Fig. 7

Properties of ICGC whole-genome sequencing of tumor (T)-blood (B) pairs. a Left panel: numbers of different genotypic changes between T- and B-stage sequences (∆TB) in ICGC Pilot-63 pan-cancer samples. Right panel: rates of different types of SNV mutations. For Pilot-63 samples, the rates were derived from WGS ∆TB/B values in the left panel; for B-N-P-T AluScan samples, from ∆TB/B values in Fig. 1a; for B-N-T AluScan samples, from ∆TB/B values in Fig. 3a; for Reference [17] samples, from AluScan results on six types of cancers [17]. b Scatter plot of the numbers of GOHs and LOHs in 22 intrahepatic cholangiocarcinoma (ICC, green triangles), 86 hepatocellular carcinomas (LIHC, red circles), and 75 non-small cell lung cancer (NSCLC, blue squares) pairs of samples (Additional file 12: Table S10). c Alteration-group plots of mutational profiles for GOHs and LOHs between B- and T-stages in Pilot-63 samples. Each plot was grouped using the six alteration types: C>A, C>G, C>T, T>A, T>C, and T>G. d Context-group plots of mutational profiles for GOHs and LOHs. Each plot is arranged by the ten context groups: A.A, C.C, A.G, C.A, A.C, G.A, C.G, A.T, T.A, and G.C, designating the different immediate 5′ and 3′ flanking nucleotides. The opposing GOH mutations (left panel) or opposing LOH mutations (right panel) are placed side-by-side (color-coded as in part c). e Representative mutation-rate diagrams, GOH-3 (left panel) and LOH-3 (right panel), were generated from the ICGC Pilot-63 dataset (see additional nine pairs of diagrams in Additional file 13: Figure S3). In these diagrams based on triplet duplexes, the rates of opposing mutations from part d were paired and labeled on bidirectional arrowheads with same color-codes as in part d. f Distribution of the observed rate ratios between opposing GOH pairs (the blue columns) and LOH pairs (the striped red column) (see Fig. 1 for abbreviations)