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 .
Applicants filed a Preliminary Amendment on September 12, 2023, in which new claims 2-17 were added. Thus, claims 1-17 are pending in this application, and are under examination.
Information Disclosure Statement
The Information Disclosure Statements filed February 20, 2023 and September 15, 2023 (2) have been considered. It is noted that the February 20, 2023 and the single page September 15, 2023 Information Disclosure Statements appear to be the same. Initialed/signed copies of both are attached.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). The sequences at page 23, lines 2 and 14 (LAGLIDADG) do not have sequence identifiers.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings (Figures 4, 20, 23, and 40) are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The use of the terms GIBSON ASSEMBLY at page 8, line 19; page 51, line 31; page 84, line 10; page 85, at lines 6-7, 7, 9, 11, 17, 22, and 24; and page 86, line 7; PRESTOBLUE at page 9, lines 4 and 14; and page 87, lines 23 and 30; PIGGYBAC at page 15, line 9; PIGGYBAC at page 15, line 9; SLEEPING BEAUTY at page 15, line 10; TALEN at page 23, lines 7, 11, 25, 28, and 33 and page 32, line 9; PICOGREEN at page 39, lines 29 and 31 and page 47, line 29; ENSPIRE at page 39, line 32 and page 87, line 27; Q5 at page 40, lines 10 and 16 and page 80, lines 3, 4, and 6; HOT START at page 10, line 10; page 46, line 28; and page 80, lines 3, 4, an 6; ZYMO at page 40, line 28, page 82, line 8; and page 83, lines 6 and 13; NANODROP at page 40, line 32; page 45, line 7; and page 46, line 14; SYBR at page 40, line 35; at page 45, line 35; and at page 49, line 24; LOBIND at page 41, lines 9 and 34; at page 42, line 29; at page 43, line 3; at page 44, lines 8, 16, 24 and 27; at page 46, line 27; and at page 47, lines 13, 20, and 34; EPICENTRE at page 41, lines 15 and 17; CUTSMART at page 42, lines 25 and 32; SEPHACRYL at page 44, line 9; NEBNEXT at page 44, line 11; GENELUTE at page 44, line 28 and page 43, line 4; GENEPULSER at page 42, line 1 and page 48, line 34; DNA CLEAN AND CONCENTRATOR at page 47, lines 7 and 26; AMPURE at page 48, lines 13 and 28; NEXTERA at page 49, line 21; HISEQ at page 49, line 28 and page 51, line 23; SUPERSCRIPT at page 51, line 6 and page 58, line 7; INTELLICYT at page 88, line 13; and ONETAQ at page 89, lines 15 and 17; which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
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 5-6 and 11 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.
At claim 5, line 2, improper Markush language is used. At line 2, “or” should be changed to “and” in order for the Markush group to be a closed group.
At claim 6, line 1, it is not clear where in the DNAs the barcode is being inserted. Is there a particular location or sequence into which the barcode should (or should not) be inserted?
At claim 11, line 2 and line 3, it is not clear what is meant by “at or near one end” or “at or near the other end” of the transposon cassette. How close to the end of one end and/or the other end must the first and second recognition sequences be?
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 1-4, 6, and 11-17 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-7 of U.S. Patent No. 11,584,931 in view of Hansen et al. (U.S. Patent Application Publication No. 2006/0019301, published January 26, 2006, and cited in the Information Disclosure Statement filed September 15, 2023).
Although the claims at issue are not identical, they are not patentably distinct from each other because the ‘931 patent claims a method of generating and identifying a defective interfering particle and the instant application claims a method of generating a deletion library where the methods have overlapping steps.
Regarding claims 1, 12, and 17 the ‘931 patent claims that the method recites the steps of inserting a target sequence for a sequence specific DNA endonuclease into a population of circular target viral DNAS, each comprising a viral genome to generate a population of sequence-inserted viral DNAS; contacting the population of DNAs with the endonuclease to generate a population of cleaved linear viral DNAs; contacting the cleaved linear viral DNA with an exonuclease to generated deletion DNAs; circularizing the deletion DNAs to generate a library of circularized deletion DNA; and sequencing members of the library to identify defective interfering particles (DIPS) (claims 1-2).
Regarding claim 2, the ‘931 patent claims that the circular target DNAs comprise a viral genome (claim 1).
Regarding claims 3 and 14, the ‘931 patent claims introducing members of the library into mammalian cells and assaying for viral infectivity (claim 5).
Regarding claim 4, the ‘931 patent claims sequencing members of the library to identify defective interfering particles (DIPS) (claim 1).
Regarding claim 6, the ‘931 patent claims insertion of a barcode sequence prior to or simultaneously with circularization of the deletion DNAs (claim 4).
Regarding claim 13, the ‘931 patent claims that the population of linear DNA molecules comprises one or more PCT products, one or more linear viral genomes, and/or one or more restriction digest products (claim 3)
Regarding claim 15, the ‘931 patent claims generating from the library of circularized deletion DNAs, at least one of linear double stranded DNA products; linear single stranded DNA products, linear single stranded RNA products, and linear double stranded RNA products (claim 6).
Regarding claim 16, the ‘931 patent claims introducing the linear dsDNA products, the linear ssDNA products, the linear ssRNA products, and/or the linear dsRNA products into mammalian cells and assaying for viral infectivity (claim 7).
The ‘931 patent does not claim insertion of a transposon cassette comprising a target sequence for a sequence specific DNA endonuclease into a population of circular target DNAs.
Regarding claim 1, Hansen discloses a method of producing mutants of a polynucleotide comprising isolating libraries of constructs where the constructs have an inserted transposon and ultimately isolating mutants of the polynucleotide from the insertion library (paragraphs [0017]-[0021]). Hansen discloses that the mutation can be a deletion mutation (paragraphs [0017]-[0021]).
Regarding claim 11, Hansen discloses that the transposon insertion can include recombination sites flanking the 5’ and 3’ ends of the polynucleotide, which is interpreted as comprising first and second recognition sites at or near the end of both ends of the transposon cassette (paragraphs [0017]-[0021]).
It would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to employ Hansen’s transposon to insert the target sequence into the circular target DNAs of the ‘931 patent because whether inserted by Hansen’s transposon or by the non-specific insertion method of the ‘931 patent, the results are the same. Because the insertion of the target sequence by any means results in a population of target sequences having a sequence that can be recognized by a sequence-specific endonuclease, the claims are not deemed to be patentably distinct.
It is noted that the instant application is a continuation application of the ‘931 patent. Should Applicants amend the Application Data Sheet to be a divisional application of the ‘931 patent, this rejection will be withdrawn. Alternatively, a Terminal Disclaimer can be filed.
Claim 5 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-7 of U.S. Patent No. 11,584,931 in view of Hansen et al. (U.S. Patent Application Publication No. 2006/0019301, published January 26, 2006, and cited in the Information Disclosure Statement filed September 15, 2023), as applied to claims 1-4, 6, and 11-17 above, and further in view of Gaj et al. (31(7) Trends in Biotechnology 397-405 (2013)).
The ’931 patent claims a method of generating and identifying a defective interfering particle and Hansen discloses the use of transposons to provide target sequences for generating deletion mutants.
The ‘931 patent does not claim the specific sequence specific endonucleases.
Gaj discloses a variety of sequence specific endonucleases that can be used for genome engineering (abstract). Gaj discloses zinc finger nucleases, transcription activator-like effector nucleases, and CRISPR/Cas-based RNA-guided DNA endonucleases (abstract).
It would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to use the endonucleases of Gaj in the method claimed/disclosed by the ‘931 patent and Hansen because the endonucleases of Gaj are well-known sequence specific endonucleases that can be used for genome editing. Thus, it would have been obvious to one with ordinary skill in the art to substitute one well-known endonucleases of Gaj for the endnuclease in the method of the ‘931 patent and Hansen because each of the endonucleases would be interchangeable in the method of generating a deletion library. One of ordinary skill in the art would have been able to switch any of the well-known nucleases with a predictable and reasonable expectation of success.
It is noted that the instant application is a continuation application of the ‘931 patent. Should Applicants amend the Application Data Sheet to be a divisional application of the ‘931 patent, this rejection will be withdrawn. Alternatively, a Terminal Disclaimer can be filed.
Claims 7-10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-7 of U.S. Patent No. 11,584,931 in view of Hansen et al. (U.S. Patent Application Publication No. 2006/0019301, published January 26, 2006, and cited in the Information Disclosure Statement filed September 15, 2023), as applied to claims 1-4, 6, and 11-17 above, and further in view of Thomas (253(2) The Journal of Biological Chemistry 424-429 (1978)) and Lovett (4(2) EcoSal Plus 1-45 (2014)).
The ’931 patent claims a method of generating and identifying a defective interfering particle and Hansen discloses the use of transposons to provide target sequences for generating deletion mutants.
The ‘931 patent does not claim the specific exonucleases.
Regarding claims 7-8, Thomas discloses a variety of DNA exonuclease that play important metabolic roles in replication, recombination, and repair (page 424, column 1, first paragraph). Thomas discloses that DNA polymerase I is an exonuclease having both 3’ to 5’ and 5’ to 3’activity (abstract). Thomas discloses the T4 DNA polymerase (abstract).
Lovett discloses a variety of DNA exonucleases that hydrolyze phosphodiester bonds in DNA from a free end and have roles in DNA repair, genetic recombination, and mutation avoidance (abstract).
Regarding claim 8, Lovett discloses that the exonucleases can a 5’-3’ exonuclease and a 3’-5’ exonuclease (Table 1).
Regarding claim 9, Lovett discloses that the exonucleases can be RecJ (Table 1).
Regarding claim 10, Lovett discloses that single stranded binding proteins (SSB) can stimulate the ability of exonucleases, including RecJ, to bind and digest DA (pages 13-15).
It would have been obvious to one with ordinary skill in the art before the effective filing date of the claimed invention to use the exonucleases of Thomas and Lovett in the method claimed/disclosed by the ‘931 patent and Hansen because the exonucleases of Thomas and Lovett are well-known exonucleases. Thus, it would have been obvious to one with ordinary skill in the art to substitute one well-known exonucleases of Thomas and/or Lovett in the method of the ‘931 patent and Hansen because each of the exonucleases would be interchangeable in the method of generating a deletion library. One of ordinary skill in the art would have been able to switch any of the well-known nucleases with a predictable and reasonable expectation of success.
It is noted that the instant application is a continuation application of the ‘931 patent. Should Applicants amend the Application Data Sheet to be a divisional application of the ‘931 patent, this rejection will be withdrawn. Alternatively, a Terminal Disclaimer can be filed.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Huang (27 Annual Review of Microbiology 101-118 (1973), and cited in the Information Disclosure Statement filed September 15, 2023) provides a background discussion relating to viral systems that contain defective interfering particles.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NANCY J LEITH whose telephone number is (313)446-4874. The examiner can normally be reached Monday - Thursday 8:00 AM - 6:30 PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, NEIL HAMMELL can be reached at (571) 270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
NANCY J. LEITH
Primary Examiner
Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636
Prosecution Insights