This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 65 arm-level events and 10 clinical features across 36 patients, no significant finding detected with Q value < 0.25.
-
No arm-level cnvs related to clinical features.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RESIDUAL TUMOR |
RACE | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-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 | Fisher's exact test | |
1p gain | 10 (28%) | 26 |
0.348 (1.00) |
0.596 (1.00) |
0.785 (1.00) |
0.345 (1.00) |
0.286 (1.00) |
0.291 (1.00) |
0.285 (1.00) |
0.452 (1.00) |
0.217 (1.00) |
0.764 (1.00) |
1q gain | 22 (61%) | 14 |
0.924 (1.00) |
0.236 (1.00) |
0.0535 (1.00) |
0.149 (1.00) |
0.624 (1.00) |
0.328 (1.00) |
1 (1.00) |
0.141 (1.00) |
0.83 (1.00) |
1 (1.00) |
2p gain | 5 (14%) | 31 |
0.344 (1.00) |
0.436 (1.00) |
0.815 (1.00) |
1 (1.00) |
0.525 (1.00) |
1 (1.00) |
0.355 (1.00) |
0.62 (1.00) |
0.465 (1.00) |
0.134 (1.00) |
2q gain | 6 (17%) | 30 |
0.309 (1.00) |
0.51 (1.00) |
0.505 (1.00) |
0.475 (1.00) |
0.173 (1.00) |
1 (1.00) |
0.672 (1.00) |
0.696 (1.00) |
0.555 (1.00) |
0.186 (1.00) |
3q gain | 7 (19%) | 29 |
0.467 (1.00) |
0.223 (1.00) |
0.443 (1.00) |
0.847 (1.00) |
0.562 (1.00) |
0.282 (1.00) |
0.204 (1.00) |
0.0911 (1.00) |
0.0931 (1.00) |
0.123 (1.00) |
5p gain | 12 (33%) | 24 |
0.807 (1.00) |
0.775 (1.00) |
0.605 (1.00) |
0.704 (1.00) |
1 (1.00) |
0.63 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.23 (1.00) |
5q gain | 11 (31%) | 25 |
0.983 (1.00) |
0.548 (1.00) |
0.504 (1.00) |
0.599 (1.00) |
1 (1.00) |
0.643 (1.00) |
1 (1.00) |
0.35 (1.00) |
0.829 (1.00) |
0.189 (1.00) |
6p gain | 8 (22%) | 28 |
0.205 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.733 (1.00) |
1 (1.00) |
1 (1.00) |
0.103 (1.00) |
0.245 (1.00) |
0.173 (1.00) |
0.474 (1.00) |
6q gain | 3 (8%) | 33 |
0.198 (1.00) |
0.144 (1.00) |
0.555 (1.00) |
0.712 (1.00) |
0.422 (1.00) |
0.4 (1.00) |
0.574 (1.00) |
0.0324 (1.00) |
0.02 (1.00) |
1 (1.00) |
7p gain | 7 (19%) | 29 |
0.164 (1.00) |
0.81 (1.00) |
0.16 (1.00) |
0.527 (1.00) |
0.241 (1.00) |
0.282 (1.00) |
1 (1.00) |
0.0906 (1.00) |
0.774 (1.00) |
0.419 (1.00) |
7q gain | 6 (17%) | 30 |
0.294 (1.00) |
0.718 (1.00) |
0.181 (1.00) |
0.703 (1.00) |
0.173 (1.00) |
0.216 (1.00) |
1 (1.00) |
0.0589 (1.00) |
0.551 (1.00) |
0.359 (1.00) |
8p gain | 5 (14%) | 31 |
0.349 (1.00) |
0.478 (1.00) |
0.746 (1.00) |
0.402 (1.00) |
1 (1.00) |
1 (1.00) |
0.637 (1.00) |
0.1 (1.00) |
0.305 (1.00) |
0.546 (1.00) |
8q gain | 11 (31%) | 25 |
0.276 (1.00) |
0.514 (1.00) |
0.742 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.483 (1.00) |
0.61 (1.00) |
1 (1.00) |
0.191 (1.00) |
10p gain | 5 (14%) | 31 |
0.465 (1.00) |
0.945 (1.00) |
0.745 (1.00) |
0.676 (1.00) |
1 (1.00) |
1 (1.00) |
0.149 (1.00) |
1 (1.00) |
1 (1.00) |
0.553 (1.00) |
11p gain | 4 (11%) | 32 |
0.0785 (1.00) |
0.743 (1.00) |
0.129 (1.00) |
0.61 (1.00) |
0.0601 (1.00) |
0.0993 (1.00) |
1 (1.00) |
0.123 (1.00) |
0.373 (1.00) |
0.0847 (1.00) |
11q gain | 4 (11%) | 32 |
0.0785 (1.00) |
0.743 (1.00) |
0.128 (1.00) |
0.61 (1.00) |
0.0601 (1.00) |
0.0993 (1.00) |
1 (1.00) |
0.12 (1.00) |
0.372 (1.00) |
0.0835 (1.00) |
12p gain | 9 (25%) | 27 |
0.223 (1.00) |
0.798 (1.00) |
1 (1.00) |
0.431 (1.00) |
1 (1.00) |
1 (1.00) |
0.146 (1.00) |
1 (1.00) |
0.52 (1.00) |
0.0165 (1.00) |
12q gain | 8 (22%) | 28 |
0.473 (1.00) |
0.805 (1.00) |
0.958 (1.00) |
0.733 (1.00) |
0.291 (1.00) |
0.302 (1.00) |
0.422 (1.00) |
0.73 (1.00) |
0.616 (1.00) |
0.0109 (1.00) |
13q gain | 3 (8%) | 33 |
0.968 (1.00) |
0.457 (1.00) |
0.0789 (1.00) |
0.537 (1.00) |
0.0601 (1.00) |
0.0532 (1.00) |
1 (1.00) |
0.0029 (0.985) |
0.278 (1.00) |
1 (1.00) |
15q gain | 6 (17%) | 30 |
0.42 (1.00) |
0.687 (1.00) |
0.31 (1.00) |
0.836 (1.00) |
0.173 (1.00) |
1 (1.00) |
1 (1.00) |
0.145 (1.00) |
0.555 (1.00) |
0.359 (1.00) |
16p gain | 7 (19%) | 29 |
0.557 (1.00) |
0.208 (1.00) |
0.698 (1.00) |
0.441 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.426 (1.00) |
0.329 (1.00) |
1 (1.00) |
0.686 (1.00) |
16q gain | 5 (14%) | 31 |
0.274 (1.00) |
0.423 (1.00) |
0.816 (1.00) |
0.831 (1.00) |
1 (1.00) |
1 (1.00) |
0.355 (1.00) |
0.185 (1.00) |
0.73 (1.00) |
0.549 (1.00) |
17p gain | 3 (8%) | 33 |
0.0127 (1.00) |
0.797 (1.00) |
0.554 (1.00) |
0.713 (1.00) |
0.301 (1.00) |
0.4 (1.00) |
1 (1.00) |
0.433 (1.00) |
0.28 (1.00) |
0.0444 (1.00) |
17q gain | 7 (19%) | 29 |
0.00303 (0.985) |
0.873 (1.00) |
0.86 (1.00) |
0.619 (1.00) |
1 (1.00) |
1 (1.00) |
0.204 (1.00) |
1 (1.00) |
0.773 (1.00) |
0.062 (1.00) |
18p gain | 7 (19%) | 29 |
0.599 (1.00) |
0.119 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.426 (1.00) |
0.331 (1.00) |
0.599 (1.00) |
0.686 (1.00) |
18q gain | 6 (17%) | 30 |
0.596 (1.00) |
0.226 (1.00) |
0.928 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.747 (1.00) |
0.622 (1.00) |
19p gain | 6 (17%) | 30 |
0.687 (1.00) |
0.396 (1.00) |
0.314 (1.00) |
0.704 (1.00) |
0.173 (1.00) |
1 (1.00) |
1 (1.00) |
0.401 (1.00) |
0.747 (1.00) |
0.358 (1.00) |
19q gain | 6 (17%) | 30 |
0.687 (1.00) |
0.396 (1.00) |
0.316 (1.00) |
0.703 (1.00) |
0.173 (1.00) |
1 (1.00) |
1 (1.00) |
0.402 (1.00) |
0.748 (1.00) |
0.361 (1.00) |
20p gain | 11 (31%) | 25 |
0.353 (1.00) |
0.0304 (1.00) |
0.577 (1.00) |
0.693 (1.00) |
1 (1.00) |
1 (1.00) |
0.0335 (1.00) |
1 (1.00) |
0.369 (1.00) |
0.188 (1.00) |
20q gain | 12 (33%) | 24 |
0.557 (1.00) |
0.0156 (1.00) |
0.504 (1.00) |
0.545 (1.00) |
1 (1.00) |
1 (1.00) |
0.0815 (1.00) |
0.634 (1.00) |
0.2 (1.00) |
0.229 (1.00) |
22q gain | 5 (14%) | 31 |
0.287 (1.00) |
0.252 (1.00) |
0.15 (1.00) |
0.831 (1.00) |
0.173 (1.00) |
0.155 (1.00) |
0.637 (1.00) |
0.185 (1.00) |
0.467 (1.00) |
1 (1.00) |
1p loss | 3 (8%) | 33 |
0.651 (1.00) |
0.529 (1.00) |
0.0806 (1.00) |
0.536 (1.00) |
0.0601 (1.00) |
0.0189 (1.00) |
0.574 (1.00) |
0.43 (1.00) |
0.278 (1.00) |
1 (1.00) |
3p loss | 24 (67%) | 12 |
0.615 (1.00) |
0.135 (1.00) |
0.0347 (1.00) |
0.0908 (1.00) |
0.0274 (1.00) |
0.304 (1.00) |
0.729 (1.00) |
0.194 (1.00) |
0.253 (1.00) |
0.588 (1.00) |
3q loss | 4 (11%) | 32 |
0.155 (1.00) |
0.65 (1.00) |
0.852 (1.00) |
0.801 (1.00) |
1 (1.00) |
1 (1.00) |
0.613 (1.00) |
1 (1.00) |
1 (1.00) |
0.0858 (1.00) |
4p loss | 11 (31%) | 25 |
0.488 (1.00) |
0.481 (1.00) |
0.767 (1.00) |
0.165 (1.00) |
1 (1.00) |
0.643 (1.00) |
0.0335 (1.00) |
1 (1.00) |
0.447 (1.00) |
0.188 (1.00) |
4q loss | 13 (36%) | 23 |
0.845 (1.00) |
0.692 (1.00) |
0.961 (1.00) |
0.243 (1.00) |
1 (1.00) |
0.63 (1.00) |
0.493 (1.00) |
0.654 (1.00) |
0.597 (1.00) |
1 (1.00) |
5q loss | 3 (8%) | 33 |
0.749 (1.00) |
0.129 (1.00) |
0.552 (1.00) |
1 (1.00) |
0.422 (1.00) |
0.4 (1.00) |
0.574 (1.00) |
0.0315 (1.00) |
0.279 (1.00) |
1 (1.00) |
6p loss | 5 (14%) | 31 |
0.669 (1.00) |
0.731 (1.00) |
0.502 (1.00) |
0.109 (1.00) |
0.56 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.728 (1.00) |
1 (1.00) |
6q loss | 20 (56%) | 16 |
0.532 (1.00) |
0.339 (1.00) |
0.897 (1.00) |
0.802 (1.00) |
0.636 (1.00) |
0.639 (1.00) |
0.091 (1.00) |
0.524 (1.00) |
0.847 (1.00) |
0.783 (1.00) |
7p loss | 4 (11%) | 32 |
0.00941 (1.00) |
0.597 (1.00) |
0.296 (1.00) |
0.438 (1.00) |
0.422 (1.00) |
1 (1.00) |
0.613 (1.00) |
1 (1.00) |
0.655 (1.00) |
0.467 (1.00) |
7q loss | 4 (11%) | 32 |
0.256 (1.00) |
0.821 (1.00) |
0.348 (1.00) |
0.25 (1.00) |
1 (1.00) |
1 (1.00) |
0.613 (1.00) |
1 (1.00) |
0.654 (1.00) |
0.463 (1.00) |
8p loss | 10 (28%) | 26 |
0.454 (1.00) |
0.536 (1.00) |
0.197 (1.00) |
0.0287 (1.00) |
0.291 (1.00) |
0.29 (1.00) |
0.285 (1.00) |
0.452 (1.00) |
0.419 (1.00) |
0.763 (1.00) |
8q loss | 5 (14%) | 31 |
0.832 (1.00) |
0.664 (1.00) |
1 (1.00) |
0.527 (1.00) |
1 (1.00) |
1 (1.00) |
0.637 (1.00) |
1 (1.00) |
0.469 (1.00) |
1 (1.00) |
9p loss | 18 (50%) | 18 |
0.709 (1.00) |
0.0515 (1.00) |
0.106 (1.00) |
0.357 (1.00) |
0.654 (1.00) |
0.0184 (1.00) |
0.315 (1.00) |
0.209 (1.00) |
1 (1.00) |
0.228 (1.00) |
9q loss | 19 (53%) | 17 |
0.825 (1.00) |
0.0493 (1.00) |
0.388 (1.00) |
0.245 (1.00) |
0.172 (1.00) |
0.152 (1.00) |
1 (1.00) |
0.433 (1.00) |
0.491 (1.00) |
0.231 (1.00) |
10p loss | 6 (17%) | 30 |
0.74 (1.00) |
0.983 (1.00) |
0.184 (1.00) |
0.705 (1.00) |
0.173 (1.00) |
0.216 (1.00) |
1 (1.00) |
0.0585 (1.00) |
0.556 (1.00) |
0.359 (1.00) |
10q loss | 5 (14%) | 31 |
0.897 (1.00) |
1 (1.00) |
0.814 (1.00) |
0.829 (1.00) |
0.525 (1.00) |
1 (1.00) |
0.637 (1.00) |
0.33 (1.00) |
1 (1.00) |
1 (1.00) |
11p loss | 8 (22%) | 28 |
0.158 (1.00) |
0.985 (1.00) |
0.727 (1.00) |
0.413 (1.00) |
0.553 (1.00) |
1 (1.00) |
0.422 (1.00) |
1 (1.00) |
0.272 (1.00) |
1 (1.00) |
11q loss | 9 (25%) | 27 |
0.0995 (1.00) |
0.715 (1.00) |
0.86 (1.00) |
0.432 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.146 (1.00) |
1 (1.00) |
0.518 (1.00) |
1 (1.00) |
12q loss | 3 (8%) | 33 |
0.481 (1.00) |
0.954 (1.00) |
0.0816 (1.00) |
0.535 (1.00) |
0.0601 (1.00) |
0.0532 (1.00) |
1 (1.00) |
0.065 (1.00) |
0.277 (1.00) |
1 (1.00) |
13q loss | 16 (44%) | 20 |
0.558 (1.00) |
0.899 (1.00) |
0.316 (1.00) |
0.243 (1.00) |
0.344 (1.00) |
0.0574 (1.00) |
1 (1.00) |
0.072 (1.00) |
0.846 (1.00) |
0.613 (1.00) |
14q loss | 13 (36%) | 23 |
0.91 (1.00) |
0.961 (1.00) |
0.507 (1.00) |
0.799 (1.00) |
0.147 (1.00) |
0.63 (1.00) |
0.731 (1.00) |
0.655 (1.00) |
1 (1.00) |
1 (1.00) |
15q loss | 5 (14%) | 31 |
0.31 (1.00) |
0.537 (1.00) |
0.5 (1.00) |
0.194 (1.00) |
0.525 (1.00) |
0.5 (1.00) |
0.637 (1.00) |
0.331 (1.00) |
0.728 (1.00) |
1 (1.00) |
16p loss | 4 (11%) | 32 |
0.281 (1.00) |
0.84 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.303 (1.00) |
1 (1.00) |
0.653 (1.00) |
0.467 (1.00) |
16q loss | 7 (19%) | 29 |
0.529 (1.00) |
0.889 (1.00) |
0.824 (1.00) |
1 (1.00) |
1 (1.00) |
0.559 (1.00) |
1 (1.00) |
0.719 (1.00) |
0.0567 (1.00) |
0.685 (1.00) |
17p loss | 10 (28%) | 26 |
0.188 (1.00) |
0.958 (1.00) |
0.882 (1.00) |
0.523 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.774 (1.00) |
0.54 (1.00) |
0.242 (1.00) |
18p loss | 6 (17%) | 30 |
0.665 (1.00) |
0.47 (1.00) |
0.93 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.374 (1.00) |
1 (1.00) |
1 (1.00) |
0.0893 (1.00) |
18q loss | 8 (22%) | 28 |
0.638 (1.00) |
0.849 (1.00) |
0.958 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.535 (1.00) |
1 (1.00) |
0.159 (1.00) |
19p loss | 4 (11%) | 32 |
0.696 (1.00) |
0.94 (1.00) |
0.498 (1.00) |
1 (1.00) |
0.525 (1.00) |
0.5 (1.00) |
1 (1.00) |
0.0616 (1.00) |
0.374 (1.00) |
1 (1.00) |
19q loss | 3 (8%) | 33 |
0.334 (1.00) |
0.567 (1.00) |
0.783 (1.00) |
0.376 (1.00) |
1 (1.00) |
1 (1.00) |
0.574 (1.00) |
0.432 (1.00) |
1 (1.00) |
1 (1.00) |
20p loss | 5 (14%) | 31 |
0.326 (1.00) |
0.537 (1.00) |
0.814 (1.00) |
0.83 (1.00) |
1 (1.00) |
0.5 (1.00) |
1 (1.00) |
0.185 (1.00) |
1 (1.00) |
0.548 (1.00) |
21q loss | 15 (42%) | 21 |
0.867 (1.00) |
0.199 (1.00) |
0.601 (1.00) |
0.412 (1.00) |
0.368 (1.00) |
0.625 (1.00) |
1 (1.00) |
0.814 (1.00) |
0.836 (1.00) |
0.778 (1.00) |
22q loss | 5 (14%) | 31 |
0.243 (1.00) |
1 (1.00) |
0.501 (1.00) |
0.108 (1.00) |
1 (1.00) |
1 (1.00) |
0.355 (1.00) |
0.622 (1.00) |
0.728 (1.00) |
0.298 (1.00) |
xp loss | 15 (42%) | 21 |
0.619 (1.00) |
0.885 (1.00) |
0.227 (1.00) |
0.587 (1.00) |
0.128 (1.00) |
1 (1.00) |
0.32 (1.00) |
0.642 (1.00) |
0.834 (1.00) |
0.202 (1.00) |
xq loss | 15 (42%) | 21 |
0.619 (1.00) |
0.885 (1.00) |
0.229 (1.00) |
0.588 (1.00) |
0.128 (1.00) |
1 (1.00) |
0.32 (1.00) |
0.641 (1.00) |
0.836 (1.00) |
0.199 (1.00) |
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Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/22519028/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CHOL-TP/22489349/CHOL-TP.merged_data.txt
-
Number of patients = 36
-
Number of significantly arm-level cnvs = 65
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Number of selected clinical features = 10
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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 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.