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 .
DETAILED ACTION
Pursuant to a preliminary amendment, claims 5, 7, 9, 12-17, 23, 26, 27, 31-33, 35-37, 40 and 57 are currently pending in the instant application.
Response to Election/Restriction
Applicant's initial election without traverse of Group I, claims 5, 7, 9, 12-17, 31-33, 35-37, 40 and 57, directed to a method for generating a circular probe, in the reply filed September 15, 2025 is acknowledged.
Claims 23, 26 and 27 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim.
The restriction requirement is still deemed proper and is therefore made FINAL.
The claims will be examined insofar as they read on the elected species.
Therefore, claims 5, 7, 9, 12-17, 31-33, 35-37, 40 and 57 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed June 16, 2022 claims the benefit of US Provisional Patent Application 63213133, filed June 21, 2021.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on August 29, 2022 and September 15, 2025 have been considered. Initialed copies of the IDSs accompany this Office Action.
Claim Objections/Rejections
Claim Interpretation: the term “upon hybridization” in claim 5 is interpreted to refer to a future step, such that “hybridization” is not carried out in instant claim 5 (e.g., claim 5 in interpreted to recite the steps of contacting and ligating).
Double Patenting Objection
Claim 14 is objected to under 37 CFR 1.75 as being a substantial duplicate of claim 13. Claim 13 recites “wherein at least one of the one or more splints hybridizes…to the one or more splints” in lines 1-4; while claim 14 recites “wherein at least one of the one or more splints hybridizes…to the one or more splints” in lines 1-4. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
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 5, 7, 9, 12-17, 31-33, 35-37, 40 and 57 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 5 is indefinite for the recitation of the term “two regions of a splint” such as recited in claim 5, line 12. There is insufficient antecedent basis for the term “two regions of a splint” in the claim. Instant claim 5 does not recite that the splint comprises two regions, such that it is unclear whether the term is referring to hybridization regions HR1’ and HR3’, or whether the term is referring to other, different regions of the one or more splints and, thus, the metes and bounds of the claim cannot be determined.
Claim 5 is indefinite for the recitation of the term “the plurality of oligonucleotides” such as recited in claim 5, lines 13 and 16-18. There is insufficient antecedent basis for the term “the plurality of oligonucleotides” in the claim because claim 5, lines 9-10 recites that the one or more splints hybridize to the ends of “one or more of the plurality of oligonucleotides.”
Claim 5 is indefinite for the recitation of the terms “a first adjacent oligonucleotide of the plurality of oligonucleotides” and “a second adjacent oligonucleotide of the plurality of oligonucleotides” such as recited in claim 5, lines 16-18. There is insufficient antecedent basis for the terms “a first adjacent oligonucleotide” and “a second adjacent oligonucleotide” in the claim because claim 5, lines 9-10 recites the term “one or more of the plurality of oligonucleotides.” Moreover, the origin of the “first adjacent oligonucleotide” and the “second adjacent oligonucleotide” is unclear because the “one or more of the plurality of oligonucleotides” are not recited to comprise “adjacent oligonucleotides” and, thus, the metes and bounds of the claim cannot be determined.
Claim 5 is indefinite for the recitation of the term “thereby forming a circular probe that is hybridized to the target nucleic acid” such as recited in claim 5, lines 18-19 because claim 5 does not recite a hybridization step. Instead, claim 5 recites what will happen upon hybridization, but does not actually recite “hybridizing,” such that no hybridized circular probe can result and, thus, the metes and bounds of the claim cannot be determined.
Claim 7 is indefinite for the recitation of the term “comprises a first probe” such as recited in claim 7, line 2 because claim 7 depends from instant claim 5, wherein claim 5, line 4 recites that the target-binding probe or probe set comprises “hybridization regions HR1, HR2 and HR3,” such that dependent claim 7 recites that the target-binding probe or probe set comprises a different limitation from the limitation as recited in independent claim 5 (e.g., a first probe comprising HR1, HR2 and HR3) and, thus, the metes and bounds of the claim cannot be determined.
Claim 9 is indefinite for the recitation of the term “target-binding probe or probe set comprises (i) a first probe…and HR3;” such as recited in claim 9, lines 6-7. There is insufficient antecedent basis for the term “target-binding probe or probe set comprises (i) a first probe…and HR3;” in the claim because claim 5 does not recite the presence of “split hybridization regions;” “adjacent hybridization regions;” “HR2a;” and/or “HR2b.”
Claim 9 is indefinite for the recitation of the term “comprises (i) a first probe that comprises HR1…that comprises HR2b and HR3” such as recited in claim 9, lines 6-7 because claim 9 depends from instant claim 5, wherein claim 5, line 4 recites that the ‘target-binding probe or probe set’ comprises “hybridization regions HR1, HR2 and HR3”, such that dependent claim 9 recites that the target-binding probe or probe set comprises something different from the limitation recited in independent claim 5, line 4 recites that the target-binding probe or probe set comprises “hybridization regions HR1, HR2 and HR3,” such that dependent claim 9 recites that the target-binding probe or probe set comprises a different limitation from the limitation as recited in independent claim 5 (e.g., a first probe comprising HR1, HR2 and HR3) and, thus, the metes and bounds of the claim cannot be determined.
Claims 13 and 14 are indefinite for the recitation of the terms “at least two oligonucleotides” such as recited in claim 13, lines 2 and 3. There is insufficient antecedent basis for the terms “at least two oligonucleotides” in the claim because claim 5 recites that the “one or more splints” comprise hybridization regions that hybridizes to “one or more of the plurality of oligonucleotides.”
Claim 14 is indefinite for the recitation of the term “the method of claim 5…to the one or more splints” such as recited in claim 14, lines 1-4 because claim 14 is a duplicate of claim 13 and, thus, the metes and bounds of the claim cannot be determined.
Claim 16 is indefinite for the recitation of the term “adjacent splints” such as recited in claim 16, line 1. There is insufficient antecedent basis for the term “adjacent splints” in the claim because claim 15, lines 1-2 recites the terms “one or more splints” and “at least two splints.”
Claim 17 is indefinite for the recitation of the terms “sample” and “in situ” such as recited in claim 17, lines 1-2. There is insufficient antecedent basis for the terms “sample” and “in situ” in the claim because claim 17 depends from instant claim 5, wherein claim 5 does not recite the presence of a “sample” and/or any location, reaction mixture, vessel, etc. Moreover, it is unclear if the term “in situ” refers to reactions carried out within the sample, within the body of a subject, or whether the term refers to something else and, thus, the metes and bounds of the claim cannot be determined.
Claim 17 is indefinite for the recitation of the term “the contacting, hybridizing, and ligating” such as recited in claim 17, line 2. There is insufficient antecedent basis for the term “the contacting, hybridizing, and ligating” in the claim because claim 17 depends from instant claim 5, wherein claim 5, lines 2 and 16 recite steps including “contacting” and “ligating” and, thus, the metes and bounds of the claim cannot be determined.
Claim 32 is indefinite for the recitation of the term “at least 1 of the plurality of oligonucleotides” such as recited in claim 32, lines 1-2. There is insufficient antecedent basis for the term “at least 1 of the plurality of oligonucleotides” in the claim because claim 5, lines 3 and 9-10 recite the terms “a plurality of oligonucleotides” and “one or more of the plurality of oligonucleotides.”
Claim 35 is indefinite for the recitation of the term “detecting a sequence in the circular probe” such as recited in claim 35, lines 1-2 because claim 35 depends from claim 5, such that without a hybridization step, claim 5 does not produce a circular probe. There is no circular probe produced for use in a subsequent reaction and, thus, the metes and bounds of the claim cannot be determined.
Claim 36 is indefinite for the recitation of the term “using the circular probe as a template” such as recited in claim 36, lines 1-2 because claim 36 depends from claim 5, wherein claim 5 does not produce a circular probe (e.g., there is no hybridization step recited in claim 5), such that a circular probe cannot be used in a further reaction and, thus, the metes and bounds of the claim cannot be determined.
Claim 36 is indefinite for the recitation of the term “the amplification product” such as recited in claim 36, lines 2-3. There is insufficient antecedent basis for the term “the amplification product” in the claim. Claim 36 depends from claim 5, wherein claim 5 does not recite the presence of an amplification product and, thus, the metes and bounds of the claim cannot be determined.
Claim 40 is indefinite for the recitation of the term “the circular probe comprises one or more cleavage sites” such as recited in claim 40, lines 1-2 because claim 40 depends from claim 5, such that without hybridization, claim 5 does not produce a circular probe. No circular probe is produced for use in a subsequent reaction and, thus, the metes and bounds of the claim cannot be determined.
Claim 40 is indefinite for the recitation of the terms “subsequent probe”; “additional oligonucleotide-additional splint hybridization”; “the one or more additional splints”; “the one or more additional oligonucleotides”; and “subsequent circular probe” such as recited in claim 40, lines 1-13 because claim 40 depends from claim 5, wherein claim 5 does recite the presence of subsequent probes; additional oligonucleotide-additional splint hybridizations; one or more additional splints; the one or more additional oligonucleotides; and subsequent circular probes and, thus, the metes and bounds of the claim cannot be determined.
Claim 57 is indefinite for the recitation of the term “sample” such as recited in claim 57, line 2. There is insufficient antecedent basis for the term “sample” in the claim because claim 57 depends from instant claims 5 and 36 wherein claims 5 and 36 do not recite the presence of a “sample” and, thus, the metes and bounds of the claim cannot be determined.
Claim 57 is indefinite for the recitation of the term “in situ” such as recited in claim 57, line 2. There is insufficient antecedent basis for the term “in situ” in the claim because claim 57 depends from instant claims 5 and 36 wherein claims 5 and 36 do not recite a specific location, vessel, reaction mixture, etc. where contacting and ligating are carried out and, thus, the metes and bounds of the claim cannot be determined.
Claims 12, 15, 31 and 37 are indefinite insofar as they ultimately depend from instant claim 5.
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.
Claims 7, 9, 16, 17, 35, 36, 40 and 57 are rejected under 35 U.S.C. 112(d) 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 7 recites (in part): “wherein the target-binding probe or probe set comprises a first probe that comprises hybridization regions HR1, HR2, and HR3” in lines 1-2 because claim 7 depends from instant claim 5, wherein claim 5 recites that the target-binding probe or probe set comprises hybridization regions HR1, HR2 and HR3, such that claim 5 does not recite the presence of a first probe. Thus, claim 7 is an improper dependent claim 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 9 recites (in part): “the target-binding probe or probe set comprises (i) a first probe that comprises HR1 and HR2a; and (ii) a second probe that comprises HR2b and HR3” in lines 6-7 because claim 9 depends from instant claim 5, wherein claim 5 recites that the target-binding probe or probe set comprises hybridization regions HR1, HR2 and HR3, such that claim 5 does not recite the presence of a first probe and a second probe. Thus, claim 9 is an improper dependent claim 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 16 recites (in part): “wherein adjacent splints of the at least two splints both hybridize to one of the plurality of oligonucleotides” in lines 1-2 because claim 16 depends from instant claims 5 and 15, wherein claims 5 and 15 do not recite the presence of “adjacent splints.” Thus, claim 16 is an improper dependent claim 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 17 recites (in part): “wherein the target nucleic acid is in a sample, and the contacting, hybridizing, and ligating are performed in situ” in lines 1-2 because claim 17 depends from instant claim 5, wherein claim 5 does not recite the step of hybridizing, the presence of a sample and/or any location, reaction mixture, vessel, etc. indicating what the term “in situ” refers. Thus, claim 17 is an improper dependent claim 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 35 recites (in part): “circular probe” in claim 35, line 2 because claim 35 depends from instant claim 5, wherein claim 5 does not recite a step of hybridization, such that no circular probe is produced in claim 5. Thus, claims 35 is an improper dependent claims 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 36 recites (in part): “a circular probe as a template and detecting a sequence in the amplification product” in claim 36, lines 2-3 because claim 36 depends from instant claim 5, wherein claim 5 does not recite a step of hybridization (e.g., no circular probe is produced in claim 5) and/or the presence or formation of an amplification product. Thus, claims 36 is an improper dependent claims 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 40 recites (in part): “wherein the circular probe comprises one or more cleavage sites…forming a subsequent circular probe” in lines 1-13 because claim 40 depends from instant claim 5, wherein the steps recited in claims 5 and 40 do not produce a circular probe; and claim 5 does not recite the presence of subsequent probes; additional oligonucleotide-additional splint hybridizations; one or more additional splints; the one or more additional oligonucleotides; and subsequent circular probes. Thus, claim 40 is an improper dependent claim 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 57 recites (in part): “wherein the target nucleic acid is in a sample, and the detecting is performed in situ” in lines 1-2 because claim 57 depends from instant claims 5 and 36, wherein claims 5 and 36 do not recite the presence of a sample, and/or any location, reaction mixture, vessel, etc. which is indicative of being “in situ” such that detection can occur. Thus, claim 57 is an improper dependent claim 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.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim 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 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 may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived 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 5, 7, 9, 12-17, 31-33, 35-37, 40 and 57 are rejected under 35 U.S.C. 103 as being unpatentable over Bava et al. (hereinafter “Bava”) (US Patent No. 10982271, issue April 20, 2021; published March 28, 2019) in view of Chen et. al. (hereinafter “Chen”) (US Patent Application Publication 20190360044, published November 28, 2019) as evidenced by Nolan (US Patent Application Publication 20150329852, published November 19, 2015).
Regarding claim 5, Bava teaches methods, compositions, kits and devices for the detection of target molecules including the multiplexed target molecule detection (Abstract). Bava teaches a plurality of SNAIL oligonucleotide primer pairs having specificity for different target nucleic acids are used (interpreted as one or more of a plurality of oligonucleotides, claim 5) (col 2, lines 23-25). Bava teaches a method for identifying whether at least one target nucleic acid is present in a plurality of cells comprising: (a) binding to the target nucleic acids at least one pair of SNAIL oligonucleotide primers comprising a Splint Primer Oligonucleotide (SPO) and a Padlock oligonucleotide (PO) (interpreted as contacting a target with a probe or probe set, claim 5), wherein each of SPO and PO comprise first complementarity regions (CR1 and CR1', respectively, wherein the CR1' is a Unique Binding Agent (UBA)) complementary to adjacent sequences on the target nucleic acid; and each of SPO and PO further comprise second complementarity regions (CR2 and CR2’, respectively) complementary to each other, wherein CR2' is a split region such that the 5' and the 3' ends of the PO hybridize to CR2 (interpreting the probe sets to comprise HR1, HR2 and HR3; and one or more splints, claim 5); (b) contacting the cell with ligase wherein the 5' and the 3' ends PO are joined to generate a closed circle (interpreted as ligating HR1 to an adjacent oligo; forming a loop; and forming a circular probe, claim 5); (c) performing rolling circle amplification using the PO as a template and SPO as a primer for a polymerase (interpreted as an amplification reaction); (d) annealing an anchor primer complementary to a region of the PO and forming an extension product which is a copy of the UBA; (e) forming a cell originating barcode (COB) by adding multiple assayable polymer subunit (APS) oligonucleotides to each extension product in the plurality of cells in an ordered manner during successive rounds of split pool synthesis wherein the APS oligonucleotides in each round anneal adjacently to the APS from a previous round via an annealing region, and covalently linking the adjacently annealed APS oligonucleotides to each other to create unique codes that represent the identities of individual cells in which the SNAIL primers are bound to targets (interpreted as comprising a barcode; and one or more of a plurality of oligonucleotides, claim 5) (col 1, lines 57-67; and col 2, lines 1-18). Bava teaches that the 5' terminus of PO is phosphorylated, so that upon annealing of both ends to CR2, the PO oligonucleotide can be circularized by ligation, using any suitable DNA ligase enzyme, e.g. T4 DNA ligase (interpreted as ligating each end to form a subsequent circular probe, claim 40) (col 21, lines 40-44). Bava teaches that a unique binding agent (UBA), an multiple assayable polymer subunit (APS), or an epitope specific barcode (ESB) comprise nucleic acids linked using a linking oligonucleotide comprising a first and second complimentary regions, and a second linking oligonucleotide is linked using a linking oligonucleotide comprising the third and the fourth complementary region to two components selected from a UBA, an APS, and an ESB (interpreting the PO and SPO probe sets; and interpreting UAB-APS-ESB, unique codes, and/or four complementary regions as encompassing HR1, HR2, and HR3, claim 5) (col 4, lines 36-39). Bava teaches that the one or more splints are used which are complementary to one or more APSs (interpreted as one or more splints, claim 5) (col 24, lines 61-62).
Regarding claim 7, Bava teaches at least one pair of SNAIL oligonucleotide primers comprising a Splint Primer Oligonucleotide (SPO) and a Padlock Oligonucleotide (PO), wherein each of SPO and PO comprise first complementarity regions (CR1 and CR1', respectively, wherein the CR1' is a Unique Binding Agent (UBA)) complementary to adjacent sequences on the target nucleic acid; and each of SPO and PO further comprise second complementarity regions (CR2 and CR2', respectively) complementary to each other, wherein CR2' is a split region such that the 5' and the 3' ends of the PO hybridize to CR2 (interpreting the PO and SPO probe sets to comprise HR1, HR2, and HR3, claim 7) (col 1, lines 60-67; and col 2, lines 1-3). Bava teaches that a unique binding agent (UBA), an multiple assayable polymer subunit (APS), or an epitope specific barcode (ESB) comprise nucleic acids linked using a linking oligonucleotide comprising a first and second complimentary regions, and a second linking oligonucleotide is linked using a linking oligonucleotide comprising the third and the fourth complementary region to two components selected from UBA, an APS, or an ESB (interpreting the PO and SPO probe sets; and interpreting UAB/APS/ESB, unique codes, and/or four complementary regions as encompassing HR1, HR2, and HR3, claim 7) (col 4, lines 36-39).
Regarding claim 9, Bava teaches that Figure 12 illustrates that each of the SPO and PO comprise first complementarity regions (CR1 and CR1’, respectively) that are complementary to adjacent sequences on the target mRNA, wherein CR1' is a Unique Binding Agent (UBA) as defined herein, such that the UBA is specific for the target nucleic acid and is referred to as Sequence Tag (SeqTag); and each SPO and PO further comprise second complementarity regions (CR2 and CR2' respectively) complementary to each other, wherein region CR2', which is present on PO, is a split region, where the 5' and the 3' ends of PO hybridize to region CR2 adjacent to one another, wherein the PO further comprises a spacer region, which in the circular form of the molecule is between CR2 and CR2' (interpreted as HR2’ is a split region comprising adjacent hybridization regions; HR2 comprises HR2a and HR2b; forming a loop; circular probe; and a first and second probe, claim 9) (col 21, lines 28-40).
Regarding claims 12 and 15, Bava teaches that the one or more splints are used which are complementary to one or more APSs, wherein one universal splint can be used with multiple binding sites for multiple APSs, wherein assembling of cell origination barcode (COB) from APSs annealing to splints is described in greater detail with multiple examples in US Patent 14/420,345 (interpreted as one or more splints; at least two splints; and encompassing between 1 and 10 splints, claims 12 and 15) (col 24, lines 61-67), where it is known that the APSs can be linked together using a splint on a complementary strand, or multiple splints are using in alternating strands as evidenced by Nolan (US Pat 14420345; paragraphs [0048], lines 1-2; and [0128], lines 1-3).
Regarding claims 13 and 14, Bava teaches that amplification requires a circular molecule, which in turn requires that the SPO and PO hybridize to directly adjacent regions of the same mRNA molecule and that the ligase successfully joins the 5' and 3' ends of the PO with or without gap filling (interpreted as a splint hybridizing to the ends of two oligonucleotides to form a loop, claims 13 and 14) (col 22, lines 1-5). Bava teaches a common linker (CL) oligonucleotide comprises pairs of loop annealing regions (Figs. 9 and 10), where APSs can be designed to hybridize to the CL in a loop geometry, hybridizing on each end to the CL along the loop annealing regions, such that the hybridization can populate the APSs along the CL (interpreted as a splint hybridized to ends of at least two oligos to form a loop, claims 13 and 14) (col 28, lines 48-54; and Figures 9 and 10).
Regarding claim 16, Bava teaches that amplification requires a circular molecule, which in turn requires that the SPO and PO hybridize to directly adjacent regions of the same mRNA molecule and that the ligase successfully joins the 5' and 3' ends of the PO with or without gap filling, wherein both probes hybridize to adjacent locations for the amplification reaction to take place (interpreted as adjacent splints hybridize to one or a plurality of oligonucleotides, claim 16) (col 22, lines 1-7).
Regarding claims 17 and 57, Bava teaches that the invention provides methods for detection at least one target molecule in a sample (interpreted as a target nucleic acid is in a sample, claims 17 and 57) (col 11, lines 37-38). Bava teaches development of an amplification system in situ for the mRNA so that the QBC process utilizing UBA, ESB and COB will give a higher signal for expression analysis (interpreted as in situ, claims 17 and 57) (col 60, lines 45-46). Bava teaches in Figure 12 that after ligation in situ and rolling circle amplification (RCA) (FIG. 12, step 2), an oligonucleotide primer containing the anchor sequence (ESB, epitope specific barcode) is added which binds proximal to the SeqTag sequence in the amplicon, (FIG. 12, step 3), which is extended in situ (FIG. 12, step 4), such that next, the COB (cell originating barcode) is formed in situ by annealing APSs (assayable polymer subunits) to a splint during rounds of split-pool synthesis (FIG. 12, steps 5-6) (interpreted as in situ reactions, claims 17 and 57) (col 60, lines 54-62).
Regarding claim 31, Bava teaches that aminomethyl macroporous polystyrene (MPPS) beads are labeled with ten different CL oligonucleotides, each with an optional first amplification primer complementary region, one of 10 different ESB sequences and a common annealing region, six rounds of split and pool syntheses is performed, and a different oligonucleotide APS is added to each container totaling 20 different APSs (interpreted as about 2 to 20 oligonucleotides, claim 31) (col 56, lines 2-9).
Regarding claims 32 and 33, Bava teaches in Figure 12 that after ligation in situ and rolling circle amplification (RCA) (FIG. 12, step 2), an oligonucleotide primer containing the anchor sequence (ESB, epitope specific barcode) is added which binds proximal to the SeqTag sequence in the amplicon, (FIG. 12, step 3), which is extended in situ (FIG. 12, step 4), such that next, the COB (cell originating barcode) is formed in situ by annealing APSs (assayable polymer subunits) to a splint during rounds of split-pool synthesis. (FIG. 12, steps 5-6) (interpreting the epitope specific barcode, SeqTag, and COB as oligonucleotides comprising a barcode; and in situ reactions, claim 32) (col 60, lines 54-62). Bava teaches in Figure 9 a loop cell originating barcode (COB) (interpreted as each loop comprises a barcode sequence, claim 33) (col 58, line 1; and Figure 9). Bava teaches labeling a target molecule of a cell in a population of cells with a cell origination barcode, comprising: (a) n sets of m assayable polymer subunits (APSs) each comprising a distinct package of information; wherein the packages of information are capable of being linked in an ordered fashion; (b) a target molecule specific unique binding agent (UBA) (interpreted as each loop comprises a barcode sequence, claim 33) ( col 5, lines 9-15).
Regarding claim 35, Bava teaches the application of quantum barcoding (QBC) to detection of nucleic acids and comprises the use of a pair of probes where upon binding of both probes to the target, one probe can form a circle that can be amplified and detected (interpreted as detecting a sequence in the circular probe, claim 35) (col 1, lines 52-56). Bava teaches the detection, identification, and quantification of target molecules in a sample; as well as, the detection of individual target molecules in single cells (interpreted as detecting a sequence in the circular probe, claim 35) (col 2, lines 34-38).
Regarding claims 36 and 37, Bava teaches that the ESBs, APSs and/or COBs can provide templates for the addition of any of another one of the ESBs, APSs and/or COBs (interpreted as using the circular probe as a template, claims 36 and 37) (col 26, lines 64-67). Bava teaches performing rolling circle amplification using the PO as a template and SPO as a primer for a polymerase (interpreted as an amplification reaction; forming an amplification product; using the circular probe as a template; and where the splint is used as a primer, claims 36 and 37) (col 2, lines 5-6). Bava teaches that upon addition of a DNA polymerase in the presence of appropriate dNTP precursors and other cofactors, the SPO probe is elongated by rolling circle replication (RCA) to form multiple copies of the PO template comprising SeqTag (FIG. 12) (interpreted as an amplification product; and using the circular probe as a template, claims 36 and 37) (col 21, lines 55-59).
Regarding claim 40, Bava teaches that the skilled artisan will appreciate that the molecular complexes and the at least part of the molecular complexes described herein can be individually detected while tethered or attached to a substrate or while in solution, depending on, among other things, the nature of the specific molecular complex or cleavable component and the SMD technique and detection apparatus employed (interpreted as comprising a cleavage site, claim 40) (col 37, lines 46-52). Bava teaches that cleavage of oligonucleotides from a solid support and deprotection is achieved by exposure to concentrated aqueous ammonia (interpreted as comprising a cleavage site, claim 40) (col 54, lines 46-48). Bava teaches in Figure 11 that cleavage sites can be inserted for post purification (interpreted as comprising a cleavage site, claim 40) (Figure 11). Bava teaches forming a cell originating barcode (COB) by adding multiple assayable polymer subunit (APS) oligonucleotides to each extension product in the plurality of cells in an ordered manner during successive rounds of split pool synthesis wherein the APS oligonucleotides in each round anneal adjacently to the APS from a previous round via an annealing region, and covalently linking the adjacently annealed APS oligonucleotides to each other to create unique codes that represent the identities of individual cells in which the SNAIL primers are bound to targets (interpreted as subsequent probes; additional splints; forming loops; ligating subsequent probes; and adjacent additional oligonucleotides, claim 40) (col 2, lines 9-18). Bava teaches that the 5' terminus of PO is phosphorylated, so that upon annealing of both ends to CR2, the PO oligonucleotide can be circularized by ligation, using any suitable DNA ligase enzyme, e.g. T4 DNA ligase (interpreted as ligating each end to form a subsequent circular probe, claim 40) (col 21, lines 40-44).
Bava does not specifically teach a single probe comprising three hybridization regions (instant claim 40, in part).
Regarding claim 7 (in part), Chen teaches a method of analyzing nucleic acids, comprising: providing at least one targeting probe to a target nucleic acid, whereby the at least one targeting probe binds to a target region in the target nucleic acid; providing a first sensing oligo, which binds to the at least one targeting probe; providing a second sensing oligo comprising a sequencing adaptor, which binds to the first sensing oligo via a hybridization region in the second sensing oligo; and attaching the second sensing oligo to the at least one targeting probe, thereby generating a sequencing construct (paragraph [0007]). Chen teaches that in the case of MIPs, padlock probes, and rolling circle probes, constructs for generating labeled target sequences are formed by circularizing a linear version of the probe in a template-driven reaction on a target polynucleotide (interpreted as generating circular probes) (paragraph [0291]). Chen teaches that multiple proximity dependent probes can bind to the same target RNA including 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 500, or 1000 proximity dependent probes can be used per target RNA, wherein increasing the number of unique MIPs or probes per target gene can lead to higher sensitivity of the probes, thus allowing for the study of target genes that are expressed at a very low level (interpreted as probes comprising HR1, HR2 and HR3, claims 5 and 7) (paragraph [0264]). Chen teaches that the method can include providing one or more targeting probes so that the targeting probes bind to a target nucleic acid (paragraph [0197]). Chen teaches providing multiple targeting probes to bind to multiple target regions in the target nucleic acid, wherein the methods can comprise providing a first and a second targeting probes, which bind to a first and a second target regions in the target nucleic acid, respectively (interpreted as probes comprising HR1, HR2 and HR3, claims 5 and 7) (paragraph [0199]). Chen teaches providing one or more sensing oligos so that the sensing oligo(s) bind to one or more targeting probes including providing a sensing oligo so that it binds to at least one, e.g., 1, 2, 3, 4, 5, 6, or more targeting probes (interpreted as probes comprising HR1, HR2 and HR3, claims 5 and 7) (paragraph [0206]). Chen teaches that the bound proximity dependent probes are linked by ligation, splinted ligation, hybridization, or proximity extension; and that the proximity dependent probes are molecular inversion probes (MIPs), HyPR probes, padlock probes, or split-ligation probes, each probe further comprising a unique molecular identifier (UMI) (paragraphs [0041]-[0042]). Chen teaches that when attached, the second sensing oligo and at least one targeting probe can form a loop structure (interpreted as forming a loop) (paragraph [0220], lines 1-3). Chen teaches that a ligase can be capable of ligating the 3’-end of an acceptor polynucleotide and a 5’-end of a donor polynucleotide (paragraph [0225], lines 4-6). Chen teaches that the respective analyte-binding domains of each proximity probe pair can have specificity for different binding sites on the analyte, which analyte can consist of a single molecule or a complex of interacting molecules, or can have identical specificities, for example in the event that the target analyte exists as a multimer; and when a proximity probe pair comes into close proximity with each other ,which will primarily occur when both are bound to their respective sites on the same analyte molecule, the nucleic acid domains are able to be joined to form a new nucleic acid sequence by means of a ligation reaction (interpreted as being adjacent), where this can be templated by a splint oligonucleotide subsequently added to the reaction, said splint oligonucleotide containing regions of complementarity for the ends of the respective nucleic acid domains of the proximity probe pair, such that the new nucleic acid sequence thereby generated serves to report the presence or amount of analyte in a sample, and can be qualitatively or quantitatively detected, for example by real-time, quantitative PCR (q-PCR) (interpreted as using a splint oligo; and subsequent probe, claim 40) (paragraph [0260]).
It is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of single-cell molecular analysis as exemplified by Chen, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of quantum barcoding for the detection of nucleic acids using a pair of probes, wherein one probe can form a circle that can be amplified and detected as disclosed by Bava to include the targeting probes, proximity probes, sensing oligonucleotides, and/or circular probes that bind at least one target region in the target nucleic acid as taught by Chen with a reasonable expectation of success in using circular probes to quantify target nucleic acids in individual cells including improving the efficiency in the detection of single-copy loci; and/or in reducing required sample quantity, while accelerating analysis and improving measurement accuracy in the multiplexed detection of target molecules in a sample.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly rejected under 35 USC §103(a) as obvious over the art.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 5, 7, 9, 12-17, 31-33, 35-37, 40 and 57 are rejected on the ground of nonstatutory double patenting as being unpatentable over:
Claims 1-10 of U.S. Patent No. 10,982,271 – A method for identifying whether at least one target nucleic acid is present in a plurality of cells comprising: a) binding to the target nucleic acids at least one pair of SNAIL oligonucleotide primers comprising a Splint Primer Oligonucleotide (SPO) and a Padlock Oligonucleotide (PO), wherein each of SPO and PO comprise first complementarity regions (CR! and CR!', respectively); b) contacting the cell with ligase wherein the 5' and the 3' ends of the PO are joined to generate a closed circle; c) performing rolling circle amplification using the PO as a template and the SPO as a primer for a polymerase; d) annealing an anchor primer complementary to a region of the PO and forming an extension product which is a copy of the UBA; e) forming a cell originating barcode (COB) by annealing a splint oligonucleotide to the anchor primer and adding multiple assayable polymer subunit (APS) oligonucleotides to each extension product in the plurality of cells (claim 1).
Claims 1-20 of U.S. Patent No. 12,275,984 - A method for analyzing a biological sample, comprising: a) contacting a biological sample with a first probe, wherein: the first probe comprises a detectable moiety D1 and a hybridization sequence H1, the biological sample comprises a nucleic acid molecule comprising a hybridization sequence H1', and H1' hybridizes to H1; and b) contacting the biological sample with a second probe, wherein the second probe comprises: (i) a hybridization sequence H2 that hybridizes to a hybridization region H2' of the nucleic acid molecule, the first probe, or a splint, (ii) a quencher Q1, and (iii) a detectable moiety D2 (claim 1). The method of claim 1, wherein the method further comprises: c) contacting the biological sample with a third probe, wherein: the third probe comprises: (i) a hybridization sequence H3 that hybridizes to a hybridization sequence H3' of the nucleic acid molecule, the probe of the previous contacting step, or a splint, (ii) a quencher Q2, and (iii) a detectable moiety D3 (claim 9).
Although the claims at issue are not identical, they are not patentably distinct from each other because: the instant claims, and the claims of U.S. Patent Nos. 10,982,271 and 12,275,984 teach a method comprising contacting a target nucleic acid with a probe or probe set comprising hybridization regions HR1, HR2 and HR3, one or more splints, and a plurality of oligonucleotides; wherein hybridization will produce a loop; and ligating HR1 to a first adjacent oligonucleotide to form a circular probe hybridized to a target nucleic acid.
Conclusion
Claims 5, 7, 9, 12-17, 31-33, 35-37, 40 and 57 are rejected.
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/AMY M BUNKER/
Primary Examiner, Art Unit 1684