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 87 (24%) 279 0.13223 0.401 0.12217 0.39 0.84292 0.956 0.97757 0.996 0.87268 0.964 0.3511 0.65 0.17138 0.464 0.94474 0.978 0.75776 0.916 0.35863 0.65 1q gain 171 (47%) 195 9.9999e-06 0.000631 0.66483 0.865 0.50076 0.752 0.50809 0.758 0.03315 0.181 0.33156 0.637 0.02303 0.14 0.053499 0.238 0.04074 0.206 0.18177 0.478 2p gain 67 (18%) 299 0.01106 0.0856 0.25842 0.559 0.41312 0.694 0.81697 0.95 0.0042 0.0463 0.0081399 0.0703 0.12228 0.39 0.00043 0.00925 0.054609 0.239 0.00155 0.0235 2q gain 65 (18%) 301 0.0081199 0.0703 0.44798 0.716 0.63766 0.854 0.34432 0.647 0.00044 0.00925 0.0121 0.0894 0.10172 0.343 0.00017 0.00516 0.070599 0.278 2e-04 0.00566 3p gain 63 (17%) 303 0.21966 0.515 0.2485 0.546 0.13068 0.401 0.02076 0.131 0.41692 0.696 0.32822 0.637 0.66599 0.865 0.33449 0.637 0.52311 0.766 0.92178 0.978 3q gain 72 (20%) 294 0.56114 0.791 0.46342 0.728 0.071129 0.278 0.04685 0.224 0.04576 0.223 0.23865 0.535 0.38498 0.675 0.57367 0.806 0.10689 0.354 0.79552 0.939 4p gain 56 (15%) 310 0.00193 0.0274 0.19163 0.486 0.19323 0.487 0.85904 0.963 0.31935 0.631 0.24569 0.544 0.64212 0.855 0.00241 0.0318 0.81672 0.95 0.54127 0.777 4q gain 47 (13%) 319 0.01174 0.0883 0.32353 0.634 0.25084 0.55 0.93407 0.978 0.21444 0.511 0.38956 0.677 0.7296 0.901 0.0038 0.0437 0.9186 0.978 0.86643 0.964 5p gain 76 (21%) 290 0.00048 0.00984 0.17144 0.464 0.71879 0.894 0.39455 0.681 0.22397 0.517 0.57996 0.81 0.1094 0.359 0.46773 0.731 1 1 0.13038 0.401 5q gain 52 (14%) 314 0.01041 0.0837 0.14059 0.415 0.25209 0.55 0.13912 0.415 0.9818 0.996 0.77721 0.924 0.30389 0.614 0.62626 0.85 0.42991 0.705 0.02017 0.129 6p gain 144 (39%) 222 0.00038 0.00911 7.9999e-05 0.00345 0.95523 0.983 0.14373 0.419 0.32502 0.635 0.0236 0.141 0.098669 0.34 0.00012 0.00428 0.00094999 0.0169 5e-04 0.01 6q gain 48 (13%) 318 0.30961 0.618 0.582 0.812 0.92394 0.978 0.33098 0.637 0.94241 0.978 0.68898 0.88 0.67831 0.875 0.20654 0.501 0.93406 0.978 0.70958 0.892 7p gain 203 (55%) 163 9.9999e-06 0.000631 0.93624 0.978 0.49439 0.752 0.37072 0.662 0.01885 0.122 0.19897 0.493 0.77463 0.923 0.71066 0.892 0.077259 0.289 0.30743 0.616 7q gain 200 (55%) 166 3e-05 0.00145 0.91036 0.978 0.71728 0.894 0.5169 0.762 0.0065299 0.0608 0.18911 0.483 0.83652 0.956 0.37399 0.662 0.00292 0.0357 0.29424 0.602 8p gain 121 (33%) 245 9.9999e-06 0.000631 0.17379 0.469 0.87926 0.967 0.84192 0.956 0.01265 0.0926 0.03585 0.186 0.60599 0.834 0.93706 0.978 0.95457 0.983 0.651 0.862 8q gain 169 (46%) 197 9.9999e-06 0.000631 0.00105 0.0179 0.69752 0.887 0.79674 0.939 0.00435 0.0463 0.11082 0.362 0.81785 0.95 0.34846 0.65 0.93395 0.978 0.69969 0.887 9p gain 16 (4%) 350 0.30544 0.614 0.2045 0.499 0.23175 0.529 0.83972 0.956 0.342 0.646 0.91256 0.978 0.89076 0.974 0.72661 0.901 0.10031 0.34 0.46021 0.727 9q gain 21 (6%) 345 0.66328 0.865 0.65768 0.864 0.14011 0.415 0.92797 0.978 0.56121 0.791 0.49291 0.752 0.73552 0.905 0.68524 0.879 0.50287 0.752 0.64346 0.855 10p gain 12 (3%) 354 0.49586 0.752 0.93143 0.978 0.93542 0.978 0.54621 0.779 0.71169 0.892 1 1 0.19901 0.493 0.3375 0.639 0.92763 0.978 0.96578 0.99 10q gain 3 (1%) 363 0.37647 0.662 0.3582 0.65 NA NA NA NA 0.63594 0.854 0.63771 0.854 0.796 0.939 0.84854 0.958 0.27509 0.578 0.70177 0.887 11p gain 35 (10%) 331 0.0068699 0.0633 0.094459 0.33 0.13366 0.402 0.18628 0.482 0.00122 0.0196 0.0075099 0.0676 0.02096 0.131 0.00435 0.0463 0.29686 0.604 0.02283 0.14 11q gain 29 (8%) 337 0.00031 0.00794 0.18766 0.482 0.14525 0.422 0.086809 0.312 0.00282 0.035 0.0012 0.0196 0.0056699 0.0574 0.00015 0.00492 0.079639 0.293 0.02023 0.129 12p gain 65 (18%) 301 0.00084999 0.0157 0.16366 0.456 0.63832 0.854 0.42409 0.699 0.01278 0.0927 0.86096 0.963 0.62246 0.848 0.39166 0.678 0.23671 0.532 0.42164 0.699 12q gain 39 (11%) 327 0.01633 0.11 1 1 0.60569 0.834 0.057939 0.245 0.54164 0.777 0.64289 0.855 0.87198 0.964 0.16303 0.456 0.42391 0.699 0.056399 0.243 13q gain 94 (26%) 272 9.9999e-06 0.000631 9.9999e-06 0.000631 0.3897 0.677 0.31317 0.621 0.00044 0.00925 0.0062199 0.0608 0.37318 0.662 0.89464 0.976 0.12462 0.393 0.74276 0.906 14q gain 41 (11%) 325 0.39562 0.681 0.40018 0.684 0.49889 0.752 0.15348 0.442 0.83432 0.956 0.91504 0.978 0.65948 0.864 0.84648 0.957 0.76712 0.92 0.9816 0.996 15q gain 85 (23%) 281 2e-05 0.00109 0.19686 0.492 0.97518 0.995 0.8161 0.95 0.00347 0.0406 0.01697 0.113 0.13126 0.401 0.14236 0.418 0.27846 0.58 0.04453 0.22 16p gain 58 (16%) 308 0.00189 0.0274 0.03414 0.182 0.83853 0.956 0.65959 0.864 4e-04 0.00911 0.12539 0.393 0.44401 0.713 0.10613 0.354 0.43756 0.712 0.41104 0.692 16q gain 44 (12%) 322 2e-04 0.00566 0.053859 0.238 0.22288 0.517 0.62789 0.85 3e-05 0.00145 0.03263 0.181 0.44945 0.716 0.12543 0.393 0.44456 0.713 0.23455 0.53 17p gain 37 (10%) 329 0.0098199 0.0803 0.00098999 0.0173 0.74194 0.906 0.52837 0.766 0.078669 0.293 0.51465 0.762 0.49696 0.752 0.40058 0.684 0.92589 0.978 0.31213 0.621 17q gain 65 (18%) 301 0.051159 0.233 0.04843 0.226 0.35097 0.65 0.27644 0.58 0.98491 0.997 0.33351 0.637 0.38932 0.677 0.4417 0.713 0.36015 0.65 0.64925 0.861 18p gain 55 (15%) 311 0.00213 0.0291 0.606 0.834 0.17993 0.478 0.39062 0.677 0.2618 0.565 0.65926 0.864 0.76672 0.92 0.82738 0.955 0.070149 0.278 0.89835 0.978 18q gain 44 (12%) 322 0.00077999 0.0149 0.67716 0.874 0.29356 0.602 0.46981 0.731 0.21702 0.514 0.82955 0.955 0.49727 0.752 0.86021 0.963 0.66026 0.864 0.71438 0.894 19p gain 57 (16%) 309 0.0053299 0.0553 0.02315 0.14 0.589 0.818 0.79733 0.939 0.00138 0.0214 0.2419 0.538 0.92044 0.978 0.36063 0.65 0.19997 0.493 0.76359 0.919 19q gain 56 (15%) 310 0.01091 0.0856 0.01859 0.121 0.58946 0.818 1 1 5e-05 0.00228 0.063509 0.26 0.6931 0.884 0.33561 0.637 0.27342 0.576 0.88424 0.971 20p gain 147 (40%) 219 9.9999e-06 0.000631 0.0094399 0.0798 0.83473 0.956 0.98435 0.997 0.00015 0.00492 0.02145 0.133 0.70172 0.887 0.24605 0.544 0.28906 0.599 0.17882 0.478 20q gain 179 (49%) 187 9.9999e-06 0.000631 0.01599 0.109 0.88777 0.973 0.97398 0.995 0.00388 0.0437 0.16125 0.455 0.72343 0.899 0.19065 0.486 0.90407 0.978 0.46841 0.731 21q gain 67 (18%) 299 0.16521 0.458 0.04849 0.226 0.86303 0.963 0.5284 0.766 0.1932 0.487 0.35663 0.65 0.16577 0.458 0.79912 0.94 0.90276 0.978 0.75878 0.916 22q gain 126 (34%) 240 0.00035 0.0087 0.11891 0.384 0.66755 0.866 0.94392 0.978 0.073139 0.28 0.25314 0.551 0.48588 0.75 0.21651 0.514 0.82965 0.955 0.54238 0.777 xp gain 41 (11%) 325 9.9999e-05 0.0041 0.00194 0.0274 0.90251 0.978 0.22705 0.52 0.0076099 0.0676 0.2211 0.517 0.2179 0.515 0.73374 0.905 0.00059999 0.0117 0.70632 0.891 xq gain 43 (12%) 323 0.00011 0.0041 0.00022 0.00582 0.32855 0.637 0.98637 0.997 0.00426 0.0463 0.18892 0.483 0.22382 0.517 0.63506 0.854 0.00021 0.00574 0.42449 0.699 1p loss 53 (14%) 313 0.04809 0.226 0.00039 0.00911 0.65364 0.864 0.31364 0.621 0.0106 0.0844 0.13183 0.401 0.04946 0.228 0.94884 0.981 0.12731 0.396 0.088669 0.315 1q loss 28 (8%) 338 0.064519 0.262 0.055529 0.242 0.96972 0.991 0.46317 0.728 0.11663 0.38 0.35449 0.65 0.50096 0.752 0.68728 0.879 0.27862 0.58 0.68246 0.877 2p loss 51 (14%) 315 0.37592 0.662 0.21147 0.509 0.0095799 0.0802 0.01467 0.102 0.92791 0.978 0.03426 0.182 0.0053099 0.0553 0.01825 0.12 0.18493 0.482 0.29265 0.602 2q loss 52 (14%) 314 0.81392 0.95 0.19373 0.487 0.00305 0.0367 0.00164 0.0245 0.76049 0.917 0.21279 0.51 0.0064099 0.0608 0.02907 0.169 0.12387 0.392 0.43409 0.71 3p loss 61 (17%) 305 0.061389 0.253 0.82111 0.952 0.36236 0.65 0.32707 0.637 0.10707 0.354 0.15518 0.443 0.03883 0.199 0.61623 0.845 0.45145 0.716 0.51669 0.762 3q loss 53 (14%) 313 0.0464 0.224 0.090359 0.319 0.40943 0.691 0.37441 0.662 0.37468 0.662 0.2513 0.55 0.067259 0.272 0.26401 0.567 0.28864 0.599 0.86847 0.964 4p loss 80 (22%) 286 0.5288 0.766 0.19938 0.493 0.36027 0.65 0.96973 0.991 0.16148 0.455 0.063739 0.26 0.73643 0.905 0.0060399 0.0604 0.91607 0.978 0.087759 0.313 4q loss 85 (23%) 281 0.52681 0.766 0.071419 0.278 0.44168 0.713 0.7505 0.912 0.21861 0.515 0.03425 0.182 0.9429 0.978 0.0027 0.0346 0.53466 0.773 0.01428 0.1 5p loss 79 (22%) 287 0.85207 0.961 0.16259 0.456 0.94061 0.978 0.86197 0.963 0.83932 0.956 0.077149 0.289 0.67214 0.869 0.30113 0.611 0.34493 0.647 0.52536 0.766 5q loss 99 (27%) 267 0.58844 0.818 0.057449 0.245 0.44256 0.713 0.3591 0.65 0.86136 0.963 0.04996 0.229 0.95092 0.982 0.74781 0.91 0.8276 0.955 0.77313 0.923 6p loss 68 (19%) 298 0.0055499 0.0569 0.46564 0.73 0.92496 0.978 0.27751 0.58 0.01318 0.0948 0.03539 0.186 0.16984 0.464 0.072609 0.28 0.074019 0.282 0.0064499 0.0608 6q loss 172 (47%) 194 9.9999e-06 0.000631 0.01407 0.0995 0.91185 0.978 0.481 0.746 0.00244 0.0318 0.084269 0.307 0.43481 0.71 0.23687 0.532 0.41556 0.696 0.27016 0.572 7p loss 18 (5%) 348 0.82906 0.955 0.052009 0.233 0.04911 0.228 0.55667 0.789 0.42292 0.699 0.84276 0.956 0.50314 0.752 0.76891 0.92 0.12987 0.401 0.78487 0.931 7q loss 17 (5%) 349 0.36338 0.651 0.0097699 0.0803 0.18751 0.482 0.43992 0.713 0.40215 0.686 0.41987 0.698 0.78654 0.932 0.83284 0.956 0.070109 0.278 0.97908 0.996 8p loss 67 (18%) 299 0.12232 0.39 0.45032 0.716 0.086279 0.312 0.29438 0.602 0.057619 0.245 0.52151 0.765 0.2484 0.546 0.04678 0.224 0.93842 0.978 0.18183 0.478 8q loss 27 (7%) 339 0.51854 0.763 0.0074199 0.0676 0.1751 0.471 0.53516 0.773 0.23289 0.53 0.74032 0.906 0.33116 0.637 0.66848 0.866 0.071509 0.278 0.13243 0.401 9p loss 236 (64%) 130 0.00017 0.00516 0.13389 0.402 0.35569 0.65 0.44884 0.716 0.00309 0.0367 0.099479 0.34 0.0303 0.175 0.069249 0.278 0.57646 0.807 0.68671 0.879 9q loss 185 (51%) 181 0.27183 0.574 0.070079 0.278 0.98861 0.998 0.14928 0.433 0.01129 0.0862 0.33567 0.637 0.01559 0.107 0.059879 0.249 0.67956 0.875 0.69703 0.887 10p loss 204 (56%) 162 9.9999e-06 0.000631 0.12736 0.396 0.8012 0.941 0.40897 0.691 0.00136 0.0214 0.01631 0.11 0.20002 0.493 0.20776 0.502 0.50074 0.752 0.75264 0.913 10q loss 224 (61%) 142 9.9999e-06 0.000631 0.20811 0.502 0.92556 0.978 0.20154 0.495 0.00011 0.0041 0.00227 0.0305 0.03224 0.181 0.21431 0.511 0.43016 0.705 0.63015 0.851 11p loss 126 (34%) 240 0.01754 0.116 0.056189 0.243 0.34373 0.647 0.29189 0.602 0.46941 0.731 0.099069 0.34 0.22712 0.52 0.12277 0.39 0.094949 0.33 0.23416 0.53 11q loss 148 (40%) 218 0.01192 0.0889 0.35004 0.65 0.86566 0.964 0.69865 0.887 0.22339 0.517 0.00211 0.0291 0.35835 0.65 0.23403 0.53 0.10645 0.354 0.04438 0.22 12p loss 59 (16%) 307 0.2192 0.515 0.10802 0.356 0.70801 0.892 0.87155 0.964 0.01408 0.0995 0.89113 0.974 0.33499 0.637 0.18695 0.482 0.89523 0.976 0.83016 0.955 12q loss 67 (18%) 299 0.03468 0.183 0.0076699 0.0676 0.81789 0.95 0.87509 0.964 0.051999 0.233 0.55643 0.789 0.3619 0.65 0.40883 0.691 0.61823 0.846 0.87414 0.964 13q loss 80 (22%) 286 0.93561 0.978 0.01096 0.0856 0.04721 0.224 0.55775 0.789 0.6605 0.864 0.03302 0.181 0.59999 0.831 0.33463 0.637 0.15756 0.447 0.63368 0.854 14q loss 112 (31%) 254 2e-05 0.00109 0.32028 0.631 0.17107 0.464 0.26954 0.572 0.0090999 0.0777 0.03332 0.181 0.35849 0.65 0.8134 0.95 0.40794 0.691 0.10595 0.354 15q loss 52 (14%) 314 0.18403 0.482 0.35547 0.65 0.26336 0.567 0.060939 0.252 0.80214 0.941 0.26668 0.571 0.71672 0.894 0.57416 0.806 0.60743 0.834 0.50225 0.752 16p loss 68 (19%) 298 0.20521 0.499 0.094639 0.33 0.0441 0.22 0.35964 0.65 0.059429 0.249 0.1549 0.443 0.18103 0.478 0.16481 0.458 0.087149 0.312 0.3594 0.65 16q loss 106 (29%) 260 0.302 0.611 0.3241 0.634 0.02732 0.16 0.75375 0.913 0.03811 0.197 0.03593 0.186 0.24168 0.538 0.16968 0.464 0.04515 0.222 0.11844 0.384 17p loss 127 (35%) 239 0.076519 0.289 0.0062399 0.0608 0.32313 0.634 0.51534 0.762 0.18703 0.482 0.053879 0.238 0.76709 0.92 0.54823 0.78 0.71645 0.894 0.52149 0.765 17q loss 64 (17%) 302 0.1435 0.419 0.13425 0.402 0.18043 0.478 0.54403 0.777 0.92427 0.978 0.49551 0.752 0.86817 0.964 0.5369 0.774 0.03202 0.181 0.91926 0.978 18p loss 104 (28%) 262 0.72973 0.901 0.60063 0.831 0.57575 0.807 0.5135 0.762 0.02641 0.156 0.16691 0.459 0.29686 0.604 0.079259 0.293 0.4546 0.72 0.46261 0.728 18q loss 100 (27%) 266 0.44802 0.716 0.87971 0.967 0.20526 0.499 0.49032 0.752 0.44462 0.713 0.43731 0.712 0.62135 0.848 0.098549 0.34 0.41681 0.696 0.48827 0.752 19p loss 77 (21%) 289 0.072959 0.28 0.65796 0.864 0.55746 0.789 0.03311 0.181 0.15013 0.433 0.25392 0.551 0.4981 0.752 0.93215 0.978 0.51188 0.762 0.52468 0.766 19q loss 73 (20%) 293 0.02427 0.144 0.04715 0.224 0.8437 0.956 0.082959 0.304 0.091269 0.321 0.49253 0.752 0.26999 0.572 0.95655 0.983 0.057519 0.245 0.64041 0.855 20p loss 26 (7%) 340 0.37158 0.662 0.6201 0.847 0.30534 0.614 0.77228 0.923 0.19642 0.492 0.02157 0.133 0.059549 0.249 0.01135 0.0862 0.85797 0.963 0.37708 0.662 20q loss 9 (2%) 357 0.3959 0.681 0.17878 0.478 NA NA NA NA 0.074229 0.282 0.0098899 0.0803 0.7373 0.905 0.38713 0.677 0.26834 0.572 0.66419 0.865 21q loss 70 (19%) 296 0.099989 0.34 0.47384 0.736 0.30873 0.617 0.93097 0.978 0.92948 0.978 0.49735 0.752 0.54369 0.777 0.74097 0.906 0.7776 0.924 0.39902 0.684 22q loss 39 (11%) 327 0.40316 0.686 0.41739 0.696 0.95337 0.983 0.93986 0.978 0.2406 0.538 0.96297 0.988 0.62751 0.85 0.74551 0.908 0.72793 0.901 0.90048 0.978 xp loss 97 (27%) 269 0.03054 0.175 9.9999e-06 0.000631 0.04459 0.22 0.22653 0.52 0.00109 0.0182 0.00389 0.0437 0.00274 0.0346 0.1407 0.415 0.084509 0.307 0.85448 0.962 xq loss 93 (25%) 273 0.03927 0.2 9.9999e-06 0.000631 0.15548 0.443 0.078909 0.293 0.00085999 0.0157 0.0064799 0.0608 0.03297 0.181 0.48529 0.75 0.051329 0.233 0.62751 0.85