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 1p gain 24 (43%) 32 0.26311 0.818 0.59801 0.961 0.98212 1 0.79877 1 0.84611 1 0.90312 1 0.73793 0.998 0.36735 0.86 0.94713 1 0.67009 0.979 1q gain 31 (55%) 25 0.94132 1 0.24717 0.81 0.87211 1 0.63638 0.97 0.56283 0.946 0.61899 0.97 0.73726 0.998 0.52591 0.93 0.76391 1 0.91632 1 2p gain 23 (41%) 33 0.34882 0.86 0.10553 0.72 0.25296 0.81 0.03513 0.697 0.02637 0.688 0.057229 0.707 0.30422 0.836 0.072209 0.72 0.31143 0.836 0.13397 0.72 2q gain 21 (38%) 35 0.36136 0.86 0.10017 0.72 0.2111 0.809 0.31827 0.844 0.00107 0.45 0.11198 0.72 0.24488 0.81 0.04877 0.707 0.36443 0.86 0.11032 0.72 3p gain 10 (18%) 46 0.4102 0.864 0.79011 1 0.36284 0.86 0.29658 0.836 0.7928 1 0.24846 0.81 1 1 0.46742 0.886 0.71455 0.997 0.40818 0.863 3q gain 22 (39%) 34 0.10147 0.72 0.13186 0.72 0.38228 0.86 0.81189 1 0.45592 0.877 0.22824 0.81 0.21979 0.81 0.40867 0.863 0.81332 1 0.27035 0.825 4p gain 10 (18%) 46 0.21205 0.809 0.59561 0.961 0.01327 0.594 0.10082 0.72 0.6373 0.97 0.88349 1 0.40722 0.863 0.351 0.86 1 1 0.22975 0.81 4q gain 3 (5%) 53 0.17399 0.786 0.39171 0.86 NA NA NA NA 0.388 0.86 0.79273 1 0.45713 0.877 0.56786 0.952 0.6925 0.991 0.69938 0.992 5p gain 23 (41%) 33 0.47925 0.897 0.21165 0.809 0.082129 0.72 0.19911 0.809 0.16482 0.786 0.24268 0.81 0.38842 0.86 0.02753 0.688 0.58315 0.957 0.14841 0.744 5q gain 8 (14%) 48 0.55207 0.944 0.51139 0.925 0.66829 0.978 0.20842 0.809 0.63295 0.97 0.24757 0.81 0.19724 0.809 0.1525 0.758 0.45448 0.877 0.19283 0.809 6p gain 31 (55%) 25 0.23123 0.81 0.34143 0.86 0.49727 0.918 0.39366 0.86 0.9328 1 0.32039 0.844 0.58087 0.957 0.17248 0.786 0.52278 0.93 0.066019 0.707 6q gain 27 (48%) 29 0.36096 0.86 0.23976 0.81 0.74147 0.998 0.62277 0.97 0.64896 0.97 0.1658 0.786 0.83514 1 0.18946 0.809 0.25424 0.81 0.13651 0.72 7p gain 21 (38%) 35 0.7793 1 0.39406 0.86 0.56077 0.946 0.29107 0.836 0.22313 0.81 0.27823 0.836 0.38267 0.86 0.12997 0.72 0.34221 0.86 0.12052 0.72 7q gain 18 (32%) 38 0.44263 0.877 0.80631 1 0.7313 0.998 0.60708 0.965 0.30675 0.836 0.65962 0.977 0.58296 0.957 0.1108 0.72 0.50828 0.925 0.063139 0.707 8p gain 18 (32%) 38 0.088209 0.72 0.31389 0.838 0.04107 0.698 0.17326 0.786 0.29565 0.836 0.77413 1 0.75498 1 0.3846 0.86 0.54966 0.944 0.23034 0.81 8q gain 30 (54%) 26 0.062039 0.707 0.1317 0.72 0.37957 0.86 0.59662 0.961 0.01016 0.573 0.50771 0.925 0.33324 0.859 0.32451 0.846 0.25717 0.81 0.12232 0.72 9p gain 6 (11%) 50 1 1 0.77879 1 0.50609 0.925 0.12118 0.72 0.93471 1 0.66485 0.977 0.8672 1 0.80351 1 0.78397 1 1 1 10p gain 20 (36%) 36 0.93909 1 0.58006 0.957 0.66397 0.977 0.54412 0.944 0.02623 0.688 0.25635 0.81 0.62636 0.97 0.30115 0.836 0.31929 0.844 0.43743 0.877 10q gain 17 (30%) 39 0.80896 1 0.88543 1 0.6282 0.97 0.46203 0.88 0.39275 0.86 0.04861 0.707 0.22121 0.81 0.18309 0.804 0.18972 0.809 0.073029 0.72 11p gain 5 (9%) 51 1 1 0.75753 1 0.7322 0.998 0.92502 1 0.28954 0.836 0.85381 1 1 1 0.11927 0.72 0.38158 0.86 0.092179 0.72 11q gain 7 (12%) 49 0.27198 0.826 0.95041 1 0.19346 0.809 0.71698 0.997 0.16035 0.786 0.37976 0.86 0.44746 0.877 0.03556 0.697 0.6793 0.985 0.03037 0.697 12p gain 22 (39%) 34 0.39458 0.86 0.01904 0.645 0.38214 0.86 0.59301 0.961 0.18287 0.804 0.04277 0.704 0.88255 1 0.97676 1 0.81257 1 0.62665 0.97 12q gain 11 (20%) 45 0.4386 0.877 0.53595 0.935 0.96566 1 0.85533 1 0.6274 0.97 0.52264 0.93 0.6865 0.988 0.29736 0.836 0.64225 0.97 0.26963 0.825 13q gain 15 (27%) 41 1 1 0.30624 0.836 0.094749 0.72 0.54496 0.944 0.03705 0.697 0.02447 0.688 0.0348 0.697 0.04606 0.707 0.059099 0.707 0.14081 0.72 14q gain 7 (12%) 49 0.45019 0.877 0.10627 0.72 0.43674 0.877 0.04988 0.707 0.20942 0.809 0.25932 0.811 0.25699 0.81 0.73527 0.998 0.11833 0.72 0.47274 0.889 15q gain 4 (7%) 52 0.34652 0.86 0.35248 0.86 0.22896 0.81 0.58114 0.957 0.40317 0.863 0.3293 0.856 0.053749 0.707 0.34614 0.86 0.57402 0.957 0.35592 0.86 16p gain 10 (18%) 46 0.0068199 0.45 0.7014 0.993 0.53385 0.935 0.82784 1 0.21736 0.81 0.27934 0.836 0.73948 0.998 0.48313 0.9 0.59141 0.961 0.40641 0.863 16q gain 6 (11%) 50 0.055459 0.707 0.48305 0.9 0.91937 1 0.92607 1 0.5134 0.926 0.96876 1 1 1 0.92488 1 1 1 0.86707 1 17p gain 9 (16%) 47 0.65103 0.97 0.62954 0.97 0.88587 1 0.82632 1 0.64638 0.97 0.56169 0.946 0.30115 0.836 0.061539 0.707 0.7633 1 0.17179 0.786 17q gain 18 (32%) 38 0.76691 1 0.74259 0.998 0.72418 0.998 0.80431 1 0.64825 0.97 0.51131 0.925 0.66554 0.977 0.30723 0.836 0.71084 0.997 0.42882 0.877 18p gain 18 (32%) 38 0.81917 1 0.34711 0.86 0.68549 0.988 0.7864 1 0.056839 0.707 0.34309 0.86 0.1188 0.72 0.19979 0.809 0.40485 0.863 0.43283 0.877 18q gain 13 (23%) 43 0.72943 0.998 0.94461 1 0.68321 0.988 0.60111 0.961 0.18106 0.804 0.29146 0.836 0.23608 0.81 0.17327 0.786 0.2512 0.81 0.28488 0.836 19p gain 24 (43%) 32 0.10698 0.72 0.52235 0.93 0.48556 0.903 0.77985 1 0.11756 0.72 0.18515 0.804 0.11497 0.72 0.03914 0.698 0.22048 0.81 0.13857 0.72 19q gain 29 (52%) 27 0.12092 0.72 0.68915 0.988 0.65786 0.977 0.87281 1 0.81012 1 0.43454 0.877 0.83424 1 0.77255 1 0.71632 0.997 0.97754 1 20p gain 36 (64%) 20 0.46022 0.878 0.73394 0.998 0.066129 0.707 0.47055 0.889 0.77854 1 0.72718 0.998 0.55427 0.944 0.35025 0.86 0.18593 0.804 0.20994 0.809 20q gain 43 (77%) 13 0.16841 0.786 0.74209 0.998 0.20687 0.809 0.71287 0.997 0.82897 1 0.95046 1 0.43957 0.877 0.2399 0.81 0.21366 0.809 0.39055 0.86 21q gain 18 (32%) 38 0.01503 0.594 0.11251 0.72 0.21409 0.809 0.78763 1 0.92252 1 0.89147 1 0.35258 0.86 0.57055 0.953 1 1 0.94705 1 22q gain 8 (14%) 48 0.48972 0.908 0.91505 1 0.52778 0.931 0.30451 0.836 0.76976 1 0.9267 1 0.89234 1 0.94315 1 0.94926 1 1 1 xp gain 18 (32%) 38 0.66661 0.977 0.03834 0.698 0.60222 0.961 0.34108 0.86 0.064369 0.707 0.4562 0.877 1 1 0.56004 0.946 0.27055 0.825 0.43432 0.877 xq gain 15 (27%) 41 0.86256 1 0.41672 0.872 0.88732 1 0.24595 0.81 0.52511 0.93 0.54166 0.943 0.17263 0.786 0.29185 0.836 0.086119 0.72 0.20271 0.809 1p loss 10 (18%) 46 0.40797 0.863 0.79082 1 0.94492 1 0.45603 0.877 0.84032 1 0.10086 0.72 0.03659 0.697 0.01392 0.594 0.51689 0.93 0.01458 0.594 1q loss 10 (18%) 46 0.24201 0.81 0.70394 0.995 0.64909 0.97 0.19733 0.809 0.69935 0.992 0.098309 0.72 0.13691 0.72 0.070339 0.72 0.41484 0.872 0.089389 0.72 3p loss 22 (39%) 34 0.44851 0.877 0.45233 0.877 0.43763 0.877 0.58282 0.957 0.01959 0.645 0.16739 0.786 0.72902 0.998 0.95326 1 0.67811 0.985 0.66349 0.977 3q loss 15 (27%) 41 0.20447 0.809 0.34737 0.86 0.50888 0.925 0.86229 1 0.065519 0.707 0.40699 0.863 0.16776 0.786 0.91134 1 0.97424 1 0.97007 1 4p loss 30 (54%) 26 0.12881 0.72 0.0091699 0.557 0.00427 0.45 0.075099 0.72 0.51812 0.93 0.44234 0.877 0.4221 0.873 0.63408 0.97 0.099019 0.72 0.45975 0.878 4q loss 34 (61%) 22 0.20471 0.809 0.00383 0.45 0.12045 0.72 0.20029 0.809 0.02478 0.688 0.056959 0.707 0.00361 0.45 0.20754 0.809 0.0050599 0.45 0.077429 0.72 5p loss 9 (16%) 47 1 1 0.25341 0.81 0.03484 0.697 0.062269 0.707 0.79597 1 0.1332 0.72 1 1 0.29805 0.836 1 1 0.4192 0.872 5q loss 18 (32%) 38 0.76509 1 0.11385 0.72 0.79421 1 0.079059 0.72 0.35536 0.86 0.23409 0.81 1 1 0.94788 1 0.5487 0.944 0.94782 1 6p loss 5 (9%) 51 0.22537 0.81 0.91778 1 0.13748 0.72 0.7515 1 0.80081 1 0.95684 1 1 1 0.91224 1 0.92307 1 1 1 6q loss 7 (12%) 49 0.082139 0.72 1 1 0.22583 0.81 0.13018 0.72 0.44868 0.877 0.92124 1 1 1 0.9363 1 0.62569 0.97 0.93448 1 7p loss 13 (23%) 43 0.51152 0.925 0.70769 0.997 0.26558 0.823 0.28859 0.836 0.6779 0.985 0.49836 0.918 0.8497 1 0.45535 0.877 0.47573 0.893 0.59844 0.961 7q loss 12 (21%) 44 0.13411 0.72 0.97042 1 0.5857 0.957 0.61812 0.97 0.96873 1 0.94358 1 0.65011 0.97 0.30849 0.836 0.46321 0.88 0.55393 0.944 8p loss 24 (43%) 32 0.04154 0.698 0.94757 1 0.41957 0.872 0.13833 0.72 0.91539 1 0.61903 0.97 1 1 0.36707 0.86 0.94694 1 0.34843 0.86 8q loss 9 (16%) 47 0.37118 0.86 0.67421 0.983 0.81216 1 0.68809 0.988 0.03993 0.698 0.71226 0.997 0.89684 1 0.75666 1 1 1 0.66569 0.977 9p loss 35 (62%) 21 0.11167 0.72 0.27006 0.825 0.0068299 0.45 0.00217 0.45 0.64443 0.97 0.21276 0.809 0.58722 0.957 0.38243 0.86 0.31873 0.844 0.091939 0.72 9q loss 40 (71%) 16 0.066189 0.707 0.30943 0.836 0.080129 0.72 0.065759 0.707 0.87418 1 0.058789 0.707 0.68816 0.988 0.22305 0.81 0.73034 0.998 0.25246 0.81 10p loss 24 (43%) 32 0.61851 0.97 0.03663 0.697 0.71703 0.997 0.8057 1 0.0178 0.645 0.22427 0.81 1 1 1 1 0.88641 1 0.97601 1 10q loss 20 (36%) 36 0.93744 1 0.44666 0.877 0.42753 0.877 0.78284 1 0.38572 0.86 0.25739 0.81 0.63 0.97 0.58759 0.957 0.35419 0.86 0.82393 1 11p loss 28 (50%) 28 0.78553 1 0.02534 0.688 0.60512 0.964 0.88966 1 0.7325 0.998 0.31225 0.836 0.33412 0.859 0.39052 0.86 0.32289 0.845 0.23116 0.81 11q loss 26 (46%) 30 0.13723 0.72 0.43551 0.877 0.11511 0.72 0.91015 1 0.84511 1 0.5353 0.935 0.37731 0.86 0.52609 0.93 0.24903 0.81 0.13714 0.72 12p loss 13 (23%) 43 0.37548 0.86 0.64831 0.97 0.2841 0.836 0.74269 0.998 0.72092 0.998 0.73403 0.998 0.78337 1 0.57768 0.957 0.77481 1 0.2171 0.81 12q loss 14 (25%) 42 0.30709 0.836 0.97267 1 0.41865 0.872 0.12506 0.72 0.88291 1 0.91614 1 1 1 0.90744 1 0.3952 0.86 0.60204 0.961 13q loss 26 (46%) 30 0.51958 0.93 0.070189 0.72 0.3042 0.836 0.14883 0.744 0.097889 0.72 0.02785 0.688 0.4004 0.863 0.11782 0.72 0.13043 0.72 0.19859 0.809 14q loss 27 (48%) 29 0.94212 1 0.17414 0.786 0.86564 1 0.11731 0.72 0.1066 0.72 0.12446 0.72 0.38208 0.86 0.89837 1 0.28451 0.836 0.93835 1 15q loss 33 (59%) 23 0.01109 0.584 0.34659 0.86 0.90262 1 0.12597 0.72 1 1 0.97967 1 1 1 0.95321 1 0.87826 1 0.90954 1 16p loss 32 (57%) 24 0.42106 0.873 0.82339 1 0.40399 0.863 0.086019 0.72 0.32192 0.845 0.098949 0.72 0.36985 0.86 0.91524 1 0.86888 1 0.89572 1 16q loss 37 (66%) 19 0.36937 0.86 0.37287 0.86 0.25045 0.81 0.12904 0.72 0.64514 0.97 0.090339 0.72 0.14118 0.72 0.92182 1 0.88178 1 0.85854 1 17p loss 34 (61%) 22 0.44497 0.877 0.34515 0.86 0.0196 0.645 0.27403 0.829 0.9267 1 0.75894 1 0.93933 1 0.89106 1 0.44411 0.877 0.88902 1 17q loss 17 (30%) 39 0.65863 0.977 0.55335 0.944 0.13178 0.72 0.62804 0.97 0.69462 0.991 0.38457 0.86 0.25959 0.811 0.21234 0.809 0.73828 0.998 0.27647 0.834 18p loss 18 (32%) 38 0.47282 0.889 0.25209 0.81 0.55888 0.946 0.29141 0.836 0.0469 0.707 0.090019 0.72 0.03206 0.697 0.078889 0.72 0.081569 0.72 0.04642 0.707 18q loss 20 (36%) 36 0.14666 0.743 0.5971 0.961 0.29754 0.836 0.29706 0.836 0.24606 0.81 0.11994 0.72 0.00142 0.45 0.0055299 0.45 0.065389 0.707 0.00255 0.45 19p loss 15 (27%) 41 0.55017 0.944 0.14126 0.72 0.1577 0.779 0.38033 0.86 0.01269 0.594 0.061329 0.707 0.16616 0.786 0.254 0.81 0.090589 0.72 0.18635 0.804 19q loss 12 (21%) 44 0.64995 0.97 0.62884 0.97 0.1054 0.72 0.816 1 0.84243 1 0.50833 0.925 0.40795 0.863 0.96116 1 0.56951 0.953 1 1 20p loss 8 (14%) 48 0.88889 1 0.58728 0.957 0.53205 0.935 0.0062699 0.45 0.1798 0.802 0.28524 0.836 0.55679 0.946 0.335 0.859 0.8383 1 0.39493 0.86 20q loss 5 (9%) 51 0.43372 0.877 0.80618 1 0.78624 1 0.2411 0.81 0.53587 0.935 0.91078 1 0.71047 0.997 0.69371 0.991 1 1 0.62733 0.97 21q loss 17 (30%) 39 0.43124 0.877 0.077609 0.72 0.056659 0.707 0.33046 0.856 0.49142 0.909 0.74747 1 0.80715 1 0.9725 1 1 1 0.94209 1 22q loss 33 (59%) 23 0.94198 1 0.89906 1 0.39422 0.86 0.02172 0.686 0.77947 1 0.90121 1 0.17857 0.802 0.29047 0.836 0.94459 1 0.75884 1 xp loss 15 (27%) 41 0.19121 0.809 0.69808 0.992 0.92414 1 0.16996 0.786 0.95229 1 0.85893 1 0.54723 0.944 0.64662 0.97 0.82875 1 0.76107 1 xq loss 18 (32%) 38 0.76625 1 0.85367 1 0.86828 1 0.03407 0.697 0.42808 0.877 0.6237 0.97 0.31097 0.836 0.64713 0.97 0.13678 0.72 0.75202 1