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 0.13108 0.402 0.12279 0.39 0.7975 0.93 0.97864 1 0.87216 0.969 0.35164 0.651 0.56747 0.779 0.92384 0.989 0.79941 0.93 0.49566 0.753 1q gain 171 (47%) 195 9.9999e-06 0.000586 0.66403 0.846 0.27064 0.578 0.5095 0.758 0.03354 0.186 0.33304 0.636 0.12483 0.392 0.31853 0.631 0.04777 0.23 0.286 0.595 2p gain 67 (18%) 299 0.01141 0.0926 0.26108 0.568 0.80136 0.931 0.81452 0.942 0.00403 0.0486 0.0077199 0.0749 0.10462 0.347 0.00012 0.00444 0.03901 0.204 0.02865 0.169 2q gain 65 (18%) 301 0.0079399 0.0749 0.45014 0.727 0.77694 0.918 0.34248 0.644 0.00050999 0.0113 0.01163 0.0926 0.1376 0.409 6.9999e-05 0.00302 0.052769 0.246 0.00212 0.0303 3p gain 63 (17%) 303 0.22029 0.519 0.25059 0.557 0.04451 0.225 0.01989 0.129 0.41748 0.699 0.33013 0.636 0.33144 0.636 0.55507 0.775 0.75494 0.909 0.97537 1 3q gain 72 (20%) 294 0.56421 0.778 0.4634 0.738 0.0184 0.122 0.046 0.228 0.04617 0.228 0.23929 0.541 0.13247 0.402 0.53252 0.762 0.20057 0.5 0.61703 0.815 4p gain 56 (15%) 310 0.00167 0.0258 0.18883 0.487 0.30481 0.617 0.85683 0.964 0.31459 0.628 0.24652 0.549 0.30488 0.617 0.04579 0.228 0.72962 0.896 0.56166 0.778 4q gain 47 (13%) 319 0.01153 0.0926 0.32084 0.632 0.26343 0.57 0.93433 0.989 0.2132 0.516 0.38653 0.675 0.68684 0.862 0.04208 0.214 0.77379 0.917 0.94212 0.989 5p gain 76 (21%) 290 0.00061999 0.0134 0.17238 0.463 0.88931 0.974 0.39706 0.684 0.22212 0.519 0.57995 0.786 0.087889 0.312 0.49811 0.753 0.98486 1 0.095809 0.329 5q gain 52 (14%) 314 0.0108 0.0904 0.13945 0.41 0.35747 0.651 0.13881 0.409 0.98184 1 0.77485 0.917 0.1049 0.347 0.52167 0.759 0.33017 0.636 0.073199 0.282 6p gain 144 (39%) 222 0.00043 0.0101 5.9999e-05 0.00273 0.98844 1 0.14383 0.42 0.32189 0.633 0.02466 0.152 0.00214 0.0303 0.056569 0.249 0.00028 0.00741 0.0018 0.0268 6q gain 48 (13%) 318 0.30821 0.619 0.58274 0.789 0.85611 0.964 0.3308 0.636 0.94262 0.989 0.68908 0.863 0.35421 0.651 0.40388 0.687 0.83368 0.955 0.64778 0.838 7p gain 203 (55%) 163 9.9999e-06 0.000586 0.93696 0.989 0.45873 0.736 0.37401 0.662 0.01894 0.124 0.19913 0.5 0.074929 0.282 0.74057 0.902 0.17331 0.463 0.57049 0.78 7q gain 200 (55%) 166 3e-05 0.00154 0.9116 0.984 0.69177 0.865 0.51493 0.758 0.0059299 0.0636 0.1899 0.487 0.68636 0.862 0.56966 0.78 0.0086499 0.0797 0.29996 0.612 8p gain 121 (33%) 245 9.9999e-06 0.000586 0.1775 0.473 0.61284 0.813 0.84357 0.957 0.01314 0.0995 0.03548 0.189 0.5241 0.76 0.84349 0.957 0.85172 0.964 0.43668 0.713 8q gain 169 (46%) 197 9.9999e-06 0.000586 0.00112 0.02 0.69444 0.865 0.79563 0.93 0.00411 0.0488 0.11198 0.364 0.63013 0.827 0.89152 0.974 0.80786 0.937 0.37573 0.662 9p gain 16 (4%) 350 0.3067 0.618 0.20408 0.504 0.37444 0.662 0.83542 0.955 0.34658 0.65 0.91159 0.984 0.90367 0.981 0.61039 0.811 0.12637 0.396 0.26611 0.574 9q gain 21 (6%) 345 0.65952 0.845 0.65698 0.845 0.13278 0.402 0.92928 0.989 0.56353 0.778 0.4931 0.753 0.88451 0.974 0.41515 0.698 0.47567 0.743 0.55557 0.775 10p gain 12 (3%) 354 0.49788 0.753 0.93049 0.989 0.86688 0.968 0.54548 0.77 0.71051 0.876 1 1 0.26246 0.569 0.55828 0.775 1 1 0.90474 0.981 10q gain 3 (1%) 363 0.378 0.662 0.3565 0.651 NA NA NA NA 0.63612 0.832 0.63911 0.835 0.77804 0.918 0.72563 0.892 0.26863 0.577 0.68938 0.863 11p gain 35 (10%) 331 0.0060899 0.0636 0.094469 0.327 0.084599 0.304 0.18859 0.487 0.0013 0.0219 0.0077699 0.0749 0.02327 0.147 0.0062799 0.0636 0.23076 0.529 0.01744 0.118 11q gain 29 (8%) 337 2e-04 0.00607 0.18972 0.487 0.076379 0.285 0.084909 0.304 0.00306 0.0392 0.00131 0.0219 0.0059799 0.0636 0.00074999 0.0152 0.057439 0.25 0.01365 0.102 12p gain 65 (18%) 301 0.00077999 0.0152 0.16368 0.451 0.53958 0.768 0.4262 0.705 0.01231 0.0961 0.86371 0.967 0.87346 0.969 0.49252 0.753 0.16614 0.454 0.3696 0.662 12q gain 39 (11%) 327 0.01638 0.114 1 1 0.61636 0.815 0.057879 0.25 0.53913 0.768 0.64589 0.838 0.81703 0.944 0.061169 0.255 0.4226 0.7 0.68026 0.861 13q gain 94 (26%) 272 9.9999e-06 0.000586 9.9999e-06 0.000586 0.45936 0.736 0.31413 0.628 0.00047 0.0107 0.0062599 0.0636 0.49873 0.753 0.83896 0.957 0.090719 0.319 0.6848 0.862 14q gain 41 (11%) 325 0.39254 0.679 0.39888 0.684 0.34846 0.651 0.15425 0.44 0.83483 0.955 0.91532 0.985 0.51282 0.758 0.50804 0.758 0.7675 0.917 0.96731 1 15q gain 85 (23%) 281 5e-05 0.00241 0.19484 0.493 0.94469 0.989 0.81813 0.944 0.00372 0.0469 0.01612 0.113 0.19339 0.493 0.17264 0.463 0.3763 0.662 0.057309 0.25 16p gain 58 (16%) 308 0.00161 0.0254 0.03417 0.187 0.98798 1 0.65661 0.845 0.00036 0.00895 0.12321 0.39 0.78498 0.924 0.075109 0.282 0.069959 0.274 0.12321 0.39 16q gain 44 (12%) 322 0.00026 0.00711 0.053529 0.246 0.27474 0.581 0.62652 0.823 2e-05 0.00109 0.03323 0.186 0.78652 0.924 0.099299 0.336 0.054959 0.246 0.14672 0.425 17p gain 37 (10%) 329 0.0090799 0.0809 0.00102 0.0195 0.57888 0.786 0.53158 0.762 0.078449 0.287 0.51234 0.758 0.57151 0.78 0.29316 0.606 0.97453 1 0.13877 0.409 17q gain 65 (18%) 301 0.050679 0.237 0.04782 0.23 0.10282 0.344 0.27566 0.581 0.98492 1 0.3338 0.636 0.48023 0.747 0.67309 0.855 0.55615 0.775 0.7618 0.913 18p gain 55 (15%) 311 0.00255 0.0343 0.60584 0.808 0.20808 0.508 0.38971 0.677 0.25958 0.568 0.66391 0.846 0.93278 0.989 0.96583 1 0.060949 0.255 0.47268 0.741 18q gain 44 (12%) 322 0.00076999 0.0152 0.67714 0.858 0.35002 0.651 0.46989 0.74 0.21743 0.519 0.8302 0.953 0.67354 0.855 0.76362 0.914 0.64396 0.838 0.79689 0.93 19p gain 57 (16%) 309 0.0050799 0.0579 0.02362 0.148 0.25278 0.559 0.79786 0.93 0.00135 0.0221 0.24024 0.541 0.90571 0.981 0.54349 0.77 0.17239 0.463 0.90085 0.981 19q gain 56 (15%) 310 0.01062 0.0904 0.01782 0.12 0.29542 0.606 1 1 0.00012 0.00444 0.062179 0.255 0.5274 0.76 0.4317 0.712 0.15516 0.44 0.85471 0.964 20p gain 147 (40%) 219 9.9999e-06 0.000586 0.0089999 0.0809 0.84314 0.957 0.98406 1 0.00015 0.00492 0.02084 0.134 0.48713 0.753 0.27081 0.578 0.27315 0.579 0.065939 0.264 20q gain 179 (49%) 187 9.9999e-06 0.000586 0.0165 0.114 0.941 0.989 0.97401 1 0.00384 0.0477 0.16278 0.451 0.47859 0.746 0.26036 0.568 0.9147 0.985 0.28029 0.586 21q gain 67 (18%) 299 0.16422 0.451 0.04831 0.23 0.88842 0.974 0.52894 0.76 0.19435 0.493 0.35747 0.651 0.10906 0.356 0.99688 1 0.94933 0.993 0.51197 0.758 22q gain 126 (34%) 240 0.00038 0.00916 0.11836 0.381 0.89383 0.975 0.94453 0.989 0.073979 0.282 0.25204 0.559 0.61683 0.815 0.15903 0.447 0.69838 0.866 0.49559 0.753 xp gain 41 (11%) 325 0.00013 0.00444 0.00161 0.0254 0.9584 0.999 0.22797 0.527 0.0072799 0.0728 0.21999 0.519 0.66393 0.846 0.3984 0.684 0.00109 0.0199 0.40629 0.69 xq gain 43 (12%) 323 7.9999e-05 0.00328 0.00031 0.00794 0.58499 0.789 0.98573 1 0.00446 0.0522 0.18822 0.487 0.38709 0.675 0.27705 0.582 0.00023 0.00674 0.75611 0.909 1p loss 53 (14%) 313 0.04792 0.23 0.00026 0.00711 0.58701 0.79 0.31453 0.628 0.01072 0.0904 0.13425 0.402 0.0093299 0.0814 0.69345 0.865 0.17946 0.476 0.054379 0.246 1q loss 28 (8%) 338 0.066509 0.265 0.054849 0.246 0.96901 1 0.46584 0.739 0.1171 0.38 0.35434 0.651 0.36777 0.661 0.93833 0.989 0.2842 0.593 0.35714 0.651 2p loss 51 (14%) 315 0.37327 0.662 0.21157 0.514 0.04566 0.228 0.01493 0.107 0.92696 0.989 0.03531 0.189 0.00306 0.0392 0.065549 0.264 0.22439 0.521 0.21175 0.514 2q loss 52 (14%) 314 0.81472 0.942 0.19624 0.495 0.01106 0.091 0.0017 0.0258 0.75854 0.911 0.21434 0.517 0.0079299 0.0749 0.11803 0.381 0.16683 0.454 0.22305 0.52 3p loss 61 (17%) 305 0.059819 0.255 0.82026 0.945 0.49478 0.753 0.32596 0.636 0.10653 0.349 0.15573 0.44 0.060509 0.255 0.65959 0.845 0.52161 0.759 0.41118 0.692 3q loss 53 (14%) 313 0.04643 0.228 0.091019 0.319 0.50929 0.758 0.3721 0.662 0.37508 0.662 0.25387 0.56 0.12879 0.4 0.63334 0.83 0.32845 0.636 0.77052 0.917 4p loss 80 (22%) 286 0.52921 0.76 0.19988 0.5 0.35226 0.651 0.96938 1 0.16273 0.451 0.066069 0.264 0.54318 0.77 0.01323 0.0995 0.87921 0.971 0.31639 0.628 4q loss 85 (23%) 281 0.52938 0.76 0.070179 0.274 0.48113 0.747 0.75093 0.908 0.21747 0.519 0.03276 0.186 0.9025 0.981 0.0055899 0.0619 0.60489 0.808 0.24285 0.543 5p loss 79 (22%) 287 0.85255 0.964 0.1613 0.451 0.88085 0.971 0.86186 0.967 0.84226 0.957 0.076939 0.285 0.51233 0.758 0.25732 0.564 0.20765 0.508 0.3905 0.677 5q loss 99 (27%) 267 0.58757 0.79 0.055599 0.248 0.64766 0.838 0.35988 0.652 0.86176 0.967 0.050349 0.237 0.90801 0.982 0.57818 0.786 0.42055 0.7 0.60861 0.81 6p loss 68 (19%) 298 0.0050399 0.0579 0.46816 0.74 0.87284 0.969 0.27737 0.582 0.01263 0.0977 0.03518 0.189 0.0419 0.214 0.089479 0.316 0.02578 0.157 0.02755 0.164 6q loss 172 (47%) 194 9.9999e-06 0.000586 0.01425 0.105 0.97817 1 0.48231 0.748 0.00249 0.034 0.081369 0.297 0.22066 0.519 0.21853 0.519 0.40325 0.687 0.16223 0.451 7p loss 18 (5%) 348 0.82957 0.953 0.054179 0.246 0.094379 0.327 0.55731 0.775 0.42256 0.7 0.84245 0.957 0.64904 0.838 0.71017 0.876 0.16919 0.459 0.75153 0.908 7q loss 17 (5%) 349 0.35896 0.652 0.01051 0.0904 0.33736 0.637 0.4367 0.713 0.40407 0.687 0.41752 0.699 0.52071 0.759 0.77167 0.917 0.096189 0.329 0.92756 0.989 8p loss 67 (18%) 299 0.1225 0.39 0.45145 0.727 0.058709 0.252 0.29581 0.606 0.057759 0.25 0.5245 0.76 0.46224 0.737 0.02933 0.172 0.43597 0.713 0.18055 0.476 8q loss 27 (7%) 339 0.51973 0.759 0.0079499 0.0749 0.31638 0.628 0.53499 0.764 0.2309 0.529 0.73822 0.902 0.40892 0.692 0.5041 0.757 0.01474 0.107 0.14551 0.423 9p loss 236 (64%) 130 0.00013 0.00444 0.13341 0.402 0.6444 0.838 0.45052 0.727 0.00275 0.0364 0.10118 0.34 0.075309 0.282 0.22086 0.519 0.73885 0.902 0.59081 0.793 9q loss 185 (51%) 181 0.27238 0.579 0.070859 0.275 0.9923 1 0.14935 0.43 0.01223 0.0961 0.33355 0.636 0.03977 0.205 0.13773 0.409 0.96939 1 0.46619 0.739 10p loss 204 (56%) 162 9.9999e-06 0.000586 0.12861 0.4 0.92387 0.989 0.4106 0.692 0.00117 0.0204 0.01614 0.113 0.060829 0.255 0.35014 0.651 0.37215 0.662 0.5642 0.778 10q loss 224 (61%) 142 9.9999e-06 0.000586 0.20789 0.508 0.9206 0.989 0.20175 0.501 0.00019 0.00599 0.00239 0.0332 0.02093 0.134 0.36258 0.653 0.32976 0.636 0.50078 0.753 11p loss 126 (34%) 240 0.01795 0.12 0.055929 0.248 0.5842 0.789 0.29447 0.606 0.46897 0.74 0.098029 0.334 0.52201 0.759 0.33542 0.637 0.083409 0.301 0.56853 0.78 11q loss 148 (40%) 218 0.01303 0.0995 0.34955 0.651 0.95247 0.994 0.69592 0.866 0.22161 0.519 0.00195 0.0286 0.73631 0.901 0.15834 0.446 0.075159 0.282 0.54976 0.775 12p loss 59 (16%) 307 0.21981 0.519 0.10613 0.349 0.85709 0.964 0.87169 0.969 0.01443 0.106 0.89242 0.974 0.12472 0.392 0.43535 0.713 0.98135 1 0.57742 0.786 12q loss 67 (18%) 299 0.03335 0.186 0.0080599 0.0751 0.98322 1 0.8758 0.97 0.050329 0.237 0.55748 0.775 0.133 0.402 0.50073 0.753 0.45052 0.727 0.69824 0.866 13q loss 80 (22%) 286 0.93522 0.989 0.0111 0.091 0.065589 0.264 0.55706 0.775 0.66123 0.846 0.03423 0.187 0.79686 0.93 0.20287 0.503 0.3226 0.633 0.47166 0.741 14q loss 112 (31%) 254 9.9999e-06 0.000586 0.32042 0.632 0.40977 0.692 0.27149 0.578 0.0090699 0.0809 0.0331 0.186 0.0057099 0.0624 0.21631 0.519 0.33437 0.636 0.23636 0.535 15q loss 52 (14%) 314 0.18245 0.478 0.35605 0.651 0.28884 0.598 0.061769 0.255 0.79891 0.93 0.26704 0.575 0.64663 0.838 0.42121 0.7 0.28825 0.598 0.46058 0.736 16p loss 68 (19%) 298 0.20474 0.504 0.094899 0.327 0.063959 0.261 0.35993 0.652 0.061369 0.255 0.15519 0.44 0.23514 0.535 0.19359 0.493 0.1339 0.402 0.30576 0.618 16q loss 106 (29%) 260 0.3019 0.614 0.32529 0.636 0.01544 0.11 0.75463 0.909 0.03724 0.196 0.03573 0.189 0.32821 0.636 0.10443 0.347 0.068159 0.27 0.18242 0.478 17p loss 127 (35%) 239 0.078449 0.287 0.0055099 0.0619 0.44416 0.722 0.51483 0.758 0.18666 0.487 0.053219 0.246 0.88 0.971 0.51931 0.759 0.62433 0.822 0.44197 0.721 17q loss 64 (17%) 302 0.14179 0.415 0.13343 0.402 0.13089 0.402 0.54112 0.769 0.92548 0.989 0.49457 0.753 0.50864 0.758 0.87 0.969 0.062289 0.255 1 1 18p loss 104 (28%) 262 0.73162 0.897 0.60098 0.804 0.37713 0.662 0.51013 0.758 0.02606 0.157 0.16433 0.451 0.02746 0.164 0.39007 0.677 0.54535 0.77 0.15201 0.436 18q loss 100 (27%) 266 0.45186 0.727 0.88036 0.971 0.29811 0.61 0.49019 0.753 0.44454 0.722 0.43523 0.713 0.75012 0.908 0.23026 0.529 0.55848 0.775 0.17324 0.463 19p loss 77 (21%) 289 0.074899 0.282 0.65826 0.845 0.78328 0.923 0.03347 0.186 0.14722 0.425 0.25584 0.562 0.56673 0.779 0.8867 0.974 0.23633 0.535 0.51609 0.758 19q loss 73 (20%) 293 0.02494 0.153 0.04721 0.23 0.9774 1 0.082209 0.298 0.091819 0.32 0.49431 0.753 0.48751 0.753 0.98865 1 0.053929 0.246 0.52727 0.76 20p loss 26 (7%) 340 0.37143 0.662 0.62045 0.818 0.23611 0.535 0.77247 0.917 0.19955 0.5 0.02156 0.137 0.13408 0.402 0.01672 0.114 0.89087 0.974 0.18785 0.487 20q loss 9 (2%) 357 0.39758 0.684 0.17983 0.476 NA NA NA NA 0.073799 0.282 0.0092999 0.0814 0.68509 0.862 0.55573 0.775 0.36204 0.653 0.68257 0.862 21q loss 70 (19%) 296 0.10058 0.339 0.47455 0.743 0.46946 0.74 0.93194 0.989 0.93004 0.989 0.49356 0.753 0.33675 0.637 0.74704 0.908 0.59532 0.798 0.76808 0.917 22q loss 39 (11%) 327 0.40298 0.687 0.42115 0.7 0.9531 0.994 0.94002 0.989 0.24139 0.541 0.96342 1 0.8644 0.967 0.69875 0.866 0.70745 0.875 0.7733 0.917 xp loss 97 (27%) 269 0.03068 0.178 9.9999e-06 0.000586 0.086549 0.309 0.22558 0.523 0.00109 0.0199 0.00396 0.0485 0.02471 0.152 0.33922 0.639 0.03091 0.178 0.75166 0.908 xq loss 93 (25%) 273 0.03952 0.205 9.9999e-06 0.000586 0.24092 0.541 0.078429 0.287 0.00069999 0.0147 0.0062499 0.0636 0.069829 0.274 0.71722 0.883 0.03534 0.189 0.74959 0.908