Table 5A. Supplementary materials Genomic regions showing significant alterations in signal intensities in samples of metastatic- as compared to localized prostate cancer. Chr. Start* End* SNPs in Region Gain/loss Region Size (Mb) p-value** 1 1 4 5 7 7 8 8 8 9 9 10 10 10 11 12 12 12 14 17 17 19 19 19 19 19 20 20 20 21 22 201.25 208.07 10.00 34.67 42.94 128.44 95.18 123.41 133.82 74.178 125.24 68.90 72.00 94.33 65.70 102.96 107.47 115.20 20.78 70.89 74.54 16.19 34.22 50.48 53.41 59.25 2.45 23.45 42.36 38.98 45.08 204.51 210.66 10.43 35.19 44.99 130.40 96.72 126.82 136.26 75.08 129.79 71.20 73.93 95.10 70.86 103.60 111.44 116.42 21.54 71.76 81.25 17.53 35.19 52.29 56.01 59.89 4.19 24.10 43.87 39.16 46.44 27 27 16 21 19 27 36 39 50 19 26 37 25 27 28 20 28 23 17 20 24 10 11 15 14 10 15 16 14 15 10 Gain Gain Loss Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain 3.26 2.59 0.43 0.52 2.05 1.96 1.54 3.41 2.44 0.90 4.55 2.31 1.93 0.78 5.16 0.64 3.98 1.23 0.76 0.88 6.71 1.33 0.97 1.81 2.59 0.64 1.74 0.64 1.50 0.19 1.36 0.009 0.009 0.01 0.01 0.007 0.003 0.008 0.006 0.004 0.008 0.001 0.002 0.005 0.005 0.004 0.009 0.004 0.007 0.007 0.003 0.002 0.007 0.004 0.002 0.003 0.007 0.006 0.006 0.007 0.006 0.009 Listed are regions with consecutive SNPs each displaying a difference at 1% significance level in signal intensity of the samples from localized compared to metastatic prostate cancer. Multiple regions at chromosomes 10 and 19 are not necessarily independent regions of altered DNA copy changes, but can be parts of larger regions. False discovery rate of chromosomes with significant segments is less than 1/22=1.5%. * The genomic positions were based on the May 2004 genome assembly (hg17) of the UCSC human genome browser (http://genome.ucsc.edu/). ** Segments with p≤ 0.01 were reported Table 5B Supplementary materials Genomic regions showing significant alterations in signal intensities between samples of metastatic prostate cancer with and without previous androgen deprivation. Chr. 2 2 2 10 Start* Region End* SNPs in (Mb) Gain/Loss Region Size p-value** 42.53 53.83 55.56 60.65 43.91 54.09 55.88 61.33 13 13 17 22 Gain Gain Gain Gain 1.37 0.26 0.32 0.68 0.043 0.043 0.022 0.013 Listed are regions with consecutive SNPs each displaying significant difference (p<0.01) in signal intensity of the samples from metastatic prostate cancer with and without antiandrogen therapy. Androgen deprivation therapy was performed as orchiectomy. Multiple regions at chromosome 2 are not necessarily independent regions of altered DNA copy changes, but can be parts of larger regions. * The genomic positions was based on the May 2004 genome assembly (hg17) of the UCSC human genome browser (http://genome.ucsc.edu/). Table 5C Supplementary materials Genomic regions showing significant alterations in signal intensities between samples of Gleason score ≥ 8 as compared to Gleason score ≤7 prostate cancer. Chr. 1 1 1 1 1 3 7 8 8 8 8 8 8 8 14 Start* Region 143.19 196.95 198.23 204.63 209.45 156.70 127.94 70.26 80.29 94.96 98.00 100.79 109.020 122.20 32.70 End* SNPs in (Mb) Gain/Loss Region Size p-value** 144.80 198.04 204.51 206.06 211.35 158.44 130.31 71.75 83.07 96.44 100.48 102.90 110.62 127.94 33.98 28 27 71 25 42 34 29 31 48 36 42 34 40 106 11 Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain Gain 1.61 1.09 6.27 1.43 1.90 1.74 2.37 1.49 2.79 1.48 2.48 2.12 1.60 5.74 1.28 0.007 0.007 0.000 0.008 0.001 0.004 0.005 0.008 0.003 0.006 0.003 0.007 0.003 0.000 0.01 Listed are regions with consecutive SNPs each displaying significant difference (p<0.01) in signal intensity of the samples from low differentiated compared to high differentiated prostate cancer. Multiple regions at chromosomes 1 and 8 are not necessarily independent regions of altered DNA copy changes, but can be parts of larger regions. FDR of chromosomes with significant segments is less than 1/5=20%. * The genomic positions was based on the May 2004 genome assembly (hg17) of the UCSC human genome browser (http://genome.ucsc.edu/). ** Segments with p≤ 0.01 were reported.