Supplementary Figure 9: Classification of tumors on the basis of TERT expression and ATRX or DAXX genomic alterations.

(a) Comparison of ATRX variant classification between samples classified as TERT^expr and samples classified as ATRX/DAXX^alt. Silent mutations, DAXX alterations, deletions and structural variants were omitted. Truncating variants consist of frameshift, nonsense and splice site variants. Non-truncating mutations consist of missense mutations and in-frame indels. P-value was calculated using a Fisher’s exact test. (b) Distribution of telomerase signature score across TERT/ATRX/DAXX groups in the core set. A small group, TERT^alt-TERT^expr-ATRX/DAXX^alt, has only 2 cases thus were excluded from the comparison. All P values are derived from comparisons with the ATRX/DAXX^alt group (blue). Red are TERT expressing groups, and purple is the double wild-type group. The group in black is TERT^alt but without expression. (c) Number of copy number segments by TERT^expr-ATRX/DAXX^alt group. Number of segments between groups was compared using two-sided t-tests. (d) Mutational burden by TERT^expr-ATRX/DAXX^alt groups. Mutational burden between groups was compared using two-sided t-tests. (e) Survival differences between TERT^expr-ATRX/DAXX^alt groups by cancer type. Number of patients included, number of events (deaths) and univariable log-rank P-values are indicated in the bottom left corner for each tumor type. Hazard ratios and 95% confidence intervals comparing survival in the double wild-type group (green) and ATRX/DAXX^alt group (blue) relative to the TERT^expr group are shown in the top right corner of each tumor type. Groups with less than six samples were omitted. ***P < 0.0001; **P < 0.001; *P < 0.05; N.S. not significant.