Clinical Features CN_CNMF METHLYATION_CNMF RPPA_CNMF RPPA_CHIERARCHICAL MRNASEQ_CNMF MRNASEQ_CHIERARCHICAL MIRSEQ_CNMF MIRSEQ_CHIERARCHICAL MIRSEQ_MATURE_CNMF MIRSEQ_MATURE_CHIERARCHICAL nCNV (%) nWild-Type Chi-square test_P Chi-square test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Chi-square test_P Chi-square test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q amp_1p36.22 48 (14%) 303 1.0128e-09 7.12e-07 0.010786 1 0.50624 1 0.11804 1 0.00023677 0.12 0.099092 1 0.33927 1 0.050512 1 0.25769 1 0.037532 1 amp_1q21.3 129 (37%) 222 1.3172e-25 1.02e-22 6.2718e-10 4.42e-07 0.033926 1 0.013076 1 1.1217e-12 8.19e-10 1.2336e-07 8.14e-05 7.7596e-12 5.6e-09 6.5632e-07 0.000425 3.07e-07 2e-04 5.7545e-08 3.84e-05 amp_1q42.3 117 (33%) 234 1.807e-16 1.37e-13 2.7289e-05 0.0156 0.3983 1 0.73607 1 3.4133e-08 2.31e-05 9.183e-05 0.0495 9.7512e-09 6.71e-06 1.2548e-07 8.27e-05 0.0010938 0.482 1.597e-07 0.000105 amp_3q27.1 123 (35%) 228 1.0569e-07 7e-05 0.00086535 0.391 0.94951 1 0.092575 1 0.31542 1 0.85191 1 0.25572 1 0.011125 1 0.25205 1 0.0050018 1 amp_5p15.33 98 (28%) 253 7.9635e-21 6.12e-18 4.5081e-09 3.13e-06 0.13163 1 0.39617 1 4.1348e-10 2.92e-07 3.5587e-06 0.00222 6.1704e-06 0.00377 6.6272e-07 0.000428 0.0001619 0.0834 1.3721e-08 9.4e-06 amp_5p13.1 98 (28%) 253 7.9635e-21 6.12e-18 3.0769e-06 0.00193 0.71636 1 0.92344 1 8.7506e-09 6.05e-06 3.8997e-05 0.022 1.8012e-05 0.0105 3.4962e-06 0.00219 0.0042151 1 2.1638e-06 0.00137 amp_6p21.1 95 (27%) 256 2.0286e-19 1.55e-16 1.5382e-12 1.12e-09 0.33826 1 0.22823 1 0.00038722 0.186 0.00060659 0.28 0.00010586 0.056 5.2029e-05 0.029 0.0022533 0.94 1.4719e-06 0.000936 amp_6q12 69 (20%) 282 9.9453e-13 7.27e-10 5.3285e-07 0.000346 0.065636 1 0.28282 1 2.2052e-05 0.0127 4.2899e-05 0.0242 0.00022552 0.114 7.8432e-05 0.0427 0.0027926 1 4.5975e-05 0.0258 amp_6q21 64 (18%) 287 1.0066e-07 6.67e-05 0.0013971 0.608 0.3688 1 0.89862 1 0.00057824 0.268 2.6632e-05 0.0153 0.0027928 1 0.0025653 1 0.0019947 0.848 0.00031025 0.152 amp_7p22.1 180 (51%) 171 5.4875e-16 4.15e-13 6.3599e-06 0.00387 0.62712 1 0.89037 1 0.00019173 0.0976 0.0074877 1 0.051846 1 0.0095045 1 0.0094606 1 2.4183e-05 0.0139 amp_7p11.2 163 (46%) 188 2.7764e-12 2.02e-09 0.00024271 0.122 0.89885 1 0.93138 1 0.041664 1 0.13726 1 0.13785 1 0.20464 1 0.04499 1 0.0090811 1 amp_7q21.2 159 (45%) 192 5.8736e-12 4.25e-09 0.0007712 0.352 0.19989 1 0.97979 1 0.51088 1 0.29654 1 0.19767 1 0.10376 1 0.082012 1 0.037262 1 amp_8p23.1 141 (40%) 210 9.1103e-05 0.0492 0.00016984 0.0868 0.59543 1 0.58515 1 0.061031 1 0.0051683 1 0.83816 1 0.11125 1 0.18298 1 0.0095801 1 amp_8q24.21 244 (70%) 107 2.0116e-07 0.000132 0.00082397 0.374 0.36968 1 0.15877 1 0.0074852 1 0.0085574 1 0.0014185 0.614 0.00047376 0.223 0.00012278 0.064 0.0011968 0.525 amp_9p24.1 55 (16%) 296 6.1822e-05 0.0342 0.443 1 0.62209 1 0.021102 1 0.13955 1 0.017583 1 0.10049 1 0.069093 1 0.10306 1 0.39697 1 amp_9p13.3 66 (19%) 285 0.0034483 1 0.22432 1 0.26328 1 0.62115 1 0.019319 1 0.020636 1 0.013549 1 0.47381 1 0.10098 1 0.31056 1 amp_9q34.3 93 (26%) 258 0.00025671 0.128 0.10893 1 0.72241 1 0.21723 1 0.033012 1 0.0036879 1 0.18336 1 0.37084 1 0.006788 1 0.082159 1 amp_10p11.22 95 (27%) 256 1.8411e-13 1.36e-10 1.7775e-06 0.00113 0.14425 1 0.60723 1 0.00064055 0.294 0.0022379 0.935 5.1079e-05 0.0286 0.00043619 0.207 0.0044695 1 0.00025644 0.128 amp_10q22.2 66 (19%) 285 1.3832e-09 9.71e-07 0.0088452 1 0.02757 1 0.47391 1 0.012941 1 0.011749 1 0.040363 1 0.14345 1 0.089456 1 0.033496 1 amp_10q26.13 71 (20%) 280 1.2894e-05 0.00762 0.0063576 1 0.037272 1 0.55366 1 0.0039336 1 0.0078824 1 0.18519 1 0.062646 1 1 1 0.028586 1 amp_11p13 66 (19%) 285 0.0029183 1 0.024317 1 0.64226 1 0.26302 1 0.00095356 0.428 1.1488e-05 0.00686 0.0048284 1 0.00010472 0.0556 0.13126 1 0.0028696 1 amp_11q13.3 85 (24%) 266 2.0564e-09 1.44e-06 0.012207 1 0.18591 1 0.76865 1 0.10673 1 0.0023605 0.973 5.6246e-06 0.00344 0.002036 0.861 6.9982e-05 0.0384 0.017575 1 amp_12p12.1 105 (30%) 246 7.4659e-06 0.00451 0.16434 1 0.42336 1 0.062255 1 0.18397 1 0.64174 1 0.04525 1 0.09113 1 0.012647 1 0.25003 1 amp_12q15 91 (26%) 260 1.999e-05 0.0116 0.44212 1 0.21104 1 0.42808 1 0.26337 1 0.50925 1 0.4838 1 0.095673 1 0.13616 1 0.54421 1 amp_13q12.3 136 (39%) 215 4.5782e-15 3.45e-12 6.2833e-05 0.0347 0.32276 1 0.54494 1 0.015211 1 0.21659 1 0.00016451 0.0844 0.00053446 0.249 0.013632 1 3.8079e-05 0.0216 amp_13q22.1 141 (40%) 210 3.5108e-15 2.65e-12 1.655e-05 0.00975 0.19505 1 0.22957 1 1.2615e-05 0.00748 0.0019977 0.848 1.2083e-05 0.0072 9.1974e-06 0.00552 0.00047711 0.224 2.4729e-08 1.68e-05 amp_15q26.1 83 (24%) 268 6.1844e-16 4.68e-13 1.9505e-05 0.0113 0.44726 1 0.69699 1 1.8814e-05 0.0109 4.3262e-06 0.00268 0.0070978 1 0.012311 1 0.010853 1 0.0036582 1 amp_17q12 110 (31%) 241 1.2312e-18 9.37e-16 9.0074e-08 6e-05 0.78008 1 0.5412 1 0.00010575 0.056 0.00029278 0.145 2.8504e-06 0.00179 0.00039953 0.191 0.04772 1 0.0010208 0.456 amp_18q11.2 112 (32%) 239 3.7922e-10 2.68e-07 0.0068623 1 0.29152 1 0.078182 1 0.01331 1 0.02659 1 0.0018022 0.768 0.0010324 0.459 0.021831 1 0.0090075 1 amp_19p13.2 40 (11%) 311 0.00044561 0.211 0.13808 1 0.86901 1 0.3264 1 0.72872 1 0.82916 1 0.73806 1 0.59397 1 0.87755 1 0.25756 1 amp_19q12 108 (31%) 243 3.9296e-22 3.03e-19 1.8802e-08 1.28e-05 0.0060919 1 0.16092 1 3.2577e-14 2.43e-11 3.3377e-08 2.26e-05 2.4594e-07 0.000161 1.3693e-13 1.02e-10 0.038423 1 1.8661e-13 1.38e-10 amp_20q13.2 233 (66%) 118 1.5839e-21 1.22e-18 5.4556e-10 3.85e-07 0.0063412 1 0.9294 1 5.6597e-08 3.79e-05 2.7609e-05 0.0158 1.0784e-07 7.13e-05 4.5543e-12 3.3e-09 0.010857 1 1.2261e-10 8.73e-08 amp_xq27.3 67 (19%) 284 0.00029078 0.144 0.0017641 0.753 0.58619 1 0.16714 1 0.17597 1 0.34489 1 0.030081 1 0.9696 1 0.04305 1 0.14856 1 del_1p36.11 100 (28%) 251 1.1793e-14 8.86e-12 3.2017e-10 2.27e-07 0.15705 1 0.23512 1 0.00032969 0.16 0.00010797 0.057 7.4629e-06 0.00451 1.398e-06 0.000891 0.0026699 1 7.8527e-06 0.00472 del_1p13.2 70 (20%) 281 9.6106e-13 7.03e-10 1.0327e-06 0.000662 0.077683 1 0.1911 1 0.00062784 0.289 0.00043072 0.205 0.0016655 0.716 0.0026401 1 0.39691 1 0.0092152 1 del_1q44 27 (8%) 324 0.022524 1 0.005429 1 0.17646 1 0.024255 1 0.35028 1 0.014264 1 0.0090895 1 0.015549 1 0.010167 1 0.092911 1 del_2q32.1 49 (14%) 302 0.010504 1 0.066047 1 0.46185 1 0.11598 1 0.11035 1 0.68317 1 0.045611 1 0.003917 1 0.47091 1 0.0158 1 del_2q37.2 53 (15%) 298 0.00020776 0.106 0.00046024 0.217 0.2682 1 0.12446 1 0.0045801 1 0.2644 1 0.00051632 0.241 7.7001e-06 0.00464 0.10306 1 1.478e-05 0.00872 del_3p26.1 109 (31%) 242 1.0227e-11 7.37e-09 0.00077159 0.352 0.33767 1 0.69262 1 0.0062731 1 0.0012264 0.536 0.00032903 0.16 0.00056859 0.264 0.011202 1 0.00016317 0.0839 del_3p14.2 127 (36%) 224 1.9822e-09 1.39e-06 1.2751e-05 0.00755 0.40193 1 0.9043 1 9.2143e-05 0.0496 3.7222e-05 0.0211 0.00031101 0.152 0.0027699 1 0.062984 1 2.9975e-05 0.0171 del_3q26.31 43 (12%) 308 3.8363e-06 0.00239 1.7685e-05 0.0103 0.12809 1 0.45595 1 0.00033771 0.163 0.00049527 0.232 0.00012845 0.0667 0.009881 1 0.012663 1 0.016619 1 del_4p16.3 135 (38%) 216 5.2491e-13 3.85e-10 0.00023664 0.12 0.45302 1 0.027909 1 1.0535e-05 0.0063 3.6612e-05 0.0208 2.4234e-06 0.00153 4.2578e-08 2.87e-05 0.00023677 0.12 9.585e-08 6.36e-05 del_4q22.1 153 (44%) 198 2.0251e-22 1.57e-19 6.1985e-06 0.00378 0.1097 1 0.3293 1 0.0023912 0.98 0.00032429 0.158 0.0023933 0.98 8.9956e-05 0.0487 0.11001 1 2.1326e-05 0.0123 del_4q34.3 155 (44%) 196 1.8614e-21 1.43e-18 1.0984e-06 0.000702 0.050961 1 0.57188 1 1.2415e-05 0.00737 2.7787e-05 0.0159 5.0264e-06 0.00309 2.9793e-07 0.000195 0.0043995 1 2.6741e-07 0.000175 del_5q11.2 129 (37%) 222 9.4094e-26 7.33e-23 4.7257e-15 3.56e-12 0.24069 1 0.42823 1 5.103e-13 3.75e-10 3.2953e-12 2.39e-09 9.6298e-11 6.87e-08 1.2096e-11 8.71e-09 2.6707e-08 1.81e-05 5.642e-15 4.24e-12 del_5q23.2 116 (33%) 235 1.6507e-25 1.28e-22 1.186e-14 8.9e-12 0.11868 1 0.46233 1 4.199e-13 3.09e-10 5.9638e-11 4.26e-08 1.5595e-11 1.12e-08 3.7487e-10 2.66e-07 9.4726e-08 6.3e-05 1.8041e-12 1.31e-09 del_6p25.3 85 (24%) 266 2.4639e-09 1.72e-06 4.3717e-05 0.0246 0.13445 1 0.090319 1 9.4835e-05 0.0508 1.8078e-05 0.0105 0.0022535 0.94 0.00061634 0.284 0.028794 1 0.011161 1 del_6q14.1 69 (20%) 282 2.4971e-08 1.7e-05 0.00037457 0.18 0.2178 1 0.86099 1 0.00042489 0.203 0.078101 1 0.81107 1 0.026336 1 0.76655 1 0.022232 1 del_6q26 77 (22%) 274 5.4211e-07 0.000352 0.0094832 1 0.77088 1 0.2273 1 0.0010363 0.46 0.0002646 0.132 0.49439 1 0.018109 1 0.22063 1 0.14472 1 del_7q31.1 50 (14%) 301 8.1092e-09 5.62e-06 6.9857e-06 0.00424 0.71098 1 0.64737 1 0.0044721 1 0.012964 1 0.0082144 1 0.034216 1 5.8893e-05 0.0326 0.067862 1 del_7q36.3 75 (21%) 276 9.5866e-21 7.34e-18 9.732e-05 0.0521 0.38825 1 0.79977 1 3.1727e-06 0.00199 5.4286e-06 0.00333 9.7828e-05 0.0522 8.1605e-07 0.000526 0.0021037 0.887 6.5235e-06 0.00397 del_8p23.2 93 (26%) 258 1.8465e-14 1.38e-11 0.00024254 0.122 0.061859 1 0.28302 1 7.1047e-06 0.00431 4.9024e-06 0.00301 0.0042104 1 1.0732e-06 0.000687 0.016897 1 1.7688e-06 0.00112 del_9p23 149 (42%) 202 2.8671e-22 2.22e-19 6.8086e-05 0.0374 0.028121 1 0.20766 1 4.4313e-06 0.00273 0.00021692 0.11 0.01108 1 0.0022996 0.952 0.55909 1 6.4396e-05 0.0355 del_9p21.3 145 (41%) 206 4.3182e-23 3.35e-20 3.7787e-07 0.000246 4.9251e-05 0.0276 0.022662 1 2.5597e-09 1.78e-06 1.7266e-05 0.0101 0.012037 1 0.00044217 0.21 0.17189 1 3.7754e-06 0.00235 del_9q21.11 90 (26%) 261 4.077e-13 3.01e-10 0.003663 1 0.14062 1 0.1247 1 0.0010886 0.481 0.018709 1 0.00081084 0.369 0.0035894 1 0.051816 1 1.7373e-05 0.0102 del_10q22.3 56 (16%) 295 3.4069e-11 2.44e-08 0.024799 1 0.73023 1 0.76077 1 0.00015142 0.0783 0.0023774 0.977 0.0012481 0.544 0.0067602 1 0.067771 1 0.013028 1 del_10q23.31 84 (24%) 267 1.4599e-13 1.08e-10 9.2553e-05 0.0497 0.065512 1 0.33174 1 8.6403e-07 0.000556 0.0021512 0.904 5.4699e-05 0.0304 0.00011634 0.061 0.09342 1 0.00031603 0.155 del_11p15.4 74 (21%) 277 6.0478e-13 4.43e-10 5.2613e-05 0.0293 1.8401e-06 0.00116 0.0016645 0.716 0.00073948 0.339 7.6642e-05 0.0418 0.17937 1 0.0057545 1 0.49832 1 0.0031319 1 del_11q23.2 75 (21%) 276 1.231e-05 0.00732 0.010483 1 0.56652 1 0.72662 1 0.0022196 0.93 0.53085 1 0.18195 1 0.074532 1 0.30118 1 0.087337 1 del_12p13.1 54 (15%) 297 1.7713e-13 1.31e-10 2.984e-08 2.02e-05 0.51926 1 1 1 2.9624e-06 0.00186 6.305e-07 0.000409 0.06055 1 0.028125 1 0.12918 1 0.00029273 0.145 del_13q12.11 50 (14%) 301 1.4443e-08 9.88e-06 0.099795 1 0.41333 1 0.13777 1 0.04605 1 0.024495 1 0.34597 1 0.15866 1 0.53304 1 0.05831 1 del_14q12 91 (26%) 260 3.4571e-12 2.51e-09 5.5368e-05 0.0307 0.58408 1 0.75459 1 0.000346 0.167 0.00016535 0.0847 0.00017612 0.0898 0.0014072 0.611 0.013631 1 0.00010377 0.0552 del_14q32.33 102 (29%) 249 1.5581e-10 1.11e-07 0.00013954 0.0723 0.97705 1 0.37771 1 0.00055669 0.259 7.4475e-06 0.00451 0.010247 1 0.041346 1 0.0029056 1 0.00087806 0.396 del_15q15.1 97 (28%) 254 3.8967e-13 2.88e-10 2.985e-07 0.000195 0.0036937 1 0.058303 1 5.6329e-08 3.77e-05 1.3234e-08 9.09e-06 4.0719e-06 0.00253 9.599e-09 6.61e-06 6.8081e-05 0.0374 9.8239e-07 0.000632 del_16p13.3 71 (20%) 280 3.9896e-14 2.98e-11 0.00046725 0.22 0.69762 1 0.95532 1 8.0643e-09 5.6e-06 2.3393e-09 1.64e-06 4.2479e-06 0.00263 1.7247e-05 0.0101 1.0236e-06 0.000657 2.4337e-06 0.00153 del_16q23.1 141 (40%) 210 1.4591e-08 9.97e-06 0.01253 1 0.46402 1 0.13498 1 0.0016053 0.692 0.00011184 0.0589 0.0010535 0.467 0.0046792 1 0.00029585 0.146 0.00012067 0.0631 del_17p12 134 (38%) 217 7.0448e-25 5.47e-22 1.3369e-14 1e-11 0.39789 1 0.88864 1 9.4025e-09 6.49e-06 5.5845e-08 3.75e-05 9.9438e-06 0.00596 4.3585e-08 2.93e-05 0.00011372 0.0598 4.3147e-11 3.08e-08 del_17q24.3 64 (18%) 287 1.3575e-08 9.31e-06 2.2883e-05 0.0132 0.1827 1 0.44773 1 0.0012058 0.528 0.0039769 1 0.0027928 1 0.0051726 1 0.023586 1 0.0054795 1 del_18q21.2 162 (46%) 189 2.5945e-18 1.97e-15 0.00011478 0.0603 0.66232 1 0.47202 1 0.00032424 0.158 0.0023481 0.97 0.00029639 0.146 0.013137 1 0.011375 1 0.021869 1 del_19p13.3 123 (35%) 228 3.9242e-29 3.06e-26 5.6652e-14 4.22e-11 0.0021027 0.887 0.34827 1 4.4591e-17 3.38e-14 8.76e-19 6.68e-16 2.6437e-09 1.84e-06 1.2125e-21 9.35e-19 4.7829e-05 0.0268 1.2235e-19 9.36e-17 del_19q13.11 53 (15%) 298 6.944e-10 4.89e-07 8.1121e-09 5.62e-06 0.20366 1 0.49942 1 0.0001212 0.0633 0.00099873 0.447 7.916e-05 0.043 2.4525e-05 0.0141 0.0011203 0.493 0.00012789 0.0665 del_20p12.1 28 (8%) 323 0.0058276 1 0.00091974 0.414 0.64401 1 1 1 0.009171 1 0.067884 1 0.0032098 1 0.17339 1 0.48199 1 0.040052 1 del_21q11.2 130 (37%) 221 4.0595e-11 2.91e-08 3.8569e-05 0.0218 0.34044 1 0.19399 1 0.0016939 0.725 1.2641e-06 0.000806 0.00033685 0.163 0.0072385 1 0.0043041 1 0.0059899 1 del_21q22.13 142 (40%) 209 4.2352e-13 3.12e-10 0.0056092 1 0.10262 1 0.44014 1 0.0015471 0.668 4.7658e-06 0.00294 0.0022604 0.94 0.0010216 0.456 0.014305 1 0.0033014 1 del_22q13.31 122 (35%) 229 4.5249e-19 3.45e-16 4.9627e-08 3.33e-05 0.048934 1 0.50256 1 0.00083712 0.379 0.0001592 0.0821 7.8522e-05 0.0427 7.4752e-08 4.99e-05 0.027395 1 4.3775e-06 0.00271 del_xp22.2 66 (19%) 285 2.44e-11 1.75e-08 7.9552e-05 0.0431 0.34916 1 0.85906 1 0.00028399 0.141 0.029362 1 0.054454 1 0.00010157 0.0541 0.33951 1 0.024855 1 del_xp21.1 63 (18%) 288 3.4786e-08 2.35e-05 0.018624 1 0.092228 1 0.57358 1 0.02426 1 0.079292 1 0.57573 1 0.18525 1 0.44391 1 0.35507 1 del_xq21.33 45 (13%) 306 7.2808e-05 0.0398 0.00041348 0.198 0.79725 1 0.76523 1 0.0077396 1 0.012211 1 0.015816 1 0.097408 1 0.031848 1 0.050816 1