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 .
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 - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825. This application contains a “Sequence Listing” as a PDF file (37 CFR 1.821(c)(2)) or as physical sheets of paper (37 CFR 1.821(c)(3)). A copy of the "Sequence Listing" in computer readable form (CRF) has been submitted; however, the content of the CRF does not comply with one or more of the requirements of 37 CFR 1.822 through 1.824, as indicated in the "Error Report" that indicates the "Sequence Listing" could not be accepted. Refer to attachment or document "Computer Readable Form (CRF) for Sequence Listing – Defective" dated 9/5/25.
Required response – Applicant must provide:
A replacement "Sequence Listing" part of the disclosure, as described above in item 1); together with
An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(b)(2);
A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.825(b)(5); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(b)(4).
If the replacement "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation-by-reference paragraph, 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 and
An amendment to the specification to remove the “Sequence Listing previously submitted as a PDF file (37 CFR 1.821(c)(2)) or as physical sheets of paper (37 CFR 1.821(c)(3))
If the replacement "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, Applicant must also provide:
A CRF in accordance with 1.821(e)(1) or 1.821(e)(2) as required by 37 CFR 1.825(b)(6)(ii); and
Statement according to item 2) a) or b) above.
The attached defective sequence listing indicates that applicant filed the sequence under ST.26 instead of ST.25. The instant application was filed on 11/19/18 and before the date of filing a sequence under ST.26.
Specification
The amendment to the specification filed on 9/4/25 has been entered.
Response to Arguments
Applicant’s arguments, see pages 4-8, filed 9/4/25, with respect to the rejections of claims 13-18 under 112 or 103 have been fully considered and are persuasive. NOTE: while the argument on page 8 is supposed to be directed against HU, the argument just repeats the argument for the rejection based on Court, US 2003/0224521 and Sharan. The rejections have been withdrawn because of the amendment to claim 13 to remove polynucleotide encoding a fluorescent protein. However, upon further consideration, a new ground(s) of rejection is made in view of the amendment to claims 13 and 17-18.
Claim Objections
Claim 13 is objected to because of the following informalities: the limitation ‘directly abuts the DSB’ appears to be redundant since the proximal homology arm is already next to the region of a DSB in the genome. The terms ‘directly abuts’ and ‘next to’ appear to be similar language. 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 14-18 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.
Claims 14-16 recite the limitation "the polynucleotide of claim 13(14,15)" in line 1. There is insufficient antecedent basis for this limitation in the claim. Claim 13 is directed to a composition comprising a double stranded linear donor polynucleotide.
Claims 17-18 recite the limitation "the linear donor polynucleotide of claim 13" in line 1. There is insufficient antecedent basis for this limitation in the claim. Claim 13 is directed to a composition comprising the double stranded linear donor polynucleotide.
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.
Claims 13-15 and 17-18 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Paix et al. (Methods, May 15, 2017, 121-122, 86-93, cited on an IDS). NOTE: there is one additional person (Andrew Falkmann) listed on the publication that is not listed as an inventor on the instant application. See MPEP 2152.
Paix et al. teach editing strategies, including crRNAs and repair templates, wherein one template is a PCR fragment, double stranded linear polynucleotide sequence, up to 1 kb (pages 88-89, Fig. 3). Inserting a PCR fragment into the DSB region would change at least one nucleotide base within 30 bases of the DSB of the target nucleic acid. The homology arms are 35 nucleotides in length. The method includes administering a Cas endonuclease, a guide RNA, and the PCR fragment to a cell.
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Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The broadest reasonable interpretation of the claimed invention reads on a composition comprising a double stranded linear polynucleotide comprising a nucleotide sequence flanked by a 5’ and 3’ homology arm, wherein the arms are substantially identical to nucleotides from a region of a target sequence to be edited. The linear polynucleotide broadly reads on a composition comprising an isolated polynucleotide or a cell comprising the polynucleotide (for example, the linear polynucleotide inserted into a circular nucleotide construct and cleaved in a cell resulting in the linear polynucleotide). The limitation ‘immediately next to a double-stranded break (DSB) in the genome to be edited and directly abuts the DSB’ is directed to an intended use of the claimed product. The limitation is directed to the product being used in a process that requires a DSB to the sequence in a genome. The specification does not appear to provide a definition of the term “immediately next to a DSB and directly abuts the DSB. However, Figure 8A indicates that immediately next and directly abuts could read on less than 30 bases from DSB. The limitation could embrace wherein the target sequence is capable of having a DSB. The limitation ‘genome’ does not appear to be define by the specification and broadly reads on the genome of a cell or a genome of a construct (e.g., plasmid). The 5’ arm is next to the region of the target sequence that will become a DSB. The 3’ arm is downstream from the nucleotide sequence. The 5’ and 3’ arm are between 30-35 bases in length.
Page 2 of the specification recites the limitation “wherein the template polynucleotide comprises an edit to the genome to be edited”. Page 11, lines 14-17 of the specification describes an “edit” as a desired modification to be introduced into the genome. An edit is any change in the genomic sequence that is included in the repair template polynucleotide. Edits can include, for example, base pair insertions, deletions, or changes. The term can be a noun or a verb directed to the action of changing a region of a genomic sequence. It appears that the claim is using the term as a noun similar to a polynucleotide encoding a protein. Even though the wording of the claims using this term is awkward, the term ‘edit’ can be used a noun. The BRI of the term ‘edit’ in the limitation will read on a verb or a noun directed to a polynucleotide encoding (comprising) a sequence that has a different nucleotide sequence than the nucleotide in the genome to be edited and when inserted into the genome results in any change in the genomic sequence including a base pair insertion, deletion, or change in the sequence it edited. Thus, edit can read on any polynucleotide sequence that can be inserted into the linear double stranded polynucleotide.
The limitation ‘donor’ does not add any structural limitations to the double stranded linear polynucleotide. The limitation ‘template’ before polynucleotide does not add any structural limitations to the polynucleotide flanked by the homology arms
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Paix et al. (Methods, May 15, 2017, 121-122, 86-93, cited on an IDS).
The rejection of claims 13-15 and 17-18 as being anticipated by Paix is incorporated herein.
Paix et al. do not specifically teach wherein the template further comprises a restriction enzyme site.
However Paix et al. suggest using a restriction enzyme site to identify edits (page 89).
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to use a restriction enzyme site in the template to identify the edit, namely to arrive at the claimed invention.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Claims 13-15 and 17-18 are rejected under 35 U.S.C. 103 as being unpatentable over Shen (WO 2016/025759, published 2/18/16).
‘759 discloses an efficient genome editing technique comprising introducing into a cell a) a RNA-guided nuclease (Cas) that cleaves the chromosome at the insertion site, b) introducing into the cell a donor construct, c) introducing an exonuclease, and d) a guide RNA (gRNA) into the cell recognizing the insertion site; wherein the donor construct is linear and comprises a 5’ and 3’ homology arm, wherein the donor sequence is inserted into the chromosome through homologous recombination (pages 24-27 and 48-53). The homology arms can be about 30 bp in length (page 30). The 5’ homology arm can be immediately upstream of the DNA cleavage site (page 30). The donor sequence can range from about 1bp to about 100 kb, including 1kb (pages 28- 29). The donor sequence can be an exogenous sequence (e.g., exogenous gene) to be inserted into the chromosome. The donor could read on a double stranded polynucleotide because a gene is a double stranded polynucleotide.
‘759 does not specifically teach a double stranded linear polynucleotide comprising a polynucleotide and two homology arms, wherein the arms are between 30-35 bases in length.
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to make a composition comprising the double stranded linear polynucleotide, namely to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to make and use the composition to study the efficiency of genome editing. ‘759 teaches that the template can be linear and up to 1 kb (pages 28-29). The template could read on a double stranded polynucleotide because a gene is a double stranded polynucleotide. Inserting a gene into the DSB region would change at least one nucleotide base within 30 bases of the DSB of the target nucleic acid. ‘759 teaches that the homology arms can be about 30 bp in length ‘759 teaches inserting the donor sequence at the DSB region of the target sequence (page 30). ‘759 makes obvious administering to a cell a composition comprising CRISPR-Cas complex, including a gRNA and the instant donor sequence.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Shen (WO 2016/025759), as applied to claims 13-15 and 17-18 above, and further in view of Gurumurthy et al. (WO 2016196887).
‘759 does not specifically teach the donor sequence comprising a restriction enzyme site.
However, ‘887 teaches making nucleotide sequence having a restriction enzyme site (pages 17, 19, 21 and 41-47).
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to combine the teaching of ‘759 taken with ‘887 to insert a restriction enzyme site into the donor sequence, namely to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to combine the teaching to detect the sequence in a cell.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Claims 13-18 are rejected under 35 U.S.C. 103 as being unpatentable over Frisch (WO2017066175).
‘175 claims a method for selecting a cell comprising a modified nucleotide sequence in its genome, the method comprising a) providing a guide polynucleotide, at least one protected polynucleotide modification template and a Cas endonuclease to a cell, wherein said Cas endonuclease and guide polynucleotide can form a complex capable of introducing a single or double stranded break at a target site in genome of said cell and selecting a cell from the step a) comprising said modified nucleotide sequence and further determining the frequency of homologous directed repair (HDR) and/or non-homologous end joining (NHEJ) in said cell, wherein the frequency of HDR is increased when compared to the frequence of HDR derived from a control method having all of the same components and steps as the method except using an unprotected polynucleotide template (pages 64 and 95-98). The polynucleotide template can be a linear double stranded sequence. The template can be a DNA sequence of interest (pages 36-47). ‘175 further discloses conventional yeasts typically exhibit specific integration donor DNA with short flanking homology arms (30-50bp) with efficiency routine over 70% (page 64).
‘175 does not specifically teach a double stranded linear polynucleotide comprising a polynucleotide and two homology arms, wherein the arms are between 30-35 bases in length.
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to use a double stranded linear polynucleotide comprising a polynucleotide and two homology arms, wherein the arms are between 30-35 bases in length as the unprotected polynucleotide template in the method of determining HDR efficiency of the protected polynucleotide template, namely to arrive at the claimed invention. The unprotected template can be any length of nucleotides, including up to 1kb (pages 26-37). One of ordinary skill in the art would have been motivated to use the restriction enzyme to detect the unprotected template in a cell (e.g., pages 19-20). ’175 makes a method of introducing into a cell a RNA-guided DNA endonuclease, a guide RNA, and the double stranded linear donor polynucleotide. Inserting a DNA sequence of interest (unprotected template) into the DSB region would change at least one nucleotide base within 30 bases of the DSB of the target nucleic acid.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Conclusion
See attached PTO-326 for disposition of claims.
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/BRIAN WHITEMAN/ Primary Examiner, Art Unit 1636