Abstract: The present disclosure generally relates to methods and systems for engineering antibodies, and antigen-binding fragments thereof, to have altered characteristics. The present disclosure also provides a high-throughput method useful for identifying the engineered antibodies, or antigen-binding fragments thereof, that acquired the altered characteristics having performed the methods. These methods and systems have implications, for example, in the rapid development of biotherapeutics having desired and/or improved, e.g., affinity, specificity and/or activity-related, characteristics.

Abstract: A method for identifying framework regions and complementarity-determining regions in an amino acid sequence. The amino acid sequence is received. A plurality of candidate start positions is identified within the amino acid sequence for a start position for a selected region of interest. A score is generated for each candidate start position of the plurality of candidate start positions via analysis of a motif window that begins at each candidate start position. The start position for the selected region of interest is identified based on a candidate start position of the plurality of candidate start positions having a highest score.

Abstract: The present disclosure relates generally to compositions, methods, kits, partitions and systems for high-throughput microfluidic identification of antigen-binding molecules and antigen binding molecule epitope mapping. Particularly, the compositions, methods, kits, partitions and systems of the disclosure relate to the characterization of cell-expressed antigen-binding molecules (e.g., antibodies) produced by a population of cells, such as B cells, that may have different binding and epitope specificity to a target antigen of interest and/or with enhanced activity.

Abstract: The present disclosure generally relates to compositions and methods for secreted analyte detection and analysis. The analytes detected and analyzed are mapped to a cell or nucleus having secreted the analyte and are useful to characterize the cell or nucleus. The ability to understand analyte secretion events has implications for the improvement of drug delivery, cell profiling, and diagnostic development.

Abstract: Methods and systems for selecting a cell of interest based on immune cell data are disclosed. For example, a method may comprise obtaining a single cell or spatial dataset, wherein the single cell or spatial dataset comprises a dataset of immune cell receptors, antibodies, or fragments thereof from a sample; identifying a clonotype group in the single cell or spatial dataset; selecting a schema to visualize selected amino acids in the clonotype group based on positions or chemical identity of the selected amino acids; visualizing the selected amino acids in the clonotype group in a graphic representation according to the schema; and selecting a cell of interest from the clonotype group based on a pre-defined criterion using the graphic representation.

Abstract: The present disclosure relates to a method for identifying opsonophagocytotic activity and/or trogocytotic activity of an antigen-binding molecule.

Abstract: The present disclosure relates generally to the field of immunology, and particularly relates to compositions, methods, and systems for the analysis and generation of antigen-binding molecules produced by immune cells obtained from tumor samples (e.g., antibodies produced by B cells obtained from tumor samples or TCRs produced by T cells obtained from tumor samples), using single-cell immune profiling methodologies, so as to produce recombinant antigen-binding molecules (e.g., antibodies, TCRs) with desired properties.

Abstract: Provided herein are methods and systems for measuring secreted antibodies or other analytes from single cells. The methods disclosed herein include the use of capture agents and reporter agents that bind to secreted antibodies, wherein the capture agent and/or the reporter agent can be analyte-specific and/or barcoded, and beads in partitions (e.g., droplets or wells) to measure secreted antibodies on a single cell basis. Further described herein are methods comprising the use of hydrogel-encapsulated cells (e.g., cell beads) to measure secreted and/or cellular analytes from single cells.

Abstract: A method is provided for identifying one or more D gene segment in a VDJ or VDDJ sequence. The method can include obtaining a B cell receptor and/or T cell receptor data set, wherein the data set includes a VDJ sequence, aligning the VDJ sequence to one or more VDJ reference sequences thereby generating a first potential alignment and a second potential alignment, determining a first score for the first potential alignment and a second score for the second potential alignment in accordance with a D gene segment alignment scoring schema, and identifying a D gene segment region associated with a highest score between the first score and the second score.

Abstract: Provided herein are methods for identification of antigen binding molecules such as antibodies from a sample by exposing the antigen binding molecules to an antigen conjugated to an oligonucleotide.

Abstract: Provided herein are compositions, systems, methods, and kits for internalizing a payload into a cell via aptamer-mediated deliver. Payloads can comprise molecules capable of hybridizing to nucleic acid sequences directly or through intermediaries (e.g. payload handles). More specifically, payloads can comprise gene editing machinery. A non-limiting example of gene editing machinery can comprise Clustered Regularly Interspaced Short Palindromic Repeats (“CRISPR”) RNP complexes or the subcomponents to those complexes (e.g. gRNA molecules and endonucleases).

Abstract: The present disclosure provides methods, compositions, and systems for selective enzymatic gelation of cells, e.g., immune cells, contained in partitions.

Abstract: The present disclosure relates in some aspects to methods and compositions for analyzing a biomolecule, such as an antibody, and/or analyzing a repertoire comprising biomolecules, such as the repertoire of antibody binding specificities in a sample comprising one or more antibodies. Exemplary samples include serum and plasma, as well as monoclonal antibody compositions.

Abstract: Provided herein are methods for enrichment from a library of nucleic acid sequences of interest using primers against identification sequences. The nucleic acid sequences of interest can be subsequently cloned, and the protein products can be analyzed.

Abstract: A method for grouping immune cells within an immune cell receptor sequence dataset, is disclosed. An immune cell receptor sequence dataset is obtained from a sample. The dataset includes a plurality of full-length immune cell receptor sequences. Each full-length immune cell receptor sequence can comprise of at least one heavy chain region sequence and one light chain region sequence. Each immune cell receptor sequence is associated with an individual immune cell in the sample. The immune cell receptor sequences associated with a first immune cell and a second immune cell from the sample is compared using a comparison protocol. The first immune cell and the second immune cell are identified as members of the same clonotype if one or more immune cell receptor sequence comparison criteria is met.

Abstract: Provided herein are methods and systems for measuring secreted cytokines or other analytes from single cells. The methods disclosed herein include the use of analyte-specific and/or barcoded binding agents (e.g., antibodies) and beads in partitions (e.g., droplets or wells) to measure such analytes on a single cell basis. Further described herein are methods comprising the use of hydrogel-encapsulated cells (e.g., cell beads) to measure secreted and/or cellular analytes from single cells.

Abstract: The present disclosure relates in some aspects to methods and compositions for assessing the target binding capacity of a binding molecule, such as an antigen binding molecule, e.g., a monoclonal antibody. In some embodiments, provided herein is a method of analyzing binding of a barcode-labeled antibody to a target antigen expressed by a cell, wherein cells expressing the candidate antigens are partitioned and wherein detection of the barcoded nucleic acid molecule is indicative of the binding between the antibody or antigen-binding fragment thereof and the candidate antigen or epitope of the cell.

Abstract: Interactive visualization systems and methods are disclosed herein. The system includes a data source, user input device, processor, and display. The data source obtains a data set comprising B cell receptor and/or T cell receptor data associated with a plurality of cells. The user input device receives a user-selected first parameter under which to analyze the data set. The processor performs the method by identifying a plurality of clonotype groups in the data set using the first parameter, identifying subclonotypes within the clonotype groups (wherein each identified subclonotype comprises cells having identical V(D)J transcripts), and processing the data to define a visualization model that can display a compressed view of the clonotype groups and of the plurality of subclonotypes. The display renders a visualization of said data set according to said visualization model.