Fig. 3

Exonic and intronic profiling of circulating tumor DNA. The non-repetitive sequence was captured for the entire gene body of TP53, PTEN, and RB1 in 165 cell-free DNA samples from 135 men. The somatic variants found in the 152 cell-free DNA samples from 124 men with detectable circulating tumor DNA are shown here. TMPRSS2-ERG gene fusions or structural rearrangements in TMPRSS2 or ERG are also shown. The upper panel displays the circulating tumor DNA fraction. The dashed lines at 0.02, 0.10, and 0.20 denote the cutoffs to reliably detect point mutations, loss of heterozygosity, and homozygous deletions, respectively. Bottom panel, heatmap of the somatic alterations detected from circulating tumor DNA profiling. Type of alteration is coded according to the bottom legend. For visualization purposes, up to two mutations or structural variants (forward and backslashes) are displayed per patient. Triangles and boxes represent single nucleotide variants and indels, respectively. Subclonal mutations are defined as having an allele frequency < 1/4 of the circulating tumor DNA fraction. The same definition was applied to structural variants after median allele frequency adjustment with respect to the mutations. Synonymous point mutations are not displayed here. Variants of unknown significance are non-synonymous single nucleotide variants outside hotspots, not annotated as pathogenic in variant databases. Structural variants of unknown significance are, for example, confined to a single intron, without affecting neighboring exons. X-axis: cell-free DNA samples sorted according to the circulating tumor DNA fraction. Patients with multiple samples are colored in blue. The asterisk indicates samples with microsatellite instability. Samples described in the main text are connected with lines