Extended Data Fig. 2: BAP1 is essential in HAP1 cells and amenable to SGE.

a. Experimental scheme and viable cell counts in polyclonal Cas9+ LIG4- HAP1 cells after targeting loci with sgRNAs, based on assumed non-homologous end joining (NHEJ). Cells targeted with BAP1 sgRNAs do not strongly increase in number between day 7 and day 9 post-transfection whereas sgRNAs to a known HAP1 non-essential gene, HPRT1 do. A plasmid not expressing a sgRNA which does not cleave the genome, shows log growth between day 5 and day 7, plateauing between day 7 and day 9 due to confluency. This demonstrates that cutting the genome at a non-essential locus has some genotoxic effects. b. Hart et al.⁶⁵, HAP1-derived Bayes factor essentiality data was scaled across all genes included in the Cancer Gene Census⁶⁶ (as of 2020). The dashed line marks the scaled value for the threshold Bayes factor (>6) above which there is a ~90% probability of essentiality. BAP1 position relative to other genes is shown. c. Cells edited in a similar manner to that shown in ‘a’ were sampled at day 5 and day 11 and indels counted and ranked by frequency, frameshift and in-frame deletions deplete over time suggesting essentiality of the BAP1 locus. d. A pilot SGE experiment using a minimal library at exon 5 shows screening by SGE at the BAP1 locus works as expected, with stop-gained variants depleting, synonymous variants generally not changing and missense variants showing a spectrum of variant effect.

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