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 1-20 are currently pending in the instant application, filed July 8, 2026.
Response to Election/Restriction
Applicant's election of Group I without traverse, claims 1-18 directed to a method of reducing deaminated nucleotide bases in a nucleic acid library; and Applicant’s election of Species without traverse as follows:
Species (A): further comprising (g) contacting the plurality of covalently closed circular library molecules with a reagent that removes deaminated nucleotide bases (claim 2);
Species (B): wherein the plurality of immobilized surface capture primers is tethered to a polymer coating on the support (claim 4); and
Species (C): wherein the plurality of immobilized concatemer template molecules is on a polymer-coated support at a density of 102-1012 per mm2 (claim 11), in the reply filed July 8, 2026 is acknowledged.
Claims 19 and 20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim.
Claims 6, 7 and 18-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, there being no allowable generic or linking claim.
Therefore, claims 1-5 and 8-17 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed June 2, 2023, claims the benefit of the US Provisional Patent Application 63349016, filed June 3, 2022.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on April 4, 2025 has been considered. An initialed copy of the IDS accompanies this Office Action.
Claim Objections/Rejections
Claim Interpretation: the term “under conditions suitable for” such as recited in claim 1 is interpreted to broadly refer to conditions under which a reaction or event can occur, but the reaction or event is not occurring and/or has not occurred.
The term “to permit” such as recited in claim 8 is interpreted to refer to an arrangement that would allow an action to occur, but the action is not occurring and/or has not occurred.
Claim Objections
Claims 3, 5, 11 and 13 are objected to because of the following informalities: Claims 3, 5, 11 and 13 recite terms “AP,” “Endo IV”, “FPG”, “Endo VIII”, “mm2”, “dATP”, “dGTP”, “dCTP”, “dTTP” and “dUTP,” where an abbreviation should be spelled out in the first encounter of the claims.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(B) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-5 and 8-17 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 1 is indefinite for the recitation of the term “reducing” such as recited in claim 1, line 1 because the term “reducing” is relative term that renders the claim indefinite. The term “reducing” is not defined by the claim, and the Specification does not provide a standard for ascertaining the requisite amount of reduction as compared to some other value that qualifies as “reducing” deaminated nucleotide bases, such that one of ordinary skill in the art would not be reasonably appraised of the scope of the invention and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “individual linear nucleic acid library molecules” such as recited in claim 1, lines 3-4. There is insufficient antecedent basis for the term “individual linear nucleic acid library molecules” in the claim because claim 1, line 3 recites the term “a plurality of linear nucleic acid library molecules.” The Examiner suggests that Applicant amend the claim to recite, for example, “wherein each of the plurality of linear nucleic acid library molecules.”
Claim 1 is indefinite for the recitation of the term “the plurality” such as recited in claim 1, line 4. There is insufficient antecedent basis for the term “the plurality” in the claim because claim 1, line 3 recites the term “a plurality of linear nucleic acid library molecules.”
Claim 1 is indefinite for the recitation of the term “the linear nucleic acid library molecules” such as recited in claim 1, lines 7-8. There is insufficient antecedent basis for the term “the linear nucleic acid library molecules” in the claim because claim 1, line 3 recites the term “a plurality of linear nucleic acid library molecules.”
Claim 1 is indefinite for the recitation of the term “deaminated nucleotide bases” such as recited in claim 1, line 10. There is insufficient antecedent basis for the term “deaminated nucleotide bases” in the claim because claim 1, line 8 recites the term “one or more deaminated nucleotide bases.”
Claim 1 is indefinite for the recitation of the term “individual covalently closed circular library molecule” such as recited in claim 1, lines 16-17. There is insufficient antecedent basis for the term “individual covalently closed circular library molecule” in the claim because claim 1, lines 12-13 recites the term “a plurality of covalently closed circular library molecules.”
Claim 1 is indefinite for the recitation of the term “individual surface capture primer” such as recited in claim 1, line 17. There is insufficient antecedent basis for the term “individual surface capture primer” in the claim because claim 1, line 15 recites the term “a plurality of immobilized surface capture primers.”
Claims 1 and 14 are indefinite for the recitation of the term “the sequence” such as recited in claim 1, line 21. There is insufficient antecedent basis for the term “the sequence” in the claim.
Claim 1 is indefinite for the recitation of the term “at least a portion of the nucleic acid concatemer template molecules” such as recited in claim 1, line 21. There is insufficient antecedent basis for the term “at least a portion of the nucleic acid concatemer template molecules” in the claim because claim 1, lines 18-19 recites the term “a plurality of nucleic acid concatemer template molecules.”
Claims 3, 5 and 15 for the recitation of the term “step” (e.g., step (b), step (e), step (f)) such as recited in claim 3, line 2. There is insufficient antecedent basis for the term “step” in the claim because claim 1 recites the terms a), b), c), d), e) and f). Moreover, claims 3 and 5 depend from instant claim 1; and claim 15 depends from claims 1, 12, 13 and 14, wherein claims 1, 12, 13 and 14 do not recite a “step” and, thus, the metes and bounds of the claim cannot be determined.
Claim 4 is indefinite for the recitation of the term “a polymer coating on the support” such as recited in claim 4, line 2 because claim 4 depends from instant claim 1, wherein claim 1 does not recite that the support comprises a polymer coating and, thus, the metes and bounds of the claim cannot be determined.
Claims 8, 10, 11, 12 and 14 are indefinite for the recitation of the term “the plurality of concatemer template molecules” such as recited in claim 8, lines 1-2. There is insufficient antecedent basis for the term “the plurality of concatemer template molecules” in the claim because claim 1, lines 18-19 recites the term “a plurality of nucleic acid concatemer template molecules.”
Claim 8 is indefinite for the recitation of the terms “fluid communication” and “flowing a solution of reagents onto the support” such as recited in claim 8, lines 2-3 because claim 8 depend from instant claim 1, wherein claim 1 does not recite a microfluidic device, channels, a solution, a solution of reagents, etc. and, thus, the metes and bounds of the claim cannot be determined.
Claim 10 is indefinite for the recitation of the term “essentially simultaneously reacted” such as recited in claim 10, line 2 because the term “essentially simultaneously” is a relative term that renders the claim indefinite. The term “essentially simultaneously” is not defined by the claim, and the Specification does not provide a standard for ascertaining the requisite timing of reaction as compared to some other value that qualifies as being ‘essentially simultaneous’ reactions between the template molecules and the solution of reagents, such that one of ordinary skill in the art would not be reasonably appraised of the scope of the invention and, thus, the metes and bounds of the claim cannot be determined.
Claim 10 is indefinite for the recitation of the term “massively parallel manner” such as recited in claim 10, line 3 because it is unclear what is meant by reacting a solution of reagents in a massively parallel manner including whether the term refers to a device such as a massively parallel sequencer, or whether the term refers to a type of reaction condition and, thus, the metes and bounds of the claim cannot be determined.
Claim 11 is indefinite for the recitation of the term “the density” such as recited in claim 11, line 2. There is insufficient antecedent basis for the term “the density” in the claim.
Claim 11 is indefinite for the recitation of the term “102 – 1012 per mm2” such as recited in claim 11, line 3 because it appears that the recited density units is missing critical information, where the units should read, for example, “102 – 1012 concatemer template molecules/mm2” and, thus, the metes and bounds of the claim cannot be determined.
Claims 12 and 14 are indefinite for the recitation of the term “a concatemer template molecule” such as recited in claim 12, line 8. There is insufficient antecedent basis for the term “a concatemer template molecule” in the claim because claim 1, lines 18-19 recites the term “a plurality of nucleic acid concatemer template molecules.”
Claim 12 is indefinite for the recitation of the terms “a plurality of soluble sequencing primers;” a sequencing polymerase;” “a nucleic acid duplex;” “a soluble sequencing primer;” a plurality of nucleotides;” and “at least one nucleotide analog labeled with a fluorophore and having a removable chain terminating moiety” because claim 12 depends from instant claim 1, wherein claim 1 does not recite the presence of a plurality of soluble sequencing primers; a sequencing polymerase; nucleic acid duplexes; a soluble sequencing primer; a plurality of nucleotides; and at least one nucleotide analog labeled with a fluorophore and having a removable chain terminating moiety and, thus, the metes and bounds of the claim cannot be determined.
Claims 12 and 14 are indefinite for the recitation of the term “a soluble sequencing primer” such as recited in claim 12, lines 8-9. There is insufficient antecedent basis for the term “a soluble sequencing primer” in the claim because claim 12, lines 4-5 recites the term “a plurality of soluble sequencing primers.”
Claims 12 and 15 are indefinite for the recitation of the term “the sugar 3’ position” such as recited in claim 12, line 14. There is insufficient antecedent basis for the term “the sugar 3’ position” in the claim.
Claim 12 is indefinite for the recitation of the term “the hybridized sequencing primers” such as recited in claim 12, lines 15-16. There is insufficient antecedent basis for the term “the hybridized sequencing primers” in the claim.
Claim 12 is indefinite for the recitation of the term “the incorporated nucleotide” such as recited in claim 12, lines 17-18. There is insufficient antecedent basis for the term “the incorporated nucleotide” in the claim because claim 12, line 15 recites the term “incorporating at least one nucleotide.”
Claim 13 is indefinite for the recitation of the term “the sugar 3’ group” and “the sugar group” such as recited in claim 13, lines 3 and 9. There is insufficient antecedent basis for the terms “the sugar 3’ group” and “the sugar group” in the claim.
Claim 14 is indefinite for the recitation of the term “the plurality of complexed polymerases” such as recited in claim 14, line 9. There is insufficient antecedent basis for the term “the plurality of complexed polymerases” in the claim because claim 14, lines 9-10 recite the term “a plurality of detectably labeled multivalent molecules” because claim 14, lines 5-6 recites the term “a plurality of first complexed polymerases.”
Claim 14 is indefinite for the recitation of the terms “a plurality of complexed polymerases;” “complementary nucleotide units;” “a plurality of detectably labeled multivalent molecules;” “a core attached to multiple nucleotide arms;” and “individual multivalent molecules” in claim 14, lines 9-22 because claim 14 depends from instant claims 1, 12 and 13, wherein claims 1, 12 and 13 do not recite the presence of a plurality of complexed polymerases; complementary nucleotide units; a plurality of detectably labeled multivalent molecules; a core attached to multiple nucleotide arms; and individual multivalent molecules and, thus, the metes and bounds of the claim cannot be determined.
Claim 14 is indefinite for the recitation of the terms “the multivalent molecules” and “individual multivalent molecules” such as recited in claim 14, lines 12 and 16. There is insufficient antecedent basis for the terms “the multivalent molecules” and “individual multivalent molecules” in the claim because claim 14, lines 9-10 recite the term “a plurality of detectably labeled multivalent molecules.”
Claims 14, 15 and 16 are indefinite for the recitation of the term “the sequencing primers” such as recited in claim 14, line 15. There is insufficient antecedent basis for the term “the sequencing primers” in the claim because claim 14, line 4-5 recites the term “a plurality of the soluble sequencing primers.”
Claim 14 is indefinite for the recitation of the term “the nucleic acid template” such as recited in claim 14, line 22. There is insufficient antecedent basis for the term “the nucleic acid template” in the claim.
Claim 15 is indefinite for the recitation of the term “their bound multivalent molecules” such as recited in claim 15, line 3. There is insufficient antecedent basis for the term “their bound multivalent molecules” in the claim because claim 14, lines 9-10 recite the term “a plurality of detectably labeled multivalent molecules.”
Claims 15 and 16 are indefinite for the recitation of the term “the nucleotide-complexed polymerases” such as recited in claim 15, lines 18-19. There is insufficient antecedent basis for the term “the nucleotide-complexed polymerases” in the claim.
Claim 16 is indefinite for the recitation of the term “optionally” such as recited in claim 16, line 3 because the claim does not particularly pointing out and distinctly claiming the subject matter which the applicant regards as the invention and, thus, the metes and bounds of the claim cannot be determined.
Claim 17 is indefinite for the recitation of the term “the support is passivated” such as recited in claim 17, line 4 because the claim 17 depends from instant claim 1, wherein claim 1 does not recite that the support comprises a coating, that the support is passivated and/or that the support has a water contact angle and, thus, the metes and bounds of the claim cannot be determined.
Claims 2 and 9 are indefinite insofar as they ultimately depend from instant claim 1.
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 3-5, 8, 10, 12, 14, 15 and 17 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.
Claims 3, 5 and 15 recite (in part): “step” such as recited in claim 3, line 2 because claims 3 and 5 depend from instant claim 1; and claim 15 depends from claims 1, 12, 13 and 14, wherein claims 1, 12, 13 and 14 do not recite a “step.” Thus, claims 3, 5 and 15 are 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 4 recite (in part): “wherein the plurality of immobilized surface capture primers is tethered to a polymer coating on the support” in lines 1-2 because claim 4 depends from instant claim 1, wherein claim 1 does not recite that the support comprises a polymer coating. Thus, claim 4 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 8 recites (in part): “wherein the plurality of concatemer template molecules immobilized to the support is in fluid communication with each other to permit flowing a solution of reagents onto the support” in lines 1-3 because claim 8 depend from instant claim 1, wherein claim 1 does not recite a microfluidic device, channels, a solution, a solution of reagents, etc. Thus, claim 8 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 10 recites (in part): “wherein the plurality of concatemer template molecules immobilized to the support…reacted with the solution of reagents in a massively parallel manner” in lines 1-3 because claim 10 depend from instant claims 1 and 8, wherein claims 1 and 8 do not recite reacting a plurality of concatemer template molecules with a solution of reagent including using a device and/or conditions for massively parallel reactions. Thus, claim 10 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 12 recites (in part): “wherein sequencing the plurality of concatemer template molecules comprises:…of the incorporated nucleotide” in lines 1-18 because claim 12 depends from instant claim 1, wherein claim 1 does not recite the presence of a plurality of soluble sequencing primers; a sequencing polymerase; a nucleic acid duplex; a soluble sequencing primer; a plurality of nucleotides; a sugar; at least one nucleotide analog labeled with a fluorophore and having a removable chain terminating moiety, etc. Thus, claim 12 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 14 recites (in part): “wherein sequencing the plurality of concatemer template molecules immobilized to the support comprises:…the nucleic acid template” in lines 1-22 because claim 14 depends from instant claims 1, 12 and 13, wherein claims 1, 12 and 13 do not recite the presence of a plurality of complexed polymerases; complementary nucleotide units; a plurality of detectably labeled multivalent molecules; a core attached to multiple nucleotide arms; and individual multivalent molecules. Thus, claim 14 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): “the support is passivated with at least one hydrophilic polymer coating having a water contact angle of no more than 45 degrees…and dextran” in lines 4-11 because the claim 17 depends from instant claim 1, wherein claim 1 does not recite that the support comprises a coating, that the support is passivated and/or that the support has a water contact angle. 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.
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 § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-5, 8-11, 13 and 17 are rejected under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Belhocine et al. (hereinafter “Belhocine”) (US Patent Application Publication No. 20190361010, published November 28, 2019; effective filing date February 12, 2018).
Regarding claim 1, Belhocine teaches compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from one or more cells, wherein polynucleotide processing can be useful for a variety of applications, including generation of labeled macromolecules (Abstract, lines 1-5). Belhocine teaches that the gDNA molecule is an enzymatically fragmented gDNA molecule including deaminated cytosines or oxidized 5-hydroxymethylcytosine bases; or the analyte is a ribonucleic acid (RNA) molecule, wherein the RNA molecule is a messenger RNA molecule (mRNA), (i) a clustered regularly interspaced short palindromic (CRISPR) RNA molecule (crRNA), or (ii) a single guide RNA (sgRNA) molecule (interpreted as a linear gDNA or RNA molecule; and carrying one or more deaminated bases, claim 1a) (paragraph [0013], lines 45-54). Belhocine teaches that co-partitioned nucleic acid molecules can comprise functional sequences useful in processing nucleic acids including targeted or random/universal amplification primer sequences for amplifying the genomic DNA from the individual biological particles within the partitions while attaching the associated barcode sequences, sequencing primers or primer recognition sites, hybridization or probing sequences, e.g., for identification of presence of the sequences or for pulling down barcoded nucleic acids, or any of a number of other potential functional sequences (interpreted as comprising a sequence of interest, a universal adaptor, a universal sequence for binding a sequencing primer, claim 1a) (paragraph [0282]). Belhocine teaches that species such as oligonucleotides comprising barcodes attached to a solid support (e.g., a bead) can comprise a U-excising element that allows the species to release from the bead, wherein the U-excising element can comprise a single-stranded DNA (ssDNA) sequence that contains at least one uracil, such that the species can be attached to a solid support via the ssDNA sequence; and the species can be released by a combination of uracil-DNA glycosylase (e.g., to remove the uracil) and an endonuclease (e.g., to induce an ssDNA break), wherein if the endonuclease generates a 5' phosphate group from the cleavage, then additional enzyme treatment can be included in downstream processing to eliminate the phosphate group, e.g., prior to ligation of additional sequencing handle elements, e.g., Illumina full P5 sequence, partial P5 sequence, full R1 sequence, and/or partial R1 sequence (interpreted as contacting linear nucleic acid molecules with a reagent that removes deaminated nucleotide bases; interpreting a P5 sequence as a universal sequence; and DNA glycosylase, claim 1b and 3) (paragraph [0397]). Belhocine teaches that an oligonucleotide comprising a capture sequence or a labelling agent can be a splint oligonucleotide, wherein a splint oligonucleotide can comprise two or more different primers that can have different functions, such as comprising two or more of the following: a poly-T primer, a random N-mer primer, and a target-specific primer (interpreted as universal adaptors having a binding sequence, claim 1a) (paragraph [0398], lines 1-2). Belhocine teaches that probe molecules that attach to the same target nucleic acid molecule can be linked to one another, such that a probe nucleic acid molecule can comprise (i) a first probe moiety at a first end that comprises a sequence complementary to a first target region of a nucleic acid molecule; and (ii) a second probe moiety at a second end that comprises a sequence complementary to a second target region of the nucleic acid molecule that is adjacent to the first target region, wherein a single probe molecule can comprise additional sequences, such as a sequencing primer binding site, or a primer site for downstream analysis, e.g., rolling circle amplification, such that upon hybridization of the first and second probe moieties to the target nucleic acid molecule, the first and second probe moieties can be adjacent and the probe molecule and target nucleic acid molecule can form a circular nucleic acid product; and the circular nucleic acid product can then be subjected to conditions sufficient for ligation of the nucleic acid product, forming a circular probe-linked nucleic acid molecule (interpreted as circularizing the linear nucleic acids, claim 1c) (paragraph [0502], lines 1-20). Belhocine teaches that the circular nucleic acid product can then be partitioned with one of more materials including one or more nucleic acid barcode molecules (e.g., coupled to a bead, as described herein) or nucleic acid binding molecules to undergo further processing; alternatively a circular nucleic acid product can be formed within a partition and hybridize with a nucleic acid barcode molecule and/or nucleic acid binding molecule within the partition to generate a barcoded circular nucleic acid product (interpreted as distributing the circular molecules onto a support having immobilized surface capture primers, claim 1d) (paragraph [0502], lines 39-48). Belhocine teaches that the circular nucleic acid product can be amplified by rolling circle amplification (RCA) prior or subsequent to partitioning of the circular nucleic acid product; and that the use of RCA can increase efficiency of a barcoding process by generating multiple targets from the same original ligation event (interpreted as RCA; and generating concatemer template molecules, claim 1e) (paragraph [0502], lines 58-62). Belhocine teaches that subsequent to amplification, cleanup of primers and sequencing can be performed (interpreted as sequencing, claim 1f) (paragraph [0501], lines 26-27).
Regarding claim 2, Belhocine teaches that circularization of nucleic acid moieties can also facilitate removal of unwanted nucleic acid species and unhybridized probes by permitting the use of exonucleases without affecting ligation products, such that circular nucleic acid product can be formed in a solution, and unwanted and unhybridized materials removed from the solution prior to barcoding or other processing (interpreted as removing deaminated nucleotide bases, claim 2) (paragraph [0502], lines 30-33 and 36-39).
Regarding claim 3, Belhocine teaches that species such as oligonucleotides comprising barcodes attached to a solid support (e.g., a bead) can comprise a U-excising element that allows the species to release from the bead, wherein the U-excising element can comprise a single-stranded DNA (ssDNA) sequence that contains at least one uracil, such that the species can be attached to a solid support via the ssDNA sequence; and the species can be released by a combination of uracil-DNA glycosylase (e.g., to remove the uracil) and an endonuclease (e.g., to induce an ssDNA break) (interpreting uracil-DNA glycosylase as a reagent that removes deaminated nucleotide bases, claim 1b and 3) (paragraph [0397], lines 1-10).
Regarding claims 4 and 11, Belhocine teaches one or more reagents attached to cell beads, wherein the one or more reagents comprise a nucleic acid molecule, wherein the nucleic acid molecule is a poly-T primer (interpreting the poly-T sequence as capture primers comprising a density >1012 per mm2) (paragraph [0010], last five lines). Belhocine teaches that a capture oligonucleotide (e.g., a barcoded oligonucleotide capable of coupling to an analyte) or a labelling agent can comprise a primer as described herein (e.g., a poly-T primer, a random N-mer primer, and/or a target-specific capture primer); as well as, a backbone, which can comprise one or more of the following elements: a sequencer primer, a barcode, and a UMI (interpreted as capture primers immobilized on a bead; and amplified primers comprising a density >1012 per mm2, claims 4 and 11) (paragraph [0393]). Belhocine teaches that the bead can be formed via covalent or non-covalent assembly of molecules (e.g., macromolecules) such as monomers or polymers including DNA or RNA (interpreted as comprising capture primer sequences, claims 4 and 11) (paragraph [0181], lines 13-15). Belhocine teaches that the bead can be a solid particle such as a metal-based particle including, but not limited to iron oxide, gold, or silver covered with a coating comprising one or more polymers, wherein such coating can be disruptable or dissolvable (interpreted as a coating on the support; and a polymer coating, claims 4 and 11) (paragraph [0181], lines 22-25).
Regarding claims 5 and 9, Belhocine teaches that species can include nucleic acid molecules (e.g., oligonucleotides), reagents for a nucleic acid amplification reaction (e.g., primers, polymerases, dNTPs, co-factors (e.g., ionic cofactors), and buffers including those described herein, reagents for enzymatic reactions (e.g., enzymes, co-factors, substrates, buffers), reagents for nucleic acid modification reactions such as polymerization, ligation, or digestion, and/or reagents for template preparation (e.g., tagmentation) for one or more sequencing platforms (e.g., Nextera for Illumina), wherein such species can include one or more enzymes including polymerase, reverse transcriptase, restriction enzymes (e.g., endonuclease), transposase, ligase, proteinase K, DNAse, etc., wherein such species can include one or more reagents described elsewhere herein (e.g., lysis agents, inhibitors, inactivating agents, chelating agents, stimulus) (interpreted as amplification comprising; and encompassing strand-displacing enzymes; and dNTPs; and reagents include enzymes, cations and nucleotides, claims 5 and 9) (paragraph [0251], lines 1-24). Belhocine teaches that the barcoded probe-linked nucleic acid molecule 11912 undergoes a nucleic acid reaction 11913 such as amplification (e.g., Phi29-based rolling circle amplification) to provide barcoded amplicons of interest (interpreted as comprising a strand displacing polymerase and dNTPs, claims 5 and 9) (paragraph [0518], lines 13-17). Belhocine teaches the formation of alginate droplets followed by exposure to divalent metal ions (e.g., Ca2+ ions), can be used as an encapsulation process using the described processes (interpreted as flowing divalent cations, claim 9) (paragraph [0205, lines 12-15]).
Regarding claim 8, Belhocine teaches in Figure 1 shows an example of a microfluidic channel structure for partitioning individual biological particles; Figure 2 shows an example of a microfluidic channel structure for delivering barcode carrying beads to droplets; Figure 3 shows an example of a microfluidic channel structure for co-partitioning biological particles and reagents; Figure 4 shows an example of a microfluidic channel structure for the controlled partitioning of beads into discrete droplets; and Figure 5 shows an example of a microfluidic channel structure for increased droplet generation throughput, wherein microfluidic channel structures 100 can have more than one channel junction, such that a microfluidic channel structure can have 2, 3, 4, or 5 channel segments each carrying particles (e.g., biological particles, cell beads, and/or gel beads) that meet at a channel junction, such that fluid can be directed to flow along one or more channels or reservoirs via one or more fluid flow units; and a fluid flow unit can comprise compressors (e.g., providing positive pressure), pumps (e.g., providing negative pressure), actuators, and the like to control flow of the fluid. Fluid may also or otherwise be controlled via applied pressure differentials, centrifugal force, electrokinetic pumping, vacuum, capillary or gravity flow, or the like (interpreted as being in fluid communication and permitting flow, claim 8) (paragraph [0197]; and Figures 1-5).
Regarding claim 10, Belhocine teaches combinatorial libraries of the chemical compounds and identifier oligonucleotides can be made through sequential additions of chemical compound subunits that concord with simultaneous or subsequent sequential additions of identifier oligonucleotides on the solid matrix (interpreted as essentially simultaneously, claim 10) (paragraph [1061], lines 5-10). Belhocine teaches that the methods can be multiplexed in a single vessel for additions of chemical compounds and identifier oligonucleotides in a massively parallel way (interpreted as reactions in a massively parallel manner, claim 10) (paragraph [1061], lines 10-13).
Regarding claim 13, Belhocine teaches that a modified nucleotide can comprise one or more modifications such as alkylations, hydroxylations, oxidation, or other modification in its nucleobase and/or sugar moieties (interpreted as chain terminating moiety comprising alkyl group, claim 13) (paragraph [0464, last 3 lines).
Regarding claim 17, Belhocine teaches that beads can be formed from materials other than polymers including lipids, micelles, ceramics, glass-ceramics, material composites, metals, other inorganic materials (interpreted as glass and plastic, claim 17) (paragraph [0224], last 4 lines). Belhocine teaches that a bead can comprise natural and/or synthetic materials including a natural polymer, a synthetic polymer or both natural and synthetic polymers, wherein natural polymers include proteins and sugars such as deoxyribonucleic acid, rubber, cellulose, starch (e.g., amylase, amylopectin), proteins, enzymes, polysaccharides, silks, polyhydroxyalkanoates, chitosan, dextran, collagen, carrageenan, ispaghula, acacia, agar, gelatin, shellac, sterculia gum, xanthan gum, agarose, alginic acid, alginate, or natural polymers thereof; and synthetic polymers include acrylics, nylons, silicones, spandex, viscose rayon, polycarboxylic acids, polyvinyl acetate, polyacrylamide, polyacrylate, polyethylene glycol, polyurethanes, polylactic acid, silica, polystyrene, polyacrylonitrile, polybutadiene, polycarbonate, polyethylene, polyethylene terephthalate, poly( chlorotrifluoroethylene), poly(ethylene oxide), poly(ethylene terephthalate), polyethylene, polyisobutylene, poly(methyl methacrylate), poly(oxy-methylene), polyformaldehyde, polypropylene, polystyrene, poly(tetrafluoroethylene), poly(vinyl acetate), poly(vinyl alcohol), poly(vinyl-chloride), poly(vinylidene dichloride), poly(vinylidene difluoride), poly(vinyl fluoride) and/or combinations (e.g., copolymers) thereof (interpreted as a polymer coated support including PEG, claims 1, 4, 11 and 17) (paragraph [0224]).
Belhocine does not specifically exemplify sequencing as recited in claim 12 (claim 12); removable chain terminating moieties recited in claim 13 (claim 13); sequencing as recited in claim 14 (claim 14); dissociating, contacting, and contacting as recited in claim 15 (claim 15); and identifying nucleobases as recited in claim 16 (claim 16).
Belhocine meets all the limitations of the claims and, therefore, anticipates the claimed invention.
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 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.
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 and 8-17 are rejected under 35 U.S.C. 103 as being unpatentable over Belhocine et al. (hereinafter “Belhocine”) (US Patent Application Publication No. 20190361010, published November 28, 2019; effective filing date February 12, 2018) in view of Previte et. al. (hereinafter “Previte”) (US Patent Application Publication 20210123098, published April 29, 2021; WO2021061841, published April 1, 2021).
The teachings of Belhocine as applied to claims 1-5, 8-11, 13 and 17 are described supra.
Belhocine does not specifically exemplify sequencing as recited in claim 12 (claim 12); removable chain terminating moieties recited in claim 13 (claim 13); sequencing as recited in claim 14 (claim 14); dissociating, contacting, and contacting as recited in claim 15 (claim 15); and identifying nucleobases as recited in claim 16 (claim 16).
Regarding claims 12, 14, 15 and 16, Previte teaches methods and systems for analyzing nucleic acids in a biological sample in a manner that retains the spatial and/or cellular origin of the nucleic acids within the biological sample (Abstract). Previte teaches that the term “sequencing” and related terms refers to a method for obtaining from a nucleic acid molecule, typically by determining the identify of at nucleotide sequence information least one nucleotides including their nucleobase components within the nucleic acid molecule (interpreted as identifying nucleobases, claim 16) (paragraph [0843], lines 1-5). Previte teaches that in any of the sequencing steps can be conducted using a sequence-by-synthesis, sequence-by-hybridization or sequence-by-binding procedures, wherein examples of massively parallel sequence-by-synthesis procedures include Polony sequencing, pyrosequencing (e.g., from 454 Life Sciences; U.S. Pat. Nos. 7,211,390, 7,244,559 and 7,264,929), chain-terminator sequencing (e.g., from II!umina; U.S. Pat. No. 7,566,537; Bentley 2006 Current Opinion Genetics and Development 16:545-552; and Bentley, et al., 2008 Nature 456:53-59, ion sensitive sequencing (e.g., from Ion Torrent), probe-anchor ligation sequencing (e.g., Complete Genomics), DNA nanoball sequencing, nanopore DNA sequencing, such that examples of single molecule sequencing include Heliscope single molecule sequencing, and single molecule real time (SMRT) sequencing; and an example of sequence-by-hybridization includes SOLiD sequencing (e.g., from Life Technologies; WO 2006/084132), wherein an example of sequence-by-binding includes Onmiome sequencing (e.g., U.S. Pat. No. 10,246,744) (interpreting claims 12 and 16 as describing sequencing-by-synthesis and chain-terminator sequencing; and interpreting claims 14 and 15 to describe sequencing-by-binding and chain-terminator sequencing, claims 12, 14, 15 and 16) (paragraph [0844]). Previte teaches a system for analyzing a biological sample comprising: a substrate comprising a surface having coupled thereto a polymer layer suitable to immobilize said biological sample to said surface, wherein: said biological sample or derivative thereof comprises a target nucleic acid molecule or derivative thereof; said polymer layer is configured to couple with (i) said biological sample or derivative thereof, or (ii) said target nucleic acid molecule or derivative thereof (paragraph [0008], lines 1-9). Previte teaches methods for identifying at least a portion of a sub-cellular component within a cell or tissue in situ, the method comprising: (a) detecting a signal from a multivalent binding complex between said sub-cellular component or derivative thereof and a detectable polymer-nucleotide conjugate; and (b) processing at least said signal detected in (a) to identify said at least said portion of said sub-cellular component or derivative thereof, wherein said sub-cellular component or derivative thereof is a nucleic acid. In some embodiments, said nucleic acid is DNA. In some embodiments, methods further comprise: (c) immobilizing said cell or said tissue on a surface of a substrate, such that the methods further comprise: (d) coupling at least a portion of said sub-cellular component to a capture molecule coupled to a said surface, such that the methods further comprise: (e) permeabilizing said tissue or lysing said cell prior to detecting in (a), wherein said surface has a water contact angle of less than or equal to 45 degrees; and coupling in (d) comprises hybridizing said capture molecule with said at least said portion of said sub-cellular component in a presence of a hybridization buffer (interpreted as multivalent binding; and sequencing by binding, claim 14) (paragraph [0007]).
Regarding claim 13, Previte teaches that the nucleotide unit has a chain terminating moiety (e.g., blocking moiety) at the sugar 2' position, at the sugar 3' position, or at the sugar 2' and 3' position, wherein the chain terminating moiety is selected from a group consisting of 3'-deoxy nucleotides, 2',3'-dideoxynucleotides, 3'-methyl, 3'-azido, 3'-azidomethyl, 3'-O-azidoalkyl, 3'-O-ethynyl, 3'-O-fluoroalkyl, 3'-fluoromethyl, 3' difluoromethyl, 3'-trifluoromethyl, 3'-malonyl, 3'-amino, 3'-0-amino, 3'-sulfhydral, 3'-aminomethyl, 3'-ethyl, 3'butyl, 3'-tert 3' Fluorenylmethyloxycarbonyl, 3' tert-Butyloxycarbonyl, 3'-O-alkyl hydroxyl-amino group, 3'-phosphorothioate, and 3-O-benzyl, or derivatives thereof (interpreted as encompassing aryl groups, alkyl group, azido, etc., claim 13) (paragraphs [09333]-[0934]).
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 identifying at least a portion of a sub-cellular component within a cell or tissue in situ as exemplified by Previte, it would have been prima facie obvious for one of ordinary skill in the art at the time the invention was made to modify the method of polynucleotide processing and analyte characterization from one or more cells comprising generating barcoded nucleic acid fragments within a plurality of partitions comprising template nucleic acid molecules; circularizing the linear nucleic acid molecules upon hybridization of probes to target regions; amplifying the barcoded template nucleic acid molecule by RCA; and sequencing the amplified products as disclosed by Belhocine to include the sequencing methods such as sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-binding, sequencing-by-nucleotide incorporation, ion-sensitive sequencing, probe-anchor sequencing, nanopore DNA sequencing, ion-sensitive sequencing, single molecule real time (SMRT) sequencing, chain-terminator sequencing, Polony sequencing, etc. as taught by Previte with a reasonable expectation of success in processing and/or analyzing multiple different nucleic acid components including different nucleic acid components from a cell; and/or in lowering non-specific binding, improving contrast-to-noise ratios, reducing costs, and/or increasing efficiency of molecular barcoding including for single-cell applications.
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.
Conclusion
Claims 1-5 and 8-17 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMY M BUNKER whose telephone number is (313) 446-4833. The examiner can normally be reached on Monday-Friday (6am-2:30pm).
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/AMY M BUNKER/Primary Examiner, Art Unit 1684
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