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_1q21.2 258 (51%) 243 0.03902 1 0.10056 1 9.9999e-06 0.00996 2e-05 0.0176 0.18011 1 0.073799 1 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 0.00112 0.824 0.00378 1 amp_2p16.1 275 (55%) 226 0.00143 1 0.00028 0.223 9.9999e-06 0.00996 2e-05 0.0176 0.94974 1 0.6719 1 9.9999e-06 0.00996 2e-05 0.0176 0.00029 0.23 0.00066999 0.511 0.03137 1 3e-05 0.026 amp_2q31.2 172 (34%) 329 0.0186 1 0.02294 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.72453 1 0.63871 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.00267 1 0.25552 1 0.0033 1 0.00057999 0.445 amp_3q26.33 452 (90%) 49 0.00034 0.267 0.00054999 0.423 9.9999e-06 0.00996 9.9999e-06 0.00996 0.26371 1 0.03247 1 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-05 0.0842 9.9999e-06 0.00996 0.01873 1 6.9999e-05 0.0593 amp_4q12 119 (24%) 382 0.88151 1 0.88204 1 0.00167 1 0.069369 1 0.29517 1 0.13211 1 0.061319 1 0.58189 1 0.03369 1 0.34995 1 0.39428 1 0.03514 1 amp_5p15.33 387 (77%) 114 0.85377 1 0.79875 1 9.9999e-06 0.00996 0.03353 1 0.40464 1 0.3709 1 0.49088 1 0.064689 1 0.53931 1 0.0057799 1 0.47805 1 0.27984 1 amp_5p12 354 (71%) 147 0.95735 1 0.76031 1 9.9999e-06 0.00996 0.01063 1 0.21906 1 0.93457 1 0.36462 1 0.9005 1 0.70934 1 0.077159 1 0.063849 1 0.71038 1 amp_6p12.1 166 (33%) 335 0.65034 1 0.49347 1 2e-05 0.0176 0.052559 1 0.92656 1 0.54408 1 0.00069999 0.532 0.062819 1 0.57173 1 0.11744 1 0.21326 1 0.00017 0.14 amp_6q12 152 (30%) 349 0.93687 1 0.72876 1 2e-05 0.0176 0.00098999 0.736 0.49638 1 0.60154 1 0.0011 0.811 0.0054999 1 0.74248 1 0.02271 1 0.052259 1 0.0066899 1 amp_7p11.2 256 (51%) 245 0.11422 1 0.0298 1 9.9999e-06 0.00996 0.00217 1 0.70267 1 0.59716 1 0.00197 1 2e-05 0.0176 0.15536 1 0.04647 1 0.0453 1 0.32993 1 amp_7q21.2 264 (53%) 237 0.10366 1 0.01539 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.075479 1 0.55537 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.00022 0.178 0.00083999 0.634 0.00175 1 0.00088999 0.667 amp_8p11.23 238 (48%) 263 0.01326 1 0.092319 1 0.00014 0.116 0.01897 1 0.19138 1 0.24834 1 0.059689 1 0.056479 1 0.87182 1 0.17299 1 0.59244 1 0.32902 1 amp_8q24.21 352 (70%) 149 0.91957 1 0.78004 1 0.02048 1 0.335 1 0.82356 1 0.57006 1 0.81398 1 0.55072 1 0.2793 1 0.25656 1 0.84568 1 0.89845 1 amp_9p13.3 136 (27%) 365 0.12264 1 0.71628 1 0.00167 1 0.00202 1 0.071329 1 0.00296 1 0.0017 1 0.00149 1 0.0059499 1 0.00319 1 0.01816 1 0.01225 1 amp_11q13.3 185 (37%) 316 0.04882 1 0.03382 1 3e-05 0.026 3e-04 0.237 0.26063 1 0.33665 1 0.03 1 0.064319 1 0.00143 1 0.00468 1 0.1907 1 0.00284 1 amp_12p13.33 255 (51%) 246 0.0080299 1 0.02194 1 9.9999e-06 0.00996 0.00088999 0.667 0.35026 1 0.63687 1 9.9999e-06 0.00996 0.00176 1 0.13408 1 0.00268 1 0.25516 1 0.0059199 1 amp_12q15 178 (36%) 323 0.13366 1 0.34462 1 4e-05 0.0343 0.0154 1 0.76651 1 0.43774 1 0.0060799 1 0.01053 1 0.35779 1 0.64417 1 0.02441 1 0.00359 1 amp_13q34 91 (18%) 410 0.98182 1 0.83318 1 0.38213 1 0.71332 1 0.87088 1 0.21516 1 0.74378 1 0.10492 1 0.01273 1 0.03471 1 0.96891 1 0.46503 1 amp_14q13.3 159 (32%) 342 0.35658 1 0.02686 1 0.15916 1 0.13416 1 0.64885 1 0.078929 1 0.10206 1 0.00239 1 0.01842 1 0.10982 1 0.74896 1 0.84262 1 amp_14q32.33 158 (32%) 343 0.03047 1 0.01527 1 0.00212 1 0.00109 0.806 0.02523 1 0.40238 1 0.00077999 0.59 0.00043 0.335 0.51784 1 0.43343 1 0.054909 1 0.12668 1 amp_15q26.3 179 (36%) 322 0.36175 1 0.050029 1 9.9999e-06 0.00996 0.00051999 0.401 0.46487 1 0.02714 1 8.9999e-05 0.0759 0.003 1 0.03858 1 0.0063799 1 0.0075999 1 0.00424 1 amp_17q25.1 236 (47%) 265 0.0087999 1 0.13609 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.40384 1 0.523 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.00046 0.357 0.00467 1 0.00129 0.939 0.00024 0.194 amp_18p11.32 179 (36%) 322 0.04295 1 0.00424 1 9.9999e-06 0.00996 3e-05 0.026 0.5027 1 0.97881 1 0.04153 1 0.00132 0.958 0.01811 1 0.095959 1 0.075399 1 0.00027 0.215 amp_18q11.2 151 (30%) 350 0.00036 0.282 0.01515 1 9.9999e-06 0.00996 3e-05 0.026 0.25446 1 0.74575 1 9.9999e-06 0.00996 5.9999e-05 0.0511 0.0123 1 0.0028 1 0.050499 1 5.9999e-05 0.0511 amp_19q12 224 (45%) 277 0.37059 1 0.64775 1 9.9999e-06 0.00996 0.00175 1 0.23208 1 0.35766 1 0.00296 1 0.02834 1 0.72453 1 0.56234 1 0.0076999 1 0.00221 1 amp_19q13.2 234 (47%) 267 0.3408 1 0.25685 1 9.9999e-06 0.00996 0.00296 1 0.37123 1 0.4896 1 0.00488 1 0.080569 1 0.79631 1 0.50316 1 0.03117 1 0.01339 1 amp_20p12.2 280 (56%) 221 0.00113 0.829 0.0022 1 9.9999e-06 0.00996 0.00021 0.171 0.90309 1 0.32934 1 0.0171 1 0.0148 1 0.089969 1 0.64823 1 0.57293 1 0.53368 1 amp_20q11.21 306 (61%) 195 0.81188 1 0.50507 1 9.9999e-06 0.00996 0.0058099 1 0.78005 1 0.73578 1 0.63353 1 0.94435 1 0.27544 1 0.36821 1 0.59185 1 0.20092 1 amp_22q11.21 256 (51%) 245 0.11383 1 0.16024 1 0.00016 0.132 0.00092999 0.696 0.85944 1 0.6174 1 0.00013 0.108 0.00016 0.132 0.16579 1 0.04205 1 0.5858 1 0.27851 1 amp_xq28 124 (25%) 377 0.88707 1 0.87239 1 0.01082 1 0.04883 1 0.03492 1 0.077379 1 0.0478 1 0.30568 1 0.20299 1 0.16517 1 0.0165 1 0.03304 1 del_1p36.11 228 (46%) 273 3e-05 0.026 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 0.054679 1 0.00352 1 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 del_1p13.1 221 (44%) 280 0.00015 0.124 3e-05 0.026 9.9999e-06 0.00996 9.9999e-06 0.00996 0.02409 1 0.20673 1 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 0.00026 0.208 9.9999e-06 0.00996 del_2p25.3 50 (10%) 451 0.12155 1 0.45859 1 0.090229 1 0.39481 1 0.25485 1 0.36581 1 0.6749 1 0.60567 1 0.0076899 1 0.36502 1 0.04681 1 0.02947 1 del_2q22.1 131 (26%) 370 0.32097 1 0.33632 1 9.9999e-06 0.00996 0.00021 0.171 0.38378 1 0.42458 1 0.00223 1 0.0070999 1 0.00021 0.171 0.00045 0.35 0.01879 1 0.02519 1 del_2q37.1 159 (32%) 342 0.00297 1 0.00058999 0.452 9.9999e-06 0.00996 9.9999e-06 0.00996 0.38531 1 0.18947 1 9.9999e-06 0.00996 2e-05 0.0176 9.9999e-06 0.00996 3e-05 0.026 9.9999e-06 0.00996 9.9999e-06 0.00996 del_3p25.3 398 (79%) 103 0.38524 1 0.20112 1 0.00173 1 0.00097999 0.729 0.88223 1 0.22815 1 0.00297 1 0.00026 0.208 0.0085199 1 0.00019 0.155 0.01503 1 0.081829 1 del_3p13 434 (87%) 67 0.25479 1 0.35271 1 9.9999e-06 0.00996 0.00025 0.201 0.78459 1 0.00099999 0.741 0.00072999 0.553 0.00083999 0.634 0.00253 1 9.9999e-06 0.00996 0.00085999 0.647 0.00025 0.201 del_3p12.3 427 (85%) 74 0.27729 1 0.22761 1 9.9999e-06 0.00996 3e-04 0.237 0.93638 1 0.00178 1 0.00071999 0.546 0.00475 1 0.02258 1 9.9999e-06 0.00996 0.00054999 0.423 0.00115 0.843 del_3p12.3 421 (84%) 80 0.22854 1 0.39765 1 9.9999e-06 0.00996 0.00027 0.215 0.96977 1 0.0064799 1 0.00244 1 0.0076899 1 0.02647 1 3e-05 0.026 0.00221 1 0.00252 1 del_3q11.1 79 (16%) 422 0.76598 1 0.77967 1 0.22554 1 0.94828 1 0.76318 1 0.60104 1 0.76947 1 0.17241 1 0.92332 1 0.51888 1 0.33843 1 0.73666 1 del_4p15.2 317 (63%) 184 0.00021 0.171 5.9999e-05 0.0511 9.9999e-06 0.00996 9.9999e-06 0.00996 0.77601 1 0.063109 1 0.00016 0.132 9.9999e-06 0.00996 0.00225 1 0.051299 1 0.00011 0.0923 3e-05 0.026 del_4q22.1 285 (57%) 216 0.00307 1 0.00486 1 9.9999e-06 0.00996 0.00144 1 0.11583 1 0.51289 1 0.00013 0.108 0.0145 1 0.01633 1 0.0058399 1 0.056659 1 0.01738 1 del_4q32.3 329 (66%) 172 0.0057999 1 0.01869 1 9.9999e-06 0.00996 5.9999e-05 0.0511 0.067119 1 0.77827 1 2e-05 0.0176 0.00028 0.223 0.00062999 0.481 0.00246 1 0.0042 1 9.9999e-06 0.00996 del_4q35.2 331 (66%) 170 0.068589 1 0.20248 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.36208 1 0.86236 1 9.9999e-06 0.00996 0.0033 1 0.00041 0.32 0.0078899 1 0.04863 1 9.9999e-06 0.00996 del_5q12.1 369 (74%) 132 0.48599 1 0.43145 1 9.9999e-06 0.00996 2e-05 0.0176 0.93703 1 0.46221 1 0.00195 1 0.00128 0.933 0.01089 1 9.9999e-06 0.00996 0.064019 1 0.00321 1 del_5q31.1 386 (77%) 115 0.15833 1 0.27555 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.36916 1 0.52196 1 0.01543 1 0.0071699 1 0.00387 1 9.9999e-06 0.00996 0.080159 1 0.00108 0.799 del_6p25.3 134 (27%) 367 0.45587 1 0.2849 1 0.00038 0.298 0.00011 0.0923 0.20143 1 0.0066899 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.13785 1 0.00085999 0.647 0.11279 1 0.18312 1 del_6q22.31 122 (24%) 379 0.03968 1 0.00342 1 0.00025 0.201 0.00191 1 0.47776 1 0.51058 1 0.00084999 0.64 0.01726 1 0.26316 1 0.20937 1 0.19838 1 0.37063 1 del_6q26 134 (27%) 367 0.04202 1 0.00407 1 0.00016 0.132 9.9999e-05 0.0842 0.92116 1 0.65741 1 0.00050999 0.394 0.0054999 1 0.01737 1 0.073059 1 0.03296 1 0.10447 1 del_7q11.22 48 (10%) 453 0.8009 1 0.70089 1 0.00117 0.855 0.78869 1 0.84829 1 0.3196 1 0.00202 1 0.00098999 0.736 0.64458 1 0.3749 1 0.65627 1 0.90587 1 del_7q36.3 104 (21%) 397 0.17065 1 0.0479 1 0.00435 1 0.29064 1 0.97427 1 0.098979 1 0.00024 0.194 0.00132 0.958 0.30385 1 0.00447 1 0.77264 1 0.04642 1 del_8p23.2 341 (68%) 160 0.59066 1 0.70565 1 2e-05 0.0176 0.01385 1 0.24302 1 0.35969 1 0.11371 1 0.092919 1 0.31825 1 0.063269 1 0.38921 1 0.04209 1 del_9p23 332 (66%) 169 0.01054 1 0.00188 1 9.9999e-06 0.00996 0.01972 1 0.19338 1 0.16885 1 0.00012 0.1 0.00109 0.806 0.01087 1 0.00019 0.155 0.62283 1 0.1283 1 del_9p21.3 388 (77%) 113 0.19732 1 0.25912 1 9.9999e-06 0.00996 0.29242 1 0.81171 1 0.59692 1 0.00058999 0.452 0.01647 1 0.45174 1 0.01166 1 0.37897 1 0.02293 1 del_9p21.1 326 (65%) 175 0.14012 1 0.28418 1 2e-05 0.0176 0.17572 1 0.70891 1 0.63033 1 0.00032 0.252 0.00028 0.223 0.35622 1 0.0091199 1 0.15608 1 0.35854 1 del_9q21.11 251 (50%) 250 0.00024 0.194 5e-05 0.0426 9.9999e-06 0.00996 9.9999e-06 0.00996 0.55616 1 0.14463 1 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 9.9999e-06 0.00996 0.051089 1 0.0090599 1 del_10p15.2 219 (44%) 282 0.2619 1 0.46712 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.14591 1 0.14225 1 9.9999e-06 0.00996 0.00015 0.124 4e-05 0.0343 9.9999e-06 0.00996 0.02415 1 0.01002 1 del_10q23.31 268 (53%) 233 0.00323 1 0.00096999 0.723 9.9999e-06 0.00996 9.9999e-06 0.00996 0.14945 1 0.2478 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.00118 0.861 4e-05 0.0343 0.02158 1 0.00019 0.155 del_11p15.5 245 (49%) 256 0.00038 0.298 0.01111 1 9.9999e-06 0.00996 0.00459 1 0.00047 0.364 0.00026 0.208 0.0063899 1 0.081729 1 0.00046 0.357 0.088819 1 0.73268 1 0.00435 1 del_11q22.1 162 (32%) 339 0.55934 1 0.2564 1 0.00134 0.97 0.00062999 0.481 0.15041 1 0.96378 1 0.01396 1 0.03949 1 0.00443 1 0.02846 1 0.21593 1 0.14716 1 del_11q25 184 (37%) 317 0.80084 1 0.70636 1 0.00167 1 0.050499 1 0.17406 1 0.68909 1 0.0167 1 0.14584 1 0.03176 1 0.14886 1 0.3781 1 0.12469 1 del_12q24.31 86 (17%) 415 0.91473 1 0.59932 1 0.40484 1 0.2584 1 0.20135 1 0.67981 1 0.51978 1 0.69796 1 0.70743 1 0.33091 1 0.39808 1 0.17132 1 del_13q12.11 331 (66%) 170 0.10526 1 0.5677 1 0.00356 1 0.1244 1 0.90976 1 0.18071 1 0.81369 1 0.97028 1 0.23141 1 0.38244 1 0.00428 1 0.00395 1 del_13q14.2 344 (69%) 157 0.11944 1 0.10047 1 0.00322 1 0.02075 1 0.70693 1 0.72985 1 0.43107 1 0.57369 1 0.073049 1 0.14653 1 0.0015 1 0.0198 1 del_14q11.2 175 (35%) 326 0.03845 1 0.03393 1 0.53596 1 0.98994 1 0.26037 1 0.16601 1 0.00014 0.116 0.00023 0.186 0.02289 1 0.01021 1 0.00068999 0.525 0.0327 1 del_15q11.2 167 (33%) 334 0.56393 1 0.52141 1 0.15937 1 0.12992 1 0.088949 1 0.02765 1 0.19339 1 0.060779 1 0.02426 1 0.53933 1 0.26306 1 0.1268 1 del_15q21.1 169 (34%) 332 0.45266 1 0.76099 1 0.01606 1 0.20089 1 0.088549 1 0.0069399 1 0.27411 1 0.24748 1 0.00305 1 0.097939 1 0.35853 1 0.17165 1 del_16p13.3 187 (37%) 314 0.25705 1 0.44514 1 0.00411 1 0.04963 1 0.20765 1 0.25869 1 0.51353 1 0.91657 1 0.17379 1 0.63284 1 0.0092999 1 0.10036 1 del_16q23.1 210 (42%) 291 0.93048 1 0.11307 1 0.01422 1 0.21239 1 0.35377 1 0.84835 1 0.069099 1 0.03872 1 0.0066899 1 0.44479 1 0.00032 0.252 0.00029 0.23 del_17p11.2 272 (54%) 229 0.24267 1 0.11275 1 0.00048 0.372 0.56571 1 0.15723 1 0.0084099 1 0.12711 1 0.01596 1 0.30888 1 0.02694 1 0.23096 1 0.15324 1 del_17q11.2 132 (26%) 369 9.9999e-05 0.0842 5.9999e-05 0.0511 9.9999e-06 0.00996 9.9999e-06 0.00996 0.38898 1 0.56396 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.00416 1 0.00116 0.849 0.27424 1 0.00043 0.335 del_17q25.3 102 (20%) 399 0.00429 1 0.01191 1 6.9999e-05 0.0593 0.03059 1 0.62322 1 0.99444 1 0.00152 1 0.00135 0.976 0.64519 1 0.01375 1 0.77474 1 0.10471 1 del_18q23 234 (47%) 267 0.59978 1 0.17159 1 0.0054999 1 0.2074 1 0.88691 1 0.18863 1 0.78986 1 0.47944 1 0.50221 1 0.53676 1 0.10594 1 0.64576 1 del_19p13.3 236 (47%) 265 0.44897 1 0.23322 1 4e-05 0.0343 0.78024 1 0.094459 1 0.16362 1 0.065739 1 0.02277 1 0.1828 1 0.00092999 0.696 0.79423 1 0.053539 1 del_19q13.32 149 (30%) 352 0.82665 1 0.591 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.16371 1 0.53566 1 0.01465 1 0.0074399 1 0.03766 1 0.50328 1 0.01389 1 0.15104 1 del_21q11.2 246 (49%) 255 0.56372 1 0.5624 1 4e-05 0.0343 0.14937 1 0.98248 1 0.72819 1 0.086299 1 0.46929 1 0.00074999 0.568 0.00018 0.147 0.18517 1 0.01516 1 del_21q22.3 281 (56%) 220 0.77594 1 0.12631 1 9.9999e-06 0.00996 0.0429 1 0.5109 1 0.061309 1 0.151 1 0.076019 1 0.0098699 1 3e-04 0.237 0.01427 1 0.04678 1 del_22q11.21 95 (19%) 406 0.02957 1 0.096699 1 0.14204 1 0.066199 1 0.13023 1 0.35491 1 0.1522 1 0.00018 0.147 0.73224 1 0.40245 1 0.25761 1 0.14352 1 del_22q13.32 128 (26%) 373 0.00017 0.14 0.01321 1 0.22419 1 0.01532 1 0.40195 1 0.21379 1 0.00012 0.1 9.9999e-06 0.00996 0.27122 1 0.00049 0.379 0.52208 1 0.1647 1 del_xp22.2 155 (31%) 346 0.71343 1 0.52389 1 2e-05 0.0176 0.00012 0.1 0.35535 1 0.71253 1 0.0118 1 0.0098699 1 0.11941 1 0.10975 1 0.00022 0.178 7.9999e-05 0.0676 del_xp21.1 152 (30%) 349 0.45692 1 0.48024 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.27257 1 0.75284 1 7.9999e-05 0.0676 0.00094999 0.709 0.0060699 1 0.00129 0.939 2e-05 0.0176 9.9999e-06 0.00996 del_xp11.3 149 (30%) 352 0.097209 1 0.40025 1 9.9999e-06 0.00996 9.9999e-06 0.00996 0.10746 1 0.064979 1 0.00016 0.132 0.00229 1 0.00012 0.1 0.00056999 0.438 2e-05 0.0176 9.9999e-06 0.00996 del_xq22.3 114 (23%) 387 0.02106 1 0.01024 1 9.9999e-06 0.00996 2e-05 0.0176 0.8697 1 0.8888 1 0.00112 0.824 0.33265 1 0.0059099 1 0.00016 0.132 0.0081199 1 0.00025 0.201