This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 75 arm-level events and 10 clinical features across 134 patients, 14 significant findings detected with Q value < 0.25.
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7q gain cnv correlated to 'ETHNICITY'.
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10p gain cnv correlated to 'YEARS_TO_BIRTH'.
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10q gain cnv correlated to 'YEARS_TO_BIRTH'.
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15q gain cnv correlated to 'YEARS_TO_BIRTH'.
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19p gain cnv correlated to 'YEARS_TO_BIRTH'.
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19q gain cnv correlated to 'YEARS_TO_BIRTH'.
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20p gain cnv correlated to 'PATHOLOGY_T_STAGE'.
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10p loss cnv correlated to 'YEARS_TO_BIRTH'.
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10q loss cnv correlated to 'YEARS_TO_BIRTH'.
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14q loss cnv correlated to 'YEARS_TO_BIRTH'.
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19p loss cnv correlated to 'PATHOLOGIC_STAGE'.
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19q loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', and 'RADIATION_THERAPY'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
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 | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
19q loss | 42 (31%) | 92 |
0.618 (1.00) |
0.00175 (0.136) |
0.00033 (0.0825) |
0.147 (0.909) |
0.105 (0.796) |
0.596 (1.00) |
0.000193 (0.0788) |
0.278 (1.00) |
1 (1.00) |
0.751 (1.00) |
7q gain | 95 (71%) | 39 |
0.933 (1.00) |
0.825 (1.00) |
0.462 (1.00) |
0.0299 (0.582) |
0.738 (1.00) |
1 (1.00) |
0.795 (1.00) |
0.626 (1.00) |
1 (1.00) |
0.00441 (0.236) |
10p gain | 6 (4%) | 128 |
0.723 (1.00) |
0.000592 (0.0942) |
0.948 (1.00) |
0.173 (0.973) |
1 (1.00) |
0.586 (1.00) |
0.596 (1.00) |
0.339 (1.00) |
1 (1.00) |
|
10q gain | 10 (7%) | 124 |
0.637 (1.00) |
0.00429 (0.236) |
0.995 (1.00) |
0.573 (1.00) |
1 (1.00) |
1 (1.00) |
0.635 (1.00) |
0.638 (1.00) |
0.528 (1.00) |
1 (1.00) |
15q gain | 48 (36%) | 86 |
0.995 (1.00) |
0.00021 (0.0788) |
0.236 (1.00) |
0.95 (1.00) |
1 (1.00) |
0.295 (1.00) |
0.808 (1.00) |
0.413 (1.00) |
1 (1.00) |
0.535 (1.00) |
19p gain | 34 (25%) | 100 |
0.325 (1.00) |
0.00146 (0.136) |
0.0849 (0.77) |
0.316 (1.00) |
0.668 (1.00) |
0.571 (1.00) |
0.169 (0.965) |
0.575 (1.00) |
1 (1.00) |
0.176 (0.973) |
19q gain | 27 (20%) | 107 |
0.403 (1.00) |
0.00104 (0.116) |
0.14 (0.886) |
0.278 (1.00) |
1 (1.00) |
0.582 (1.00) |
0.0334 (0.611) |
0.483 (1.00) |
1 (1.00) |
0.0666 (0.725) |
20p gain | 31 (23%) | 103 |
0.365 (1.00) |
0.908 (1.00) |
0.0939 (0.77) |
0.00322 (0.201) |
0.426 (1.00) |
0.207 (0.978) |
0.402 (1.00) |
0.55 (1.00) |
0.839 (1.00) |
1 (1.00) |
10p loss | 68 (51%) | 66 |
0.464 (1.00) |
0.00109 (0.116) |
0.11 (0.804) |
0.353 (1.00) |
0.0575 (0.695) |
0.619 (1.00) |
0.031 (0.582) |
0.0547 (0.686) |
0.0888 (0.77) |
1 (1.00) |
10q loss | 62 (46%) | 72 |
0.289 (1.00) |
0.00201 (0.137) |
0.0719 (0.733) |
0.295 (1.00) |
0.0303 (0.582) |
0.328 (1.00) |
0.0304 (0.582) |
0.011 (0.436) |
0.535 (1.00) |
0.0353 (0.63) |
14q loss | 17 (13%) | 117 |
0.606 (1.00) |
0.000628 (0.0942) |
0.195 (0.973) |
0.467 (1.00) |
0.0623 (0.725) |
0.374 (1.00) |
0.307 (1.00) |
0.903 (1.00) |
0.77 (1.00) |
0.627 (1.00) |
19p loss | 39 (29%) | 95 |
0.549 (1.00) |
0.0192 (0.558) |
0.00182 (0.136) |
0.1 (0.788) |
0.0549 (0.686) |
0.583 (1.00) |
0.00747 (0.311) |
0.491 (1.00) |
1 (1.00) |
1 (1.00) |
1p gain | 32 (24%) | 102 |
0.824 (1.00) |
0.0543 (0.686) |
0.342 (1.00) |
0.0563 (0.693) |
0.187 (0.973) |
1 (1.00) |
0.158 (0.939) |
0.895 (1.00) |
0.717 (1.00) |
0.495 (1.00) |
1q gain | 54 (40%) | 80 |
0.774 (1.00) |
0.381 (1.00) |
0.429 (1.00) |
0.0385 (0.656) |
0.344 (1.00) |
0.638 (1.00) |
0.474 (1.00) |
0.251 (1.00) |
0.516 (1.00) |
0.0269 (0.577) |
2p gain | 40 (30%) | 94 |
0.865 (1.00) |
0.915 (1.00) |
0.946 (1.00) |
0.455 (1.00) |
0.517 (1.00) |
1 (1.00) |
0.797 (1.00) |
0.0869 (0.77) |
0.399 (1.00) |
1 (1.00) |
2q gain | 38 (28%) | 96 |
0.697 (1.00) |
0.432 (1.00) |
0.937 (1.00) |
0.525 (1.00) |
0.738 (1.00) |
1 (1.00) |
0.294 (1.00) |
0.352 (1.00) |
0.385 (1.00) |
0.73 (1.00) |
3p gain | 22 (16%) | 112 |
0.464 (1.00) |
0.342 (1.00) |
0.909 (1.00) |
0.467 (1.00) |
1 (1.00) |
0.131 (0.869) |
0.197 (0.974) |
0.422 (1.00) |
0.792 (1.00) |
0.411 (1.00) |
3q gain | 31 (23%) | 103 |
0.942 (1.00) |
0.994 (1.00) |
0.426 (1.00) |
0.0466 (0.675) |
0.481 (1.00) |
0.221 (0.993) |
0.781 (1.00) |
0.408 (1.00) |
0.836 (1.00) |
0.725 (1.00) |
4p gain | 3 (2%) | 131 |
0.818 (1.00) |
0.609 (1.00) |
0.855 (1.00) |
0.368 (1.00) |
1 (1.00) |
1 (1.00) |
0.652 (1.00) |
0.216 (0.978) |
1 (1.00) |
|
5p gain | 6 (4%) | 128 |
0.714 (1.00) |
0.0197 (0.558) |
0.405 (1.00) |
0.411 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.589 (1.00) |
0.0144 (0.535) |
1 (1.00) |
0.467 (1.00) |
5q gain | 3 (2%) | 131 |
0.821 (1.00) |
0.101 (0.788) |
0.124 (0.844) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.267 (1.00) |
|||
6p gain | 21 (16%) | 113 |
0.341 (1.00) |
0.353 (1.00) |
0.616 (1.00) |
0.546 (1.00) |
1 (1.00) |
0.526 (1.00) |
0.194 (0.973) |
0.749 (1.00) |
0.461 (1.00) |
0.411 (1.00) |
6q gain | 17 (13%) | 117 |
0.505 (1.00) |
0.623 (1.00) |
0.264 (1.00) |
0.325 (1.00) |
0.643 (1.00) |
0.465 (1.00) |
0.073 (0.733) |
0.872 (1.00) |
0.545 (1.00) |
0.37 (1.00) |
7p gain | 111 (83%) | 23 |
0.727 (1.00) |
1 (1.00) |
0.712 (1.00) |
1 (1.00) |
1 (1.00) |
0.526 (1.00) |
1 (1.00) |
0.476 (1.00) |
0.807 (1.00) |
0.0257 (0.577) |
8p gain | 102 (76%) | 32 |
0.26 (1.00) |
0.466 (1.00) |
0.554 (1.00) |
0.939 (1.00) |
1 (1.00) |
0.0361 (0.63) |
0.404 (1.00) |
0.37 (1.00) |
0.841 (1.00) |
0.732 (1.00) |
8q gain | 104 (78%) | 30 |
0.271 (1.00) |
0.23 (1.00) |
0.24 (1.00) |
0.552 (1.00) |
1 (1.00) |
0.0288 (0.582) |
0.0437 (0.675) |
0.173 (0.973) |
0.702 (1.00) |
0.278 (1.00) |
9p gain | 14 (10%) | 120 |
0.408 (1.00) |
0.546 (1.00) |
0.54 (1.00) |
0.336 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.402 (1.00) |
1 (1.00) |
0.0945 (0.77) |
|
9q gain | 15 (11%) | 119 |
0.385 (1.00) |
0.285 (1.00) |
0.199 (0.974) |
0.8 (1.00) |
1 (1.00) |
0.35 (1.00) |
1 (1.00) |
0.645 (1.00) |
0.327 (1.00) |
1 (1.00) |
11p gain | 8 (6%) | 126 |
0.471 (1.00) |
0.557 (1.00) |
0.18 (0.973) |
0.497 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.354 (1.00) |
0.821 (1.00) |
1 (1.00) |
1 (1.00) |
11q gain | 3 (2%) | 131 |
0.528 (1.00) |
0.662 (1.00) |
0.411 (1.00) |
0.62 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|||
12p gain | 130 (97%) | 4 |
0.754 (1.00) |
0.969 (1.00) |
0.195 (0.973) |
0.709 (1.00) |
1 (1.00) |
0.504 (1.00) |
0.122 (0.844) |
1 (1.00) |
1 (1.00) |
|
12q gain | 91 (68%) | 43 |
0.559 (1.00) |
0.0477 (0.675) |
0.21 (0.978) |
0.554 (1.00) |
0.738 (1.00) |
1 (1.00) |
0.124 (0.844) |
0.923 (1.00) |
0.569 (1.00) |
0.339 (1.00) |
14q gain | 45 (34%) | 89 |
0.392 (1.00) |
0.0993 (0.788) |
0.183 (0.973) |
0.948 (1.00) |
0.307 (1.00) |
1 (1.00) |
0.206 (0.978) |
0.125 (0.844) |
1 (1.00) |
0.212 (0.978) |
16p gain | 14 (10%) | 120 |
0.178 (0.973) |
0.713 (1.00) |
0.759 (1.00) |
0.142 (0.886) |
0.643 (1.00) |
0.35 (1.00) |
1 (1.00) |
0.906 (1.00) |
0.697 (1.00) |
0.0945 (0.77) |
16q gain | 14 (10%) | 120 |
0.202 (0.978) |
0.357 (1.00) |
0.759 (1.00) |
0.212 (0.978) |
0.643 (1.00) |
0.35 (1.00) |
1 (1.00) |
0.906 (1.00) |
0.695 (1.00) |
0.0945 (0.77) |
17p gain | 32 (24%) | 102 |
0.435 (1.00) |
0.204 (0.978) |
0.0927 (0.77) |
0.166 (0.96) |
0.513 (1.00) |
0.278 (1.00) |
0.025 (0.577) |
0.227 (1.00) |
0.603 (1.00) |
0.729 (1.00) |
17q gain | 42 (31%) | 92 |
0.118 (0.836) |
0.228 (1.00) |
0.239 (1.00) |
0.393 (1.00) |
1 (1.00) |
0.592 (1.00) |
0.0748 (0.739) |
0.373 (1.00) |
0.304 (1.00) |
0.751 (1.00) |
18p gain | 4 (3%) | 130 |
0.78 (1.00) |
0.794 (1.00) |
0.44 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.398 (1.00) |
0.13 (0.868) |
1 (1.00) |
20q gain | 34 (25%) | 100 |
0.44 (1.00) |
0.967 (1.00) |
0.015 (0.535) |
0.0186 (0.558) |
0.712 (1.00) |
0.235 (1.00) |
0.277 (1.00) |
0.452 (1.00) |
0.608 (1.00) |
0.291 (1.00) |
21q gain | 113 (84%) | 21 |
0.109 (0.804) |
0.0417 (0.672) |
0.498 (1.00) |
0.305 (1.00) |
0.713 (1.00) |
0.486 (1.00) |
1 (1.00) |
0.936 (1.00) |
0.322 (1.00) |
1 (1.00) |
22q gain | 36 (27%) | 98 |
0.311 (1.00) |
0.0682 (0.731) |
0.333 (1.00) |
0.3 (1.00) |
0.432 (1.00) |
0.573 (1.00) |
0.00619 (0.29) |
0.483 (1.00) |
0.619 (1.00) |
1 (1.00) |
xp gain | 18 (13%) | 116 |
0.371 (1.00) |
0.158 (0.939) |
0.692 (1.00) |
0.609 (1.00) |
0.185 (0.973) |
0.108 (0.804) |
0.073 (0.733) |
0.0801 (0.77) |
1 (1.00) |
0.688 (1.00) |
xq gain | 18 (13%) | 116 |
0.371 (1.00) |
0.0926 (0.77) |
0.578 (1.00) |
0.384 (1.00) |
0.0979 (0.788) |
0.486 (1.00) |
0.073 (0.733) |
0.133 (0.875) |
1 (1.00) |
0.688 (1.00) |
1p loss | 19 (14%) | 115 |
0.00522 (0.261) |
0.75 (1.00) |
0.841 (1.00) |
0.692 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
0.0212 (0.567) |
0.272 (1.00) |
1 (1.00) |
1q loss | 9 (7%) | 125 |
0.0533 (0.686) |
0.673 (1.00) |
0.89 (1.00) |
0.295 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.635 (1.00) |
0.091 (0.77) |
0.0634 (0.725) |
1 (1.00) |
2p loss | 4 (3%) | 130 |
0.754 (1.00) |
0.395 (1.00) |
1 (1.00) |
0.19 (0.973) |
1 (1.00) |
0.504 (1.00) |
0.694 (1.00) |
1 (1.00) |
0.34 (1.00) |
|
2q loss | 5 (4%) | 129 |
0.723 (1.00) |
0.655 (1.00) |
0.403 (1.00) |
0.721 (1.00) |
1 (1.00) |
1 (1.00) |
0.937 (1.00) |
1 (1.00) |
0.407 (1.00) |
|
3p loss | 31 (23%) | 103 |
0.815 (1.00) |
0.0397 (0.661) |
0.19 (0.973) |
0.491 (1.00) |
0.712 (1.00) |
0.578 (1.00) |
1 (1.00) |
0.291 (1.00) |
0.174 (0.973) |
1 (1.00) |
3q loss | 23 (17%) | 111 |
0.318 (1.00) |
0.11 (0.804) |
0.539 (1.00) |
0.617 (1.00) |
0.268 (1.00) |
1 (1.00) |
0.762 (1.00) |
0.139 (0.886) |
0.292 (1.00) |
1 (1.00) |
4p loss | 86 (64%) | 48 |
0.215 (0.978) |
0.0816 (0.77) |
0.752 (1.00) |
0.103 (0.79) |
0.334 (1.00) |
1 (1.00) |
0.808 (1.00) |
0.463 (1.00) |
0.87 (1.00) |
0.751 (1.00) |
4q loss | 100 (75%) | 34 |
0.313 (1.00) |
0.152 (0.926) |
0.346 (1.00) |
0.0476 (0.675) |
0.0259 (0.577) |
1 (1.00) |
0.41 (1.00) |
0.364 (1.00) |
0.103 (0.79) |
0.732 (1.00) |
5p loss | 93 (69%) | 41 |
0.951 (1.00) |
0.75 (1.00) |
0.453 (1.00) |
0.0167 (0.552) |
1 (1.00) |
0.583 (1.00) |
0.119 (0.836) |
0.271 (1.00) |
0.646 (1.00) |
0.752 (1.00) |
5q loss | 91 (68%) | 43 |
0.997 (1.00) |
0.744 (1.00) |
0.0548 (0.686) |
0.00721 (0.311) |
0.334 (1.00) |
0.596 (1.00) |
0.0201 (0.558) |
0.196 (0.973) |
0.565 (1.00) |
1 (1.00) |
6p loss | 11 (8%) | 123 |
0.616 (1.00) |
0.0421 (0.672) |
0.876 (1.00) |
0.856 (1.00) |
0.322 (1.00) |
1 (1.00) |
1 (1.00) |
0.338 (1.00) |
0.6 (1.00) |
1 (1.00) |
6q loss | 14 (10%) | 120 |
0.416 (1.00) |
0.0825 (0.77) |
0.382 (1.00) |
0.693 (1.00) |
1 (1.00) |
0.325 (1.00) |
0.698 (1.00) |
0.866 (1.00) |
0.667 (1.00) |
1 (1.00) |
7q loss | 3 (2%) | 131 |
0.777 (1.00) |
0.351 (1.00) |
0.854 (1.00) |
0.369 (1.00) |
1 (1.00) |
1 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.267 (1.00) |
|
8p loss | 10 (7%) | 124 |
0.438 (1.00) |
0.632 (1.00) |
0.0466 (0.675) |
0.576 (1.00) |
0.119 (0.836) |
0.0169 (0.552) |
1 (1.00) |
0.236 (1.00) |
0.529 (1.00) |
1 (1.00) |
8q loss | 4 (3%) | 130 |
0.514 (1.00) |
0.844 (1.00) |
0.0664 (0.725) |
0.0733 (0.733) |
0.0664 (0.725) |
1 (1.00) |
0.214 (0.978) |
1 (1.00) |
||
9p loss | 56 (42%) | 78 |
0.809 (1.00) |
0.406 (1.00) |
0.252 (1.00) |
0.589 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.0535 (0.686) |
0.734 (1.00) |
0.524 (1.00) |
0.557 (1.00) |
9q loss | 50 (37%) | 84 |
0.698 (1.00) |
0.65 (1.00) |
0.452 (1.00) |
0.906 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.625 (1.00) |
0.541 (1.00) |
0.769 (1.00) |
0.37 (1.00) |
11p loss | 90 (67%) | 44 |
0.595 (1.00) |
0.189 (0.973) |
0.958 (1.00) |
0.562 (1.00) |
0.307 (1.00) |
1 (1.00) |
0.206 (0.978) |
0.77 (1.00) |
1 (1.00) |
1 (1.00) |
11q loss | 106 (79%) | 28 |
0.191 (0.973) |
0.372 (1.00) |
0.852 (1.00) |
0.581 (1.00) |
0.0523 (0.686) |
0.582 (1.00) |
0.0454 (0.675) |
0.0912 (0.77) |
0.0852 (0.77) |
0.696 (1.00) |
13q loss | 104 (78%) | 30 |
0.336 (1.00) |
0.31 (1.00) |
0.885 (1.00) |
0.137 (0.883) |
0.26 (1.00) |
1 (1.00) |
0.158 (0.939) |
0.805 (1.00) |
0.377 (1.00) |
1 (1.00) |
15q loss | 22 (16%) | 112 |
0.71 (1.00) |
0.214 (0.978) |
0.0667 (0.725) |
0.722 (1.00) |
0.455 (1.00) |
0.119 (0.836) |
0.0237 (0.577) |
0.652 (1.00) |
0.346 (1.00) |
0.688 (1.00) |
16p loss | 43 (32%) | 91 |
0.44 (1.00) |
0.981 (1.00) |
0.561 (1.00) |
0.501 (1.00) |
0.721 (1.00) |
0.305 (1.00) |
0.804 (1.00) |
0.476 (1.00) |
0.863 (1.00) |
1 (1.00) |
16q loss | 46 (34%) | 88 |
0.212 (0.978) |
0.894 (1.00) |
0.622 (1.00) |
0.261 (1.00) |
1 (1.00) |
0.297 (1.00) |
0.452 (1.00) |
0.592 (1.00) |
0.672 (1.00) |
1 (1.00) |
17p loss | 35 (26%) | 99 |
0.989 (1.00) |
0.166 (0.96) |
0.83 (1.00) |
0.742 (1.00) |
0.693 (1.00) |
0.571 (1.00) |
0.0263 (0.577) |
0.637 (1.00) |
0.25 (1.00) |
0.296 (1.00) |
17q loss | 17 (13%) | 117 |
0.51 (1.00) |
0.141 (0.886) |
0.686 (1.00) |
0.463 (1.00) |
0.643 (1.00) |
1 (1.00) |
0.0221 (0.572) |
0.855 (1.00) |
0.768 (1.00) |
1 (1.00) |
18p loss | 106 (79%) | 28 |
0.373 (1.00) |
0.346 (1.00) |
0.785 (1.00) |
0.229 (1.00) |
0.26 (1.00) |
1 (1.00) |
1 (1.00) |
0.643 (1.00) |
0.674 (1.00) |
1 (1.00) |
18q loss | 110 (82%) | 24 |
0.411 (1.00) |
0.159 (0.939) |
0.625 (1.00) |
0.0929 (0.77) |
0.432 (1.00) |
0.564 (1.00) |
0.764 (1.00) |
0.349 (1.00) |
0.644 (1.00) |
1 (1.00) |
20p loss | 27 (20%) | 107 |
0.291 (1.00) |
0.951 (1.00) |
0.309 (1.00) |
0.701 (1.00) |
0.135 (0.882) |
0.194 (0.973) |
0.243 (1.00) |
0.836 (1.00) |
0.572 (1.00) |
0.716 (1.00) |
20q loss | 14 (10%) | 120 |
0.424 (1.00) |
0.449 (1.00) |
0.458 (1.00) |
0.334 (1.00) |
0.605 (1.00) |
0.398 (1.00) |
1 (1.00) |
0.662 (1.00) |
1 (1.00) |
0.627 (1.00) |
22q loss | 36 (27%) | 98 |
0.728 (1.00) |
0.769 (1.00) |
0.15 (0.922) |
0.165 (0.96) |
0.738 (1.00) |
0.293 (1.00) |
0.062 (0.725) |
0.275 (1.00) |
0.456 (1.00) |
0.732 (1.00) |
xp loss | 23 (17%) | 111 |
0.329 (1.00) |
0.732 (1.00) |
0.375 (1.00) |
0.618 (1.00) |
0.185 (0.973) |
1 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.808 (1.00) |
0.429 (1.00) |
xq loss | 23 (17%) | 111 |
0.329 (1.00) |
0.922 (1.00) |
0.5 (1.00) |
0.405 (1.00) |
0.18 (0.973) |
0.526 (1.00) |
1 (1.00) |
0.434 (1.00) |
0.808 (1.00) |
0.429 (1.00) |
P value = 0.00441 (Fisher's exact test), Q value = 0.24
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 12 | 111 |
7Q GAIN MUTATED | 4 | 84 |
7Q GAIN WILD-TYPE | 8 | 27 |
P value = 0.000592 (Wilcoxon-test), Q value = 0.094
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
10P GAIN MUTATED | 6 | 48.3 (10.7) |
10P GAIN WILD-TYPE | 128 | 31.2 (8.5) |
P value = 0.00429 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
10Q GAIN MUTATED | 10 | 41.6 (12.2) |
10Q GAIN WILD-TYPE | 124 | 31.2 (8.6) |
P value = 0.00021 (Wilcoxon-test), Q value = 0.079
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
15Q GAIN MUTATED | 48 | 35.9 (10.1) |
15Q GAIN WILD-TYPE | 86 | 29.8 (8.1) |
P value = 0.00146 (Wilcoxon-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
19P GAIN MUTATED | 34 | 35.6 (8.4) |
19P GAIN WILD-TYPE | 100 | 30.8 (9.3) |
P value = 0.00104 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
19Q GAIN MUTATED | 27 | 36.3 (8.3) |
19Q GAIN WILD-TYPE | 107 | 30.9 (9.3) |
P value = 0.00322 (Fisher's exact test), Q value = 0.2
nPatients | T1 | T2 | T3 |
---|---|---|---|
ALL | 76 | 51 | 6 |
20P GAIN MUTATED | 10 | 18 | 3 |
20P GAIN WILD-TYPE | 66 | 33 | 3 |
P value = 0.00109 (Wilcoxon-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
10P LOSS MUTATED | 68 | 29.6 (8.6) |
10P LOSS WILD-TYPE | 66 | 34.4 (9.4) |
P value = 0.00201 (Wilcoxon-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
10Q LOSS MUTATED | 62 | 29.6 (8.9) |
10Q LOSS WILD-TYPE | 72 | 34.1 (9.2) |
P value = 0.000628 (Wilcoxon-test), Q value = 0.094
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
14Q LOSS MUTATED | 17 | 25.4 (5.7) |
14Q LOSS WILD-TYPE | 117 | 32.9 (9.4) |
P value = 0.00182 (Fisher's exact test), Q value = 0.14
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
19P LOSS MUTATED | 15 | 2 | 2 | 3 | 3 | 4 | 0 | 0 | 0 | 0 | 4 | 3 |
19P LOSS WILD-TYPE | 31 | 16 | 24 | 8 | 1 | 2 | 1 | 1 | 2 | 1 | 2 | 2 |
P value = 0.00175 (Wilcoxon-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 134 | 32.0 (9.3) |
19Q LOSS MUTATED | 42 | 29.0 (10.1) |
19Q LOSS WILD-TYPE | 92 | 33.4 (8.6) |
P value = 0.00033 (Fisher's exact test), Q value = 0.082
nPatients | IS | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 46 | 18 | 26 | 11 | 4 | 6 | 1 | 1 | 2 | 1 | 6 | 5 |
19Q LOSS MUTATED | 16 | 2 | 2 | 3 | 4 | 4 | 0 | 0 | 1 | 0 | 4 | 3 |
19Q LOSS WILD-TYPE | 30 | 16 | 24 | 8 | 0 | 2 | 1 | 1 | 1 | 1 | 2 | 2 |
P value = 0.000193 (Fisher's exact test), Q value = 0.079
nPatients | NO | YES |
---|---|---|
ALL | 111 | 21 |
19Q LOSS MUTATED | 42 | 0 |
19Q LOSS WILD-TYPE | 69 | 21 |
-
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/TGCT-TP/22533661/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/TGCT-TP/22507091/TGCT-TP.merged_data.txt
-
Number of patients = 134
-
Number of significantly arm-level cnvs = 75
-
Number of selected clinical features = 10
-
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.