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 10 (11%) 77 0.01423 0.229 0.78036 0.953 0.38208 0.793 0.44165 0.822 0.76812 0.953 0.68304 0.925 0.43985 0.822 0.82117 0.972 0.23199 0.668 0.34311 0.772 1q gain 21 (24%) 66 0.0091899 0.184 0.03171 0.356 0.84124 0.977 0.77144 0.953 0.10248 0.535 0.15538 0.565 0.22831 0.667 0.20506 0.641 0.57482 0.893 0.50741 0.855 2p gain 4 (5%) 83 0.10381 0.535 0.37463 0.791 0.96613 1 0.74416 0.948 0.60443 0.906 0.78613 0.953 0.12173 0.543 0.14163 0.549 0.35633 0.779 0.18524 0.615 2q gain 7 (8%) 80 0.51584 0.86 0.46191 0.831 0.90392 0.991 0.60411 0.906 0.35963 0.779 0.42539 0.811 0.24683 0.697 0.91234 0.992 0.13541 0.547 0.064379 0.501 3p gain 17 (20%) 70 0.00055999 0.0296 0.93054 0.997 0.10686 0.535 0.40723 0.799 0.61868 0.916 0.62589 0.921 0.88614 0.985 0.88272 0.985 0.43967 0.822 0.60845 0.908 3q gain 19 (22%) 68 0.00012 0.012 0.76775 0.953 0.23049 0.668 0.43075 0.815 0.66808 0.925 0.38814 0.793 0.45577 0.829 0.46678 0.831 0.32831 0.767 0.54019 0.865 5p gain 24 (28%) 63 0.19649 0.638 0.32896 0.767 0.096109 0.529 0.93734 0.997 0.51383 0.86 0.58048 0.893 0.03881 0.399 0.43325 0.818 0.49448 0.852 0.44642 0.823 5q gain 15 (17%) 72 0.060369 0.496 0.3543 0.779 0.50102 0.852 0.99197 1 0.30005 0.75 0.69024 0.925 0.15111 0.565 0.36703 0.785 0.3398 0.772 0.34485 0.772 6p gain 7 (8%) 80 0.075699 0.509 0.095269 0.529 0.86563 0.984 0.12548 0.547 0.068059 0.501 0.38571 0.793 0.071899 0.502 0.96581 1 0.88429 0.985 0.71483 0.94 6q gain 4 (5%) 83 0.10246 0.535 0.63268 0.921 0.90692 0.991 0.74624 0.948 0.40077 0.799 0.69409 0.925 0.6744 0.925 0.93561 0.997 0.67955 0.925 0.75244 0.948 7p gain 25 (29%) 62 0.01412 0.229 0.39082 0.793 0.37135 0.787 0.26329 0.704 0.095449 0.529 0.071899 0.502 0.096589 0.529 0.04213 0.414 0.3192 0.764 0.02443 0.309 7q gain 22 (25%) 65 0.02408 0.309 0.44699 0.823 0.65852 0.925 0.11417 0.535 0.14318 0.549 0.03004 0.342 0.22771 0.667 0.18318 0.611 0.52783 0.865 0.11558 0.535 8p gain 12 (14%) 75 0.04634 0.429 0.52277 0.865 0.34078 0.772 0.23105 0.668 0.66371 0.925 0.75955 0.951 0.14062 0.549 0.03824 0.399 0.60024 0.906 0.2487 0.697 8q gain 14 (16%) 73 0.04884 0.441 0.93418 0.997 0.22772 0.667 0.72268 0.944 0.7001 0.929 0.74971 0.948 0.26242 0.704 0.58582 0.896 0.74605 0.948 0.54101 0.865 9p gain 3 (3%) 84 0.70205 0.929 0.53341 0.865 NA NA NA NA 0.31681 0.764 1 1 0.11188 0.535 0.80695 0.968 0.1003 0.535 0.02632 0.314 9q gain 4 (5%) 83 0.50023 0.852 0.071099 0.502 0.44968 0.824 1 1 0.47317 0.838 0.63624 0.921 0.058569 0.487 0.46846 0.831 0.81443 0.972 0.69314 0.925 10p gain 3 (3%) 84 0.078539 0.51 0.77494 0.953 NA NA NA NA 0.88296 0.985 0.91847 0.992 1 1 0.26498 0.704 1 1 0.88625 0.985 10q gain 3 (3%) 84 0.080789 0.512 0.77463 0.953 NA NA NA NA 0.88478 0.985 0.92051 0.992 1 1 0.2653 0.704 1 1 0.88997 0.987 11p gain 11 (13%) 76 0.0074499 0.153 0.66388 0.925 0.63593 0.921 0.82291 0.972 0.29388 0.749 0.092089 0.529 0.38962 0.793 0.66605 0.925 1 1 0.82625 0.972 11q gain 12 (14%) 75 0.0096799 0.189 0.38083 0.793 0.75074 0.948 0.95526 1 0.065489 0.501 0.03528 0.378 0.52912 0.865 0.54532 0.87 0.56574 0.885 0.48193 0.847 12p gain 18 (21%) 69 0.00031 0.0197 0.81312 0.972 0.4868 0.847 0.14087 0.549 0.89314 0.988 0.85191 0.977 0.75061 0.948 0.92236 0.992 1 1 0.86203 0.983 12q gain 18 (21%) 69 0.00032 0.0197 0.81462 0.972 0.48125 0.847 0.14067 0.549 0.89102 0.987 0.85301 0.977 0.74857 0.948 0.9218 0.992 1 1 0.86103 0.983 13q gain 5 (6%) 82 0.42062 0.807 0.097989 0.533 0.34756 0.772 0.88277 0.985 0.02673 0.314 0.04539 0.425 0.6109 0.91 0.43061 0.815 0.85105 0.977 0.38565 0.793 15q gain 11 (13%) 76 0.02504 0.309 0.0043 0.111 0.17806 0.603 0.01168 0.211 0.01969 0.291 0.12974 0.547 0.00352 0.109 0.078179 0.51 0.77403 0.953 0.22582 0.667 16p gain 17 (20%) 70 0.0066599 0.145 0.56674 0.885 0.5274 0.865 0.75608 0.948 0.01201 0.212 0.066329 0.501 0.17797 0.603 0.18707 0.618 0.63426 0.921 0.080979 0.512 16q gain 16 (18%) 71 0.00238 0.0881 0.8055 0.968 0.5285 0.865 0.87795 0.985 0.0229 0.309 0.10679 0.535 0.56055 0.882 0.66031 0.925 0.8752 0.985 0.37635 0.791 17p gain 7 (8%) 80 0.22102 0.665 1 1 0.15127 0.565 0.070549 0.502 0.4421 0.822 0.68419 0.925 0.69616 0.927 0.11299 0.535 0.46828 0.831 0.24451 0.697 17q gain 17 (20%) 70 0.092879 0.529 0.31848 0.764 0.30025 0.75 0.11409 0.535 0.02169 0.303 0.04435 0.421 0.14551 0.552 0.86806 0.985 0.74046 0.948 0.84572 0.977 18p gain 8 (9%) 79 0.067269 0.501 0.31769 0.764 0.40156 0.799 0.8248 0.972 0.11754 0.54 0.18277 0.611 0.11951 0.54 0.13489 0.547 0.60467 0.906 0.13366 0.547 18q gain 4 (5%) 83 0.085149 0.521 1 1 0.2629 0.704 0.27868 0.721 0.30087 0.75 0.63737 0.921 0.03352 0.369 0.083239 0.518 0.60642 0.907 0.19269 0.628 19p gain 14 (16%) 73 0.27127 0.712 0.03387 0.369 0.85687 0.98 0.58124 0.893 0.16104 0.573 0.17232 0.596 0.4633 0.831 0.17413 0.599 0.69001 0.925 0.20626 0.641 19q gain 10 (11%) 77 0.80237 0.965 0.11841 0.54 0.48421 0.847 0.59066 0.898 0.3254 0.767 0.68613 0.925 0.53181 0.865 0.71154 0.939 0.54121 0.865 0.89521 0.988 20p gain 8 (9%) 79 0.69298 0.925 0.72935 0.947 0.66481 0.925 0.49081 0.851 0.38433 0.793 0.78265 0.953 0.58141 0.893 0.44471 0.823 0.64063 0.921 0.6702 0.925 20q gain 10 (11%) 77 0.20595 0.641 0.9066 0.991 0.84679 0.977 0.75218 0.948 0.64106 0.921 0.93666 0.997 0.32058 0.765 0.74746 0.948 0.52485 0.865 0.59108 0.898 21q gain 6 (7%) 81 0.25213 0.704 0.61408 0.912 0.63929 0.921 0.60458 0.906 0.224 0.667 0.21712 0.658 0.074389 0.505 0.34355 0.772 0.03951 0.401 0.15908 0.571 xp gain 7 (8%) 80 0.13286 0.547 0.36021 0.779 0.98565 1 0.44186 0.822 0.24646 0.697 0.77653 0.953 0.78705 0.953 0.96581 1 0.78273 0.953 0.90565 0.991 xq gain 6 (7%) 81 0.22905 0.667 0.49902 0.852 1 1 0.68535 0.925 0.15586 0.565 0.64329 0.923 0.48759 0.847 0.83798 0.977 1 1 0.88142 0.985 1p loss 8 (9%) 79 0.02505 0.309 0.22654 0.667 0.53585 0.865 0.31481 0.764 0.42081 0.807 0.91239 0.992 0.28479 0.732 0.20762 0.643 0.055189 0.478 0.6477 0.925 2p loss 6 (7%) 81 0.68789 0.925 0.38371 0.793 0.63931 0.921 0.11464 0.535 0.25639 0.704 0.068409 0.501 0.074259 0.505 0.58589 0.896 0.84959 0.977 0.15908 0.571 2q loss 4 (5%) 83 0.63534 0.921 0.3449 0.772 0.75621 0.948 0.42455 0.811 0.30027 0.75 0.50618 0.855 0.55707 0.881 0.39099 0.793 1 1 1 1 3p loss 8 (9%) 79 0.36809 0.785 0.089679 0.529 0.48408 0.847 0.54114 0.865 0.1645 0.58 0.11964 0.54 0.45868 0.831 0.71317 0.939 0.19897 0.64 0.062339 0.501 3q loss 6 (7%) 81 0.72271 0.944 0.091019 0.529 0.39723 0.797 0.26995 0.712 0.1816 0.611 0.41886 0.807 1 1 0.50247 0.853 0.65509 0.925 0.62091 0.917 4p loss 32 (37%) 55 5e-05 0.0074 0.32287 0.766 0.057949 0.487 0.38756 0.793 0.27244 0.712 0.00422 0.111 0.13075 0.547 0.33263 0.769 0.39018 0.793 0.51169 0.86 4q loss 33 (38%) 54 9.9999e-06 0.00247 0.10112 0.535 0.03602 0.381 0.1541 0.565 0.004 0.111 0.00029 0.0197 0.057909 0.487 0.14491 0.552 0.77579 0.953 0.089969 0.529 5p loss 4 (5%) 83 0.49944 0.852 0.69275 0.925 0.34541 0.772 0.53603 0.865 0.36434 0.782 0.63588 0.921 0.35961 0.779 0.93542 0.997 1 1 0.44308 0.822 5q loss 9 (10%) 78 0.02565 0.311 0.8381 0.977 0.27199 0.712 0.20969 0.644 0.49545 0.852 0.10516 0.535 0.36444 0.782 0.66954 0.925 0.4082 0.799 0.91808 0.992 6p loss 9 (10%) 78 0.83713 0.977 0.3214 0.765 0.077469 0.51 0.79451 0.958 0.24787 0.697 0.50598 0.855 0.90192 0.991 0.1708 0.593 0.20328 0.641 0.11154 0.535 6q loss 29 (33%) 58 0.00331 0.106 0.21397 0.652 0.57773 0.893 0.6595 0.925 0.395 0.794 0.64987 0.925 0.65302 0.925 0.52095 0.865 0.11305 0.535 0.081679 0.512 8p loss 13 (15%) 74 0.86966 0.985 0.68981 0.925 0.89623 0.988 0.93487 0.997 0.66369 0.925 0.75216 0.948 0.32879 0.767 0.75053 0.948 0.74722 0.948 0.2816 0.726 8q loss 4 (5%) 83 0.10504 0.535 0.37498 0.791 0.26106 0.704 0.27734 0.72 0.51484 0.86 0.55513 0.881 0.16405 0.58 0.12062 0.541 1 1 0.10647 0.535 9p loss 28 (32%) 59 9.9999e-06 0.00247 0.01497 0.236 0.092529 0.529 0.11312 0.535 0.04169 0.414 0.01055 0.195 0.95779 1 0.48737 0.847 0.91403 0.992 0.15368 0.565 9q loss 21 (24%) 66 0.00181 0.0744 0.20615 0.641 0.0061799 0.139 0.067489 0.501 0.1416 0.549 0.16102 0.573 0.9495 1 0.53784 0.865 0.57762 0.893 0.25939 0.704 10p loss 24 (28%) 63 0.00434 0.111 0.00073999 0.0342 0.12727 0.547 0.59321 0.9 0.1334 0.547 0.13599 0.547 0.87054 0.985 0.30387 0.752 0.70703 0.934 0.7294 0.947 10q loss 19 (22%) 68 0.02328 0.309 0.01708 0.263 0.12911 0.547 0.92124 0.992 0.5005 0.852 0.31805 0.764 0.2582 0.704 0.72109 0.944 1 1 0.83706 0.977 11p loss 4 (5%) 83 0.68237 0.925 0.82879 0.974 0.1673 0.584 0.20367 0.641 0.29574 0.749 0.26551 0.704 0.81857 0.972 0.39324 0.794 0.56703 0.885 0.91246 0.992 11q loss 5 (6%) 82 0.57728 0.893 0.61775 0.916 0.25591 0.704 0.34634 0.772 0.00447 0.111 0.00276 0.0973 0.84793 0.977 0.35797 0.779 0.56132 0.882 0.91293 0.992 12p loss 4 (5%) 83 0.25991 0.704 0.069359 0.502 0.1353 0.547 0.17838 0.603 0.47496 0.839 0.46478 0.831 0.28743 0.736 0.81595 0.972 0.46348 0.831 0.59815 0.905 13q loss 33 (38%) 54 0.10506 0.535 0.73592 0.948 0.70158 0.929 0.11164 0.535 0.16672 0.584 0.66496 0.925 0.75247 0.948 0.18887 0.621 0.02078 0.302 0.46659 0.831 14q loss 35 (40%) 52 0.00055999 0.0296 0.3598 0.779 0.77702 0.953 0.42632 0.811 0.00026 0.0197 9.9999e-06 0.00247 0.04883 0.441 0.00059999 0.0296 0.01415 0.229 0.00167 0.0727 15q loss 11 (13%) 76 0.1153 0.535 0.76051 0.951 0.31349 0.764 0.50071 0.852 0.27454 0.715 0.30033 0.75 0.32893 0.767 0.30382 0.752 0.74592 0.948 0.40582 0.799 16p loss 7 (8%) 80 0.0099399 0.189 0.19205 0.628 0.96501 1 0.32969 0.767 0.53151 0.865 0.34663 0.772 0.41544 0.807 0.36397 0.782 1 1 1 1 16q loss 10 (11%) 77 0.0495 0.441 0.90532 0.991 0.95462 1 0.88349 0.985 0.21903 0.662 0.45188 0.826 0.69335 0.925 0.12605 0.547 1 1 0.87943 0.985 17p loss 23 (26%) 64 0.34995 0.773 0.38052 0.793 0.19813 0.64 0.02987 0.342 0.7656 0.953 0.62664 0.921 0.15273 0.565 0.14023 0.549 0.51256 0.86 0.2616 0.704 17q loss 7 (8%) 80 0.55692 0.881 0.1555 0.565 0.44836 0.823 0.078249 0.51 0.67005 0.925 0.72758 0.947 0.24552 0.697 0.53248 0.865 0.42064 0.807 0.21378 0.652 18p loss 9 (10%) 78 0.13915 0.549 0.78111 0.953 0.085829 0.521 0.54011 0.865 0.67744 0.925 0.69301 0.925 0.33115 0.768 0.75618 0.948 0.40028 0.799 0.68564 0.925 18q loss 14 (16%) 73 0.40274 0.799 0.68533 0.925 0.45315 0.826 0.40624 0.799 0.84772 0.977 0.86421 0.984 0.12251 0.543 0.093539 0.529 0.34048 0.772 0.17856 0.603 19p loss 4 (5%) 83 0.68495 0.925 0.20084 0.641 1 1 0.096229 0.529 0.55566 0.881 0.46492 0.831 1 1 0.34907 0.773 0.20904 0.644 0.37092 0.787 19q loss 7 (8%) 80 0.55818 0.881 0.051029 0.45 0.85025 0.977 0.02161 0.303 1 1 0.93336 0.997 0.78796 0.953 0.79002 0.954 0.31203 0.764 0.82244 0.972 20p loss 14 (16%) 73 0.02456 0.309 0.10925 0.535 0.04435 0.421 0.77071 0.953 0.14246 0.549 0.58854 0.898 0.3437 0.772 0.72342 0.944 0.5697 0.888 0.12662 0.547 20q loss 3 (3%) 84 0.24024 0.689 0.33963 0.772 0.04255 0.414 0.42079 0.807 0.78812 0.953 0.20546 0.641 0.2572 0.704 0.01822 0.275 1 1 0.44344 0.822 21q loss 11 (13%) 76 0.10804 0.535 0.01288 0.222 0.39477 0.794 0.77998 0.953 0.22198 0.665 0.080259 0.512 0.65497 0.925 0.29467 0.749 0.84584 0.977 0.82418 0.972 22q loss 67 (77%) 20 0.0053899 0.125 3e-05 0.00555 0.8207 0.972 0.97286 1 0.055499 0.478 0.0045 0.111 1 1 0.64056 0.921 0.13108 0.547 0.83229 0.976 xp loss 27 (31%) 60 0.0052699 0.125 0.00013 0.012 0.068339 0.501 0.12999 0.547 0.068209 0.501 0.0072399 0.153 0.091659 0.529 0.41785 0.807 0.074119 0.505 0.30484 0.752 xq loss 28 (32%) 59 0.00196 0.0763 0.00012 0.012 0.13358 0.547 0.40542 0.799 0.085929 0.521 0.003 0.101 0.15451 0.565 0.41024 0.801 0.067919 0.501 0.31272 0.764