Detection of genome editing

A method of generating partitions containing amplified target genomic regions, wherein at least some target genomic regions contain a mutation, the method comprising:

• providing a sample comprising a nucleic acid comprising the target genomic region;
• partitioning the sample into a plurality of partitions, wherein the partitions comprise:
• (i) the nucleic acid comprising the target genomic region;
• (ii) a DNA-dependent DNA polymerase;
• (iii) a forward and a reverse oligonucleotide amplification primer, wherein the forward and reverse primers hybridize to opposite strands of and flank, the target genomic region, and wherein the primers are configured to amplify the target genomic region in the presence of the polymerase;
• (iv) a detectably labeled oligonucleotide reference probe that hybridizes to the target genomic region regardless of allele present at the target genomic region;
• (v) a detectably labeled oligonucleotide mutation probe, wherein the mutation probe hybridizes to target genomic regions containing the mutation and (vi) a detectably labeled drop-off probe that hybridizes to a wild-type target genomic region but does not hybridize when the mutation is present at the target genomic region, wherein
• the partitions further comprise a non-extendible dark probe that blocks cross-reactivity of the mutation probe to the wild-type target genomic region by competing with the mutation probe for binding to the wild-type target genomic region, but not when the mutation is present at the target genomic region, or
• the drop-off probe hybridizes to a region overlapping a region to which the mutation probe hybridizes;
• amplifying the target genomic region in the plurality of partitions;
• and
• determining a quantity of wild-type target genomic regions and a quantity of target genomic regions containing the mutation by detecting hybridization of the labeled probes to the target genomic regions in the plurality of partitions.