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 11 clinical features across 285 patients, 3 significant findings detected with Q value < 0.25.
-
4q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
-
11q gain cnv correlated to 'AGE'.
-
1q loss cnv correlated to 'Time to Death'.
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%) | 277 |
0.617 (1.00) |
0.555 (1.00) |
0.149 (1.00) |
7.42e-05 (0.0612) |
0.0927 (1.00) |
0.367 (1.00) |
0.508 (1.00) |
0.645 (1.00) |
0.315 (1.00) |
1 (1.00) |
|
11q gain | 34 (12%) | 251 |
0.48 (1.00) |
0.000302 (0.249) |
0.0658 (1.00) |
0.701 (1.00) |
0.771 (1.00) |
0.568 (1.00) |
0.704 (1.00) |
0.56 (1.00) |
0.233 (1.00) |
0.659 (1.00) |
1 (1.00) |
1q loss | 10 (4%) | 275 |
4.11e-06 (0.00339) |
0.468 (1.00) |
0.521 (1.00) |
0.59 (1.00) |
0.553 (1.00) |
0.229 (1.00) |
1 (1.00) |
0.0765 (1.00) |
0.378 (1.00) |
1 (1.00) |
|
1p gain | 37 (13%) | 248 |
0.818 (1.00) |
0.00446 (1.00) |
0.86 (1.00) |
0.553 (1.00) |
0.971 (1.00) |
0.675 (1.00) |
0.0147 (1.00) |
0.687 (1.00) |
0.0105 (1.00) |
1 (1.00) |
0.807 (1.00) |
1q gain | 111 (39%) | 174 |
0.761 (1.00) |
0.517 (1.00) |
0.715 (1.00) |
0.551 (1.00) |
0.606 (1.00) |
0.748 (1.00) |
0.0825 (1.00) |
0.387 (1.00) |
0.0456 (1.00) |
1 (1.00) |
0.175 (1.00) |
2p gain | 36 (13%) | 249 |
0.13 (1.00) |
0.0628 (1.00) |
0.0307 (1.00) |
0.685 (1.00) |
0.793 (1.00) |
0.0679 (1.00) |
0.676 (1.00) |
0.0929 (1.00) |
0.123 (1.00) |
0.672 (1.00) |
0.803 (1.00) |
2q gain | 30 (11%) | 255 |
0.196 (1.00) |
0.228 (1.00) |
0.248 (1.00) |
0.238 (1.00) |
0.287 (1.00) |
0.963 (1.00) |
0.0978 (1.00) |
0.236 (1.00) |
1 (1.00) |
1 (1.00) |
|
3p gain | 9 (3%) | 276 |
0.126 (1.00) |
0.65 (1.00) |
0.737 (1.00) |
0.91 (1.00) |
0.0718 (1.00) |
0.626 (1.00) |
0.547 (1.00) |
0.427 (1.00) |
0.347 (1.00) |
0.629 (1.00) |
|
3q gain | 18 (6%) | 267 |
0.138 (1.00) |
0.491 (1.00) |
0.809 (1.00) |
0.962 (1.00) |
0.864 (1.00) |
0.313 (1.00) |
0.91 (1.00) |
0.551 (1.00) |
0.194 (1.00) |
0.492 (1.00) |
|
4p gain | 21 (7%) | 264 |
0.651 (1.00) |
0.0135 (1.00) |
0.364 (1.00) |
0.0634 (1.00) |
0.217 (1.00) |
0.85 (1.00) |
0.0913 (1.00) |
0.266 (1.00) |
1 (1.00) |
1 (1.00) |
|
5p gain | 111 (39%) | 174 |
0.527 (1.00) |
0.299 (1.00) |
0.715 (1.00) |
0.791 (1.00) |
0.267 (1.00) |
0.457 (1.00) |
0.805 (1.00) |
0.864 (1.00) |
0.976 (1.00) |
0.383 (1.00) |
0.735 (1.00) |
5q gain | 36 (13%) | 249 |
0.696 (1.00) |
0.831 (1.00) |
0.378 (1.00) |
0.82 (1.00) |
0.582 (1.00) |
0.641 (1.00) |
0.576 (1.00) |
0.804 (1.00) |
0.217 (1.00) |
0.0839 (1.00) |
|
6p gain | 40 (14%) | 245 |
0.883 (1.00) |
0.65 (1.00) |
0.495 (1.00) |
0.833 (1.00) |
0.685 (1.00) |
0.511 (1.00) |
0.188 (1.00) |
0.829 (1.00) |
0.762 (1.00) |
1 (1.00) |
0.636 (1.00) |
6q gain | 11 (4%) | 274 |
0.5 (1.00) |
0.0906 (1.00) |
0.0129 (1.00) |
0.991 (1.00) |
0.84 (1.00) |
0.507 (1.00) |
0.531 (1.00) |
0.445 (1.00) |
1 (1.00) |
0.674 (1.00) |
|
7p gain | 99 (35%) | 186 |
0.248 (1.00) |
0.0494 (1.00) |
0.901 (1.00) |
0.246 (1.00) |
0.445 (1.00) |
0.177 (1.00) |
0.0214 (1.00) |
0.0982 (1.00) |
0.0477 (1.00) |
1 (1.00) |
0.73 (1.00) |
7q gain | 71 (25%) | 214 |
0.906 (1.00) |
0.00363 (1.00) |
0.41 (1.00) |
0.976 (1.00) |
0.678 (1.00) |
0.344 (1.00) |
0.226 (1.00) |
0.0639 (1.00) |
0.0479 (1.00) |
0.322 (1.00) |
0.702 (1.00) |
8p gain | 34 (12%) | 251 |
0.211 (1.00) |
0.00123 (1.00) |
0.142 (1.00) |
0.865 (1.00) |
0.701 (1.00) |
1 (1.00) |
0.315 (1.00) |
0.981 (1.00) |
0.659 (1.00) |
0.197 (1.00) |
|
8q gain | 89 (31%) | 196 |
0.899 (1.00) |
0.000456 (0.375) |
0.202 (1.00) |
0.37 (1.00) |
0.443 (1.00) |
0.892 (1.00) |
0.428 (1.00) |
0.316 (1.00) |
0.572 (1.00) |
0.761 (1.00) |
0.722 (1.00) |
9p gain | 7 (2%) | 278 |
0.207 (1.00) |
0.297 (1.00) |
0.254 (1.00) |
0.993 (1.00) |
0.338 (1.00) |
0.499 (1.00) |
0.474 (1.00) |
1 (1.00) |
1 (1.00) |
0.599 (1.00) |
|
9q gain | 3 (1%) | 282 |
0.0591 (1.00) |
0.225 (1.00) |
1 (1.00) |
1 (1.00) |
0.707 (1.00) |
1 (1.00) |
0.629 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
10p gain | 32 (11%) | 253 |
0.93 (1.00) |
0.17 (1.00) |
0.26 (1.00) |
0.977 (1.00) |
0.234 (1.00) |
0.557 (1.00) |
0.214 (1.00) |
0.894 (1.00) |
0.626 (1.00) |
0.374 (1.00) |
0.798 (1.00) |
10q gain | 19 (7%) | 266 |
0.997 (1.00) |
0.602 (1.00) |
0.343 (1.00) |
0.11 (1.00) |
0.468 (1.00) |
0.5 (1.00) |
0.387 (1.00) |
0.594 (1.00) |
1 (1.00) |
0.748 (1.00) |
|
11p gain | 23 (8%) | 262 |
0.731 (1.00) |
0.104 (1.00) |
0.383 (1.00) |
0.703 (1.00) |
0.681 (1.00) |
0.52 (1.00) |
1 (1.00) |
0.455 (1.00) |
1 (1.00) |
0.761 (1.00) |
|
12p gain | 39 (14%) | 246 |
0.869 (1.00) |
0.00338 (1.00) |
0.605 (1.00) |
0.704 (1.00) |
0.142 (1.00) |
0.0704 (1.00) |
1 (1.00) |
0.0456 (1.00) |
1 (1.00) |
0.812 (1.00) |
|
12q gain | 31 (11%) | 254 |
0.743 (1.00) |
0.00098 (0.806) |
0.448 (1.00) |
0.78 (1.00) |
0.134 (1.00) |
0.141 (1.00) |
0.735 (1.00) |
0.0704 (1.00) |
0.373 (1.00) |
0.794 (1.00) |
|
13q gain | 15 (5%) | 270 |
0.569 (1.00) |
0.525 (1.00) |
1 (1.00) |
0.983 (1.00) |
0.112 (1.00) |
0.424 (1.00) |
0.137 (1.00) |
0.532 (1.00) |
0.513 (1.00) |
0.481 (1.00) |
|
14q gain | 33 (12%) | 252 |
0.169 (1.00) |
0.189 (1.00) |
0.269 (1.00) |
0.777 (1.00) |
0.0528 (1.00) |
0.628 (1.00) |
0.552 (1.00) |
0.702 (1.00) |
0.879 (1.00) |
1 (1.00) |
0.439 (1.00) |
15q gain | 10 (4%) | 275 |
0.275 (1.00) |
0.375 (1.00) |
0.758 (1.00) |
0.0967 (1.00) |
0.67 (1.00) |
0.351 (1.00) |
0.443 (1.00) |
0.21 (1.00) |
1 (1.00) |
1 (1.00) |
|
16p gain | 40 (14%) | 245 |
0.583 (1.00) |
0.155 (1.00) |
0.865 (1.00) |
0.342 (1.00) |
0.616 (1.00) |
0.461 (1.00) |
0.608 (1.00) |
0.669 (1.00) |
0.583 (1.00) |
1 (1.00) |
0.159 (1.00) |
16q gain | 26 (9%) | 259 |
0.652 (1.00) |
0.261 (1.00) |
0.417 (1.00) |
0.302 (1.00) |
0.467 (1.00) |
0.345 (1.00) |
0.519 (1.00) |
0.42 (1.00) |
0.558 (1.00) |
0.616 (1.00) |
0.565 (1.00) |
17p gain | 16 (6%) | 269 |
0.786 (1.00) |
0.63 (1.00) |
0.202 (1.00) |
0.208 (1.00) |
0.421 (1.00) |
0.901 (1.00) |
0.508 (1.00) |
0.397 (1.00) |
0.348 (1.00) |
0.0295 (1.00) |
0.717 (1.00) |
17q gain | 48 (17%) | 237 |
0.213 (1.00) |
0.344 (1.00) |
1 (1.00) |
0.379 (1.00) |
0.259 (1.00) |
0.0287 (1.00) |
0.518 (1.00) |
0.0246 (1.00) |
0.0301 (1.00) |
0.049 (1.00) |
0.506 (1.00) |
18p gain | 19 (7%) | 266 |
0.572 (1.00) |
0.34 (1.00) |
0.343 (1.00) |
0.228 (1.00) |
0.851 (1.00) |
0.75 (1.00) |
1 (1.00) |
0.923 (1.00) |
0.6 (1.00) |
0.503 (1.00) |
|
18q gain | 14 (5%) | 271 |
0.462 (1.00) |
0.204 (1.00) |
0.422 (1.00) |
0.0765 (1.00) |
0.886 (1.00) |
0.798 (1.00) |
0.527 (1.00) |
0.867 (1.00) |
0.488 (1.00) |
0.239 (1.00) |
|
19p gain | 4 (1%) | 281 |
0.985 (1.00) |
0.605 (1.00) |
0.627 (1.00) |
0.993 (1.00) |
0.485 (1.00) |
0.342 (1.00) |
0.245 (1.00) |
0.164 (1.00) |
1 (1.00) |
0.482 (1.00) |
|
19q gain | 11 (4%) | 274 |
0.781 (1.00) |
0.68 (1.00) |
0.556 (1.00) |
0.993 (1.00) |
0.172 (1.00) |
0.908 (1.00) |
0.288 (1.00) |
0.73 (1.00) |
1 (1.00) |
0.381 (1.00) |
|
20p gain | 42 (15%) | 243 |
0.861 (1.00) |
0.318 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.791 (1.00) |
0.35 (1.00) |
0.444 (1.00) |
0.715 (1.00) |
0.38 (1.00) |
0.416 (1.00) |
0.0586 (1.00) |
20q gain | 49 (17%) | 236 |
0.73 (1.00) |
0.163 (1.00) |
0.529 (1.00) |
0.153 (1.00) |
0.768 (1.00) |
0.127 (1.00) |
0.924 (1.00) |
0.47 (1.00) |
0.701 (1.00) |
0.705 (1.00) |
0.0766 (1.00) |
21q gain | 26 (9%) | 259 |
0.501 (1.00) |
0.58 (1.00) |
0.147 (1.00) |
0.645 (1.00) |
0.659 (1.00) |
0.61 (1.00) |
0.42 (1.00) |
0.934 (1.00) |
1 (1.00) |
0.25 (1.00) |
|
22q gain | 13 (5%) | 272 |
0.479 (1.00) |
0.0886 (1.00) |
1 (1.00) |
0.455 (1.00) |
0.208 (1.00) |
0.0716 (1.00) |
0.881 (1.00) |
0.405 (1.00) |
0.462 (1.00) |
0.115 (1.00) |
|
Xq gain | 14 (5%) | 271 |
0.359 (1.00) |
0.237 (1.00) |
0.179 (1.00) |
0.695 (1.00) |
0.345 (1.00) |
0.928 (1.00) |
0.779 (1.00) |
0.908 (1.00) |
1 (1.00) |
0.451 (1.00) |
|
1p loss | 22 (8%) | 263 |
0.223 (1.00) |
0.825 (1.00) |
0.118 (1.00) |
0.902 (1.00) |
0.681 (1.00) |
0.861 (1.00) |
0.334 (1.00) |
0.0442 (1.00) |
1 (1.00) |
0.547 (1.00) |
|
2p loss | 3 (1%) | 282 |
1 (1.00) |
0.998 (1.00) |
1 (1.00) |
1 (1.00) |
0.629 (1.00) |
1 (1.00) |
1 (1.00) |
0.389 (1.00) |
|||
3p loss | 56 (20%) | 229 |
0.874 (1.00) |
0.694 (1.00) |
0.766 (1.00) |
0.025 (1.00) |
0.917 (1.00) |
0.699 (1.00) |
0.479 (1.00) |
0.158 (1.00) |
0.00424 (1.00) |
0.724 (1.00) |
0.534 (1.00) |
3q loss | 30 (11%) | 255 |
0.872 (1.00) |
0.717 (1.00) |
0.441 (1.00) |
0.0533 (1.00) |
0.996 (1.00) |
0.481 (1.00) |
0.633 (1.00) |
0.598 (1.00) |
0.231 (1.00) |
1 (1.00) |
0.788 (1.00) |
4p loss | 26 (9%) | 259 |
0.462 (1.00) |
0.0256 (1.00) |
0.103 (1.00) |
0.723 (1.00) |
0.666 (1.00) |
0.329 (1.00) |
0.279 (1.00) |
0.65 (1.00) |
0.48 (1.00) |
0.336 (1.00) |
0.565 (1.00) |
4q loss | 31 (11%) | 254 |
0.516 (1.00) |
0.046 (1.00) |
0.0126 (1.00) |
0.984 (1.00) |
0.957 (1.00) |
0.144 (1.00) |
0.00685 (1.00) |
0.542 (1.00) |
0.0602 (1.00) |
0.157 (1.00) |
0.794 (1.00) |
5p loss | 6 (2%) | 279 |
0.918 (1.00) |
0.177 (1.00) |
0.419 (1.00) |
0.462 (1.00) |
0.568 (1.00) |
0.841 (1.00) |
0.404 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.225 (1.00) |
|
5q loss | 38 (13%) | 247 |
0.591 (1.00) |
0.0634 (1.00) |
0.0136 (1.00) |
0.101 (1.00) |
0.834 (1.00) |
0.0656 (1.00) |
0.727 (1.00) |
0.359 (1.00) |
1 (1.00) |
0.328 (1.00) |
|
6p loss | 24 (8%) | 261 |
0.354 (1.00) |
0.182 (1.00) |
0.017 (1.00) |
0.421 (1.00) |
0.798 (1.00) |
0.69 (1.00) |
0.373 (1.00) |
0.688 (1.00) |
1 (1.00) |
1 (1.00) |
|
6q loss | 64 (22%) | 221 |
0.962 (1.00) |
0.502 (1.00) |
0.322 (1.00) |
0.0174 (1.00) |
0.632 (1.00) |
0.29 (1.00) |
0.472 (1.00) |
0.467 (1.00) |
0.515 (1.00) |
0.739 (1.00) |
1 (1.00) |
7p loss | 10 (4%) | 275 |
0.815 (1.00) |
0.237 (1.00) |
1 (1.00) |
0.445 (1.00) |
1 (1.00) |
0.284 (1.00) |
0.443 (1.00) |
0.237 (1.00) |
0.378 (1.00) |
1 (1.00) |
|
7q loss | 11 (4%) | 274 |
0.72 (1.00) |
0.193 (1.00) |
0.556 (1.00) |
0.0208 (1.00) |
0.89 (1.00) |
0.627 (1.00) |
1 (1.00) |
0.654 (1.00) |
0.407 (1.00) |
0.674 (1.00) |
|
8p loss | 73 (26%) | 212 |
0.591 (1.00) |
0.839 (1.00) |
1 (1.00) |
0.148 (1.00) |
0.0896 (1.00) |
0.137 (1.00) |
0.796 (1.00) |
0.761 (1.00) |
0.943 (1.00) |
0.745 (1.00) |
0.85 (1.00) |
8q loss | 10 (4%) | 275 |
0.304 (1.00) |
0.55 (1.00) |
0.758 (1.00) |
0.5 (1.00) |
0.712 (1.00) |
0.815 (1.00) |
0.0967 (1.00) |
1 (1.00) |
1 (1.00) |
0.651 (1.00) |
|
9p loss | 89 (31%) | 196 |
0.00761 (1.00) |
0.0646 (1.00) |
0.202 (1.00) |
0.853 (1.00) |
0.606 (1.00) |
0.232 (1.00) |
0.0259 (1.00) |
0.847 (1.00) |
0.0548 (1.00) |
0.552 (1.00) |
0.375 (1.00) |
9q loss | 74 (26%) | 211 |
0.325 (1.00) |
0.381 (1.00) |
1 (1.00) |
0.984 (1.00) |
0.306 (1.00) |
0.328 (1.00) |
0.185 (1.00) |
0.624 (1.00) |
0.39 (1.00) |
1 (1.00) |
0.85 (1.00) |
10p loss | 23 (8%) | 262 |
0.31 (1.00) |
0.61 (1.00) |
0.132 (1.00) |
0.334 (1.00) |
0.896 (1.00) |
0.462 (1.00) |
0.388 (1.00) |
0.904 (1.00) |
0.609 (1.00) |
1 (1.00) |
|
10q loss | 25 (9%) | 260 |
0.34 (1.00) |
0.167 (1.00) |
1 (1.00) |
0.00132 (1.00) |
0.336 (1.00) |
0.0985 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.613 (1.00) |
0.777 (1.00) |
|
11p loss | 22 (8%) | 263 |
0.162 (1.00) |
0.0045 (1.00) |
0.824 (1.00) |
0.572 (1.00) |
0.407 (1.00) |
0.976 (1.00) |
0.0679 (1.00) |
0.047 (1.00) |
0.038 (1.00) |
1 (1.00) |
1 (1.00) |
11q loss | 18 (6%) | 267 |
0.16 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.344 (1.00) |
0.534 (1.00) |
1 (1.00) |
0.741 (1.00) |
0.0344 (1.00) |
0.9 (1.00) |
0.194 (1.00) |
0.164 (1.00) |
12p loss | 25 (9%) | 260 |
0.359 (1.00) |
0.786 (1.00) |
0.837 (1.00) |
0.572 (1.00) |
0.0963 (1.00) |
0.633 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.534 (1.00) |
0.613 (1.00) |
0.392 (1.00) |
12q loss | 18 (6%) | 267 |
0.0727 (1.00) |
0.882 (1.00) |
0.468 (1.00) |
0.0795 (1.00) |
0.495 (1.00) |
0.377 (1.00) |
0.366 (1.00) |
0.308 (1.00) |
1 (1.00) |
1 (1.00) |
|
13q loss | 64 (22%) | 221 |
0.147 (1.00) |
0.333 (1.00) |
0.203 (1.00) |
0.0273 (1.00) |
0.326 (1.00) |
0.877 (1.00) |
0.109 (1.00) |
0.454 (1.00) |
0.432 (1.00) |
1 (1.00) |
0.427 (1.00) |
14q loss | 27 (9%) | 258 |
0.56 (1.00) |
0.96 (1.00) |
0.548 (1.00) |
0.666 (1.00) |
0.143 (1.00) |
0.783 (1.00) |
1 (1.00) |
0.281 (1.00) |
0.8 (1.00) |
0.114 (1.00) |
0.151 (1.00) |
15q loss | 63 (22%) | 222 |
0.734 (1.00) |
0.0673 (1.00) |
0.474 (1.00) |
0.889 (1.00) |
0.0627 (1.00) |
0.666 (1.00) |
0.979 (1.00) |
0.933 (1.00) |
0.908 (1.00) |
1 (1.00) |
0.553 (1.00) |
16p loss | 22 (8%) | 263 |
0.876 (1.00) |
0.313 (1.00) |
0.824 (1.00) |
0.494 (1.00) |
1 (1.00) |
0.949 (1.00) |
0.00376 (1.00) |
0.0595 (1.00) |
0.0688 (1.00) |
0.755 (1.00) |
|
16q loss | 40 (14%) | 245 |
0.0654 (1.00) |
0.231 (1.00) |
0.611 (1.00) |
0.825 (1.00) |
0.113 (1.00) |
0.229 (1.00) |
0.509 (1.00) |
0.107 (1.00) |
0.219 (1.00) |
0.403 (1.00) |
0.812 (1.00) |
17p loss | 75 (26%) | 210 |
0.501 (1.00) |
0.613 (1.00) |
0.688 (1.00) |
0.156 (1.00) |
0.915 (1.00) |
0.357 (1.00) |
0.359 (1.00) |
0.62 (1.00) |
0.31 (1.00) |
0.525 (1.00) |
0.709 (1.00) |
17q loss | 12 (4%) | 273 |
0.155 (1.00) |
0.955 (1.00) |
1 (1.00) |
0.59 (1.00) |
0.498 (1.00) |
0.65 (1.00) |
0.751 (1.00) |
0.459 (1.00) |
1 (1.00) |
0.0894 (1.00) |
|
18p loss | 47 (16%) | 238 |
0.542 (1.00) |
0.035 (1.00) |
0.874 (1.00) |
0.01 (1.00) |
0.303 (1.00) |
0.29 (1.00) |
0.479 (1.00) |
0.0333 (1.00) |
0.00838 (1.00) |
0.701 (1.00) |
0.659 (1.00) |
18q loss | 73 (26%) | 212 |
0.0085 (1.00) |
0.234 (1.00) |
1 (1.00) |
0.529 (1.00) |
0.464 (1.00) |
0.113 (1.00) |
0.325 (1.00) |
0.228 (1.00) |
0.00356 (1.00) |
0.526 (1.00) |
0.453 (1.00) |
19p loss | 80 (28%) | 205 |
0.0417 (1.00) |
0.381 (1.00) |
0.00814 (1.00) |
0.758 (1.00) |
0.507 (1.00) |
0.232 (1.00) |
0.0185 (1.00) |
0.101 (1.00) |
0.127 (1.00) |
0.761 (1.00) |
0.357 (1.00) |
19q loss | 44 (15%) | 241 |
0.0948 (1.00) |
0.391 (1.00) |
0.412 (1.00) |
0.146 (1.00) |
0.232 (1.00) |
0.372 (1.00) |
0.0458 (1.00) |
0.31 (1.00) |
0.431 (1.00) |
1 (1.00) |
|
20p loss | 42 (15%) | 243 |
0.0859 (1.00) |
0.35 (1.00) |
0.868 (1.00) |
0.314 (1.00) |
0.199 (1.00) |
0.0335 (1.00) |
0.19 (1.00) |
0.0739 (1.00) |
0.7 (1.00) |
1 (1.00) |
|
20q loss | 14 (5%) | 271 |
0.0936 (1.00) |
0.27 (1.00) |
0.789 (1.00) |
0.297 (1.00) |
0.85 (1.00) |
0.547 (1.00) |
0.393 (1.00) |
0.375 (1.00) |
1 (1.00) |
0.702 (1.00) |
|
21q loss | 42 (15%) | 243 |
0.856 (1.00) |
0.701 (1.00) |
0.0293 (1.00) |
0.0916 (1.00) |
0.598 (1.00) |
0.844 (1.00) |
0.751 (1.00) |
0.83 (1.00) |
0.751 (1.00) |
1 (1.00) |
1 (1.00) |
22q loss | 64 (22%) | 221 |
0.986 (1.00) |
0.122 (1.00) |
0.0655 (1.00) |
0.499 (1.00) |
0.802 (1.00) |
0.785 (1.00) |
0.919 (1.00) |
0.211 (1.00) |
0.964 (1.00) |
0.497 (1.00) |
0.845 (1.00) |
Xq loss | 6 (2%) | 279 |
0.33 (1.00) |
0.0991 (1.00) |
1 (1.00) |
0.0101 (1.00) |
0.568 (1.00) |
0.841 (1.00) |
0.54 (1.00) |
0.816 (1.00) |
0.026 (1.00) |
1 (1.00) |
P value = 7.42e-05 (Chi-square test), Q value = 0.061
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 | 180 | 3 | 9 | 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 | 174 | 3 | 9 | 2 | 3 | 2 | 10 | 0 | 4 |
P value = 0.000302 (t-test), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 254 | 65.4 (9.7) |
11Q GAIN MUTATED | 31 | 59.2 (9.4) |
11Q GAIN WILD-TYPE | 223 | 66.3 (9.4) |
P value = 4.11e-06 (logrank test), Q value = 0.0034
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 251 | 81 | 0.0 - 224.0 (13.2) |
1Q LOSS MUTATED | 8 | 5 | 0.1 - 21.5 (8.4) |
1Q LOSS WILD-TYPE | 243 | 76 | 0.0 - 224.0 (13.9) |
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = LUAD.clin.merged.picked.txt
-
Number of patients = 285
-
Number of significantly arm-level cnvs = 79
-
Number of selected clinical features = 11
-
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.