DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
As detailed on the Filing Receipt filed 3/6/2024, the instant application claims priority to as early as 2/23/2021. At this point in prosecution, all claims are accorded the earliest claimed priority date.
Information Disclosure Statement
The Information Disclosure Statement filed on 8/6/2024 is in compliance with the provisions of 37 CFR 1.97 and has been considered in full. A signed copy of the IDS is included with this Office Action.
Claim Status
Claims 2, 9-12, 14, 16, 18, 21, 25, 27-28, 30-32, 34-39, 41-42, 44-69, 71-96 and 98 are canceled.
Claims 1, 3-8, 13, 15, 17, 19-20, 22-24, 26, 29, 33, 40, 43, 70 and 97 are pending, and under examination.
Objection to the Specification
The specification is objected to for improper usage of trade names and/or marks used in commerce. 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 specification includes at least the following terms, which reference trade names and/or marks used in commerce, that are not appropriately formatted:
GlyCLICK (para. 0178)
Abcam (para. 0149)
ProImmune (para. 0155)
Illumina (para. 0261)
Sigma-Aldrich; Triton; Tween (para. 0302)
10X Genomics (para. 0343)
iPad; Galaxy Tab; iPhone; Android (para. 0413)
These terms should, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Additionally, the specification is objected to for a minor typographic error. The recited term “Aortase A” (para. 0175) should read “Sortase A”.
Appropriate correction is required.
Claim Objections
Claims 1, 3 and 5-6 are objected to because of the following informalities: periods have been used to label constituent steps (e.g., “i).”, “a.”) therein. Each claim must end with a period, and periods may not be used elsewhere in the claims except for in abbreviations (MPEP 608.01(m)).
Appropriate correction is required. Please note that the use of letters and parentheses to label constituent steps conforms to the form of claims requirements.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 USC § 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.
Claims 13 and 20 are rejected under 35 USC § 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor, or a joint inventor, regards as the invention.
With respect to claim 13, the recited terms “the first capture sequence” and “the second capture sequence” lack antecedent basis in the claims. Claim 13 depends on claim 3, and thereby on claim 1. Neither of claims 1 or 3 refers to first or second capture sequences. For purposes of further prosecution, claim 13 is interpreted as dependent on claim 8 (which does refer to said capture sequences).
With respect to claim 20, the claim is directed to a further-limited embodiment of the method of claim “Error! Reference source not found. ”, which does not exist in the antecedent portion of the claim set. For purposes of further prosecution herein, claim 20 is interpreted as dependent on claim 1.
Thus, the scope of the claimed invention is indefinite.
The following is a quotation of 35 USC § 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.
Claim 13 is rejected under 35 USC § 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends.
With respect to claim 13, this dependent claim does not appear to further limit the method of claim 8 (see rejection under 35 USC §112(b)). The unique limitations of claim 13 pertain to the first and second capture sequences, and alternatively require that:
the first capture sequence and the second capture sequence are identical; or
the first capture sequence and the second capture sequence are different.
These alternatives appear to encompass every claimed embodiment of the method of claim 8, with respect to the identical nature of the first and second capture sequences. In this way, claim 13 does not appear to further limit the subject matter of claim 8.
Applicant may cancel the claims, amend the claims to place the claims in proper dependent form, rewrite the claims in independent form, or present a sufficient showing that the dependent claims comply with the statutory requirements.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 USC §§ 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 USC § 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 USC § 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 USC § 102(b)(2)(C) for any potential 35 USC 102(a)(2) prior art against the later invention.
Claims 1, 3-8, 13, 15, 17, 19-20, 22-24, 26, 29, 33, 40, 43, 70 and 97 are rejected under 35 USC § 103 as being unpatentable over Setliff (WO 2020/033164; effectively filed 8/8/2018), in view of Chan (SLAS Discovery 23(7): 613-623; published 5/21/2018; on IDS filed 8/6/2024).
Claim 1 is directed to a method, comprising:
obtaining a first epitope specificity of a first plurality of cells and a second epitope specificity of a second plurality of cells by contacting an antigen with the first plurality of cells and the second plurality of cells, wherein:
the antigen is labeled with a reporter oligonucleotide comprising a reporter sequence,
the first plurality of cells is engineered to express a known antibody, and
the second plurality of cells is engineered to express a candidate antibody;
generating,
a first reduced dimension representation of the first epitope specificity of the first plurality of cells expressing the known antibody; and
a second reduced dimension representation of the second epitope specificity of the second plurality of cells expressing the candidate antibody;
determining, based at least on the first reduced dimension representation and the second reduced dimension representation, whether the second plurality of cells exhibit a novel epitope specificity or an epitope specificity associated with the first plurality of cells.
With respect to claim 1, Setliff discloses LIBRA-seq, a system for simultaneous detection of antigens and antigen specific antibodies (Abstract), and describes application of LIBRA-seq for antibody discovery via epitope mapping including steps of:
recovering specificities of B cells, from cell lines and donor samples, against antigen variants with particular epitope-knockout mutations (pg. 35, para. 2 – pg. 37, para. 1; see pg. 25, para. 3 – pg. 26, para. 2), wherein:
the antigens are labeled with oligonucleotides comprising antigen barcodes, i.e., reporter sequences (pg. 35, para. 4; see pg. 29, para. 2),
cell lines are engineered to express specific B cell receptors (BCRs) corresponding to well-characterized antibodies (pg. 35, para. 3; see pg. 25, para. 3), while donor B cells express a wide variety of BCRs (pg. 26, para. 2);
generating,
a principal component representation of the epitope specificities of different cell lines expressing well-characterized antibodies (Fig. 9 and pg. 8, paras. 2-3; see Fig. 1G and description at pg. 26, para. 1); and
characterizing donor (i.e., candidate) antibodies as members of a known antibody lineage or as not belonging to a known lineage (pg. 26, para. 1 – pg. 27, para. 2).
Setliff particularly discusses the application of LIBRA-seq to characterizing epitope specificities for the purpose of antibody discovery (pg. 34, para. 3). Setliff also discusses application of LIBRA-seq to a constructed library of mammalian cells, engineered to express mutated candidate antibodies, for identification of mutations that still meet particular antibody discovery goals (pg. 41, para. 4 – pg. 42, para. 1). In this way Setliff is considered to disclose recovering epitope specificities from said cells, as well as generating representations of the epitope specificities on a single principal component therefrom.
The depicted principal component graph includes two labeled distributions, showing separation of cell lines on a single principal component based on antigen specificity scores (Fig. 9; see description at pg. 8, paras. 1-2). Joint principal component representation of specificities of different cell lines is considered functionally equivalent to generating a first reduced dimension representation of a first plurality of cells and a second reduced dimension representation of a second plurality of cells.
However, Setliff does not disclose, or make obvious, characterization of antibodies as members, or non-members, of a known lineage based on the principal component representations. Setliff instead specifically describes characterization of antibodies via phylogenetic clustering with known antibody sequences (pg. 32, para. 3), rather than directly based on reduced dimensional representations of epitope specificities as claimed.
Chan describes an epitope binning method that leverages cellular barcoding to characterize candidate antibodies, raised against cellular protein targets, based on relatedness of their binding profiles with those of a set of reference antibodies (pg. 613, Abstract). Chan teaches that antibodies that bind to similar target epitopes often share similar target functions (pg. 613, r. column). Chan presents findings that antibodies within a particular sequence lineage typically cluster to the same epitope bin, but notes observation that a few antibodies within a particular sequence lineage fell into overlapping bins where antibodies assigned to one of the bins displayed additional complementarity-determining mutations relative to antibodies assigned to the other (pg. 618, r. column). In this way, Chan indicates that comparison of epitope binding properties functionally clusters antibodies more robustly than comparison of sequence lineage.
Chan additionally teaches that their method overcomes common epitope binning obstacles via comparison of antibody binding profiles, rather than individual antibody-antibody reactions, providing the ability to bin larger panel sizes of antibodies with low-volume samples and broad applicability across all host species used for antibody discovery (pg. 614, r. column).
With respect to claim 3, Setliff discloses an antigen-specific cell enrichment process comprising: staining suspended cells with fluorescently labeled antigen-oligo conjugates; antigen-specific bulk cell sorting (thus creating pluralities of cells bound to or not bound to the antigen); and processing single-cell suspensions to generate, and sequence, cell line libraries of antigen barcodes and BCR (e.g., V(D)J) transcripts (pg. 19, paras. 1-4; pg. 22, para. 1; pg. 30, para. 2 – pg. 31, para. 1). The disclosed antigen barcodes and BCR transcripts are considered respectively analogous to reporter sequences and sequences corresponding to immune receptors as claimed.
With respect to claims 4 and 15, Setliff discloses separating an antigen-positive cell population into single cell emulsions including cellular transcripts and antigen barcodes, and co-encapsulating single cells with unique bead-delivered oligos, using droplet fluidics (pg. 3, para. 7; pg. 18, paras. 4-5; pg. 25, para. 2; Fig. 1C). Setliff states that the bead-delivered oligos contain cell barcodes, which are considered analogous to partition barcodes as claimed.
With respect to claim 5, Setliff discloses steps of tagging antigen barcodes with bead-delivered cell barcodes; preparing a cDNA library from the tagged antigen barcodes; and performing PCR amplification reactions to produce a plurality of amplicons comprising the cell barcode and the antigen barcode (pg. 22, para. 1). Setliff states that bead-delivered oligos, which contain the cell barcodes, directly anneal to (i.e., couple to) the antigen barcode-containing oligos from the antigen (pg. 13, para. 6).
With respect to claim 6, Setliff discloses preparing a single-cell cDNA library from the single cell emulsions, wherein cellular BCR transcripts are made into cDNA; incubating the single cell cDNA library to allow hybridization of the unique cell barcode-labeled bead with immunoglobulin heavy chain (VDJ) and immunoglobulin light chain (VJ) cDNAs (pg. 19, paras. 1-2). The disclosed hybridization process is considered analogous to coupling a nucleic acid barcode molecule, that comprises the partition barcode sequence, to a nucleic acid analyte of the cell bound to the antigen, that comprises a sequence of an immune receptor expressed by the cell bound to the antigen as claimed.
Setliff discloses further performing a PCR amplification reaction to produce a plurality of amplicons therefrom, wherein the amplicons comprise the cell barcode and an immunoglobulin heavy chain (VDJ) or immunoglobulin light chain (VJ) sequence (pg. 19, para. 2). The generated amplicons are considered analogous to second barcoded nucleic acid molecules that comprise the sequence of the immune receptor expressed by the cell bound to the antigen as claimed.
With respect to claim 7, Setliff discloses introducing into each single cell emulsion a unique cell barcode-labeled bead (pg. 19, para. 1). In other words, each cell barcode uniquely identifies a bead to which it is attached.
With respect to claim 8, Setliff states that bead-delivered oligos contain a template switch oligo, while the antigen oligos (comprising the antigen barcodes) contain a sequence capable of annealing to the template switch oligo (pg. 13, para. 6 – pg. 14, para. 1; pg. 28, para. 4 – pg. 29, para. 1). The disclosed template switch oligo is considered analogous to a first capture sequence configured to couple to the reporter oligonucleotide as claimed.
With respect to claim 13, Setliff states that bead-delivered oligos contain a template switch oligo, while the antigen oligos (comprising the antigen barcodes) contain a sequence capable of annealing to the template switch oligo (pg. 13, para. 6 – pg. 14, para. 1; pg. 28, para. 4 – pg. 29, para. 1). In this way, Setliff indicates that the disclosed template switch oligo functions as a first capture sequence as claimed.
Setliff also states that the cell-barcode labeled oligos enable amplification of cellular mRNA transcripts through their constituent template switch oligo (pg. 13, para. 6). In this way, Setliff indicates that the template switch oligo additionally functions as a second capture sequence as claimed. Thus, Setliff is considered to disclose an embodiment wherein the first capture sequence and the second capture sequence are identical.
With respect to claim 17, Setliff discloses introducing into each single cell emulsion a unique cell barcode-labeled bead (pg. 16, para. 3). In other words, a unique bead-delivered oligonucleotide (comprising a unique cell barcode) is used to label each sorted cell.
With respect to claim 19, Setliff discloses performing PCR amplification reactions to produce a plurality of amplicons, wherein the amplicons comprise 1) the cell barcode and the antigen barcode, and 2) the cell barcode and an immunoglobulin heavy chain (VDJ) or immunoglobulin light chain (VJ) sequence; and sequencing the plurality of amplicons (pg. 3, para. 4).
With respect to claim 20, Setliff describes generation of a cell barcode-antigen barcode UMI count matrix, and performance of further analysis therefrom (pg. 31, para. 2 – pg. 32, para. 2). The disclosed cell barcode-antigen barcode UMI count matrix is considered equivalent to the union of a first matrix including a first dataset indicating the epitope specificity of a first plurality of cells and a second matrix including a second dataset indicating the epitope specificity of a second plurality of cells as claimed. One of ordinary skill in the art would understand that generating a principal component representation would necessarily involve decomposing this matrix.
With respect to claim 22, the claimed limitation of the matrix structure (i.e., rows correspond to antigens and columns correspond to pluralities of cells) is viewed as mere data formatting, and is not considered to distinguish from the disclosure of a cell barcode-antigen barcode UMI count matrix in Setliff.
With respect to claim 23, Setliff discloses generating a cell barcode-antigen barcode UMI count matrix (pg. 31, para. 2 – pg. 32, para. 2).
With respect to claim 24, Setliff depicts representations of epitope specificities on a single principal component (Figs. 1G and 9; pg. 8, paras. 2-3; pg. 26, para. 1). One of ordinary skill in the art would understand that generating the depicted representations on a single principal component would necessarily involve embedding a reduced dimensional space.
With respect to claim 26, Setliff depicts separation of cell lines on a single principal component based on antigen scores (Fig. 9; see description at pg. 8, paras. 1-2). One of ordinary skill in the art would understand that principal component analysis is a graph-based embedding and reduction technique.
With respect to claim 29, Setliff discloses embodiments wherein the antigen is a particular viral or human protein, e.g., vascular epithelial growth factor (pg. 3, para. 1; pg. 14, paras. 5-6; pg. 38, Table 1). Setliff also discloses use of antigen libraries including oligo-labeled recombinant antigen proteins, and states that pseudovirus can contain internal barcode (pg. 20, para. 2). Setliff is thus considered to also disclose embodiments wherein the antigen is a pseudovirus, i.e., a synthetic virus-like particle.
With respect to claim 33, Setliff discloses generating a principal component representation of the epitope specificities of different cell lines (Fig. 9 and pg. 8, paras. 2-3; see Fig. 1G and description at pg. 26, para. 1).
With respect to claim 40, Chan teaches quantifying similarity between (i.e., comparison between) antibody binding profiles by generating a heat map of correlation coefficients (i.e., distributions of scores) between net fluorescent signal values for each screened antibody relative to each reference antibody, and grouping antibodies into epitope bins based on the similarity (pg. 617, l-r. columns; pg. 619, Figs. 4B-C). The disclosed analytical methodology is considered to read on that claimed.
Claim 43 is directed to a system comprising at least one data processor; and at least one memory storing instructions, which when executed by the at least one data processor, result in operations comprising:
generating, based on at least a first dataset indicating a first epitope specificity of a first plurality of cells expressing a known antibody, a first reduced dimension representation of the first dataset;
generating, based on at least a second dataset indicating a second epitope specificity of a first plurality of cells expressing a candidate antibody, a second reduced dimension representation of the second dataset; and
determining, based at least on the first reduced dimension representation and the second reduced dimension representation, whether the second plurality of cells exhibit a novel epitope specificity or an epitope specificity of the epitope bin associated with the first plurality of cells.
With respect to claim 43, Setliff indicates performance of various analytical steps in a computer environment, e.g., processing of barcode reads in the form of input fastq files (pg. 31, para. 2). Processors and memories are conventional computer hardware components. Before the effective filing date of the claimed invention, one of ordinary skill in the art would have found it obvious to implement computerized steps on a system comprising one or more processors and one or more memories storing instructions as claimed.
Setliff discloses analytical steps of:
generating a principal component representation of the epitope specificities of different cell lines expressing well-characterized antibodies (Fig. 9 and pg. 8, paras. 2-3; see Fig. 1G and description at pg. 26, para. 1); and
characterizing donor (i.e., candidate) antibodies as members of a known antibody lineage or as not belonging to a known lineage (pg. 26, para. 1 – pg. 27, para. 2).
Setliff particularly discusses the application of their methodology to characterizing epitope specificities for the purpose of antibody discovery (pg. 34, para. 3). Setliff also discusses application to a constructed library of mammalian cells, engineered to express mutated candidate antibodies, for identification of mutations that still meet particular antibody discovery goals (pg. 41, para. 4 – pg. 42, para. 1). In this way Setliff is considered to disclose recovering epitope specificities from said cells, as well as generating representations of the epitope specificities on a single principal component therefrom.
The depicted principal component graph includes two labeled distributions, showing separation of cell lines on a single principal component based on antigen specificity scores (Fig. 9; see description at pg. 8, paras. 1-2). Joint principal component representation of specificities of different cell lines is considered functionally equivalent to generating a first reduced dimension representation of a first plurality of cells and a second reduced dimension representation of a second plurality of cells.
However, Setliff does not disclose, or make obvious, characterization of antibodies as members, or non-members, of a known lineage based on the principal component representations. Setliff instead specifically describes characterization of antibodies via phylogenetic clustering with known antibody sequences (pg. 32, para. 3), rather than directly based on reduced dimensional representations of epitope specificities as claimed.
Chan describes an epitope binning method that leverages cellular barcoding to characterize candidate antibodies, raised against cellular protein targets, based on relatedness of their binding profiles with those of a set of reference antibodies (pg. 613, Abstract). Chan teaches that antibodies that bind to similar target epitopes often share similar target functions (pg. 613, r. column). Chan presents findings that antibodies within a particular sequence lineage typically cluster to the same epitope bin, but notes observation that a few antibodies within a particular sequence lineage fell into overlapping bins where antibodies assigned to one of the bins displayed additional complementarity-determining mutations relative to antibodies assigned to the other (pg. 618, r. column). In this way, Chan indicates that comparison of epitope binding properties functionally clusters antibodies more robustly than comparison of sequence lineage.
Chan additionally teaches that their method overcomes common epitope binning obstacles via comparison of antibody binding profiles, rather than individual antibody-antibody reactions, providing the ability to bin larger panel sizes of antibodies with low-volume samples and broad applicability across all host species used for antibody discovery (pg. 614, r. column).
Claim 70 is directed to a computer-implemented method, comprising steps of substantive similarity to functional limitations of the system of claim 43.
With respect to claim 70, Setliff indicates performance of various analytical steps in a computer environment, e.g., processing of barcode reads in the form of input fastq files (pg. 31, para. 2). In other words, computer implementation of their methodology.
The combined teachings of Setliff and Chan are considered to read on the further limitations of the claim in the same way as outlined above with respect to the functional limitations of claim 43.
Claim 97 is directed to a non-transitory computer readable medium storing instructions, which when executed by at least one data processor, result in operations with substantive similarity to functional limitations of the system of claim 43.
With respect to claim 97, Setliff indicates performance of various analytical steps in a computer environment, e.g., processing of barcode reads in the form of input fastq files (pg. 31, para. 2). Non-transitory computer readable media are conventional computer hardware components. Before the effective filing date of the claimed invention, one of ordinary skill in the art would have found it obvious to implement computerized steps on non-transitory computer readable media storing instructions as claimed.
The combined teachings of Setliff and Chan are considered to read on the further limitations of the claim in the same way as outlined above with respect to the functional limitations of claim 43.
An invention would have been obvious to one of ordinary skill in the art if some teaching in the prior art would have led that person to combine prior art reference teachings to arrive at the claimed invention. Before the effective filing date of the claimed invention, said practitioner would have combined the epitope binning method of Chan, with the LIBRA-seq system and methods of Setliff, because Chan presents findings indicating that comparison of epitope binding properties functionally clusters antibodies more robustly than comparison of sequence lineage (pg. 618, r. column), i.e., the basis employed for antibody clustering by the methods of Setliff. Chan additionally teaches that their method can characterize large panels of antibodies from low-volume samples, and is broadly applicable for cell-based antibody discovery (pg. 614, r. column). Said practitioner would have had a reasonable expectation of success because Setliff and Chan are directed to similar fields of endeavor. For example, both discuss methods of characterizing candidate antibodies involving analytical comparison of antigen binding properties between candidate and reference antibodies expressed by barcoded cell populations.
In this way the disclosure of Setliff, in view of Chan, makes obvious the limitations of claims 1, 3-8, 13, 15, 17, 19-20, 22-24, 26, 29, 33, 40, 43, 70 and 97. Thus, the claimed invention is prima facie obvious.
Conclusion
At this point in prosecution, no claim is allowed.
The following prior art, made of record and not relied upon, is considered pertinent to applicant's disclosure:
Cheng (US 2023/0087348; effectively filed 1/11/2019) discloses methods of using Hepatitis B virus peptides to characterize T cell binding (Abstract), involving: sorting T cell populations, sequencing epitope-specific T cell receptors (TCRs), generating a similarity matrix, clustering data, and reduced-dimensional visualizing to produce a map of TCR-epitope associations (para. 0206, 0216-7);
Moyle (US 2010/0034807; effectively filed 10/29/2008) discloses methods and compositions for discovery of antibodies, based on analysis of B-cell expression libraries and functional epitope clustering (Abstract); and
Venkat (‘High-Throughput Epitope Determination of HIV-1 Polyclonal B Cell Repertoires’ [thesis], Vanderbilt University; published 12/12/2020) discloses application of LIBRA-seq to mapping epitope specificities of polyclonal B cells against oligonucleotide-labeled antigens (pg. 2, para. 3 – pg. 3, para. 2; pg. 9, para. 3 – pg. 10, para. 1).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Theodore C. Striegel whose telephone number is (571)272-1860. The examiner can normally be reached Mon-Fri 12pm-8pm ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia M. Wise can be reached at (571)272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/T.C.S./Examiner, Art Unit 1685
/JESSE P FRUMKIN/Primary Examiner, Art Unit 1685 September 28, 2026
