This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 82 arm-level events and 15 clinical features across 501 patients, no significant finding detected with Q value < 0.25.
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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 |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
NUMBER PACK YEARS SMOKED |
YEAR OF TOBACCO SMOKING ONSET |
RESIDUAL TUMOR |
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 | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
1p gain | 91 (18%) | 410 |
0.531 (0.917) |
0.865 (1.00) |
0.0996 (0.709) |
0.755 (0.962) |
0.655 (0.945) |
0.0313 (0.599) |
0.792 (0.973) |
0.262 (0.845) |
0.858 (1.00) |
0.0275 (0.57) |
0.388 (0.883) |
0.814 (0.981) |
0.654 (0.945) |
0.884 (1.00) |
1 (1.00) |
1q gain | 202 (40%) | 299 |
0.736 (0.954) |
0.327 (0.855) |
0.0342 (0.61) |
0.0913 (0.705) |
0.764 (0.962) |
0.0451 (0.612) |
0.213 (0.816) |
0.882 (1.00) |
0.448 (0.906) |
0.00194 (0.271) |
0.804 (0.981) |
0.467 (0.906) |
0.959 (1.00) |
0.754 (0.962) |
0.72 (0.954) |
2p gain | 223 (45%) | 278 |
0.00708 (0.458) |
0.696 (0.953) |
0.315 (0.855) |
0.139 (0.733) |
0.204 (0.807) |
1 (1.00) |
0.00286 (0.271) |
0.0773 (0.689) |
0.135 (0.733) |
0.0349 (0.61) |
0.258 (0.845) |
0.189 (0.802) |
0.334 (0.855) |
0.316 (0.855) |
0.0827 (0.691) |
2q gain | 143 (29%) | 358 |
0.0459 (0.612) |
0.663 (0.945) |
0.382 (0.883) |
0.222 (0.836) |
0.479 (0.906) |
1 (1.00) |
0.0425 (0.612) |
0.264 (0.845) |
0.11 (0.711) |
0.0431 (0.612) |
0.53 (0.917) |
0.586 (0.927) |
0.474 (0.906) |
0.684 (0.951) |
0.443 (0.906) |
3p gain | 108 (22%) | 393 |
0.49 (0.909) |
0.881 (1.00) |
0.0932 (0.705) |
0.849 (0.998) |
0.52 (0.917) |
0.356 (0.872) |
0.0843 (0.691) |
0.0512 (0.617) |
0.897 (1.00) |
0.54 (0.917) |
0.768 (0.962) |
0.292 (0.855) |
0.319 (0.855) |
0.565 (0.923) |
1 (1.00) |
3q gain | 315 (63%) | 186 |
0.79 (0.973) |
0.73 (0.954) |
0.138 (0.733) |
0.321 (0.855) |
0.863 (1.00) |
0.0491 (0.613) |
0.598 (0.929) |
0.651 (0.945) |
0.621 (0.939) |
0.00309 (0.271) |
0.423 (0.906) |
0.333 (0.855) |
0.97 (1.00) |
0.346 (0.869) |
1 (1.00) |
4p gain | 31 (6%) | 470 |
0.328 (0.855) |
0.808 (0.981) |
0.541 (0.917) |
0.661 (0.945) |
0.827 (0.987) |
1 (1.00) |
0.0943 (0.705) |
0.54 (0.917) |
0.0206 (0.57) |
1 (1.00) |
0.995 (1.00) |
0.729 (0.954) |
0.677 (0.948) |
0.462 (0.906) |
1 (1.00) |
4q gain | 21 (4%) | 480 |
0.345 (0.869) |
0.0105 (0.521) |
0.172 (0.769) |
0.922 (1.00) |
0.858 (1.00) |
1 (1.00) |
0.309 (0.855) |
0.722 (0.954) |
0.116 (0.731) |
0.62 (0.939) |
0.37 (0.883) |
0.551 (0.917) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
5p gain | 309 (62%) | 192 |
0.294 (0.855) |
0.0833 (0.691) |
0.49 (0.909) |
0.509 (0.917) |
0.161 (0.766) |
0.715 (0.954) |
0.53 (0.917) |
0.653 (0.945) |
0.773 (0.963) |
0.333 (0.855) |
0.0369 (0.612) |
0.133 (0.733) |
0.0275 (0.57) |
0.204 (0.807) |
0.267 (0.845) |
5q gain | 97 (19%) | 404 |
0.381 (0.883) |
0.237 (0.845) |
0.981 (1.00) |
0.497 (0.914) |
0.923 (1.00) |
1 (1.00) |
0.442 (0.906) |
0.204 (0.807) |
0.396 (0.886) |
0.727 (0.954) |
0.173 (0.771) |
0.0377 (0.612) |
0.238 (0.845) |
0.279 (0.853) |
1 (1.00) |
6p gain | 108 (22%) | 393 |
0.716 (0.954) |
0.23 (0.84) |
0.924 (1.00) |
0.827 (0.987) |
0.379 (0.883) |
1 (1.00) |
0.536 (0.917) |
0.0454 (0.612) |
0.136 (0.733) |
0.166 (0.769) |
0.856 (1.00) |
0.0653 (0.679) |
0.345 (0.869) |
0.107 (0.711) |
1 (1.00) |
6q gain | 92 (18%) | 409 |
0.994 (1.00) |
0.859 (1.00) |
0.454 (0.906) |
0.958 (1.00) |
0.0721 (0.679) |
0.612 (0.933) |
0.694 (0.952) |
0.0874 (0.702) |
0.435 (0.906) |
0.246 (0.845) |
0.991 (1.00) |
0.657 (0.945) |
0.722 (0.954) |
0.44 (0.906) |
0.201 (0.807) |
7p gain | 238 (48%) | 263 |
0.0263 (0.57) |
0.0726 (0.679) |
0.1 (0.709) |
0.00256 (0.271) |
0.576 (0.927) |
0.715 (0.954) |
0.126 (0.731) |
0.884 (1.00) |
0.159 (0.766) |
0.38 (0.883) |
0.138 (0.733) |
0.166 (0.769) |
0.848 (0.998) |
0.0168 (0.569) |
0.297 (0.855) |
7q gain | 220 (44%) | 281 |
0.153 (0.76) |
0.146 (0.747) |
0.272 (0.845) |
0.116 (0.731) |
0.369 (0.883) |
0.251 (0.845) |
0.101 (0.709) |
0.376 (0.883) |
0.0873 (0.702) |
0.544 (0.917) |
0.191 (0.803) |
0.12 (0.731) |
0.72 (0.954) |
0.00658 (0.45) |
0.474 (0.906) |
8p gain | 129 (26%) | 372 |
0.899 (1.00) |
0.0263 (0.57) |
0.0641 (0.679) |
0.0517 (0.618) |
0.658 (0.945) |
0.0816 (0.691) |
0.908 (1.00) |
0.244 (0.845) |
0.643 (0.945) |
0.269 (0.845) |
0.95 (1.00) |
0.736 (0.954) |
0.025 (0.57) |
0.109 (0.711) |
0.431 (0.906) |
8q gain | 256 (51%) | 245 |
0.293 (0.855) |
0.322 (0.855) |
0.0222 (0.57) |
0.18 (0.783) |
0.377 (0.883) |
0.123 (0.731) |
0.839 (0.991) |
0.464 (0.906) |
0.0573 (0.656) |
0.481 (0.906) |
0.188 (0.802) |
0.489 (0.909) |
0.128 (0.731) |
0.0606 (0.667) |
0.724 (0.954) |
9p gain | 62 (12%) | 439 |
0.587 (0.927) |
0.347 (0.869) |
0.0498 (0.613) |
0.33 (0.855) |
0.00443 (0.321) |
1 (1.00) |
0.759 (0.962) |
0.658 (0.945) |
0.918 (1.00) |
0.273 (0.847) |
0.426 (0.906) |
0.947 (1.00) |
0.667 (0.945) |
0.303 (0.855) |
0.228 (0.839) |
9q gain | 91 (18%) | 410 |
0.914 (1.00) |
0.628 (0.943) |
0.181 (0.786) |
0.541 (0.917) |
0.0495 (0.613) |
1 (1.00) |
0.512 (0.917) |
0.852 (1.00) |
0.729 (0.954) |
0.509 (0.917) |
0.862 (1.00) |
0.719 (0.954) |
0.601 (0.929) |
0.461 (0.906) |
0.637 (0.945) |
10p gain | 78 (16%) | 423 |
0.553 (0.917) |
0.992 (1.00) |
0.193 (0.803) |
0.693 (0.952) |
0.639 (0.945) |
0.299 (0.855) |
0.0239 (0.57) |
0.839 (0.991) |
0.671 (0.947) |
0.902 (1.00) |
0.0504 (0.614) |
0.0155 (0.547) |
0.321 (0.855) |
0.0662 (0.679) |
1 (1.00) |
10q gain | 44 (9%) | 457 |
0.906 (1.00) |
0.452 (0.906) |
0.687 (0.951) |
0.811 (0.981) |
0.815 (0.981) |
0.48 (0.906) |
0.149 (0.751) |
0.609 (0.932) |
0.743 (0.959) |
1 (1.00) |
0.263 (0.845) |
0.00878 (0.508) |
0.771 (0.962) |
0.132 (0.733) |
0.591 (0.927) |
11p gain | 75 (15%) | 426 |
0.58 (0.927) |
0.269 (0.845) |
0.721 (0.954) |
0.864 (1.00) |
0.148 (0.751) |
0.602 (0.929) |
0.253 (0.845) |
0.832 (0.99) |
0.00908 (0.508) |
1 (1.00) |
0.675 (0.948) |
0.736 (0.954) |
0.508 (0.917) |
0.299 (0.855) |
1 (1.00) |
11q gain | 89 (18%) | 412 |
0.356 (0.872) |
0.587 (0.927) |
0.583 (0.927) |
0.246 (0.845) |
0.214 (0.816) |
0.12 (0.731) |
1 (1.00) |
0.432 (0.906) |
0.649 (0.945) |
1 (1.00) |
0.494 (0.91) |
0.789 (0.973) |
0.54 (0.917) |
0.503 (0.917) |
1 (1.00) |
12p gain | 226 (45%) | 275 |
0.75 (0.962) |
0.751 (0.962) |
0.425 (0.906) |
0.125 (0.731) |
0.416 (0.906) |
0.464 (0.906) |
0.00295 (0.271) |
0.659 (0.945) |
0.0743 (0.679) |
0.933 (1.00) |
0.131 (0.733) |
0.872 (1.00) |
0.886 (1.00) |
0.924 (1.00) |
1 (1.00) |
12q gain | 151 (30%) | 350 |
0.989 (1.00) |
0.542 (0.917) |
0.356 (0.872) |
0.232 (0.841) |
0.0987 (0.709) |
1 (1.00) |
0.00376 (0.308) |
0.205 (0.809) |
0.084 (0.691) |
0.857 (1.00) |
0.767 (0.962) |
0.555 (0.917) |
0.947 (1.00) |
0.875 (1.00) |
0.701 (0.954) |
13q gain | 39 (8%) | 462 |
0.182 (0.787) |
0.442 (0.906) |
0.681 (0.949) |
0.394 (0.886) |
0.469 (0.906) |
0.409 (0.897) |
0.568 (0.927) |
0.256 (0.845) |
0.15 (0.751) |
0.384 (0.883) |
0.317 (0.855) |
0.269 (0.845) |
0.724 (0.954) |
0.0383 (0.612) |
1 (1.00) |
14q gain | 126 (25%) | 375 |
0.0152 (0.547) |
0.0834 (0.691) |
0.17 (0.769) |
0.128 (0.731) |
0.276 (0.852) |
1 (1.00) |
0.814 (0.981) |
0.74 (0.956) |
0.989 (1.00) |
1 (1.00) |
0.469 (0.906) |
0.514 (0.917) |
0.608 (0.932) |
0.521 (0.917) |
0.0203 (0.57) |
15q gain | 107 (21%) | 394 |
0.809 (0.981) |
0.612 (0.933) |
0.167 (0.769) |
0.311 (0.855) |
0.0971 (0.705) |
0.201 (0.807) |
0.172 (0.769) |
0.861 (1.00) |
0.132 (0.733) |
0.537 (0.917) |
0.316 (0.855) |
0.268 (0.845) |
0.787 (0.973) |
0.8 (0.978) |
0.687 (0.951) |
16p gain | 86 (17%) | 415 |
0.889 (1.00) |
0.544 (0.917) |
0.678 (0.948) |
0.726 (0.954) |
0.395 (0.886) |
1 (1.00) |
0.177 (0.78) |
0.691 (0.951) |
0.872 (1.00) |
0.193 (0.803) |
0.118 (0.731) |
0.753 (0.962) |
0.936 (1.00) |
0.479 (0.906) |
1 (1.00) |
16q gain | 85 (17%) | 416 |
0.748 (0.961) |
0.294 (0.855) |
0.225 (0.839) |
0.501 (0.915) |
0.725 (0.954) |
0.36 (0.876) |
0.0143 (0.547) |
0.546 (0.917) |
0.59 (0.927) |
0.299 (0.855) |
0.262 (0.845) |
0.55 (0.917) |
0.79 (0.973) |
0.134 (0.733) |
1 (1.00) |
17p gain | 65 (13%) | 436 |
0.161 (0.766) |
0.0662 (0.679) |
0.769 (0.962) |
0.456 (0.906) |
0.966 (1.00) |
1 (1.00) |
0.45 (0.906) |
0.675 (0.948) |
0.598 (0.929) |
0.518 (0.917) |
0.124 (0.731) |
0.011 (0.521) |
0.332 (0.855) |
0.918 (1.00) |
0.326 (0.855) |
17q gain | 158 (32%) | 343 |
0.952 (1.00) |
0.0889 (0.705) |
0.259 (0.845) |
0.0149 (0.547) |
0.0851 (0.693) |
0.684 (0.951) |
0.000962 (0.271) |
0.529 (0.917) |
0.0966 (0.705) |
0.752 (0.962) |
0.293 (0.855) |
0.0464 (0.612) |
0.624 (0.941) |
0.166 (0.769) |
0.249 (0.845) |
18p gain | 148 (30%) | 353 |
0.581 (0.927) |
0.15 (0.751) |
0.44 (0.906) |
0.544 (0.917) |
0.167 (0.769) |
0.679 (0.948) |
0.264 (0.845) |
0.0171 (0.569) |
0.0202 (0.57) |
0.769 (0.962) |
0.701 (0.954) |
0.334 (0.855) |
0.234 (0.845) |
0.0156 (0.547) |
1 (1.00) |
18q gain | 102 (20%) | 399 |
0.977 (1.00) |
0.772 (0.962) |
0.425 (0.906) |
0.0803 (0.691) |
0.556 (0.917) |
0.354 (0.872) |
0.448 (0.906) |
0.104 (0.711) |
0.0155 (0.547) |
0.788 (0.973) |
0.0392 (0.612) |
0.471 (0.906) |
0.353 (0.872) |
0.02 (0.57) |
0.667 (0.945) |
19p gain | 115 (23%) | 386 |
0.121 (0.731) |
0.809 (0.981) |
0.59 (0.927) |
0.464 (0.906) |
0.405 (0.892) |
1 (1.00) |
0.546 (0.917) |
0.167 (0.769) |
0.293 (0.855) |
0.139 (0.733) |
0.722 (0.954) |
0.0708 (0.679) |
1 (1.00) |
0.618 (0.938) |
1 (1.00) |
19q gain | 163 (33%) | 338 |
0.354 (0.872) |
0.146 (0.747) |
0.556 (0.917) |
0.336 (0.857) |
0.199 (0.807) |
0.689 (0.951) |
0.828 (0.987) |
1 (1.00) |
0.19 (0.803) |
0.0691 (0.679) |
0.133 (0.733) |
0.00178 (0.271) |
0.633 (0.943) |
0.157 (0.763) |
0.703 (0.954) |
20p gain | 263 (52%) | 238 |
0.38 (0.883) |
0.174 (0.771) |
0.402 (0.886) |
0.0902 (0.705) |
0.578 (0.927) |
0.128 (0.731) |
0.00423 (0.321) |
0.189 (0.802) |
0.243 (0.845) |
0.401 (0.886) |
0.374 (0.883) |
0.812 (0.981) |
0.853 (1.00) |
0.731 (0.954) |
0.0693 (0.679) |
20q gain | 251 (50%) | 250 |
0.6 (0.929) |
0.372 (0.883) |
0.467 (0.906) |
0.252 (0.845) |
0.154 (0.761) |
0.122 (0.731) |
0.0011 (0.271) |
0.38 (0.883) |
0.74 (0.956) |
0.143 (0.745) |
0.735 (0.954) |
0.64 (0.945) |
0.804 (0.981) |
0.679 (0.948) |
0.284 (0.855) |
21q gain | 57 (11%) | 444 |
0.0441 (0.612) |
0.322 (0.855) |
0.152 (0.756) |
0.0233 (0.57) |
0.0316 (0.599) |
1 (1.00) |
0.263 (0.845) |
0.0221 (0.57) |
0.172 (0.769) |
0.0283 (0.57) |
0.833 (0.99) |
0.461 (0.906) |
0.0753 (0.679) |
0.306 (0.855) |
1 (1.00) |
22q gain | 222 (44%) | 279 |
0.175 (0.774) |
0.0337 (0.61) |
0.0653 (0.679) |
0.107 (0.711) |
0.315 (0.855) |
0.255 (0.845) |
0.125 (0.731) |
0.187 (0.801) |
0.372 (0.883) |
0.447 (0.906) |
0.108 (0.711) |
0.0322 (0.6) |
0.442 (0.906) |
0.117 (0.731) |
1 (1.00) |
xp gain | 64 (13%) | 437 |
0.783 (0.973) |
0.453 (0.906) |
0.64 (0.945) |
0.323 (0.855) |
0.913 (1.00) |
1 (1.00) |
0.88 (1.00) |
0.517 (0.917) |
0.964 (1.00) |
0.0445 (0.612) |
0.144 (0.745) |
0.75 (0.962) |
0.49 (0.909) |
0.659 (0.945) |
0.603 (0.929) |
xq gain | 79 (16%) | 422 |
0.878 (1.00) |
0.587 (0.927) |
0.108 (0.711) |
0.0154 (0.547) |
0.594 (0.928) |
0.319 (0.855) |
0.402 (0.886) |
0.84 (0.991) |
0.564 (0.922) |
0.819 (0.982) |
0.905 (1.00) |
0.554 (0.917) |
0.688 (0.951) |
0.319 (0.855) |
0.361 (0.878) |
1p loss | 155 (31%) | 346 |
0.694 (0.952) |
0.0437 (0.612) |
0.518 (0.917) |
0.973 (1.00) |
0.0235 (0.57) |
0.445 (0.906) |
0.0779 (0.69) |
0.158 (0.763) |
0.478 (0.906) |
0.902 (1.00) |
0.317 (0.855) |
0.826 (0.987) |
0.854 (1.00) |
0.761 (0.962) |
0.0569 (0.656) |
1q loss | 60 (12%) | 441 |
0.248 (0.845) |
0.632 (0.943) |
0.0715 (0.679) |
0.755 (0.962) |
0.272 (0.845) |
1 (1.00) |
0.346 (0.869) |
0.0743 (0.679) |
0.371 (0.883) |
0.376 (0.883) |
0.324 (0.855) |
0.492 (0.909) |
0.0373 (0.612) |
0.193 (0.803) |
0.238 (0.845) |
2p loss | 24 (5%) | 477 |
0.272 (0.845) |
0.18 (0.783) |
0.639 (0.945) |
0.699 (0.954) |
0.367 (0.883) |
1 (1.00) |
0.0927 (0.705) |
0.71 (0.954) |
0.763 (0.962) |
0.667 (0.945) |
0.245 (0.845) |
0.49 (0.909) |
1 (1.00) |
0.796 (0.975) |
0.352 (0.872) |
2q loss | 44 (9%) | 457 |
0.388 (0.883) |
0.196 (0.806) |
0.708 (0.954) |
0.33 (0.855) |
0.121 (0.731) |
0.47 (0.906) |
0.37 (0.883) |
1 (1.00) |
0.771 (0.962) |
0.808 (0.981) |
0.0362 (0.612) |
0.958 (1.00) |
1 (1.00) |
0.892 (1.00) |
1 (1.00) |
3p loss | 310 (62%) | 191 |
0.864 (1.00) |
0.397 (0.886) |
0.446 (0.906) |
0.965 (1.00) |
0.827 (0.987) |
0.0476 (0.612) |
0.347 (0.869) |
0.449 (0.906) |
0.236 (0.845) |
0.885 (1.00) |
0.588 (0.927) |
0.963 (1.00) |
0.24 (0.845) |
0.382 (0.883) |
0.479 (0.906) |
3q loss | 73 (15%) | 428 |
0.668 (0.945) |
0.155 (0.761) |
0.366 (0.883) |
0.107 (0.711) |
0.504 (0.917) |
0.604 (0.929) |
0.665 (0.945) |
0.839 (0.991) |
0.474 (0.906) |
0.381 (0.883) |
0.0828 (0.691) |
0.125 (0.731) |
0.895 (1.00) |
0.522 (0.917) |
1 (1.00) |
4p loss | 315 (63%) | 186 |
0.535 (0.917) |
0.123 (0.731) |
0.166 (0.769) |
0.299 (0.855) |
0.764 (0.962) |
0.433 (0.906) |
0.461 (0.906) |
0.0676 (0.679) |
0.74 (0.956) |
0.0566 (0.656) |
0.786 (0.973) |
0.52 (0.917) |
0.513 (0.917) |
0.0836 (0.691) |
1 (1.00) |
4q loss | 297 (59%) | 204 |
0.547 (0.917) |
0.357 (0.872) |
0.134 (0.733) |
0.2 (0.807) |
0.57 (0.927) |
0.451 (0.906) |
0.917 (1.00) |
0.135 (0.733) |
0.542 (0.917) |
0.169 (0.769) |
0.186 (0.801) |
0.983 (1.00) |
0.529 (0.917) |
0.59 (0.927) |
0.731 (0.954) |
5p loss | 79 (16%) | 422 |
0.156 (0.763) |
0.643 (0.945) |
0.534 (0.917) |
0.28 (0.853) |
0.269 (0.845) |
0.602 (0.929) |
0.263 (0.845) |
0.314 (0.855) |
0.421 (0.906) |
0.49 (0.909) |
0.0352 (0.61) |
0.0446 (0.612) |
0.124 (0.731) |
0.928 (1.00) |
0.109 (0.711) |
5q loss | 290 (58%) | 211 |
0.481 (0.906) |
0.588 (0.927) |
0.72 (0.954) |
0.464 (0.906) |
0.341 (0.866) |
0.247 (0.845) |
0.68 (0.948) |
0.304 (0.855) |
0.364 (0.882) |
0.473 (0.906) |
0.419 (0.906) |
0.0104 (0.521) |
0.766 (0.962) |
0.207 (0.809) |
1 (1.00) |
6p loss | 114 (23%) | 387 |
0.386 (0.883) |
0.69 (0.951) |
0.432 (0.906) |
0.458 (0.906) |
0.172 (0.769) |
0.666 (0.945) |
0.627 (0.943) |
1 (1.00) |
0.392 (0.885) |
0.929 (1.00) |
0.732 (0.954) |
0.553 (0.917) |
0.437 (0.906) |
0.892 (1.00) |
1 (1.00) |
6q loss | 114 (23%) | 387 |
0.397 (0.886) |
0.627 (0.943) |
0.503 (0.917) |
0.577 (0.927) |
0.386 (0.883) |
0.666 (0.945) |
0.546 (0.917) |
0.302 (0.855) |
0.893 (1.00) |
0.28 (0.853) |
0.775 (0.965) |
0.66 (0.945) |
0.521 (0.917) |
1 (1.00) |
0.392 (0.885) |
7p loss | 60 (12%) | 441 |
0.581 (0.927) |
0.516 (0.917) |
0.231 (0.841) |
0.436 (0.906) |
0.365 (0.882) |
0.585 (0.927) |
0.53 (0.917) |
0.818 (0.982) |
0.384 (0.883) |
1 (1.00) |
0.0756 (0.679) |
0.819 (0.982) |
0.0966 (0.705) |
0.762 (0.962) |
1 (1.00) |
7q loss | 50 (10%) | 451 |
0.592 (0.927) |
0.533 (0.917) |
0.901 (1.00) |
0.458 (0.906) |
0.902 (1.00) |
1 (1.00) |
0.611 (0.933) |
0.0444 (0.612) |
0.256 (0.845) |
1 (1.00) |
0.0973 (0.705) |
0.111 (0.715) |
0.272 (0.845) |
0.471 (0.906) |
0.556 (0.917) |
8p loss | 243 (49%) | 258 |
0.491 (0.909) |
0.00308 (0.271) |
0.543 (0.917) |
0.392 (0.885) |
0.658 (0.945) |
0.451 (0.906) |
0.31 (0.855) |
0.0279 (0.57) |
0.349 (0.87) |
0.275 (0.85) |
0.431 (0.906) |
0.198 (0.807) |
0.878 (1.00) |
0.787 (0.973) |
0.727 (0.954) |
8q loss | 54 (11%) | 447 |
0.579 (0.927) |
0.137 (0.733) |
0.0795 (0.691) |
0.24 (0.845) |
0.605 (0.93) |
0.561 (0.92) |
0.249 (0.845) |
0.0468 (0.612) |
0.617 (0.938) |
0.619 (0.938) |
0.0936 (0.705) |
0.00168 (0.271) |
0.71 (0.954) |
0.0415 (0.612) |
0.556 (0.917) |
9p loss | 315 (63%) | 186 |
0.955 (1.00) |
0.616 (0.938) |
0.339 (0.862) |
0.739 (0.956) |
0.216 (0.816) |
0.716 (0.954) |
0.674 (0.948) |
1 (1.00) |
0.319 (0.855) |
0.0632 (0.679) |
0.146 (0.747) |
0.447 (0.906) |
0.795 (0.975) |
0.918 (1.00) |
0.465 (0.906) |
9q loss | 247 (49%) | 254 |
0.56 (0.92) |
0.00119 (0.271) |
0.542 (0.917) |
0.198 (0.807) |
0.747 (0.961) |
0.271 (0.845) |
0.919 (1.00) |
0.041 (0.612) |
0.95 (1.00) |
0.0727 (0.679) |
0.706 (0.954) |
0.0202 (0.57) |
0.353 (0.872) |
0.56 (0.92) |
0.067 (0.679) |
10p loss | 215 (43%) | 286 |
0.38 (0.883) |
0.699 (0.954) |
0.534 (0.917) |
0.942 (1.00) |
0.809 (0.981) |
0.142 (0.744) |
0.472 (0.906) |
0.77 (0.962) |
0.941 (1.00) |
0.899 (1.00) |
0.332 (0.855) |
0.227 (0.839) |
0.31 (0.855) |
0.416 (0.906) |
0.733 (0.954) |
10q loss | 229 (46%) | 272 |
0.169 (0.769) |
0.106 (0.711) |
0.323 (0.855) |
0.298 (0.855) |
0.919 (1.00) |
0.133 (0.733) |
0.306 (0.855) |
0.305 (0.855) |
0.314 (0.855) |
0.793 (0.973) |
0.878 (1.00) |
0.194 (0.803) |
0.259 (0.845) |
0.291 (0.855) |
1 (1.00) |
11p loss | 169 (34%) | 332 |
0.811 (0.981) |
0.139 (0.733) |
0.47 (0.906) |
0.479 (0.906) |
0.317 (0.855) |
0.24 (0.845) |
0.332 (0.855) |
0.878 (1.00) |
0.228 (0.839) |
0.428 (0.906) |
0.208 (0.809) |
0.476 (0.906) |
0.968 (1.00) |
0.241 (0.845) |
0.718 (0.954) |
11q loss | 143 (29%) | 358 |
0.713 (0.954) |
0.0479 (0.612) |
0.666 (0.945) |
0.542 (0.917) |
0.048 (0.612) |
1 (1.00) |
0.178 (0.78) |
0.15 (0.751) |
0.458 (0.906) |
0.72 (0.954) |
0.827 (0.987) |
0.195 (0.803) |
0.329 (0.855) |
0.471 (0.906) |
1 (1.00) |
12p loss | 39 (8%) | 462 |
0.607 (0.932) |
0.585 (0.927) |
0.376 (0.883) |
0.399 (0.886) |
0.431 (0.906) |
1 (1.00) |
0.707 (0.954) |
0.289 (0.855) |
0.641 (0.945) |
0.057 (0.656) |
0.0197 (0.57) |
0.364 (0.882) |
1 (1.00) |
0.192 (0.803) |
1 (1.00) |
12q loss | 47 (9%) | 454 |
0.765 (0.962) |
0.732 (0.954) |
0.285 (0.855) |
0.688 (0.951) |
0.652 (0.945) |
1 (1.00) |
0.6 (0.929) |
0.452 (0.906) |
0.699 (0.954) |
0.0598 (0.667) |
0.115 (0.731) |
0.758 (0.962) |
0.641 (0.945) |
0.208 (0.809) |
1 (1.00) |
13q loss | 311 (62%) | 190 |
0.0907 (0.705) |
0.511 (0.917) |
0.17 (0.769) |
0.278 (0.853) |
0.386 (0.883) |
0.432 (0.906) |
0.834 (0.99) |
0.879 (1.00) |
0.451 (0.906) |
0.00275 (0.271) |
0.592 (0.927) |
0.322 (0.855) |
0.858 (1.00) |
0.0607 (0.667) |
0.023 (0.57) |
14q loss | 167 (33%) | 334 |
0.0965 (0.705) |
0.814 (0.981) |
0.0926 (0.705) |
0.0924 (0.705) |
0.105 (0.711) |
0.101 (0.709) |
0.59 (0.927) |
0.756 (0.962) |
0.489 (0.909) |
0.161 (0.766) |
0.295 (0.855) |
0.526 (0.917) |
0.629 (0.943) |
0.809 (0.981) |
0.269 (0.845) |
15q loss | 141 (28%) | 360 |
0.632 (0.943) |
0.42 (0.906) |
0.0824 (0.691) |
0.421 (0.906) |
0.118 (0.731) |
0.397 (0.886) |
0.573 (0.927) |
0.251 (0.845) |
0.0205 (0.57) |
0.243 (0.845) |
0.609 (0.932) |
0.782 (0.972) |
0.691 (0.951) |
0.0975 (0.705) |
1 (1.00) |
16p loss | 163 (33%) | 338 |
0.441 (0.906) |
0.917 (1.00) |
0.0999 (0.709) |
0.337 (0.857) |
0.44 (0.906) |
0.435 (0.906) |
0.328 (0.855) |
0.643 (0.945) |
0.652 (0.945) |
0.0698 (0.679) |
0.243 (0.845) |
0.835 (0.991) |
0.144 (0.745) |
0.0583 (0.658) |
1 (1.00) |
16q loss | 184 (37%) | 317 |
0.185 (0.8) |
0.508 (0.917) |
0.534 (0.917) |
0.668 (0.945) |
0.746 (0.961) |
0.263 (0.845) |
0.0909 (0.705) |
0.651 (0.945) |
0.45 (0.906) |
0.16 (0.766) |
0.043 (0.612) |
0.877 (1.00) |
0.483 (0.907) |
0.263 (0.845) |
0.717 (0.954) |
17p loss | 292 (58%) | 209 |
0.496 (0.914) |
0.117 (0.731) |
0.919 (1.00) |
0.499 (0.914) |
0.0351 (0.61) |
0.704 (0.954) |
0.757 (0.962) |
0.769 (0.962) |
0.632 (0.943) |
0.597 (0.929) |
0.0483 (0.612) |
0.307 (0.855) |
0.332 (0.855) |
0.389 (0.883) |
1 (1.00) |
17q loss | 91 (18%) | 410 |
0.126 (0.731) |
0.0281 (0.57) |
0.948 (1.00) |
0.279 (0.853) |
0.0394 (0.612) |
0.621 (0.939) |
0.29 (0.855) |
0.575 (0.927) |
0.157 (0.763) |
0.202 (0.807) |
0.0739 (0.679) |
0.379 (0.883) |
0.92 (1.00) |
0.0704 (0.679) |
0.663 (0.945) |
18p loss | 141 (28%) | 360 |
0.815 (0.981) |
0.598 (0.929) |
0.0576 (0.656) |
0.464 (0.906) |
0.901 (1.00) |
0.0228 (0.57) |
0.311 (0.855) |
0.245 (0.845) |
0.862 (1.00) |
0.848 (0.998) |
0.79 (0.973) |
0.729 (0.954) |
0.834 (0.99) |
0.586 (0.927) |
0.69 (0.951) |
18q loss | 190 (38%) | 311 |
0.388 (0.883) |
0.4 (0.886) |
0.0289 (0.574) |
0.203 (0.807) |
0.459 (0.906) |
0.108 (0.711) |
0.529 (0.917) |
0.291 (0.855) |
0.324 (0.855) |
0.885 (1.00) |
0.516 (0.917) |
0.135 (0.733) |
0.17 (0.769) |
0.479 (0.906) |
0.716 (0.954) |
19p loss | 162 (32%) | 339 |
0.283 (0.855) |
0.668 (0.945) |
0.653 (0.945) |
0.665 (0.945) |
0.0276 (0.57) |
0.223 (0.839) |
0.327 (0.855) |
0.212 (0.816) |
0.214 (0.816) |
0.593 (0.927) |
0.474 (0.906) |
0.327 (0.855) |
0.552 (0.917) |
0.839 (0.991) |
1 (1.00) |
19q loss | 110 (22%) | 391 |
0.529 (0.917) |
0.0635 (0.679) |
0.385 (0.883) |
0.817 (0.982) |
0.672 (0.948) |
0.657 (0.945) |
0.0658 (0.679) |
0.0316 (0.599) |
0.109 (0.711) |
0.225 (0.839) |
0.195 (0.803) |
0.0119 (0.543) |
0.758 (0.962) |
0.846 (0.998) |
1 (1.00) |
20p loss | 42 (8%) | 459 |
0.635 (0.945) |
0.715 (0.954) |
0.883 (1.00) |
0.343 (0.868) |
0.592 (0.927) |
1 (1.00) |
0.359 (0.876) |
1 (1.00) |
0.231 (0.841) |
1 (1.00) |
0.332 (0.855) |
0.428 (0.906) |
0.711 (0.954) |
0.885 (1.00) |
1 (1.00) |
20q loss | 49 (10%) | 452 |
0.862 (1.00) |
0.499 (0.914) |
0.509 (0.917) |
0.106 (0.711) |
0.654 (0.945) |
1 (1.00) |
1 (1.00) |
0.632 (0.943) |
0.542 (0.917) |
0.587 (0.927) |
0.415 (0.906) |
0.784 (0.973) |
0.42 (0.906) |
1 (1.00) |
0.556 (0.917) |
21q loss | 264 (53%) | 237 |
0.513 (0.917) |
0.0747 (0.679) |
0.228 (0.839) |
0.674 (0.948) |
0.536 (0.917) |
0.134 (0.733) |
0.000493 (0.271) |
0.464 (0.906) |
0.255 (0.845) |
0.535 (0.917) |
0.792 (0.973) |
0.207 (0.809) |
0.88 (1.00) |
0.399 (0.886) |
0.285 (0.855) |
22q loss | 98 (20%) | 403 |
0.431 (0.906) |
0.00272 (0.271) |
0.328 (0.855) |
0.524 (0.917) |
0.0244 (0.57) |
0.625 (0.943) |
0.798 (0.976) |
0.00813 (0.5) |
0.498 (0.914) |
0.212 (0.816) |
0.897 (1.00) |
0.0108 (0.521) |
0.485 (0.909) |
0.215 (0.816) |
0.64 (0.945) |
xp loss | 145 (29%) | 356 |
0.335 (0.857) |
0.228 (0.839) |
0.561 (0.92) |
0.295 (0.855) |
0.265 (0.845) |
0.679 (0.948) |
0.653 (0.945) |
0.872 (1.00) |
0.397 (0.886) |
1 (1.00) |
0.591 (0.927) |
0.935 (1.00) |
0.266 (0.845) |
0.593 (0.927) |
0.449 (0.906) |
xq loss | 114 (23%) | 387 |
0.257 (0.845) |
0.472 (0.906) |
0.491 (0.909) |
0.0134 (0.547) |
0.564 (0.922) |
0.357 (0.872) |
0.331 (0.855) |
0.728 (0.954) |
0.482 (0.906) |
0.226 (0.839) |
0.215 (0.816) |
0.547 (0.917) |
0.575 (0.927) |
0.257 (0.845) |
0.211 (0.816) |
-
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/LUSC-TP/22533933/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUSC-TP/22506957/LUSC-TP.merged_data.txt
-
Number of patients = 501
-
Number of significantly arm-level cnvs = 82
-
Number of selected clinical features = 15
-
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.