Fig. 3: Tumour phylogenetic trees.

Trees were reconstructed from non-silent and synonymous mutations and trunk and branch lengths are proportional to the number of mutations acquired. Trees are rooted at the germline DNA sequence, determined by exome sequencing of DNA from tumour adjacent normal tissue. Subclones that define the tips of the tree are labelled with the tumour region in which they were identified. Numbers were added where several subclones were identified by the phylogenetic deconvolution algorithm within a tumour region, with 1 defining the largest intra-regional subclone and 2, 3 increasingly smaller subclones. Private mutations were furthermore split into those that were clonal in the analysed region (present in >0.7 of the cancer cell fraction in that region) and those that were subclonal (present in ≤ 0.7 of the cancer cell fraction). Likely driver mutations and relevant loss of heterozygosity (LOH) events were mapped onto the branch of the trees where they likely occurred. Genes affected by more than one genetic aberration within a tumour are labelled with the genetic aberration type that occurred. Arrows labelled ‘CIN’ indicate the likely onset of chromosomal instability.