Figure 2. RLOH in GCTs.

a, Representative allelic somatic copy number data. Top, coverage-derived copy number events in a tumour. Bottom, the allele fraction of germ-line variants observed in the tumour. Regions in which there is LOH are coloured in purple and orange for the retained and lost allele, respectively. b, Arm level amplification rates in GCTs and 19 other tumour types (see https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations for abbreviations). Shown are the distributions of counts of arm level amplifications, after controlling for whole-genome doubling, in samples from each tumour type. The distributions are estimated using a Gaussian kernel density³¹ and the median count is indicated by the black bar. GCTs (purple, with the independent replication series denoted as ICR GCT) have significantly more arm level amplifications than other tumour types (gold) (P < 0.0001; Mann–Whitney). c, Rate of reciprocal deletion on arms with amplification in GCTs and 19 other tumour types. For each sample, we counted the number of arm level amplifications with and without a reciprocal deletion. Shown are the mean fractions of amplified arms with a reciprocal arm level deletion, after controlling for whole-genome doubling. GCTs (purple) have significantly more reciprocal deletions than other tumour types (gold) (P < 0.0001; Mann–Whitney). d, Permutation test of arm level deletions. To generate a null distribution of reciprocal deletions, we shuffled arm level deletions within samples²³ and for each permutation we counted the number of observed reciprocal arm level deletions. Shown is a histogram of the counts of reciprocal deletions observed in permutations. The red line indicates the number observed in our dataset corresponding to an empirical P < 0.0001.