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 4/20/2026.
Applicant’s election of the species of ZFP36L1, DCXR and Chr4:90790001-90792000 in the reply filed on 6/08/2022 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)).
4. Claims 2, 5-6, 10, 12-13 are pending. Claim 1, 3-4, 7-9 and 11 has been cancelled. Claims 5-6 has been withdrawn as being drawn to nonelected species.
5. The following rejections for claims 2, 10, 12-13 are newly applied necessitated by amendment.
6. This action is FINAL.
Withdrawn Rejections
The 35 USC 112a rejection made in the previous office action is withdrawn based upon amendments to the claims.
The 35 USC 112b rejection made in the previous office action is withdrawn based upon the amendments that cancel the “optional” step.
Claim Interpretation
The claims have been amended to delete the requirement that FPKM value is greater than or equal to 10, and as such the claims have been broaden in the interpretation for obviousness. Further, it is noted that “consisting essentially of” is being interpreted as “comprising”. This interpretation is based upon the response to arguments stating that the language may be construed equivalently to comprising for examination purposes (see page 7 of reply).
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.
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) 2, 10, 12-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Erbenstein et al. (WO 2014/191981 December 4, 2014) in view of Dor et al. (WO2015/159293 April 14, 2025) and Lee et al. (US Patent Application Publication 2015/0376612 Dec 31, 2015)
With regard to claim 2, Erbenstein et al. teaches obtaining samples and incubating the DNA with β-glucosyltransferase and UDP and placing 5hmc on a solid support (p 3 , 6, and 24).
Erbenstein et al. does not teach that the sample is from cfDNA.
Erbenstein et al. teaches providing a reference hydroxy methylome reference (p. 44-45). Erbenstein et al. teaches dividing the full length of DNA to give a normalized value for 5hmC, however, does not teach FPKM (p 43-44 and 48). Erbenstein et al. teaches mapping to determine differences (p. 44). Erbenstein et al. teaches measurement of increased expression of hydroxy methylation (p. 30). Erbenstein et al. teaches that 5hmC levels vary greatly between different tissues and suggests detection of epigenetic modifications in tissue distribution (p 1, 6 and 47).
With regard to claim 2, Dor et al teaches that cfDNA can be used in tissue of origin methodologies (p. 12-16). Dor et al. teaches that 5 hydroxymethylcytosine can be detected in cfDNA (p. 12-16).
With regard to claims 10, 12, Dor et a. teaches that cfDNA profiles can be used to compare to particular tissue references (p 12-16). Dor et al teaches methylome comparisons and as such these steps can be combined with Erbenstein et al. to measure and compare 5hmC.
With regard to claim 2, Lee et al. teaches methods of assembling transcript expression data (para 41-46 and 145 and 244). Lee et al. teaches that one method of calculating and assembling is by used FPKM (para 41-46).
Therefore it would be prima facie obvious to one of ordinary skill at the time of the effective filing date to modify the method of Erbenstein et al. to use the method steps and sample type of Dor et al. and Lee et al in order to screen easily obtained cfDNA from fluid samples and use the comparison methodology for large number of expression products as taught by Lee et al. The ordinary artisan would have a reasonable expectation of success of combining known steps of determining 5mC differences.
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.
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, Wu Cheng (Winston) Shen can be reached on 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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