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 79 arm-level results and 14 clinical features across 327 patients, 5 significant findings detected with Q value < 0.25.
-
11q gain cnv correlated to 'AGE'.
-
1q loss cnv correlated to 'Time to Death'.
-
7q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
-
10q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
-
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 79 arm-level results and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 5 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 | STOPPEDSMOKINGYEAR | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET | ||
| 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 | t-test | Fisher's exact test | t-test | |
| 11q gain | 37 (11%) | 290 |
0.359 (1.00) |
5.13e-05 (0.0544) |
0.161 (1.00) |
0.751 (1.00) |
0.774 (1.00) |
0.321 (1.00) |
0.419 (1.00) |
0.58 (1.00) |
0.165 (1.00) |
0.262 (1.00) |
0.191 (1.00) |
0.00166 (1.00) |
0.0515 (1.00) |
0.11 (1.00) |
| 1q loss | 9 (3%) | 318 |
5.79e-05 (0.0613) |
0.731 (1.00) |
0.737 (1.00) |
0.00169 (1.00) |
0.791 (1.00) |
0.087 (1.00) |
1 (1.00) |
0.329 (1.00) |
0.437 (1.00) |
0.34 (1.00) |
0.0402 (1.00) |
0.695 (1.00) |
||
| 7q loss | 12 (4%) | 315 |
0.705 (1.00) |
0.207 (1.00) |
0.557 (1.00) |
9.89e-05 (0.105) |
0.902 (1.00) |
1 (1.00) |
1 (1.00) |
0.96 (1.00) |
0.537 (1.00) |
0.192 (1.00) |
0.116 (1.00) |
0.123 (1.00) |
||
| 10q loss | 28 (9%) | 299 |
0.336 (1.00) |
0.124 (1.00) |
0.845 (1.00) |
1.23e-05 (0.013) |
0.264 (1.00) |
0.0921 (1.00) |
0.872 (1.00) |
0.131 (1.00) |
0.237 (1.00) |
0.116 (1.00) |
0.468 (1.00) |
0.224 (1.00) |
0.961 (1.00) |
|
| 18p loss | 55 (17%) | 272 |
0.55 (1.00) |
0.0363 (1.00) |
0.299 (1.00) |
0.00531 (1.00) |
0.13 (1.00) |
0.0307 (1.00) |
0.324 (1.00) |
0.0437 (1.00) |
0.00932 (1.00) |
0.218 (1.00) |
0.000226 (0.239) |
0.508 (1.00) |
0.337 (1.00) |
0.0165 (1.00) |
| 1p gain | 41 (13%) | 286 |
0.89 (1.00) |
0.00104 (1.00) |
0.869 (1.00) |
0.492 (1.00) |
0.983 (1.00) |
0.701 (1.00) |
0.000714 (0.752) |
0.651 (1.00) |
0.000269 (0.283) |
0.488 (1.00) |
0.829 (1.00) |
0.913 (1.00) |
0.478 (1.00) |
0.734 (1.00) |
| 1q gain | 127 (39%) | 200 |
0.862 (1.00) |
0.372 (1.00) |
0.734 (1.00) |
0.512 (1.00) |
0.528 (1.00) |
0.21 (1.00) |
0.0268 (1.00) |
0.287 (1.00) |
0.0261 (1.00) |
0.816 (1.00) |
0.941 (1.00) |
0.822 (1.00) |
0.43 (1.00) |
0.639 (1.00) |
| 2p gain | 41 (13%) | 286 |
0.0816 (1.00) |
0.0548 (1.00) |
0.0431 (1.00) |
0.851 (1.00) |
0.683 (1.00) |
0.108 (1.00) |
0.766 (1.00) |
0.0926 (1.00) |
0.22 (1.00) |
1 (1.00) |
0.563 (1.00) |
0.0617 (1.00) |
0.0736 (1.00) |
0.645 (1.00) |
| 2q gain | 33 (10%) | 294 |
0.188 (1.00) |
0.209 (1.00) |
0.274 (1.00) |
0.472 (1.00) |
0.416 (1.00) |
0.932 (1.00) |
0.0666 (1.00) |
0.278 (1.00) |
0.706 (1.00) |
0.553 (1.00) |
0.997 (1.00) |
0.174 (1.00) |
0.86 (1.00) |
|
| 3p gain | 10 (3%) | 317 |
0.117 (1.00) |
0.61 (1.00) |
0.76 (1.00) |
0.964 (1.00) |
0.069 (1.00) |
0.336 (1.00) |
0.577 (1.00) |
0.257 (1.00) |
0.473 (1.00) |
0.754 (1.00) |
0.495 (1.00) |
0.4 (1.00) |
0.228 (1.00) |
|
| 3q gain | 19 (6%) | 308 |
0.157 (1.00) |
0.548 (1.00) |
1 (1.00) |
0.99 (1.00) |
0.659 (1.00) |
0.141 (1.00) |
0.762 (1.00) |
0.371 (1.00) |
0.326 (1.00) |
0.848 (1.00) |
0.336 (1.00) |
0.434 (1.00) |
0.0559 (1.00) |
|
| 4p gain | 23 (7%) | 304 |
0.671 (1.00) |
0.0183 (1.00) |
0.284 (1.00) |
0.781 (1.00) |
0.648 (1.00) |
1 (1.00) |
0.0715 (1.00) |
0.311 (1.00) |
1 (1.00) |
0.0586 (1.00) |
0.252 (1.00) |
0.318 (1.00) |
0.935 (1.00) |
|
| 4q gain | 7 (2%) | 320 |
0.577 (1.00) |
0.869 (1.00) |
0.251 (1.00) |
0.995 (1.00) |
0.237 (1.00) |
0.344 (1.00) |
0.183 (1.00) |
0.622 (1.00) |
0.36 (1.00) |
0.0439 (1.00) |
0.781 (1.00) |
0.531 (1.00) |
0.0241 (1.00) |
|
| 5p gain | 124 (38%) | 203 |
0.694 (1.00) |
0.15 (1.00) |
1 (1.00) |
0.786 (1.00) |
0.386 (1.00) |
0.822 (1.00) |
0.679 (1.00) |
0.534 (1.00) |
0.581 (1.00) |
0.152 (1.00) |
0.083 (1.00) |
0.036 (1.00) |
0.443 (1.00) |
0.827 (1.00) |
| 5q gain | 39 (12%) | 288 |
0.958 (1.00) |
0.716 (1.00) |
0.396 (1.00) |
0.782 (1.00) |
0.667 (1.00) |
0.848 (1.00) |
0.247 (1.00) |
0.488 (1.00) |
0.0746 (1.00) |
0.662 (1.00) |
0.807 (1.00) |
0.186 (1.00) |
0.317 (1.00) |
|
| 6p gain | 47 (14%) | 280 |
0.818 (1.00) |
0.931 (1.00) |
0.528 (1.00) |
0.902 (1.00) |
0.584 (1.00) |
0.413 (1.00) |
0.224 (1.00) |
0.847 (1.00) |
0.926 (1.00) |
0.75 (1.00) |
0.968 (1.00) |
0.861 (1.00) |
0.415 (1.00) |
0.0988 (1.00) |
| 6q gain | 11 (3%) | 316 |
0.559 (1.00) |
0.26 (1.00) |
0.0142 (1.00) |
0.986 (1.00) |
0.454 (1.00) |
0.679 (1.00) |
0.434 (1.00) |
0.39 (1.00) |
1 (1.00) |
0.894 (1.00) |
0.774 (1.00) |
0.0657 (1.00) |
0.453 (1.00) |
|
| 7p gain | 113 (35%) | 214 |
0.237 (1.00) |
0.176 (1.00) |
0.642 (1.00) |
0.193 (1.00) |
0.535 (1.00) |
0.127 (1.00) |
0.0157 (1.00) |
0.199 (1.00) |
0.0639 (1.00) |
0.469 (1.00) |
0.674 (1.00) |
0.702 (1.00) |
0.473 (1.00) |
0.976 (1.00) |
| 7q gain | 81 (25%) | 246 |
0.878 (1.00) |
0.0525 (1.00) |
0.44 (1.00) |
0.82 (1.00) |
0.614 (1.00) |
0.402 (1.00) |
0.252 (1.00) |
0.082 (1.00) |
0.0561 (1.00) |
0.595 (1.00) |
0.965 (1.00) |
0.731 (1.00) |
0.892 (1.00) |
0.797 (1.00) |
| 8p gain | 39 (12%) | 288 |
0.417 (1.00) |
0.00097 (1.00) |
0.494 (1.00) |
0.814 (1.00) |
0.211 (1.00) |
0.937 (1.00) |
0.429 (1.00) |
0.846 (1.00) |
0.718 (1.00) |
0.524 (1.00) |
0.116 (1.00) |
0.0357 (1.00) |
0.0403 (1.00) |
|
| 8q gain | 101 (31%) | 226 |
0.842 (1.00) |
0.000962 (1.00) |
0.337 (1.00) |
0.321 (1.00) |
0.537 (1.00) |
0.411 (1.00) |
0.354 (1.00) |
0.384 (1.00) |
0.494 (1.00) |
0.627 (1.00) |
0.524 (1.00) |
0.191 (1.00) |
0.0725 (1.00) |
0.031 (1.00) |
| 9p gain | 8 (2%) | 319 |
0.2 (1.00) |
0.461 (1.00) |
0.476 (1.00) |
0.731 (1.00) |
0.629 (1.00) |
0.455 (1.00) |
1 (1.00) |
0.808 (1.00) |
1 (1.00) |
0.269 (1.00) |
0.0309 (1.00) |
0.426 (1.00) |
0.52 (1.00) |
|
| 9q gain | 4 (1%) | 323 |
0.0591 (1.00) |
0.288 (1.00) |
1 (1.00) |
0.996 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.853 (1.00) |
1 (1.00) |
0.634 (1.00) |
0.274 (1.00) |
1 (1.00) |
0.758 (1.00) |
|
| 10p gain | 35 (11%) | 292 |
0.976 (1.00) |
0.371 (1.00) |
0.153 (1.00) |
0.82 (1.00) |
0.564 (1.00) |
0.53 (1.00) |
0.196 (1.00) |
0.901 (1.00) |
0.443 (1.00) |
0.708 (1.00) |
0.0437 (1.00) |
0.0636 (1.00) |
0.00215 (1.00) |
0.512 (1.00) |
| 10q gain | 20 (6%) | 307 |
0.887 (1.00) |
0.957 (1.00) |
0.246 (1.00) |
0.349 (1.00) |
0.167 (1.00) |
0.176 (1.00) |
0.323 (1.00) |
0.155 (1.00) |
1 (1.00) |
0.132 (1.00) |
0.513 (1.00) |
0.0592 (1.00) |
0.275 (1.00) |
|
| 11p gain | 26 (8%) | 301 |
0.715 (1.00) |
0.0594 (1.00) |
0.414 (1.00) |
0.72 (1.00) |
0.711 (1.00) |
0.476 (1.00) |
0.436 (1.00) |
0.926 (1.00) |
0.293 (1.00) |
0.666 (1.00) |
0.366 (1.00) |
0.4 (1.00) |
0.806 (1.00) |
0.894 (1.00) |
| 12p gain | 41 (13%) | 286 |
0.846 (1.00) |
0.00254 (1.00) |
0.408 (1.00) |
0.558 (1.00) |
0.288 (1.00) |
0.106 (1.00) |
1 (1.00) |
0.0789 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.0879 (1.00) |
0.0626 (1.00) |
0.104 (1.00) |
|
| 12q gain | 36 (11%) | 291 |
0.694 (1.00) |
0.00428 (1.00) |
0.48 (1.00) |
0.48 (1.00) |
0.3 (1.00) |
0.344 (1.00) |
0.719 (1.00) |
0.234 (1.00) |
0.71 (1.00) |
0.0356 (1.00) |
0.104 (1.00) |
0.0421 (1.00) |
0.006 (1.00) |
|
| 13q gain | 15 (5%) | 312 |
0.588 (1.00) |
0.564 (1.00) |
1 (1.00) |
0.98 (1.00) |
0.0834 (1.00) |
0.411 (1.00) |
0.111 (1.00) |
0.452 (1.00) |
1 (1.00) |
0.767 (1.00) |
0.395 (1.00) |
0.354 (1.00) |
0.75 (1.00) |
|
| 14q gain | 37 (11%) | 290 |
0.461 (1.00) |
0.474 (1.00) |
0.221 (1.00) |
0.901 (1.00) |
0.311 (1.00) |
0.434 (1.00) |
0.19 (1.00) |
0.5 (1.00) |
0.538 (1.00) |
0.145 (1.00) |
0.345 (1.00) |
0.877 (1.00) |
0.727 (1.00) |
0.513 (1.00) |
| 15q gain | 10 (3%) | 317 |
0.284 (1.00) |
0.402 (1.00) |
1 (1.00) |
0.108 (1.00) |
0.625 (1.00) |
0.266 (1.00) |
0.431 (1.00) |
0.176 (1.00) |
1 (1.00) |
0.807 (1.00) |
0.55 (1.00) |
0.136 (1.00) |
0.931 (1.00) |
|
| 16p gain | 44 (13%) | 283 |
0.547 (1.00) |
0.148 (1.00) |
1 (1.00) |
0.314 (1.00) |
0.7 (1.00) |
0.6 (1.00) |
0.416 (1.00) |
0.354 (1.00) |
0.351 (1.00) |
1 (1.00) |
0.316 (1.00) |
0.107 (1.00) |
0.0199 (1.00) |
0.779 (1.00) |
| 16q gain | 30 (9%) | 297 |
0.743 (1.00) |
0.114 (1.00) |
0.442 (1.00) |
0.292 (1.00) |
0.284 (1.00) |
0.836 (1.00) |
0.183 (1.00) |
0.2 (1.00) |
0.184 (1.00) |
0.236 (1.00) |
0.0478 (1.00) |
0.0423 (1.00) |
0.391 (1.00) |
0.353 (1.00) |
| 17p gain | 18 (6%) | 309 |
0.749 (1.00) |
0.861 (1.00) |
0.223 (1.00) |
0.265 (1.00) |
0.384 (1.00) |
0.781 (1.00) |
0.692 (1.00) |
0.353 (1.00) |
0.501 (1.00) |
0.0179 (1.00) |
0.0775 (1.00) |
0.387 (1.00) |
0.641 (1.00) |
0.929 (1.00) |
| 17q gain | 55 (17%) | 272 |
0.266 (1.00) |
0.879 (1.00) |
1 (1.00) |
0.437 (1.00) |
0.362 (1.00) |
0.0603 (1.00) |
0.889 (1.00) |
0.0324 (1.00) |
0.0907 (1.00) |
0.0562 (1.00) |
0.0375 (1.00) |
0.168 (1.00) |
0.389 (1.00) |
0.414 (1.00) |
| 18p gain | 28 (9%) | 299 |
0.252 (1.00) |
0.294 (1.00) |
0.234 (1.00) |
0.109 (1.00) |
0.868 (1.00) |
0.368 (1.00) |
0.221 (1.00) |
0.95 (1.00) |
1 (1.00) |
0.0618 (1.00) |
0.11 (1.00) |
0.432 (1.00) |
0.934 (1.00) |
|
| 18q gain | 17 (5%) | 310 |
0.666 (1.00) |
0.188 (1.00) |
0.619 (1.00) |
0.787 (1.00) |
0.746 (1.00) |
0.56 (1.00) |
0.822 (1.00) |
0.954 (1.00) |
1 (1.00) |
0.656 (1.00) |
0.0594 (1.00) |
0.634 (1.00) |
0.222 (1.00) |
|
| 19p gain | 6 (2%) | 321 |
0.841 (1.00) |
0.479 (1.00) |
0.693 (1.00) |
0.999 (1.00) |
0.647 (1.00) |
0.169 (1.00) |
0.393 (1.00) |
0.336 (1.00) |
0.317 (1.00) |
0.922 (1.00) |
0.464 (1.00) |
1 (1.00) |
0.398 (1.00) |
|
| 19q gain | 16 (5%) | 311 |
0.963 (1.00) |
0.571 (1.00) |
0.308 (1.00) |
0.946 (1.00) |
0.108 (1.00) |
0.813 (1.00) |
0.501 (1.00) |
0.802 (1.00) |
1 (1.00) |
0.824 (1.00) |
0.0144 (1.00) |
0.183 (1.00) |
0.268 (1.00) |
|
| 20p gain | 46 (14%) | 281 |
0.7 (1.00) |
0.615 (1.00) |
0.751 (1.00) |
0.561 (1.00) |
0.787 (1.00) |
0.84 (1.00) |
0.483 (1.00) |
0.701 (1.00) |
0.316 (1.00) |
1 (1.00) |
0.552 (1.00) |
0.844 (1.00) |
0.0278 (1.00) |
0.536 (1.00) |
| 20q gain | 57 (17%) | 270 |
0.604 (1.00) |
0.28 (1.00) |
0.243 (1.00) |
0.141 (1.00) |
0.572 (1.00) |
0.533 (1.00) |
0.773 (1.00) |
0.533 (1.00) |
0.694 (1.00) |
0.219 (1.00) |
0.0403 (1.00) |
0.585 (1.00) |
0.0189 (1.00) |
0.59 (1.00) |
| 21q gain | 29 (9%) | 298 |
0.527 (1.00) |
0.532 (1.00) |
0.246 (1.00) |
0.701 (1.00) |
0.525 (1.00) |
0.535 (1.00) |
0.522 (1.00) |
0.941 (1.00) |
1 (1.00) |
0.789 (1.00) |
0.0502 (1.00) |
0.00664 (1.00) |
0.8 (1.00) |
|
| 22q gain | 14 (4%) | 313 |
0.46 (1.00) |
0.144 (1.00) |
1 (1.00) |
0.32 (1.00) |
0.387 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.535 (1.00) |
0.594 (1.00) |
0.512 (1.00) |
0.681 (1.00) |
0.682 (1.00) |
0.4 (1.00) |
|
| Xq gain | 15 (5%) | 312 |
0.165 (1.00) |
0.0271 (1.00) |
0.6 (1.00) |
0.588 (1.00) |
0.351 (1.00) |
0.865 (1.00) |
0.785 (1.00) |
0.913 (1.00) |
1 (1.00) |
0.428 (1.00) |
0.992 (1.00) |
0.172 (1.00) |
0.0438 (1.00) |
|
| 1p loss | 26 (8%) | 301 |
0.207 (1.00) |
0.674 (1.00) |
0.22 (1.00) |
0.377 (1.00) |
0.574 (1.00) |
0.916 (1.00) |
0.34 (1.00) |
0.292 (1.00) |
0.205 (1.00) |
0.172 (1.00) |
0.0672 (1.00) |
0.143 (1.00) |
0.692 (1.00) |
|
| 2p loss | 4 (1%) | 323 |
0.187 (1.00) |
0.313 (1.00) |
1 (1.00) |
0.81 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.602 (1.00) |
1 (1.00) |
0.46 (1.00) |
0.267 (1.00) |
|||
| 3p loss | 66 (20%) | 261 |
0.905 (1.00) |
0.814 (1.00) |
1 (1.00) |
0.0134 (1.00) |
0.859 (1.00) |
0.474 (1.00) |
0.306 (1.00) |
0.216 (1.00) |
0.00911 (1.00) |
1 (1.00) |
0.77 (1.00) |
0.765 (1.00) |
0.0331 (1.00) |
0.252 (1.00) |
| 3q loss | 38 (12%) | 289 |
0.937 (1.00) |
0.971 (1.00) |
0.863 (1.00) |
0.016 (1.00) |
0.852 (1.00) |
0.116 (1.00) |
0.482 (1.00) |
0.627 (1.00) |
0.195 (1.00) |
1 (1.00) |
0.167 (1.00) |
0.455 (1.00) |
0.515 (1.00) |
0.815 (1.00) |
| 4p loss | 29 (9%) | 298 |
0.45 (1.00) |
0.0136 (1.00) |
0.329 (1.00) |
0.646 (1.00) |
0.548 (1.00) |
0.11 (1.00) |
0.231 (1.00) |
0.674 (1.00) |
0.696 (1.00) |
0.404 (1.00) |
0.824 (1.00) |
0.0369 (1.00) |
0.0681 (1.00) |
0.451 (1.00) |
| 4q loss | 34 (10%) | 293 |
0.522 (1.00) |
0.0509 (1.00) |
0.0183 (1.00) |
0.88 (1.00) |
0.777 (1.00) |
0.111 (1.00) |
0.00429 (1.00) |
0.508 (1.00) |
0.0364 (1.00) |
0.141 (1.00) |
0.46 (1.00) |
0.358 (1.00) |
0.0405 (1.00) |
0.88 (1.00) |
| 5p loss | 11 (3%) | 316 |
0.786 (1.00) |
0.94 (1.00) |
0.234 (1.00) |
0.0863 (1.00) |
0.841 (1.00) |
0.449 (1.00) |
0.434 (1.00) |
0.665 (1.00) |
1 (1.00) |
0.485 (1.00) |
0.000691 (0.728) |
0.352 (1.00) |
0.779 (1.00) |
|
| 5q loss | 44 (13%) | 283 |
0.593 (1.00) |
0.179 (1.00) |
0.052 (1.00) |
0.0529 (1.00) |
0.954 (1.00) |
0.0485 (1.00) |
0.909 (1.00) |
0.308 (1.00) |
0.494 (1.00) |
0.254 (1.00) |
0.0479 (1.00) |
0.0966 (1.00) |
0.975 (1.00) |
|
| 6p loss | 30 (9%) | 297 |
0.929 (1.00) |
0.0816 (1.00) |
0.248 (1.00) |
0.535 (1.00) |
0.493 (1.00) |
0.439 (1.00) |
0.225 (1.00) |
0.359 (1.00) |
0.411 (1.00) |
0.314 (1.00) |
0.295 (1.00) |
0.286 (1.00) |
0.242 (1.00) |
|
| 6q loss | 73 (22%) | 254 |
0.814 (1.00) |
0.256 (1.00) |
0.894 (1.00) |
0.0305 (1.00) |
0.577 (1.00) |
0.192 (1.00) |
0.322 (1.00) |
0.596 (1.00) |
0.342 (1.00) |
0.409 (1.00) |
0.162 (1.00) |
0.982 (1.00) |
0.595 (1.00) |
0.362 (1.00) |
| 7p loss | 11 (3%) | 316 |
0.827 (1.00) |
0.255 (1.00) |
1 (1.00) |
0.27 (1.00) |
0.892 (1.00) |
0.679 (1.00) |
0.474 (1.00) |
0.542 (1.00) |
0.506 (1.00) |
0.593 (1.00) |
0.817 (1.00) |
0.31 (1.00) |
0.313 (1.00) |
|
| 8p loss | 89 (27%) | 238 |
0.719 (1.00) |
0.796 (1.00) |
1 (1.00) |
0.189 (1.00) |
0.0819 (1.00) |
0.213 (1.00) |
0.936 (1.00) |
0.731 (1.00) |
0.833 (1.00) |
0.607 (1.00) |
0.351 (1.00) |
0.159 (1.00) |
0.0134 (1.00) |
0.232 (1.00) |
| 8q loss | 12 (4%) | 315 |
0.316 (1.00) |
0.92 (1.00) |
0.775 (1.00) |
0.0165 (1.00) |
1 (1.00) |
0.914 (1.00) |
0.643 (1.00) |
0.89 (1.00) |
1 (1.00) |
0.22 (1.00) |
0.0403 (1.00) |
|||
| 9p loss | 99 (30%) | 228 |
0.00585 (1.00) |
0.235 (1.00) |
0.148 (1.00) |
0.975 (1.00) |
0.398 (1.00) |
0.184 (1.00) |
0.00744 (1.00) |
0.905 (1.00) |
0.038 (1.00) |
1 (1.00) |
0.881 (1.00) |
0.151 (1.00) |
0.0855 (1.00) |
0.603 (1.00) |
| 9q loss | 84 (26%) | 243 |
0.203 (1.00) |
0.995 (1.00) |
0.899 (1.00) |
0.882 (1.00) |
0.391 (1.00) |
0.169 (1.00) |
0.115 (1.00) |
0.695 (1.00) |
0.232 (1.00) |
0.427 (1.00) |
0.447 (1.00) |
0.95 (1.00) |
0.0285 (1.00) |
0.741 (1.00) |
| 10p loss | 26 (8%) | 301 |
0.301 (1.00) |
0.296 (1.00) |
0.152 (1.00) |
0.225 (1.00) |
0.842 (1.00) |
0.377 (1.00) |
0.796 (1.00) |
0.929 (1.00) |
0.386 (1.00) |
0.668 (1.00) |
0.781 (1.00) |
0.0924 (1.00) |
0.425 (1.00) |
|
| 11p loss | 25 (8%) | 302 |
0.51 (1.00) |
0.00322 (1.00) |
0.299 (1.00) |
0.681 (1.00) |
1 (1.00) |
0.177 (1.00) |
0.0416 (1.00) |
0.0464 (1.00) |
1 (1.00) |
0.193 (1.00) |
0.208 (1.00) |
0.0462 (1.00) |
0.00121 (1.00) |
|
| 11q loss | 20 (6%) | 307 |
0.424 (1.00) |
0.552 (1.00) |
0.817 (1.00) |
0.715 (1.00) |
0.256 (1.00) |
0.69 (1.00) |
0.286 (1.00) |
0.0151 (1.00) |
0.417 (1.00) |
0.35 (1.00) |
0.0335 (1.00) |
0.458 (1.00) |
0.487 (1.00) |
0.21 (1.00) |
| 12p loss | 29 (9%) | 298 |
0.354 (1.00) |
0.816 (1.00) |
1 (1.00) |
0.541 (1.00) |
0.641 (1.00) |
0.327 (1.00) |
0.887 (1.00) |
0.289 (1.00) |
0.578 (1.00) |
0.694 (1.00) |
0.733 (1.00) |
0.627 (1.00) |
0.025 (1.00) |
0.0736 (1.00) |
| 12q loss | 19 (6%) | 308 |
0.0679 (1.00) |
0.756 (1.00) |
0.636 (1.00) |
0.536 (1.00) |
0.344 (1.00) |
0.438 (1.00) |
0.512 (1.00) |
0.389 (1.00) |
0.617 (1.00) |
0.788 (1.00) |
0.569 (1.00) |
0.152 (1.00) |
0.298 (1.00) |
|
| 13q loss | 74 (23%) | 253 |
0.134 (1.00) |
0.34 (1.00) |
0.895 (1.00) |
0.0181 (1.00) |
0.143 (1.00) |
0.526 (1.00) |
0.161 (1.00) |
0.346 (1.00) |
0.162 (1.00) |
0.785 (1.00) |
0.606 (1.00) |
0.633 (1.00) |
0.113 (1.00) |
0.229 (1.00) |
| 14q loss | 34 (10%) | 293 |
0.63 (1.00) |
0.316 (1.00) |
0.589 (1.00) |
0.814 (1.00) |
0.294 (1.00) |
0.401 (1.00) |
0.901 (1.00) |
0.0274 (1.00) |
0.907 (1.00) |
0.449 (1.00) |
0.0647 (1.00) |
0.161 (1.00) |
0.755 (1.00) |
0.348 (1.00) |
| 15q loss | 70 (21%) | 257 |
0.802 (1.00) |
0.0448 (1.00) |
0.137 (1.00) |
0.746 (1.00) |
0.15 (1.00) |
0.968 (1.00) |
0.943 (1.00) |
0.939 (1.00) |
0.925 (1.00) |
0.778 (1.00) |
0.582 (1.00) |
0.711 (1.00) |
0.345 (1.00) |
0.549 (1.00) |
| 16p loss | 26 (8%) | 301 |
0.976 (1.00) |
0.169 (1.00) |
0.414 (1.00) |
0.558 (1.00) |
0.78 (1.00) |
0.835 (1.00) |
0.0123 (1.00) |
0.0917 (1.00) |
0.205 (1.00) |
0.748 (1.00) |
0.394 (1.00) |
0.0957 (1.00) |
0.643 (1.00) |
|
| 16q loss | 46 (14%) | 281 |
0.0969 (1.00) |
0.233 (1.00) |
0.751 (1.00) |
0.746 (1.00) |
0.0466 (1.00) |
0.653 (1.00) |
0.288 (1.00) |
0.181 (1.00) |
0.136 (1.00) |
1 (1.00) |
0.815 (1.00) |
0.766 (1.00) |
0.218 (1.00) |
0.389 (1.00) |
| 17p loss | 82 (25%) | 245 |
0.81 (1.00) |
0.468 (1.00) |
0.799 (1.00) |
0.1 (1.00) |
0.865 (1.00) |
0.572 (1.00) |
0.933 (1.00) |
0.738 (1.00) |
0.716 (1.00) |
0.425 (1.00) |
0.23 (1.00) |
0.063 (1.00) |
0.0721 (1.00) |
0.112 (1.00) |
| 17q loss | 13 (4%) | 314 |
0.357 (1.00) |
0.47 (1.00) |
0.778 (1.00) |
0.502 (1.00) |
0.406 (1.00) |
0.389 (1.00) |
0.669 (1.00) |
0.435 (1.00) |
1 (1.00) |
0.03 (1.00) |
0.124 (1.00) |
0.232 (1.00) |
0.118 (1.00) |
|
| 18q loss | 84 (26%) | 243 |
0.0252 (1.00) |
0.309 (1.00) |
0.703 (1.00) |
0.452 (1.00) |
0.257 (1.00) |
0.047 (1.00) |
0.295 (1.00) |
0.284 (1.00) |
0.00793 (1.00) |
0.117 (1.00) |
0.175 (1.00) |
0.362 (1.00) |
0.232 (1.00) |
0.312 (1.00) |
| 19p loss | 90 (28%) | 237 |
0.0491 (1.00) |
0.303 (1.00) |
0.0466 (1.00) |
0.649 (1.00) |
0.682 (1.00) |
0.212 (1.00) |
0.0529 (1.00) |
0.1 (1.00) |
0.253 (1.00) |
1 (1.00) |
0.449 (1.00) |
0.343 (1.00) |
0.126 (1.00) |
0.362 (1.00) |
| 19q loss | 51 (16%) | 276 |
0.147 (1.00) |
0.347 (1.00) |
0.878 (1.00) |
0.00456 (1.00) |
0.0858 (1.00) |
0.435 (1.00) |
0.575 (1.00) |
0.0732 (1.00) |
0.4 (1.00) |
0.531 (1.00) |
0.254 (1.00) |
0.701 (1.00) |
0.326 (1.00) |
0.302 (1.00) |
| 20p loss | 46 (14%) | 281 |
0.172 (1.00) |
0.619 (1.00) |
1 (1.00) |
0.678 (1.00) |
0.148 (1.00) |
0.0348 (1.00) |
0.195 (1.00) |
0.131 (1.00) |
1 (1.00) |
0.814 (1.00) |
0.422 (1.00) |
0.498 (1.00) |
0.0416 (1.00) |
|
| 20q loss | 17 (5%) | 310 |
0.523 (1.00) |
0.483 (1.00) |
1 (1.00) |
0.379 (1.00) |
0.938 (1.00) |
0.768 (1.00) |
0.194 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.752 (1.00) |
0.424 (1.00) |
0.36 (1.00) |
0.299 (1.00) |
|
| 21q loss | 47 (14%) | 280 |
0.905 (1.00) |
0.991 (1.00) |
0.0395 (1.00) |
0.116 (1.00) |
0.585 (1.00) |
0.647 (1.00) |
0.604 (1.00) |
0.574 (1.00) |
0.416 (1.00) |
0.506 (1.00) |
0.16 (1.00) |
0.025 (1.00) |
0.00988 (1.00) |
0.974 (1.00) |
| 22q loss | 71 (22%) | 256 |
0.793 (1.00) |
0.232 (1.00) |
0.225 (1.00) |
0.59 (1.00) |
0.829 (1.00) |
0.916 (1.00) |
0.856 (1.00) |
0.273 (1.00) |
0.942 (1.00) |
0.16 (1.00) |
0.36 (1.00) |
0.87 (1.00) |
0.00719 (1.00) |
0.251 (1.00) |
| Xq loss | 8 (2%) | 319 |
0.272 (1.00) |
0.252 (1.00) |
0.147 (1.00) |
0.0116 (1.00) |
0.105 (1.00) |
0.859 (1.00) |
0.798 (1.00) |
0.302 (1.00) |
0.0798 (1.00) |
0.491 (1.00) |
0.269 (1.00) |
0.72 (1.00) |
0.865 (1.00) |
'11q gain mutation analysis' versus 'AGE'
P value = 5.13e-05 (t-test), Q value = 0.054
Table S1. Gene #22: '11q gain mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 296 | 65.3 (9.8) |
| 11Q GAIN MUTATED | 34 | 58.4 (9.5) |
| 11Q GAIN WILD-TYPE | 262 | 66.2 (9.5) |
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 = 5.79e-05 (logrank test), Q value = 0.061
Table S2. Gene #42: '1q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 291 | 82 | 0.0 - 224.0 (10.0) |
| 1Q LOSS MUTATED | 7 | 3 | 0.1 - 12.2 (5.7) |
| 1Q LOSS WILD-TYPE | 284 | 79 | 0.0 - 224.0 (10.7) |
Figure S2. Get High-res Image Gene #42: '1q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'
'7q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'
P value = 9.89e-05 (Chi-square test), Q value = 0.1
Table S3. Gene #53: '7q loss 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 | 10 | 74 | 199 | 3 | 14 | 2 | 3 | 2 | 13 | 2 | 5 |
| 7Q LOSS MUTATED | 0 | 0 | 8 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 2 |
| 7Q LOSS WILD-TYPE | 10 | 74 | 191 | 3 | 14 | 1 | 3 | 2 | 12 | 2 | 3 |
Figure S3. Get High-res Image Gene #53: '7q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
'10q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'
P value = 1.23e-05 (Chi-square test), Q value = 0.013
Table S4. Gene #59: '10q loss 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 | 10 | 74 | 199 | 3 | 14 | 2 | 3 | 2 | 13 | 2 | 5 |
| 10Q LOSS MUTATED | 1 | 5 | 16 | 1 | 0 | 0 | 2 | 0 | 0 | 2 | 1 |
| 10Q LOSS WILD-TYPE | 9 | 69 | 183 | 2 | 14 | 2 | 1 | 2 | 13 | 0 | 4 |
Figure S4. Get High-res Image Gene #59: '10q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
'18p loss mutation analysis' versus 'NUMBERPACKYEARSSMOKED'
P value = 0.000226 (t-test), Q value = 0.24
Table S5. Gene #71: '18p loss mutation analysis' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 228 | 39.8 (26.2) |
| 18P LOSS MUTATED | 37 | 28.5 (17.6) |
| 18P LOSS WILD-TYPE | 191 | 42.0 (27.1) |
Figure S5. Get High-res Image Gene #71: '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 = 327
-
Number of significantly arm-level cnvs = 79
-
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.