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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 1/7/2026 has been entered.
Applicant’s arguments and amendments have been thoroughly reviewed and considered. Claims 26-32 and 35-37 remain withdrawn. Claims 1-2, 4-6, and 8-23 are pending and are examined on the merits herein.
Response to Applicant’s Arguments and Amendments
Claims 1-2, 4-6, 8-15, 17-19, and 22-23 were rejected under 35 U.S.C. 103 as being unpatentable over Wendt et al. (International Patent Application No. WO 2018/001884 A1). Claim 16 was rejected under 35 U.S.C. 103 as being unpatentable over Wendt et al. (International Patent Application No. WO 2018/001884 A1) in view of Johnson et al. (Nucleic Acids Research, 2004). Claim 20 was rejected under 35 U.S.C. 103 as being unpatentable over Wendt et al. (International Patent Application No. WO 2018/001884 A1) in view of Barker et al. (Genetic Epidemiology, 1996). Claim 21 was rejected under 35 U.S.C. 103 as being unpatentable over Wendt et al. (International Patent Application No. WO 2018/001884 A1) in view of Jenkins et al. (mBio, 2015).
Regarding the 35 USC 103 Rejections, Applicant argues that Wendt, the primary reference used in the Final Rejection mailed 10/7/2025, does not teach a single-step PCR reaction that includes the claimed primers and probes, as allegedly required by the claims (Remarks, pages 10-11).
In instant claim 1, the claim recites the elements of a solution that must undergo a polymerase chain reaction. In terms of the steps required for the PCR, none are specified, as the claim simply states “performing a polymerase chain reaction (PCR) on a solution…thereby discriminating the target sequence from the reference sequence.” PCR is not specifically defined or limited to a particular type in the instant specification (see para. 5, for example). However, the newly amended claim does specifically require that the labeled probe, PBNJ, and primers be together in solution.
In Wendt, page 38, para. 2 states “In some embodiments, the PCR reagents comprise a set of probes consisting of a mutant detection probe and a reference detection probe. The "set of probes" is preferably capable of competing for the binding site(s) at the NOl(s) when added to a PCR amplification together with a nucleic acid comprising the target sequence, PCR reagents and the set of primers under conditions allowing amplification of said target sequence.” Thus, Wendt specifically teaches that these elements may be used together in a single PCR amplification. This PCR reaction clearly involves primers for amplification of the target sequence, which involves a forward and reverse primer (page 8, para. 4), and PCR reagents include a nucleic acid polymerase (page 7, para. 5, and see page 32, paras. 5-6, which specifically recite the use of DNA polymerases). The primers are preferably designed to amplify both a reference sequence and a sequence with a mutation (page 36, para. 3).
Regarding the blocking probes of Wendt, these are not actually suggested to be in solution with the PCR primers and the mutant/reference probe in the obviousness rejection. In para. 19 of the Final Rejection, it is stated that one or more of the detection probes (e.g. the mutant and reference probes) may be blocked at their 3’ ends to prevent extension by a polymerase. This is separate to the references teachings regarding blocking probes. The reference then specifically teaches 3’ C3 spacers as a means to block extension, where said spacer is taught on the blocking probes of Wendt. Then, a prima facie obviousness determination was made to use the specific 3’ blocking means already taught by the reference as the 3’ blocking means used in one or more of the detection probes. The actual use of the blocking probes of Wendt is not relevant to how the reference as a whole reads on the instant claims. The blocking probes of Wendt are not required to be in the PCR amplification described on page 38, para. 2 of the reference (as described above), and the use of the blocking probes generally can be considered a separate enriching step in the reference – see page 51, para. 2 and Examples 16 and 17, where Example 16 details using the blocking probes to enrich super pools and Example 17 then teaches performing additional PCR on said super pools, specifically with wild-type and mutant detection probes (pages 78-79). Thus, even if performing enriching amplification with blocking probes were required by every embodiment of Wendt, which the Examiner does not argue, such enrichment is separate from the use of the detection probes in an amplification reaction, and it is this second amplification that reads on the instant claim. Because this second amplification contains the claimed components and achieves the claimed results, it is considered to teach each limitation of the claim.
On pages 11-13 of their Remarks, Applicant argues that Wendt does not teach the PBNJ as claimed, specifically because the reference allegedly does not teach the claimed signal suppression, as the reference allegedly does not clearly teach that the reference detection probe may be unlabeled, and allegedly provides no examples of how detection of the probes would proceed with an unlabeled probe.
On page 38, para 4, Wendt states, “The methods of the invention may comprise use of both a mutant detection probe and a reference detection probe. In such cases, preferably, the probes are differentially labelled, e.g. such that one of the probes is associated with, or covalently linked to, detectable means, whereas the other is not.” The reference then goes on in para. 5 to describe separate embodiments, where in one the reference detection probe is detectably labeled, and in another the mutant detection probe is detectably labeled. Though pages 39-40 describe various types of probes that the detection probes may comprise (e.g. TaqMan, Sunrise, Scorpion, etc.), none of these are required to be used with the detection probes. Page 42, para. 3 describes several ways in which signals may be measured and evaluated. These include the comparison of signals generated from a target sample with a control sample, where the control may or may not generate a signal from the reference sequence. Additionally, signals may be “associated with a mutant detection probe and/or a wild-type detection probe,” (emphasis added). Page 9, para. 2 of the reference states that the reference detection probe, which may also be referred to as a wild-type probe, is optionally linked to detectable means. In detecting PCR products, page 36, para. 5 states that detection may be adapted to particular mutations. These teachings support the Examiner’s conclusion that Wendt does not require that both the mutant and reference detection probes be labeled for detection to occur, and thus, one of these probes may be unlabeled. The fact that Wendt does not specifically teach working examples of their invention in which this particular probe set up is used does not disqualify these teachings from being used in an obviousness rejection, as prior art references must be considered as a whole. This is described in MPEP 2141.02 VI, which specifically states, “"the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed…." In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir. 2004).” Thus, the fact that Wendt teaches embodiments in which both detection probes may be labeled does not teach away or discourage alternative embodiments also taught by the reference in which only a single detection probe is labeled.
Additionally, Wendt is not limited to any particular detection means, and teaches detection comparisons with a control sample, as noted in the paragraph above. MPEP 2141.03 I, “"A person of ordinary skill in the art is also a person of ordinary creativity, not an automaton." KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 421, 82 USPQ2d 1385, 1397 (2007). "[I]n many cases a person of ordinary skill will be able to fit the teachings of multiple patents together like pieces of a puzzle." Id. at 420, 82 USPQ2d 1397. Office personnel may also take into account "the inferences and creative steps that a person of ordinary skill in the art would employ." Id. at 418, 82 USPQ2d at 1396.” As Wendt teaches differentially labeled detection probes where only one such probe is labeled, and the use of such probes with detection means, it is the Examiner’s position that the ordinary artisan would be capable of performing such detecting using such probes using the teachings of the Wendt, along with ordinary skill, knowledge, and creativity in the art, even though the reference does not provide an explicit working example of such detection. Such detection would not lead Wendt to be inoperable for its intended purpose because, as noted above, there are several teachings in the reference that recite said detection.
As to the claimed wherein clause concerning the PBNJ, Applicant is directed to the explanations of para. 20 in the Final Rejection. Specifically, para. 20 uses the general structure of the mutant and reference detection probes to describe how they would each specifically and non-specifically bind to either the mutant or reference sequence, keeping the scope of non-specific binding in line with that described by the instant specification. This paragraph states that “If the probes are competing for binding sites, it would follow that the reference detection probe, which would be a perfect match for the reference sequence, would bind to the reference sequence more often than the mutant detection probe, which is an imperfect match. This would lead to suppression of mutant detection probe binding to the reference sequence.” Applicant does not appear to address the rationale provided in this paragraph.
It is noted that instant claim 1 has been amended to additionally recite that the PBNJ sequence reduces signal detection of the reference sequence – though see the 35 USC 112(b) Rejections below. This is considered a function of the specific structure and suppressive binding of the PBNJ sequence. In other words, the PBNJ is preferentially binding to the reference sequence compared to the labeled probe, and the PBNJ is unlabeled. Thus, very little signal will be associated with the reference sequence, as any such signal would only be generated from any labeled probe that is able to bind to said reference sequence. This would be considered to read on the claimed reduction. As to the discrimination of the target sequence and the reference sequence, “discriminating” is defined by the instant specification in para. 71 as making a distinction between two or more things, though there is no limit as to how this distinction may be made. Thus, this term encompasses simply detecting a signal from a target sequence that is distinguishable to that generated by a reference sequence. This can be done by the detection comparison with a control sample described by Wendt above. Additionally, this discrimination could also amount to the confirmation that a particular target sequence is present in a sample, which could also be accomplished by the detection comparison with a control sample described by Wendt above. Thus, Wendt is considered to teach a reference detection probe and a detection step that reads on the PBNJ and the discriminating steps of claim 1, respectively.
On page 14 of their Remarks, Applicant argues that there is no clear reason or sufficient motivation provided to combine the teachings of Wendt in the manner described by the Examiner to arrive at the claimed invention. Applicant argues that it is impermissible hindsight reconstruction to “contemplate repurposing a blocking oligonucleotide to suppress probe binding as part of a detection strategy.”
Regarding impermissible hindsight, MPEP 2145 X (A) states, “"[a]ny judgment on obviousness is in a sense necessarily a reconstruction based on hindsight reasoning, but so long as it takes into account only knowledge which was within the level of ordinary skill in the art at the time the claimed invention was made and does not include knowledge gleaned only from applicant’s disclosure, such a reconstruction is proper." In re McLaughlin, 443 F.2d 1392, 1395, 170 USPQ 209, 212 (CCPA 1971).” In the Final Rejection, the instant specification is only cited in order to make clear the scope of claimed terms as they relate to the prior art (see paras. 18 and 20 of the Final Rejection), and is not used to develop obviousness rationale or to provide information that would not have been available to the ordinary artisan. Therefore, the Examiner is not considered to make use of impermissible hindsight.
Regarding the repurposing of a blocking oligonucleotide of Wendt, this is a mischaracterization of the teachings of Wendt used and the obviousness rejection generally. As noted above, Wendt teaches blocking probes with specific 3’ C3 spacers, and these were only mentioned in the Final Rejection to provide reasoning for why the ordinary artisan would place a 3’ C3 spacer on the reference detection probe, as this probe is already taught by Wendt as having a 3’ extension blocker (on page 41, para. 2 it states “The 3' terminal nucleotide of the detection probe(s) can be blocked or rendered incapable of extension by a nucleic acid polymerase.”). Regarding this specific combination, para. 19 of the Final Rejection states, “One or more of the detection probes can be blocked at the 3’ end to prevent extension by a polymerase (page 41, para. 2). Wendt also teaches that a blocking probe, which operates separately from the detection probes, may have a 3’ C3 spacer as a blocking agent (page 52, para. 2). In an example, the blocking probe in particular, which is based on the sequence of a reference detection probe, can have a 3’ C3 spacer and an unmodified 5’ end (page 102, para. 1 and lines 21-22). Thus, it would be prima facie obvious to use the 3’ C3 polymerase extension blocking means taught by Wendt (in a probe based on the reference detection probe) as the polymerase extension blocker for the reference detection probes themselves. Additionally, given that Wendt teaches labelling of only one of the detection probes, and the obviousness of including a spacer on the 3’ end of the reference detection probe, it would additionally be obvious to leave the reference detection probe with an unlabeled 5’ end. Because the detection methods of Wendt generally involve 5’ fluorophores and 3’ quenchers (page 38, para. 4), and the 3’ end of the reference detection probe already contains a spacer, it would be prima facie obvious to make the mutant detection probe the single probe that is detectable with a 5’ fluorophore and 3’ quencher in order to prevent overly complex reference detection probe design. Thus, Wendt teaches a mutant detection probe with a fluorophore and quencher, and a reference detection probe that contains an unmodified 5’ end and a C3 spacer at the 3’ end.”
Essentially, the teachings of Wendt regarding extension blocking on the blocking probes are being used to inform a particular type of extension blocker that can be used with the detection probes, as such detection probe blocking is not particularly limited by the reference. Then, as Wendt teaches that either the mutant or reference detection probe may be blocked, and that both probes need not be detectably labeled (see additional teachings on this point above), logic is applied to such a scenario in which the reference probe is blocked to arrive at the labeled probe and PBNJ of the claimed invention. This combination of teachings still results in an embodiment that is encompassed by the overall teachings of Wendt. MPEP 2143.01 states that motivation to establish an obviousness rejection need not be made explicit in a particular reference, but may originate from “background knowledge, creativity, and common sense of the person of ordinary skill." Zup v. Nash Mfg., 896 F.3d 1365, 1371, 127 USPQ2d 1423, 1427 (Fed. Cir. 2018).” Section V also states, “‘[a] given course of action often has simultaneous advantages and disadvantages, and this does not necessarily obviate motivation to combine’." Taken together, the fact that Wendt teaches other embodiments of detection probes that may have distinct advantages and disadvantages compared to those of the combination of teachings described here does not obviate the finding of obviousness, and though Wendt does not provide explicit motivation for the combination of teachings described in the rejection, this is not required to make an obviousness determination.
On pages 15-16 of their Remarks, Applicant argues that the existing obviousness rejections have no reasonable expectation of success for arriving at the claimed invention, particularly in that the reference allegedly does not sufficiently describe simultaneous amplification and detection or an unlabeled probe suppressing signal generation. Applicant argues that fluorescence generation is essential to the operation of Wendt and that the current obviousness rejections rely on impermissible hindsight.
Impermissible hindsight arguments were addressed above, and are not repeated here for the sake of conciseness. Additionally, the presence of an unlabeled probe suppressing signal generation in Wendt is already addressed above, as is the methods of detection in relation to the detection probes described by the reference.
Regarding the alleged simultaneous amplification and detection, it is noted that claim 1 is directed to performing a PCR reaction on a solution containing primers and probes, where one probe is labeled. Thus, the detection Applicant is considered to be referring to is simply detecting the signal associated with the label on the labeled probe, and “discriminating” a target from a reference sequence, though the actual measuring of a signal provided by the labeled probe is not required to occur within or during the PCR in claim 1.
In Wendt, the detection probes are provided with the PCR reagents (see the discussion of page 38, para. 2 of the reference above). Thus, the signal generated by the mutant detection probe would be capable of being detected once mutant detection probe binding occurred, and Wendt teaches detection of amplification products throughout their invention in association with the detection probes (e.g. page 38, para. 5, page 38-39 joining para., and page 42, para. 3). Thus, Wendt is considered to teach the amplification and detection associated with the instant claims.
On pages 16-18 of their Remarks, Applicant argues that the Examiner has not provided sufficient explanation to dispute Applicant’s evidence demonstrating inoperability of a one-step PCR employing a 5’ blocked probe in relation to the discussion of Figure D3 of Applicant’s declaration.
In Applicant’s Remarks, page 17, para. 2 is focused on the use of particular polymerases – where the model of the alleged Wendt protocol is done using Q5 polymerase, while the protocol following the instant invention uses Taq polymerase. The model of the Wendt protocol also involves the use of TaqMan chemistry and ddPCR. This model narrows features of Wendt in a manner inconsistent with the disclosure of Wendt – for example, page 32, paras. 5-6 provide a list of polymerases that may be used with the methods of the invention, including the use of Taq polymerase. While TaqMan probes may be used in the invention of Wendt, this is in no way a requirement (see page 39, para. 2, “In some embodiments, the detection probe is a TaqMan® probe,”). ddPCR, though recited throughout Wendt, is also not the only PCR method that may be used in Wendt (page 28, para. 2 states, “The entire PCR reaction comprising a plurality of compartmentalised PCR amplifications may be prepared in a number of different manners. In one embodiment, the PCR amplification comprising a plurality of compartmentalised PCR amplifications may be conducted as a digital PCR (dPCR) amplification. Any dPCR amplification known to the skilled person may be used with the invention.”) Thus, Applicant’s experiment does not accurately reflect the breadth of teachings in Wendt, and additionally does not demonstrate inoperability of the combination of the teachings of Wendt described in the obviousness rejections, as this combination does not rely on the combination of features used by Applicant.
As to Applicant’s allegedly unexpected results shown in this declaration, Applicant has not provided any additional specific Remarks or arguments concerning these alleged results. Regarding the claimed PBNJ functions, the Examiner’s position is that the combination of the teachings of Wendt render the claimed PBNJ structure obvious, and as this structure is what produces the claimed PBNJ functions, said combination of teachings would also produce the claimed function. A discussion of said PBNJ functions has also already been provided above, and was addressed in the Final Rejection.
Thus, Applicant’s arguments are not considered persuasive. The rejections presented in the Final Rejection mailed 10/7/2025 have been maintained. Additional teachings from Wendt are provided to clearly address the claim amendments and to elaborate upon the teachings cited previously, but these additional teachings do not change the rationale or thrust of the rejections.
Claim Objections
Claims 1 objected to because of the following informalities: in (c), “the reference and template sequence” should read “the reference and template sequences”. Additionally, if it is Applicant’s intention, it is recommended that in (i), “elongation by a polymerase” should read “elongation by the DNA polymerase” to clearly link the blocker to the polymerase recited earlier in the claim. Finally, in the final wherein clause of the claim, it is recommended that “non-specific” read “nonspecific” to match the use of “nonspecifically” earlier in the claim. Appropriate correction is required.
Claim 2 objected to because of the following informality: in the recitation of circulating cell free tumor DNA, line 1 should read “a somatic, wild-type”. Appropriate correction is required.
Claim 10 is objected to because of the following informality: in line 3, “non-specific” should read “nonspecific”. Appropriate correction is required.
Claim 17 is objected to because of the following informalities: in the final limitation of the claim regarding the complementarity and binding affinity of the PBNJ, each recitation of “a binding affinity” should read “the binding affinity,” as for a given PBNJ or labeled probe, there will be a single binding affinity of that sequence to a particular target or reference sequence. Appropriate correction is required.
Claim 22 is objected to because of the following informalities: line 2 should read “wastewater, an environmental sample, bodily fluid, tissue, a cell culture, or a tumor.” Appropriate correction is required.
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 1-2, 4-6, and 8-23 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 rejected due to the addition of the phrase “reduces signal detection of the reference sequence.” Specifically, this is because it is unclear what this signal reduction is in relation to. No specific signal detection is recited by the claim, and the only signal that would be produced is that of the labeled probe, which unspecifically binds to the reference sequence. Thus, this phrase is indefinite, as the scope of the described function is not clear. This claim will be interpreted as though this reduction in signal detection is in comparison to a signal that may be detected for the reference sequence in a sample or scenario in which a signal generated from the reference sequence is not inhibited.
Claims 2, 4-6, and 8-23 are rejected due to their dependence on rejected claim 1.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-2, 4-6, 8-15, 17-19, and 22-23 are rejected under 35 U.S.C. 103 as being unpatentable over Wendt et al. (International Patent Application No. WO 2018/001884 A1).
Wendt teaches methods for finding mutants in a population of nucleotides of interest (NOI; page 1, para. 1). This population can identify an organism or any predefined species (page 14, para. 5). This specifically includes bacteria, fungi, animals, and plants. (page 15, paras. 1-2). This method preferably involves dPCR (page 28, paras. 1-2; instant claim 6). Wendt explicitly teaches the use of genomic DNA, but teaches that the method can be performed in “any nucleic acid,” meaning that RNA can also be used (page 10, part g. and page 14, para. 4; instant claim 5). The mutation can be any mutation where the NOI of interest differs from a corresponding reference NOI. Wendt specifically states that the reference sequence can be a wild-type sequence, and the mutation can be an insertion, deletion or substitution (and more specifically a single nucleotide substitution; page 13, “Nucleotide of Interest (NOI),” paras. 1-5; instant claims 2, 4, 9, and 12-14). Regarding claim 12, it is noted that a “short nucleotide polymorphism” can be an insertion or deletion, as described in para. 86 of the instant specification.
Wendt teaches a PCR reaction involving mutant detection probes and reference detection probes that may compete for binding sites on NOIs when added together (page 38, para. 2). This PCR reaction clearly involves primers for amplification of the target sequence, which include a forward and reverse primer (page 8, para. 4), and PCR reagents include a nucleic acid polymerase (page 7, para. 5, and see page 32, paras. 5-6, which specifically recite the use of DNA polymerases). The primers are preferably designed to amplify both a reference sequence and a sequence with a mutation (page 36, para. 3). Though the probes are not required to be associated with specific detection means, the detection probes may be labelled with a fluorophore at the 5’ end and a quencher at the 3’ end, and in a particularly preferred embodiment, one probe may be linked to detectable means while the other is not (page 38, para. 4). Thus, the reference detection probe may be entirely unlabeled. Both detection probes can comprise a sequence that is identical or complementary to the NOI (page 38, para. 5, page 39, para. 2, and page 37, paras. 3-4). Both the mutant and reference detection probes can be 10-30 nucleotides in length, and therefore may be the same length, meeting the length requirements of instant claim 1. One or more of the detection probes can be blocked at the 3’ end to prevent extension by a polymerase (page 41, para. 2). Wendt also teaches that a blocking probe, which operates separately from the detection probes, may have a 3’ C3 spacer as a blocking agent (page 52, para. 2). In an example, the blocking probe in particular, which is based on the sequence of a reference detection probe, can have a 3’ C3 spacer and an unmodified 5’ end (page 102, para. 1 and lines 21-22). Thus, it would be prima facie obvious to use the 3’ C3 polymerase extension blocking means taught by Wendt (in a probe based on the reference detection probe) as the polymerase extension blocker for the reference detection probes themselves. Additionally, given that Wendt teaches labelling of only one of the detection probes, and the obviousness of including a spacer on the 3’ end of the reference detection probe, it would additionally be obvious to leave the reference detection probe with an unlabeled 5’ end. Because the detection methods of Wendt generally involve 5’ fluorophores and 3’ quenchers (page 38, para. 4), and the 3’ end of the reference detection probe already contains a spacer, it would be prima facie obvious to make the mutant detection probe the single probe that is detectable with a 5’ fluorophore and 3’ quencher in order to prevent overly complex reference detection probe design. Thus, Wendt teaches a mutant detection probe with a fluorophore and quencher, and a reference detection probe that contains an unmodified 5’ end and a C3 spacer at the 3’ end (instant claims 8 and 15).
Wendt does not explicitly teach that the competing mutant and reference detection probes will result in suppression of the mutation detection probe bound to the reference sequence. However, because the probes can be identical or complementary to a target or reference sequence, and the two sequences may only differ by an insertion, deletion, or single nucleotide substitution, this means the mutation detection probe will non-specifically bind to the reference NOI, and the reference detection probe will non-specifically bind to the mutated NOI, as they would still be majority complementary. If the probes are competing for binding sites, it would follow that the reference detection probe, which would be a perfect match for the reference sequence, would bind to the reference sequence more often than the mutant detection probe, which is an imperfect match. This would lead to suppression of mutant detection probe binding to the reference sequence. It should be noted that para. 73 of the instant specification states that “non-specifically binds” can include when “the binding agent is an oligonucleotide which non-specifically hybridizes to an oligonucleotide sequence which is not completely complementary to the sequence of the oligonucleotide binding agent.”
On page 42, para. 3, Wendt describes several ways in which signals may be measured and evaluated. These include the comparison of signals generated from a target sample with a control sample, where the control may or may not generate a signal from the reference sequence. Additionally, signals may be “associated with a mutant detection probe and/or a wild-type detection probe,” (emphasis added). Page 9, para. 2 of the reference states that the reference detection probe, which may also be referred to as a wild-type probe, is optionally linked to detectable means. In detecting PCR products, page 36, para. 5 states that detection may be adapted to particular mutations. Thus, detection with a singular labeled detection probe is contemplated by the reference, and this detection can be compared to scenarios in which a reference signal is uninhibited. Thus, taken together, these teachings of Wendt, in light of the claim interpretations provided in the “Response to Applicant’s Arguments” and 35 USC 112(b) Rejections sections above, meet each limitation of instant claim 1.
Wendt also teaches that in some cases, the mutant detection probe may be provided in excess compared to the reference detection probe (page 38, para. 6 through page 39, para. 1). Wendt describes how the detection of PCR amplification products may involve comparing signals between the mutation and reference NOI, where the signal may be fluorescent, such as in the case of the mutation detection probe (page 42, para. 3). This reference also teaches that fluorescence may be measured by “any useful means,” (page 39, para. 2), and specifically mentions using Quantasoft Software (page 42, para. 4). In an example of their method, Wendt uses the Quantasoft software, and teaches that it has multiple channels that can measure the amplitude of a plurality of signals during amplification (page 82, para. 3). It would be obvious for one of ordinary skill in the art to use the devices taught by Wendt to perform the method of Wendt. Therefore, claim 11 is prima facie obvious.
In measuring the signals resulting from fluorescence emission, Wendt teaches that a “positive signal” can be a signal for the target NOI only. Wendt teaches that this positive signal can be considered anything stronger than the signal from control PCR amplification (i.e. amplification comprising only the reference sequence). This positive signal can be detected via threshold determined by the Quantasoft software. The detection and analysis of only the positive signal would mean that there is no active detection of the reference signal, thus eliminating detection of non-specific amplification of the reference sequence (page 42, paras. 3-4). The use of Quantasoft software as taught by Wendt can be used in conjunction with a QX200 Droplet Reader, and therefore can occur in the context of droplet-based PCR (page 42, para. 4, page 54, para. 2, bullet 1, page 71, para. 1, and page 8, para. 1; instant claim 10).
Wendt specifically states that the detection probes can range from 10 to 30 nucleotides in length, overlapping with the stated range in instant claim 19 (page 37, paras. 3-4 and page 40, para. 5). In addition, if the detection probes are identical or complementary to an NOI sequence as taught above, it would follow that the target sequence can also be 10 to 30 nucleotides in length as well (page 37, para. 3; instant claim 19). MPEP 2144.05 states, “In the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists.” In addition, no evidence of unexpected results has been presented with regard to the 10 to 30 nucleotide length range recited in claim 19. Therefore, claim 19 is prima facie obvious.
Additionally, given that the reference detection probe can be entirely complementary to the reference sequence and that the target sequence may differ from the reference sequence by a single nucleotide substitution, as described above, the reference detection probe could then still be 90-95% complementary to the target sequence (page 37, para. 3 and page 13, “Nucleotide of Interest (NOI),” paras. 1-5). For example, if the sequences are all 10 nucleotides long, and the mutant sequence differs from the reference sequence by a single nucleotide substitution and the reference detection probe is completely complementary to the reference sequence, then the reference detection probe would still be 90% complementary to the mutant sequence. These teachings of Wendt also mean that the reference detection probe would have greater binding affinity to the reference sequence over the target sequence, and that the mutant detection probe, which is completely complementary to the mutant sequence, would have greater binding affinity to said mutant sequence over the reference sequence (instant claims 17 and 23).
Wendt describes that pools of organisms, from which the NOIs are derived, is preferred to theoretically comprise “all possible mutations in all genes,” (page 16, para. 6). This would therefore include every possible SNP at a specific location in the reference sequence. When organisms are pooled and then sub-pooled according to the method of Wendt, samples containing DNA may be compartmentalized to detect multiple mutations and compartmentalized PCR can occur (pages 23-24, “Identifying sub-pools”). This compartmentalized PCR can include the detection probes (page 33, para. 3). Thus, it would be prima facie obvious to one of ordinary skill in the art that multiple reference detection probes, each made to detect a specific SNP at a specific location in the reference sequence, could be used in different compartments, and could therefore be used in the method of Wendt. Therefore, claim 18 is prima facie obvious.
Wendt teaches that when the organisms of interest are unicellular, such as in the case of bacteria, they may be incubated in a cell culture before being used in the method (page 45, para. 3; instant claim 22).
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Wendt et al. (International Patent Application No. WO 2018/001884 A1) in view of Johnson et al. (Nucleic Acids Research, 2004).
Regarding claim 16, Wendt teaches the method of claim 1, as described above. While Wendt does teach locked nucleic acids, it is in the context of the composition of forward and reverse PCR primers, and not in the detection probes (page 34, para. 5).
Johnson teaches fluorogenic locked nucleic acid probes that are specific to particular SNPs in humans (Abstract and page 2, column 1, para. 3). These probes were used in real-time PCR (e.g. page 2, “Real-time PCR optimization”). Johnson teaches that the use of these probes allows the user to obtain raw fluorescence data, and is effective, reliable, efficient, and capable of aiding in high throughput SNP genotyping (page 8, column 2, paras. 1-2).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to combine the SNP specific locked nucleic acids probes with the existing detection probes of Wendt. This would result in probes with all the features initially described by Wendt, with the additional SNP specific locked nucleic acid structure of Johnson. One would be motivated to make this combination in order to increase the efficiency and ease of performing SNP genotyping via a PCR assay, as taught by Johnson, as this would aid in detecting mutant sequences in a population of sequences, which is the purpose of the invention of Wendt. There would be a reasonable expectation of success with this combination because many different probe configurations are taught by Wendt, and the context of the probes of Johnson is very similar to those of Wendt. Therefore, the method of claim 16 is prima facie obvious over Wendt in view of Johnson.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Wendt et al. (International Patent Application No. WO 2018/001884 A1) in view of Barker et al. (Genetic Epidemiology, 1996).
Regarding claim 20, Wendt teaches the method of claim 1, as described above. Wendt does not teach that the method may be used to test mutations that result in an elevated risk or presence of cancer.
Barker teaches the BRCA1 mutation in humans that leads to an increased risk of breast and ovarian cancers (Abstract and page 601, para. 4 through page 602, para. 1). The BRCA1 mutation in particular is a single nucleotide variant, where a C is mutated to a T (Figure 1).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use human DNA containing the BRCA1 gene in the method of Wendt, and to specifically compare wild-type BRACA1 versus mutated BRCA1 as taught by Barker. One of ordinary skill in the art would be motivated to use the method of Wendt to detect the mutated BRAC1 gene as this can be an indicator for increased risk of breast and ovarian cancers, and thus can be used in cancer screening and in preventative tests and treatments. There would be a reasonable expectation of success with detecting the BRAC1 mutation in the method of Wendt because this method specifically points out that it can be used with animals, and substitutions are taught as a possible mutation that can be detected (e.g. page 36, para. 5). Thus, claim 20 is prima facie obvious over Wendt in view of Barker.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Wendt et al. (International Patent Application No. WO 2018/001884 A1) in view of Jenkins et al. (mBio, 2015).
Regarding claim 21, Wendt teaches the method of claim 1, as described above. Wendt also teaches various genera that the bacteria used in the method may be from, including Staphylococcus (page 15, para. 1). However, Wendt does not teach any specific pathogenic strain of bacteria.
Jenkins teaches gene expression of S. aureus, and states that there is step-wise mutation progression from strains of S. aureus that are commensal (i.e. non-pathogenic) in humans, to strains that are pathogenic (page 1, column 2, para. 1). To mimic this progression, Jenkins created various mutant strains of S. aureus involving deletions of certain genes (page 2, column 2, para. 4).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use S. aureus as the organism of choice in the method of Wendt, and to specifically compare a commensal strain of the bacterium with a pathogenic strain (i.e. as the reference and mutant sequences in the method of Wendt, respectively). Jenkins teaches that S. aureus is prevalent in the noses of humans, and can cause mild to severe infections, including sepsis (page 1, column 1, para. 1). Thus, one of ordinary skill in the art would be motivated to use the method of Wendt to detect pathogenic S. aureus strains that have the potential to cause severe infection in order to better diagnose and treat sick individuals. There would be a reasonable expectation of success with detecting S. aureus in the method of Wendt because this method specifically points out that it can be used with Staphylococcus bacteria, and deletions are taught as a possible mutation that can be detected (e.g. page 36, para. 5). Thus, claim 21 is prima facie obvious over Wendt in view of Jenkins.
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.
Claim 1 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 2 of copending Application No. 19/199,885 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because claim 2 of the ‘885 application contains nearly each limitation of instant claim 1, though the terms used are not precisely the same. The labeled probe of the ‘885 application has the same structure as the instant labeled probe and hybridizes to a target sequence, while the MEOW probe contains a 3’ extension blocker and hybridizes to a reference sequence, thus making it similar to the instant PBNJ. Both are then used in a PCR reaction with a sample containing both the reference and target sequence, primers, and PCR reagents (which the ordinary artisan would recognize would include a polymerase for extension, and would therefore encompass a DNA polymerase). The labeled probe and MEOW each specifically hybridize to the target and reference sequences, respectively, and each non-specifically bind to the reference and target sequences, respectively. Detection of the target sequence in an amplicon is performed. Though the MEOW probe is not specifically stated to be unlabeled, no label is recited in claim 2 of the ‘885 application, and as the 5’ and 3’ ends of the probe are attached to various components, 5’ or 3’ fluorophores and quenchers could not be used.
Additionally, though claim 2 of the ‘885 application does not recite the specific functions of the PBNJ specific binding that are recited in the instant claim, such functions would naturally arise from the structures of the labeled and MEOW probes, as the MEOW probe would preferentially bind to the reference region, and thus suppress potential detection of the labeled probe (i.e. signal) on the reference region.
Though the primers of claim 2 of the ‘885 application are not stated to be for both the reference and target sequences, the use of such primers would be prima facie obvious to the ordinary artisan, as the intention of the probes is to bind to both the target and reference sequence – if only one of these sequences were amplified, then the specific/non-specific binding described by the claim would not occur in an appreciable manner
Finally, though the instant claim requires that the PBNJ have a length of at least 80% the length of the labeled probe, length requirements are not discussed in claim 2 of the ‘885 application. However, this means that the length requirements of the probes of claim 2 of the ‘885 application are not particularly limited, and so overlap in scope with those of instant claim 1.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are currently allowable.
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/FRANCESCA FILIPPA GIAMMONA/Examiner, Art Unit 1681
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