Table 1.
Methods for detection of off-target CRISPR cleavage.
| Method | References | Acronym disambiguation | Description |
|---|---|---|---|
| Surveyor | Guschin et al., 2010 | Surveyor assay | Mismatch cleavage |
| T7E1 | Kim et al., 2009 | T7E1 assay | Mismatch cleavage |
| IDAA | Yang et al., 2015 | Indel detection by amplicon analysis | DNA capillary electrophoresis |
| TIDE | Brinkman et al., 2014 | Tracking of indels by decomposition | Indel frequency detection |
| TIDER | Brinkman et al., 2018 | Tracking of insertions, deletions and recombination events | Mutation frequency detection |
| qEva-CRISPR | Dabrowska et al., 2018 | Quantitative evaluation of CRISPR/Cas9-mediated editing | Mutation frequency detection |
| WGS | Smith et al., 2014; Suzuki et al., 2014; Veres et al., 2014; Iyer et al., 2015 | Whole-genome sequencing | Whole genome sequencing |
| Digenome-seq | Kim et al., 2015 | In vitro nuclease-digested genome sequencing | In vitro, genomic DNA cleavage, WGS |
| Multiplex Digenome-seq | Kim et al., 2016 | Multiplex Digenome-seq | In vitro, genomic DNA cleavage, WGS |
| DIG-Seq | Kim and Kim, 2018 | DIG-seq | In vitro, genomic DNA cleavage, WGS |
| SITE-Seq | Cameron et al., 2017 | Selective enrichment and identification of tagged genomic DNA ends by sequencing | In vitro, genomic DNA cleavage |
| GOTI | Zuo et al., 2019 | Genome-wide off-target analysis by two-cell embryo Injection | In vivo cleavage, WGS |
| In vitro selection | Pattanayak et al., 2013 | In vitro selection with high throughput sequencing | In vitro, synthetic library |
| CIRCLE-seq | Tsai et al., 2017 | Circularization for in vitro reporting of cleavage effects by sequencing | In vitro, genomic library |
| CHANGE-seq | Lazzarotto et al., 2020 | Circularization for high-throughput analysis of nuclease genome-wide effects by sequencing | In vitro, genomic library |
| VIVO | Akcakaya et al., 2018 | Verification of in vivo off-targets | In vitro, genomic library, in vivo validation |
| AMP | Zheng et al., 2014 | Anchored multiplex PCR sequencing | Anchored-primer target enrichment |
| IDLV assay | Wang et al., 2015 | Integrase-defective lentiviral vector assay | Anchored-primer target enrichment |
| GUIDE-seq | Tsai et al., 2015 | Genome-wide, unbiased identification of DSBs enabled by sequencing | Anchored-primer target enrichment |
| iGUIDE | Nobles et al., 2019 | Improvement of the GUIDE-seq method | Anchored-primer target enrichment |
| UDiTaS | Giannoukos et al., 2018 | Uni-directional targeted sequencing | Anchored-primer target enrichment |
| TTISS | Schmid-Burgk et al., 2020 | Tagmentation-based tag integration site sequencing | Anchored-primer target enrichment |
| TC-Seq | Klein et al., 2011 | Translocation capture sequencing | Translocation enrichment |
| HTGTS | Chiarle et al., 2011 | High-throughput, genome-wide, translocation sequencing | Translocation enrichment |
| LAM-PCR HTGTS | Frock et al., 2015; Hu et al., 2016 | Linear-amplification-mediated-polymerase chain reaction high-throughput genome-wide translocation sequencing | Translocation enrichment |
| ChIP-Seq | Iacovoni et al., 2010; Kuscu et al., 2014; Wu et al., 2014; O'Geen et al., 2015 | Chromatin immunoprecipitation sequencing | ChIP-seq |
| DISCOVER-Seq | Wienert et al., 2019, 2020 | Discovery of in situ Cas off-targets and verification by sequencing | ChIP-seq |
| BLESS | Crosetto et al., 2013 | Direct in situ breaks labeling, enrichment on streptavidin and next-generation sequencing | In situ end-capture |
| DSB-Seq | Baranello et al., 2014 | Double-strand break sequencing | In situ end-capture |
| END-Seq | Canela et al., 2016 | END-Seq | In situ end-capture |
| DSBCapture | Lensing et al., 2016 | Double-strand break capture | In situ end-capture |
| BLISS | Yan et al., 2017 | Breaks labeling in situ and sequencing | In situ end-capture |
| iBLESS | Biernacka et al., 2018 | Immobilized-direct in situ breaks labeling, enrichment on streptavidin and next-generation sequencing | In situ end-capture |