Intra-tumor heterogeneity and clonal exclusivity in renal cell carcinoma

Tumorigenesis is an evolutionary process in which different clones evolve over time. Interactions between clones can affect tumor evolution and hence disease progression and treatment outcome. We analyzed 178 tumor samples in 89 clear cell renal cell carcinoma patients and found high intra-tumor heterogeneity with 62% of mutations detected in only one of two biopsies per patient. We developed a novel statistical test to identify gene pairs that are altered in co-occurring clones of the same tumor, including the pairs TP53 and MUC16, as well as BAP1 and TP53. The mutations in these gene pairs are clonally exclusive meaning that they occurred in different branches of the tumor phylogeny, suggesting a synergistic effect between the two clones carrying these mutations. Our analysis sheds new light on tumor development and implies that clonal interactions are common within tumors, which may eventually open up novel treatment strategies to improve cancer treatment.