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 .
Claims Status
Claims 1, 2, 5, 12, 13, 21, 22, 26, 36, 38, 41, 43, 45, 51, & 54-58 filed on 01/20/2026 are pending. All the amendments and arguments have been thoroughly reviewed but are deemed insufficient to place this application in condition for allowance. The following rejections are either newly applied, as necessitated by amendment, or are reiterated. They constitute the complete set being presently applied to the instant application. Response to Applicant’s argument follow. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.
Claim Rejections - 35 USC § 103
Claim(s) 1, 5, 12, 13, 21, 26, 41, & 43 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fritsch (US Patent Application Publication US 2019/0376147 A1), in view of Lutz (Lutz et al.; Nano Research, Vol. 11, pages 6141-6154, December 2017).
Regarding newly amended claim 1, Fritsch teaches a method for selectively amplifying and detecting a mutant variant of a polynucleotide relative to a wild-type polynucleotide by contacting a first strand of a double stranded polynucleotide (first target nucleic acid sequence) with a first primer (first probe) which includes a portion complementary to a region comprising a mutation within the first polynucleotide strand (first probe comprises a recognition sequence capable of hybridizing to the first target nucleic acid sequence), contacting the second polynucleotide strand of the double stranded polynucleotide (second target nucleic acid sequence) with a second primer (second probe) which includes a sequence substantially complementary to a sequence on the wildtype second strand sequence (second probe comprises a recognition sequence capable of hybridizing to the second target nucleic acid sequence), and a blocking oligonucleotide (interfering agent) that includes a portion complementary to a reference sequence (wildtype sequence/second target nucleic acid sequence) (paragraph [0059] lines 1-2 & 11-12) and competes for binding to inhibit amplification of the wildtype polynucleotide (second target nucleic acid sequence) (hybridization of the second probe to the second target nucleic acid sequence is interfered with by the interfering agent) and permit amplification of the mutant variant polynucleotide (first target nucleic acid sequence) where detection of an amplicon (detecting a first signal indicative of hybridization of the first probe to the first target nucleic acid sequence whereas a second signal indicative of the hybridization of the second probe to the second target nucleic acid is not detected or detected at a lower level thereby preventing optical crowding of the first signal) indicated the presence of the mutant variant of the polynucleotide in the sample (detecting the first target nucleic acid in the sample) (paragraph [0010] lines 1-26; paragraph [0012] lines 1-23; paragraph [0037] lines 1-4 & 7-21; paragraph [0074] lines 1-18; FIGS. 2A-2C).
Fritsch does not teach that the blocking oligonucleotide (interfering agent) is capable of hybridizing to the recognition sequence of the second probe but not to the recognition sequence of the first probe.
Lutz teaches a method to analyze oligonucleotides in which quencher strands (interfering agent) bind to imager oligonucleotides and prevent them from hybridizing to their target docking strands in order to effectively quench the fluorophore on the imager oligonucleotide (interfere or block an oligonucleotide) allowing for the detection of a different imager oligonucleotide (detection of a different nucleic acid sequence) through the ability to bind to their docking targets (abstract lines 3-9 & 12-23; Figure 1). In addition, Lutz teaches that this method of quenching (blocking/interfering with) oligonucleotides enables efficient multiplexing for the detection of oligonucleotides (abstract lines 22-23).
Fritsch and Lutz are considered to be analogous to the claimed invention because they are all in the same field of detection of nucleic acid sequences. Therefore, 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 have modified the method contacting a mutant polynucleotide (first target nucleic acid sequence) and a wildtype polynucleotide (second target nucleic acid strand) polynucleotide with a first primer (first probe), a second primer (second probe), and a blocking oligonucleotide (interfering agent) that inhibits amplification of the wildtype polynucleotide (second target nucleic acid sequence) in Fritsch to incorporate the use of a quencher strand (interfering agent) that hybridizes to an oligonucleotide (second probe) to prevent hybridization of the oligonucleotide (second probe) to its target docking strand (second target nucleic acid sequence) as taught in Lutz because Lutz teaches that doing so would enable efficient multiplexing for the detection of oligonucleotides.
Regarding claim 5, Lutz teaches the quencher strand (interfering agent) is contacted with the complement oligonucleotide (second probe) (red quencher and oligonucleotide strands in bottom row of Figure 1 of Lutz) and then a different oligonucleotide (first probe) (green oligonucleotide strand in bottom row of Figure 1 of Lutz) and the quencher oligonucleotide complex (second probe/interfering complex) is contacted with the respective target docking strands (first and second target nucleic acid sequence) in the sample (forming a second probe/interfering agent hybridization complex and contacting the first probe and the second probe/interfering hybridization complex with the sample) (Figure 1).
Regarding claim 12, Lutz teaches that the quencher strand (interfering agent) is contacted with the complement oligonucleotide (second probe) (red quencher and oligonucleotide strands in bottom row of Figure 1 of Lutz) (interfering agent comprises a sequence to the recognition sequence of the second probe) (Figure 1).
Regarding claim 13, Lutz teaches that the quencher strand (interfering agent) is contacted with the complement oligonucleotide (second probe) (red quencher and oligonucleotide strands in bottom row of Figure 1 of Lutz) and does not hybridize to a different oligonucleotide (first probe) (green oligonucleotide strand in bottom row of Figure 1 of Lutz) (interfering agent hybridizes to the recognition sequence of the second probe but not to the recognition sequence of the first probe) (Figure 1).
Regarding claim 21, Fritsch teaches that at least one of the primers (first and second probes) is modified to contain a marker moiety including a ligand that can be detected with a labeled antibody (the first and/or second probe indirectly binds to a detectably labelled probe).
Regarding claim 26, Fritsch teaches the method is used to amplify and detect a mutant variant of a polynucleotide relative to a wildtype polynucleotide that are present in biological samples that include an excess of wildtype sequence (second target nucleic acid sequence) (paragraph [0078] lines 1-12) and that the mutant variant polynucleotide (first nucleic acid sequence) and the wildtype polynucleotide (second nucleic acid sequence) to be amplified and detected are analytes (first analyte and second analyte) (paragraph [0044] lines 1-2).
Regarding claim 41, Fritsch teaches that the mutant variant polynucleotide (first target nucleic acid sequence) and the wildtype polynucleotide (second target nucleic acid sequence) are comprised in an amplification product of a nucleic acid analyte in the sample for PCR or isothermal amplification (paragraph [0101] lines 1-11; paragraph [0105] lines 1-6; paragraph [0109] lines 1-5).
Regarding claim 43, Fritsch teaches that the amplification product includes isothermal nucleic acid amplification including rolling circle amplification (RCA) (paragraph [0109] lines 1-5).
Claim(s) 2 & 51 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fritsch (US Patent Application Publication US 2019/0376147 A1) and Lutz (Lutz et al.; Nano Research, Vol. 11, pages 6141-6154, December 2017), as applied to claims 1, 12, 13, 26, 41, & 43 above, and further in view of Nadeau (Nadeau & Hellyer; US Patent Application Publication US 2015/0315636).
The teachings of Fritsch and Lutz with respect to claim 1 are discussed above.
Regarding claim 2, Fritsch and Lutz does not teach that the sample comprises a plurality of the first target nucleic acid sequences that are different from each other.
Nadeau teaches a method for detecting a first variant target nucleic acid sequence (first target nucleic acid sequence) in a sample comprising nucleic acids by contacting the biological sample with a pair of amplification primers comprising a forward primer 1 (second probe that comprises a recognition sequence for the first and second target nucleic acid sequence) and a reverse primer 2 configured to amplify a variant target sequence (first target nucleic acid sequence) and a wildtype target sequence (second target nucleic acid sequence), a blocking primer (interfering agent) that preferentially hybridizes to the wildtype target sequence (second target nucleic acid sequence), and a reporter probe. Nadeau teaches the method further comprising a second variant target sequence (plurality of first target nucleic acid sequences) and contacting the second variant target sequence (plurality of first target nucleic acid sequences) with amplification primers and a second reporter probe (plurality of first probes) that preferentially hybridizes to the second variant target nucleic acid sequence (plurality of first probes each capable of hybridizing to one of the plurality of first target nucleic acid sequences) to measure a detectable signal indicative of presence or amount of the second variant target sequences (plurality of first target nucleic acid sequences) in the biological sample (pg. 19 claim 5 lines 1-19). In addition, Nadeau teaches the method is used to detect and quantify sequence variants (first target nucleic acid sequences) that are present in biological samples that include an excess of wildtype sequence (second target nucleic acid sequence) (paragraph [0004] lines 4-7).
Fritsch, Lutz, and Nadeau are considered to be analogous to the claimed invention because they are all in the same field of detection of nucleic acid sequences. Therefore, 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 have modified the method amplifying and detecting a mutant polynucleotide (first target nucleic acid sequence) in Fritsch to incorporate the detection of multiple of different variant target sequences (plurality of first tater nucleic acid sequences) as taught in Nadeau because Nadeau teaches that doing so would provide a method to quantify sequence variants (first target nucleic acid sequences) present in a sample including an excess of wildtype sequences (second target nucleic acid sequences).
Regarding claim 51, Fritsch and Lutz does not teach that the first and/or second target nucleic acid sequences are detected in situ in the sample.
Nadeau teaches this method is used for the detection of variant nucleic acid sequences in a biological sample in which the biological sample is analyzed directly without prior nucleic acid extraction and/or isolation (in situ) (paragraph [0029] lines 2-10; paragraph [0030] lines 5-7; pg. 19 claim 1 lines 1-4). In addition, Nadeau teaches the method is used to detect and quantify sequence variants (first target nucleic acid sequences) that are present in biological samples that include an excess of wildtype sequence (second target nucleic acid sequence) (paragraph [0004] lines 4-7).
Fritsch, Lutz, and Nadeau are considered to be analogous to the claimed invention because they are all in the same field of detection of nucleic acid sequences. Therefore, 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 have modified the method amplifying and detecting a mutant polynucleotide (first target nucleic acid sequence) in Fritsch to incorporate the detection of variant nucleic acid sequences (first target nucleic acid sequences) in situ as taught in Nadeau because Nadeau teaches that doing so would provide a method to quantify sequence variants (first target nucleic acid sequences) present in a sample including an excess of wildtype sequences (second target nucleic acid sequences).
Claim(s) 36 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fritsch (US Patent Application Publication US 2019/0376147 A1) and Lutz (Lutz et al.; Nano Research, Vol. 11, pages 6141-6154, December 2017), as applied to claims 1, 12, 13, 26, 41, & 43 above, and further in view of Agerholm (Agerholm et al.; Human Reproduction, Vol. 20, pages 1072-1077, January 21st, 2005).
The teachings of Fritsch and Lutz with respect to claim 1 are discussed above.
Regarding claim 36, Fritsch and Lutz does not teach removing the first probe hybridized to the first target nucleic acid sequence in the sample and contacting the sample with the second probe but not the interfering agent and detecting a signal indicative of the hybridization of the second probe to the second target nucleic acid sequence to detect the second target nucleic acid in the sample.
Agerholm teaches a method of sequential fluorescence in-situ hybridization (FISH) analysis with peptide nucleic acid (PNA) probes in which the sample is contacted with labeled probe set A (containing probe 1) for detection of nucleic acids of chromosomes 13 and 21 (first target nucleic acid sequence) in the sample (pg. 1073 column 2 3rd full paragraph line 1), followed by a cycle of contacting the sample with probe set B which contains unlabeled probes for chromosomes 13 and 21 and labeled probes for chromosome 1, 16, & 17 (containing probe 2). The unlabeled probes in probe set B dissociate the bound labelled probe set A (containing probe 1) (removal of fist probe hybridized to the first target nucleic acid sequence) (pg. 1075 2nd full paragraph lines 1-10) while the labeled probes of probe set B (containing probe 2) detect the nucleic acids of chromosomes 1, 16, and 17 (second target nucleic acid sequence) (Pg. 1072 method paragraph lines 1-2; pg. 1073 column 2 3rd full paragraph lines 2-3; Figure 2). In addition, Agerholm teaches that PNA probes minimize loss of signal and allow for several sequential analysis of targets to be carried out before errors occur (pg. 1072 conclusions paragraph lines 1-3).
Fritsch, Lutz, and Agerholm are considered to be analogous to the claimed invention because they are all in the same field of detection of nucleic acid sequences. Therefore, 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 have modified the method taught in Fritsch to incorporate the removal of the first probe to the first target nucleic acid sequence and detection of the second nucleic acid sequence as taught in Agerholm because Agerholm teaches that this method minimizes the loss of signal and allows sequential analysis of nucleic acid targets to be carried out by removing the first identified target nucleic acid sequence and then detecting the next (second) target nucleic acid sequence before errors occur thus allowing the detection of multiple nucleic acid sequences in a sample.
Claim(s) 38 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fritsch (US Patent Application Publication US 2019/0376147 A1) and Lutz (Lutz et al.; Nano Research, Vol. 11, pages 6141-6154, December 2017), as applied to claims 1, 12, 13, 26, 41, & 43 above, and further in view of Morlan (Morlan, Baker, & Sinicropi; PLOS One, Vol. 4, Pages 1-11, February 25th, 2009).
The teachings of Fritsch and Lutz with respect to claim 1 are discussed above.
Regarding claim 38, Fritsch and Lutz does not teach a method of contacting the sample with the first and second probes but not with the interfering agent, wherein the signal indicative of the hybridization of the first probe to the first target nucleic acid sequence in the sample has a lower amplitude that the reference signal which is indictive of the hybridization of the second probe to the second target nucleic acid sequence in the sample without the interfering agent.
Morlan teaches a method of amplifying a mutation sequence (first nucleic acid sequence) and a wildtype sequence (second nucleic acid sequence) with and without a blocking oligonucleotide to compare the assays selectivity (pg. 3 paragraph bridging column 1 & 2 lines 14-17). Morlan also teaches that the assay that amplifies without a blocking oligonucleotide (interfering agent) has a reduced selectivity as wildtype sequence (second target nucleic acid sequence) and a reduced change in CT value indicating there is overlap in the mutation sequence (first nucleic acid sequence) and the wildtype sequence (second nucleic acid sequence) (Figure 2A; Table 2).
Fritsch, Lutz, and Morlan are considered to be analogous to the claimed invention because they are all in the same field of detection of detection of target nucleic acid sequences. Therefore, 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 have modified the method taught in Fritsch to incorporate comparison of signals obtained from a first and second nucleic acid sequence with and without a blocking probe (interfering agent) as taught in Morlan because Morlan teaches that an assay without a blocking probe can serve as a control to an assay with a blocking probe to obtain accurate selectivity values of each assay.
Claim(s) 45 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fritsch (US Patent Application Publication US 2019/0376147 A1) and Lutz (Lutz et al.; Nano Research, Vol. 11, pages 6141-6154, December 2017), as applied to claims 1, 12, 13, 26, 41, & 43 above, and further in view of Goo (Goo & Kim; BioChip Journal, Vol. 10, pages 262-271, July 29th, 2016).
The teachings of Fritsch and Lutz with respect to claim 1 are discussed above.
Regarding claim 45, Fritsch teaches that the mutant variant polynucleotide (first target nucleic acid sequence) and the wildtype polynucleotide (second target nucleic acid sequence) are comprised in an amplification product of a nucleic acid analyte in the sample for PCR or isothermal amplification including rolling circle amplification (RCA) (paragraph [0101] lines 1-11; paragraph [0105] lines 1-6; paragraph [0109] lines 1-5).
Fritsch and Lutz do not teach that the product is a rolling circle amplification product of a circular or padlock probe.
Goo teaches that rolling circle amplification (RCA) is a widely used and efficient isothermal amplification method and that RCA amplifies sequences with high fidelity and specificity (abstract lines 1-6). Goo teaches that the target nucleic acid with the addition of DNA polymerases leads to an RCA product of a single-stranded DNA after the isothermal amplification (pg. 1 paragraph bridging column 1 & 2 lines 3-12). In addition, Goo teaches padlock probes are designed to hybridize to target nucleotides such as genomic DNA or microRNA (pg. 262 2nd column 1st full paragraph lines 1-6).
Fritsch, Lutz, and Goo are considered to be analogous to the claimed invention because they are all in the same field of detection of target nucleic acid sequences. Therefore, 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 have modified the method taught in Fritsch to incorporate the use of a RCA product and padlock probes as taught in Goo because Goo teaches that RCA amplifies target nucleic acid sequences with high fidelity and specificity.
Claim(s) 22 & 54-58 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fritsch (US Patent Application Publication US 2019/0376147 A1) and Lutz (Lutz et al.; Nano Research, Vol. 11, pages 6141-6154, December 2017), as applied to claims 1, 12, 13, 26, 41, & 43 above, and further in view of Hauling (Hauling & Kühnemund; U.S. Patent Application Publication US 2019/0161796).
The teachings of Fritsch and Lutz with respect to claim 1 are discussed above.
Regarding claim 22 & 54-58, Fritsch teaches contacting the sample with a blocking oligonucleotide (interfering agent).
Fritsch and Lutz does not teach that the first and/or second probe comprise one or more overhangs that do not hybridize to the first and second target nucleic acid sequences and wherein at least one or more of the overhangs is capable of hybridizing to a detectably labelled detection probe (claim 22). In addition, Fritsch and Lutz does not teach a method wherein a unique signal code is assigned to each target nucleic acid sequence, wherein a set of probes is provided for decoding of each signal code sequence for each target nucleic acid sequence, wherein each probe in a set comprises the same recognition sequence that hybridizes to the target nucleic acid sequence and a detection hybridization region or the absence of a detection hybridization region, wherein the detection hybridization region or the absence thereof may be the same or different among probes in the set, wherein the detection hybridization region, if present, is specific for a detection probe comprising a detectable label or lacking a detectable label, and wherein the probes of the set are used sequentially in multiple cycles of decoding in a pre-determined sequence which corresponds to the signal code sequence (claims 54-58).
Hauling teaches a method of nucleic acid sequencing where a set of oligonucleotide probes N (set of probes for decoding) that have a different nucleic acid sequence from the other oligonucleotide probes (unique signal code sequence) and each oligonucleotide having a different label (detectably labelled detection probe) are used sequentially to perform measurements in each time instance M (cycle) to determine a sequences base of a target nucleic acid sequence (claims 54 & 55) (pg. 20 claim 1 lines 1-31). Hauling also teaches that this method of sequencing is significantly faster than other sequencing methods since the measurements are performed during the hybridization reactions and that this method may also improve the accuracy of nucleic acid sequencing (paragraph [0015] lines 1-8).
Fritsch, Lutz, and Hauling are considered to be analogous to the claimed invention because they are all in the same field of detection of target nucleic acid sequences. Therefore, 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 have modified the method of detecting a mutant variant polynucleotide (first target nucleic acid sequence) with a blocking oligonucleotide (interfering agent) as taught in Fritsch to incorporate the use of a sequential method of decoding for target nucleic acid detection and sequencing as taught in Hauling because Hauling teaches that this sequential method of decoding to sequence a target nucleic acid sequence can be conducted faster and with higher accuracy than other methods of sequencing. In addition, with regard to claims 57 & 58, one of ordinary skill in the art would need to use an interfering agent that interferes with a plurality of second probes as every hybridization of a second probe to a second target nucleic acid sequence (a nucleic acid sequence that is not the first target nucleic acid sequence and exists in excess in the sample) would need to be interfered to detect the first target nucleic acid sequence.
Response to Arguments
The response traverses the rejection. The response asserts that claim 1 as amended recites “whereas a second signal indicative of the hybridization of the second probe to the second target nucleic acid sequence in the sample is not detected thereby preventing optical crowding of the first signal” and that Fritsch is silent regarding a method that prevents optical crowding of a signal indicative of hybridization of a first probe to a target sequence. This argument has been thoroughly reviewed but was not found persuasive. First, preventing optical crowding of the first signal, as recited in amended claim 1, is an outcome of the recited steps of amended claim 1 comprising detecting a first signal indicative of the first probe to the first target nucleic acid sequence whereas a second signal indicative of hybridization of the second probe to the second target nucleic acid sequence is not detected. Therefore, as Fritsch teaches the steps of claim 1 as currently amended, Fritsch teaches this outcome. Second, Fritsch also explicitly teaches that this method is for detecting a mutated polynucleotide in a sample as the normal DNA (wildtype polynucleotide) exist in large excess leading to a high level of background noise (optical crowding) and Fritsch teaches that this method permits amplification of the mutant variant polynucleotide (first target nucleic acid sequence) where detection of an amplicon indicated the presence of the mutant variant of the polynucleotide in the sample (detecting a first signal indicative of hybridization of the first probe to the first target nucleic acid sequence whereas a second signal indicative of the hybridization of the second probe to the second target nucleic acid is not detected or detected at a lower level thereby preventing optical crowding of the first signal) (paragraph [0004] lines 13-16; paragraph [0006] lines 1-4; paragraph [0010] lines 1-26).
The response also asserts that one skilled in the art would not have been motivated to modify the method taught by Fritsch as suggested by the examiner because doing so would render the Fritsch method unsatisfactory for its intended purpose. Specifically, the response asserts that the method taught in Fritsch is for selectively amplifying and detecting a mutant variant of a polynucleotide relative to a wildtype polynucleotide and thus any proposed modification that prevents amplification of the mutant variant would render the method unsatisfactory for its intended purpose. Further, the response asserts that as explained in paragraph [0010] of Fritsch when a first primer binds a first polynucleotide strand and the second primer binds the second polynucleotide strand, the first and second primers function as forward a reverse amplification primers. Further, the response asserts that paragraph [0010] of Fritsch explains the first primer and the blocking oligonucleotide competing for binding to the first polynucleotide strand corresponding to the position of the mutation, thereby inhibiting amplification of the wildtype polynucleotide, and thus, according to the Fritsch method, when the first polynucleotide strand includes the mutant variant the first primer outcompetes the blocking oligonucleotide and is used along with the second primer bound to the second polynucleotide strand to amplify the mutant variant, however when the first polynucleotide strand includes a wildtype sequence the blocking oligonucleotide outcompetes the first primer and no amplification product results. Finally, the response asserts that it is necessary for both the first primer and the second primer to bind to their respective target sequences as if the blocking oligonucleotide hybridized to either primer neither amplification of the wildtype nor mutant would occur and thus one skilled in the art would not have modified the method taught in Fritsch such that the blocking strand hybridizes to the second primer, as proposed by the examiner, because doing so would prevent any amplification of either the wildtype or mutant thus rendering the prior art method inoperable. These arguments have been thoroughly reviewed but were not found persuasive. First, Fritsch does not teach that the first and second primers must function of forward and reverse primers. While Fritsch teaches a first primer (first probe) having a 3’ end region complementary to a region comprising a mutation within the first polynucleotide strand (first target nucleic acid sequence) and a second primer (second probe) complementary to a sequence on the second strand of the polynucleotide (wildtype sequence/ second target nucleic acid sequence) that is 5’ upstream of where the first primer (first probe) binds, Fritsch does not teach that these primers exclusively function as forward and reverse primers. This is further exemplified in Figs. 2A-2C, and for discussions of Figs. 2A-2C, it is noted that Fritsch teaches that a mutation detection probe as complementary to a mutation on a polynucleotide strand (first target nucleic acid) and Fritsch also teaches a first primer that is complementary to a mutation on a polynucleotide strand (first target nucleic acid), therefore both recitations of a mutation detection probe and a first primer are interpreted to comprise a first probe as recited in amended claim 1 and, further, Fritsch teachings that the probe to the left in Fig. 2A and teachings of a second primer is complementary to wildtype sequence (second target nucleic acid), therefore both recitations of a probe to the left of Fig. 2A and a second primer are interpreted to comprise a second probe as recited in amended claim 1. Further as exemplified in Figs. 2A-2C, that depict a mutation detection probe (first probe) that is complementary to a mutation on a polynucleotide strand and a probe (second probe) to the left (5’ upstream to mutation detection probe (first probe)) that is complementary to the wild-type sequence and that the probes (first and second probes) compete and bind according to the probe with the greater degree of correct base pairing to the strand forms (i.e. the first probe binds to mutation if mutated polynucleotide strand (first target nucleic acid sequence) and second probe binds to wildtype if wildtype polynucleotide strand (second target nucleic acid sequence)) (paragraph [0075] lines 4-18). Therefore, Fritsch teaches a first primer (first probe) having a 3’ end region complementary to a mutation in the first polynucleotide strand (first target nucleic acid strand) and a second primer (second probe) complementary to the wildtype polynucleotide sequence (second target nucleic acid sequence) that is 5’ upstream where the first primer (first probe) binds to describe their spatial relation to each other (see annotated Figs. 2A-C from Fritsch below). Further, it is noted that teachings of primer oligonucleotides complementary to a wildtype sequence (second target nucleic acid sequence) is interpreted to comprise the teachings of a second primer (which is complementary to wildtype/second target nucleic acid sequence)as taught in Fritsch and teachings of primer oligonucleotides complementary to a mutation sequence (first target nucleic acid) is interpreted to comprise the teachings of a first primer (which is complementary to mutation/first target nucleic acid sequence) as taught in Fritsch. With this noted, Fritsch teaches that Fig. 3A shows an displacement of an exemplary forward primer oligonucleotide (second probe) from a template having a wildtype sequence after an exemplary blocking oligonucleotide binds to an exemplary wildtype sequence (second target nucleic acid sequence) and Fig. 3B shows an exemplary forward primer oligonucleotide (first probe) to a template polynucleotide having a mutation (first target nucleic acid) and displacement of the blocking oligonucleotide to bind the forward primer oligonucleotide (first probe) to mutant polynucleotide sequence (first target nucleic acid sequence) (first probe outcompetes blocking oligonucleotide to bind to mutated polynucleotide strand (first target nucleic acid strand)) (paragraph 0075] lines 1-20). Therefore, the teachings of Fritsch refer to both the first primer complementary to the mutated polynucleotide strand (first probe) and the second primer complementary to wildtype polynucleotide strand (second probe) as forward primers, respective to their target, and not as a set of forward and reverse primers. Therefore, modification of the method taught in Fritsch such that the blocking strand hybridizes to the second primer (second forward probe complementary to wildtype (second target nucleic acid sequence)), as proposed by the examiner, would not prevent amplification of mutant and thus enables the intended purpose of Fritsch to detect target in lower excess (mutant polynucleotide/first polynucleotide strand) and does not render the method unsatisfactory for its intended purpose.
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The response also asserts that as discussed above claim 1 is not obvious of Fritsch in view of lutz and as claims 5, 12, 13, 21, 26, 41, & 43 depend from claim 1 are not obvious at least for the same reason. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
The response also asserts that as discusses above claim 1 is not obvious over Fritsch in view of Lutz and further that nothing in any one of Nadeau, Agerholm, Morlan, Goo, or Hauling cures the deficiencies of Fritsch and Lutz and accordingly claim 1 is not obvious over Fritsch in view of Lutz and further in view of any one of Nadeau, Agerholm, Morlan, Goo, or Hauling and as claims 2, 22, 36, 38, 45, 51, & 54-58 depend from claim 1 are also not obvious at least for the same reason. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Double Patenting
Claims 1, 21, 22, 38, 41, 43, 45, & 54-56 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 88, 92, 99, 104, & 110 of copending Application No. 17/860,960 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because each patent application provides a method for identifying target nucleic acid sequences in a biological sample through the use of a sequential decoding method for detection of a first and second nucleic acid sequence with an interfering agent.
Regarding claims 1, 38, & 54-56, the instant application claims a method for nucleic acid sequence detection by contacting a first and second target nucleic acid sequence with a first and second probe and an interfering agent that interferes with the hybridization of the second probe to the second target nucleic acid sequence therefore allowing for the detection of the first target nucleic acid sequence (claim 1). The instant application also claims prior to contacting the sample with the interfering agent that the sample is contacted with the first and second probes and not the interfering agent leading to detection of the first and second target nucleic acid sequences that are spatially overlapped (claim 38). Finally, the instant application claims a method of sequential decoding wherein each cycle of decoding comprises contacting the sample with a probe library and an interfering agent or a set of interfering agents (claims 54-56). Copending Application No. 17/860,960 claims a method for identifying target nucleic acid sequences with a sequential cycles comprising contacting the sample with probes in which the signal associated with the first probe bound to the first target nucleic acid sequence and the signal associated with the second probe bound to the second target nucleic acid sequence spatially overlap without the use of an interfering agent, then in the next cycle blocking the hybridization of the second probe to the second target nucleic acid sequence with an interfering oligonucleotide, and in the third cycle blocking the hybridization of the first probe to the first target nucleic acid sequence with an interfering oligonucleotide in order to identify the first and second target nucleic acid sequences (see claim 88). In addition, Copending Application No. 17/860,960 claims contacting the biological sample with a plurality of the first and/or second interfering oligonucleotides (see claim 99).
Regarding claims 21 & 22, the instant application claims that the first probe and/or second probe directly or indirectly bind to a detectably labelled detection probe (claim 21). The instant application also claims that the first and/or second probe comprise one or more overhangs wherein at least one or more of the overhangs in capable of hybridizing to a detectably labelled detection probe (claim 22). Copending Application No. 17/860,960 claims the first, second, third, and fourth probe each comprises a detection hybridization region for binding to a detectably labeled probe (see claim 92).
Regarding claims 41 & 43, the instant application claims the first and/or second target nucleic acid sequence are comprised in a product wherein the product is a rolling circle amplification (RCA) product. Copending Application No. 17/860,960 claims the first and second target nucleic acid sequences are each in a rolling circle amplification product (see claim 104).
Regarding claim 45, the instant application claims the first and/or second target nucleic acid sequences are comprised in an RCA product of a circular or padlock probe that hybridizes to a DNA or RNA analyte in the sample. Copending Application No. 17/860,960 claims the RCA product is generated using a circular probe that hybridizes to a nucleic acid analyte in the biological sample (see claim 110).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
The response traverses the rejection. The response asserts that the instant application has an earlier patent term filing date than the co-pending Application No. 17/860,960 and that the nonstatutory double patenting rejections should be withdrawn according to MPEP §804.I.B.1.(b).(i). as all other rejections in this instant application have been addressed. These arguments have been thoroughly reviewed but were not found persuasive as MPEP §804.I.B.1.(b).(i). requires that a provisional nonstatutory double patenting rejection should be withdrawn if it is the only rejection remaining in an application having an earlier patent term filing date. Claims 1, 2, 5, 12, 13, 21, 22, 26, 36, 38, 41, 43, 45, 51, & 54-58 have 103 rejections that have been applied to the newly amended claims. Therefore, as there are other rejections remining in the instant application MPEP §804.I.B.1.(b).(i). does not apply.
For these reasons and reasons already made of record, the rejections are maintained and applied to the newly amended claims.
Conclusion
Claims 1, 2, 5, 12, 13, 21, 22, 26, 36, 38, 41, 43, 45, 51, & 54-58 are rejected.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BAILEY C BUCHANAN whose telephone number is (703)756-1315. The examiner can normally be reached Monday-Friday 8:00am-5:00pm ET.
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/BAILEY BUCHANAN/Examiner, Art Unit 1682
/JEHANNE S SITTON/Primary Examiner, Art Unit 1682
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