Table 2.

CRISPR-based mammalian deep mutational scanning studies (non-exhaustive)

Target	Search space	Variants	Assay	Sequencing
Saturation genome editing: Homology-directed repair with repair template library (repair template sublibraries based on gRNA; haploid target locusa)
Murine anti-HEL antibodies HEL23/HEL24 CDRH1/2/334	6–10 aa	108–189	PPI with mammalian surface display	Illumina sequencing of short variable region in endogenous locus (per sublibrary)
Anti-HER2 CAR CDRH341	10 aa	189	PPI with intrinsic surface display and CAR T cell signaling	Illumina sequencing of short variable region in endogenous locus (per sublibrary)
BRCA1 RING and BRCT domains67	exons 2–5, 15–23 (1,342 bp)	3,893	survival	Illumina sequencing of short variable region in endogenous locus (per sublibrary)
CARD11 CARD, LATCH, and N-terminal coiled-coil domains68	exons 3–5 (143 aa)	2,542	survival and drug resistance	Illumina sequencing of short variable region in endogenous locus (per sublibrary)
Saturation prime editing: Prime editing with pegRNA library (pegRNA sublibraries based on target region; haploid target locusb)
BRCA269	10 sites (140 bp)	426	survival	Illumina sequencing of short variable region in endogenous locus (per sublibrary)
NPC169	16 sites (523 bp)	978	cholesterol accumulation	Illumina sequencing of short variable region in endogenous locus (per sublibrary)
Base editing with tiling gRNA library: lentiviral transduction gRNA library at low multiplicity of infection
BRCA170	endogenous locus	660	survival (drug-induced)	Illumina sequencing of genome-integrated gRNA representative for mutation introduced in endogenous gene
BRCA1, BRCA271	endogenous locus	NR	survival	Illumina sequencing of genome-integrated gRNA representative for mutation introduced in endogenous gene
MCL1, BCL2L171	endogenous locus	NR	drug sensitivity/resistance	Illumina sequencing of genome-integrated gRNA representative for mutation introduced in endogenous gene
19 drug target genes71	endogenous locus	NR	drug resistance	Illumina sequencing of genome-integrated gRNA representative for mutation introduced in endogenous gene
3584 genes71	endogenous locus	52,034	survival	Illumina sequencing of genome-integrated gRNA representative for mutation introduced in endogenous gene
86 DNA damage response genes72	endogenous locus	NR	survival upon DNA damage	Illumina sequencing of genome-integrated gRNA representative for mutation introduced in endogenous gene
BRCA1, BRCA236	endogenous locus	NR	survival	Illumina sequencing of genome-integrated gRNA representative for mutation introduced in endogenous gene
MAP2K1, KRAS, NRAS73	endogenous locus	NR	drug resistance	Illumina sequencing of genome-integrated gRNA representative for mutation introduced in endogenous gene

NR, not reported.

^aHigh biallelic and silent HDR rates allow reliable assessment of dominant effects in a diploid cell line.⁶⁸

^bLow-MOI lentiviral transduction of the entire pegRNA library could eliminate the need for a haploid target locus.⁶⁹