This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 82 arm-level events and 12 clinical features across 625 patients, 11 significant findings detected with Q value < 0.25.
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7p gain cnv correlated to 'GENDER'.
-
7q gain cnv correlated to 'GENDER'.
-
12q gain cnv correlated to 'RACE'.
-
20q gain cnv correlated to 'GENDER'.
-
xp gain cnv correlated to 'RACE'.
-
xq gain cnv correlated to 'RACE'.
-
5p loss cnv correlated to 'PATHOLOGIC_STAGE'.
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5q loss cnv correlated to 'PATHOLOGIC_STAGE'.
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8p loss cnv correlated to 'GENDER'.
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18q loss cnv correlated to 'PATHOLOGY_T_STAGE'.
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xp loss cnv correlated to 'GENDER'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
NUMBER PACK YEARS SMOKED |
RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
7p gain | 308 (49%) | 317 |
0.768 (0.987) |
0.551 (0.938) |
0.378 (0.84) |
0.0408 (0.437) |
0.907 (1.00) |
1 (1.00) |
0.000449 (0.138) |
0.918 (1.00) |
0.99 (1.00) |
0.171 (0.644) |
0.0754 (0.515) |
0.124 (0.565) |
7q gain | 257 (41%) | 368 |
0.68 (0.962) |
0.975 (1.00) |
0.333 (0.811) |
0.0625 (0.494) |
0.606 (0.96) |
1 (1.00) |
0.00246 (0.239) |
0.834 (1.00) |
0.163 (0.626) |
0.655 (0.96) |
0.123 (0.561) |
0.12 (0.558) |
12q gain | 116 (19%) | 509 |
0.89 (1.00) |
0.0289 (0.401) |
0.373 (0.838) |
0.134 (0.586) |
0.112 (0.552) |
0.134 (0.586) |
0.176 (0.656) |
1 (1.00) |
0.0616 (0.494) |
0.0249 (0.38) |
0.00253 (0.239) |
0.466 (0.901) |
20q gain | 395 (63%) | 230 |
0.0863 (0.525) |
0.129 (0.578) |
0.436 (0.891) |
0.166 (0.634) |
0.0642 (0.494) |
0.499 (0.914) |
0.00267 (0.239) |
0.134 (0.586) |
0.291 (0.793) |
0.779 (0.994) |
0.855 (1.00) |
0.547 (0.938) |
xp gain | 75 (12%) | 550 |
0.513 (0.923) |
0.98 (1.00) |
0.3 (0.793) |
0.453 (0.9) |
0.199 (0.688) |
0.295 (0.793) |
0.686 (0.963) |
0.274 (0.783) |
0.699 (0.968) |
0.64 (0.96) |
0.00019 (0.123) |
1 (1.00) |
xq gain | 93 (15%) | 532 |
0.982 (1.00) |
0.252 (0.748) |
0.603 (0.959) |
0.544 (0.938) |
0.318 (0.796) |
1 (1.00) |
0.806 (1) |
0.772 (0.992) |
0.829 (1.00) |
0.822 (1.00) |
0.00056 (0.138) |
0.225 (0.718) |
5p loss | 110 (18%) | 515 |
0.0153 (0.341) |
0.197 (0.688) |
0.00088 (0.144) |
0.0115 (0.341) |
0.205 (0.698) |
0.657 (0.96) |
0.25 (0.748) |
0.592 (0.957) |
0.671 (0.962) |
0.765 (0.987) |
0.446 (0.9) |
1 (1.00) |
5q loss | 195 (31%) | 430 |
0.139 (0.586) |
0.832 (1.00) |
0.00136 (0.191) |
0.197 (0.688) |
0.031 (0.404) |
0.369 (0.838) |
0.22 (0.713) |
0.825 (1.00) |
0.262 (0.767) |
0.901 (1.00) |
0.209 (0.707) |
1 (1.00) |
8p loss | 156 (25%) | 469 |
0.914 (1.00) |
0.743 (0.977) |
0.113 (0.552) |
0.22 (0.713) |
0.0657 (0.494) |
1 (1.00) |
0.0023 (0.239) |
0.721 (0.972) |
0.974 (1.00) |
0.142 (0.586) |
0.286 (0.793) |
0.136 (0.586) |
18q loss | 257 (41%) | 368 |
0.92 (1.00) |
0.258 (0.761) |
0.906 (1.00) |
0.0008 (0.144) |
0.97 (1.00) |
0.736 (0.972) |
0.214 (0.713) |
0.601 (0.959) |
0.316 (0.795) |
0.294 (0.793) |
0.805 (1) |
0.347 (0.823) |
xp loss | 123 (20%) | 502 |
0.282 (0.793) |
0.494 (0.912) |
0.393 (0.853) |
0.295 (0.793) |
0.0387 (0.437) |
0.205 (0.698) |
0.000249 (0.123) |
0.6 (0.959) |
0.864 (1.00) |
0.00766 (0.331) |
0.38 (0.841) |
0.233 (0.734) |
1p gain | 84 (13%) | 541 |
0.293 (0.793) |
0.0299 (0.404) |
0.0985 (0.533) |
0.0528 (0.486) |
0.965 (1.00) |
0.21 (0.707) |
0.0944 (0.528) |
0.0316 (0.404) |
0.537 (0.938) |
0.959 (1.00) |
0.33 (0.807) |
0.664 (0.96) |
1q gain | 170 (27%) | 455 |
0.186 (0.665) |
0.0904 (0.528) |
0.828 (1.00) |
0.203 (0.698) |
0.96 (1.00) |
0.574 (0.95) |
0.0487 (0.461) |
0.0642 (0.494) |
0.818 (1.00) |
0.465 (0.901) |
0.0217 (0.373) |
0.523 (0.927) |
2p gain | 137 (22%) | 488 |
0.945 (1.00) |
0.47 (0.901) |
0.216 (0.713) |
0.0564 (0.488) |
0.677 (0.962) |
0.838 (1.00) |
0.525 (0.928) |
0.804 (1) |
0.437 (0.891) |
0.167 (0.635) |
0.0438 (0.444) |
1 (1.00) |
2q gain | 113 (18%) | 512 |
0.79 (0.995) |
0.876 (1.00) |
0.0996 (0.533) |
0.11 (0.548) |
0.692 (0.966) |
1 (1.00) |
0.649 (0.96) |
0.507 (0.923) |
0.703 (0.968) |
0.955 (1.00) |
0.399 (0.859) |
1 (1.00) |
3p gain | 85 (14%) | 540 |
0.515 (0.923) |
0.554 (0.938) |
0.4 (0.859) |
0.674 (0.962) |
0.493 (0.912) |
1 (1.00) |
0.612 (0.96) |
0.237 (0.74) |
0.929 (1.00) |
0.712 (0.972) |
0.478 (0.904) |
0.0325 (0.41) |
3q gain | 170 (27%) | 455 |
0.6 (0.959) |
0.00422 (0.279) |
0.118 (0.557) |
0.922 (1.00) |
0.686 (0.963) |
0.71 (0.972) |
0.325 (0.806) |
0.0284 (0.401) |
0.884 (1.00) |
0.0882 (0.526) |
0.0931 (0.528) |
0.148 (0.599) |
4p gain | 37 (6%) | 588 |
0.436 (0.891) |
0.988 (1.00) |
0.0569 (0.488) |
0.62 (0.96) |
0.545 (0.938) |
1 (1.00) |
0.0928 (0.528) |
0.655 (0.96) |
0.389 (0.853) |
0.333 (0.811) |
0.274 (0.783) |
0.102 (0.533) |
4q gain | 30 (5%) | 595 |
0.735 (0.972) |
0.856 (1.00) |
0.402 (0.86) |
0.619 (0.96) |
0.648 (0.96) |
1 (1.00) |
0.15 (0.604) |
0.813 (1.00) |
0.737 (0.972) |
0.956 (1.00) |
0.221 (0.713) |
1 (1.00) |
5p gain | 179 (29%) | 446 |
0.472 (0.901) |
0.743 (0.977) |
0.801 (1) |
0.00346 (0.277) |
0.972 (1.00) |
0.46 (0.901) |
0.628 (0.96) |
0.909 (1.00) |
0.975 (1.00) |
0.841 (1.00) |
0.825 (1.00) |
1 (1.00) |
5q gain | 64 (10%) | 561 |
0.536 (0.938) |
0.357 (0.833) |
0.271 (0.783) |
0.105 (0.534) |
0.222 (0.715) |
0.785 (0.994) |
0.471 (0.901) |
0.737 (0.972) |
0.263 (0.768) |
0.817 (1.00) |
0.857 (1.00) |
0.61 (0.96) |
6p gain | 118 (19%) | 507 |
0.0854 (0.525) |
0.87 (1.00) |
0.141 (0.586) |
0.273 (0.783) |
0.941 (1.00) |
0.401 (0.859) |
1 (1.00) |
0.437 (0.891) |
0.0849 (0.525) |
0.463 (0.901) |
0.115 (0.554) |
1 (1.00) |
6q gain | 100 (16%) | 525 |
0.021 (0.373) |
0.787 (0.994) |
0.009 (0.335) |
0.291 (0.793) |
0.85 (1.00) |
0.0369 (0.433) |
0.633 (0.96) |
1 (1.00) |
0.0849 (0.525) |
0.266 (0.775) |
0.0564 (0.488) |
0.681 (0.962) |
8p gain | 248 (40%) | 377 |
0.807 (1.00) |
0.0585 (0.488) |
0.469 (0.901) |
0.944 (1.00) |
0.577 (0.95) |
1 (1.00) |
0.0158 (0.341) |
0.916 (1.00) |
0.537 (0.938) |
0.14 (0.586) |
0.826 (1.00) |
0.541 (0.938) |
8q gain | 337 (54%) | 288 |
0.799 (1) |
0.0875 (0.525) |
0.286 (0.793) |
0.957 (1.00) |
0.443 (0.9) |
0.407 (0.864) |
0.16 (0.622) |
0.408 (0.864) |
0.964 (1.00) |
0.786 (0.994) |
0.865 (1.00) |
0.554 (0.938) |
9p gain | 78 (12%) | 547 |
0.00857 (0.335) |
0.631 (0.96) |
0.909 (1.00) |
0.937 (1.00) |
0.493 (0.912) |
0.457 (0.9) |
0.895 (1.00) |
0.0188 (0.363) |
0.309 (0.793) |
0.0196 (0.363) |
0.233 (0.734) |
0.646 (0.96) |
9q gain | 109 (17%) | 516 |
0.0577 (0.488) |
0.273 (0.783) |
0.995 (1.00) |
0.927 (1.00) |
0.995 (1.00) |
0.517 (0.924) |
0.106 (0.535) |
0.0224 (0.373) |
0.0934 (0.528) |
0.0423 (0.439) |
0.163 (0.626) |
0.431 (0.891) |
10p gain | 136 (22%) | 489 |
0.654 (0.96) |
0.921 (1.00) |
0.136 (0.586) |
0.0824 (0.525) |
0.899 (1.00) |
0.544 (0.938) |
0.832 (1.00) |
0.62 (0.96) |
0.175 (0.656) |
0.274 (0.783) |
0.221 (0.713) |
0.134 (0.586) |
10q gain | 98 (16%) | 527 |
0.829 (1.00) |
0.104 (0.534) |
0.0233 (0.373) |
0.0251 (0.38) |
0.367 (0.838) |
1 (1.00) |
1 (1.00) |
0.781 (0.994) |
0.454 (0.9) |
0.0163 (0.341) |
0.304 (0.793) |
0.225 (0.718) |
11p gain | 98 (16%) | 527 |
0.497 (0.912) |
0.32 (0.798) |
0.391 (0.853) |
0.0655 (0.494) |
0.0757 (0.515) |
0.644 (0.96) |
0.718 (0.972) |
0.396 (0.857) |
0.705 (0.968) |
0.505 (0.922) |
0.0761 (0.515) |
1 (1.00) |
11q gain | 102 (16%) | 523 |
0.412 (0.866) |
0.0482 (0.46) |
0.21 (0.707) |
0.385 (0.849) |
0.0045 (0.279) |
0.658 (0.96) |
0.407 (0.864) |
0.329 (0.807) |
0.581 (0.95) |
0.797 (1) |
0.219 (0.713) |
1 (1.00) |
12p gain | 149 (24%) | 476 |
0.563 (0.945) |
0.347 (0.823) |
0.118 (0.557) |
0.0155 (0.341) |
0.539 (0.938) |
0.326 (0.806) |
0.0647 (0.494) |
0.185 (0.665) |
0.0996 (0.533) |
0.181 (0.661) |
0.0956 (0.528) |
0.483 (0.907) |
13q gain | 197 (32%) | 428 |
0.599 (0.959) |
0.768 (0.987) |
0.366 (0.838) |
0.872 (1.00) |
0.141 (0.586) |
0.858 (1.00) |
0.346 (0.823) |
0.374 (0.838) |
0.73 (0.972) |
0.046 (0.457) |
0.153 (0.607) |
0.748 (0.978) |
14q gain | 76 (12%) | 549 |
0.306 (0.793) |
0.0115 (0.341) |
0.076 (0.515) |
0.301 (0.793) |
0.484 (0.907) |
0.452 (0.9) |
0.0227 (0.373) |
0.0918 (0.528) |
0.73 (0.972) |
0.75 (0.98) |
0.52 (0.925) |
0.636 (0.96) |
15q gain | 67 (11%) | 558 |
0.0766 (0.515) |
0.729 (0.972) |
0.215 (0.713) |
0.555 (0.938) |
0.299 (0.793) |
0.579 (0.95) |
0.119 (0.557) |
1 (1.00) |
0.788 (0.994) |
0.0734 (0.515) |
0.00791 (0.331) |
1 (1.00) |
16p gain | 100 (16%) | 525 |
0.154 (0.608) |
0.801 (1) |
0.0704 (0.51) |
0.776 (0.992) |
0.936 (1.00) |
0.159 (0.622) |
0.0423 (0.439) |
0.196 (0.687) |
0.148 (0.599) |
0.658 (0.96) |
0.0263 (0.392) |
1 (1.00) |
16q gain | 86 (14%) | 539 |
0.0161 (0.341) |
0.654 (0.96) |
0.047 (0.457) |
0.731 (0.972) |
0.703 (0.968) |
0.0207 (0.373) |
0.0743 (0.515) |
0.0655 (0.494) |
0.783 (0.994) |
0.941 (1.00) |
0.0309 (0.404) |
0.653 (0.96) |
17p gain | 61 (10%) | 564 |
0.308 (0.793) |
0.87 (1.00) |
0.00799 (0.331) |
0.609 (0.96) |
0.0758 (0.515) |
0.377 (0.84) |
0.0778 (0.515) |
0.115 (0.554) |
0.957 (1.00) |
0.923 (1.00) |
0.581 (0.95) |
0.611 (0.96) |
17q gain | 108 (17%) | 517 |
0.746 (0.978) |
0.998 (1.00) |
0.312 (0.793) |
0.496 (0.912) |
0.859 (1.00) |
0.257 (0.761) |
0.0108 (0.341) |
0.00596 (0.326) |
0.661 (0.96) |
0.339 (0.818) |
0.0875 (0.525) |
1 (1.00) |
18p gain | 135 (22%) | 490 |
0.0228 (0.373) |
0.612 (0.96) |
0.638 (0.96) |
0.584 (0.953) |
0.46 (0.901) |
0.685 (0.963) |
1 (1.00) |
0.455 (0.9) |
0.541 (0.938) |
0.924 (1.00) |
0.773 (0.992) |
0.703 (0.968) |
18q gain | 79 (13%) | 546 |
0.166 (0.634) |
0.722 (0.972) |
0.0975 (0.533) |
0.029 (0.401) |
0.618 (0.96) |
0.801 (1) |
0.511 (0.923) |
0.437 (0.891) |
0.549 (0.938) |
0.507 (0.923) |
0.884 (1.00) |
1 (1.00) |
19p gain | 83 (13%) | 542 |
0.182 (0.661) |
0.303 (0.793) |
0.932 (1.00) |
0.0872 (0.525) |
0.458 (0.9) |
0.306 (0.793) |
0.606 (0.96) |
0.764 (0.987) |
0.722 (0.972) |
0.514 (0.923) |
0.518 (0.924) |
1 (1.00) |
19q gain | 119 (19%) | 506 |
0.95 (1.00) |
0.401 (0.859) |
0.876 (1.00) |
0.152 (0.607) |
0.176 (0.656) |
0.666 (0.96) |
0.181 (0.661) |
1 (1.00) |
0.931 (1.00) |
0.934 (1.00) |
0.242 (0.742) |
0.697 (0.968) |
20p gain | 349 (56%) | 276 |
0.0119 (0.341) |
0.363 (0.838) |
0.544 (0.938) |
0.282 (0.793) |
0.204 (0.698) |
0.622 (0.96) |
0.00808 (0.331) |
0.0223 (0.373) |
0.0408 (0.437) |
0.628 (0.96) |
0.957 (1.00) |
1 (1.00) |
21q gain | 39 (6%) | 586 |
0.943 (1.00) |
0.717 (0.972) |
0.925 (1.00) |
0.682 (0.962) |
0.465 (0.901) |
0.5 (0.915) |
0.718 (0.972) |
0.669 (0.962) |
0.687 (0.963) |
0.681 (0.962) |
0.218 (0.713) |
0.603 (0.959) |
22q gain | 63 (10%) | 562 |
0.428 (0.889) |
0.0192 (0.363) |
0.228 (0.724) |
0.146 (0.594) |
0.0156 (0.341) |
1 (1.00) |
0.471 (0.901) |
0.408 (0.864) |
0.239 (0.742) |
0.931 (1.00) |
0.00725 (0.331) |
0.37 (0.838) |
1p loss | 97 (16%) | 528 |
0.237 (0.74) |
0.984 (1.00) |
0.32 (0.798) |
0.896 (1.00) |
0.643 (0.96) |
0.0313 (0.404) |
0.547 (0.938) |
0.393 (0.853) |
0.312 (0.793) |
0.791 (0.995) |
0.247 (0.748) |
1 (1.00) |
1q loss | 47 (8%) | 578 |
0.0385 (0.437) |
0.155 (0.609) |
0.73 (0.972) |
0.446 (0.9) |
0.666 (0.96) |
0.283 (0.793) |
0.869 (1.00) |
0.556 (0.938) |
0.321 (0.799) |
0.262 (0.767) |
1 (1.00) |
0.603 (0.959) |
2p loss | 36 (6%) | 589 |
0.457 (0.9) |
0.31 (0.793) |
0.251 (0.748) |
0.0719 (0.515) |
0.855 (1.00) |
0.156 (0.611) |
0.258 (0.761) |
0.135 (0.586) |
0.95 (1.00) |
1 (1.00) |
0.884 (1.00) |
1 (1.00) |
2q loss | 49 (8%) | 576 |
0.786 (0.994) |
0.439 (0.892) |
0.659 (0.96) |
0.679 (0.962) |
0.815 (1.00) |
0.356 (0.833) |
1 (1.00) |
0.0581 (0.488) |
0.294 (0.793) |
0.453 (0.9) |
0.242 (0.742) |
1 (1.00) |
3p loss | 187 (30%) | 438 |
0.856 (1.00) |
0.0543 (0.488) |
0.079 (0.515) |
0.488 (0.911) |
0.0142 (0.341) |
0.47 (0.901) |
0.444 (0.9) |
0.372 (0.838) |
0.875 (1.00) |
0.586 (0.953) |
0.0823 (0.525) |
1 (1.00) |
3q loss | 92 (15%) | 533 |
0.798 (1) |
0.811 (1.00) |
0.351 (0.828) |
0.0963 (0.529) |
0.279 (0.793) |
0.252 (0.748) |
0.806 (1) |
0.473 (0.901) |
0.364 (0.838) |
0.368 (0.838) |
0.856 (1.00) |
0.673 (0.962) |
4p loss | 274 (44%) | 351 |
0.139 (0.586) |
0.629 (0.96) |
0.0843 (0.525) |
0.102 (0.533) |
0.557 (0.938) |
0.183 (0.663) |
0.078 (0.515) |
0.177 (0.656) |
0.99 (1.00) |
0.152 (0.607) |
0.0401 (0.437) |
0.766 (0.987) |
4q loss | 256 (41%) | 369 |
0.0191 (0.363) |
0.0842 (0.525) |
0.199 (0.688) |
0.0693 (0.507) |
0.335 (0.813) |
0.866 (1.00) |
0.328 (0.807) |
0.917 (1.00) |
0.914 (1.00) |
0.892 (1.00) |
0.285 (0.793) |
0.758 (0.984) |
6p loss | 93 (15%) | 532 |
0.812 (1.00) |
0.592 (0.957) |
0.63 (0.96) |
0.128 (0.578) |
0.377 (0.84) |
0.145 (0.594) |
0.112 (0.551) |
0.884 (1.00) |
0.656 (0.96) |
0.178 (0.656) |
0.495 (0.912) |
0.681 (0.962) |
6q loss | 112 (18%) | 513 |
0.731 (0.972) |
0.664 (0.96) |
0.67 (0.962) |
0.0289 (0.401) |
0.756 (0.984) |
0.177 (0.656) |
0.0397 (0.437) |
0.786 (0.994) |
0.884 (1.00) |
0.162 (0.626) |
0.579 (0.95) |
1 (1.00) |
7p loss | 33 (5%) | 592 |
0.481 (0.907) |
0.849 (1.00) |
0.389 (0.853) |
0.678 (0.962) |
0.108 (0.541) |
0.714 (0.972) |
0.847 (1.00) |
0.818 (1.00) |
0.269 (0.781) |
0.0236 (0.373) |
0.236 (0.74) |
1 (1.00) |
7q loss | 50 (8%) | 575 |
0.76 (0.986) |
0.0789 (0.515) |
0.188 (0.671) |
0.101 (0.533) |
0.243 (0.742) |
0.237 (0.74) |
0.63 (0.96) |
0.704 (0.968) |
0.581 (0.95) |
0.122 (0.561) |
0.751 (0.98) |
1 (1.00) |
8q loss | 59 (9%) | 566 |
0.539 (0.938) |
0.862 (1.00) |
0.0461 (0.457) |
0.00682 (0.331) |
0.732 (0.972) |
0.785 (0.994) |
0.0528 (0.486) |
0.727 (0.972) |
0.452 (0.9) |
0.413 (0.866) |
0.0195 (0.363) |
0.567 (0.948) |
9p loss | 249 (40%) | 376 |
0.524 (0.927) |
0.965 (1.00) |
0.0334 (0.416) |
0.138 (0.586) |
0.106 (0.535) |
0.736 (0.972) |
0.18 (0.661) |
0.115 (0.554) |
0.545 (0.938) |
0.352 (0.828) |
0.3 (0.793) |
0.114 (0.554) |
9q loss | 173 (28%) | 452 |
0.305 (0.793) |
0.409 (0.864) |
0.121 (0.56) |
0.227 (0.722) |
0.874 (1.00) |
0.578 (0.95) |
0.0502 (0.471) |
0.305 (0.793) |
0.311 (0.793) |
0.103 (0.534) |
0.141 (0.586) |
0.19 (0.676) |
10p loss | 118 (19%) | 507 |
0.0937 (0.528) |
0.484 (0.907) |
0.828 (1.00) |
0.058 (0.488) |
0.35 (0.828) |
0.835 (1.00) |
0.314 (0.793) |
0.431 (0.891) |
0.0415 (0.439) |
0.538 (0.938) |
0.0239 (0.373) |
0.426 (0.887) |
10q loss | 118 (19%) | 507 |
0.496 (0.912) |
0.938 (1.00) |
0.626 (0.96) |
0.384 (0.849) |
0.495 (0.912) |
0.836 (1.00) |
0.434 (0.891) |
0.36 (0.835) |
0.522 (0.927) |
0.353 (0.828) |
0.00454 (0.279) |
0.455 (0.9) |
11p loss | 117 (19%) | 508 |
0.249 (0.748) |
0.747 (0.978) |
0.018 (0.363) |
0.426 (0.887) |
0.454 (0.9) |
0.664 (0.96) |
0.0927 (0.528) |
0.0346 (0.424) |
0.105 (0.534) |
0.935 (1.00) |
0.305 (0.793) |
0.118 (0.557) |
11q loss | 122 (20%) | 503 |
0.0747 (0.515) |
0.129 (0.578) |
0.014 (0.341) |
0.34 (0.818) |
0.193 (0.683) |
0.666 (0.96) |
0.0149 (0.341) |
0.0696 (0.507) |
0.661 (0.96) |
0.476 (0.904) |
0.518 (0.924) |
0.0395 (0.437) |
12p loss | 98 (16%) | 527 |
0.104 (0.534) |
0.0609 (0.494) |
0.858 (1.00) |
0.0848 (0.525) |
0.766 (0.987) |
0.819 (1.00) |
0.631 (0.96) |
0.0651 (0.494) |
0.655 (0.96) |
0.0776 (0.515) |
0.559 (0.941) |
1 (1.00) |
12q loss | 87 (14%) | 538 |
0.13 (0.578) |
0.184 (0.663) |
0.288 (0.793) |
0.0126 (0.341) |
0.569 (0.949) |
0.805 (1) |
0.613 (0.96) |
0.551 (0.938) |
0.138 (0.586) |
0.0281 (0.401) |
0.0373 (0.433) |
0.37 (0.838) |
13q loss | 103 (16%) | 522 |
0.961 (1.00) |
0.065 (0.494) |
0.00596 (0.326) |
0.0354 (0.424) |
0.0156 (0.341) |
0.25 (0.748) |
0.0131 (0.341) |
0.0546 (0.488) |
0.121 (0.56) |
0.848 (1.00) |
0.0473 (0.457) |
0.387 (0.852) |
14q loss | 157 (25%) | 468 |
0.776 (0.992) |
0.544 (0.938) |
0.0686 (0.507) |
0.241 (0.742) |
0.218 (0.713) |
0.244 (0.743) |
0.84 (1.00) |
0.637 (0.96) |
0.477 (0.904) |
0.41 (0.864) |
0.688 (0.963) |
0.472 (0.901) |
15q loss | 149 (24%) | 476 |
0.546 (0.938) |
0.31 (0.793) |
0.603 (0.959) |
0.0152 (0.341) |
0.646 (0.96) |
0.701 (0.968) |
0.682 (0.962) |
0.091 (0.528) |
0.689 (0.963) |
0.827 (1.00) |
0.71 (0.972) |
0.297 (0.793) |
16p loss | 154 (25%) | 471 |
0.935 (1.00) |
0.101 (0.533) |
0.757 (0.984) |
0.215 (0.713) |
0.242 (0.742) |
0.119 (0.557) |
1 (1.00) |
0.906 (1.00) |
0.976 (1.00) |
0.847 (1.00) |
0.871 (1.00) |
0.714 (0.972) |
16q loss | 167 (27%) | 458 |
0.554 (0.938) |
0.342 (0.821) |
0.308 (0.793) |
0.41 (0.864) |
0.901 (1.00) |
0.0581 (0.488) |
0.621 (0.96) |
0.357 (0.833) |
0.828 (1.00) |
0.548 (0.938) |
0.665 (0.96) |
0.14 (0.586) |
17p loss | 237 (38%) | 388 |
0.917 (1.00) |
0.415 (0.868) |
0.579 (0.95) |
0.28 (0.793) |
0.855 (1.00) |
0.396 (0.857) |
0.0472 (0.457) |
0.168 (0.635) |
0.0953 (0.528) |
0.592 (0.957) |
0.51 (0.923) |
0.196 (0.687) |
17q loss | 102 (16%) | 523 |
0.344 (0.823) |
0.847 (1.00) |
0.569 (0.949) |
0.305 (0.793) |
0.285 (0.793) |
0.372 (0.838) |
0.722 (0.972) |
0.776 (0.992) |
0.105 (0.534) |
0.565 (0.947) |
0.295 (0.793) |
0.0921 (0.528) |
18p loss | 187 (30%) | 438 |
0.33 (0.807) |
0.306 (0.793) |
0.956 (1.00) |
0.0639 (0.494) |
0.847 (1.00) |
0.586 (0.953) |
0.0849 (0.525) |
0.312 (0.793) |
0.866 (1.00) |
0.146 (0.594) |
0.642 (0.96) |
0.314 (0.793) |
19p loss | 182 (29%) | 443 |
0.0553 (0.488) |
0.745 (0.978) |
0.462 (0.901) |
0.575 (0.95) |
0.458 (0.9) |
0.716 (0.972) |
0.21 (0.707) |
0.572 (0.95) |
0.813 (1.00) |
0.0315 (0.404) |
0.00976 (0.335) |
1 (1.00) |
19q loss | 142 (23%) | 483 |
0.653 (0.96) |
0.904 (1.00) |
0.867 (1.00) |
0.592 (0.957) |
0.653 (0.96) |
1 (1.00) |
0.347 (0.823) |
0.712 (0.972) |
0.934 (1.00) |
0.0592 (0.49) |
0.0152 (0.341) |
0.704 (0.968) |
20p loss | 42 (7%) | 583 |
0.423 (0.884) |
0.696 (0.968) |
0.627 (0.96) |
0.494 (0.912) |
0.956 (1.00) |
0.726 (0.972) |
0.601 (0.959) |
0.0374 (0.433) |
0.392 (0.853) |
0.704 (0.968) |
0.51 (0.923) |
0.485 (0.907) |
20q loss | 8 (1%) | 617 |
0.339 (0.818) |
0.577 (0.95) |
0.245 (0.743) |
0.0353 (0.424) |
0.649 (0.96) |
1 (1.00) |
0.447 (0.9) |
0.678 (0.962) |
0.642 (0.96) |
0.512 (0.923) |
1 (1.00) |
|
21q loss | 287 (46%) | 338 |
0.71 (0.972) |
0.142 (0.586) |
0.339 (0.818) |
0.364 (0.838) |
0.665 (0.96) |
0.317 (0.795) |
0.726 (0.972) |
0.214 (0.713) |
0.199 (0.688) |
0.129 (0.578) |
0.375 (0.838) |
0.375 (0.838) |
22q loss | 218 (35%) | 407 |
0.095 (0.528) |
0.481 (0.907) |
0.00988 (0.335) |
0.0437 (0.444) |
0.434 (0.891) |
0.607 (0.96) |
0.358 (0.833) |
0.0678 (0.505) |
0.475 (0.904) |
0.953 (1.00) |
0.366 (0.838) |
0.752 (0.98) |
xq loss | 98 (16%) | 527 |
0.6 (0.959) |
0.832 (1.00) |
0.621 (0.96) |
0.291 (0.793) |
0.515 (0.923) |
0.0999 (0.533) |
0.00367 (0.277) |
0.314 (0.793) |
0.666 (0.96) |
0.00965 (0.335) |
0.95 (1.00) |
0.664 (0.96) |
P value = 0.000449 (Fisher's exact test), Q value = 0.14
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
7P GAIN MUTATED | 71 | 237 |
7P GAIN WILD-TYPE | 114 | 203 |
P value = 0.00246 (Fisher's exact test), Q value = 0.24
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
7Q GAIN MUTATED | 59 | 198 |
7Q GAIN WILD-TYPE | 126 | 242 |
P value = 0.00253 (Fisher's exact test), Q value = 0.24
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
12Q GAIN MUTATED | 39 | 1 | 0 | 62 |
12Q GAIN WILD-TYPE | 95 | 16 | 1 | 330 |
P value = 0.00267 (Fisher's exact test), Q value = 0.24
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
20Q GAIN MUTATED | 100 | 295 |
20Q GAIN WILD-TYPE | 85 | 145 |
P value = 0.00019 (Fisher's exact test), Q value = 0.12
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
XP GAIN MUTATED | 20 | 7 | 1 | 37 |
XP GAIN WILD-TYPE | 114 | 10 | 0 | 355 |
P value = 0.00056 (Fisher's exact test), Q value = 0.14
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 134 | 17 | 1 | 392 |
XQ GAIN MUTATED | 29 | 6 | 1 | 48 |
XQ GAIN WILD-TYPE | 105 | 11 | 0 | 344 |
P value = 0.00088 (Fisher's exact test), Q value = 0.14
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 10 | 21 | 47 | 33 | 87 | 87 | 28 | 95 | 72 | 46 | 49 | 4 |
5P LOSS MUTATED | 7 | 3 | 2 | 3 | 13 | 18 | 9 | 18 | 11 | 6 | 5 | 1 |
5P LOSS WILD-TYPE | 3 | 18 | 45 | 30 | 74 | 69 | 19 | 77 | 61 | 40 | 44 | 3 |
P value = 0.00136 (Fisher's exact test), Q value = 0.19
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 10 | 21 | 47 | 33 | 87 | 87 | 28 | 95 | 72 | 46 | 49 | 4 |
5Q LOSS MUTATED | 7 | 7 | 8 | 9 | 26 | 29 | 11 | 42 | 17 | 11 | 9 | 3 |
5Q LOSS WILD-TYPE | 3 | 14 | 39 | 24 | 61 | 58 | 17 | 53 | 55 | 35 | 40 | 1 |
P value = 0.0023 (Fisher's exact test), Q value = 0.24
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
8P LOSS MUTATED | 31 | 125 |
8P LOSS WILD-TYPE | 154 | 315 |
P value = 8e-04 (Fisher's exact test), Q value = 0.14
nPatients | T0+T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 55 | 136 | 283 | 124 |
18Q LOSS MUTATED | 18 | 56 | 136 | 34 |
18Q LOSS WILD-TYPE | 37 | 80 | 147 | 90 |
P value = 0.000249 (Fisher's exact test), Q value = 0.12
nPatients | FEMALE | MALE |
---|---|---|
ALL | 185 | 440 |
XP LOSS MUTATED | 20 | 103 |
XP LOSS WILD-TYPE | 165 | 337 |
-
Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/22532763/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STES-TP/22507048/STES-TP.merged_data.txt
-
Number of patients = 625
-
Number of significantly arm-level cnvs = 82
-
Number of selected clinical features = 12
-
Exclude regions that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.