Fig. 3

Copy Number Comparison. A) Median Copyome derived aneuploidy with 99% CI for normal and late-stage cancer samples. Copyome derived aneuploidy was computed as the fraction of Copyome bins where Copyome pillar value was < −0.1 or > 0.1. Asterisks (*) indicate significance in Copyome aneuploidy between specific cancer samples and normal. B) Mean z-transformed Copyome pillar values for 2655 normal samples vs. 178 late-stage NSCLC samples with 95% CI error band. The highlighted regions show the cytobands known to harbor higher number of CNV variants in NSCLC. The 2 sample ks-test with mean Copyome value for the given band between normal and NSCLC samples showed a p-value of 3.33e-16 (KS test statistic: 0.39) for 3p, 5.37e-9 (KS test statistic: 0.24) for 3q26-29, and 6.68e-7 (KS test statistic: 0.21) for 6q25-24. C) Mean z-transformed Copyome pillar values for 2655 normal samples vs. 189 late-stage CRC samples with 95% CI error band. The highlighted regions show the cytobands known to harbor higher number of CNV variants in CRC. The 2 sample ks-test with mean Copyome value for the given band between normal and CRC samples showed p-value of 2.89e-15 (KS test statistic: 0.31) for 7p, 7.77e-16 (KS test statistic: 0.33) for 8p, 7.77e-16 (KS test statistic: 0.44) for 13q, 7.77e-16 (KS test statistic: 0.42) for 17p, and 7.77e-16 (KS test statistic: 0.45) for 20q. D) Mean z-transformed Copyome pillar values for 2655 normal samples vs. 72 late stage breast cancer samples with 95% CI error band. The highlighted regions show the cytobands known to harbor higher number of CNV variants in breast cancer. The 2 sample ks-test with mean Copyome value for the given band between normal and breast cancer samples showed p-value 2.82e-9 (KS test statistic: 0.37) for 1q, 9.26e-7 (KS test statistic: 0.32) for 8p, 4.11e-6 (KS test statistic: 0.30) for 8q, 3.45e-5 (KS test statistic: 0.28) for 13q, 1.4e-14 (KS test statistic: 0.47) for 16q, and 2.33e-9 (KS test statistic: 0.38) for 17p. E) Mean z-transformed Copyome pillar values for 2655 normal samples vs. 38 late stage prostate cancer samples with 95% CI error band. The highlighted regions show the cytobands known to harbor higher number of CNV variants in prostate cancer. The 2 sample ks-test with mean Copyome value for the given band between normal and prostate cancer samples showed p-value 3.74e-3 (KS test statistic: 0.28) for 8p, 3.66e-5 (KS test statistic: 0.37) for 8q, 3.16e-4 (KS test statistic: 0.33) for 13q, 1.91e-11 (KS test statistic: 0.56) for 16q. High Grade Sample N numbers can be found in Supplementary Table 2. Abbreviations: BLAD, Bladder; BRCA, Breast Cancer; CHOL, Cholangiocarcinoma; CRC, Colorectal Cancer; ESO, Esophageal; GAS, Gastric; H&N, Head and Neck; NSCLC, Non-small-cell Lung Cancer; N, Normal; OV, Ovarian; PANC, Pancreatic; PRAD, Prostate Adenocarcinoma; UTER, Uterus.