Table 2 Methods for the detection of byproducts generated by Cas9*

Method	In vivo/ In vitro/ In silico		Assay type	Comment
Cas-OFFinder	In silico	Off-target	Sequence alignment	High false positive
CAST-seq	In vivo	Chromosomal structural variations, indels	Map translocations with induced DSBs	High-sensitivity; not applicable to limited material
CIRCLE-seq	In vitro	Off-target	Sequence cleaved linear DNA from circularized genomic DNA	High-sensitivity; Requires in vivo cleavage confirmation
Dig-seq	In vitro	Off-target	Whole-genome sequencing for cleaved chromatin	High-sensitivity;
Digenome-seq	In vitro	Off-target	Whole-genome sequencing for cleaved naked genomic DNA	High-sensitivity; Requires in vivo cleavage confirmation
DISCOVER-seq	In vivo	Off-target	Pull down Mre11 binding to broken ends	Narrow time-window (only maps unjoined ends); low resolution
GUIDE-seq	In vivo	Off-target	Integrate dsODNs into DSB sites	Unbiased; limited use for blunt-ended DSBs
LAM-HTGTS	In vivo	Off-target, chromosomal structural variations	Map translocations with induced DSBs or recurrent DSBs	High-sensitivity; not applicable to limited material
PEM-seq	In vivo	Off-target, chromosomal structural variations, indels	Map translocations with induced DSBs or recurrent DSBs	High-sensitivity; not applicable to limited material
SITE-seq	In vitro	Off-target	Map broken ends with biotinylatedadapters	High-sensitivity; Requires in vivo cleavage confirmation
UDiTaS	In vivo	Chromosomal structural variations, indels	Map translocations with induced DSBs	Low sensitivity due to no nested PCR

*Because of space limitation, only typical methods are cited here.