Fig. 6: Altered DNA methylation patterns associated with SV breakpoints near genes.

a Histogram of t-statistics for correlation between gene expression and DNA methylation (by Pearson’s using log-transformed expression and logit-transformed methylation), for both the entire set of 8256 genes (blue) associated with CpG islands represented on DNA methylation array platform and the subset of 263 genes (red) on methylation platform and positively correlated in expression (p < 0.001 and FDR < 4%, “OE” for “overexpressed”) with occurrence of upstream SV breakpoint (for either 0–20 kb, 20–50 kb, or 50–100 kb SV sets). b Histogram of t-statistics for correlation between gene expression and SV event (by Pearson’s using logit-transformed methylation), for both the entire set of 2316 genes (blue) with at least three cases with SV breakpoints 0–20 kb upstream and represented on methylation platform and the subset of 97 genes (red) on methylation platform and positively correlated in expression (p < 0.001 and FDR < 4%) with occurrence of SV breakpoint 0–20 kb upstream. c DNA methylation of the CpG site cg02545192 proximal to the TERT core promoter in cases with SV breakpoint 0–20 kb or 20–50 kb upstream of TERT, in cases with TERT promoter (PM) activation mutation (SNV), in cases with TERT amplification (“amp.”), and in the rest of cases (unaligned). P-values by t-test on logit-transformed methylation beta values; “*” denotes significant differences versus unaligned group with p < = 0.0001. Box plots represent 5, 25, 50, 75, and 95%. Points in box plots are colored according to tumor type as indicated. See also Supplementary Data 6 and Supplementary Fig. 2.