Fig. 3: High-throughput prime editing sensor screens identify pathogenic TP53 variants.
From: High-throughput evaluation of genetic variants with prime editing sensor libraries
a, Schematic of the sensor-calibrated filtration approach, where the editing rate of a pegRNA is determined by the sensor locus and pegRNAs below a given editing threshold are filtered. b, Number of significantly enriching or depleting pegRNAs (FDR < 0.05) as a function of the minimum correct editing percentage threshold at D34 in both conditions. c, LFC of each pegRNA ≥10% editing with at least ten sensor reads at D34 relative to D4 in the untreated condition, with pegRNAs colored by editing efficiency. d, Same as c, but for the Nutlin-treated condition. e, Plot as in a, but with pegRNAs colored by variant type. Enriching pegRNAs with LFC ≥ 2 and FDR < 0.05 labeled. Depleting pegRNAs with FDR < 0.05 labeled. f, Plot as in b, but with pegRNAs colored by variant type. Selected enriching pegRNAs with FDR < 0.05 labeled. Depleting pegRNAs with FDR < 0.05 labeled. g,h, Boxplots of LFC in pegRNAs at D34 in Nutlin-treated condition separated by variant class for pegRNAs ≥10% editing and ≥20% editing. Statistics shown for two-sided t-test with Bonferroni correction. *P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001; ****P ≤ 0.0001; NS, not significant (P > 0.05). g, Nonsense versus missense (P = 0.02996), versus INS (P = 0.05716), versus DEL (P = 1.0), versus silent (P = 0.0002895). h, Nonsense versus missense (P = 0.009422), versus INS (P = 0.02487), versus DEL (P = 1.0), versus silent (P = 0.001592). i, Boxplot of the LFC at D34 in the Nutlin-treated condition for pegRNAs ≥20% editing with annotated residue functions. In all boxplots (g–i), boxes indicate the median and interquartile range (IQR) for each sample with whiskers extending 1.5× IQR past the upper and lower quartiles. LFC calculated from the median values across n = 3 biologically independent samples using MAGeCK. j, Spearman correlation between LFC of SNV-generating variants and CADD score at D34 in both conditions, as a function of the minimum correct editing threshold. k, Sensor editing for selected pegRNAs at D34 in the Nutlin-treated condition. Source data and code to reproduce this figure can be found at https://github.com/samgould2/p53-prime-editing-sensor/blob/main/figure3.ipynb.
