Extended Data Fig. 3: PEER-seq evaluation of SNVs in BRCA1.

a, Flow cytometry gating strategy used to isolate haploid cells. b, Correlation between PEER-seq LFC values of SNVs in BRCA1 from two biological replicates. The Pearson correlation coefficient (r) is shown. The number of SNVs n = 239. c, Correlation between HDR function scores obtained by Findlay et al. (2018) and PEER-seq LFC values for SNVs in exon 19 of BRCA1. The Pearson correlation coefficient (r) is shown. The number of SNVs n = 239. d, Kernel density estimation plots of adjusted LFCs of SNVs in the region encoding exon 19 of BRCA1 as a function of the category of SNV. For each category, the number and percentage of SNVs with adjusted LFC values lower than a cutoff value (the gray dashed vertical line), representing the 5th percentile of adjusted LFC values of synoynous mutations, are shown. ‘Canonical splice’ denotes the two intronic positions immediately flanking exon 19 of BRCA1 and ‘splice region’ denotes three other intronic positions. e,f, ROC curves for adjusted LFCs of SNVs determined by PEER-seq (blue) and HDR function scores (red) for sets of SNVs with pathogenic/likely pathogenic classifications (the number of SNVs n = 10) vs. SNVs with benign/likely benign classifications (n = 6) from ClinVar in exon 19 of BRCA1 (e) or sets of nonsense and canonical splice sites (n = 17) vs. synonymous SNVs (n = 44) (f). Area under curve values are shown.