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
This application 17/758,656 filed on 07/12/2022 is a 371 national phase of PCT/US2021/013598 filed on 01/15/2021, and claims the benefit of provisional U.S. Patent Application No. PRO 63/009,603, filed on 04/14/2020 and provisional U.S. Patent Application No. PRO 62/962,777, filed on 01/17/2020.
The priority date of claims 23-27, 29-36 and 39 is determined to be 01/17/2020, the filing date of PRO 62/962,777.
The priority date of claims 37-38 and 40-42 is determined to be 04/14/2020, the filing date of PRO 63/009,603 because the provisional application 62/962,777, filed on 01/17/2020 does not support the limitations recited in those claims. For instance, no support can be found in provisional application 62/962,777 filed on 01/17/2020 regarding the limitation “wherein the isolated cleaved affinity
molecule-coupled double stranded DNA molecule comprises a long read sequencing nucleic acid” recited in newly added claim 37 filed on 01/17/2023.
Status of Claims
Applicant’s amendments to claims filed 11/06/2025 in response to the Non-Final Rejection mailed 05/06/2025 are acknowledged.
Claims 23 and 29 are amended.
Claim 28 has been canceled.
Claims 23-27 and 29-42 are pending and under examination.
Response to Remarks filed 11/06/2025
The amendments and arguments presented in the papers filed 11/06/2025 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 05/06/2025 listed below have been reconsidered as indicated.
a) The objections to the specification regarding the presence of a hyperlink and the use of trade names or marks are withdrawn in view of the amendments to the specification.
b) The rejection of claims 23-27 and 32-40 under 35 U.S.C. 102 as being as being anticipated by Mandell et al. (US PGPub 20190136303, published on 05/09/2019 for US application number 16/099,953, with PCT/US2017/032021) are withdrawn in view of the amendments to the claims.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Claim Objections
Claim 24 is objected to because of the following informalities: Claim 24 recites the limitation “isolating in step (d)” from claim 23. Claim 23 has been amended to recite “(d) removing the cleaved ---“. Appropriate correction is required.
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 23-27 and 29-40 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Mandell et al. (US PGPub 20190136303) in view of Wilson (US PGPub 20170362639).
These are new rejections necessitated by claim amendments filed on 11/06/2025.
Regarding claim 23, Mandell teaches methods for enriching or amplifying polynucleotides using CRISPR-Cas systems (para 1), the method comprising embodiments that include: a double-stranded DNA (dsDNA) target nucleic acid (para 79) and ligating a biotinylated adapter (i.e. affinity molecule) to the first double-stranded DNA break end (para 87), which reads on forming the limitation of an affinity molecule-coupled double stranded DNA molecule; Mandell further teaches adding magnetic streptavidin beads (i.e. affinity molecule binding agents) to enrich biotinylated target nucleic acid (para 80), which reads on the limitation of a captured affinity molecule-coupled double stranded DNA molecule; contacting the target double-stranded nucleic acid with an endonuclease system (para 60). Mandell states the method can be used to isolate DNA fragments from genomic DNA by selective amplification of a specific region of DNA (para 180). Mandell also teaches using bead elution to pull down (i.e. removal) cleaved DNA fragments (para 235). Mandell teaches the use of the method to generate a nucleic acid library (paras 96, 185).
Mandell teaches the ligation of biotinylated adapters (affinity molecules) on one end of a target nucleic acid.
However, Mandell does not teach selective ligation of the affinity molecule to one end of the double-stranded DNA molecule where the one end is the 3’ end.
Wilson teaches methods for generating asymmetrically-tagged nucleic acid constructs for downstream genetic analysis (para 5). Wilson teaches the method comprises attaching a hairpin adapter to the 5’ ends of a double-stranded nucleic acid fragment to produce a first ligation product and ligating a second adapter to the end opposite the hairpin adapter (i.e.’ the 3’ end) (para 7). Wilson further teaches the second adapter can include capture moieties such as biotin (para 45).
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 Mandell and Wilson to arrive at the instantly claimed method with a reasonable expectation of success. The modification would have entailed using the method of asymmetrically labelling nucleic acids as in Wilson in the method of Mandell to generate the affinity molecule-coupled double stranded DNA molecule. The ordinary artisan would have been motivated to use the asymmetrically labeled nucleic acids of Wilson for the advantage of, for example, incorporating different functionalities at each end (para 78). In addition, it would have been obvious to the ordinary artisan that the known techniques of the cited prior art could have been combined with predictable results because both Mandel and Wilson relied on the known techniques of adapter ligation and capture. 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 24, Mandell teaches cleaved DNA fragments detected from bead elution (para 235).
Regarding claim 25, Mandell teaches enriching or amplifying a target DNA sequence using endonuclease (i.e. enzymes) systems, e.g., CRISPR-Cas systems (para 7) and that “CRISPR-Cas system” refers to an enzyme system including a guide RNA sequence that contains a nucleotide sequence complementary or substantially complementary to a region of a target polynucleotide, and a protein with nuclease activity (para 118).
Regarding claim 26, Mandell teaches that the endonuclease system provided herein is derived from a CRISPR-Cas system (para 231) and includes Cas proteins such as Cas9 (para 234).
Regarding claim 27, Mandell teaches ligating a biotinylated adapter to the end of DNA with a first double-stranded break (para 87).
Regarding claims 29-31, Mandell does not teach that blocking prevents affinity molecule tagging (claim 29) via a hairpin adapter (claim 30) or dephosphorylating one strand (claim 31).
Wilson teaches methods for generating asymmetrically-tagged nucleic acid constructs for downstream genetic analysis (para 5).
Regarding claim 29, Wilson teaches attaching a hairpin adapter to the 5’ ends of a double-stranded nucleic acid fragment to produce a first ligation product (para 7), thus satisfying the requirement of preventing ligation to the one end of the double-stranded nucleic acid.
Regarding claim 30, Wilson teaches attaching a hairpin adapter to the 5’ ends of a double-stranded nucleic acid fragment (para 7), thus preventing a second adapter (i.e. affinity molecule) attaching to that end as required in claim 30.
Regarding claim 31, Wilson teaches dephosphorylating the 5’ ends of a nucleic acid fragment (para 7) which is processed to generate an asymmetrically-tagged product (para 64). Thus preventing coupling on one end of the double-stranded nucleic acid as required by claim 31.
It would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Mandell and Wilson to arrive at the instantly claimed method/system with a reasonable expectation of success. The ordinary artisan would have been motivated to use the asymmetrically labeled nucleic acids of Wilson for the advantage of , for example, incorporating different functionalities at each end (para 78). In addition, it would have been obvious to the ordinary artisan that the known techniques of the cited prior art could have been combined with predictable results because both Mandell and Wilson relied on the known techniques of adapter ligation and capture.
Regarding claim 32, Mandell teaches the adapter (i.e. affinity molecule) is a biotinylated adapter (i.e. a biochemical tag) (para 87).
Regarding claim 33, Mandell teaches the adapter (i.e. affinity molecule) is a biotinylated adapter (i.e. a biochemical tag) (para 87).
Regarding claim 34, Mandell teaches adding magnetic streptavidin beads (i.e. affinity molecule binding agents) (para 80).
Regarding claim 35, Mandell teaches adding magnetic streptavidin beads (i.e. affinity molecule binding agents) (para 80).
Regarding claim 36, Mandell teaches adding magnetic streptavidin beads (i.e. affinity molecule binding agents) (para 80).
Regarding claim 37, Mandell teaches sequencing the target nucleic acid or target nucleic acid fragments, including by nanopore sequencing (i.e. long read sequencing) (para 35). Mandell further explicitly teaches enrichment of long nucleic acid fragments (para 305)
Regarding claim 38, Mandell teaches sequencing the target nucleic acid or target nucleic acid fragments (para 35) and the addition of sequencing adapters (para 333)
Regarding claim 39, Mandell teaches that cleaved DNA fragments are detected from the bead elution (i.e. Purified by the magnetic streptavidin beads that enrich the target nucleic acid) (para 235).
Regarding claim 40, Mandell teaches that nucleic acids in the method include nucleic acids from DNA or RNA viruses (para 108).
Claims 41-42 are rejected under 35 U.S.C. 103 as being unpatentable over Mandell et al. (US PGPub 20190136303) in view of Wilson (US PGPub 20170362639) as applied to claims 23-27 and 29-40 above, and further in view of Schmid-Burgk et al. (BioRxiv. Posted 4/08/2020.17 pages. Retrieved from the internet on 4/30/2025: https://www. https://www.biorxiv.org/content/10.1101/2020.04.06.025635v1).
These rejections are modified as necessitated by the amendments to the claims.
Mandell teaches target nucleic acids include nucleic acids from DNA or RNA viruses (para 108) and Wilson teaches the double-stranded nucleic acid fragments can come from samples such as virus (para 44).
However, neither Mandell nor Wilson teaches the virus is an influenza virus, a coronavirus, a rhinovirus, a herpesvirus, or a human immunodeficiency virus (claim 41) or that the coronavirus is a SARS-CoV2 (claim 42).
Regarding claim 41, Schmid-Burgk teaches sequencing target nucleic acids that are the SARS-CoV-2 (coronavirus) genome (p. 4).
Regarding claim 42, Schmid-Burgk teaches sequencing target nucleic acids that are the SARS-CoV-2 (coronavirus) genome (p. 4).
Schmid-Burgk states the importance of having a method to detect COVID-19 (SARS-COV2) spread by sequencing during the pandemic (p.2, Summary).
It would therefore have been prima facie obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Mandell and Wilson with Schmid-Burgk to arrive at the instantly claimed method/system with a reasonable expectation of success. The ordinary artisan would have been motivated to sequence SARS-COV2 to help break the cycle of isolation and spread in the population during the covid-19 pandemic (p.2, Summary). In addition, it would have been obvious to the ordinary artisan that the known techniques of the cited prior art could have been combined with predictable results because all of Mandell, Wilson, and Schmid-Burgk relied on the known techniques of nucleic acid sequencing.
Response to Arguments against Claim Rejection - 35 U.S. C § 102
The response asserts that the amendments to claim 23 overcome the 35 U.S. C § 102 rejection of claims 23-27 and 32-40 (p. 6).
Applicant's arguments with respect to the rejection(s) of claim(s) 23-27 and 32-40 under 35 U.S. C § 102 over Mandell have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection for claims 23-27 and 29-40 is made over Mandell in view of Wilson as described above in the new rejections of the claims.
Response to Arguments against Claim Rejection - 35 U.S. C § 103
Claims 28-31
Because claim 28 is cancelled and the features of claim 28 are now found in claim 23 as amended, the applicant addresses the rejection as it may apply to claim 32 as amended. The response asserts a person of ordinary skill in the art does not have a reasonable expectation of success in achieving the claimed method based on the teaching of Mandell and Wilson and further that, while elements of the claim may be found in one of Mandell and/or Wilson, one of ordinary skill in the art would not necessarily expect success in creating a nucleic acid library using the claimed method (p. 7).
Applicant's arguments have been fully considered but are not persuasive.
It is the Examiner's position that Mandell in view of Wilson does teach the limitations of claim 23 and motivations to modify the cited art to arrive at the present claims as outlined in the rejections provided above
Claims 41-42
The response asserts that Mandell does not teach all of the elements of claim 23, much
less the combination of elements of claims 41-42, and Schmid-Burgk does not cure the abovementioned deficiencies of Mandell (p. 8).
Applicant's arguments have been fully considered but are not persuasive.
The rejection of claim 23 over Mandell in view of Wilson is presented above. No amendments were made to claims 41 or 42. It is the Examiner’s position that the limitations of claims 14 and 42 are taught by Schmid-Burgk and motivations to combine the elements of Schmid-Burgk with Mandell and Wilson are presented above.
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