Extended Data Fig. 9: Recurrent parallel evolution and LOH across the genome.

a, Across-genome plot showing the frequency of parallel gain/amplification events in red and frequency of parallel LOH events in blue. The dashed red lines indicate the significance threshold determined by a permutation test. b, Example of parallel evolution on chromosome 1 in CRUK0005. log₂[R], B-allele frequency (BAF) and allele-specific expression (ASE) plots are shown for chromosome 1 in samples 3 and 4. On the phylogenetic tree, we indicate the branches in which the parallel gains of chromosome 1 were identified. c, Correlating intra-tumour heterogeneity (ITH) for each gene at the DNA and RNA levels. The scatter plot shows that the percentage of expressed genes with allele-specific DNA intratumour heterogeneity correlates with the percentage of expressed genes with allele-specific RNA intratumour heterogeneity. Only the 43 tumours, for which we had paired multi-sample exome-sequencing and multi-sample RNA sequencing data, were included in this analysis. d, Prevalence of single haploid copies in WGD tumours. Across-genome plot showing the frequency of loss to a single haploid copy in WGD tumours at the cytoband level. Clonal loss to a single haploid copy is shown in grey. Subclonal loss to a single haploid copy is shown in orange. The solid black line indicates the total frequency, including both clonal and subclonal events, of loss to a single haploid copy. HLA LOH is not shown as only the whole-exome sequencing subset of our cohort could be analysed using the LOHHLA bioinformatics tool (see Methods, ‘HLA LOH detection’). e, Prevalence of LOH in WGD tumours. This across-genome plot at the cytoband level shows the proportion of tumours with LOH. The solid black line indicates the total proportion of tumours with either subclonal or clonal LOH; the yellow shading indicates the proportion of tumours with WGD in the cohort that had subclonal LOH at these cytobands. The dashed grey lines demarcate the borders between separate chromosomes. f, Prevalence of HLA LOH across tumour types. We indicate for each tumour type the count and proportion of tumours in which HLA LOH was observed. Dark grey and orange bars show tumours for which HLA LOH was observed clonally or subclonally, respectively; light grey bars show tumours for which no HLA LOH was observed.