Fig. 1

A proof-of-concept screen for pathogenic variants in BRCA1 and BRCA2 using cytosine and adenine base editors. a Schematic workflow of the base editing screen. sgRNAs targeting all the possible C/G or A/T bases across the exon regions of BRCA1 and BRCA2 were cloned and delivered into eHAP cells through lentivirus. After puromycin selection, cells were transfected with base editors and selected by EGFP signals through fluorescence-activated cell sorting. sgRNA cassettes were PCR amplified from cells at day 0 and day 10 and sequenced. b Cell viability analysis of eHAP cells after base editing with different sgRNAs using CCK-8 assay. The control group was infected with the sgRNA targeting wild type GFP gene. The three sgRNAs were expected to generate Q1200*, Y1509Y, and Y1703C mutations, respectively. Error bars represent SEMs from three independent experiments. c The relative frequency of the substitution variants induced by three sgRNAs, measured at day 0, day 4, and day 8 after base editing. The frequency was normalized to 100% at day 0. d–g The essentiality scores (β scores) and their P values reported by the MAGeCK-MLE algorithm for the four base editing screens: BRCA1-AT-NGG (d), BRCA1-CG-NGG (e), BRCA2-AT-NGG (f), and BRCA2-CG-NGG (g). The dashed lines indicate P = 0.05. The black dots indicate the sgRNAs targeting the SINE/Alu repeats. The red dots indicate the sgRNAs that were significantly depleted after base editing (fold change < 0.8, P < 0.05)