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 93 (25%) 274 0.33776 0.606 0.44386 0.685 0.31461 0.588 0.40155 0.668 0.053449 0.236 0.70576 0.865 0.63287 0.821 0.98624 0.995 0.28105 0.557 0.60679 0.806 1q gain 173 (47%) 194 3e-05 0.00145 0.60772 0.806 0.01367 0.102 0.1545 0.429 0.0032 0.0426 0.1189 0.372 0.01853 0.129 0.068159 0.263 0.01951 0.133 0.32976 0.597 2p gain 67 (18%) 300 0.00194 0.0325 0.00285 0.0399 0.83191 0.917 0.4168 0.673 0.0083099 0.0741 0.00423 0.051 0.3112 0.588 0.00095999 0.0199 0.21248 0.507 0.00122 0.0238 2q gain 65 (18%) 302 0.00131 0.025 0.00222 0.035 0.94331 0.971 0.13161 0.398 0.00152 0.0271 0.0051999 0.0566 0.22815 0.511 3e-04 0.00946 0.28269 0.557 0.00243 0.0367 3p gain 64 (17%) 303 0.32779 0.596 0.69301 0.855 0.71106 0.87 0.80064 0.907 0.65459 0.837 0.73592 0.878 0.2868 0.56 0.2657 0.549 0.83801 0.919 0.87602 0.934 3q gain 74 (20%) 293 0.76023 0.885 0.22527 0.507 0.46814 0.697 0.5383 0.749 0.3132 0.588 0.50525 0.724 0.18755 0.487 0.49625 0.719 0.40467 0.668 0.81934 0.917 4p gain 57 (16%) 310 0.2097 0.505 0.052819 0.234 0.74402 0.883 0.62149 0.818 0.43563 0.683 0.23819 0.519 0.13558 0.402 0.00246 0.0367 0.23179 0.515 0.61397 0.813 4q gain 48 (13%) 319 0.37074 0.639 0.11502 0.366 0.1774 0.472 0.61436 0.813 0.31168 0.588 0.41207 0.67 0.10733 0.346 0.0055899 0.0574 0.32468 0.592 0.79779 0.906 5p gain 74 (20%) 293 9.9999e-06 0.000683 0.35268 0.618 0.64332 0.829 0.39266 0.663 0.40621 0.668 0.21661 0.507 0.078969 0.289 0.54017 0.751 0.30447 0.578 0.031 0.172 5q gain 52 (14%) 315 9.9999e-06 0.000683 0.32979 0.597 0.79565 0.905 0.30206 0.576 0.3419 0.608 0.87481 0.934 0.21383 0.507 0.43416 0.682 0.10644 0.346 0.44253 0.685 6p gain 148 (40%) 219 0.00076999 0.0186 0.01288 0.0982 0.58376 0.787 0.20872 0.505 0.01688 0.119 0.03845 0.195 0.04002 0.199 0.00036 0.0102 3e-05 0.00145 9.9999e-05 0.0039 6q gain 50 (14%) 317 0.52497 0.742 0.91309 0.954 0.76871 0.888 0.69188 0.855 1 1 0.39396 0.663 0.55307 0.762 0.2544 0.536 0.22677 0.509 0.55151 0.761 7p gain 204 (56%) 163 0.00095999 0.0199 0.27317 0.555 0.17974 0.477 0.16108 0.442 0.097199 0.321 0.19991 0.495 0.95985 0.98 0.7366 0.878 0.51529 0.736 0.28846 0.56 7q gain 199 (54%) 168 0.0055899 0.0574 0.18127 0.477 0.22349 0.507 0.24291 0.527 0.01458 0.108 0.080869 0.291 0.95246 0.976 0.41778 0.673 0.068229 0.263 0.04654 0.214 8p gain 123 (34%) 244 2e-05 0.00109 0.090499 0.312 0.1954 0.491 0.25804 0.539 0.0336 0.18 0.023 0.146 0.48486 0.713 0.93312 0.966 0.4983 0.719 0.79555 0.905 8q gain 172 (47%) 195 5e-05 0.00216 9.9999e-06 0.000683 0.49854 0.719 0.69085 0.855 0.00046 0.0122 0.01868 0.129 0.81065 0.911 0.32443 0.592 0.43011 0.68 0.38746 0.662 9p gain 16 (4%) 351 0.52438 0.742 0.27741 0.555 0.083279 0.296 0.04601 0.214 0.57435 0.781 0.89925 0.944 0.49487 0.719 0.72073 0.876 0.495 0.719 0.52306 0.742 9q gain 20 (5%) 347 0.1324 0.398 0.32329 0.592 0.076339 0.282 0.095629 0.321 0.91723 0.956 0.33941 0.608 0.83912 0.919 0.76128 0.885 0.75197 0.885 0.56683 0.774 10p gain 12 (3%) 355 0.27603 0.555 0.97226 0.985 0.72456 0.876 0.77412 0.892 0.93464 0.966 0.93321 0.966 0.23428 0.515 0.32284 0.592 0.68435 0.855 0.4542 0.692 10q gain 3 (1%) 364 0.18984 0.49 0.04324 0.209 NA NA NA NA 0.69789 0.859 1 1 0.86412 0.932 0.84995 0.923 0.35648 0.622 0.50112 0.721 11p gain 34 (9%) 333 0.079929 0.29 0.03778 0.192 0.11786 0.372 0.02832 0.164 0.00401 0.0498 0.00243 0.0367 0.1921 0.491 0.0070699 0.0659 0.63101 0.821 0.089109 0.308 11q gain 28 (8%) 339 0.12715 0.388 0.096559 0.321 0.19109 0.491 0.01129 0.0908 0.00142 0.0259 0.00353 0.0452 0.13976 0.411 0.00032 0.00972 0.22097 0.507 0.067099 0.263 12p gain 64 (17%) 303 0.0082199 0.0741 0.16976 0.459 0.44854 0.687 0.094999 0.321 0.23266 0.515 0.93849 0.968 0.88294 0.935 0.41413 0.671 0.31825 0.59 0.46678 0.696 12q gain 40 (11%) 327 0.054979 0.239 0.64034 0.827 0.97379 0.986 0.15899 0.438 0.79849 0.906 0.69917 0.86 0.95601 0.979 0.22243 0.507 0.57915 0.785 0.03322 0.179 13q gain 92 (25%) 275 4e-05 0.00182 0.00012 0.00428 0.1024 0.336 0.18658 0.487 0.00011 0.0041 0.056969 0.24 0.22114 0.507 0.96627 0.984 0.03054 0.17 0.03253 0.177 14q gain 42 (11%) 325 0.87564 0.934 0.89298 0.941 0.39543 0.663 0.04299 0.209 0.82823 0.917 0.72736 0.876 0.53365 0.748 0.82363 0.917 0.48986 0.717 0.23437 0.515 15q gain 84 (23%) 283 0.04704 0.214 0.27488 0.555 0.83355 0.917 0.63521 0.822 0.0057999 0.058 0.0065199 0.0622 0.03032 0.17 0.11832 0.372 0.14441 0.415 0.04408 0.211 16p gain 57 (16%) 310 6.9999e-05 0.00287 0.00085999 0.0198 0.95928 0.98 0.87719 0.934 0.0056699 0.0574 0.062399 0.254 0.30678 0.581 0.19314 0.491 0.36366 0.632 0.0082499 0.0741 16q gain 45 (12%) 322 2e-05 0.00109 0.0054999 0.0574 0.68545 0.855 0.45709 0.692 0.00337 0.0439 0.01521 0.11 0.20872 0.505 0.21687 0.507 0.39025 0.663 0.00096999 0.0199 17p gain 40 (11%) 327 0.093939 0.318 0.01007 0.0834 0.56947 0.776 0.24376 0.527 0.73351 0.878 0.34793 0.614 0.26982 0.554 0.43822 0.683 0.9077 0.951 0.45559 0.692 17q gain 67 (18%) 300 0.22414 0.507 0.04217 0.207 0.84683 0.922 0.90484 0.949 0.98948 0.996 0.42168 0.676 0.19835 0.494 0.357 0.622 0.46275 0.695 0.15706 0.435 18p gain 56 (15%) 311 0.01293 0.0982 0.054109 0.237 0.38418 0.659 0.72677 0.876 0.68961 0.855 0.45697 0.692 0.85557 0.928 0.81332 0.912 0.0066399 0.0626 0.45805 0.692 18q gain 45 (12%) 322 0.00271 0.0397 0.37 0.639 0.32328 0.592 0.40554 0.668 0.54511 0.755 0.5848 0.787 0.81115 0.911 0.86712 0.933 0.19604 0.492 0.61848 0.815 19p gain 58 (16%) 309 0.02359 0.146 0.18016 0.477 0.53586 0.749 0.49354 0.719 0.02611 0.153 0.060409 0.25 0.98641 0.995 0.49872 0.719 0.062589 0.254 0.41467 0.671 19q gain 56 (15%) 311 0.00375 0.0473 0.073119 0.273 0.56688 0.774 0.16854 0.458 0.02476 0.15 0.02393 0.146 0.94484 0.971 0.29635 0.572 0.073379 0.273 0.40142 0.668 20p gain 147 (40%) 220 9.9999e-06 0.000683 0.00041 0.0112 0.2574 0.539 0.10971 0.353 0.00086999 0.0198 0.01317 0.0991 0.12743 0.388 0.25698 0.539 0.41293 0.67 0.059229 0.247 20q gain 180 (49%) 187 9.9999e-06 0.000683 0.0084799 0.0745 0.14851 0.421 0.04553 0.214 0.084219 0.298 0.04686 0.214 0.45425 0.692 0.21001 0.505 0.93177 0.966 0.14772 0.421 21q gain 67 (18%) 300 0.19021 0.49 0.19443 0.491 0.28679 0.56 0.28513 0.559 0.27094 0.554 0.7535 0.885 0.43231 0.681 0.77248 0.891 0.76051 0.885 0.41141 0.67 22q gain 126 (34%) 241 0.0060399 0.059 0.055569 0.24 0.26212 0.544 0.25823 0.539 0.082229 0.294 0.15371 0.429 0.4436 0.685 0.14692 0.42 0.72293 0.876 0.04301 0.209 xp gain 42 (11%) 325 0.19878 0.494 0.00489 0.0566 0.63283 0.821 0.28117 0.557 0.01264 0.0978 0.0097499 0.0824 0.34107 0.608 0.67941 0.854 0.01181 0.094 0.48622 0.713 xq gain 44 (12%) 323 0.04613 0.214 0.0050499 0.0566 0.40429 0.668 0.69053 0.855 0.00215 0.035 0.0052399 0.0566 0.28734 0.56 0.7166 0.873 0.00056999 0.0146 0.60331 0.803 1p loss 51 (14%) 316 0.00284 0.0399 0.0056299 0.0574 0.68362 0.855 0.3041 0.578 0.50578 0.724 0.27529 0.555 0.20485 0.502 0.84779 0.922 0.0096999 0.0824 0.12517 0.384 1q loss 27 (7%) 340 0.073489 0.273 0.054859 0.239 0.89727 0.943 0.65121 0.836 0.68628 0.855 0.76466 0.885 0.64415 0.829 0.93889 0.968 0.67451 0.851 0.62458 0.819 2p loss 50 (14%) 317 0.31675 0.59 0.084849 0.299 0.13589 0.402 0.25155 0.533 0.29834 0.573 0.03129 0.172 0.00292 0.0399 0.02183 0.14 0.15303 0.429 0.63348 0.821 2q loss 51 (14%) 316 0.15135 0.428 0.02561 0.153 0.067079 0.263 0.03923 0.197 0.22142 0.507 0.13955 0.411 0.0085399 0.0745 0.03573 0.187 0.10719 0.346 0.71353 0.871 3p loss 60 (16%) 307 0.31415 0.588 0.79041 0.904 0.8028 0.907 0.4376 0.683 0.20709 0.504 0.46411 0.696 0.0065199 0.0622 0.66161 0.842 0.9306 0.966 0.1432 0.413 3q loss 51 (14%) 316 0.19529 0.491 0.39535 0.663 0.59039 0.794 0.14264 0.413 0.42329 0.677 0.60276 0.803 0.02341 0.146 0.42798 0.677 0.21537 0.507 0.53489 0.748 4p loss 80 (22%) 287 0.27559 0.555 0.59327 0.795 0.73933 0.88 0.46483 0.696 0.35268 0.618 0.01505 0.11 0.49782 0.719 0.0059599 0.0589 0.72713 0.876 0.83448 0.917 4q loss 85 (23%) 282 0.24885 0.533 0.74762 0.885 0.82343 0.917 0.55653 0.764 0.23384 0.515 0.01632 0.116 0.48095 0.709 0.00322 0.0426 0.64522 0.829 0.47313 0.7 5p loss 79 (22%) 288 9.9999e-06 0.000683 0.75629 0.885 0.096289 0.321 0.85991 0.929 0.42028 0.676 0.75904 0.885 0.75997 0.885 0.34493 0.611 0.40257 0.668 0.46699 0.696 5q loss 97 (26%) 270 9.9999e-06 0.000683 0.43703 0.683 0.03455 0.184 0.93358 0.966 0.35567 0.622 0.27174 0.554 0.9482 0.973 0.66739 0.847 0.83315 0.917 0.98769 0.995 6p loss 70 (19%) 297 0.063489 0.255 0.86718 0.933 0.46896 0.697 0.87976 0.935 0.00072999 0.0181 0.051009 0.23 0.50218 0.721 0.069789 0.266 0.12109 0.374 0.01254 0.0978 6q loss 172 (47%) 195 9.9999e-06 0.000683 0.04457 0.212 0.096649 0.321 0.53212 0.748 0.0051299 0.0566 0.056149 0.24 0.526 0.742 0.23462 0.515 0.45067 0.689 0.28882 0.56 7p loss 18 (5%) 349 0.4614 0.694 0.25217 0.533 0.29212 0.565 0.56725 0.774 0.068109 0.263 0.78355 0.9 0.40943 0.669 0.77773 0.894 0.2177 0.507 0.82397 0.917 7q loss 17 (5%) 350 0.39773 0.666 0.53288 0.748 0.59938 0.802 0.20069 0.496 0.02374 0.146 0.48473 0.713 0.82805 0.917 0.83416 0.917 0.14157 0.412 0.97019 0.985 8p loss 66 (18%) 301 0.067979 0.263 0.36658 0.636 0.0183 0.128 0.072809 0.273 0.03762 0.192 0.84015 0.919 0.24531 0.528 0.052349 0.233 0.51905 0.738 0.58434 0.787 8q loss 25 (7%) 342 0.16345 0.447 0.02358 0.146 0.02063 0.135 0.1736 0.467 0.3229 0.592 0.83408 0.917 0.091739 0.313 0.25116 0.533 0.02096 0.135 0.02016 0.134 9p loss 235 (64%) 132 0.00034 0.00996 0.03509 0.186 0.01119 0.0908 0.057019 0.24 0.080949 0.291 0.04958 0.225 0.44325 0.685 0.099079 0.326 0.96799 0.985 0.0081799 0.0741 9q loss 185 (50%) 182 0.02074 0.135 0.141 0.412 0.091559 0.313 0.56207 0.771 0.14592 0.418 0.74762 0.885 0.21818 0.507 0.02868 0.164 0.87043 0.934 0.0090499 0.0781 10p loss 204 (56%) 163 9.9999e-06 0.000683 0.00427 0.051 0.6295 0.821 0.82782 0.917 0.02592 0.153 0.0098699 0.0826 0.88399 0.935 0.19355 0.491 0.15384 0.429 0.40858 0.669 10q loss 224 (61%) 143 9.9999e-06 0.000683 0.00122 0.0238 0.81832 0.917 0.90951 0.951 0.0052199 0.0566 0.0029 0.0399 0.59257 0.795 0.19203 0.491 0.23425 0.515 0.21069 0.505 11p loss 126 (34%) 241 0.00222 0.035 0.38469 0.659 0.87373 0.934 0.70518 0.865 0.88696 0.937 0.8817 0.935 0.62894 0.821 0.13437 0.401 0.44464 0.685 0.28146 0.557 11q loss 149 (41%) 218 0.0017 0.0297 0.85888 0.929 0.89713 0.943 0.40541 0.668 0.48079 0.709 0.26312 0.545 0.7539 0.885 0.24468 0.528 0.30132 0.576 0.02966 0.168 12p loss 61 (17%) 306 0.24852 0.533 0.18766 0.487 0.9928 0.998 0.76481 0.885 0.3508 0.617 0.79241 0.904 0.28496 0.559 0.13054 0.396 0.8022 0.907 0.1741 0.467 12q loss 68 (19%) 299 0.02054 0.135 0.051379 0.23 0.4484 0.687 0.31316 0.588 0.29845 0.573 0.71305 0.871 0.26983 0.554 0.33349 0.602 0.63115 0.821 0.2768 0.555 13q loss 82 (22%) 285 0.37018 0.639 0.62281 0.818 0.28266 0.557 0.81068 0.911 0.22305 0.507 0.39273 0.663 0.4324 0.681 0.38874 0.663 0.28112 0.557 0.11818 0.372 14q loss 112 (31%) 255 0.00013 0.00444 0.061699 0.254 0.40908 0.669 0.03549 0.187 0.02576 0.153 0.057129 0.24 0.32171 0.592 0.8252 0.917 0.42186 0.676 0.6924 0.855 15q loss 54 (15%) 313 0.51745 0.737 0.7334 0.878 0.15209 0.429 0.063459 0.255 0.34618 0.612 0.616 0.813 0.86899 0.934 0.67035 0.848 0.22497 0.507 0.87625 0.934 16p loss 69 (19%) 298 0.00028 0.00918 0.02935 0.167 0.31825 0.59 0.54589 0.755 0.15929 0.438 0.27008 0.554 0.1975 0.494 0.14175 0.412 0.11244 0.359 0.67297 0.85 16q loss 105 (29%) 262 9.9999e-06 0.000683 0.080049 0.29 0.087259 0.304 0.55417 0.762 0.059269 0.247 0.066289 0.263 0.22513 0.507 0.2017 0.497 0.18138 0.477 0.13448 0.401 17p loss 124 (34%) 243 0.4437 0.685 0.03148 0.172 0.070159 0.266 0.069299 0.266 0.42753 0.677 0.20548 0.502 0.75671 0.885 0.63288 0.821 0.72937 0.877 0.22272 0.507 17q loss 62 (17%) 305 0.68874 0.855 0.97155 0.985 0.02767 0.161 0.20559 0.502 0.67694 0.853 0.42596 0.677 0.84561 0.922 0.51793 0.737 0.23497 0.515 0.80864 0.911 18p loss 104 (28%) 263 0.25111 0.533 0.49298 0.719 0.30076 0.576 0.46024 0.694 0.078319 0.288 0.23553 0.515 0.98771 0.995 0.072429 0.273 0.69023 0.855 0.75914 0.885 18q loss 100 (27%) 267 0.22119 0.507 0.27693 0.555 0.16841 0.458 0.83738 0.919 0.54524 0.755 0.85795 0.929 0.88039 0.935 0.088579 0.308 0.91489 0.954 0.84572 0.922 19p loss 77 (21%) 290 0.0397 0.198 0.74313 0.883 0.53725 0.749 0.72406 0.876 0.12045 0.374 0.66474 0.845 0.22263 0.507 0.94035 0.969 0.66076 0.842 0.76455 0.885 19q loss 73 (20%) 294 0.03721 0.192 0.12147 0.374 0.24129 0.525 0.33586 0.604 0.12064 0.374 0.42455 0.677 0.17403 0.467 0.96352 0.983 0.34124 0.608 0.73209 0.878 20p loss 25 (7%) 342 0.75168 0.885 0.11082 0.355 0.37503 0.645 0.22188 0.507 0.32135 0.592 0.064039 0.256 0.067609 0.263 0.01243 0.0978 0.79137 0.904 0.18686 0.487 20q loss 9 (2%) 358 0.76159 0.885 0.10571 0.345 0.44531 0.685 0.04077 0.201 0.46981 0.697 0.0052499 0.0566 0.26028 0.542 0.38996 0.663 0.57509 0.781 0.45658 0.692 21q loss 70 (19%) 297 0.0106 0.0869 0.39395 0.663 0.53265 0.748 0.67046 0.848 0.25172 0.533 0.33575 0.604 0.01595 0.115 0.72717 0.876 0.13205 0.398 0.73674 0.878 22q loss 39 (11%) 328 0.78702 0.901 0.4058 0.668 0.65906 0.842 0.60193 0.803 0.21889 0.507 0.69167 0.855 0.78513 0.9 0.65383 0.837 0.42546 0.677 0.89043 0.94 xp loss 96 (26%) 271 0.03599 0.187 9.9999e-06 0.000683 0.086479 0.303 0.17526 0.468 0.0014 0.0259 0.00179 0.0306 0.02012 0.134 0.062169 0.254 0.093719 0.318 0.02512 0.151 xq loss 92 (25%) 275 0.04687 0.214 2e-05 0.00109 0.082859 0.295 0.58373 0.787 0.00091999 0.0199 0.00429 0.051 0.04633 0.214 0.34439 0.611 0.056919 0.24 0.01971 0.134