Extended Data Fig. 2. Interaction of TMB and fraction of mutations in single- and multi-copy regions across 31 cancer types.
A combined analysis of TMB ranks in relation to the fraction of mutations in multi-copy (a) and only-copy (b) regions of the genome revealed a complex landscape, where a wide range of multi-copy or single-copy mutation fraction was observed at any given TMB value in 9,256 tumors across 31 cancer types from TCGA. These findings highlight tumors with a low or intermediate TMB that at the same time harbor a large fraction of mutations in multi-copy or single-copy states, therefore suggesting the independent nature of these features. A weak correlation was noted between TMB rank and fraction of mutations in multi-copy regions of the genome for BLCA (Pearson’s R = 0.26), KICH (Pearson’s R = 0.45), LUAD (Pearson’s R = 0.34), LUSC (Pearson’s R = 0.21), SARC (Pearson’s R = 0.24) while these features were weakly anti-correlated in COAD and UCEC (Pearson’s R = -0.23 and -0.35 respectively). TMB was weakly anti-correlated with the fraction of mutations in haploid regions for COAD, STAD and UCEC (Pearson’s R = -0.22, −0.25 and −0.25 respectively). The heatmaps indicate the distribution of tumors within a tumor type, and each black dot represents an analyzed tumor sample.