Correlation between copy number variations of arm-level result and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
23 September 2013
|
analyses__2013_09_23
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as
Broad Institute TCGA Genome Data Analysis Center
(2013):
Correlation between copy number variations of arm-level result and selected clinical features.
Broad Institute of MIT and Harvard.
doi:10.7908/C1WW7G0J
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 80 arm-level events and 13 clinical features across 450 patients, one significant finding detected with Q value < 0.25.
-
17P GAIN MUTATION ANALYSIS cnv correlated to 'NUMBERPACKYEARSSMOKED'.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.
|
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | YEAROFTOBACCOSMOKINGONSET |
COMPLETENESS OF RESECTION |
||
| nCNV (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | t-test | Chi-square test | Fisher's exact test | t-test | t-test | Fisher's exact test | |
| 17P GAIN MUTATION ANALYSIS | 74 (16%) | 376 |
0.231 (1.00) |
0.0174 (1.00) |
0.525 (1.00) |
0.711 (1.00) |
0.122 (1.00) |
0.212 (1.00) |
0.0299 (1.00) |
0.666 (1.00) |
0.263 (1.00) |
0.0314 (1.00) |
0.000228 (0.237) |
0.391 (1.00) |
0.137 (1.00) |
| 1P GAIN MUTATION ANALYSIS | 122 (27%) | 328 |
0.764 (1.00) |
0.0158 (1.00) |
0.93 (1.00) |
0.867 (1.00) |
0.0413 (1.00) |
0.68 (1.00) |
0.916 (1.00) |
0.538 (1.00) |
0.482 (1.00) |
0.61 (1.00) |
0.64 (1.00) |
0.951 (1.00) |
0.584 (1.00) |
| 1Q GAIN MUTATION ANALYSIS | 265 (59%) | 185 |
0.693 (1.00) |
0.425 (1.00) |
0.549 (1.00) |
0.611 (1.00) |
0.769 (1.00) |
0.405 (1.00) |
0.293 (1.00) |
0.301 (1.00) |
0.187 (1.00) |
0.817 (1.00) |
0.763 (1.00) |
0.489 (1.00) |
0.72 (1.00) |
| 2P GAIN MUTATION ANALYSIS | 142 (32%) | 308 |
0.549 (1.00) |
0.0108 (1.00) |
0.878 (1.00) |
0.855 (1.00) |
0.194 (1.00) |
0.92 (1.00) |
0.761 (1.00) |
0.695 (1.00) |
0.51 (1.00) |
1 (1.00) |
0.238 (1.00) |
0.162 (1.00) |
0.528 (1.00) |
| 2Q GAIN MUTATION ANALYSIS | 126 (28%) | 324 |
0.661 (1.00) |
0.416 (1.00) |
0.869 (1.00) |
0.895 (1.00) |
0.32 (1.00) |
0.95 (1.00) |
0.344 (1.00) |
0.557 (1.00) |
0.653 (1.00) |
1 (1.00) |
0.132 (1.00) |
0.574 (1.00) |
0.735 (1.00) |
| 3P GAIN MUTATION ANALYSIS | 31 (7%) | 419 |
0.828 (1.00) |
0.566 (1.00) |
0.829 (1.00) |
0.125 (1.00) |
0.0952 (1.00) |
0.926 (1.00) |
0.853 (1.00) |
0.26 (1.00) |
0.975 (1.00) |
0.152 (1.00) |
0.602 (1.00) |
0.184 (1.00) |
0.0839 (1.00) |
| 3Q GAIN MUTATION ANALYSIS | 72 (16%) | 378 |
0.271 (1.00) |
0.497 (1.00) |
0.706 (1.00) |
0.589 (1.00) |
0.657 (1.00) |
0.711 (1.00) |
0.7 (1.00) |
0.403 (1.00) |
0.789 (1.00) |
0.343 (1.00) |
0.377 (1.00) |
0.216 (1.00) |
0.271 (1.00) |
| 4P GAIN MUTATION ANALYSIS | 70 (16%) | 380 |
0.769 (1.00) |
0.0197 (1.00) |
0.0965 (1.00) |
0.448 (1.00) |
0.41 (1.00) |
0.796 (1.00) |
0.897 (1.00) |
0.253 (1.00) |
0.326 (1.00) |
0.752 (1.00) |
0.449 (1.00) |
0.784 (1.00) |
1 (1.00) |
| 4Q GAIN MUTATION ANALYSIS | 38 (8%) | 412 |
0.145 (1.00) |
0.867 (1.00) |
0.113 (1.00) |
0.315 (1.00) |
1 (1.00) |
0.965 (1.00) |
0.497 (1.00) |
0.511 (1.00) |
0.711 (1.00) |
1 (1.00) |
0.21 (1.00) |
0.999 (1.00) |
0.815 (1.00) |
| 5P GAIN MUTATION ANALYSIS | 244 (54%) | 206 |
0.196 (1.00) |
0.0908 (1.00) |
0.486 (1.00) |
0.246 (1.00) |
0.857 (1.00) |
0.477 (1.00) |
0.155 (1.00) |
0.368 (1.00) |
0.135 (1.00) |
0.366 (1.00) |
0.00208 (1.00) |
0.589 (1.00) |
0.48 (1.00) |
| 5Q GAIN MUTATION ANALYSIS | 109 (24%) | 341 |
0.799 (1.00) |
0.918 (1.00) |
0.904 (1.00) |
0.541 (1.00) |
0.776 (1.00) |
0.82 (1.00) |
0.0773 (1.00) |
0.625 (1.00) |
0.289 (1.00) |
0.285 (1.00) |
0.747 (1.00) |
0.856 (1.00) |
0.949 (1.00) |
| 6P GAIN MUTATION ANALYSIS | 133 (30%) | 317 |
0.103 (1.00) |
0.126 (1.00) |
0.367 (1.00) |
0.39 (1.00) |
0.309 (1.00) |
0.347 (1.00) |
1 (1.00) |
0.787 (1.00) |
0.696 (1.00) |
0.455 (1.00) |
0.467 (1.00) |
0.928 (1.00) |
0.709 (1.00) |
| 6Q GAIN MUTATION ANALYSIS | 56 (12%) | 394 |
0.688 (1.00) |
0.0987 (1.00) |
0.861 (1.00) |
0.787 (1.00) |
0.977 (1.00) |
0.783 (1.00) |
0.668 (1.00) |
0.458 (1.00) |
0.909 (1.00) |
0.492 (1.00) |
0.818 (1.00) |
0.312 (1.00) |
0.669 (1.00) |
| 7P GAIN MUTATION ANALYSIS | 234 (52%) | 216 |
0.34 (1.00) |
0.038 (1.00) |
0.38 (1.00) |
0.303 (1.00) |
0.00333 (1.00) |
0.705 (1.00) |
0.85 (1.00) |
0.497 (1.00) |
0.0752 (1.00) |
0.648 (1.00) |
0.0714 (1.00) |
0.242 (1.00) |
0.689 (1.00) |
| 7Q GAIN MUTATION ANALYSIS | 192 (43%) | 258 |
0.981 (1.00) |
0.00299 (1.00) |
0.247 (1.00) |
0.709 (1.00) |
0.0107 (1.00) |
0.306 (1.00) |
0.567 (1.00) |
0.717 (1.00) |
0.211 (1.00) |
0.259 (1.00) |
0.187 (1.00) |
0.529 (1.00) |
0.334 (1.00) |
| 8P GAIN MUTATION ANALYSIS | 112 (25%) | 338 |
0.58 (1.00) |
0.14 (1.00) |
0.713 (1.00) |
0.0558 (1.00) |
0.825 (1.00) |
0.963 (1.00) |
0.00443 (1.00) |
0.362 (1.00) |
0.808 (1.00) |
0.294 (1.00) |
0.634 (1.00) |
0.908 (1.00) |
0.255 (1.00) |
| 8Q GAIN MUTATION ANALYSIS | 215 (48%) | 235 |
0.0516 (1.00) |
0.0407 (1.00) |
0.925 (1.00) |
0.265 (1.00) |
0.107 (1.00) |
0.706 (1.00) |
0.22 (1.00) |
0.866 (1.00) |
0.061 (1.00) |
1 (1.00) |
0.883 (1.00) |
0.296 (1.00) |
0.546 (1.00) |
| 9P GAIN MUTATION ANALYSIS | 38 (8%) | 412 |
0.278 (1.00) |
0.535 (1.00) |
0.807 (1.00) |
0.0951 (1.00) |
0.396 (1.00) |
0.611 (1.00) |
0.401 (1.00) |
0.673 (1.00) |
0.143 (1.00) |
1 (1.00) |
0.588 (1.00) |
0.643 (1.00) |
0.334 (1.00) |
| 9Q GAIN MUTATION ANALYSIS | 26 (6%) | 424 |
0.134 (1.00) |
0.324 (1.00) |
0.396 (1.00) |
0.575 (1.00) |
0.955 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.796 (1.00) |
0.974 (1.00) |
1 (1.00) |
0.673 (1.00) |
0.905 (1.00) |
1 (1.00) |
| 10P GAIN MUTATION ANALYSIS | 97 (22%) | 353 |
0.718 (1.00) |
0.145 (1.00) |
0.653 (1.00) |
0.123 (1.00) |
0.0156 (1.00) |
0.865 (1.00) |
0.00278 (1.00) |
0.328 (1.00) |
0.587 (1.00) |
0.271 (1.00) |
0.202 (1.00) |
0.833 (1.00) |
0.223 (1.00) |
| 10Q GAIN MUTATION ANALYSIS | 69 (15%) | 381 |
0.979 (1.00) |
0.106 (1.00) |
0.448 (1.00) |
0.136 (1.00) |
0.0423 (1.00) |
0.445 (1.00) |
0.0039 (1.00) |
0.123 (1.00) |
0.348 (1.00) |
0.752 (1.00) |
0.85 (1.00) |
0.672 (1.00) |
0.404 (1.00) |
| 11P GAIN MUTATION ANALYSIS | 84 (19%) | 366 |
0.243 (1.00) |
0.763 (1.00) |
0.418 (1.00) |
0.512 (1.00) |
0.0943 (1.00) |
0.475 (1.00) |
0.115 (1.00) |
0.321 (1.00) |
0.546 (1.00) |
1 (1.00) |
0.111 (1.00) |
0.8 (1.00) |
0.9 (1.00) |
| 11Q GAIN MUTATION ANALYSIS | 104 (23%) | 346 |
0.767 (1.00) |
0.00625 (1.00) |
0.585 (1.00) |
0.86 (1.00) |
0.405 (1.00) |
0.382 (1.00) |
0.503 (1.00) |
0.199 (1.00) |
0.228 (1.00) |
0.79 (1.00) |
0.0432 (1.00) |
0.05 (1.00) |
1 (1.00) |
| 12P GAIN MUTATION ANALYSIS | 120 (27%) | 330 |
0.0394 (1.00) |
0.0122 (1.00) |
0.195 (1.00) |
0.934 (1.00) |
0.6 (1.00) |
0.76 (1.00) |
0.11 (1.00) |
0.459 (1.00) |
0.341 (1.00) |
1 (1.00) |
0.187 (1.00) |
0.0232 (1.00) |
0.616 (1.00) |
| 12Q GAIN MUTATION ANALYSIS | 116 (26%) | 334 |
0.228 (1.00) |
0.0774 (1.00) |
0.883 (1.00) |
0.854 (1.00) |
0.579 (1.00) |
0.547 (1.00) |
0.28 (1.00) |
0.399 (1.00) |
0.415 (1.00) |
1 (1.00) |
0.332 (1.00) |
0.00051 (0.53) |
0.572 (1.00) |
| 13Q GAIN MUTATION ANALYSIS | 38 (8%) | 412 |
0.977 (1.00) |
1 (1.00) |
0.249 (1.00) |
0.637 (1.00) |
0.16 (1.00) |
0.0811 (1.00) |
0.867 (1.00) |
0.126 (1.00) |
0.976 (1.00) |
0.682 (1.00) |
0.523 (1.00) |
0.814 (1.00) |
0.518 (1.00) |
| 14Q GAIN MUTATION ANALYSIS | 109 (24%) | 341 |
0.121 (1.00) |
0.0974 (1.00) |
0.92 (1.00) |
0.981 (1.00) |
0.297 (1.00) |
0.00289 (1.00) |
0.508 (1.00) |
0.279 (1.00) |
0.716 (1.00) |
0.182 (1.00) |
0.13 (1.00) |
0.274 (1.00) |
0.321 (1.00) |
| 15Q GAIN MUTATION ANALYSIS | 31 (7%) | 419 |
0.115 (1.00) |
0.989 (1.00) |
0.0717 (1.00) |
0.543 (1.00) |
0.0451 (1.00) |
0.322 (1.00) |
0.194 (1.00) |
0.748 (1.00) |
0.371 (1.00) |
0.64 (1.00) |
0.611 (1.00) |
0.613 (1.00) |
0.879 (1.00) |
| 16P GAIN MUTATION ANALYSIS | 111 (25%) | 339 |
0.405 (1.00) |
0.712 (1.00) |
0.973 (1.00) |
0.697 (1.00) |
0.351 (1.00) |
0.474 (1.00) |
1 (1.00) |
0.176 (1.00) |
0.662 (1.00) |
0.793 (1.00) |
0.104 (1.00) |
0.975 (1.00) |
0.885 (1.00) |
| 16Q GAIN MUTATION ANALYSIS | 83 (18%) | 367 |
0.351 (1.00) |
0.393 (1.00) |
0.859 (1.00) |
0.81 (1.00) |
0.709 (1.00) |
0.852 (1.00) |
0.716 (1.00) |
0.311 (1.00) |
0.449 (1.00) |
1 (1.00) |
0.147 (1.00) |
0.617 (1.00) |
0.605 (1.00) |
| 17Q GAIN MUTATION ANALYSIS | 170 (38%) | 280 |
0.877 (1.00) |
0.0413 (1.00) |
0.223 (1.00) |
0.273 (1.00) |
0.387 (1.00) |
0.543 (1.00) |
0.845 (1.00) |
0.197 (1.00) |
0.13 (1.00) |
0.49 (1.00) |
0.0463 (1.00) |
0.907 (1.00) |
0.0182 (1.00) |
| 18P GAIN MUTATION ANALYSIS | 87 (19%) | 363 |
0.597 (1.00) |
0.581 (1.00) |
0.522 (1.00) |
0.904 (1.00) |
0.922 (1.00) |
0.756 (1.00) |
0.188 (1.00) |
0.676 (1.00) |
0.586 (1.00) |
0.777 (1.00) |
0.00944 (1.00) |
0.435 (1.00) |
0.185 (1.00) |
| 18Q GAIN MUTATION ANALYSIS | 57 (13%) | 393 |
0.777 (1.00) |
0.0825 (1.00) |
0.803 (1.00) |
0.96 (1.00) |
0.73 (1.00) |
0.603 (1.00) |
0.322 (1.00) |
0.232 (1.00) |
0.492 (1.00) |
1 (1.00) |
0.0242 (1.00) |
0.467 (1.00) |
0.0109 (1.00) |
| 19P GAIN MUTATION ANALYSIS | 28 (6%) | 422 |
0.182 (1.00) |
0.42 (1.00) |
0.671 (1.00) |
0.106 (1.00) |
0.644 (1.00) |
0.405 (1.00) |
0.7 (1.00) |
0.681 (1.00) |
0.00527 (1.00) |
1 (1.00) |
0.143 (1.00) |
0.79 (1.00) |
0.662 (1.00) |
| 19Q GAIN MUTATION ANALYSIS | 65 (14%) | 385 |
0.771 (1.00) |
0.684 (1.00) |
0.66 (1.00) |
0.0491 (1.00) |
0.752 (1.00) |
0.843 (1.00) |
0.0431 (1.00) |
0.231 (1.00) |
0.312 (1.00) |
0.334 (1.00) |
0.0642 (1.00) |
0.914 (1.00) |
0.885 (1.00) |
| 20P GAIN MUTATION ANALYSIS | 147 (33%) | 303 |
0.417 (1.00) |
0.851 (1.00) |
0.124 (1.00) |
0.293 (1.00) |
0.272 (1.00) |
0.137 (1.00) |
0.841 (1.00) |
0.201 (1.00) |
0.234 (1.00) |
1 (1.00) |
0.0802 (1.00) |
0.0921 (1.00) |
0.693 (1.00) |
| 20Q GAIN MUTATION ANALYSIS | 169 (38%) | 281 |
0.387 (1.00) |
0.104 (1.00) |
0.344 (1.00) |
0.319 (1.00) |
0.831 (1.00) |
0.297 (1.00) |
0.38 (1.00) |
0.0477 (1.00) |
0.102 (1.00) |
0.345 (1.00) |
0.00309 (1.00) |
0.624 (1.00) |
0.892 (1.00) |
| 21Q GAIN MUTATION ANALYSIS | 86 (19%) | 364 |
0.0699 (1.00) |
0.448 (1.00) |
0.503 (1.00) |
0.844 (1.00) |
0.016 (1.00) |
0.896 (1.00) |
0.118 (1.00) |
0.454 (1.00) |
0.376 (1.00) |
0.778 (1.00) |
0.568 (1.00) |
0.644 (1.00) |
0.734 (1.00) |
| 22Q GAIN MUTATION ANALYSIS | 52 (12%) | 398 |
0.0719 (1.00) |
0.409 (1.00) |
0.577 (1.00) |
0.306 (1.00) |
0.217 (1.00) |
0.429 (1.00) |
0.241 (1.00) |
0.903 (1.00) |
0.418 (1.00) |
0.493 (1.00) |
0.819 (1.00) |
0.345 (1.00) |
0.526 (1.00) |
| XQ GAIN MUTATION ANALYSIS | 71 (16%) | 379 |
0.301 (1.00) |
0.45 (1.00) |
0.698 (1.00) |
0.841 (1.00) |
0.657 (1.00) |
0.778 (1.00) |
0.301 (1.00) |
0.582 (1.00) |
0.472 (1.00) |
1 (1.00) |
0.359 (1.00) |
0.524 (1.00) |
0.48 (1.00) |
| 1P LOSS MUTATION ANALYSIS | 69 (15%) | 381 |
0.104 (1.00) |
0.502 (1.00) |
0.0253 (1.00) |
0.347 (1.00) |
0.00358 (1.00) |
0.409 (1.00) |
0.296 (1.00) |
0.752 (1.00) |
0.36 (1.00) |
0.21 (1.00) |
0.506 (1.00) |
0.872 (1.00) |
0.76 (1.00) |
| 1Q LOSS MUTATION ANALYSIS | 26 (6%) | 424 |
0.722 (1.00) |
0.871 (1.00) |
0.0374 (1.00) |
0.893 (1.00) |
0.104 (1.00) |
0.254 (1.00) |
0.692 (1.00) |
0.216 (1.00) |
0.557 (1.00) |
0.101 (1.00) |
0.0445 (1.00) |
0.472 (1.00) |
1 (1.00) |
| 2P LOSS MUTATION ANALYSIS | 24 (5%) | 426 |
0.392 (1.00) |
0.523 (1.00) |
0.000551 (0.572) |
0.791 (1.00) |
0.432 (1.00) |
0.97 (1.00) |
0.68 (1.00) |
0.985 (1.00) |
0.383 (1.00) |
0.615 (1.00) |
0.964 (1.00) |
0.776 (1.00) |
0.372 (1.00) |
| 2Q LOSS MUTATION ANALYSIS | 24 (5%) | 426 |
0.219 (1.00) |
0.779 (1.00) |
0.373 (1.00) |
0.887 (1.00) |
0.712 (1.00) |
0.635 (1.00) |
0.408 (1.00) |
0.737 (1.00) |
0.0983 (1.00) |
0.615 (1.00) |
0.0132 (1.00) |
0.833 (1.00) |
0.781 (1.00) |
| 3P LOSS MUTATION ANALYSIS | 190 (42%) | 260 |
0.171 (1.00) |
0.619 (1.00) |
0.428 (1.00) |
0.0175 (1.00) |
0.227 (1.00) |
0.732 (1.00) |
0.774 (1.00) |
0.367 (1.00) |
0.387 (1.00) |
1 (1.00) |
0.27 (1.00) |
0.0783 (1.00) |
0.203 (1.00) |
| 3Q LOSS MUTATION ANALYSIS | 130 (29%) | 320 |
0.164 (1.00) |
0.52 (1.00) |
0.498 (1.00) |
0.506 (1.00) |
0.0649 (1.00) |
0.295 (1.00) |
1 (1.00) |
0.612 (1.00) |
0.636 (1.00) |
0.457 (1.00) |
0.19 (1.00) |
0.102 (1.00) |
0.383 (1.00) |
| 4P LOSS MUTATION ANALYSIS | 104 (23%) | 346 |
0.459 (1.00) |
0.251 (1.00) |
0.605 (1.00) |
0.989 (1.00) |
0.2 (1.00) |
0.84 (1.00) |
0.911 (1.00) |
0.212 (1.00) |
0.431 (1.00) |
0.426 (1.00) |
0.271 (1.00) |
0.0515 (1.00) |
0.35 (1.00) |
| 4Q LOSS MUTATION ANALYSIS | 118 (26%) | 332 |
0.608 (1.00) |
0.244 (1.00) |
0.095 (1.00) |
0.753 (1.00) |
0.00419 (1.00) |
0.719 (1.00) |
0.83 (1.00) |
0.106 (1.00) |
0.4 (1.00) |
0.434 (1.00) |
0.268 (1.00) |
0.22 (1.00) |
0.244 (1.00) |
| 5P LOSS MUTATION ANALYSIS | 35 (8%) | 415 |
0.402 (1.00) |
0.155 (1.00) |
0.785 (1.00) |
0.484 (1.00) |
0.683 (1.00) |
0.354 (1.00) |
0.112 (1.00) |
0.077 (1.00) |
0.135 (1.00) |
1 (1.00) |
0.323 (1.00) |
0.0108 (1.00) |
0.614 (1.00) |
| 5Q LOSS MUTATION ANALYSIS | 126 (28%) | 324 |
0.0956 (1.00) |
0.0101 (1.00) |
0.889 (1.00) |
0.988 (1.00) |
0.66 (1.00) |
0.911 (1.00) |
0.0736 (1.00) |
0.529 (1.00) |
0.307 (1.00) |
0.611 (1.00) |
0.0625 (1.00) |
0.722 (1.00) |
0.0439 (1.00) |
| 6P LOSS MUTATION ANALYSIS | 90 (20%) | 360 |
0.0731 (1.00) |
0.682 (1.00) |
0.406 (1.00) |
0.298 (1.00) |
0.8 (1.00) |
0.896 (1.00) |
0.345 (1.00) |
0.0384 (1.00) |
0.976 (1.00) |
0.569 (1.00) |
0.119 (1.00) |
0.339 (1.00) |
1 (1.00) |
| 6Q LOSS MUTATION ANALYSIS | 192 (43%) | 258 |
0.994 (1.00) |
0.136 (1.00) |
0.807 (1.00) |
0.588 (1.00) |
0.557 (1.00) |
0.822 (1.00) |
0.445 (1.00) |
0.0999 (1.00) |
0.845 (1.00) |
0.822 (1.00) |
0.263 (1.00) |
0.0324 (1.00) |
0.878 (1.00) |
| 7P LOSS MUTATION ANALYSIS | 30 (7%) | 420 |
0.831 (1.00) |
0.908 (1.00) |
0.987 (1.00) |
0.789 (1.00) |
0.672 (1.00) |
0.778 (1.00) |
0.259 (1.00) |
0.931 (1.00) |
0.431 (1.00) |
0.635 (1.00) |
0.977 (1.00) |
0.93 (1.00) |
0.448 (1.00) |
| 7Q LOSS MUTATION ANALYSIS | 34 (8%) | 416 |
0.43 (1.00) |
0.0514 (1.00) |
0.876 (1.00) |
0.986 (1.00) |
0.545 (1.00) |
0.476 (1.00) |
0.859 (1.00) |
0.284 (1.00) |
0.306 (1.00) |
1 (1.00) |
0.784 (1.00) |
0.488 (1.00) |
0.701 (1.00) |
| 8P LOSS MUTATION ANALYSIS | 171 (38%) | 279 |
0.892 (1.00) |
0.956 (1.00) |
0.904 (1.00) |
0.688 (1.00) |
0.958 (1.00) |
0.435 (1.00) |
0.0522 (1.00) |
0.559 (1.00) |
0.0324 (1.00) |
0.103 (1.00) |
0.252 (1.00) |
0.809 (1.00) |
0.28 (1.00) |
| 8Q LOSS MUTATION ANALYSIS | 45 (10%) | 405 |
0.617 (1.00) |
0.933 (1.00) |
0.126 (1.00) |
0.769 (1.00) |
0.0854 (1.00) |
0.0525 (1.00) |
0.156 (1.00) |
0.274 (1.00) |
0.0983 (1.00) |
0.708 (1.00) |
0.393 (1.00) |
0.827 (1.00) |
1 (1.00) |
| 9P LOSS MUTATION ANALYSIS | 229 (51%) | 221 |
0.115 (1.00) |
0.18 (1.00) |
0.631 (1.00) |
0.988 (1.00) |
0.114 (1.00) |
0.491 (1.00) |
0.059 (1.00) |
0.381 (1.00) |
0.647 (1.00) |
0.652 (1.00) |
0.383 (1.00) |
0.547 (1.00) |
0.778 (1.00) |
| 9Q LOSS MUTATION ANALYSIS | 213 (47%) | 237 |
0.636 (1.00) |
0.897 (1.00) |
0.89 (1.00) |
0.373 (1.00) |
0.518 (1.00) |
0.724 (1.00) |
0.777 (1.00) |
0.615 (1.00) |
0.248 (1.00) |
0.36 (1.00) |
0.0803 (1.00) |
0.839 (1.00) |
0.767 (1.00) |
| 10P LOSS MUTATION ANALYSIS | 95 (21%) | 355 |
0.628 (1.00) |
0.684 (1.00) |
0.657 (1.00) |
0.161 (1.00) |
0.45 (1.00) |
0.943 (1.00) |
0.00363 (1.00) |
0.576 (1.00) |
0.0372 (1.00) |
0.272 (1.00) |
0.284 (1.00) |
0.378 (1.00) |
0.745 (1.00) |
| 10Q LOSS MUTATION ANALYSIS | 112 (25%) | 338 |
0.328 (1.00) |
0.713 (1.00) |
0.522 (1.00) |
0.197 (1.00) |
0.21 (1.00) |
0.799 (1.00) |
0.0631 (1.00) |
0.576 (1.00) |
0.0122 (1.00) |
0.183 (1.00) |
0.0629 (1.00) |
0.15 (1.00) |
0.742 (1.00) |
| 11P LOSS MUTATION ANALYSIS | 99 (22%) | 351 |
0.889 (1.00) |
0.0691 (1.00) |
0.366 (1.00) |
0.655 (1.00) |
0.625 (1.00) |
0.39 (1.00) |
0.00136 (1.00) |
0.576 (1.00) |
0.7 (1.00) |
0.586 (1.00) |
0.633 (1.00) |
0.157 (1.00) |
0.673 (1.00) |
| 11Q LOSS MUTATION ANALYSIS | 78 (17%) | 372 |
0.457 (1.00) |
0.994 (1.00) |
0.493 (1.00) |
0.956 (1.00) |
0.84 (1.00) |
0.481 (1.00) |
0.00388 (1.00) |
0.61 (1.00) |
0.885 (1.00) |
0.549 (1.00) |
0.828 (1.00) |
0.376 (1.00) |
0.88 (1.00) |
| 12P LOSS MUTATION ANALYSIS | 92 (20%) | 358 |
0.15 (1.00) |
0.402 (1.00) |
0.638 (1.00) |
0.803 (1.00) |
0.911 (1.00) |
0.245 (1.00) |
0.0141 (1.00) |
0.21 (1.00) |
0.709 (1.00) |
0.393 (1.00) |
0.217 (1.00) |
0.51 (1.00) |
0.904 (1.00) |
| 12Q LOSS MUTATION ANALYSIS | 77 (17%) | 373 |
0.119 (1.00) |
0.647 (1.00) |
0.542 (1.00) |
0.476 (1.00) |
0.195 (1.00) |
0.133 (1.00) |
0.00838 (1.00) |
0.561 (1.00) |
0.447 (1.00) |
0.222 (1.00) |
0.226 (1.00) |
0.732 (1.00) |
0.797 (1.00) |
| 13Q LOSS MUTATION ANALYSIS | 213 (47%) | 237 |
0.869 (1.00) |
0.193 (1.00) |
0.827 (1.00) |
0.544 (1.00) |
0.713 (1.00) |
0.35 (1.00) |
0.705 (1.00) |
0.848 (1.00) |
0.325 (1.00) |
0.648 (1.00) |
0.0908 (1.00) |
0.205 (1.00) |
0.546 (1.00) |
| 14Q LOSS MUTATION ANALYSIS | 101 (22%) | 349 |
0.587 (1.00) |
0.405 (1.00) |
0.516 (1.00) |
0.482 (1.00) |
0.147 (1.00) |
0.652 (1.00) |
0.497 (1.00) |
0.317 (1.00) |
0.909 (1.00) |
1 (1.00) |
0.16 (1.00) |
0.451 (1.00) |
0.283 (1.00) |
| 15Q LOSS MUTATION ANALYSIS | 210 (47%) | 240 |
0.744 (1.00) |
0.00468 (1.00) |
0.533 (1.00) |
0.928 (1.00) |
0.931 (1.00) |
0.763 (1.00) |
0.571 (1.00) |
0.0337 (1.00) |
0.00866 (1.00) |
0.821 (1.00) |
0.174 (1.00) |
0.222 (1.00) |
0.907 (1.00) |
| 16P LOSS MUTATION ANALYSIS | 100 (22%) | 350 |
0.296 (1.00) |
0.769 (1.00) |
0.161 (1.00) |
0.625 (1.00) |
0.0769 (1.00) |
0.359 (1.00) |
0.427 (1.00) |
0.967 (1.00) |
0.836 (1.00) |
0.784 (1.00) |
0.734 (1.00) |
0.797 (1.00) |
0.602 (1.00) |
| 16Q LOSS MUTATION ANALYSIS | 128 (28%) | 322 |
0.735 (1.00) |
0.328 (1.00) |
0.599 (1.00) |
0.965 (1.00) |
0.33 (1.00) |
0.624 (1.00) |
0.464 (1.00) |
0.264 (1.00) |
0.395 (1.00) |
1 (1.00) |
0.392 (1.00) |
0.862 (1.00) |
0.248 (1.00) |
| 17P LOSS MUTATION ANALYSIS | 190 (42%) | 260 |
0.705 (1.00) |
0.126 (1.00) |
0.453 (1.00) |
0.366 (1.00) |
0.738 (1.00) |
0.468 (1.00) |
0.069 (1.00) |
0.589 (1.00) |
0.555 (1.00) |
0.0613 (1.00) |
0.0376 (1.00) |
0.011 (1.00) |
0.756 (1.00) |
| 17Q LOSS MUTATION ANALYSIS | 50 (11%) | 400 |
0.676 (1.00) |
0.704 (1.00) |
0.37 (1.00) |
0.165 (1.00) |
0.426 (1.00) |
0.971 (1.00) |
0.551 (1.00) |
0.981 (1.00) |
0.893 (1.00) |
0.713 (1.00) |
0.738 (1.00) |
0.0816 (1.00) |
0.649 (1.00) |
| 18P LOSS MUTATION ANALYSIS | 152 (34%) | 298 |
0.389 (1.00) |
0.0348 (1.00) |
0.0429 (1.00) |
0.599 (1.00) |
0.164 (1.00) |
0.161 (1.00) |
0.00509 (1.00) |
0.282 (1.00) |
0.557 (1.00) |
0.475 (1.00) |
0.037 (1.00) |
0.00192 (1.00) |
0.0784 (1.00) |
| 18Q LOSS MUTATION ANALYSIS | 190 (42%) | 260 |
0.048 (1.00) |
0.392 (1.00) |
0.0197 (1.00) |
0.31 (1.00) |
0.0605 (1.00) |
0.403 (1.00) |
0.069 (1.00) |
0.849 (1.00) |
0.574 (1.00) |
0.355 (1.00) |
0.172 (1.00) |
0.0935 (1.00) |
0.00368 (1.00) |
| 19P LOSS MUTATION ANALYSIS | 221 (49%) | 229 |
0.0239 (1.00) |
0.155 (1.00) |
0.0975 (1.00) |
0.415 (1.00) |
0.278 (1.00) |
0.0615 (1.00) |
0.0106 (1.00) |
0.54 (1.00) |
0.6 (1.00) |
0.254 (1.00) |
0.967 (1.00) |
0.593 (1.00) |
0.236 (1.00) |
| 19Q LOSS MUTATION ANALYSIS | 142 (32%) | 308 |
0.0547 (1.00) |
0.193 (1.00) |
0.145 (1.00) |
0.0988 (1.00) |
0.398 (1.00) |
0.02 (1.00) |
0.309 (1.00) |
0.895 (1.00) |
0.731 (1.00) |
0.628 (1.00) |
0.509 (1.00) |
0.966 (1.00) |
0.272 (1.00) |
| 20P LOSS MUTATION ANALYSIS | 109 (24%) | 341 |
0.206 (1.00) |
0.585 (1.00) |
0.37 (1.00) |
0.329 (1.00) |
0.118 (1.00) |
0.329 (1.00) |
0.912 (1.00) |
0.328 (1.00) |
0.257 (1.00) |
0.794 (1.00) |
0.329 (1.00) |
0.243 (1.00) |
0.581 (1.00) |
| 20Q LOSS MUTATION ANALYSIS | 68 (15%) | 382 |
0.464 (1.00) |
0.226 (1.00) |
0.136 (1.00) |
0.417 (1.00) |
0.373 (1.00) |
0.305 (1.00) |
1 (1.00) |
0.000895 (0.929) |
0.0573 (1.00) |
0.752 (1.00) |
0.833 (1.00) |
0.948 (1.00) |
0.662 (1.00) |
| 21Q LOSS MUTATION ANALYSIS | 143 (32%) | 307 |
0.544 (1.00) |
0.837 (1.00) |
0.575 (1.00) |
0.808 (1.00) |
0.609 (1.00) |
0.596 (1.00) |
0.0536 (1.00) |
0.854 (1.00) |
0.171 (1.00) |
0.221 (1.00) |
0.165 (1.00) |
0.309 (1.00) |
0.51 (1.00) |
| 22Q LOSS MUTATION ANALYSIS | 190 (42%) | 260 |
0.646 (1.00) |
0.00142 (1.00) |
0.54 (1.00) |
1 (1.00) |
0.846 (1.00) |
0.248 (1.00) |
0.0559 (1.00) |
0.0521 (1.00) |
0.319 (1.00) |
0.82 (1.00) |
0.786 (1.00) |
0.0045 (1.00) |
0.752 (1.00) |
| XQ LOSS MUTATION ANALYSIS | 61 (14%) | 389 |
0.968 (1.00) |
0.747 (1.00) |
0.288 (1.00) |
0.805 (1.00) |
0.838 (1.00) |
0.392 (1.00) |
0.214 (1.00) |
0.928 (1.00) |
0.133 (1.00) |
0.17 (1.00) |
0.804 (1.00) |
0.284 (1.00) |
0.772 (1.00) |
'17P GAIN MUTATION STATUS' versus 'NUMBERPACKYEARSSMOKED'
P value = 0.000228 (t-test), Q value = 0.24
Table S1. Gene #30: '17P GAIN MUTATION STATUS' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 312 | 42.0 (27.2) |
| 17P GAIN MUTATED | 52 | 56.4 (29.9) |
| 17P GAIN WILD-TYPE | 260 | 39.1 (25.8) |
Figure S1. Get High-res Image Gene #30: '17P GAIN MUTATION STATUS' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
Methods & Data
Input
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = LUAD-TP.clin.merged.picked.txt
-
Number of patients = 450
-
Number of significantly arm-level cnvs = 80
-
Number of selected clinical features = 13
-
Exclude regions 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
Chi-square test
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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
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.
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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[5] 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 © 2013
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.