Clinical Features MRNA_CNMF MRNA_CHIERARCHICAL 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 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 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 Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q amp_1p34.3 138 (27%) 377 0.55185 1 0.58033 1 9.9999e-06 0.00888 0.25989 1 0.01097 1 0.16 1 0.052449 1 0.00191 1 0.11397 1 0.0094399 1 0.30461 1 0.0065199 1 amp_1p22.3 141 (27%) 374 0.87619 1 1 1 9.9999e-06 0.00888 0.12466 1 0.01658 1 0.50761 1 0.04186 1 0.01572 1 0.12271 1 0.03791 1 0.42443 1 0.17648 1 amp_1q21.3 376 (73%) 139 0.36088 1 0.521 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.10966 1 0.0293 1 0.00464 1 9.9999e-06 0.00888 0.00396 1 0.00072999 0.415 0.00441 1 0.24021 1 amp_3q26.2 170 (33%) 345 0.00029 0.174 0.00145 0.795 9.9999e-06 0.00888 9.9999e-06 0.00888 0.4739 1 0.01737 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.46258 1 2e-05 0.0136 amp_4q12 96 (19%) 419 0.70437 1 0.25608 1 9.9999e-06 0.00888 0.11738 1 0.14106 1 0.01451 1 0.00428 1 0.0073899 1 0.0069499 1 0.00169 0.913 0.82674 1 0.0011 0.613 amp_5p15.33 334 (65%) 181 0.87789 1 0.8051 1 9.9999e-06 0.00888 0.069059 1 0.01541 1 0.0125 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.00132 0.73 0.00093999 0.528 0.40641 1 9.9999e-06 0.00888 amp_5p13.1 304 (59%) 211 0.26247 1 1 1 9.9999e-06 0.00888 0.00487 1 0.10054 1 0.04959 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-05 0.0626 0.00026 0.156 0.22499 1 9.9999e-06 0.00888 amp_6p21.1 189 (37%) 326 0.67422 1 0.25448 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.10006 1 0.46736 1 0.00357 1 0.00079999 0.454 0.02577 1 0.00471 1 0.34854 1 0.02747 1 amp_7p11.2 273 (53%) 242 0.95939 1 0.90178 1 9.9999e-06 0.00888 0.00132 0.73 0.0016 0.87 0.0060999 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 6.9999e-05 0.0447 9.9999e-06 0.00888 amp_7q31.2 216 (42%) 299 0.48157 1 0.3111 1 9.9999e-06 0.00888 0.00148 0.808 0.082819 1 0.12 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.00055999 0.322 0.00305 1 0.14434 1 9.9999e-06 0.00888 amp_8p11.23 137 (27%) 378 0.29389 1 0.10075 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.6921 1 0.96046 1 9.9999e-06 0.00888 0.00017 0.105 0.01684 1 0.0051399 1 0.50406 1 0.01744 1 amp_8p11.21 174 (34%) 341 0.2529 1 0.44457 1 9.9999e-06 0.00888 0.00032 0.19 0.29965 1 0.92741 1 9.9999e-06 0.00888 2e-05 0.0136 3e-04 0.179 9.9999e-05 0.0626 0.0194 1 0.00019 0.116 amp_8q11.1 234 (45%) 281 0.0049 1 0.03931 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.25518 1 0.9575 1 9.9999e-06 0.00888 9.9999e-06 0.00888 2e-05 0.0136 0.00014 0.0868 0.00111 0.617 9.9999e-06 0.00888 amp_8q24.21 324 (63%) 191 0.03493 1 0.087769 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.50533 1 0.79026 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.00102 0.571 0.074299 1 9.9999e-06 0.00888 amp_10p15.1 141 (27%) 374 0.0229 1 0.01586 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.0068199 1 0.055649 1 4e-05 0.0261 9.9999e-06 0.00888 5e-05 0.0324 2e-05 0.0136 0.03788 1 0.00067999 0.388 amp_11q13.3 174 (34%) 341 0.0066199 1 0.00265 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.03027 1 0.91073 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.57145 1 0.00017 0.105 amp_12p12.1 179 (35%) 336 0.19633 1 0.03819 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.03798 1 0.44704 1 9.9999e-06 0.00888 9.9999e-06 0.00888 2e-05 0.0136 3e-05 0.0199 0.67723 1 9.9999e-06 0.00888 amp_12q14.1 170 (33%) 345 0.40795 1 0.28622 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.33835 1 0.55092 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.34793 1 9.9999e-06 0.00888 amp_12q15 171 (33%) 344 0.22204 1 0.1369 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.20908 1 0.097089 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.35225 1 9.9999e-06 0.00888 amp_13q33.3 77 (15%) 438 0.46401 1 0.51997 1 0.090229 1 7.9999e-05 0.0506 0.19387 1 0.92334 1 0.47416 1 0.02112 1 0.15197 1 0.11983 1 0.65207 1 0.04149 1 amp_14q13.3 230 (45%) 285 0.79669 1 0.53936 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.057099 1 0.86616 1 9.9999e-06 0.00888 9.9999e-06 0.00888 2e-05 0.0136 9.9999e-06 0.00888 0.18506 1 0.00013 0.0809 amp_16p11.2 168 (33%) 347 0.80185 1 0.39158 1 9.9999e-06 0.00888 0.0070399 1 0.1554 1 0.22557 1 0.33066 1 0.058749 1 0.03453 1 0.10456 1 0.40609 1 0.1821 1 amp_17q12 227 (44%) 288 0.090149 1 0.0334 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.31008 1 0.01687 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.54274 1 9.9999e-06 0.00888 amp_17q23.1 249 (48%) 266 0.078849 1 0.30265 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.24061 1 0.056599 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 3e-05 0.0199 0.7007 1 3e-05 0.0199 amp_18q11.2 104 (20%) 411 0.19352 1 0.01956 1 0.00099999 0.561 9.9999e-06 0.00888 0.078519 1 0.23157 1 7.9999e-05 0.0506 0.00012 0.0749 0.00014 0.0868 5e-05 0.0324 0.45734 1 6.9999e-05 0.0447 amp_19q12 139 (27%) 376 0.050879 1 0.0104 1 7.9999e-05 0.0506 9.9999e-06 0.00888 0.7659 1 0.35285 1 2e-04 0.122 9.9999e-06 0.00888 9.9999e-06 0.00888 0.00032 0.19 0.061089 1 4e-05 0.0261 amp_20q13.33 250 (49%) 265 0.0055499 1 0.04468 1 9.9999e-06 0.00888 3e-05 0.0199 0.04353 1 0.36316 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.058699 1 3e-05 0.0199 amp_22q11.22 90 (17%) 425 0.2701 1 0.12682 1 9.9999e-06 0.00888 0.36166 1 0.01288 1 0.21073 1 0.5607 1 0.061949 1 0.03976 1 0.04191 1 0.72857 1 0.01657 1 amp_xq28 158 (31%) 357 0.29918 1 0.24264 1 9.9999e-06 0.00888 6.9999e-05 0.0447 0.31963 1 0.55241 1 5e-05 0.0324 4e-05 0.0261 0.0101 1 0.089619 1 0.26017 1 5e-04 0.289 del_1p36.13 120 (23%) 395 0.79631 1 0.38128 1 9.9999e-06 0.00888 0.0025 1 0.69466 1 0.10326 1 8.9999e-05 0.0566 9.9999e-06 0.00888 0.01129 1 0.13399 1 0.01101 1 0.02454 1 del_1p13.1 151 (29%) 364 0.61916 1 0.45436 1 9.9999e-06 0.00888 0.00090999 0.513 0.12644 1 0.054749 1 0.00017 0.105 0.00024 0.144 0.15631 1 0.00222 1 0.84128 1 0.77738 1 del_2q22.1 45 (9%) 470 0.86936 1 0.78082 1 0.00036 0.212 0.01126 1 0.1857 1 0.44887 1 0.02412 1 0.0051699 1 0.01693 1 0.00468 1 0.94775 1 0.03799 1 del_3p26.2 232 (45%) 283 0.094249 1 0.24063 1 2e-05 0.0136 0.00045 0.263 0.055139 1 0.37743 1 0.093259 1 9.9999e-06 0.00888 3e-05 0.0199 0.00013 0.0809 0.8131 1 0.00026 0.156 del_3p21.31 247 (48%) 268 0.13274 1 0.34772 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.0345 1 0.21926 1 0.01693 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.66039 1 2e-05 0.0136 del_3q11.1 139 (27%) 376 0.6122 1 0.6864 1 0.13039 1 0.02198 1 0.7704 1 0.76598 1 0.084369 1 0.0016 0.87 0.21533 1 0.69373 1 0.60348 1 0.859 1 del_3q29 135 (26%) 380 0.71125 1 0.61572 1 0.12492 1 0.00021 0.127 0.13939 1 0.02808 1 7.9999e-05 0.0506 9.9999e-06 0.00888 0.85329 1 0.04256 1 0.14677 1 0.24636 1 del_4p16.3 130 (25%) 385 0.59614 1 0.30881 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.83733 1 0.39769 1 2e-05 0.0136 2e-05 0.0136 9.9999e-06 0.00888 9.9999e-06 0.00888 0.6107 1 0.00035 0.207 del_4q34.3 186 (36%) 329 0.00193 1 0.00309 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.13601 1 0.25468 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.02394 1 9.9999e-06 0.00888 del_5q12.1 179 (35%) 336 0.25982 1 0.16626 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.03009 1 0.40498 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.02284 1 9.9999e-06 0.00888 del_5q31.1 210 (41%) 305 0.092979 1 0.242 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.083559 1 0.42928 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.35889 1 9.9999e-06 0.00888 del_6q11.1 139 (27%) 376 0.95289 1 1 1 0.31155 1 0.088539 1 0.3937 1 0.92388 1 0.66381 1 0.83465 1 0.03077 1 0.20063 1 0.73165 1 0.077359 1 del_6q22.31 255 (50%) 260 0.54206 1 0.14077 1 0.00483 1 9.9999e-06 0.00888 0.12902 1 0.01609 1 0.02736 1 0.00015 0.0927 0.70597 1 0.00147 0.804 0.6658 1 0.28711 1 del_6q26 257 (50%) 258 0.36885 1 0.33363 1 0.00037 0.218 0.00069999 0.398 0.075259 1 0.082329 1 0.10276 1 0.00489 1 0.77114 1 0.01351 1 0.51561 1 0.19086 1 del_8p23.2 252 (49%) 263 0.00497 1 0.0098099 1 9.9999e-06 0.00888 0.00060999 0.35 0.02244 1 0.00038 0.223 9.9999e-06 0.00888 9.9999e-06 0.00888 5e-05 0.0324 0.00448 1 0.01372 1 0.00017 0.105 del_8p11.21 125 (24%) 390 0.79431 1 0.5076 1 9.9999e-06 0.00888 0.17522 1 0.77982 1 0.03512 1 0.0083599 1 0.059009 1 0.1519 1 0.57276 1 0.5411 1 0.13021 1 del_9p23 286 (56%) 229 0.52246 1 0.80582 1 0.00047 0.274 0.2617 1 0.79432 1 0.2426 1 0.00353 1 5.9999e-05 0.0385 0.12009 1 0.02811 1 0.28453 1 0.21478 1 del_9p21.3 292 (57%) 223 0.52216 1 0.80449 1 0.00023 0.139 0.13236 1 0.51097 1 0.02943 1 2e-05 0.0136 2e-05 0.0136 0.13989 1 0.0024 1 0.04424 1 0.10568 1 del_9q21.11 257 (50%) 258 0.03375 1 0.48416 1 3e-05 0.0199 5.9999e-05 0.0385 0.24231 1 0.04168 1 0.00264 1 5.9999e-05 0.0385 5e-05 0.0324 9.9999e-06 0.00888 0.21947 1 0.00019 0.116 del_10p15.3 125 (24%) 390 1 1 0.84523 1 5e-05 0.0324 0.01074 1 0.13792 1 0.12128 1 0.0053099 1 0.00083999 0.475 0.00142 0.78 0.01661 1 0.03255 1 0.0126 1 del_10q26.3 147 (29%) 368 0.61597 1 0.33855 1 9.9999e-06 0.00888 0.01404 1 0.00131 0.726 0.00316 1 3e-05 0.0199 9.9999e-06 0.00888 0.0079099 1 0.00021 0.127 0.02287 1 0.00031 0.185 del_11p15.5 142 (28%) 373 0.26524 1 0.03182 1 9.9999e-06 0.00888 0.00139 0.764 0.62366 1 0.33424 1 0.00043 0.252 9.9999e-06 0.00888 0.00019 0.116 0.00043 0.252 0.069549 1 0.00046 0.268 del_11q23.2 120 (23%) 395 0.43093 1 0.84634 1 9.9999e-06 0.00888 0.00441 1 0.03765 1 0.33584 1 6.9999e-05 0.0447 0.00289 1 0.00199 1 0.04066 1 0.04563 1 0.30951 1 del_11q25 116 (23%) 399 0.10678 1 0.48508 1 3e-05 0.0199 0.01102 1 0.00419 1 0.14768 1 0.00023 0.139 0.01111 1 0.086029 1 0.17486 1 0.11922 1 0.4558 1 del_12p13.2 139 (27%) 376 0.25603 1 0.89867 1 0.00106 0.593 0.0052899 1 0.16611 1 0.063269 1 0.00163 0.883 0.00292 1 0.80168 1 0.9765 1 0.49115 1 0.085179 1 del_12q12 98 (19%) 417 0.59954 1 0.75101 1 0.00033 0.195 0.11692 1 0.13587 1 0.067609 1 0.0063699 1 0.02286 1 0.056179 1 0.21183 1 0.90197 1 0.02634 1 del_12q24.33 130 (25%) 385 0.062409 1 0.071619 1 9.9999e-06 0.00888 0.068579 1 0.062649 1 0.18468 1 4e-05 0.0261 9.9999e-06 0.00888 0.14695 1 0.01798 1 0.55358 1 0.46291 1 del_13q12.11 293 (57%) 222 0.00106 0.593 0.03843 1 9.9999e-06 0.00888 0.01137 1 0.0066699 1 0.00047 0.274 9.9999e-06 0.00888 9.9999e-06 0.00888 0.00319 1 0.00375 1 0.24463 1 0.00047 0.274 del_13q12.13 292 (57%) 223 0.0086499 1 0.063779 1 9.9999e-06 0.00888 0.00482 1 0.0088299 1 0.00082999 0.47 9.9999e-06 0.00888 9.9999e-06 0.00888 0.00442 1 0.0056799 1 0.21279 1 0.00053999 0.311 del_13q14.2 282 (55%) 233 0.0086699 1 0.064889 1 9.9999e-06 0.00888 0.02338 1 0.00478 1 0.00148 0.808 9.9999e-06 0.00888 9.9999e-06 0.00888 0.00168 0.909 0.0069799 1 0.04925 1 8.9999e-05 0.0566 del_13q34 241 (47%) 274 0.03578 1 0.11227 1 9.9999e-06 0.00888 0.16558 1 0.00133 0.733 0.01478 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.0097799 1 0.02712 1 0.22633 1 0.01772 1 del_14q32.33 150 (29%) 365 0.70121 1 0.2864 1 0.00472 1 0.73829 1 0.7708 1 0.3469 1 0.21292 1 0.097119 1 0.02096 1 0.287 1 0.21787 1 0.072249 1 del_15q11.2 263 (51%) 252 0.1676 1 0.29992 1 9.9999e-06 0.00888 0.00051999 0.3 0.03599 1 0.00177 0.954 9.9999e-06 0.00888 9.9999e-06 0.00888 2e-05 0.0136 0.0154 1 0.27085 1 9.9999e-06 0.00888 del_16q23.1 169 (33%) 346 0.060339 1 0.87713 1 2e-05 0.0136 8.9999e-05 0.0566 0.21906 1 0.00091999 0.518 9.9999e-06 0.00888 9.9999e-06 0.00888 0.0278 1 0.00255 1 0.86102 1 0.00059999 0.344 del_17p13.3 278 (54%) 237 0.38542 1 0.78738 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.00049 0.284 0.00062999 0.36 9.9999e-06 0.00888 9.9999e-06 0.00888 0.0087899 1 0.01825 1 0.60327 1 0.00113 0.627 del_18q21.32 254 (49%) 261 0.11281 1 0.079469 1 9.9999e-06 0.00888 0.76822 1 0.01934 1 0.00016 0.0987 3e-05 0.0199 5.9999e-05 0.0385 0.01092 1 0.16511 1 0.86216 1 0.055499 1 del_18q23 249 (48%) 266 0.02916 1 0.02548 1 9.9999e-06 0.00888 0.59552 1 0.0071999 1 6.9999e-05 0.0447 9.9999e-06 0.00888 4e-05 0.0261 0.0074699 1 0.18274 1 0.80419 1 0.056979 1 del_19p13.3 275 (53%) 240 0.57275 1 0.81318 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.51082 1 0.23463 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.1199 1 0.00031 0.185 del_19p13.2 268 (52%) 247 0.69329 1 1 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.89528 1 0.082199 1 2e-05 0.0136 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.055729 1 0.00012 0.0749 del_19q13.33 194 (38%) 321 0.27436 1 0.25572 1 9.9999e-06 0.00888 0.00066999 0.383 0.20411 1 0.21174 1 0.00192 1 2e-05 0.0136 2e-05 0.0136 9.9999e-06 0.00888 0.57651 1 0.01186 1 del_20p13 130 (25%) 385 0.10562 1 0.22341 1 9.9999e-06 0.00888 0.00236 1 0.00344 1 0.00044 0.257 2e-05 0.0136 9.9999e-06 0.00888 0.95384 1 0.70585 1 0.36814 1 0.01566 1 del_20q13.12 82 (16%) 433 0.17086 1 0.57856 1 0.44992 1 0.26385 1 0.10954 1 0.12945 1 0.18518 1 0.04146 1 0.14686 1 0.15771 1 0.04403 1 0.25685 1 del_21q11.2 176 (34%) 339 0.060619 1 0.04748 1 9.9999e-06 0.00888 0.00022 0.133 0.0124 1 0.23264 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 2e-05 0.0136 0.48985 1 9.9999e-06 0.00888 del_22q13.32 250 (49%) 265 0.02547 1 0.080829 1 9.9999e-06 0.00888 9.9999e-06 0.00888 0.73858 1 0.44265 1 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 9.9999e-06 0.00888 0.01597 1 9.9999e-06 0.00888 del_xp22.2 144 (28%) 371 0.68934 1 0.89222 1 9.9999e-06 0.00888 0.00205 1 0.092049 1 0.01138 1 0.00017 0.105 3e-04 0.179 0.34134 1 0.58602 1 0.96154 1 0.10431 1