This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 57 arm-level events and 17 clinical features across 495 patients, 9 significant findings detected with Q value < 0.25.
-
1q gain cnv correlated to 'AGE', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.
-
5p gain cnv correlated to 'AGE'.
-
5q gain cnv correlated to 'PATHOLOGY.M.STAGE'.
-
12q gain cnv correlated to 'PATHOLOGY.M.STAGE'.
-
20p gain cnv correlated to 'PATHOLOGY.M.STAGE'.
-
20q gain cnv correlated to 'PATHOLOGY.M.STAGE'.
-
11q loss cnv correlated to 'AGE'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
RADIATIONEXPOSURE |
EXTRATHYROIDAL EXTENSION |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
MULTIFOCALITY |
TUMOR SIZE |
RACE | ETHNICITY | ||
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 | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
1q gain | 25 (5%) | 470 |
0.0256 (1.00) |
4.07e-05 (0.0386) |
2e-05 (0.019) |
4e-05 (0.038) |
0.000655 (0.612) |
0.325 (1.00) |
0.493 (1.00) |
0.0191 (1.00) |
0.521 (1.00) |
0.611 (1.00) |
0.00031 (0.292) |
0.017 (1.00) |
0.0646 (1.00) |
0.0239 (1.00) |
0.00925 (1.00) |
0.00801 (1.00) |
0.264 (1.00) |
5p gain | 20 (4%) | 475 |
0.0914 (1.00) |
0.000226 (0.213) |
0.00339 (1.00) |
0.468 (1.00) |
0.202 (1.00) |
0.00347 (1.00) |
0.796 (1.00) |
0.129 (1.00) |
0.443 (1.00) |
1 (1.00) |
0.0386 (1.00) |
0.512 (1.00) |
0.0254 (1.00) |
0.651 (1.00) |
0.0568 (1.00) |
0.43 (1.00) |
1 (1.00) |
5q gain | 16 (3%) | 479 |
0.0163 (1.00) |
0.0107 (1.00) |
0.00564 (1.00) |
0.682 (1.00) |
0.00571 (1.00) |
0.00014 (0.133) |
0.773 (1.00) |
0.0401 (1.00) |
0.373 (1.00) |
1 (1.00) |
0.0287 (1.00) |
0.466 (1.00) |
0.00054 (0.506) |
0.803 (1.00) |
0.144 (1.00) |
0.798 (1.00) |
1 (1.00) |
12q gain | 15 (3%) | 480 |
0.524 (1.00) |
0.168 (1.00) |
0.127 (1.00) |
0.92 (1.00) |
0.00176 (1.00) |
0.00023 (0.217) |
0.769 (1.00) |
0.00612 (1.00) |
1 (1.00) |
1 (1.00) |
0.199 (1.00) |
0.606 (1.00) |
0.000938 (0.874) |
1 (1.00) |
0.953 (1.00) |
0.778 (1.00) |
1 (1.00) |
20p gain | 12 (2%) | 483 |
0.304 (1.00) |
0.0768 (1.00) |
0.0103 (1.00) |
0.551 (1.00) |
0.0679 (1.00) |
0.00015 (0.142) |
0.526 (1.00) |
0.00411 (1.00) |
1 (1.00) |
1 (1.00) |
0.0221 (1.00) |
0.861 (1.00) |
0.00496 (1.00) |
1 (1.00) |
0.0933 (1.00) |
1 (1.00) |
1 (1.00) |
20q gain | 12 (2%) | 483 |
0.304 (1.00) |
0.0768 (1.00) |
0.00954 (1.00) |
0.549 (1.00) |
0.0679 (1.00) |
0.00013 (0.123) |
0.526 (1.00) |
0.00462 (1.00) |
1 (1.00) |
1 (1.00) |
0.0218 (1.00) |
0.857 (1.00) |
0.00496 (1.00) |
1 (1.00) |
0.0933 (1.00) |
1 (1.00) |
1 (1.00) |
11q loss | 9 (2%) | 486 |
0.00232 (1.00) |
0.000177 (0.167) |
0.00383 (1.00) |
0.195 (1.00) |
0.503 (1.00) |
0.118 (1.00) |
0.00176 (1.00) |
1 (1.00) |
0.229 (1.00) |
1 (1.00) |
0.796 (1.00) |
0.522 (1.00) |
0.358 (1.00) |
1 (1.00) |
0.00223 (1.00) |
0.532 (1.00) |
1 (1.00) |
1p gain | 4 (1%) | 491 |
0.0101 (1.00) |
0.196 (1.00) |
0.00353 (1.00) |
0.253 (1.00) |
0.372 (1.00) |
0.00717 (1.00) |
1 (1.00) |
0.336 (1.00) |
1 (1.00) |
0.113 (1.00) |
1 (1.00) |
0.0491 (1.00) |
0.639 (1.00) |
0.628 (1.00) |
0.72 (1.00) |
1 (1.00) |
1 (1.00) |
3p gain | 3 (1%) | 492 |
0.0093 (1.00) |
0.0147 (1.00) |
0.0347 (1.00) |
0.114 (1.00) |
1 (1.00) |
0.0109 (1.00) |
0.569 (1.00) |
0.224 (1.00) |
1 (1.00) |
1 (1.00) |
0.607 (1.00) |
0.0238 (1.00) |
1 (1.00) |
0.546 (1.00) |
1 (1.00) |
||
4p gain | 5 (1%) | 490 |
0.0203 (1.00) |
0.0281 (1.00) |
0.184 (1.00) |
0.632 (1.00) |
0.0611 (1.00) |
0.029 (1.00) |
1 (1.00) |
0.179 (1.00) |
0.134 (1.00) |
1 (1.00) |
1 (1.00) |
0.396 (1.00) |
0.027 (1.00) |
0.187 (1.00) |
0.24 (1.00) |
1 (1.00) |
1 (1.00) |
4q gain | 5 (1%) | 490 |
0.0203 (1.00) |
0.0281 (1.00) |
0.184 (1.00) |
0.63 (1.00) |
0.0611 (1.00) |
0.0285 (1.00) |
1 (1.00) |
0.181 (1.00) |
0.134 (1.00) |
1 (1.00) |
1 (1.00) |
0.395 (1.00) |
0.027 (1.00) |
0.187 (1.00) |
0.24 (1.00) |
1 (1.00) |
1 (1.00) |
7p gain | 17 (3%) | 478 |
0.337 (1.00) |
0.0611 (1.00) |
0.00602 (1.00) |
0.808 (1.00) |
0.00301 (1.00) |
0.00577 (1.00) |
1 (1.00) |
0.0164 (1.00) |
1 (1.00) |
1 (1.00) |
0.00936 (1.00) |
0.463 (1.00) |
0.00031 (0.292) |
1 (1.00) |
0.57 (1.00) |
0.796 (1.00) |
1 (1.00) |
7q gain | 19 (4%) | 476 |
0.351 (1.00) |
0.0503 (1.00) |
0.0095 (1.00) |
0.947 (1.00) |
0.00301 (1.00) |
0.00794 (1.00) |
0.792 (1.00) |
0.0106 (1.00) |
1 (1.00) |
1 (1.00) |
0.0219 (1.00) |
0.262 (1.00) |
0.00031 (0.292) |
1 (1.00) |
0.577 (1.00) |
0.555 (1.00) |
1 (1.00) |
8p gain | 6 (1%) | 489 |
0.621 (1.00) |
0.64 (1.00) |
0.71 (1.00) |
0.906 (1.00) |
0.623 (1.00) |
0.186 (1.00) |
1 (1.00) |
0.781 (1.00) |
1 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.464 (1.00) |
0.2 (1.00) |
0.224 (1.00) |
0.335 (1.00) |
0.656 (1.00) |
1 (1.00) |
8q gain | 7 (1%) | 488 |
0.119 (1.00) |
0.337 (1.00) |
0.0564 (1.00) |
0.407 (1.00) |
1 (1.00) |
0.0954 (1.00) |
0.681 (1.00) |
0.815 (1.00) |
1 (1.00) |
1 (1.00) |
0.00813 (1.00) |
0.396 (1.00) |
0.2 (1.00) |
0.13 (1.00) |
0.222 (1.00) |
0.723 (1.00) |
1 (1.00) |
9p gain | 3 (1%) | 492 |
0.712 (1.00) |
0.0764 (1.00) |
0.0474 (1.00) |
0.805 (1.00) |
0.248 (1.00) |
0.605 (1.00) |
1 (1.00) |
0.227 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.598 (1.00) |
0.0597 (1.00) |
1 (1.00) |
||
9q gain | 4 (1%) | 491 |
0.707 (1.00) |
0.031 (1.00) |
0.0404 (1.00) |
0.629 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.286 (1.00) |
0.454 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.269 (1.00) |
0.34 (1.00) |
0.025 (1.00) |
1 (1.00) |
1 (1.00) |
11p gain | 6 (1%) | 489 |
0.571 (1.00) |
0.773 (1.00) |
0.713 (1.00) |
0.695 (1.00) |
0.123 (1.00) |
0.185 (1.00) |
0.192 (1.00) |
0.249 (1.00) |
1 (1.00) |
1 (1.00) |
0.348 (1.00) |
0.465 (1.00) |
0.0482 (1.00) |
0.224 (1.00) |
0.621 (1.00) |
1 (1.00) |
1 (1.00) |
11q gain | 5 (1%) | 490 |
0.574 (1.00) |
0.759 (1.00) |
0.793 (1.00) |
0.797 (1.00) |
0.248 (1.00) |
0.246 (1.00) |
0.612 (1.00) |
0.56 (1.00) |
1 (1.00) |
1 (1.00) |
0.443 (1.00) |
0.395 (1.00) |
0.0877 (1.00) |
0.0648 (1.00) |
0.967 (1.00) |
1 (1.00) |
1 (1.00) |
12p gain | 14 (3%) | 481 |
0.527 (1.00) |
0.193 (1.00) |
0.0932 (1.00) |
0.916 (1.00) |
0.00176 (1.00) |
0.00051 (0.478) |
1 (1.00) |
0.016 (1.00) |
1 (1.00) |
1 (1.00) |
0.24 (1.00) |
0.462 (1.00) |
0.000938 (0.874) |
0.792 (1.00) |
0.953 (1.00) |
0.757 (1.00) |
1 (1.00) |
13q gain | 5 (1%) | 490 |
0.739 (1.00) |
0.147 (1.00) |
0.0574 (1.00) |
0.704 (1.00) |
0.123 (1.00) |
0.245 (1.00) |
1 (1.00) |
0.178 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0482 (1.00) |
0.666 (1.00) |
0.685 (1.00) |
1 (1.00) |
|
14q gain | 11 (2%) | 484 |
0.55 (1.00) |
0.0334 (1.00) |
0.00701 (1.00) |
0.376 (1.00) |
0.0679 (1.00) |
0.033 (1.00) |
0.303 (1.00) |
0.0594 (1.00) |
1 (1.00) |
1 (1.00) |
0.824 (1.00) |
0.497 (1.00) |
0.0662 (1.00) |
0.123 (1.00) |
0.271 (1.00) |
1 (1.00) |
1 (1.00) |
16p gain | 15 (3%) | 480 |
0.209 (1.00) |
0.187 (1.00) |
0.0383 (1.00) |
0.876 (1.00) |
0.0201 (1.00) |
0.0155 (1.00) |
0.769 (1.00) |
0.0965 (1.00) |
1 (1.00) |
1 (1.00) |
0.0378 (1.00) |
0.146 (1.00) |
0.00163 (1.00) |
0.794 (1.00) |
0.682 (1.00) |
0.796 (1.00) |
1 (1.00) |
16q gain | 13 (3%) | 482 |
0.202 (1.00) |
0.123 (1.00) |
0.0216 (1.00) |
0.713 (1.00) |
0.0372 (1.00) |
0.0095 (1.00) |
1 (1.00) |
0.0458 (1.00) |
1 (1.00) |
1 (1.00) |
0.0169 (1.00) |
0.271 (1.00) |
0.00284 (1.00) |
1 (1.00) |
0.621 (1.00) |
0.758 (1.00) |
1 (1.00) |
17p gain | 16 (3%) | 479 |
0.434 (1.00) |
0.075 (1.00) |
0.00392 (1.00) |
0.849 (1.00) |
0.0361 (1.00) |
0.00734 (1.00) |
1 (1.00) |
0.039 (1.00) |
1 (1.00) |
1 (1.00) |
0.763 (1.00) |
0.332 (1.00) |
0.0139 (1.00) |
1 (1.00) |
0.52 (1.00) |
1 (1.00) |
1 (1.00) |
17q gain | 17 (3%) | 478 |
0.434 (1.00) |
0.141 (1.00) |
0.00546 (1.00) |
0.861 (1.00) |
0.0206 (1.00) |
0.00525 (1.00) |
1 (1.00) |
0.0679 (1.00) |
1 (1.00) |
1 (1.00) |
0.69 (1.00) |
0.333 (1.00) |
0.0082 (1.00) |
0.806 (1.00) |
0.828 (1.00) |
1 (1.00) |
0.608 (1.00) |
18p gain | 6 (1%) | 489 |
0.629 (1.00) |
0.705 (1.00) |
0.711 (1.00) |
0.695 (1.00) |
0.0611 (1.00) |
0.471 (1.00) |
0.658 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.392 (1.00) |
0.0482 (1.00) |
0.691 (1.00) |
0.806 (1.00) |
1 (1.00) |
1 (1.00) |
18q gain | 6 (1%) | 489 |
0.629 (1.00) |
0.705 (1.00) |
0.712 (1.00) |
0.695 (1.00) |
0.0611 (1.00) |
0.471 (1.00) |
0.658 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.391 (1.00) |
0.0482 (1.00) |
0.691 (1.00) |
0.806 (1.00) |
1 (1.00) |
1 (1.00) |
19p gain | 8 (2%) | 487 |
0.742 (1.00) |
0.0504 (1.00) |
0.624 (1.00) |
0.581 (1.00) |
0.0302 (1.00) |
0.00258 (1.00) |
0.217 (1.00) |
0.00803 (1.00) |
1 (1.00) |
1 (1.00) |
0.591 (1.00) |
0.465 (1.00) |
0.00867 (1.00) |
0.152 (1.00) |
0.153 (1.00) |
1 (1.00) |
1 (1.00) |
19q gain | 10 (2%) | 485 |
0.0293 (1.00) |
0.0148 (1.00) |
0.601 (1.00) |
0.313 (1.00) |
0.0149 (1.00) |
0.00105 (0.976) |
0.139 (1.00) |
0.00477 (1.00) |
0.251 (1.00) |
1 (1.00) |
0.513 (1.00) |
0.82 (1.00) |
0.00496 (1.00) |
0.525 (1.00) |
0.0814 (1.00) |
1 (1.00) |
1 (1.00) |
21q gain | 5 (1%) | 490 |
0.629 (1.00) |
0.328 (1.00) |
0.576 (1.00) |
0.558 (1.00) |
0.248 (1.00) |
0.687 (1.00) |
0.612 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.641 (1.00) |
0.317 (1.00) |
0.0877 (1.00) |
0.0648 (1.00) |
0.124 (1.00) |
1 (1.00) |
1 (1.00) |
xq gain | 9 (2%) | 486 |
0.0737 (1.00) |
0.0529 (1.00) |
0.0157 (1.00) |
0.479 (1.00) |
0.285 (1.00) |
0.0247 (1.00) |
0.456 (1.00) |
0.334 (1.00) |
1 (1.00) |
0.304 (1.00) |
0.0247 (1.00) |
0.0869 (1.00) |
0.108 (1.00) |
0.314 (1.00) |
0.467 (1.00) |
1 (1.00) |
1 (1.00) |
1p loss | 4 (1%) | 491 |
0.613 (1.00) |
0.532 (1.00) |
0.154 (1.00) |
0.628 (1.00) |
0.248 (1.00) |
0.369 (1.00) |
0.577 (1.00) |
0.454 (1.00) |
1 (1.00) |
1 (1.00) |
0.635 (1.00) |
1 (1.00) |
0.628 (1.00) |
0.116 (1.00) |
0.474 (1.00) |
1 (1.00) |
|
1q loss | 3 (1%) | 492 |
0.616 (1.00) |
0.808 (1.00) |
0.331 (1.00) |
0.692 (1.00) |
0.499 (1.00) |
0.133 (1.00) |
0.569 (1.00) |
0.228 (1.00) |
1 (1.00) |
1 (1.00) |
0.607 (1.00) |
1 (1.00) |
1 (1.00) |
0.116 (1.00) |
1 (1.00) |
||
2p loss | 10 (2%) | 485 |
0.728 (1.00) |
0.273 (1.00) |
0.0291 (1.00) |
0.695 (1.00) |
0.00733 (1.00) |
0.0135 (1.00) |
0.729 (1.00) |
0.00543 (1.00) |
1 (1.00) |
1 (1.00) |
0.141 (1.00) |
0.455 (1.00) |
0.00284 (1.00) |
1 (1.00) |
0.987 (1.00) |
1 (1.00) |
1 (1.00) |
2q loss | 10 (2%) | 485 |
0.588 (1.00) |
0.248 (1.00) |
0.0282 (1.00) |
0.821 (1.00) |
0.0149 (1.00) |
0.0134 (1.00) |
0.729 (1.00) |
0.00523 (1.00) |
1 (1.00) |
1 (1.00) |
0.141 (1.00) |
0.455 (1.00) |
0.00496 (1.00) |
1 (1.00) |
0.355 (1.00) |
1 (1.00) |
1 (1.00) |
3p loss | 3 (1%) | 492 |
0.672 (1.00) |
0.56 (1.00) |
0.329 (1.00) |
0.688 (1.00) |
0.499 (1.00) |
0.133 (1.00) |
1 (1.00) |
0.636 (1.00) |
1 (1.00) |
1 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.598 (1.00) |
0.0773 (1.00) |
1 (1.00) |
1 (1.00) |
|
3q loss | 4 (1%) | 491 |
0.61 (1.00) |
0.585 (1.00) |
0.152 (1.00) |
0.627 (1.00) |
0.248 (1.00) |
0.105 (1.00) |
1 (1.00) |
0.453 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
0.0877 (1.00) |
1 (1.00) |
0.0941 (1.00) |
1 (1.00) |
1 (1.00) |
6p loss | 4 (1%) | 491 |
0.645 (1.00) |
0.315 (1.00) |
0.735 (1.00) |
0.87 (1.00) |
1 (1.00) |
0.105 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.638 (1.00) |
0.555 (1.00) |
1 (1.00) |
0.0571 (1.00) |
1 (1.00) |
1 (1.00) |
|
6q loss | 7 (1%) | 488 |
0.00549 (1.00) |
0.0767 (1.00) |
0.199 (1.00) |
0.789 (1.00) |
0.372 (1.00) |
0.00921 (1.00) |
0.388 (1.00) |
0.818 (1.00) |
0.183 (1.00) |
0.214 (1.00) |
0.38 (1.00) |
0.76 (1.00) |
0.2 (1.00) |
0.459 (1.00) |
0.00901 (1.00) |
1 (1.00) |
1 (1.00) |
8p loss | 4 (1%) | 491 |
0.876 (1.00) |
0.89 (1.00) |
0.173 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.37 (1.00) |
0.0587 (1.00) |
0.454 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
0.0482 (1.00) |
1 (1.00) |
0.741 (1.00) |
1 (1.00) |
|
8q loss | 4 (1%) | 491 |
0.876 (1.00) |
0.89 (1.00) |
0.176 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.372 (1.00) |
0.0587 (1.00) |
0.452 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
0.0482 (1.00) |
1 (1.00) |
0.741 (1.00) |
1 (1.00) |
|
9p loss | 19 (4%) | 476 |
0.448 (1.00) |
0.0881 (1.00) |
0.0281 (1.00) |
0.435 (1.00) |
1 (1.00) |
0.0535 (1.00) |
0.296 (1.00) |
0.766 (1.00) |
1 (1.00) |
1 (1.00) |
0.894 (1.00) |
0.565 (1.00) |
0.281 (1.00) |
0.485 (1.00) |
0.116 (1.00) |
1 (1.00) |
0.378 (1.00) |
9q loss | 23 (5%) | 472 |
0.0349 (1.00) |
0.00461 (1.00) |
0.00047 (0.441) |
0.218 (1.00) |
0.493 (1.00) |
0.0228 (1.00) |
0.342 (1.00) |
0.719 (1.00) |
0.491 (1.00) |
0.594 (1.00) |
0.0778 (1.00) |
0.735 (1.00) |
0.494 (1.00) |
0.527 (1.00) |
0.0568 (1.00) |
0.891 (1.00) |
1 (1.00) |
10p loss | 7 (1%) | 488 |
0.6 (1.00) |
0.319 (1.00) |
0.122 (1.00) |
0.291 (1.00) |
0.0302 (1.00) |
0.0942 (1.00) |
0.388 (1.00) |
0.387 (1.00) |
1 (1.00) |
1 (1.00) |
0.753 (1.00) |
1 (1.00) |
0.027 (1.00) |
0.709 (1.00) |
0.0111 (1.00) |
0.657 (1.00) |
1 (1.00) |
10q loss | 6 (1%) | 489 |
0.659 (1.00) |
0.298 (1.00) |
0.259 (1.00) |
0.306 (1.00) |
0.0611 (1.00) |
0.187 (1.00) |
0.192 (1.00) |
0.78 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0482 (1.00) |
0.422 (1.00) |
0.00806 (1.00) |
0.657 (1.00) |
1 (1.00) |
11p loss | 7 (1%) | 488 |
0.00076 (0.709) |
0.00061 (0.571) |
0.00554 (1.00) |
0.216 (1.00) |
0.449 (1.00) |
0.0954 (1.00) |
0.0159 (1.00) |
0.817 (1.00) |
0.183 (1.00) |
1 (1.00) |
0.544 (1.00) |
0.53 (1.00) |
0.239 (1.00) |
0.709 (1.00) |
0.00754 (1.00) |
0.466 (1.00) |
1 (1.00) |
13q loss | 14 (3%) | 481 |
0.343 (1.00) |
0.0281 (1.00) |
0.46 (1.00) |
0.573 (1.00) |
0.0108 (1.00) |
0.363 (1.00) |
0.538 (1.00) |
0.458 (1.00) |
0.334 (1.00) |
0.000664 (0.62) |
0.623 (1.00) |
0.678 (1.00) |
0.00677 (1.00) |
0.792 (1.00) |
0.0937 (1.00) |
1 (1.00) |
0.608 (1.00) |
15q loss | 8 (2%) | 487 |
0.573 (1.00) |
0.774 (1.00) |
0.241 (1.00) |
0.682 (1.00) |
0.122 (1.00) |
0.059 (1.00) |
0.688 (1.00) |
0.05 (1.00) |
1 (1.00) |
1 (1.00) |
0.59 (1.00) |
0.785 (1.00) |
0.155 (1.00) |
0.731 (1.00) |
0.0755 (1.00) |
0.657 (1.00) |
0.404 (1.00) |
17p loss | 7 (1%) | 488 |
0.589 (1.00) |
0.851 (1.00) |
0.254 (1.00) |
0.163 (1.00) |
0.449 (1.00) |
0.343 (1.00) |
0.681 (1.00) |
0.13 (1.00) |
0.0144 (1.00) |
0.246 (1.00) |
0.184 (1.00) |
0.758 (1.00) |
0.582 (1.00) |
1 (1.00) |
0.0423 (1.00) |
0.573 (1.00) |
1 (1.00) |
17q loss | 4 (1%) | 491 |
0.812 (1.00) |
0.476 (1.00) |
0.471 (1.00) |
0.625 (1.00) |
0.123 (1.00) |
0.37 (1.00) |
1 (1.00) |
0.457 (1.00) |
0.109 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0877 (1.00) |
1 (1.00) |
0.401 (1.00) |
1 (1.00) |
|
18p loss | 4 (1%) | 491 |
0.765 (1.00) |
0.69 (1.00) |
0.175 (1.00) |
0.339 (1.00) |
1 (1.00) |
0.37 (1.00) |
1 (1.00) |
0.456 (1.00) |
1 (1.00) |
1 (1.00) |
0.64 (1.00) |
1 (1.00) |
0.2 (1.00) |
0.628 (1.00) |
0.638 (1.00) |
0.187 (1.00) |
|
18q loss | 4 (1%) | 491 |
0.765 (1.00) |
0.69 (1.00) |
0.176 (1.00) |
0.342 (1.00) |
1 (1.00) |
0.371 (1.00) |
1 (1.00) |
0.454 (1.00) |
1 (1.00) |
1 (1.00) |
0.641 (1.00) |
1 (1.00) |
0.2 (1.00) |
0.628 (1.00) |
0.638 (1.00) |
0.187 (1.00) |
|
19p loss | 5 (1%) | 490 |
0.114 (1.00) |
0.481 (1.00) |
0.252 (1.00) |
1 (1.00) |
1 (1.00) |
0.686 (1.00) |
0.612 (1.00) |
1 (1.00) |
1 (1.00) |
0.0135 (1.00) |
1 (1.00) |
0.639 (1.00) |
0.38 (1.00) |
0.00904 (1.00) |
1 (1.00) |
1 (1.00) |
|
21q loss | 8 (2%) | 487 |
0.854 (1.00) |
0.111 (1.00) |
0.0137 (1.00) |
0.174 (1.00) |
0.724 (1.00) |
0.771 (1.00) |
0.442 (1.00) |
0.85 (1.00) |
1 (1.00) |
1 (1.00) |
0.214 (1.00) |
1 (1.00) |
0.642 (1.00) |
0.152 (1.00) |
0.506 (1.00) |
0.224 (1.00) |
1 (1.00) |
22q loss | 87 (18%) | 408 |
0.529 (1.00) |
0.578 (1.00) |
0.591 (1.00) |
0.644 (1.00) |
0.321 (1.00) |
0.452 (1.00) |
0.424 (1.00) |
0.208 (1.00) |
0.481 (1.00) |
0.331 (1.00) |
0.375 (1.00) |
0.297 (1.00) |
0.601 (1.00) |
0.188 (1.00) |
0.608 (1.00) |
0.529 (1.00) |
1 (1.00) |
xq loss | 3 (1%) | 492 |
0.76 (1.00) |
0.413 (1.00) |
0.00622 (1.00) |
0.221 (1.00) |
0.248 (1.00) |
0.131 (1.00) |
0.172 (1.00) |
0.637 (1.00) |
1 (1.00) |
1 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.0877 (1.00) |
1 (1.00) |
1 (1.00) |
P value = 4.07e-05 (Wilcoxon-test), Q value = 0.039
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 495 | 47.1 (15.6) |
1Q GAIN MUTATED | 25 | 60.4 (15.4) |
1Q GAIN WILD-TYPE | 470 | 46.4 (15.4) |
P value = 2e-05 (Fisher's exact test), Q value = 0.019
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 280 | 51 | 109 | 2 | 45 | 6 |
1Q GAIN MUTATED | 6 | 0 | 10 | 1 | 7 | 1 |
1Q GAIN WILD-TYPE | 274 | 51 | 99 | 1 | 38 | 5 |
P value = 4e-05 (Fisher's exact test), Q value = 0.038
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 140 | 166 | 165 | 21 |
1Q GAIN MUTATED | 2 | 3 | 15 | 5 |
1Q GAIN WILD-TYPE | 138 | 163 | 150 | 16 |
P value = 0.000226 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 495 | 47.1 (15.6) |
5P GAIN MUTATED | 20 | 60.8 (15.5) |
5P GAIN WILD-TYPE | 475 | 46.5 (15.4) |
P value = 0.00014 (Fisher's exact test), Q value = 0.13
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 273 | 9 | 212 |
5Q GAIN MUTATED | 1 | 0 | 15 |
5Q GAIN WILD-TYPE | 272 | 9 | 197 |
P value = 0.00023 (Fisher's exact test), Q value = 0.22
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 273 | 9 | 212 |
12Q GAIN MUTATED | 1 | 0 | 14 |
12Q GAIN WILD-TYPE | 272 | 9 | 198 |
P value = 0.00015 (Fisher's exact test), Q value = 0.14
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 273 | 9 | 212 |
20P GAIN MUTATED | 0 | 0 | 12 |
20P GAIN WILD-TYPE | 273 | 9 | 200 |
P value = 0.00013 (Fisher's exact test), Q value = 0.12
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 273 | 9 | 212 |
20Q GAIN MUTATED | 0 | 0 | 12 |
20Q GAIN WILD-TYPE | 273 | 9 | 200 |
P value = 0.000177 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 495 | 47.1 (15.6) |
11Q LOSS MUTATED | 9 | 67.0 (8.9) |
11Q LOSS WILD-TYPE | 486 | 46.7 (15.5) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = THCA-TP.merged_data.txt
-
Number of patients = 495
-
Number of significantly arm-level cnvs = 57
-
Number of selected clinical features = 17
-
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.