Plasma-Seq conducted with blood from male individuals without cancer.
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1 Supplementary Figures Supplementary Figure 1 Plasma-Seq conducted with blood from male individuals without cancer. Copy number patterns established from plasma samples of male individuals without cancer (n=50). Chromosome positions are indicated along the X-axis, the Y-axis represents relative abundance of respective aberrations in percentage. The averages of gained and lost regions were 0.1% and 0.5% after removing centromeric regions (indicated as red bars), respectively, which were either homologue regions in the vicinity of repetitive regions (e.g. centromeres) or likely constitutional CNVs present in the germline.
2 2 Supplementary Figure 2 GISTIC (genomic identification of significant targets in cancer) analyses. GISTIC analyses of the TCGA and plasma samples: Amplifications are illustrated in red and deletions in blue. Chromosome positions are indicated along the X-axis. Significance thresholds are indicated by the green lines, the statistical significance of the aberrations is displayed as false discovery rate (FDR) q values on the Y-axis.
3 3 Supplementary Figure 3 Head to head comparisons between plasma and tissue samples. A pairwise comparison of genomic position-mapped profiles between plasma and tissue samples revealed strong correlations in cases P2 (Pearson correlation coefficient: 0.92), P59 (Pearson correlation coefficient: 0.85), P112 (Pearson correlation coefficient: 0.88), and P127
4 4 (Pearson correlation coefficient: 0.95), and low correlations in cases P29 (Pearson correlation coefficient: 0.65) and P33 (Pearson correlation coefficient: 0.45).
5 5 Supplementary Figure 4 Definition of focal SCs and detection limits. (a) Copy number profiles obtained with undiluted VCaP D employing the CytoScan HD SNP-array (top) and whole-genome sequencing of VCaP (bottom).
6 6 (b) Correlation coefficients (Spearman correlation) obtained by comparison of log2-ratios of focal events identified in undiluted VCaP D between whole-genome sequencing and the CytoScan HD SNP-array of two biological replicates (shown in blue and red, respectively) with various dilutions of cell line VCaP. (c) Scatter plot with copy numbers (inferred from log2-ratios) obtained with CytoScan HD SNP-array (Y-axis) and whole-genome sequencing (X-axis), of focal events identified from whole-genome sequencing of undiluted VCaP D, illustrating the correlation and also the higher dynamic range of whole-genome sequencing. (d) Detection of the AR amplicon in cell line VCaP undiluted (100%) and in a dilution series (50%, 20%, 5%, and 1%). (e) Validation of copy numbers of three focally amplified genes (AR, left panel; FGFR1 center panel; MYC right panel) using quantitative real-time PCR.
7 7 Supplementary Tables Supplementary Table 1 Summary of clinical data of our prostate cancer patient cohort. = within normal range; NSE < 17: normale range; : not available Sample ID Age (years) Histology CRPC/ CSPC PSA (ng/ml) NSE (ng/ml) Therapy P2_1 73 Adenocarcinoma CSPC 19,1 / P10_1 67 Adenocarcinoma CRPC 10,4 P19_1 444,1 P19_2 69 Adenocarcinoma CRPC 397,3 P19_3 131,5 poorly P29_1 73 differentiated PC CSPC 394,0 / poorly differentiated PC CSPC 58,3 P33_1 75 P40_1 poorly CSPC 773,7 83 P40_2 differentiated PC CRPC 656,0 P55_1 63 Adenocarcinoma CRPC 49,2, Chemotherapy, P59_1 6471,1 P59_2 62 Adenocarcinoma CRPC 7532,5 P59_3 6863,3 P65_1 303,0 73 Adenocarcinoma CRPC P65_2, Chemotherapy P98_1 / / CRPC 35,6 RTX P106_1 761,5 79 Adenocarcinoma CRPC P106_2 P112_1 146,9 No therapy applied 80 Adenocarcinoma CSPC P112_2 31,5 P116_1 506,7 85 Adenocarcinoma CRPC P116_2 2489,0 P118_1 1604,0 68 Adenocarcinoma CRPC P118_2 1689,0 P119_1 67 poorly differentiated PC CRPC 161,4 P120_1 68 Adenocarcinoma CRPC 867,7, Chemotherapy P125_1 61 Adenocarcinoma CRPC 58,8 P127_1 57 Adenocarcinoma CRPC 2,8 P136_1 208,2 75 Adenocarcinoma CRPC P136_2 254,9
8 8 P137_1 77 Adenocarcinoma CSPC 5,5 P140_1 63 Adenocarcinoma CRPC 593,0, Chemotherapy, P143_1 0,0, Chemotherapy P143_2 45 Adenocarcinoma CRPC 0,2 P143_3 8,7 >370 Chemotherapy P144_1 34,2, Chemotherapy 68 Adenocarcinoma CRPC P144_2 33,0 P147_1 205,0, Chemotherapy, P147_2 60 Adenocarcinoma CRPC 263,0 P147_3 863,0 >370 P148_1 694,0, Chemotherapy P148_2 63 Adenocarcinoma CRPC 48,0 Chemotherapy P148_3 52,0 >370 P151_1 471,0 P151_2 66 Adenocarcinoma CRPC 0,7, P151_3 0,0 P152_1 69 Adenocarcinoma CRPC, Chemotherapy P153_1 68 Adenocarcinoma CRPC 531,3 P154_1 P154_2 67,7 51 Adenocarcinoma CRPC, P154_3 201,4 Enazalutamide P154_4 337,7 Chemotherapy P155_1 134,0, Chemotherapy, P155_2 67 undiff. CRPC 124,6, Enzalutamide P155_3 P156_1 6,1 P156_2 3,2 poorly,, P156_3 59 CRPC differentiated PC Chemotherapy P156_4 2,2 P156_5 P158_1 43,1 P158_2 9,2 61 Adenocarcinoma CRPC P158_3 19,6 Enzalutamide P158_4 P159_1 319,5, 54 Adenocarcinoma CRPC Chemotherapy, P159_2 599,0 Enzalutamide P162_1, Chemotherapy 72 Adenocarcinoma CRPC P162_2 69,9 P164_1 69 Adenocarcinoma CRPC 292,7 RTX, Chemotherapy P165_1 21,7 49 Adenocarcinoma CRPC P165_2 38,2, Chemotherapy P167_1 593,2, 56 Adenocarcinoma CRPC P167_2 327,5 Enzalutamide
9 9 P167_3 P167_4 7570,0 P167_5 7605,2 Chemotherapy P169_1 595,8, Chemotherapy, P169_2 58 Adenocarcinoma CRPC 615,2 Enzalutamide P169_3 960,4 P169_4 1244,4 Chemotherapy P170_1 16,0, Chemotherapy P170_2 3,5 133,0 63 Adenocarcinoma CRPC P170_3 2,6 14,2 Chemotherapy P170_4 3,6 13,8 P178_1 209,1 RTX, P178_2 62 Adenocarcinoma CRPC 196,1 P178_3 92,2 P179_1 0,4 59,0 P179_2 P179_3 64 Adenocarcinoma CRPC P179_4 0,6 218,0 P181_1 111,0 66 Adenocarcinoma CRPC P181_2 P182_1 122,9 P182_2 52 glandular CRPC 194,5 P182_3 RTX, Chemotherapy,, Chemotherapy, Enzalutamide
10 10 Supplementary Table 2 List of 74 cancer-related genes for which targeted resequencing was performed. Genes AKAP9 AKT1 APC AR ARID1A ASXL1 ATM AXIN1 BAX BRAF BRCA1 BRCA2 BRIP1 CDH1 CDKN2A CDKN2B CHEK2 CREBBP CTN1 CTNNB1 DAPK3 EGFR EP300 ERBB2 FBXW7 FGFR3 FOXA1 GATA3 GATA4 HNF1A HRAS KDM6A FOCAD KLF6 KMT2D KRAS MAP2K4 MDM2 MED12 MLH1 KMT2A
11 11 KMT2C MLLT3 MSH2 MSH6 MUTYH MYH9 KAT6B NF1 NOTCH1 NRAS PALB2 PDE4D PIK3CA PIK3R1 PMS1 PMS2 PTCH1 PTEN RAD51C RB1 RUNX1 SMAD4 SMO SPOP STK11 TMEM135 TP53 TRRAP UBR5 VHL ZBTB7A TMPRSS2 ERG
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