DETAILED ACTION
Response to Amendment
Applicant’s response to the office action filed on December 3, 2025 has been entered. The claims pending in this application are claims 7 and 18-33 wherein claims 7 and 18-28 have been withdrawn due to the restriction requirement mailed on January 30, 2019. The objection/rejections not reiterated from the previous office action are hereby withdrawn in view of applicant’s amendment filed on December 3, 2025. Claims 29-33 will be examined.
Claim Objections
Claim 29 is objected to because of the following informalities: (1) “PTO (Probing and Tagging Oligonucleotide)” in step (a-1)” should be “Probing and Tagging Oligonucleotide (PTO)”; (2) “the first and the second upstream oligonucleotide” in step (a-1) should be “each of the first upstream oligonucleotide and the second upstream oligonucleotide”; (3) “the first and the second PTO” in step (a-1) should be “the first PTO and the second PTO”; (4) “each of the resultants” in steps (a-2) and (a-4) should be “the hybridizing mixture”; (5) “CTO (Capturing and Tagging Oligonucleotide)” in step (a-3)” should be “Capturing and Tagging Oligonucleotide (CTO)”; (6) “the first and the second CTO” in step (a-3) should be “the first CTO and the second CTO”; (7) “the first and the second fragment hybridized to the first and the second CTO, respectively, are extended to form an extended strand” in step (a-4) should be “the first fragment and the second fragment hybridized to the first CTO and the second CTO, respectively, are extended to form extended strands”; and (8) “RFU (relative fluorescence unit)” in step (f-1) should be “relative fluorescence unit (RFU)”.
Claim 30 is objected to because of the following informality: “the first detection temperature and the second detection temperature are implemented in each cycle or in the selected cycles of the real-time PCR” should be “the first detection temperature and the second detection temperature are identical in each cycle or in the selected cycles of the real-time PCR”.
Claim 31 is objected to because of the following informalities: (1) “a third and a fourth upstream oligonucleotides, a third and a fourth PTO, and a third and a fourth CTO” should be “a third upstream oligonucleotide and a fourth upstream oligonucleotide, a third PTO and a fourth PTO, and a third CTO and a fourth CTO”; and (2) “these additional two signal-generating means” should be “the additional two signal-generating means”.
Appropriate correction is required.
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.
New Matter
Note that this rejection is different from the new matter rejection mailed on September 10, 2025.
Claims 29-33 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.
Step (f) of newly amended claim 29 contains a limitation “(f-1) determining the presence of the first target nucleic acid sequence by a formula (i) or (ii): (i) [(signal intensity of the test sample incubation product at the first detection temperature) - (signal intensity of the test sample incubation product at the second detection temperature) * (the second reference value)]; (ii) [(signal intensity of the test sample incubation product at the second detection temperature) - (signal intensity of the test sample incubation product at the first detection temperature) / (the second reference value)], wherein a resulting value of formula (i) greater than a first threshold of RFU (relative fluorescence unit) 300 for distinguishing the presence and absence of the first target nucleic acid or a resulting value of formula (ii) smaller than a second threshold of RFU -200 indicates the presence of the first target nucleic acid, and (f-2) determining the presence of the second target nucleic acid sequence by a formula (iii) or (iv): (iii) [(signal intensity of the test sample incubation product at the first detection temperature) - (signal intensity of the test sample incubation product at the second detection temperature) * (the first reference value)]; (iv) [(signal intensity of the test sample incubation product at the second detection temperature) - (signal intensity of the test sample incubation product at the first detection temperature) / (the first reference value)], wherein a resulting value of formula (iii) smaller than a third threshold of RFU -1000 for distinguishing the presence and absence of the second target nucleic acid or a resulting value of formula (iv) greater than a fourth threshold of RFU 150 indicates the presence of the second target nucleic acid”. Although applicant stated that “[T]he horizontal line in Figure 1D (ii), RFU 300, represents the first threshold in claim 29”, “[T]he horizontal line in Figure 1D (ii), RFU-200, represents the second threshold in claim 29”, “[T]he horizontal line in Figure 1C (ii), RFU -1000, represents the third threshold in claim 29”, and “[T]he horizontal line in Figure 1C (i), RFU 150, represents the fourth threshold in claim 29” (see pages 21 and 22 of applicant’s remarks), above limitation recited in claim 29 is considered as a new matter since the specification only describes that “[F]IG. 1C schematically represents determination of the presence of a target nucleic acid sequence (genome DNA of Neisseria gonorrhoeae, NG) by using the reference value of CT obtained in FIG. 16 and the signals detected in FIG. 1A. The dotted lines denote a threshold value” and “[F]IG. 1D schematically represents determination of the presence of a target nucleic acid sequence (genome DNA of Chlamydia trachomatis, CT) by using the reference value of NG obtained in FIG. 1B and the signals detected in FIG. 1A. The dotted line denotes a threshold value. The dotted lines denote a threshold value” (see paragraphs [0020] and [0021] of US 2017/0362646 A1, which is US Publication of this instant case), the first threshold and the second threshold recited in claim 29 are obtained based on determination of the presence of a genome DNA of Chlamydia trachomatis (CT) by using the reference value of genome DNA of Neisseria gonorrhoeae (NG) obtained in FIG. 1B and the signals detected in FIG. 1A, the third threshold and the fourth threshold recited in claim 29 are obtained based on determination of the presence of a genome DNA of Neisseria gonorrhoeae (NG) by using the reference value of genome DNA of Chlamydia trachomatis (CT) by using the reference value of CT obtained in FIG. 16 and the signals detected in FIG. 1A, and claim 29 does not limit the reference sample and the test sample to genomic DNAs from specific sources.
MPEP 2163.06 notes “If new matter is added to the claims, the examiner should reject the claims under 35 U.S.C. 112, first paragraph - written description requirement. In re Rasmussen, 650 F.2d 1212, 211 USPQ 323 (CCPA 1981).” MPEP 2163.02 teaches that “Whenever the issue arises, the fundamental factual inquiry is whether a claim defines an invention that is clearly conveyed to those skilled in the art at the time the application was filed...If a claim is amended to include subject matter, limitations, or terminology not present in the application as filed, involving a departure from, addition to, or deletion from the disclosure of the application as filed, the examiner should conclude that the claimed subject matter is not described in that application.” MPEP 2163.06 further notes “When an amendment is filed in reply to an objection or rejection based on 35 U.S.C. 112, first paragraph, a study of the entire application is often necessary to determine whether or not “new matter” is involved. Applicant should therefore specifically point out the support for any amendments made to the disclosure” (emphasis added).
Scope of Enablement
Note that this rejection is different from the scope of enablement rejection mailed on September 10, 2025.
Claims 29-33 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for incubating a test sample in a single reaction vessel with the first upstream oligonucleotide and the second upstream oligonucleotide, the first PTO and the second PTO, the first CTO and the second CTO, and the template-dependent nucleic acid polymerase by real-time PCR under conditions suitable to perform the hybridizing, contacting, and extending steps, does not reasonably provide enablement for detecting a first target nucleic acid sequence and a second target nucleic acid sequence in a test sample using different detection temperatures and reference values as recited in claims 29-33. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). Wands states at page 1404,
“Factors to be considered in determining whether a disclosure would require undue experimentation have been summarized by the board in Ex parte Forman. They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.”
The Nature of The Invention
The claims are drawn to a method for detecting a first target nucleic acid sequence and a second target nucleic acid sequence in a sample using different detection temperatures and reference values. The invention is a class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001).
The Breadth of The Claims
Claims 29-33 encompass a method for detecting a first target nucleic acid sequence and a second target nucleic acid sequence in a sample using different detection temperatures and reference values, comprising: (a) performing a reaction on a reference sample containing the first target nucleic acid sequence and the second target nucleic acid sequence to obtain reference signals, comprising: (a-1) hybridizing the first target nucleic acid sequence in the reference sample with a first upstream oligonucleotide and a first PTO (Probing and Tagging Oligonucleotide), and hybridizing the second target nucleic acid sequence in the reference sample with a second upstream oligonucleotide and a second PTO, wherein each of the first and the second upstream oligonucleotide comprises a hybridizing nucleotide sequence complementary to the first and the second target nucleic acid sequences, respectively; wherein the first PTO comprises (i) a first 3’-targeting portion complementary to the first target nucleic acid sequence and (ii) a first 5’-tagging portion that is non-complementary to the first target nucleic acid sequence, and the second PTO comprises (i) a second 3’-targeting portion complementary to the second target nucleic acid sequence and (ii) a second 5’-tagging portion that is non-complementary to the second target nucleic acid sequence; and wherein the first and the second upstream oligonucleotides are located upstream of the first and the second PTO, respectively; (a-2) contacting each of the resultants of step (a-1) with a template-dependent nucleic acid polymerase having 5’ nuclease activity under conditions that induce cleavage of the first PTO and the second PTO, wherein each of the first and the second upstream oligonucleotides or its extended strand causes cleavage of each of the first and the second PTO, respectively, thereby releasing a first fragment comprising the first 5’-tagging portion or a part thereof and a second fragment comprising the second 5’ -tagging portion or a part thereof, respectively; (a-3) hybridizing each of the first and the second fragments of step (a-2) with a first and a second CTO (Capturing and Templating Oligonucleotide), respectively; (a-3) hybridizing each of the first and the second fragments of step (a-2) with a first and a second CTO (Capturing and Templating Oligonucleotide), respectively, wherein the first and the second CTO is labeled with a fluorescent label and a quencher; wherein the first CTO comprises, in a 3' to 5' direction, (i) a first capturing portion complementary to the first 5'-tagging portion or a part thereof and (ii) a first templating portion that is non-complementary to both the first 5’-tagging portion and the first 3’-targeting portion of the first PTO such that the fluorescent label is quenched unless and until the first fragment hybridizes to the first capturing portion and an extension occurs; and wherein the second CTO comprises, in a 3’ to 5’ direction, (i) a second capturing portion complementary to the second 5’-tagging portion or a part thereof and (ii) a second templating portion that is non-complementary to both the second 5’-tagging portion and the second 3’-targeting portion of the second PTO such that the fluorescent label is quenched unless and until the second fragment hybridizes to the second capturing portion and an extension occurs; and (a-4) performing an extension reaction on each of the resultants of step (a-3) with a template-dependent nucleic acid polymerase having 5' nuclease activity, such that the first and the second fragment hybridized to the first and the second CTO, respectively, are extended to form an extended strand, thereby generating a first reference signal and a second reference signal, respectively; (b) detecting the first reference signal and the second reference signal at a first detection temperature of 60 °C and at a second detection temperature of 72 °C; (c) obtaining (c-1) a first reference value for the first target nucleic acid sequence, the first reference value representing a ratio of the first reference signal at the first detection temperature to the first reference signal at the second detection temperature, and (c-2) a second reference value for the second target nucleic acid sequence, the second reference value representing a ratio of the second reference signal at the first detection temperature to the second reference signal at the second detection temperature, wherein the first reference value is at least 1.1 fold larger than the second reference value or vice versa, wherein both the first reference value and the second reference value are obtained from fluorescence measurements made in a single fluorescence detection channel and are derived solely from signals generated upon formation of the extended strand; (d) incubating the test sample in a single reaction vessel with the first and second upstream oligonucleotides, the first and second PTOs, the first and second CTOs, and the template-
dependent nucleic acid polymerase by real-time PCR under conditions suitable to perform the hybridizing, contacting, and extending steps defined in the steps (a-1) through (a-4), to give a test
sample incubation product, (e) detecting signals from the test sample incubation product at the first detection temperature and at the second detection temperature, wherein the signals are obtained from fluorescence measurements made in a single fluorescence detection channel and are derived solely from signals generated upon formation of the extended strand, and (f) (f-1) determining the presence of the first target nucleic acid sequence by a formula (i) or (ii): (i)
[(signal intensity of the test sample incubation product at the first detection temperature) - (signal intensity of the test sample incubation product at the second detection temperature) * (the second reference value)]; (ii) [(signal intensity of the test sample incubation product at the second detection temperature) - (signal intensity of the test sample incubation product at the first detection temperature) / (the second reference value)], wherein a resulting value of formula (i) greater than a first threshold of RFU (relative fluorescence unit) 300 for distinguishing the presence and absence of the first target nucleic acid or a resulting value of formula (ii) smaller than a second threshold of RFU -200 indicates the presence of the first target nucleic acid, and (f-2) determining the presence of the second target nucleic acid sequence by a formula (iii) or (iv):(iii) [(signal intensity of the test sample incubation product at the first detection temperature) - (signal intensity of the test sample incubation product at the second detection temperature) * (the first reference value)]; (iv) [(signal intensity of the test sample incubation product at the second detection temperature) - (signal intensity of the test sample incubation product at the first detection temperature) / (the first reference value)], wherein a resulting value of formula (iii) smaller than a third threshold of RFU -1000 for distinguishing the presence and absence of the second target nucleic acid or a resulting value of formula (iv) greater than a fourth threshold of RFU 150 indicates the presence of the second target nucleic acid.
Working Examples
The specification provides working examples (see pages 64-73) for: (1) Multiple Target Detection by TaqMan real-time PCR Using Different Detection Temperatures and Reference Values; (2) Multiple target detection by PTOCE real-time PCR comprising Using Different Detection Temperatures and Reference Values; and (3) SNP Genotyping Using Different Detection Temperatures and Reference Values. However, the specification provides no working example for detecting a first target nucleic acid sequence and a second target nucleic acid sequence in a test sample using different detection temperatures and reference values as recited in claims 29-33.
The Amount of Direction or Guidance Provided and The State of The Prior Art
Although the specification provides working examples (see pages 64-73) for: (1) Multiple Target Detection by TaqMan real-time PCR Using Different Detection Temperatures and Reference Values; (2) Multiple target detection by PTOCE real-time PCR comprising Using Different Detection Temperatures and Reference Values; and (3) SNP Genotyping Using Different Detection Temperatures and Reference Values, the specification does not provide a guidance to show that a first target nucleic acid sequence and a second target nucleic acid sequence in a test sample can be detected using different detection temperatures and reference values as recited in claims 29-33. Furthermore, there is no experimental condition and/or experimental data in the specification to support the claimed invention. During the process of the prior art search, the examiner has not found any prior art which is related to detect a first target nucleic acid sequence and a second target nucleic acid sequence in a test sample using different detection temperatures and reference values as recited in claims 29-33.
Level of Skill in The Art, The Unpredictability of The Art, and The Quantity of Experimentation Necessary
While the relative skill in the art is very high (the Ph.D. degree with laboratory experience), there is no predictability whether a first target nucleic acid sequence and a second target nucleic acid sequence in a test sample can be detect using different detection temperatures and reference values as recited in claims 29-33.
Although steps (b) and (c) of claim 29 require detecting the first reference signal and the second reference signal at a first detection temperature of 60 °C and at a second detection temperature of 72 °C and obtaining a first reference value for the first target nucleic acid sequence, the first reference value representing a ratio of the first reference signal at the first detection temperature to the first reference signal at the second detection temperature, and a second reference value for the second target nucleic acid sequence, the second reference value representing a ratio of the second reference signal at the first detection temperature to the second reference signal at the second detection temperature, wherein the first reference value is at least 1.1 fold larger than the second reference value or vice versa, wherein both the first reference value and the second reference value are obtained from fluorescence measurements made in a single fluorescence detection channel and are derived solely from signals generated upon formation of the extended strand, since steps (a) to (c) of claim 29 do not indicate how to differentiate the first reference signal from the second reference signal based on fluorescence measurements at each of the first detection temperature and the second detection temperature, it is unpredictable how a first reference value can be obtained based on a ratio of the first reference signal at the first detection temperature to the first reference signal at the second detection temperature and a second reference value can be obtained based on a ratio of the second reference signal at the first detection temperature to the second reference signal at the second detection temperature such that the presence of the first target nucleic acid sequence cannot be determined by a formula (i) or (ii) and the presence of the second target nucleic acid sequence cannot be determined by a formula (iii) or (iv) as recited in step (f) of claim 29. Furthermore, although step (d) of claim 29 requires incubating the test sample in a single reaction vessel with the first upstream oligonucleotide and the second upstream oligonucleotide, the first PTO and the second PTO, the first CTO and the second CTO, and the template-dependent nucleic acid polymerase by real-time PCR under conditions suitable to perform the hybridizing, contacting, and extending steps defined in the steps (a-1) through (a-4), since steps (a-1) through (a-4) of claim 29 do not require to perform a real-time PCR, if steps (a-1) through (a-4) of claim 29 do not include a real-time PCR, it is unclear how signal intensities of the test sample incubation product from the test sample incubation product at the first detection temperature and at the second detection temperature obtained from step (d) of claim 29 can be used together with the first reference value and the second reference value obtained from steps (a) to (c) of claim 29 in
a formula (i) or (ii) for determining the presence of the first target nucleic acid sequence and in a formula (iii) or (iv) for determining the presence of the second target nucleic acid sequence as recited in step (f) of claim 29. In addition, although claim 31 requires that the single reaction vessel in step (d) further comprises at least one additional set of two signal-generating means, which comprises a third upstream oligonucleotide and a fourth upstream oligonucleotide, a third PTO and a fourth PTO, and a third CTO and a fourth CTO, for detecting additional two target nucleic acid sequences, since claim 31 does not indicate how to differentiate the signals generated by the additional two signal-generating means, it is unpredictable how the additional two target nucleic acid sequences can be detected.
Case law has established that “(t)o be enabling, the specification of a patent must teach those skilled in the art how to make and use the full scope of the claimed invention without ‘undue experimentation’.” In re Wright 990 F.2d 1557, 1561. In re Fisher, 427 F.2d 833, 839, 166 USPQ 18, 24 (CCPA 1970) it was determined that “[T]he scope of the claims must bear a reasonable correlation to the scope of enablement provided by the specification to persons of ordinary skill in the art”. The amount of guidance needed to enable the invention is related to the amount of knowledge in the art as well as the predictability in the art. Furthermore, the Court in Genentech Inc. v Novo Nordisk 42 USPQ2d 1001 held that “[I]t is the specification, not the knowledge of one skilled in the art that must supply the novel aspects of the invention in order to constitute adequate enablement”.
In view of above discussion, the skilled artisan will have no way to predict the experimental results. Accordingly, it is concluded that undue experimentation is required to make the invention as it is claimed. These undue experimentation at least includes to test whether a first target nucleic acid sequence and a second target nucleic acid sequence in a sample can be detect using different detection temperatures and reference values as recited in claims 29-33.
Conclusion
In the instant case, as discussed above, the level of unpredictability in the art is high, the specification provides one with no guidance that leads one to claimed methods. One of skill in the art cannot readily anticipate the effect of a change within the subject matter to which the claimed invention pertains. Thus given the broad claims in an art whose nature is identified as unpredictable, the unpredictability of that art, the large quantity of research required to define these unpredictable variables, the lack of guidance provided in the specification, the absence of any working example related to claimed invention and the no teaching in the prior art balanced only against the high skill level in the art, it is the position of the examiner that it would require undue experimentation for one of skill in the art to perform the method of the claim as broadly written.
Response to Arguments
Applicant’s arguments with respect to claims 29-33 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Conclusion
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.
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Frank Lu, Ph. D., whose telephone number is (571)272-0746. The examiner can normally be reached Monday to Friday, 9 AM to 5 PM.
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/FRANK W LU/
Primary Examiner, Art Unit 1683
February 23, 2026