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 .
Status of Claims
Applicant’s amendment filed 6/21/2024 is acknowledged. Claims 3-23 and 27 have been amended. Claims 28-42 have been added. Claims 1-42 are pending in the instant application and the subject of this non-final office action.
Specification
The use of the terms including ”Cy”, “Triton”, “Igepal”, “Tergitol”, “Tween”, “StarSeal”, (as “Star Seal” in the specification), and “Spark”, each which is a trade name or a mark used in commerce, has been noted in this application. Such terms should be accompanied by the generic terminology; furthermore such terms should be capitalized (each letter) wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
A hyperlink was identified at the top of pg. 17.
Drawings
The drawings are objected to because Fig. 5 contains the trademarked term “Tergitol”. See Specification section above regarding form of trademarked terms.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 2, 8, 11, 24, 26, 33, and 40 are objected to because of the following informalities:
Claims 2, 8, 24, and 33: The plurality of elements in each claim should be set forth by a line indentation.
Claims 11 and 36: The quotations around “hot-start” should be deleted.
Claims 14 and 38: The claims recite “1 to 10 or 2 to 5 oligonucleotides in length”. This appears to be a typo of “nucleotides in length”.
Claim 26: The claim has a line break after “Igepal,”. This differs from claim 6 and may be unintentional.
Claim 40: The claim appears to have an unintentional line break after “or” in the first line.
Appropriate correction is required.
Claim Order
A series of singular dependent claims is permissible in which a dependent claim refers to a preceding claim which, in turn, refers to another preceding claim.
A claim which depends from a dependent claim should not be separated by any claim which does not also depend from said dependent claim. It should be kept in mind that a dependent claim may refer to any preceding independent claim. In general, applicant's sequence will not be changed. See MPEP § 608.01(n).
It is noted that the instant claim sequence has intervening independent claims and the sequence may be reordered if allowable claims are found.
Claim Interpretation
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP 2111.
The term “working concentration” is interpreted to be a diluted, i.e., 1X, concentration. This is consistent with the usage in the specification in at least pg. 22, Buffer Composition 3 at 2x, para 2.
The term “buffer” has been defined as “solution containing a buffering agent or a mixture of buffering agents and further components (e.g. other salts, compounds, enzymes
etc.)” (pg. 14, para 1).
Claim Rejections - 35 USC § 112(b)
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 1-42 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.
Regarding claims 1 and 2, the claims recite “the tag sequence of a forward primer”. It is not clear if this is intended to be the tag sequence of the one or more forward oligonucleotide primers and if so which one as this phrase recites only “a forward primer”. This is an antecedent basis rejection.
Similarly, the claims recite “the sequence of a probe”, where it is not clear whether this is intended to be the sequence having at least 50% identity to the tag sequence of a forward oligonucleotide primer and which probe. This is an antecedent basis rejection.
Claims 3-23 and 28-42 are indefinite for depending on claims 1 or 2 and not rectifying the deficiency.
Regarding claims 3 and 28, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, the claim recites the broad recitation “no more than 60 mM, and the claims also recite “about 40 mM to about 60 mM”, “about 45 mM to about 55 mM” which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Regarding claims 5-6, 25-26, and 30-31, the claims recite “Tergitol”, “Triton”, and “Igepal”, each of which is a trademark/trade name. 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 non-ionic surfactants and, accordingly, the identification/description is indefinite.
Regarding claims 8 and 33, the claims recite “TMAC”. No definition was identified for this abbreviation in the specification. TMAC is known in the art to refer to tetramethylammonium chloride and multiple classes of proteins (e.g., testis-specific meiotic arrest complex and transmembrane adenylyl cyclase).
Regarding claims 15-16 and 39-40, the claims recite “the tag sequence of a forward oligonucleotide primer”. As in claims 1-2, it is not clear which forward primer being referred to and if the tag sequence is that of (i). This is an antecedent basis rejection.
Regarding claims 17-18 and 41-42, the claims recite “the sequence of a probe”. As in claims 1-2, it is not clear which probe is being referred to and thus which sequence. This is an antecedent basis rejection.
Regarding claim 24, the claim recites “a buffer composition”. As noted in the Claim Interpretations section, a buffer composition is defined to comprise a buffer. KCl and a non-ionic surfactants are not known in the art to perform the functions of buffering agents.
Claims 25-27 are rejected for depending on claim 24 and not rectifying the deficiency.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1-22 and 24-42 is/are rejected under 35 U.S.C. 103 as being unpatentable over Holme (WO 2020/144480 A1; published 07/16/2020; as cited in the IDS dated 06/25/2024) in view of Zhao (US 2002/0119465 A1; published 08/29/2002).
Regarding claim 1, Holme teaches a method for detecting one or more target sequences in a sample by amplification (pg. 2; claim 1; Examples 1, 3-6), the method comprising:
providing an aqueous composition comprising:
i) one or more forward oligonucleotide primers having a 5' region which is a tag sequence and a 3' region specific for a target sequence;
ii) a reverse oligonucleotide primer, such that a forward and the reverse primer operably form a primer pair;
iii) one or more probes having a reporter label and a quencher label, each probe comprising a sequence having at least 50% identity to the tag sequence of a forward oligonucleotide primer; and
iv) one or more enhancer oligonucleotide primers comprising a sequence having at least 50% identity to the sequence of a probe;
incubating the primers and probes with the sample and at least one polymerase; and
performing polymerase chain reaction (PCR) on the sample to generate tagged nucleic acids, whereby the probe(s) can bind the tagged nucleic acids (pg. 2; claim 1).
Holme teaches that a polymerases include RNA-dependent DNA polymerases include reverse transcriptases and DNA-dependent DNA polymerases (pg. 18, lines 28-30). Holme teaches the sample may be a biological sample such as a biological fluid or a sample of cells (pg. 10, para 1). Holme teaches that its methods and kits are directed to nucleic acid amplification (Title, Field of the Invention).
Holme teaches detecting target sequences by amplification using PCR and said components using a genotyping master mix that comprises a buffer Tris-HCl (Example 1, pgs. 20-22: 2x genotyping master mix on pg. 21).
Regarding claims 3-8, Holme teaches performing the method with a 2X genotyping master mix in which the KCl concentration is 100 mM (pg. 27, line 7), i.e., the working concentration is about 50 mM (instant claim 3).
Holme teaches that in the same master mix, there is 0.05% Igepal (pg. 27, line 22; instant claims 4-7), i.e., at a working concentration of about 0.025%.
While not required by the claims, it is noted that the concentration of 0.05% is not determined to be critical as both Examples 3 and 4 utilize a working concentration of about 0.025% of an alternative non-ionic surfactant provided in claim 6.
Holme teaches that said master mix further comprises MgCl (pg. 27, line 19); glycerol (pg. 27, line 23); and TMAC (pg. 27, line 24) (instant claim 8). It is also noted that the master mix contains TRIS pH 8.3 (pg. 27, line 17).
Regarding claims 9-11, Holme teaches the polymerase may be a DNA polymerase (claim 3; instant claim 9), a fragment/domain/derivative of Taq (claim 4; instant claims 9-10), modified (claim 5; instant claim 10), modified to remove exo-nuclease activity (claim 6; instant claim 11), and/or modified to be hot-start (claim 7; instant claim 11).
Regarding claim 13-14, Holme teaches wherein the one or more enhancer oligonucleotide primers comprise at least two distinct regions, each region comprising a sequence having at least 50% identity to that of the one or more probes (claim 8; instant claim 13) and wherein the two distinct regions are separated by a linker region (claim 9; instant claim 14) wherein the linker region is 1 to 10 “oligonucleotides” in length (claim 10) or wherein the linker region is 2 to 5 “oligonucleotides” in length (claim 11).
It is noted that the enhancer oligos are optionally claimed and that these limitations would be met by no enhancer oligos.
Regarding claims 15-16, Holme teaches wherein the one or more probes comprise a sequence having at least 60%, 70%, 80%, 90%, 95%, 98% or 99% identity to the tag sequence of a forward oligonucleotide primer (claim 12-13; instant claim 15) or a sequence identical to the tag sequence of a forward oligonucleotide primer (claim 13; instant claim 16).
Regarding claims 17-18, Holme teaches wherein the one or more enhancer oligonucleotide primers comprise a sequence having at least 60%, 70%, 80%, 90%, 95%, 98% or 99% identity to the sequence of a probe (claim 14; instant claim 17) or a sequence identical to the sequence of a probe (claim 15; instant claim 18).
It is noted that the claims, as written, do not require the enhancer oligonucleotides and that this limitation is also met by having no enhancer oligonucleotide primers.
Regarding claim 19, Holme teaches at least 4 cycles (claim 16), at least 20 cycles (claim 17), and at least 30 cycles (claim 18) of PCR are performed.
Regarding claim 21, Holme teaches that the method further comprises:
measuring the signal generated by the binding of the probes to the tagged nucleic acids (claim 19).
Regarding claim 22, Holme teaches that the measurement is made in real time (claim 20) or at the end of the reaction (claim 21).
Regarding claim 24-27, Holme teaches the buffer composition of the genotyping master mix with a 1X concentration of about 50 mM KCl and about 0.025% Igepal, as cited in claims 3-7 above. See also Examples 1, 3-6.
Regarding claim 2, Holme teaches A kit for use in a nucleic acid amplification process (claim 2; pg. 2-3; Examples 1, 3-6), comprising:
i) one or more forward oligonucleotide primers having a 5' region which is a tag sequence and a 3' region specific for a target sequence;
ii) a reverse oligonucleotide primer, such that a forward and the reverse primer operably form a primer pair;
iii) one or more probes having a reporter label and a quencher label, each probe comprising a sequence having at least 50% identity to the tag sequence of a forward oligonucleotide primer;
iv) one or more enhancer oligonucleotide primers comprising a sequence having at least 50% identity to the sequence of a probe; and
v) a polymerase.
Holme further teaches that the kit comprises a quaternary ammonium salt (claim 22) and teaches a kit for performing nucleic acid amplification comprising a quaternary ammonium salt contained in an aqueous composition comprising a buffer, a DNA polymerase, and a source of divalent cations (claims 64 and 62).
Regarding claim 28-33, Holme teaches the exemplary buffer composition of the genotyping master mix with a 1X concentration of about 50 mM KCl (instant claim 28) and about 0.025% Igepal (instant claims 29-32), as cited in claims 3-7 above, which also comprises:
MgCl (pg. 27, line 19) [i.e., a source of divalent cations]; glycerol (pg. 27, line 23); and TMAC (pg. 27, line 24) [i.e., a quaternary ammonium salt; see, e.g., claims 36-28] (instant claim 33). It is also noted that the master mix contains TRIS pH 8.3 (pg. 27, line 17).
Regarding claim 34-36, Holme teaches that the polymerase of the kit may be a DNA polymerase (claim 3; instant claim 34), a fragment/domain/derivative of Taq (claim 4; instant claims 34-35), modified (claims 3 and 5; instant claim 25), modified to remove exo-nuclease activity (claim 6; instant claim 66), and/or modified to be hot-start (claim 7; instant claim 36).
Regarding claims 37-38, Holmes teaches that the one or more enhancer oligonucleotides of the kit have at least two distinct regions, each with at least 50% identity to that of the one or more probes (instant claim 37) with a linker region (instant claim 38), optionally wherein the linker is 1-10 or 2-5 “oligonucleotides” in length, as cited in claims 13-14.
It is noted that the claims, as written, do not require the enhancer oligonucleotides and that this limitation would also be met by having no enhancer oligonucleotide primers.
Regarding claims 39-40, Holmes teaches that the probes of the kit comprise a sequence having that is identical to the tag sequence of a forward oligonucleotide primer (instant claims 39-40), as cited in claims 15-16).
Regarding claims 41-42, Holmes teaches that the one or more enhancer oligo primers have a sequence that is at least 99% identity to the sequence of a probe (instant claim 41) or is identical to the sequence of a probe (instant claim 42), as cited in claims 17-18.
It is noted that the claims, as written, do not require the enhancer oligonucleotides and that this limitation would also be met by having no enhancer oligonucleotide primers.
In teaching RNA-dependent DNA polymerases and “at least one”, Holme suggests but fails to explicitly teach RNA as a template/sample and suggests more than one polymerase but that the combining includes both a polymerase and a reverse transcriptase (claim 1).
In teaching the quaternary ammonium salt kit in a composition comprising a DNA polymerase for the same purpose, Holme suggests but fails to explicitly teach a kit with a buffer, a polymerase, and a reverse transcriptase (claim 2).
Holme fails to teach:
that the RT is a modified RT (claim 12); and
that the one-step PCR comprises an RT step prior to the PCR cycles (claim 20).
Zhao teaches preparing a reaction mixture comprising an RNA template [i.e., a sample comprising RNA], a mutant thermostable DNA polymerase, a mutant reverse transcriptase (instant claim 12), buffer reagents, and at least one nucleic acid primer, and performing PCR (claim 17).
Zhao teaches subjecting the reaction mixture to a set of reverse transcription conditions prior to the PCR cycles (claim 17; para [0058-59], [0072-78]; instant claim 20).
Zhao teaches that the methods are for one-step RT-PCR (e.g., Abstract; para [0084]) and that such method have the advantage of the ability to perform the entire RT-PCR reaction in a single container without the addition of additional reagents during the process, which reduces the possibility of contamination and high sensitivity (para [0084]).
Zhao teaches that cDNA synthesis occurs in conditions sufficient for reverse transcription (para [0058]).
Zhao teaches a kit for one step nucleic acid amplification comprising: a mutant thermostable DNA polymerase; a mutant reverse transcriptase; and a buffer (claim 12; instant claim 2).
It is noted that Zhao teaches performing the method with RNase inhibitor (para [0048]; [0071]; instant claim 8) and including the RNase inhibitor in the kit (claim 16; instant claim 33).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the sample of Holme for a sample comprising RNA such as the RNA template of Zhao, motivated by the desire to extend the method to an obvious species of the genus of nucleic acids, as suggested by Holme and as taught by Zhao. In adapting the method for RNA, it would have been obvious to the POSITA before the EFD of the claimed invention to have added the mutant RT of Zhao and to have subjected the combination to RT conditions prior to PCR in a one-step method, motivated by the desire to synthesize cDNA for the PCR cycles and to reduce potential for contamination, as taught by Zhao.
It further would have been obvious to the POSITA before the EFD of the claimed invention to have combined the kits of Holme according to the exemplary concentrations of Holme, as they were taught to be compositions suitable for the same purpose, see MPEP 2144.06(I). It further would have been obvious to the POSITA before the EFD of the claimed invention have utilized a polymerase and a reverse transcriptase to enable one-step RT-PCR, as taught by Zhao, motivated by the advantages above including the ability to perform methods that utilize the kit on an obvious species of the nucleic acid genus, RNA, and to allow the user of such a kit to reduce contamination by practicing one-step methods, as taught and suggested by Zhao. In so far as the kit implies a separation of the polymerases from the buffer, it also would have been obvious to the POSITA before the EFD of the claimed invention to have separated each polymerase from the buffer composition, as taught by Zhao, under at least MPEP 2144.04(V)(C) Making Separable and 2144.04(II) Omission of an Element and Its Function Is Obvious if the Function of the Element Is Not Desired. Zhao teaches the element separately indicating a desire in the art for a buffer absent the function of the polymerase, e.g., for more flexible/optimized storage conditions of each component.
There would have been a strong expectation of success as Holme teaches the methods are compatible with multiple polymerases, including a reverse transcriptase, and kits each of which are broadly directed to nucleic acid amplification.
Claim(s) 23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Holme (WO 2020/144480 A1; published 07/16/2020; as cited in the IDS dated 06/25/2024) in view of Zhao (US 2002/0119465 A1; published 08/29/2002) as applied to claims 1-22 and 24-42 above, and further in view of Heijnen (Heijnen L, et al. Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Sci Total Environ. 2021 Dec 10;799:149456. Epub 2021 Aug 4).
Regarding claim 23, Holme and Zhao fail to teach a total volume of the reaction mix under 1 uL.
Heijnen teaches a droplet digital RT-PCR (entire document, e.g., title and abstract) to detect variants of concern from SARS-CoV2 RNA, finding that detection of mutation N501Y was possible in mixtures of WT with low proportions (0.5%) B.1.351 lineage SARS-CoV2 RNA (Abstract). Heijnen concludes that RT-ddPCR could be used for sensitive and accurate monitoring of current or future mutations in variants of concern, which can be used to obtain insight into the spread of VOC and support public health decision-making (Abstract). Heijnen teaches that the ability to perform the PCR assay in discrete self-contained droplets makes it possible to discriminate between droplets containing mutant fragments at low frequences in a background of wild-type fragments (pg. 3, col 2, para 1; see also pg. 2, col 1, para 1).
Heijnen teaches its assay uses a one-step supermix with probes in with a 20 uL volume (pg. 3, 2.6. RT-ddPCR for the N501Y mutation), wherein said volume is partition into ~10,000-20,000 droplets (pg. 2, col 1, para 1), i.e., the reaction volume of the mixture is about 20 ul/10,000, which is less than 1 uL. Heijnen teaches applying the assay to samples from cell culture (pg. 2, 2.2. SARS-CoV-2 viral RNA; 2.3.Virus concentration and nucleic acid extraction) and from wastewater (entire document, e.g., Abstract).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have used the known technique of RT-ddPCR of Heijnen to improve the method of Holme in view of Zhao, thereby reducing the volume of the reaction mixture to under 1 uL, motivated by the desire to improve the sensitivity and accuracy of monitoring, e.g., for variants of concern for public health decision making and/or for other applications that have a low level of mutant fragments in a background of wild-type fragments, as taught by Heijnen . There would have been a strong expectation of success as Heijnen is also directed to one-step RT-PCR using probes and teaches methods for producing and analyzing droplets.
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 and 3-23 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-24 of U.S. Patent No. 12680134 in view of Holme (WO 2020/144480 A1; published 07/16/2020; as cited in the IDS dated 06/25/2024), Zhao (US 2002/0119465 A1; published 08/29/2002), and Heijnen (Heijnen L, et al. Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Sci Total Environ. 2021 Dec 10;799:149456. Epub 2021 Aug 4).
Both sets of claims are directed to a method for detecting one or more target sequences in a sample by amplification, the method comprising:
providing an aqueous composition comprising:
one or more forward oligonucleotide primers having a 5' region which is a tag sequence and a 3' region specific for a target sequence;
a reverse oligonucleotide primer, such that a forward oligonucleotide primer from the one or more forward oligonucleotide primers and the reverse primer operably form a primer pair;
one or more probes having a reporter label and a quencher label, each of the one or more probes comprising a sequence having at least 90% identity to the tag sequence of the forward oligonucleotide primer from the one or more forward oligonucleotide primers (instant claim 15); and
one or more enhancer oligonucleotide primers comprising a sequence having at least 90% identity to the sequence of a probe from the one or more probes (instant claim 17);
incubating the primers and the probes with the sample and at least a DNA polymerase, wherein the DNA polymerase is a 5' nuclease-deleted DNA polymerase; and
performing polymerase chain reaction (PCR) in a single reaction master mix comprising the sample to generate tagged nucleic acids, whereby the probes can bind to the tagged nucleic acids and label the one or more target sequences by generating a signal (claim 1).
Claims 22-23 teach that the aqueous composition comprises TMAC (instant claim 8).
Claims 2-3 teach that the one or more enhancer oligo primers comprise at least two distinct regions, each comprising a sequence having at least 90% identity to a sequence of the one or more probes, wherein the distinct regions are separated by a linker and the linker region is 1-10 or 2-5 “oligonucleotides” in length, corresponding to instant claims 13-14.
Claim 7 teaches that the sequence having shared identity to the forward primer may be 100% identity to the sequence of the probe from the one or more probes (instant claims 15-16).
Regarding instant claim 18, it is noted that such enhancers are optional given the claim construction and that an oligonucleotide primer that is identical to the sequence of another oligonucleotide wherein the enhancer is not restricted from also comprising the reporter/quencher may be considered a matter of nomenclature.
Claim 6 teaches performing at least 4, 20, or 30 cycles of PCR (instant claim 19).
Claims 8-9 teaches measuring the signal generated by probe binding (instant claim 21), wherein the measurement is made in real time or at the end of the reaction (instant claim 22).
The claims of US Pat. ‘134 fail to teach or explicitly teach:
that the method utilizes a buffer and that the combination includes a combination with a reverse transcriptase (claim 1), and that the reverse transcriptase is a modified reverse transcriptase (claim 12);
a sample comprising RNA (claim 1);
that the buffer comprises KCl (claim 3) or a non-ionic surfactant (claims 4-7);
that the DNA polymerase is a fragment/derivative/domain of Taq (claim 9) or hot-start/exo-nuclease removed polymerase (claim 11);
that the one-step PCR step comprises a RT step prior to the PCR cycles (claim 20); and
that the total volume is less than 1 uL (claim 23).
As described and cited in the 103 above, Holme teaches:
a buffer comprising KCl at a working concentration of about 50 mM (claim 3), a non-ionic surfactant that may be Igepal at a working concentration of about 0.025% (claims 4-7), and that the buffer comprise TMAC (claim 8);
that the DNA polymerase may be a fragment/derivative/domain of Taq or a hot-start and/or exo-nuclease remove pol (claim 11);
Holme teaches that its buffer is intended for PCR (pg. 21, Examples 1, 3-6) and that modification of polymerase structure can confer certain properties (pg. 19, para 1), wherein a modification for hot-start allows reduction of non-specific amplification (pg. 19, para 3). Holmes teaches its invention to improve sensitivity and accuracy of PCR-based genotyping systems (pg. 2, para 1).
As described and cited in the 103 above, Zhao teaches:
a method that utilizes a sample comprising RNA and a combination that includes a modified reverse transcriptase (claims 1 and 12), wherein the one-step PCR comprises an RT step prior to the PCR cycles ( claim 20).
Zhao also teaches mutant thermostable N-terminal deletion Taq polymerases (entire document, e.g., para [0020] and claim 17) and that it may be a hot-start Taq enzyme system (para [0056]).
Zhao teaches that the methods are for one-step RT-PCR (e.g., Abstract; para [0084]) and that such method have the advantage of the ability to perform the entire RT-PCR reaction in a single container without the addition of additional reagents during the process, which reduces the possibility of contamination and high sensitivity (para [0084]).
Zhao teaches that cDNA synthesis occurs in conditions sufficient for reverse transcription (para [0058]).
As described and cited in the 103 above, Heijnen teaches:
a digital droplet one step genotyping RT-PCR with a reaction volume of about 20/~10,000 uL.
Heijnen concludes that RT-ddPCR could be used for sensitive and accurate monitoring of current or future mutations in variants of concern, which can be used to obtain insight into the spread of VOC and support public health decision-making (Abstract). Heijnen teaches that the ability to perform the PCR assay in discrete self-contained droplets makes it possible to discriminate between droplets containing mutant fragments at low frequences in a background of wild-type fragments (pg. 3, col 2, para 1; see also pg. 2, col 1, para 1).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized the buffer conditions of Holme and have substituted the DNA polymerase(s) of Holme and/or Zhao in order to improve the sensitivity and accuracy of the PCR, as taught by Holme, and/or to have taken advantage of the thermostable and/or hot-start abilities of the modified Taq fragment of Zhao, as taught by Zhao.
It further would have been obvious to the POSITA before the EFD of the claimed invention to have substituted the sample of the combined method for a sample comprising RNA such as the RNA template of Zhao, motivated by the desire to extend the method to an obvious species of the genus of nucleic acids, as suggested by Holme and as taught by Zhao. In adapting the method for RNA, it would have been obvious to the POSITA before the EFD of the claimed invention to have added the mutant RT of Zhao and to have subjected the combination to RT conditions prior to PCR in a one-step method, motivated by the desire to synthesize cDNA for the PCR cycles and to reduce potential for contamination, as taught by Zhao.
It also would have been obvious to the POSITA before the EFD of the claimed invention to have used the known technique of RT-ddPCR of Heijnen to improve the combined method, thereby reducing the volume of the reaction mixture to under 1 uL, motivated by the desire to improve the sensitivity and accuracy of monitoring, e.g., for variants of concern for public health decision making and/or for other applications that have a low level of mutant fragments in a background of wild-type fragments, as taught by Heijnen .
There would have been a strong expectation of success as each of Holme, Zhao and Heijnen are directed at methods of nucleic acid amplification comprising PCR, wherein Holme teaches buffer conditions for probe-based one-step quantitative PCR, Zhao teaches methods for one-step RT-PCR, and Heijnen teaches dd RT-PCR.
Conclusion
No claims are allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Hemken (WO 2022/147178 A1; effectively filed 12/30/2020) teaches non-ionic surfactants that may be Tergitol (entire document, e.g., para [0014-15]) and optimizing an amount of Tergitol for viral inactivation (para [0013] and [0029]; Fig. 1: 0.01% to 0.5%). Hemken teaches that the Tergitol may be Tergitol 15-S-40 (para [0070]). Hemken teaches that the method of inactivating Beta-coronavirus including SARS-CoV2 may be used in conjunction with PCR or other nucleic acid amplification-based assays (para [0079]).
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/EMMA R HOPPE/Examiner, Art Unit 1683
/NANCY J LEITH/Primary Examiner, Art Unit 1636
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