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
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office Action has been withdrawn pursuant to 37 CFR 1.114.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 February 4, 2026 has been entered.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Status of Claims
Claims 1-4, 6-9, 14, 17, 18, 20-25, 27-29, 32-37 and 39-42 are currently pending. Claims 1, 17 and 18 have been amended by Applicants’ amendment filed 02-04-2026. Claim 19 has been canceled by Applicants’ amendment filed 02-04-2026. No claims have been added by Applicants’ amendment filed 02-04-2026.
Applicant's election of Group I with traverse of claims 1-9, 14-19, 32, 34 and 35, directed to a method for preparing a sequencing library; and the election of Species without traverse as follows:
Species (A): wherein processing comprises contacting subsets with reverse transcriptase (claim 2);
Species (B): wherein the primer comprises a poly-T nucleotide sequence (claim 3);
Species (C): wherein the predetermined RNA nucleic acids are mRNA (claim 14);
Species (D): wherein the nucleotide label comprises a nucleotide analog, a hapten-labeled nucleotide, etc. (claim 17);
Species (E): wherein the predetermined condition comprises exposure to an agent (claim 21);
Species (F): wherein the agent comprises a protein, a non-ribosomal protein, etc. (claim 22);
Species (G): wherein distributing comprises dilution (claim 28);
Species (H): wherein adding comprises contacting nucleic acid fragments comprising one or more index sequence (claim 31);
Species (I): wherein the compartment comprises a well or a droplet (claim 34);
Species (J): wherein the primer comprises RNA nucleic acids (claim 45);
Species (K): wherein the primer comprises a poly-T nucleotide sequence that anneals to mRNA poly(A) tail (claim 46);
Species (L): wherein the label comprises a nucleotide analog, a hapten-labeled nucleotide, etc. that can be modified (claim 57);
Species (M): adding one or more of the first, second or third compartment comprises contacting nucleic acid fragments with a transposome complex (claim 69); and
Species (N): all compartments are wells or droplets (instant claim 71), in the reply filed on July 13, 2022 was previously acknowledged.
Response to Arguments
Applicant’s arguments filed February 4, 2026 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) claims 2-4 are drawn to the elected species of Group I, in the Restriction Requirement mailed April 14, 2022. Applicant maintains the request for rejoinder and examination (Applicant Remarks, pgs. 9-10, Status of Claims and Rejoinder).
Regarding (a), in the response filed July 13, 2022, Applicant elected Species (A) through (N) without traverse. In relevant part, Applicant elected: for Species (A) - claim 2; for Species (B) - claim 3; and Species (H) – claim 31. The restriction requirement was deemed proper and was made final in the Office Action mailed August 31, 2022. However, in the response filed November 12, 2024, Applicant amended claim 2, such that amended claim 2 read on elected Species (H). Thus, claim 2 was withdrawn as reading on a non-elected species, while claims 3 and 4 were withdrawn as depending from withdrawn claim 2 (please see the Office Action mailed April 28, 2025). As indicated in MPEP § 1.144, Applicant may petition the Director to review the requirement for restriction.
Claims 10-13, 20-25, 31 and 36-86 were previously 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. Applicant timely traversed the restriction (election) requirement in the reply filed on July 13, 2022.
Claims 2-4, 6-9, 14, 27, 29, 32, 33 and 35 were previously 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.
The restriction requirement was deemed proper was made FINAL.
The claims will be examined insofar as they read on the elected species.
Therefore, claims 1, 17, 18, 28 and 34 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed December 20, 2019 is a 35 U.S.C. 371 national stage filing of
International Application No. PCT/US2019/035422, filed June 4, 2019; which claims the benefit of US
Provisional Patent 62/821,678, filed March 21, 2019; and US Provisional Patent 62/680,259, filed June 4,
2018.
Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 120 as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of the first paragraph of 35 U.S.C. 112. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosures of the prior-filed applications including US Provisional Patent Application 62/680,259, filed June 4, 2018; and US Provisional Patent Application 62/821,678, filed March 21, 2019, which fail to provide adequate support or enablement in the manner provided by the first paragraph of 35 U.S.C. 112 for one or more claims of this application. The specific method steps recited in independent claim 1 does not have support for: “incorporating a label into RNA as it is synthesized in the subsets of nuclei or cells to result in labeled RNA nucleic acids and unlabeled pre-existing RNA nucleic acids” in lines 5-7.
Therefore, the priority date for the presently claimed invention is June 4, 2019, the filing date of PCT/US2019/035422.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed February 4, 2026 are acknowledged and have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or objection not specifically addressed below are herein withdrawn.
Maintained Objections/Rejections
Claim Interpretation: the term “a first plurality of compartments comprising subsets of nuclei or cells” as recited in claim 1 is interpreted to refer to: (i) subsets of nuclei or cells that are themselves compartments; and/or (ii) subsets of nuclei or cells that reside in a separate compartment (e.g., emulsion, well-plate, droplet, etc.).
The term “to result in RNA comprising the labeled and unlabeled pre-existing RNA” as recited in claim 1 is interpreted to mean that incorporating individual labeled nucleotides into RNA results in RNA, wherein a portion of the RNA does not comprise one or more labeled nucleotides (e.g., unlabeled pre-existing RNA), and another portion of RNA does comprise one or more labeled nucleotides (e.g., labeled RNA). The labeled RNA and unlabeled pre-existing RNA can be present as a mixture within a cell or nuclei and/or the labeled RNA and unlabeled pre-existing RNA can be located in separate compartments (e.g., cells, wells, droplets, emulsions, etc.).
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1, 17, 18, 28 and 34 is maintained under 35 U.S.C. 112(b) paragraph 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 “individual labeled nucleotides” such as recited in claim 1, line 5 because the as-filed Specification and original claims do not teach incorporating “individual labeled nucleotides” and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “the labeled and unlabeled pre-existing RNA” such as recited in claim 1, lines 6-8 and 10-11. There is insufficient antecedent basis for the term “the labeled and unlabeled pre-existing RNA” in the claim. The Examiner suggests that Applicant amend the claim to recite, for example, “subsets of nuclei or cells comprising unlabeled pre-existing RNA…to result in RNA comprising labeled RNA and unlabeled pre-existing RNA.”
Claim 1 is indefinite for the recitation of the term “present in indexed nuclei or cells” such as recited in claim 1, line 12 because processing (claim 1, line 10) generates RNA comprising the first compartment specific index sequence, such that it is unclear how “processing” results in indexed nucleic acids being present in “indexed nuclei or cells” since the nuclei and/or cells have not been indexed prior to “processing” and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “the other compartments” such as recited in claim 1, line 15. There is insufficient antecedent basis for the term “the other compartments” in the claim.
Claim 1 is indefinite for the recitation of the term “a second compartment specific sequence index sequence” such as recited in claim 1, lines 22-23 because the structure of a “second compartment specific sequence index sequence” is unclear including whether the sequence comprises two separate index sequences (e.g., a compartment specific index and an index sequence), one index sequence, or whether the term refers to something else and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “dual-indexed nuclei or cells comprising dual-indexed nucleic acids” such as recited in claim 1, lines 23-24 because claim 1, line 1 recites that the method is for “preparing indexed nucleic acids,” such that purpose of the method is unclear because the method is not recited to be directed to preparing “dual-indexed nucleic acids” and/or “preparing multi-indexed nucleic acids” and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “adding to the indexed nucleic acid comprises ligating a hairpin ligation duplex” such as recited in claim 1, lines 25-26 because claim 1, line 17-18 recite that “adding comprises ligation, primer extension, hybridization, amplification, or a combination thereof” wherein hybridization and ligation are different reactions, such that “adding” cannot instead comprise “ligating a hairpin ligation duplex,” while also comprising “hybridization” and, thus, the metes and bounds of the claim cannot be determined.
The rejection of claim 1 is maintained as being indefinite for the recitation of the term “ligating a hairpin ligation duplex to the indexed nucleic acids” such as recited in claim 1, lines 25-26 because the as-filed Specification, filed 12-20-2019 teaches that the “hairpin ligation duplex” is inserted into nucleic acid fragments (paragraphs [00127]; [00161]; and [00169]); however, instant claim 1 does not recite that the RNA within the nuclei or cells are fragmented. Claim 1 appears to be emitting an essential step and, thus, the metes and bounds of the claim cannot be determined.
Claims 17 and 18 are indefinite for the recitation of the term “the labeled nucleotides” such as recited in claim 17, line 2. There is insufficient antecedent basis for the term “the labeled nucleotides” in the claim because claim 1, line 5-6 recites the term “individual labeled nucleotides.” The Examiner suggests that Applicant amend the claim to recite, for example, “wherein the individually labeled nucleotides comprise.”
Claim 17 is indefinite for the recitation of the term “a nucleotide that can be modified by a chemical reaction” such as recited in claim 17, line 4 because the term “a nucleotide that can be modified by a chemical reaction” encompasses every RNA nucleotide (e.g., all RNA nucleotides can be modified via a chemical reaction) as evidenced by Ontiveros (Abstract), such that it is unclear what labeled nucleotides are encompassed by the term and, thus, the metes and bounds of the claim cannot be determined.
Claim 18 is indefinite for the recitation of the term “more than one of the labeled nucleotides is incorporated into the RNA as RNA is synthesized” such as recited in claim 18, lines 1-2 because claim 18 depends from claim 1 and 17, wherein claim 1, lines 5-6 recites that “individual labeled nucleotides” are incorporated into RNA as RNA is synthesized, such that claim 1 already recites that more than one individual labeled nucleotide is incorporated into RNA and, thus, the metes and bounds of the claim cannot be determined.
Claims 28 and 32 are indefinite insofar as they ultimately depend from instant claim 1.
Response to Arguments
Applicant’s arguments filed February 4, 2026 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) Figure 4A of the application shows indexed reverse transcription of RNA present in mouse embryo cells followed by indexed hairpin ligation, such that a person of ordinary skill would recognize that the term defines the metes and bounds of the claim (Applicant Remarks, pg. 11, second full paragraph)
Regarding (a), regarding the term “ligating a hairpin ligation duplex to the indexed nucleic acids” as recited in claim 1, although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26USPQ2d 1057 (Fed. Cir. 1993). The as-filed Specification teaches that ‘ligating a hairpin ligation duplex’ is carried out on fragmented nucleic acids, wherein extraction is known to cause nucleic acid fragmentation during nuclei isolation. Additionally, regarding Figure 4A, the as-filed Specification teaches that the FACS sorting step is omitted, and sonication and filtration steps are added (paragraph [00321]). Moreover, there is no recitation that hairpin ligation is carried out on full-length RNA; and/or that the indexed nucleic acids encompassed by claim 1 will be produced using full-length RNA. Thus, the rejection is maintained.
Claim Rejections - 35 USC § 112(d)
The rejection of claims 18 is maintained under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 18 recites (in part) “wherein more than one of the labeled nucleotides is incorporated into the RNA as the RNA is synthesized” in lines 1-2. Claim 18 depends from instant claims 1 and 17, wherein claims 1, lines 5-6 already recites that ‘individual labeled nucleotides are incorporated into RNA as RNA is synthesized’ (e.g., that more than one individual labeled nucleotide is incorporated as the RNA is synthesized). Thus, claim 18 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 103
The rejection of claims 1, 17, 18, 28 and 34 is maintained under 35 U.S.C. 103 as being unpatentable over unpatentable Seelig et al. (hereinafter “Seelig”) (US Patent No. 10900065, issued January 26, 2021; effective filing date November 13, 2015; of record) in view of New England Biolabs (Instruction Manual, 2016, 1-25); as evidenced by NEBNext (Illumina, 2025, 1-5; of record); and Boone et. al. (hereinafter “Boone”) (Nucleic Acids Research, March 2018, 46(6), 2701-2721; of record).
Regarding claims 1 (in part), 17, 18, 28 and 34, Seelig teaches methods of uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue, wherein the molecules to be labeled can include, but are not limited to, RNAs, DNAs, cDNAs, proteins, peptides and/or antigens, wherein Figure 1 depicts ligation of nucleic acid tags to form a label or a barcode (interpreting nucleotides that make up RNA and that can be modified by chemical reaction as incorporating individual labeled nucleotides into RNA within a cell or nuclei as it is synthesized; including by ligation, claim 1) (Abstract; and col 1, lines 60-61; and Figure 1). Seelig teaches that next generation sequencing (NGS) can be used to identify and/or quantify individual transcripts from a sample of cells (col 1, lines 32-34). Seelig teaches that in an aspect of the disclosure relates to methods of labeling nucleic acids in a first cell, wherein the method can comprise: (a) generating complementary DNAs (cDNAs) within a plurality of cells comprising the first cell by reverse transcribing RNAs using a reverse transcription primer comprising a 5' overhang sequence; (b) dividing the plurality of cells into a number (n) of aliquots; (c) providing a plurality of nucleic acid tags to each of then aliquots, wherein each labeling sequence of the plurality of nucleic acid tags provided into a given aliquot is the same, and wherein a different labeling sequence is provided into each of the n aliquots; (d) binding at least one of the cDNAs in each of the n aliquots to the nucleic acid tags; (e) combining then aliquots; and (f) repeating steps (b), (c), (d), and (e) with the combined aliquot (interpreting reverse transcription to include labeling nucleotides that were incorporated during RNA synthesis; interpreting dividing aliquots as disturbing comprising dilution; generating indexed nuclei or cells; compartment specific index; the index in other compartments is different; pooling the indexed nuclei or cells in step (e) to carry out steps 1(a)-1(c); repeating combining, providing tags in each aliquot, binding tags, and combining aliquots as encompassing distributing into a second compartment comprising indexed nucleic acids; indexing again; pooling the indexed nuclei nucleic acids in steps 1(d), 1(e) and 1(f); interpreting that different labeling sequence is provided into each of the n aliquots as nucleotide labels are different for different compartments; obtaining dual indexed nuclei or cells; and the nucleotide label comprises a nucleotide analog, claims 1, 17, 18, 28 and 34) (col 3, lines 11-26). Seelig teaches that a method of the disclosure can be useful in assessing, analyzing, or studying the transcriptome including different RNA species transcribed from the genome of a given cell of one or more individual cells (col 4, lines 7-11). Seelig teaches that cells in a single sample can be separated into a number of different reaction vessels, such as four 1.5 ml centrifuge tubes, a plurality of wells of a 96-well plate, or another suitable number and type of reaction vessels (interpreting wells as a plurality of first compartments, claims 1 and 34) (col 4, lines 25-29). Seelig teaches that the methods of labeling nucleic acids in the first cell may comprise ligating at least two of the nucleic acid tags that are bound to the cDNAs (interpreted as incorporating individual labeled nucleotides into RNA in a cell or nuclei; including chemical reactions such as reverse transcription-ligation, claims 1 and 17) (col 5, lines 27-29). Seelig teaches that Figure 2 illustrates the formation of cDNA by in situ reverse transcription, wherein: (i) Panel A depicts a cell that is fixed and permeabilized; (ii) Panel B depicts addition of a poly(T) primer, which can template the reverse transcription of polyadenylated transcripts (interpreted as reverse transcriptase and a poly(T) nucleotide sequence as a first primer and as a label); (iii) Panel C depicts addition of a random hexamer, which can template the reverse transcription of substantially any transcript (interpreting a hexamer as a compartment specific index); (iv) Panel D depicts the addition of a primer that is designed to target a specific transcript, such that only a subset of transcripts can be amplified (interpreted as adding a second primer; and a transcript-specific primer), wherein the reverse transcription primer can be configured to reverse transcribe predetermined RNAs (e.g., a transcript-specific primer); and (v) Panel E depicts the cell of Panel A after reverse transcription, illustrating a cDNA hybridized to an RNA, wherein reverse transcription can be conducted or performed on the plurality of cells (interpreted as reverse transcriptase; interpreting a poly(T) nucleotide sequence as a primer and a poly-T sequence; labeling RNA as it is synthesized in the cell; first primers; second primers; and interpreting random hexamers as a compartment specific index, claims 1-5) (col 7, lines 1-14; and Figure 2). Figure 2 is shown below:
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Figure 2
Seelig teaches that methods can comprise: (a) binding an adapter sequence, or universal adapter, to molecules within the plurality of cells (interpreted as incorporating a label into RNA as it is synthesized in the subsets of cells; indexed RNA and pre-existing RNA nucleic acids; and ligation); (b) dividing the plurality of cells into at least two primary aliquots, wherein the at least two primary aliquots comprise at least a first primary aliquot and a second primary aliquot (interpreting aliquots as subsets; interpreting an adapter as an label; and interpreting binding an adaptor sequence as incorporating a label into RNA as it is synthesized in the subsets of cells); (c) providing primary nucleic acid tags to the at least two primary aliquots, wherein the primary nucleic acid tags provided to the first primary aliquot are different from the primary nucleic acid tags provided to the second primary aliquot (interpreting tags as indexes, and aliquots as subsets; different tags as compartment specific indexes; and generating labeled RNA and unlabeled pre-existing RNA); (d) binding the adapter sequences within each of the at least two primary aliquots with the provided primary nucleic acid tags; (e) combining the at least two primary aliquots (interpreted as combining the indexed nuclei or cells to generate a pool of nucleic or cells); (f) dividing the combined primary aliquots into at least two secondary aliquots, the at least two secondary aliquots comprising at least a first secondary aliquot and a second secondary aliquot; (g) providing secondary nucleic acid tags to the at least two secondary aliquots, wherein the secondary nucleic acid tags provided to the first secondary aliquot are different from the secondary nucleic acid tags provided to the second secondary aliquot; and (h) binding the molecules within each of the at least two secondary aliquots with the provided secondary nucleic acid tags, wherein the method can further comprise steps (i), such that steps (e), (f), (g), (h) are repeated with subsequent aliquots for a suitable number of times; and wherein the molecules such as RNA, cDNA, DNA, proteins, peptides and/or antigens can be disposed within the cell or within the plurality of cells (interpreted as providing cells/nuclei; incorporating a label into RNA as it is synthesized in the subsets; processing to generate indexed nuclei or cells; labeled RNA and unlabeled pre-existing RNA; combining indexed nuclei or cells; interpreting combining as pooling; interpreting repeating as distributing a second subset, etc.; and adapter sequences are nucleotides that can be modified by chemical reaction, or a nucleotide analog; and including a third plurality of compartments, wherein adding comprises ligation and/or primer extension, claims 1, 17, 18 and 28) (col 7, lines 32-66; and col 8, lines 19-22). Seelig teaches that subsequent to (b), coupling an adapter sequence to each of the cDNA molecules by integrating the adapter sequence into the cDNA molecules using a transposase and releasing the transposase to expose the adapter sequence (interpreted as adding comprises transposition, claim 27) (col 31, claim 9).
Seelig teaches that adapter sequences can be integrated (e.g., directly integrated) into genomic DNA using Tn5 transposase and the transposase can be released to expose the adapter sequences by addition of sodium dodecyl sulfate (SDS), such that other transposases and methods of integrating the adapter sequences into genomic DNA are also within the scope of this disclosure (interpreted as adding comprises transposition, claim 27) (col 9, lines 34-40). Seelig teaches that methods related to binding or coupling an adapter sequence to an RNA can be used, for example, in RNA transcriptome sequencing, ribosome profiling, small RNA sequencing, non-coding RNA sequencing, and/or RNA structure profiling, including wherein the plurality of cells can be fixed and/or permeabilized; the 5' end of a single-stranded adapter sequence can be ligated to the 3' end of an RNA (see Figures 3A and 3B) (interpreted as a sequencing library; and ligation, claims 1 and 34) (col 8, lines 32-39). Seelig teaches that third round barcode oligos can include a domain corresponding to part of the Illumina TruSeq adapter; and that following PCR, the full Illumina adapter sequences can be introduced (interpreted as encompassing dual-index adapters, claim 1) (col 15, lines 38-40; and col 19, lines 25-26). Seelig teaches that following PCR, full Illumina adapter sequences can be introduced, wherein BC_0063 includes a flow cell binding sequence and the TruSeq multiplex read 2 and index binding sequence, wherein there is a region for the sample index (interpreted as adaptors comprising an index sequence, claim 1) (col 19, lines 25-26 and 31-33). Seelig teaches that Figure 11 depicts an annealed, first-round barcode oligo; Figure 12 depicts an annealed second-round barcode oligo; and Figure 13 depicts an annealed, third-round barcode oligo, which can be synthesized with unique molecular identifiers and can include a domain corresponding to part of the ILLUMINA TruSeq adapter (interpreted as adaptors comprising a barcode sequence, claim 1) (col 15, lines 41-43 and 62-63; col 15, lines 16-18 and 33-40; and Figures 11-13).
Seelig does not specifically exemplify a hairpin ligation duplex (claim 1, in part).
Regarding claim 1 (in part), New England Biolabs teaches that the NEBNext Multiplex Oligos for Illumina (96 Index Primers) contains adaptors and primers that are ideally suited for multiplex sample preparation for next-generation sequencing on the Illumina platform (pg. 2, Applications, first full paragraph). New England Biolabs teaches that NEBNext Adaptors are designed for use in library prep for DNA, ChIP DNA and RNA (but not Small RNA), which enables high-efficiency adaptor ligation and high library yields, with minimized adaptor-dimer formation, wherein incorporating a novel hairpin loop structure, the NEBNext Adaptor ligates with increased efficiency to end-repaired, dA-tailed DNA, wherein the loop contains a uracil (U), which is removed by treatment with USER Enzyme (a combination of UDG and Endo VIII), to open up the loop and make it available as a substrate for PCR, such that during PCR, barcodes can be incorporated by use of the NEBNext index primers, thereby enabling multiplexing; and that the 96 8-base index primers included in this kit are pre-mixed with the universal primer and are packaged in a single-use 96-well plate with a pierceable foil seal, such that NEBNext Oligos can be used with NEBNext products, and with other standard Illumina-compatible library preparation protocols (pg. 2, Workflow Overview, last full paragraph), where it is known that unique-dual indices include 96 pre-mixed unique pairs of index primers or NEBNext multiplex oligos, which provide increased sample identification specificity, enables complete filtering of index-hoped reads, highly efficient adaptor ligation, minimizes adapter-dimer formation, includes index primers for library multiplexing, and can be combined with sets of barcodes as evidenced by NEBNext (pg. 1, first and second paragraphs); and where it is known that for Y-shaped or hairpin adaptors are efficient, and the formation of side products is strongly reduced, such that they can be used in the clever ‘tagmentation’ approach, which used hyperactive Tn5 transposase for simultaneous DNA fragmentation and tag (or adaptor) insertion as evidenced by Boone (pg. 2709, col 1, last partial paragraph; and col 2, first partial paragraph). New England Biolabs teaches in Figure 1 an NEBNext adaptor comprising a barcode, wherein Figure 1 (in part) is shown below:
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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 using hairpin adaptors, index primers and/or barcodes as exemplified by New England Biolabs, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of uniquely labeling and/or barcoding molecules including RNA as disclosed by Seelig to include the incorporation of adaptors, index primers and/or barcodes as taught by New England Biolabs with a reasonable expectation of success in uniquely labeling RNAs, cDNAs, DNAs, proteins, peptides, and/or antigens within a cell, plurality of cells and/or tissues; for multiplex sample preparation for next-generation sequencing on the Illumina platform, wherein the NEBNext hairpin loop adaptors ligate with high-efficiency and high library yields, while minimizing adaptor-dimer formation including within separate reaction vessels; and/or for simultaneous nucleic acid fragmentation, tag insertion and/or adaptor insertion using hyperactive Tn5 transposase.
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.
Response to Arguments
Applicant’s arguments filed February 4, 2026 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) claim 1 has been amended to recite “incorporating individual labeled nucleotides into RNA as RNA is synthesized,” where incorporation of a label occurs during synthesis of an RNA molecules, which is not taught by Seelig (Applicant Remarks, pg. 13, first full paragraph through pg. 14, second full paragraph); and (b) because none of the cited art teaches or suggests "incorporating individual labeled nucleotides into RNA as RNA is synthesized," even if the skilled person combined or modified the cited art, the resulting combination or modification could not include all elements of the claimed invention (Applicant Remarks, pg. 14, last partial paragraph through pg. 15, first full paragraph).
Regarding (a) and (b), it is noted that none of the references has to teach each and every claim limitation. If they did, this would have been anticipation and not an obviousness-type rejection. One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). As noted in MPEP 2112.01(I),
where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990) (underline added).
Applicant’s assertion that Seelig does not teach “incorporating individual labeled nucleotides into RNA as RNA is synthesized,” is not found persuasive. As recited in dependent claim 17 (and, as taught in the as-filed Specification at paragraph [00115]), a label is incorporated into the nucleic acids as they are synthesized, where the method includes incorporation of a nucleotide that can be modified with a chemical reaction. Consequently, the RNA as taught by Seelig inherently comprises nucleotides incorporated during RNA synthesis because all of the incorporated nucleotides can be modified by a chemical reaction (for example, see Ontiveros as discussed supra). It is noted that chemical reactions can include, for example: ligation, transposition, reverse transcription, PCR, etc. Thus, Seelig clearly teaches individual labeled nucleotides that are incorporated during RNA synthesis in cells or nuclei. For example -
Seelig teaches:
Methods of uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue, wherein the molecules include RNAs, wherein Figure 1 depicts ligation of nucleic acid tags to form a label or a barcode (interpreting the incorporation of nucleotides into RNA as it is being synthesized as incorporating individual labeled nucleotides into RNA within a cell or nuclei, wherein the nucleotides can be modified by chemical reaction including by ligation, claim 1) (Abstract; col 1, lines 60-61; col 2, lines 54-60; and Figure 1).
The methods of labeling nucleic acids in the first cell can comprise ligating at least two of the nucleic acid tags that are bound to the cDNAs (interpreted as incorporating individual labeled nucleotides into RNA within a cell or nuclei; and nucleotides modified by a chemical reaction including by reverse transcription-ligation, claim 1) (col 5, lines 27-29).
Wherein each labeling sequence of the plurality of nucleic acid tags provided into a given aliquot is the same; and a different labelling sequence is provided into each of the n aliquots (interpreted as each compartment-specific index is different from the others, claim 1) (col 3, lines 18-23).
The combined references of Seelig and New England Biolabs teach all of the limitations of the claims. Thus, the claims remain rejected.
The rejection of claims 1, 17, 18, 28 and 34 is maintained under 35 U.S.C. 103 as being unpatentable over unpatentable Cao et al. (hereinafter “Cao”) (bioRxiv Preprint, Feb 2017, 1-35; of record) in view of New England Biolabs (Instruction Manual, 2016, 1-25); as evidenced by NEBNext (Illumina, 2025, 1-5); and Boone et. al. (hereinafter “Boone”) (Nucleic Acids Research, March 2018, 46(6), 2701-2721).
Regarding claims 1 (in part), 17, 18, 28 and 34, Cao teaches that single cell RNA sequencing has emerged as a powerful strategy for resolving such heterogeneity (Abstract, lines 1-3). Cao teaches a combinatorial indexing strategy to profile the transcriptomes of large numbers of single cells or single nuclei without requiring the physical isolation of each cell (Single cell Combinatorial Indexing RNA-seq or sci-RNA-seq), wherein sci-RNA-seq can be used to efficiently profile the transcriptomes of tens-of-thousands of single cells per experiment, and demonstrate that we can stratify cell types from these data; and that key advantages of sci-RNA-seq over contemporary alternatives such as droplet-based single cell RNA-seq include sublinear cost scaling, a reliance on widely available reagents and equipment, the ability to concurrently process many samples within a single workflow, compatibility with methanol fixation of cells, cell capture based on DNA content rather than cell size, and the flexibility to profile either cells or nuclei, such that sci-RNA-seq profiled the transcriptomes of 42,035 single cells from C. elegans at the L2 stage, effectively 50-fold “shotgun cellular coverage” of the somatic cell composition of this organism at this stage, and identified 27 distinct cell types, including rare cell types (interpreted as a cell or nuclei, claim 1) (Abstract, lines 5-17). Cao teaches that methods for single cell RNA-seq universally rely on the isolation of individual cells within physical compartments, whether by pipetting, sorting, microfluidics-based deposition to microwells, or by dilution to emulsion-based droplets (interpreted as providing subsets of RNA in compartments, wherein the RNA comprises individual labeled nucleotides (e.g., nucleotides that can be modified by chemical reaction; and dilution, claims 1 and 28) (pg. 2, last full paragraph). Cao teaches that the expression levels of mRNA species are linked to cellular function and therefore can be used to classify cell types in heterogeneous samples; as well as, to order cell states; and that although methods for single-cell RNA sequencing (RNA seq) have proliferated, they rely on the isolation of individual cells within physical compartments, such that preparing single cell RNA-seq libraries with these methods can be expensive, the cost scaling linearly with the numbers of cells processed (pg. 3, second full paragraph). Cao teaches the development of combinatorial indexing that uses split-pool barcoding of nucleic acids to uniquely label a large number of single molecules or single cells, such that single-cell combinatorial indexing (“sci”) can be used to profile chromatin accessibility (sci-ATAC-seq), genome sequence (sci-DNA-seq), genome-wide chromosome conformation (sci-Hi-C), and DNA methylation (sci-MET) in large numbers of single cells (interpreting DNA methylation as labeling with an identifiable mutation; and indexing with different labels, claim 1) (pg. 3, third full paragraph). Cao teaches sci-RNA-seq for profiling the transcriptomes of large numbers of single cells or nuclei per experiment, wherein sci-RNA-seq is applied to profile the transcriptomes of ~16,000 mammalian cells in a single experiment, and show that synthetic mixtures of inter- or intraspecies cell types can separated (interpreted as cells or nucleic, claim 1) (pg. 4, last full paragraph). Cao teaches that sci-RNA-seq comprises the steps illustrated in Figure 1A: (i) cells are fixed and permeabilized with methanol, then distributed across 96- or 384-well pates (interpreted as a plurality of cells; distributing subsets of cells in compartments; and RNA, claims 1 and 34); (ii) a first molecular index is introduced to the mRNA of cells within each well (interpreted as labeling RNA), with in situ reverse transcription (RT) incorporating the barcode-bearing, well-specific polyT primer containing unique molecular identifiers (UMIs) (interpreted as providing subsets of RNA in compartments, wherein the RNA comprises individual labeled nucleotides/nucleotides that can be modified by chemical reaction into RNA as it is synthesized in nuclei or cells; barcodes and UMIs as labeling nuclei or cells during RNA synthesis; first primer and second primer; polyT sequence; and a barcode or UMI as a compartment-specific index, claims 1); (iii) all cells are pooled and redistributed by fluorescence-activated cell sorting (FACS) to 96- or 384-well plates in limiting numbers such as 10 to 100 cells per well, wherein cells are gated on the basis of DAPI staining to discriminate single cells from doublets during sorting (interpreted as a plurality of single cells; wells; transcriptase; and pooling, claims 1 and 34); (iv) second-strand synthesis, transposition with transposon 5 (Tn5) transposase, lysis, and polymerase chain reaction (PCR) amplification are performed, wherein the PCR amplicons preferentially capture the 3’ ends of transcripts, and introduce a second barcode that is specific to each well of the PCR plate (interpreted as identifying the origin of at least one single cells in the combined labeled sample); and (v) amplicons are pooled and subjected to massively parallel sequencing, resulting in 3’-tag digital gene expression profiles, with each read associated with two barcodes corresponding to the first and second rounds of cellular indexing (FIG. 1B), such that most cells pass through a unique combination of wells, resulting in a unique combination of barcodes for each cell that tags its transcripts (interpreting barcoding and UMI as labeling RNA; cellular index; subsets of cells or nuclei in a plurality of compartments; index sequences; processing to result in compartment-specific barcodes; cDNA as double stranded nucleic acid; barcodes as a nucleotide label; a plurality of wells; and first and second barcoded primers, claims 1-5, 16 and 34) (pg. 4, first and second full paragraphs; and pg. 25, Figure 1). Figures 1A and 1B are shown below:
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Cao teaches that sci-RNA-seq was performed on mammalian cells, optimizing the protocol and reaction conditions, demonstrating scalability with 384 x 384-well sci-RNA-seq using pure populations of either human [human embryonic kidney 293T (HEK293T) and/or HeLa S3] or mouse (NIH/3T3) cells, and the other half contained mixed human and mouse cells (table S1), such that 15,997 single-cell transcriptomes were recovered and readily assigned cells and human or mouse (Fig. 1C) (interpreted as mammalian cells; and interpreting wells as compartments, claims 1 and 34) (pg. 4, last full paragraph; and last partial paragraph; and pg. 5, first partial paragraph). Cao teaches uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, and read 2 end coordinate (i.e. reads with identical UMI, RT index, and tagmentation site were considered duplicates); and mixed-species experiment, the percentage of uniquely mapping reads for genomes of each species was calculated, wherein cells with over 85% of UMIs assigned to one species were regarded as species-specific cells, with the remaining cells classified as mixed cells, such that the collision rate was calculated as twice the ratio of mixed cells (interpreted as reverse transcription; UMI, insertions and deletions interpreted to encompass a nucleotide analog or a mutagenic nucleotide; labels incorporated into newly synthesized RNA nucleic acids; ratio of nucleotide labels are different for different compartments, claims 17-19) (pg. 12, second full paragraph). Cao teaches second strand synthesis followed by tagmentation; and that tagmented cDNA was purified; and PCR, purification and quantification were performed (pg. 14, first partial paragraph). Cao teaches that the PCR primers target the barcoded polyT primer on one end, and the Tn5 adaptor insertion on the other end, wherein these primer introduce a second barcode, specific to each well of the PCR plate (interpreted as adaptors comprising barcodes, claim 1) (pg. 3, last partial paragraph, lines 8-9; and pg. 4, first partial paragraph). Cao teaches in Figure 1 that the sci-RNA-seq workflow includes tagmentation and PCR with well-specific barcode combinations (second round of barcoding), wherein the resulting PCR amplicons are pooled and deep sequenced to generate single cell 3' digital gene expression profiles; and the sci-RNA-seq library amplicons include lllumina adapters, PCR indices (i5 and i7), a reverse transcription barcode and UMI, in addition to the cDNA fragment to be sequenced (interpreting Illumina adaptors comprising indices, claim 1) (pg. 4, Figure 1).
Cao et al. do not specifically exemplify a hairpin ligation duplex (claim 1, in part).
Regarding claim 1 (in part), New England Biolabs teaches that the NEBNext Multiplex Oligos for Illumina (96 Index Primers) contains adaptors and primers that are ideally suited for multiplex sample preparation for next-generation sequencing on the Illumina platform (pg. 2, Applications, first full paragraph). New England Biolabs teaches that NEBNext Adaptors are designed for use in library prep for DNA, ChIP DNA and RNA (but not Small RNA), which enables high-efficiency adaptor ligation and high library yields, with minimized adaptor-dimer formation, wherein incorporating a novel hairpin loop structure, the NEBNext Adaptor ligates with increased efficiency to end-repaired, dA-tailed DNA, wherein the loop contains a uracil (U), which is removed by treatment with USER Enzyme (a combination of UDG and Endo VIII), to open up the loop and make it available as a substrate for PCR, such that during PCR, barcodes can be incorporated by use of the NEBNext index primers, thereby enabling multiplexing; and that the 96 8-base index primers included in this kit are pre-mixed with the universal primer and are packaged in a single-use 96-well plate with a pierceable foil seal, such that NEBNext Oligos can be used with NEBNext products, and with other standard Illumina-compatible library preparation protocols (pg. 2, Workflow Overview, last full paragraph), where it is known that unique-dual indices include 96 pre-mixed unique pairs of index primers or NEBNext multiplex oligos, which provide increased sample identification specificity, enables complete filtering of index-hoped reads, highly efficient adaptor ligation, minimizes adapter-dimer formation, includes index primers for library multiplexing, and can be combined with sets of barcodes as evidenced by NEBNext (pg. 1, first and second paragraphs); and where it is known that for Y-shaped or hairpin adaptors are efficient, and the formation of side products is strongly reduced, such that they can be used in the clever ‘tagmentation’ approach, which used hyperactive Tn5 transposase for simultaneous DNA fragmentation and tag (or adaptor) insertion as evidenced by Boone (pg. 2709, col 1, last partial paragraph; and col 2, first partial paragraph). New England Biolabs teaches in Figure 1 an NEBNext adaptor comprising a barcode, wherein Figure 1 (in part) is shown below:
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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 using hairpin adaptors, index primers and/or barcodes as exemplified by New England Biolabs, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method for sci-RNA-seq as disclosed by Cao et al. to include the incorporation of adaptors, index primers and/or barcodes as taught by New England Biolabs with a reasonable expectation of success in combinatorially labeling a large number of single molecules or single cells without requiring the physical isolation of each molecule or cell; for profiling the transcriptomes of a large number of single cell or nuclei per experiment including the identification of distinct cell types; for efficient multiplex sample preparation for next-generation sequencing on the Illumina platform; and/or for simultaneous nucleic acid fragmentation, tag insertion and/or adaptor insertion using hyperactive Tn5 transposase.
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.
Response to Arguments
Applicant’s arguments filed February 4, 2026 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) Cao teaches labeling, but like Seelig, the labeling taught by Cao is combinatorial indexing to add a unique molecular index of nucleic acid sequences to the RNA molecules in cells; and Cao's addition of unique molecular index of nucleic acid sequences to the RNA molecules in cells is not "incorporating individual labeled nucleotides into RNA as RNA is synthesized" (Applicant Remarks, pg. 15, last full paragraph through pg. 16, first full paragraph).
Regarding (a), please see the discussion supra regarding the Examiner’s response to Applicant’s arguments. Applicant’s assertion that Cao does not teach incorporating individual labeled nucleotides into RNA as recited in instant claim 1, is not found persuasive. As noted supra, instant claim 1 recites that incorporating individual labeled nucleotides into RNA as RNA is synthesized; while claim 17 recites that labeled nucleotides include nucleotides that can be modified by a chemical reaction. Thus, the RNA taught by Cao inherently comprises nucleotides incorporated into RNA during RNA synthesis, wherein the nucleotides can be modified by a chemical reaction. To that end -
Cao teaches:
A first molecular index is introduced to the mRNA of cells within each well (interpreted as labeling RNA), with in situ reverse transcription (RT) incorporating the barcode-bearing, well-specific polyT primer containing unique molecular identifiers (UMIs) (interpreted as providing subsets of RNA in compartments, wherein the RNA comprises individual labeled nucleotides/nucleotides that can be modified by chemical reaction into RNA as it is synthesized in nuclei or cells, claim 1) (pg. 3, last partial paragraph).
Cellular indexing (Figure 1B), such that most cells pass through a unique combination of wells, resulting in a unique combination of barcodes for each cell that tags its transcripts (interpreted as providing subsets of RNA in compartments, wherein the RNA comprises individual labeled nucleotides/nucleotides that can be modified by chemical reaction into RNA as it is synthesized in nuclei or cells, claims 1 and 17) (pg. 4, first and second full paragraphs; and Figure 1).
The combined references of Cao and New England Biolabs teach all of the limitations of the claims. Thus, the claims remain rejected.
New Objections/Rejections
Notice of Non-Compliant Amendment (37 CFR 1.121)
The amendment to the claims filed on November 17, 2025 does not comply with the requirements of 37 CFR 1.121(c) because the status identifier and text of claim 47 is not submitted with markings to indicate the changes that have been made relative to the immediate prior version of claims filed on August 1, 2025.
Amendments to the claims filed on or after July 30, 2003 comply with 37 CFR 1.121(c), which states:
(c) Claims - Amendments to a claim must be made by rewriting the entire claim with all changes (e.g., additions and deletions) as indicated in this subsection, except when the claim is being canceled. Each amendment document that includes a change to an existing claim, cancellation of an existing claim or addition of a new claim, must include a complete listing of all claims ever presented, including the text of all pending and withdrawn claims, in the application. The claim listing, including the text of the claims, in the amendment document will serve to replace all prior versions of the claims, in the application. In the claim listing, the status of every claim must be indicated after its claim number by using one of the following identifiers in a parenthetical expression: (Original), (Currently amended), (Canceled), (Withdrawn), (Previously presented), (New), and (Not entered).
Specifically, the amendments to the claims filed February 4, 2026 include amendments to the claims that do not recite proper status identifiers. For example, claims 9, 22, 36, 39 and 40 recite the status identifier “(Withdrawn-Previously Presented).”
To be fully responsible, Applicant is required to comply with the Notice of Non-Compliant Amendment (37 CFR 1.121). In the interests of compact prosecution, an action on the merits has been prepared. However, future amendments must comply with 37 CFR 1.121(c) in order to avoid a notice of non-compliant amendment.
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, 17, 18, 28 and 34 are rejected under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Cao et al. (hereinafter “Cao”) (Seattle Organism Molecular Atlases, 2018, 1-9).
Regarding claims 1, 17, 18, 28 and 34, Cao teaches a workflow comprising: Steps (1)-(4): nuclei extraction from tissue, nuclei fixation by paraformaldehyde, permeabilization, sonication and filtering, indexed reverse transcription, pooling, and redistributing:
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(5) Indexed hairpin ligation, pool and redistribute:
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(6) Second strand synthesis, tagmentation, purification, USER treatment, indexed PCR:
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; and
(7) Library purification and sequencing (interpreted as including hairpin ligation duplex, claim 1) (pg. 1, entire page). Cao teaches Step 5: Reverse Transcription, wherein each well of 4 x 96 well plate comprises 80,0000 nuclei in nuclei buffer, dNTP, and indexed oligo-dT, incubate, prepare the reverse transcription reaction mix, start RT reaction, after the reaction add NBB into each well, pool the nuclei from all wells, and pellet the nuclei (interpreted as providing compartments; and incorporating individual labeled nucleotides into RNA as RNA is synthesized in the subset of nuclei; including wells, claims 1, 17, 18 and 34) (pg. 5, Step 5; and pg. 6, Step 5). Cao teaches Step 6: Ligation, wherein cells are resuspended in NSB in the wells of 4 x 96 well plates, indexed ligation primers are added into each well, ligate, pool the nuclei from all wells, add another NBB to the nuclei mix, pellet the nuclei, dump the supernatant, resuspend the cells in NBB, filter nuclei, count the nuclei concentration with hemacytometer, distribute the diluted nuclei (in NBB) into several 96 well plates (interpreted as processing the RNA; first compartment specific index; adding comprising ligation; combining and pooling; distributing subsets of pooled indexed nuclei or cells into second compartments; adding indexed nucleic acids by ligating a hairpin ligation duplex; including wells; combining the dual indexed nuclei or cells; and dilution, claims 1 and 28) (pg. 6, Step 6; and pg. 7, Step 6).
Cao meets all the limitations of the claims and, therefore, anticipates the claimed invention.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 17, 18, 28 and 34 are rejected on the ground of nonstatutory double patenting as being unpatentable over: Claims 1-24 of U.S. Patent No. 11981891, which recites a method comprising: providing a plurality of isolated single nuclei or cells; distributing the isolated single nuclei or cells into a first plurality of compartments; processing each subset of isolated single nuclei or cells; combining the indexed nuclei or cells to generate pooled nuclei or cells; distributing the pooled indexed nuclei or cells; processing each subset of indexed nuclei or cells to generate dual-indexed nuclei or cells; combining the dual indexed nuclei or cells; distributing the pooled dual indexed nuclei or cells; processing each subset of dual indexed nuclei or cells; and combining the triple-indexed nucleic acids (claim 1).
Although the claims at issue are not identical, they are not patentably distinct from each other because the pending claims of US Patents 11981891 encompass the steps of providing, incorporating, processing, combining, distributing, and combining the dual indexed nuclei or cells as recited in the claims of US16625100.
Conclusion
Claims 1, 17, 18, 28 and 34 are rejected.
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/AMY M BUNKER/Primary Examiner, Art Unit 1684