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 486 patients, 8 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'.
-
20p gain cnv correlated to 'PATHOLOGY.M.STAGE'.
-
20q gain cnv correlated to 'PATHOLOGY.M.STAGE'.
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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 | 24 (5%) | 462 |
0.193 (1.00) |
9.33e-05 (0.0886) |
0.00012 (0.114) |
0.00013 (0.123) |
0.00115 (1.00) |
0.704 (1.00) |
0.478 (1.00) |
0.022 (1.00) |
0.513 (1.00) |
0.601 (1.00) |
0.00031 (0.292) |
0.0341 (1.00) |
0.0325 (1.00) |
0.0368 (1.00) |
0.0185 (1.00) |
0.00232 (1.00) |
0.259 (1.00) |
5p gain | 20 (4%) | 466 |
0.108 (1.00) |
0.000239 (0.225) |
0.00337 (1.00) |
0.423 (1.00) |
0.202 (1.00) |
0.0041 (1.00) |
0.796 (1.00) |
0.135 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.0402 (1.00) |
0.5 (1.00) |
0.0263 (1.00) |
0.651 (1.00) |
0.0508 (1.00) |
0.47 (1.00) |
1 (1.00) |
5q gain | 16 (3%) | 470 |
0.0208 (1.00) |
0.0113 (1.00) |
0.0053 (1.00) |
0.687 (1.00) |
0.00571 (1.00) |
0.00019 (0.179) |
0.773 (1.00) |
0.0422 (1.00) |
0.378 (1.00) |
1 (1.00) |
0.0285 (1.00) |
0.409 (1.00) |
0.000546 (0.512) |
0.802 (1.00) |
0.134 (1.00) |
0.766 (1.00) |
0.607 (1.00) |
20p gain | 12 (2%) | 474 |
0.33 (1.00) |
0.0798 (1.00) |
0.0105 (1.00) |
0.555 (1.00) |
0.0678 (1.00) |
0.00011 (0.104) |
0.528 (1.00) |
0.00425 (1.00) |
1 (1.00) |
1 (1.00) |
0.0229 (1.00) |
0.855 (1.00) |
0.005 (1.00) |
0.779 (1.00) |
0.087 (1.00) |
1 (1.00) |
1 (1.00) |
20q gain | 12 (2%) | 474 |
0.33 (1.00) |
0.0798 (1.00) |
0.0105 (1.00) |
0.552 (1.00) |
0.0678 (1.00) |
0.00015 (0.142) |
0.528 (1.00) |
0.00434 (1.00) |
1 (1.00) |
1 (1.00) |
0.0218 (1.00) |
0.854 (1.00) |
0.005 (1.00) |
0.779 (1.00) |
0.087 (1.00) |
1 (1.00) |
1 (1.00) |
11q loss | 9 (2%) | 477 |
0.00326 (1.00) |
0.000181 (0.171) |
0.00347 (1.00) |
0.198 (1.00) |
0.503 (1.00) |
0.12 (1.00) |
0.00179 (1.00) |
1 (1.00) |
0.233 (1.00) |
1 (1.00) |
0.797 (1.00) |
0.511 (1.00) |
0.362 (1.00) |
1 (1.00) |
0.00211 (1.00) |
0.36 (1.00) |
1 (1.00) |
1p gain | 3 (1%) | 483 |
0.921 (1.00) |
0.457 (1.00) |
0.0403 (1.00) |
1 (1.00) |
0.623 (1.00) |
0.135 (1.00) |
1 (1.00) |
0.341 (1.00) |
1 (1.00) |
0.0783 (1.00) |
1 (1.00) |
0.234 (1.00) |
0.969 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
3p gain | 3 (1%) | 483 |
0.0117 (1.00) |
0.0148 (1.00) |
0.0336 (1.00) |
0.118 (1.00) |
1 (1.00) |
0.0117 (1.00) |
0.569 (1.00) |
0.232 (1.00) |
1 (1.00) |
1 (1.00) |
0.606 (1.00) |
0.0224 (1.00) |
1 (1.00) |
0.533 (1.00) |
1 (1.00) |
||
4p gain | 5 (1%) | 481 |
0.025 (1.00) |
0.0283 (1.00) |
0.186 (1.00) |
0.631 (1.00) |
0.0611 (1.00) |
0.0293 (1.00) |
1 (1.00) |
0.184 (1.00) |
0.137 (1.00) |
1 (1.00) |
1 (1.00) |
0.385 (1.00) |
0.0271 (1.00) |
0.185 (1.00) |
0.231 (1.00) |
1 (1.00) |
1 (1.00) |
4q gain | 5 (1%) | 481 |
0.025 (1.00) |
0.0283 (1.00) |
0.183 (1.00) |
0.631 (1.00) |
0.0611 (1.00) |
0.0286 (1.00) |
1 (1.00) |
0.181 (1.00) |
0.137 (1.00) |
1 (1.00) |
1 (1.00) |
0.388 (1.00) |
0.0271 (1.00) |
0.185 (1.00) |
0.231 (1.00) |
1 (1.00) |
1 (1.00) |
7p gain | 17 (3%) | 469 |
0.365 (1.00) |
0.0638 (1.00) |
0.00588 (1.00) |
0.793 (1.00) |
0.003 (1.00) |
0.00612 (1.00) |
1 (1.00) |
0.0179 (1.00) |
1 (1.00) |
1 (1.00) |
0.0099 (1.00) |
0.413 (1.00) |
0.000315 (0.296) |
1 (1.00) |
0.543 (1.00) |
0.766 (1.00) |
0.607 (1.00) |
7q gain | 19 (4%) | 467 |
0.379 (1.00) |
0.0526 (1.00) |
0.00895 (1.00) |
0.947 (1.00) |
0.003 (1.00) |
0.00854 (1.00) |
0.792 (1.00) |
0.0114 (1.00) |
1 (1.00) |
1 (1.00) |
0.0219 (1.00) |
0.256 (1.00) |
0.000315 (0.296) |
1 (1.00) |
0.549 (1.00) |
0.641 (1.00) |
0.607 (1.00) |
8p gain | 6 (1%) | 480 |
0.631 (1.00) |
0.652 (1.00) |
0.71 (1.00) |
0.906 (1.00) |
0.623 (1.00) |
0.19 (1.00) |
1 (1.00) |
0.785 (1.00) |
1 (1.00) |
1 (1.00) |
0.351 (1.00) |
0.457 (1.00) |
0.202 (1.00) |
0.225 (1.00) |
0.319 (1.00) |
0.633 (1.00) |
1 (1.00) |
8q gain | 7 (1%) | 479 |
0.104 (1.00) |
0.345 (1.00) |
0.0561 (1.00) |
0.41 (1.00) |
1 (1.00) |
0.0933 (1.00) |
0.681 (1.00) |
0.821 (1.00) |
1 (1.00) |
1 (1.00) |
0.00861 (1.00) |
0.386 (1.00) |
0.202 (1.00) |
0.131 (1.00) |
0.21 (1.00) |
0.699 (1.00) |
1 (1.00) |
9p gain | 3 (1%) | 483 |
0.705 (1.00) |
0.0768 (1.00) |
0.0463 (1.00) |
0.806 (1.00) |
0.248 (1.00) |
0.608 (1.00) |
1 (1.00) |
0.232 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.597 (1.00) |
0.0577 (1.00) |
1 (1.00) |
||
9q gain | 4 (1%) | 482 |
0.699 (1.00) |
0.0312 (1.00) |
0.0413 (1.00) |
0.63 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.288 (1.00) |
0.458 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.271 (1.00) |
0.338 (1.00) |
0.0237 (1.00) |
1 (1.00) |
1 (1.00) |
11p gain | 6 (1%) | 480 |
0.562 (1.00) |
0.759 (1.00) |
0.711 (1.00) |
0.696 (1.00) |
0.123 (1.00) |
0.19 (1.00) |
0.193 (1.00) |
0.255 (1.00) |
1 (1.00) |
1 (1.00) |
0.352 (1.00) |
0.46 (1.00) |
0.0485 (1.00) |
0.225 (1.00) |
0.605 (1.00) |
1 (1.00) |
1 (1.00) |
11q gain | 5 (1%) | 481 |
0.565 (1.00) |
0.745 (1.00) |
0.796 (1.00) |
0.799 (1.00) |
0.248 (1.00) |
0.248 (1.00) |
0.612 (1.00) |
0.565 (1.00) |
1 (1.00) |
1 (1.00) |
0.442 (1.00) |
0.386 (1.00) |
0.088 (1.00) |
0.0652 (1.00) |
0.982 (1.00) |
1 (1.00) |
1 (1.00) |
12p gain | 14 (3%) | 472 |
0.516 (1.00) |
0.199 (1.00) |
0.0948 (1.00) |
0.916 (1.00) |
0.00176 (1.00) |
0.00066 (0.617) |
1 (1.00) |
0.0166 (1.00) |
1 (1.00) |
1 (1.00) |
0.245 (1.00) |
0.455 (1.00) |
0.000949 (0.884) |
0.791 (1.00) |
0.925 (1.00) |
0.731 (1.00) |
1 (1.00) |
12q gain | 15 (3%) | 471 |
0.516 (1.00) |
0.173 (1.00) |
0.127 (1.00) |
0.922 (1.00) |
0.00176 (1.00) |
0.00036 (0.338) |
0.769 (1.00) |
0.00661 (1.00) |
1 (1.00) |
1 (1.00) |
0.203 (1.00) |
0.544 (1.00) |
0.000949 (0.884) |
1 (1.00) |
0.925 (1.00) |
0.749 (1.00) |
1 (1.00) |
13q gain | 5 (1%) | 481 |
0.732 (1.00) |
0.149 (1.00) |
0.0575 (1.00) |
0.705 (1.00) |
0.123 (1.00) |
0.247 (1.00) |
1 (1.00) |
0.184 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0485 (1.00) |
0.665 (1.00) |
0.673 (1.00) |
1 (1.00) |
|
14q gain | 11 (2%) | 475 |
0.539 (1.00) |
0.0343 (1.00) |
0.00668 (1.00) |
0.378 (1.00) |
0.0678 (1.00) |
0.0344 (1.00) |
0.302 (1.00) |
0.0625 (1.00) |
1 (1.00) |
1 (1.00) |
0.824 (1.00) |
0.492 (1.00) |
0.0671 (1.00) |
0.122 (1.00) |
0.253 (1.00) |
1 (1.00) |
1 (1.00) |
16p gain | 15 (3%) | 471 |
0.23 (1.00) |
0.193 (1.00) |
0.0384 (1.00) |
0.878 (1.00) |
0.0201 (1.00) |
0.016 (1.00) |
0.769 (1.00) |
0.101 (1.00) |
1 (1.00) |
1 (1.00) |
0.0349 (1.00) |
0.128 (1.00) |
0.00165 (1.00) |
0.794 (1.00) |
0.651 (1.00) |
0.769 (1.00) |
1 (1.00) |
16q gain | 13 (3%) | 473 |
0.222 (1.00) |
0.128 (1.00) |
0.0206 (1.00) |
0.713 (1.00) |
0.0372 (1.00) |
0.00997 (1.00) |
1 (1.00) |
0.0515 (1.00) |
1 (1.00) |
1 (1.00) |
0.0167 (1.00) |
0.235 (1.00) |
0.00287 (1.00) |
1 (1.00) |
0.591 (1.00) |
0.731 (1.00) |
1 (1.00) |
17p gain | 16 (3%) | 470 |
0.422 (1.00) |
0.078 (1.00) |
0.00386 (1.00) |
0.849 (1.00) |
0.036 (1.00) |
0.0086 (1.00) |
1 (1.00) |
0.0413 (1.00) |
1 (1.00) |
1 (1.00) |
0.767 (1.00) |
0.325 (1.00) |
0.0144 (1.00) |
1 (1.00) |
0.494 (1.00) |
1 (1.00) |
0.607 (1.00) |
17q gain | 17 (3%) | 469 |
0.422 (1.00) |
0.145 (1.00) |
0.00562 (1.00) |
0.863 (1.00) |
0.0206 (1.00) |
0.00558 (1.00) |
1 (1.00) |
0.0639 (1.00) |
1 (1.00) |
1 (1.00) |
0.692 (1.00) |
0.327 (1.00) |
0.00847 (1.00) |
0.806 (1.00) |
0.797 (1.00) |
1 (1.00) |
0.607 (1.00) |
18p gain | 6 (1%) | 480 |
0.62 (1.00) |
0.717 (1.00) |
0.713 (1.00) |
0.699 (1.00) |
0.0611 (1.00) |
0.473 (1.00) |
0.658 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.389 (1.00) |
0.0485 (1.00) |
0.692 (1.00) |
0.789 (1.00) |
1 (1.00) |
1 (1.00) |
18q gain | 6 (1%) | 480 |
0.62 (1.00) |
0.717 (1.00) |
0.711 (1.00) |
0.697 (1.00) |
0.0611 (1.00) |
0.474 (1.00) |
0.658 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.39 (1.00) |
0.0485 (1.00) |
0.692 (1.00) |
0.789 (1.00) |
1 (1.00) |
1 (1.00) |
19p gain | 8 (2%) | 478 |
0.735 (1.00) |
0.0519 (1.00) |
0.623 (1.00) |
0.581 (1.00) |
0.0302 (1.00) |
0.00245 (1.00) |
0.217 (1.00) |
0.00852 (1.00) |
1 (1.00) |
1 (1.00) |
0.592 (1.00) |
0.456 (1.00) |
0.00874 (1.00) |
0.151 (1.00) |
0.147 (1.00) |
1 (1.00) |
1 (1.00) |
19q gain | 10 (2%) | 476 |
0.0315 (1.00) |
0.0154 (1.00) |
0.602 (1.00) |
0.318 (1.00) |
0.0149 (1.00) |
0.00088 (0.821) |
0.139 (1.00) |
0.00538 (1.00) |
0.256 (1.00) |
1 (1.00) |
0.513 (1.00) |
0.684 (1.00) |
0.005 (1.00) |
0.524 (1.00) |
0.0771 (1.00) |
1 (1.00) |
1 (1.00) |
21q gain | 5 (1%) | 481 |
0.62 (1.00) |
0.317 (1.00) |
0.578 (1.00) |
0.557 (1.00) |
0.248 (1.00) |
0.689 (1.00) |
0.612 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.637 (1.00) |
0.311 (1.00) |
0.088 (1.00) |
0.0652 (1.00) |
0.129 (1.00) |
1 (1.00) |
1 (1.00) |
xq gain | 9 (2%) | 477 |
0.0849 (1.00) |
0.0536 (1.00) |
0.015 (1.00) |
0.485 (1.00) |
0.285 (1.00) |
0.0242 (1.00) |
0.456 (1.00) |
0.339 (1.00) |
1 (1.00) |
0.309 (1.00) |
0.0231 (1.00) |
0.0826 (1.00) |
0.108 (1.00) |
0.313 (1.00) |
0.45 (1.00) |
1 (1.00) |
1 (1.00) |
1p loss | 4 (1%) | 482 |
0.604 (1.00) |
0.539 (1.00) |
0.154 (1.00) |
0.63 (1.00) |
0.248 (1.00) |
0.372 (1.00) |
0.578 (1.00) |
0.459 (1.00) |
1 (1.00) |
1 (1.00) |
0.64 (1.00) |
1 (1.00) |
0.628 (1.00) |
0.11 (1.00) |
0.452 (1.00) |
1 (1.00) |
|
1q loss | 3 (1%) | 483 |
0.608 (1.00) |
0.816 (1.00) |
0.332 (1.00) |
0.692 (1.00) |
0.499 (1.00) |
0.137 (1.00) |
0.569 (1.00) |
0.23 (1.00) |
1 (1.00) |
1 (1.00) |
0.608 (1.00) |
1 (1.00) |
1 (1.00) |
0.11 (1.00) |
1 (1.00) |
||
2p loss | 10 (2%) | 476 |
0.722 (1.00) |
0.28 (1.00) |
0.0283 (1.00) |
0.695 (1.00) |
0.00732 (1.00) |
0.0141 (1.00) |
0.729 (1.00) |
0.00575 (1.00) |
1 (1.00) |
1 (1.00) |
0.145 (1.00) |
0.555 (1.00) |
0.00287 (1.00) |
1 (1.00) |
0.986 (1.00) |
1 (1.00) |
1 (1.00) |
2q loss | 10 (2%) | 476 |
0.579 (1.00) |
0.256 (1.00) |
0.0277 (1.00) |
0.825 (1.00) |
0.0149 (1.00) |
0.013 (1.00) |
0.729 (1.00) |
0.00538 (1.00) |
1 (1.00) |
1 (1.00) |
0.142 (1.00) |
0.556 (1.00) |
0.005 (1.00) |
1 (1.00) |
0.335 (1.00) |
1 (1.00) |
1 (1.00) |
3p loss | 3 (1%) | 483 |
0.664 (1.00) |
0.568 (1.00) |
0.332 (1.00) |
0.693 (1.00) |
0.499 (1.00) |
0.135 (1.00) |
1 (1.00) |
0.643 (1.00) |
1 (1.00) |
1 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.597 (1.00) |
0.0748 (1.00) |
1 (1.00) |
1 (1.00) |
|
3q loss | 4 (1%) | 482 |
0.601 (1.00) |
0.593 (1.00) |
0.153 (1.00) |
0.631 (1.00) |
0.248 (1.00) |
0.106 (1.00) |
1 (1.00) |
0.462 (1.00) |
1 (1.00) |
1 (1.00) |
0.637 (1.00) |
1 (1.00) |
0.088 (1.00) |
1 (1.00) |
0.0896 (1.00) |
1 (1.00) |
1 (1.00) |
6p loss | 4 (1%) | 482 |
0.636 (1.00) |
0.32 (1.00) |
0.735 (1.00) |
0.868 (1.00) |
1 (1.00) |
0.107 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
0.55 (1.00) |
1 (1.00) |
0.0547 (1.00) |
1 (1.00) |
1 (1.00) |
|
6q loss | 7 (1%) | 479 |
0.00749 (1.00) |
0.0784 (1.00) |
0.199 (1.00) |
0.79 (1.00) |
0.372 (1.00) |
0.00967 (1.00) |
0.389 (1.00) |
0.822 (1.00) |
0.186 (1.00) |
0.218 (1.00) |
0.384 (1.00) |
0.755 (1.00) |
0.202 (1.00) |
0.46 (1.00) |
0.00834 (1.00) |
1 (1.00) |
1 (1.00) |
8p loss | 4 (1%) | 482 |
0.873 (1.00) |
0.903 (1.00) |
0.175 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.369 (1.00) |
0.0591 (1.00) |
0.462 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
0.0485 (1.00) |
1 (1.00) |
0.728 (1.00) |
1 (1.00) |
|
8q loss | 4 (1%) | 482 |
0.873 (1.00) |
0.903 (1.00) |
0.174 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.372 (1.00) |
0.0591 (1.00) |
0.461 (1.00) |
1 (1.00) |
1 (1.00) |
0.64 (1.00) |
1 (1.00) |
0.0485 (1.00) |
1 (1.00) |
0.728 (1.00) |
1 (1.00) |
|
9p loss | 19 (4%) | 467 |
0.481 (1.00) |
0.0918 (1.00) |
0.0282 (1.00) |
0.45 (1.00) |
1 (1.00) |
0.0548 (1.00) |
0.297 (1.00) |
0.766 (1.00) |
1 (1.00) |
1 (1.00) |
0.895 (1.00) |
0.563 (1.00) |
0.29 (1.00) |
0.486 (1.00) |
0.107 (1.00) |
0.733 (1.00) |
0.378 (1.00) |
9q loss | 23 (5%) | 463 |
0.0433 (1.00) |
0.00485 (1.00) |
0.00063 (0.59) |
0.228 (1.00) |
0.493 (1.00) |
0.0259 (1.00) |
0.343 (1.00) |
0.723 (1.00) |
0.498 (1.00) |
0.601 (1.00) |
0.0793 (1.00) |
0.681 (1.00) |
0.507 (1.00) |
0.528 (1.00) |
0.0513 (1.00) |
0.78 (1.00) |
1 (1.00) |
10p loss | 7 (1%) | 479 |
0.59 (1.00) |
0.327 (1.00) |
0.123 (1.00) |
0.243 (1.00) |
0.0302 (1.00) |
0.096 (1.00) |
0.389 (1.00) |
0.392 (1.00) |
1 (1.00) |
1 (1.00) |
0.753 (1.00) |
1 (1.00) |
0.0271 (1.00) |
0.708 (1.00) |
0.0104 (1.00) |
0.632 (1.00) |
1 (1.00) |
10q loss | 6 (1%) | 480 |
0.651 (1.00) |
0.305 (1.00) |
0.257 (1.00) |
0.31 (1.00) |
0.0611 (1.00) |
0.188 (1.00) |
0.193 (1.00) |
0.783 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0485 (1.00) |
0.421 (1.00) |
0.00765 (1.00) |
0.63 (1.00) |
1 (1.00) |
11p loss | 7 (1%) | 479 |
0.00114 (1.00) |
0.000622 (0.583) |
0.00586 (1.00) |
0.216 (1.00) |
0.449 (1.00) |
0.0959 (1.00) |
0.0161 (1.00) |
0.822 (1.00) |
0.186 (1.00) |
1 (1.00) |
0.546 (1.00) |
0.524 (1.00) |
0.242 (1.00) |
0.708 (1.00) |
0.00714 (1.00) |
0.418 (1.00) |
1 (1.00) |
13q loss | 14 (3%) | 472 |
0.372 (1.00) |
0.0292 (1.00) |
0.462 (1.00) |
0.562 (1.00) |
0.0108 (1.00) |
0.363 (1.00) |
0.538 (1.00) |
0.465 (1.00) |
0.34 (1.00) |
0.000713 (0.666) |
0.624 (1.00) |
0.67 (1.00) |
0.00689 (1.00) |
0.791 (1.00) |
0.0858 (1.00) |
1 (1.00) |
0.607 (1.00) |
15q loss | 8 (2%) | 478 |
0.563 (1.00) |
0.76 (1.00) |
0.241 (1.00) |
0.685 (1.00) |
0.122 (1.00) |
0.0612 (1.00) |
0.688 (1.00) |
0.0535 (1.00) |
1 (1.00) |
1 (1.00) |
0.592 (1.00) |
0.784 (1.00) |
0.156 (1.00) |
0.731 (1.00) |
0.0706 (1.00) |
0.632 (1.00) |
0.412 (1.00) |
17p loss | 7 (1%) | 479 |
0.579 (1.00) |
0.838 (1.00) |
0.259 (1.00) |
0.14 (1.00) |
0.449 (1.00) |
0.337 (1.00) |
0.681 (1.00) |
0.133 (1.00) |
0.0149 (1.00) |
0.25 (1.00) |
0.183 (1.00) |
0.752 (1.00) |
0.589 (1.00) |
1 (1.00) |
0.04 (1.00) |
0.546 (1.00) |
1 (1.00) |
17q loss | 4 (1%) | 482 |
0.807 (1.00) |
0.467 (1.00) |
0.473 (1.00) |
0.628 (1.00) |
0.123 (1.00) |
0.371 (1.00) |
1 (1.00) |
0.459 (1.00) |
0.111 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.088 (1.00) |
1 (1.00) |
0.389 (1.00) |
1 (1.00) |
|
18p loss | 4 (1%) | 482 |
0.76 (1.00) |
0.681 (1.00) |
0.176 (1.00) |
0.342 (1.00) |
1 (1.00) |
0.373 (1.00) |
1 (1.00) |
0.459 (1.00) |
1 (1.00) |
1 (1.00) |
0.64 (1.00) |
1 (1.00) |
0.202 (1.00) |
0.628 (1.00) |
0.657 (1.00) |
0.191 (1.00) |
|
18q loss | 4 (1%) | 482 |
0.76 (1.00) |
0.681 (1.00) |
0.176 (1.00) |
0.343 (1.00) |
1 (1.00) |
0.374 (1.00) |
1 (1.00) |
0.459 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
1 (1.00) |
0.202 (1.00) |
0.628 (1.00) |
0.657 (1.00) |
0.191 (1.00) |
|
19p loss | 5 (1%) | 481 |
0.123 (1.00) |
0.489 (1.00) |
0.251 (1.00) |
1 (1.00) |
1 (1.00) |
0.686 (1.00) |
0.612 (1.00) |
1 (1.00) |
1 (1.00) |
0.014 (1.00) |
1 (1.00) |
0.632 (1.00) |
0.38 (1.00) |
0.00887 (1.00) |
1 (1.00) |
1 (1.00) |
|
21q loss | 8 (2%) | 478 |
0.85 (1.00) |
0.113 (1.00) |
0.0121 (1.00) |
0.174 (1.00) |
0.724 (1.00) |
0.774 (1.00) |
0.443 (1.00) |
0.856 (1.00) |
1 (1.00) |
1 (1.00) |
0.218 (1.00) |
1 (1.00) |
0.646 (1.00) |
0.151 (1.00) |
0.489 (1.00) |
0.302 (1.00) |
1 (1.00) |
22q loss | 85 (17%) | 401 |
0.506 (1.00) |
0.771 (1.00) |
0.554 (1.00) |
0.474 (1.00) |
0.261 (1.00) |
0.58 (1.00) |
0.502 (1.00) |
0.271 (1.00) |
0.481 (1.00) |
0.332 (1.00) |
0.3 (1.00) |
0.483 (1.00) |
0.482 (1.00) |
0.276 (1.00) |
0.82 (1.00) |
0.666 (1.00) |
1 (1.00) |
xq loss | 3 (1%) | 483 |
0.754 (1.00) |
0.418 (1.00) |
0.00625 (1.00) |
0.225 (1.00) |
0.248 (1.00) |
0.135 (1.00) |
0.173 (1.00) |
0.645 (1.00) |
1 (1.00) |
1 (1.00) |
0.608 (1.00) |
1 (1.00) |
0.088 (1.00) |
1 (1.00) |
1 (1.00) |
P value = 9.33e-05 (Wilcoxon-test), Q value = 0.089
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 486 | 47.2 (15.6) |
1Q GAIN MUTATED | 24 | 60.2 (15.7) |
1Q GAIN WILD-TYPE | 462 | 46.5 (15.3) |
P value = 0.00012 (Fisher's exact test), Q value = 0.11
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 275 | 50 | 107 | 2 | 44 | 6 |
1Q GAIN MUTATED | 6 | 0 | 10 | 1 | 7 | 0 |
1Q GAIN WILD-TYPE | 269 | 50 | 97 | 1 | 37 | 6 |
P value = 0.00013 (Fisher's exact test), Q value = 0.12
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 139 | 163 | 161 | 21 |
1Q GAIN MUTATED | 2 | 3 | 15 | 4 |
1Q GAIN WILD-TYPE | 137 | 160 | 146 | 17 |
P value = 0.000239 (Wilcoxon-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 486 | 47.2 (15.6) |
5P GAIN MUTATED | 20 | 60.8 (15.5) |
5P GAIN WILD-TYPE | 466 | 46.6 (15.4) |
P value = 0.00019 (Fisher's exact test), Q value = 0.18
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 267 | 9 | 209 |
5Q GAIN MUTATED | 1 | 0 | 15 |
5Q GAIN WILD-TYPE | 266 | 9 | 194 |
P value = 0.00011 (Fisher's exact test), Q value = 0.1
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 267 | 9 | 209 |
20P GAIN MUTATED | 0 | 0 | 12 |
20P GAIN WILD-TYPE | 267 | 9 | 197 |
P value = 0.00015 (Fisher's exact test), Q value = 0.14
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 267 | 9 | 209 |
20Q GAIN MUTATED | 0 | 0 | 12 |
20Q GAIN WILD-TYPE | 267 | 9 | 197 |
P value = 0.000181 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 486 | 47.2 (15.6) |
11Q LOSS MUTATED | 9 | 67.0 (8.9) |
11Q LOSS WILD-TYPE | 477 | 46.8 (15.5) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = THCA-TP.merged_data.txt
-
Number of patients = 486
-
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.