Page 4, [0036] and Page 5, [0040]). Betts teaches contacting the plurality of nucleic acids comprising 3' tails with a plurality of first adapters and a reverse transcriptase under conditions sufficient for first strand complementary DNA (cDNA) synthesis to occur, thereby generating a plurality of cDNAs (Page 3, [0025] and [0027], Pages 4-5, [0034]-[0040], Pages 7-8, [0054]-[0055] and [0059], Page 9, [0067], Page 10-11, [0070]-[0074] and Pages 13-14, [0092]). Betts teaches contacting the plurality of cDNAs with a second adapter under conditions sufficient to allow generation of double stranded DNA from the plurality of cDNAs to generate a plurality of double stranded DNAs (Page 4, [0033]-[0035], Page 8, [0059], Pages 12-13, [0084] and Page 14, [0100]). Betts teaches preparing a library of nucleic acids with adapters at the 5' and 3' ends (Page 1, [0005]), Pages 2-3, [0021], Pages 6-7, [0050], Page 8, [0058]-[0059], Page 10, [0073], Page 11, [0075], Page 12, [0082] and Pages 12-13, [0084]).
Regarding claim 60, Betts teaches the plurality of first adapters comprise a sequence complementary to the 3' tails and a first UMI sequence (Page 4, [0034], Page 6, [0046], Page 8, [0058], Page 9, [0067] and Pages 10-11, [0071]-[0074]).
Regarding claim 61, Betts teaches the plurality of second adapters comprise a second UMI and a polyG sequence (Page 5, [0040], Page 6, [0046], Page 8, [0058], Page 9, [0067] and Pages 10-11, [0071]-[0074]).
Regarding claim 62, Betts teaches the nucleic acids comprise ribonucleic acids (RNAs) (Page 3, [0026]-[0028]).
Regarding claim 63, Betts teaches the reverse transcriptase comprises Moloney Murine Leukemia Virus (MMLV) reverse transcriptase (Page 5, [0038]-[0039]).
Regarding claim 64, Betts teaches (d) comprises adding a polymerase (Page 4, [0033]-[0035], Pages 12-13, [0084]-[0085] and Page 14, [0100]).
Regarding claim 65, Betts teaches step (d) comprises PCR amplification of the plurality of double stranded DNAs (Page 4, [0033]-[0035], Pages 12-13, [0084]-[0085] and Page 14, [0100]).
Regarding claim 66, Betts teaches the first unique molecular identifier sequence (UMI) comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 nucleotides (Page 6, [0046]).
Regarding claim 67, Betts teaches the first UMI is a random sequence (Page 6, [0046]).
Regarding claim 68, Betts teaches the first adapter comprises a sequence of a first sequencing adapter (Page 6, [0047]).
Regarding claim 69, Betts teaches the second UMI comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 nucleotides (Page 6, [0046]-[0047]).
Regarding claim 70, Betts teaches the second UMI is a random sequence (Page 6, [0046]).
Regarding claim 71, Betts teaches the second adapter comprises a sequence of a second sequencing adapter (Page 11, [0074], Pages 11-12, [0080]).
Regarding claim 74, Betts teaches the sample is degraded (Page 9, [0068] and Page 11, [0080]).
Regarding claim 76, Betts teaches the at least one sequence of interest comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 500, 1000, 10,000, 50,000, 100,000 or 200,000 unique sequences of interest (Page 2, [0019]).
Regarding claim 77, Betts teaches the sample of nucleic acids comprises ribonucleic acids (RNAs) (Page 3, [0026]-[0028]).
Regarding claim 78, Betts teaches sequencing the library of nucleic acids (Pages 12-13, [0084]).
Regarding claim 79, Betts teaches the sequencing comprises high-throughput sequencing (Pages 12-13, [0084]).
Regarding claim 90, Betts teaches the plurality of cDNAs comprise 3' polyC sequences (Page 5, [0040]).
Betts teaches each and every limitation of claims 59-71, 74 and 76-79, and therefore Betts anticipates claims 59-71, 74, 76-79 and 90.
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 72 and 73 are rejected under pre-AIA 35 U.S.C. 103 as being unpatentable over Betts et al. (U.S. Patent Application Publication 2017/0327882 A1, published November 16, 2017), cited on the IDS filed November 14, 2025, as applied to claims 59-71, 74, 76-79 and 90 above, in view of Zong (WIPO International Publication 2017/173328 A1, published October 05, 2017), cited on the IDS filed November 14, 2025.
Regarding claims 72 and 73, Betts teaches a selectable marker that is a genetic element that confers on a host organism resistance to a selection agent (Page 9, [0064]).
Betts does not teach or suggest specifically that the marker comprises a single nucleotide polymorphism (SNP), a miniSTR (mini short tandem repeat), a mitochondrial marker, a Y chromosome marker, a taxonomic marker, or a disease trait marker. Betts does not teach or suggest the disease trait marker comprises a marker for pathogenicity, virulence, resistance or strain identification.
Zong teaches a method of preparing a library of nucleic acids (Pages 4-5, [0011] and Page 40, [0132]). Zong teaches providing a sample of RNA molecules comprising at least one sequence of interest (Page 2, [0005]-[0006]). Zong teaches contacting the sample of nucleic acids with a terminal transferase and NTPs under conditions sufficient to transfer NTPs to the 3' end of the nucleic acids thereby generating a plurality of nucleic acids comprising 3' tails (Pages 6-7, [0016] and Pages 39-40, [0130]-[0131]). Zong teaches contacting the plurality of nucleic acids comprising 3' tails and a reverse transcriptase under conditions sufficient for first strand complementary DNA (cDNA) synthesis to occur, thereby generating a plurality of cDNAs (Page 3, [0009], Pages 39-40, [0129]-[0130]). Zong teaches the plurality of cDNAs comprise 3' polyC sequences (Page 10, [0029] and Page 20, [0066]). Zong teaches contacting the plurality of cDNAs with a second adapter comprising a polyG sequence under conditions sufficient to allow generation of double stranded DNA from the plurality of cDNAs to generate a plurality of double stranded DNAs (Page 3, [0009] and Page 20, [0066]-[0068]). Zong teaches preparing a library of nucleic acids with adapters at the 5' and 3' ends (Page 8, [0020], Page 40, [0132] and Page 43, [0145]). Zong teaches a single nucleotide polymorphism (SNP) and a disease trait marker (Page 43, [0145] and Pages 29-30, [0098]). Zong teaches the disease trait marker comprises a marker for pathogenicity (Pages 29-30, [0098]). Zong teaches one or more of the amplified amplicons may be analyzed for the emergence of one or more of mutations or insertions, or deletions associated with antibiotic resistance (Page 10, [0025]). Zong teaches this allows panning or other screening methods to generate a sample of one or more immune cells before the total RNA is amplified and sequenced (Pages 29-30, [0098]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the invention to have modified the teachings of Betts by using the markers as taught by Zong without unexpected or surprising results because both Betts and Zong teach markers that are genetic elements that confer on a host organism resistance to a selection agent. Additionally using these methods would allow panning and/or other screening methods to generate a sample of one or more immune cells before the total RNA is amplified and sequenced as taught by Zong (Pages 29-30, [0098]).
Claims 75 and 80-89 are rejected under pre-AIA 35 U.S.C. 103 as being unpatentable over Betts et al. (U.S. Patent Application Publication 2017/0327882 A1, published November 16, 2017), cited on the IDS filed November 14, 2025, as applied to claims 59-71, 74, 76-79 and 90 above, and in view of Carpenter et al. (WIPO International Publication Number WO2016/100955 A2, published June 23, 2016), cited on the IDS filed November 14, 2025.
Regarding claim 75, Betts teaches a nucleic acid sample as discussed above.
Regarding claim 80, Betts teaches a method of preparing a library of nucleic acids as discussed above.
Regarding claim 81, Betts teaches PCR amplifying the library of nucleic acids following step (c) (Page 4, [0033]-[0035], Pages 12-13, [0084]-[0085] and Page 14, [0100]).
Regarding claim 82-87, Betts teaches a method of preparing a library of nucleic acids as discussed above.
Regarding claim 88, Betts teaches sequencing the library of nucleic acids (Pages 12-13, [0084]).
Regarding claim 89, Betts teaches the sequencing is high throughput sequencing (Pages 12-13, [0084]).
Betts does not teach or suggest the sample is a forensics sample. Betts does not teach or suggest providing a plurality of guide nucleic acid (gNA)-CRISPR/Cas system protein complexes. Betts does not teach or suggest the gNAs are configured to hybridize to at least one sequence targeted for depletion. Betts does not teach or suggest mixing the library of nucleic acids with the plurality of gNA-CRISPR/Cas system protein complexes. Betts does not teach or suggest at least a portion of the gNA-CRISPR/Cas system protein complexes hybridize to the at least one sequence targeted for depletion. Betts does not teach or suggest incubating the mixture to cleave the at least one sequence targeted for depletion. Betts does not teach or suggest the CRISPR/Cas system protein comprises Cpfl, Cas9, Cas3, Cas8a-c, Cas10, CasX, CasY, Cas13, Casl4, Csel, Csyl, Csn2, Cas4, Csm2, Cm5 or a combination thereof. Betts does not teach or suggest the CRISPR/Cas system protein comprises Cas9, Cpfl or a combination thereof. Betts does not teach or suggest CRISPR/Cas system protein is a Cas9 or Cpfl nickase. Betts does not teach or suggest CRISPR/Cas system protein is thermostable. Betts does not teach or suggest the gNAs are guide deoxyribonucleic acids (gDNAs) or guide ribonucleic acids (gRNAs). Betts does not teach or suggest the plurality of gNAs comprise at least 2, 10, 102, 103,104,105 or 106 unique gNAs.
Carpenter teaches the sample is a forensic sample (Page 15, [0021]). Carpenter teaches providing a plurality of guide nucleic acid (gNA)-CRISPR/Cas system protein complexes, wherein the gNAs are configured to hybridize to at least one sequence targeted for depletion (Page 14, [0021]). Carpenter teaches mixing nucleic acids with the plurality of gNA-CRISPR/Cas system protein complexes (Page 14, [0021]). Carpenter teaches at least a portion of the gNA-CRISPR/Cas system protein complexes hybridize to the at least one sequence targeted for depletion (Page 14, [0021]). Carpenter teaches incubating the sample to cleave the at least one sequence targeted for depletion (Page 14, [0021]). Carpenter teaches PCR amplifying the library of nucleic acids following step (g) (Page 11, [0016]). Carpenter teaches the CRISPR/Cas system protein comprises Cpfl, Cas9, Cas3, Cas8a-c, CaslO, Csel, Csyl, Csn2, Cas4, Csm2, Cm5 or a combination thereof (Page 5, [0010]). Carpenter teaches the CRISPR/Cas system protein comprises Cas9, Cpfl or a combination thereof. Carpenter teaches CRISPR/Cas system protein is a Cas9 or Cpfl nickase (Page 39, [0165]). Carpenter teaches CRISPR/Cas system protein is thermostable (Page 5, [0010]). Carpenter teaches the gNAs are guide ribonucleic acids (gRNAs) (Page 14, [0021]). Carpenter teaches the plurality of gNAs comprise at least 2, 10, 102, 103,104,105 or 106 unique gNAs (Page 33, [0138] and Page 54, [0210]-[0211]). Carpenter teaches sequencing the library of nucleic acids (Page 22, [0066]-[0067]). Carpenter teaches the methods and compositions, applicable to biological and forensic samples, for depleting targeted nucleic acid sequences, enriching for sequences of interest, and/or partitioning of sequences from a sample (Page 2, [0009]). Carpenter teaches the methods and compositions provided achieve a low cost and more efficient method for metagenomic analysis (Page 2, [0007]).
As a common field of endeavor both Betts and Carpenter disclose a method for sequencing nucleic acids.
It would have been obvious to one having ordinary skill in the art before the effective filing date of the invention to have modified the method Betts by mixing the library of nucleic acids as taught by Betts with the nucleic acid sample of Carpenter with guide nucleic acid (gNA)-CRISPR/Cas system protein complexes wherein the gNAs are configured to hybridize to at least one sequence targeted for depletion because Carpenter teaches methods and compositions, for depleting targeted nucleic acid sequences, enriching for sequences of interest, and/or partitioning of sequences from a sample. This would allow for a lower cost and more efficient method for metagenomic analysis as taught by Carpenter (Page 2, [0007] and [0009]). Additionally Carpenter teaches methods and compositions provided within are applicable to biological and forensic samples (i.e., biological sample of Betts) (Page 2, [0009]).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA DANIELLE PARISI whose telephone number is (571)272-8025. The examiner can normally be reached Mon - Friday 7:30-5:00 Eastern with alternate Fridays off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
