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 without traverse of Group I, species SEQ ID NO: 7 in the reply filed on 9/15/2025 is acknowledged.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1, 4, 6, 8, 12, 15, 17, 19, 20, and 21 is/are rejected under 35 U.S.C. 103 as being unpatentable over Yu et al. (World Neurosurg. (2017) 105:28-36), as evidenced by Infinium HumanMethylation450 BeadChip Product information sheet, 2011, 2 pages, and Illumina Infinium HD Assay Methylation Protocol guide, 244 pages in view of GenBank GU143399 (7 Dec 2009, Homo sapiens myosin, heavy chain 11, smooth muscle isoform 1 (MYH11) gene; 52 pages).
Yu et al. teach bisulfite conversion of genomic DNA and analysis of samples using the manufacturer’s instructions. Yu et al. teach preparing the bisulfite treated DNA via manufacturer’s instructions and then hybridization to the HumanMethylation450 beadchip microarray. Preparing the DNA via manufacturer’s instructions inherently includes a step of producing an amplicon from the bisulfite treated DNA. The amplicon inherently included at least DNA comprising CpG cg01828111which is present at nucleotide 204 of instant SEQ ID NO: 1- and is identified as AMP3968:204 in the instant specification. This is evidenced by query of data set GSE75434 from the NCBI Gene Expression Ominibus database. Yu et al. teach that the methylation data from their beadchip analysis was submitted to the database under GSE75434 (p. 30, 2nd column). The graph below shows results of detection of the nucleotide present at AMP3698:204, also called cg01828111, which evidences bisulfite treated DNA was amplified and then the nucleotides present at that position were determined, as these are steps inherent to the Illumina beadchip assay. See Illumina documentation cited as evidence.
PNG
media_image1.png
390
787
media_image1.png
Greyscale
The final “wherein” clause in claim 1 defines that one CpG in the region corresponding to SEQ ID NO: 1 must comprise a bisulfite convertible cytosine. The method taught by Yu included producing an amplicon that comprises at least position 204 of instant AMP 3968, SEQ ID NO: 2, which is inherently in an MYH11 intron, thus meeting the limitations of at least claims 1 and 17. The fact there was at least one bisulfite convertible cytosine is evidenced by the fact that none of the sample values (indicating percent methylation) in the figure above are 100%. That means in each sample both methylated and unmethylated CpG were present in some copies of the assayed position.
With regard to claim 4, the assay carried out by Yu et al. is a type of bisulfite sequencing, since the nucleotide sequence of a particular region is determined. It is also an “other” method that relies on detection of amplified DNA.
With regard to claims 6 and 19, the reference teaches human aneurysm tissue samples and matched artery tissue, which are a tissue sample. With regard to claim 21, the reference does not mention that the tissue is trypsinized, therefore the evidence supports that the tissue is “non-trypsinized tissue.”
With regard to claim 8, Yu does not teach enriching cells from the tissue prior to extraction.
With regard to claim 12, the sample is from patients with the cardiovascular disease aneurysm.
With regard to claim 20, the reference teaches bisulfite treating.
Yu et al. teaches PCR amplification of a portion of the MYH11 gene using primers selected with PyroMark assay design software (p. 29, 2nd column).
Yu et al. does not teach a method wherein the amplicon is disclosed to comprise SEQ ID NO: 2.
Yu et al. does not teach whether analysis comprised the sequence of SEQ ID NO: 2, however the sequence of MYH11 was known in the art prior to the effective filing date, as taught by GenBank Accession number GU143399. Instant SEQ ID NO: 2 is identical to the complement of nucleotides 150536-151009.
Therefore, it would have been prima facie obvious to the ordinary artisan prior to the effective filing date to perform methylation analysis of the entire MYH11 sequence so as to provide a comprehensive analysis of the methylation status of MYH11 throughout the entire gene, given that Yu et al. teaches methylation of this gene is associated with the occurrence and development of intracranial aneurysms. Absent secondary considerations, creating amplicons throughout the gene and in particular comprising SEQ ID NO: 2 would have been routine and obvious in view of the level of skill in the art of methylation analysis prior to the effective filing date.
Response to Remarks
The claims have been extensively amended in response to the previous Office action. Any objection or rejection which has not been reiterated or otherwise addressed was overcome by amendment to the claims.
Applicant argues that there is not any evidence that Yu amplified a sequence wherein the original sequence had a bisulfite convertible CpG at position 204. However, this is not convincing in view of the data provided by Yu which shows that the methylation status was not 100% in any sample, indicating that each sample had some bisulfite convertible and some not convertible CpG at the subject position 204.
Claims 2 and 3 are free of the prior art because there is no evidence as to the methylation status of the CpG at these positions. Therefore, the claims are non-obvious.
Allowable Subject Matter
Claims 2 and 3 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Brodowski teaches methylation analysis of endothelial progenitor cells from patients with preeclampsia using the Illuminia Infinium EPIC BeadChip Kit. This BeadChip has probes for detection of cg01780913 and cg01828111 which are both within instant SEQ ID NO: 2. (Brodowski et al. (2019) Preeclampsia-Associated Alteration of DNA Methylation in Fetal Endothelial Progenitor Cells. Front. Cell Dev. Biol. 7:32. doi: 10.3389/fcell.2019.00032).
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 Juliet Switzer whose telephone number is (571)272-0753. The examiner can normally be reached Monday to Thursday, 8:00 AM-3:30 PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
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.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/Primary Examiner, Art Unit 1682