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 Chi-square test_P Chi-square 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 Chi-square test_P Chi-square 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 38 (11%) 313 6.7625e-06 0.00473 0.042228 1 0.004446 1 0.065245 1 0.007579 1 0.38289 1 0.080371 1 0.18343 1 0.00049771 0.305 0.13082 1 1q gain 83 (24%) 268 2.1269e-09 1.61e-06 0.0022808 1 0.041351 1 0.14454 1 9.0897e-06 0.00628 0.0076403 1 0.00059454 0.36 0.0012016 0.699 0.0051229 1 0.0026352 1 2p gain 60 (17%) 291 1.1331e-06 0.000822 0.0080795 1 0.021114 1 0.96726 1 0.11728 1 0.25536 1 0.00048261 0.296 0.0079869 1 0.0054616 1 0.0001508 0.0961 2q gain 51 (15%) 300 1.7764e-05 0.0121 0.11429 1 0.2228 1 0.7355 1 0.028488 1 0.071467 1 0.025015 1 0.062398 1 0.033376 1 0.013765 1 3p gain 39 (11%) 312 0.0019939 1 0.026764 1 0.78912 1 0.076053 1 0.64795 1 0.43651 1 0.565 1 0.1253 1 0.42024 1 0.045522 1 3q gain 66 (19%) 285 0.0092565 1 0.22727 1 0.85153 1 0.32571 1 0.19291 1 0.062772 1 0.93174 1 0.77013 1 0.75512 1 0.37942 1 4p gain 14 (4%) 337 0.34483 1 0.81018 1 0.9125 1 1 1 0.31069 1 0.46946 1 0.72867 1 0.67333 1 0.78455 1 0.66983 1 4q gain 9 (3%) 342 0.38457 1 1 1 0.69166 1 0.48788 1 0.041814 1 0.87839 1 1 1 0.69513 1 0.51664 1 0.58296 1 5p gain 79 (23%) 272 1.5122e-14 1.18e-11 1.0077e-05 0.00694 0.25975 1 0.72392 1 1.5854e-06 0.00114 2.645e-05 0.0178 0.00010954 0.0703 6.9775e-06 0.00488 0.0027075 1 1.3129e-06 0.000949 5q gain 34 (10%) 317 0.00047038 0.289 0.066462 1 0.64401 1 0.73335 1 0.093264 1 0.12498 1 0.05405 1 0.16976 1 0.15753 1 0.078278 1 6p gain 65 (19%) 286 1.6755e-12 1.3e-09 5.1227e-09 3.84e-06 0.079076 1 0.27329 1 7.3612e-05 0.0479 3.1973e-05 0.0214 5.497e-06 0.00386 9.3452e-05 0.0604 6.8347e-05 0.0446 1.3775e-06 0.000993 6q gain 54 (15%) 297 1.0039e-10 7.69e-08 1.3616e-05 0.00934 0.086773 1 0.44116 1 1.771e-05 0.0121 0.00021964 0.138 2.4486e-05 0.0165 0.011892 1 0.00018949 0.12 2.9091e-05 0.0195 7p gain 155 (44%) 196 2.7781e-11 2.13e-08 0.00075705 0.453 0.63884 1 0.92502 1 0.3899 1 0.1012 1 0.39519 1 0.22296 1 0.13435 1 0.0090199 1 7q gain 134 (38%) 217 4.83e-09 3.63e-06 0.021316 1 0.84787 1 0.64881 1 0.51104 1 0.31768 1 0.92883 1 0.86991 1 0.62355 1 0.22746 1 8p gain 148 (42%) 203 1.9218e-05 0.013 0.013204 1 0.64214 1 0.54783 1 0.25723 1 0.097719 1 0.64355 1 0.72747 1 0.063756 1 0.50225 1 8q gain 200 (57%) 151 0.0040775 1 0.011449 1 0.86493 1 0.071542 1 0.015533 1 0.26377 1 0.022005 1 0.042572 1 0.0011095 0.649 0.038733 1 9p gain 44 (13%) 307 0.080057 1 0.82076 1 0.55124 1 0.59035 1 0.35906 1 0.41467 1 0.67626 1 0.71036 1 0.80836 1 0.33282 1 9q gain 56 (16%) 295 0.10196 1 0.67325 1 0.31958 1 0.73152 1 0.60993 1 0.49297 1 0.83734 1 0.82855 1 0.8751 1 0.48421 1 10p gain 84 (24%) 267 4.6709e-12 3.61e-09 1.671e-05 0.0114 0.10391 1 0.42873 1 0.00075022 0.45 0.019925 1 0.0079774 1 0.0005482 0.333 0.084886 1 0.0020873 1 10q gain 59 (17%) 292 4.1231e-10 3.13e-07 0.010134 1 0.090576 1 0.47369 1 0.0045028 1 0.042747 1 0.020972 1 0.045257 1 0.35397 1 0.0053646 1 11p gain 42 (12%) 309 0.020931 1 0.067992 1 0.89736 1 0.80951 1 0.24773 1 0.0071981 1 0.0014849 0.854 0.033142 1 0.20078 1 0.05157 1 11q gain 51 (15%) 300 0.0015257 0.876 0.013211 1 0.79898 1 0.70257 1 0.26288 1 0.0027327 1 0.0003982 0.246 0.009195 1 0.0089668 1 0.0084045 1 12p gain 74 (21%) 277 0.057142 1 0.46181 1 0.24003 1 0.14063 1 0.15425 1 0.31244 1 0.070956 1 0.78958 1 0.010887 1 0.21687 1 12q gain 64 (18%) 287 0.35069 1 0.97374 1 0.4072 1 0.17937 1 0.95777 1 0.77667 1 0.68768 1 0.74544 1 0.1404 1 0.77857 1 13q gain 121 (34%) 230 8.412e-12 6.49e-09 0.0012159 0.706 0.56677 1 0.34827 1 0.022201 1 0.79604 1 0.0013259 0.768 0.0025096 1 0.011681 1 0.00022315 0.14 14q gain 23 (7%) 328 0.00090275 0.534 0.21109 1 0.79893 1 0.77669 1 0.58904 1 0.84842 1 0.040515 1 0.89708 1 0.2578 1 0.7639 1 15q gain 31 (9%) 320 2.9259e-05 0.0196 0.0015906 0.908 0.23328 1 0.78275 1 0.026629 1 0.065976 1 0.62497 1 0.20937 1 0.56913 1 0.027464 1 16p gain 52 (15%) 299 0.072045 1 0.011047 1 0.38046 1 0.15083 1 0.066742 1 0.34266 1 0.76028 1 0.089634 1 0.94335 1 0.4946 1 16q gain 41 (12%) 310 0.14598 1 0.32948 1 0.6881 1 0.14579 1 0.12131 1 0.5136 1 0.58603 1 0.21376 1 0.94053 1 0.88295 1 17p gain 22 (6%) 329 0.011523 1 0.66344 1 0.72668 1 0.20022 1 0.28335 1 0.73364 1 0.54203 1 0.094373 1 0.6014 1 0.79105 1 17q gain 46 (13%) 305 0.0038428 1 0.49009 1 0.93671 1 0.94044 1 0.4767 1 0.38769 1 0.6638 1 0.8943 1 0.75774 1 0.94717 1 18p gain 66 (19%) 285 2.5722e-06 0.00183 4.6575e-06 0.00328 0.056644 1 0.50205 1 0.015848 1 0.076015 1 0.0027234 1 0.00012601 0.0808 0.059501 1 0.0010625 0.624 18q gain 45 (13%) 306 0.003469 1 0.021792 1 0.47308 1 0.48096 1 0.32454 1 0.64913 1 0.039531 1 0.022854 1 0.082549 1 0.1181 1 19p gain 44 (13%) 307 0.028737 1 0.82569 1 0.47308 1 0.037394 1 0.66526 1 0.86566 1 0.69173 1 0.5577 1 0.40825 1 0.58218 1 19q gain 61 (17%) 290 0.0015477 0.887 0.40076 1 0.21395 1 0.079547 1 0.021462 1 0.082715 1 0.11223 1 0.13227 1 0.22552 1 0.14305 1 20p gain 194 (55%) 157 1.1409e-12 8.86e-10 6.5713e-05 0.043 0.084157 1 0.70427 1 0.00077729 0.463 0.0086284 1 0.00043762 0.27 5.9801e-05 0.0392 0.016774 1 0.00014161 0.0905 20q gain 223 (64%) 128 1.8631e-18 1.47e-15 3.1104e-09 2.34e-06 0.052735 1 0.96693 1 1.8369e-06 0.00132 9.3145e-05 0.0603 3.3017e-06 0.00234 1.2748e-09 9.66e-07 0.03132 1 2.972e-09 2.24e-06 21q gain 21 (6%) 330 2.5361e-05 0.0171 0.00020582 0.13 0.14016 1 0.66643 1 0.010089 1 0.06556 1 0.01748 1 0.00015325 0.0975 0.11862 1 3.8414e-05 0.0255 22q gain 27 (8%) 324 0.010469 1 0.17914 1 0.83356 1 0.39183 1 0.23605 1 0.64508 1 0.45603 1 0.63886 1 0.3728 1 0.57548 1 xq gain 43 (12%) 308 1.3461e-05 0.00925 0.00014854 0.0948 0.60757 1 0.14069 1 0.026652 1 0.34364 1 0.011206 1 0.45054 1 0.062274 1 0.036168 1 1p loss 45 (13%) 306 2.4089e-06 0.00172 6.2183e-05 0.0407 0.0562 1 0.58642 1 0.035341 1 0.059196 1 0.006568 1 0.003413 1 0.2144 1 0.0158 1 1q loss 20 (6%) 331 0.00024462 0.153 0.00021127 0.133 0.032817 1 0.073549 1 0.4875 1 0.042426 1 0.35357 1 0.22144 1 0.45068 1 0.15547 1 2p loss 18 (5%) 333 0.0028663 1 0.00082112 0.489 0.51989 1 0.76945 1 0.066288 1 0.28868 1 0.12768 1 0.10776 1 0.33316 1 0.53794 1 2q loss 22 (6%) 329 0.00020188 0.128 8.3241e-05 0.0539 0.85248 1 0.65263 1 0.050182 1 0.51104 1 0.050365 1 0.019811 1 0.22651 1 0.17129 1 3p loss 72 (21%) 279 5.9409e-08 4.4e-05 0.05215 1 0.33146 1 0.45508 1 0.001772 1 0.00087074 0.516 0.0013946 0.806 0.056914 1 0.060689 1 0.014784 1 3q loss 45 (13%) 306 4.1293e-07 0.000301 0.0031548 1 0.19823 1 0.29154 1 7.4966e-06 0.00522 4.3125e-05 0.0285 4.7024e-05 0.031 0.0012581 0.73 0.0058427 1 0.00447 1 4p loss 130 (37%) 221 1.5281e-16 1.19e-13 3.2876e-05 0.0219 0.21178 1 0.33984 1 0.00052736 0.321 0.00074975 0.45 4.6911e-05 0.031 6.0052e-07 0.000437 0.0038423 1 8.8658e-06 0.00614 4q loss 128 (36%) 223 5.3709e-18 4.22e-15 4.3482e-06 0.00307 0.050617 1 0.24917 1 0.0059663 1 0.0015593 0.892 0.00027323 0.17 2.9347e-06 0.00209 0.022455 1 2.2259e-05 0.015 5p loss 46 (13%) 305 3.221e-06 0.00229 0.00050287 0.307 0.22712 1 0.5119 1 0.0034459 1 0.010593 1 0.02202 1 0.032816 1 0.0077151 1 0.0044144 1 5q loss 76 (22%) 275 1.3692e-11 1.05e-08 1.1087e-07 8.18e-05 0.61455 1 0.92903 1 2.3428e-07 0.000172 6.6329e-06 0.00465 0.00055472 0.337 9.5497e-07 0.000694 0.0010266 0.606 9.7675e-08 7.22e-05 6p loss 41 (12%) 310 1.7631e-07 0.000129 0.020562 1 0.14556 1 0.25578 1 0.024782 1 0.04082 1 0.21189 1 0.004332 1 0.1679 1 0.001145 0.669 6q loss 53 (15%) 298 1.5991e-07 0.000118 0.01706 1 0.7487 1 0.75213 1 0.030795 1 0.15389 1 0.55795 1 0.032012 1 0.70593 1 0.029602 1 7p loss 12 (3%) 339 0.003461 1 0.0018695 1 0.4444 1 0.57746 1 0.00058351 0.354 0.13908 1 0.1981 1 0.11769 1 0.010072 1 0.033412 1 7q loss 23 (7%) 328 2.4274e-05 0.0164 0.00084091 0.5 0.43127 1 0.52764 1 0.0057253 1 0.048633 1 0.03809 1 0.041717 1 0.0014708 0.847 0.056991 1 8p loss 62 (18%) 289 1.7418e-08 1.3e-05 0.02984 1 0.38798 1 0.34086 1 0.0051747 1 0.0029042 1 0.0016588 0.946 0.0011003 0.645 0.0059593 1 0.039432 1 8q loss 17 (5%) 334 0.025038 1 0.52207 1 1 1 0.76945 1 0.85117 1 0.41865 1 0.46631 1 0.56475 1 0.8141 1 0.47033 1 9p loss 113 (32%) 238 5.9502e-21 4.69e-18 1.7563e-05 0.012 0.0010367 0.611 0.03881 1 1.7164e-08 1.28e-05 5.8796e-05 0.0386 0.00031725 0.197 8.3034e-06 0.00576 0.22891 1 4.0559e-06 0.00287 9q loss 78 (22%) 273 2.372e-10 1.81e-07 0.0017752 1 0.18343 1 0.28695 1 3.5094e-05 0.0233 0.0035671 1 0.0079252 1 0.0028547 1 0.074351 1 0.00037513 0.232 10p loss 44 (13%) 307 9.9591e-06 0.00687 0.024125 1 0.53356 1 0.26822 1 0.020959 1 0.013719 1 0.014746 1 0.051586 1 0.1439 1 0.055992 1 10q loss 49 (14%) 302 1.586e-08 1.19e-05 0.0059009 1 0.63191 1 0.64021 1 0.0026487 1 0.0081732 1 0.028032 1 0.043667 1 0.40687 1 0.10949 1 11p loss 50 (14%) 301 2.4522e-07 0.00018 0.012177 1 0.0090483 1 0.50348 1 0.07472 1 0.01681 1 0.69329 1 0.019082 1 0.43164 1 0.022777 1 11q loss 46 (13%) 305 0.00030911 0.192 0.18673 1 0.51708 1 0.95544 1 0.71352 1 0.52845 1 0.63565 1 0.22111 1 0.71168 1 0.23603 1 12p loss 47 (13%) 304 5.2928e-14 4.12e-11 3.2443e-10 2.48e-07 0.24882 1 0.51032 1 1.9188e-05 0.013 0.00051941 0.317 0.0031587 1 3.7773e-05 0.0251 0.055086 1 1.7047e-07 0.000125 12q loss 37 (11%) 314 4.0276e-10 3.07e-07 2.1891e-06 0.00157 0.49706 1 1 1 0.0025631 1 0.10126 1 0.20042 1 0.0011744 0.685 0.4975 1 0.0025502 1 13q loss 31 (9%) 320 7.0809e-05 0.0462 0.63725 1 0.67576 1 0.13801 1 0.27893 1 0.53939 1 0.72789 1 0.44538 1 0.31466 1 0.81864 1 14q loss 84 (24%) 267 3.5499e-09 2.67e-06 2.9316e-05 0.0196 0.55905 1 0.47075 1 0.00060778 0.367 0.00025041 0.156 0.00046547 0.286 0.0023839 1 0.033075 1 2.0845e-05 0.0141 15q loss 72 (21%) 279 2.019e-08 1.51e-05 0.0014326 0.827 0.0051223 1 0.069268 1 7.7436e-05 0.0503 7.5199e-05 0.0489 0.00020942 0.132 1.2462e-05 0.00857 0.0024492 1 9.8419e-05 0.0635 16p loss 74 (21%) 277 3.1336e-17 2.46e-14 0.00010067 0.0648 0.81171 1 0.80704 1 4.0839e-10 3.11e-07 5.3023e-07 0.000387 1.7087e-06 0.00123 0.00018322 0.116 3.1044e-06 0.00221 4.8594e-06 0.00342 16q loss 83 (24%) 268 2.8853e-16 2.25e-13 1.0172e-06 0.000738 0.046392 1 0.56385 1 4.9862e-08 3.7e-05 8.211e-06 0.00571 1.9593e-05 0.0133 5.6371e-05 0.0371 0.0044318 1 8.9896e-06 0.00622 17p loss 123 (35%) 228 1.6995e-21 1.34e-18 1.3282e-11 1.02e-08 0.46291 1 0.80875 1 4.4449e-06 0.00314 1.7356e-06 0.00125 0.00013374 0.0856 1.3807e-05 0.00946 0.0027818 1 4.5927e-08 3.41e-05 17q loss 56 (16%) 295 3.9159e-08 2.91e-05 7.4643e-06 0.00521 0.28263 1 1 1 0.0019296 1 0.00041315 0.255 0.0010455 0.615 0.00076728 0.458 0.077144 1 0.00015822 0.1 18p loss 100 (28%) 251 0.00010171 0.0654 0.56906 1 0.68014 1 0.083559 1 0.45118 1 0.30897 1 0.10042 1 0.4402 1 0.049827 1 0.31948 1 18q loss 124 (35%) 227 1.8854e-09 1.43e-06 0.038932 1 0.33752 1 0.3656 1 0.012505 1 0.024223 1 0.0025468 1 0.013796 1 0.11751 1 0.012556 1 19p loss 89 (25%) 262 2.3831e-23 1.88e-20 2.0266e-12 1.57e-09 0.0080979 1 0.56806 1 3.2017e-12 2.48e-09 8.8282e-12 6.81e-09 1.2226e-06 0.000885 1.1273e-12 8.77e-10 0.00036791 0.228 2.23e-10 1.71e-07 19q loss 69 (20%) 282 1.3134e-16 1.03e-13 8.3337e-10 6.33e-07 0.017418 1 0.10031 1 1.5523e-07 0.000114 2.4302e-06 0.00174 3.4151e-05 0.0227 1.6973e-09 1.28e-06 0.00065592 0.396 5.0201e-08 3.72e-05 20p loss 18 (5%) 333 0.01642 1 0.00069137 0.416 1 1 0.52548 1 0.00024897 0.156 0.26758 1 0.06761 1 0.75575 1 0.72614 1 0.35592 1 21q loss 132 (38%) 219 1.5634e-11 1.2e-08 0.0062232 1 0.1266 1 0.25368 1 0.024283 1 4.4728e-05 0.0296 0.0035839 1 0.0051463 1 0.0161 1 0.010023 1 22q loss 111 (32%) 240 3.0248e-17 2.37e-14 7.4685e-06 0.00521 0.015069 1 0.4842 1 0.00097082 0.574 0.0017344 0.987 5.7469e-06 0.00403 3.8914e-08 2.9e-05 0.034187 1 1.3373e-06 0.000966 xq loss 43 (12%) 308 3.4818e-07 0.000255 0.00070132 0.421 0.26206 1 0.80613 1 0.056306 1 0.014434 1 0.032601 1 0.44614 1 0.014157 1 0.85529 1