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 1p gain 32 (7%) 406 0.81076 1 0.63643 1 0.079269 1 0.76508 1 0.01125 1 0.073969 1 0.84021 1 0.25919 1 0.67669 1 0.10173 1 0.79492 1 0.74199 1 1q gain 79 (18%) 359 0.87263 1 0.66623 1 0.0098499 1 0.15684 1 0.23922 1 0.01297 1 0.35876 1 0.39475 1 0.88382 1 0.086779 1 0.03277 1 0.80165 1 2p gain 77 (18%) 361 0.071399 1 0.02096 1 7.9999e-05 0.0641 0.0070999 1 0.11132 1 0.13063 1 3e-05 0.0247 0.01004 1 0.40514 1 0.01469 1 0.29522 1 0.00154 1 2q gain 73 (17%) 365 0.071039 1 0.02185 1 5.9999e-05 0.0486 0.00399 1 0.28807 1 0.14534 1 0.00069999 0.528 0.0076999 1 0.49214 1 0.072639 1 0.49287 1 0.10149 1 3p gain 43 (10%) 395 0.13888 1 0.0071799 1 2e-05 0.0166 0.25117 1 0.14393 1 0.12513 1 0.38231 1 0.36636 1 0.68864 1 0.84881 1 0.63148 1 0.25486 1 3q gain 62 (14%) 376 0.094759 1 0.00013 0.103 9.9999e-06 0.00927 0.050929 1 0.091619 1 0.2839 1 0.11607 1 0.04133 1 0.67007 1 0.63898 1 0.15238 1 0.66088 1 4p gain 11 (3%) 427 NA NA NA NA 0.0074699 1 0.12616 1 0.31522 1 0.92314 1 0.32522 1 0.86155 1 0.6101 1 0.57656 1 0.5063 1 0.7144 1 4q gain 16 (4%) 422 0.12682 1 0.1189 1 0.00175 1 0.79286 1 0.0068899 1 0.12029 1 0.10986 1 0.41589 1 0.14761 1 0.13292 1 0.39319 1 0.78227 1 5p gain 66 (15%) 372 0.41543 1 0.18021 1 0.00045 0.346 0.41419 1 0.46729 1 0.99755 1 0.1049 1 0.12266 1 0.81894 1 0.36118 1 0.22657 1 0.78622 1 5q gain 41 (9%) 397 0.87406 1 0.77528 1 0.00255 1 0.50026 1 0.47425 1 0.64016 1 0.098859 1 0.074949 1 0.50907 1 0.095209 1 0.77444 1 0.9473 1 6p gain 82 (19%) 356 0.21368 1 3e-05 0.0247 9.9999e-06 0.00927 0.2262 1 0.56443 1 0.98886 1 0.0054799 1 0.01815 1 0.58952 1 0.97438 1 0.00193 1 0.11457 1 6q gain 74 (17%) 364 0.18542 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.32959 1 0.95686 1 0.5198 1 0.079359 1 0.15553 1 0.52478 1 0.95485 1 0.00017 0.134 0.12686 1 7p gain 238 (54%) 200 0.0057099 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.00032 0.248 2e-04 0.157 0.00209 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.53755 1 0.47777 1 3e-05 0.0247 0.0097299 1 7q gain 215 (49%) 223 0.00371 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.01344 1 0.0058199 1 0.0097799 1 4e-05 0.0326 9.9999e-06 0.00927 0.46847 1 0.65727 1 2e-05 0.0166 0.01407 1 8p gain 126 (29%) 312 0.97526 1 0.96484 1 3e-05 0.0247 0.96055 1 0.43794 1 0.16382 1 0.0060599 1 0.063299 1 0.51201 1 0.11651 1 0.96602 1 0.059009 1 8q gain 217 (50%) 221 0.88294 1 0.01675 1 9.9999e-06 0.00927 0.02994 1 0.12778 1 0.04063 1 0.00354 1 0.00038 0.293 0.71493 1 0.01999 1 0.0246 1 0.066179 1 9p gain 76 (17%) 362 0.19432 1 0.13671 1 0.086489 1 0.82129 1 0.00198 1 0.38407 1 0.76756 1 0.25782 1 0.87557 1 0.92407 1 0.078089 1 0.77909 1 9q gain 66 (15%) 372 0.16602 1 0.20159 1 0.35949 1 0.49377 1 0.00039 0.301 0.56994 1 0.93652 1 0.65264 1 0.42253 1 0.26313 1 0.31054 1 0.76408 1 10p gain 32 (7%) 406 0.59832 1 1 1 0.0059999 1 0.86466 1 0.02113 1 0.070439 1 0.060319 1 0.50759 1 0.42622 1 0.72074 1 0.0084299 1 0.37603 1 10q gain 18 (4%) 420 0.16952 1 0.44143 1 0.0082599 1 0.10716 1 0.36426 1 0.5961 1 0.78293 1 0.88871 1 0.75507 1 0.86392 1 0.03732 1 0.45639 1 11p gain 52 (12%) 386 0.00060999 0.464 0.00012 0.0955 9.9999e-06 0.00927 0.00019 0.15 0.091929 1 0.43233 1 0.0084599 1 0.00013 0.103 0.82046 1 0.00471 1 0.03141 1 0.04701 1 11q gain 49 (11%) 389 0.00023 0.18 9.9999e-06 0.00927 9.9999e-06 0.00927 0.0023 1 0.02885 1 0.60002 1 8.9999e-05 0.0719 9.9999e-06 0.00927 0.62715 1 0.0063099 1 0.0073399 1 0.02413 1 12p gain 90 (21%) 348 0.17665 1 1 1 0.01944 1 0.0068799 1 0.72706 1 0.7669 1 0.97352 1 0.14391 1 0.28086 1 0.41767 1 0.46146 1 0.73427 1 12q gain 83 (19%) 355 0.19744 1 0.89793 1 0.01163 1 0.0053399 1 0.54628 1 0.79289 1 0.90983 1 0.22083 1 0.11109 1 0.10229 1 0.26993 1 0.63118 1 13q gain 250 (57%) 188 5.9999e-05 0.0486 9.9999e-06 0.00927 9.9999e-06 0.00927 0.00058999 0.449 0.03149 1 0.093179 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.43273 1 0.73926 1 9.9999e-06 0.00927 0.00388 1 14q gain 34 (8%) 404 0.33798 1 0.63491 1 0.00225 1 0.92374 1 0.40581 1 0.75858 1 0.2703 1 0.19663 1 0.67338 1 0.18141 1 0.32255 1 0.89213 1 15q gain 12 (3%) 426 1 1 0.80875 1 0.02531 1 0.8096 1 0.081009 1 0.080389 1 1 1 0.94053 1 0.92179 1 0.76496 1 0.67524 1 0.76093 1 16p gain 103 (24%) 335 9.9999e-05 0.0797 9.9999e-06 0.00927 9.9999e-06 0.00927 0.16538 1 0.1583 1 0.10384 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.57122 1 0.18648 1 0.01183 1 0.01495 1 16q gain 101 (23%) 337 3e-05 0.0247 9.9999e-06 0.00927 9.9999e-06 0.00927 0.25418 1 0.18266 1 0.15483 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.80549 1 0.18159 1 0.00202 1 0.00182 1 17p gain 27 (6%) 411 0.83901 1 0.56442 1 0.28876 1 0.44674 1 0.20944 1 0.4296 1 0.86221 1 0.17948 1 0.51984 1 0.82771 1 0.9391 1 0.18842 1 17q gain 80 (18%) 358 0.1208 1 0.056039 1 9.9999e-06 0.00927 0.00037 0.286 0.36184 1 0.027 1 9.9999e-06 0.00927 0.00037 0.286 0.0070999 1 0.096579 1 0.073229 1 0.03747 1 18p gain 22 (5%) 416 0.091219 1 0.67358 1 2e-04 0.157 0.00095999 0.718 0.82973 1 0.89342 1 0.12358 1 5.9999e-05 0.0486 0.27041 1 0.17682 1 0.45182 1 0.47639 1 18q gain 13 (3%) 425 0.14376 1 1 1 0.0072899 1 0.0084499 1 0.67692 1 0.47339 1 0.01118 1 9.9999e-06 0.00927 0.5575 1 0.18798 1 0.2434 1 0.43972 1 19p gain 68 (16%) 370 0.14809 1 0.074999 1 3e-05 0.0247 0.04535 1 0.25798 1 0.26666 1 0.43762 1 0.00105 0.783 0.074469 1 0.23954 1 0.0057699 1 0.11954 1 19q gain 77 (18%) 361 0.11379 1 0.055009 1 0.00312 1 0.21938 1 0.04235 1 0.04092 1 0.35264 1 0.00023 0.18 0.14835 1 0.64316 1 0.02394 1 0.057369 1 20p gain 236 (54%) 202 0.00317 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.00054999 0.42 0.04307 1 0.23474 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.70349 1 0.070849 1 0.00128 0.951 0.00476 1 20q gain 312 (71%) 126 9.9999e-06 0.00927 9.9999e-06 0.00927 9.9999e-06 0.00927 9.9999e-06 0.00927 0.00046 0.353 0.00056999 0.435 9.9999e-06 0.00927 9.9999e-06 0.00927 0.79581 1 0.00109 0.811 9.9999e-06 0.00927 9.9999e-06 0.00927 21q gain 22 (5%) 416 0.0359 1 0.29842 1 0.04511 1 0.81375 1 0.72951 1 0.97259 1 0.95545 1 0.46621 1 0.2209 1 0.26598 1 0.37133 1 1 1 22q gain 12 (3%) 426 1 1 0.79056 1 0.16182 1 0.12831 1 0.60474 1 0.32136 1 0.36926 1 0.37874 1 1 1 0.68644 1 0.51721 1 0.40714 1 xq gain 71 (16%) 367 0.01327 1 0.26382 1 0.0065999 1 0.11659 1 0.19927 1 0.43867 1 0.14922 1 0.59171 1 0.37518 1 0.95231 1 0.1572 1 0.71047 1 1p loss 96 (22%) 342 0.0261 1 0.17977 1 9.9999e-06 0.00927 0.00198 1 0.58268 1 0.77246 1 5.9999e-05 0.0486 9.9999e-06 0.00927 0.77924 1 0.02189 1 0.00464 1 0.00062999 0.478 1q loss 54 (12%) 384 0.4092 1 0.58015 1 2e-05 0.0166 0.080659 1 0.64586 1 0.78253 1 0.0051799 1 0.01472 1 0.64397 1 0.00179 1 0.0069399 1 0.0066599 1 2p loss 6 (1%) 432 0.89799 1 0.81268 1 0.0134 1 NA NA 0.70087 1 0.78849 1 0.14383 1 0.44357 1 0.64047 1 0.48102 1 NA NA NA NA 2q loss 7 (2%) 431 1 1 0.50562 1 0.093219 1 NA NA 0.30924 1 0.43908 1 0.0462 1 0.28623 1 0.38689 1 0.24412 1 NA NA NA NA 3p loss 53 (12%) 385 0.77877 1 0.48832 1 0.00191 1 0.34777 1 0.59622 1 0.62605 1 0.03105 1 0.15234 1 0.61153 1 0.6047 1 0.00057999 0.442 0.21375 1 3q loss 33 (8%) 405 0.82228 1 1 1 0.01987 1 0.76219 1 0.40686 1 0.87186 1 0.19912 1 0.46128 1 0.2614 1 0.93293 1 0.01488 1 0.60856 1 4p loss 132 (30%) 306 6.9999e-05 0.0563 0.00139 1 9.9999e-06 0.00927 0.00016 0.127 0.10333 1 0.36204 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.46108 1 0.38123 1 2e-05 0.0166 0.03274 1 4q loss 120 (27%) 318 0.00027 0.21 0.0091899 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.10598 1 0.25187 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.25726 1 0.25138 1 4e-05 0.0326 0.0060199 1 5p loss 54 (12%) 384 0.78054 1 0.94573 1 5.9999e-05 0.0486 0.00447 1 0.36247 1 0.7309 1 0.01113 1 0.01847 1 0.8367 1 0.73079 1 0.098739 1 0.78004 1 5q loss 74 (17%) 364 0.16514 1 0.30316 1 9.9999e-06 0.00927 0.01256 1 0.02349 1 0.14481 1 8.9999e-05 0.0719 0.0062399 1 0.90317 1 0.69681 1 0.00218 1 0.57075 1 6p loss 33 (8%) 405 1 1 0.45587 1 0.00178 1 0.36746 1 0.17443 1 0.13827 1 0.50503 1 0.95927 1 0.61702 1 0.78524 1 0.03211 1 0.6585 1 6q loss 45 (10%) 393 0.82346 1 1 1 0.00327 1 0.42422 1 0.19918 1 0.097809 1 0.32414 1 0.5187 1 0.61007 1 0.96366 1 0.32518 1 0.67848 1 7q loss 3 (1%) 435 NA NA NA NA 0.14239 1 0.48104 1 NA NA NA NA 0.71357 1 0.91361 1 0.56229 1 0.62798 1 NA NA NA NA 8p loss 137 (31%) 301 0.02329 1 0.00093999 0.705 9.9999e-06 0.00927 3e-04 0.233 0.01755 1 0.02018 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.58281 1 0.15288 1 9.9999e-06 0.00927 0.00404 1 8q loss 24 (5%) 414 0.81042 1 0.40121 1 0.01446 1 0.3663 1 0.27116 1 0.46732 1 0.01717 1 0.055329 1 0.52601 1 0.54912 1 0.13911 1 0.145 1 9p loss 51 (12%) 387 0.56818 1 0.064429 1 9.9999e-06 0.00927 0.00106 0.79 0.90887 1 0.35993 1 0.00087999 0.662 0.00067999 0.514 0.3717 1 0.2783 1 0.00070999 0.535 0.27739 1 9q loss 51 (12%) 387 0.11857 1 0.060089 1 9.9999e-06 0.00927 6.9999e-05 0.0563 0.97639 1 0.66206 1 0.00081999 0.617 0.0027 1 0.44631 1 0.16518 1 3e-05 0.0247 0.090369 1 10p loss 66 (15%) 372 0.02079 1 0.02476 1 9.9999e-06 0.00927 0.00142 1 0.0134 1 0.35277 1 0.011 1 0.00027 0.21 0.49707 1 0.2334 1 0.00144 1 0.01528 1 10q loss 70 (16%) 368 0.0237 1 0.04188 1 9.9999e-06 0.00927 0.00039 0.301 0.01225 1 0.17587 1 0.00133 0.986 9.9999e-06 0.00927 0.61159 1 0.39144 1 0.00017 0.134 0.0056099 1 11p loss 49 (11%) 389 0.22449 1 0.19349 1 0.00025 0.195 0.0071599 1 0.8079 1 0.87064 1 0.01175 1 0.03018 1 0.90974 1 0.24011 1 2e-05 0.0166 0.20831 1 11q loss 61 (14%) 377 0.04076 1 0.01507 1 0.00021 0.165 0.00098999 0.74 0.60431 1 0.93052 1 0.02756 1 0.00302 1 0.84027 1 0.68225 1 0.00023 0.18 0.058159 1 12p loss 46 (11%) 392 0.060369 1 0.0075599 1 9.9999e-06 0.00927 0.0060899 1 0.41103 1 0.79897 1 0.00354 1 6.9999e-05 0.0563 0.88 1 0.40825 1 0.00281 1 0.084789 1 12q loss 49 (11%) 389 0.10981 1 0.0072199 1 9.9999e-06 0.00927 0.0073299 1 0.52369 1 0.687 1 0.00046 0.353 0.00017 0.134 0.95398 1 0.68334 1 0.00065999 0.5 0.01546 1 13q loss 12 (3%) 426 0.87368 1 0.43837 1 0.054439 1 0.04081 1 0.00155 1 0.091259 1 0.17181 1 0.9711 1 0.59907 1 0.10431 1 0.078399 1 0.15944 1 14q loss 134 (31%) 304 9.9999e-06 0.00927 3e-05 0.0247 9.9999e-06 0.00927 2e-05 0.0166 0.00187 1 0.02372 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.25127 1 0.02124 1 4e-05 0.0326 0.00175 1 15q loss 150 (34%) 288 0.00153 1 0.00154 1 9.9999e-06 0.00927 0.00061999 0.471 0.01174 1 0.03824 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.86229 1 0.77311 1 5.9999e-05 0.0486 0.00087999 0.662 16p loss 31 (7%) 407 0.40594 1 0.68781 1 0.24528 1 0.3859 1 0.38781 1 0.01299 1 0.50403 1 0.43648 1 0.50064 1 0.48096 1 0.24963 1 0.97968 1 16q loss 28 (6%) 410 0.40378 1 0.68847 1 0.066299 1 0.5767 1 0.21668 1 0.03312 1 0.57207 1 0.7794 1 0.52272 1 0.75443 1 0.22904 1 1 1 17p loss 229 (52%) 209 9.9999e-06 0.00927 9.9999e-06 0.00927 9.9999e-06 0.00927 9.9999e-06 0.00927 0.01974 1 0.00409 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.7975 1 0.03899 1 9.9999e-06 0.00927 0.00093999 0.705 17q loss 62 (14%) 376 0.11076 1 0.516 1 0.00219 1 0.0079899 1 0.56627 1 0.61959 1 0.00025 0.195 0.04546 1 0.36063 1 0.30221 1 0.0064899 1 0.00015 0.119 18p loss 245 (56%) 193 9.9999e-06 0.00927 9.9999e-06 0.00927 9.9999e-06 0.00927 9.9999e-06 0.00927 0.00139 1 0.00404 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.99073 1 0.01904 1 9.9999e-06 0.00927 4e-05 0.0326 18q loss 262 (60%) 176 9.9999e-06 0.00927 9.9999e-06 0.00927 9.9999e-06 0.00927 9.9999e-06 0.00927 0.0062799 1 0.00342 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.74614 1 0.01227 1 9.9999e-06 0.00927 7.9999e-05 0.0641 19p loss 41 (9%) 397 1 1 0.34288 1 0.01335 1 0.25161 1 0.61053 1 0.38659 1 0.01621 1 0.0072799 1 0.04027 1 0.00256 1 0.48563 1 0.04765 1 19q loss 36 (8%) 402 0.73444 1 0.70713 1 0.01116 1 0.37202 1 0.2312 1 0.13018 1 0.01497 1 0.01114 1 0.28924 1 0.067479 1 0.26609 1 0.13567 1 20p loss 43 (10%) 395 0.088959 1 0.00227 1 9.9999e-06 0.00927 0.092249 1 0.90871 1 0.25967 1 0.080659 1 0.02355 1 0.8265 1 0.04595 1 0.060229 1 0.23732 1 20q loss 4 (1%) 434 NA NA NA NA 0.73469 1 NA NA NA NA NA NA 0.20803 1 0.58465 1 0.38819 1 0.30445 1 NA NA NA NA 21q loss 120 (27%) 318 0.0095399 1 0.085289 1 9.9999e-06 0.00927 0.052289 1 0.22538 1 0.59652 1 0.00131 0.972 0.01814 1 0.45472 1 0.051589 1 0.00174 1 0.069369 1 22q loss 141 (32%) 297 3e-04 0.233 4e-04 0.308 9.9999e-06 0.00927 0.00143 1 0.17735 1 0.30527 1 9.9999e-06 0.00927 9.9999e-06 0.00927 0.18708 1 0.39955 1 5e-05 0.0405 0.00238 1 xq loss 51 (12%) 387 0.01605 1 0.24682 1 0.00049 0.375 0.13528 1 0.11219 1 0.38643 1 0.088529 1 0.22178 1 0.079749 1 0.59746 1 0.04745 1 0.19451 1