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 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'.
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 | 38 (12%) | 289 |
0.355 (1.00) |
0.000118 (0.125) |
0.119 (1.00) |
0.751 (1.00) |
0.746 (1.00) |
0.24 (1.00) |
0.489 (1.00) |
0.62 (1.00) |
0.124 (1.00) |
0.269 (1.00) |
0.169 (1.00) |
0.00166 (1.00) |
0.0357 (1.00) |
0.124 (1.00) |
1q loss | 11 (3%) | 316 |
3.31e-06 (0.00351) |
0.483 (1.00) |
0.554 (1.00) |
0.00831 (1.00) |
0.711 (1.00) |
0.267 (1.00) |
1 (1.00) |
0.192 (1.00) |
0.14 (1.00) |
0.417 (1.00) |
0.675 (1.00) |
0.93 (1.00) |
0.934 (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 (0.0131) |
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 | 43 (13%) | 284 |
0.919 (1.00) |
0.00042 (0.443) |
1 (1.00) |
0.492 (1.00) |
0.984 (1.00) |
0.786 (1.00) |
0.000989 (1.00) |
0.798 (1.00) |
0.000382 (0.404) |
0.491 (1.00) |
0.666 (1.00) |
0.712 (1.00) |
0.387 (1.00) |
0.632 (1.00) |
1q gain | 127 (39%) | 200 |
0.796 (1.00) |
0.263 (1.00) |
0.571 (1.00) |
0.512 (1.00) |
0.528 (1.00) |
0.299 (1.00) |
0.0268 (1.00) |
0.287 (1.00) |
0.0261 (1.00) |
0.483 (1.00) |
0.974 (1.00) |
0.726 (1.00) |
0.416 (1.00) |
0.709 (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 | 20 (6%) | 307 |
0.122 (1.00) |
0.73 (1.00) |
1 (1.00) |
0.93 (1.00) |
0.804 (1.00) |
0.21 (1.00) |
0.762 (1.00) |
0.527 (1.00) |
0.35 (1.00) |
0.848 (1.00) |
0.336 (1.00) |
0.426 (1.00) |
0.0559 (1.00) |
|
4p gain | 24 (7%) | 303 |
0.671 (1.00) |
0.0183 (1.00) |
0.205 (1.00) |
0.328 (1.00) |
0.568 (1.00) |
0.953 (1.00) |
0.0732 (1.00) |
0.297 (1.00) |
1 (1.00) |
0.04 (1.00) |
0.504 (1.00) |
0.355 (1.00) |
0.935 (1.00) |
|
4q gain | 9 (3%) | 318 |
0.576 (1.00) |
0.692 (1.00) |
0.309 (1.00) |
0.0386 (1.00) |
0.26 (1.00) |
0.266 (1.00) |
0.431 (1.00) |
0.548 (1.00) |
0.437 (1.00) |
0.0138 (1.00) |
0.421 (1.00) |
0.343 (1.00) |
0.2 (1.00) |
|
5p gain | 124 (38%) | 203 |
0.503 (1.00) |
0.164 (1.00) |
0.82 (1.00) |
0.786 (1.00) |
0.367 (1.00) |
0.75 (1.00) |
0.731 (1.00) |
0.611 (1.00) |
0.855 (1.00) |
0.152 (1.00) |
0.0484 (1.00) |
0.0297 (1.00) |
0.373 (1.00) |
0.885 (1.00) |
5q gain | 39 (12%) | 288 |
0.687 (1.00) |
0.758 (1.00) |
0.396 (1.00) |
0.799 (1.00) |
0.822 (1.00) |
0.798 (1.00) |
0.567 (1.00) |
0.789 (1.00) |
0.0746 (1.00) |
0.342 (1.00) |
0.638 (1.00) |
0.318 (1.00) |
0.293 (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 | 10 (3%) | 317 |
0.445 (1.00) |
0.434 (1.00) |
0.0251 (1.00) |
0.993 (1.00) |
0.935 (1.00) |
0.808 (1.00) |
0.577 (1.00) |
0.5 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.774 (1.00) |
0.148 (1.00) |
0.591 (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 |
0.266 (1.00) |
0.0013 (1.00) |
0.304 (1.00) |
0.814 (1.00) |
0.17 (1.00) |
0.772 (1.00) |
0.644 (1.00) |
1 (1.00) |
0.718 (1.00) |
0.515 (1.00) |
0.0856 (1.00) |
0.0357 (1.00) |
0.0247 (1.00) |
|
8q gain | 101 (31%) | 226 |
1 (1.00) |
0.00362 (1.00) |
0.337 (1.00) |
0.321 (1.00) |
0.539 (1.00) |
0.527 (1.00) |
0.288 (1.00) |
0.424 (1.00) |
0.696 (1.00) |
0.627 (1.00) |
0.578 (1.00) |
0.209 (1.00) |
0.111 (1.00) |
0.0399 (1.00) |
9p gain | 9 (3%) | 318 |
0.199 (1.00) |
0.277 (1.00) |
0.737 (1.00) |
0.552 (1.00) |
0.542 (1.00) |
0.347 (1.00) |
0.67 (1.00) |
0.94 (1.00) |
1 (1.00) |
0.289 (1.00) |
0.0309 (1.00) |
0.248 (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 | 27 (8%) | 300 |
0.513 (1.00) |
0.0383 (1.00) |
0.314 (1.00) |
0.72 (1.00) |
0.754 (1.00) |
0.464 (1.00) |
0.328 (1.00) |
1 (1.00) |
0.225 (1.00) |
0.675 (1.00) |
0.328 (1.00) |
0.4 (1.00) |
0.612 (1.00) |
0.683 (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 | 36 (11%) | 291 |
0.348 (1.00) |
0.346 (1.00) |
0.288 (1.00) |
0.901 (1.00) |
0.348 (1.00) |
0.528 (1.00) |
0.218 (1.00) |
0.682 (1.00) |
0.607 (1.00) |
0.145 (1.00) |
0.292 (1.00) |
0.75 (1.00) |
0.702 (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 | 45 (14%) | 282 |
0.471 (1.00) |
0.194 (1.00) |
0.873 (1.00) |
0.314 (1.00) |
0.685 (1.00) |
0.7 (1.00) |
0.449 (1.00) |
0.326 (1.00) |
0.496 (1.00) |
0.745 (1.00) |
0.316 (1.00) |
0.107 (1.00) |
0.0199 (1.00) |
0.779 (1.00) |
16q gain | 31 (9%) | 296 |
0.635 (1.00) |
0.17 (1.00) |
0.343 (1.00) |
0.292 (1.00) |
0.269 (1.00) |
0.74 (1.00) |
0.298 (1.00) |
0.148 (1.00) |
0.357 (1.00) |
0.706 (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 | 56 (17%) | 271 |
0.319 (1.00) |
0.988 (1.00) |
0.769 (1.00) |
0.437 (1.00) |
0.365 (1.00) |
0.0145 (1.00) |
0.87 (1.00) |
0.158 (1.00) |
0.242 (1.00) |
0.0579 (1.00) |
0.0259 (1.00) |
0.15 (1.00) |
0.36 (1.00) |
0.517 (1.00) |
18p gain | 30 (9%) | 297 |
0.579 (1.00) |
0.336 (1.00) |
0.442 (1.00) |
0.124 (1.00) |
0.878 (1.00) |
0.605 (1.00) |
0.731 (1.00) |
0.817 (1.00) |
1 (1.00) |
0.0617 (1.00) |
0.171 (1.00) |
0.603 (1.00) |
0.934 (1.00) |
|
18q gain | 19 (6%) | 308 |
0.418 (1.00) |
0.224 (1.00) |
1 (1.00) |
0.646 (1.00) |
0.773 (1.00) |
0.587 (1.00) |
0.913 (1.00) |
0.922 (1.00) |
1 (1.00) |
0.666 (1.00) |
0.115 (1.00) |
0.67 (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 | 47 (14%) | 280 |
0.738 (1.00) |
0.715 (1.00) |
0.636 (1.00) |
0.561 (1.00) |
0.778 (1.00) |
0.85 (1.00) |
0.436 (1.00) |
0.675 (1.00) |
0.252 (1.00) |
1 (1.00) |
0.651 (1.00) |
0.731 (1.00) |
0.0299 (1.00) |
0.341 (1.00) |
20q gain | 59 (18%) | 268 |
0.649 (1.00) |
0.303 (1.00) |
0.149 (1.00) |
0.141 (1.00) |
0.564 (1.00) |
0.497 (1.00) |
0.762 (1.00) |
0.488 (1.00) |
0.6 (1.00) |
0.142 (1.00) |
0.0554 (1.00) |
0.524 (1.00) |
0.0168 (1.00) |
0.446 (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 | 15 (5%) | 312 |
0.221 (1.00) |
0.284 (1.00) |
0.793 (1.00) |
0.312 (1.00) |
0.164 (1.00) |
0.107 (1.00) |
1 (1.00) |
0.483 (1.00) |
1 (1.00) |
0.512 (1.00) |
0.757 (1.00) |
0.82 (1.00) |
0.4 (1.00) |
|
Xq gain | 16 (5%) | 311 |
0.332 (1.00) |
0.0711 (1.00) |
0.443 (1.00) |
0.635 (1.00) |
0.188 (1.00) |
1 (1.00) |
0.704 (1.00) |
0.896 (1.00) |
1 (1.00) |
0.128 (1.00) |
0.991 (1.00) |
0.152 (1.00) |
0.0431 (1.00) |
|
1p loss | 26 (8%) | 301 |
0.0952 (1.00) |
0.781 (1.00) |
0.101 (1.00) |
0.307 (1.00) |
0.302 (1.00) |
0.875 (1.00) |
0.16 (1.00) |
0.116 (1.00) |
0.205 (1.00) |
0.196 (1.00) |
0.26 (1.00) |
0.265 (1.00) |
0.821 (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 | 67 (20%) | 260 |
0.908 (1.00) |
0.749 (1.00) |
0.891 (1.00) |
0.0134 (1.00) |
0.921 (1.00) |
0.866 (1.00) |
0.336 (1.00) |
0.263 (1.00) |
0.0123 (1.00) |
1 (1.00) |
0.903 (1.00) |
0.895 (1.00) |
0.0237 (1.00) |
0.134 (1.00) |
3q loss | 39 (12%) | 288 |
0.941 (1.00) |
0.94 (1.00) |
0.732 (1.00) |
0.016 (1.00) |
0.839 (1.00) |
0.211 (1.00) |
0.407 (1.00) |
0.78 (1.00) |
0.224 (1.00) |
1 (1.00) |
0.531 (1.00) |
0.589 (1.00) |
0.494 (1.00) |
0.782 (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 | 10 (3%) | 317 |
0.943 (1.00) |
0.395 (1.00) |
0.357 (1.00) |
0.0576 (1.00) |
0.717 (1.00) |
0.336 (1.00) |
0.577 (1.00) |
0.625 (1.00) |
1 (1.00) |
0.65 (1.00) |
0.00406 (1.00) |
0.41 (1.00) |
0.489 (1.00) |
|
5q loss | 43 (13%) | 284 |
0.56 (1.00) |
0.0582 (1.00) |
0.0142 (1.00) |
0.715 (1.00) |
0.0345 (1.00) |
0.897 (1.00) |
0.0737 (1.00) |
0.435 (1.00) |
0.42 (1.00) |
0.491 (1.00) |
0.528 (1.00) |
0.0459 (1.00) |
0.0983 (1.00) |
0.406 (1.00) |
6p loss | 28 (9%) | 299 |
0.939 (1.00) |
0.0693 (1.00) |
0.234 (1.00) |
0.277 (1.00) |
0.855 (1.00) |
0.492 (1.00) |
0.455 (1.00) |
0.6 (1.00) |
0.397 (1.00) |
0.232 (1.00) |
0.344 (1.00) |
0.353 (1.00) |
0.398 (1.00) |
|
6q loss | 73 (22%) | 254 |
0.616 (1.00) |
0.201 (1.00) |
0.689 (1.00) |
0.0305 (1.00) |
0.435 (1.00) |
0.238 (1.00) |
0.322 (1.00) |
0.596 (1.00) |
0.397 (1.00) |
0.409 (1.00) |
0.162 (1.00) |
0.895 (1.00) |
0.619 (1.00) |
0.359 (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 |
0.181 (1.00) |
0.807 (1.00) |
0.389 (1.00) |
0.0165 (1.00) |
1 (1.00) |
0.914 (1.00) |
0.267 (1.00) |
0.89 (1.00) |
1 (1.00) |
0.0977 (1.00) |
0.0434 (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 | 83 (25%) | 244 |
0.299 (1.00) |
0.89 (1.00) |
0.899 (1.00) |
0.882 (1.00) |
0.383 (1.00) |
0.196 (1.00) |
0.11 (1.00) |
0.733 (1.00) |
0.224 (1.00) |
0.426 (1.00) |
0.448 (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 | 24 (7%) | 303 |
0.494 (1.00) |
0.00409 (1.00) |
0.674 (1.00) |
0.613 (1.00) |
0.94 (1.00) |
0.328 (1.00) |
0.0395 (1.00) |
0.0629 (1.00) |
1 (1.00) |
0.176 (1.00) |
0.208 (1.00) |
0.024 (1.00) |
0.0112 (1.00) |
|
11q loss | 21 (6%) | 306 |
0.248 (1.00) |
0.668 (1.00) |
0.825 (1.00) |
0.715 (1.00) |
0.327 (1.00) |
0.765 (1.00) |
0.377 (1.00) |
0.0124 (1.00) |
0.564 (1.00) |
0.373 (1.00) |
0.0334 (1.00) |
0.426 (1.00) |
0.52 (1.00) |
0.241 (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 | 76 (23%) | 251 |
0.127 (1.00) |
0.287 (1.00) |
0.896 (1.00) |
0.525 (1.00) |
0.171 (1.00) |
0.597 (1.00) |
0.138 (1.00) |
0.34 (1.00) |
0.251 (1.00) |
0.79 (1.00) |
0.606 (1.00) |
0.773 (1.00) |
0.181 (1.00) |
0.185 (1.00) |
14q loss | 35 (11%) | 292 |
0.522 (1.00) |
0.437 (1.00) |
0.721 (1.00) |
0.814 (1.00) |
0.148 (1.00) |
0.52 (1.00) |
0.904 (1.00) |
0.0967 (1.00) |
0.863 (1.00) |
0.46 (1.00) |
0.0489 (1.00) |
0.112 (1.00) |
0.631 (1.00) |
0.348 (1.00) |
15q loss | 71 (22%) | 256 |
0.803 (1.00) |
0.0707 (1.00) |
0.18 (1.00) |
0.746 (1.00) |
0.143 (1.00) |
0.979 (1.00) |
0.856 (1.00) |
0.94 (1.00) |
0.909 (1.00) |
0.779 (1.00) |
0.501 (1.00) |
0.711 (1.00) |
0.249 (1.00) |
0.655 (1.00) |
16p loss | 27 (8%) | 300 |
0.718 (1.00) |
0.132 (1.00) |
0.314 (1.00) |
0.539 (1.00) |
0.743 (1.00) |
1 (1.00) |
0.0161 (1.00) |
0.0843 (1.00) |
0.222 (1.00) |
0.748 (1.00) |
0.394 (1.00) |
0.0957 (1.00) |
0.643 (1.00) |
|
16q loss | 47 (14%) | 280 |
0.165 (1.00) |
0.191 (1.00) |
0.636 (1.00) |
0.746 (1.00) |
0.0637 (1.00) |
0.591 (1.00) |
0.432 (1.00) |
0.188 (1.00) |
0.18 (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 |
0.944 (1.00) |
0.379 (1.00) |
1 (1.00) |
0.1 (1.00) |
0.865 (1.00) |
0.593 (1.00) |
0.811 (1.00) |
0.609 (1.00) |
0.581 (1.00) |
0.425 (1.00) |
0.365 (1.00) |
0.107 (1.00) |
0.0721 (1.00) |
0.113 (1.00) |
17q loss | 14 (4%) | 313 |
0.16 (1.00) |
0.614 (1.00) |
0.587 (1.00) |
0.579 (1.00) |
0.314 (1.00) |
0.535 (1.00) |
0.785 (1.00) |
0.581 (1.00) |
1 (1.00) |
0.0333 (1.00) |
0.124 (1.00) |
0.232 (1.00) |
0.118 (1.00) |
|
18q loss | 83 (25%) | 244 |
0.00969 (1.00) |
0.298 (1.00) |
0.704 (1.00) |
0.452 (1.00) |
0.173 (1.00) |
0.0568 (1.00) |
0.273 (1.00) |
0.297 (1.00) |
0.00549 (1.00) |
0.118 (1.00) |
0.194 (1.00) |
0.416 (1.00) |
0.208 (1.00) |
0.312 (1.00) |
19p loss | 89 (27%) | 238 |
0.0441 (1.00) |
0.392 (1.00) |
0.034 (1.00) |
0.649 (1.00) |
0.723 (1.00) |
0.322 (1.00) |
0.0545 (1.00) |
0.11 (1.00) |
0.202 (1.00) |
1 (1.00) |
0.464 (1.00) |
0.259 (1.00) |
0.104 (1.00) |
0.415 (1.00) |
19q loss | 52 (16%) | 275 |
0.147 (1.00) |
0.347 (1.00) |
1 (1.00) |
0.00456 (1.00) |
0.1 (1.00) |
0.438 (1.00) |
0.524 (1.00) |
0.0811 (1.00) |
0.395 (1.00) |
0.538 (1.00) |
0.173 (1.00) |
0.954 (1.00) |
0.382 (1.00) |
0.299 (1.00) |
20p loss | 45 (14%) | 282 |
0.166 (1.00) |
0.666 (1.00) |
1 (1.00) |
0.691 (1.00) |
0.172 (1.00) |
0.05 (1.00) |
0.179 (1.00) |
0.0948 (1.00) |
0.745 (1.00) |
0.814 (1.00) |
0.609 (1.00) |
0.491 (1.00) |
0.0519 (1.00) |
|
20q loss | 16 (5%) | 311 |
0.37 (1.00) |
0.391 (1.00) |
1 (1.00) |
0.411 (1.00) |
0.934 (1.00) |
0.661 (1.00) |
0.203 (1.00) |
0.558 (1.00) |
1 (1.00) |
0.634 (1.00) |
0.213 (1.00) |
0.431 (1.00) |
0.101 (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 | 7 (2%) | 320 |
0.232 (1.00) |
0.109 (1.00) |
0.251 (1.00) |
0.00378 (1.00) |
0.177 (1.00) |
0.722 (1.00) |
0.358 (1.00) |
0.271 (1.00) |
0.0621 (1.00) |
0.891 (1.00) |
0.269 (1.00) |
0.68 (1.00) |
0.865 (1.00) |
P value = 0.000118 (t-test), Q value = 0.12
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 | 35 | 58.8 (9.6) |
11Q GAIN WILD-TYPE | 261 | 66.1 (9.5) |
Figure S1. Get High-res Image Gene #22: '11q gain mutation analysis' versus Clinical Feature #2: 'AGE'
![](D22V2.png)
P value = 3.31e-06 (logrank test), Q value = 0.0035
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 | 9 | 5 | 0.1 - 21.5 (8.4) |
1Q LOSS WILD-TYPE | 282 | 77 | 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'
![](D42V1.png)
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'
![](D53V5.png)
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'
![](D59V5.png)
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'
![](D71V11.png)
-
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
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.