DETAILED ACTION
Applicant’s response filed 12/08/2025 has been fully considered. The following rejections and/or objections are either reiterated or newly applied.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/08/2025 has been entered.
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 .
Claim Status
Claims 19, 24 and 30 are cancelled by Applicant.
Claims 1-18, 20-23, 25-29 and 31 are currently pending.
Claims 26-27 and 29 are withdrawn as discussed in the Election of Species section in the Office action mailed 09/09/2024.
Claims 1-18, 20-23, 25, 28 and 31 are herein under examination.
Claims 1-18, 20-23, 25, 28 and 31 are rejected.
Priority
The instant application claims domestic benefit as a continuation of U.S. Application No. PCT/US2022/037785 filed 07/21/2022, which claims domestic benefit to U.S. Provisional Application No. 63/346,307 filed 05/26/2022, U.S. Provisional Application No. 63/345,866 filed 05/25/2022, U.S. Provisional Application No. 63/332,245 filed 04/18/2022, U.S. Provisional Application No. 63/329,781 filed 04/11/2022, and International Application No. PCT/US2021/060647 filed on 11/23/2021. The claims to the benefit of domestic priority for claims 1-18, 20-23, 25, 28 and 31 are acknowledged. As such, the effective filing date for claims 1-18, 20-23, 25, 28 and 31 is 11/23/2021.
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:
This application contains sequence disclosures in accordance with the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.831(a) and 1.831(b). However, this application fails to comply with the requirements of 37 CFR 1.831-1.834. The examiner has noted that Figure 16B contains sequences that are not present in the Sequence Listing or the CRF. Applicant must provide:
• A replacement “Sequence Listing XML” part of the disclosure, as described above in item 1. or 2., as well as
• A statement that identifies the location of all additions, deletions, or replacements of sequence information in the “Sequence Listing XML” as required by 1.835(b)(3);
• A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.835(b)(4);
• A statement that the “Sequence Listing XML” includes no new matter in accordance with 1.835(b)(5); 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(b)(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
A statement that the substitute specification contains no new matter.
Drawings
The drawings filed 12/04/2024 are objected to because the view numbers are not in compliance with 37 CFR 1.84(u)(1). “FIG. 16” should be amended to recite “FIG. 16A” and “FIG. 16B”. “FIG. 28” should be amended to recite “FIG. 28A”, “FIG. 28B” and “FIG. 28C”.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Withdrawn Rejections
Double Patenting
All provisional rejections on the ground of nonstatutory double patenting over copending Application No. 18/253,803 are withdrawn in view of claim amendments. However, a new rejection has been applied below.
All rejections on the ground of nonstatutory double patenting over allowed Application No. 18/150,661 are withdrawn in view of further consideration of the claims.
All rejections on the ground of nonstatutory double patenting over allowed Application No. 18/150,669 are withdrawn in view of further consideration of the claims.
All provisional rejections on the ground of nonstatutory double patenting over copending Application No. 18/670,364 are withdrawn in view of claim amendments. However, a new rejection has been applied below.
All provisional rejections on the ground of nonstatutory double patenting over copending Application No. 18/670,329 are withdrawn in view of claim amendments. However, a new rejection has been applied below.
Claim Objections
The objection to claim 16 is withdrawn in view of claim amendment.
Claim Rejections - 35 USC § 112
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 3-6, 15 and 28 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.
This rejection is newly recited in view of further consideration of the claims.
Claim 3 recites the phrase “the at least one segment of the code” which renders the claim indefinite. It is unclear which at least one segment from which code is being referenced because each recognition element has a code wherein each code contains at least one segment, as recited in claim 1, lines 6-11. To overcome this rejection, clarify which code is being referenced.
Furthermore, claim 4 is rejected because it depends on claim 3, which is rejected, and because it does not resolve the issue of indefiniteness.
Claim 5 is indefinite because the limiting effect of the wherein clause is unclear. It is unclear whether the claim recites an intended use of the at least one segment of the code by “is interrogated”, or if the claim requires an active step of interrogating. See MPEP 2111.04.I. To overcome this rejection, clarify if the claim requires an active step of interrogating.
Claim 5 recites the phrase “the at least one segment of the code” which renders the claim indefinite. It is unclear which at least one segment from which code is being referenced because each recognition element has a code wherein each code contains at least one segment, as recited in claim 1, lines 6-11. To overcome this rejection, clarify which code is being referenced.
Claim 6, lines 1-2, recites the phrases “wherein the code comprises” and “wherein the code is interrogated”, which render the claim indefinite. It is unclear which code is being referenced because claim 1, lines 6-7, recites “each coded recognition element comprising … a code from a set of codes”. To overcome this rejection, clarify which code is being referenced.
Claim 6, lines 2-3, recites the phrase “wherein the code is interrogated” which renders the claim indefinite. The limiting effect of the wherein clause is unclear. It is unclear whether the claim recites an intended use of the code by “is interrogated”, or if the claim requires an active step of interrogating. See MPEP 2111.04.I. To overcome this rejection, clarify if the claim requires an active step of interrogating.
Claim 15, line 3, recites the relative phrase “about 23,000 to about 110,000”, which renders the claim indefinite. Although specification paras. [89] and [401-402] provide examples for what “about” may mean, they do not clarify what the exact metes and bounds are for the relative phrase. For example, it is unclear if a prior art reference of “10,000 to 12,000” is encompassed by the claimed range. To overcome this rejection, clarify the metes and bounds of the relative phrase.
Claim 28, line 3, recites the relative phrase “about 10 pM to about 100 pM”, which renders the claim indefinite. Although specification paras. [89] and [401-402] provide examples for what “about” may mean, they do not clarify what the exact metes and bounds are for the relative phrase. For example, it is unclear if a prior art reference of “2 pM to 3 pM” is encompassed by the claimed range. To overcome this rejection, clarify the metes and bounds of the relative phrase.
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 1-5, 7-13, 15, 18, 20, 22-23 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Church et al. (“Church”; ref. 033 on IDS filed 01/26/2024; US 2008/0269068 A1; previously cited on PTO892 mailed 07/14/2025) in view of Kühnemund et al. (“Kühnemund”; Nucleic Acids Research 45, no. 8 (2017): e59-e59; previously cited on PTO892 mailed 09/09/2024), and Galanti et al. (“Galanti”; BMC bioinformatics 22 (2021): 1-16; published July 2021; previously cited on PTO892 mailed 07/14/2025), as evidenced by Margeridon et al. (“Margeridon”; Antimicrobial agents and chemotherapy 52, no. 9 (2008): 3068-3073; previously cited on PTO892 mailed 07/14/2025).
Any newly recited portions herein are necessitated by claim amendment.
The bold and italicized text below are the limitations of the instant claims, and the italicized text serves to map the prior art onto the instant claims.
Claim 1:
(a) subjecting the set of DNA targets extracted from a biological sample to a recognition event, in which each DNA target of the set of DNA targets is uniquely recognized by and bound to at least one coded recognition element from a set of coded recognition elements,
Church discloses “Methods of analyzing an array of nucleic acid sequences including providing a plurality of immobilized query oligonucleotide sequences, providing a plurality of molecular inversion probes, each molecular inversion probe having a tag sequence, a barcode sequence, and two guide sequences, hybridizing the molecular inversion probes with the immobilized oligonucleotide sequences”. The immobilized query oligonucleotide sequences may be DNA [47-48].
Church does not recite extracting DNA from a biological sample.
Kühnemund discloses a sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules. Figure 1 displays the single-molecule analysis through microfluidic enrichments of RCA products. The procedure in Figure 1 uses bacterial genomic DNA extracted from cultured strains (pg. 4, col. 2, para. 1; pg. 6, col. 2, last para.).
It would have been prima facie obvious to one of ordinary skill in the art to have modified the method of Church for performing RCA on DNA by extracting genomic DNA from a biological sample as taught by Kuhnemund because extracted genomic DNA detects pathogenic genomic DNA in samples containing different pathogenic species, as discussed by Kuhnemund (pg. 7, col. 2, para. 2). One of ordinary skill in the art would have had a reasonable expectation of success for extracting DNA to perform RCA because extracting nucleic acids from samples is a common procedure for performing molecular amplification such as in RCA, as taught above by Kuhnemund, and as evidenced by Margeridon who also extracts DNA from biological samples to perform RCA (pg. 3069, col. 1).
each coded recognition element comprising a target-specific binding site and a code from a set of codes, wherein the target-specific binding site is complementary to a known 3’ region and a know 5’ region of a DNA target of the set of DNA targets, wherein each code of the set of codes comprises at least one segment encoding one or more symbols, to yield a set of coded DNA targets, wherein each coded DNA target of the set of coded DNA targets comprises a DNA target of the set of DNA targets bound to a coded recognition element of the set of coded recognition elements;
Church discloses that the MIPs contain one or more guide sequences that are complementary to specific position on a template target, such as a bead-bound oligonucleotide, and thus hybridize with this sequence (target-specific binding site) [2]. Figure 2A shows two guide sequences “ACT” and “TCG” that are complementary to known 3’ and 5’ positions in the template target. The known positions are TGA and AGC (wherein the target-specific binding site is complementary to a known 3’ region and a know 5’ region of a DNA target of the set of DNA targets). The MIP also contain barcodes that refer “to a unique oligonucleotide sequence that allows a corresponding nucleic acid base and/or nucleic acid sequence to be identified” (a code from a set of codes) [22]. The barcodes contain symbols (i.e., the nucleotide sequence of the barcode). Church states “performing rolling circle amplification such that the barcode sequence of one molecular inversion probe is transferred to one immobilized query oligonucleotide sequence, arraying the immobilized query oligonucleotide sequences, and identifying barcodes present on an immobilized query oligonucleotide sequence are provided” [7].
(b) subjecting the set of coded recognition elements bound to the set of coded DNA targets to a molecular transformation event to yield a set of circularized coded recognition elements;
Church shows in Figures 2A-2B the MIPs before and after ligation [72]. Church discusses that an MIP forms a circular structure when hybridized to a template target via hybridization of two or more guide sequences to the template target [20] [28] [42].
(c) introducing an exonuclease to the set of circularized coded recognition elements to reduce one or more recognition elements of the set of coded recognition elements that were not uniquely recognized by and bound to a DNA target of the set of DNA targets;
Church discloses “Such probes are desirable because non-circularized probes can be digested with single stranded exonucleases thereby greatly reducing background noise due to spurious amplifications, and the like. In the case of molecular inversion probes (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 oligonucleotide followed by digestion of non-circularized oligonucleotides in the reaction mixture, such as target oligonucleotides, unligated probe, probe concatemers, and the like, with an exonuclease, such as exonuclease I” [42].
(d) performing rolling circle amplification of the set of circularized coded recognition elements to produce amplified circularized coded recognition elements; and
Church discloses “performing rolling circle amplification such that the barcode sequence of one molecular inversion probe is transferred to one immobilized query oligonucleotide sequence” [7]. See Figures 3A-3B and para. [28].
(e) detecting the set of DNA targets associated with the amplified circularized coded recognition elements by decoding amplified codes of the amplified circularized coded recognition elements, wherein the decoding comprises performing soft decision decoding.
Church discloses “identifying barcodes present on an immobilized query oligonucleotide sequence” [7]. However, Church does not disclose decoding the amplified barcodes using soft decision decoding.
Galanti discloses Pheniqs 2.0 for high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing (title). Galanti discloses “We developed a flexible, robustly engineered software that performs probabilistic decoding and supports arbitrarily complex barcoding designs. Pheniqs computes the full posterior decoding error probability of observed barcodes by consulting base calling quality scores and prior distributions, and reports sequences and confidence scores in Sequence Alignment/Map (SAM) fields. The product of posteriors for multiple independent barcodes provides an overall confidence score for each read.” Galanti describes on pg. 4-5 and in Figure 1 the method for decoding with posterior probability.
It would have been prima facie obvious to one of ordinary skill in the art to have modified the method of Church for multiplex decoding sequence tags in barcodes by using the Pheniqs 2.0 software of Galanti because Galanti states that decoding and classifying barcodes is essential for demultiplexing pooled bulk sequence libraries (pg. 2, para. 3). Galanti also provides motivation for doing so by stating that sequencing platforms generally tie in demultiplexing as a preprocessing step (pg. 2, last para.). One of ordinary skill in the art would have had a reasonable expectation of success for using Galanti’s Pheniqs barcode decoding strategy to decode the barcodes of Church because Galanti states that Pheniqs can handle arbitrarily complex barcoding designs and generalizes to multiple combinatorial tags (pg. 14, para. 5). Pheniqs is widely applicable to current experimental designs and is easily adaptable to the rapidly evolving landscape of sequencing applications (pg. 14, para. 5). Church even discloses that determining presence of the barcodes can be performed with next generation sequencing methods, for example, at each cycle of a sequencing reaction, oligonucleotide sequences complementary to four barcodes, each bearing one of four detectable markers or labels, is hybridized, and images are captured [50-51]. The sequencing results of Church could then be used in Galanti.
Claim 2:
Church discloses “each barcode specifies a tag position and the base identity at that position. To determine 12 base pairs of sequence in a population of beads will require 4*12=48 ‘query ligation barcodes’” [63] [67].
Claim 3:
Church recites “Each barcode circle has … a barcode which correlates with the identity of one base in the degenerate ‘query’ portion and is interrogated by hybridization once on the instrument. Each barcode specifies a tag position and the base identity at that position” [63].
Claim 4:
Church discloses that the presence and/or location of barcodes can be determined using sequencing methods such as pyrosequencing [50-51].
Claim 5:
Church recites “sequential hybridization is used to determine the presence and/or location of one or more barcode sequences. For example, at each cycle of a sequencing reaction, oligonucleotide sequences complementary to four barcodes, each bearing one of four detectable markers or labels, is hybridized, and images are captured” [51].
Claim 7:
Church discloses ligating the barcode sequence to the bead-bound strand before performing RCA [72]. Figures 2A-2B show the ligation process [13].
Claim 8:
Church discloses using a DNA ligase to perform circularization [28].
Claim 9:
Church discloses padlock probes and MIPs [42].
Claim 10:
Church shows the 5’ and 3’ arms of the MIPs. Church shows in Figure 5 that the probes also have anchors at the 5’ and 3’ ends (splint oligonucleotide).
Claim 11:
Church shows in Figure 5 a restriction enzyme site called EcoP15l on the probe.
Claim 12:
Church shows in Figure 5 that the probes contain an invariant anchor primer sequence [16].
Claim 13:
Church discloses performing RCA (Figures 3A-3B) and uses solid support surfaces [34]-[36].
Claim 15:
Church discloses “Arrays range from high density to low density, having from about 10,000,000 to about 2,000,000,000 beads per cm2 (high density) to about 100 to about 500 beads per cm2 (low density)” [34]. MPEP 2144.05.I recites “In the case where the claimed ranges ‘overlap or lie inside ranges disclosed by the prior art’ a prima facie case of obviousness exists.” Therefore, it would have been prima facie obvious to have a density of about 23,000 to about 110,000 mm2 in Church because the claimed range of about 23,000 to about 110,000 mm2 overlaps with the range disclosed by Church of 10,000,000 to about 2,000,000,000 beads per cm2.
Claim 18:
Church discloses barcodes [20] but does not disclose that they are error corrected. Galanti discloses filtering noise in barcodes (pg. 4, last para.; Figure 1B; pg. 6, para. 1; pg. 11, para. 3; Figure 4). It would have been prima facie to have modified the method of multiplex decoding of sequence tags in barcodes of Church with the barcode decoding method of Galanti that filters for noise in barcodes because Galanti states that using noise filtering increases the recovery of true barcodes and reduces the number of misclassified reads (pg. 11 last para.). One of ordinary skill in the art would have had a reasonable expectation of success for using Pheniqs of Galanti with Church because Church states that barcodes can be sequences with next generation sequencing technology [50-51], wherein the input to Pheniqs is next-gen bulk sequencing with multiplexed sample barcodes (pg. 2, para. 1; Figure 1A).
Claim 20:
Church states “barcodes can each have a length within a range of from 4 to 36 nucleotides, or from 6 to 30 nucleotides, or from 8 to 20 nucleotides” [20]. Figure 2A shows that the barcodes are contiguous. MPEP 2144.05.I recites “In the case where the claimed ranges ‘overlap or lie inside ranges disclosed by the prior art’ a prima facie case of obviousness exists.” Therefore, it would have been prima facie obvious to have a barcode length of 5 to 100 contiguous nucleotides in Church because the claimed range of about 5 to 100 overlaps with the range disclosed by Church of 4 to 36.
Claim 22:
Church discloses that the barcodes can range from 4 to 30 nucleotides [22].
Claim 23:
Church discloses detecting target nucleotides [20], but Church does not specifically recite detecting at least 100 DNA targets. Kuhnemund shows in Figures 2A and 4A the number of molecules detected (i.e., DNA fragments), which exceeds 100 molecules. It would have been prima facie obvious to target more than 100 DNA templates in Church, as taught by Kuhnemund, in order to determine detect DNA of targets given a scenario, such as in Kuhnemund, when there are more than 100 molecules of interest. One of ordinary skill would have a reasonable expectation of success because Kuhnemund shows that RCA can be performed on more than 100 target DNA molecules.
Claim 25:
Church discloses that the barcodes can detect specific nucleic acid sequences or singular nucleotides [22]. However, Church does not disclose detecting substitution, insertions, deletions or copy number variations. Kuhnemund discloses detecting point mutations in KRAS DNA fragments by RCA (Figure 5; pg. 7, col. 2, last para.). It would have been prima facie to have modified the method of Church for detecting target nucleic acids that may be single bases or multiple bases [22] to detect point mutations as taught by Kuhnemund. Kuhnemund states that RCA can be used to detect rare molecule aberrations such as single nucleotide variations (pg. 8, col. 2, para. 1), particularly associated with cancer (abstract). One of ordinary skill in the art would have had a reasonable expectation for success because Kuhnemund uses probes in RCA to detect point mutations (pg. 8, col. 1, para. 2), and Church’s probes used in RCA are capable of detecting single nucleotides [22].
Claims 14, 16-17 and 28 are rejected under 35 U.S.C. 103 as being unpatentable over Church et al. (“Church”; ref. 033 on IDS filed 01/26/2024; US 2008/0269068 A1; previously cited on PTO892 mailed 07/14/2025) in view of Kühnemund et al. (“Kühnemund”; Nucleic Acids Research 45, no. 8 (2017): e59-e59; previously cited on PTO892 mailed 09/09/2024), and Galanti et al. (“Galanti”; BMC bioinformatics 22 (2021): 1-16; published July 2021; previously cited on PTO892 mailed 07/14/2025), as evidenced by Margeridon et al. (“Margeridon”; Antimicrobial agents and chemotherapy 52, no. 9 (2008): 3068-3073; previously cited on PTO892 mailed 07/14/2025), as applied to claim 1 in the rejection above, and in further view of Lizardi et al. (“Lizardi”; Nature genetics 19, no. 3 (1998): 225-232; previously cited on PTO892 mailed 09/09/2024), Pourjahed et al. (“Pourjahed”; Iranian Journal of Basic Medical Sciences 16, no. 12 (2013): 1259; previously cited on PTO892 mailed 09/09/2024), and Clausson et al. (“Clausson”; Scientific reports 5, no. 1 (2015): 12317; previously cited on PTO892 mailed 09/09/2024).
Any newly recited portions herein are necessitated by claim amendment.
The bold and italicized text below are the limitations of the instant claims, and the italicized text serves to map the prior art onto the instant claims.
The limitations of claim 1 have been taught in the rejection above by Church, Kühnemund, Galanti, and Margeridon.
Claims 14:
wherein the rolling circle amplification.
Church discloses performing RCA on a surface [36] [39] (Figures 3A-3C). Neither Church, Kühnemund, nor Galanti nor disclose performing RCA on a surface with a cation-coating layer.
Lizardi discloses a study on mutation detection and single-molecule counting using isothermal rolling-circle amplification (RCA) (title). Lizardi discloses ligating padlock probes onto genomic DNA that was immobilized and denatured on a polylysine coated glass slide (cation-coating layer), wherein an RCA reaction was carried out on the ligated padlock probes (pg. 229, col. 1, para. 2).
Claim 16:
further comprising condensing the amplified circularized coded recognition elements by addition of one or more condensing agents, wherein the one or more condensing agents comprises: (i) one or more cationic additives; or (ii) one or more multivalent oligonucleotide sequences configured to crosslink sites on the amplified circularized coded recognition elements.
Church discloses amplifying MIPs [27-29] (Figures 3A-3C). Neither Church, Kühnemund, nor Galanti disclose adding condensing agents after amplifying MIPs by circularizing the MIP [28].
Lizardi states that the DNA generated by RCA is labelled with fluorescent DNP-oligonucleotide tags that hybridize at multiple sites in the tandem DNA sequence. The labeled DNA is then condensed into small objects by cross-linking with a multivalent anti-DNA IgM (pg. 227, col. 2, para. 2 – pg. 228, col. 1). Figure 6 shows the process.
Claim 17:
wherein the amplified circularized coded recognition elements comprise one or more modified nucleotides that participate in a crosslinking reaction with the one or more multivalent oligonucleotide sequences.
Church discloses circularizing padlock probes and MIPs [42]. Neither Church, Kühnemund, nor Galanti disclose probes with modified nucleotides that participate in crosslinking with multivalent oligonucleotides.
Lizardi states that the DNA generated by RCA is labelled with fluorescent DNP-oligonucleotide tags that hybridize at multiple sites in the tandem DNA sequence. The labeled DNA is then condensed into small objects by cross-linking with a multivalent anti-DNA IgM (pg. 227, col. 2, para. 2 – pg. 228, col. 1). Figure 6 shows the process.
Claim 28:
wherein the subjecting the set of targets to the recognition event comprises introducing the set of targets at an input concentration of about 10 picomolar (pM) to about 100 pM to the set of coded recognition elements.
Church shows in Figures 2-5 probes interacting with target nucleic acids and performing RCA. Neither Church, Kühnemund, nor Galanti disclose using target DNA with a specific concentration.
Lizardi states that target concentration was in the 0.1—0.2 nM range (pg. 231, col. 2, para. 3). MPEP 2144.05.I recites “In the case where the claimed ranges ‘overlap or lie inside ranges disclosed by the prior art’ a prima facie case of obviousness exists.” Therefore, it would have been prima facie obvious to use a concentration of about 10 pM to about 100 pM in Church because the claimed range of about 10 pM to about 100 pM overlaps with the range disclosed by Lizardi of 0.1—0.2 nM.
Prima facie case for obviousness:
Pourjahed states that polylysine is a material used to modify glass surfaces for preparing microarrays and can provide less interference with background signal (pg. 1263, col. 2, para. 2). Clausson states that reducing the size of fluorophore-labeled RCA products increase the local concentration of fluorophores and as a result increases signal intensity and signal-to-noise ratio (abstract). Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the instant invention to have modified the RCA procedure of Church, Kühnemund, and Galanti to include using polylysine, a specific target RNA concentration, and condensing the DNA generated by RCA because it would have allowed amplification of fewer starting molecules, less interference from background signals, and increased fluorophore intensity and signal-to-noise ratio. One of ordinary skill in the art would have had a reasonable expectation of success because these references all relate to using probes for detection of DNA/RNA.
Claims 6, 21 and 31 are rejected under 35 U.S.C. 103 as being unpatentable over Church et al. (“Church”; ref. 033 on IDS filed 01/26/2024; US 2008/0269068 A1; previously cited on PTO892 mailed 07/14/2025) in view of Kühnemund et al. (“Kühnemund”; Nucleic Acids Research 45, no. 8 (2017): e59-e59; previously cited on PTO892 mailed 09/09/2024), and Galanti et al. (“Galanti”; BMC bioinformatics 22 (2021): 1-16; published July 2021; previously cited on PTO892 mailed 07/14/2025), as evidenced by Margeridon et al. (“Margeridon”; Antimicrobial agents and chemotherapy 52, no. 9 (2008): 3068-3073; previously cited on PTO892 mailed 07/14/2025), as applied to claim 1 in the rejection above, and in further view of Kühnemund et al. (“Kühnemund 2020”; WO 2020/240025 A1; previously cited on PTO892 mailed 07/14/2025).
Any newly recited portions herein are necessitated by claim amendment.
The limitations of claim 1 have been taught in the rejection above by Church, Kühnemund, Galanti, and Margeridon.
Regarding claims 6, 21 and 31, Church discloses using barcodes containing at least one segment, wherein the barcodes contain at least 4-36 nucleotides (symbols) [22]. Church teaches barcodes are hybridized with complementary oligonucleotide sequences that each contain one of four detectable markers/labels for which images are taken (the code is interrogated by nucleic acid hybridization; each probe comprises a label distinct from the other probes) [51].
However, Church, Kühnemund, Galanti, and Margeridon do not teach that the barcodes contain at least 3 or 4 segments.
Kuhnemund 2020 discloses “a method of coding and decoding a nucleotide barcode sequence in a nucleic acid molecule to differentiate said nucleotide barcode sequence from other nucleotide barcode sequences. The method is based on a nucleotide barcode sequence design which comprises multiple sequential barcode positions, which can be interrogated separately, and sequentially. The nucleotide barcode sequence is essentially split into multiple sequential barcode positions, each of which comprises at least one barcode subunit. This sequential analysis of multiple barcode positions dramatically increases the coding capacity of the system. In a representative example, a nucleotide barcode sequence according to the present invention may comprise any one of 16 barcode subunit sequences at each barcode position” (pg. 3, last para. – pg. 4, para. 1).
It would have been prima facie to have modified the barcodes of Church to contain at least 16 barcode subunits as taught by Kuhnemund 2020 because Kuhnemund 2020 states that the subunits dramatically increase the coding capacity of the system (pg. 3, last para. – pg. 4, para. 1). One of ordinary skill in the art would have had a reasonable expectation of success because Kuhnemund 2020 states that the barcodes can be used with padlock probes in RCA (pg. 48, lines 14-22), wherein Church also uses barcoded padlock probes in RCA [27].
Response to Arguments under 35 USC 103
Applicant's arguments filed 12/08/2025 have been fully considered but they are not persuasive.
Applicant argues that Church, Kuhnemund, Galanti, and Margeridon do not disclose the limitation in claim 1 step (a) of “wherein the target-specific binding site is complementary to a known 3' region and a known 5' region of a DNA target of the set of DNA targets” (pg. 7, para. 2 – pg. 8, para. 4 of Applicant’s remarks). Applicant’s argument is not persuasive for the following reasons:
Examiner agrees that tags of the molecular inversion probes (MIP) contain degenerate sequences complementary to an unknown query nucleic acid sequence. See Figure 2A and paras. [20] and [63] of Church. However, the MIP also contains “one or more ‘guide sequences’ that are complementary to specific position on a template target (such as a bead-bound oligonucleotide) and thus hybridize with this sequence” [20]. Figure 2A in Church shows these guide sequences as “ACT” and “TCG”, which are complementary to known 5’ and 3’ ends of the template DNA sequence, respectively. As such, these guide sequences are target-specific binding sites (i.e., specific to the template DNA target) and bind to known 3’ and 5’ regions of the template DNA target.
Applicant’s remarks regarding not modifying the tags of Church to bind known target DNA sequences are considered but are not persuasive because the “guide sequences” of Church disclose the new limitation in claim 1 (pg. 8, para. 1 of Applicant’s remarks).
Applicant’s remarks regarding the dependent claims are considered but are not persuasive because Church discloses the new limitation in claim 1 (pg. 9 – pg. 10, para. 1 of Applicant’s remarks).
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.
Double Patenting Rejection over 18/253,803
Claims 1, 7-8, 11-12, 18, 20, 23 and 25 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 14, 23, 40 and 161 of copending Application No. 18/253,803 (Application ‘803) in view of Gataric et al. (“Gataric”; bioRxiv (2021): 2021-10; published 10/14/2021; previously cited on PTO892 mailed 09/09/2024) and Kühnemund et al. (“Kühnemund”; Nucleic Acids Research 45, no. 8 (2017): e59-e59; previously cited on PTO892 mailed 09/09/2024).
This rejection is newly recited and is necessitated by claim amendment.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are an obvious variation of the claims in Application ‘803. The following table sets forth the limitations of Application ‘803 that read on the limitations of the instant claims. The limitations that are struck through indicate limitations that Application ‘803 does not teach.
Instant Application
Application ‘803
Claims
Limitations
Claims
Limitations
1
(a) subjecting the set of
1
(a) providing a sample comprising a set of targets; (b) subjecting the sample to a recognition event, in which one or more targets in the set of targets in the sample is hybridized to a recognition element comprising a code from a set of codes, thereby yielding a set of coded targets comprising one or more targets and the recognition element; (c) subjecting each recognition element of the set of coded targets to a transformation event, in which a molecular transformation of each recognition element of the set of coded targets produces a circular recognition element, thereby yielding a set of circular recognition elements comprising the code; (d) subjecting each circular recognition element to a rolling circle amplification event to produce a set of amplified codes; and (e) subjecting each amplified code of the set of amplified codes to a detection event, wherein the detection event determines the presence of the coded targets.
2
subjecting the amplified codes to an exonuclease cleanup step.
5
wherein each code from the set of codes has a length of 3 to 75 nucleotides.
7 and 8
wherein the molecular transformation event comprises a ligation reaction in which each coded recognition element of the set of coded targets is ligated to form the set of circularized coded recognition elements.
wherein the subjecting the set of coded recognition elements of the set of coded targets to the molecular transformation event comprises introducing the set of coded recognition elements to a ligase enzyme under conditions sufficient to ligate and circularize the coded recognition elements.
23
wherein the transformation event comprises ligating termini of the recognition element together in the presence of the target but not in the absence of the target.
11 and 12
wherein the set of coded recognition elements further comprises:(a) one or more sequencing primer binding sequences;
wherein the one or more amplification primer binding sequences comprises a universal primer binding sequence that is common to all coded recognition elements of the set of coded recognition elements.
14
wherein the recognition element comprises one or more universal primers associated with the code.
20
wherein each code of the set of codes has a length comprising 5 to 100 contiguous nucleotides.
5
wherein each code from the set of codes has a length of 3 to 75 nucleotides.
23
wherein the set of targets comprises hundreds or more targets.
161
wherein the set of targets comprises 100 targets, and wherein the subjecting in (e) determines a presence of 100 codes of the set of codes in a multiplexed method.
25
wherein the set of targets comprises:(a) one or more substitutions, insertions and/or deletions; or (b) a copy number variation.
40
wherein the target of the set of targets comprises one or more substitutions, insertions and/or deletions.
Regarding claim 1, Kühnemund in Figure 1 uses bacterial genomic DNA extracted from cultured strains (DNA targets extracted from a biological sample) (pg. 4, col. 2, para. 1; pg. 6, col. 2, last para.). Kühnemund shows in Table 1 that the padlock probes contain sequences that are complementary to the target DNA sequence (wherein the target-specific binding site is complementary to a known 3’ region and a known 5’ region of a DNA target of the set of DNA targets). It would have been prima facie obvious to one of ordinary skill in the art to have modified Application ‘803 by extracting genomic DNA from a biological sample as taught by Kuhnemund because extracted genomic DNA detects pathogenic genomic DNA in samples containing different pathogenic species, as discussed by Kuhnemund (pg. 7, col. 2, para. 2). One of ordinary skill in the art would have had a reasonable expectation of success for extracting DNA to perform RCA because Kuhnemund uses MIPs with RCA on extracted DNA.
Regarding claim 1, Gataric discloses PoSTcode, a probabilistic image-based spatial transcriptomics decoder that can decode hundreds of thousands of fluorescent signals each derived from single molecules of mRNA (abstract). Figure 1C demonstrates how PoSTcode performs the decoding, which includes computing posterior probabilities to decode barcodes. Gataric also states that PoSTcode improves decoding results due to a novel probabilistic model used to assign barcodes to image values extracted at detected locations of an RNA signal (by decoding the amplified codes of the amplified circularized coded recognition elements, wherein the decoding comprises performing soft decision decoding).
Regarding claim 18, Gataric states that PoSTcode includes a process called registration correction that corrects for imagining errors of the barcodes (pg. 7, para. 1). Figure 3a shows the detection of a barcode in situ when using the registration correction and when not using registration correction. Gataric states that PoSTcode recovers up to 50% more confidently decoded molecules while simultaneously decreasing transcript mislabeling when compared to existing decoding techniques. Application ‘803 is related to using coded recognition elements detecting the presence of coded targets. One of ordinary skill in the art would have been motivated to combine PoSTcode from Gataric to the method of Application ‘803 because it would have improved detection of the coded targets. One of ordinary skill in the art would have had a reasonable expectation of success because Gataric achieves success in decoding barcodes in comparison to other techniques.
Double Patenting Rejection over 18/670,329
Claims 1, 3-7, 11-12 and 21-22 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4-9, 11, 13-14 and 16-17 of copending Application No. 18/670,329 (Application ‘329) in view of Church et al. (“Church”; ref. 033 on IDS filed 01/26/2024; US 2008/0269068 A1; previously cited on PTO892 mailed 07/14/2025).
This rejection is newly recited and is necessitated by claim amendment.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are an obvious variation of the claims in Application ‘329. The following table sets forth the limitations of Application ‘329 that read on the limitations of the instant claims. The limitations that are struck through indicate limitations that Application ‘329 does not teach.
Instant Application
Application ‘329
Claims
Limitations
Claims
Limitations
1
(a) subjecting the set of DNA targets extracted from a biological sample to a recognition event, in which each DNA target of the set of DNA targets is uniquely recognized by and bound to at least one coded recognition element from a set of coded recognition elements, each coded recognition element comprising a target- specific binding site and a code from a set of codes, recognition elements by decoding amplified codes of the amplified circularized coded recognition elements, wherein the decoding comprises performing soft decision decoding.
1
c) hybridizing an encoded detection probe from a set of encoded detection probes to each target nucleic acid sequence in the set of target nucleic acid sequences of the set of subsamples, each encoded detection probe in the set of encoded detection probes comprising a target specific binding site and a nucleic acid sequence code from a set of nucleic acid sequence codes, each nucleic acid sequence code comprising at least one segment encoding one or more symbols that corresponds to a sequence of one or more nucleotides, to yield a set of coded targets comprising a target nucleic acid sequence of the set of target nucleic acid sequences and the encoded detection probe; d) performing a molecular transformation on the set of coded targets in which a set of modified probes comprising the set of nucleic acid sequence codes is produced to enable differentiation of a methylated status and an unmethylated status of each target nucleic acid sequence in the methylation specific analysis sample; and e) amplifying and detecting the set of nucleic acid sequence codes of the set of modified probes in the non-methylation specific analysis sample, wherein the target nucleic acid sequences are detected by decoding the amplified codes associated therewith.
4
b) upon completion of the interrogation, determining a probability of the presence of each of the nucleic acid sequence codes by applying a soft decision probabilistic decoding algorithm to the recorded signal, wherein the presence of the nucleic acid sequence code is indicative of the presence of that target nucleic acid sequence.
8
wherein the amplifying comprises rolling circle amplification or PCR amplification.
9
further comprises performing an exonuclease reaction to digest single stranded nucleic acid that is present after the amplifying.
11
Wherein the sample and set of target nucleic acid sequences comprises one or more of: e) cell free DNA
3 and 4
wherein the decoding the amplified codes comprises interrogating the at least one segment of the code with a method comprising nucleic acid sequencing or nucleic acid hybridization.
wherein the nucleic acid sequencing comprises nanopore sequencing, Sanger sequencing, sequencing by synthesis, pyrosequencing, single molecule real-time sequencing, or sequencing by ligation.
5
wherein decoding the set of nucleic acid sequence codes that are amplified comprises one or a combination of nanopore sequencing, next-generation sequencing, massively parallel sequencing, Sanger sequencing, sequencing by synthesis, pyrosequencing, sequencing by hybridization, decoding by hybridization, single molecule real-time sequencing, sequencing by ligation, microarray detection, oligonucleotide probes in a hybridization based reaction, electronic or electrical sensing mechanism, and in situ sequencing.
5 and 6
wherein the at least one segment of the code is interrogated by nucleic acid hybridization with one or more hybridization probes having at least one label to produce a detectable signal.
wherein the code comprises a plurality of segments including the at least one segment, and wherein the code is interrogated by nucleic acid hybridization with a plurality of hybridization probes, wherein each hybridization probe comprises a label that is distinct from the other hybridization probes of the plurality to produce multiple detectable signals.
4 and 5
wherein the interrogation of each segment of each code of the set of nucleic acid sequence codes comprises decoding by hybridization and at least one of the segments is interrogated more than one time by hybridization with one or more hybridization probes each having at least one label to produce the signal, wherein at least four different labels are utilized in the decoding by hybridization
7
wherein the molecular transformation event comprises a ligation reaction in which each coded recognition element of the set of coded targets is ligated to form the set of circularized coded recognition elements.
16 and 17
c) performing a ligation reaction in which the detection probe is circularized;
wherein the encoded detection probe is a linear encoded detection probe and the ligation reaction is performed to circularize the probe.
11
wherein the set of coded recognition elements further comprises:(a) one or more sequencing primer binding sequences; (b) one or more amplification primer binding sequences; (c) a unique identifier sequence (UMI); (d) a sample index;
6
wherein the encoded detection probe comprises one or a combination of sequencing primers, one or more amplification primer sequences, unique identifiers sequences or sample indexes.
12
wherein the one or more amplification primer binding sequences comprises a universal primer binding sequence that is common to all coded recognition elements of the set of coded recognition elements.
7
wherein the one or more amplification primer sequences comprise a universal primer sequence that is common to each encoded detection probe in the set of encoded detection probes.
21
wherein each code comprises 3 or more segments including the at least one segment.
13
wherein each nucleic acid sequence code from the set of nucleotide sequence codes comprises two or more segments.
22
wherein each code comprises at least 16 symbols including the one or more symbols.
14
and optionally wherein each code comprises at least four segments and at least sixteen symbols.
Regarding claim 1, Church discloses a method for RCA using MIP and padlock probes (abstract). Church discloses that the MIPs contains one or more guide sequences that are complementary to specific position on a template target, such as a bead-bound oligonucleotide, and thus hybridize with this sequence (target-specific binding site) [2]. Figure 2A shows two guide sequences “ACT” and “TCG” that are complementary to known 3’ and 5’ positions in the template target. The known positions are TGA and AGC (wherein the target-specific binding site is complementary to a known 3’ region and a know 5’ region of a DNA target of the set of DNA targets).
It would have been prima facie obvious to one of ordinary skill in the art to have modified the target specific binding sites in Application ‘364 by making them complementary to known sequences of a target sequence as taught by Church in order to target a desired sequence. One of ordinary skill in the art would have had a reasonable expectation of success because the probes of Application ‘364 already have a target specific binding site, wherein the modification of Church would have further specified it to be complementary to a know target sequence, which is what Church achieves in their method.
This is a provisional nonstatutory double patenting rejection.
Double Patenting Rejection over 18/670,364
Claims 1, 3-6 and 21-23 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 6-7, 13 and 15-17 of copending Application No. 18/670,364 (Application ‘364) in view of Church et al. (“Church”; ref. 033 on IDS filed 01/26/2024; US 2008/0269068 A1; previously cited on PTO892 mailed 07/14/2025).
This rejection is newly recited and is necessitated by claim amendment.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are an obvious variation of the claims in Application ‘364. The following table sets forth the limitations of Application ‘364 that read on the limitations of the instant claims. The limitations that are struck through indicate limitations that Application ‘364 does not teach.
Instant Application
Application ‘364
Claims
Limitations
Claims
Limitations
1
(a) subjecting the set of DNA targets extracted from a biological sample to a recognition event, in which each DNA target of the set of DNA targets is uniquely recognized by and bound to at least one coded recognition element from a set of coded recognition elements, each coded recognition element comprising event to yield a set of circularized coded recognition elements;(c)
1
b) performing a recognition event on the set of capture agent-target complexes comprising use of a set of encoded probes, wherein: i) each encoded probe of the set of encoded probes comprises a code from a set of codes, and ii) each code of the set of codes comprises at least one segment encoding one or more symbols that correspond to a sequence of one or more nucleotides, to yield a set of coded targets each comprising the capture agent-target complex of the set of capture agent-target complexes and an encoded probe of the set of encoded probes; c) performing a molecular transformation event for each encoded probe of the set of encoded probes to yield a set of modified encoded probes comprising a code of the set of codes in the presence of the polypeptide target and a set of unmodified encoded probes comprising a code of the set of codes in the absence of the polypeptide target, in which the modified encoded probes of the set of modified encoded probes can be amplified and the unmodified encoded probes of the set of unmodified encoded probes cannot be amplified in an amplification event; d) performing the amplification event for each modified encoded probe of the set of modified encoded probes and detecting the polypeptide target by decoding the codes of the set of codes that are amplified; wherein decoding the codes comprises recording a signal produced in response to interrogation of each segment of the codes of each amplified and modified encoded probe; and e) determining a probability of the presence of each of the codes by applying a soft- decision probabilistic decoding algorithm to the recorded signal, wherein the presence of the code is indicative of the presence of the polypeptide target.
15-17
wherein the polypeptide targets are extracted from the sample prior to a).
16. The method of claim 1, where the sample comprising polypeptide targets is extracted from whole blood, serum, plasma, or saliva prior to a).
17. The method of claim 1, wherein the sample comprising polypeptide targets is extracted from one or more of a biological fluid, a mammal, a non-mammal, a plant, a sample comprising a virus, and a sample comprising a pathogen prior to a).
3 and 5-6
wherein the decoding the amplified codes comprises interrogating the at least one segment of the code with a method comprising nucleic acid sequencing or nucleic acid hybridization.
wherein the at least one segment of the code is interrogated by nucleic acid hybridization with one or more hybridization probes having at least one label to produce a detectable signal.
wherein the code comprises a plurality of segments including the at least one segment, and wherein the code is interrogated by nucleic acid hybridization with a plurality of hybridization probes, wherein each hybridization probe comprises a label that is distinct from the other hybridization probes of the plurality to produce multiple detectable signals.
1 and 6
wherein decoding the codes comprises recording a signal produced in response to interrogation of each segment of the codes of each amplified and modified encoded probe.
wherein the interrogation of the segments comprises decoding by hybridization, and wherein at least one of the segments is interrogated more than one time by hybridization with one or more hybridization probes, wherein each of the one or more hybridization probes comprises at least one different label to produce a signal.
4
wherein the decoding the amplified codes comprises interrogating the at least one segment of the code with a method comprising nucleic acid sequencing or nucleic acid hybridization.
2
wherein the signal produced is from one or a combination of nanopore sequencing, next generation sequencing, massively parallel sequencing, avidity sequencing, sequencing by synthesis, pyrosequencing, sequencing by hybridization, decoding by hybridization, single molecule real-time sequencing and sequencing by ligation.
23
wherein the set of targets comprises hundreds or more targets.
13
wherein the set of encoded probes comprises tens, hundreds, thousands, or up to tens of thousands of encoded probes,
21-22
wherein each code comprises 3 or more segments including the at least one segment.
wherein each code comprises at least 16 symbols including the one or more symbols.
7
wherein each code comprises at least four segments and at least sixteen symbols.
Regarding claim 1, Church discloses a method for RCA using MIP and padlock probes (abstract). Church discloses that the MIPs contains one or more guide sequences that are complementary to specific position on a template target, such as a bead-bound oligonucleotide, and thus hybridize with this sequence (target-specific binding site) [2]. Figure 2A shows two guide sequences “ACT” and “TCG” that are complementary to known 3’ and 5’ positions in the template target. The known positions are TGA and AGC (wherein the target-specific binding site is complementary to a known 3’ region and a know 5’ region of a DNA target of the set of DNA targets). Church discloses “Such probes are desirable because non-circularized probes can be digested with single stranded exonucleases thereby greatly reducing background noise due to spurious amplifications, and the like.” [42]. Church discloses “performing rolling circle amplification such that the barcode sequence of one molecular inversion probe is transferred to one immobilized query oligonucleotide sequence” [7].
It would have been prima facie obvious to one of ordinary skill in the art to have modified the method Application ‘364 by using RCA as the amplification event for probes and by using an exonuclease as taught by Church. The motivation for doing so is that using RCA and exonuclease for MIP or padlock probes reduces background noise as taught by Church [42]. One of ordinary skill in the art would have had a reasonable expectation of success for the combination because Church provides specific techniques to perform an amplification event described in Application ‘364 (i.e., RCA, exonuclease, MIPs and padlock probes).
This is a provisional nonstatutory double patenting rejection.
Response to Arguments under Double Patenting
Applicant argues that the new limitation in claim 1 renders the instant application patentably distinct from copending Applications (pg. 10-14 of Applicant’s remarks). Applicant’s argument is not persuasive because the Double Patenting rejections have been updated to reflect the new limitation in claim 1.
Conclusion
No claims are allowed.
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/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685