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 455 patients, 2 significant findings detected with Q value < 0.25.
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17p gain cnv correlated to 'NUMBERPACKYEARSSMOKED'.
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19p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.
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 | Chi-square test | Fisher's exact test | t-test | Chi-square test | Fisher's exact test | t-test | t-test | Fisher's exact test | |
17p gain | 76 (17%) | 379 |
0.122 (1.00) |
0.0269 (1.00) |
0.567 (1.00) |
0.478 (1.00) |
0.256 (1.00) |
0.207 (1.00) |
0.0587 (1.00) |
0.623 (1.00) |
0.366 (1.00) |
0.139 (1.00) |
0.000172 (0.179) |
0.613 (1.00) |
0.147 (1.00) |
19p gain | 29 (6%) | 426 |
0.215 (1.00) |
0.508 (1.00) |
0.71 (1.00) |
0.128 (1.00) |
0.549 (1.00) |
0.319 (1.00) |
0.343 (1.00) |
0.655 (1.00) |
0.000139 (0.145) |
1 (1.00) |
0.22 (1.00) |
0.943 (1.00) |
0.655 (1.00) |
1p gain | 122 (27%) | 333 |
0.738 (1.00) |
0.00741 (1.00) |
0.85 (1.00) |
0.807 (1.00) |
0.0351 (1.00) |
0.536 (1.00) |
0.751 (1.00) |
0.579 (1.00) |
0.505 (1.00) |
0.614 (1.00) |
0.855 (1.00) |
0.651 (1.00) |
0.569 (1.00) |
1q gain | 269 (59%) | 186 |
0.75 (1.00) |
0.287 (1.00) |
0.741 (1.00) |
0.863 (1.00) |
0.599 (1.00) |
0.599 (1.00) |
0.34 (1.00) |
0.324 (1.00) |
0.242 (1.00) |
0.364 (1.00) |
0.953 (1.00) |
0.626 (1.00) |
0.752 (1.00) |
2p gain | 141 (31%) | 314 |
0.349 (1.00) |
0.0489 (1.00) |
0.801 (1.00) |
0.86 (1.00) |
0.312 (1.00) |
0.895 (1.00) |
0.684 (1.00) |
0.537 (1.00) |
0.494 (1.00) |
0.63 (1.00) |
0.234 (1.00) |
0.147 (1.00) |
0.495 (1.00) |
2q gain | 127 (28%) | 328 |
0.468 (1.00) |
0.699 (1.00) |
0.654 (1.00) |
0.945 (1.00) |
0.338 (1.00) |
0.923 (1.00) |
0.676 (1.00) |
0.417 (1.00) |
0.526 (1.00) |
0.806 (1.00) |
0.153 (1.00) |
0.654 (1.00) |
0.735 (1.00) |
3p gain | 36 (8%) | 419 |
0.807 (1.00) |
0.575 (1.00) |
0.826 (1.00) |
0.235 (1.00) |
0.193 (1.00) |
0.949 (1.00) |
1 (1.00) |
0.289 (1.00) |
0.603 (1.00) |
0.226 (1.00) |
0.315 (1.00) |
0.295 (1.00) |
0.0265 (1.00) |
3q gain | 75 (16%) | 380 |
0.453 (1.00) |
0.649 (1.00) |
0.665 (1.00) |
0.758 (1.00) |
0.563 (1.00) |
0.784 (1.00) |
1 (1.00) |
0.427 (1.00) |
0.786 (1.00) |
0.763 (1.00) |
0.173 (1.00) |
0.278 (1.00) |
0.23 (1.00) |
4p gain | 75 (16%) | 380 |
0.969 (1.00) |
0.0193 (1.00) |
0.0864 (1.00) |
0.31 (1.00) |
0.578 (1.00) |
0.601 (1.00) |
0.801 (1.00) |
0.456 (1.00) |
0.285 (1.00) |
0.551 (1.00) |
0.202 (1.00) |
0.894 (1.00) |
1 (1.00) |
4q gain | 42 (9%) | 413 |
0.125 (1.00) |
0.418 (1.00) |
0.0519 (1.00) |
0.199 (1.00) |
0.862 (1.00) |
0.925 (1.00) |
0.63 (1.00) |
0.695 (1.00) |
0.51 (1.00) |
0.709 (1.00) |
0.0878 (1.00) |
0.74 (1.00) |
0.762 (1.00) |
5p gain | 249 (55%) | 206 |
0.209 (1.00) |
0.0779 (1.00) |
0.253 (1.00) |
0.13 (1.00) |
0.98 (1.00) |
0.515 (1.00) |
0.131 (1.00) |
0.217 (1.00) |
0.334 (1.00) |
0.37 (1.00) |
0.0159 (1.00) |
0.307 (1.00) |
0.498 (1.00) |
5q gain | 109 (24%) | 346 |
0.853 (1.00) |
0.662 (1.00) |
0.947 (1.00) |
0.454 (1.00) |
0.675 (1.00) |
0.691 (1.00) |
0.037 (1.00) |
0.462 (1.00) |
0.368 (1.00) |
0.123 (1.00) |
0.676 (1.00) |
0.99 (1.00) |
0.949 (1.00) |
6p gain | 129 (28%) | 326 |
0.135 (1.00) |
0.377 (1.00) |
0.204 (1.00) |
0.362 (1.00) |
0.294 (1.00) |
0.297 (1.00) |
0.835 (1.00) |
0.738 (1.00) |
0.535 (1.00) |
0.806 (1.00) |
0.624 (1.00) |
0.724 (1.00) |
0.465 (1.00) |
6q gain | 56 (12%) | 399 |
0.419 (1.00) |
0.302 (1.00) |
0.751 (1.00) |
1 (1.00) |
0.87 (1.00) |
0.709 (1.00) |
0.668 (1.00) |
0.388 (1.00) |
0.956 (1.00) |
0.495 (1.00) |
0.834 (1.00) |
0.708 (1.00) |
0.663 (1.00) |
7p gain | 236 (52%) | 219 |
0.406 (1.00) |
0.044 (1.00) |
0.337 (1.00) |
0.374 (1.00) |
0.00316 (1.00) |
0.699 (1.00) |
1 (1.00) |
0.687 (1.00) |
0.0993 (1.00) |
0.504 (1.00) |
0.119 (1.00) |
0.312 (1.00) |
0.672 (1.00) |
7q gain | 195 (43%) | 260 |
0.982 (1.00) |
0.00488 (1.00) |
0.179 (1.00) |
0.793 (1.00) |
0.00483 (1.00) |
0.318 (1.00) |
0.776 (1.00) |
0.922 (1.00) |
0.245 (1.00) |
0.184 (1.00) |
0.278 (1.00) |
0.536 (1.00) |
0.319 (1.00) |
8p gain | 113 (25%) | 342 |
0.488 (1.00) |
0.0719 (1.00) |
0.815 (1.00) |
0.0753 (1.00) |
0.793 (1.00) |
0.956 (1.00) |
0.00662 (1.00) |
0.287 (1.00) |
0.812 (1.00) |
0.436 (1.00) |
0.487 (1.00) |
0.195 (1.00) |
0.233 (1.00) |
8q gain | 219 (48%) | 236 |
0.0356 (1.00) |
0.0292 (1.00) |
0.901 (1.00) |
0.218 (1.00) |
0.123 (1.00) |
0.783 (1.00) |
0.452 (1.00) |
0.909 (1.00) |
0.0608 (1.00) |
0.824 (1.00) |
0.928 (1.00) |
0.0784 (1.00) |
0.645 (1.00) |
9p gain | 40 (9%) | 415 |
0.238 (1.00) |
0.569 (1.00) |
0.833 (1.00) |
0.204 (1.00) |
0.363 (1.00) |
0.632 (1.00) |
0.251 (1.00) |
0.392 (1.00) |
0.159 (1.00) |
0.706 (1.00) |
0.674 (1.00) |
0.635 (1.00) |
0.332 (1.00) |
9q gain | 28 (6%) | 427 |
0.121 (1.00) |
0.509 (1.00) |
0.281 (1.00) |
0.727 (1.00) |
0.956 (1.00) |
0.308 (1.00) |
0.845 (1.00) |
0.765 (1.00) |
0.993 (1.00) |
1 (1.00) |
0.389 (1.00) |
0.911 (1.00) |
1 (1.00) |
10p gain | 101 (22%) | 354 |
0.794 (1.00) |
0.131 (1.00) |
0.611 (1.00) |
0.11 (1.00) |
0.0234 (1.00) |
0.713 (1.00) |
0.00152 (1.00) |
0.37 (1.00) |
0.65 (1.00) |
0.187 (1.00) |
0.229 (1.00) |
0.824 (1.00) |
0.111 (1.00) |
10q gain | 72 (16%) | 383 |
0.876 (1.00) |
0.142 (1.00) |
0.391 (1.00) |
0.179 (1.00) |
0.0377 (1.00) |
0.19 (1.00) |
0.00305 (1.00) |
0.171 (1.00) |
0.448 (1.00) |
0.552 (1.00) |
0.913 (1.00) |
0.659 (1.00) |
0.458 (1.00) |
11p gain | 87 (19%) | 368 |
0.452 (1.00) |
0.896 (1.00) |
0.313 (1.00) |
0.377 (1.00) |
0.0814 (1.00) |
0.704 (1.00) |
0.0556 (1.00) |
0.393 (1.00) |
0.571 (1.00) |
0.778 (1.00) |
0.141 (1.00) |
0.435 (1.00) |
0.937 (1.00) |
11q gain | 107 (24%) | 348 |
0.789 (1.00) |
0.0293 (1.00) |
0.439 (1.00) |
0.679 (1.00) |
0.521 (1.00) |
0.375 (1.00) |
0.32 (1.00) |
0.261 (1.00) |
0.266 (1.00) |
0.6 (1.00) |
0.0585 (1.00) |
0.121 (1.00) |
1 (1.00) |
12p gain | 123 (27%) | 332 |
0.337 (1.00) |
0.0191 (1.00) |
0.0969 (1.00) |
0.898 (1.00) |
0.628 (1.00) |
0.504 (1.00) |
0.112 (1.00) |
0.981 (1.00) |
0.501 (1.00) |
1 (1.00) |
0.159 (1.00) |
0.0618 (1.00) |
0.378 (1.00) |
12q gain | 118 (26%) | 337 |
0.885 (1.00) |
0.108 (1.00) |
0.72 (1.00) |
0.735 (1.00) |
0.648 (1.00) |
0.322 (1.00) |
0.284 (1.00) |
0.896 (1.00) |
0.412 (1.00) |
1 (1.00) |
0.384 (1.00) |
0.00258 (1.00) |
0.359 (1.00) |
13q gain | 41 (9%) | 414 |
0.592 (1.00) |
0.793 (1.00) |
0.203 (1.00) |
0.536 (1.00) |
0.427 (1.00) |
0.0178 (1.00) |
1 (1.00) |
0.74 (1.00) |
0.98 (1.00) |
1 (1.00) |
0.288 (1.00) |
0.539 (1.00) |
0.398 (1.00) |
14q gain | 111 (24%) | 344 |
0.0964 (1.00) |
0.212 (1.00) |
0.974 (1.00) |
0.975 (1.00) |
0.244 (1.00) |
0.00465 (1.00) |
0.381 (1.00) |
0.287 (1.00) |
0.693 (1.00) |
0.123 (1.00) |
0.124 (1.00) |
0.533 (1.00) |
0.357 (1.00) |
15q gain | 32 (7%) | 423 |
0.161 (1.00) |
0.892 (1.00) |
0.0326 (1.00) |
0.474 (1.00) |
0.0148 (1.00) |
0.283 (1.00) |
0.273 (1.00) |
0.909 (1.00) |
0.335 (1.00) |
0.652 (1.00) |
0.634 (1.00) |
0.619 (1.00) |
0.884 (1.00) |
16p gain | 115 (25%) | 340 |
0.359 (1.00) |
0.912 (1.00) |
0.886 (1.00) |
0.687 (1.00) |
0.559 (1.00) |
0.509 (1.00) |
0.914 (1.00) |
0.201 (1.00) |
0.371 (1.00) |
0.614 (1.00) |
0.187 (1.00) |
0.959 (1.00) |
0.906 (1.00) |
16q gain | 86 (19%) | 369 |
0.285 (1.00) |
0.768 (1.00) |
0.87 (1.00) |
0.728 (1.00) |
0.742 (1.00) |
0.92 (1.00) |
0.633 (1.00) |
0.993 (1.00) |
0.317 (1.00) |
0.778 (1.00) |
0.15 (1.00) |
0.576 (1.00) |
0.556 (1.00) |
17q gain | 172 (38%) | 283 |
0.562 (1.00) |
0.0799 (1.00) |
0.228 (1.00) |
0.311 (1.00) |
0.403 (1.00) |
0.454 (1.00) |
0.846 (1.00) |
0.503 (1.00) |
0.173 (1.00) |
1 (1.00) |
0.0308 (1.00) |
0.878 (1.00) |
0.0174 (1.00) |
18p gain | 87 (19%) | 368 |
0.615 (1.00) |
0.423 (1.00) |
0.316 (1.00) |
0.905 (1.00) |
0.937 (1.00) |
0.496 (1.00) |
0.404 (1.00) |
0.571 (1.00) |
0.666 (1.00) |
0.778 (1.00) |
0.00419 (1.00) |
0.595 (1.00) |
0.599 (1.00) |
18q gain | 62 (14%) | 393 |
0.49 (1.00) |
0.0808 (1.00) |
0.794 (1.00) |
0.907 (1.00) |
0.629 (1.00) |
0.788 (1.00) |
0.412 (1.00) |
0.233 (1.00) |
0.267 (1.00) |
0.753 (1.00) |
0.011 (1.00) |
0.579 (1.00) |
0.0561 (1.00) |
19q gain | 65 (14%) | 390 |
0.638 (1.00) |
0.925 (1.00) |
0.55 (1.00) |
0.117 (1.00) |
0.72 (1.00) |
0.872 (1.00) |
0.0104 (1.00) |
0.282 (1.00) |
0.25 (1.00) |
0.336 (1.00) |
0.0881 (1.00) |
0.999 (1.00) |
0.936 (1.00) |
20p gain | 151 (33%) | 304 |
0.611 (1.00) |
0.997 (1.00) |
0.336 (1.00) |
0.264 (1.00) |
0.265 (1.00) |
0.204 (1.00) |
0.921 (1.00) |
0.138 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.0367 (1.00) |
0.0439 (1.00) |
0.643 (1.00) |
20q gain | 174 (38%) | 281 |
0.531 (1.00) |
0.155 (1.00) |
0.421 (1.00) |
0.27 (1.00) |
0.59 (1.00) |
0.36 (1.00) |
0.562 (1.00) |
0.035 (1.00) |
0.189 (1.00) |
0.25 (1.00) |
0.00271 (1.00) |
0.416 (1.00) |
0.796 (1.00) |
21q gain | 84 (18%) | 371 |
0.169 (1.00) |
0.366 (1.00) |
0.656 (1.00) |
0.873 (1.00) |
0.0509 (1.00) |
0.914 (1.00) |
0.115 (1.00) |
0.409 (1.00) |
0.343 (1.00) |
1 (1.00) |
0.525 (1.00) |
0.655 (1.00) |
0.94 (1.00) |
22q gain | 58 (13%) | 397 |
0.117 (1.00) |
0.197 (1.00) |
0.517 (1.00) |
0.232 (1.00) |
0.307 (1.00) |
0.745 (1.00) |
0.205 (1.00) |
0.356 (1.00) |
0.53 (1.00) |
0.498 (1.00) |
0.759 (1.00) |
0.13 (1.00) |
0.496 (1.00) |
xq gain | 66 (15%) | 389 |
0.498 (1.00) |
0.847 (1.00) |
0.723 (1.00) |
0.633 (1.00) |
0.85 (1.00) |
0.722 (1.00) |
0.286 (1.00) |
0.356 (1.00) |
0.436 (1.00) |
1 (1.00) |
0.385 (1.00) |
0.312 (1.00) |
0.527 (1.00) |
1p loss | 74 (16%) | 381 |
0.156 (1.00) |
0.616 (1.00) |
0.0133 (1.00) |
0.139 (1.00) |
0.00376 (1.00) |
0.268 (1.00) |
0.162 (1.00) |
0.729 (1.00) |
0.376 (1.00) |
0.761 (1.00) |
0.38 (1.00) |
0.475 (1.00) |
0.644 (1.00) |
1q loss | 27 (6%) | 428 |
0.836 (1.00) |
0.579 (1.00) |
0.103 (1.00) |
1 (1.00) |
0.217 (1.00) |
0.382 (1.00) |
0.559 (1.00) |
0.257 (1.00) |
0.96 (1.00) |
0.121 (1.00) |
0.0525 (1.00) |
0.898 (1.00) |
1 (1.00) |
2p loss | 24 (5%) | 431 |
0.71 (1.00) |
0.281 (1.00) |
0.00085 (0.881) |
0.777 (1.00) |
0.711 (1.00) |
0.969 (1.00) |
0.407 (1.00) |
0.983 (1.00) |
0.679 (1.00) |
1 (1.00) |
0.963 (1.00) |
0.784 (1.00) |
0.366 (1.00) |
2q loss | 23 (5%) | 432 |
0.341 (1.00) |
0.942 (1.00) |
0.34 (1.00) |
0.828 (1.00) |
0.775 (1.00) |
0.893 (1.00) |
0.526 (1.00) |
0.621 (1.00) |
0.0763 (1.00) |
0.615 (1.00) |
0.00306 (1.00) |
0.717 (1.00) |
0.726 (1.00) |
3p loss | 191 (42%) | 264 |
0.231 (1.00) |
0.355 (1.00) |
0.531 (1.00) |
0.0659 (1.00) |
0.379 (1.00) |
0.709 (1.00) |
1 (1.00) |
0.17 (1.00) |
0.641 (1.00) |
1 (1.00) |
0.241 (1.00) |
0.0599 (1.00) |
0.204 (1.00) |
3q loss | 132 (29%) | 323 |
0.244 (1.00) |
0.252 (1.00) |
0.586 (1.00) |
0.635 (1.00) |
0.0874 (1.00) |
0.449 (1.00) |
0.756 (1.00) |
0.137 (1.00) |
0.496 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.0454 (1.00) |
0.504 (1.00) |
4p loss | 106 (23%) | 349 |
0.428 (1.00) |
0.177 (1.00) |
0.523 (1.00) |
0.967 (1.00) |
0.207 (1.00) |
0.824 (1.00) |
0.579 (1.00) |
0.2 (1.00) |
0.461 (1.00) |
0.598 (1.00) |
0.321 (1.00) |
0.039 (1.00) |
0.15 (1.00) |
4q loss | 121 (27%) | 334 |
0.827 (1.00) |
0.203 (1.00) |
0.0999 (1.00) |
0.963 (1.00) |
0.0112 (1.00) |
0.729 (1.00) |
0.457 (1.00) |
0.0869 (1.00) |
0.489 (1.00) |
0.804 (1.00) |
0.275 (1.00) |
0.227 (1.00) |
0.125 (1.00) |
5p loss | 38 (8%) | 417 |
0.394 (1.00) |
0.352 (1.00) |
0.719 (1.00) |
0.975 (1.00) |
0.679 (1.00) |
0.916 (1.00) |
0.0165 (1.00) |
0.191 (1.00) |
0.286 (1.00) |
1 (1.00) |
0.586 (1.00) |
0.206 (1.00) |
0.72 (1.00) |
5q loss | 133 (29%) | 322 |
0.0401 (1.00) |
0.00481 (1.00) |
0.749 (1.00) |
0.974 (1.00) |
0.416 (1.00) |
0.482 (1.00) |
0.013 (1.00) |
0.377 (1.00) |
0.32 (1.00) |
0.339 (1.00) |
0.0254 (1.00) |
0.898 (1.00) |
0.0568 (1.00) |
6p loss | 94 (21%) | 361 |
0.144 (1.00) |
0.733 (1.00) |
0.265 (1.00) |
0.134 (1.00) |
0.514 (1.00) |
0.876 (1.00) |
0.486 (1.00) |
0.0922 (1.00) |
0.946 (1.00) |
0.782 (1.00) |
0.107 (1.00) |
0.419 (1.00) |
0.851 (1.00) |
6q loss | 193 (42%) | 262 |
0.924 (1.00) |
0.122 (1.00) |
0.719 (1.00) |
0.671 (1.00) |
0.519 (1.00) |
0.825 (1.00) |
0.298 (1.00) |
0.137 (1.00) |
0.942 (1.00) |
0.656 (1.00) |
0.325 (1.00) |
0.042 (1.00) |
0.878 (1.00) |
7p loss | 30 (7%) | 425 |
0.541 (1.00) |
0.792 (1.00) |
0.958 (1.00) |
0.911 (1.00) |
0.887 (1.00) |
0.772 (1.00) |
0.261 (1.00) |
0.659 (1.00) |
0.829 (1.00) |
0.641 (1.00) |
0.844 (1.00) |
0.71 (1.00) |
0.414 (1.00) |
7q loss | 35 (8%) | 420 |
0.323 (1.00) |
0.199 (1.00) |
0.87 (1.00) |
0.885 (1.00) |
0.759 (1.00) |
0.427 (1.00) |
0.861 (1.00) |
0.713 (1.00) |
0.678 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.377 (1.00) |
0.626 (1.00) |
8p loss | 176 (39%) | 279 |
0.991 (1.00) |
0.814 (1.00) |
0.927 (1.00) |
0.541 (1.00) |
0.979 (1.00) |
0.417 (1.00) |
0.0673 (1.00) |
0.802 (1.00) |
0.0292 (1.00) |
0.175 (1.00) |
0.212 (1.00) |
0.663 (1.00) |
0.163 (1.00) |
8q loss | 49 (11%) | 406 |
0.748 (1.00) |
0.572 (1.00) |
0.125 (1.00) |
0.503 (1.00) |
0.202 (1.00) |
0.0721 (1.00) |
0.29 (1.00) |
0.102 (1.00) |
0.136 (1.00) |
0.715 (1.00) |
0.389 (1.00) |
0.297 (1.00) |
0.926 (1.00) |
9p loss | 235 (52%) | 220 |
0.104 (1.00) |
0.345 (1.00) |
0.583 (1.00) |
0.931 (1.00) |
0.0524 (1.00) |
0.527 (1.00) |
0.0609 (1.00) |
0.434 (1.00) |
0.635 (1.00) |
0.824 (1.00) |
0.538 (1.00) |
0.789 (1.00) |
0.965 (1.00) |
9q loss | 221 (49%) | 234 |
0.657 (1.00) |
0.849 (1.00) |
0.844 (1.00) |
0.352 (1.00) |
0.376 (1.00) |
0.787 (1.00) |
0.779 (1.00) |
0.741 (1.00) |
0.351 (1.00) |
0.659 (1.00) |
0.257 (1.00) |
0.518 (1.00) |
0.935 (1.00) |
10p loss | 98 (22%) | 357 |
0.523 (1.00) |
0.98 (1.00) |
0.609 (1.00) |
0.161 (1.00) |
0.371 (1.00) |
0.906 (1.00) |
0.0116 (1.00) |
0.611 (1.00) |
0.0471 (1.00) |
0.274 (1.00) |
0.545 (1.00) |
0.62 (1.00) |
0.82 (1.00) |
10q loss | 118 (26%) | 337 |
0.293 (1.00) |
0.675 (1.00) |
0.509 (1.00) |
0.2 (1.00) |
0.189 (1.00) |
0.782 (1.00) |
0.108 (1.00) |
0.468 (1.00) |
0.0193 (1.00) |
0.122 (1.00) |
0.11 (1.00) |
0.264 (1.00) |
0.612 (1.00) |
11p loss | 104 (23%) | 351 |
0.902 (1.00) |
0.0555 (1.00) |
0.397 (1.00) |
0.416 (1.00) |
0.445 (1.00) |
0.426 (1.00) |
0.000497 (0.516) |
0.809 (1.00) |
0.542 (1.00) |
0.433 (1.00) |
0.689 (1.00) |
0.137 (1.00) |
0.427 (1.00) |
11q loss | 83 (18%) | 372 |
0.604 (1.00) |
0.702 (1.00) |
0.525 (1.00) |
0.904 (1.00) |
0.983 (1.00) |
0.31 (1.00) |
0.00332 (1.00) |
0.875 (1.00) |
0.783 (1.00) |
0.394 (1.00) |
0.896 (1.00) |
0.337 (1.00) |
0.705 (1.00) |
12p loss | 97 (21%) | 358 |
0.177 (1.00) |
0.415 (1.00) |
0.522 (1.00) |
0.637 (1.00) |
0.942 (1.00) |
0.127 (1.00) |
0.0119 (1.00) |
0.0709 (1.00) |
0.866 (1.00) |
0.588 (1.00) |
0.126 (1.00) |
0.443 (1.00) |
0.88 (1.00) |
12q loss | 85 (19%) | 370 |
0.149 (1.00) |
0.739 (1.00) |
0.652 (1.00) |
0.56 (1.00) |
0.308 (1.00) |
0.102 (1.00) |
0.00773 (1.00) |
0.217 (1.00) |
0.39 (1.00) |
0.393 (1.00) |
0.121 (1.00) |
0.906 (1.00) |
0.852 (1.00) |
13q loss | 218 (48%) | 237 |
0.846 (1.00) |
0.184 (1.00) |
0.614 (1.00) |
0.362 (1.00) |
0.443 (1.00) |
0.509 (1.00) |
0.851 (1.00) |
0.804 (1.00) |
0.521 (1.00) |
0.381 (1.00) |
0.0509 (1.00) |
0.164 (1.00) |
0.582 (1.00) |
14q loss | 103 (23%) | 352 |
0.477 (1.00) |
0.136 (1.00) |
0.505 (1.00) |
0.363 (1.00) |
0.0532 (1.00) |
0.701 (1.00) |
0.262 (1.00) |
0.552 (1.00) |
0.784 (1.00) |
0.796 (1.00) |
0.132 (1.00) |
0.38 (1.00) |
0.225 (1.00) |
15q loss | 214 (47%) | 241 |
0.639 (1.00) |
0.000984 (1.00) |
0.756 (1.00) |
0.986 (1.00) |
0.715 (1.00) |
0.713 (1.00) |
0.573 (1.00) |
0.22 (1.00) |
0.0277 (1.00) |
0.659 (1.00) |
0.324 (1.00) |
0.175 (1.00) |
0.746 (1.00) |
16p loss | 100 (22%) | 355 |
0.553 (1.00) |
0.726 (1.00) |
0.0415 (1.00) |
0.418 (1.00) |
0.0349 (1.00) |
0.312 (1.00) |
0.428 (1.00) |
0.961 (1.00) |
0.861 (1.00) |
0.791 (1.00) |
0.61 (1.00) |
0.78 (1.00) |
0.615 (1.00) |
16q loss | 127 (28%) | 328 |
0.629 (1.00) |
0.404 (1.00) |
0.556 (1.00) |
0.986 (1.00) |
0.286 (1.00) |
0.621 (1.00) |
0.403 (1.00) |
0.274 (1.00) |
0.439 (1.00) |
0.806 (1.00) |
0.395 (1.00) |
0.886 (1.00) |
0.283 (1.00) |
17p loss | 191 (42%) | 264 |
0.923 (1.00) |
0.15 (1.00) |
0.393 (1.00) |
0.459 (1.00) |
0.739 (1.00) |
0.451 (1.00) |
0.154 (1.00) |
0.631 (1.00) |
0.351 (1.00) |
0.0396 (1.00) |
0.0213 (1.00) |
0.0139 (1.00) |
0.951 (1.00) |
17q loss | 51 (11%) | 404 |
0.335 (1.00) |
0.477 (1.00) |
0.295 (1.00) |
0.226 (1.00) |
0.286 (1.00) |
0.973 (1.00) |
0.657 (1.00) |
0.681 (1.00) |
0.664 (1.00) |
1 (1.00) |
0.914 (1.00) |
0.109 (1.00) |
0.617 (1.00) |
18p loss | 155 (34%) | 300 |
0.403 (1.00) |
0.0638 (1.00) |
0.0335 (1.00) |
0.345 (1.00) |
0.331 (1.00) |
0.0343 (1.00) |
0.00732 (1.00) |
0.296 (1.00) |
0.706 (1.00) |
0.356 (1.00) |
0.0172 (1.00) |
0.00469 (1.00) |
0.149 (1.00) |
18q loss | 190 (42%) | 265 |
0.0505 (1.00) |
0.49 (1.00) |
0.0176 (1.00) |
0.217 (1.00) |
0.0717 (1.00) |
0.308 (1.00) |
0.0364 (1.00) |
0.929 (1.00) |
0.646 (1.00) |
0.26 (1.00) |
0.0869 (1.00) |
0.125 (1.00) |
0.00345 (1.00) |
19p loss | 221 (49%) | 234 |
0.0309 (1.00) |
0.0784 (1.00) |
0.0631 (1.00) |
0.477 (1.00) |
0.15 (1.00) |
0.0514 (1.00) |
0.0114 (1.00) |
0.619 (1.00) |
0.749 (1.00) |
0.183 (1.00) |
0.946 (1.00) |
0.369 (1.00) |
0.245 (1.00) |
19q loss | 142 (31%) | 313 |
0.132 (1.00) |
0.131 (1.00) |
0.109 (1.00) |
0.143 (1.00) |
0.412 (1.00) |
0.0173 (1.00) |
0.225 (1.00) |
0.968 (1.00) |
0.688 (1.00) |
0.334 (1.00) |
0.51 (1.00) |
0.779 (1.00) |
0.254 (1.00) |
20p loss | 107 (24%) | 348 |
0.213 (1.00) |
0.64 (1.00) |
0.6 (1.00) |
0.419 (1.00) |
0.256 (1.00) |
0.332 (1.00) |
0.825 (1.00) |
0.502 (1.00) |
0.382 (1.00) |
0.794 (1.00) |
0.433 (1.00) |
0.174 (1.00) |
0.863 (1.00) |
20q loss | 64 (14%) | 391 |
0.762 (1.00) |
0.407 (1.00) |
0.374 (1.00) |
0.443 (1.00) |
0.411 (1.00) |
0.163 (1.00) |
0.787 (1.00) |
0.00245 (1.00) |
0.0655 (1.00) |
0.336 (1.00) |
0.795 (1.00) |
0.481 (1.00) |
0.571 (1.00) |
21q loss | 148 (33%) | 307 |
0.492 (1.00) |
0.448 (1.00) |
0.686 (1.00) |
0.808 (1.00) |
0.912 (1.00) |
0.665 (1.00) |
0.108 (1.00) |
0.877 (1.00) |
0.0752 (1.00) |
0.153 (1.00) |
0.16 (1.00) |
0.176 (1.00) |
0.781 (1.00) |
22q loss | 194 (43%) | 261 |
0.506 (1.00) |
0.00174 (1.00) |
0.624 (1.00) |
0.998 (1.00) |
0.98 (1.00) |
0.272 (1.00) |
0.0371 (1.00) |
0.0442 (1.00) |
0.294 (1.00) |
0.822 (1.00) |
0.915 (1.00) |
0.00449 (1.00) |
0.732 (1.00) |
xq loss | 55 (12%) | 400 |
0.632 (1.00) |
0.268 (1.00) |
0.26 (1.00) |
0.711 (1.00) |
0.953 (1.00) |
0.464 (1.00) |
0.199 (1.00) |
0.945 (1.00) |
0.0757 (1.00) |
0.158 (1.00) |
0.543 (1.00) |
0.528 (1.00) |
0.808 (1.00) |
P value = 0.000172 (t-test), Q value = 0.18
Table S1. Gene #30: '17p gain' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 315 | 42.2 (27.3) |
17P GAIN MUTATED | 53 | 56.7 (29.6) |
17P GAIN WILD-TYPE | 262 | 39.3 (25.9) |
Figure S1. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
![](D30V11.png)
P value = 0.000139 (Chi-square test), Q value = 0.14
Table S2. Gene #34: '19p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'
nPatients | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG SIGNET RING ADENOCARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 13 | 92 | 292 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 4 | 7 |
19P GAIN MUTATED | 2 | 4 | 17 | 0 | 0 | 0 | 1 | 0 | 2 | 1 | 2 | 0 |
19P GAIN WILD-TYPE | 11 | 88 | 275 | 4 | 17 | 2 | 2 | 2 | 16 | 0 | 2 | 7 |
Figure S2. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'
![](D34V9.png)
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = LUAD-TP.merged_data.txt
-
Number of patients = 455
-
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.