Genomewide unbiased identification of DSBs evaluated by sequencing (GUIDE-Seq)
First Claim
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1. A method for detecting double stranded breaks (DSBs) in genomic DNA (gDNA) of a cell, the method comprising:
- contacting the cell with a blunt-ended double-stranded oligodeoxynucleotide (dsODN), wherein both strands of the dsODN are orthogonal to the genome of the cell, and further wherein (a) the 5′
ends of the dsODN are phosphorylated, and (b) phosphorothioate linkages are present on both 3′
ends, or phosphorothioate linkages are present on both 3′
ends and both 5′
ends;
expressing or activating an exogenous engineered nuclease in the cell, for a time sufficient for the nuclease to induce DSBs in the genomic DNA of the cell, and for the cell to repair the DSBs, integrating a dsODN at one or more DSBs;
amplifying a portion of genomic DNA comprising an integrated dsODN; and
sequencing the amplified portion of the genomic DNA,thereby detecting a DSB in the genomic DNA of the cell.
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Abstract
Unbiased, genomewide and highly sensitive methods for detecting mutations, e.g., off-target mutations, induced by engineered nucleases.
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Citations
12 Claims
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1. A method for detecting double stranded breaks (DSBs) in genomic DNA (gDNA) of a cell, the method comprising:
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contacting the cell with a blunt-ended double-stranded oligodeoxynucleotide (dsODN), wherein both strands of the dsODN are orthogonal to the genome of the cell, and further wherein (a) the 5′
ends of the dsODN are phosphorylated, and (b) phosphorothioate linkages are present on both 3′
ends, or phosphorothioate linkages are present on both 3′
ends and both 5′
ends;expressing or activating an exogenous engineered nuclease in the cell, for a time sufficient for the nuclease to induce DSBs in the genomic DNA of the cell, and for the cell to repair the DSBs, integrating a dsODN at one or more DSBs; amplifying a portion of genomic DNA comprising an integrated dsODN; and sequencing the amplified portion of the genomic DNA, thereby detecting a DSB in the genomic DNA of the cell. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A method of determining which of a plurality of guide RNAs is most specific, the method comprising:
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contacting a first population of cells with a first guide RNA and a blunt-ended double-stranded oligodeoxynucleotide (dsODN), wherein both strands of the dsODN are orthogonal to the genome of the cell, and further wherein (a) the 5′
ends of the dsODN are phosphorylated, and (b) phosphorothioate linkages are present on both 3′
ends, or phosphorothioate linkages are present on both 3′
ends and both 5′
ends;expressing or activating an exogenous Cas9 engineered nuclease in the first population of cells, for a time sufficient for the nuclease to induce DSBs in the genomic DNA of the cells, and for the cells to repair the DSBs, integrating a dsODN at one or more DSBs; amplifying a portion of genomic DNA from the first population of cells comprising an integrated dsODN; sequencing the amplified portion of the genomic DNA from the first population of cells; determining a number of sites at which the dsODN integrated into the genomic DNA of the first population of cells; contacting a second population of cells with a second guide RNA and a blunt-ended double-stranded oligodeoxynucleotide (dsODN), wherein both strands of the dsODN are orthogonal to the genome of the cell, and further wherein (a) the 5′
ends of the dsODN are phosphorylated, and (b) phosphorothioate linkages are present on both 3′
ends, or phosphorothioate linkages are present on both 3′
ends and both 5′
ends;expressing or activating an exogenous Cas9 engineered nuclease in the second population of cells, for a time sufficient for the nuclease to induce DSBs in the genomic DNA of the second population of cells, and for the cells to repair the DSBs, integrating a dsODN at one or more DSBs; amplifying a portion of genomic DNA comprising an integrated dsODN from the second population of cells; sequencing the amplified portion of the genomic DNA from the second population of cells; determining a number of sites at which the dsODN integrated into the genomic DNA of the second population of cells; and comparing the number of sites at which the dsODN integrated into the genomic DNA of the first population of cells to the number of sites at which the dsODN integrated into the genomic DNA of the second population of cells to determine if the first or second guide RNA is more specific.
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Specification