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 12 (7%) 153 0.51004 0.899 0.94082 1 0.8289 1 0.52737 0.906 0.03091 0.337 0.01732 0.267 0.3316 0.8 0.59512 0.929 0.9405 1 0.45887 0.889 0.86975 1 0.65271 0.951 1q gain 34 (21%) 131 0.58334 0.924 0.65042 0.951 0.136 0.618 0.31143 0.771 0.068699 0.496 0.21195 0.71 0.45235 0.885 0.99568 1 0.53552 0.907 0.87877 1 0.86962 1 0.36588 0.826 2p gain 41 (25%) 124 0.50777 0.899 0.01974 0.267 0.25906 0.721 0.025 0.311 0.66908 0.957 0.64137 0.951 0.04651 0.439 0.01906 0.267 0.18823 0.698 0.076069 0.514 0.72645 0.987 0.50067 0.899 2q gain 43 (26%) 122 0.092959 0.553 0.057469 0.481 0.12107 0.597 0.060969 0.488 0.72148 0.987 0.82792 1 0.088109 0.551 0.0025 0.0828 0.21851 0.71 0.3071 0.768 0.15775 0.652 0.18835 0.698 3p gain 27 (16%) 138 1 1 0.90207 1 0.00061999 0.0397 0.65471 0.951 0.087419 0.551 0.45857 0.889 0.11031 0.581 0.92793 1 0.37834 0.826 0.36105 0.826 0.65434 0.951 0.82498 1 3q gain 34 (21%) 131 0.60538 0.934 0.61159 0.938 0.00018 0.0192 0.86838 1 0.25087 0.717 0.42306 0.866 0.10297 0.567 0.7378 0.989 0.22032 0.71 0.31539 0.776 0.65905 0.951 0.89647 1 4p gain 9 (5%) 156 1 1 0.79123 1 0.96544 1 0.76455 1 0.089709 0.552 0.17244 0.672 0.48774 0.899 0.62751 0.947 0.2233 0.71 0.37376 0.826 0.74359 0.989 0.94936 1 4q gain 5 (3%) 160 0.29795 0.763 0.64821 0.951 0.67494 0.958 NA NA 0.21906 0.71 0.48825 0.899 0.71226 0.984 1 1 0.88915 1 1 1 NA NA NA NA 5p gain 36 (22%) 129 0.20354 0.71 0.098049 0.556 0.00174 0.0795 0.098509 0.556 0.21468 0.71 0.68948 0.967 0.11287 0.582 5.9999e-05 0.0072 0.19029 0.703 0.92311 1 0.49216 0.899 0.62676 0.947 5q gain 24 (15%) 141 0.2438 0.717 0.087779 0.551 0.0072099 0.169 0.073859 0.51 0.18647 0.697 0.96079 1 0.44862 0.885 0.091099 0.553 0.24817 0.717 0.52224 0.902 1 1 0.65191 0.951 6p gain 41 (25%) 124 0.33489 0.801 0.56463 0.912 0.0088999 0.178 0.00328 0.0984 0.77337 1 0.25704 0.721 0.79737 1 0.46738 0.892 0.2407 0.715 0.29766 0.763 0.27779 0.745 0.81103 1 6q gain 36 (22%) 129 0.67079 0.957 0.22984 0.71 0.01739 0.267 0.0067099 0.169 0.84246 1 0.47006 0.894 0.67257 0.958 0.50904 0.899 0.34108 0.803 0.58165 0.923 0.20161 0.71 0.56278 0.912 7p gain 102 (62%) 63 0.00229 0.0828 0.00261 0.0835 9.9999e-06 0.0048 0.00316 0.0979 0.48628 0.899 0.37566 0.826 0.00024 0.023 2e-05 0.0048 0.0415 0.419 0.097939 0.556 0.59357 0.929 0.81404 1 7q gain 85 (52%) 80 0.04596 0.439 0.0081299 0.174 2e-05 0.0048 0.13975 0.619 0.61886 0.941 0.94828 1 0.0045 0.123 0.00213 0.0828 0.50111 0.899 0.82744 1 0.85639 1 0.85553 1 8p gain 42 (25%) 123 0.42159 0.866 0.23564 0.71 0.00224 0.0828 0.51746 0.899 0.45253 0.885 0.093279 0.553 0.51356 0.899 0.3406 0.803 0.81412 1 0.28696 0.749 0.91798 1 0.13987 0.619 8q gain 89 (54%) 76 0.03638 0.384 0.27657 0.745 5e-05 0.0072 0.20998 0.71 0.54807 0.912 0.78819 1 0.6043 0.934 0.22043 0.71 0.24447 0.717 0.067509 0.494 0.0208 0.27 0.37324 0.826 9p gain 42 (25%) 123 0.01756 0.267 0.19604 0.71 0.44209 0.881 0.16344 0.662 0.65237 0.951 0.2287 0.71 0.051249 0.457 0.27847 0.745 0.27284 0.745 0.32769 0.792 0.86388 1 0.86743 1 9q gain 33 (20%) 132 0.01526 0.253 0.21091 0.71 0.2799 0.745 0.4682 0.892 0.5605 0.912 0.097949 0.556 0.3711 0.826 0.090859 0.553 0.78636 1 0.62232 0.942 0.82989 1 0.93156 1 10p gain 13 (8%) 152 1 1 0.91795 1 0.33619 0.801 0.71626 0.985 0.66558 0.957 0.75006 0.989 0.52209 0.902 0.12636 0.607 0.65288 0.951 0.91894 1 0.61564 0.941 0.79109 1 10q gain 7 (4%) 158 0.51837 0.899 0.081659 0.533 0.25357 0.72 1 1 1 1 0.87236 1 1 1 0.50262 0.899 0.77449 1 0.86394 1 NA NA NA NA 11p gain 32 (19%) 133 0.13418 0.618 0.38924 0.836 0.0085199 0.174 0.41863 0.866 0.71961 0.987 0.35899 0.826 0.13315 0.618 0.14135 0.62 0.02052 0.27 0.20887 0.71 0.65692 0.951 0.53187 0.907 11q gain 26 (16%) 139 0.23676 0.71 0.42844 0.87 0.00202 0.0828 0.01947 0.267 0.57409 0.917 0.30173 0.766 0.00249 0.0828 0.00043 0.035 0.02526 0.311 0.58868 0.929 0.11921 0.596 0.1582 0.652 12p gain 33 (20%) 132 0.69184 0.968 0.48135 0.899 0.23518 0.71 0.7279 0.987 0.181 0.688 0.12213 0.598 0.083959 0.541 0.20217 0.71 0.37365 0.826 0.55003 0.912 0.28094 0.745 0.86913 1 12q gain 24 (15%) 141 0.77574 1 0.51856 0.899 0.73955 0.989 0.30738 0.768 0.26492 0.733 0.21267 0.71 0.04201 0.42 0.50976 0.899 0.22424 0.71 0.74201 0.989 0.053179 0.464 0.94948 1 13q gain 113 (68%) 52 0.28486 0.749 0.37639 0.826 9.9999e-06 0.0048 0.071339 0.5 0.83618 1 0.3174 0.777 0.00050999 0.035 0.00047 0.035 0.00351 0.102 0.065959 0.494 0.71143 0.984 0.47557 0.897 14q gain 8 (5%) 157 0.83204 1 0.91626 1 0.11244 0.582 0.22347 0.71 0.51853 0.899 0.54371 0.912 0.49373 0.899 0.913 1 0.12925 0.614 0.8617 1 NA NA NA NA 15q gain 3 (2%) 162 NA NA NA NA 0.41731 0.866 0.48053 0.899 NA NA NA NA 0.35615 0.826 0.64418 0.951 NA NA NA NA NA NA NA NA 16p gain 41 (25%) 124 0.14432 0.621 0.85317 1 0.00108 0.0576 0.27012 0.743 0.92397 1 1 1 0.11619 0.593 0.36927 0.826 0.1514 0.647 0.67544 0.958 0.33514 0.801 0.98144 1 16q gain 41 (25%) 124 0.051439 0.457 0.59407 0.929 3e-05 0.00576 0.23303 0.71 1 1 0.66973 0.957 0.01005 0.193 0.10673 0.572 0.01974 0.267 0.24473 0.717 0.23279 0.71 0.91638 1 17p gain 8 (5%) 157 0.10822 0.577 0.3801 0.826 0.23289 0.71 0.46604 0.892 1 1 0.87224 1 0.4234 0.866 0.68545 0.966 0.4899 0.899 0.44299 0.881 NA NA NA NA 17q gain 32 (19%) 133 0.19858 0.71 0.9434 1 0.0070299 0.169 0.42106 0.866 0.87929 1 0.93974 1 0.36648 0.826 0.49278 0.899 0.053689 0.464 0.46011 0.889 0.12005 0.597 0.6368 0.951 18p gain 8 (5%) 157 0.51648 0.899 0.39081 0.837 0.21637 0.71 0.72849 0.987 0.80727 1 0.73807 0.989 0.67849 0.959 0.38325 0.827 0.50015 0.899 0.55809 0.912 1 1 0.89302 1 18q gain 6 (4%) 159 NA NA NA NA 0.79243 1 0.37925 0.826 0.49173 0.899 0.89336 1 0.53351 0.907 0.22696 0.71 0.65428 0.951 0.63186 0.949 1 1 0.89241 1 19p gain 33 (20%) 132 0.065239 0.494 0.41718 0.866 0.1056 0.572 0.76558 1 0.54443 0.912 0.46273 0.89 0.56613 0.912 0.0277 0.315 0.13756 0.618 0.95661 1 1 1 0.97296 1 19q gain 32 (19%) 133 0.082009 0.533 0.53346 0.907 0.074799 0.513 0.52985 0.907 0.95812 1 0.5937 0.929 0.22574 0.71 0.12842 0.613 0.35346 0.826 0.58086 0.923 1 1 0.9727 1 20p gain 109 (66%) 56 0.095439 0.556 0.7255 0.987 0.13832 0.618 0.25071 0.717 0.13423 0.618 0.83064 1 0.6043 0.934 0.56572 0.912 0.097259 0.556 0.04681 0.439 0.30403 0.766 0.077669 0.514 20q gain 145 (88%) 20 0.0073999 0.169 0.16114 0.661 0.00071999 0.0432 0.23268 0.71 0.16221 0.662 0.33769 0.802 0.44343 0.881 0.00247 0.0828 0.04467 0.438 0.36072 0.826 0.36213 0.826 1 1 21q gain 10 (6%) 155 0.53468 0.907 0.65878 0.951 0.63746 0.951 1 1 0.62022 0.941 0.79221 1 0.9469 1 0.9205 1 0.28902 0.75 0.7239 0.987 NA NA NA NA 22q gain 9 (5%) 156 0.72923 0.987 0.060789 0.488 0.075399 0.513 1 1 0.42196 0.866 0.23416 0.71 0.3507 0.823 0.20105 0.71 1 1 1 1 NA NA NA NA xp gain 34 (21%) 131 0.01094 0.206 0.14298 0.621 0.11071 0.581 0.40021 0.853 0.5928 0.929 0.62051 0.941 0.27095 0.743 0.66889 0.957 0.81035 1 0.84631 1 0.83054 1 0.64299 0.951 xq gain 34 (21%) 131 0.1558 0.647 0.3822 0.826 0.04541 0.439 0.28785 0.749 0.81791 1 0.30235 0.766 0.10387 0.567 0.64712 0.951 0.98096 1 1 1 0.45331 0.885 0.21174 0.71 1p loss 46 (28%) 119 0.69028 0.967 0.02726 0.315 0.050779 0.457 0.18471 0.693 0.9351 1 0.20652 0.71 0.36589 0.826 0.16901 0.67 0.44225 0.881 0.60981 0.937 0.55863 0.912 0.56728 0.912 1q loss 26 (16%) 139 0.91178 1 0.057609 0.481 0.25687 0.721 0.02878 0.321 0.84292 1 0.53214 0.907 0.065439 0.494 0.4628 0.89 0.56052 0.912 0.22605 0.71 0.49983 0.899 0.27539 0.745 2p loss 11 (7%) 154 0.63838 0.951 0.74994 0.989 0.00384 0.108 0.48317 0.899 0.90723 1 0.54182 0.912 0.52631 0.905 0.059349 0.487 0.43527 0.876 0.60523 0.934 NA NA NA NA 2q loss 6 (4%) 159 1 1 0.56886 0.912 0.052339 0.461 NA NA 0.10257 0.567 0.30363 0.766 0.81026 1 0.065559 0.494 0.20276 0.71 0.46637 0.892 NA NA NA NA 3p loss 15 (9%) 150 1 1 0.36478 0.826 0.2033 0.71 0.77358 1 0.25835 0.721 0.89481 1 0.1538 0.647 0.5571 0.912 0.45346 0.885 0.13369 0.618 0.098299 0.556 0.04447 0.438 3q loss 10 (6%) 155 0.51802 0.899 0.79274 1 0.19505 0.71 0.4095 0.863 0.32597 0.791 0.65674 0.951 0.10374 0.567 0.22013 0.71 0.49354 0.899 0.0094199 0.185 0.42196 0.866 0.36483 0.826 4p loss 59 (36%) 106 0.66598 0.957 0.37489 0.826 0.00196 0.0828 0.02733 0.315 0.97115 1 0.51399 0.899 0.7127 0.984 0.56919 0.912 0.97448 1 0.099789 0.557 0.22443 0.71 0.21053 0.71 4q loss 66 (40%) 99 0.77922 1 0.2696 0.743 0.00106 0.0576 0.04007 0.409 0.82037 1 0.51586 0.899 0.76827 1 0.43509 0.876 0.81237 1 0.21724 0.71 0.56689 0.912 0.91642 1 5p loss 26 (16%) 139 0.23854 0.713 0.81585 1 0.1371 0.618 0.17772 0.68 0.52463 0.904 0.065159 0.494 0.87787 1 0.12522 0.607 0.7238 0.987 0.57731 0.921 0.1736 0.672 0.24565 0.717 5q loss 40 (24%) 125 0.091929 0.553 0.01167 0.215 0.21639 0.71 0.1682 0.67 1 1 0.54844 0.912 0.92608 1 0.22103 0.71 0.91175 1 0.20721 0.71 0.11335 0.582 0.22744 0.71 6p loss 13 (8%) 152 0.54577 0.912 0.93061 1 0.7001 0.975 0.12122 0.597 0.3109 0.771 0.35936 0.826 0.74926 0.989 0.27757 0.745 0.56563 0.912 0.25552 0.721 NA NA NA NA 6q loss 22 (13%) 143 0.16958 0.67 0.64415 0.951 0.15508 0.647 0.42157 0.866 0.45188 0.885 0.60366 0.934 0.15288 0.647 0.15233 0.647 0.26433 0.733 0.40941 0.863 0.01323 0.235 0.55323 0.912 7q loss 3 (2%) 162 NA NA NA NA 0.35744 0.826 NA NA 0.7848 1 0.77282 1 0.03748 0.391 0.75868 0.996 0.85834 1 1 1 NA NA NA NA 8p loss 73 (44%) 92 0.12303 0.6 0.24634 0.717 0.13412 0.618 0.96409 1 0.78513 1 0.25229 0.719 0.02402 0.303 0.11701 0.593 0.89445 1 0.97305 1 0.73313 0.989 0.22946 0.71 8q loss 11 (7%) 154 0.68736 0.966 0.71372 0.984 0.40971 0.863 0.46774 0.892 0.79383 1 0.27927 0.745 0.54539 0.912 0.32646 0.791 0.86583 1 0.30241 0.766 0.16901 0.67 0.40503 0.858 9p loss 23 (14%) 142 0.63364 0.95 0.61621 0.941 0.32085 0.782 0.14116 0.62 0.74896 0.989 0.56438 0.912 0.81104 1 0.5148 0.899 0.30836 0.769 0.04812 0.444 0.71268 0.984 0.03911 0.404 9q loss 23 (14%) 142 0.20979 0.71 0.44682 0.885 0.28143 0.745 0.13771 0.618 0.94124 1 0.90533 1 0.51567 0.899 0.19545 0.71 0.071299 0.5 0.00166 0.0795 0.4599 0.889 0.01511 0.253 10p loss 33 (20%) 132 0.14404 0.621 0.17194 0.672 0.13742 0.618 0.067169 0.494 0.14386 0.621 0.24043 0.715 0.20062 0.71 0.45508 0.886 0.83701 1 0.11748 0.593 0.81646 1 0.74866 0.989 10q loss 38 (23%) 127 0.17733 0.68 0.1553 0.647 0.059349 0.487 0.093379 0.553 0.12995 0.615 0.03237 0.348 0.37412 0.826 0.073439 0.51 0.68211 0.963 0.088439 0.551 0.89918 1 0.53747 0.908 11p loss 23 (14%) 142 0.24424 0.717 0.37067 0.826 0.0060299 0.159 0.20502 0.71 0.2237 0.71 0.1742 0.672 0.01935 0.267 0.23403 0.71 0.97659 1 0.74083 0.989 0.60159 0.934 0.29073 0.75 11q loss 30 (18%) 135 0.055379 0.47 0.20493 0.71 0.0069799 0.169 0.02603 0.315 0.60614 0.934 0.38492 0.829 0.0083899 0.174 0.0083799 0.174 0.20261 0.71 0.37727 0.826 0.41457 0.866 0.66754 0.957 12p loss 22 (13%) 143 0.42416 0.866 0.27833 0.745 0.65403 0.951 0.40057 0.853 0.69333 0.969 0.077509 0.514 0.7518 0.99 0.43277 0.875 0.44977 0.885 0.77514 1 0.066179 0.494 0.51198 0.899 12q loss 19 (12%) 146 0.50202 0.899 0.77098 1 0.23663 0.71 0.93011 1 0.55549 0.912 0.25849 0.721 0.83373 1 0.25439 0.72 0.37852 0.826 0.31718 0.777 0.27443 0.745 0.86771 1 13q loss 8 (5%) 157 0.51804 0.899 1 1 0.65656 0.951 0.1066 0.572 0.054359 0.466 0.431 0.873 1 1 0.49153 0.899 0.17439 0.672 1 1 NA NA NA NA 14q loss 67 (41%) 98 0.50138 0.899 0.25035 0.717 0.01996 0.267 0.5671 0.912 0.80204 1 0.49279 0.899 0.38213 0.826 0.077689 0.514 0.33549 0.801 0.20213 0.71 0.74829 0.989 0.78124 1 15q loss 73 (44%) 92 0.45081 0.885 0.11068 0.581 0.00048 0.035 1 1 0.086479 0.551 0.24905 0.717 0.43923 0.88 0.47744 0.899 0.8172 1 0.63106 0.949 0.90551 1 0.74598 0.989 16p loss 9 (5%) 156 0.37764 0.826 0.7563 0.995 0.099599 0.557 0.062399 0.494 0.65368 0.951 0.63159 0.949 0.18416 0.693 0.91288 1 0.56296 0.912 1 1 0.25046 0.717 0.4857 0.899 16q loss 15 (9%) 150 0.28186 0.745 0.67769 0.959 0.04713 0.439 0.33399 0.801 0.7227 0.987 0.89816 1 0.40237 0.855 0.99574 1 0.86879 1 1 1 0.93934 1 0.96386 1 17p loss 107 (65%) 58 0.20552 0.71 0.37623 0.826 0.094599 0.556 0.19917 0.71 0.97078 1 0.31928 0.78 0.61728 0.941 0.59329 0.929 0.98086 1 0.39824 0.851 0.28765 0.749 0.66448 0.957 17q loss 26 (16%) 139 0.90417 1 0.73692 0.989 0.02779 0.315 0.089409 0.552 0.74641 0.989 0.97385 1 0.1127 0.582 0.33964 0.803 0.86988 1 0.94698 1 0.42311 0.866 0.4758 0.897 18p loss 128 (78%) 37 0.060089 0.488 0.70741 0.984 0.00133 0.0672 0.0263 0.315 0.60097 0.934 0.15188 0.647 0.11805 0.593 0.01463 0.251 0.16816 0.67 0.16329 0.662 0.61859 0.941 0.59418 0.929 18q loss 138 (84%) 27 0.02006 0.267 0.17442 0.672 5.9999e-05 0.0072 0.01204 0.218 0.79602 1 0.48384 0.899 0.071179 0.5 0.01984 0.267 0.42652 0.867 0.02792 0.315 0.51625 0.899 0.53822 0.908 19p loss 21 (13%) 144 0.72908 0.987 0.83416 1 0.13458 0.618 0.03038 0.335 0.64956 0.951 0.80796 1 0.59067 0.929 0.56557 0.912 0.37715 0.826 0.01833 0.267 0.96362 1 0.74039 0.989 19q loss 20 (12%) 145 0.82879 1 0.5031 0.899 0.070119 0.5 0.082109 0.533 0.82039 1 0.77508 1 0.5534 0.912 0.71551 0.985 0.067519 0.494 0.0084499 0.174 1 1 0.74934 0.989 20p loss 23 (14%) 142 1 1 0.9521 1 0.050749 0.457 0.28414 0.749 0.37839 0.826 0.98519 1 0.43891 0.88 0.67376 0.958 0.0326 0.348 0.02272 0.291 0.30399 0.766 0.01452 0.251 21q loss 68 (41%) 97 0.28541 0.749 0.24686 0.717 0.41336 0.866 1 1 0.97279 1 0.53101 0.907 0.81981 1 0.68738 0.966 0.01574 0.256 0.18269 0.69 0.22429 0.71 0.067959 0.494 22q loss 58 (35%) 107 0.85322 1 0.31162 0.771 0.064159 0.494 0.77558 1 0.74983 0.989 0.29651 0.763 0.34007 0.803 0.16882 0.67 0.0061399 0.159 0.18134 0.688 0.12599 0.607 0.0186 0.267 xp loss 25 (15%) 140 0.28969 0.75 0.89898 1 0.30477 0.766 0.47513 0.897 0.50439 0.899 0.84006 1 0.42579 0.867 0.85791 1 0.97749 1 0.57874 0.921 0.57079 0.913 0.77989 1 xq loss 24 (15%) 141 0.60933 0.937 0.47828 0.899 0.70874 0.984 0.31486 0.776 0.6945 0.969 0.90142 1 0.56347 0.912 0.95447 1 0.8405 1 0.3656 0.826 0.47398 0.897 0.80585 1