A method for enriching clonal populations includes, for a population of target nucleic acids, includes exposing the population of target nucleic acids to a plurality of supports; amplifying the bound target nucleic acids in the presence of a primer to form supports including a plurality of copies of the target nucleic acids of the population of target nucleic acids; applying to the supports a capture primer; applying a magnetic bead functionalize with a moiety to bind to the binder moiety; and separating the first set of supports from the second and third set of supports.

The present disclosure provides compositions comprising nucleic acid single-stranded splint strands, including kits, and methods that employ the single-stranded splint strands. The single-stranded splint strands can hybridize to portions of linear library molecules to form circularized library-splint complexes having a nick, where the nick can be ligated to form covalently closed circular molecules which can be subjected to downstream amplification and sequencing workflows.

The present disclosure provides compositions comprising nucleic acid double-stranded splint adaptors, including kits, and methods that employ the double-stranded splint adaptors. The double-stranded splint adaptors (200) can be used in a one-pot, multi-enzyme reaction to introduce one or more new adaptor sequences into a library molecule. The double-stranded splint adaptor (200) comprises a first splint strand (long splint strand (300)) and a second splint strand (short splint strand (400)), where the first and second splint strands are hybridized together to form the double-stranded splint adaptor (200) having a double-stranded region and two flanking single-stranded regions. The second splint strand (400) carries the new adaptor sequence(s) to be introduced, such as for example a universal binding sequence and/or an index sequence.

The present invention provides novel microfluidic substrates and methods that are useful for performing biological, chemical and diagnostic assays. The substrates can include a plurality of electrically addressable, channel bearing fluidic modules integrally arranged such that a continuous channel is provided for flow of immiscible fluids.

Methods and compositions are described herein that are useful for analyzing and identifying retron systems with improved replication fidelity and efficiency. The methods and compositions described herein facilitate the engineering, quantification, and identification of retron elements for precise genome engineering.

Provided are a CAR library used to screen scFvs that can be functional in CAR-T cells, and an scFv manufacturing method in which the CAR library is used. A chimeric antigen receptor (CAR) library of the present invention includes nucleic acids coding for first CARs. Each of the first CARs includes a first antigen-binding domain, a first transmembrane domain, and a first intracellular signaling domain. The first antigen-binding domain includes a first single-chain antibody (scFv) to be screened for the ability to bind to a target antigen. The first scFv includes a first heavy-chain variable region and a first light-chain variable region. The first heavy-chain variable region and the first light-chain variable region meet a predetermined condition.

Provided herein are methods and compositions to make guide nucleic acids (gNAs), nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs from any source nucleic acid. Also provided herein are methods and compositions to use the resulting gNAs, nucleic acids encoding gNAs, collections of gNAs, and nucleic acids encoding for a collection of gNAs in a variety of applications.

Herein is reported a method for selecting a variant of a parental antibody variable domain encoding nucleic acid, wherein the parental antibody variable domain amino acid sequence encoded by said encoding nucleic acid has at least one developability hot spot, the method comprising the steps of (i) providing a multitude of DNA-containing samples (genomic material of antibody secreting B-cell) each including one or more antibody variable domain encoding nucleic acids; (ii) performing PCR amplification of said antibody variable domain encoding nucleic acids of (i) using consensus sequence-specific primers to obtain amplification products (wherein said consensus sequence-specific primers bind to consensus sequences that are common to a plurality of genes within the genetic loci set, thereby generating a pool of amplification products); (iii) sequencing a plurality of said amplification products obtained in step (ii) in order to determine the relative proportion of each nucleotide at each position in a sequencing read; (iv) performing a sequence alignment between the sequencing read results of (iii) and the parental antibody variable domain encoding nucleic acid; (v) performing a sequence-identity/homology-based ranking of the antibody variable domain encoding nucleic acids in said sequence alignment with the parental antibody variable domain encoding nucleic acid being the perfect/template/reference sequence; and (vi) selecting the variant antibody variable domain encoding nucleic acid based on the sequence ranking of step (v), whereby the variant selected in step (vi) is selected so that the developability hot-spot is removed.

Cancer immunology provides promising new avenues for cancer treatment but validation of potential neoantigens to target is costly and expensive. Analysis of MHC binding affinity, antigen processing, similarity to known antigens, predicted expression levels (as mRNA or proteins), self-similarity, and mutant allele frequency, provides screening method to identify and prioritize candidate neoantigens using sequencing data. Methods of the invention thereby save time and money by identifying the priority candidate neoantigens for further experimental validation.

A method of library construction for peptide generation and, more particularly, to a method of construction of a DNA library built for selection of peptides that starts with a protein sequence known to bind to a target, wherein the protein sequence is used to generate DNA sequences which are then recombined and wherein each codon of the recombined DNA sequences has degenerate bases that cover between 1 and 20 of 20 possible amino acids.