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 37 (11%) 294 8.7457e-06 0.00609 0.16804 1 0.0028436 1 0.095565 1 0.012413 1 0.38634 1 0.068329 1 0.20034 1 0.00038401 0.238 0.082666 1 1q gain 80 (24%) 251 1.5191e-10 1.16e-07 0.0031666 1 0.027419 1 0.1551 1 1.3883e-05 0.00951 0.0048394 1 0.00081084 0.488 0.001517 0.878 0.0070105 1 0.0034455 1 2p gain 56 (17%) 275 4.7241e-06 0.00334 0.017958 1 0.048369 1 0.94043 1 0.066113 1 0.23847 1 0.00025371 0.16 0.0038383 1 0.0036872 1 7.0046e-05 0.0461 2q gain 49 (15%) 282 0.00016011 0.103 0.28222 1 0.35161 1 0.55488 1 0.013353 1 0.081335 1 0.015464 1 0.037222 1 0.022177 1 0.0070926 1 3p gain 38 (11%) 293 0.015043 1 0.13214 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 62 (19%) 269 0.062067 1 0.25163 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 12 (4%) 319 0.26029 1 0.85433 1 1 1 1 1 0.51693 1 0.47015 1 0.53573 1 0.3672 1 0.91477 1 0.45213 1 4q gain 8 (2%) 323 0.6455 1 0.8476 1 0.86675 1 0.72284 1 0.15796 1 0.62039 1 1 1 0.59736 1 0.78471 1 0.61154 1 5p gain 73 (22%) 258 5.7521e-16 4.5e-13 6.2019e-06 0.00435 0.27483 1 0.64047 1 8.1668e-06 0.0057 6.291e-05 0.0416 2.567e-05 0.0174 2.4247e-05 0.0164 0.00064884 0.394 5.1084e-06 0.0036 5q gain 29 (9%) 302 0.0020026 1 0.18589 1 0.64401 1 0.73335 1 0.093264 1 0.12498 1 0.091903 1 0.11806 1 0.1908 1 0.14352 1 6p gain 59 (18%) 272 2.1483e-09 1.63e-06 6.8716e-08 5.11e-05 0.10589 1 0.26568 1 0.00021885 0.139 7.5199e-05 0.0493 1.0494e-05 0.00726 0.00020581 0.131 0.00011605 0.0753 3.8027e-06 0.00271 6q gain 49 (15%) 282 1.0016e-08 7.55e-06 2.0137e-05 0.0137 0.12298 1 0.5549 1 5.9052e-05 0.0392 0.00049941 0.308 5.1503e-05 0.0342 0.02272 1 0.00034859 0.218 7.2155e-05 0.0474 7p gain 145 (44%) 186 1.2754e-11 9.82e-09 0.00029927 0.188 0.79402 1 0.90734 1 0.21727 1 0.10339 1 0.27288 1 0.10757 1 0.090369 1 0.0022724 1 7q gain 124 (37%) 207 1.184e-10 9.07e-08 0.0020462 1 0.93624 1 0.67188 1 0.57286 1 0.36252 1 0.94674 1 0.79482 1 0.63775 1 0.151 1 8p gain 140 (42%) 191 0.00023745 0.15 0.27418 1 0.48805 1 0.62074 1 0.29624 1 0.10594 1 0.7454 1 0.84995 1 0.040956 1 0.51602 1 8q gain 186 (56%) 145 0.0061755 1 0.012969 1 0.7121 1 0.071542 1 0.025644 1 0.30162 1 0.029064 1 0.042572 1 0.0007345 0.444 0.055726 1 9p gain 42 (13%) 289 0.15351 1 0.53442 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 52 (16%) 279 0.21947 1 0.19563 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 80 (24%) 251 4.4036e-14 3.43e-11 1.6955e-05 0.0116 0.10391 1 0.42873 1 0.00075022 0.453 0.019925 1 0.0079774 1 0.0005482 0.336 0.084886 1 0.0020873 1 10q gain 55 (17%) 276 1.2586e-12 9.77e-10 0.014041 1 0.12839 1 0.56216 1 0.010578 1 0.035786 1 0.017754 1 0.079787 1 0.2873 1 0.011747 1 11p gain 35 (11%) 296 0.040892 1 0.013306 1 0.89736 1 0.80951 1 0.24773 1 0.0071981 1 0.0014849 0.861 0.033142 1 0.20078 1 0.05157 1 11q gain 43 (13%) 288 0.0014084 0.82 0.0040734 1 0.87798 1 0.60774 1 0.27019 1 0.0059587 1 0.00032555 0.203 0.0093921 1 0.01401 1 0.0084291 1 12p gain 66 (20%) 265 0.012866 1 0.095296 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 58 (18%) 273 0.038904 1 0.026825 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 111 (34%) 220 7.5801e-11 5.82e-08 0.0021194 1 0.56677 1 0.34827 1 0.022201 1 0.79604 1 0.0013259 0.776 0.0025096 1 0.011681 1 0.00022315 0.142 14q gain 19 (6%) 312 0.0064689 1 0.27449 1 0.9326 1 0.5409 1 0.77801 1 0.92979 1 0.11507 1 0.93667 1 0.20218 1 0.72866 1 15q gain 26 (8%) 305 0.0016631 0.958 0.053579 1 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 45 (14%) 286 0.14484 1 0.0548 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 34 (10%) 297 0.27554 1 0.34214 1 0.6881 1 0.14579 1 0.19754 1 0.37282 1 0.70724 1 0.12968 1 1 1 0.88677 1 17p gain 21 (6%) 310 0.020162 1 0.59572 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 40 (12%) 291 0.011753 1 0.28306 1 0.93671 1 0.94044 1 0.47311 1 0.35994 1 0.78749 1 0.80486 1 0.75078 1 1 1 18p gain 62 (19%) 269 6.4501e-05 0.0426 3.8134e-06 0.00271 0.10552 1 0.60964 1 0.015848 1 0.076015 1 0.0057434 1 0.00013264 0.0859 0.059501 1 0.0013403 0.783 18q gain 43 (13%) 288 0.0036774 1 0.002397 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 41 (12%) 290 0.081537 1 0.55809 1 0.38239 1 0.057413 1 0.7426 1 0.73143 1 0.80648 1 0.63676 1 0.47243 1 0.74571 1 19q gain 56 (17%) 275 0.013816 1 0.19187 1 0.19205 1 0.11356 1 0.042381 1 0.1216 1 0.15713 1 0.19812 1 0.28512 1 0.23687 1 20p gain 182 (55%) 149 9.2617e-12 7.14e-09 0.00066863 0.405 0.084157 1 0.70427 1 0.00077729 0.469 0.0086284 1 0.00043762 0.271 5.9801e-05 0.0396 0.016774 1 0.00014161 0.0915 20q gain 209 (63%) 122 3.8705e-16 3.04e-13 9.5728e-10 7.29e-07 0.044012 1 0.97131 1 1.0186e-06 0.000743 7.5999e-05 0.0497 2.2642e-06 0.00163 1.0344e-09 7.87e-07 0.046325 1 2.3655e-09 1.79e-06 21q gain 20 (6%) 311 1.0633e-06 0.000774 0.00088233 0.528 0.14016 1 0.66643 1 0.010089 1 0.06556 1 0.01748 1 0.00015325 0.0988 0.11862 1 3.8414e-05 0.0257 22q gain 26 (8%) 305 0.00976 1 0.19382 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 42 (13%) 289 0.00041119 0.255 0.019464 1 0.45962 1 0.15224 1 0.061565 1 0.34364 1 0.011206 1 0.45054 1 0.062274 1 0.036168 1 1p loss 43 (13%) 288 7.1949e-08 5.33e-05 0.0089249 1 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%) 311 3.5709e-05 0.024 0.0073767 1 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%) 313 0.0054312 1 0.019439 1 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 20 (6%) 311 0.003145 1 0.0082866 1 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 63 (19%) 268 5.1447e-06 0.00362 0.00092891 0.554 0.33146 1 0.45508 1 0.001772 1 0.00087074 0.522 0.0013946 0.813 0.056914 1 0.060689 1 0.014784 1 3q loss 38 (11%) 293 2.4461e-06 0.00176 2.585e-06 0.00186 0.19823 1 0.29154 1 7.4966e-06 0.00524 4.3125e-05 0.0289 4.7024e-05 0.0313 0.0012581 0.738 0.0058427 1 0.00447 1 4p loss 122 (37%) 209 4.2669e-16 3.35e-13 3.4557e-06 0.00247 0.28393 1 0.56048 1 0.00034921 0.218 0.001131 0.668 1.4668e-05 0.01 4.3289e-08 3.24e-05 0.0079152 1 2.22e-06 0.0016 4q loss 121 (37%) 210 7.1568e-18 5.63e-15 1.7235e-06 0.00125 0.070869 1 0.37419 1 0.0068676 1 0.001131 0.668 0.00017667 0.113 3.9811e-07 0.000292 0.030634 1 9.8079e-06 0.0068 5p loss 42 (13%) 289 1.1228e-05 0.00776 0.0013086 0.767 0.31692 1 0.44135 1 0.00060508 0.37 0.0036804 1 0.061322 1 0.017934 1 0.024088 1 0.0015935 0.921 5q loss 72 (22%) 259 4.3622e-12 3.37e-09 4.6763e-06 0.00331 0.61455 1 0.92903 1 2.3428e-07 0.000172 6.6329e-06 0.00464 0.00029954 0.188 1.1499e-06 0.000836 0.00064157 0.391 2.986e-08 2.24e-05 6p loss 36 (11%) 295 2.1085e-05 0.0143 0.0053109 1 0.14556 1 0.25578 1 0.024782 1 0.04082 1 0.21189 1 0.004332 1 0.1679 1 0.001145 0.674 6q loss 47 (14%) 284 0.00019211 0.123 0.0079498 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 11 (3%) 320 0.0060993 1 0.097834 1 0.40456 1 0.78023 1 0.00053786 0.33 0.13908 1 0.1981 1 0.11769 1 0.010072 1 0.033412 1 7q loss 21 (6%) 310 2.8394e-05 0.0192 0.033217 1 0.44506 1 0.78203 1 0.0021568 1 0.055131 1 0.068593 1 0.034637 1 0.0023358 1 0.051079 1 8p loss 57 (17%) 274 7.8675e-07 0.000574 0.11525 1 0.38798 1 0.34086 1 0.0051747 1 0.0029042 1 0.0016588 0.957 0.0011003 0.651 0.0059593 1 0.039432 1 8q loss 17 (5%) 314 0.023176 1 0.44623 1 1 1 0.67906 1 0.86806 1 0.25492 1 0.31547 1 0.61369 1 0.8141 1 0.47033 1 9p loss 103 (31%) 228 6.8882e-18 5.43e-15 1.4347e-07 0.000106 0.0010367 0.616 0.03881 1 1.7164e-08 1.29e-05 5.8796e-05 0.039 0.00031725 0.199 8.3034e-06 0.00579 0.22891 1 4.0559e-06 0.00288 9q loss 72 (22%) 259 1.361e-08 1.02e-05 0.00086787 0.521 0.12991 1 0.31604 1 1.3103e-05 0.00903 0.0017511 1 0.0046699 1 0.0014257 0.828 0.074351 1 0.00037513 0.233 10p loss 38 (11%) 293 9.183e-06 0.00638 0.043116 1 0.60439 1 0.39936 1 0.019723 1 0.013874 1 0.014426 1 0.047078 1 0.1439 1 0.055992 1 10q loss 44 (13%) 287 4.7327e-08 3.53e-05 0.0017257 0.992 0.59277 1 0.5397 1 0.0010708 0.635 0.009405 1 0.058659 1 0.022854 1 0.53122 1 0.059332 1 11p loss 47 (14%) 284 2.9953e-06 0.00214 0.00086453 0.52 0.019592 1 0.70549 1 0.063472 1 0.019091 1 0.56526 1 0.022087 1 0.39832 1 0.030309 1 11q loss 43 (13%) 288 0.0065611 1 0.10703 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 45 (14%) 286 5.5621e-12 4.29e-09 7.669e-08 5.68e-05 0.24882 1 0.51032 1 1.9188e-05 0.0131 0.00051941 0.319 0.0031587 1 3.7773e-05 0.0253 0.055086 1 1.7047e-07 0.000126 12q loss 34 (10%) 297 3.8533e-09 2.91e-06 1.8923e-05 0.0129 0.49706 1 1 1 0.0025631 1 0.10126 1 0.20042 1 0.0011744 0.691 0.4975 1 0.0025502 1 13q loss 30 (9%) 301 0.00016733 0.107 0.95104 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 81 (24%) 250 4.7592e-08 3.55e-05 0.0052852 1 0.55905 1 0.47075 1 0.00060778 0.371 0.00025041 0.158 0.00046547 0.288 0.0023839 1 0.033075 1 2.0845e-05 0.0142 15q loss 67 (20%) 264 2.9901e-07 0.000219 4.5987e-05 0.0307 0.0051223 1 0.069268 1 7.7436e-05 0.0505 7.5199e-05 0.0493 0.00020942 0.133 1.2462e-05 0.0086 0.0024492 1 9.8419e-05 0.0641 16p loss 70 (21%) 261 5.545e-16 4.35e-13 3.4795e-06 0.00248 0.81171 1 0.80704 1 4.0839e-10 3.12e-07 5.3023e-07 0.000388 1.7087e-06 0.00124 0.00018322 0.117 3.1044e-06 0.00222 4.8594e-06 0.00343 16q loss 79 (24%) 252 1.1858e-13 9.24e-11 1.83e-07 0.000135 0.046392 1 0.56385 1 6.9722e-08 5.17e-05 1.3866e-05 0.00951 9.5166e-06 0.0066 7.6138e-05 0.0497 0.0029643 1 1.3331e-05 0.00917 17p loss 115 (35%) 216 2.8089e-20 2.22e-17 1.7645e-09 1.34e-06 0.46291 1 0.80875 1 4.4449e-06 0.00315 1.7356e-06 0.00125 0.00013374 0.0865 1.3807e-05 0.00949 0.0027818 1 4.5927e-08 3.43e-05 17q loss 54 (16%) 277 8.0678e-09 6.09e-06 3.3321e-05 0.0225 0.28263 1 1 1 0.0023238 1 0.00049941 0.308 0.00057635 0.353 0.00090041 0.538 0.054114 1 0.00023643 0.15 18p loss 92 (28%) 239 4.4081e-05 0.0294 0.62961 1 0.70275 1 0.13093 1 0.45118 1 0.30897 1 0.065836 1 0.47773 1 0.049827 1 0.365 1 18q loss 116 (35%) 215 2.1657e-08 1.63e-05 0.036353 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 81 (24%) 250 2.6518e-19 2.09e-16 3.1056e-12 2.4e-09 0.0099561 1 0.48511 1 6.1804e-13 4.8e-10 2.2237e-12 1.72e-09 5.4337e-07 0.000397 2.9459e-13 2.29e-10 0.00022803 0.145 5.7409e-11 4.41e-08 19q loss 62 (19%) 269 1.6224e-14 1.27e-11 5.8797e-10 4.49e-07 0.017418 1 0.10031 1 1.5523e-07 0.000115 2.4302e-06 0.00175 3.4151e-05 0.023 1.6973e-09 1.29e-06 0.00065592 0.398 5.0201e-08 3.73e-05 20p loss 16 (5%) 315 0.019282 1 0.00011287 0.0734 1 1 0.52548 1 0.00024897 0.157 0.26758 1 0.06761 1 0.75575 1 0.72614 1 0.35592 1 21q loss 120 (36%) 211 8.6661e-11 6.65e-08 0.00015444 0.0995 0.10129 1 0.27989 1 0.031027 1 6.6486e-05 0.0438 0.0055944 1 0.0066346 1 0.011693 1 0.012865 1 22q loss 101 (31%) 230 1.9651e-15 1.54e-12 2.6601e-06 0.00191 0.015069 1 0.4842 1 0.00097082 0.578 0.0017344 0.996 5.7469e-06 0.00403 3.8914e-08 2.91e-05 0.034187 1 1.3373e-06 0.000971 xq loss 41 (12%) 290 5.3265e-06 0.00374 0.0071426 1 0.47903 1 0.90111 1 0.037024 1 0.012185 1 0.048808 1 0.49937 1 0.022481 1 0.87916 1