(primary solid tumor cohort)
This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 75 arm-level results and 9 clinical features across 162 patients, one significant finding detected with Q value < 0.25.
-
20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
||
nCNV (%) | nWild-Type | logrank test | t-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 | Fisher's exact test | |
20q gain | 132 (81%) | 30 |
0.0358 (1.00) |
0.13 (1.00) |
0.686 (1.00) |
2.52e-05 (0.0168) |
0.395 (1.00) |
0.193 (1.00) |
0.264 (1.00) |
0.192 (1.00) |
0.308 (1.00) |
1p gain | 4 (2%) | 158 |
0.0152 (1.00) |
0.859 (1.00) |
0.332 (1.00) |
0.296 (1.00) |
0.0399 (1.00) |
0.0312 (1.00) |
1 (1.00) |
0.431 (1.00) |
1 (1.00) |
1q gain | 27 (17%) | 135 |
0.417 (1.00) |
0.383 (1.00) |
0.53 (1.00) |
0.233 (1.00) |
0.00248 (1.00) |
0.133 (1.00) |
0.829 (1.00) |
0.749 (1.00) |
1 (1.00) |
2p gain | 20 (12%) | 142 |
0.284 (1.00) |
0.451 (1.00) |
0.0073 (1.00) |
0.221 (1.00) |
0.536 (1.00) |
0.265 (1.00) |
0.298 (1.00) |
0.677 (1.00) |
1 (1.00) |
2q gain | 21 (13%) | 141 |
0.153 (1.00) |
0.443 (1.00) |
0.0174 (1.00) |
0.218 (1.00) |
0.231 (1.00) |
0.0589 (1.00) |
0.708 (1.00) |
0.714 (1.00) |
1 (1.00) |
3p gain | 17 (10%) | 145 |
0.814 (1.00) |
0.748 (1.00) |
1 (1.00) |
0.363 (1.00) |
0.841 (1.00) |
0.251 (1.00) |
0.0925 (1.00) |
0.261 (1.00) |
0.121 (1.00) |
3q gain | 23 (14%) | 139 |
0.506 (1.00) |
0.668 (1.00) |
0.27 (1.00) |
0.218 (1.00) |
0.606 (1.00) |
0.296 (1.00) |
0.107 (1.00) |
0.406 (1.00) |
0.203 (1.00) |
4p gain | 4 (2%) | 158 |
0.574 (1.00) |
0.233 (1.00) |
0.626 (1.00) |
1 (1.00) |
0.459 (1.00) |
0.814 (1.00) |
0.252 (1.00) |
0.133 (1.00) |
1 (1.00) |
4q gain | 3 (2%) | 159 |
0.354 (1.00) |
0.251 (1.00) |
1 (1.00) |
1 (1.00) |
0.293 (1.00) |
0.548 (1.00) |
0.877 (1.00) |
1 (1.00) |
|
5p gain | 20 (12%) | 142 |
0.854 (1.00) |
0.0481 (1.00) |
0.638 (1.00) |
0.221 (1.00) |
0.744 (1.00) |
0.723 (1.00) |
0.335 (1.00) |
0.497 (1.00) |
0.552 (1.00) |
5q gain | 12 (7%) | 150 |
0.462 (1.00) |
0.0508 (1.00) |
1 (1.00) |
0.601 (1.00) |
1 (1.00) |
0.845 (1.00) |
0.214 (1.00) |
0.36 (1.00) |
1 (1.00) |
6p gain | 27 (17%) | 135 |
0.858 (1.00) |
0.947 (1.00) |
0.834 (1.00) |
0.127 (1.00) |
0.851 (1.00) |
0.491 (1.00) |
0.374 (1.00) |
0.481 (1.00) |
0.0587 (1.00) |
6q gain | 27 (17%) | 135 |
0.228 (1.00) |
0.356 (1.00) |
1 (1.00) |
0.128 (1.00) |
0.52 (1.00) |
0.306 (1.00) |
0.135 (1.00) |
0.146 (1.00) |
0.262 (1.00) |
7p gain | 90 (56%) | 72 |
0.338 (1.00) |
0.363 (1.00) |
0.874 (1.00) |
0.00225 (1.00) |
0.18 (1.00) |
0.106 (1.00) |
0.804 (1.00) |
0.303 (1.00) |
1 (1.00) |
7q gain | 79 (49%) | 83 |
0.425 (1.00) |
0.351 (1.00) |
1 (1.00) |
0.00232 (1.00) |
0.492 (1.00) |
0.046 (1.00) |
0.443 (1.00) |
0.0214 (1.00) |
1 (1.00) |
8p gain | 27 (17%) | 135 |
0.361 (1.00) |
0.15 (1.00) |
0.834 (1.00) |
1 (1.00) |
0.846 (1.00) |
0.624 (1.00) |
0.713 (1.00) |
0.29 (1.00) |
0.591 (1.00) |
8q gain | 72 (44%) | 90 |
0.0685 (1.00) |
0.525 (1.00) |
1 (1.00) |
0.145 (1.00) |
0.747 (1.00) |
0.228 (1.00) |
0.0966 (1.00) |
0.447 (1.00) |
0.228 (1.00) |
9p gain | 35 (22%) | 127 |
0.827 (1.00) |
0.296 (1.00) |
0.706 (1.00) |
1 (1.00) |
0.328 (1.00) |
0.542 (1.00) |
0.56 (1.00) |
0.418 (1.00) |
0.342 (1.00) |
9q gain | 26 (16%) | 136 |
0.358 (1.00) |
0.0862 (1.00) |
0.831 (1.00) |
1 (1.00) |
0.455 (1.00) |
0.807 (1.00) |
0.9 (1.00) |
0.293 (1.00) |
0.591 (1.00) |
10p gain | 8 (5%) | 154 |
0.993 (1.00) |
0.988 (1.00) |
0.471 (1.00) |
1 (1.00) |
1 (1.00) |
0.35 (1.00) |
0.573 (1.00) |
1 (1.00) |
1 (1.00) |
10q gain | 4 (2%) | 158 |
0.332 (1.00) |
0.171 (1.00) |
0.0416 (1.00) |
1 (1.00) |
0.774 (1.00) |
0.316 (1.00) |
0.655 (1.00) |
0.774 (1.00) |
1 (1.00) |
11p gain | 21 (13%) | 141 |
0.459 (1.00) |
0.195 (1.00) |
0.249 (1.00) |
0.218 (1.00) |
0.211 (1.00) |
0.951 (1.00) |
0.306 (1.00) |
0.428 (1.00) |
1 (1.00) |
11q gain | 17 (10%) | 145 |
0.937 (1.00) |
0.0317 (1.00) |
0.8 (1.00) |
0.363 (1.00) |
0.144 (1.00) |
0.589 (1.00) |
0.198 (1.00) |
0.0863 (1.00) |
1 (1.00) |
12p gain | 28 (17%) | 134 |
0.999 (1.00) |
0.0797 (1.00) |
1 (1.00) |
1 (1.00) |
0.218 (1.00) |
0.373 (1.00) |
0.565 (1.00) |
0.731 (1.00) |
0.277 (1.00) |
12q gain | 19 (12%) | 143 |
0.507 (1.00) |
0.0205 (1.00) |
0.328 (1.00) |
1 (1.00) |
0.417 (1.00) |
0.9 (1.00) |
0.93 (1.00) |
0.691 (1.00) |
1 (1.00) |
13q gain | 102 (63%) | 60 |
0.0286 (1.00) |
0.489 (1.00) |
0.871 (1.00) |
0.000377 (0.252) |
0.238 (1.00) |
0.037 (1.00) |
0.213 (1.00) |
0.178 (1.00) |
0.671 (1.00) |
14q gain | 4 (2%) | 158 |
0.345 (1.00) |
0.447 (1.00) |
0.0416 (1.00) |
1 (1.00) |
0.774 (1.00) |
0.112 (1.00) |
0.252 (1.00) |
0.76 (1.00) |
0.141 (1.00) |
16p gain | 29 (18%) | 133 |
0.229 (1.00) |
0.636 (1.00) |
0.539 (1.00) |
0.129 (1.00) |
0.743 (1.00) |
0.508 (1.00) |
0.441 (1.00) |
0.571 (1.00) |
0.292 (1.00) |
16q gain | 30 (19%) | 132 |
0.871 (1.00) |
0.596 (1.00) |
1 (1.00) |
0.0747 (1.00) |
0.865 (1.00) |
0.211 (1.00) |
0.158 (1.00) |
0.375 (1.00) |
0.308 (1.00) |
17p gain | 3 (2%) | 159 |
0.257 (1.00) |
0.593 (1.00) |
1 (1.00) |
0.0728 (1.00) |
0.171 (1.00) |
0.548 (1.00) |
0.573 (1.00) |
1 (1.00) |
|
17q gain | 18 (11%) | 144 |
0.652 (1.00) |
0.469 (1.00) |
0.621 (1.00) |
0.365 (1.00) |
0.751 (1.00) |
0.127 (1.00) |
0.459 (1.00) |
0.739 (1.00) |
1 (1.00) |
18p gain | 7 (4%) | 155 |
0.964 (1.00) |
0.622 (1.00) |
1 (1.00) |
0.463 (1.00) |
0.245 (1.00) |
0.262 (1.00) |
0.194 (1.00) |
0.47 (1.00) |
0.236 (1.00) |
18q gain | 4 (2%) | 158 |
0.747 (1.00) |
0.626 (1.00) |
1 (1.00) |
0.0399 (1.00) |
0.0671 (1.00) |
0.0325 (1.00) |
0.0939 (1.00) |
0.141 (1.00) |
|
19p gain | 20 (12%) | 142 |
0.859 (1.00) |
0.365 (1.00) |
0.473 (1.00) |
0.221 (1.00) |
0.176 (1.00) |
0.856 (1.00) |
0.287 (1.00) |
0.385 (1.00) |
1 (1.00) |
19q gain | 23 (14%) | 139 |
0.827 (1.00) |
0.645 (1.00) |
0.27 (1.00) |
0.218 (1.00) |
0.188 (1.00) |
0.956 (1.00) |
0.148 (1.00) |
0.307 (1.00) |
0.595 (1.00) |
20p gain | 95 (59%) | 67 |
0.874 (1.00) |
0.962 (1.00) |
0.2 (1.00) |
0.00182 (1.00) |
0.99 (1.00) |
0.209 (1.00) |
0.714 (1.00) |
0.536 (1.00) |
0.692 (1.00) |
21q gain | 7 (4%) | 155 |
0.829 (1.00) |
0.0302 (1.00) |
0.703 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.289 (1.00) |
0.586 (1.00) |
1 (1.00) |
22q gain | 5 (3%) | 157 |
0.0152 (1.00) |
0.781 (1.00) |
0.661 (1.00) |
1 (1.00) |
1 (1.00) |
0.217 (1.00) |
0.737 (1.00) |
0.327 (1.00) |
1 (1.00) |
Xq gain | 7 (4%) | 155 |
0.808 (1.00) |
0.718 (1.00) |
1 (1.00) |
0.463 (1.00) |
0.0691 (1.00) |
0.191 (1.00) |
0.289 (1.00) |
0.0613 (1.00) |
1 (1.00) |
1p loss | 21 (13%) | 141 |
0.806 (1.00) |
0.388 (1.00) |
0.105 (1.00) |
0.221 (1.00) |
0.459 (1.00) |
0.461 (1.00) |
0.93 (1.00) |
0.572 (1.00) |
0.571 (1.00) |
1q loss | 7 (4%) | 155 |
0.789 (1.00) |
0.629 (1.00) |
0.455 (1.00) |
1 (1.00) |
1 (1.00) |
0.0231 (1.00) |
1 (1.00) |
0.0851 (1.00) |
0.236 (1.00) |
2p loss | 5 (3%) | 157 |
0.611 (1.00) |
0.0489 (1.00) |
0.661 (1.00) |
0.296 (1.00) |
1 (1.00) |
1 (1.00) |
0.737 (1.00) |
1 (1.00) |
1 (1.00) |
3p loss | 8 (5%) | 154 |
0.849 (1.00) |
0.91 (1.00) |
0.292 (1.00) |
0.106 (1.00) |
0.425 (1.00) |
0.629 (1.00) |
0.161 (1.00) |
0.47 (1.00) |
0.266 (1.00) |
3q loss | 4 (2%) | 158 |
0.877 (1.00) |
0.766 (1.00) |
0.626 (1.00) |
0.00175 (1.00) |
0.774 (1.00) |
1 (1.00) |
0.548 (1.00) |
0.76 (1.00) |
0.141 (1.00) |
4p loss | 39 (24%) | 123 |
0.276 (1.00) |
0.132 (1.00) |
0.581 (1.00) |
0.304 (1.00) |
0.381 (1.00) |
0.433 (1.00) |
0.766 (1.00) |
0.717 (1.00) |
0.151 (1.00) |
4q loss | 46 (28%) | 116 |
0.109 (1.00) |
0.306 (1.00) |
0.301 (1.00) |
0.188 (1.00) |
0.259 (1.00) |
0.676 (1.00) |
0.787 (1.00) |
0.91 (1.00) |
0.353 (1.00) |
5p loss | 11 (7%) | 151 |
0.153 (1.00) |
0.788 (1.00) |
0.114 (1.00) |
0.601 (1.00) |
0.935 (1.00) |
0.378 (1.00) |
0.672 (1.00) |
0.919 (1.00) |
0.349 (1.00) |
5q loss | 23 (14%) | 139 |
0.58 (1.00) |
0.6 (1.00) |
0.27 (1.00) |
0.695 (1.00) |
0.55 (1.00) |
0.76 (1.00) |
0.414 (1.00) |
0.467 (1.00) |
0.00392 (1.00) |
6p loss | 8 (5%) | 154 |
0.102 (1.00) |
0.504 (1.00) |
1 (1.00) |
0.106 (1.00) |
1 (1.00) |
0.176 (1.00) |
1 (1.00) |
0.357 (1.00) |
1 (1.00) |
6q loss | 14 (9%) | 148 |
0.657 (1.00) |
0.434 (1.00) |
0.577 (1.00) |
0.0643 (1.00) |
0.604 (1.00) |
0.162 (1.00) |
0.738 (1.00) |
0.36 (1.00) |
1 (1.00) |
8p loss | 56 (35%) | 106 |
0.268 (1.00) |
0.555 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.94 (1.00) |
0.928 (1.00) |
0.427 (1.00) |
0.801 (1.00) |
0.183 (1.00) |
8q loss | 3 (2%) | 159 |
0.679 (1.00) |
1 (1.00) |
1 (1.00) |
0.244 (1.00) |
1 (1.00) |
0.548 (1.00) |
0.0431 (1.00) |
1 (1.00) |
|
9p loss | 12 (7%) | 150 |
0.0169 (1.00) |
0.122 (1.00) |
1 (1.00) |
1 (1.00) |
0.476 (1.00) |
0.852 (1.00) |
0.253 (1.00) |
0.289 (1.00) |
1 (1.00) |
9q loss | 11 (7%) | 151 |
0.00797 (1.00) |
0.677 (1.00) |
1 (1.00) |
0.592 (1.00) |
0.131 (1.00) |
0.713 (1.00) |
0.672 (1.00) |
0.705 (1.00) |
1 (1.00) |
10p loss | 17 (10%) | 145 |
0.221 (1.00) |
0.00571 (1.00) |
1 (1.00) |
0.0377 (1.00) |
0.312 (1.00) |
0.403 (1.00) |
0.78 (1.00) |
0.982 (1.00) |
0.492 (1.00) |
10q loss | 21 (13%) | 141 |
0.534 (1.00) |
0.0482 (1.00) |
0.491 (1.00) |
0.0773 (1.00) |
0.864 (1.00) |
0.901 (1.00) |
0.634 (1.00) |
0.785 (1.00) |
0.571 (1.00) |
11p loss | 19 (12%) | 143 |
0.464 (1.00) |
0.578 (1.00) |
0.626 (1.00) |
0.046 (1.00) |
0.707 (1.00) |
0.584 (1.00) |
0.698 (1.00) |
0.0468 (1.00) |
0.533 (1.00) |
11q loss | 23 (14%) | 139 |
0.353 (1.00) |
0.656 (1.00) |
0.508 (1.00) |
0.0137 (1.00) |
0.5 (1.00) |
0.794 (1.00) |
0.396 (1.00) |
0.278 (1.00) |
0.0379 (1.00) |
12p loss | 12 (7%) | 150 |
0.177 (1.00) |
0.642 (1.00) |
0.0397 (1.00) |
0.601 (1.00) |
0.529 (1.00) |
0.368 (1.00) |
0.496 (1.00) |
0.374 (1.00) |
1 (1.00) |
12q loss | 8 (5%) | 154 |
0.0971 (1.00) |
0.466 (1.00) |
1 (1.00) |
1 (1.00) |
0.908 (1.00) |
0.231 (1.00) |
0.245 (1.00) |
0.652 (1.00) |
1 (1.00) |
13q loss | 5 (3%) | 157 |
0.98 (1.00) |
1 (1.00) |
0.357 (1.00) |
0.47 (1.00) |
0.273 (1.00) |
0.102 (1.00) |
0.551 (1.00) |
1 (1.00) |
|
14q loss | 51 (31%) | 111 |
0.635 (1.00) |
0.881 (1.00) |
0.735 (1.00) |
0.00981 (1.00) |
0.266 (1.00) |
0.245 (1.00) |
0.503 (1.00) |
0.488 (1.00) |
1 (1.00) |
15q loss | 58 (36%) | 104 |
0.0719 (1.00) |
0.415 (1.00) |
0.511 (1.00) |
1 (1.00) |
0.173 (1.00) |
0.742 (1.00) |
0.923 (1.00) |
0.166 (1.00) |
0.668 (1.00) |
16p loss | 6 (4%) | 156 |
0.238 (1.00) |
0.413 (1.00) |
0.357 (1.00) |
0.641 (1.00) |
0.28 (1.00) |
1 (1.00) |
0.0351 (1.00) |
1 (1.00) |
|
16q loss | 10 (6%) | 152 |
0.877 (1.00) |
0.532 (1.00) |
1 (1.00) |
0.553 (1.00) |
1 (1.00) |
0.0935 (1.00) |
1 (1.00) |
0.377 (1.00) |
0.322 (1.00) |
17p loss | 89 (55%) | 73 |
0.44 (1.00) |
0.0299 (1.00) |
0.527 (1.00) |
0.572 (1.00) |
0.133 (1.00) |
0.757 (1.00) |
0.435 (1.00) |
0.285 (1.00) |
0.691 (1.00) |
17q loss | 15 (9%) | 147 |
0.465 (1.00) |
0.864 (1.00) |
0.788 (1.00) |
1 (1.00) |
0.845 (1.00) |
0.825 (1.00) |
1 (1.00) |
1 (1.00) |
0.0967 (1.00) |
18p loss | 114 (70%) | 48 |
0.65 (1.00) |
0.0737 (1.00) |
0.863 (1.00) |
0.00925 (1.00) |
0.0102 (1.00) |
0.487 (1.00) |
0.321 (1.00) |
0.579 (1.00) |
1 (1.00) |
18q loss | 126 (78%) | 36 |
0.407 (1.00) |
0.0453 (1.00) |
0.448 (1.00) |
0.482 (1.00) |
0.00609 (1.00) |
0.5 (1.00) |
0.603 (1.00) |
0.262 (1.00) |
0.615 (1.00) |
19p loss | 7 (4%) | 155 |
0.0864 (1.00) |
0.794 (1.00) |
0.703 (1.00) |
1 (1.00) |
0.88 (1.00) |
0.689 (1.00) |
1 (1.00) |
0.678 (1.00) |
1 (1.00) |
19q loss | 7 (4%) | 155 |
0.0462 (1.00) |
0.403 (1.00) |
1 (1.00) |
1 (1.00) |
0.496 (1.00) |
0.778 (1.00) |
0.799 (1.00) |
0.181 (1.00) |
1 (1.00) |
20p loss | 18 (11%) | 144 |
1 (1.00) |
0.689 (1.00) |
0.803 (1.00) |
0.636 (1.00) |
0.851 (1.00) |
1 (1.00) |
0.923 (1.00) |
0.295 (1.00) |
1 (1.00) |
21q loss | 43 (27%) | 119 |
0.162 (1.00) |
0.807 (1.00) |
0.476 (1.00) |
0.517 (1.00) |
0.291 (1.00) |
0.0616 (1.00) |
1 (1.00) |
0.153 (1.00) |
0.656 (1.00) |
22q loss | 42 (26%) | 120 |
0.0236 (1.00) |
0.284 (1.00) |
0.475 (1.00) |
0.745 (1.00) |
0.628 (1.00) |
0.0953 (1.00) |
0.598 (1.00) |
0.244 (1.00) |
0.181 (1.00) |
Xq loss | 6 (4%) | 156 |
0.518 (1.00) |
0.0974 (1.00) |
0.689 (1.00) |
1 (1.00) |
0.846 (1.00) |
0.236 (1.00) |
0.221 (1.00) |
0.152 (1.00) |
1 (1.00) |
P value = 2.52e-05 (Fisher's exact test), Q value = 0.017
nPatients | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 143 | 13 |
20Q GAIN MUTATED | 124 | 4 |
20Q GAIN WILD-TYPE | 19 | 9 |
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = READ-TP.clin.merged.picked.txt
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Number of patients = 162
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Number of significantly arm-level cnvs = 75
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Number of selected clinical features = 9
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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 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.