Fig. 2.

False colour plots of allelic imbalances, somatic DNA variant (SNV) and structural variants in primary testicular germ cell cancer (TGCC) (nonseminoma (NS)) and various purified tumour components of two cases (T6107 (panels a, b) and T618 (panels c, d)). Data from (tumour) samples analysed more than once were averaged. Top panels a, c Each line represents the amplicon averaged lesser allele frequencies (LAF) of heterozygote SNPs using the LAF colour scheme in panel e (LAF). Blue indicates heterozygosity and red refers to loss of heterozygosity (LOH). Ordering is based on chromosomal position (indicated on the right). For comparison, the 100 kb interval WGS LAF (CG-LAF) is also shown. In addition, the WGS relative read coverage (CGrelCov) data of the primary NS are provided for the specific chromosomal regions using the colour scheme (Rel Cov) in panel e. Missing data are white. Sample types have been marked by coloured dashed lines (germ cell neoplasia in situ (GCNIS): orange, histological components: red and metastases: purple). (*) Formalin-fixed paraffin-embedded (FFPE) tissue blocks derived DNA samples. Bottom panels b, d Occurrence of tumour-specific SNV and structural variants in the different tumour samples (grey indicates absence, black indicates >3% of the reads carrying the variant, missing data in white). Tumour-specific structural variants are indicated with green arrow heads. Genes with a mutation resulting in amino-acid change (T618: only those observed in GCNIS) have been indicated (see Table 1). A red arrow marks a SNV present in all samples (except PBL) from case T6107 (chr19:56131557), residing in a 2-kb region between two Zn-finger genes. The number at the bottom indicates the months after surgery of the primary tumour for the removal of the metastasis. e Colour keys for the different categories. Sample information and targeted sequence data details are provided in Supplementary Table S1 and Table S8