33 results about "Homology directed repair" patented technology

This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

The invention relates to the unexpected discovery of a system and methods for precise homology directed repair after CRISPR / Cas9 cleavage. The invention includes a DNA cleavage and repair system comprising a CRISPR / Cas9 system and an oligonucleotide 100% complementary to cleaved DNA to promote homology directed DNA repair. The invention further includes methods for inducing homology directed repair of cleaved DNA and repairing a CRISPR / Cas9 cleavage.

This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of homologous recombination deficiency (HRD) or an HRD signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an HRD signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

Methods for use with Type II CRISPR-Cas9 systems for increasing Cas9-mediated genome engineering efficiency are disclosed. The methods can be used to decrease the number of off-target nucleic acid double-stranded breaks and / or to enhance homology-directed repair of a cleaved target nucleic acid.

This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of homologous recombination deficiency (HRD) or an HRD signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an HRD signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

In certain embodiments, the disclosure provides a method for increasing the efficiency of homology directed repair (HDR) in the genome of a cell, comprising: (a) introducing into the cell: (i) a nuclease; and (ii) a donor nucleic acid which comprises a modification sequence to be inserted into the genome; and (b) subjecting the cell to a temperature shift from 37 DEG C to a lower temperature; wherein the nuclease cleaves the genome at a cleavage site in the cell, and the donor nucleic acid directs the repair of the genome sequence with the modification sequence through an increased rate of HDR.

Administration of TH-302 or another hypoxia activated prodrug in combination with a pharmacological agent that down-regulates or inhibits homology directed repair (HDR) is useful for treating cancer.

Methods for use with Type II CRISPR-Cas9 systems for increasing Cas9-mediated genome engineering efficiency are disclosed. The methods can be used to decrease the number of off-target nucleic acid double-stranded breaks and / or to enhance homology-directed repair of a cleaved target nucleic acid.

The present disclosure relates to the multiplex production and phenotyping of genetically engineered cells by using RNA-guided nucleases and genomic barcoding. In particular, the high-throughput multiplex genome editing is achieved by utilizing a system that facilitates the precise genome editing at desired target chromosomal loci by homology directed repair. The integration of guide RNA and donorDNA sequences as a genomic barcode at a separate chromosomal locus allows identification, isolation, and massively-parallel validation of individual variants from a pool of transformants. Strains canbe arrayed according to their precise genetic modifications, as specified by donor DNA incorporation in heterologous or native genes. The present disclosure further relates to a method of editing codons outside of canonical guide RNA recognition regions, which enables the complete saturation mutagenesis of protein-coding genes, a marker-based internal cloning method which removes background due to oligonucleotide synthesis errors and incomplete vector backbone cleavage, and a method of enhancing homology directed repair by the active donor recruitment.

Provided here are methods for editing of a host genome to knock out or debilitate genes responsible for the growth and / or differentiation of a target organ and injecting that animal at an embryo stagewith donor stem cells to complement the missing genetic information for the growth and development of the organ. The result is a chimeric animal in which the complemented tissue (human / humanized organ) matches the genotype and phenotype of the donor. Such organs may be made in a single generation and the stem cell may be taken or generated from the patient's own body. As disclosed herein, it is possible to do so by simultaneously editing multiple genes in a cell or embryo creating a 'niche"' for the complemented tissue. Multiple genes can be targeted for editing using targeted nucleases and homology directed repair (HDR) templates in vertebrate cells or embryos.

Methods and compositions are provided for the improvement of homology-directed repair of a double strand break in a plant cell, via the use of a polynucleotide comprising sequences homologous to the target site. In some aspects, the double strand break is created by an RNA-guided Cas endonuclease. The homology-directed repair of the double-strand break may include incorporation of a heterologous polynucleotide, for example a gene encoding a trait of agronomic importance. The homology-directed repair of the double-strand break may occur as a result of template-directed repair using a polynucleotide repair template.

Constructs, vectors, and methods for enhancing homology directed repair using the CRISPR / Cas9 gene editing platform are disclosed.

Human or humanized tissues and organs suitable for transplant are disclosed herein. Gene editing of a host animal provides a niche for complementation of the missing genetic information by donor stem cells. Editing of a host genome to knock out or disrupt genes responsible for the growth and / or differentiation of a target organ and injecting that animal at an embryo stage with donor stem cells to complement the missing genetic information for the growth and development of the organ. The result is a chimeric animal in which the complemented tissue (human / humanized organ) matches the genotype and phenotype of the donor. Such organs may be made in a single generation and the stem cell may be taken or generated from the patient's own body. As disclosed herein, it is possible to do so by simultaneously editing multiple genes in a cell or embryo creating a “niche” for the complemented tissue. Multiple genes can be targeted for editing using targeted nucleases and homology directed repair (HDR) templates in vertebrate cells or embryos.

The invention relates to the unexpected discovery of a system and methods for precise homology directed repair after CRISPR / Cas9 cleavage. The invention includes a DNA cleavage and repair system comprising a CRISPR / Cas9 system and an oligonucleotide 100% complementary to cleaved DNA to promote homology directed DNA repair. The invention further includes methods for inducing homology directed repair of cleaved DNA and repairing a CRISPR / Cas9 cleavage.

Methods and compositions are provided for the improvement of homology-directed repair of a double strand break in a plant cell, via the use of a polynucleotide comprising sequences homologous to the target site. In some aspects, the double strand break is created by an RNA-guided Cas endonuclease. The homology-directed repair of the double-strand break may include incorporation of a heterologous polynucleotide, for example a gene encoding a trait of agronomic importance. The homology-directed repair of the double-strand break may occur as a result of template-directed repair using a polynucleotide repair template.

Methods for use with Type II CRISPR-Cas9 systems for increasing Cas9-mediated genome engineering efficiency are disclosed. The methods can be used to decrease the number of off-target nucleic acid double-stranded breaks and / or to enhance homology-directed repair of a cleaved target nucleic acid.

Human or humanized tissues and organs suitable for transplant are disclosed herein. Gene editing of a host animal provides a niche for complementation of the missing genetic information by donor stemcells. Editing of a host genome to knock out or disrupt genes responsible for the growth and / or differentiation of a target organ and injecting that animal at an embryo stage with donor stem cells tocomplement the missing genetic information for the growth and development of the organ. The result is a chimeric animal in which the complemented tissue (human / humanized organ) matches the genotype and phenotype of the donor. Such organs may be made in a single generation and the stem cell may be taken or generated from the patient's own body. As disclosed herein, it is possible to do so by simultaneously editing multiple genes in a cell or embryo creating a 'niche' for the complemented tissue. Multiple genes can be targeted for editing using targeted nucleases and homology directed repair (HDR) templates in vertebrate cells or embryos.

The invention relates to a method to determine a homology directed repair (HDR) event within a eukaryotic cell, wherein the cell expresses a first isoform of a surface protein, which is different from a second isoform of said surface protein with regard to an amino acid marker. The method comprises the steps of inducing a DNA double strand break, providing a HDR template DNA construct comprising the amino acid marker corresponding to the second isoform of the surface protein and subsequently determining the expression of the first or second isoform of said surface protein on said cell, wherein expression of the second isoform indicates a successful HDR event. The invention also relates to a method for editing a genomic location of interest within a eukaryotic cell, and to a method of selectively depleting or enriching an edited cell in a composition of non-edited and edited cells.

Disclosed are methods of genomic modification of skeletal and cardiac muscle using sequence-targeting nucleases and a donor sequence delivered via a virus.

Human or humanized tissues and organs suitable for transplant are disclosed herein. Gene editing of a host animal provides a niche for complementation of the missing genetic information by donor stem cells. Editing of a host genome to knock out or debilitate genes responsible for the growth and / or differentiation of a target organ and injecting that animal at an embryo stage with donor stem cells to complement the missing genetic information for the growth and development of the organ. The result is a chimeric animal in which the complemented tissue (human / humanized organ) matches the genotype and phenotype of the donor. Such organs may be made in a single generation and the stem cell may be taken or generated from the patient's own body. As disclosed herein, it is possible to do so by simultaneously editing multiple genes in a cell or embryo creating a “niche” for the complemented tissue. Multiple genes can be targeted for editing using targeted nucleases and homology directed repair (HDR) templates in vertebrate cells or embryos.

The disclosure provides compositions and methods for modifying a target nucleic acid. In some embodiments, a composition can include a targetable nuclease, a DNA-binding protein, and a donor template comprising a homology directed repair (HDR) template and one or more DNA-binding protein target sequences. In some embodiments, a composition can include a Cas protein, one or more single guide RNAs (sgRNAs), and an anionic polymer.

Provided herein are systems and methods for performing repair of mutant chromosomes in cells by using the homologous chromosome as a template for homology directed repair. Also provided herein are CopyCatcher systems, methods, and organisms for the study and measurement of homologous chromosome template repair and related mechanisms in cells and organisms.

Described are methods of homology directed repair (e.g., for treating a disease or disorder) and fusion proteins, polynucleotides (e.g., guide polynucleotides (e.g., guide RNAs) and polynucleotides encoding the fusion proteins), vectors containing the polynucleotides, viral or non-viral delivery vehicles containing the vectors, and compositions (e.g., pharmaceutical compositions) containing the same for use in methods of homology directed repair.

The present invention relates to compositions and methods for increasing the rate of site specific insertion of a donor DNA sequence to the genome. More specifically, the method introduces a donor DNA template containing at least one transcription factor binding site to a cell in order to favor specific insertion of a donor template sequence at a target site by homology directed repair (HDR).

Compositions and methods are provided for editing nucleotides or altering target sites in the genome of a cell. The methods and compositions employ a guide RNA / Cas endonuclease system and at least one component selected from the group consisting of (i) an inhibitor of end joining (NHEJ), (ii) an activator of homology-directed repair (HDR) or (iii) any one combination of (i) and (ii), to provide an effective system for editing nucleotides or altering target sites within the genome of a cell. The present disclosure also describes methods for editing a nucleotide sequence in the genome of a microbial cell employing a guide RNA / Cas endonuclease system and at least one component selected from the group consisting of (i) an inhibitor of NHEJ, (ii) an activator of HDR, or (iii) any one combination of (i) and (ii), wherein said microbial cell has reduced or no off-target site effects.

Human or humanized tissues and organs suitable for transplant are disclosed herein. Gene editing of a host animal provides a niche for complementation of the missing genetic information by donor stem cells. Editing of a host genome to knock out or disrupt genes responsible for the growth and / or differentiation of a target organ and injecting that animal at an embryo stage with donor stem cells to complement the missing genetic information for the growth and development of the organ. The result is a chimeric animal in which the complemented tissue (human / humanized organ) matches the genotype and phenotype of the donor. Such organs may be made in a single generation and the stem cell may be taken or generated from the patient's own body. As disclosed herein, it is possible to do so by simultaneously editing multiple genes in a cell or embryo creating a “niche” for the complemented tissue. Multiple genes can be targeted for editing using targeted nucleases and homology directed repair (HDR) templates in vertebrate cells or embryos.