Lung Adenocarcinoma: Correlation between copy number variations of arm-level result and selected clinical features
Maintained by TCGA GDAC Team
(Broad Institute/Dana-Farber Cancer Institute/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 79 arm-level results and 11 clinical features across 287 patients, 3 significant findings detected with Q value < 0.25.
-
4q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
-
8q gain cnv correlated to 'AGE'.
-
1q loss cnv correlated to 'Time to Death'.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 11 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 |
NEOADJUVANT THERAPY |
||
| 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 | Fisher's exact test | |
| 4q gain | 8 (3%) | 279 |
0.619 (1.00) |
0.557 (1.00) |
0.149 (1.00) |
6.68e-05 (0.0551) |
0.0824 (1.00) |
0.365 (1.00) |
0.506 (1.00) |
0.645 (1.00) |
0.426 (1.00) |
1 (1.00) |
|
| 8q gain | 90 (31%) | 197 |
0.918 (1.00) |
0.000246 (0.203) |
0.253 (1.00) |
0.37 (1.00) |
0.417 (1.00) |
0.829 (1.00) |
0.453 (1.00) |
0.356 (1.00) |
0.494 (1.00) |
0.799 (1.00) |
0.599 (1.00) |
| 1q loss | 10 (3%) | 277 |
3.77e-06 (0.00311) |
0.467 (1.00) |
0.521 (1.00) |
0.58 (1.00) |
0.559 (1.00) |
0.228 (1.00) |
1 (1.00) |
0.0794 (1.00) |
0.136 (1.00) |
1 (1.00) |
|
| 1p gain | 37 (13%) | 250 |
0.809 (1.00) |
0.00458 (1.00) |
0.86 (1.00) |
0.553 (1.00) |
0.969 (1.00) |
0.656 (1.00) |
0.0145 (1.00) |
0.686 (1.00) |
0.00909 (1.00) |
0.485 (1.00) |
0.81 (1.00) |
| 1q gain | 113 (39%) | 174 |
0.744 (1.00) |
0.507 (1.00) |
0.63 (1.00) |
0.551 (1.00) |
0.628 (1.00) |
0.657 (1.00) |
0.066 (1.00) |
0.347 (1.00) |
0.0627 (1.00) |
0.628 (1.00) |
0.133 (1.00) |
| 2p gain | 36 (13%) | 251 |
0.133 (1.00) |
0.0639 (1.00) |
0.0308 (1.00) |
0.685 (1.00) |
0.785 (1.00) |
0.0749 (1.00) |
0.674 (1.00) |
0.0871 (1.00) |
0.121 (1.00) |
1 (1.00) |
0.806 (1.00) |
| 2q gain | 30 (10%) | 257 |
0.198 (1.00) |
0.23 (1.00) |
0.248 (1.00) |
0.226 (1.00) |
0.282 (1.00) |
0.963 (1.00) |
0.0975 (1.00) |
0.232 (1.00) |
0.704 (1.00) |
1 (1.00) |
|
| 3p gain | 9 (3%) | 278 |
0.124 (1.00) |
0.653 (1.00) |
0.737 (1.00) |
0.906 (1.00) |
0.0853 (1.00) |
0.624 (1.00) |
0.547 (1.00) |
0.427 (1.00) |
0.465 (1.00) |
0.632 (1.00) |
|
| 3q gain | 18 (6%) | 269 |
0.135 (1.00) |
0.494 (1.00) |
0.809 (1.00) |
0.96 (1.00) |
0.866 (1.00) |
0.293 (1.00) |
0.91 (1.00) |
0.56 (1.00) |
0.338 (1.00) |
0.494 (1.00) |
|
| 4p gain | 21 (7%) | 266 |
0.645 (1.00) |
0.0137 (1.00) |
0.364 (1.00) |
0.0607 (1.00) |
0.234 (1.00) |
0.896 (1.00) |
0.0908 (1.00) |
0.269 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 5p gain | 111 (39%) | 176 |
0.541 (1.00) |
0.308 (1.00) |
0.715 (1.00) |
0.791 (1.00) |
0.303 (1.00) |
0.404 (1.00) |
0.805 (1.00) |
0.907 (1.00) |
0.976 (1.00) |
0.0898 (1.00) |
0.506 (1.00) |
| 5q gain | 36 (13%) | 251 |
0.703 (1.00) |
0.836 (1.00) |
0.378 (1.00) |
0.813 (1.00) |
0.571 (1.00) |
0.663 (1.00) |
0.547 (1.00) |
0.798 (1.00) |
0.0731 (1.00) |
0.133 (1.00) |
|
| 6p gain | 40 (14%) | 247 |
0.892 (1.00) |
0.655 (1.00) |
0.495 (1.00) |
0.833 (1.00) |
0.696 (1.00) |
0.466 (1.00) |
0.193 (1.00) |
0.793 (1.00) |
0.762 (1.00) |
1 (1.00) |
0.641 (1.00) |
| 6q gain | 11 (4%) | 276 |
0.496 (1.00) |
0.0912 (1.00) |
0.0129 (1.00) |
0.99 (1.00) |
0.845 (1.00) |
0.505 (1.00) |
0.62 (1.00) |
0.429 (1.00) |
1 (1.00) |
0.679 (1.00) |
|
| 7p gain | 99 (34%) | 188 |
0.245 (1.00) |
0.0518 (1.00) |
1 (1.00) |
0.246 (1.00) |
0.443 (1.00) |
0.179 (1.00) |
0.0174 (1.00) |
0.0907 (1.00) |
0.051 (1.00) |
0.618 (1.00) |
0.606 (1.00) |
| 7q gain | 71 (25%) | 216 |
0.904 (1.00) |
0.00384 (1.00) |
0.411 (1.00) |
0.976 (1.00) |
0.666 (1.00) |
0.365 (1.00) |
0.207 (1.00) |
0.0601 (1.00) |
0.0486 (1.00) |
0.582 (1.00) |
0.449 (1.00) |
| 8p gain | 34 (12%) | 253 |
0.215 (1.00) |
0.00127 (1.00) |
0.142 (1.00) |
0.861 (1.00) |
0.67 (1.00) |
1 (1.00) |
0.315 (1.00) |
0.972 (1.00) |
0.48 (1.00) |
0.201 (1.00) |
|
| 9p gain | 7 (2%) | 280 |
0.208 (1.00) |
0.299 (1.00) |
0.254 (1.00) |
0.993 (1.00) |
0.344 (1.00) |
0.569 (1.00) |
0.474 (1.00) |
1 (1.00) |
1 (1.00) |
0.6 (1.00) |
|
| 9q gain | 3 (1%) | 284 |
0.0592 (1.00) |
0.226 (1.00) |
1 (1.00) |
1 (1.00) |
0.709 (1.00) |
1 (1.00) |
0.632 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 10p gain | 32 (11%) | 255 |
0.938 (1.00) |
0.173 (1.00) |
0.26 (1.00) |
0.977 (1.00) |
0.22 (1.00) |
0.551 (1.00) |
0.213 (1.00) |
0.845 (1.00) |
0.621 (1.00) |
0.706 (1.00) |
0.798 (1.00) |
| 10q gain | 19 (7%) | 268 |
0.991 (1.00) |
0.606 (1.00) |
0.343 (1.00) |
0.104 (1.00) |
0.487 (1.00) |
0.498 (1.00) |
0.386 (1.00) |
0.604 (1.00) |
1 (1.00) |
0.748 (1.00) |
|
| 11p gain | 23 (8%) | 264 |
0.736 (1.00) |
0.105 (1.00) |
0.384 (1.00) |
0.689 (1.00) |
0.726 (1.00) |
0.494 (1.00) |
1 (1.00) |
0.443 (1.00) |
1 (1.00) |
0.764 (1.00) |
|
| 11q gain | 34 (12%) | 253 |
0.485 (1.00) |
0.000312 (0.257) |
0.066 (1.00) |
0.701 (1.00) |
0.761 (1.00) |
0.59 (1.00) |
0.702 (1.00) |
0.56 (1.00) |
0.227 (1.00) |
0.48 (1.00) |
1 (1.00) |
| 12p gain | 39 (14%) | 248 |
0.86 (1.00) |
0.00349 (1.00) |
0.605 (1.00) |
0.689 (1.00) |
0.153 (1.00) |
0.0651 (1.00) |
1 (1.00) |
0.0495 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 12q gain | 31 (11%) | 256 |
0.75 (1.00) |
0.00101 (0.828) |
0.448 (1.00) |
0.766 (1.00) |
0.147 (1.00) |
0.129 (1.00) |
0.692 (1.00) |
0.0738 (1.00) |
0.705 (1.00) |
0.596 (1.00) |
|
| 13q gain | 15 (5%) | 272 |
0.573 (1.00) |
0.527 (1.00) |
1 (1.00) |
0.982 (1.00) |
0.112 (1.00) |
0.424 (1.00) |
0.137 (1.00) |
0.542 (1.00) |
1 (1.00) |
0.26 (1.00) |
|
| 14q gain | 33 (11%) | 254 |
0.166 (1.00) |
0.192 (1.00) |
0.269 (1.00) |
0.777 (1.00) |
0.0499 (1.00) |
0.608 (1.00) |
0.571 (1.00) |
0.703 (1.00) |
0.863 (1.00) |
0.708 (1.00) |
0.798 (1.00) |
| 15q gain | 10 (3%) | 277 |
0.276 (1.00) |
0.377 (1.00) |
0.758 (1.00) |
0.0919 (1.00) |
0.679 (1.00) |
0.351 (1.00) |
0.443 (1.00) |
0.21 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 16p gain | 40 (14%) | 247 |
0.59 (1.00) |
0.158 (1.00) |
0.865 (1.00) |
0.342 (1.00) |
0.611 (1.00) |
0.474 (1.00) |
0.569 (1.00) |
0.635 (1.00) |
0.563 (1.00) |
0.736 (1.00) |
0.234 (1.00) |
| 16q gain | 26 (9%) | 261 |
0.658 (1.00) |
0.264 (1.00) |
0.417 (1.00) |
0.302 (1.00) |
0.47 (1.00) |
0.354 (1.00) |
0.518 (1.00) |
0.418 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.569 (1.00) |
| 17p gain | 16 (6%) | 271 |
0.79 (1.00) |
0.634 (1.00) |
0.203 (1.00) |
0.208 (1.00) |
0.41 (1.00) |
0.966 (1.00) |
0.507 (1.00) |
0.396 (1.00) |
0.342 (1.00) |
0.0151 (1.00) |
0.282 (1.00) |
| 17q gain | 48 (17%) | 239 |
0.208 (1.00) |
0.349 (1.00) |
1 (1.00) |
0.379 (1.00) |
0.243 (1.00) |
0.0286 (1.00) |
0.517 (1.00) |
0.0257 (1.00) |
0.0278 (1.00) |
0.104 (1.00) |
0.272 (1.00) |
| 18p gain | 19 (7%) | 268 |
0.566 (1.00) |
0.342 (1.00) |
0.343 (1.00) |
0.218 (1.00) |
0.854 (1.00) |
0.749 (1.00) |
1 (1.00) |
0.923 (1.00) |
1 (1.00) |
0.507 (1.00) |
|
| 18q gain | 14 (5%) | 273 |
0.466 (1.00) |
0.205 (1.00) |
0.422 (1.00) |
0.0724 (1.00) |
0.923 (1.00) |
0.797 (1.00) |
0.528 (1.00) |
0.867 (1.00) |
1 (1.00) |
0.242 (1.00) |
|
| 19p gain | 4 (1%) | 283 |
0.988 (1.00) |
0.606 (1.00) |
0.627 (1.00) |
0.993 (1.00) |
0.491 (1.00) |
0.338 (1.00) |
0.245 (1.00) |
0.164 (1.00) |
0.241 (1.00) |
0.488 (1.00) |
|
| 19q gain | 11 (4%) | 276 |
0.776 (1.00) |
0.678 (1.00) |
0.556 (1.00) |
0.993 (1.00) |
0.16 (1.00) |
0.833 (1.00) |
0.288 (1.00) |
0.704 (1.00) |
0.536 (1.00) |
0.225 (1.00) |
|
| 20p gain | 42 (15%) | 245 |
0.851 (1.00) |
0.323 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.773 (1.00) |
0.332 (1.00) |
0.457 (1.00) |
0.716 (1.00) |
0.375 (1.00) |
0.747 (1.00) |
0.0381 (1.00) |
| 20q gain | 49 (17%) | 238 |
0.72 (1.00) |
0.167 (1.00) |
0.529 (1.00) |
0.153 (1.00) |
0.747 (1.00) |
0.111 (1.00) |
0.924 (1.00) |
0.47 (1.00) |
0.698 (1.00) |
0.215 (1.00) |
0.0513 (1.00) |
| 21q gain | 26 (9%) | 261 |
0.496 (1.00) |
0.577 (1.00) |
0.148 (1.00) |
0.636 (1.00) |
0.627 (1.00) |
0.558 (1.00) |
0.418 (1.00) |
0.934 (1.00) |
1 (1.00) |
0.256 (1.00) |
|
| 22q gain | 13 (5%) | 274 |
0.474 (1.00) |
0.0892 (1.00) |
1 (1.00) |
0.449 (1.00) |
0.199 (1.00) |
0.0702 (1.00) |
0.881 (1.00) |
0.403 (1.00) |
0.598 (1.00) |
0.0336 (1.00) |
|
| Xq gain | 14 (5%) | 273 |
0.361 (1.00) |
0.235 (1.00) |
0.179 (1.00) |
0.686 (1.00) |
0.341 (1.00) |
0.928 (1.00) |
0.779 (1.00) |
0.907 (1.00) |
1 (1.00) |
0.457 (1.00) |
|
| 1p loss | 22 (8%) | 265 |
0.22 (1.00) |
0.821 (1.00) |
0.118 (1.00) |
0.894 (1.00) |
0.726 (1.00) |
0.819 (1.00) |
0.333 (1.00) |
0.0474 (1.00) |
0.169 (1.00) |
1 (1.00) |
|
| 2p loss | 3 (1%) | 284 |
1 (1.00) |
0.998 (1.00) |
1 (1.00) |
1 (1.00) |
0.632 (1.00) |
1 (1.00) |
1 (1.00) |
0.394 (1.00) |
|||
| 3p loss | 56 (20%) | 231 |
0.864 (1.00) |
0.688 (1.00) |
0.766 (1.00) |
0.025 (1.00) |
0.908 (1.00) |
0.64 (1.00) |
0.467 (1.00) |
0.159 (1.00) |
0.00376 (1.00) |
0.771 (1.00) |
0.308 (1.00) |
| 3q loss | 30 (10%) | 257 |
0.866 (1.00) |
0.712 (1.00) |
0.442 (1.00) |
0.0533 (1.00) |
0.996 (1.00) |
0.483 (1.00) |
0.656 (1.00) |
0.567 (1.00) |
0.218 (1.00) |
1 (1.00) |
0.428 (1.00) |
| 4p loss | 26 (9%) | 261 |
0.467 (1.00) |
0.0261 (1.00) |
0.103 (1.00) |
0.723 (1.00) |
0.664 (1.00) |
0.328 (1.00) |
0.266 (1.00) |
0.651 (1.00) |
0.49 (1.00) |
0.396 (1.00) |
0.569 (1.00) |
| 4q loss | 31 (11%) | 256 |
0.522 (1.00) |
0.0469 (1.00) |
0.0127 (1.00) |
0.984 (1.00) |
0.969 (1.00) |
0.162 (1.00) |
0.00701 (1.00) |
0.514 (1.00) |
0.065 (1.00) |
0.135 (1.00) |
0.798 (1.00) |
| 5p loss | 6 (2%) | 281 |
0.914 (1.00) |
0.178 (1.00) |
0.419 (1.00) |
0.453 (1.00) |
0.576 (1.00) |
0.84 (1.00) |
0.404 (1.00) |
0.448 (1.00) |
1 (1.00) |
0.23 (1.00) |
|
| 5q loss | 38 (13%) | 249 |
0.598 (1.00) |
0.0648 (1.00) |
0.0136 (1.00) |
0.0946 (1.00) |
0.871 (1.00) |
0.0698 (1.00) |
0.726 (1.00) |
0.344 (1.00) |
0.485 (1.00) |
0.146 (1.00) |
|
| 6p loss | 24 (8%) | 263 |
0.358 (1.00) |
0.184 (1.00) |
0.017 (1.00) |
0.406 (1.00) |
0.786 (1.00) |
0.659 (1.00) |
0.342 (1.00) |
0.721 (1.00) |
0.665 (1.00) |
1 (1.00) |
|
| 6q loss | 64 (22%) | 223 |
0.973 (1.00) |
0.509 (1.00) |
0.323 (1.00) |
0.0174 (1.00) |
0.623 (1.00) |
0.296 (1.00) |
0.441 (1.00) |
0.467 (1.00) |
0.536 (1.00) |
0.775 (1.00) |
0.846 (1.00) |
| 7p loss | 10 (3%) | 277 |
0.819 (1.00) |
0.236 (1.00) |
1 (1.00) |
0.437 (1.00) |
1 (1.00) |
0.283 (1.00) |
0.443 (1.00) |
0.246 (1.00) |
0.502 (1.00) |
1 (1.00) |
|
| 7q loss | 11 (4%) | 276 |
0.716 (1.00) |
0.192 (1.00) |
0.556 (1.00) |
0.0196 (1.00) |
0.893 (1.00) |
0.692 (1.00) |
1 (1.00) |
0.653 (1.00) |
0.536 (1.00) |
0.679 (1.00) |
|
| 8p loss | 73 (25%) | 214 |
0.58 (1.00) |
0.847 (1.00) |
1 (1.00) |
0.148 (1.00) |
0.0946 (1.00) |
0.111 (1.00) |
0.826 (1.00) |
0.786 (1.00) |
0.946 (1.00) |
0.79 (1.00) |
0.711 (1.00) |
| 8q loss | 10 (3%) | 277 |
0.305 (1.00) |
0.547 (1.00) |
0.758 (1.00) |
0.492 (1.00) |
0.678 (1.00) |
0.814 (1.00) |
0.124 (1.00) |
1 (1.00) |
1 (1.00) |
0.654 (1.00) |
|
| 9p loss | 89 (31%) | 198 |
0.00716 (1.00) |
0.0636 (1.00) |
0.203 (1.00) |
0.853 (1.00) |
0.558 (1.00) |
0.231 (1.00) |
0.0239 (1.00) |
0.825 (1.00) |
0.0483 (1.00) |
1 (1.00) |
0.479 (1.00) |
| 9q loss | 74 (26%) | 213 |
0.317 (1.00) |
0.376 (1.00) |
1 (1.00) |
0.984 (1.00) |
0.281 (1.00) |
0.293 (1.00) |
0.177 (1.00) |
0.625 (1.00) |
0.366 (1.00) |
0.419 (1.00) |
0.852 (1.00) |
| 10p loss | 23 (8%) | 264 |
0.305 (1.00) |
0.615 (1.00) |
0.132 (1.00) |
0.326 (1.00) |
0.898 (1.00) |
0.484 (1.00) |
0.425 (1.00) |
0.892 (1.00) |
0.38 (1.00) |
1 (1.00) |
|
| 10q loss | 25 (9%) | 262 |
0.335 (1.00) |
0.169 (1.00) |
1 (1.00) |
0.00119 (0.976) |
0.325 (1.00) |
0.102 (1.00) |
1 (1.00) |
0.159 (1.00) |
0.389 (1.00) |
1 (1.00) |
|
| 11p loss | 22 (8%) | 265 |
0.164 (1.00) |
0.00458 (1.00) |
0.825 (1.00) |
0.572 (1.00) |
0.399 (1.00) |
0.977 (1.00) |
0.0629 (1.00) |
0.0427 (1.00) |
0.036 (1.00) |
1 (1.00) |
1 (1.00) |
| 11q loss | 18 (6%) | 269 |
0.162 (1.00) |
0.572 (1.00) |
1 (1.00) |
0.344 (1.00) |
0.54 (1.00) |
1 (1.00) |
0.74 (1.00) |
0.0343 (1.00) |
0.9 (1.00) |
0.338 (1.00) |
0.168 (1.00) |
| 12p loss | 25 (9%) | 262 |
0.354 (1.00) |
0.782 (1.00) |
0.837 (1.00) |
0.572 (1.00) |
0.108 (1.00) |
0.603 (1.00) |
1 (1.00) |
0.309 (1.00) |
0.539 (1.00) |
0.675 (1.00) |
0.391 (1.00) |
| 12q loss | 18 (6%) | 269 |
0.0711 (1.00) |
0.878 (1.00) |
0.468 (1.00) |
0.0796 (1.00) |
0.516 (1.00) |
0.375 (1.00) |
0.366 (1.00) |
0.299 (1.00) |
0.618 (1.00) |
1 (1.00) |
|
| 13q loss | 65 (23%) | 222 |
0.157 (1.00) |
0.249 (1.00) |
0.26 (1.00) |
0.0273 (1.00) |
0.381 (1.00) |
0.876 (1.00) |
0.118 (1.00) |
0.414 (1.00) |
0.348 (1.00) |
0.777 (1.00) |
0.437 (1.00) |
| 14q loss | 27 (9%) | 260 |
0.565 (1.00) |
0.964 (1.00) |
0.548 (1.00) |
0.666 (1.00) |
0.139 (1.00) |
0.785 (1.00) |
1 (1.00) |
0.28 (1.00) |
0.8 (1.00) |
0.403 (1.00) |
0.154 (1.00) |
| 15q loss | 64 (22%) | 223 |
0.758 (1.00) |
0.045 (1.00) |
0.394 (1.00) |
0.889 (1.00) |
0.0799 (1.00) |
0.752 (1.00) |
1 (1.00) |
0.934 (1.00) |
0.906 (1.00) |
0.775 (1.00) |
0.431 (1.00) |
| 16p loss | 22 (8%) | 265 |
0.881 (1.00) |
0.316 (1.00) |
0.825 (1.00) |
0.495 (1.00) |
1 (1.00) |
0.949 (1.00) |
0.0038 (1.00) |
0.0586 (1.00) |
0.169 (1.00) |
0.757 (1.00) |
|
| 16q loss | 40 (14%) | 247 |
0.0666 (1.00) |
0.235 (1.00) |
0.611 (1.00) |
0.825 (1.00) |
0.116 (1.00) |
0.207 (1.00) |
0.524 (1.00) |
0.107 (1.00) |
0.215 (1.00) |
0.736 (1.00) |
0.813 (1.00) |
| 17p loss | 75 (26%) | 212 |
0.491 (1.00) |
0.621 (1.00) |
0.689 (1.00) |
0.156 (1.00) |
0.9 (1.00) |
0.316 (1.00) |
0.372 (1.00) |
0.64 (1.00) |
0.292 (1.00) |
0.174 (1.00) |
0.71 (1.00) |
| 17q loss | 12 (4%) | 275 |
0.153 (1.00) |
0.958 (1.00) |
1 (1.00) |
0.58 (1.00) |
0.532 (1.00) |
0.648 (1.00) |
0.751 (1.00) |
0.459 (1.00) |
1 (1.00) |
0.0939 (1.00) |
|
| 18p loss | 47 (16%) | 240 |
0.535 (1.00) |
0.0359 (1.00) |
0.874 (1.00) |
0.01 (1.00) |
0.288 (1.00) |
0.294 (1.00) |
0.476 (1.00) |
0.0352 (1.00) |
0.00805 (1.00) |
0.331 (1.00) |
0.665 (1.00) |
| 18q loss | 73 (25%) | 214 |
0.00807 (1.00) |
0.24 (1.00) |
1 (1.00) |
0.529 (1.00) |
0.471 (1.00) |
0.121 (1.00) |
0.306 (1.00) |
0.203 (1.00) |
0.00331 (1.00) |
0.173 (1.00) |
0.573 (1.00) |
| 19p loss | 81 (28%) | 206 |
0.0447 (1.00) |
0.292 (1.00) |
0.0124 (1.00) |
0.758 (1.00) |
0.595 (1.00) |
0.168 (1.00) |
0.019 (1.00) |
0.0801 (1.00) |
0.141 (1.00) |
1 (1.00) |
0.275 (1.00) |
| 19q loss | 44 (15%) | 243 |
0.0922 (1.00) |
0.396 (1.00) |
0.413 (1.00) |
0.134 (1.00) |
0.28 (1.00) |
0.381 (1.00) |
0.0457 (1.00) |
0.313 (1.00) |
0.507 (1.00) |
0.824 (1.00) |
|
| 20p loss | 42 (15%) | 245 |
0.0875 (1.00) |
0.353 (1.00) |
0.868 (1.00) |
0.299 (1.00) |
0.227 (1.00) |
0.0293 (1.00) |
0.198 (1.00) |
0.0747 (1.00) |
0.747 (1.00) |
0.817 (1.00) |
|
| 20q loss | 14 (5%) | 273 |
0.092 (1.00) |
0.271 (1.00) |
0.789 (1.00) |
0.287 (1.00) |
0.923 (1.00) |
0.546 (1.00) |
0.392 (1.00) |
0.393 (1.00) |
1 (1.00) |
0.703 (1.00) |
|
| 21q loss | 42 (15%) | 245 |
0.848 (1.00) |
0.707 (1.00) |
0.0295 (1.00) |
0.0916 (1.00) |
0.575 (1.00) |
0.885 (1.00) |
0.729 (1.00) |
0.831 (1.00) |
0.783 (1.00) |
0.497 (1.00) |
1 (1.00) |
| 22q loss | 64 (22%) | 223 |
0.997 (1.00) |
0.126 (1.00) |
0.066 (1.00) |
0.499 (1.00) |
0.796 (1.00) |
0.741 (1.00) |
0.9 (1.00) |
0.183 (1.00) |
0.973 (1.00) |
0.15 (1.00) |
1 (1.00) |
| Xq loss | 6 (2%) | 281 |
0.327 (1.00) |
0.0987 (1.00) |
1 (1.00) |
0.00946 (1.00) |
0.576 (1.00) |
0.84 (1.00) |
0.538 (1.00) |
0.816 (1.00) |
0.0532 (1.00) |
1 (1.00) |
'4q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'
P value = 6.68e-05 (Chi-square test), Q value = 0.055
Table S1. Gene #8: '4q gain mutation analysis' versus Clinical Feature #5: '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 SOLID PATTERN PREDOMINANT ADENOCARCINOMA | MUCINOUS (COLLOID) ADENOCARCINOMA |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 6 | 65 | 181 | 3 | 10 | 2 | 3 | 2 | 10 | 1 | 4 |
| 4Q GAIN MUTATED | 0 | 1 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 4Q GAIN WILD-TYPE | 6 | 64 | 175 | 3 | 10 | 2 | 3 | 2 | 10 | 0 | 4 |
Figure S1. Get High-res Image Gene #8: '4q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
'8q gain mutation analysis' versus 'AGE'
P value = 0.000246 (t-test), Q value = 0.2
Table S2. Gene #16: '8q gain mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 256 | 65.4 (9.7) |
| 8Q GAIN MUTATED | 79 | 62.2 (9.1) |
| 8Q GAIN WILD-TYPE | 177 | 66.9 (9.6) |
Figure S2. Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #2: 'AGE'
'1q loss mutation analysis' versus 'Time to Death'
P value = 3.77e-06 (logrank test), Q value = 0.0031
Table S3. Gene #42: '1q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 253 | 81 | 0.0 - 224.0 (13.2) |
| 1Q LOSS MUTATED | 8 | 5 | 0.1 - 21.5 (8.4) |
| 1Q LOSS WILD-TYPE | 245 | 76 | 0.0 - 224.0 (13.7) |
Figure S3. Get High-res Image Gene #42: '1q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'
Methods & Data
Input
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = LUAD.clin.merged.picked.txt
-
Number of patients = 287
-
Number of significantly arm-level cnvs = 79
-
Number of selected clinical features = 11
-
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 © 2012
Broad Institute TCGA GDAC as part of the TCGA Research Network.
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