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 13 clinical features across 488 patients, 2 significant findings detected with Q value < 0.25.
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18p gain cnv correlated to 'GENDER'.
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9p loss cnv correlated to 'NUMBERPACKYEARSSMOKED'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED |
NUMBER OF LYMPH NODES |
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 | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
18p gain | 112 (23%) | 376 |
0.508 (1.00) |
0.141 (1.00) |
0.202 (1.00) |
0.179 (1.00) |
0.165 (1.00) |
0.0522 (1.00) |
0.000152 (0.158) |
1 (1.00) |
0.661 (1.00) |
0.273 (1.00) |
0.279 (1.00) |
0.479 (1.00) |
0.619 (1.00) |
9p loss | 175 (36%) | 313 |
0.0149 (1.00) |
0.707 (1.00) |
0.818 (1.00) |
0.875 (1.00) |
0.952 (1.00) |
0.244 (1.00) |
0.203 (1.00) |
1 (1.00) |
1 (1.00) |
4.61e-05 (0.0479) |
0.826 (1.00) |
0.159 (1.00) |
1 (1.00) |
1p gain | 64 (13%) | 424 |
0.301 (1.00) |
0.528 (1.00) |
0.62 (1.00) |
0.686 (1.00) |
0.429 (1.00) |
0.0566 (1.00) |
0.88 (1.00) |
0.00451 (1.00) |
0.856 (1.00) |
0.473 (1.00) |
0.248 (1.00) |
0.0414 (1.00) |
0.228 (1.00) |
1q gain | 112 (23%) | 376 |
0.216 (1.00) |
0.0954 (1.00) |
0.714 (1.00) |
0.226 (1.00) |
0.236 (1.00) |
0.456 (1.00) |
0.333 (1.00) |
0.00421 (1.00) |
0.306 (1.00) |
0.996 (1.00) |
0.442 (1.00) |
0.00201 (1.00) |
0.453 (1.00) |
2p gain | 91 (19%) | 397 |
0.277 (1.00) |
0.405 (1.00) |
0.984 (1.00) |
0.757 (1.00) |
0.409 (1.00) |
0.866 (1.00) |
0.0126 (1.00) |
0.516 (1.00) |
1 (1.00) |
0.0102 (1.00) |
0.869 (1.00) |
0.137 (1.00) |
1 (1.00) |
2q gain | 72 (15%) | 416 |
0.686 (1.00) |
0.687 (1.00) |
0.862 (1.00) |
0.945 (1.00) |
0.253 (1.00) |
0.7 (1.00) |
0.15 (1.00) |
0.466 (1.00) |
0.392 (1.00) |
0.0568 (1.00) |
0.691 (1.00) |
0.193 (1.00) |
0.765 (1.00) |
3p gain | 77 (16%) | 411 |
0.312 (1.00) |
0.371 (1.00) |
0.494 (1.00) |
0.402 (1.00) |
0.29 (1.00) |
0.00971 (1.00) |
0.78 (1.00) |
1 (1.00) |
0.401 (1.00) |
0.978 (1.00) |
0.115 (1.00) |
0.962 (1.00) |
0.781 (1.00) |
3q gain | 237 (49%) | 251 |
0.159 (1.00) |
0.449 (1.00) |
0.882 (1.00) |
0.842 (1.00) |
0.0316 (1.00) |
0.699 (1.00) |
0.104 (1.00) |
1 (1.00) |
0.0196 (1.00) |
0.799 (1.00) |
0.00442 (1.00) |
1 (1.00) |
0.534 (1.00) |
4p gain | 39 (8%) | 449 |
0.222 (1.00) |
0.0347 (1.00) |
0.329 (1.00) |
0.23 (1.00) |
0.519 (1.00) |
0.746 (1.00) |
1 (1.00) |
1 (1.00) |
0.495 (1.00) |
0.747 (1.00) |
0.548 (1.00) |
0.0614 (1.00) |
0.103 (1.00) |
4q gain | 35 (7%) | 453 |
0.852 (1.00) |
0.278 (1.00) |
0.0219 (1.00) |
0.562 (1.00) |
0.0582 (1.00) |
0.55 (1.00) |
0.694 (1.00) |
0.559 (1.00) |
0.243 (1.00) |
0.746 (1.00) |
0.484 (1.00) |
0.136 (1.00) |
0.0714 (1.00) |
5p gain | 187 (38%) | 301 |
0.428 (1.00) |
0.204 (1.00) |
0.15 (1.00) |
0.927 (1.00) |
0.0326 (1.00) |
0.0347 (1.00) |
0.175 (1.00) |
0.187 (1.00) |
0.0163 (1.00) |
0.28 (1.00) |
0.0429 (1.00) |
0.296 (1.00) |
0.132 (1.00) |
5q gain | 64 (13%) | 424 |
0.322 (1.00) |
0.444 (1.00) |
0.138 (1.00) |
0.287 (1.00) |
0.137 (1.00) |
0.0881 (1.00) |
0.228 (1.00) |
0.0772 (1.00) |
0.102 (1.00) |
0.734 (1.00) |
0.0118 (1.00) |
0.664 (1.00) |
0.0298 (1.00) |
6p gain | 76 (16%) | 412 |
0.517 (1.00) |
0.0734 (1.00) |
0.579 (1.00) |
0.554 (1.00) |
0.731 (1.00) |
0.516 (1.00) |
0.574 (1.00) |
0.714 (1.00) |
0.0405 (1.00) |
0.215 (1.00) |
0.205 (1.00) |
0.0191 (1.00) |
0.772 (1.00) |
6q gain | 58 (12%) | 430 |
0.0569 (1.00) |
0.0404 (1.00) |
0.242 (1.00) |
0.649 (1.00) |
0.179 (1.00) |
0.431 (1.00) |
0.64 (1.00) |
0.416 (1.00) |
0.0128 (1.00) |
0.00989 (1.00) |
0.0946 (1.00) |
0.232 (1.00) |
0.014 (1.00) |
7p gain | 172 (35%) | 316 |
0.907 (1.00) |
0.916 (1.00) |
0.872 (1.00) |
0.591 (1.00) |
0.819 (1.00) |
0.832 (1.00) |
0.67 (1.00) |
0.294 (1.00) |
0.441 (1.00) |
0.0497 (1.00) |
0.742 (1.00) |
0.632 (1.00) |
1 (1.00) |
7q gain | 123 (25%) | 365 |
0.944 (1.00) |
0.0915 (1.00) |
0.822 (1.00) |
0.759 (1.00) |
0.578 (1.00) |
0.685 (1.00) |
0.815 (1.00) |
0.349 (1.00) |
0.397 (1.00) |
0.115 (1.00) |
0.487 (1.00) |
0.467 (1.00) |
0.338 (1.00) |
8p gain | 146 (30%) | 342 |
0.267 (1.00) |
0.65 (1.00) |
0.959 (1.00) |
0.304 (1.00) |
0.331 (1.00) |
1 (1.00) |
0.0106 (1.00) |
0.103 (1.00) |
0.788 (1.00) |
0.82 (1.00) |
0.902 (1.00) |
0.397 (1.00) |
0.651 (1.00) |
8q gain | 291 (60%) | 197 |
0.182 (1.00) |
0.185 (1.00) |
0.236 (1.00) |
0.643 (1.00) |
0.291 (1.00) |
0.467 (1.00) |
1 (1.00) |
1 (1.00) |
0.618 (1.00) |
0.939 (1.00) |
0.167 (1.00) |
0.666 (1.00) |
0.288 (1.00) |
9p gain | 93 (19%) | 395 |
0.133 (1.00) |
0.286 (1.00) |
0.49 (1.00) |
0.629 (1.00) |
0.192 (1.00) |
0.761 (1.00) |
0.0271 (1.00) |
0.755 (1.00) |
0.273 (1.00) |
0.0132 (1.00) |
0.951 (1.00) |
0.582 (1.00) |
0.289 (1.00) |
9q gain | 129 (26%) | 359 |
0.766 (1.00) |
0.0868 (1.00) |
0.238 (1.00) |
0.108 (1.00) |
0.473 (1.00) |
1 (1.00) |
0.489 (1.00) |
0.801 (1.00) |
0.677 (1.00) |
0.415 (1.00) |
0.413 (1.00) |
0.942 (1.00) |
0.0957 (1.00) |
10p gain | 34 (7%) | 454 |
0.451 (1.00) |
0.705 (1.00) |
0.853 (1.00) |
0.7 (1.00) |
0.308 (1.00) |
0.734 (1.00) |
0.695 (1.00) |
0.552 (1.00) |
0.81 (1.00) |
0.461 (1.00) |
0.0787 (1.00) |
0.831 (1.00) |
0.243 (1.00) |
10q gain | 31 (6%) | 457 |
0.686 (1.00) |
0.688 (1.00) |
0.631 (1.00) |
0.839 (1.00) |
0.714 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.316 (1.00) |
0.893 (1.00) |
0.687 (1.00) |
0.255 (1.00) |
0.667 (1.00) |
11p gain | 60 (12%) | 428 |
0.575 (1.00) |
0.446 (1.00) |
0.159 (1.00) |
0.351 (1.00) |
0.0778 (1.00) |
0.211 (1.00) |
0.877 (1.00) |
0.665 (1.00) |
0.58 (1.00) |
0.262 (1.00) |
0.171 (1.00) |
0.0734 (1.00) |
0.754 (1.00) |
11q gain | 69 (14%) | 419 |
0.467 (1.00) |
0.679 (1.00) |
0.436 (1.00) |
0.63 (1.00) |
0.0806 (1.00) |
0.239 (1.00) |
0.38 (1.00) |
0.459 (1.00) |
0.296 (1.00) |
0.239 (1.00) |
0.0287 (1.00) |
0.798 (1.00) |
0.757 (1.00) |
12p gain | 139 (28%) | 349 |
0.247 (1.00) |
0.811 (1.00) |
0.951 (1.00) |
0.975 (1.00) |
0.875 (1.00) |
0.555 (1.00) |
0.216 (1.00) |
0.807 (1.00) |
0.892 (1.00) |
0.32 (1.00) |
0.991 (1.00) |
0.249 (1.00) |
0.49 (1.00) |
12q gain | 81 (17%) | 407 |
0.295 (1.00) |
0.156 (1.00) |
0.709 (1.00) |
0.798 (1.00) |
0.277 (1.00) |
0.499 (1.00) |
1 (1.00) |
1 (1.00) |
0.0679 (1.00) |
0.27 (1.00) |
0.175 (1.00) |
0.838 (1.00) |
0.571 (1.00) |
13q gain | 55 (11%) | 433 |
0.406 (1.00) |
0.0881 (1.00) |
0.392 (1.00) |
0.332 (1.00) |
0.891 (1.00) |
1 (1.00) |
0.748 (1.00) |
1 (1.00) |
0.0535 (1.00) |
0.72 (1.00) |
0.979 (1.00) |
0.703 (1.00) |
0.33 (1.00) |
14q gain | 139 (28%) | 349 |
0.192 (1.00) |
0.849 (1.00) |
0.806 (1.00) |
0.98 (1.00) |
0.948 (1.00) |
0.548 (1.00) |
0.366 (1.00) |
0.0699 (1.00) |
0.586 (1.00) |
0.382 (1.00) |
0.948 (1.00) |
0.0833 (1.00) |
0.819 (1.00) |
15q gain | 69 (14%) | 419 |
0.697 (1.00) |
0.259 (1.00) |
0.871 (1.00) |
0.0389 (1.00) |
0.726 (1.00) |
0.845 (1.00) |
0.38 (1.00) |
0.692 (1.00) |
1 (1.00) |
0.977 (1.00) |
0.313 (1.00) |
0.834 (1.00) |
0.227 (1.00) |
16p gain | 103 (21%) | 385 |
0.581 (1.00) |
0.311 (1.00) |
0.726 (1.00) |
0.911 (1.00) |
0.573 (1.00) |
0.536 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.655 (1.00) |
0.299 (1.00) |
0.133 (1.00) |
0.133 (1.00) |
0.294 (1.00) |
16q gain | 104 (21%) | 384 |
0.354 (1.00) |
0.446 (1.00) |
0.654 (1.00) |
0.871 (1.00) |
0.922 (1.00) |
0.528 (1.00) |
0.534 (1.00) |
1 (1.00) |
0.764 (1.00) |
0.87 (1.00) |
0.883 (1.00) |
0.241 (1.00) |
0.302 (1.00) |
17p gain | 64 (13%) | 424 |
0.118 (1.00) |
0.557 (1.00) |
0.0938 (1.00) |
0.04 (1.00) |
0.573 (1.00) |
0.848 (1.00) |
0.228 (1.00) |
0.11 (1.00) |
0.856 (1.00) |
0.909 (1.00) |
0.533 (1.00) |
0.628 (1.00) |
0.108 (1.00) |
17q gain | 81 (17%) | 407 |
0.544 (1.00) |
0.816 (1.00) |
0.0611 (1.00) |
0.0222 (1.00) |
0.35 (1.00) |
0.231 (1.00) |
0.218 (1.00) |
0.167 (1.00) |
0.869 (1.00) |
0.184 (1.00) |
0.985 (1.00) |
0.776 (1.00) |
0.0446 (1.00) |
18q gain | 48 (10%) | 440 |
0.64 (1.00) |
0.919 (1.00) |
0.255 (1.00) |
0.808 (1.00) |
0.661 (1.00) |
0.0731 (1.00) |
0.00171 (1.00) |
0.33 (1.00) |
1 (1.00) |
0.652 (1.00) |
0.777 (1.00) |
0.598 (1.00) |
1 (1.00) |
19p gain | 50 (10%) | 438 |
0.163 (1.00) |
0.189 (1.00) |
0.825 (1.00) |
0.2 (1.00) |
0.243 (1.00) |
0.195 (1.00) |
0.178 (1.00) |
0.348 (1.00) |
0.84 (1.00) |
0.111 (1.00) |
0.0321 (1.00) |
0.624 (1.00) |
0.731 (1.00) |
19q gain | 71 (15%) | 417 |
0.342 (1.00) |
0.415 (1.00) |
0.987 (1.00) |
0.811 (1.00) |
0.595 (1.00) |
0.209 (1.00) |
0.083 (1.00) |
0.287 (1.00) |
0.862 (1.00) |
0.285 (1.00) |
0.0891 (1.00) |
0.115 (1.00) |
1 (1.00) |
20p gain | 178 (36%) | 310 |
0.0178 (1.00) |
0.61 (1.00) |
0.25 (1.00) |
0.445 (1.00) |
0.122 (1.00) |
0.646 (1.00) |
0.916 (1.00) |
1 (1.00) |
0.203 (1.00) |
0.361 (1.00) |
0.611 (1.00) |
0.97 (1.00) |
0.188 (1.00) |
20q gain | 189 (39%) | 299 |
0.3 (1.00) |
0.956 (1.00) |
0.228 (1.00) |
0.251 (1.00) |
0.674 (1.00) |
0.667 (1.00) |
0.917 (1.00) |
0.843 (1.00) |
0.313 (1.00) |
0.803 (1.00) |
0.732 (1.00) |
0.68 (1.00) |
0.518 (1.00) |
21q gain | 32 (7%) | 456 |
0.561 (1.00) |
0.779 (1.00) |
0.0427 (1.00) |
0.384 (1.00) |
0.265 (1.00) |
1 (1.00) |
0.0636 (1.00) |
0.0109 (1.00) |
0.33 (1.00) |
0.466 (1.00) |
0.43 (1.00) |
0.573 (1.00) |
0.0645 (1.00) |
22q gain | 108 (22%) | 380 |
0.995 (1.00) |
0.708 (1.00) |
0.967 (1.00) |
0.686 (1.00) |
0.817 (1.00) |
0.367 (1.00) |
0.221 (1.00) |
0.321 (1.00) |
0.461 (1.00) |
0.0554 (1.00) |
0.722 (1.00) |
0.467 (1.00) |
0.0769 (1.00) |
xq gain | 81 (17%) | 407 |
0.571 (1.00) |
0.0927 (1.00) |
0.332 (1.00) |
0.0398 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.494 (1.00) |
1 (1.00) |
0.00498 (1.00) |
0.381 (1.00) |
0.171 (1.00) |
0.401 (1.00) |
1 (1.00) |
1p loss | 55 (11%) | 433 |
0.665 (1.00) |
0.0181 (1.00) |
0.809 (1.00) |
0.849 (1.00) |
0.949 (1.00) |
0.83 (1.00) |
0.63 (1.00) |
1 (1.00) |
0.697 (1.00) |
0.00316 (1.00) |
0.489 (1.00) |
0.718 (1.00) |
1 (1.00) |
1q loss | 36 (7%) | 452 |
0.223 (1.00) |
0.371 (1.00) |
0.65 (1.00) |
0.312 (1.00) |
0.828 (1.00) |
0.435 (1.00) |
0.848 (1.00) |
1 (1.00) |
1 (1.00) |
0.72 (1.00) |
0.995 (1.00) |
0.109 (1.00) |
1 (1.00) |
2p loss | 32 (7%) | 456 |
0.775 (1.00) |
0.822 (1.00) |
0.292 (1.00) |
0.51 (1.00) |
0.288 (1.00) |
0.131 (1.00) |
0.013 (1.00) |
1 (1.00) |
0.139 (1.00) |
0.108 (1.00) |
0.391 (1.00) |
0.73 (1.00) |
0.0714 (1.00) |
2q loss | 44 (9%) | 444 |
0.946 (1.00) |
0.992 (1.00) |
0.116 (1.00) |
0.359 (1.00) |
0.127 (1.00) |
0.823 (1.00) |
0.00686 (1.00) |
0.294 (1.00) |
0.0298 (1.00) |
0.715 (1.00) |
0.942 (1.00) |
0.206 (1.00) |
0.258 (1.00) |
3p loss | 283 (58%) | 205 |
0.0955 (1.00) |
0.72 (1.00) |
0.491 (1.00) |
0.0874 (1.00) |
0.201 (1.00) |
0.0644 (1.00) |
0.00714 (1.00) |
0.335 (1.00) |
0.321 (1.00) |
0.0279 (1.00) |
0.409 (1.00) |
0.00938 (1.00) |
0.674 (1.00) |
3q loss | 59 (12%) | 429 |
0.0859 (1.00) |
0.484 (1.00) |
0.233 (1.00) |
0.135 (1.00) |
0.205 (1.00) |
0.358 (1.00) |
0.435 (1.00) |
0.664 (1.00) |
0.707 (1.00) |
0.0693 (1.00) |
0.198 (1.00) |
0.163 (1.00) |
0.754 (1.00) |
4p loss | 183 (38%) | 305 |
0.802 (1.00) |
0.48 (1.00) |
0.469 (1.00) |
0.0916 (1.00) |
0.453 (1.00) |
0.065 (1.00) |
0.293 (1.00) |
0.693 (1.00) |
1 (1.00) |
0.0754 (1.00) |
0.171 (1.00) |
0.107 (1.00) |
0.395 (1.00) |
4q loss | 141 (29%) | 347 |
0.401 (1.00) |
0.88 (1.00) |
0.109 (1.00) |
0.109 (1.00) |
0.163 (1.00) |
0.0862 (1.00) |
0.823 (1.00) |
0.81 (1.00) |
0.104 (1.00) |
0.161 (1.00) |
0.157 (1.00) |
0.0619 (1.00) |
0.363 (1.00) |
5p loss | 48 (10%) | 440 |
0.725 (1.00) |
0.371 (1.00) |
0.916 (1.00) |
0.617 (1.00) |
0.643 (1.00) |
0.822 (1.00) |
0.734 (1.00) |
0.331 (1.00) |
0.0129 (1.00) |
0.596 (1.00) |
0.629 (1.00) |
0.356 (1.00) |
0.449 (1.00) |
5q loss | 156 (32%) | 332 |
0.0676 (1.00) |
0.365 (1.00) |
0.699 (1.00) |
0.131 (1.00) |
0.632 (1.00) |
0.537 (1.00) |
0.191 (1.00) |
0.817 (1.00) |
1 (1.00) |
0.0845 (1.00) |
0.963 (1.00) |
0.0921 (1.00) |
1 (1.00) |
6p loss | 64 (13%) | 424 |
0.629 (1.00) |
0.637 (1.00) |
0.455 (1.00) |
0.455 (1.00) |
0.637 (1.00) |
0.412 (1.00) |
0.367 (1.00) |
1 (1.00) |
0.585 (1.00) |
0.278 (1.00) |
0.886 (1.00) |
0.135 (1.00) |
0.102 (1.00) |
6q loss | 62 (13%) | 426 |
0.184 (1.00) |
0.77 (1.00) |
0.753 (1.00) |
0.591 (1.00) |
0.759 (1.00) |
0.299 (1.00) |
0.169 (1.00) |
1 (1.00) |
0.463 (1.00) |
0.855 (1.00) |
0.795 (1.00) |
0.135 (1.00) |
1 (1.00) |
7p loss | 28 (6%) | 460 |
0.571 (1.00) |
0.773 (1.00) |
0.164 (1.00) |
0.831 (1.00) |
0.114 (1.00) |
0.0367 (1.00) |
0.517 (1.00) |
0.48 (1.00) |
0.598 (1.00) |
0.766 (1.00) |
0.355 (1.00) |
1 (1.00) |
1 (1.00) |
7q loss | 39 (8%) | 449 |
0.642 (1.00) |
0.123 (1.00) |
0.875 (1.00) |
0.0964 (1.00) |
0.12 (1.00) |
0.46 (1.00) |
0.577 (1.00) |
0.252 (1.00) |
0.82 (1.00) |
0.918 (1.00) |
0.743 (1.00) |
0.927 (1.00) |
0.71 (1.00) |
8p loss | 175 (36%) | 313 |
0.669 (1.00) |
0.33 (1.00) |
0.564 (1.00) |
0.228 (1.00) |
0.613 (1.00) |
0.543 (1.00) |
0.0714 (1.00) |
0.684 (1.00) |
0.898 (1.00) |
0.743 (1.00) |
0.203 (1.00) |
0.298 (1.00) |
0.519 (1.00) |
8q loss | 28 (6%) | 460 |
0.709 (1.00) |
0.785 (1.00) |
0.841 (1.00) |
0.889 (1.00) |
0.794 (1.00) |
0.783 (1.00) |
0.662 (1.00) |
0.482 (1.00) |
0.43 (1.00) |
0.129 (1.00) |
0.604 (1.00) |
1 (1.00) |
0.646 (1.00) |
9q loss | 81 (17%) | 407 |
0.987 (1.00) |
0.982 (1.00) |
0.478 (1.00) |
0.316 (1.00) |
0.721 (1.00) |
0.23 (1.00) |
0.682 (1.00) |
0.482 (1.00) |
0.512 (1.00) |
0.0827 (1.00) |
0.596 (1.00) |
0.169 (1.00) |
0.241 (1.00) |
10p loss | 149 (31%) | 339 |
0.0272 (1.00) |
0.894 (1.00) |
0.463 (1.00) |
0.0765 (1.00) |
0.558 (1.00) |
0.91 (1.00) |
0.0766 (1.00) |
0.0473 (1.00) |
0.35 (1.00) |
0.647 (1.00) |
0.534 (1.00) |
0.0233 (1.00) |
1 (1.00) |
10q loss | 104 (21%) | 384 |
0.0416 (1.00) |
0.894 (1.00) |
0.651 (1.00) |
0.256 (1.00) |
0.181 (1.00) |
0.783 (1.00) |
0.0467 (1.00) |
0.314 (1.00) |
0.23 (1.00) |
0.435 (1.00) |
0.886 (1.00) |
0.0889 (1.00) |
0.614 (1.00) |
11p loss | 135 (28%) | 353 |
0.761 (1.00) |
0.645 (1.00) |
0.0164 (1.00) |
0.795 (1.00) |
0.0798 (1.00) |
0.636 (1.00) |
0.362 (1.00) |
0.0417 (1.00) |
0.784 (1.00) |
0.533 (1.00) |
0.0236 (1.00) |
0.0947 (1.00) |
0.098 (1.00) |
11q loss | 160 (33%) | 328 |
0.624 (1.00) |
0.0765 (1.00) |
0.221 (1.00) |
0.856 (1.00) |
0.0771 (1.00) |
0.067 (1.00) |
0.000774 (0.803) |
0.117 (1.00) |
0.117 (1.00) |
0.906 (1.00) |
0.00124 (1.00) |
0.0359 (1.00) |
0.182 (1.00) |
12p loss | 33 (7%) | 455 |
0.0655 (1.00) |
0.178 (1.00) |
0.658 (1.00) |
0.702 (1.00) |
0.523 (1.00) |
1 (1.00) |
0.419 (1.00) |
1 (1.00) |
0.461 (1.00) |
0.909 (1.00) |
0.666 (1.00) |
0.37 (1.00) |
0.205 (1.00) |
12q loss | 29 (6%) | 459 |
0.672 (1.00) |
0.477 (1.00) |
0.868 (1.00) |
0.155 (1.00) |
0.709 (1.00) |
1 (1.00) |
0.831 (1.00) |
0.495 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.346 (1.00) |
0.141 (1.00) |
0.164 (1.00) |
13q loss | 154 (32%) | 334 |
0.726 (1.00) |
0.588 (1.00) |
0.329 (1.00) |
0.87 (1.00) |
0.91 (1.00) |
0.481 (1.00) |
0.585 (1.00) |
0.522 (1.00) |
0.895 (1.00) |
0.408 (1.00) |
0.354 (1.00) |
0.0977 (1.00) |
0.493 (1.00) |
14q loss | 53 (11%) | 435 |
0.000538 (0.559) |
0.883 (1.00) |
0.22 (1.00) |
0.452 (1.00) |
0.681 (1.00) |
0.406 (1.00) |
0.19 (1.00) |
0.183 (1.00) |
0.556 (1.00) |
0.786 (1.00) |
0.198 (1.00) |
0.322 (1.00) |
1 (1.00) |
15q loss | 95 (19%) | 393 |
0.468 (1.00) |
0.379 (1.00) |
0.769 (1.00) |
0.575 (1.00) |
0.392 (1.00) |
0.454 (1.00) |
0.701 (1.00) |
0.0651 (1.00) |
0.438 (1.00) |
0.983 (1.00) |
0.521 (1.00) |
0.612 (1.00) |
0.106 (1.00) |
16p loss | 57 (12%) | 431 |
0.0385 (1.00) |
0.0269 (1.00) |
0.968 (1.00) |
0.0143 (1.00) |
0.0405 (1.00) |
0.0432 (1.00) |
0.429 (1.00) |
0.409 (1.00) |
0.126 (1.00) |
0.894 (1.00) |
0.0751 (1.00) |
0.693 (1.00) |
0.515 (1.00) |
16q loss | 72 (15%) | 416 |
0.697 (1.00) |
0.09 (1.00) |
0.933 (1.00) |
0.26 (1.00) |
0.169 (1.00) |
0.288 (1.00) |
0.25 (1.00) |
0.0937 (1.00) |
0.488 (1.00) |
0.77 (1.00) |
0.458 (1.00) |
0.749 (1.00) |
1 (1.00) |
17p loss | 101 (21%) | 387 |
0.357 (1.00) |
0.191 (1.00) |
0.0642 (1.00) |
0.582 (1.00) |
0.742 (1.00) |
0.111 (1.00) |
0.802 (1.00) |
1 (1.00) |
0.449 (1.00) |
0.506 (1.00) |
0.671 (1.00) |
0.669 (1.00) |
0.0671 (1.00) |
17q loss | 32 (7%) | 456 |
0.0786 (1.00) |
0.613 (1.00) |
0.52 (1.00) |
0.411 (1.00) |
0.403 (1.00) |
0.0524 (1.00) |
1 (1.00) |
0.53 (1.00) |
0.21 (1.00) |
0.83 (1.00) |
0.923 (1.00) |
0.801 (1.00) |
0.205 (1.00) |
18p loss | 96 (20%) | 392 |
0.281 (1.00) |
0.923 (1.00) |
0.901 (1.00) |
0.996 (1.00) |
0.825 (1.00) |
1 (1.00) |
0.126 (1.00) |
0.162 (1.00) |
0.645 (1.00) |
0.855 (1.00) |
0.868 (1.00) |
0.582 (1.00) |
0.031 (1.00) |
18q loss | 198 (41%) | 290 |
0.995 (1.00) |
0.0586 (1.00) |
0.993 (1.00) |
0.994 (1.00) |
0.466 (1.00) |
0.212 (1.00) |
0.47 (1.00) |
0.0344 (1.00) |
0.381 (1.00) |
0.211 (1.00) |
0.18 (1.00) |
0.0373 (1.00) |
0.394 (1.00) |
19p loss | 90 (18%) | 398 |
0.205 (1.00) |
0.226 (1.00) |
0.124 (1.00) |
0.281 (1.00) |
0.0809 (1.00) |
0.266 (1.00) |
0.189 (1.00) |
0.365 (1.00) |
0.158 (1.00) |
0.618 (1.00) |
0.776 (1.00) |
0.441 (1.00) |
0.425 (1.00) |
19q loss | 79 (16%) | 409 |
0.254 (1.00) |
0.0922 (1.00) |
0.0242 (1.00) |
0.0507 (1.00) |
0.568 (1.00) |
0.6 (1.00) |
0.408 (1.00) |
1 (1.00) |
0.504 (1.00) |
0.837 (1.00) |
0.934 (1.00) |
0.139 (1.00) |
0.565 (1.00) |
20p loss | 46 (9%) | 442 |
0.381 (1.00) |
0.829 (1.00) |
0.558 (1.00) |
0.919 (1.00) |
0.303 (1.00) |
0.238 (1.00) |
0.728 (1.00) |
0.644 (1.00) |
0.528 (1.00) |
0.26 (1.00) |
0.198 (1.00) |
0.701 (1.00) |
1 (1.00) |
20q loss | 28 (6%) | 460 |
0.779 (1.00) |
0.534 (1.00) |
0.151 (1.00) |
0.262 (1.00) |
0.929 (1.00) |
0.696 (1.00) |
0.662 (1.00) |
0.484 (1.00) |
1 (1.00) |
0.0311 (1.00) |
0.259 (1.00) |
0.877 (1.00) |
1 (1.00) |
21q loss | 177 (36%) | 311 |
0.686 (1.00) |
0.957 (1.00) |
0.882 (1.00) |
0.0762 (1.00) |
0.367 (1.00) |
0.0675 (1.00) |
0.916 (1.00) |
1 (1.00) |
0.703 (1.00) |
0.0256 (1.00) |
0.524 (1.00) |
0.0129 (1.00) |
1 (1.00) |
22q loss | 69 (14%) | 419 |
0.617 (1.00) |
0.879 (1.00) |
0.46 (1.00) |
0.328 (1.00) |
0.295 (1.00) |
1 (1.00) |
0.143 (1.00) |
0.46 (1.00) |
0.161 (1.00) |
0.667 (1.00) |
0.198 (1.00) |
0.191 (1.00) |
0.36 (1.00) |
xq loss | 77 (16%) | 411 |
0.218 (1.00) |
0.0949 (1.00) |
0.0426 (1.00) |
0.0566 (1.00) |
0.4 (1.00) |
0.0882 (1.00) |
0.264 (1.00) |
0.107 (1.00) |
0.737 (1.00) |
0.0463 (1.00) |
0.0276 (1.00) |
0.855 (1.00) |
0.4 (1.00) |
P value = 0.000152 (Fisher's exact test), Q value = 0.16
nPatients | FEMALE | MALE |
---|---|---|
ALL | 132 | 356 |
18P GAIN MUTATED | 15 | 97 |
18P GAIN WILD-TYPE | 117 | 259 |
P value = 4.61e-05 (Wilcoxon-test), Q value = 0.048
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 272 | 45.8 (35.8) |
9P LOSS MUTATED | 108 | 52.5 (30.7) |
9P LOSS WILD-TYPE | 164 | 41.4 (38.2) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = HNSC-TP.merged_data.txt
-
Number of patients = 488
-
Number of significantly arm-level cnvs = 80
-
Number of selected clinical features = 13
-
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.