DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
Claims 25-48 (6/16/2022) are under examination.
Priority
Claims 25-48 receive a priority date of 12/16/2019, the filing date of Italian Republic Provisional IT102019000024159.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
The Information Disclosure Statements from 6/16/2022, 9/23/2022, 4/25/2025 and 6/26/2025 are considered.
Drawings
Nucleotide and/or Amino Acid Sequence Disclosures
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings (Figures 10 and 16) are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities (see MPEP § 608.01):
The use of the term “Agilent Bioanalyzer” (p.19, 50), “Perkin Elmer LabChip” (p.19), “Kapa Biosystems” (p. 19, 50), “Illumina” (p. 20 and used throughout the Specification), “IonTorrent” (p. 20), “ThermoFisher Scientific” (p. 20), “Pacific Biosciences” (p.20) “Oxford Nanopore” (p. 20), “Miltenyi Biotec” (p. 45), “Beckman-Coulter” (p. 50) and “Menarini Silicon Biosystems” (p. 52-53) is a trade name or mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore, the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (p. 2, 3, 4, 5, 6, 7, and 26 in reference to links for citations used). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Rejections - 35 USC § 112
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 25-48 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 25 is rejected. Claim 25 recites the limitation "the number" in step h. There is insufficient antecedent basis for this limitation in the claim.
Claims 26-48 are included in this rejection due to their dependency on claim 25.
Claim 27 is further rejected. Claim 27 recites the limitation "the range" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 37 is further rejected. Claim 37 recites the limitation "the extension" in step c. There is insufficient antecedent basis for this limitation in the claim.
Claim 40 is further rejected. Claim 40 recites the limitation "the sequence reverse complementary" in line 5. There is insufficient antecedent basis for this limitation in the claim.
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 (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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 25-42 and 44 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Belgrader et al. (US PGPub 2018/0179591 A1; published 6/28/2018).
Regarding claim 25, Belgrader teaches the need for methods, compositions and systems for analyzing genomic and proteomic information from individual cells or a small population of cells including, but not limited to, cancer cells, fetal cells, and immune cells involved in immune responses (Paragraph 5, lines 1-5). Further Belgrader teaches the amplification of the cell's nucleic acids is carried out until the barcoded overlapping fragments within the partition constitute at least 1× coverage of the particular portion or all of the cell's genome, at least 2×, at least 3×, at least 4×, at least 5×, at least 10×, at least 20×, at least 40× or more coverage of the genome or its relevant portion of interest and once the barcoded fragments are produced, they may be directly sequenced on an appropriate sequencing system, e.g., an Illumina Hiseq®, Miseq® or X10 system, or they may be subjected to additional processing, such as further amplification, attachment of other functional sequences, e.g., second sequencing primers, for reverse reads, sample index sequences, and the like (Paragraph 226, lines 1-10). Specifically, Belgrader teaches that the labelling agents may be coupled, through the coupling approaches as described herein, to a reporter oligonucleotide comprising a nucleic acid barcode sequence that permits identification of the labelling agent, as described herein and in some embodiments, the nucleic acid barcode sequence coupled to the labelling agent may comprise a unique molecular identifier (UMI) sequence segment (Paragraph 192, lines 1-20). Further, Belgrader teaches the inclusion of an identifier which may be an oligonucleotide comprising a nucleic acid barcode sequence or binding agent barcode sequence (Paragraph 332, lines 1-5). Belgrader also teaches that prior to co-partitioning, the cells may be incubated with the library of labelling agents, that may represent antibodies to a broad panel of different cell surface features, e.g., receptors, proteins, etc., and which include their associated reporter oligonucleotides where unbound labelling agents may be washed from the cells, and the cells may then be co-partitioned along with the barcode oligonucleotides described above and as a result, the partitions may include the cell or cells, as well as the bound labelling agents and their known, associated reporter oligonucleotides (Paragraph 232, lines 15-25). Belgrader additionally teaches that in some cases, the methods and compositions may be used for sequencing the genome and transcriptome from a single cell in parallel (Paragraph 348, lines 1-5).
Regarding claim 26, Belgrader teaches that the previously described method can be applied to the first amplification products and/or second amplification products, which may be subject to sequencing for sequence analysis (Paragraph 296, lines 15-20).
Regarding claim 27, Belgrader teaches that the previously described method includes a UMI identifying sequence that in some instances, in which the cell may be bound to at least about 5 different labelling agents, at least about 10 different labelling agents, at least about 50 different labelling agents or nucleotides (Paragraph 316m lines 10-15).
Regarding claims 28-31, Belgrader teaches that the previously described method includes a method for RNA expression analysis in individual cells using the methods described, where shown, at operation 602 a cell containing sample is sorted for viable cells, which are quantified and diluted for subsequent partitioning and the individual cells separately co-partitioned with gel beads or droplets bearing the barcoding oligonucleotides as described herein (Figure 6; Paragraph 257, lines 1-5).
Regarding claim 32, Belgrader teaches that the previously described method includes following the generation of amplification products, subsequent operations may include purification (e.g., via solid phase reversible immobilization (SPRI)), further processing (e.g., shearing, ligation of functional sequences, and subsequent amplification (e.g., via PCR)). These operations may occur in bulk (e.g., outside the partition) (Paragraph 296, lines 1-5).
Regarding claims 33-34, Belgrader teaches that the previously described method includes methods, compositions and systems for analyzing individual cells or a small population of cells, including the analysis and attribution of nucleic acids and proteins from and to these individual cells or cell populations (Paragraph 5, lines 1-5).
Regarding claims 35-39, Belgrader teaches that the previously described method includes a labelling agent (e.g., antibody) and 5221 is indirectly (e.g., via hybridization) coupled to an oligonucleotide 5222 comprising a barcode sequence 5223 that identifies the label agent 5221 and the labelling agent 5221 is directly (e.g., covalently bound, bound via a protein-protein interaction, such as with Protein G) coupled to a hybridization oligonucleotide 5232 that hybridizes with sequence 5231 of oligonucleotide 5222, where hybridization of oligonucleotide 5232 to oligonucleotide 5231 couples label agent 5221 to oligonucleotide 5222 (Figure 52B; Paragraph 367, lines 1-10). Further Belgrader teaches that the oligonucleotide 5222 also includes additional sequences (sequence 5224 comprising a reverse complement of a template switch oligo and sequence 5225 comprising a PCR handle) suitable for downstream reactions and FIG. 52B (panel II) also shows an additional oligonucleotide 5226 (e.g., which may have been released from a bead as described elsewhere herein) comprising a barcode sequence 5228, a UMI sequence 5229 and additional sequences (sequence 5227 comprising a sequencing read primer binding site ‘pR1’ and sequence 5220 comprising a template switch oligo) suitable for downstream reactions (Paragraph 367, lines 10-20).
Further, Belgrader teaches that the first individual barcode molecule or the second individual barcode molecule may be capable of coupling to the labelling agent via a third nucleic acid molecule coupled to the labelling agent and the third nucleic acid molecule can be coupled to the labelling agent and comprise a third nucleic acid barcode sequence that identifies the coupled labelling agent (and, thus, a cell surface feature to which the labelling agent is bound), where in a primer extension reaction, the first individual barcode molecule or the second individual barcode molecule can be extended such that a complement of the third barcode sequence is added to the first or second individual barcode molecule and during sequencing, the first or second barcode sequence of these molecules can identify the partition from which the molecules were synthesized and, where a partition comprises a single cell, the third barcode sequence can associate a particular cell surface feature with that single cell (Paragraph 384, lines 1-10).
Regarding claim 40, Belgrader teaches that the previously described method includes and also provided is at least one labelling agent, such as a library of labelling agents, capable of binding to a cell surface feature of interest, where a labelling agent may include, but is not limited to, an antibody, an antibody fragment, a cell surface receptor binding molecule, a receptor ligand, a small molecule, a bi-specific antibody, a bi-specific T-cell engager, a T-cell receptor engager, a B-cell receptor engager, a pro-body, an aptamer, a monobody, an affimer, a darpin, and a protein scaffold, or any combination thereof (Paragraph 317, lines 10-20).
Regarding claims 41-42, 44, Belgrader teaches the need for methods, compositions and systems for analyzing genomic and proteomic information from individual cells or a small population of cells including, but not limited to, cancer cells, fetal cells, and immune cells involved in immune responses (Paragraph 5, lines 1-5). Specifically, Belgrader teaches kits comprising antibody-binding proteins conjugated with reporter oligonucleotides, e.g., in well plates (Paragraph 324, lines 1-5). Further Belgrader teaches the amplification of the cell's nucleic acids is carried out until the barcoded overlapping fragments within the partition constitute at least 1× coverage of the particular portion or all of the cell's genome, at least 2×, at least 3×, at least 4×, at least 5×, at least 10×, at least 20×, at least 40× or more coverage of the genome or its relevant portion of interest and once the barcoded fragments are produced, they may be directly sequenced on an appropriate sequencing system, e.g., an Illumina Hiseq®, Miseq® or X10 system, or they may be subjected to additional processing, such as further amplification, attachment of other functional sequences, e.g., second sequencing primers, for reverse reads, sample index sequences, and the like (Paragraph 226, lines 1-10). Specifically, Belgrader teaches that the labelling agents may be coupled, through the coupling approaches as described herein, to a reporter oligonucleotide comprising a nucleic acid barcode sequence that permits identification of the labelling agent, as described herein and in some embodiments, the nucleic acid barcode sequence coupled to the labelling agent may comprise a unique molecular identifier (UMI) sequence segment (Paragraph 192, lines 1-20). Further, Belgrader teaches the inclusion of an identifier which may be an oligonucleotide comprising a nucleic acid barcode sequence or binding agent barcode sequence (Paragraph 332, lines 1-5). Belgrader also teaches that prior to co-partitioning, the cells may be incubated with the library of labelling agents, that may represent antibodies to a broad panel of different cell surface features, e.g., receptors, proteins, etc., and which include their associated reporter oligonucleotides where unbound labelling agents may be washed from the cells, and the cells may then be co-partitioned along with the barcode oligonucleotides described above and as a result, the partitions may include the cell or cells, as well as the bound labelling agents and their known, associated reporter oligonucleotides (Paragraph 232, lines 15-25). Belgrader additionally teaches that in some cases, the methods and compositions may be used for sequencing the genome and transcriptome from a single cell in parallel (Paragraph 348, lines 1-5).
Belgrader also teaches that the previously described method can be applied to the first amplification products and/or second amplification products, which may be subject to sequencing for sequence analysis (Paragraph 296, lines 15-20).
Belgrader teaches each and every limitation of claims 25-42 and 44, and therefore Belgrader anticipates claims 25-42 and 44.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 43, 45-48 is rejected under 35 U.S.C. 103 as being unpatentable over Belgrader et al. (US PGPub 2018/0179591 A1; published 6/28/2018), as applied to claims 25-42 and 44 above, in view of Ritter et al. (US PG Pub 2015/0337368 A1; published 11/26/2015); Huang et al. (US PG Pub 2015/0322492 A1; published 11/12/2015); and Fontana et al. (US Patent No. 9938574 B2; issued 4/10/2018).
As described above, Belgrader teaches the need for methods, compositions and systems for analyzing genomic and proteomic information from individual cells or a small population of cells including, but not limited to, cancer cells, fetal cells, and immune cells involved in immune responses (Paragraph 5, lines 1-5). Further Belgrader teaches the amplification of the cell's nucleic acids is carried out until the barcoded overlapping fragments within the partition constitute at least 1× coverage of the particular portion or all of the cell's genome, at least 2×, at least 3×, at least 4×, at least 5×, at least 10×, at least 20×, at least 40× or more coverage of the genome or its relevant portion of interest and once the barcoded fragments are produced, they may be directly sequenced on an appropriate sequencing system, e.g., an Illumina Hiseq®, Miseq® or X10 system, or they may be subjected to additional processing, such as further amplification, attachment of other functional sequences, e.g., second sequencing primers, for reverse reads, sample index sequences, and the like (Paragraph 226, lines 1-10). Specifically, Belgrader teaches that the labelling agents may be coupled, through the coupling approaches as described herein, to a reporter oligonucleotide comprising a nucleic acid barcode sequence that permits identification of the labelling agent, as described herein and in some embodiments, the nucleic acid barcode sequence coupled to the labelling agent may comprise a unique molecular identifier (UMI) sequence segment (Paragraph 192, lines 1-20). Further, Belgrader teaches the inclusion of an identifier which may be an oligonucleotide comprising a nucleic acid barcode sequence or binding agent barcode sequence (Paragraph 332, lines 1-5). Belgrader also teaches that prior to co-partitioning, the cells may be incubated with the library of labelling agents, that may represent antibodies to a broad panel of different cell surface features, e.g., receptors, proteins, etc., and which include their associated reporter oligonucleotides where unbound labelling agents may be washed from the cells, and the cells may then be co-partitioned along with the barcode oligonucleotides described above and as a result, the partitions may include the cell or cells, as well as the bound labelling agents and their known, associated reporter oligonucleotides (Paragraph 232, lines 15-25). Belgrader additionally teaches that in some cases, the methods and compositions may be used for sequencing the genome and transcriptome from a single cell in parallel (Paragraph 348, lines 1-5).
Belgrader also teaches that the previously described method can be applied to the first amplification products and/or second amplification products, which may be subject to sequencing for sequence analysis (Paragraph 296, lines 15-20).
Belgrader does not teach or suggest the specific SEQ ID NOs corresponding to the library primers or tagged oligonucleotides, including, SEQ ID NO: 1, 2, 3, 8-15, 16-27, 28-29, 30-37 and/or 38-49.
Ritter teaches a method for amplifying a target nucleic acid sequence comprising a first amplification using specified first and second primer pairs (Abstract). Specifically, Ritter teaches SEQ ID NO:
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77, a 100% similarity match to SEQ ID NO: 2 of the instant application.
Huang teaches compositions with uniquely designed oligonucleotide primers for identifying a plurality of microorganism in a sample (Abstract). Huang also teaches SEQ ID NO: 44, a 100% similarity match to SEQ ID NO: 8 and 30 of the instant application.
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Huang also teaches SEQ ID NO: 52, a 100% similarity match to SEQ ID NO: 16 of the instant application.
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Fontana teaches a method for detecting a first and or a second target DNA sequence from a DNA library, differing in that a mutation generates/eliminates a restriction site for a restriction endonuclease (Abstract). Fontana also teaches SEQ ID NO: 1, a 100% similarity match to SEQ ID NO: 29 of the instant application.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the methods of Belgrader with the specific primer and oligonucleotide artificial sequences as taught by Ritter, Huang and Fontana because Belgrader expressly teaches that its reporter oligonucleotides may incorporate known primer sequences, amplification handles, index sequences and functional adapters to enable downstream sequencing (Paragraphs 192, 226, 232, 296). Specifically, Ritter, Huang and Fontana each teach primer sequences or oligonucleotide tags that are identical to SEQ ID NOs 2, 8, 16, 29 and 30 of the instant application. One skilled in the art would have been motivated to use these known primers in Belgrader’s modular system in order to facilitate amplification and sequencing with standard sequencing platforms/workflows, as Belgrader specifically instructs the user to select appropriate amplification primers based on the desired sequencing method. Further, substituting the known primer or tagged sequences of Ritter, Huang or Fontana into Belgrader’s reporter oligo design would have represented a routine design choice that predictably yields an amplifiable, sequence-ready construct, and the art provides a reasonable expectation of success because each reference teaches functional primers of conventional length, structure and compatibility with the same sequencing platforms as Belgrader.
Conclusions
No claim is allowed. As an aside, SEQ ID NOs: 1, 3, 28 and 38-49 are free of the prior art.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELIZABETH ROSE LAFAVE whose telephone number is (703)756-4747. The examiner can normally be reached Compressed Bi-Week: M-F 7:30-4:30.
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/ELIZABETH ROSE LAFAVE/
Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684