Lung Adenocarcinoma: Correlation between copy number variations of arm-level result and selected clinical features
(primary solid tumor cohort)
(primary solid tumor cohort)
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction
This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Summary
Testing the association between copy number variation 80 arm-level results and 14 clinical features across 370 patients, 3 significant findings detected with Q value < 0.25.
-
11q gain cnv correlated to 'AGE'.
-
1q loss cnv correlated to 'Time to Death'.
-
18p loss cnv correlated to 'NUMBERPACKYEARSSMOKED'.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 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 | |
| 11q gain | 42 (11%) | 328 |
0.219 (1.00) |
9.1e-05 (0.0973) |
0.102 (1.00) |
0.751 (1.00) |
0.76 (1.00) |
0.197 (1.00) |
0.286 (1.00) |
0.327 (1.00) |
0.083 (1.00) |
0.264 (1.00) |
0.158 (1.00) |
0.0546 (1.00) |
0.131 (1.00) |
1 (1.00) |
| 1q loss | 10 (3%) | 360 |
3.78e-05 (0.0404) |
0.692 (1.00) |
0.759 (1.00) |
0.0292 (1.00) |
1 (1.00) |
0.106 (1.00) |
0.85 (1.00) |
0.332 (1.00) |
0.0963 (1.00) |
0.364 (1.00) |
0.748 (1.00) |
1 (1.00) |
||
| 18p loss | 65 (18%) | 305 |
0.507 (1.00) |
0.137 (1.00) |
0.17 (1.00) |
0.00531 (1.00) |
0.293 (1.00) |
0.139 (1.00) |
0.661 (1.00) |
0.102 (1.00) |
0.0559 (1.00) |
0.222 (1.00) |
0.000163 (0.174) |
0.533 (1.00) |
0.0471 (1.00) |
0.246 (1.00) |
| 1p gain | 49 (13%) | 321 |
0.818 (1.00) |
0.000809 (0.861) |
1 (1.00) |
0.492 (1.00) |
0.919 (1.00) |
0.905 (1.00) |
0.00562 (1.00) |
0.784 (1.00) |
0.00495 (1.00) |
0.494 (1.00) |
0.792 (1.00) |
0.637 (1.00) |
0.826 (1.00) |
0.378 (1.00) |
| 1q gain | 146 (39%) | 224 |
0.758 (1.00) |
0.183 (1.00) |
0.394 (1.00) |
0.512 (1.00) |
0.251 (1.00) |
0.593 (1.00) |
0.0323 (1.00) |
0.316 (1.00) |
0.0367 (1.00) |
0.24 (1.00) |
0.624 (1.00) |
0.387 (1.00) |
0.509 (1.00) |
0.145 (1.00) |
| 2p gain | 43 (12%) | 327 |
0.0909 (1.00) |
0.0426 (1.00) |
0.0349 (1.00) |
0.851 (1.00) |
0.691 (1.00) |
0.0352 (1.00) |
0.748 (1.00) |
0.114 (1.00) |
0.311 (1.00) |
1 (1.00) |
0.88 (1.00) |
0.078 (1.00) |
0.727 (1.00) |
0.673 (1.00) |
| 2q gain | 37 (10%) | 333 |
0.198 (1.00) |
0.163 (1.00) |
0.297 (1.00) |
0.762 (1.00) |
0.223 (1.00) |
1 (1.00) |
0.0673 (1.00) |
0.162 (1.00) |
0.707 (1.00) |
0.492 (1.00) |
0.103 (1.00) |
0.869 (1.00) |
1 (1.00) |
|
| 3p gain | 10 (3%) | 360 |
0.104 (1.00) |
0.613 (1.00) |
0.759 (1.00) |
0.967 (1.00) |
0.0746 (1.00) |
0.255 (1.00) |
0.603 (1.00) |
0.238 (1.00) |
0.43 (1.00) |
0.826 (1.00) |
0.446 (1.00) |
0.251 (1.00) |
0.402 (1.00) |
|
| 3q gain | 23 (6%) | 347 |
0.14 (1.00) |
0.957 (1.00) |
0.522 (1.00) |
0.999 (1.00) |
0.758 (1.00) |
0.398 (1.00) |
0.939 (1.00) |
0.617 (1.00) |
0.358 (1.00) |
0.543 (1.00) |
0.883 (1.00) |
0.364 (1.00) |
0.658 (1.00) |
|
| 4p gain | 27 (7%) | 343 |
0.628 (1.00) |
0.014 (1.00) |
0.316 (1.00) |
0.42 (1.00) |
0.553 (1.00) |
0.955 (1.00) |
0.0349 (1.00) |
0.126 (1.00) |
1 (1.00) |
0.037 (1.00) |
0.257 (1.00) |
0.967 (1.00) |
0.695 (1.00) |
|
| 4q gain | 9 (2%) | 361 |
0.587 (1.00) |
0.694 (1.00) |
0.309 (1.00) |
0.155 (1.00) |
0.242 (1.00) |
0.292 (1.00) |
0.327 (1.00) |
0.582 (1.00) |
0.397 (1.00) |
0.0181 (1.00) |
0.374 (1.00) |
0.179 (1.00) |
1 (1.00) |
|
| 5p gain | 138 (37%) | 232 |
0.294 (1.00) |
0.184 (1.00) |
0.746 (1.00) |
0.786 (1.00) |
0.182 (1.00) |
0.783 (1.00) |
0.532 (1.00) |
0.775 (1.00) |
0.819 (1.00) |
0.101 (1.00) |
0.0183 (1.00) |
0.378 (1.00) |
0.898 (1.00) |
0.0953 (1.00) |
| 5q gain | 41 (11%) | 329 |
0.703 (1.00) |
0.816 (1.00) |
0.506 (1.00) |
0.796 (1.00) |
0.786 (1.00) |
0.802 (1.00) |
0.704 (1.00) |
0.831 (1.00) |
0.0574 (1.00) |
0.454 (1.00) |
0.213 (1.00) |
0.306 (1.00) |
0.753 (1.00) |
|
| 6p gain | 56 (15%) | 314 |
0.652 (1.00) |
0.831 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.313 (1.00) |
0.487 (1.00) |
0.39 (1.00) |
0.636 (1.00) |
0.919 (1.00) |
0.75 (1.00) |
0.6 (1.00) |
0.52 (1.00) |
0.114 (1.00) |
0.939 (1.00) |
| 6q gain | 15 (4%) | 355 |
0.632 (1.00) |
0.256 (1.00) |
0.0148 (1.00) |
0.966 (1.00) |
0.53 (1.00) |
0.926 (1.00) |
0.094 (1.00) |
0.432 (1.00) |
1 (1.00) |
0.536 (1.00) |
0.0859 (1.00) |
0.412 (1.00) |
0.644 (1.00) |
|
| 7p gain | 124 (34%) | 246 |
0.281 (1.00) |
0.0901 (1.00) |
0.74 (1.00) |
0.193 (1.00) |
0.449 (1.00) |
0.137 (1.00) |
0.00771 (1.00) |
0.224 (1.00) |
0.0439 (1.00) |
0.474 (1.00) |
0.554 (1.00) |
0.639 (1.00) |
0.859 (1.00) |
0.668 (1.00) |
| 7q gain | 90 (24%) | 280 |
0.659 (1.00) |
0.011 (1.00) |
0.627 (1.00) |
0.82 (1.00) |
0.315 (1.00) |
0.396 (1.00) |
0.223 (1.00) |
0.114 (1.00) |
0.0358 (1.00) |
0.593 (1.00) |
0.875 (1.00) |
0.968 (1.00) |
0.983 (1.00) |
0.529 (1.00) |
| 8p gain | 47 (13%) | 323 |
0.899 (1.00) |
0.00293 (1.00) |
0.273 (1.00) |
0.448 (1.00) |
0.0582 (1.00) |
0.494 (1.00) |
0.637 (1.00) |
0.805 (1.00) |
0.729 (1.00) |
0.374 (1.00) |
0.0106 (1.00) |
0.021 (1.00) |
0.737 (1.00) |
|
| 8q gain | 117 (32%) | 253 |
0.677 (1.00) |
0.00502 (1.00) |
0.37 (1.00) |
0.321 (1.00) |
0.212 (1.00) |
0.266 (1.00) |
0.227 (1.00) |
0.303 (1.00) |
0.55 (1.00) |
0.626 (1.00) |
0.55 (1.00) |
0.123 (1.00) |
0.0472 (1.00) |
0.701 (1.00) |
| 9p gain | 11 (3%) | 359 |
0.189 (1.00) |
0.282 (1.00) |
0.554 (1.00) |
0.751 (1.00) |
0.666 (1.00) |
0.395 (1.00) |
0.0961 (1.00) |
0.747 (1.00) |
1 (1.00) |
0.2 (1.00) |
0.183 (1.00) |
0.568 (1.00) |
0.6 (1.00) |
|
| 9q gain | 5 (1%) | 365 |
0.0584 (1.00) |
0.158 (1.00) |
0.661 (1.00) |
0.998 (1.00) |
1 (1.00) |
0.416 (1.00) |
0.0734 (1.00) |
0.375 (1.00) |
1 (1.00) |
0.303 (1.00) |
0.815 (1.00) |
0.779 (1.00) |
1 (1.00) |
|
| 10p gain | 41 (11%) | 329 |
0.889 (1.00) |
0.762 (1.00) |
0.0448 (1.00) |
0.82 (1.00) |
0.763 (1.00) |
0.254 (1.00) |
0.313 (1.00) |
0.551 (1.00) |
0.482 (1.00) |
0.711 (1.00) |
0.0168 (1.00) |
0.001 (1.00) |
0.414 (1.00) |
0.446 (1.00) |
| 10q gain | 23 (6%) | 347 |
0.732 (1.00) |
0.731 (1.00) |
0.0528 (1.00) |
0.379 (1.00) |
0.127 (1.00) |
0.12 (1.00) |
0.389 (1.00) |
0.0783 (1.00) |
1 (1.00) |
0.114 (1.00) |
0.0778 (1.00) |
0.285 (1.00) |
0.0818 (1.00) |
|
| 11p gain | 30 (8%) | 340 |
0.443 (1.00) |
0.0438 (1.00) |
0.444 (1.00) |
0.72 (1.00) |
0.677 (1.00) |
0.498 (1.00) |
0.274 (1.00) |
0.346 (1.00) |
0.25 (1.00) |
0.671 (1.00) |
0.289 (1.00) |
0.819 (1.00) |
0.862 (1.00) |
0.759 (1.00) |
| 12p gain | 47 (13%) | 323 |
0.696 (1.00) |
0.0114 (1.00) |
0.755 (1.00) |
0.587 (1.00) |
0.09 (1.00) |
0.131 (1.00) |
0.64 (1.00) |
0.0629 (1.00) |
1 (1.00) |
0.505 (1.00) |
0.0833 (1.00) |
0.171 (1.00) |
0.762 (1.00) |
|
| 12q gain | 39 (11%) | 331 |
0.938 (1.00) |
0.0575 (1.00) |
0.867 (1.00) |
0.496 (1.00) |
0.118 (1.00) |
0.193 (1.00) |
0.786 (1.00) |
0.125 (1.00) |
0.708 (1.00) |
0.0198 (1.00) |
0.0281 (1.00) |
0.0447 (1.00) |
0.602 (1.00) |
|
| 13q gain | 14 (4%) | 356 |
0.818 (1.00) |
0.489 (1.00) |
0.788 (1.00) |
0.961 (1.00) |
0.0868 (1.00) |
0.478 (1.00) |
0.125 (1.00) |
0.387 (1.00) |
0.547 (1.00) |
0.69 (1.00) |
0.452 (1.00) |
0.882 (1.00) |
1 (1.00) |
|
| 14q gain | 38 (10%) | 332 |
0.438 (1.00) |
0.653 (1.00) |
0.306 (1.00) |
0.901 (1.00) |
0.449 (1.00) |
0.722 (1.00) |
0.227 (1.00) |
0.753 (1.00) |
0.6 (1.00) |
0.245 (1.00) |
0.488 (1.00) |
0.676 (1.00) |
0.791 (1.00) |
0.884 (1.00) |
| 15q gain | 10 (3%) | 360 |
0.299 (1.00) |
0.405 (1.00) |
1 (1.00) |
0.157 (1.00) |
0.573 (1.00) |
0.292 (1.00) |
0.327 (1.00) |
0.152 (1.00) |
1 (1.00) |
0.853 (1.00) |
0.148 (1.00) |
0.869 (1.00) |
0.6 (1.00) |
|
| 16p gain | 49 (13%) | 321 |
0.493 (1.00) |
0.297 (1.00) |
1 (1.00) |
0.314 (1.00) |
0.663 (1.00) |
0.851 (1.00) |
0.553 (1.00) |
0.628 (1.00) |
0.517 (1.00) |
0.737 (1.00) |
0.56 (1.00) |
0.00976 (1.00) |
0.466 (1.00) |
0.463 (1.00) |
| 16q gain | 33 (9%) | 337 |
0.656 (1.00) |
0.111 (1.00) |
0.468 (1.00) |
0.292 (1.00) |
0.245 (1.00) |
0.874 (1.00) |
0.335 (1.00) |
0.224 (1.00) |
0.423 (1.00) |
1 (1.00) |
0.0789 (1.00) |
0.326 (1.00) |
0.393 (1.00) |
0.799 (1.00) |
| 17p gain | 21 (6%) | 349 |
0.762 (1.00) |
0.6 (1.00) |
0.12 (1.00) |
0.265 (1.00) |
0.372 (1.00) |
0.911 (1.00) |
0.678 (1.00) |
0.128 (1.00) |
0.203 (1.00) |
0.0205 (1.00) |
0.0994 (1.00) |
0.745 (1.00) |
0.711 (1.00) |
0.471 (1.00) |
| 17q gain | 63 (17%) | 307 |
0.248 (1.00) |
0.819 (1.00) |
1 (1.00) |
0.437 (1.00) |
0.312 (1.00) |
0.0441 (1.00) |
0.79 (1.00) |
0.0443 (1.00) |
0.0686 (1.00) |
0.0582 (1.00) |
0.075 (1.00) |
0.76 (1.00) |
0.464 (1.00) |
0.019 (1.00) |
| 18p gain | 33 (9%) | 337 |
0.696 (1.00) |
0.238 (1.00) |
0.0684 (1.00) |
0.0875 (1.00) |
0.867 (1.00) |
0.517 (1.00) |
0.18 (1.00) |
0.851 (1.00) |
1 (1.00) |
0.091 (1.00) |
0.776 (1.00) |
0.738 (1.00) |
0.892 (1.00) |
|
| 18q gain | 20 (5%) | 350 |
0.521 (1.00) |
0.158 (1.00) |
0.368 (1.00) |
0.704 (1.00) |
0.569 (1.00) |
0.592 (1.00) |
0.749 (1.00) |
0.924 (1.00) |
1 (1.00) |
0.599 (1.00) |
0.556 (1.00) |
0.428 (1.00) |
0.75 (1.00) |
|
| 19p gain | 6 (2%) | 364 |
0.334 (1.00) |
0.049 (1.00) |
1 (1.00) |
0.999 (1.00) |
0.645 (1.00) |
0.0363 (1.00) |
0.0159 (1.00) |
0.0247 (1.00) |
1 (1.00) |
0.437 (1.00) |
0.895 (1.00) |
0.413 (1.00) |
0.434 (1.00) |
|
| 19q gain | 19 (5%) | 351 |
0.978 (1.00) |
0.883 (1.00) |
0.637 (1.00) |
0.491 (1.00) |
0.0312 (1.00) |
0.224 (1.00) |
0.1 (1.00) |
0.254 (1.00) |
0.613 (1.00) |
0.317 (1.00) |
0.084 (1.00) |
0.252 (1.00) |
0.75 (1.00) |
|
| 20p gain | 50 (14%) | 320 |
0.895 (1.00) |
0.507 (1.00) |
1 (1.00) |
0.561 (1.00) |
0.729 (1.00) |
0.918 (1.00) |
0.899 (1.00) |
0.692 (1.00) |
0.166 (1.00) |
0.742 (1.00) |
0.925 (1.00) |
0.0136 (1.00) |
0.607 (1.00) |
0.494 (1.00) |
| 20q gain | 65 (18%) | 305 |
0.731 (1.00) |
0.155 (1.00) |
0.218 (1.00) |
0.141 (1.00) |
0.644 (1.00) |
0.531 (1.00) |
0.775 (1.00) |
0.448 (1.00) |
0.694 (1.00) |
0.222 (1.00) |
0.0272 (1.00) |
0.0083 (1.00) |
0.82 (1.00) |
0.898 (1.00) |
| 21q gain | 31 (8%) | 339 |
0.796 (1.00) |
0.646 (1.00) |
0.346 (1.00) |
0.746 (1.00) |
0.497 (1.00) |
0.165 (1.00) |
0.552 (1.00) |
0.773 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.0408 (1.00) |
0.836 (1.00) |
1 (1.00) |
|
| 22q gain | 15 (4%) | 355 |
0.35 (1.00) |
0.348 (1.00) |
0.794 (1.00) |
0.264 (1.00) |
0.549 (1.00) |
0.151 (1.00) |
1 (1.00) |
0.676 (1.00) |
0.573 (1.00) |
0.286 (1.00) |
0.56 (1.00) |
0.48 (1.00) |
0.75 (1.00) |
|
| Xq gain | 17 (5%) | 353 |
0.352 (1.00) |
0.116 (1.00) |
0.32 (1.00) |
0.749 (1.00) |
0.677 (1.00) |
0.817 (1.00) |
0.144 (1.00) |
0.538 (1.00) |
1 (1.00) |
0.173 (1.00) |
0.121 (1.00) |
0.0815 (1.00) |
0.718 (1.00) |
|
| 1p loss | 26 (7%) | 344 |
0.199 (1.00) |
0.694 (1.00) |
0.221 (1.00) |
0.554 (1.00) |
0.621 (1.00) |
0.836 (1.00) |
0.391 (1.00) |
0.16 (1.00) |
0.158 (1.00) |
0.203 (1.00) |
0.31 (1.00) |
0.977 (1.00) |
0.287 (1.00) |
|
| 2p loss | 5 (1%) | 365 |
0.247 (1.00) |
0.145 (1.00) |
1 (1.00) |
0.899 (1.00) |
1 (1.00) |
0.83 (1.00) |
1 (1.00) |
0.773 (1.00) |
1 (1.00) |
0.504 (1.00) |
0.709 (1.00) |
1 (1.00) |
||
| 2q loss | 3 (1%) | 367 |
1 (1.00) |
0.401 (1.00) |
0.366 (1.00) |
1 (1.00) |
0.632 (1.00) |
1 (1.00) |
1 (1.00) |
0.601 (1.00) |
||||||
| 3p loss | 76 (21%) | 294 |
0.467 (1.00) |
0.799 (1.00) |
1 (1.00) |
0.0134 (1.00) |
0.707 (1.00) |
0.622 (1.00) |
0.514 (1.00) |
0.191 (1.00) |
0.0664 (1.00) |
1 (1.00) |
0.482 (1.00) |
0.0866 (1.00) |
0.149 (1.00) |
0.783 (1.00) |
| 3q loss | 46 (12%) | 324 |
0.435 (1.00) |
0.791 (1.00) |
0.752 (1.00) |
0.016 (1.00) |
0.567 (1.00) |
0.213 (1.00) |
0.39 (1.00) |
0.263 (1.00) |
0.459 (1.00) |
1 (1.00) |
0.0767 (1.00) |
0.927 (1.00) |
0.59 (1.00) |
0.852 (1.00) |
| 4p loss | 34 (9%) | 336 |
0.453 (1.00) |
0.0222 (1.00) |
0.59 (1.00) |
0.646 (1.00) |
0.596 (1.00) |
0.237 (1.00) |
0.169 (1.00) |
0.883 (1.00) |
0.583 (1.00) |
0.413 (1.00) |
0.986 (1.00) |
0.0465 (1.00) |
0.458 (1.00) |
0.779 (1.00) |
| 4q loss | 41 (11%) | 329 |
0.564 (1.00) |
0.0462 (1.00) |
0.139 (1.00) |
0.88 (1.00) |
0.927 (1.00) |
0.0761 (1.00) |
0.0029 (1.00) |
0.278 (1.00) |
0.0141 (1.00) |
0.258 (1.00) |
0.582 (1.00) |
0.058 (1.00) |
0.963 (1.00) |
0.631 (1.00) |
| 5p loss | 12 (3%) | 358 |
0.73 (1.00) |
0.905 (1.00) |
0.149 (1.00) |
0.0453 (1.00) |
1 (1.00) |
0.469 (1.00) |
0.215 (1.00) |
0.511 (1.00) |
1 (1.00) |
0.727 (1.00) |
0.15 (1.00) |
0.513 (1.00) |
0.357 (1.00) |
|
| 5q loss | 48 (13%) | 322 |
0.626 (1.00) |
0.032 (1.00) |
0.12 (1.00) |
0.0496 (1.00) |
0.777 (1.00) |
0.0707 (1.00) |
0.235 (1.00) |
0.328 (1.00) |
0.492 (1.00) |
0.216 (1.00) |
0.0403 (1.00) |
0.498 (1.00) |
0.417 (1.00) |
|
| 6p loss | 31 (8%) | 339 |
0.676 (1.00) |
0.0868 (1.00) |
0.137 (1.00) |
0.57 (1.00) |
0.232 (1.00) |
0.516 (1.00) |
0.239 (1.00) |
0.375 (1.00) |
0.229 (1.00) |
0.304 (1.00) |
0.324 (1.00) |
0.285 (1.00) |
0.615 (1.00) |
|
| 6q loss | 83 (22%) | 287 |
0.669 (1.00) |
0.113 (1.00) |
0.534 (1.00) |
0.0305 (1.00) |
0.402 (1.00) |
0.196 (1.00) |
0.325 (1.00) |
0.191 (1.00) |
0.422 (1.00) |
0.412 (1.00) |
0.135 (1.00) |
0.304 (1.00) |
0.186 (1.00) |
0.934 (1.00) |
| 7p loss | 11 (3%) | 359 |
0.841 (1.00) |
0.254 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.832 (1.00) |
0.742 (1.00) |
0.364 (1.00) |
0.562 (1.00) |
0.462 (1.00) |
0.524 (1.00) |
0.315 (1.00) |
0.302 (1.00) |
0.31 (1.00) |
|
| 7q loss | 12 (3%) | 358 |
0.691 (1.00) |
0.207 (1.00) |
0.558 (1.00) |
0.000309 (0.329) |
0.896 (1.00) |
1 (1.00) |
0.859 (1.00) |
0.96 (1.00) |
0.492 (1.00) |
0.164 (1.00) |
0.122 (1.00) |
0.261 (1.00) |
||
| 8p loss | 97 (26%) | 273 |
0.783 (1.00) |
0.664 (1.00) |
0.553 (1.00) |
0.267 (1.00) |
0.0993 (1.00) |
0.139 (1.00) |
0.71 (1.00) |
0.613 (1.00) |
0.618 (1.00) |
1 (1.00) |
0.558 (1.00) |
0.0664 (1.00) |
0.43 (1.00) |
0.525 (1.00) |
| 8q loss | 11 (3%) | 359 |
0.186 (1.00) |
0.96 (1.00) |
0.554 (1.00) |
0.0211 (1.00) |
0.941 (1.00) |
0.668 (1.00) |
0.738 (1.00) |
0.775 (1.00) |
1 (1.00) |
0.241 (1.00) |
0.113 (1.00) |
1 (1.00) |
||
| 9p loss | 113 (31%) | 257 |
0.0169 (1.00) |
0.278 (1.00) |
0.0309 (1.00) |
0.975 (1.00) |
0.764 (1.00) |
0.408 (1.00) |
0.00931 (1.00) |
0.389 (1.00) |
0.012 (1.00) |
1 (1.00) |
0.544 (1.00) |
0.0824 (1.00) |
0.721 (1.00) |
0.698 (1.00) |
| 9q loss | 96 (26%) | 274 |
0.415 (1.00) |
0.747 (1.00) |
0.722 (1.00) |
0.882 (1.00) |
0.672 (1.00) |
0.476 (1.00) |
0.128 (1.00) |
0.252 (1.00) |
0.167 (1.00) |
0.305 (1.00) |
0.316 (1.00) |
0.161 (1.00) |
0.864 (1.00) |
0.343 (1.00) |
| 10p loss | 26 (7%) | 344 |
0.291 (1.00) |
0.662 (1.00) |
0.154 (1.00) |
0.185 (1.00) |
0.712 (1.00) |
0.362 (1.00) |
0.746 (1.00) |
0.942 (1.00) |
0.381 (1.00) |
0.656 (1.00) |
0.129 (1.00) |
0.716 (1.00) |
0.63 (1.00) |
|
| 10q loss | 30 (8%) | 340 |
0.339 (1.00) |
0.222 (1.00) |
1 (1.00) |
0.000271 (0.289) |
0.21 (1.00) |
0.0925 (1.00) |
0.952 (1.00) |
0.117 (1.00) |
0.39 (1.00) |
0.123 (1.00) |
0.312 (1.00) |
0.948 (1.00) |
1 (1.00) |
|
| 11p loss | 27 (7%) | 343 |
0.283 (1.00) |
0.0108 (1.00) |
0.841 (1.00) |
0.525 (1.00) |
1 (1.00) |
0.378 (1.00) |
0.297 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.158 (1.00) |
0.0452 (1.00) |
0.0166 (1.00) |
0.892 (1.00) |
|
| 11q loss | 24 (6%) | 346 |
0.339 (1.00) |
0.98 (1.00) |
0.4 (1.00) |
0.715 (1.00) |
0.252 (1.00) |
0.599 (1.00) |
0.477 (1.00) |
0.0114 (1.00) |
0.346 (1.00) |
0.378 (1.00) |
0.0432 (1.00) |
0.238 (1.00) |
0.351 (1.00) |
0.759 (1.00) |
| 12p loss | 32 (9%) | 338 |
0.346 (1.00) |
0.88 (1.00) |
1 (1.00) |
0.541 (1.00) |
0.828 (1.00) |
0.391 (1.00) |
0.829 (1.00) |
0.358 (1.00) |
0.407 (1.00) |
0.688 (1.00) |
0.869 (1.00) |
0.129 (1.00) |
0.0653 (1.00) |
0.867 (1.00) |
| 12q loss | 21 (6%) | 349 |
0.0651 (1.00) |
0.935 (1.00) |
0.507 (1.00) |
0.804 (1.00) |
0.456 (1.00) |
0.486 (1.00) |
0.54 (1.00) |
0.424 (1.00) |
0.617 (1.00) |
0.966 (1.00) |
0.108 (1.00) |
0.248 (1.00) |
1 (1.00) |
|
| 13q loss | 85 (23%) | 285 |
0.205 (1.00) |
0.219 (1.00) |
0.62 (1.00) |
0.525 (1.00) |
0.167 (1.00) |
0.651 (1.00) |
0.371 (1.00) |
0.377 (1.00) |
0.211 (1.00) |
0.788 (1.00) |
0.734 (1.00) |
0.248 (1.00) |
0.0921 (1.00) |
0.491 (1.00) |
| 14q loss | 41 (11%) | 329 |
0.655 (1.00) |
0.445 (1.00) |
0.622 (1.00) |
0.814 (1.00) |
0.425 (1.00) |
0.594 (1.00) |
0.834 (1.00) |
0.248 (1.00) |
0.831 (1.00) |
0.475 (1.00) |
0.45 (1.00) |
0.553 (1.00) |
0.302 (1.00) |
0.447 (1.00) |
| 15q loss | 77 (21%) | 293 |
0.838 (1.00) |
0.0665 (1.00) |
0.248 (1.00) |
0.746 (1.00) |
0.147 (1.00) |
0.941 (1.00) |
1 (1.00) |
0.811 (1.00) |
0.831 (1.00) |
0.58 (1.00) |
0.254 (1.00) |
0.5 (1.00) |
0.688 (1.00) |
0.358 (1.00) |
| 16p loss | 30 (8%) | 340 |
0.628 (1.00) |
0.121 (1.00) |
0.251 (1.00) |
0.407 (1.00) |
0.674 (1.00) |
0.922 (1.00) |
0.0107 (1.00) |
0.0317 (1.00) |
0.214 (1.00) |
0.699 (1.00) |
0.252 (1.00) |
0.455 (1.00) |
0.387 (1.00) |
|
| 16q loss | 49 (13%) | 321 |
0.235 (1.00) |
0.193 (1.00) |
0.644 (1.00) |
0.746 (1.00) |
0.0144 (1.00) |
0.525 (1.00) |
0.461 (1.00) |
0.114 (1.00) |
0.19 (1.00) |
0.737 (1.00) |
0.631 (1.00) |
0.255 (1.00) |
0.3 (1.00) |
0.538 (1.00) |
| 17p loss | 94 (25%) | 276 |
0.985 (1.00) |
0.4 (1.00) |
0.631 (1.00) |
0.1 (1.00) |
0.687 (1.00) |
0.748 (1.00) |
0.984 (1.00) |
0.844 (1.00) |
0.679 (1.00) |
0.428 (1.00) |
0.496 (1.00) |
0.0519 (1.00) |
0.0908 (1.00) |
0.218 (1.00) |
| 17q loss | 16 (4%) | 354 |
0.189 (1.00) |
0.365 (1.00) |
0.31 (1.00) |
0.59 (1.00) |
0.561 (1.00) |
0.699 (1.00) |
0.831 (1.00) |
0.801 (1.00) |
1 (1.00) |
0.54 (1.00) |
0.44 (1.00) |
0.0532 (1.00) |
0.718 (1.00) |
|
| 18q loss | 93 (25%) | 277 |
0.0279 (1.00) |
0.429 (1.00) |
0.547 (1.00) |
0.452 (1.00) |
0.286 (1.00) |
0.0785 (1.00) |
0.446 (1.00) |
0.34 (1.00) |
0.00844 (1.00) |
0.182 (1.00) |
0.124 (1.00) |
0.335 (1.00) |
0.387 (1.00) |
0.0255 (1.00) |
| 19p loss | 98 (26%) | 272 |
0.0371 (1.00) |
0.207 (1.00) |
0.0759 (1.00) |
0.649 (1.00) |
0.792 (1.00) |
0.161 (1.00) |
0.0609 (1.00) |
0.0474 (1.00) |
0.248 (1.00) |
1 (1.00) |
0.342 (1.00) |
0.0807 (1.00) |
0.22 (1.00) |
0.0959 (1.00) |
| 19q loss | 56 (15%) | 314 |
0.0802 (1.00) |
0.372 (1.00) |
0.885 (1.00) |
0.00456 (1.00) |
0.514 (1.00) |
0.398 (1.00) |
0.467 (1.00) |
0.144 (1.00) |
0.549 (1.00) |
0.522 (1.00) |
0.283 (1.00) |
0.26 (1.00) |
0.341 (1.00) |
0.0321 (1.00) |
| 20p loss | 50 (14%) | 320 |
0.16 (1.00) |
0.931 (1.00) |
0.76 (1.00) |
0.727 (1.00) |
0.164 (1.00) |
0.223 (1.00) |
0.247 (1.00) |
0.241 (1.00) |
0.742 (1.00) |
0.684 (1.00) |
0.9 (1.00) |
0.0857 (1.00) |
0.941 (1.00) |
|
| 20q loss | 21 (6%) | 349 |
0.313 (1.00) |
0.337 (1.00) |
1 (1.00) |
0.49 (1.00) |
0.776 (1.00) |
0.804 (1.00) |
0.509 (1.00) |
0.783 (1.00) |
1 (1.00) |
0.819 (1.00) |
0.481 (1.00) |
0.256 (1.00) |
0.532 (1.00) |
|
| 21q loss | 52 (14%) | 318 |
0.84 (1.00) |
0.35 (1.00) |
0.025 (1.00) |
0.116 (1.00) |
0.443 (1.00) |
0.551 (1.00) |
0.623 (1.00) |
0.869 (1.00) |
0.55 (1.00) |
0.503 (1.00) |
0.331 (1.00) |
0.0717 (1.00) |
0.857 (1.00) |
0.669 (1.00) |
| 22q loss | 77 (21%) | 293 |
0.828 (1.00) |
0.0622 (1.00) |
0.0718 (1.00) |
0.689 (1.00) |
0.798 (1.00) |
0.963 (1.00) |
0.787 (1.00) |
0.0276 (1.00) |
0.895 (1.00) |
0.151 (1.00) |
0.201 (1.00) |
0.0112 (1.00) |
0.111 (1.00) |
0.22 (1.00) |
| Xq loss | 10 (3%) | 360 |
0.291 (1.00) |
0.0666 (1.00) |
0.0477 (1.00) |
0.0221 (1.00) |
0.0474 (1.00) |
1 (1.00) |
0.85 (1.00) |
0.266 (1.00) |
0.0963 (1.00) |
0.288 (1.00) |
0.537 (1.00) |
0.909 (1.00) |
1 (1.00) |
'11q gain mutation analysis' versus 'AGE'
P value = 9.1e-05 (t-test), Q value = 0.097
Table S1. Gene #22: '11q gain mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 339 | 65.3 (9.8) |
| 11Q GAIN MUTATED | 39 | 59.3 (9.3) |
| 11Q GAIN WILD-TYPE | 300 | 66.0 (9.6) |
Figure S1. Get High-res Image Gene #22: '11q gain mutation analysis' versus Clinical Feature #2: 'AGE'
'1q loss mutation analysis' versus 'Time to Death'
P value = 3.78e-05 (logrank test), Q value = 0.04
Table S2. Gene #42: '1q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 331 | 85 | 0.0 - 224.0 (8.5) |
| 1Q LOSS MUTATED | 8 | 4 | 0.1 - 21.5 (7.0) |
| 1Q LOSS WILD-TYPE | 323 | 81 | 0.0 - 224.0 (8.7) |
Figure S2. Get High-res Image Gene #42: '1q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'
'18p loss mutation analysis' versus 'NUMBERPACKYEARSSMOKED'
P value = 0.000163 (t-test), Q value = 0.17
Table S3. Gene #72: '18p loss mutation analysis' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 260 | 41.0 (27.1) |
| 18P LOSS MUTATED | 45 | 30.7 (17.0) |
| 18P LOSS WILD-TYPE | 215 | 43.1 (28.3) |
Figure S3. Get High-res Image Gene #72: '18p loss mutation analysis' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
Methods & Data
Input
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = LUAD-TP.clin.merged.picked.txt
-
Number of patients = 370
-
Number of significantly arm-level cnvs = 80
-
Number of selected clinical features = 14
-
Exclude genes that fewer than K tumors have mutations, K = 3
Survival analysis
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
Student's t-test analysis
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
Fisher's exact test
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
Chi-square test
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
Q value calculation
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.
Download Results
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.
References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2013
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.