Table 1.
Prevalence of LOH of heterozygous SNPs following CRISPR/Cas9 targeting.
| Cell line | Targeted gene | crRNA | Clones analysed | Clones with indels | Number of clones with indels at |
Any SNP LOH | All dsa SNP LOH | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Target site ‘A’ | Target site ‘B’ | Target site ‘C’ | Target site ‘D’ | Target site ‘E’ | |||||||
| HCT116 | Nontargeting | Pool of 5 (Exp 1) | 66 | 0 | 0 | 0 | 0 | 0 | — | 2 (3%) | 0 |
| HCT116 | ZNF516 | Pool of 4 (Exp 1) | 96 | 65 (68%) | 0 | 57 (59%) | 21 (22%) | 22 (23%) | — | 35 (36%) | 6 (6%) |
| HCT116 | Nontargeting | Pool of 5 (Exp 2) | 41 | 0 | 0 | 0 | 0 | 0 | — | 1 (2%) | 1 (2%) |
| HCT116 | ZNF516 | Pool of 4 (Exp 2) | 59 | 24 (40%) | 20 (33%) | 6 (10%) | 1 (2%) | 2 (3%) | — | 6 (10%) | 4 (7%) |
| HCT116 | ZNF516 | crRNA ‘A’ | 58 | 33 (57%) | 33 (57%) | — | — | — | — | 5 (9%) | 4 (7%) |
| HCT116 | ZNF516 | crRNA ‘B’ | 48 | 17 (35%) | — | 17 (35%) | — | — | — | 2 (4%) | 1 (2%) |
| HCT116 | ZNF516 | crRNA ‘C’ | 47 | 4 (9%) | — | — | 4 (9%) | — | — | 3 (6%) | 1 (2%) |
| HCT116 | ZNF516 | crRNA ‘D’ | 53 | 13 (25%) | — | — | — | 13 (25%) | — | 3 (6%) | 2 (4%) |
| HCT116 | Nontargeting | Pool of 5 | 58 | 0 | 0 | 0 | 0 | 0 | 0 | 1 (2%) | 0 |
| HCT116 | MEX3C | Pool of 5 | 52 | 15 (29%) | 0 | 5 (10%) | 2 (4%) | 10 (19%) | 1 (2%) | 0 | 0 |
crRNA, CRISPR (clustered regularly interspaced short palindromic repeats) RNA; LOH, loss of heterozygosity; SNP, single-nucleotide polymorphism.
a
ds, downstream from the targeted gene towards the telomere.