Head and Neck Squamous Cell Carcinoma: Correlation between copy number variations of arm-level result and selected clinical features
Maintained by TCGA GDAC Team
(Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction
This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Summary
Testing the association between copy number variation 79 arm-level results and 8 clinical features across 288 patients, no significant finding detected with Q value < 0.25.
-
No arm-level cnvs related to clinical features.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.
|
Clinical Features |
Time to Death |
AGE | GENDER |
PATHOLOGY T |
PATHOLOGY N |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NEOADJUVANT THERAPY |
||
| nCNV (%) | nWild-Type | logrank test | t-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 | 11 (4%) | 277 |
0.714 (1.00) |
0.507 (1.00) |
0.0798 (1.00) |
0.369 (1.00) |
0.74 (1.00) |
0.881 (1.00) |
0.733 (1.00) |
1 (1.00) |
| 1q gain | 37 (13%) | 251 |
0.925 (1.00) |
0.955 (1.00) |
0.846 (1.00) |
0.456 (1.00) |
0.0322 (1.00) |
0.428 (1.00) |
0.11 (1.00) |
0.636 (1.00) |
| 2p gain | 29 (10%) | 259 |
0.707 (1.00) |
0.694 (1.00) |
0.393 (1.00) |
0.869 (1.00) |
0.819 (1.00) |
0.514 (1.00) |
0.657 (1.00) |
1 (1.00) |
| 2q gain | 20 (7%) | 268 |
0.708 (1.00) |
0.994 (1.00) |
0.606 (1.00) |
0.804 (1.00) |
0.823 (1.00) |
0.951 (1.00) |
1 (1.00) |
0.547 (1.00) |
| 3p gain | 25 (9%) | 263 |
0.112 (1.00) |
0.843 (1.00) |
0.485 (1.00) |
0.667 (1.00) |
0.869 (1.00) |
0.716 (1.00) |
0.485 (1.00) |
0.575 (1.00) |
| 3q gain | 95 (33%) | 193 |
0.375 (1.00) |
0.358 (1.00) |
0.126 (1.00) |
0.922 (1.00) |
0.463 (1.00) |
0.168 (1.00) |
0.00271 (1.00) |
0.000613 (0.388) |
| 4p gain | 13 (5%) | 275 |
0.597 (1.00) |
0.103 (1.00) |
0.762 (1.00) |
0.854 (1.00) |
0.565 (1.00) |
0.438 (1.00) |
0.338 (1.00) |
0.0433 (1.00) |
| 4q gain | 9 (3%) | 279 |
0.646 (1.00) |
0.838 (1.00) |
1 (1.00) |
0.227 (1.00) |
0.575 (1.00) |
0.443 (1.00) |
1 (1.00) |
0.644 (1.00) |
| 5p gain | 70 (24%) | 218 |
0.632 (1.00) |
0.364 (1.00) |
0.0937 (1.00) |
0.728 (1.00) |
0.83 (1.00) |
0.466 (1.00) |
0.279 (1.00) |
0.355 (1.00) |
| 5q gain | 23 (8%) | 265 |
0.843 (1.00) |
0.825 (1.00) |
0.334 (1.00) |
0.371 (1.00) |
0.951 (1.00) |
0.0964 (1.00) |
0.215 (1.00) |
0.234 (1.00) |
| 6p gain | 24 (8%) | 264 |
0.451 (1.00) |
0.0409 (1.00) |
0.816 (1.00) |
0.434 (1.00) |
0.282 (1.00) |
0.252 (1.00) |
0.0499 (1.00) |
0.145 (1.00) |
| 6q gain | 17 (6%) | 271 |
0.651 (1.00) |
0.227 (1.00) |
1 (1.00) |
0.0774 (1.00) |
0.225 (1.00) |
0.0302 (1.00) |
0.0497 (1.00) |
0.0849 (1.00) |
| 7p gain | 64 (22%) | 224 |
0.375 (1.00) |
0.0539 (1.00) |
0.27 (1.00) |
0.763 (1.00) |
0.887 (1.00) |
0.874 (1.00) |
1 (1.00) |
0.849 (1.00) |
| 7q gain | 38 (13%) | 250 |
0.52 (1.00) |
0.938 (1.00) |
0.339 (1.00) |
0.678 (1.00) |
0.676 (1.00) |
0.674 (1.00) |
1 (1.00) |
1 (1.00) |
| 8p gain | 44 (15%) | 244 |
0.0148 (1.00) |
0.551 (1.00) |
0.275 (1.00) |
0.483 (1.00) |
0.79 (1.00) |
0.698 (1.00) |
0.71 (1.00) |
0.385 (1.00) |
| 8q gain | 121 (42%) | 167 |
0.0897 (1.00) |
0.0959 (1.00) |
0.792 (1.00) |
0.14 (1.00) |
0.175 (1.00) |
0.329 (1.00) |
0.892 (1.00) |
0.747 (1.00) |
| 9p gain | 34 (12%) | 254 |
0.284 (1.00) |
0.143 (1.00) |
0.102 (1.00) |
0.984 (1.00) |
0.585 (1.00) |
0.463 (1.00) |
0.837 (1.00) |
1 (1.00) |
| 9q gain | 41 (14%) | 247 |
0.431 (1.00) |
0.0656 (1.00) |
0.578 (1.00) |
0.628 (1.00) |
0.878 (1.00) |
0.746 (1.00) |
0.445 (1.00) |
0.359 (1.00) |
| 10p gain | 12 (4%) | 276 |
0.957 (1.00) |
0.638 (1.00) |
0.52 (1.00) |
0.649 (1.00) |
0.366 (1.00) |
1 (1.00) |
0.523 (1.00) |
1 (1.00) |
| 10q gain | 6 (2%) | 282 |
0.0913 (1.00) |
0.446 (1.00) |
1 (1.00) |
0.403 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.0437 (1.00) |
0.057 (1.00) |
| 11p gain | 15 (5%) | 273 |
0.409 (1.00) |
0.243 (1.00) |
1 (1.00) |
0.0933 (1.00) |
1 (1.00) |
0.195 (1.00) |
0.552 (1.00) |
1 (1.00) |
| 11q gain | 16 (6%) | 272 |
0.829 (1.00) |
0.197 (1.00) |
0.399 (1.00) |
0.603 (1.00) |
0.929 (1.00) |
0.402 (1.00) |
0.77 (1.00) |
1 (1.00) |
| 12p gain | 58 (20%) | 230 |
0.114 (1.00) |
0.348 (1.00) |
0.192 (1.00) |
0.532 (1.00) |
1 (1.00) |
0.796 (1.00) |
0.319 (1.00) |
0.232 (1.00) |
| 12q gain | 25 (9%) | 263 |
0.229 (1.00) |
0.897 (1.00) |
0.0653 (1.00) |
0.844 (1.00) |
0.737 (1.00) |
0.653 (1.00) |
0.485 (1.00) |
1 (1.00) |
| 13q gain | 17 (6%) | 271 |
0.62 (1.00) |
0.986 (1.00) |
1 (1.00) |
0.498 (1.00) |
0.0745 (1.00) |
0.269 (1.00) |
1 (1.00) |
1 (1.00) |
| 14q gain | 48 (17%) | 240 |
0.988 (1.00) |
0.92 (1.00) |
0.223 (1.00) |
0.976 (1.00) |
0.648 (1.00) |
0.429 (1.00) |
0.213 (1.00) |
0.287 (1.00) |
| 15q gain | 11 (4%) | 277 |
0.667 (1.00) |
0.885 (1.00) |
0.51 (1.00) |
0.146 (1.00) |
0.837 (1.00) |
0.236 (1.00) |
0.299 (1.00) |
1 (1.00) |
| 16p gain | 19 (7%) | 269 |
0.576 (1.00) |
0.00395 (1.00) |
1 (1.00) |
0.883 (1.00) |
0.0863 (1.00) |
0.184 (1.00) |
0.789 (1.00) |
1 (1.00) |
| 16q gain | 24 (8%) | 264 |
0.9 (1.00) |
0.187 (1.00) |
1 (1.00) |
0.64 (1.00) |
0.354 (1.00) |
0.446 (1.00) |
1 (1.00) |
1 (1.00) |
| 17p gain | 17 (6%) | 271 |
0.462 (1.00) |
0.948 (1.00) |
0.166 (1.00) |
0.249 (1.00) |
0.853 (1.00) |
0.312 (1.00) |
1 (1.00) |
0.324 (1.00) |
| 17q gain | 19 (7%) | 269 |
0.728 (1.00) |
0.991 (1.00) |
0.294 (1.00) |
0.0109 (1.00) |
0.129 (1.00) |
0.0964 (1.00) |
0.789 (1.00) |
0.33 (1.00) |
| 18p gain | 47 (16%) | 241 |
0.217 (1.00) |
0.657 (1.00) |
0.000642 (0.405) |
0.00664 (1.00) |
0.531 (1.00) |
0.0365 (1.00) |
0.471 (1.00) |
0.134 (1.00) |
| 18q gain | 18 (6%) | 270 |
0.0687 (1.00) |
0.913 (1.00) |
0.111 (1.00) |
0.665 (1.00) |
0.518 (1.00) |
0.896 (1.00) |
1 (1.00) |
0.747 (1.00) |
| 19p gain | 10 (3%) | 278 |
0.036 (1.00) |
0.213 (1.00) |
0.731 (1.00) |
0.397 (1.00) |
0.886 (1.00) |
0.357 (1.00) |
0.727 (1.00) |
1 (1.00) |
| 19q gain | 20 (7%) | 268 |
0.129 (1.00) |
0.89 (1.00) |
1 (1.00) |
0.0936 (1.00) |
0.639 (1.00) |
0.24 (1.00) |
0.607 (1.00) |
0.547 (1.00) |
| 20p gain | 62 (22%) | 226 |
0.091 (1.00) |
0.136 (1.00) |
0.524 (1.00) |
0.362 (1.00) |
0.135 (1.00) |
0.213 (1.00) |
0.0153 (1.00) |
0.00359 (1.00) |
| 20q gain | 65 (23%) | 223 |
0.416 (1.00) |
0.0252 (1.00) |
0.211 (1.00) |
0.357 (1.00) |
0.609 (1.00) |
0.5 (1.00) |
0.00643 (1.00) |
0.00731 (1.00) |
| 21q gain | 8 (3%) | 280 |
0.882 (1.00) |
0.0909 (1.00) |
1 (1.00) |
0.907 (1.00) |
1 (1.00) |
0.455 (1.00) |
1 (1.00) |
1 (1.00) |
| 22q gain | 37 (13%) | 251 |
0.415 (1.00) |
0.237 (1.00) |
0.435 (1.00) |
0.879 (1.00) |
0.126 (1.00) |
0.987 (1.00) |
0.844 (1.00) |
0.812 (1.00) |
| Xq gain | 20 (7%) | 268 |
0.0808 (1.00) |
0.648 (1.00) |
0.606 (1.00) |
0.467 (1.00) |
0.263 (1.00) |
0.97 (1.00) |
0.607 (1.00) |
0.752 (1.00) |
| 1p loss | 16 (6%) | 272 |
0.272 (1.00) |
0.126 (1.00) |
0.569 (1.00) |
0.0127 (1.00) |
0.381 (1.00) |
0.26 (1.00) |
0.38 (1.00) |
0.307 (1.00) |
| 2p loss | 4 (1%) | 284 |
0.298 (1.00) |
0.841 (1.00) |
0.315 (1.00) |
0.701 (1.00) |
0.809 (1.00) |
0.707 (1.00) |
0.285 (1.00) |
0.126 (1.00) |
| 2q loss | 7 (2%) | 281 |
0.28 (1.00) |
0.888 (1.00) |
0.406 (1.00) |
0.129 (1.00) |
0.809 (1.00) |
0.385 (1.00) |
0.68 (1.00) |
0.604 (1.00) |
| 3p loss | 112 (39%) | 176 |
0.0242 (1.00) |
0.666 (1.00) |
0.0109 (1.00) |
0.422 (1.00) |
0.00941 (1.00) |
0.847 (1.00) |
0.892 (1.00) |
0.745 (1.00) |
| 3q loss | 19 (7%) | 269 |
0.141 (1.00) |
0.298 (1.00) |
0.294 (1.00) |
0.573 (1.00) |
0.137 (1.00) |
0.451 (1.00) |
0.595 (1.00) |
0.526 (1.00) |
| 4p loss | 69 (24%) | 219 |
0.113 (1.00) |
0.546 (1.00) |
0.219 (1.00) |
0.239 (1.00) |
0.464 (1.00) |
0.07 (1.00) |
1 (1.00) |
0.35 (1.00) |
| 4q loss | 47 (16%) | 241 |
0.936 (1.00) |
0.874 (1.00) |
0.726 (1.00) |
0.211 (1.00) |
0.705 (1.00) |
0.345 (1.00) |
0.589 (1.00) |
0.832 (1.00) |
| 5p loss | 8 (3%) | 280 |
0.475 (1.00) |
0.137 (1.00) |
0.691 (1.00) |
0.866 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.115 (1.00) |
0.361 (1.00) |
| 5q loss | 58 (20%) | 230 |
0.315 (1.00) |
0.132 (1.00) |
0.329 (1.00) |
0.263 (1.00) |
0.608 (1.00) |
0.302 (1.00) |
1 (1.00) |
1 (1.00) |
| 6p loss | 18 (6%) | 270 |
0.308 (1.00) |
0.522 (1.00) |
0.416 (1.00) |
0.00369 (1.00) |
0.658 (1.00) |
0.146 (1.00) |
0.581 (1.00) |
0.508 (1.00) |
| 6q loss | 21 (7%) | 267 |
0.71 (1.00) |
0.141 (1.00) |
0.453 (1.00) |
0.0176 (1.00) |
0.584 (1.00) |
0.219 (1.00) |
1 (1.00) |
0.545 (1.00) |
| 7p loss | 5 (2%) | 283 |
0.721 (1.00) |
0.52 (1.00) |
1 (1.00) |
0.778 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.592 (1.00) |
| 7q loss | 9 (3%) | 279 |
0.908 (1.00) |
0.766 (1.00) |
0.715 (1.00) |
0.303 (1.00) |
0.575 (1.00) |
0.769 (1.00) |
0.453 (1.00) |
1 (1.00) |
| 8p loss | 60 (21%) | 228 |
0.0297 (1.00) |
0.829 (1.00) |
1 (1.00) |
0.0241 (1.00) |
0.978 (1.00) |
0.171 (1.00) |
0.743 (1.00) |
0.239 (1.00) |
| 8q loss | 7 (2%) | 281 |
0.3 (1.00) |
0.672 (1.00) |
0.677 (1.00) |
1 (1.00) |
0.325 (1.00) |
0.6 (1.00) |
1 (1.00) |
0.32 (1.00) |
| 9p loss | 81 (28%) | 207 |
0.388 (1.00) |
0.227 (1.00) |
0.309 (1.00) |
0.794 (1.00) |
0.941 (1.00) |
0.442 (1.00) |
1 (1.00) |
0.726 (1.00) |
| 9q loss | 29 (10%) | 259 |
0.355 (1.00) |
0.266 (1.00) |
1 (1.00) |
0.878 (1.00) |
0.787 (1.00) |
0.271 (1.00) |
0.828 (1.00) |
0.439 (1.00) |
| 10p loss | 42 (15%) | 246 |
0.205 (1.00) |
0.368 (1.00) |
0.356 (1.00) |
0.116 (1.00) |
0.434 (1.00) |
0.632 (1.00) |
1 (1.00) |
0.824 (1.00) |
| 10q loss | 23 (8%) | 265 |
0.261 (1.00) |
0.696 (1.00) |
0.144 (1.00) |
0.375 (1.00) |
0.749 (1.00) |
0.38 (1.00) |
0.628 (1.00) |
0.776 (1.00) |
| 11p loss | 37 (13%) | 251 |
0.424 (1.00) |
0.993 (1.00) |
0.435 (1.00) |
0.745 (1.00) |
0.0175 (1.00) |
0.108 (1.00) |
0.69 (1.00) |
0.0913 (1.00) |
| 11q loss | 53 (18%) | 235 |
0.524 (1.00) |
0.692 (1.00) |
0.0618 (1.00) |
1 (1.00) |
0.21 (1.00) |
0.462 (1.00) |
0.0239 (1.00) |
0.00155 (0.976) |
| 12p loss | 11 (4%) | 277 |
0.155 (1.00) |
0.00829 (1.00) |
0.191 (1.00) |
0.0794 (1.00) |
0.0174 (1.00) |
0.116 (1.00) |
0.0409 (1.00) |
0.0857 (1.00) |
| 12q loss | 8 (3%) | 280 |
0.607 (1.00) |
0.377 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.245 (1.00) |
1 (1.00) |
0.439 (1.00) |
0.621 (1.00) |
| 13q loss | 55 (19%) | 233 |
0.777 (1.00) |
0.649 (1.00) |
0.0311 (1.00) |
0.389 (1.00) |
0.785 (1.00) |
0.203 (1.00) |
0.734 (1.00) |
0.84 (1.00) |
| 14q loss | 12 (4%) | 276 |
0.491 (1.00) |
0.979 (1.00) |
0.52 (1.00) |
0.35 (1.00) |
0.886 (1.00) |
0.238 (1.00) |
0.312 (1.00) |
0.422 (1.00) |
| 15q loss | 21 (7%) | 267 |
0.411 (1.00) |
0.84 (1.00) |
0.803 (1.00) |
0.736 (1.00) |
0.342 (1.00) |
0.731 (1.00) |
0.8 (1.00) |
0.759 (1.00) |
| 16p loss | 9 (3%) | 279 |
0.132 (1.00) |
0.553 (1.00) |
1 (1.00) |
0.339 (1.00) |
0.18 (1.00) |
0.758 (1.00) |
1 (1.00) |
0.364 (1.00) |
| 16q loss | 18 (6%) | 270 |
0.598 (1.00) |
0.48 (1.00) |
0.416 (1.00) |
0.959 (1.00) |
1 (1.00) |
0.485 (1.00) |
0.789 (1.00) |
0.324 (1.00) |
| 17p loss | 38 (13%) | 250 |
0.329 (1.00) |
0.0725 (1.00) |
0.0818 (1.00) |
0.181 (1.00) |
0.699 (1.00) |
0.0613 (1.00) |
0.554 (1.00) |
1 (1.00) |
| 17q loss | 5 (2%) | 283 |
0.753 (1.00) |
0.5 (1.00) |
0.326 (1.00) |
1 (1.00) |
0.398 (1.00) |
0.421 (1.00) |
0.117 (1.00) |
0.188 (1.00) |
| 18p loss | 27 (9%) | 261 |
0.813 (1.00) |
0.632 (1.00) |
0.508 (1.00) |
0.941 (1.00) |
0.414 (1.00) |
1 (1.00) |
0.653 (1.00) |
0.171 (1.00) |
| 18q loss | 76 (26%) | 212 |
0.0701 (1.00) |
0.0381 (1.00) |
0.373 (1.00) |
0.908 (1.00) |
0.669 (1.00) |
0.829 (1.00) |
0.764 (1.00) |
0.105 (1.00) |
| 19p loss | 26 (9%) | 262 |
0.0172 (1.00) |
0.67 (1.00) |
0.0122 (1.00) |
0.173 (1.00) |
0.0885 (1.00) |
0.0705 (1.00) |
0.488 (1.00) |
0.59 (1.00) |
| 19q loss | 19 (7%) | 269 |
0.0818 (1.00) |
0.417 (1.00) |
0.111 (1.00) |
0.00809 (1.00) |
0.108 (1.00) |
0.0225 (1.00) |
1 (1.00) |
0.21 (1.00) |
| 20p loss | 19 (7%) | 269 |
0.413 (1.00) |
0.254 (1.00) |
0.294 (1.00) |
0.566 (1.00) |
0.315 (1.00) |
0.482 (1.00) |
0.789 (1.00) |
1 (1.00) |
| 20q loss | 8 (3%) | 280 |
0.386 (1.00) |
0.855 (1.00) |
0.111 (1.00) |
0.28 (1.00) |
0.731 (1.00) |
0.758 (1.00) |
1 (1.00) |
1 (1.00) |
| 21q loss | 50 (17%) | 238 |
0.855 (1.00) |
0.0766 (1.00) |
0.086 (1.00) |
0.411 (1.00) |
0.0399 (1.00) |
0.924 (1.00) |
1 (1.00) |
0.833 (1.00) |
| 22q loss | 22 (8%) | 266 |
0.153 (1.00) |
0.905 (1.00) |
0.334 (1.00) |
0.279 (1.00) |
0.269 (1.00) |
0.418 (1.00) |
0.805 (1.00) |
1 (1.00) |
| Xq loss | 9 (3%) | 279 |
0.608 (1.00) |
0.858 (1.00) |
0.123 (1.00) |
0.27 (1.00) |
0.0978 (1.00) |
0.0363 (1.00) |
0.703 (1.00) |
1 (1.00) |
Methods & Data
Input
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = HNSC.clin.merged.picked.txt
-
Number of patients = 288
-
Number of significantly arm-level cnvs = 79
-
Number of selected clinical features = 8
-
Exclude genes that fewer than K tumors have mutations, K = 3
Survival analysis
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
Student's t-test analysis
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
Fisher's exact test
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
Q value calculation
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.
Download Results
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.
References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2012
Broad Institute TCGA GDAC as part of the TCGA Research Network.
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