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 .
Election/Restrictions
Applicant’s election of the invention of Group 1 (methods comprising DNA amplification), and the particular combination of loci that are positions 13992930, 113993052, 113993142, 13993304 and 113993313 of chromosome 2, in the reply filed on 09/19/2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 2, 4-10, 28, 30-36 and 45 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species (claims 2, 4-10, 28, and 30-36) or nonelected invention (claim 45), there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 09/19/2025.
It is noted that Applicants reply asserts that claims 2 and 28 are included in the elected invention, but these claims are withdrawn as they do not recite positions 13992930, 113993052 of chromosome 2. As such they are in fact directed to non-elected subcombinations and nonelected combinations.
Information Disclosure Statement
The information disclosure statement filed 05/04/2023 has been considered. Please note that the citations of Berry et al (2012) and Day et al (2004) have been lined through and not considered because these citations fail to comply with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. The IDS has been placed in the application file, but the information regarding the aforementioned citations has not been considered.
Claim Rejections – Improper Markush Group
Claims 1, 3, 27 and 29 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 § 2117.
The Markush grouping of alternative chromosomal loci in the limitations recited in claims 1, 3, 27 and 29, is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use. Here it is noted that the election provides for the particular combination that is “positions 13992930, 113993052, 113993142, 13993304 and 113993313 of chromosome 2”. The different gene loci recited in the claims are each unique, with different sequences of nucleotides required for their detection and analysis; and they are related to different encoded proteins with distinct biological roles in a cellular environment. Additionally, with regard to any association with the hypersomnolence phenotype, as asserted in the specificity, any particular gene locus may have a different strengths of association with the phenotype (e.g.: Tables 1 and 2 of the specification) indicating that each individual locus, may be used to determine risk of hypersomnolence with a different level of reliability.
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.
Claim(s) 1 and 3 are is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Finer et al (2016), including the Supplementary Information.
Regarding the methods of the rejected claims, Finer et al teaches the analysis of genomic DNA from whole blood samples (e.g.: p.3, left col), including the treatment of the DNA with bisulfite to generate bisulfite modified DNA (e.g.: p.3, right col) and the amplification of the modified DNA with a primer pair that includes positions 13992930, 113993052, 113993142, 13993304 and 113993313 of chromosome 2 and quantifying methylation at the positions (e.g.: p.3, right col: Forward and reverse primers (one of them being biotinylated) flanking the region of interest were designed using the Pyromark Assay Design v2.0.1.15 software and used with Platinum Taq DNA Polymerase to amplify 20 ng of BS-converted DNA. Quantitative short read sequencing of amplified BS-DNA was performed…). See also page 4 - Targeted DNA methylation analysis, and p.5, right col (Quantitative methylation values derived from the 450k array at PAX8 were validated against a BS-pyrosequencing amplicon targeted to 8 CpG sites overlying and adjacent to the metastable epiallele), and Supplementary table 3.
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.
Claim(s) 27 and 29 is/are rejected under 35 U.S.C. 103 as being unpatentable over Finer et al (2016), including the Supplementary Information in view of Mikeska et al (2011).
Regarding the methods of the rejected claims, Finer et al teaches the analysis of genomic DNA from whole blood samples (e.g.: p.3, left col), including the treatment of the DNA with bisulfite to generate bisulfite modified DNA (e.g.: p.3, right col) and the amplification of the modified DNA with a primer pair that includes positions 13992930, 113993052, 113993142, 13993304 and 113993313 of chromosome 2 and quantifying methylation at the positions (e.g.: p.3, right col: Forward and reverse primers (one of them being biotinylated) flanking the region of interest were designed using the Pyromark Assay Design v2.0.1.15 software and used with Platinum Taq DNA Polymerase to amplify 20 ng of BS-converted DNA. Quantitative short read sequencing of amplified BS-DNA was performed…). See also page 4 - Targeted DNA methylation analysis, and p.5, right col (Quantitative methylation values derived from the 450k array at PAX8 were validated against a BS-pyrosequencing amplicon targeted to 8 CpG sites overlying and adjacent to the metastable epiallele), and Supplementary table 3.
Finer et al recites using Platinum Taq DNA Polymerase to amplify 20 ng of BS-converted DNA, but does not explicitly disclose repeated steps of heating and cooling, as recited in claim 27.
However, such steps were typically used in the analysis of DNA methylation using bisulphite pyrosequencing, and are taught by Mikeska et al (e.g.: p.43 – 3.3. Bisulphite-Specific PCR).
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have used the methods of Mikeska et al in the analysis of BS-converted DNA taught by Finer et al. The skilled artisan would have been motivated to use the methods of Mikeska et al, and would have had a reasonable expectation of success, based on the expressed teaching of Mikeska et al that such methods provide accurate quantitative information pertaining to DNA methylation in a sample.
Conclusion
No claim is allowed.
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Stephen Kapushoc
Primary Examiner
Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683