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 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 3p gain 8 (12%) 58 0.25953 0.501 0.50733 0.745 0.46014 0.694 0.04473 0.157 0.83873 0.929 0.64626 0.826 0.20417 0.441 0.69047 0.855 0.03853 0.139 0.62499 0.81 3q gain 8 (12%) 58 0.26017 0.501 0.50636 0.745 0.45759 0.691 0.04371 0.155 0.84073 0.929 0.64817 0.826 0.20525 0.441 0.68949 0.855 0.03903 0.14 0.6263 0.81 4p gain 23 (35%) 43 0.90314 0.971 0.64252 0.826 0.50722 0.745 0.17389 0.397 0.00103 0.00865 0.00037 0.00359 1 1 0.01372 0.0697 0.01034 0.0557 0.00366 0.0245 4q gain 24 (36%) 42 0.81046 0.918 0.80532 0.917 0.34443 0.585 0.1503 0.357 9.9999e-05 0.00137 8.9999e-05 0.00129 0.95078 0.997 0.0090799 0.0502 0.01147 0.0607 0.01523 0.0737 5p gain 8 (12%) 58 0.77206 0.898 0.79705 0.915 0.71013 0.863 0.19941 0.439 0.3865 0.628 0.44571 0.679 0.42642 0.661 0.059919 0.195 0.31118 0.552 0.12902 0.329 5q gain 8 (12%) 58 0.77293 0.898 0.79996 0.915 0.70908 0.863 0.19749 0.439 0.38553 0.628 0.44644 0.679 0.42715 0.661 0.060179 0.195 0.31126 0.552 0.12883 0.329 7p gain 24 (36%) 42 0.57144 0.788 0.89773 0.968 0.099619 0.276 0.13501 0.338 0.076789 0.228 0.061029 0.197 0.844 0.931 0.11729 0.316 0.03419 0.127 0.14027 0.344 7q gain 24 (36%) 42 0.57481 0.791 0.89608 0.968 0.095889 0.267 0.13623 0.338 0.075299 0.228 0.061539 0.198 0.84019 0.929 0.1171 0.316 0.03485 0.128 0.14157 0.344 8p gain 16 (24%) 50 0.32938 0.575 0.13124 0.329 0.38155 0.628 0.1494 0.357 0.091469 0.256 0.077159 0.228 0.30491 0.552 0.14415 0.349 0.02073 0.0888 0.0467 0.163 8q gain 17 (26%) 49 0.23958 0.482 0.14538 0.35 0.39012 0.63 0.13036 0.329 0.03367 0.126 0.03071 0.118 0.4436 0.678 0.12097 0.322 0.0096099 0.0526 0.055269 0.183 9p gain 10 (15%) 56 0.64862 0.826 0.5633 0.785 0.25737 0.499 0.23391 0.475 0.41709 0.655 0.81334 0.918 0.75463 0.89 0.60163 0.805 0.30062 0.552 0.30394 0.552 9q gain 10 (15%) 56 0.6491 0.826 0.56211 0.785 0.25577 0.499 0.23529 0.477 0.4178 0.655 0.81276 0.918 0.75789 0.891 0.59723 0.805 0.30066 0.552 0.3051 0.552 10p gain 4 (6%) 62 1 1 0.28528 0.538 1 1 0.55031 0.776 0.47799 0.716 0.20511 0.441 1 1 0.16667 0.385 0.25491 0.499 0.77726 0.899 11p gain 15 (23%) 51 1 1 0.87039 0.95 0.56061 0.785 0.088859 0.251 0.00051999 0.00475 3e-04 0.00315 0.83036 0.924 0.02749 0.106 0.33695 0.583 0.052849 0.176 11q gain 15 (23%) 51 1 1 0.86789 0.949 0.21473 0.452 0.087869 0.251 2e-05 0.000371 2e-05 0.000371 0.7475 0.889 0.01997 0.0862 0.090369 0.254 0.02566 0.101 12p gain 19 (29%) 47 0.89229 0.968 0.73748 0.88 0.83719 0.929 0.46265 0.696 0.12799 0.329 0.15918 0.377 0.66959 0.837 0.066419 0.208 0.00036 0.00359 0.19791 0.439 12q gain 20 (30%) 46 1 1 0.51913 0.754 0.7871 0.905 0.41285 0.651 0.03312 0.124 0.083709 0.241 0.94347 0.992 0.03166 0.12 0.00081999 0.00726 0.17688 0.401 14q gain 21 (32%) 45 1 1 0.94352 0.992 0.20022 0.439 0.29317 0.55 0.01673 0.0787 0.00483 0.0317 0.76668 0.898 0.058589 0.193 0.02143 0.0899 0.066079 0.208 15q gain 21 (32%) 45 0.30134 0.552 0.94309 0.992 0.19989 0.439 0.2967 0.551 0.13618 0.338 0.061859 0.198 0.94537 0.993 0.21256 0.451 0.28836 0.542 0.41022 0.649 16p gain 22 (33%) 44 1 1 0.79905 0.915 0.49248 0.732 0.29457 0.55 0.00161 0.0121 0.00053999 0.00486 0.65575 0.826 0.0058299 0.036 0.0056699 0.0354 0.0090599 0.0502 16q gain 21 (32%) 45 1 1 0.94328 0.992 0.26435 0.506 0.36445 0.608 0.00037 0.00359 0.00014 0.00184 0.40078 0.642 0.0051499 0.0331 0.0019 0.0138 0.0054699 0.0345 18p gain 17 (26%) 49 1 1 0.72107 0.863 0.76091 0.893 0.65156 0.826 0.02169 0.0899 0.01289 0.066 1 1 0.04798 0.167 0.00247 0.0171 0.01283 0.066 18q gain 16 (24%) 50 0.87377 0.952 0.93531 0.992 0.92886 0.992 0.55529 0.78 0.04979 0.17 0.01984 0.0862 1 1 0.050609 0.171 0.00188 0.0138 0.01619 0.0767 19p gain 20 (30%) 46 0.71132 0.863 0.22475 0.465 0.069929 0.216 0.02638 0.103 0.01918 0.0845 0.0227 0.0929 0.88127 0.957 0.13003 0.329 0.35578 0.598 0.6073 0.805 19q gain 18 (27%) 48 1 1 0.26131 0.502 0.10931 0.297 0.073409 0.225 0.00357 0.0242 0.0062999 0.0385 0.69604 0.856 0.14613 0.35 0.32615 0.572 0.50601 0.745 20p gain 22 (33%) 44 0.72082 0.863 0.71144 0.863 0.16598 0.385 0.065669 0.208 0.01749 0.081 0.02377 0.0957 0.42903 0.661 0.02239 0.0922 0.01524 0.0737 0.2032 0.441 20q gain 22 (33%) 44 0.72179 0.863 0.71445 0.863 0.16738 0.385 0.066499 0.208 0.01819 0.0836 0.02346 0.0954 0.42709 0.661 0.02165 0.0899 0.01532 0.0737 0.20109 0.439 21q gain 4 (6%) 62 1 1 0.28179 0.533 0.5559 0.78 0.8104 0.918 0.33935 0.584 0.1067 0.292 0.67532 0.842 0.16556 0.385 0.75843 0.891 0.71878 0.863 22q gain 19 (29%) 47 1 1 0.54134 0.773 0.25398 0.499 0.2426 0.487 0.33545 0.583 0.36232 0.607 0.48051 0.716 0.02385 0.0957 0.0099299 0.0539 0.00227 0.0159 xp gain 8 (12%) 58 0.7725 0.898 0.30625 0.552 0.40348 0.644 0.38379 0.628 0.0076099 0.0443 0.01965 0.086 0.075219 0.228 0.083759 0.241 0.0073399 0.0436 0.03083 0.118 xq gain 8 (12%) 58 0.77232 0.898 0.30587 0.552 0.40554 0.645 0.3855 0.628 0.0078199 0.0448 0.01854 0.0845 0.075659 0.228 0.083879 0.241 0.0079499 0.0451 0.0321 0.121 1p loss 53 (80%) 13 0.41352 0.651 9.9999e-06 0.000233 0.71892 0.863 0.5964 0.805 0.00027 0.00298 0.00028 0.00304 0.39569 0.638 0.00123 0.00993 0.00048 0.00451 0.00204 0.0144 1q loss 51 (77%) 15 0.54207 0.773 9.9999e-06 0.000233 0.21736 0.453 0.33624 0.583 2e-05 0.000371 5.9999e-05 0.000969 0.26903 0.512 0.00031 0.0032 0.0048 0.0317 0.01189 0.0619 2p loss 46 (70%) 20 0.71238 0.863 9.9999e-06 0.000233 0.12608 0.328 0.51195 0.745 9.9999e-06 0.000233 9.9999e-06 0.000233 0.45009 0.683 2e-05 0.000371 9.9999e-06 0.000233 0.00041 0.00391 2q loss 46 (70%) 20 0.71007 0.863 9.9999e-06 0.000233 0.12668 0.328 0.51086 0.745 9.9999e-06 0.000233 9.9999e-06 0.000233 0.45267 0.686 9.9999e-06 0.000233 9.9999e-06 0.000233 0.00050999 0.00472 3p loss 9 (14%) 57 0.60463 0.805 0.43576 0.668 0.81661 0.92 0.16688 0.385 0.12662 0.328 0.0027 0.0185 0.42833 0.661 0.20139 0.439 0.66779 0.836 0.85331 0.938 3q loss 8 (12%) 58 0.42451 0.661 0.16696 0.385 0.89646 0.968 0.38492 0.628 0.088479 0.251 0.00196 0.014 0.30585 0.552 0.18013 0.407 0.30861 0.552 0.65579 0.826 5p loss 10 (15%) 56 0.0080699 0.0454 0.20951 0.448 1 1 0.82219 0.922 0.01438 0.0719 0.01897 0.0845 0.22656 0.465 0.0148 0.0728 0.3836 0.628 0.64867 0.826 5q loss 10 (15%) 56 0.0067999 0.0412 0.20972 0.448 1 1 0.82213 0.922 0.01473 0.0728 0.01915 0.0845 0.22963 0.47 0.01435 0.0719 0.3811 0.628 0.65178 0.826 6p loss 51 (77%) 15 0.6239 0.81 9.9999e-06 0.000233 0.16091 0.378 0.10478 0.29 9.9999e-06 0.000233 9.9999e-06 0.000233 0.60906 0.805 0.00133 0.0105 0.00026 0.00298 6.9999e-05 0.00108 6q loss 51 (77%) 15 0.6242 0.81 9.9999e-06 0.000233 0.15982 0.377 0.10528 0.29 9.9999e-06 0.000233 9.9999e-06 0.000233 0.609 0.805 0.00129 0.0103 0.00015 0.00193 0.00012 0.00161 8p loss 10 (15%) 56 2e-05 0.000371 0.02159 0.0899 0.02438 0.0972 0.02689 0.105 0.3446 0.585 0.076469 0.228 0.14581 0.35 0.54703 0.774 0.21452 0.452 0.01912 0.0845 8q loss 9 (14%) 57 0.00019 0.00235 0.01699 0.0793 0.070409 0.216 0.082039 0.24 0.58599 0.802 0.12028 0.322 0.24872 0.494 0.58704 0.802 0.21626 0.453 0.0187 0.0845 9p loss 9 (14%) 57 1 1 0.90583 0.972 0.66355 0.833 0.81054 0.918 0.01166 0.0612 0.0050399 0.0327 0.25703 0.499 0.54663 0.774 0.22543 0.465 0.9976 1 9q loss 10 (15%) 56 0.80358 0.917 0.82873 0.924 0.50964 0.745 0.55008 0.776 0.02089 0.0889 0.01563 0.0746 0.076619 0.228 0.60044 0.805 0.70818 0.863 0.92473 0.991 10p loss 48 (73%) 18 0.5945 0.805 3e-05 0.000525 0.088269 0.251 0.10749 0.293 9.9999e-06 0.000233 9.9999e-06 0.000233 0.59478 0.805 0.00022 0.00267 0.00159 0.0121 0.0072599 0.0436 10q loss 49 (74%) 17 0.42342 0.661 2e-05 0.000371 0.17524 0.399 0.23758 0.48 9.9999e-06 0.000233 9.9999e-06 0.000233 0.569 0.786 0.00036 0.00359 0.0054299 0.0345 0.00178 0.0132 11p loss 7 (11%) 59 0.75273 0.89 0.69445 0.856 0.53337 0.767 0.25268 0.499 0.34422 0.585 0.31769 0.559 0.34469 0.585 0.93821 0.992 0.93664 0.992 0.60438 0.805 11q loss 7 (11%) 59 0.75273 0.89 0.69528 0.856 0.53004 0.766 0.2545 0.499 0.34133 0.585 0.31596 0.558 0.34692 0.586 0.93725 0.992 0.9386 0.992 0.60314 0.805 13q loss 43 (65%) 23 0.37462 0.623 0.00027 0.00298 0.29489 0.55 0.052079 0.175 0.00016 0.00202 4e-05 0.000681 0.082299 0.24 0.19801 0.439 0.00088999 0.00758 0.0076599 0.0443 16p loss 3 (5%) 63 0.60182 0.805 0.61347 0.805 0.3505 0.59 0.59146 0.805 0.24797 0.494 0.12366 0.326 0.75237 0.89 0.48068 0.716 0.78097 0.901 0.62399 0.81 16q loss 5 (8%) 61 0.47988 0.716 0.43381 0.667 0.8528 0.938 0.22619 0.465 0.0347 0.128 0.0074899 0.0441 0.27555 0.523 0.04969 0.17 0.53936 0.773 0.65663 0.826 17p loss 50 (76%) 16 0.56762 0.786 9.9999e-06 0.000233 0.13952 0.343 0.068829 0.214 9.9999e-06 0.000233 9.9999e-06 0.000233 0.31014 0.552 5e-05 0.000829 6.9999e-05 0.00108 0.0011 0.00912 17q loss 50 (76%) 16 0.56926 0.786 9.9999e-06 0.000233 0.14071 0.344 0.068789 0.214 9.9999e-06 0.000233 9.9999e-06 0.000233 0.30945 0.552 7.9999e-05 0.00117 9.9999e-05 0.00137 0.00121 0.0099 18p loss 7 (11%) 59 0.38077 0.628 0.051389 0.173 0.53357 0.767 0.51179 0.745 0.39896 0.641 0.13952 0.343 0.77421 0.898 0.93808 0.992 0.3008 0.552 0.82511 0.923 18q loss 9 (14%) 57 0.12982 0.329 0.04064 0.145 0.39003 0.63 0.40689 0.646 0.0364 0.132 0.16836 0.386 0.58267 0.8 0.78324 0.902 0.12195 0.323 0.49619 0.736 19q loss 3 (5%) 63 1 1 1 1 0.6131 0.805 0.30842 0.552 0.05 0.17 0.82128 0.922 1 1 0.86522 0.948 0.77754 0.899 0.62411 0.81 20p loss 4 (6%) 62 1 1 0.56731 0.786 0.36488 0.608 0.33837 0.584 0.54375 0.773 0.21547 0.452 0.74389 0.886 0.65659 0.826 0.34609 0.586 0.54144 0.773 20q loss 3 (5%) 63 1 1 0.24881 0.494 0.61182 0.805 0.58951 0.804 0.24957 0.494 0.058929 0.193 0.64488 0.826 0.82743 0.924 0.079639 0.234 0.62409 0.81 21q loss 35 (53%) 31 0.40238 0.643 0.03555 0.129 0.12546 0.328 0.1885 0.424 0.26485 0.506 0.19476 0.437 0.98413 1 0.127 0.328 0.12089 0.322 0.22546 0.465 22q loss 8 (12%) 58 1 1 0.02468 0.0978 0.87917 0.957 1 1 0.5284 0.765 0.233 0.475 0.61073 0.805 0.21252 0.451 0.85951 0.943 0.31603 0.558 xp loss 38 (58%) 28 0.90084 0.97 0.00026 0.00298 0.68988 0.855 0.72212 0.863 3e-04 0.00315 0.00027 0.00298 0.32954 0.575 3e-05 0.000525 2e-05 0.000371 0.01099 0.0587 xq loss 38 (58%) 28 1 1 0.00158 0.0121 0.69075 0.855 0.71949 0.863 0.00086999 0.00751 0.00144 0.0112 0.65252 0.826 0.00082999 0.00726 7.9999e-05 0.00117 0.04984 0.17