This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 79 arm-level results and 14 clinical features across 325 patients, 11 significant findings detected with Q value < 0.25.
-
1p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
-
2q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
-
11p gain cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
-
17p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
-
19p gain cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE' and 'HISTOLOGICAL.TYPE'.
-
21q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
-
12p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
-
12q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
-
16q loss cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
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Xq loss cnv correlated to 'HISTOLOGICAL.TYPE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 11 significant findings detected.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET |
COMPLETENESS OF RESECTION |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | Fisher's exact test | t-test | Fisher's exact test | |
19p gain | 0 (0%) | 292 |
0.438 (1.00) |
0.227 (1.00) |
0.675 (1.00) |
1.77e-06 (0.00192) |
5.63e-06 (0.0061) |
0.634 (1.00) |
0.378 (1.00) |
0.566 (1.00) |
0.63 (1.00) |
0.309 (1.00) |
0.592 (1.00) |
0.656 (1.00) |
0.83 (1.00) |
0.89 (1.00) |
1p gain | 0 (0%) | 302 |
0.858 (1.00) |
0.853 (1.00) |
0.0489 (1.00) |
2.88e-08 (3.14e-05) |
0.0379 (1.00) |
1 (1.00) |
0.0321 (1.00) |
0.017 (1.00) |
0.56 (1.00) |
0.566 (1.00) |
0.368 (1.00) |
0.415 (1.00) |
0.602 (1.00) |
|
2q gain | 0 (0%) | 289 |
0.198 (1.00) |
0.474 (1.00) |
0.425 (1.00) |
0.903 (1.00) |
8.58e-05 (0.0926) |
0.208 (1.00) |
0.486 (1.00) |
0.168 (1.00) |
0.00299 (1.00) |
0.11 (1.00) |
0.13 (1.00) |
0.938 (1.00) |
0.295 (1.00) |
1 (1.00) |
11p gain | 0 (0%) | 305 |
0.902 (1.00) |
0.32 (1.00) |
0.426 (1.00) |
2e-06 (0.00217) |
0.954 (1.00) |
0.0123 (1.00) |
0.324 (1.00) |
1 (1.00) |
0.516 (1.00) |
0.508 (1.00) |
0.148 (1.00) |
0.851 (1.00) |
0.541 (1.00) |
0.785 (1.00) |
17p gain | 0 (0%) | 316 |
0.346 (1.00) |
0.839 (1.00) |
0.118 (1.00) |
3.79e-07 (0.000412) |
0.55 (1.00) |
0.419 (1.00) |
0.294 (1.00) |
0.095 (1.00) |
1 (1.00) |
0.948 (1.00) |
0.143 (1.00) |
0.0232 (1.00) |
0.5 (1.00) |
|
21q gain | 0 (0%) | 307 |
0.268 (1.00) |
0.682 (1.00) |
1 (1.00) |
0.949 (1.00) |
5.96e-05 (0.0645) |
0.239 (1.00) |
0.249 (1.00) |
0.72 (1.00) |
0.191 (1.00) |
0.471 (1.00) |
0.865 (1.00) |
0.488 (1.00) |
0.631 (1.00) |
0.0937 (1.00) |
12p loss | 0 (0%) | 321 |
0.51 (1.00) |
0.0145 (1.00) |
0.27 (1.00) |
1.32e-16 (1.44e-13) |
0.532 (1.00) |
1 (1.00) |
0.364 (1.00) |
0.549 (1.00) |
1 (1.00) |
0.256 (1.00) |
0.339 (1.00) |
1 (1.00) |
||
12q loss | 0 (0%) | 321 |
0.864 (1.00) |
0.185 (1.00) |
0.27 (1.00) |
1.32e-16 (1.44e-13) |
0.185 (1.00) |
0.543 (1.00) |
0.364 (1.00) |
0.35 (1.00) |
1 (1.00) |
0.195 (1.00) |
0.327 (1.00) |
1 (1.00) |
||
16q loss | 0 (0%) | 265 |
0.133 (1.00) |
0.164 (1.00) |
0.141 (1.00) |
1.77e-06 (0.00192) |
0.674 (1.00) |
0.8 (1.00) |
0.434 (1.00) |
0.138 (1.00) |
0.792 (1.00) |
0.433 (1.00) |
0.0755 (1.00) |
0.299 (1.00) |
0.59 (1.00) |
0.251 (1.00) |
Xq loss | 0 (0%) | 312 |
0.884 (1.00) |
0.284 (1.00) |
0.329 (1.00) |
0.949 (1.00) |
6.63e-05 (0.0716) |
0.729 (1.00) |
0.15 (1.00) |
1 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.681 (1.00) |
1 (1.00) |
0.788 (1.00) |
1 (1.00) |
1q gain | 0 (0%) | 256 |
0.386 (1.00) |
0.468 (1.00) |
0.878 (1.00) |
0.358 (1.00) |
0.00453 (1.00) |
0.182 (1.00) |
0.832 (1.00) |
0.267 (1.00) |
0.452 (1.00) |
1 (1.00) |
0.259 (1.00) |
1 (1.00) |
0.52 (1.00) |
0.558 (1.00) |
2p gain | 0 (0%) | 249 |
0.515 (1.00) |
0.875 (1.00) |
0.0706 (1.00) |
0.126 (1.00) |
0.0106 (1.00) |
0.125 (1.00) |
0.14 (1.00) |
0.173 (1.00) |
0.103 (1.00) |
0.137 (1.00) |
0.021 (1.00) |
0.726 (1.00) |
0.0201 (1.00) |
0.789 (1.00) |
3p gain | 0 (0%) | 291 |
0.495 (1.00) |
0.127 (1.00) |
0.0609 (1.00) |
0.197 (1.00) |
0.977 (1.00) |
0.0403 (1.00) |
0.796 (1.00) |
0.498 (1.00) |
0.52 (1.00) |
1 (1.00) |
0.356 (1.00) |
0.0688 (1.00) |
0.0561 (1.00) |
0.791 (1.00) |
3q gain | 0 (0%) | 178 |
0.876 (1.00) |
0.211 (1.00) |
0.899 (1.00) |
0.248 (1.00) |
0.352 (1.00) |
0.373 (1.00) |
0.871 (1.00) |
0.437 (1.00) |
0.669 (1.00) |
0.554 (1.00) |
0.771 (1.00) |
0.0417 (1.00) |
0.0246 (1.00) |
0.878 (1.00) |
4p gain | 0 (0%) | 311 |
0.33 (1.00) |
0.636 (1.00) |
0.0248 (1.00) |
0.712 (1.00) |
0.763 (1.00) |
0.131 (1.00) |
1 (1.00) |
0.692 (1.00) |
0.632 (1.00) |
1 (1.00) |
0.354 (1.00) |
0.758 (1.00) |
0.404 (1.00) |
0.199 (1.00) |
4q gain | 0 (0%) | 319 |
0.922 (1.00) |
0.14 (1.00) |
0.344 (1.00) |
0.188 (1.00) |
0.306 (1.00) |
0.663 (1.00) |
1 (1.00) |
0.266 (1.00) |
1 (1.00) |
0.154 (1.00) |
0.122 (1.00) |
1 (1.00) |
||
5p gain | 0 (0%) | 173 |
0.411 (1.00) |
0.0716 (1.00) |
0.525 (1.00) |
0.809 (1.00) |
0.328 (1.00) |
0.0376 (1.00) |
0.382 (1.00) |
0.63 (1.00) |
0.671 (1.00) |
1 (1.00) |
0.489 (1.00) |
0.0412 (1.00) |
0.815 (1.00) |
0.0193 (1.00) |
5q gain | 0 (0%) | 291 |
0.862 (1.00) |
0.286 (1.00) |
0.839 (1.00) |
0.453 (1.00) |
0.977 (1.00) |
0.933 (1.00) |
0.427 (1.00) |
1 (1.00) |
0.598 (1.00) |
0.323 (1.00) |
0.906 (1.00) |
0.638 (1.00) |
0.295 (1.00) |
0.791 (1.00) |
6p gain | 0 (0%) | 294 |
0.885 (1.00) |
0.327 (1.00) |
1 (1.00) |
0.286 (1.00) |
0.0337 (1.00) |
0.111 (1.00) |
0.657 (1.00) |
0.395 (1.00) |
0.123 (1.00) |
0.283 (1.00) |
0.416 (1.00) |
0.603 (1.00) |
0.013 (1.00) |
0.203 (1.00) |
6q gain | 0 (0%) | 307 |
0.638 (1.00) |
0.43 (1.00) |
1 (1.00) |
0.463 (1.00) |
0.00148 (1.00) |
0.646 (1.00) |
1 (1.00) |
0.75 (1.00) |
0.959 (1.00) |
0.471 (1.00) |
0.288 (1.00) |
0.71 (1.00) |
0.186 (1.00) |
0.125 (1.00) |
7p gain | 0 (0%) | 235 |
0.228 (1.00) |
0.158 (1.00) |
0.478 (1.00) |
0.807 (1.00) |
0.379 (1.00) |
0.00393 (1.00) |
0.742 (1.00) |
0.326 (1.00) |
0.448 (1.00) |
0.734 (1.00) |
0.0605 (1.00) |
0.427 (1.00) |
0.355 (1.00) |
0.5 (1.00) |
7q gain | 0 (0%) | 240 |
0.5 (1.00) |
0.393 (1.00) |
0.314 (1.00) |
0.355 (1.00) |
0.469 (1.00) |
0.00914 (1.00) |
0.721 (1.00) |
0.12 (1.00) |
0.323 (1.00) |
0.734 (1.00) |
0.772 (1.00) |
0.786 (1.00) |
0.52 (1.00) |
0.458 (1.00) |
8p gain | 0 (0%) | 280 |
0.887 (1.00) |
0.255 (1.00) |
0.855 (1.00) |
0.00638 (1.00) |
0.0959 (1.00) |
0.598 (1.00) |
0.404 (1.00) |
0.0312 (1.00) |
0.191 (1.00) |
0.184 (1.00) |
0.677 (1.00) |
0.708 (1.00) |
0.615 (1.00) |
0.291 (1.00) |
8q gain | 0 (0%) | 230 |
0.323 (1.00) |
0.301 (1.00) |
0.781 (1.00) |
0.209 (1.00) |
0.869 (1.00) |
0.209 (1.00) |
0.715 (1.00) |
0.0377 (1.00) |
0.0943 (1.00) |
0.309 (1.00) |
0.284 (1.00) |
0.273 (1.00) |
0.262 (1.00) |
0.19 (1.00) |
9p gain | 0 (0%) | 306 |
0.214 (1.00) |
0.72 (1.00) |
0.279 (1.00) |
0.00127 (1.00) |
0.532 (1.00) |
0.704 (1.00) |
1 (1.00) |
0.795 (1.00) |
1 (1.00) |
0.928 (1.00) |
0.879 (1.00) |
0.882 (1.00) |
0.525 (1.00) |
|
9q gain | 0 (0%) | 297 |
0.198 (1.00) |
0.402 (1.00) |
0.657 (1.00) |
0.537 (1.00) |
0.423 (1.00) |
0.382 (1.00) |
0.837 (1.00) |
0.177 (1.00) |
0.725 (1.00) |
0.608 (1.00) |
0.666 (1.00) |
0.619 (1.00) |
0.74 (1.00) |
1 (1.00) |
10p gain | 0 (0%) | 308 |
0.981 (1.00) |
0.746 (1.00) |
1 (1.00) |
0.936 (1.00) |
0.966 (1.00) |
0.57 (1.00) |
0.0693 (1.00) |
0.231 (1.00) |
0.03 (1.00) |
0.451 (1.00) |
0.179 (1.00) |
0.235 (1.00) |
0.327 (1.00) |
0.223 (1.00) |
10q gain | 0 (0%) | 318 |
0.571 (1.00) |
0.699 (1.00) |
1 (1.00) |
0.994 (1.00) |
0.387 (1.00) |
0.419 (1.00) |
1 (1.00) |
0.327 (1.00) |
0.216 (1.00) |
0.582 (1.00) |
0.0471 (1.00) |
0.771 (1.00) |
1 (1.00) |
|
11q gain | 0 (0%) | 303 |
0.735 (1.00) |
0.588 (1.00) |
0.216 (1.00) |
0.521 (1.00) |
0.932 (1.00) |
0.0512 (1.00) |
0.217 (1.00) |
0.776 (1.00) |
0.123 (1.00) |
0.543 (1.00) |
0.562 (1.00) |
0.478 (1.00) |
0.987 (1.00) |
1 (1.00) |
12p gain | 0 (0%) | 235 |
0.868 (1.00) |
0.939 (1.00) |
0.00437 (1.00) |
0.0774 (1.00) |
0.884 (1.00) |
0.149 (1.00) |
0.804 (1.00) |
0.862 (1.00) |
0.903 (1.00) |
0.505 (1.00) |
0.965 (1.00) |
0.404 (1.00) |
0.404 (1.00) |
0.698 (1.00) |
12q gain | 0 (0%) | 284 |
0.569 (1.00) |
0.872 (1.00) |
0.0122 (1.00) |
0.378 (1.00) |
0.978 (1.00) |
0.275 (1.00) |
0.0891 (1.00) |
0.304 (1.00) |
0.201 (1.00) |
0.636 (1.00) |
0.48 (1.00) |
0.343 (1.00) |
0.987 (1.00) |
0.61 (1.00) |
13q gain | 0 (0%) | 317 |
0.275 (1.00) |
0.937 (1.00) |
0.685 (1.00) |
0.992 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.671 (1.00) |
1 (1.00) |
0.566 (1.00) |
0.123 (1.00) |
0.681 (1.00) |
1 (1.00) |
|
14q gain | 0 (0%) | 294 |
0.0308 (1.00) |
0.0644 (1.00) |
0.83 (1.00) |
0.858 (1.00) |
0.974 (1.00) |
0.492 (1.00) |
0.338 (1.00) |
0.552 (1.00) |
0.756 (1.00) |
1 (1.00) |
0.612 (1.00) |
0.245 (1.00) |
0.752 (1.00) |
0.382 (1.00) |
15q gain | 0 (0%) | 295 |
0.68 (1.00) |
0.97 (1.00) |
1 (1.00) |
0.389 (1.00) |
0.482 (1.00) |
0.642 (1.00) |
0.412 (1.00) |
0.834 (1.00) |
0.745 (1.00) |
1 (1.00) |
0.447 (1.00) |
0.0237 (1.00) |
0.365 (1.00) |
0.499 (1.00) |
16p gain | 0 (0%) | 310 |
0.779 (1.00) |
0.311 (1.00) |
0.371 (1.00) |
0.0681 (1.00) |
0.799 (1.00) |
0.0156 (1.00) |
0.678 (1.00) |
1 (1.00) |
0.61 (1.00) |
1 (1.00) |
0.806 (1.00) |
0.437 (1.00) |
0.121 (1.00) |
1 (1.00) |
16q gain | 0 (0%) | 306 |
0.856 (1.00) |
0.109 (1.00) |
0.175 (1.00) |
0.366 (1.00) |
0.958 (1.00) |
0.00407 (1.00) |
0.228 (1.00) |
0.292 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.94 (1.00) |
0.922 (1.00) |
0.0125 (1.00) |
0.802 (1.00) |
17q gain | 0 (0%) | 290 |
0.704 (1.00) |
0.383 (1.00) |
0.0421 (1.00) |
0.12 (1.00) |
0.609 (1.00) |
0.477 (1.00) |
0.0206 (1.00) |
0.168 (1.00) |
0.0505 (1.00) |
0.336 (1.00) |
0.791 (1.00) |
0.567 (1.00) |
0.0558 (1.00) |
0.0641 (1.00) |
18p gain | 0 (0%) | 271 |
0.329 (1.00) |
0.149 (1.00) |
0.233 (1.00) |
0.198 (1.00) |
0.858 (1.00) |
0.331 (1.00) |
0.0336 (1.00) |
0.0714 (1.00) |
0.268 (1.00) |
1 (1.00) |
0.642 (1.00) |
0.158 (1.00) |
0.646 (1.00) |
0.607 (1.00) |
18q gain | 0 (0%) | 286 |
0.648 (1.00) |
0.248 (1.00) |
0.697 (1.00) |
0.378 (1.00) |
0.69 (1.00) |
0.452 (1.00) |
0.329 (1.00) |
0.283 (1.00) |
0.925 (1.00) |
0.628 (1.00) |
0.163 (1.00) |
0.696 (1.00) |
0.242 (1.00) |
0.914 (1.00) |
19q gain | 0 (0%) | 279 |
0.667 (1.00) |
0.82 (1.00) |
1 (1.00) |
0.139 (1.00) |
0.000565 (0.609) |
0.854 (1.00) |
0.112 (1.00) |
0.0747 (1.00) |
0.0574 (1.00) |
0.659 (1.00) |
0.879 (1.00) |
0.863 (1.00) |
0.162 (1.00) |
0.86 (1.00) |
20p gain | 0 (0%) | 234 |
0.765 (1.00) |
0.0637 (1.00) |
0.0231 (1.00) |
0.279 (1.00) |
0.173 (1.00) |
0.942 (1.00) |
0.622 (1.00) |
0.0408 (1.00) |
0.152 (1.00) |
0.19 (1.00) |
0.741 (1.00) |
0.779 (1.00) |
0.198 (1.00) |
0.297 (1.00) |
20q gain | 0 (0%) | 245 |
0.673 (1.00) |
0.266 (1.00) |
0.139 (1.00) |
0.77 (1.00) |
0.0985 (1.00) |
0.97 (1.00) |
0.501 (1.00) |
0.0805 (1.00) |
0.13 (1.00) |
0.147 (1.00) |
0.658 (1.00) |
0.661 (1.00) |
0.572 (1.00) |
0.253 (1.00) |
22q gain | 0 (0%) | 248 |
0.0826 (1.00) |
0.361 (1.00) |
0.458 (1.00) |
0.782 (1.00) |
0.906 (1.00) |
0.204 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.113 (1.00) |
0.726 (1.00) |
0.938 (1.00) |
0.328 (1.00) |
0.604 (1.00) |
0.372 (1.00) |
Xq gain | 0 (0%) | 316 |
0.881 (1.00) |
0.287 (1.00) |
1 (1.00) |
0.891 (1.00) |
0.99 (1.00) |
0.483 (1.00) |
0.89 (1.00) |
0.642 (1.00) |
0.694 (1.00) |
1 (1.00) |
0.563 (1.00) |
1 (1.00) |
0.964 (1.00) |
1 (1.00) |
1p loss | 0 (0%) | 277 |
0.622 (1.00) |
0.793 (1.00) |
0.0021 (1.00) |
0.45 (1.00) |
0.119 (1.00) |
0.4 (1.00) |
0.333 (1.00) |
0.359 (1.00) |
0.195 (1.00) |
0.212 (1.00) |
0.592 (1.00) |
0.664 (1.00) |
0.546 (1.00) |
0.574 (1.00) |
1q loss | 0 (0%) | 318 |
0.775 (1.00) |
0.0214 (1.00) |
0.683 (1.00) |
0.994 (1.00) |
0.294 (1.00) |
0.419 (1.00) |
0.549 (1.00) |
0.165 (1.00) |
0.216 (1.00) |
0.257 (1.00) |
0.539 (1.00) |
0.187 (1.00) |
0.119 (1.00) |
|
2q loss | 0 (0%) | 317 |
0.0784 (1.00) |
0.148 (1.00) |
1 (1.00) |
0.992 (1.00) |
0.607 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.112 (1.00) |
0.0353 (1.00) |
0.731 (1.00) |
1 (1.00) |
|
3p loss | 0 (0%) | 184 |
0.885 (1.00) |
0.345 (1.00) |
0.799 (1.00) |
0.138 (1.00) |
0.406 (1.00) |
0.961 (1.00) |
0.916 (1.00) |
0.701 (1.00) |
0.967 (1.00) |
0.541 (1.00) |
0.557 (1.00) |
0.593 (1.00) |
0.396 (1.00) |
0.936 (1.00) |
3q loss | 0 (0%) | 301 |
0.0955 (1.00) |
0.336 (1.00) |
0.808 (1.00) |
0.65 (1.00) |
0.0101 (1.00) |
0.488 (1.00) |
0.0374 (1.00) |
0.307 (1.00) |
0.0914 (1.00) |
1 (1.00) |
0.107 (1.00) |
0.864 (1.00) |
0.0536 (1.00) |
0.0415 (1.00) |
4p loss | 0 (0%) | 187 |
0.108 (1.00) |
0.863 (1.00) |
1 (1.00) |
0.271 (1.00) |
0.406 (1.00) |
0.356 (1.00) |
0.318 (1.00) |
0.248 (1.00) |
0.0568 (1.00) |
1 (1.00) |
0.567 (1.00) |
0.87 (1.00) |
0.293 (1.00) |
0.66 (1.00) |
4q loss | 0 (0%) | 206 |
0.0759 (1.00) |
0.507 (1.00) |
0.148 (1.00) |
0.138 (1.00) |
0.235 (1.00) |
0.525 (1.00) |
0.891 (1.00) |
0.322 (1.00) |
0.256 (1.00) |
0.539 (1.00) |
0.569 (1.00) |
0.624 (1.00) |
0.685 (1.00) |
0.868 (1.00) |
5p loss | 0 (0%) | 303 |
0.0876 (1.00) |
0.238 (1.00) |
0.613 (1.00) |
0.491 (1.00) |
0.00604 (1.00) |
0.318 (1.00) |
0.36 (1.00) |
0.336 (1.00) |
0.879 (1.00) |
0.166 (1.00) |
0.992 (1.00) |
0.596 (1.00) |
0.174 (1.00) |
0.19 (1.00) |
5q loss | 0 (0%) | 208 |
0.261 (1.00) |
0.723 (1.00) |
0.691 (1.00) |
0.684 (1.00) |
0.235 (1.00) |
0.0207 (1.00) |
0.245 (1.00) |
0.558 (1.00) |
0.0379 (1.00) |
0.533 (1.00) |
0.555 (1.00) |
0.253 (1.00) |
0.0221 (1.00) |
0.231 (1.00) |
6p loss | 0 (0%) | 292 |
0.922 (1.00) |
0.44 (1.00) |
0.0897 (1.00) |
0.818 (1.00) |
0.0188 (1.00) |
0.0775 (1.00) |
0.254 (1.00) |
0.701 (1.00) |
0.138 (1.00) |
0.611 (1.00) |
0.821 (1.00) |
0.542 (1.00) |
0.923 (1.00) |
0.277 (1.00) |
6q loss | 0 (0%) | 291 |
0.55 (1.00) |
0.647 (1.00) |
0.839 (1.00) |
0.789 (1.00) |
0.0227 (1.00) |
0.0294 (1.00) |
0.569 (1.00) |
0.712 (1.00) |
0.182 (1.00) |
0.613 (1.00) |
0.259 (1.00) |
0.624 (1.00) |
0.283 (1.00) |
0.114 (1.00) |
7p loss | 0 (0%) | 305 |
0.739 (1.00) |
0.467 (1.00) |
0.792 (1.00) |
0.796 (1.00) |
0.954 (1.00) |
0.294 (1.00) |
0.214 (1.00) |
1 (1.00) |
0.547 (1.00) |
0.508 (1.00) |
0.103 (1.00) |
0.421 (1.00) |
0.394 (1.00) |
0.0477 (1.00) |
7q loss | 0 (0%) | 315 |
0.485 (1.00) |
0.818 (1.00) |
0.462 (1.00) |
0.988 (1.00) |
0.124 (1.00) |
0.423 (1.00) |
1 (1.00) |
0.923 (1.00) |
0.295 (1.00) |
0.165 (1.00) |
0.386 (1.00) |
0.596 (1.00) |
0.23 (1.00) |
|
8p loss | 0 (0%) | 230 |
0.382 (1.00) |
0.0983 (1.00) |
0.578 (1.00) |
0.519 (1.00) |
0.869 (1.00) |
0.134 (1.00) |
0.692 (1.00) |
0.36 (1.00) |
0.634 (1.00) |
0.186 (1.00) |
0.0531 (1.00) |
0.0366 (1.00) |
0.35 (1.00) |
0.843 (1.00) |
8q loss | 0 (0%) | 316 |
0.849 (1.00) |
0.863 (1.00) |
0.457 (1.00) |
0.463 (1.00) |
0.464 (1.00) |
0.516 (1.00) |
0.692 (1.00) |
1 (1.00) |
0.542 (1.00) |
1 (1.00) |
0.801 (1.00) |
0.405 (1.00) |
0.0476 (1.00) |
0.548 (1.00) |
9p loss | 0 (0%) | 191 |
0.763 (1.00) |
0.374 (1.00) |
0.44 (1.00) |
0.3 (1.00) |
0.404 (1.00) |
0.854 (1.00) |
0.482 (1.00) |
0.654 (1.00) |
0.752 (1.00) |
0.766 (1.00) |
0.108 (1.00) |
0.736 (1.00) |
0.312 (1.00) |
0.292 (1.00) |
9q loss | 0 (0%) | 241 |
0.928 (1.00) |
0.00442 (1.00) |
0.772 (1.00) |
0.768 (1.00) |
0.16 (1.00) |
0.204 (1.00) |
0.713 (1.00) |
0.173 (1.00) |
0.717 (1.00) |
1 (1.00) |
0.663 (1.00) |
0.609 (1.00) |
0.0714 (1.00) |
0.593 (1.00) |
10p loss | 0 (0%) | 254 |
0.431 (1.00) |
0.592 (1.00) |
0.222 (1.00) |
0.963 (1.00) |
0.363 (1.00) |
0.797 (1.00) |
0.327 (1.00) |
0.441 (1.00) |
0.327 (1.00) |
0.13 (1.00) |
0.929 (1.00) |
0.421 (1.00) |
0.556 (1.00) |
0.605 (1.00) |
10q loss | 0 (0%) | 255 |
0.378 (1.00) |
0.998 (1.00) |
0.878 (1.00) |
0.832 (1.00) |
0.353 (1.00) |
0.98 (1.00) |
0.877 (1.00) |
0.211 (1.00) |
0.339 (1.00) |
0.13 (1.00) |
0.186 (1.00) |
0.734 (1.00) |
0.0797 (1.00) |
0.582 (1.00) |
11p loss | 0 (0%) | 278 |
0.406 (1.00) |
0.609 (1.00) |
0.857 (1.00) |
0.712 (1.00) |
0.18 (1.00) |
0.674 (1.00) |
0.431 (1.00) |
0.404 (1.00) |
0.846 (1.00) |
0.202 (1.00) |
0.358 (1.00) |
0.548 (1.00) |
0.963 (1.00) |
0.715 (1.00) |
11q loss | 0 (0%) | 297 |
0.626 (1.00) |
0.13 (1.00) |
0.496 (1.00) |
0.963 (1.00) |
0.914 (1.00) |
0.511 (1.00) |
0.0796 (1.00) |
0.812 (1.00) |
0.485 (1.00) |
0.243 (1.00) |
0.883 (1.00) |
0.803 (1.00) |
0.937 (1.00) |
0.319 (1.00) |
13q loss | 0 (0%) | 203 |
0.0324 (1.00) |
0.485 (1.00) |
0.694 (1.00) |
0.0744 (1.00) |
0.34 (1.00) |
0.958 (1.00) |
0.116 (1.00) |
0.417 (1.00) |
0.0154 (1.00) |
0.753 (1.00) |
0.727 (1.00) |
0.261 (1.00) |
0.00734 (1.00) |
0.686 (1.00) |
14q loss | 0 (0%) | 265 |
0.195 (1.00) |
0.211 (1.00) |
0.0719 (1.00) |
0.227 (1.00) |
0.167 (1.00) |
0.0193 (1.00) |
0.159 (1.00) |
0.433 (1.00) |
0.434 (1.00) |
0.433 (1.00) |
0.758 (1.00) |
0.427 (1.00) |
0.19 (1.00) |
0.904 (1.00) |
15q loss | 0 (0%) | 287 |
0.685 (1.00) |
0.445 (1.00) |
0.0469 (1.00) |
0.836 (1.00) |
0.0678 (1.00) |
0.031 (1.00) |
0.223 (1.00) |
0.462 (1.00) |
0.0532 (1.00) |
1 (1.00) |
0.447 (1.00) |
0.135 (1.00) |
0.834 (1.00) |
0.506 (1.00) |
16p loss | 0 (0%) | 277 |
0.188 (1.00) |
0.754 (1.00) |
0.858 (1.00) |
0.453 (1.00) |
0.775 (1.00) |
0.75 (1.00) |
0.561 (1.00) |
0.789 (1.00) |
0.914 (1.00) |
1 (1.00) |
0.319 (1.00) |
0.931 (1.00) |
0.684 (1.00) |
0.865 (1.00) |
17p loss | 0 (0%) | 210 |
0.203 (1.00) |
0.875 (1.00) |
0.354 (1.00) |
0.0135 (1.00) |
0.542 (1.00) |
0.346 (1.00) |
0.196 (1.00) |
0.315 (1.00) |
0.942 (1.00) |
0.528 (1.00) |
0.361 (1.00) |
0.28 (1.00) |
0.759 (1.00) |
0.948 (1.00) |
17q loss | 0 (0%) | 306 |
0.791 (1.00) |
0.76 (1.00) |
0.0317 (1.00) |
0.453 (1.00) |
0.958 (1.00) |
0.473 (1.00) |
0.74 (1.00) |
0.117 (1.00) |
0.296 (1.00) |
0.49 (1.00) |
0.332 (1.00) |
0.516 (1.00) |
0.136 (1.00) |
0.051 (1.00) |
18p loss | 0 (0%) | 292 |
0.599 (1.00) |
0.378 (1.00) |
0.675 (1.00) |
0.753 (1.00) |
0.884 (1.00) |
0.952 (1.00) |
0.392 (1.00) |
0.27 (1.00) |
0.345 (1.00) |
0.611 (1.00) |
0.0936 (1.00) |
0.871 (1.00) |
0.23 (1.00) |
0.599 (1.00) |
18q loss | 0 (0%) | 262 |
0.351 (1.00) |
0.115 (1.00) |
0.203 (1.00) |
0.963 (1.00) |
0.313 (1.00) |
0.482 (1.00) |
0.802 (1.00) |
0.224 (1.00) |
0.905 (1.00) |
0.698 (1.00) |
0.219 (1.00) |
0.319 (1.00) |
0.29 (1.00) |
0.412 (1.00) |
19p loss | 0 (0%) | 272 |
0.0716 (1.00) |
0.818 (1.00) |
0.864 (1.00) |
0.118 (1.00) |
0.142 (1.00) |
0.377 (1.00) |
0.0954 (1.00) |
0.158 (1.00) |
0.172 (1.00) |
0.0204 (1.00) |
0.961 (1.00) |
0.146 (1.00) |
0.111 (1.00) |
0.411 (1.00) |
19q loss | 0 (0%) | 289 |
0.572 (1.00) |
0.197 (1.00) |
0.839 (1.00) |
0.26 (1.00) |
0.00187 (1.00) |
0.566 (1.00) |
0.248 (1.00) |
0.595 (1.00) |
0.882 (1.00) |
0.11 (1.00) |
0.156 (1.00) |
0.261 (1.00) |
0.035 (1.00) |
0.0086 (1.00) |
20p loss | 0 (0%) | 309 |
0.06 (1.00) |
0.868 (1.00) |
1 (1.00) |
0.97 (1.00) |
0.387 (1.00) |
0.524 (1.00) |
0.72 (1.00) |
0.0663 (1.00) |
1 (1.00) |
0.909 (1.00) |
0.795 (1.00) |
0.705 (1.00) |
0.728 (1.00) |
|
20q loss | 0 (0%) | 308 |
0.376 (1.00) |
0.907 (1.00) |
0.575 (1.00) |
0.966 (1.00) |
0.945 (1.00) |
0.406 (1.00) |
0.735 (1.00) |
0.839 (1.00) |
1 (1.00) |
0.12 (1.00) |
0.89 (1.00) |
0.178 (1.00) |
0.19 (1.00) |
|
21q loss | 0 (0%) | 226 |
0.454 (1.00) |
0.314 (1.00) |
0.0125 (1.00) |
0.564 (1.00) |
0.53 (1.00) |
0.504 (1.00) |
0.719 (1.00) |
0.29 (1.00) |
0.1 (1.00) |
0.741 (1.00) |
0.253 (1.00) |
0.945 (1.00) |
0.374 (1.00) |
0.729 (1.00) |
22q loss | 0 (0%) | 292 |
0.648 (1.00) |
0.126 (1.00) |
0.0605 (1.00) |
0.327 (1.00) |
0.00119 (1.00) |
0.235 (1.00) |
0.000422 (0.455) |
0.282 (1.00) |
0.00292 (1.00) |
1 (1.00) |
0.715 (1.00) |
0.402 (1.00) |
0.0836 (1.00) |
0.184 (1.00) |
P value = 2.88e-08 (Chi-square test), Q value = 3.1e-05
Table S1. Gene #1: '1p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|
ALL | 7 | 1 | 1 | 1 | 315 |
1P GAIN CNV | 4 | 0 | 0 | 1 | 18 |
1P GAIN WILD-TYPE | 3 | 1 | 1 | 0 | 297 |
Figure S1. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D1V5.png)
P value = 8.58e-05 (Chi-square test), Q value = 0.093
Table S2. Gene #4: '2q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|
ALL | 7 | 1 | 1 | 1 | 315 |
2Q GAIN CNV | 4 | 1 | 0 | 0 | 31 |
2Q GAIN WILD-TYPE | 3 | 0 | 1 | 1 | 284 |
Figure S2. Get High-res Image Gene #4: '2q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D4V5.png)
P value = 2e-06 (t-test), Q value = 0.0022
Table S3. Gene #21: '11p gain' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 28.5 (39.7) |
11P GAIN CNV | 4 | 0.0 (0.0) |
11P GAIN WILD-TYPE | 50 | 30.8 (40.4) |
Figure S3. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D21V4.png)
P value = 3.79e-07 (Chi-square test), Q value = 0.00041
Table S4. Gene #30: '17p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|
ALL | 7 | 1 | 1 | 1 | 315 |
17P GAIN CNV | 0 | 1 | 0 | 0 | 8 |
17P GAIN WILD-TYPE | 7 | 0 | 1 | 1 | 307 |
Figure S4. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D30V5.png)
P value = 1.77e-06 (t-test), Q value = 0.0019
Table S5. Gene #34: '19p gain' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 28.5 (39.7) |
19P GAIN CNV | 6 | 0.0 (0.0) |
19P GAIN WILD-TYPE | 48 | 32.1 (40.7) |
Figure S5. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D34V4.png)
P value = 5.63e-06 (Chi-square test), Q value = 0.0061
Table S6. Gene #34: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|
ALL | 7 | 1 | 1 | 1 | 315 |
19P GAIN CNV | 5 | 0 | 0 | 0 | 28 |
19P GAIN WILD-TYPE | 2 | 1 | 1 | 1 | 287 |
Figure S6. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D34V5.png)
P value = 5.96e-05 (Chi-square test), Q value = 0.064
Table S7. Gene #38: '21q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|
ALL | 7 | 1 | 1 | 1 | 315 |
21Q GAIN CNV | 2 | 0 | 0 | 1 | 15 |
21Q GAIN WILD-TYPE | 5 | 1 | 1 | 0 | 300 |
Figure S7. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D38V5.png)
P value = 1.32e-16 (Chi-square test), Q value = 1.4e-13
Table S8. Gene #62: '12p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|
ALL | 7 | 1 | 1 | 1 | 315 |
12P LOSS CNV | 0 | 0 | 0 | 1 | 3 |
12P LOSS WILD-TYPE | 7 | 1 | 1 | 0 | 312 |
Figure S8. Get High-res Image Gene #62: '12p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D62V5.png)
P value = 1.32e-16 (Chi-square test), Q value = 1.4e-13
Table S9. Gene #63: '12q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|
ALL | 7 | 1 | 1 | 1 | 315 |
12Q LOSS CNV | 0 | 0 | 0 | 1 | 3 |
12Q LOSS WILD-TYPE | 7 | 1 | 1 | 0 | 312 |
Figure S9. Get High-res Image Gene #63: '12q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D63V5.png)
P value = 1.77e-06 (t-test), Q value = 0.0019
Table S10. Gene #68: '16q loss' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 54 | 28.5 (39.7) |
16Q LOSS CNV | 6 | 0.0 (0.0) |
16Q LOSS WILD-TYPE | 48 | 32.1 (40.7) |
Figure S10. Get High-res Image Gene #68: '16q loss' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'
![](D68V4.png)
P value = 6.63e-05 (Chi-square test), Q value = 0.072
Table S11. Gene #79: 'Xq loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) |
---|---|---|---|---|---|
ALL | 7 | 1 | 1 | 1 | 315 |
XQ LOSS CNV | 0 | 0 | 0 | 1 | 12 |
XQ LOSS WILD-TYPE | 7 | 1 | 1 | 0 | 303 |
Figure S11. Get High-res Image Gene #79: 'Xq loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D79V5.png)
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = LUSC-TP.clin.merged.picked.txt
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Number of patients = 325
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Number of significantly arm-level cnvs = 79
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Number of selected clinical features = 14
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Exclude genes 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 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 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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.