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48 Life Technologies ™ | Genome editing When using genome editing tools such as CRISPRs, TAL effectors, or zinc finger nucleases to obtain targeted mutations, it is necessary to determine the efficiency with which these nucleases cleave the target sequence, prior to continuing with labor-intensive and expensive experiments. We have developed a set of tools that will enable you to quickly determine which cells have been edited. Detect and analyze Essential tools for monitoring the efficiency of your genome editing experiments Table 3. Comparison of the three genomic analysis methodologies. Methodology Advantages Limitations When to use GeneArt ® Genomic Cleavage Detection Assay • Can detect small changes in genomic DNA—NHEJ and HDR editing • Limited by detection sensitive to the low rate of modification • Triaging colonies from editing via NHEJ repair GeneArt ® Genomic Cleavage Selection Assay • Fast-live detection as early as 24 hours post- transfection • Visual indication and allows clone enrichment • Detecting cleavage on the reporter construct not actually genomic loci • Triaging colonies from editing via NHEJ repair TaqMan ® SNP Genotyping Assay • Fast • Clearly distinguishes changes in allele status • Only detects changes in alleles that the assay is designed for—may not detect indels from NHEJ repair • Triaging colonies from editing via homologous recombination Ion PGM ™ sequencing • Can specifically detect all changes in a population • Quantitative results • Higher cost compared to other assays • Longer workflow • Best used as a secondary assay— for confirmation and quantitation of editing in populations identified from primary screens When combined, these genetic analysis methodologies can streamline the genome editing process. Table 3 compares the advantages, limitations, and suggested applications of each method.