This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 80 arm-level events and 8 clinical features across 123 patients, no significant finding detected with Q value < 0.25.
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No arm-level cnvs related to clinical features.
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
COMPLETENESS OF RESECTION |
||
nCNV (%) | nWild-Type | logrank 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 | |
1p gain | 17 (14%) | 106 |
0.406 (1.00) |
0.682 (1.00) |
0.719 (1.00) |
0.0695 (1.00) |
1 (1.00) |
0.23 (1.00) |
0.282 (1.00) |
0.249 (1.00) |
1q gain | 70 (57%) | 53 |
0.0459 (1.00) |
0.634 (1.00) |
0.0423 (1.00) |
0.0617 (1.00) |
0.0846 (1.00) |
0.629 (1.00) |
0.262 (1.00) |
0.885 (1.00) |
2p gain | 17 (14%) | 106 |
0.889 (1.00) |
0.445 (1.00) |
0.0473 (1.00) |
0.347 (1.00) |
0.0449 (1.00) |
0.283 (1.00) |
0.0612 (1.00) |
0.094 (1.00) |
2q gain | 15 (12%) | 108 |
0.776 (1.00) |
0.552 (1.00) |
0.206 (1.00) |
0.922 (1.00) |
0.323 (1.00) |
0.293 (1.00) |
0.0849 (1.00) |
0.249 (1.00) |
3p gain | 11 (9%) | 112 |
0.288 (1.00) |
0.486 (1.00) |
0.975 (1.00) |
0.81 (1.00) |
0.172 (1.00) |
1 (1.00) |
0.534 (1.00) |
0.561 (1.00) |
3q gain | 12 (10%) | 111 |
0.149 (1.00) |
0.42 (1.00) |
0.975 (1.00) |
0.961 (1.00) |
0.172 (1.00) |
0.765 (1.00) |
1 (1.00) |
0.706 (1.00) |
4p gain | 8 (7%) | 115 |
0.364 (1.00) |
0.341 (1.00) |
0.999 (1.00) |
0.934 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.4 (1.00) |
4q gain | 4 (3%) | 119 |
0.877 (1.00) |
0.315 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.142 (1.00) |
5p gain | 49 (40%) | 74 |
0.952 (1.00) |
0.422 (1.00) |
0.319 (1.00) |
0.0911 (1.00) |
0.281 (1.00) |
0.411 (1.00) |
1 (1.00) |
1 (1.00) |
5q gain | 37 (30%) | 86 |
0.822 (1.00) |
0.433 (1.00) |
0.514 (1.00) |
0.365 (1.00) |
0.553 (1.00) |
0.909 (1.00) |
0.544 (1.00) |
0.715 (1.00) |
6p gain | 27 (22%) | 96 |
0.262 (1.00) |
0.754 (1.00) |
0.2 (1.00) |
0.927 (1.00) |
1 (1.00) |
0.0731 (1.00) |
0.66 (1.00) |
0.355 (1.00) |
6q gain | 17 (14%) | 106 |
0.289 (1.00) |
0.0771 (1.00) |
0.0579 (1.00) |
0.813 (1.00) |
1 (1.00) |
0.0155 (1.00) |
0.282 (1.00) |
0.0847 (1.00) |
7p gain | 39 (32%) | 84 |
0.819 (1.00) |
0.0605 (1.00) |
0.646 (1.00) |
0.667 (1.00) |
0.199 (1.00) |
0.829 (1.00) |
0.689 (1.00) |
0.615 (1.00) |
7q gain | 40 (33%) | 83 |
0.999 (1.00) |
0.271 (1.00) |
0.352 (1.00) |
0.442 (1.00) |
0.214 (1.00) |
0.528 (1.00) |
1 (1.00) |
0.895 (1.00) |
8p gain | 27 (22%) | 96 |
0.767 (1.00) |
0.104 (1.00) |
0.357 (1.00) |
0.3 (1.00) |
0.568 (1.00) |
0.205 (1.00) |
0.378 (1.00) |
0.271 (1.00) |
8q gain | 65 (53%) | 58 |
0.696 (1.00) |
0.607 (1.00) |
0.194 (1.00) |
0.345 (1.00) |
0.616 (1.00) |
0.911 (1.00) |
0.0621 (1.00) |
0.717 (1.00) |
9p gain | 6 (5%) | 117 |
0.416 (1.00) |
0.66 (1.00) |
0.367 (1.00) |
0.218 (1.00) |
1 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.443 (1.00) |
9q gain | 6 (5%) | 117 |
0.0815 (1.00) |
0.827 (1.00) |
0.948 (1.00) |
0.748 (1.00) |
1 (1.00) |
1 (1.00) |
0.195 (1.00) |
0.443 (1.00) |
10p gain | 18 (15%) | 105 |
0.835 (1.00) |
0.0461 (1.00) |
0.193 (1.00) |
0.25 (1.00) |
1 (1.00) |
0.295 (1.00) |
0.796 (1.00) |
1 (1.00) |
10q gain | 10 (8%) | 113 |
0.648 (1.00) |
0.222 (1.00) |
0.142 (1.00) |
0.563 (1.00) |
1 (1.00) |
0.183 (1.00) |
1 (1.00) |
0.822 (1.00) |
11p gain | 7 (6%) | 116 |
0.89 (1.00) |
0.638 (1.00) |
0.0375 (1.00) |
0.853 (1.00) |
1 (1.00) |
0.069 (1.00) |
0.255 (1.00) |
0.0606 (1.00) |
11q gain | 8 (7%) | 115 |
0.593 (1.00) |
0.933 (1.00) |
0.0304 (1.00) |
0.32 (1.00) |
1 (1.00) |
0.0539 (1.00) |
0.256 (1.00) |
0.0824 (1.00) |
12p gain | 9 (7%) | 114 |
0.205 (1.00) |
0.309 (1.00) |
0.81 (1.00) |
0.719 (1.00) |
1 (1.00) |
0.728 (1.00) |
0.292 (1.00) |
0.562 (1.00) |
12q gain | 13 (11%) | 110 |
0.749 (1.00) |
0.2 (1.00) |
0.147 (1.00) |
0.437 (1.00) |
0.323 (1.00) |
0.44 (1.00) |
0.0164 (1.00) |
0.706 (1.00) |
13q gain | 7 (6%) | 116 |
0.302 (1.00) |
0.905 (1.00) |
0.502 (1.00) |
0.853 (1.00) |
0.172 (1.00) |
1 (1.00) |
0.423 (1.00) |
0.443 (1.00) |
14q gain | 8 (7%) | 115 |
0.906 (1.00) |
0.634 (1.00) |
0.0783 (1.00) |
0.934 (1.00) |
1 (1.00) |
0.175 (1.00) |
1 (1.00) |
0.0824 (1.00) |
15q gain | 11 (9%) | 112 |
0.396 (1.00) |
0.933 (1.00) |
0.847 (1.00) |
0.27 (1.00) |
1 (1.00) |
0.748 (1.00) |
0.534 (1.00) |
1 (1.00) |
16p gain | 10 (8%) | 113 |
0.886 (1.00) |
0.36 (1.00) |
0.266 (1.00) |
0.362 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
16q gain | 4 (3%) | 119 |
0.609 (1.00) |
0.23 (1.00) |
0.844 (1.00) |
0.246 (1.00) |
1 (1.00) |
1 (1.00) |
0.629 (1.00) |
1 (1.00) |
17p gain | 12 (10%) | 111 |
0.34 (1.00) |
0.42 (1.00) |
0.0776 (1.00) |
0.504 (1.00) |
1 (1.00) |
0.765 (1.00) |
1 (1.00) |
0.48 (1.00) |
17q gain | 34 (28%) | 89 |
0.246 (1.00) |
0.533 (1.00) |
0.304 (1.00) |
0.162 (1.00) |
1 (1.00) |
0.0643 (1.00) |
0.536 (1.00) |
0.119 (1.00) |
18p gain | 10 (8%) | 113 |
0.388 (1.00) |
0.187 (1.00) |
0.0424 (1.00) |
0.211 (1.00) |
1 (1.00) |
0.135 (1.00) |
0.742 (1.00) |
0.0525 (1.00) |
18q gain | 9 (7%) | 114 |
0.388 (1.00) |
0.368 (1.00) |
0.0533 (1.00) |
0.309 (1.00) |
1 (1.00) |
0.157 (1.00) |
1 (1.00) |
0.0431 (1.00) |
19p gain | 27 (22%) | 96 |
0.404 (1.00) |
0.949 (1.00) |
0.0421 (1.00) |
0.294 (1.00) |
0.547 (1.00) |
0.0731 (1.00) |
0.114 (1.00) |
0.257 (1.00) |
19q gain | 29 (24%) | 94 |
0.41 (1.00) |
0.637 (1.00) |
0.0583 (1.00) |
0.464 (1.00) |
0.547 (1.00) |
0.0742 (1.00) |
0.0813 (1.00) |
0.266 (1.00) |
20p gain | 36 (29%) | 87 |
0.234 (1.00) |
0.999 (1.00) |
0.671 (1.00) |
0.967 (1.00) |
1 (1.00) |
0.111 (1.00) |
0.313 (1.00) |
0.445 (1.00) |
20q gain | 38 (31%) | 85 |
0.294 (1.00) |
0.998 (1.00) |
0.726 (1.00) |
0.92 (1.00) |
1 (1.00) |
0.106 (1.00) |
0.546 (1.00) |
0.305 (1.00) |
21q gain | 11 (9%) | 112 |
0.35 (1.00) |
0.773 (1.00) |
0.61 (1.00) |
0.622 (1.00) |
1 (1.00) |
1 (1.00) |
0.327 (1.00) |
0.234 (1.00) |
22q gain | 15 (12%) | 108 |
0.837 (1.00) |
0.782 (1.00) |
0.892 (1.00) |
0.828 (1.00) |
0.351 (1.00) |
1 (1.00) |
1 (1.00) |
0.198 (1.00) |
xq gain | 21 (17%) | 102 |
0.516 (1.00) |
0.0527 (1.00) |
0.797 (1.00) |
0.6 (1.00) |
1 (1.00) |
0.571 (1.00) |
0.461 (1.00) |
0.729 (1.00) |
1p loss | 34 (28%) | 89 |
0.777 (1.00) |
0.952 (1.00) |
0.24 (1.00) |
0.728 (1.00) |
0.17 (1.00) |
0.0757 (1.00) |
1 (1.00) |
0.414 (1.00) |
1q loss | 11 (9%) | 112 |
0.638 (1.00) |
0.14 (1.00) |
0.111 (1.00) |
0.956 (1.00) |
0.0178 (1.00) |
0.748 (1.00) |
0.534 (1.00) |
0.234 (1.00) |
2p loss | 10 (8%) | 113 |
0.128 (1.00) |
0.796 (1.00) |
0.901 (1.00) |
0.264 (1.00) |
1 (1.00) |
1 (1.00) |
0.742 (1.00) |
0.52 (1.00) |
2q loss | 10 (8%) | 113 |
0.86 (1.00) |
0.982 (1.00) |
0.982 (1.00) |
0.563 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.246 (1.00) |
3p loss | 16 (13%) | 107 |
0.0846 (1.00) |
0.972 (1.00) |
0.0926 (1.00) |
0.0439 (1.00) |
0.378 (1.00) |
0.256 (1.00) |
0.28 (1.00) |
0.607 (1.00) |
3q loss | 8 (7%) | 115 |
0.0337 (1.00) |
0.195 (1.00) |
0.784 (1.00) |
0.417 (1.00) |
0.204 (1.00) |
1 (1.00) |
0.471 (1.00) |
1 (1.00) |
4p loss | 30 (24%) | 93 |
0.656 (1.00) |
0.575 (1.00) |
0.0982 (1.00) |
0.733 (1.00) |
0.105 (1.00) |
0.09 (1.00) |
0.668 (1.00) |
0.391 (1.00) |
4q loss | 40 (33%) | 83 |
0.6 (1.00) |
0.519 (1.00) |
0.375 (1.00) |
0.672 (1.00) |
0.199 (1.00) |
0.168 (1.00) |
0.551 (1.00) |
0.282 (1.00) |
5p loss | 9 (7%) | 114 |
0.407 (1.00) |
0.888 (1.00) |
0.331 (1.00) |
0.757 (1.00) |
0.204 (1.00) |
1 (1.00) |
0.481 (1.00) |
0.462 (1.00) |
5q loss | 13 (11%) | 110 |
0.154 (1.00) |
0.687 (1.00) |
0.575 (1.00) |
0.339 (1.00) |
0.235 (1.00) |
0.785 (1.00) |
1 (1.00) |
0.445 (1.00) |
6p loss | 17 (14%) | 106 |
0.799 (1.00) |
0.989 (1.00) |
0.958 (1.00) |
0.777 (1.00) |
0.455 (1.00) |
0.0441 (1.00) |
0.424 (1.00) |
1 (1.00) |
6q loss | 37 (30%) | 86 |
0.686 (1.00) |
0.0867 (1.00) |
0.496 (1.00) |
0.909 (1.00) |
0.214 (1.00) |
0.34 (1.00) |
0.106 (1.00) |
0.942 (1.00) |
7p loss | 8 (7%) | 115 |
0.426 (1.00) |
0.639 (1.00) |
0.864 (1.00) |
0.395 (1.00) |
1 (1.00) |
0.711 (1.00) |
0.0513 (1.00) |
0.562 (1.00) |
7q loss | 10 (8%) | 113 |
0.34 (1.00) |
0.553 (1.00) |
0.906 (1.00) |
0.42 (1.00) |
1 (1.00) |
0.735 (1.00) |
0.0391 (1.00) |
0.301 (1.00) |
8p loss | 57 (46%) | 66 |
0.155 (1.00) |
0.00123 (0.787) |
0.0757 (1.00) |
0.175 (1.00) |
0.054 (1.00) |
0.242 (1.00) |
0.853 (1.00) |
0.712 (1.00) |
8q loss | 12 (10%) | 111 |
0.414 (1.00) |
0.128 (1.00) |
0.0188 (1.00) |
0.00707 (1.00) |
0.204 (1.00) |
0.288 (1.00) |
0.129 (1.00) |
0.852 (1.00) |
9p loss | 40 (33%) | 83 |
0.0787 (1.00) |
0.842 (1.00) |
0.132 (1.00) |
0.347 (1.00) |
0.23 (1.00) |
0.131 (1.00) |
0.32 (1.00) |
0.119 (1.00) |
9q loss | 42 (34%) | 81 |
0.0171 (1.00) |
0.778 (1.00) |
0.079 (1.00) |
0.542 (1.00) |
0.0283 (1.00) |
0.0667 (1.00) |
0.559 (1.00) |
0.0984 (1.00) |
10p loss | 15 (12%) | 108 |
0.926 (1.00) |
0.0217 (1.00) |
0.14 (1.00) |
0.458 (1.00) |
0.294 (1.00) |
1 (1.00) |
0.0476 (1.00) |
0.758 (1.00) |
10q loss | 27 (22%) | 96 |
0.117 (1.00) |
0.53 (1.00) |
0.295 (1.00) |
0.211 (1.00) |
0.455 (1.00) |
0.874 (1.00) |
0.184 (1.00) |
0.227 (1.00) |
11p loss | 22 (18%) | 101 |
0.919 (1.00) |
0.0227 (1.00) |
0.453 (1.00) |
0.655 (1.00) |
0.0534 (1.00) |
0.849 (1.00) |
1 (1.00) |
0.68 (1.00) |
11q loss | 24 (20%) | 99 |
0.995 (1.00) |
0.0609 (1.00) |
0.424 (1.00) |
0.481 (1.00) |
0.0723 (1.00) |
0.727 (1.00) |
0.815 (1.00) |
0.313 (1.00) |
12p loss | 23 (19%) | 100 |
0.234 (1.00) |
0.413 (1.00) |
0.369 (1.00) |
0.836 (1.00) |
0.0827 (1.00) |
0.308 (1.00) |
1 (1.00) |
0.153 (1.00) |
12q loss | 15 (12%) | 108 |
0.523 (1.00) |
0.194 (1.00) |
0.187 (1.00) |
1 (1.00) |
1 (1.00) |
0.235 (1.00) |
0.785 (1.00) |
0.111 (1.00) |
13q loss | 43 (35%) | 80 |
0.756 (1.00) |
0.153 (1.00) |
0.25 (1.00) |
0.00701 (1.00) |
1 (1.00) |
0.547 (1.00) |
1 (1.00) |
0.153 (1.00) |
14q loss | 40 (33%) | 83 |
0.707 (1.00) |
0.579 (1.00) |
0.132 (1.00) |
0.0556 (1.00) |
1 (1.00) |
0.469 (1.00) |
0.551 (1.00) |
0.176 (1.00) |
15q loss | 25 (20%) | 98 |
0.533 (1.00) |
0.527 (1.00) |
0.531 (1.00) |
0.306 (1.00) |
0.0936 (1.00) |
0.154 (1.00) |
0.357 (1.00) |
0.921 (1.00) |
16p loss | 38 (31%) | 85 |
0.0486 (1.00) |
0.259 (1.00) |
0.0942 (1.00) |
0.21 (1.00) |
0.246 (1.00) |
0.157 (1.00) |
0.841 (1.00) |
0.104 (1.00) |
16q loss | 47 (38%) | 76 |
0.17 (1.00) |
0.162 (1.00) |
0.2 (1.00) |
0.196 (1.00) |
0.565 (1.00) |
0.235 (1.00) |
0.702 (1.00) |
0.0688 (1.00) |
17p loss | 60 (49%) | 63 |
0.293 (1.00) |
0.331 (1.00) |
0.0753 (1.00) |
0.295 (1.00) |
0.242 (1.00) |
0.306 (1.00) |
0.71 (1.00) |
0.0692 (1.00) |
17q loss | 14 (11%) | 109 |
0.771 (1.00) |
0.0519 (1.00) |
0.15 (1.00) |
0.886 (1.00) |
0.0178 (1.00) |
0.79 (1.00) |
0.771 (1.00) |
0.858 (1.00) |
18p loss | 20 (16%) | 103 |
0.142 (1.00) |
0.392 (1.00) |
0.825 (1.00) |
0.538 (1.00) |
0.351 (1.00) |
0.834 (1.00) |
0.805 (1.00) |
1 (1.00) |
18q loss | 22 (18%) | 101 |
0.308 (1.00) |
0.385 (1.00) |
0.476 (1.00) |
0.912 (1.00) |
0.378 (1.00) |
0.303 (1.00) |
0.468 (1.00) |
0.908 (1.00) |
19p loss | 15 (12%) | 108 |
0.0249 (1.00) |
0.824 (1.00) |
0.959 (1.00) |
0.658 (1.00) |
0.294 (1.00) |
0.795 (1.00) |
0.409 (1.00) |
0.0995 (1.00) |
19q loss | 11 (9%) | 112 |
0.113 (1.00) |
0.731 (1.00) |
0.969 (1.00) |
0.956 (1.00) |
0.235 (1.00) |
0.55 (1.00) |
0.534 (1.00) |
0.197 (1.00) |
20p loss | 8 (7%) | 115 |
0.899 (1.00) |
0.408 (1.00) |
0.536 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
20q loss | 5 (4%) | 118 |
0.488 (1.00) |
0.71 (1.00) |
0.142 (1.00) |
0.784 (1.00) |
1 (1.00) |
0.616 (1.00) |
1 (1.00) |
1 (1.00) |
21q loss | 33 (27%) | 90 |
0.0135 (1.00) |
0.616 (1.00) |
0.198 (1.00) |
0.695 (1.00) |
0.143 (1.00) |
0.11 (1.00) |
0.0347 (1.00) |
0.343 (1.00) |
22q loss | 25 (20%) | 98 |
0.281 (1.00) |
0.904 (1.00) |
0.856 (1.00) |
0.296 (1.00) |
1 (1.00) |
0.544 (1.00) |
0.491 (1.00) |
0.0659 (1.00) |
xq loss | 15 (12%) | 108 |
0.593 (1.00) |
0.244 (1.00) |
0.944 (1.00) |
0.458 (1.00) |
0.294 (1.00) |
0.795 (1.00) |
0.409 (1.00) |
0.505 (1.00) |
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = LIHC-TP.merged_data.txt
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Number of patients = 123
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Number of significantly arm-level cnvs = 80
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Number of selected clinical features = 8
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Exclude regions 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 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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.