Abstract: Methods and compositions are described herein for primer extension target enrichment of immune receptor (BCR or TCR) sequences.

Abstract: Methods and systems for quantification of an abundance of one or more payloads (e.g. proteins) in a mixture (e.g. a complex mixture (e.g. in vivo)) using barcodes (e.g. peptide barcodes), binders (e.g. polypeptide binders), and binding agents (e.g. phage) are provided herein.

Abstract: This disclosure describes compositions, methods, and systems for constructing defined variation in a contiguous functional genetic unit in association with a unique sequence identifier (“a barcode”) in a combinatorial manner.

Abstract: The present disclosure relates to designs and applications of Variable Heavy Only (VHO) domain regions. The present disclosure provides a VHO library of polynucleotides encoding VHO domains, wherein the VHO domains are designed based on the Vh domain of a human Vh family, and a method of generating the VHO library. The present disclosure also provides a phage library displaying the VHO domains encoded by the VHO library through the use of M13 bacteriophage minor coat proteins such as pIX and pVII and a method of generating the phage library. The present disclosure also provides a method of screening the phage library to identify VHO candidates that are capable of binding a target of interest.

Abstract: Aspects of the invention relate to methods for preparing and analyzing a sequencing library from a mixed cell-free DNA (cfDNA) sample, wherein the mixed sample includes double-stranded DNA (dsDNA), damaged dsDNA (e.g., nicked dsDNA), and single-stranded DNA (ssDNA) molecules. The subject methods facilitate the collection of information from dsDNA, ssDNA and damaged DNA (e.g., nicked DNA) molecules in a sample, thereby providing enhanced diagnostic information as compared to sequencing libraries that are prepared from dsDNA alone.

Abstract: The present invention overcomes the inadequacies inherent in the known methods for generating libraries of antibody-encoding polynucleotides by specifically designing the libraries with directed sequence and length diversity.

Abstract: Described herein is a method of preparing an unbiased library of phage variants, comprising (a) preparing a population of “acceptor phage”; (b) removing an endogenous target gene and inserting gene variants into the acceptor phage genomes; (c) enriching the recombined phages; and (d) expressing the library for selection. The acceptor phage is a lytic phage comprising a synthetic genome wherein the target gene of interest is flanked by recombinase sites. The acceptor phage infects a first host bacteria expressing a recombination plasmid facilitating recombination. The phages then infect a second host bacteria expressing a counterselection system that accumulates recombined phage variants and selecting against non-recombined phages. The accumulated phage variants infect a third host bacteria. The phage library may then be sequenced and characterized.

Abstract: The present technology is related to methods for detecting genetic alterations underlying intracranial neoplasms such as pituitary adenomas, meningiomas, and craniopharyngiomas. The methods disclosed herein are useful in determining whether a patient harboring an intracranial tumor will benefit from or is predicted to be responsive to treatment with an individual therapeutic agent or a specific combination of therapeutic agents. Kits for use in practicing the methods are also provided.

Abstract: The invention refers to a replicable genetic package displaying a peptide having at least one intramolecular cyclic bond between two heteroatoms of amino acid side chains, a method of preparing a replicable genetic package, a method of producing a library and a library of replicable genetic package.

Abstract: The present invention generally relates to specificity assays using cell cultures, in particular to chimeric antigen receptor (CAR) expressing reporter T (CAR-T) cell assays to test novel antigen binding moieties in different formats. Furthermore, the present invention relates to the use of CAR-T cells, transfected/transduced with an engineered chimeric antigen receptor (CAR) comprising a target antigen binding moiety capable of specific binding to a recognition domain of an antigen binding molecule. The invention also relates to methods and kits for specificity testing of a candidate antigen binding moiety and/or nucleic acid molecules and vectors expressing engineered CARs.

Abstract: Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence ?X?, wherein X is the desired peptide epitope, wherein each of ? and ? comprise an amino acid, using the peptide library to select an affinity reagent.

Abstract: Oligonucleotide constructs are described, each comprising a functional element and a coding element, wherein the functional element comprises a functional sequence, the functional sequence comprising a sequence of nucleotides in which one or more, or each, nucleotide is modified and the coding element comprises a coding sequence, the coding sequence comprising a sequence of nucleotides which do not contain the modifications of the functional sequence, wherein the coding sequence encodes the sequence structure of the functional sequence.

Abstract: This disclosure provides compositions and methods for expressing and displaying isolated integral membrane proteins (IMPs) or fragments thereof in a native conformation on poxvirus extracellular virions and methods for screening, selecting, and identifying antibodies or antibody-like molecules that bind to a target IMP of interest.

Abstract: Methods and systems for quantification of an abundance of one or more payloads (e.g. proteins) in a mixture (e.g. a complex mixture (e.g. in vivo)) using barcodes (e.g. peptide barcodes), binders (e.g. polypeptide binders), and binding agents (e.g. phage) are provided herein.

Abstract: The present disclosure relates to oligonucleotide biosensors that bind to a fluorophore through a reporter domain and to one or more target ligand(s) through one or more target domain(s), which is connected to the reporter domain through one or more linker domain(s). The binding of the target ligand to the target domain affects the fluorescence of the fluorophore when excited by the appropriate wavelength of energy, either by causing dimming or allosteric fluorescence. Methods of selecting biosensors and their use to detect target ligands are also described.

Abstract: The present disclosure provides methods of integrating therapeutic protein and antibody generation and/or selection, evolution and expression in a eukaryotic host for manufacturing in a single system. Therapeutic proteins, including antibodies, are generated, optimized and manufactured in the same eukaryotic host system. The disclosed system of Comprehensive Integrated Antibody Optimization (CIAO!™) allows for simultaneous evolution of protein performance and expression optimization.

Abstract: The present disclosure provides methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire. In one aspect, target-specific primer panels provide for the effective amplification of sequences of T cell receptor and/or B cell receptor chains with improved sequencing accuracy and resolution over the repertoire. Variable regions associated with the immune cell receptor are resolved to effectively portray clonal diversity of a biological sample and/or differences associated with the immune cell repertoire of a biological sample.

Abstract: The invention relates to methods and products for generating diverse libraries of genetic material. The products include libraries and constructed nucleic acids as well as kits and databases and systems thereof.

Abstract: The invention describes a novel system for identifying optimized gRNAs for use in CRISPR/Cas9 genome editing platforms. The invention allows for the determination of specific gene alterations rendered by a particular gRNA, thereby permitting the generation of optimized gRNA libraries.

Abstract: The present invention relates to a polypeptide comprising an antigen binding domain and a carrying moiety having an inhibiting domain that inhibits the antigen binding activity of the antigen binding domain, and having a longer half-life than that of the antigen binding domain existing alone, methods for producing and screening for the polypeptide, a pharmaceutical composition comprising the polypeptide, methods for producing and screening for a single-domain antibody whose antigen binding activity is inhibited by associating with particular VL, VH or VHH, and a fusion polypeptide library including a single-domain antibody whose antigen binding activity is inhibited by associating with particular VL, VH or VHH.