Fig. 3. Widespread allelic imbalance (AI) and loss of heterozygosity (LOH) in metastatic melanoma.

A Left: genomic proportions of each tissue sample affected by allelic imbalance. Horizontal bars indicate the fraction of each genome with the indicated allelic state. Middle: allelic imbalances in each sample at the cytogenetic band level. Regions of allelic balance have the same paternal and maternal allele copy number; regions of AI have different allele-specific copy numbers. AIs including an LOH event are shown separately. Undetermined regions are indicated in grey. Right: relationship between LOH and mutations lost during disease progression. Shown are proportions of all lost mutations that co-occur with acquisition of LOH events. B B-allele frequencies of single nucleotide polymorphisms in regional and distant metastases in patient CAS-B. A mirrored imbalance of heterozygous SNPs on chromosome 10 was evident between these lesions. C The impact of LOH events on neoantigenic mutations. Analysis of predicted neoantigenic mutations lost via LOH events across the cohort. X-axis indicates the number of neoantigenic mutations lost per LOH event. D Impact of LOH events on structural variants (SVs). Shown are Circos plots of large SVs detected in two liver metastases in patient CAS-D. Inner track indicates the allelic state for each chromosome.