Molecular subtypes MRNA_CNMF MRNA_CHIERARCHICAL MIR_CNMF MIR_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 Fisher's exact test_P Fisher's exact test_Q Fisher's exact test_P Fisher's exact test_Q Amp Peak 1(1p34.3) 0 (0%) 288 0.28519 1 0.13763 1 0.071972 1 0.20016 1 4.7527e-06 0.00445 0.15339 1 0.12133 1 0.7837 1 0.60208 1 0.1044 1 0.069358 1 0.092226 1 0.047893 1 0.53567 1 Amp Peak 2(1q21.3) 0 (0%) 213 0.1858 1 0.11218 1 0.53581 1 0.18765 1 2.9346e-11 2.84e-08 0.0001027 0.0938 0.06009 1 0.0099903 1 0.62753 1 0.27957 1 0.91555 1 0.97204 1 0.78448 1 0.97836 1 Amp Peak 3(1q42.2) 0 (0%) 257 0.020382 1 0.043502 1 0.87255 1 0.12823 1 5.5536e-09 5.31e-06 5.8886e-06 0.0055 0.27927 1 0.20673 1 0.61994 1 0.41838 1 0.18305 1 0.26977 1 0.25807 1 0.21879 1 Amp Peak 4(2p23.2) 0 (0%) 330 0.30202 1 0.16926 1 0.40928 1 0.050084 1 2.1875e-08 2.08e-05 0.004492 1 0.2232 1 0.65841 1 0.031553 1 0.75122 1 0.91142 1 0.11482 1 0.9605 1 0.63774 1 Amp Peak 5(2q31.2) 0 (0%) 319 0.047364 1 0.086451 1 0.15133 1 0.32485 1 1.9013e-10 1.83e-07 0.0027652 1 0.057514 1 0.50728 1 0.22903 1 0.52213 1 0.4562 1 0.66373 1 0.21844 1 0.085553 1 Amp Peak 6(3q26.2) 0 (0%) 96 0.0070511 1 0.057035 1 0.63748 1 0.095416 1 4.0093e-11 3.87e-08 0.083523 1 0.55374 1 0.55333 1 0.016628 1 0.046345 1 0.12268 1 0.43241 1 0.56208 1 0.65945 1 Amp Peak 7(4p16.3) 0 (0%) 414 0.9548 1 0.4729 1 0.044712 1 0.92727 1 0.0001028 0.0938 0.042062 1 0.24406 1 0.76876 1 0.7495 1 0.45544 1 0.6437 1 0.66442 1 0.67608 1 0.42174 1 Amp Peak 8(4q13.3) 0 (0%) 464 0.88726 1 0.97999 1 0.2452 1 0.93385 1 4.5911e-06 0.0043 0.11695 1 0.31225 1 0.14892 1 0.14795 1 0.93527 1 0.97634 1 0.10761 1 0.82891 1 0.47991 1 Amp Peak 9(5p15.33) 0 (0%) 270 0.66712 1 0.92826 1 0.8622 1 0.040392 1 2.2615e-07 0.000215 0.061365 1 0.98199 1 0.4769 1 0.17489 1 0.92737 1 0.013829 1 0.43615 1 0.067736 1 0.38166 1 Amp Peak 10(6p22.3) 0 (0%) 278 0.086057 1 0.042485 1 0.67026 1 0.41747 1 1.6854e-09 1.61e-06 0.12701 1 0.0709 1 0.052988 1 0.83343 1 0.070896 1 0.30352 1 0.43388 1 0.12391 1 0.29539 1 Amp Peak 11(7q36.3) 0 (0%) 265 0.067654 1 0.035878 1 0.51287 1 0.95282 1 7.0246e-06 0.00655 0.41153 1 0.068269 1 0.24191 1 0.96189 1 0.76385 1 0.1648 1 0.14332 1 0.022747 1 0.21057 1 Amp Peak 12(8p11.21) 0 (0%) 367 0.068767 1 0.13628 1 0.11711 1 0.26306 1 8.8309e-08 8.39e-05 0.003506 1 0.036499 1 0.26168 1 0.35177 1 0.21615 1 0.90478 1 0.67237 1 0.59857 1 0.69348 1 Amp Peak 13(8q24.21) 0 (0%) 122 3.9697e-07 0.000376 1.5723e-05 0.0146 0.25383 1 0.00078931 0.704 1.7577e-17 1.72e-14 0.0026451 1 0.9599 1 0.59521 1 4.5152e-07 0.000427 2.4637e-05 0.0228 0.14209 1 0.040558 1 0.083995 1 0.083616 1 Amp Peak 14(10p15.3) 0 (0%) 329 0.87711 1 0.37736 1 0.073199 1 0.12147 1 4.1528e-12 4.03e-09 2.8521e-05 0.0264 0.56203 1 0.40842 1 0.34409 1 0.30582 1 0.46509 1 0.94504 1 0.79793 1 0.65187 1 Amp Peak 15(10q22.3) 0 (0%) 394 0.78566 1 0.69335 1 0.65207 1 0.11616 1 0.35453 1 0.99317 1 0.52683 1 0.9776 1 0.074943 1 0.33248 1 0.11244 1 0.15069 1 0.68998 1 0.33593 1 Amp Peak 16(11q14.1) 0 (0%) 319 0.0064817 1 0.0049999 1 0.56336 1 0.21298 1 1.1906e-09 1.14e-06 0.021087 1 0.60018 1 0.22203 1 0.0037819 1 0.0040494 1 0.20461 1 0.82698 1 0.23264 1 0.89979 1 Amp Peak 17(12p13.33) 0 (0%) 251 0.028147 1 0.023934 1 0.16177 1 0.08021 1 1.0241e-10 9.86e-08 3.0438e-05 0.0281 0.31408 1 0.61446 1 0.012405 1 0.13745 1 0.31956 1 0.9209 1 0.6568 1 0.35729 1 Amp Peak 18(12p12.1) 0 (0%) 268 0.32495 1 0.14473 1 0.88945 1 0.14199 1 9.0547e-15 8.84e-12 5.7299e-06 0.00536 0.81857 1 0.49251 1 0.021381 1 0.13261 1 0.20164 1 0.69951 1 0.50396 1 0.58053 1 Amp Peak 19(12q15) 0 (0%) 359 0.0044953 1 0.0027565 1 0.85303 1 0.32525 1 1.4297e-08 1.36e-05 3.1575e-05 0.0291 0.20395 1 0.32802 1 0.0032364 1 0.00033957 0.307 0.66489 1 0.6198 1 0.7172 1 0.53986 1 Amp Peak 20(14q11.2) 0 (0%) 426 0.0072273 1 0.033396 1 0.37444 1 0.0045106 1 0.045837 1 0.22791 1 0.393 1 0.28794 1 0.25505 1 0.33311 1 0.2343 1 0.33494 1 0.26707 1 0.27863 1 Amp Peak 21(14q32.33) 0 (0%) 419 0.27132 1 0.049598 1 0.74162 1 0.28692 1 0.00015466 0.14 0.31792 1 1 1 0.67109 1 0.18485 1 0.57834 1 0.50815 1 0.7803 1 0.51279 1 0.58436 1 Amp Peak 22(15q26.3) 0 (0%) 413 0.090797 1 0.19582 1 0.82011 1 0.72512 1 8.6878e-10 8.34e-07 0.75745 1 0.97809 1 0.25265 1 0.15745 1 0.94533 1 0.11883 1 0.36343 1 0.18081 1 0.40422 1 Amp Peak 23(17q25.3) 0 (0%) 362 0.53106 1 0.84653 1 0.83099 1 0.12467 1 0.0025792 1 0.90414 1 0.093596 1 0.11207 1 0.016232 1 0.024064 1 0.4061 1 0.16901 1 0.33235 1 0.13449 1 Amp Peak 24(18q11.2) 0 (0%) 431 0.87634 1 0.69903 1 0.81921 1 0.614 1 1.8327e-06 0.00172 0.0093201 1 0.20545 1 0.45327 1 0.042716 1 0.10889 1 0.31304 1 0.82502 1 0.31701 1 0.46882 1 Amp Peak 25(19p13.12) 0 (0%) 264 0.0008114 0.722 3.2437e-06 0.00305 0.021202 1 0.064513 1 6.5967e-13 6.42e-10 1.4279e-06 0.00135 0.00066159 0.594 0.0037834 1 0.21537 1 0.26956 1 0.48203 1 0.59549 1 0.96113 1 0.65605 1 Amp Peak 26(19q12) 0 (0%) 255 0.064554 1 0.0013398 1 0.031597 1 0.54096 1 9.1092e-29 8.93e-26 2.194e-10 2.11e-07 0.080336 1 0.82035 1 0.5507 1 0.85952 1 0.33501 1 0.59597 1 0.73844 1 0.43835 1 Amp Peak 27(19q13.2) 0 (0%) 331 0.92182 1 0.73273 1 0.48052 1 0.75278 1 2.3798e-13 2.32e-10 7.3301e-05 0.0672 0.45652 1 0.38234 1 0.45755 1 0.98471 1 1 1 0.3794 1 0.66406 1 0.37393 1 Amp Peak 28(20p13) 0 (0%) 259 0.25693 1 0.15409 1 0.17352 1 0.056261 1 1.178e-11 1.14e-08 3.2509e-05 0.03 0.32141 1 0.97078 1 0.071585 1 0.6862 1 0.24165 1 0.89627 1 0.72297 1 0.29928 1 Amp Peak 29(20q11.21) 0 (0%) 237 0.005101 1 0.00046421 0.419 0.26114 1 0.012946 1 1.4322e-25 1.4e-22 4.0574e-12 3.94e-09 0.14036 1 0.039225 1 0.00013753 0.125 0.59878 1 0.5432 1 0.25099 1 0.96791 1 0.57291 1 Amp Peak 30(20q13.33) 0 (0%) 177 0.0096003 1 0.0037262 1 0.7387 1 0.36413 1 1.8239e-17 1.78e-14 8.5028e-08 8.09e-05 0.89923 1 0.56042 1 0.0080012 1 0.79319 1 0.4765 1 0.60408 1 0.68875 1 0.31859 1 Amp Peak 31(22q12.2) 0 (0%) 482 0.49083 1 0.48681 1 0.10514 1 0.016494 1 0.00072466 0.648 0.001446 1 1 1 0.057451 1 0.098624 1 0.195 1 0.10137 1 0.011408 1 0.048885 1 0.039466 1 Amp Peak 32(Xp11.23) 0 (0%) 406 0.94261 1 0.3063 1 0.28586 1 0.03835 1 3.287e-06 0.00309 8.7305e-05 0.0799 0.70289 1 0.2224 1 0.28613 1 0.2156 1 0.36494 1 0.87915 1 0.46716 1 0.72007 1 Amp Peak 33(Xq28) 0 (0%) 346 0.13651 1 0.38392 1 0.70232 1 0.46399 1 1.9282e-05 0.0179 0.11531 1 0.35856 1 0.7908 1 0.5486 1 0.4349 1 0.91696 1 0.011929 1 0.89127 1 0.82138 1 Del Peak 1(1p36.11) 0 (0%) 304 0.90668 1 0.69351 1 0.12546 1 0.60592 1 3.3244e-06 0.00312 0.046165 1 0.18884 1 0.41581 1 0.96084 1 0.80721 1 0.22128 1 0.14443 1 0.34491 1 0.16097 1 Del Peak 2(1q32.3) 0 (0%) 475 0.082276 1 0.23709 1 0.46655 1 0.45884 1 3.4574e-07 0.000327 0.2267 1 0.78069 1 0.10493 1 0.11541 1 0.33037 1 0.897 1 0.56961 1 0.95847 1 0.85714 1 Del Peak 3(2p25.3) 0 (0%) 452 0.98178 1 0.92813 1 0.21298 1 0.52397 1 0.28615 1 0.73947 1 0.14867 1 0.11212 1 0.050061 1 0.73405 1 0.90478 1 0.50594 1 0.93266 1 0.55261 1 Del Peak 4(2q22.1) 0 (0%) 436 0.11454 1 0.29925 1 0.41554 1 0.0073213 1 0.038288 1 0.36055 1 0.28134 1 0.70968 1 0.98287 1 0.35733 1 0.56696 1 0.57438 1 0.56518 1 0.15393 1 Del Peak 5(2q37.3) 0 (0%) 396 0.015975 1 0.063316 1 0.5261 1 9.0251e-05 0.0825 3.3292e-05 0.0307 0.12355 1 0.72491 1 0.89364 1 0.01988 1 0.028864 1 0.01865 1 0.012482 1 0.072817 1 0.02752 1 Del Peak 6(3p26.2) 0 (0%) 359 0.1456 1 0.03524 1 0.015236 1 0.10778 1 7.9488e-05 0.0728 0.00022594 0.205 0.96999 1 0.094852 1 0.0031158 1 0.67425 1 0.62801 1 0.61119 1 0.95898 1 0.024851 1 Del Peak 7(4q22.1) 0 (0%) 186 0.050228 1 0.31562 1 0.90732 1 0.25336 1 0.045759 1 0.58009 1 0.059333 1 0.0090796 1 0.10929 1 0.42446 1 0.19509 1 0.0073341 1 0.02275 1 0.11901 1 Del Peak 8(4q34.3) 0 (0%) 157 0.021525 1 0.023864 1 0.010815 1 0.36837 1 0.28284 1 0.69382 1 0.4294 1 0.21123 1 0.08514 1 0.030251 1 0.33715 1 0.17663 1 0.11655 1 0.25189 1 Del Peak 9(5q11.2) 0 (0%) 228 0.76991 1 0.59311 1 0.19791 1 0.26373 1 2.6912e-07 0.000255 0.00052806 0.476 0.73119 1 0.85153 1 0.1817 1 0.12795 1 0.034107 1 0.00055831 0.503 0.015281 1 0.011863 1 Del Peak 10(5q13.2) 0 (0%) 163 0.69869 1 0.49876 1 0.84689 1 0.4775 1 3.8927e-11 3.76e-08 0.12243 1 0.76159 1 0.82409 1 0.3536 1 0.0030253 1 0.12125 1 0.0088524 1 0.10307 1 0.068307 1 Del Peak 11(6q27) 0 (0%) 189 0.13998 1 0.0057951 1 0.55514 1 0.56628 1 8.4624e-09 8.08e-06 2.3467e-05 0.0218 0.42773 1 0.91712 1 2.6855e-05 0.0249 0.24953 1 0.4568 1 0.94464 1 0.31139 1 0.092705 1 Del Peak 12(7p22.1) 0 (0%) 323 0.26027 1 0.69394 1 0.61033 1 0.82723 1 1.4021e-13 1.37e-10 0.8023 1 0.80093 1 0.78182 1 0.28221 1 0.10438 1 0.32752 1 0.56375 1 0.66773 1 0.56365 1 Del Peak 13(8p23.3) 0 (0%) 188 0.10086 1 0.26047 1 0.78833 1 0.003137 1 5.6331e-11 5.43e-08 0.14967 1 0.87324 1 0.61599 1 0.89476 1 0.60024 1 0.23462 1 0.15946 1 0.18727 1 0.40225 1 Del Peak 14(8p21.2) 0 (0%) 171 0.065758 1 0.24788 1 0.11591 1 0.0022215 1 1.3533e-08 1.29e-05 0.20187 1 0.79353 1 0.84768 1 0.36021 1 0.25 1 0.54086 1 0.48426 1 0.90146 1 0.97638 1 Del Peak 15(9p24.3) 0 (0%) 315 0.00090475 0.804 0.0058255 1 0.67942 1 0.01121 1 0.012307 1 6.6032e-05 0.0606 0.45165 1 0.59747 1 0.072551 1 0.074551 1 0.087932 1 0.13694 1 0.058961 1 0.13266 1 Del Peak 16(9q34.13) 0 (0%) 232 0.016563 1 0.019619 1 0.91485 1 0.015657 1 6.6278e-07 0.000626 0.057831 1 0.34379 1 0.37086 1 0.27207 1 1 1 0.03707 1 0.099525 1 0.10195 1 0.057026 1 Del Peak 17(10p15.3) 0 (0%) 449 0.093979 1 0.10327 1 0.036364 1 0.042599 1 0.10053 1 0.36001 1 0.28282 1 0.068751 1 0.014455 1 0.060723 1 0.25458 1 0.33814 1 0.11299 1 0.28842 1 Del Peak 18(10q23.31) 0 (0%) 350 0.22245 1 0.0025812 1 0.00012391 0.113 0.71858 1 0.00066198 0.594 0.0011957 1 0.036002 1 0.012118 1 0.96084 1 0.50205 1 0.073452 1 0.38278 1 0.083633 1 0.16491 1 Del Peak 19(10q26.3) 0 (0%) 381 0.0062108 1 0.00063645 0.572 0.1535 1 0.26008 1 1.5273e-05 0.0142 0.15526 1 0.0924 1 0.01349 1 0.060288 1 0.12159 1 0.016338 1 0.22053 1 0.051276 1 0.23322 1 Del Peak 20(11p15.5) 0 (0%) 231 0.07044 1 0.27925 1 0.76894 1 0.24191 1 1.8916e-11 1.83e-08 0.024875 1 0.96331 1 0.59561 1 0.71737 1 0.272 1 0.12946 1 0.023987 1 0.15703 1 0.28366 1 Del Peak 21(11q25) 0 (0%) 374 0.80036 1 0.32102 1 0.26979 1 0.46151 1 0.052942 1 0.55423 1 0.31973 1 0.17519 1 0.93094 1 0.87676 1 0.5974 1 0.13818 1 0.58935 1 0.2122 1 Del Peak 22(12q24.33) 0 (0%) 353 0.00069507 0.623 0.00058047 0.522 0.21185 1 0.0040363 1 2.1767e-09 2.08e-06 0.015392 1 0.3814 1 0.50179 1 0.069961 1 0.0031356 1 0.017165 1 0.0056917 1 0.021087 1 0.009768 1 Del Peak 23(13q14.2) 0 (0%) 215 0.00355 1 0.025242 1 0.61181 1 0.88534 1 6.6348e-07 0.000626 4.3185e-05 0.0397 0.0014027 1 0.00080734 0.719 0.09885 1 0.25006 1 0.37539 1 0.89057 1 0.45142 1 0.65689 1 Del Peak 24(14q23.3) 0 (0%) 272 0.029491 1 0.11591 1 0.59583 1 0.81462 1 6.1231e-05 0.0563 0.53722 1 0.18481 1 0.24683 1 0.85595 1 0.20068 1 0.8034 1 0.66168 1 0.58532 1 0.20873 1 Del Peak 25(15q15.1) 0 (0%) 212 0.028672 1 0.019469 1 0.011059 1 0.0061803 1 2.1189e-11 2.05e-08 7.2118e-06 0.00672 0.12115 1 0.045597 1 0.01805 1 0.76761 1 0.46434 1 0.67584 1 0.24277 1 0.21388 1 Del Peak 26(16p13.3) 0 (0%) 267 0.46676 1 0.069184 1 0.12356 1 0.18301 1 0.075948 1 0.4141 1 0.92114 1 0.23886 1 0.50761 1 0.78608 1 0.20404 1 0.85155 1 0.096862 1 0.81256 1 Del Peak 27(16q22.1) 0 (0%) 118 0.49177 1 0.89434 1 0.03763 1 0.37173 1 0.00025699 0.233 0.57634 1 0.55204 1 0.35943 1 0.30349 1 0.30528 1 0.41225 1 0.12574 1 0.074694 1 0.19003 1 Del Peak 28(16q23.1) 0 (0%) 127 0.12137 1 0.22782 1 0.12174 1 0.17059 1 0.00012924 0.117 0.60367 1 0.6021 1 0.92483 1 0.39459 1 0.44854 1 0.08924 1 0.039284 1 0.066765 1 0.056936 1 Del Peak 29(17p12) 0 (0%) 89 0.18115 1 0.021349 1 0.94315 1 0.86158 1 0.80236 1 0.28915 1 0.93821 1 0.36217 1 0.1874 1 0.51545 1 0.61003 1 0.62084 1 0.55078 1 0.8327 1 Del Peak 30(17q11.2) 0 (0%) 104 0.95058 1 0.043437 1 0.76496 1 0.076609 1 0.00071136 0.637 0.0049803 1 0.76734 1 0.066573 1 0.37712 1 0.57142 1 0.20232 1 0.56529 1 0.039787 1 0.42715 1 Del Peak 31(18q23) 0 (0%) 197 1 1 0.97975 1 0.088359 1 0.17808 1 0.0020758 1 0.4391 1 0.22796 1 0.275 1 0.21987 1 0.3983 1 0.68926 1 0.68941 1 0.12254 1 0.79313 1 Del Peak 32(19p13.3) 0 (0%) 68 0.38567 1 0.029362 1 0.85169 1 0.54048 1 0.0023957 1 0.012682 1 0.59172 1 0.22869 1 0.33265 1 0.015723 1 0.47594 1 0.85014 1 0.4401 1 0.89881 1 Del Peak 33(19q13.33) 0 (0%) 275 0.0018817 1 0.00076484 0.683 0.022217 1 0.15948 1 0.081044 1 0.005848 1 0.034225 1 0.21418 1 0.0078351 1 0.084428 1 0.25918 1 0.15122 1 0.2444 1 0.4317 1 Del Peak 34(19q13.43) 0 (0%) 290 0.043249 1 0.0079892 1 0.15472 1 0.050803 1 0.0046372 1 0.00010774 0.0981 0.17832 1 0.27795 1 0.5553 1 0.15411 1 0.52674 1 0.45469 1 0.42687 1 0.61885 1 Del Peak 35(21q22.3) 0 (0%) 348 0.43454 1 0.53286 1 0.53531 1 0.5781 1 0.75474 1 0.266 1 0.57876 1 0.62599 1 0.18866 1 0.27222 1 0.73978 1 0.65237 1 0.18512 1 0.41057 1 Del Peak 36(22q13.32) 0 (0%) 76 0.1091 1 0.047806 1 0.043619 1 0.025755 1 0.014892 1 0.066656 1 0.071142 1 0.34908 1 0.068042 1 0.17968 1 0.023586 1 0.29558 1 0.020204 1 0.47952 1 Del Peak 37(Xp21.1) 0 (0%) 206 0.27623 1 0.88103 1 0.12023 1 0.45224 1 0.081775 1 0.028462 1 0.32266 1 0.043386 1 0.90769 1 0.40881 1 0.93591 1 0.42976 1 0.70161 1 0.47574 1