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 .
Election/Restrictions
Applicant’s election without traverse of group I, claims 1-28 in the reply filed on 06/17/2025 is acknowledged.
Claim 29 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 06/17/2025.
Claims 1-28 are under examination.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 62/944922, fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application.
62/944922 does not disclose SEQ ID NO 3 or SEQ ID NO 4. While ‘922 discloses mutant and wildtype probe (see table, pg. 1) the sequence of the mutant and wildtype probe is 11 net long whereas SEQ ID NO 3 and SEQ ID NO 4 is a 10 nucleotide length sequence, as such the sequences are not the same. Additionally it is noted that the reverse primer of ‘922 is SEQ ID NO 2. Because ‘922 does not provide support for SEQ ID NO 3 and 4 the effective filing date of the instant claims is 5/21/2020.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Figure 1B provides sequences without a SEQ ID NO for the sequence depicted in the figure. It is noted that the description indicates that the sequence illustrates forward and reverse primers (see pg. 4, lines 6-7) and teaches an example of a pair of amplification primers comprising a forward primer, SEQ ID NO 1 and reverse primer, SEQ ID NO 2 is shown in Fig 1B. The reverse primer depicted in Fig 1B is not the sequence of SEQ ID NO 2. Applicant is required to provide a sequence identifiers for the sequence in Fig 1B. Applicant should further correct the reverse primer sequence, SEQ ID NO 2 with the depicted sequence in Fig 1B, if the reverse primer sequence is the sequence depicted in Fig 1B.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-28 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites “a pair of detection primers”, “wherein the mutant primer comprises SEQ ID NO 3 and the wild-type primer comprises SEQ ID NO 4” however the working example refers to SEQ ID NO 3 and SEQ ID NO 4 as probes. SEQ ID NO 3 and SEQ ID NO 4 are not primers, the sequence of each is 10 nucleotides in length and hybridize to either the TERT promoter mutant or TERT promoter wild type sequence. These sequences do not amplify any nucleic acids. The recitation of mutant primer and wild-type primer renders the claim indefinite because it is unclear if SEQ ID NO 3 and SEQ ID NO 4 as claimed amplify the TERT promoter or as described in the specification detect the TERT promoter by hybridization (see pg. 25, TERT ddPCR). Accordingly the recitation of mutant primer and wild-type primer renders the claim indefinite because the claim does not reasonably apprise one of ordinary skill in the art the scope of the claims, the metes and bounds of the claim are unclear and it would not be readily apparent if one was infringing on the claimed invention.
Claim 1 is indefinite for the recitation of reverse primer comprises SEQ ID NO 2. While the sequence listing and working example (see pg. 25, TERT ddPCR) indicates SEQ ID NO 2 is the following sequence : AGAGCGGAAAGGAAGGGGA, figure 1B indicates SEQ ID NO 2 is CTCCCCTTCCTTTCCGCGG, or the reverse complement would be CCGCGGAAAGGAAGGGAG. The specification on page 10 indicates the forward primer (SEQ ID NO 1) and a reverse primer (SEQ ID NO 2) is shown in Fig 1B. It is unclear if the reverse primer sequence is intended to be the sequence indicated in Fig 1B or the sequence in the sequence listing. On 8/13/2025, the Examiner contacted Janice Kugler DeYoung to clarify if the sequence listing or the drawing was the correct sequence. A return phone call on 9/4/2025 indicated that the correct sequence was the sequence in figure 1B and not the sequence in the sequence listing. Because the claims recite SEQ ID NO 2 but the drawing indicates a different reverse primers, the claims are indefinite for what is encompassed by the reverse primer. If applicant updates the sequence listing accordingly the rejection will be withdrawn.
Claim 2, 17, and 18 contains the trademark/trade name. Claim 2 recites ExoLution PLUS kit. Claims 17 recites FAM, HEX, Cy3, Cy5, Texas Red and claim 18 recites Iowa Black FQ, Iowa Black RQ, ZEN Quencher and TAMRA. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe nucleic extraction (claim 2), fluorophores (claim 17) and quenchers (claim 18) and, accordingly, the identification/description is indefinite.
Claim 27 and claim 28 are indefinite over the recitation of “detecting the TERT promoter sequence in the DNA sample from the biological fluid of the subject according to the method of claim 1”. It is unclear what is encompassed by according to the method of claim 1. Does the detecting step require all of the method steps of claim 1 or does the detecting step require only some unstated part of claim 1. Would using SEQ ID NO 1 as a primer be according to the method of claim 1? Would detecting a mutation be according to the method of claim 1? Because it is unclear what is encompassed by the detecting step, the metes and bounds of the claimed invention are indefinite and one of ordinary skill in the art would not be apprised of infringing on the claimed method. Additionally because claim 27 and claim 28 are according to the method, claim 27 and claim 28 are also indefinite for the reasons applied to claim 1. Claim 27-28 recites the limitation "the TERT promoter", “the DNA sample”, “the biological fluid” in 3-4 of the claims. There is insufficient antecedent basis for this limitation in the claim. Claim 27-28 do not directly depend from claim 1, claim 27-28 only recite according to the method of claim 1.
Claims 2-26 depend from claim 1 and are indefinite for the reasons applied to claim 1.
Claim Interpretation
As addressed in the 112 section above, claim 1 recites a reverse primer comprising SEQ ID NO 2. SEQ ID NO 2 in the sequence listing and working example is different from the reverse primer sequence in Figure 1B. Applicant clarified on 9/4/2025 that the figure is the correct sequence for the reverse primer. For the purposes of the following art rejection, claim 1 has been interpreted as requiring the reverse primer sequence of CTCCCCTTCCTTTCCGCGG as depicted in Figure 1B. It is noted that a reverse primer of SEQ ID NO 2 is free of the art as this sequence has a 3 bp mismatch at the 5’ end of the primer to the TERT promoter sequence in Fig 1B.
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.
Claims 27-28 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Song (US20170369947A1, cited on IDS)
Song teaches detecting or monitoring recurrence in hepatocellular carcinoma (HCC) by determining a level of mutation in TERT (See para 23) in a biological sample. Song teaches the biological sample can be blood, serum, fluid, bile (see para 24). Song teaches performing PCR to determine the level of mutation in TERT (see para 29-32). Song teaches mutations at -124 in the promoter of TERT (see para 49). Song teaches identifying subject patients for treatment by mutant TERT associated cancers (see para 78). Song teaches determining TERT before and after treatment (see para 130-131). Therefore Song teaches detecting TERT promoter sequence in DNA sample from biological fluid of a subject according to claim 1, determining whether the subject has reoccurrence of cancer based on the level of mutant TERT, determining whether the cancer therapy is effective and administering a cancer therapy. Because the claim recites “according to claim 1” this has been interpreted as using PCR to detect a mutation in TERT as the claim does not require what according to claim 1 is required for the method.
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 1-2, 4-26 are rejected under 35 U.S.C. 103 as being unpatentable over McEvoy (2017, cited on IDS) in view of Krug (Annals of Oncology, 29:700-706, 2018), Ali Mosrati (Oncotarget, 2015, vol 6, pp 16663-16673), and Untergasser (NAR, 2007, Vol 35, W71-W74).
McEvoy teaches a method of droplet digital PCR for detection of TERT promoter mutations in cell free DNA from patients with cancer. McEvoy teaches isolating cfDNA from plasma of patients with melanoma (see DNA extraction from plasma). McEvoy teaches droplet digital PCR (claim 4-5) to detect C228T and C250T mutation. McEvoy teaches primers for TERT promoter region. The reverse primer comprises instant SEQ ID NO 1 (claim 9). McEvoy teaches a mutation and wildtype probe, see TERT Mut and TERT WT. The sequences of McEvoy are instant SEQ ID NO 3 and SEQ ID NO 4 (claim 11-12). The probes of McEvoy comprise LNA bases at position 4, 5, 6, 7 of the wild type probe and 5, 6, 7 of mutant probe (claim 6-7 and claim 8). The mutant probe comprises a first fluorophore and a first quencher and the wild type probe comprises a second fluorophore and a second quencher (claim 13-14). McEvoy teaches the probes comprise FAM or HEX as a fluorophore (claim 15, 17) and the same quencher IABkFq (claim 16, 18). McEvoy teaches the blood samples were collected from stage IV melanoma patients prior to treatment (see plasma sample preparation) (claim 19-22). McEvoy does not teach the reverse primer comprising SEQ ID NO 2. McEvoy does not teach exosomal DNA, cancer that is glioma or the reverse primer depicted in Fig 1B.
Krug teaches isolating plasma exoNA (exosomal DNA and RNA along with present cfDNA) was co-isolated from samples using ExoLution Plus (claim 2). Krug demonstrates the exoNA isolates and purifies the nucleic acids. Krug teaches mutation detection of exoNA allows for monitoring patient response to treatment and predicting treatment outcome. Krug teaches identification of non-responders to treatment switching patients to a different treatment (see pg. 704, 1st column). The isolation method of Krug allows for analysis of nucleic acid carried in exosome of living cells and ctDNA released by dying cells and beneficial in cases with low levels of nucleic acids in circulation.
Ali Mosrati teaches TERT promoter mutations in primary glioblastoma. Al Mostrati teaches detecting C228T and C250T in primary GBM and in oligodendroglioma (See mutation analysis, pg. 16664). Al Mostrati teaches that poor survival was detected in patients with a C alleles at rs2853669 (see pg. 16669). Al Mostrati teaches obtaining samples from blood and tumor tissues (see DNA extraction). Al Mostrati teaches mutation analysis of TERT promoter was performed by PCR using primers found in the literature (see mutation analysis).
Untergasser teaches a web interface for primer design. Untergasser teaches a program that allows primer design of a known target. Untergasser teaches the detection task that designs standard PCR primers to detect a given sequence and Primer List which generates all possible primers that can be designed ton a target sequence and meet current requirements (see pg. W73).
It would have been prima facie obvious to one having ordinary skill in the art before the effective filing to apply familiar primer design parameters to yield the primers of SEQ ID NO 1 and SEQ ID NO 2 (the sequence depicted in Fig 1B) with a reasonable expectation of success. As many primers were known at the time of filing to amplify the promoter sequence of TERT as taught by Ali Mostrati and McEvoy, McEvoy teaches the same forward primer as claimed but a different reverse primer. Because McEvoy and Ali Mostrati teaches primers to amplify the same promoter region a skilled artisan would have applied familiar primer design parameters to yield primers to amplify the promoter region, including SEQ ID NO 1 and 2. To this end, a skilled artisan at the time of filing would have designed primers and probes to known sequences (such as the sequences disclosed in the above references) with a high expectation of success. To design such primers constituted routine and conventional optimization at the time of filing. See In re Aller, 220 F.2d 454, at 456 (CCAP 1955) (“where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.”). Numerous references describe how to design and optimize primers and probes for PCR applications. For example, Untergasser teach how to design primers and probes from known sequences using known online primer/probe design programs for use in PCR assays. Untergasser teaches how to use Primer3Plus online program to design primers and probes to known sequences (Untergasser at pgs. W71-74). In other words, Untergasser (as provide specific guidance and parameters to optimize primer, probe and PCR assay design to yield optimal results; thus, designing PCR assays for particular applications constitutes well-known routine optimization. As noted in In re Aller, 105 USPQ 233 at 235, where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation. Routine optimization is not considered inventive and no evidence has been presented that the primer selection performed was other than routine, that the products resulting from the optimization have any unexpected properties, or that the results should be considered unexpected in any way as compared to the closest prior art. In sum, the claimed primers are prima facie obvious because there was clear motivation to design PCR primers to detect the same mutations in the TERT promoter sequence; and designing and optimizing such primers constitutes a well-known, routine and conventional technique which would yield the claimed primers with a reasonable expectation of success.
With regard to claim 2 and 25-26, it would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to improve the isolation of plasma in the method of McEvoy with DNA extraction kit as taught by Krug to include isolation of both exosomal nucleic acid and cell free DNA. Additionally it would have been obvious to include analysis of cancer therapy and administration of cancer therapy based on the analysis of both exosomal nucleic acid and cell free DNA as taught by Krug. The ordinary artisan would have been motivated to improve the isolation of nucleic acids from plasma samples as taught by McEvoy and replace the step with the isolation method and use the ExoLution PLUS kit as taught by Krug to allow for analysis of both exosomal nucleic acid and cell free DNA as taught by Krug. The ordinary arista would have had a reasonable expectation of success that isolation of both exosomal nucleic acids and cell free DNA could have been used in the method of McEvoy because both McEvoy and Krug teach isolation kits using plasma and detection of mutations in cancer.
With regard to claim 23-24, it would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to include analysis of glioma patients, including oligodendrogliomas in the method of McEvoy, because both McEvoy and Ali Mostrati teach detection of mutations at C228T and C250T in blood samples. The ordinary artisan would have been motivated to include additional cancers in the method of McEvoy to allow for a more robust analysis of C228T and C250T mutations in cancer. The ordinary artisan would have had a reasonable expectation of success that the method of McEvoy could be used for analysis of glioma because both McEvoy and Ali Mostrati teach PCR amplification to detect mutations in the promoter region of TERT.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over McEvoy in view of Krug, Ali Mosrati and Untergasser as applied to claims 1-2, 4-26 above, and further in view of Colebatch (Clin Chem, 64:4 (2018) 745-747, cited on IDS).
McEvoy in view of Krug, Ali Mosrati and Untergasser is set forth in section 16 above. McEvoy in view of Krug, Ali Mosrati and Untergasser does not teach the ddPCR reaction mixture comprises 7-deaza-GTP.
Colebatch teaches ddPCR assay for detection of C228T and C250T in the TERT promoter. Colebatch teaches an alternative assay for using locked nucleic acids for the probes of McEvoy. Colebatch teaches using 7-deaza-dGTP to improve the performance of ddPCR for the detection of TERT mutation (See pg. 745, 1st column). Colebatch teaches the addition of 7-deaza-GTP does not require the use of LNA and is successful to monitor circulating tumor DNA. Colebatch teaches that using 7-deaza-dGTP would improve the performance of ddPCR in high GC targets.
Therefore, it would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to improve the method of detecting C228T or C250T mutation in TERT as taught by McEvoy in view of Krug, Ali Mosrati and Untergasser by replacing the LNA probes of McEvoy with 7-deaza-dGTP to improve the performance of the ddPCR method of McEvoy in view of Krug, Ali Mosrati and Untergasser. The ordinary artisan would have been motivated to improve the method of ddPCR analysis for detection of C228T and C250T in TERT promoter of McEvoy in view of Krug, Ali Mosrati and Untergasser and replace the use of LNA labels in the probe of McEvoy and use 7-deaza-dGTP because Colebatch teaches the use of 7-deaza-dGTP improves the performance of ddPCR. The ordinary artisan would have had a reasonable expectation of success to use 7-deaza-dGTP in the method of McEvoy in view of Krug, Ali Mosrati and Untergasser because both McEvoy in view of Krug, Ali Mosrati and Untergasser and Colebatch teach analysis of C250T and C228T in the TERT promoter by ddPCR.
Conclusion
No claims are allowable.
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/SARAE L BAUSCH/ Primary Examiner, Art Unit 1699