Pan-cancer analysis of the extent and consequences of intratumor heterogeneity

Intratumor heterogeneity (ITH) drives neoplastic progression and therapeutic resistance. We used the bioinformatics tools ‘expanding ploidy and allele frequency on nested subpopulations’ (EXPANDS) and PyClone to detect clones that are present at a >= 10% frequency in 1,165 exome sequences from tumors in The Cancer Genome Atlas. 86% of tumors across 12 cancer types had at least two clones. ITH in the morphology of nuclei was associated with genetic ITH (Spearman’s correlation coefficient, rho = 0.24-0.41; P 2 clones coexisted in the same tumor sample (HR = 1.49, 95% CI: 1.20-1.87). In two independent data sets, copy-number alterations affecting either 75% of a tumor’s genome predicted reduced risk (HR = 0.15, 95% CI: 0.08-0.29). Mortality risk also declined when > 4 clones coexisted in the sample, suggesting a trade-off between the costs and benefits of genomic instability. ITH and genomic instability thus have the potential to be useful measures that can universally be applied to all cancers