This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 80 arm-level events and 13 clinical features across 406 patients, no significant finding detected with Q value < 0.25.
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No arm-level cnvs related to clinical features.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | YEAROFTOBACCOSMOKINGONSET |
COMPLETENESS OF RESECTION |
||
nCNV (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | Fisher's exact test | Fisher's exact test | t-test | t-test | Fisher's exact test | |
1p gain | 77 (19%) | 329 |
0.87 (1.00) |
0.941 (1.00) |
0.047 (1.00) |
0.206 (1.00) |
0.86 (1.00) |
0.0669 (1.00) |
1 (1.00) |
0.563 (1.00) |
0.00541 (1.00) |
1 (1.00) |
0.396 (1.00) |
0.205 (1.00) |
0.469 (1.00) |
1q gain | 168 (41%) | 238 |
0.326 (1.00) |
0.423 (1.00) |
0.125 (1.00) |
0.233 (1.00) |
0.692 (1.00) |
0.239 (1.00) |
0.415 (1.00) |
0.283 (1.00) |
0.000622 (0.647) |
0.134 (1.00) |
0.322 (1.00) |
0.318 (1.00) |
0.505 (1.00) |
2p gain | 174 (43%) | 232 |
0.0989 (1.00) |
0.485 (1.00) |
0.507 (1.00) |
0.281 (1.00) |
0.134 (1.00) |
1 (1.00) |
0.0106 (1.00) |
0.392 (1.00) |
0.00613 (1.00) |
0.137 (1.00) |
0.2 (1.00) |
0.0755 (1.00) |
0.148 (1.00) |
2q gain | 115 (28%) | 291 |
0.267 (1.00) |
0.458 (1.00) |
0.391 (1.00) |
0.695 (1.00) |
0.303 (1.00) |
0.619 (1.00) |
0.163 (1.00) |
0.717 (1.00) |
0.00539 (1.00) |
0.107 (1.00) |
0.425 (1.00) |
0.23 (1.00) |
0.224 (1.00) |
3p gain | 88 (22%) | 318 |
0.215 (1.00) |
0.952 (1.00) |
0.0839 (1.00) |
0.787 (1.00) |
0.131 (1.00) |
0.777 (1.00) |
0.21 (1.00) |
0.646 (1.00) |
0.68 (1.00) |
0.728 (1.00) |
0.457 (1.00) |
0.928 (1.00) |
0.595 (1.00) |
3q gain | 257 (63%) | 149 |
0.994 (1.00) |
0.916 (1.00) |
0.438 (1.00) |
0.899 (1.00) |
0.867 (1.00) |
0.21 (1.00) |
0.478 (1.00) |
0.817 (1.00) |
0.00166 (1.00) |
0.548 (1.00) |
0.851 (1.00) |
0.871 (1.00) |
0.813 (1.00) |
4p gain | 26 (6%) | 380 |
0.062 (1.00) |
0.74 (1.00) |
0.71 (1.00) |
0.422 (1.00) |
0.929 (1.00) |
1 (1.00) |
0.157 (1.00) |
0.362 (1.00) |
0.724 (1.00) |
0.553 (1.00) |
0.98 (1.00) |
0.395 (1.00) |
0.428 (1.00) |
4q gain | 18 (4%) | 388 |
0.295 (1.00) |
0.0446 (1.00) |
0.619 (1.00) |
0.784 (1.00) |
0.796 (1.00) |
1 (1.00) |
0.58 (1.00) |
0.524 (1.00) |
0.586 (1.00) |
0.424 (1.00) |
0.667 (1.00) |
0.825 (1.00) |
0.759 (1.00) |
5p gain | 256 (63%) | 150 |
0.28 (1.00) |
0.139 (1.00) |
0.86 (1.00) |
0.447 (1.00) |
0.217 (1.00) |
0.872 (1.00) |
0.722 (1.00) |
0.513 (1.00) |
0.401 (1.00) |
0.766 (1.00) |
0.119 (1.00) |
0.445 (1.00) |
0.0109 (1.00) |
5q gain | 78 (19%) | 328 |
0.5 (1.00) |
0.505 (1.00) |
0.178 (1.00) |
0.375 (1.00) |
0.849 (1.00) |
0.936 (1.00) |
0.561 (1.00) |
0.794 (1.00) |
0.761 (1.00) |
1 (1.00) |
0.433 (1.00) |
0.12 (1.00) |
0.442 (1.00) |
6p gain | 90 (22%) | 316 |
0.581 (1.00) |
0.563 (1.00) |
0.757 (1.00) |
0.351 (1.00) |
0.499 (1.00) |
0.882 (1.00) |
0.581 (1.00) |
0.0179 (1.00) |
0.226 (1.00) |
0.733 (1.00) |
0.775 (1.00) |
0.224 (1.00) |
0.416 (1.00) |
6q gain | 74 (18%) | 332 |
0.437 (1.00) |
0.712 (1.00) |
0.244 (1.00) |
0.594 (1.00) |
0.288 (1.00) |
0.872 (1.00) |
1 (1.00) |
0.0028 (1.00) |
0.259 (1.00) |
1 (1.00) |
0.824 (1.00) |
0.739 (1.00) |
0.772 (1.00) |
7p gain | 197 (49%) | 209 |
0.0556 (1.00) |
0.061 (1.00) |
0.0634 (1.00) |
0.00127 (1.00) |
0.212 (1.00) |
0.621 (1.00) |
0.171 (1.00) |
0.15 (1.00) |
0.351 (1.00) |
0.383 (1.00) |
0.0325 (1.00) |
0.134 (1.00) |
0.655 (1.00) |
7q gain | 186 (46%) | 220 |
0.804 (1.00) |
0.437 (1.00) |
0.114 (1.00) |
0.0404 (1.00) |
0.299 (1.00) |
0.193 (1.00) |
0.167 (1.00) |
0.0195 (1.00) |
0.438 (1.00) |
0.558 (1.00) |
0.0728 (1.00) |
0.335 (1.00) |
0.402 (1.00) |
8p gain | 106 (26%) | 300 |
0.41 (1.00) |
0.0286 (1.00) |
0.0346 (1.00) |
0.011 (1.00) |
0.794 (1.00) |
0.199 (1.00) |
0.361 (1.00) |
0.146 (1.00) |
0.361 (1.00) |
0.52 (1.00) |
0.643 (1.00) |
0.829 (1.00) |
0.0938 (1.00) |
8q gain | 207 (51%) | 199 |
0.497 (1.00) |
0.263 (1.00) |
0.0211 (1.00) |
0.0967 (1.00) |
0.16 (1.00) |
0.0831 (1.00) |
0.569 (1.00) |
0.22 (1.00) |
0.351 (1.00) |
0.382 (1.00) |
0.302 (1.00) |
0.605 (1.00) |
0.0589 (1.00) |
9p gain | 45 (11%) | 361 |
0.819 (1.00) |
0.166 (1.00) |
0.0687 (1.00) |
0.636 (1.00) |
0.192 (1.00) |
0.189 (1.00) |
0.36 (1.00) |
0.414 (1.00) |
0.339 (1.00) |
0.376 (1.00) |
0.839 (1.00) |
0.75 (1.00) |
0.846 (1.00) |
9q gain | 75 (18%) | 331 |
0.584 (1.00) |
0.895 (1.00) |
0.345 (1.00) |
0.969 (1.00) |
0.0684 (1.00) |
0.0114 (1.00) |
0.138 (1.00) |
0.639 (1.00) |
0.629 (1.00) |
0.134 (1.00) |
0.619 (1.00) |
0.982 (1.00) |
0.462 (1.00) |
10p gain | 59 (15%) | 347 |
0.499 (1.00) |
0.516 (1.00) |
0.156 (1.00) |
0.575 (1.00) |
0.57 (1.00) |
0.712 (1.00) |
0.144 (1.00) |
0.173 (1.00) |
0.691 (1.00) |
1 (1.00) |
0.186 (1.00) |
0.0156 (1.00) |
0.406 (1.00) |
10q gain | 34 (8%) | 372 |
0.329 (1.00) |
0.375 (1.00) |
0.528 (1.00) |
0.475 (1.00) |
0.68 (1.00) |
1 (1.00) |
0.408 (1.00) |
0.771 (1.00) |
1 (1.00) |
1 (1.00) |
0.63 (1.00) |
0.023 (1.00) |
0.686 (1.00) |
11p gain | 61 (15%) | 345 |
0.824 (1.00) |
0.0701 (1.00) |
0.824 (1.00) |
0.195 (1.00) |
0.612 (1.00) |
1 (1.00) |
0.34 (1.00) |
0.0264 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.858 (1.00) |
0.438 (1.00) |
0.786 (1.00) |
11q gain | 74 (18%) | 332 |
0.653 (1.00) |
0.437 (1.00) |
0.908 (1.00) |
0.087 (1.00) |
0.356 (1.00) |
0.345 (1.00) |
0.882 (1.00) |
0.773 (1.00) |
0.902 (1.00) |
0.703 (1.00) |
0.82 (1.00) |
0.901 (1.00) |
0.645 (1.00) |
12p gain | 183 (45%) | 223 |
0.764 (1.00) |
0.681 (1.00) |
0.174 (1.00) |
0.14 (1.00) |
0.396 (1.00) |
0.573 (1.00) |
0.00185 (1.00) |
0.0577 (1.00) |
0.926 (1.00) |
0.389 (1.00) |
0.875 (1.00) |
0.985 (1.00) |
0.981 (1.00) |
12q gain | 126 (31%) | 280 |
0.858 (1.00) |
0.866 (1.00) |
0.175 (1.00) |
0.332 (1.00) |
0.0462 (1.00) |
0.783 (1.00) |
0.00442 (1.00) |
0.147 (1.00) |
0.893 (1.00) |
1 (1.00) |
0.798 (1.00) |
0.804 (1.00) |
0.931 (1.00) |
13q gain | 31 (8%) | 375 |
0.997 (1.00) |
0.555 (1.00) |
0.927 (1.00) |
0.498 (1.00) |
0.601 (1.00) |
0.368 (1.00) |
1 (1.00) |
0.552 (1.00) |
0.453 (1.00) |
1 (1.00) |
0.0145 (1.00) |
0.285 (1.00) |
0.495 (1.00) |
14q gain | 102 (25%) | 304 |
0.017 (1.00) |
0.0452 (1.00) |
0.284 (1.00) |
0.0411 (1.00) |
0.454 (1.00) |
0.211 (1.00) |
0.895 (1.00) |
0.413 (1.00) |
1 (1.00) |
0.738 (1.00) |
0.869 (1.00) |
0.243 (1.00) |
0.9 (1.00) |
15q gain | 88 (22%) | 318 |
0.674 (1.00) |
0.756 (1.00) |
0.485 (1.00) |
0.373 (1.00) |
0.0737 (1.00) |
0.259 (1.00) |
0.487 (1.00) |
0.632 (1.00) |
0.918 (1.00) |
0.475 (1.00) |
0.037 (1.00) |
0.351 (1.00) |
0.888 (1.00) |
16p gain | 68 (17%) | 338 |
0.498 (1.00) |
0.234 (1.00) |
0.436 (1.00) |
0.764 (1.00) |
0.487 (1.00) |
0.402 (1.00) |
0.0899 (1.00) |
0.568 (1.00) |
0.241 (1.00) |
1 (1.00) |
0.123 (1.00) |
0.639 (1.00) |
0.955 (1.00) |
16q gain | 69 (17%) | 337 |
0.96 (1.00) |
0.0521 (1.00) |
0.51 (1.00) |
0.773 (1.00) |
0.861 (1.00) |
0.633 (1.00) |
0.0139 (1.00) |
0.69 (1.00) |
0.286 (1.00) |
1 (1.00) |
0.686 (1.00) |
0.0823 (1.00) |
0.423 (1.00) |
17p gain | 53 (13%) | 353 |
0.318 (1.00) |
0.0571 (1.00) |
0.952 (1.00) |
0.873 (1.00) |
0.986 (1.00) |
0.244 (1.00) |
0.737 (1.00) |
0.923 (1.00) |
0.653 (1.00) |
0.379 (1.00) |
0.00438 (1.00) |
0.0287 (1.00) |
0.751 (1.00) |
17q gain | 129 (32%) | 277 |
0.631 (1.00) |
0.123 (1.00) |
0.34 (1.00) |
0.0729 (1.00) |
0.0435 (1.00) |
0.342 (1.00) |
0.00298 (1.00) |
0.815 (1.00) |
0.764 (1.00) |
0.531 (1.00) |
0.317 (1.00) |
0.076 (1.00) |
0.652 (1.00) |
18p gain | 128 (32%) | 278 |
0.35 (1.00) |
0.167 (1.00) |
0.724 (1.00) |
0.468 (1.00) |
0.335 (1.00) |
0.602 (1.00) |
0.267 (1.00) |
0.563 (1.00) |
0.894 (1.00) |
0.207 (1.00) |
0.663 (1.00) |
0.519 (1.00) |
0.33 (1.00) |
18q gain | 97 (24%) | 309 |
0.59 (1.00) |
0.769 (1.00) |
0.811 (1.00) |
0.566 (1.00) |
0.63 (1.00) |
0.384 (1.00) |
0.423 (1.00) |
0.0872 (1.00) |
0.511 (1.00) |
0.168 (1.00) |
0.0795 (1.00) |
0.945 (1.00) |
0.514 (1.00) |
19p gain | 90 (22%) | 316 |
0.85 (1.00) |
0.469 (1.00) |
0.48 (1.00) |
0.525 (1.00) |
0.383 (1.00) |
0.616 (1.00) |
1 (1.00) |
0.109 (1.00) |
0.107 (1.00) |
0.149 (1.00) |
0.806 (1.00) |
0.155 (1.00) |
0.763 (1.00) |
19q gain | 128 (32%) | 278 |
0.786 (1.00) |
0.308 (1.00) |
0.59 (1.00) |
0.268 (1.00) |
0.277 (1.00) |
0.91 (1.00) |
0.805 (1.00) |
0.285 (1.00) |
0.0478 (1.00) |
0.76 (1.00) |
0.394 (1.00) |
0.0086 (1.00) |
0.664 (1.00) |
20p gain | 209 (51%) | 197 |
0.405 (1.00) |
0.105 (1.00) |
0.392 (1.00) |
0.72 (1.00) |
0.586 (1.00) |
0.395 (1.00) |
0.0846 (1.00) |
0.91 (1.00) |
0.648 (1.00) |
0.383 (1.00) |
0.337 (1.00) |
0.849 (1.00) |
0.61 (1.00) |
20q gain | 198 (49%) | 208 |
0.362 (1.00) |
0.302 (1.00) |
0.543 (1.00) |
0.466 (1.00) |
0.185 (1.00) |
0.414 (1.00) |
0.0216 (1.00) |
0.715 (1.00) |
0.364 (1.00) |
0.567 (1.00) |
0.589 (1.00) |
0.583 (1.00) |
0.665 (1.00) |
21q gain | 46 (11%) | 360 |
0.0647 (1.00) |
0.831 (1.00) |
0.00134 (1.00) |
0.00938 (1.00) |
0.0201 (1.00) |
0.793 (1.00) |
0.277 (1.00) |
0.915 (1.00) |
0.0502 (1.00) |
0.144 (1.00) |
0.748 (1.00) |
0.473 (1.00) |
0.0278 (1.00) |
22q gain | 183 (45%) | 223 |
0.47 (1.00) |
0.052 (1.00) |
0.184 (1.00) |
0.314 (1.00) |
0.495 (1.00) |
0.842 (1.00) |
0.731 (1.00) |
0.468 (1.00) |
0.455 (1.00) |
0.559 (1.00) |
0.48 (1.00) |
0.138 (1.00) |
0.0585 (1.00) |
xq gain | 63 (16%) | 343 |
0.614 (1.00) |
0.751 (1.00) |
0.345 (1.00) |
0.157 (1.00) |
0.913 (1.00) |
0.275 (1.00) |
0.433 (1.00) |
0.75 (1.00) |
0.62 (1.00) |
0.701 (1.00) |
0.985 (1.00) |
0.335 (1.00) |
0.446 (1.00) |
1p loss | 120 (30%) | 286 |
0.364 (1.00) |
0.184 (1.00) |
0.581 (1.00) |
0.548 (1.00) |
0.0439 (1.00) |
0.394 (1.00) |
0.0165 (1.00) |
0.883 (1.00) |
0.89 (1.00) |
0.349 (1.00) |
0.277 (1.00) |
0.961 (1.00) |
0.471 (1.00) |
1q loss | 48 (12%) | 358 |
0.526 (1.00) |
0.548 (1.00) |
0.248 (1.00) |
0.549 (1.00) |
0.156 (1.00) |
0.8 (1.00) |
0.595 (1.00) |
0.809 (1.00) |
0.446 (1.00) |
0.0417 (1.00) |
0.344 (1.00) |
0.934 (1.00) |
0.125 (1.00) |
2p loss | 15 (4%) | 391 |
0.646 (1.00) |
0.185 (1.00) |
0.607 (1.00) |
0.405 (1.00) |
0.134 (1.00) |
0.368 (1.00) |
0.542 (1.00) |
0.583 (1.00) |
1 (1.00) |
0.368 (1.00) |
0.087 (1.00) |
0.935 (1.00) |
1 (1.00) |
2q loss | 30 (7%) | 376 |
0.769 (1.00) |
0.252 (1.00) |
0.859 (1.00) |
0.343 (1.00) |
0.035 (1.00) |
0.249 (1.00) |
0.827 (1.00) |
0.679 (1.00) |
1 (1.00) |
0.607 (1.00) |
0.034 (1.00) |
0.776 (1.00) |
0.686 (1.00) |
3p loss | 252 (62%) | 154 |
0.404 (1.00) |
0.0714 (1.00) |
0.721 (1.00) |
0.988 (1.00) |
0.391 (1.00) |
0.697 (1.00) |
0.237 (1.00) |
0.434 (1.00) |
0.91 (1.00) |
0.547 (1.00) |
0.304 (1.00) |
0.386 (1.00) |
0.582 (1.00) |
3q loss | 61 (15%) | 345 |
0.83 (1.00) |
0.591 (1.00) |
0.922 (1.00) |
0.0509 (1.00) |
0.823 (1.00) |
0.148 (1.00) |
0.525 (1.00) |
0.934 (1.00) |
0.443 (1.00) |
1 (1.00) |
0.107 (1.00) |
0.249 (1.00) |
0.696 (1.00) |
4p loss | 253 (62%) | 153 |
0.272 (1.00) |
0.317 (1.00) |
0.169 (1.00) |
0.343 (1.00) |
0.51 (1.00) |
0.228 (1.00) |
0.407 (1.00) |
0.787 (1.00) |
0.0889 (1.00) |
0.225 (1.00) |
0.568 (1.00) |
0.792 (1.00) |
0.364 (1.00) |
4q loss | 235 (58%) | 171 |
0.292 (1.00) |
0.865 (1.00) |
0.222 (1.00) |
0.221 (1.00) |
0.573 (1.00) |
0.21 (1.00) |
1 (1.00) |
0.439 (1.00) |
0.264 (1.00) |
0.0811 (1.00) |
0.342 (1.00) |
0.28 (1.00) |
0.757 (1.00) |
5p loss | 63 (16%) | 343 |
0.178 (1.00) |
0.505 (1.00) |
0.627 (1.00) |
0.103 (1.00) |
0.32 (1.00) |
1 (1.00) |
0.433 (1.00) |
0.866 (1.00) |
0.62 (1.00) |
0.409 (1.00) |
0.143 (1.00) |
0.205 (1.00) |
0.327 (1.00) |
5q loss | 238 (59%) | 168 |
0.353 (1.00) |
0.494 (1.00) |
0.108 (1.00) |
0.772 (1.00) |
0.272 (1.00) |
0.386 (1.00) |
0.561 (1.00) |
0.303 (1.00) |
0.463 (1.00) |
0.374 (1.00) |
0.562 (1.00) |
0.0885 (1.00) |
0.759 (1.00) |
6p loss | 91 (22%) | 315 |
0.503 (1.00) |
0.776 (1.00) |
0.366 (1.00) |
0.177 (1.00) |
0.305 (1.00) |
0.882 (1.00) |
0.495 (1.00) |
0.454 (1.00) |
1 (1.00) |
1 (1.00) |
0.917 (1.00) |
0.857 (1.00) |
0.357 (1.00) |
6q loss | 94 (23%) | 312 |
0.483 (1.00) |
0.81 (1.00) |
0.281 (1.00) |
0.293 (1.00) |
0.604 (1.00) |
0.941 (1.00) |
1 (1.00) |
0.705 (1.00) |
0.852 (1.00) |
1 (1.00) |
0.76 (1.00) |
0.295 (1.00) |
0.694 (1.00) |
7p loss | 50 (12%) | 356 |
0.199 (1.00) |
0.284 (1.00) |
0.104 (1.00) |
0.473 (1.00) |
0.466 (1.00) |
0.592 (1.00) |
0.295 (1.00) |
0.975 (1.00) |
1 (1.00) |
0.649 (1.00) |
0.0704 (1.00) |
0.986 (1.00) |
0.111 (1.00) |
7q loss | 45 (11%) | 361 |
0.429 (1.00) |
0.637 (1.00) |
0.959 (1.00) |
0.789 (1.00) |
0.929 (1.00) |
0.793 (1.00) |
0.719 (1.00) |
0.802 (1.00) |
1 (1.00) |
1 (1.00) |
0.0624 (1.00) |
0.547 (1.00) |
0.636 (1.00) |
8p loss | 196 (48%) | 210 |
0.485 (1.00) |
0.00809 (1.00) |
0.159 (1.00) |
0.171 (1.00) |
0.826 (1.00) |
0.103 (1.00) |
0.207 (1.00) |
0.44 (1.00) |
0.315 (1.00) |
1 (1.00) |
0.423 (1.00) |
0.435 (1.00) |
0.98 (1.00) |
8q loss | 37 (9%) | 369 |
0.951 (1.00) |
0.222 (1.00) |
0.296 (1.00) |
0.598 (1.00) |
0.459 (1.00) |
0.645 (1.00) |
0.432 (1.00) |
0.0621 (1.00) |
0.317 (1.00) |
0.612 (1.00) |
0.151 (1.00) |
0.0672 (1.00) |
0.718 (1.00) |
9p loss | 255 (63%) | 151 |
0.678 (1.00) |
0.242 (1.00) |
0.157 (1.00) |
0.367 (1.00) |
0.548 (1.00) |
0.761 (1.00) |
0.724 (1.00) |
0.848 (1.00) |
0.054 (1.00) |
1 (1.00) |
0.158 (1.00) |
0.27 (1.00) |
0.98 (1.00) |
9q loss | 194 (48%) | 212 |
0.965 (1.00) |
0.00113 (1.00) |
0.361 (1.00) |
0.212 (1.00) |
0.8 (1.00) |
0.116 (1.00) |
0.731 (1.00) |
0.673 (1.00) |
0.0876 (1.00) |
0.386 (1.00) |
0.85 (1.00) |
0.0334 (1.00) |
0.712 (1.00) |
10p loss | 175 (43%) | 231 |
0.669 (1.00) |
0.838 (1.00) |
0.387 (1.00) |
0.948 (1.00) |
0.558 (1.00) |
0.263 (1.00) |
0.134 (1.00) |
0.267 (1.00) |
0.961 (1.00) |
0.566 (1.00) |
0.227 (1.00) |
0.0775 (1.00) |
0.386 (1.00) |
10q loss | 184 (45%) | 222 |
0.726 (1.00) |
0.185 (1.00) |
0.324 (1.00) |
0.455 (1.00) |
0.784 (1.00) |
0.349 (1.00) |
0.205 (1.00) |
0.243 (1.00) |
0.892 (1.00) |
0.559 (1.00) |
0.731 (1.00) |
0.0888 (1.00) |
0.179 (1.00) |
11p loss | 140 (34%) | 266 |
0.914 (1.00) |
0.131 (1.00) |
0.305 (1.00) |
0.835 (1.00) |
0.407 (1.00) |
0.0408 (1.00) |
0.904 (1.00) |
0.301 (1.00) |
0.532 (1.00) |
1 (1.00) |
0.0752 (1.00) |
0.827 (1.00) |
0.709 (1.00) |
11q loss | 116 (29%) | 290 |
0.499 (1.00) |
0.0547 (1.00) |
0.847 (1.00) |
0.471 (1.00) |
0.0456 (1.00) |
0.728 (1.00) |
0.162 (1.00) |
0.868 (1.00) |
0.697 (1.00) |
1 (1.00) |
0.159 (1.00) |
0.451 (1.00) |
0.122 (1.00) |
12p loss | 31 (8%) | 375 |
0.58 (1.00) |
0.991 (1.00) |
0.697 (1.00) |
0.114 (1.00) |
0.628 (1.00) |
0.85 (1.00) |
0.386 (1.00) |
0.504 (1.00) |
0.0471 (1.00) |
0.611 (1.00) |
0.19 (1.00) |
0.363 (1.00) |
0.769 (1.00) |
12q loss | 38 (9%) | 368 |
0.896 (1.00) |
0.719 (1.00) |
0.745 (1.00) |
0.434 (1.00) |
0.788 (1.00) |
0.645 (1.00) |
0.556 (1.00) |
0.887 (1.00) |
0.0485 (1.00) |
1 (1.00) |
0.341 (1.00) |
0.661 (1.00) |
1 (1.00) |
13q loss | 245 (60%) | 161 |
0.114 (1.00) |
0.43 (1.00) |
0.653 (1.00) |
0.359 (1.00) |
0.715 (1.00) |
0.644 (1.00) |
0.641 (1.00) |
0.928 (1.00) |
0.0077 (1.00) |
1 (1.00) |
0.781 (1.00) |
0.647 (1.00) |
0.612 (1.00) |
14q loss | 137 (34%) | 269 |
0.226 (1.00) |
0.433 (1.00) |
0.455 (1.00) |
0.135 (1.00) |
0.0827 (1.00) |
0.317 (1.00) |
0.274 (1.00) |
0.373 (1.00) |
0.108 (1.00) |
1 (1.00) |
0.547 (1.00) |
0.406 (1.00) |
0.475 (1.00) |
15q loss | 107 (26%) | 299 |
0.981 (1.00) |
0.0827 (1.00) |
0.167 (1.00) |
0.235 (1.00) |
0.0291 (1.00) |
0.521 (1.00) |
0.434 (1.00) |
0.145 (1.00) |
0.365 (1.00) |
0.0896 (1.00) |
0.582 (1.00) |
0.477 (1.00) |
0.723 (1.00) |
16p loss | 125 (31%) | 281 |
0.131 (1.00) |
0.783 (1.00) |
0.491 (1.00) |
0.123 (1.00) |
0.624 (1.00) |
0.515 (1.00) |
0.171 (1.00) |
0.533 (1.00) |
0.0451 (1.00) |
1 (1.00) |
0.247 (1.00) |
0.649 (1.00) |
0.421 (1.00) |
16q loss | 143 (35%) | 263 |
0.344 (1.00) |
0.275 (1.00) |
0.788 (1.00) |
0.371 (1.00) |
0.703 (1.00) |
0.149 (1.00) |
0.0922 (1.00) |
0.382 (1.00) |
0.139 (1.00) |
0.358 (1.00) |
0.398 (1.00) |
0.845 (1.00) |
0.389 (1.00) |
17p loss | 233 (57%) | 173 |
0.6 (1.00) |
0.00933 (1.00) |
0.847 (1.00) |
0.431 (1.00) |
0.0628 (1.00) |
0.916 (1.00) |
1 (1.00) |
0.111 (1.00) |
0.63 (1.00) |
0.0789 (1.00) |
0.00767 (1.00) |
0.11 (1.00) |
0.576 (1.00) |
17q loss | 75 (18%) | 331 |
0.733 (1.00) |
0.089 (1.00) |
0.299 (1.00) |
0.198 (1.00) |
0.0312 (1.00) |
0.816 (1.00) |
0.0177 (1.00) |
0.914 (1.00) |
0.283 (1.00) |
0.247 (1.00) |
0.0918 (1.00) |
0.405 (1.00) |
0.928 (1.00) |
18p loss | 108 (27%) | 298 |
0.809 (1.00) |
0.386 (1.00) |
0.11 (1.00) |
0.29 (1.00) |
0.994 (1.00) |
0.0826 (1.00) |
0.517 (1.00) |
0.652 (1.00) |
0.77 (1.00) |
0.195 (1.00) |
0.546 (1.00) |
0.852 (1.00) |
0.874 (1.00) |
18q loss | 143 (35%) | 263 |
0.55 (1.00) |
0.966 (1.00) |
0.175 (1.00) |
0.219 (1.00) |
0.764 (1.00) |
0.202 (1.00) |
0.282 (1.00) |
0.196 (1.00) |
0.406 (1.00) |
0.552 (1.00) |
0.127 (1.00) |
0.396 (1.00) |
0.451 (1.00) |
19p loss | 136 (33%) | 270 |
0.104 (1.00) |
0.116 (1.00) |
0.562 (1.00) |
0.785 (1.00) |
0.0124 (1.00) |
0.286 (1.00) |
0.395 (1.00) |
0.0197 (1.00) |
0.622 (1.00) |
0.228 (1.00) |
0.426 (1.00) |
0.393 (1.00) |
0.728 (1.00) |
19q loss | 89 (22%) | 317 |
0.698 (1.00) |
0.154 (1.00) |
0.296 (1.00) |
0.914 (1.00) |
0.56 (1.00) |
0.939 (1.00) |
0.0523 (1.00) |
0.011 (1.00) |
0.294 (1.00) |
0.306 (1.00) |
0.0719 (1.00) |
0.01 (1.00) |
0.455 (1.00) |
20p loss | 36 (9%) | 370 |
0.399 (1.00) |
0.841 (1.00) |
0.818 (1.00) |
0.261 (1.00) |
0.403 (1.00) |
0.867 (1.00) |
0.313 (1.00) |
0.583 (1.00) |
1 (1.00) |
1 (1.00) |
0.613 (1.00) |
0.74 (1.00) |
0.399 (1.00) |
20q loss | 40 (10%) | 366 |
0.95 (1.00) |
0.904 (1.00) |
0.0677 (1.00) |
0.24 (1.00) |
0.644 (1.00) |
0.677 (1.00) |
0.701 (1.00) |
0.429 (1.00) |
0.817 (1.00) |
0.618 (1.00) |
0.342 (1.00) |
0.927 (1.00) |
0.282 (1.00) |
21q loss | 217 (53%) | 189 |
0.5 (1.00) |
0.876 (1.00) |
0.554 (1.00) |
0.964 (1.00) |
0.4 (1.00) |
0.0971 (1.00) |
0.000797 (0.828) |
0.994 (1.00) |
0.438 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.441 (1.00) |
0.466 (1.00) |
22q loss | 74 (18%) | 332 |
0.813 (1.00) |
0.0155 (1.00) |
0.139 (1.00) |
0.845 (1.00) |
0.0159 (1.00) |
0.372 (1.00) |
0.767 (1.00) |
0.696 (1.00) |
0.144 (1.00) |
0.464 (1.00) |
0.912 (1.00) |
0.0277 (1.00) |
0.664 (1.00) |
xq loss | 87 (21%) | 319 |
0.812 (1.00) |
0.485 (1.00) |
0.796 (1.00) |
0.0325 (1.00) |
0.467 (1.00) |
0.726 (1.00) |
0.263 (1.00) |
0.621 (1.00) |
0.382 (1.00) |
0.725 (1.00) |
0.369 (1.00) |
0.264 (1.00) |
0.83 (1.00) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = LUSC-TP.merged_data.txt
-
Number of patients = 406
-
Number of significantly arm-level cnvs = 80
-
Number of selected clinical features = 13
-
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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' 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.