DETAILED ACTION
Election/Restrictions
Applicant’s election without traverse of Species a): PARP8 as the gene in chromosome band 5q1 and PARP15 as the gene in chromosome band 3q2; and Species b): PARP8 as the gene in chromosome band 5q1 and PARP15 as the gene in chromosome band 3q2 in the reply filed on 01/12/2026 is acknowledged. Claims 1, 4, 5, and 6 read on the elected species.
Claims Status
Claims 1-11,13,16-17,20-22,24 and 28-29 are pending and currently under examination.
Priority
This application claims the benefit of U.S. Provisional Patent Application Serial Nos. 63/125,938, filed on December 15, 2020. The priority date of claim set filed on January 12, 2026, is determined to be December 15, 2020.
Specification
The listing of references in the specification is not a proper information disclosure statement. The specification filed on 06/14/2023 includes a list of references on pages 1-2, 21, 24-25, 27-50, 59-61, 66, etc.. 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.
Claim Objections
Claims 1, 4-5 and 8-11 are objected to because of the following informalities:
the preamble recites “a method of treating a cancer in a subject” (ln 1). The limitation of treatment in step (c) is optional, thus the preamble in claim 1 does not seem to adequately describe the method required by the limitations of claim 1. (Claim 1)
“wherein: the” (ln 1) should be amended to omit the colon. (Claims 4-5 and 8-11)
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 1-11,13,16-17,20-22,24 and 28-29 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.
Claim 1 is indefinite over the limitations “optionally” (ln 8) and “based on the assessment of step (b)” (ln 9). It is unclear as to what the metes and bounds of the assessment comprise. Furthermore, it unclear if even if a certain assessment is determined, if the step (c) remains optional, or whether determination of the assessment of step (b) makes step (c) optional. Claims 2-11,13,16-17,20-22,24 and 28-29 depend on claim 1.
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, 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 1-6,13, 20-22,24 and 28-29 are rejected under 35 U.S.C. 103 as being unpatentable over Regev et al. (“Regev”; Patent App. Pub. US 20200157633 A1, May 21, 2020).
Claim interpretations: The limitation(s) reciting “optionally” in claim 1 is interpreted as rendering the phrase thereafter as an optional limitation to the claim. Therefore, dependent claims 7-11 and 16-17, drawn to the optional limitation are also interpreted as optional.
Regev discloses “The subject matter disclosed herein is generally directed to detecting and modulating novel gene signatures for the treatment and prognosis of cancer. The novel gene signatures predict overall survival in cancer and can be targeted therapeutically.” (Abstract).
Regarding claim 1, Regev teaches a method comprising “a method of treating a cancer in a subject in need thereof comprising detecting the expression or activity of an ICR and/or exclusion signature according to any embodiment herein in a tumor obtained from the subject” (Para. 24). Regev teaches a method comprising “Cell type signatures that were derived from the analysis of the scRNA-seq data… PARP8…PARP15” (Table S4). Thus, Regev suggests a method of treating a cancer in a subject, the method comprising:(a) obtaining at least one biological sample comprising cells and/or cell free materials derived from the cancer in the subject; (b) performing at least one assay on the at least one biological sample to assess a presence or level of chromosome arm 5q or a portion thereof and chromosome arm 3q or a portion thereof, and(c) optionally, administering a PARP inhibitor chemotherapy and/or a platinum-based chemotherapy to the subject based on the assessment of step (b).
Regarding claim 2, Regev teaches a method wherein “a target nucleic acid molecule (e.g., RNA molecule), may be sequenced by any method known in the art, for example, methods of high-throughput sequencing, also known as next generation sequencing or deep sequencing.” (Para.383). Regev teaches a method wherein “Applicants distinguished malignant from non-malignant cells (materials and methods) according to (1) their inferred CNV profiles” (Para. 406). Thus, Regev suggests a method wherein performing the at least one assay in step (b) comprises a DNA analysis and/or an expression analysis, wherein: i. the DNA analysis comprises determining DNA copy number and is performed using next generation sequencing (NGS); and/or ii. the expression analysis comprises analysis of messenger RNA transcripts and is performed using NGS.
Regarding claim 3-6, Regev teaches a method comprising “Cell type signatures that were derived from the analysis of the scRNA-seq data… PARP8…PARP15” (Table S4). Thus, Regev suggests a method wherein the portion of chromosome arm 5q comprises band 5q1 or a portion thereof, and/or the portion of chromosome arm 3q comprises band 3q1 or a portion thereof; wherein: the portion of chromosome arm 5q comprises at least one gene located in band 5q1; and/or the portion of chromosome arm 3q comprises at least one gene located in band 3q2; and wherein: the at least one gene in chromosome band 5q1 comprises at least one gene selected from PARP8 and/or the at least one gene in chromosome band 3q2 comprises at least one gene selected from PARP15; and wherein the at least one gene in chromosome band 5q1 comprises PARP8, and/or the at least one gene in chromosome band 3q2 comprises PARP15.
Regarding claim 13, Regev teaches a method wherein “detecting the expression or activity of an ICR and/or exclusion signature according to any embodiment herein in a tumor obtained from the subject before the treatment” (Para.24). Thus, Regev suggests a method wherein the subject has not previously been treated with chemotherapy, the PARP inhibitor chemotherapy, and/or the platinum- based chemotherapy.
Regarding claim 20, Regev teaches a method wherein “tumor sample” (Para. 20). Thus, Regev suggests a method wherein the at least one biological sample comprises a bodily fluid, a tumor sample, a tissue sample, or any combination thereof.
Regarding claim 21, Regev teaches a method wherein “solid tumors” (Para. 266). Thus, Regev suggests a method herein the cells and/or cell free materials derived from the cancer are from a solid tumor.
Regarding claims 22 and 24, Regev teaches a method wherein “blood collected from a subject” and “plasma” (Para.242). “plasma” reads on cell-free. Thus, Regev suggests a method wherein the at least one biological sample comprises a bodily fluid and the cell free materials derived from cancer comprise cell free nucleic acids; and wherein the bodily fluid comprises peripheral blood, sera, or plasma.
Regarding claim 28, Regev teaches a method wherein “solid tumors include, but are not limited to… ovarian carcinoma (e.g., ovarian epithelial carcinoma or surface epithelial-stromal tumour including serous tumour, endometrioid tumor and mucinous cystadenocarcinoma, sex-cord-stromal tumor)” (Para. 266). Thus, Regev suggests a method wherein the cancer comprises ovarian cancer.
Regarding claim 29, Regev teaches a method wherein “classification of malignant and non-malignant cells. (A) Inferred large-scale CNVs distinguish malignant (right) from nonmalignant (left) cells. Shown are the inferred CNVs (amplification, blue, deletion) along the chromosomes (x axis) for cells (y axis) in two representative tumors.” (Para.73). Thus, Regev suggests a method wherein the cancer comprises a solid tumor that exhibits DNA replication errors selected from the group consisting of mutations, insertions, deletions, mismatch repair deficiency (MMRd), microsatellite instability (MSI-H), high tumor mutational burden (TMB), copy number variations (CNV), and any combination thereof.
Therefore, the invention as recited in claims 1-6,13, 20-22,24 and 28-29 are prima facie obvious over the prior art Regev et al. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of the claims. It would have been obvious to provide a method for monitoring a cancer in a subject comprising detecting the expression signature according to the limitations of the instant application claims 1-6,13, 20-22,24 and 28-29 based on Regev et al. (Patent App. Pub. No. US 20200157633 A1, May 21, 2020).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's
disclosure: Burgess et al. (“Burgess”; Patent App. Pub. CA 3099335 A1, Nov. 14, 2019 (Pg.12-13 and Pg 52 Claims 1-2 - PARP8 and PARP15;PARP inhibitor), (Pg. 50-ovarian cancer).
No claims are in condition for allowance.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENDRA R VANN-OJUEKAIYE whose telephone number is (571)270-7529. The examiner can normally be reached M-F 9:00 AM- 5:00 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Winston Shen can be reached at (571)272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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