Correlation between copy number variations of arm-level result and selected clinical features
Mesothelioma (Primary solid tumor)
28 January 2016
|
analyses__2016_01_28
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
(2016):
Correlation between copy number variations of arm-level result and selected clinical features.
Broad Institute of MIT and Harvard.
doi:10.7908/C1959H06
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 72 arm-level events and 11 clinical features across 87 patients, 3 significant findings detected with Q value < 0.25.
-
7q gain cnv correlated to 'PATHOLOGY_N_STAGE'.
-
9p loss cnv correlated to 'Time to Death'.
-
10q loss cnv correlated to 'Time to Death'.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 72 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.
|
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 |
RESIDUAL TUMOR |
||
| 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 | Fisher's exact test | |
| 7q gain | 22 (25%) | 65 |
0.332 (1.00) |
0.336 (1.00) |
0.463 (1.00) |
0.733 (1.00) |
0.00063 (0.168) |
0.545 (1.00) |
0.538 (1.00) |
0.783 (1.00) |
1 (1.00) |
0.951 (1.00) |
0.205 (1.00) |
| 9p loss | 28 (32%) | 59 |
0.000635 (0.168) |
0.669 (1.00) |
0.416 (1.00) |
0.216 (1.00) |
0.793 (1.00) |
0.551 (1.00) |
0.249 (1.00) |
1 (1.00) |
0.813 (1.00) |
0.332 (1.00) |
0.652 (1.00) |
| 10q loss | 19 (22%) | 68 |
5.53e-05 (0.0438) |
0.662 (1.00) |
0.169 (1.00) |
0.487 (1.00) |
0.654 (1.00) |
0.099 (1.00) |
0.505 (1.00) |
1 (1.00) |
0.192 (1.00) |
0.496 (1.00) |
0.352 (1.00) |
| 1p gain | 8 (9%) | 79 |
0.0276 (0.817) |
0.803 (1.00) |
0.317 (1.00) |
0.907 (1.00) |
0.501 (1.00) |
1 (1.00) |
0.636 (1.00) |
0.211 (1.00) |
0.328 (1.00) |
0.175 (1.00) |
|
| 1q gain | 20 (23%) | 67 |
0.127 (1.00) |
0.762 (1.00) |
0.333 (1.00) |
0.339 (1.00) |
0.763 (1.00) |
0.545 (1.00) |
0.511 (1.00) |
0.0852 (1.00) |
0.00767 (0.675) |
0.537 (1.00) |
0.707 (1.00) |
| 2p gain | 4 (5%) | 83 |
0.953 (1.00) |
0.655 (1.00) |
0.218 (1.00) |
0.472 (1.00) |
1 (1.00) |
1 (1.00) |
0.563 (1.00) |
0.573 (1.00) |
0.0786 (1.00) |
||
| 2q gain | 6 (7%) | 81 |
0.769 (1.00) |
0.645 (1.00) |
0.236 (1.00) |
0.598 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.179 (1.00) |
0.11 (1.00) |
0.565 (1.00) |
|
| 3p gain | 17 (20%) | 70 |
0.444 (1.00) |
0.524 (1.00) |
0.0538 (0.948) |
0.333 (1.00) |
0.742 (1.00) |
1 (1.00) |
0.506 (1.00) |
0.548 (1.00) |
1 (1.00) |
0.505 (1.00) |
0.481 (1.00) |
| 3q gain | 19 (22%) | 68 |
0.232 (1.00) |
0.611 (1.00) |
0.0441 (0.948) |
0.308 (1.00) |
0.71 (1.00) |
0.558 (1.00) |
0.327 (1.00) |
0.774 (1.00) |
0.407 (1.00) |
0.428 (1.00) |
0.259 (1.00) |
| 5p gain | 24 (28%) | 63 |
0.877 (1.00) |
0.374 (1.00) |
0.802 (1.00) |
0.149 (1.00) |
0.347 (1.00) |
1 (1.00) |
0.761 (1.00) |
0.789 (1.00) |
0.798 (1.00) |
0.727 (1.00) |
0.345 (1.00) |
| 5q gain | 14 (16%) | 73 |
0.682 (1.00) |
0.711 (1.00) |
0.697 (1.00) |
0.0763 (1.00) |
0.539 (1.00) |
1 (1.00) |
0.279 (1.00) |
0.522 (1.00) |
0.869 (1.00) |
0.42 (1.00) |
0.585 (1.00) |
| 6p gain | 7 (8%) | 80 |
0.0951 (1.00) |
0.612 (1.00) |
0.405 (1.00) |
0.172 (1.00) |
0.131 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.393 (1.00) |
0.644 (1.00) |
0.817 (1.00) |
0.651 (1.00) |
| 6q gain | 4 (5%) | 83 |
0.925 (1.00) |
0.243 (1.00) |
0.105 (1.00) |
0.0479 (0.948) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.31 (1.00) |
1 (1.00) |
0.863 (1.00) |
|
| 7p gain | 25 (29%) | 62 |
0.351 (1.00) |
0.398 (1.00) |
0.386 (1.00) |
0.933 (1.00) |
0.00135 (0.267) |
0.545 (1.00) |
0.769 (1.00) |
1 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.33 (1.00) |
| 8p gain | 12 (14%) | 75 |
0.474 (1.00) |
0.534 (1.00) |
0.667 (1.00) |
0.1 (1.00) |
0.586 (1.00) |
1 (1.00) |
0.452 (1.00) |
1 (1.00) |
0.825 (1.00) |
0.506 (1.00) |
0.927 (1.00) |
| 8q gain | 14 (16%) | 73 |
0.997 (1.00) |
0.544 (1.00) |
0.202 (1.00) |
0.0797 (1.00) |
0.495 (1.00) |
0.462 (1.00) |
0.451 (1.00) |
0.522 (1.00) |
0.494 (1.00) |
0.668 (1.00) |
0.745 (1.00) |
| 9q gain | 3 (3%) | 84 |
0.00538 (0.533) |
0.65 (1.00) |
0.291 (1.00) |
0.292 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
| 10p gain | 3 (3%) | 84 |
0.96 (1.00) |
0.322 (1.00) |
0.125 (1.00) |
0.294 (1.00) |
0.364 (1.00) |
1 (1.00) |
0.461 (1.00) |
1 (1.00) |
0.103 (1.00) |
0.817 (1.00) |
|
| 10q gain | 3 (3%) | 84 |
0.96 (1.00) |
0.322 (1.00) |
0.123 (1.00) |
0.294 (1.00) |
0.364 (1.00) |
1 (1.00) |
0.461 (1.00) |
1 (1.00) |
0.106 (1.00) |
0.813 (1.00) |
|
| 11p gain | 12 (14%) | 75 |
0.603 (1.00) |
0.292 (1.00) |
0.914 (1.00) |
0.831 (1.00) |
0.0945 (1.00) |
1 (1.00) |
1 (1.00) |
0.278 (1.00) |
0.0585 (0.953) |
1 (1.00) |
|
| 11q gain | 12 (14%) | 75 |
0.401 (1.00) |
0.183 (1.00) |
0.915 (1.00) |
0.829 (1.00) |
0.0943 (1.00) |
1 (1.00) |
0.452 (1.00) |
0.491 (1.00) |
0.895 (1.00) |
0.0604 (0.953) |
0.928 (1.00) |
| 12p gain | 18 (21%) | 69 |
0.177 (1.00) |
0.809 (1.00) |
0.325 (1.00) |
0.695 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.506 (1.00) |
1 (1.00) |
0.429 (1.00) |
0.925 (1.00) |
|
| 12q gain | 18 (21%) | 69 |
0.177 (1.00) |
0.809 (1.00) |
0.322 (1.00) |
0.697 (1.00) |
0.155 (1.00) |
1 (1.00) |
0.506 (1.00) |
1 (1.00) |
0.432 (1.00) |
0.924 (1.00) |
|
| 13q gain | 5 (6%) | 82 |
0.456 (1.00) |
0.763 (1.00) |
0.444 (1.00) |
0.629 (1.00) |
0.411 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
| 15q gain | 10 (11%) | 77 |
0.588 (1.00) |
0.936 (1.00) |
0.305 (1.00) |
0.28 (1.00) |
0.4 (1.00) |
1 (1.00) |
0.383 (1.00) |
1 (1.00) |
0.692 (1.00) |
1 (1.00) |
0.747 (1.00) |
| 16p gain | 16 (18%) | 71 |
0.74 (1.00) |
0.167 (1.00) |
0.27 (1.00) |
0.919 (1.00) |
0.0887 (1.00) |
1 (1.00) |
0.725 (1.00) |
0.365 (1.00) |
0.295 (1.00) |
0.294 (1.00) |
0.151 (1.00) |
| 16q gain | 16 (18%) | 71 |
0.722 (1.00) |
0.194 (1.00) |
0.268 (1.00) |
0.816 (1.00) |
0.306 (1.00) |
1 (1.00) |
1 (1.00) |
0.365 (1.00) |
0.295 (1.00) |
0.295 (1.00) |
0.0272 (0.817) |
| 17p gain | 8 (9%) | 79 |
0.763 (1.00) |
0.0505 (0.948) |
0.315 (1.00) |
0.906 (1.00) |
0.761 (1.00) |
1 (1.00) |
0.342 (1.00) |
0.68 (1.00) |
0.169 (1.00) |
0.864 (1.00) |
|
| 17q gain | 17 (20%) | 70 |
0.967 (1.00) |
0.5 (1.00) |
0.542 (1.00) |
0.961 (1.00) |
0.169 (1.00) |
0.566 (1.00) |
0.728 (1.00) |
0.365 (1.00) |
0.0709 (1.00) |
0.737 (1.00) |
|
| 18p gain | 8 (9%) | 79 |
0.297 (1.00) |
0.78 (1.00) |
0.445 (1.00) |
1 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.636 (1.00) |
0.433 (1.00) |
0.328 (1.00) |
0.861 (1.00) |
|
| 18q gain | 4 (5%) | 83 |
0.103 (1.00) |
0.887 (1.00) |
0.153 (1.00) |
0.749 (1.00) |
1 (1.00) |
1 (1.00) |
0.563 (1.00) |
1 (1.00) |
0.145 (1.00) |
0.862 (1.00) |
|
| 19p gain | 14 (16%) | 73 |
0.963 (1.00) |
0.37 (1.00) |
0.696 (1.00) |
0.888 (1.00) |
0.398 (1.00) |
1 (1.00) |
1 (1.00) |
0.502 (1.00) |
0.114 (1.00) |
0.512 (1.00) |
0.745 (1.00) |
| 19q gain | 11 (13%) | 76 |
0.402 (1.00) |
0.269 (1.00) |
0.416 (1.00) |
0.493 (1.00) |
0.713 (1.00) |
1 (1.00) |
0.681 (1.00) |
0.719 (1.00) |
0.391 (1.00) |
0.264 (1.00) |
0.927 (1.00) |
| 20p gain | 8 (9%) | 79 |
0.123 (1.00) |
0.494 (1.00) |
0.188 (1.00) |
0.868 (1.00) |
0.63 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.448 (1.00) |
0.651 (1.00) |
|
| 20q gain | 11 (13%) | 76 |
0.609 (1.00) |
0.632 (1.00) |
0.285 (1.00) |
0.885 (1.00) |
0.713 (1.00) |
1 (1.00) |
0.204 (1.00) |
1 (1.00) |
1 (1.00) |
0.926 (1.00) |
|
| 21q gain | 6 (7%) | 81 |
0.0623 (0.953) |
0.154 (1.00) |
0.924 (1.00) |
0.829 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.025 (0.817) |
1 (1.00) |
0.11 (1.00) |
| xp gain | 7 (8%) | 80 |
0.839 (1.00) |
0.382 (1.00) |
0.946 (1.00) |
0.819 (1.00) |
0.45 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.393 (1.00) |
1 (1.00) |
0.0314 (0.858) |
|
| xq gain | 6 (7%) | 81 |
0.673 (1.00) |
0.476 (1.00) |
0.691 (1.00) |
0.599 (1.00) |
0.306 (1.00) |
1 (1.00) |
0.304 (1.00) |
0.67 (1.00) |
0.799 (1.00) |
0.0865 (1.00) |
|
| 1p loss | 9 (10%) | 78 |
0.14 (1.00) |
0.686 (1.00) |
0.478 (1.00) |
0.227 (1.00) |
0.536 (1.00) |
1 (1.00) |
0.357 (1.00) |
0.705 (1.00) |
0.578 (1.00) |
0.159 (1.00) |
|
| 2p loss | 6 (7%) | 81 |
0.171 (1.00) |
0.383 (1.00) |
1 (1.00) |
0.831 (1.00) |
0.712 (1.00) |
1 (1.00) |
0.304 (1.00) |
0.179 (1.00) |
0.165 (1.00) |
0.141 (1.00) |
|
| 2q loss | 5 (6%) | 82 |
0.103 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.859 (1.00) |
1 (1.00) |
1 (1.00) |
0.0413 (0.948) |
0.316 (1.00) |
0.348 (1.00) |
0.0506 (0.948) |
|
| 3p loss | 8 (9%) | 79 |
0.144 (1.00) |
0.895 (1.00) |
0.258 (1.00) |
0.867 (1.00) |
0.314 (1.00) |
1 (1.00) |
0.342 (1.00) |
0.68 (1.00) |
0.843 (1.00) |
0.654 (1.00) |
|
| 3q loss | 7 (8%) | 80 |
0.0981 (1.00) |
0.0499 (0.948) |
0.135 (1.00) |
0.817 (1.00) |
0.124 (1.00) |
1 (1.00) |
0.34 (1.00) |
1 (1.00) |
0.343 (1.00) |
1 (1.00) |
|
| 4p loss | 33 (38%) | 54 |
0.0477 (0.948) |
0.248 (1.00) |
0.855 (1.00) |
0.5 (1.00) |
0.558 (1.00) |
0.251 (1.00) |
0.776 (1.00) |
0.626 (1.00) |
0.213 (1.00) |
0.221 (1.00) |
0.0469 (0.948) |
| 4q loss | 34 (39%) | 53 |
0.0482 (0.948) |
0.267 (1.00) |
0.599 (1.00) |
0.0802 (1.00) |
0.402 (1.00) |
0.258 (1.00) |
0.398 (1.00) |
0.811 (1.00) |
0.0471 (0.948) |
0.243 (1.00) |
0.0237 (0.817) |
| 5p loss | 4 (5%) | 83 |
0.0377 (0.948) |
0.648 (1.00) |
0.887 (1.00) |
0.539 (1.00) |
1 (1.00) |
1 (1.00) |
0.563 (1.00) |
0.0641 (0.953) |
0.698 (1.00) |
0.816 (1.00) |
|
| 5q loss | 9 (10%) | 78 |
0.0222 (0.817) |
0.712 (1.00) |
0.81 (1.00) |
1 (1.00) |
0.41 (1.00) |
1 (1.00) |
1 (1.00) |
0.258 (1.00) |
0.871 (1.00) |
0.887 (1.00) |
|
| 6p loss | 8 (9%) | 79 |
0.0492 (0.948) |
0.065 (0.953) |
0.00236 (0.312) |
0.184 (1.00) |
0.527 (1.00) |
1 (1.00) |
0.342 (1.00) |
0.433 (1.00) |
0.236 (1.00) |
1 (1.00) |
|
| 6q loss | 29 (33%) | 58 |
0.189 (1.00) |
0.953 (1.00) |
0.00871 (0.687) |
0.43 (1.00) |
0.138 (1.00) |
1 (1.00) |
1 (1.00) |
0.446 (1.00) |
0.0873 (1.00) |
0.641 (1.00) |
0.378 (1.00) |
| 8p loss | 13 (15%) | 74 |
0.349 (1.00) |
0.283 (1.00) |
0.208 (1.00) |
0.605 (1.00) |
1 (1.00) |
0.427 (1.00) |
1 (1.00) |
0.502 (1.00) |
0.262 (1.00) |
0.149 (1.00) |
0.0255 (0.817) |
| 8q loss | 4 (5%) | 83 |
0.204 (1.00) |
0.655 (1.00) |
0.0195 (0.817) |
0.0911 (1.00) |
1 (1.00) |
1 (1.00) |
0.563 (1.00) |
1 (1.00) |
0.0801 (1.00) |
0.13 (1.00) |
|
| 9q loss | 22 (25%) | 65 |
0.0107 (0.706) |
0.969 (1.00) |
0.275 (1.00) |
0.835 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.339 (1.00) |
1 (1.00) |
0.62 (1.00) |
0.467 (1.00) |
1 (1.00) |
| 10p loss | 25 (29%) | 62 |
0.00196 (0.31) |
0.936 (1.00) |
0.25 (1.00) |
0.673 (1.00) |
0.681 (1.00) |
1 (1.00) |
0.137 (1.00) |
0.431 (1.00) |
0.058 (0.953) |
0.565 (1.00) |
0.488 (1.00) |
| 11p loss | 4 (5%) | 83 |
0.211 (1.00) |
0.147 (1.00) |
0.016 (0.817) |
0.385 (1.00) |
0.699 (1.00) |
1 (1.00) |
0.563 (1.00) |
1 (1.00) |
0.0531 (0.948) |
0.815 (1.00) |
|
| 11q loss | 5 (6%) | 82 |
0.0279 (0.817) |
0.391 (1.00) |
0.0189 (0.817) |
0.147 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.316 (1.00) |
0.0225 (0.817) |
0.817 (1.00) |
|
| 12p loss | 4 (5%) | 83 |
0.119 (1.00) |
0.081 (1.00) |
0.508 (1.00) |
1 (1.00) |
0.25 (1.00) |
1 (1.00) |
0.563 (1.00) |
0.31 (1.00) |
0.191 (1.00) |
||
| 13q loss | 33 (38%) | 54 |
0.00954 (0.687) |
0.612 (1.00) |
0.473 (1.00) |
0.956 (1.00) |
0.59 (1.00) |
0.0591 (0.953) |
0.776 (1.00) |
1 (1.00) |
0.724 (1.00) |
0.966 (1.00) |
0.832 (1.00) |
| 14q loss | 35 (40%) | 52 |
0.0135 (0.817) |
0.24 (1.00) |
0.165 (1.00) |
0.0293 (0.83) |
0.169 (1.00) |
0.258 (1.00) |
0.0532 (0.948) |
1 (1.00) |
0.113 (1.00) |
0.0186 (0.817) |
0.75 (1.00) |
| 15q loss | 11 (13%) | 76 |
0.00354 (0.401) |
0.462 (1.00) |
0.135 (1.00) |
0.573 (1.00) |
0.454 (1.00) |
1 (1.00) |
0.681 (1.00) |
0.491 (1.00) |
0.111 (1.00) |
1 (1.00) |
|
| 16p loss | 8 (9%) | 79 |
0.72 (1.00) |
0.116 (1.00) |
0.142 (1.00) |
0.376 (1.00) |
0.152 (1.00) |
1 (1.00) |
1 (1.00) |
0.433 (1.00) |
0.0756 (1.00) |
0.408 (1.00) |
|
| 16q loss | 11 (13%) | 76 |
0.461 (1.00) |
0.173 (1.00) |
0.0364 (0.948) |
0.357 (1.00) |
0.132 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.109 (1.00) |
0.0637 (0.953) |
|
| 17p loss | 23 (26%) | 64 |
0.257 (1.00) |
0.0182 (0.817) |
0.45 (1.00) |
0.202 (1.00) |
0.0753 (1.00) |
0.556 (1.00) |
0.754 (1.00) |
1 (1.00) |
0.687 (1.00) |
0.912 (1.00) |
1 (1.00) |
| 17q loss | 7 (8%) | 80 |
0.561 (1.00) |
0.725 (1.00) |
0.135 (1.00) |
0.164 (1.00) |
1 (1.00) |
1 (1.00) |
0.608 (1.00) |
0.183 (1.00) |
0.391 (1.00) |
0.673 (1.00) |
0.211 (1.00) |
| 18p loss | 9 (10%) | 78 |
0.344 (1.00) |
0.244 (1.00) |
0.761 (1.00) |
1 (1.00) |
0.782 (1.00) |
1 (1.00) |
1 (1.00) |
0.0567 (0.953) |
0.582 (1.00) |
0.179 (1.00) |
|
| 18q loss | 14 (16%) | 73 |
0.315 (1.00) |
0.945 (1.00) |
0.611 (1.00) |
0.595 (1.00) |
0.915 (1.00) |
1 (1.00) |
0.124 (1.00) |
0.332 (1.00) |
0.928 (1.00) |
0.37 (1.00) |
|
| 19p loss | 4 (5%) | 83 |
0.451 (1.00) |
0.367 (1.00) |
0.133 (1.00) |
1 (1.00) |
0.226 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.697 (1.00) |
||
| 19q loss | 7 (8%) | 80 |
0.212 (1.00) |
0.857 (1.00) |
0.137 (1.00) |
0.714 (1.00) |
0.583 (1.00) |
1 (1.00) |
1 (1.00) |
0.393 (1.00) |
1 (1.00) |
0.274 (1.00) |
|
| 20p loss | 14 (16%) | 73 |
0.353 (1.00) |
0.949 (1.00) |
0.3 (1.00) |
0.728 (1.00) |
0.382 (1.00) |
1 (1.00) |
1 (1.00) |
0.748 (1.00) |
0.692 (1.00) |
0.135 (1.00) |
0.0262 (0.817) |
| 21q loss | 11 (13%) | 76 |
0.106 (1.00) |
0.954 (1.00) |
0.0786 (1.00) |
0.334 (1.00) |
0.694 (1.00) |
1 (1.00) |
0.681 (1.00) |
0.271 (1.00) |
0.366 (1.00) |
0.453 (1.00) |
|
| 22q loss | 67 (77%) | 20 |
0.0881 (1.00) |
0.936 (1.00) |
0.465 (1.00) |
0.229 (1.00) |
0.869 (1.00) |
0.556 (1.00) |
0.511 (1.00) |
0.57 (1.00) |
0.377 (1.00) |
0.454 (1.00) |
0.853 (1.00) |
| xp loss | 27 (31%) | 60 |
0.395 (1.00) |
0.24 (1.00) |
0.968 (1.00) |
0.881 (1.00) |
0.893 (1.00) |
0.212 (1.00) |
0.766 (1.00) |
0.801 (1.00) |
0.838 (1.00) |
0.415 (1.00) |
0.715 (1.00) |
| xq loss | 28 (32%) | 59 |
0.334 (1.00) |
0.298 (1.00) |
0.938 (1.00) |
0.833 (1.00) |
0.897 (1.00) |
0.233 (1.00) |
0.568 (1.00) |
0.611 (1.00) |
0.838 (1.00) |
0.401 (1.00) |
1 (1.00) |
'7q gain' versus 'PATHOLOGY_N_STAGE'
P value = 0.00063 (Fisher's exact test), Q value = 0.17
Table S1. Gene #12: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
| nPatients | N0 | N1 | N2+N3 |
|---|---|---|---|
| ALL | 44 | 10 | 29 |
| 7Q GAIN MUTATED | 7 | 0 | 15 |
| 7Q GAIN WILD-TYPE | 37 | 10 | 14 |
Figure S1. Get High-res Image Gene #12: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
'9p loss' versus 'Time to Death'
P value = 0.000635 (logrank test), Q value = 0.17
Table S2. Gene #50: '9p loss' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
| 9P LOSS MUTATED | 27 | 26 | 0.7 - 41.5 (13.3) |
| 9P LOSS WILD-TYPE | 58 | 47 | 1.3 - 91.7 (22.2) |
Figure S2. Get High-res Image Gene #50: '9p loss' versus Clinical Feature #1: 'Time to Death'
'10q loss' versus 'Time to Death'
P value = 5.53e-05 (logrank test), Q value = 0.044
Table S3. Gene #53: '10q loss' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 85 | 73 | 0.7 - 91.7 (17.3) |
| 10Q LOSS MUTATED | 19 | 17 | 0.7 - 24.1 (10.8) |
| 10Q LOSS WILD-TYPE | 66 | 56 | 1.3 - 91.7 (22.2) |
Figure S3. Get High-res Image Gene #53: '10q loss' versus Clinical Feature #1: 'Time to Death'
Methods & Data
Input
-
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/MESO-TP/22533659/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/MESO-TP/22507181/MESO-TP.merged_data.txt
-
Number of patients = 87
-
Number of significantly arm-level cnvs = 72
-
Number of selected clinical features = 11
-
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
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] 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)
[3] 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 © 2016
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.