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 .
DETAILED ACTION
Acknowledgement is hereby made of receipt and entry of the communication filed on Sep. 5, 2025. Claims 1-10 and 17-20 are pending and currently examined.
Election/Restrictions
Applicant's election without traverse of Group I (Claims 1-10 and 17-20), directed to a method of detecting an integration pattern of HPV in genome DNA of a subject, in the reply filed on Sep. 5, 2025, is acknowledged. Non-elected claims 11-16 are canceled.
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 of this title, 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 1-10 and 17-20 are rejected under 35 U.S.C. 103 as being unpatentable over Artesi et al. (bioRxiv preprint doi: https://doi.org/10.1101/558130; this version posted February 24, 2019; submitted in IDS filed on Jun 22, 2022) in view of Groves et al. (J Pathol 2018; 245: 9–18; submitted in IDS filed on Sep. 13, 2022).
These claims are directed to a method for detecting an integration pattern of human papillomavirus (HPV) in genomic DNA of a subject, the method comprising: (a) fragmenting genomic DNA isolated from a sample of the subject; (b) circularizing the DNA fragments to generate circular DNA; (c) removing non-circularized DNA fragments; (d) linearizing the circular DNA using an RNA-guided DNA endonuclease and at least one guide RNA or at least one pool of guide RNAs, which target a region in the viral genome, to generate linearized DNA molecules; (e) amplifying the linearized DNA molecules by an inverse amplification reaction using a pair of primers arranged about and oriented outwardly with respect to the linearization site; (f) sequencing the amplified DNA; (g) mapping the sequenced DNA to human genomic DNA sequence; and (h) optionally mapping the sequenced DNA to the HPV genome.
Artesi teaches a Pooled CRISPR Inverse PCR sequencing (PCIP-seq) method that can be used to simultaneously sequencing retroviral insertion points and the associated provirus in thousands of cells with long reads. Artesi teaches that the method leverages long reads on the Oxford Nanopore MinION platform to sequence the insertion site and its associated provirus. The authors have applied the technique to three exogenous retroviruses, HTLV HTLV-1, HIV -1 and BLV, as well as endogenous retroviruses in both cattle and sheep. The long reads of PCIP-seq improved the accuracy of insertion site identification in repetitive regions of the genome. See Abstract.
Specifically, about the PCIP-seq, Artesi teaches that high molecular weight DNA was sheared to ~8kb, followed by end-repair; intramolecular circularization was achieved by DNA Ligase; remaining linear DNA was removed with DNAse; guide RNAs were designed using chop (http://chopchop.cbu.uib.no/index.php ); selective linearization reactions were performed with the Cas-9 nuclease; PCR primers flanking the cut sites were designed using primer3 (http://bioinfo.ut.ee/primer3/ primer3/); primers were tailed to facilitate the addition of Oxford Nanopore indexes in a subsequent PCR reaction. The linearized fragments were PCR amplified with LongAmp Taq DNA Polymerase (New England Biolabs) and a second PCR added the appropriate Oxford Nanopore index. PCR products were visualized on a 1% agarose gel and quantified on a Nanodrop spectrophotometer. Indexed PCR products were multiplexed and Oxford Nanopore libraries prepared with either the Ligation Sequencing Kit 1D (SQK SQK-LSK108) or 1D^2 Sequencing Kit (SQK SQK-LSK308). The result resulting libraries were sequence sequenced on Oxford Nanopore MinION R9.4 or R9.5 flow cells respectively and base called using albacore2.3.1. Only the 1D reads from both flow cell versions were used. See para spanning pages 13 and 14. Accordingly, Artesi teaches a method for detecting an integration pattern of a retrovirus in genomic DNA of a subject, comprising the steps as specified in claim 1.
Artesi further teaches that it is estimated that 10-15% of all cancers have a viral cause, HTLV-1 only represent represents a small fraction of this number, with human papillomaviruses (HPV) and hepatitis B virus (HBV) playing a much bigger role. These viruses are often found integrated into the genome of the cancers they provoke. In contrast to retroviruses, the viral sequence immediately adjacent to the integration site is not consistent, reducing the utility of ligation mediated PCR approaches. As a consequence, probe-based capture methods are required to obtain a genome-wide picture of integration sites in these viruses. Using PCIP-seq guides and primers, multiplexed at different points in the viral genome, combined with long-reads, it will be possible to identify the viral insertion site while also sequencing the virus. This could open many more viral integration sites and viral sequences to interrogation, while also exploring precancerous tissue for rare viral integrations. See page 9, para 3. These teachings indicate that application of the PCIP-seq method to the study of HPV integration in host genomic DNA is contemplated and guidance provided.
Groves et al. (J Pathol 2018; 245: 9–18; submitted in IDS filed on Sep. 13, 2022) reviews the studies on HPV genome integration in squamous carcinogenesis based on next-generation sequencing studies. It provides teachings necessary for the design and analysis of studies on HPV genome integrations of clinical relevance. See throughout the article.
It would have been prima facie obvious for one of skill in the art before the effective filing date of the current invention to extent the studies of Artesi or to combine the teachings of Artesi and Groves to arrive at the invention as claimed. One would have been motivated to apply the PCIP-seq method to the study of HPV integration in host genomic DNA, as suggested in Artesi.
Artesi is silent on the sample types, HPV types and HPV genes used in studies of HPV integration specified in claims 6-8; Artesi is also silent on the guide RNA sequences specified in claims 9-10. Regarding claims 6-8, studies on HPV genome integration are well known at the time of study and, therefore, one of skill in the art would have found it obvious to use the sample types and target HPV types and genes (e.g., E6 and E7) deemed as proper at the time of invention. Regarding claims 9-10, Artesi provides guidance on how guide RNA can be designed for the PCIP-seq method, one of skill in the art would have found it obvious to design guide RNAs for HPV integration studies, including the sequences as claimed, based on combined teachings of Artesi and Groves. The claimed sequences can be arrived through routine experimental optimization unless there is evidence that the claimed sequences are critical.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NIANXIANG (NICK) ZOU whose telephone number is (571)272-2850. The examiner can normally be reached on Monday - Friday, 8:30 am - 5:00 pm, EST. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, JANET ANDRES, on (571) 272-0867, can be reached. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/NIANXIANG ZOU/
Primary Examiner, Art Unit 1671