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 .
Election/Restrictions
Applicant's election with traverse of Species A (claim 6) in the reply filed on 2/3/2026 is acknowledged. The traversal is on the ground(s) that it would allegedly not be undue burden to examine all of the claims to their full scope. This is not found persuasive because undue burden is not a factor under restrictions related to applications submitted under 35 USC 371, which is the case in the instant application.
The requirement is still deemed proper and is therefore made FINAL.
Claims 10 and 14 withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim.
Claims 1-2, 4-9, 15, 26-27, 30, and 33 are pending and are examined on the merits herein.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 8/15/2023 and 3/25/2024 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.831-1.834 because it does not contain a “Sequence Listing XML” as a separate part of the disclosure. A “Sequence Listing XML” is required because the application was filed on or after July 1, 2022, and so must abide by the guidelines of ST.26. It is noted that Applicant has provided a Sequence Listing, but this is in ASCII format, which was the requirement under ST.25, and not ST.26.
Required response - Applicant must provide:
• A “Sequence Listing XML” part of the disclosure, as described above in item 1. or 2.; together with
o A statement that indicates the basis for the amendment, with specific references to particular parts of the application as originally filed, as required by 37 CFR 1.835(a)(3);
o A statement that the “Sequence Listing XML” includes no new matter as required by 37 CFR 1.835(a)(4)
AND
• A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph as required by 37 CFR 1.835(a)(2), consisting of:
o A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
o A copy of the amended specification without markings (clean version); and
o A statement that the substitute specification contains no new matter.
Claim Objections
Claim 1 is objected to because of the following informalities: the claim contains periods that do not appear at the end of the claim (i.e. i., ii., and iii. in (b)). Note MPEP 608.01(m) which states, “Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations.” Additionally, in the final line of the claim, “the polynucleotide target sequence” should read “the target polynucleotide sequence” in order to better match the language used in the preamble. Finally, in the final line of the claim “the analyte” should read “the given nucleic acid analyte,” also to better match the language used in the preamble. Appropriate correction is required.
Claim 4 is objected to because of the following informalities: in line 4, “(dNTP)” should read “(dNTPs)” and in line 5, “present in a sample” should read “present in the sample,” as a sample is already recited in claim 1, from which this claim depends. Appropriate correction is required.
Claim 5 is objected to because of the following informalities: the claim contains periods that do not appear at the end of the claim (i.e. i., ii., and iii. in (b)). Note MPEP 608.01(m) which states, “Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations.” Additionally, in the final line of the claim, “the polynucleotide target sequence” should read “the target polynucleotide sequence” in order to better match the language used in the previous claims. Finally, in the final line of the claim “the analyte” should read “the given nucleic acid analyte,” also to better match the language used in previous claims. Appropriate correction is required.
Claim 7 is objected to because of the following informality: in the final line of the claim, it is recommended to amend “pyrophosphorolysis enzyme” to “pyrophosphorolysing enzyme,” as the latter is the language used in claim 1, from which this claim depends. Appropriate correction is required.
Claim 8 is objected to because of the following informality: in paragraph 2 of the claim, in the final line, “the extent needed for it to melt from the non-target molecule” should read “the extent needed for the blocking oligonucleotide to melt from the non-target nucleic acid analyte,” though see the 35 USC 112(b) Rejections below concerning this latter term. Appropriate correction is required.
Claim 15 is objected to because of the following informality: in the final line of the first option for the third reaction mixture, “amplification of the target of interest, in this case A2 which is then detected” should read “amplification of A2, which is then detected.” Appropriate correction is required.
Claim 30 is objected to because of the following informalities: for better clarity, in line 2, it is recommended to amend “multiple probes A0” to read “multiple A0 probes,” as the former can be read as an alternative definition for the A0 probes rather than a statement that multiple A0 probes as described in claim 1 may be used. Additionally, in line 4, “wherein the amplicons of A2” should read ““wherein the multiple copies of A2,” as the latter language is what is used in claim 1. 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, 4-9, 15, 26-27, 30, and 33 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 because in line 1 of the wherein clause of step (b), “the target analyte” is recited. No target analyte is recited earlier in the claim, and so this phrase lacks antecedent basis. It will be interpreted as though this target analyte is the same as the “target polynucleotide sequence” of the preamble of the claim.
Claims 2, 4-9, 15, 26-27, 30, and 33 are rejected based on their dependence on rejected claim 1.
Claim 2 is also rejected because in line 2, the claim recites “a biological sample.” It is unclear if this biological sample is referring to the same “sample” as stated in the preamble of claim 1, or if a new sample is required. Thus, the scope of the claim is indefinite. It will be interpreted as though the biological sample of claim 2 and the sample of claim 1 are the same.
Claim 5 is also rejected because it is generally written as though it is an independent claim even though it depends on claim 1, and this renders the scope of the claim unclear and indefinite. For instance, the components of the mixture are written with “a” language, even though they have already been established in claim 1, and the wherein clause similarly uses the same language as claim 1 (e.g. “a subset of non-target polynucleotide sequences,” “a first intermediate product,” etc.), which appears to indicate that the claim is drawn to an entirely new mixture and set of reactions than those of claim 1.See also the 35 USC 112(d) Rejections below.
In light of these rejections and the 35 USC 112(d) Rejection to claim 5, it is noted that if this claim is amended to be an independent claim, the same issue with the use of “the target analyte” that is described in the rejection of claim 1 above would apply here to the use of the phrase in line 2 of the wherein clause.
Claim 7 is also rejected because in line 3 the claim recites “the biological sample,” which lacks antecedent basis, as “a biological sample” is not recited in claim 1, from which this claim depends. It is also unclear if this biological sample is referring to the same “sample” as stated in the preamble of claim 1, or if a new sample is required. Thus, the scope of the claim is indefinite. It will be interpreted as though the biological sample of claim 7 and the sample of claim 1 are the same.
Claim 8 is also rejected for reasons similar to claim 5, in that it appears to be written as though it is an independent claim even though it depends on claim 1, and this renders the scope of the claim unclear and indefinite. Particularly, the fourth and fifth paragraphs of the claim reiterate the limitations stated in the wherein clause of (b) of claim 1, and use the same language “a” language as claim 1 for the reaction components (e.g. “a first intermediate product,” “a partially digested strand,” etc.), rendering it unclear if this claim is attempting to recite a distinct reaction from that of claim 1. It will be interpreted as though this is not the case, and that the fourth and fifth paragraphs are merely intended to reiterate the method of claim 1, but Applicant is required to amend the language to make this clear.
Additionally, in claim 8, in line 3, the phrase “a target nucleic acid analyte” is unclear, as it is unknown if this is intended to be the same element as “the target analyte” of claim 1 (though see the 35 USC 112(b) rejection with this phrase described above). It is noted that “the target nucleic acid analyte” also appears throughout the claim, and these instances should be changed depending on Applicant’s amendments to “a target nucleic acid analyte.” Similarly, throughout the claim there is reference to “non-target nucleic acid analytes,” and it is unknown if these are intended to be the same as the “non-target polynucleotide sequences” recited in claim 1. Finally, in the final paragraph of the claim, line 1 references “the previous step,” but the claim does not recite any distinct steps, making it unclear to what element of the claim this is referring to. As this paragraph is being interpreted as the same as the detecting step of claim 1, “the previous step” will be interpreted as referring to step (b) of claim 1.
Claim 15 is also rejected because in line 3, “the products of the pyrophosphorolysis reaction” renders the scope of the claim unclear. Specifically, in claim 1, from which this claim depends, the second reaction mixture, which contains the pyrophosphorolysing enzyme, is not only used to perform a pyrophosphorolysis reaction – for example, a ligation reaction is also performed. Therefore, it is unclear which specific products should be used in the third reaction mixture described by claim 15 – e.g. if the products of the pyrophosphorolysis reaction must be removed before ligation and placed in the third reaction mixture. If so, the ligation to form A2 would not occur. This does not appear to be Applicant’s intention, as each option for the third reaction mixture in claim 15 utilizes A2. It will be interpreted as though “the products of the pyrophosphorolysis reaction” are the products formed at the end of step (b) of claim 1.
Additionally in claim 15, line 5 of the second third reaction mixture option states “the labelled oligonucleotides.” This lacks antecedent basis, as “a labelled oligonucleotide” does not appear earlier in the claim or in claim 1, from which this claim depends. It will be interpreted as though this labelled oligonucleotide is the oligonucleotide comprising the one or multiple fluorophores recited earlier in claim 15.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 5 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 1 requires the distinct use of two reaction mixtures, and in step (b) of the claim, the reaction mixture formed in (a) is further introduced to a second reaction mixture. In claim 5, the first and second reaction mixtures are combined, and the nucleic acid analytes are introduced to the combined reaction mixture. With this combination, the step (b) of claim 1 would not be able to occur, as the reaction mixture formed in (a) of claim 1 could not be introduced to a second reaction mixture, as only one reaction mixture would be present. Thus, claim 5 fails to include all the limitations of the claim upon which it depends.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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, 9, 26, 30, and 33 are rejected under 35 U.S.C. 103 as being unpatentable over Balmforth et al. (WO 2020/016590 A1; cited in Applicant’s IDS).
Balmforth teaches a method for detecting a target polynucleotide in a given nucleic acid analyte. This method is described on page 6, and involves the following:
annealing the analyte to a single-stranded probe oligonucleotide A0 to create a first intermediate product which is at least partially double-stranded and in which the 3' end of A0 forms a double-stranded complex with the analyte target sequence;
pyrophosphorolysing the first intermediate product with a pyrophosphorolysing enzyme in the 3'-5' direction from the 3' end of Ao to create partially digested strand A1 and the analyte;
(i) annealing A1 to a single-stranded trigger oligonucleotide B and extending the A1 strand in the 5'-3' direction against B; or (ii) circularising A1 through ligation of its 3' and 5' ends; or (iii) ligating the 3' end of A1 to the 5' end of a ligation probe oligonucleotide C; in each case to create an oligonucleotide A2;
priming A2 with at least one single-stranded primer oligonucleotide and creating multiple copies of A2, or a region of A2; and
detecting a signal derived from the multiple copies and inferring therefrom the presence or absence of the polynucleotide target sequence in the analyte.
Note that option c.iii) reads on instant claim 1, and that this method may specifically involve the use of a ligase (see that final para. on page 13). Additionally, Balmforth teaches that blocking oligonucleotides may be used (pages 25-27), where said blocking oligonucleotide can anneal to wild-type, non-target sequences, while the A0 probe anneals to mutant, target sequences. At the bottom of page 26, when the blocking oligonucleotide is used with the method described above, it is described as being introduced in the step before A0 is annealed to target sequences, where the blocking oligonucleotide anneals “to at least a subset of non-target polynucleotide sequences.”
However, Balmforth does not make clear the specific reaction mixes used with the described components in their method, nor does the method restrict the specific configuration of reaction mixes for their invention.
MPEP 2143.01 V states, “‘[a] given course of action often has simultaneous advantages and disadvantages, and this does not necessarily obviate motivation to combine’" (quoting Medichem, S.A. v. Rolabo, S.L., 437 F.3d 1157, 1165, 77 USPQ2d 1865, 1870 (Fed. Cir. 2006).” MPEP 2144 I states, "The rationale to modify or combine the prior art does not have to be expressly stated in the prior art; the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art, established scientific principles, or legal precedent established by prior case law." MPEP 2141.03 I states, "'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.".
Regarding claims 1 and 5, the ordinary artisan, using ordinary skill, knowledge, and creativity in the art, would be capable of arriving at the reaction mixture(s) described by the claims. For claim 1 specifically, the ordinary artisan would recognize the advantages of separating the blocking oligonucleotide reaction from the subsequent method steps, as this would allow for the non-target sequences to be blocked before additional manipulation of the sample occurred, thus reducing the amount of non-target sequence available to potentially bind to A0 and create background noise in the method. This would increase overall accuracy in the method. Then, by combining the A0 probe, the pyrophosphorolysing enzyme, and the ligase in a second reaction mixture that the target sequence is then exposed to, this would allow the transformation of A0 to A2 to occur in said single reaction mixture, without the need for moving the A oligonucleotides or the analyte into multiple vessels, ensuring that these components are preserved, while also saving time and equipment.
For claim 5 specifically, including the blocking oligonucleotide and the A0 probe, the pyrophosphorolysing enzyme, and the ligase in a single reaction mixture would even further save time and equipment compared to the two reaction mixture method described above. Though the blocking oligonucleotide would be competing with the A0 oligonucleotide in this scenario, as the blocking oligonucleotide can be designed to hybridize perfectly with a non-target sequence and have sequence mismatches with a target sequence, the A0 oligonucleotide is designed to specifically hybridize to the target analyte, and so would bind to this sequence with much more efficiency compared to the blocking oligonucleotide. As A2 is eventually amplified, this early competition would not have an appreciable effect on the detection of the target. There would be a reasonable expectation of success with both of these reaction configurations as Balmforth does not require a specific reaction mixture configuration, as noted above, and the reactions performed (hybridization, pyrophosphorylation, ligation, amplification, etc.) would all be known to the ordinary artisan (see Balmforth page 1, para. 2, page 2, para. 2, page 10, para. 2, and pages 13-14).
Thus, though the configurations of instant claims 1 and 5 may have distinct advantages and disadvantages, the presence of disadvantages do not obviate a finding of obviousness, and using the teachings provided by Balmforth and the capabilities of the ordinary artisan described above, motivation to arrive at the configurations of both claims exists, even though an explicit motivation is not provided by Balmforth.
Hence, claims 1 and 5 are prima facie obvious over Balmforth.
Regarding claim 2, Balmforth teaches on page 18, para. 2 that, “…there is provided a method for preparing at least one single-stranded analyte of a nucleic acid comprised of a target polynucleotide region characterised by the steps of (i) producing amplicons of the analyte(s) by subjecting a biological sample comprised of corresponding double-stranded versions of the analyte(s) and optionally background genomic DNA to cycles of amplification. In one preferred embodiment amplification is carried out using the polymerase chain reaction (PCR) in the presence of a polymerase, nucleoside triphosphates and at least one corresponding primer pair wherein one of the primers includes a 5'-3' exonuclease blocking group…” Page 9, para. 2 and page 19, para. 4 of the reference note that exonuclease blocking groups can be DNA spacers, inverted bases, or other oligonucleotide modifications, though these are not taught directly in conjunction with the primers of the PCR of page 18, para. 2. However, it would be prima facie obvious to the ordinary artisan to use components taught by Balmforth as being for exonuclease blocking for the exonuclease blocking groups recited throughout the invention, as such blocking groups are indicated to perform as desired by Balmforth, and would therefore have a reasonable expectation of success with their use. Thus, as the primers of page 18, para. 2 of Balmforth have a 5’ exonuclease blocking group in order to prevent 5’-3’ exonuclease activity from acting upon said primers, and Balmforth teaches that exonuclease blocking groups can be DNA spacers or otherwise modified oligonucleotides, this would result in primers with 5’ tails that are not complementary to the analytes from the biological sample.
Thus, claim 2 is prima facie obvious over Balmforth.
Regarding claim 4, page 18, para. 2 of Balmforth describes PCR amplification of target sequences before they undergo contact with the A0 probe. This is a preliminary step designed to separate the target from background noise from genomic DNA, which is “typically present in significant excess.” The amplification reaction is specifically noted to utilize “polymerase, nucleoside triphosphates and at least one corresponding primer pair.” After this amplification, the product may be treated with a proteinase.
Though Balmforth does not specifically teach that this amplification can occur in a reaction mixture with blocking oligonucleotide, it would be prima facie obvious to the ordinary artisan that this could be done, particularly as the reference teaches that the blocking oligonucleotide is introduced before the A0 probe, and is specifically designed to anneal to non-target sequences in a manner that is not disrupted during PCR (pages 25-26). Thus, the use of the blocking oligonucleotide with this PCR amplification would bolster the noise-reducing effects of said amplification, as it would ensure that non-target, potentially noise creating sequences are not also amplified.
Thus, claim 4 is prima facie obvious over Balmforth.
Regarding claim 6, Balmforth teaches that phosphorolysis can be performed “in the presence of a polymerase exhibiting pyrophosphorolysis activity and a source of pyrophosphate ion,” (page 10, para. 2).
Regarding claim 9, page 26, paras. 1 and 3 of Balmforth note that the blocking oligonucleotides can have modifications to prevent digestion, such as 3’ end modifications.
Regarding claim 26, Balmforth teaches that after the ligation step, an exonuclease can be added to the reaction mixture can be treated with an exonuclease to digest any non-ligated nucleic acid material (claim 5).
Regarding claim 30, page 21, para. 3 of Balmforth states that the method can be used in multiplex, where multiple different A0 probes are used for multiple target regions. Page 9, para. 1 teaches that A0 sequences may have identification regions, and page 9, para. 3 states that the identification regions have unique sequences that can be used in the detection/inferring step of the method. When multiple A0 probes are employed with identification regions, where the A0 probes are selective for different target sequences, the resulting amplicons will also have the identification region (page 15, para. 3). Page 21, para. 3 then specifically notes that the A2 amplicons/copies will have this identification region.
Regarding claim 33, the joining para. of pages 15-16 states that in one embodiment, “the analyte is split into multiple reaction volumes with each volume having a different probe oligonucleotide A0 or plurality thereof designed to detect different target sequence(s).” This paragraph also notes that the different A0 probes can include a common priming site allowing a single or single set of primers to be used for amplification.
Claims 7 and 27 are rejected under 35 U.S.C. 103 as being unpatentable over Balmforth et al. (WO 2020/016590 A1) in view of Liu et al. (US 2009/0239283 A1; cited in Applicant’s IDS).
Regarding claim 7, Balmforth teaches that the analytes of the invention can be RNA molecules (page 2, final para.). However, in each of the working examples (pages 27-34), it is noted that the oligonucleotides used appear to be exclusively DNA, indicating that the use of DNA primers and probes is preferable in the invention of Balmforth. Additionally, this reference does not teach that when RNA is used, it can be reverse transcribed.
Liu teaches methods for pyrophosphorolysis activated polymerization (PAP). The method for PAP is shown in Figure 1, where blocked primers, when matched to a template, can be pyrophosphorolysed and amplified. When the blocked primer is mismatched with the template, extension and amplification generally do not occur (though there can be exceptions, see Figure 1 and para. 165). Liu teaches that RNA can be used with PAP methods, and when RNA is used, reverse transcriptase can also be used (para. 21).
Liu provides evidence that phosphorylation reactions can be performed with DNA or RNA, but also describes using reverse transcriptase on RNA in the context of phosphorylation reactions. As Balmforth does not specify that their A0, blocking, and other oligonucleotides can be either DNA or RNA, and the reference provides exclusively DNA examples for these oligonucleotides, the ordinary artisan would be motivated to use DNA for these oligonucleotides. As Balmforth does teach that a target can be RNA, it would therefore be prima facie obvious to the ordinary artisan that the RNA would need to be reverse transcribed before hybridizing to these oligonucleotides to ensure efficient hybridization. Liu provides a similar context in which RNA can be reverse transcribed before being used in pyrophosphorylation reactions, providing a reasonable expectation of success.
Thus, claim 7 is prima facie obvious over Balmforth in view of Liu.
Regarding claim 27, Balmforth does not teach that the same enzyme can perform pyrophosphorolysis and amplification within their methods. In their working examples, Balmforth appears to use different polymerases for these purposes (see page 28, which shows using Mako DNA polymerase for pyrophosphorylation and page 31, which uses Phusion Hot Start Flex DNA polymerase).
Liu teaches that in their PAP methods, the same polymerase can be used for both pyrophosphorolysis and extension (e.g. paras. 21 and 131). Such polymerases can be Taq polymerases (paras. 21 and 138)
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 the guidance of Liu, which teaches pyrophosphorylation reactions and amplifications reactions (i.e. a context similar to that of Balmforth), to use the same enzyme for pyrophosphorylation and amplification in the method of Balmforth. Balmforth does not particularly limit the polymerases/enzymes that may be used in their invention, and so using a well-known polymerase such as Taq would be possible and accessible for the ordinary artisan. Additionally, the ordinary artisan would see the benefit of using a single enzyme for both reactions, as it would prevent the need for both acquiring a second polymerase and adding an additional polymerase to the second reaction mixture, thus simplifying the overall method of Balmforth. As Liu teaches that Taq can be used for both of these reaction types, there would be a reasonable expectation of success.
Thus, claim 27 is prima facie obvious over Balmforth in view of Liu.
Claims 15 is rejected under 35 U.S.C. 103 as being unpatentable over Balmforth et al. (WO 2020/016590 A1), hereby Balmforth 1, in view of Balmforth et al. (WO 2016/012789 A1), hereby Balmforth 2.
Regarding claim 15, Balmforth 1 teaches that their detection methods can include a sequence-specific molecular probe, such as a molecular beacon or hairpin probe (page 15, para. 2). However, this reference does not provide specifics of how such molecular probes would work in a detection reaction.
Balmforth 2 teaches a probe system that can be used for sequencing that comprises a first single-stranded oligonucleotide that is labelled with detectable elements in an undetectable state, second and third oligonucleotides that hybridize to complementary regions of the first oligonucleotide, making a double-stranded oligonucleotide, and then digesting the probe to release the detectable elements. Repeating this digestion process leads to the detection of the detectable elements (pages 2-3, joining para.). The second and third oligonucleotides can be joined to one another before contact with the first oligonucleotide (page 5, para. 1). Page 6 notes that the detectable element can be a fluorophore, and rendering them undetectable can be done via close proximity to a second fluorophore or between a fluorophore and a quencher. Though this probe is taught as part of a sequencing system, the probe system itself can exist on its own (page 10, para. 2).
In Balmforth 1, the c.iii) option that reads on instant claim 1 is shown in Figure 12, where A1 is ligated with a C oligonucleotide via a D oligonucleotide splint to create A2, and then A2 undergoes amplification. Thus, the ligation point would be near the center of the ligated product. Balmforth 1 also teaches that detecting amplification products can be done with sequence-specific probes. In order to ensure that the detecting is detecting products that successfully underwent ligation to create A2, it would be prima facie obvious to the ordinary artisan to make the sequence-specific probe complementary to the ligation point. If this point was not included in the probe, than the probe may release signal when hybridizing to errant A1 or C sequences that did not undergo ligation.
In relating this to the teachings of Balmforth 2, this reference teaches a fluorescent probe (the first oligonucleotide) that binds to an oligonucleotide (in the presence of ligase), undergoes digestion, and then releases a fluorescent signal. As the context for the use of this probe is similar to that of Balmforth 1 (especially as Balmforth 2 teaches pyrophosphorolysis methods in their invention, see page 4, para. 2). Thus, the ordinary artisan would recognize that this first oligonucleotide of Balmforth 2 could hybridize to the copies of A2 (overlapping with the ligation point, as described above), and then the digestion and detection associated with the first oligonucleotide of Balmforth 2 would proceed as described in the reference. As Balmforth 1 does not require a particular probe method, this would amount to substituting the probe and probe detection of Balmforth 1 with the probe and probe detection described by Balmforth 2. MPEP 2143 I (B) states, “The rationale to support a conclusion that the claim would have been obvious is that the substitution of one known element for another yields predictable results to one of ordinary skill in the art.” As Balmforth 1 teaches the use of a sequence-specific probe, and generally teaches design methods for the oligonucleotides of their invention (e.g. page 9, para. 1, page 15, para. 3, and page 21, para. 1), designing oligonucleotides for specific target sequences is encompassed by their invention. Balmforth 2 then teaches a specific single-stranded oligonucleotide probe designed for hybridization with a single-stranded sequence, of which A2 would be, and the digestion of the oligonucleotide of Balmforth 2 and the subsequent fluorophore signal release would simply rely on this hybridization. As Balmforth 2 teaches that the second and third oligonucleotides can be linked to one another, forming one single-stranded oligonucleotide, the fact that A2 is one single-stranded oligonucleotide would not change the operation of the probe detection of Balmforth 2, and the subsequent signal generation would be predictable. Additionally, as this detecting is taught by Balmforth 1 to occur with A2 specifically, it would be prima facie obvious to not add the detection probe/digestion methods until after the generation of A2 and its amplicons is complete, so that these components do not interfere with the earlier steps of the method.
Thus, claim 15 is prima facie obvious over Balmforth 1 in view of Balmforth 2.
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 5 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 31 of U.S. Patent No. 12,545,951 B2. It is noted that although this patent number has been issued for this application, this patent has not yet been published. The claim numbers used in reference to this patent refer to those of the patent application, 17/757,861.
Although the claims at issue are not identical, they are not patentably distinct from each other because claim 31 of the ‘951 patent teaches the same reaction mixture as the combined reaction mixture of instant claim 5. The blocking oligonucleotide of the ‘951 patent operates in the same manner as in the instant claims (binding to a non-target sequence), and the transformation of A0 to A2 occurs in a manner encompassed by the instant claims – in other words, though the ligation reaction of A1 to form A2 is more detailed in the ‘591 patent than in the instant claim, the instant claim does not specify how the ligation must occur. Additionally, the ‘591 patent then describes a detecting step to identify the presence of a target that reads on that of the instant claim.
Claims 1, 6, 26-27, and 30 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 19, 23, and 27 of U.S. Patent No. 11,332,780 B2 in view of Balmforth et al. (WO 2020/016590 A1).
Claim 1 of the ‘780 patent provides a first mixture that is the same as the second mixture of instant claim 1. The transformation of A0 to A2 occurs in a manner encompassed by the instant claims – in other words, though the ligation reaction of A1 to form A2 is more detailed in the ‘780 patent than in the instant claim, the instant claim does not specify how the ligation must occur. Additionally, the ‘780 patent then describes a detecting step to identify the presence of a target that reads on that of the instant claim.
However, claim 1 of the ‘780 patent does not describe the use of a blocking oligonucleotide.
Balmforth teaches a method on page 6 that is also encompassed by claim 1 of the ’780 patent. Additionally, Balmforth teaches that blocking oligonucleotides may be used (pages 25-27), where said blocking oligonucleotide can anneal to wild-type, non-target sequences, while the A0 probe anneals to mutant, target sequences. At the bottom of page 26, when the blocking oligonucleotide is used with the method described above, it is described as being introduced in the step before A0 is annealed to target sequences, where the blocking oligonucleotide anneals “to at least a subset of non-target polynucleotide sequences.”
Thus, the ordinary artisan would be motivated to incorporate a blocking oligonucleotide as described by Balmforth into the method of claim 1 of the ‘780 patent, as this blocking oligonucleotide would ensure that non-target sequences do not hybridize to the A0 sequences, which could cause background noise in the method. Thus, the blocking oligonucleotide would increase accuracy. Additionally, the ordinary artisan would recognize the advantages of separating the blocking oligonucleotide/analyte reaction from the subsequent method steps, as this would allow for the non-target sequences to be blocked before additional manipulation of the sample occurred, thus reducing the amount of non-target sequence available to potentially bind to A0 and create background noise in the method. This would increase overall accuracy in the method. Then, by combining the A0 probe, the pyrophosphorolysing enzyme, and the ligase in a second reaction mixture that the target analyte is then exposed to, this would allow the transformation of A0 to A2 to occur in said single reaction mixture, without the need for moving the A oligonucleotides or the analyte into multiple vessels, ensuring that these components are preserved, while also saving time and equipment.
Thus, claim 1 of the ‘780 patent in view of Balmforth reads on instant claim 1.
Claim 2 of the ‘780 patent states the use of pyrophosphate ions in their reaction mixture, and so reads on instant claim 6.
Claim 19 of the ‘780 patent states that before the detection step, the products of step (a) are treated with a pyrophosphatase or an exonuclease, and so reads on instant claim 26.
Claim 23 of the ‘780 patent states the use of an enzyme with the same function as in instant claim 27, and so reads on this claim.
Claim 27 of the ’780 patent recites the same multiplex/identification region limitations as instant claim 30, and so reads on this claim.
Claims 1, 4, 26, and 30 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1, 5, 19, and 22 of U.S. Patent No. 10,961,569 B2 in view of Balmforth et al. (WO 2020/016590 A1).
Steps (a)-(c) of claim 1 of the ‘569 patent provide a method that is the same as the steps that occur in (b) of instant claim 1 (specifically where (c)(iii) reads on the ligation in the instant claim). Step (e) also describes a detecting step to identify the presence of a target that reads on step (c) of the instant claim.
However, claim 1 of the ‘569 patent does not describe the use of a blocking oligonucleotide.
Balmforth teaches a method on page 6 that is also encompassed by claim 1 of the ‘569 patent. Additionally, Balmforth teaches that blocking oligonucleotides may be used (pages 25-27), where said blocking oligonucleotide can anneal to wild-type, non-target sequences, while the A0 probe anneals to mutant, target sequences. At the bottom of page 26, when the blocking oligonucleotide is used with the method described above, it is described as being introduced in the step before A0 is annealed to target sequences, where the blocking oligonucleotide anneals “to at least a subset of non-target polynucleotide sequences.”
Thus, the ordinary artisan would be motivated to incorporate a blocking oligonucleotide as described by Balmforth into the method of claim 1 of the ‘569 patent, as this blocking oligonucleotide would ensure that non-target sequences do not hybridize to the A0 sequences, which could cause background noise in the method. Thus, the blocking oligonucleotide would increase accuracy.
As to the reaction mixtures described by the instant claim, claim 1 of the ‘569 does not specify particular reaction mixtures that must be used with their method, and therefore encompasses the mixture configuration of instant claim 1.
Thus, claim 1 of the ‘569 patent in view of Balmforth reads on instant claim 1.
Claim 5 of the ‘569 patent states that before the detection step (i.e. after step (c)), the products of step (c) are treated with an exonuclease, and so reads on instant claim 26.
Claim 19 of the ‘569 patent depends on claim 17, which describes amplifying the analyte in the biological sample before performing the method of claim 1. Then claim 19 describes treating the amplification product with a proteinase. Thus, the scope of claim 19 as a whole reads on instant claim 4, which requires amplification and proteinase treatment.
Claim 22 of the ‘569 patent depends on claim 21, which recites multiple A0 probes that are selective for different targets and each include an identification region that is present in amplification products. Claim 22 then states that the presence of the analyte is inferred through the detection of the identification region. Thus, the scope of claim 22 as a whole reads on instant claim 30, which requires the identification regions, the multiple selective A0 probes, and detection based on the identification region.
Free of the Prior Art
Claim 8 is considered to be free of the prior art. No known prior art could be found wherein a blocker oligonucleotide is used to bind to target and non-target sequences in conjunction with pyrophosphorolysis and a probe analogous to the A0 probe as described in the instant claim.
Balmforth (WO 2020/016590 A1) describes their general principle of blocking oligonucleotides, where for a wild-type and mutant sequence, the blocking oligonucleotide fully anneals to the wild-type sequence, while being mismatched with the mutant sequence. When the blocking oligonucleotide and its wild-type or mutant hybridized partner undergo PCR amplification conditions, these differences in annealing lead to the blocking oligonucleotide remaining annealing to the wild-type sequence with dissociating from the mismatched mutant sequence (page 25, final para.). This is the opposite of the set up described in the instant claim. Additionally, Balmforth teaches that it can be beneficial to ensure that the blocking oligonucleotides are resistant to pyrophosphorolysing, furthering distancing these blocking oligonucleotides from those of instant claim 8 (page 26, para. 3).
Concerning pyrophosphorolysing and blocking entities, the prior art focuses on blocking amplification primers themselves. Liu and Sommer (Human Mutation, 2004; cited in Applicant’s IDS) teaches P* oligonucleotides, which are blocked at their 3’ termini with nucleotides that must be removed by pyrophosphorolysis for extension to occur (pages 427-428 joining para.). Figure 3 shows a basic outline of their method, where when the P* oligonucleotide is a perfect match for a template, the end is pyrophosphorolysed, and extension occurs, while such pyrophosphorolysing cannot occur when the P* has a mismatch relative to the template. This differs from the invention of instant claim 8 in that the P* is used for extension, and the match with the template facilitates such extension. Additionally, no intermediate product is formed with the mismatched hybridization as required in the instant claims. Morlan et al. (PLoS ONE, 2009; cited in Applicant’s IDS) shows blocking oligonucleotides that act with primers, but these blockers mainly bind to the wild-type sequence, preventing amplification, while mutant sequences are unbound by the blockers and can be amplified. No pyrophosphorylation is described.
Conclusion
No claims are currently allowable.
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/FRANCESCA FILIPPA GIAMMONA/Examiner, Art Unit 1681
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