Benchmarking of SpCas9 variants enables deeper base editor screens of BRCA1 and BCL2

Numerous rationally-designed and directed-evolution variants of SpCas9 have been reported to expand the utility of CRISPR technology. Here, we benchmark PAM preferences, on-target activity, and off-target susceptibility of 11 variants of SpCas9 in cell culture assays with thousands of guides targeting endogenous genes. To enhance the coverage and thus utility of base editing screens, we demonstrate that the SpCas9-NG and SpG variants are compatible with both A>G and C>T base editors, more than tripling the number of guides and assayable residues. We demonstrate the performance of these technologies by screening for loss-of-function mutations in BRCA1 and Venetoclax-resistant mutations of BCL2, identifying both known and new insights into these clinically-relevant genes. We anticipate that the tools and methodologies described here will facilitate the investigation of genetic variants at a finer and deeper resolution for any locus of interest. BRCA1 tiling library: Base editor (BE): CBE and ABE Cas9 variants: WT, NG, SpG Cell lines: HAP1, Meljuso Reference: pDNA Number of replicates: 2 or 3 BCL2 tiling library: Base editor (BE): CBE and ABE Cas9 variants: Cas9-NG Cell lines: MOLM13 Reference: pDNA (for Dropout arm) and untreated arm (for Venetoclax arm) Number of replicates: 3 High-fidelity (HF) variant off-target library: Cas9 variants: WT, eCas9-1.1, HiFi Cas9 Cell line: A375 Number of replicates: 2 PAM-flexible variant off-target library: Cas9 variants: SpG, NG Cell line: A375 Number of replicates: 2 PAM-mapping library: Cas9 variants: WT, Cas9-HF1, eCas9-1.1, evoCas9, HypaCas9, xCas9-3.7, Cas9-VQR, Cas9-VRER, Cas9-NG, SpG Cell line: A375 Number of replicates: 2