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 11/05/2025.
Applicant’s election without traverse of Group I, ZNG790-AS1 and MSCAS1 in the reply filed on 3/05/2025 is acknowledged.
Claims 1-11, 16-20 are pending. Claims 12-15 has been cancelled.
Claims 16-18 are withdrawn as being drawn to a nonelected invention.
The following rejections for claims 1-11 and 19-20 are maintained or modified with response to arguetmsn following.
This action is FINAL.
Withdrawn Objections and Rejections
The claim objection made in the previous office action is withdrawn based upon amendments to the claims.
The 35 USC 112b, 35 USC 101 rejection made in the previous office action is withdrawn based upon amendments to the claims.
The 35 USC 102 rejection made in the previous office is withdrawn based upon amendments to the claims. However, it is noted that the reference used in the 35 USC 102 is used in the 35 USC 103 rejection proved below.
Maintained Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-11 and 19-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims are drawn to methods of determining levels or amounts of methylation in any biological sample in any subject and further diagnosing or identifying as suffering from a gastric cancer when the genes are hypermethylated.
The claims are drawn to a very large genus of examining methylation levels or amounts of any samples from any type of individual to diagnosing gastric cancer. Based upon the description in the specification although the skilled artisan could readily use a methylation analysis, the artisan would first need to determine if it functionally detectable of diagnosing gastric cancer, in the samples from any of the different species as such the specification has not provided written support for the structures with the recited functionality.
In analyzing whether the written description requirement is met for genus claims, it is first determined whether a representative number of species have been described by their complete structure. The instant specification has not provided the critical structures in any species in any sample to functionally determine gastric cancer using hypermethylated methylation of MSC-AS1 and ZNF790-AS1 rather the specification provides a specific human and a specific sample type.
Further, the art does not provide guidance to sufficiently describe relevant identifying characteristics or functional attributes that would distinguish different members of the claimed genus. In the instant case it is not clear that the functionality of bladder cancer can be extrapolated to non-human individuals or in any sample type based upon methylation levels of MSC-AS1 and ZNF790-AS1 particular sample from a specific species. This finding is supported by Feng (PNAS 2010 Vol 107 No 19 pages 8689-8694). Specifically, Feng teaches that although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms (abstract).
Herein the claims are drawn to any type of sample in any subject however, there is no written support that methylation detection or levels would between the different types of samples and species would be functionally the same.
In analysis of the claims for compliance with the written description requirement of 35 U.S.C. 112, first paragraph, the written description guidelines note regarding genus/species situations that "Satisfactory disclosure of a ``representative number'' depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features of the elements possessed by the members of the genus in view of the species disclosed." (See: 'Written Description" Requirement, Federal Register, Vol. 66, No. 4, pages 1099-1111, Friday January 5, 2001.) As such, one of skill in the art would not recognize that applicant was in possession of the genus of markers, encompassed by the broadly claimed invention.
Response to Arguments
The reply traverses the rejection. A summary of the arguments is provided below with response to arguments following. The reply asserts that a specific subset of patients that have or are suspected of having gastric cancer (p. 5). The reply asserts that the specification provides that hypermethylation of the genes are assessed (p. 5). The reply asserts that claim 3 and 19 both limit the biological sample to blood and humans (p. 5-6).
These arguetmsn have been reviewed but have not been found persuasive.
The independent claims are not limited to hypermethylation, blood or humans and as such the breadth of the claims is larger than the examples pointed to in the reply. As noted above such correlations without critical structures would not be described by the specification. The reply asserts that claim 1 is limited to subjects that has or is suspected of having gastric cancer. Although the limitation of “subjects that have gastric cancer” would be limiting, the specification has not described which limitations are necessary to be “suspected”. The specification does not describe the limitations of “suspected” and as such it is broadly interpreted as any subject that has the capability of having gastric cancer, as the phrase is not limited to clinical determinations.
Modified 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) 1-5, 7 is/are rejected under 35 U.S.C. 103 as being unpatentable over Vrba et al. (WO2019/068082 April 4, 2019).
With regard to claim 1, Vrba et al. teaches a method of determining the level of methylation of MSC-AS1 and KCNA3 (p. 15 SKCM 6 marker set and para 36). However, Vrba et al. does not teach ZNF790-AS1.
Vrba et al. suggests that the subject can have a stomach cancer (p 34) and as such suggests a subject that is suspected of gastric cancer.
With regard to claim 2, the claim is interpreted as an optional limitation. In particular the correlation to gastric cancer only needs to be determined “when” there is hypermethylation. As Vrba et al. teaches any level of methylation it would encompass the breadth of the claims.
With regard to claim 3, Vrba et al. teaches that the biological sample is a human blood sample (para 28).
With regard to claim 4, Vrba et al. teaches a method of methylation detection by next generation sequencing (para 67).
With regard to claim 5, Vrba et al. teaches determination of methylation of the entirety of the gens and therefore teaches that methylation is determined of the recited regions within the gene.
With regard to claim 7, as VRBA teaches NGS sequencing it suggests determination of methylation simultaneously. However, Vrba et al. does not teach ZNF790-AS1.
Response to Arguments
The reply traverses the rejection. A summary of the arguments is provided below with response to arguments following. The reply asserts that the claims require that the subject has or is suspected of having gastric cancer. The reply asserts that the combination was used for testing skin cutaneous melanoma (p. 7). It is noted that the rejection of Bernstein has been withdrawn.
These arguments have been reviewed but have not been found persuasive.
Vrba et al. suggests that the subject can have a stomach cancer (p 34) and as such suggests a subject that is suspected of gastric cancer. Although the specific genes were found associated with skin cutaneous melanoma, Vrba et al. teaches screening the genes across a number of sample types with a variety of cancer. As such Vrba et al. suggests that at least one of the samples was suspected of gastric cancer.
Claim(s) 8,11,19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Vrba et al. (WO2019/068082 April 4, 2019) as applied to claims 1-5, 7 in view of Ahlquist et al. (US Patent Application Publication 2017/0058356 March 2, 2017).
Vrba et al. teaches a method of determining the level of methylation of MSC-AS1 and KCNA3 (p. 15 SKCM 6 marker set and para 36). Vrba et al. suggests that the subject can have a stomach cancer (p 34) and as such suggests a subject that is suspected of gastric cancer.
However, Vrba et al. do not teach determining methylation levels at different time points.
With regard to claim 8, Ahlquist et al. teaches methods of determining levels of methylation at multiple time points in genes including KCNA3 (para 15,20,40, 211).
With regard to claim 10, as VRBA teaches NGS sequencing it suggests determination of methylation simultaneously
With regard to claim 19, Vrba et al. teaches that the biological sample is a human blood sample (para 28).
With regard to claim 11, Ahlquist et al teaches comparison with a reference (para 211-218).
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 Vrba and Bernstein to measure methylation at more than one time point as suggested by Ahlquist et al.. The ordinary artisan would be motivated in order to measure changes in methylation in a sample across time to determine how external changes effect methylation.
Response to Arguments
The reply traverses the rejection. A summary of the arguments is provided below with response to arguments following. The reply is traverses based upon the arguetmsn set forth and replied to above.
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 at 5712723157. 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.
/KATHERINE D SALMON/ Primary Examiner, Art Unit 1682