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 .
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The IDS received on December 25, 2024 is proper and is being considered by the Examiner.
Drawings
New corrected drawings in compliance with 37 CFR 1.121(d) are required in this application because the drawings filed on September 14, 2024 are poor in quality and the labels of the x- and y- axes are not legible (see Figs. 1-8). Applicant is advised to employ the services of a competent patent draftsperson outside the Office, as the U.S. Patent and Trademark Office no longer prepares new drawings. The corrected drawings are required in reply to the Office action to avoid abandonment of the application. The requirement for corrected drawings will not be held in abeyance.
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 1-10 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 is indefinite for missing a conjunction between the recitation of the wild-type amplification blockers (i.e., between the Tm1 limitation and the blocking group limitation).
Claim 1 is also indefinite for reciting the phrase, “wild-type amplification blocker specifically binding to a mutant template” because the term, “specific binding” is conventionally understood in the art to be non-cross hybridizing. Therefore, a wild-type blocker, which is to block amplification of a wildtype sequence of a gene, cannot be at the same time specific to a mutant template.
Claim 4 is indefinite for the following reasons.
The term, “Tm value of probe specifically binding to the wild-type template of the gene” lacks a proper antecedent basis. The parent claim 3 (which depends from claim 1) defines a “blocker-probe combination” as comprising a probe and the wild type amplification blocker (referring to that which is described in parent claim 1). The “probe,” according to parent claim 1, appears to be directed to a mutant sequence of a gene and the wild-type amplification blocker appears to be directed to the same gene region cover this mutant sequence, but is perfectly complementary to the non-mutant sequence (i.e., wildtype) of the gene. Therefore, the only probe that specifically binds to the wild-type template is the wild-type blocker, and not the probe. While the probe can bind to a wild-type version of the gene, it is not a specific binding according to the meaning accepted in the art. The Office has construed this limitation to mean that the probe that is specific for the mutant has a melting temperature Tm3 when bound to the wild-type sequence. Indeed this appears to be the correct interpretation as the claim recites that Tm1 is greater than Tm3, meaning that the wild-type blocker (which is specific for the wildtype) should have a higher melting temperature than the probe which is mis-bound thereto, and Tm3 is greater than Tm2 since Tm2 defines the wild-type blocker mis annealing to the mutant sequence.
Claim 5 is indefinite for reciting a trademarked element, ECLIPSE. The usage of a trademark in a claim renders the claim indefinite because a trademark identifies the source of the good and not the good itself. Because the product can change over time while retaining the same tradename (e.g., Coke®), the metes and bounds of a product defined by its trademark becomes vague and indefinite.
Claim 7 appears to contain a typographical error as reciting “RCR buffer”. This term does not appear anywhere else in the application. however, the specification does disclose a “PCR buffer” (see section [0031]), as well as claim 8 referring to claim 8, further reciting “the PCR buffer”. Therefore, the subject-term has been construed to mean a “PCR buffer.”
Claim 8 is indefinite because the claim recites limitations which appears to be an intended usage. The phrase, “in the nucleic acid detection system, a final concentration of the wild-type amplification blocker is 0.02-0.5 mM”. A convention usage of the term, “final concentration” is when a reagent is placed and results in a final concentration after all other reagents for an assay is added. However, claim 8 is directed to a product. Therefore, if the concentration is a final concentration as conventionally used in the art, then the metes and bounds surrounding what the concentration of the product is before the final concentration is reached remains unclear and indefinite.
Claims 2-10 are indefinite by way of their dependency on claim 1.
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 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Huang et al. (Molecular and Cellular Probes, 2010, vol. 24, pages 376-380).
With regard to claim 1, Huang et al. teach a wild-type amplification blocker, wherein the Tm value of the wild-type blocker is higher when perfectly matched to the wild-type sequence than when the wild-type blocker is mismatched to the mutant sequence (see below):
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Because the wild-type blocker (i.e., LNA/DNA chimeras) is perfectly matched to the wild-type sequence of a gene, the probe stays bound, whereas the mismatches present result in the lower Tm and becomes displaced.
As well, Huang et al. teach that the wild-type blocker is blocked at its 3’ end to prevent extension (“[t]o avoid the extension of WTB by DNA polymerase in PCR procedures, a phosphorylation group was modified at its 3’-terminus” (page 377, 2nd column, 1st paragraph).
Therefore, Huang et al. anticipate the invention as claimed.
Claims 1, 3, 5, 7, and 9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Hellyer et al. (US 2014/0193819 A1, published July 10, 2014).
With regard to claim 1, Hellyer et al. teach a wild-type amplification blocker wherein the Tm value of the wild-type blocker is higher when perfectly matched to the wild-type sequence than when the wild-type blocker is mismatched to the mutant sequence (see below, Fig. 2):
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Because the wild-type blocker (i.e., the modulator) is perfectly matched to the wild-type sequence of a gene, the probe stays bound, whereas the mismatches present result in the lower Tm and becomes displaced (“the modulator oligonucleotide preferentially binds to the more abundant, e.g., wild-type target sequence compared to the rare, e.g., mutant or variant target sequence”, section [0083]).
As well, Hellyer et al. teach that the wild-type blocker is blocked at its 3’ end to prevent extension (“[m]odulator oligonucleotides are disclosed herein refer to oligonucleotides that are incapable of extension by a polymerase, for example, when hybridized to its complementary sequence in an amplification assay, e.g., PCR) … modifying oligonucleotides to render them incapable of extension by a polymerase … 3’-OH modification and dideoxy nucleotides”, section [0070]).
With regard to claim 3, the artisans teach a system comprising a forward primer, a reverse primer, and at least one blocker-probe combination which comprises a probe and the wild-type amplification blocker (see above, modulator is the wild-type amplification blocker as discussed above, and the mutant allele probe (A/T), also “detect the presence and/or amount of multiple target sequences in the sample, for example variant target sequence(s), including rare variant or mutant template nucleic acids, the sample is contacted with one or more sequence-specific reporter probes … detector probes”, section [0084]), wherein the forward and reverse primers are used to amplify the gene to be detected and they are located upstream and downstream of the gene to be detected (see above).
With regard to claim 5, the probe is comprised of FRET dye pair including FAM and quencher and TAMRA, wherein the probe is considered a molecular beacon (see section [0086]), having an LNA modification (see section [0077]).
With regard to claim 7, the system further comprises PCR buffer, a DNA polymerase, and dNTPs (see section [0068] and section [0094]).
With regard to claim 9, the artisans teach a kit comprising the above-discussed reagents (see section [0041]).
Therefore, Hellyer et al. anticipate the invention as claimed.
Claim Rejections - 35 USC § 103
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.
Claims 2, 4, 6, 8, and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Hellyer et al. (US 2014/0193819 A1, published July 10, 2014) in view of Marras et al. (Clinica Chimica Acta, 2006, vol. 363, pages 48-60).
The teachings of Hellyer et al. have already been discussed above.
Hellyer et al. teach that the wild-type amplification blocker and the probe overlap in bases (see above), and the overlapping base is not less than 80-20% of the total number of basses of the probe (“reporter probe(s) and the modular oligonucleotide [i.e., wild-type blocker] exists over 10% … 85% or more … of the length of the modulator oligonucleotide and/or reporter probe(s)”, section [0090]). With regard to Tm3 being defined as Tm1> Tm3> Tm2, this is inherent owning to the fact that the melting temperature, Tm3, of mutant specific probe to the wild-type sequence must be lower than that of the melting temperature, Tm1, of wild-type blocker to the its completely complementary wild-type template sequence, and the melting temperature of the wild-type blocker to the mutant template sequence, Tm2 should be less than the melting temperature of the mutant probe to the complete complementary sequence of the mutant template.
However, the Hellyer et al. do not explicitly teach the difference in Tm between the wild-type blocker (to the wild-type sequence) and that of the mismatch TM of the mutant probe (to the wild-type sequence) (claim 4).
Similarly, Hellyer et al. do not explicitly teach that the Tm values of the forward and the reverse primers and their relation to the Tm values of the wild-type blocker (to wild-type template) (claim 6).
Hellyer et al. teach that LNA could comprise ribonucleotide bases (“modulator oligonucleotide can contain one or more lockend nucleic acid (LNA)-type modification. LNA modifications useful in the embodiments disclosed herein can involve alterations to the pentose sugar or ribo- and deoxyribonucleotides that contains, or ‘locks’ the sugar …”, section [0077]), but do not explicitly teach the Tm conditions as discussed above (claim 2).
While Hellyer et al. teach the additional reagents of PCR buffer, such as KCl, MgCl2, or ammonium sulfate (see section [0094]), and the use of a Pfu DNA polymerase (see section [0092], a known DNA polymerase without 5’-3’ exonuclease activity and no 3’ to 5’ endouclease activity) the artisans do not explicitly teach their concentration of the wild-type amplification blocker, the reporter probe, the primers, and the dNTPs (claim 8).
Hellyer et al. do not teach the recited method of PCR and melting point analysis under the recited conditions in claim 10.
Marras et al. teach a method of performing a melting analysis with molecular beacon probes (see page 55, Fig. 7).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Hellyer et al. with the teachings of Marras et al. and conventionally applied protocols, thereby arriving at the invention as claimed for the following reasons.
With regard to the determination of the optimal melting temperature to utilize for the wild-type blocker and a mutant specific probe in an amplification reaction, given the teachings of Hellyer et al. who expressly teach the use of a wild-type blocker to suppress the amplification of more abundant wild-type nucleic acid molecules in a sample, so as to allow the detection of the more rare mutation molecules to be detected by the reporter probe, one of ordinary skill in the art would have been motivated to empirically determine the melting temperatures of the wild-type blocker, the mutant specific reporter probe, and the forward and reverse primers, allowing the amplification to occur while suppressing the amplification of wild-type template nucleic acids in the sample. Optimization of assay parameters have been conventional and routine in the art of molecular diagnostics as conditions such as buffer, reagent, and temperature of the assay have been known to be result-effective variable.
In In re Antonie, 559 F.2d 618, 195 USPQ 6 (CCPA 1977), the CCPA held that a particular parameter must first be recognized as a result-effective variable, i.e., a variable which achieves a recognized result, before the determination of the optimum or workable ranges of said variable might be characterized as routine experimentation.
With regard to the application of the method of Hellyer et al. to extend the amplification to a melting point assay of the mutant nucleic acids, doing so would have been obvious to ascertain the presence of the mutant nucleic acid by further performing a melting point analysis with the probe of Hellyer et al., which was expressly taught as being a molecular beacon, which is also shown in Marras et al. Indeed, combining the amplification assay of Hellyer et al. would have provided an amplification reaction with suppressed wild-type nucleic acid in the sample with reporter probe providing the presence of the mutant nucleic acid therein, and applying a melting point assay with the same molecular beacon probe would have further confirmed the presence of said mutant nucleic acid. One of ordinary skill in the art would have also had a reasonable expectation of success given that the reporter probe of Hellyer et al. was a molecular beacon which was also employed by Marras et al. in the melting point assay.
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 September 25, 2026
/YJK/
