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 applicants correspondence mailed 12/22/2022. The amendment to the claims mailed 12/22/2022 has been entered.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 12 is rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims recite a mental process and law of nature. This judicial exception is not integrated into a practical application and the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons that follow.
The following three inquiries are used to determine whether a claim is drawn to patent-eligible subject matter:
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? Yes, all of the claims are directed to a process.
Step 2A. Is the claim directed to a law of nature, a natural phenomenon or an abstract idea (judicially recognized exception) and does the claim recite additional elements that integrate the judicial exception into a practical application?
Yes, the claims are directed to law of nature/natural phenomenon. The claims recite the correlation between risk of developing esophageal cancer and presence of extrachromosomal DNA. The recited relationship is a natural phenomenon that exists apart from any human action.
The claims also recite the judicial exception of an abstract idea and particularly mental processes.
With regard to claim 12, the claim recites the abstract idea of a mental process, the judgement or comparison step of the presence of ecDNA in a plurality of esophageal cells relative to a subject wherein the presence of ecDNA is not detected in the plurality of esophageal cells. The broadest reasonable interpretation of the wherein clause includes a judgement or comparison step that is accomplished mentally by evaluating data and includes critical thinking wherein one mentally reads information of the presence of ecDNA then draws a mental conclusion of risk of esophageal cancer.
Having determined that the claims recite a judicial exception, it is then determined whether the claims recite additional elements that integrate the judicial exception into a practical application.
Herein, claim 12 does not recite additional steps or elements that integrate the recited judicial exceptions into a practical application of the exceptions. While the claims recite obtaining a biological sample and detecting ecDNA, none of limitations of the independent claim result in an practical application of the judicial exception recited in claim 12.
Step 2B - Does the claim recite additional elements that amount to significantly more than the judicial exception? No.
Herein the claims as a whole are not considered to recite any additional steps or elements that amount to significantly more than well-understood, routine, and conventional activities in the art and do not add something “significantly more” so as to render the claims patent-eligible. The step of obtaining a biological sample and detecting ecDNA merely instructs a scientist to use well established, routine and conventional nucleic acid techniques to gather samples for diagnostic analysis. As addressed in the instant specification methods of determining the number of ecDNA within a cell are known in the art (see para 123). The claims do not require a particular, non-conventional primer or probe consisting of or comprising a specific nucleotide sequence or any other specific reagent that is used to accomplish such determining such that the claims would recite significantly more than the judicial exception. The targets to be detected are part of the judicial exception and thereby the naming of the targets does not add something “significantly more” to the recited judicial exceptions.
The additional steps and elements are recited at a high degree of generality and are all routine, well understood and conventional in the prior art. The recited steps and elements do not provide inventive concept necessary to render the claims patient eligible. There is no combination of elements in this step that distinguishes it from well-understood, routine and conventional data gathering activity engaged in by scientists prior to applicant’s invention and at the time the application was filed. Many cited prior art references in this record demonstrate that these techniques were conventional at the time of the invention. The prior art demonstrates detecting extrachromosomal DNA in esophageal cancer samples (see Mischel US2018/0355416 A1,. Kim (Nature Genetics 2020, vol 52, pp 891-897) and Nones (Nature Communication, 2014, 5:5224, p 1-9)). Thus the prior art and specification demonstrates it was routine, well-known and conventional in the art to detect extrachromosomal DNA in biological samples, including esophageal cancer.
Claim Rejections - 35 USC § 102
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 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 1 and 9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Mischel (US2018/0355416 A1).
Mischel teaches a method to detect and treat cancer by identification of extrachromosomal oncogenes. Mischel teaches obtaining a biological sample from a subject and detecting amplified extrachromosomal oncogene present (sese para 6). Mischel teaches administering to the subject an effective amount of anti-cancer agent (see para 7). Mischel teaches the cancer includes esophageal cancer (see para 117). Mischel teaches the biological sample includes a tumor sample or a tumor fluid sample (see para 147, 151). Mischel teaches the tumor includes esophageal cancer, as such Mischel teaches obtaining a biological sample containing a plurality of esophageal cells from the subject. Mischel teaches a method of treating cancer by obtaining a biological sample, detecting oncogene amplification on circular extrachromosomal DNA and administering a therapeutically effective amount of an anti-cancer drug (see para 151).
Claims 1, 8-9, 12 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kim (Nature Genetics 2020, vol 52, pp 891-897)
Kim teaches obtaining tumor samples and detecting the presence of ecDNA by amplification (see fig 1c and pg. 893, 1st column). Kim teaches ecDNA based amplicons were found in esophageal carcinoma (see pg. 893, 1st column) (claim 9), thus teaching obtaining in a sample containing a plurality of esophageal cells from a subject with esophageal cancer and detecting the presence of ecDNA in the esophageal cells. Kim teaches the count of ecDNA per cell (see pg. 893, 1st column and supplementary table 2) (claim 8).
Claims 1, 8-9, and 12 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Nones (Nature Communication, 2014, 5:5224, p 1-9).
Nones teaches obtaining biological samples comprising esophagus cells from tissue samples (see samples). Nones teaches both tumor and matched DNA was assay for copy number, WGS, and FISH (see methods pg. 7-8). The fresh tissue samples comprise a plurality of esophageal cells from the subject. Nones teaches gene amplification is due to detecting the presence of extrachromosomal DNA in the sample by FISH (see pg. 5, 2nd column) (claim 8-9).
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.
Claims 2-4, 6, 8, 12-13, 15, 17, 20-23, 25, 27, 31, 33, 35 is/are rejected under 35 U.S.C. 103 as being unpatentable over Mischel (US2018/0355416 A1) in view of Bandla (Annals of Surgery, 2014, vol 260, 72-80).
Mischel teaches a method to detect and treat cancer by identification of extrachromosomal oncogenes. Mischel teaches obtaining a biological sample from a subject and detecting amplified extrachromosomal oncogene present (sese para 6). Mischel teaches administering to the subject an effective amount of anti-cancer agent (see para 7). Mischel teaches the cancer includes esophageal cancer (see para 117). Mischel teaches the biological sample includes a tumor sample or a tumor fluid sample (see para 147, 151). Mischel teaches the tumor includes esophageal cancer, as such Mischel teaches obtaining a biological sample containing a plurality of esophageal cells from the subject. Mischel teaches a method of treating cancer by obtaining a biological sample, detecting oncogene amplification on circular extrachromosomal DNA and administering a therapeutically effective amount of an anti-cancer drug (see para 151). Mischel does not teach a subject with Barrett’s esophagus, biological sample comprising epithelium tissue, cells having metaplasia or dysplasia including columnar epithelial cells. Mischel does not teach preventative treatment of esophageal cancer.
Bandla teaches obtaining esophageal mucosa specimens from subject diagnosed with EAC having dysplasia and intestinal metaplasia (see specimen screening and subject cohort). Bandla teaches mucosal tissue pieces were obtained from 4 subjects that underwent esophagectomies (see pg. 73, 1st column) (administering treatment, esophagectomy) (claim 17, 20, 35). Bandla teaches patients underwent upper endoscopy (see subject cohort) (preventative treatment, diagnostic test) (claim 13, 15, 31, 33), Bandla teaches isolating DNA and performing FISH analysis. Bandla teaches isolating columnar cell metaplasia (Barrett’s esophagus) (see specimen screening) (claim 3-4 and 6, 22-23, and 25). Bandla teaches analysis of metaplasia versus EAC to determine disease progression (see pg. 78, 1st column) (claim 12).
Given Mischel teaches detecting extrachromosomal DNA in esophageal carcinoma and teaches administering therapy to subjects with extrachromosomal DNA, it would have been prima facie obvious to the ordinary artisan at the time the invention was to include different types of samples from different tissues of esophagus cells, including samples from Barrett’s esophagus, epithelium samples and metaplasia for the analysis of extrachromosomal DNA as taught by Mischel. The skilled artisan would have been motivated to include analysis of different cell samples because both Mischel and Bandla teaches analysis of esophageal cells including esophageal carcinoma and the skilled artisan would have been motivated to include additional samples of esophageal cells in the method of Mischel for a more robust analysis of different cancer samples and different cell samples. The skilled artisan would have been motivated to include treatment of subjects with or at risk of developing EAC in the method of Mischel with anticancer therapy including esophagectomy because Bandla teaches endoscopy as a diagnostic test and preventative as well as teaches esophagectomy as a treatment. The skilled artisan would have a reasonable expectation of success that extrachromosomal DNA can be tested in additional esophageal samples including Barrett’s esophagus, epithelium samples and metaplasia for extrachromosomal DNA because Mischel teaches extrachromosomal DNA detection in EAC and Bandla teaches analysis of chromosomal DNA in Barrett’s esophagus, epithelium samples and metaplasia.
Claims 2-4, 6, 13, 15, 17, 20-23, 25, 27, 31, 33, 35 are rejected under 35 U.S.C. 103 as being unpatentable over Nones (Nature Communication, 2014, 5:5224, p 1-9) in view of Bandla (Annals of Surgery, 2014, vol 260, pp 72-80)
Nones teaches detecting extrachromosomal DNA in esophageal adenocarcinoma. Nones teaches extrachromosomal amplification of MYC in EAC (see figure 2, pg. 5, 2nd column). Nones does not teach samples of EAC having dysplasia or metaplasia.
Bandla teaches obtaining esophageal mucosa specimens from subject diagnosed with EAC having dysplasia and intestinal metaplasia (see specimen screening and subject cohort). Bandla teaches mucosal tissue pieces were obtained from 4 subjects that underwent esophagectomies (see pg. 73, 1st column) (administering treatment, esophagectomy) (claim 17, 20, 35). Bandla teaches patients underwent upper endoscopy (see subject cohort) (preventative treatment, diagnostic test) (claim 13, 15, 31, 33), Bandla teaches isolating DNA and performing FISH analysis. Bandla teaches isolating columnar cell metaplasia (Barrett’s esophagus) (see specimen screening) (claim 3-4 and 6, 22-23, and 25). Bandla teaches analysis of metaplasia versus EAC to determine disease progression (see pg. 78, 1st column).
Given the prior art teaches detecting extrachromosomal DNA in esophageal carcinoma, it would have been prima facie obvious to the ordinary artisan at the time the invention was made to screen and test different types of samples from different tissues of esophagus cells, including samples from Barrett’s esophagus, epithelium samples and metaplasia for extrachromosomal DNA as taught by None. The skilled artisan would have been motivated to include analysis of different cell samples because both None and Bandla teaches FISH analysis of esophageal cells and the skilled artisan would have been motivated to include additional samples in the method of None for a more robust analysis of progression of esophageal cancer. The skilled artisan would have been motivated to include diagnostic testing, preventative treatment and treatment of subjects with or at risk of developing EAC in the method of None because Bandla teaches endoscopy as a diagnostic test and preventative as well as teaches esophagectomy as a treatment. The skilled artisan would have a reasonable expectation of success that extrachromosomal DNA can be tested in additional esophageal samples including Barrett’s esophagus, epithelium samples and metaplasia for extrachromosomal DNA because None teaches extrachromosomal DNA detection in EAC and Bandla teaches analysis of chromosomal DNA in Barrett’s esophagus, epithelium samples and metaplasia.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-4, 6, 8-9, 12-13, 15, 17, 20-23, 25, 27, 31, 33, 35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of U.S. Patent No. 11193164 in view of Bandla (Annals of Surgery, 2014, vol 260, 72-80).
Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-10 of ‘164 in view of Bandla would render obvious claims 1-4, 6, 8-9, 12-13, 15, 17, 20-23, 25, 27, 31, 33, and 35. Claims 1-10 of ‘164 do not claim esophageal cells, cancer, a subject with Barrett’s esophagus, biological sample comprising epithelium tissue, cells having metaplasia or dysplasia including columnar epithelial cells. ‘164 does not teach preventative treatment of esophageal cancer.
Bandla teaches obtaining esophageal mucosa specimens from subject diagnosed with EAC having dysplasia and intestinal metaplasia (see specimen screening and subject cohort). Bandla teaches mucosal tissue pieces were obtained from 4 subjects that underwent esophagectomies (see pg. 73, 1st column) (administering treatment, esophagectomy) (claim 17, 20, 35). Bandla teaches patients underwent upper endoscopy (see subject cohort) (preventative treatment, diagnostic test) (claim 13, 15, 31, 33), Bandla teaches isolating DNA and performing FISH analysis. Bandla teaches isolating columnar cell metaplasia (Barrett’s esophagus) (see specimen screening) (claim 3-4 and 6, 22-23, and 25). Bandla teaches analysis of metaplasia versus EAC to determine disease progression (see pg. 78, 1st column) (claim 12). Bandla teaches amplification of c-myc in EAC.
Therefore it would have been obvious to include detecting extrachromosomal oncogene in esophageal carcinoma and administering therapy to subjects and to include different types of samples from different tissues of esophagus cells, including samples from Barrett’s esophagus, epithelium samples and metaplasia as taught by Bandla. The skilled artisan would have been motivated to include analysis of different cell samples because Bandla teaches analysis of esophageal cells including esophageal carcinoma and the skilled artisan would have been motivated to include additional samples of esophageal cells for a more robust analysis of different cancer samples and different cell samples. The skilled artisan would have been motivated to include treatment of subjects with or at risk of developing EAC with anticancer therapy including esophagectomy because Bandla teaches endoscopy as a diagnostic test and preventative as well as teaches esophagectomy as a treatment. The skilled artisan would have a reasonable expectation of success that extrachromosomal DNA can be tested in additional cancers and samples including esophageal samples, Barrett’s esophagus, epithelium samples and metaplasia for extrachromosomal DNA because Bandla teaches analysis of chromosomal DNA including c-myc amplification in Barrett’s esophagus, epithelium samples and metaplasia.
Conclusion
No claims are allowed.
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/SARAE L BAUSCH/ Primary Examiner, Art Unit 1699