Extended Data Fig. 2: Whole genome sequencing of treatment-naive and drug resistant fate type clones.

a. We performed a pairwise hypergeometric test for variants in all clones to determine statistical significance of variant overlap between clones. This was calculated with the following parameters (M = all CADD > 15 variants, n = # Variants in Sample 1, N = # Variants in Sample 2, X = # Variants in intersection of Samples 1 & 2). P-values are plotted on the heatmap where the p-value represents the probability of observing at least as large an overlap as observed if the two clones in fact had independently randomly selected variants from the full list of CADD > 15 variants. P-values below 0.05 represent two clones that are not genetically independent. b. Heatmap of genes with deleterious variants (CADD > 15) that were present with allele frequencies between 25% and 75% in both naive and resistant clones, colored by their CADD deleteriousness score. For genes that include multiple, unique variants, the variants were collapsed into one row, where the variant with the highest CADD score was plotted for that sample. The curated gene set represents the lack of variation in (Shaffer et al. 2017; Garman et al. 2017). Differentially expressed genes from the FateMap dataset show eight genes with variation. c. The expression patterns of the eight genes from the DEG list from FateMap with heterogeneously present genetic variants, visualized on UMAP (Cell counts available in Supplementary Table 11). d. To evaluate for acquired genetic resistance to therapy in the resistant clones, we next plotted variants on a heatmap (colored by their CADD deleteriousness score) if there was a significant difference in the allele frequencies of variants between naive and resistant clones by Fisher’s exact test (P < 0.05). Variants were only included if they were not present in any naive clones. The curated gene set represents the lack of acquired variants in genes from [2017 paper genes], [FateMap DEG], [Clone Genes], [Top 500 most Variable Genes], [Known Epigenetic Modifiers]. The [“all variants with CAAD > 15”] includes all variants with CADD c-scores over 15. e. We analyzed 143 genes classified as epigenetic modifiers for deleterious variants (CADD > 15) within naive clones. The chart shows the number of genes with variants in a subset of naive clones (2 genes) and in all naive clones (10 genes). f. Heatmap of deleterious variants in epigenetic modifier genes, colored by their CADD deleteriousness score.