Supplementary Figure 1 - Nature

Kanu_Figure_S1 Figure S1. Schematic diagram illustrating analysis of H3K36me3 frequency within defined breakpoint regions and analysis of chromosomal complexity of SETD2 mutant tumors in the TCGA ccRCC dataset.

a Copy number

3

Breakpoint

2

Sample-wise copy number profiling Breakpoint identification

1

0 Chromosome location

Multiple samples (either SETD2 mutant or WT)

Sample 1

Breakpoints in samples

Sample 2

Random breakpoints

Sample 3

5,000 sample-set-based randomisations

Genome H3K36me3 sites Expected H3K36me3 frequencies

Observed H3k36me3 frequency

Sample 1 breakpoints

Number of bp in breakpoints overlapping with H3K36me3 sites / Total number of bp in breakpoints

Sample 2 breakpoints

Comparison

b P = 0.33

Weighted genome instability index (wGII)

1.0

0.8

0.6

0.4

0.2

0 SETD2mut (n = 29)

SETD2LOH (n = 210)

Sample 3 breakpoints

Observed frequency

H3k36me3 frequency distribution (background)