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
Applicant’s amendments filed April 3, 2026, amending claims 9 and 11 and adding new claim 16 is acknowledged. Claims 1-16 are pending and under examination.
The amendment to claims 9 and 11 overcome the §112(b) rejection. The rejection for indefiniteness is withdrawn.
Any other rejection or objection not reiterated herein has been overcome by amendment. Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Drawings
The drawings filed April 3, 2026 are objected to because:
The numbers and letters of FIGs 1B, 1D, 1E, 3, 4D, 4E, and 5B are still 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 the above 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. For instance, the “function score” text in the Table of FIG. 5B is completely illegible. In FIG 1D, the nucleotide letters over shading cannot be discerned due to the same color font for some of the letters and the shading behind it. Thus is likely due to a color drawing being copied inot black and white without correction of the shading.
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.
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 1-16 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]). This is a maintained rejection.
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 and 16, 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).
Response to Arguments
Applicant argues that Findlay does not anticipate the claims because of two differences between the claimed method and Findlay’s method: 1) step (c) of the claimed method only discloses a determination of the genetic variants in a single population of haploid cells, and 2) the claimed method requires the generation of a silent/benign mutation at the PAM sequence and silent/benign mutation at the site of the genetic variant in a second population of cells. Applicant also argues that the purpose of Findlay – to characterize all possible BRCA1 VUSs – only uses a single population of cells (Remarks, page 10, ¶1-3). This argument has been fully considered but is not persuasive for the following reasons.
The Specification does not define a “population of cells” and there is no requirement for the two claimed populations of cells to be physically separated from each other either in the contacting steps or in the “determining the occurrence” step. The broadest reasonable interpretation (BRI) of “a population of cells” is two or more cells. Findlay teaches recovering cells that have the c.63C>A and cells that have the c.63C>G, variant. So, even though Findlay provided the HDR templates to the cells in a single container, there were inherently two populations of cells – a first population that received the donor template that comprised the c.63C>G change and a silent PAM mutation and a second population that received the donor template that comprised the c.63C>A change and a silent PAM mutation. Findlay teaches that the c.63C>A change is a synonymous (i.e., silent) mutation (Fig 4, blue outline box) and that the c.63C>G is a “functional” missense variant (Fig 4, green outline box). ClinVar evidences that the c.63C>G variant is found in the human population. Thus, Findlay’s method includes all the limitations of steps (a) and (b).
The Specification also does not define or describe limitations of “determining the occurrence of” genetic variants. Although the working examples use a “function score determination”, which appears to be a ratio of the mutation frequency in one population to the silent mutation in the second population, there is no such “function score” recited in the claims. The BRI of “determining the occurrence of” encompasses any means to detect/determine the presence of variant. Findlay teaches calculating “function scores” by comparing the frequence of the SNV on day 11 (i.e., determining the occurrence) to the frequency of the input HDR template (page 2018, ¶5). Thus, Findlay determined the occurrence of the c.63C>G variant in each of the cells that received the c.63C>G template (i.e., in the first population of cells). Likewise, Findlay determined the occurrence of the c.63C>A variant in each of the cells that received the c.63C>A template (i.e., in the second population of cells. Thus, Findlay’s method also includes the limitations of steps (c).
Examiner concedes that Applicant’s working example of a low-throughput method for introducing individual VUSs into haploid cells in physically separate populations and calculating a “function score determination” based on the frequencies of the variant to the frequence of the PAM sequence mutation is distinct from Findlay’s high throughput, saturation genome editing method. However, the features of Applicant’s working example that distinguishes it from Findlay’s method are not recited in any of the claims. To overcome the §102 rejection it is suggested to incorporate additional steps and/or parameters from the working examples to distinguish the claimed method for Findlay’s.
Conclusion
No claims are allowable.
THIS ACTION IS MADE FINAL. 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.
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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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Ram Shukla can be reached at (571)272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CATHERINE KONOPKA/Primary Examiner, Art Unit 1635
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