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 .
This action is in response to papers filed 4/22/2026.
Applicant's election with traverse of Group III and the species of PARP3, Neil3, Nthl1, Nbn, Rbbpb, and Rad45l in the reply filed on 11/10/2025 is acknowledged.
Claims 48, 50-55, 57-58, 65, 76, 82-85 are pending. 1-47, 49, 56, 59-64, 66-75, 77-81 are cancelled.
The following rejections are newly applied or maintained with response to arguments following.
This action is FINAL.
Withdrawn Rejections
The 35 USC 112b rejection made in the previous office action is withdrawn based upon amendments to the claims.
Newly Applied 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 48, 50-55, 57-58, 65, 76, 82-85 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 48, 50-55, 57-58, 65, 76, 82-85 are indefinite over the amendment to the claims that require “one or more…comprise”. These phrases are unclear as it is not clear if the claims require the measurement of all the DDR genes or if the claim still requires one or more of the genes.
Improper Markush
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 48, 50-55, 57-58, 65, 76, 82-85 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 706.03(y).
The Markush groupings of the combinations of at least one of the genes HR pathway and at least one of the genes of BER pathway in claim 48 are improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons:
It is first noted that MPEP 706.03(y) states that “A Markush claim may be rejected under judicially approved “improper Markush grouping” principles when the claim contains an improper grouping of alternatively useable members. A Markush claim contains an “improper Markush grouping” if either: (1) the members of the Markush group do not share a “single structural similarity” or (2) the members do not share a common use. Supplementary Guidelines at 7166 (citing In re Harnisch, 631 F.2d 716, 721-22, 206 USPQ 300, 305 (CCPA 1980)). “ Members of a Markush group share a “single structural similarity” when they belong to the same recognized physical or chemical class or to the same art-recognized class (prong 1) and the members of a Markush group share a common function or use when they are disclosed in the specification or known in the art to be functionally equivalent (prong 2).
The phrase “significant structural element is shared by all of the alternatives” refers to cases where the compounds share a common chemical structure which occupies a large portion of their structures, or in case the compounds have in common only a small portion of their structures, the commonly shared structure constitutes a structurally distinctive portion in view of existing prior art, and the common structure is essential to the common property or activity.
A recognized physical class, a recognized chemical class, or an art-recognized class is a class wherein “there is an expectation from the knowledge in the art that members of the class will behave in the same way in the context of the claimed invention. In other words, each member could be substituted one for the other, with the expectation that the same intended result would be achieved” (see MPEP 706.03(y)IIA).
Herein, the recited alternative species do not share a single structural similarity, as each gene has a different chemical structure in that it consists of a different nucleotide sequence. The only structural similarity present is that all of the comprise the generic structure of nucleotides. The fact that the genes have a generic structure per se does not support a conclusion that they have a common single structural similarity because the structure of comprising nucleotides alone is not essential to the asserted common activity of the being correlated to breast cancer and they do not share a substantial structural similarity essential to this activity.
Further, the recited genes do not belong to a chemical or art-recognized class because there is no expectation from the knowledge in the prior art that genes behave in the same manner and can be substituted for one another with the same intended result achieved. There is no evidence of record to establish that it is clear from their very nature that the recited sequences possess the common property of being associated with urine cancer treatment. There is no evidence of record to establish that it is clear from their very nature that the recited markers possess the common property of being having a relationship of susceptible to treatment.
Response to arguments
The reply asserts that the claims have been amended (p. 7). It is noted that the claim amendments are indefinite. It is noted that should the claims be amended to require the entire combination of HR and BER genes listed that the rejection would be overcome. However, it is noted that the claims are not clear if the claims only require one or combinations of the genes.
Claim Rejections - 35 USC § 103
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 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.
Claim(s) 48,50-55,57,58,65,70 is/are rejected under 35 U.S.C. 103 as being unpatentable over Knudsen et al. (Oncotarget August 2016 Vol 7 p. 69111) as evidenced by Kalady et al. (US Patent Application Publication 2019/0376145 December 12, 2019) in view of Craig et al. (US Patent Application Publication 2014/0024539 January 23,2014).
With regard to claim 48, Knudsen et al. teaches screening human samples for expression with the Affymetrix U133 gene chip (p. 69120 last paragraph). Knudsen et al. does not teach PARP3, Neil3, Nthl1, Nbn, Rbbpb, and Rad45l however as evidenced by Kalady the Affymetrix U133 gene chip comprises these genes (para 54 and table 2). Knudsen et al. teaches comparison to a control (figure 3).
Knudsen et al teaches human tissues of ER positive breast cancer was measured (p. 69120) but does not specifically describe the human population.
Knudsen et al. teaches administering to the subject CDKN2 inhibitors of CDK4 and CDK6 (p. 69112 2nd column). The claim does not require any particular expression level, rather, the claims require treating a subject with a CDKN2 inhibitor wherein a sample of the subject had expression measured.
With regard to claim 51, Knudsen et al. teaches human tissue (biopsy) (p. 69120 last two paragraphs).
With regard to claim 52, as the sample is from a breast cancer subject, that subject would have had to be clinically diagnosed with breast cancer and therefore have had performed a breast test.
With regard to claim 54, Knudsen et al. teaches a method of using a microarray (p 69120 last parpaghra).
With regard to claim 57, Knudsen et al. teaches administering endocrine therapy (p. 69111 1st paragraph).
With regard to claim 58, Knudsen et al. teaches a luteinizing hormone releasing agent (figure 1 legend).
With regard to claim 65, Knudsen et al. teaches using a method that includes florescence (figure 3).
With regard to claim 70, Knudsen et al. teaches the use of palbociclib (p. 69112 1st column last full paragraph).
However Knudsen et al. does not describe the human subject treated.
With regard to claims 48, 50, Craig et al. teaches obtaining a sample from an ER positive breast cancer human subject considered to be an African American for expression analysis (para 68, 118).
With regard to claim 53,55 Craig et al. teaches that the sample can be from a patient with recurrent breast cancer which would be considered a poor survival rate (para 61).
Therefore it would be prima facie obvious to one of ordinary skill in the art at the time of the effective filing date to modify the sample of Knudsen so that the sample is from a known subject including the human subjects of Craig et al. It would be obvious to one of ordinary skill in the art to use samples from any human subject from a human population in order to screen expression and treat that subject with a known treatment (CDKN2 inhibitor) with breast cancer.
Response to arguments
The reply traverse the rejection. A summary of the arguments is provided below with response to arguments following. The reply asserts that Knudsen does not teach the wherein clause (p. 8). This arguments has been reviewed but has not been found persuasive. In particular the wherein clause appears to be one embodiment of the claimed steps. The wherein combination does not require being performed if the particular lower or higher expression is not determined. It is suggested that the wherein clause be amended to be a positive active step.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 KATHERINE D SALMON whose telephone number is (571)272-3316. The examiner can normally be reached 9-530.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu Cheng (Winston) Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KATHERINE D SALMON/Primary Examiner, Art Unit 1682
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