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 .
Application Status
The preliminary amendment filed November 10, 2022 is acknowledged. Claims 1-15 are pending and under examination.
Drawings
The drawings are objected to for two reasons.
First, the figures are referred to as “Figure” in the drawings. MPEP §608.02.V states that according to 37 C.F.R. 1.84(u)(1) “View numbers must be preceded by the abbreviation "FIG.".
Second, the numbers and letters of FIGs 1-5 are not sufficient to provide satisfactory reproduction characteristics. 37 CFR 1.84(l) states that “all drawings must be made by a process which will give them satisfactory reproduction characteristics. Every line, number, and letter must be durable, clean, black (except for color drawings), sufficiently dense and dark, and uniformly thick and well-defined.” In the instant case, the text in all FIGs is light grey or otherwise not sufficiently dense and dark to permit satisfactory reproduction characteristics and/or the text is very small and of poor resolution.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) 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. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. 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.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on pages 25 and 36. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Additionally, the use of the terms Lipofectamine®, CRISPRMAX®, BigDye®, Oncomine®, Ion®, ALT-RTM, which are trade names or marks used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears 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(b)
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 9 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.
Claims 9 and 11 recite the phrase “preferably” and “in particular” before reciting a species that falls within a previously recited genus. The phrases render the claims indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d). It is not clear if the endonuclease in claim 9 must be Cas9 or Cpf1. Likewise, it is not clear if the cells in claim 11 must be cultured for at least 96 hours.
To remedy the indefiniteness, it is suggested that the claims remove the phrases, and either delete the species or make clear that the claims are limited to the species recited.
Claim Rejections - 35 USC § 102
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 1-15 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Findlay (Findlay et al., Nature (2018), 562: 217-222 and Supplemental contents) and evidenced by ClinVar (NM_007294.4(BRCA1):c.63C>G (p.Ile21Met), https://www.ncbi.nlm.nih.gov/clinvar/variation/865054/ [retrieved December 31, 2025]).
Regarding claims 1 and 5, Findlay teaches characterizing variants of uncertain significance (VUS) in the BRCA1 gene using genome editing (Abstract). Findlay teaches introducing into HAP1 cells (i.e., haploid cells), an expression construct for Cas9 and a guide RNA (i.e., an expression system capable of expressing a CRISPR-Cas endonuclease) (Methods, page 1, column 2, ¶4). Findlay teaches transfecting HAP1 cells with an SNV library (i.e., a first and second nucleic acid) (Methods, page 1, column 2, ¶4). Findlay teaches that the SNV library comprised homology directed repair (HDR) oligonucleotides designed to incorporate (i) a single nucleotide polymorphism (SNP) at each location in an exon and (ii) a synonymous substitution (i.e., a silent mutation) in the Cas9 PAM site (Methods, page 1, column 1, ¶5). Findlay teaches culturing the transfected HAP1 cells (Methods, page 1, column 2, ¶5). Findlay teaches determining the frequency of the genetic variant after culturing the cells by sequencing gDNA and determining the frequency of the genetic variant in the cells (Methods, page 1, column 2, ¶7 through page 2, ¶5). Findlay teaches characterizing each of the SNVs as non-functional, intermediate or functional based on detection of the SNVs from the cultured cell population (Fig 4). Findley teaches changing the C at c.63 to A is a synonymous/silent mutation while changing c.63 to a G is a missense mutation (i.e., an SNV) (Fig 4). Because Findley teaches characterization of both the c.63C>A and c.63C>G, Findley’s method must have inherently included providing a donor comprising c.63C>A to a first population of cells and the c.63C>G to a second population of cells. There is no requirement for the claimed populations of cells to be physically separated from each other. Although Findley is silent regarding whether c.63C>G variant has been identified in patients, ClinVar teaches the c.63C>G results in a p.Ile21Met missense mutation was first identified as a clinical variant (i.e., present in a patient) in April 2020 (page 1). Therefore, the HDR oligos used in Findlay to produce the c.63C>G BRCA1 variant in a population of cells inherently introduced a mutation found in a patient.
Regarding claim 2, Findlay teaches designing the gRNAs to target sequences with PAMs that were permissive to synonymous substitution (i.e., silent mutation) (Methods, ¶3) and designing HDR oligos that introduced synonymous substitutions at the PAM site (Methods, ¶5).
Regarding claim 3, Findlay teaches the c.63 is in BRCA1 (Fig 4) and loss of function of BRCA1 in HAP1 cells reduces cell variability (Extended Data Fig. 1).
Regarding claim 4, Findlay teaches the BRCA1 SNVs tested have uncertain significance (Fig 3c) and ClinVar teaches specifically the c.63C>G variant has been classified as having uncertain significance (page 1, bottom).
Regarding claim 6, ClinVar teaches BRCA1 c.63C>G variant has been identified in Hereditary breast ovarian cancer syndrome (page 1, bottom).
Regarding claim 7, Findlay teaches for each guide RNA, three HDR oligos, one for each nucleotide substitution, was generated (Methods, ¶3 and 5).
Regarding claims 8-9, Findlay teaches transfecting the HAP1 cell populations (i.e., contacting the cells) with a plasmid encoding Cas9 (i.e., a type II Cas endonuclease) as indicated above for claim 1 (Methods, ¶3).
Regarding claim 10, there is no indication in Findlay that the HAP1 cells were diluted between transfection of the Cas9/gRNA/HDR oligo and culturing (Methods, page 1, column 2, ¶4-5).
Regarding claim 11, Findlay teaches culturing the transfected cells for 5 days or 11 days (at least 48 hours) before analyzing the genomic changes in the BRCA 1 gene (Methods, page 1, column 2, ¶6).
Regarding claim 12, Findlay teaches harvesting transfected cells from the culture media at day 5 and 12 (i.e., recovering the cells that had the c.63C>A and c.63C>G mutations) (Methods, page 1, column 2, ¶6).
Regarding claims 13-14, Findlay teaches recovering genomic DNA from the transfected cells and sequencing it (Methods, page 1, column 2, ¶7 through page 2, column 1, ¶5).
Regarding claim 15, Findlay teaches comparing the occurrence of the c.63C>G mutation to the occurrence of the c.63C>A mutation and determining that cell populations comprising both SNVs were present after culturing as determined by sequence analysis and determined to be functional variants (Fig 4; Methods, page 2, column 2, ¶8-9).
Conclusion
No claims are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CATHERINE KONOPKA whose telephone number is (571)272-0330. The examiner can normally be reached Mon - Fri 7- 4.
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/CATHERINE KONOPKA/Examiner, Art Unit 1635