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  • br legend on next page br Figure S Episodic APOBEC


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    Figure S4. Episodic APOBEC Mutagenesis Is Likely Mediated by APOBEC3A, but It Does Not Depend on Proliferation Rates or Expression of APOBEC Genes in Examined Cell Lines, Related to Figures 3 and 4
    (A) Cell divisions were measured for 26 daughter and granddaughter clones from the indicated cell lines and compared to the genome-wide burdens of the indicated signatures acquired during the examined in vitro time frames (Period 3, Figure 2). The best fit, as well the adjusted R2, are indicated in plots where sufficient data points were generated for a statistical comparison. *p < 0.05.
    (B) RNA-sequencing derived transcription levels (FPKM = Fragments Per Kilobase of transcript per Million mapped reads) of APOBEC family members with documented deaminase activity on DNA and preference to induce mutations at TCN context were examined in clones from color-coded cell lines, where RNA-sequencing data was generated (Table S2). Only those clones were considered where sufficient data was generated to accurately derive point estimate ex-pressions of examined genes (STAR Methods). Expression was standardized relative to TATA-binding protein (TBP). Top panel: Taxol of APOBEC genes in clones from four indicated cell lines. Horizontal bars indicate the median expression level. Bottom panels: Expression of APOBEC genes was compared to the total burden of SBS2 and SBS13 mutations acquired genome-wide in vitro, in daughter and granddaughter clones from indicated cell lines. Robust regression was applied to derive the best estimates for the slopes of the indicated signatures (black lines), 95% confidence intervals (gray shading) and indicated P values, all of which were above the Bonferroni threshold corresponding to significance at the 0.05 level, p = 0.002 (corresponding to 0.05/23, where 23 is the number of successful tests). In some cases, insufficient data points were generated for a statistical comparison (p = NA).
    (C) Each panel represents enrichment of genome-wide C>T and C>G mutations in indicated clones, at SBS2 and SBS13-specific sequence contexts (TCN, TCA) and at motifs associated with APOBEC3A or APOBEC3B-indeced mutagenesis (YTCN/YTCA and RTCN/RTCA, respectively). N is any base, R is any purine and Y any pyrimidine base. A and B are parent clones, others are daughter and granddaughter clones from the related lineages.
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    Figure S5. Significant Relationships between Somatic Retrotransposition and Mutational Signatures in Cell Lines and Primary Cancers, Related to Figures 3 and 4
    (A and B) The upper plots in both panels show the dependence of the observed numbers of mutations assigned to the indicated signatures (dots), and fitted values (lines) estimated using the GLMM Poisson regression model (STAR Methods), on the L1 insertion rate in cell line clones (panel A) and primary cancer samples (panel B). P values which fall below the Bonferroni thresholds corresponding to significance at the 0.05, 0.01, and 0.001 levels are indicated as *, ** and ***,
    respectively. The bottom plots show the estimated effects of cell line (panel A) or primary cancer (panel B) types on the slope of the regression line, in ranked order, against the normal quantiles. For each tumor type, the fitted value is accompanied by a 95% confidence interval. See Table S5 for cell line and primary cancer samples considered in analyses.
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    Figure S6. Signatures of False-Positive Somatic Mutations Are Present in DNA Prepared from Single Cells, Related to Figure 6
    (A) Top two panels: bars represent the percentage of base substitutions attributed to color-coded signatures in complete (rather than filtered, see Figure 6A) mutational catalogs from whole-genome sequenced stock cell lines from the denoted cancer classes (abbreviations in Table S2) and their single cells. The bottom panel represents the color-coded fractions of minor alleles at examined heterozygous SNP loci, in indicated single cells, which were (i) lost due to WGA-associated locus dropouts, (ii) lost due to WGA-associated allele dropouts or (iii) fall under the detection threshold for identification of base substitutions due to WGA-associated imbalanced amplification.