Tumor types/samples and cell lines analyzed and schematic visualization of genomic functional categories of interest.

<p><b>(A)</b> GCT subtypes in the hypothesized context of normal germ cell development as proposed in earlier studies (grey box). Developmental schemes are indicated in blue (male), red (female) or when possible in both sexes (white). DG does not originate from CIS but is indicated together with SE for reasons of consistency. <b>(B)</b> Samples included in this study. Abbreviations match Fig 1A and roman numbers indicate the GCT type to which the histological subtypes belongs. n indicates the number of tumor samples per group. All samples are from male patients except the DGs, DCs and a subset of the type I TEs. Please note that when only TE is denoted, this indicates the group of all type I TEs together. Otherwise II.TE (type II pure TE) or the abbreviations for specific localizations are used as indicated in this figure. Four GCT cell lines were included; tumor of origin between brackets. <b>(C)</b> Reference to (abbreviations of) the functional genomic regions as mentioned in the rest of the manuscript. Probes were classified according to their relation to gene coding regions, micro-RNA (MIR) coding regions, CpG islands and/or transposon elements (LINE/SINE). The distance to the transcription start site (TSS) was used in accordance with the Illumina manifest: 200 or 1500 bp. Of note, the TSSAssociated category contains all probes with a distance < 1500 bp to the TSS in contrast to the TSS1500 category from Illumina which is only contains probes 200-1500bp from the TSS. Probes within imprinting associated regions were classified as (1) mapped inside a known imprinting control region (ICR) or (2) either mapped inside an ICR or mapped close to the TSS of a transcript of an imprinted gene (200/1500bp upstream, not mutually exclusive). P/M indicates the expressed allele, i.e. paternal/maternal respectively. Numbers between brackets indicate the number of valid probes within each specific category (total number of valid probes: 437,881). *The visualization did not permit including the probe count for all categories. The counts for the empty categories are: 5’UTR = 59,338; ISLAND = 136,339; IMPR_P200 = 638; IMPR_P1500 = 1,659; IMPR_M200 = 610; IMPR_M1500 = 2,265.