This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 80 arm-level events and 11 clinical features across 165 patients, no significant finding detected with Q value < 0.25.
-
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 |
HISTOLOGICAL TYPE |
RESIDUAL TUMOR |
NUMBER OF LYMPH NODES |
||
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 | Fisher's exact test | Fisher's exact test | Wilcoxon-test | |
1p gain | 12 (7%) | 153 |
0.144 (0.823) |
0.564 (0.996) |
0.157 (0.827) |
0.0264 (0.582) |
0.443 (0.996) |
1 (1.00) |
0.774 (1.00) |
0.648 (0.996) |
0.0483 (0.662) |
0.217 (0.881) |
0.588 (0.996) |
1q gain | 33 (20%) | 132 |
0.463 (0.996) |
0.61 (0.996) |
0.297 (0.942) |
0.00306 (0.444) |
0.275 (0.919) |
0.785 (1.00) |
0.33 (0.98) |
0.135 (0.814) |
0.283 (0.933) |
0.559 (0.996) |
0.0587 (0.716) |
2p gain | 40 (24%) | 125 |
0.497 (0.996) |
0.674 (0.997) |
0.518 (0.996) |
0.386 (0.996) |
0.159 (0.827) |
0.432 (0.996) |
0.0187 (0.542) |
0.593 (0.996) |
0.0395 (0.648) |
0.0864 (0.73) |
0.941 (1.00) |
2q gain | 41 (25%) | 124 |
0.994 (1.00) |
0.787 (1.00) |
0.667 (0.997) |
0.257 (0.9) |
0.168 (0.833) |
0.445 (0.996) |
0.0311 (0.588) |
0.42 (0.996) |
0.0222 (0.542) |
0.148 (0.827) |
0.97 (1.00) |
3p gain | 27 (16%) | 138 |
0.257 (0.9) |
0.819 (1.00) |
0.192 (0.879) |
0.848 (1.00) |
0.411 (0.996) |
0.226 (0.887) |
0.533 (0.996) |
0.525 (0.996) |
0.698 (1.00) |
0.885 (1.00) |
0.198 (0.881) |
3q gain | 33 (20%) | 132 |
0.444 (0.996) |
0.903 (1.00) |
0.373 (0.996) |
0.856 (1.00) |
0.427 (0.996) |
0.399 (0.996) |
0.33 (0.98) |
0.558 (0.996) |
0.305 (0.949) |
0.717 (1.00) |
0.296 (0.942) |
4p gain | 9 (5%) | 156 |
0.558 (0.996) |
0.914 (1.00) |
0.746 (1.00) |
0.554 (0.996) |
0.245 (0.898) |
1 (1.00) |
0.18 (0.852) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0286 (0.588) |
4q gain | 5 (3%) | 160 |
0.962 (1.00) |
0.857 (1.00) |
0.803 (1.00) |
1 (1.00) |
0.707 (1.00) |
0.59 (0.996) |
0.0626 (0.716) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.447 (0.996) |
5p gain | 35 (21%) | 130 |
0.748 (1.00) |
0.772 (1.00) |
0.547 (0.996) |
0.234 (0.892) |
0.582 (0.996) |
0.588 (0.996) |
0.13 (0.813) |
0.25 (0.898) |
0.0734 (0.716) |
0.359 (0.996) |
0.401 (0.996) |
5q gain | 24 (15%) | 141 |
0.653 (0.996) |
0.936 (1.00) |
0.168 (0.833) |
0.602 (0.996) |
0.298 (0.942) |
0.757 (1.00) |
0.386 (0.996) |
0.315 (0.966) |
0.22 (0.881) |
0.541 (0.996) |
0.2 (0.881) |
6p gain | 40 (24%) | 125 |
0.0655 (0.716) |
0.571 (0.996) |
0.158 (0.827) |
0.256 (0.9) |
0.0314 (0.588) |
0.0611 (0.716) |
0.467 (0.996) |
0.396 (0.996) |
0.189 (0.873) |
0.826 (1.00) |
0.045 (0.648) |
6q gain | 35 (21%) | 130 |
0.346 (0.995) |
0.873 (1.00) |
0.00831 (0.444) |
0.445 (0.996) |
0.0202 (0.542) |
0.00857 (0.444) |
0.45 (0.996) |
0.545 (0.996) |
0.0721 (0.716) |
0.216 (0.881) |
0.0417 (0.648) |
7p gain | 102 (62%) | 63 |
0.502 (0.996) |
0.628 (0.996) |
0.107 (0.791) |
0.41 (0.996) |
0.133 (0.813) |
0.649 (0.996) |
0.63 (0.996) |
1 (1.00) |
0.00466 (0.444) |
0.385 (0.996) |
0.0374 (0.643) |
7q gain | 87 (53%) | 78 |
0.564 (0.996) |
0.47 (0.996) |
0.005 (0.444) |
0.528 (0.996) |
0.0489 (0.662) |
0.268 (0.903) |
0.535 (0.996) |
0.468 (0.996) |
0.0068 (0.444) |
0.199 (0.881) |
0.0792 (0.716) |
8p gain | 40 (24%) | 125 |
0.953 (1.00) |
0.98 (1.00) |
0.0638 (0.716) |
0.245 (0.898) |
0.382 (0.996) |
0.291 (0.942) |
0.716 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.112 (0.805) |
0.338 (0.989) |
8q gain | 90 (55%) | 75 |
0.0428 (0.648) |
0.529 (0.996) |
0.00629 (0.444) |
0.151 (0.827) |
0.103 (0.791) |
0.0728 (0.716) |
0.877 (1.00) |
0.813 (1.00) |
0.0855 (0.73) |
0.0193 (0.542) |
0.163 (0.827) |
9p gain | 43 (26%) | 122 |
0.105 (0.791) |
0.218 (0.881) |
0.483 (0.996) |
0.851 (1.00) |
0.718 (1.00) |
0.617 (0.996) |
1 (1.00) |
0.589 (0.996) |
0.331 (0.98) |
0.426 (0.996) |
0.991 (1.00) |
9q gain | 35 (21%) | 130 |
0.351 (0.996) |
0.131 (0.813) |
0.105 (0.791) |
0.967 (1.00) |
0.902 (1.00) |
0.786 (1.00) |
0.706 (1.00) |
0.565 (0.996) |
0.478 (0.996) |
0.808 (1.00) |
0.659 (0.997) |
10p gain | 12 (7%) | 153 |
0.893 (1.00) |
0.91 (1.00) |
0.925 (1.00) |
0.578 (0.996) |
0.726 (1.00) |
0.691 (1.00) |
0.774 (1.00) |
0.607 (0.996) |
0.601 (0.996) |
1 (1.00) |
0.4 (0.996) |
10q gain | 7 (4%) | 158 |
0.724 (1.00) |
0.51 (0.996) |
0.709 (1.00) |
0.682 (1.00) |
0.876 (1.00) |
1 (1.00) |
0.25 (0.898) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.993 (1.00) |
11p gain | 32 (19%) | 133 |
0.147 (0.827) |
0.469 (0.996) |
0.998 (1.00) |
0.57 (0.996) |
0.72 (1.00) |
0.785 (1.00) |
0.845 (1.00) |
0.763 (1.00) |
0.0724 (0.716) |
1 (1.00) |
0.296 (0.942) |
11q gain | 27 (16%) | 138 |
0.093 (0.765) |
0.123 (0.813) |
0.921 (1.00) |
0.401 (0.996) |
0.559 (0.996) |
0.242 (0.898) |
1 (1.00) |
0.737 (1.00) |
0.127 (0.813) |
0.794 (1.00) |
0.234 (0.892) |
12p gain | 33 (20%) | 132 |
0.895 (1.00) |
0.421 (0.996) |
0.781 (1.00) |
0.376 (0.996) |
0.361 (0.996) |
0.415 (0.996) |
0.699 (1.00) |
0.0727 (0.716) |
0.298 (0.942) |
0.397 (0.996) |
0.524 (0.996) |
12q gain | 21 (13%) | 144 |
0.454 (0.996) |
0.281 (0.929) |
0.958 (1.00) |
0.206 (0.881) |
0.429 (0.996) |
1 (1.00) |
0.641 (0.996) |
0.467 (0.996) |
1 (1.00) |
0.853 (1.00) |
0.246 (0.898) |
13q gain | 114 (69%) | 51 |
0.729 (1.00) |
0.715 (1.00) |
0.259 (0.9) |
0.158 (0.827) |
0.0143 (0.526) |
0.814 (1.00) |
0.404 (0.996) |
0.3 (0.942) |
0.000486 (0.292) |
0.955 (1.00) |
0.0106 (0.519) |
14q gain | 8 (5%) | 157 |
0.457 (0.996) |
0.894 (1.00) |
0.721 (1.00) |
1 (1.00) |
0.399 (0.996) |
1 (1.00) |
0.472 (0.996) |
0.566 (0.996) |
1 (1.00) |
1 (1.00) |
0.628 (0.996) |
15q gain | 4 (2%) | 161 |
0.114 (0.808) |
0.518 (0.996) |
0.343 (0.995) |
0.0987 (0.782) |
0.177 (0.844) |
1 (1.00) |
0.335 (0.985) |
0.392 (0.996) |
0.0339 (0.621) |
1 (1.00) |
0.526 (0.996) |
16p gain | 41 (25%) | 124 |
0.259 (0.9) |
0.777 (1.00) |
0.121 (0.813) |
0.734 (1.00) |
0.272 (0.914) |
0.798 (1.00) |
1 (1.00) |
0.411 (0.996) |
0.0222 (0.542) |
0.393 (0.996) |
0.276 (0.919) |
16q gain | 41 (25%) | 124 |
0.97 (1.00) |
0.853 (1.00) |
0.409 (0.996) |
0.958 (1.00) |
0.128 (0.813) |
0.291 (0.942) |
0.857 (1.00) |
1 (1.00) |
0.0222 (0.542) |
0.623 (0.996) |
0.2 (0.881) |
17p gain | 10 (6%) | 155 |
0.22 (0.881) |
0.927 (1.00) |
0.537 (0.996) |
0.0161 (0.526) |
0.418 (0.996) |
0.638 (0.996) |
0.754 (1.00) |
1 (1.00) |
0.585 (0.996) |
0.714 (1.00) |
1 (1.00) |
17q gain | 31 (19%) | 134 |
0.514 (0.996) |
0.777 (1.00) |
0.915 (1.00) |
0.799 (1.00) |
0.177 (0.844) |
0.162 (0.827) |
0.691 (1.00) |
0.764 (1.00) |
0.466 (0.996) |
0.518 (0.996) |
0.65 (0.996) |
18p gain | 8 (5%) | 157 |
0.127 (0.813) |
0.425 (0.996) |
0.151 (0.827) |
0.373 (0.996) |
0.496 (0.996) |
1 (1.00) |
0.727 (1.00) |
0.0446 (0.648) |
0.131 (0.813) |
0.152 (0.827) |
0.238 (0.893) |
18q gain | 6 (4%) | 159 |
0.0546 (0.696) |
0.391 (0.996) |
0.127 (0.813) |
0.162 (0.827) |
0.0854 (0.73) |
0.509 (0.996) |
0.219 (0.881) |
0.0247 (0.558) |
0.406 (0.996) |
0.0477 (0.662) |
0.0288 (0.588) |
19p gain | 33 (20%) | 132 |
0.634 (0.996) |
0.732 (1.00) |
0.816 (1.00) |
0.344 (0.995) |
0.812 (1.00) |
0.588 (0.996) |
0.559 (0.996) |
0.76 (1.00) |
0.0718 (0.716) |
0.497 (0.996) |
0.854 (1.00) |
19q gain | 33 (20%) | 132 |
0.226 (0.887) |
0.672 (0.997) |
0.833 (1.00) |
0.336 (0.985) |
0.87 (1.00) |
0.279 (0.928) |
0.559 (0.996) |
0.525 (0.996) |
0.0718 (0.716) |
0.262 (0.9) |
0.802 (1.00) |
20p gain | 105 (64%) | 60 |
0.762 (1.00) |
0.525 (0.996) |
0.0146 (0.526) |
0.5 (0.996) |
0.416 (0.996) |
0.249 (0.898) |
0.33 (0.98) |
0.607 (0.996) |
0.0672 (0.716) |
0.511 (0.996) |
0.46 (0.996) |
20q gain | 146 (88%) | 19 |
0.479 (0.996) |
0.235 (0.892) |
0.207 (0.881) |
0.602 (0.996) |
0.038 (0.643) |
0.308 (0.956) |
1 (1.00) |
0.723 (1.00) |
0.000663 (0.292) |
0.184 (0.859) |
0.162 (0.827) |
21q gain | 10 (6%) | 155 |
0.788 (1.00) |
0.482 (0.996) |
0.561 (0.996) |
0.741 (1.00) |
0.904 (1.00) |
0.638 (0.996) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.674 (0.997) |
0.913 (1.00) |
22q gain | 9 (5%) | 156 |
0.197 (0.881) |
0.858 (1.00) |
0.583 (0.996) |
0.699 (1.00) |
0.391 (0.996) |
1 (1.00) |
1 (1.00) |
0.594 (0.996) |
1 (1.00) |
0.624 (0.996) |
0.346 (0.995) |
xp gain | 31 (19%) | 134 |
0.48 (0.996) |
0.566 (0.996) |
0.353 (0.996) |
0.299 (0.942) |
0.083 (0.73) |
0.138 (0.82) |
0.32 (0.975) |
0.362 (0.996) |
0.13 (0.813) |
0.264 (0.9) |
0.459 (0.996) |
xq gain | 32 (19%) | 133 |
0.965 (1.00) |
0.553 (0.996) |
0.868 (1.00) |
0.125 (0.813) |
0.35 (0.996) |
0.399 (0.996) |
0.432 (0.996) |
0.365 (0.996) |
0.465 (0.996) |
0.855 (1.00) |
0.5 (0.996) |
1p loss | 46 (28%) | 119 |
0.481 (0.996) |
0.549 (0.996) |
0.838 (1.00) |
0.712 (1.00) |
0.587 (0.996) |
0.808 (1.00) |
0.489 (0.996) |
0.433 (0.996) |
0.0203 (0.542) |
0.883 (1.00) |
0.341 (0.993) |
1q loss | 28 (17%) | 137 |
0.526 (0.996) |
0.476 (0.996) |
0.669 (0.997) |
0.598 (0.996) |
0.816 (1.00) |
0.545 (0.996) |
0.145 (0.823) |
0.752 (1.00) |
0.127 (0.813) |
0.618 (0.996) |
0.922 (1.00) |
2p loss | 11 (7%) | 154 |
0.534 (0.996) |
0.00649 (0.444) |
0.642 (0.996) |
0.648 (0.996) |
0.494 (0.996) |
1 (1.00) |
0.756 (1.00) |
0.648 (0.996) |
0.585 (0.996) |
0.718 (1.00) |
0.263 (0.9) |
2q loss | 7 (4%) | 158 |
0.248 (0.898) |
0.0611 (0.716) |
0.551 (0.996) |
1 (1.00) |
0.134 (0.813) |
0.598 (0.996) |
0.704 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.176 (0.844) |
3p loss | 15 (9%) | 150 |
0.0507 (0.676) |
0.673 (0.997) |
0.106 (0.791) |
0.189 (0.873) |
0.142 (0.823) |
0.00454 (0.444) |
0.0544 (0.696) |
0.416 (0.996) |
0.0758 (0.716) |
0.0124 (0.526) |
0.0515 (0.677) |
3q loss | 10 (6%) | 155 |
0.0689 (0.716) |
0.516 (0.996) |
0.141 (0.823) |
0.418 (0.996) |
0.168 (0.833) |
0.0236 (0.55) |
0.11 (0.797) |
0.625 (0.996) |
0.00277 (0.444) |
0.0205 (0.542) |
0.0786 (0.716) |
4p loss | 60 (36%) | 105 |
0.134 (0.813) |
0.799 (1.00) |
0.573 (0.996) |
0.769 (1.00) |
0.322 (0.976) |
0.82 (1.00) |
0.629 (0.996) |
0.209 (0.881) |
0.77 (1.00) |
0.396 (0.996) |
0.155 (0.827) |
4q loss | 67 (41%) | 98 |
0.0871 (0.73) |
0.715 (1.00) |
0.437 (0.996) |
0.713 (1.00) |
0.573 (0.996) |
0.649 (0.996) |
0.427 (0.996) |
0.624 (0.996) |
0.567 (0.996) |
0.217 (0.881) |
0.408 (0.996) |
5p loss | 27 (16%) | 138 |
0.665 (0.997) |
0.982 (1.00) |
0.982 (1.00) |
0.866 (1.00) |
0.591 (0.996) |
1 (1.00) |
0.145 (0.823) |
1 (1.00) |
0.698 (1.00) |
1 (1.00) |
0.432 (0.996) |
5q loss | 40 (24%) | 125 |
0.649 (0.996) |
0.145 (0.823) |
0.603 (0.996) |
0.685 (1.00) |
1 (1.00) |
0.61 (0.996) |
0.589 (0.996) |
0.401 (0.996) |
0.189 (0.873) |
0.568 (0.996) |
0.759 (1.00) |
6p loss | 14 (8%) | 151 |
0.0372 (0.643) |
0.928 (1.00) |
0.0921 (0.764) |
0.381 (0.996) |
0.0238 (0.55) |
1 (1.00) |
0.786 (1.00) |
0.111 (0.797) |
0.0758 (0.716) |
0.33 (0.98) |
0.456 (0.996) |
6q loss | 23 (14%) | 142 |
0.987 (1.00) |
0.605 (0.996) |
0.12 (0.813) |
0.325 (0.98) |
0.068 (0.716) |
1 (1.00) |
0.268 (0.903) |
0.103 (0.791) |
0.0159 (0.526) |
0.777 (1.00) |
0.672 (0.997) |
7q loss | 3 (2%) | 162 |
0.538 (0.996) |
0.227 (0.887) |
0.951 (1.00) |
0.675 (0.997) |
0.43 (0.996) |
1 (1.00) |
0.595 (0.996) |
0.392 (0.996) |
0.227 (0.887) |
1 (1.00) |
0.126 (0.813) |
8p loss | 75 (45%) | 90 |
0.064 (0.716) |
0.152 (0.827) |
0.719 (1.00) |
0.841 (1.00) |
0.163 (0.827) |
1 (1.00) |
0.642 (0.996) |
1 (1.00) |
0.773 (1.00) |
0.956 (1.00) |
0.0446 (0.648) |
8q loss | 10 (6%) | 155 |
0.883 (1.00) |
0.808 (1.00) |
0.755 (1.00) |
0.201 (0.881) |
0.828 (1.00) |
1 (1.00) |
0.00194 (0.444) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.718 (1.00) |
9p loss | 23 (14%) | 142 |
0.251 (0.898) |
0.643 (0.996) |
0.117 (0.813) |
0.0969 (0.775) |
1 (1.00) |
0.0608 (0.716) |
0.507 (0.996) |
0.723 (1.00) |
1 (1.00) |
0.00564 (0.444) |
0.489 (0.996) |
9q loss | 23 (14%) | 142 |
0.472 (0.996) |
0.6 (0.996) |
0.511 (0.996) |
0.0469 (0.662) |
0.697 (1.00) |
0.213 (0.881) |
0.507 (0.996) |
1 (1.00) |
1 (1.00) |
0.00811 (0.444) |
0.842 (1.00) |
10p loss | 34 (21%) | 131 |
0.0155 (0.526) |
0.00343 (0.444) |
0.426 (0.996) |
0.705 (1.00) |
0.736 (1.00) |
0.291 (0.942) |
0.567 (0.996) |
0.0369 (0.643) |
0.0294 (0.588) |
0.181 (0.854) |
0.255 (0.9) |
10q loss | 38 (23%) | 127 |
0.0699 (0.716) |
0.0428 (0.648) |
0.447 (0.996) |
0.802 (1.00) |
1 (1.00) |
0.0668 (0.716) |
0.458 (0.996) |
0.0212 (0.542) |
0.0786 (0.716) |
0.159 (0.827) |
0.618 (0.996) |
11p loss | 24 (15%) | 141 |
0.938 (1.00) |
0.609 (0.996) |
0.118 (0.813) |
0.198 (0.881) |
0.173 (0.842) |
0.529 (0.996) |
1 (1.00) |
0.167 (0.833) |
0.0846 (0.73) |
0.401 (0.996) |
0.0161 (0.526) |
11q loss | 30 (18%) | 135 |
0.717 (1.00) |
0.746 (1.00) |
0.725 (1.00) |
0.511 (0.996) |
0.963 (1.00) |
0.0797 (0.716) |
1 (1.00) |
0.227 (0.887) |
0.0404 (0.648) |
0.319 (0.974) |
0.688 (1.00) |
12p loss | 23 (14%) | 142 |
0.086 (0.73) |
0.513 (0.996) |
0.489 (0.996) |
0.576 (0.996) |
0.634 (0.996) |
0.749 (1.00) |
0.653 (0.996) |
0.737 (1.00) |
0.217 (0.881) |
1 (1.00) |
0.522 (0.996) |
12q loss | 24 (15%) | 141 |
0.209 (0.881) |
0.142 (0.823) |
0.265 (0.9) |
0.849 (1.00) |
1 (1.00) |
0.757 (1.00) |
0.665 (0.997) |
0.505 (0.996) |
0.694 (1.00) |
1 (1.00) |
0.673 (0.997) |
13q loss | 6 (4%) | 159 |
0.301 (0.942) |
0.764 (1.00) |
0.335 (0.985) |
0.738 (1.00) |
0.736 (1.00) |
1 (1.00) |
0.416 (0.996) |
0.109 (0.797) |
0.077 (0.716) |
0.5 (0.996) |
0.726 (1.00) |
14q loss | 67 (41%) | 98 |
0.41 (0.996) |
0.858 (1.00) |
0.548 (0.996) |
0.663 (0.997) |
0.228 (0.887) |
0.824 (1.00) |
0.427 (0.996) |
0.215 (0.881) |
0.0155 (0.526) |
0.21 (0.881) |
0.716 (1.00) |
15q loss | 72 (44%) | 93 |
0.742 (1.00) |
0.954 (1.00) |
0.42 (0.996) |
0.424 (0.996) |
0.408 (0.996) |
1 (1.00) |
0.21 (0.881) |
0.633 (0.996) |
0.778 (1.00) |
0.882 (1.00) |
0.0777 (0.716) |
16p loss | 9 (5%) | 156 |
0.865 (1.00) |
0.373 (0.996) |
0.291 (0.942) |
0.37 (0.996) |
0.0945 (0.768) |
1 (1.00) |
0.734 (1.00) |
1 (1.00) |
0.503 (0.996) |
1 (1.00) |
0.795 (1.00) |
16q loss | 14 (8%) | 151 |
0.646 (0.996) |
0.531 (0.996) |
0.625 (0.996) |
0.909 (1.00) |
0.0144 (0.526) |
0.694 (1.00) |
0.786 (1.00) |
0.416 (0.996) |
1 (1.00) |
0.752 (1.00) |
0.962 (1.00) |
17p loss | 105 (64%) | 60 |
0.653 (0.996) |
0.125 (0.813) |
0.658 (0.997) |
0.0415 (0.648) |
0.843 (1.00) |
1 (1.00) |
0.42 (0.996) |
0.62 (0.996) |
0.23 (0.888) |
0.811 (1.00) |
0.925 (1.00) |
17q loss | 28 (17%) | 137 |
0.866 (1.00) |
0.945 (1.00) |
0.45 (0.996) |
0.63 (0.996) |
0.576 (0.996) |
0.767 (1.00) |
0.299 (0.942) |
0.76 (1.00) |
1 (1.00) |
0.172 (0.842) |
0.515 (0.996) |
18p loss | 128 (78%) | 37 |
0.206 (0.881) |
0.413 (0.996) |
0.63 (0.996) |
0.356 (0.996) |
0.635 (0.996) |
0.107 (0.791) |
1 (1.00) |
0.771 (1.00) |
0.0294 (0.588) |
0.737 (1.00) |
0.467 (0.996) |
18q loss | 138 (84%) | 27 |
0.372 (0.996) |
0.263 (0.9) |
0.668 (0.997) |
0.0951 (0.768) |
0.757 (1.00) |
0.127 (0.813) |
0.674 (0.997) |
0.315 (0.966) |
0.432 (0.996) |
0.723 (1.00) |
0.54 (0.996) |
19p loss | 24 (15%) | 141 |
0.674 (0.997) |
0.846 (1.00) |
0.171 (0.842) |
0.779 (1.00) |
0.492 (0.996) |
0.536 (0.996) |
0.825 (1.00) |
0.304 (0.949) |
0.217 (0.881) |
1 (1.00) |
0.176 (0.844) |
19q loss | 22 (13%) | 143 |
0.863 (1.00) |
0.444 (0.996) |
0.265 (0.9) |
0.73 (1.00) |
0.463 (0.996) |
0.529 (0.996) |
0.492 (0.996) |
0.737 (1.00) |
0.374 (0.996) |
0.509 (0.996) |
0.645 (0.996) |
20p loss | 24 (15%) | 141 |
0.328 (0.98) |
0.5 (0.996) |
0.0311 (0.588) |
0.578 (0.996) |
0.588 (0.996) |
0.531 (0.996) |
1 (1.00) |
0.243 (0.898) |
1 (1.00) |
0.508 (0.996) |
0.796 (1.00) |
21q loss | 68 (41%) | 97 |
0.97 (1.00) |
0.491 (0.996) |
0.638 (0.996) |
0.159 (0.827) |
0.232 (0.89) |
0.258 (0.9) |
0.636 (0.996) |
0.62 (0.996) |
0.242 (0.898) |
0.237 (0.893) |
0.216 (0.881) |
22q loss | 58 (35%) | 107 |
0.25 (0.898) |
0.102 (0.791) |
0.539 (0.996) |
0.469 (0.996) |
0.00777 (0.444) |
0.645 (0.996) |
0.871 (1.00) |
0.802 (1.00) |
1 (1.00) |
0.877 (1.00) |
0.151 (0.827) |
xp loss | 28 (17%) | 137 |
0.66 (0.997) |
0.806 (1.00) |
0.648 (0.996) |
0.294 (0.942) |
0.136 (0.814) |
1 (1.00) |
0.411 (0.996) |
0.315 (0.966) |
0.23 (0.888) |
0.791 (1.00) |
0.208 (0.881) |
xq loss | 26 (16%) | 139 |
0.793 (1.00) |
0.872 (1.00) |
0.661 (0.997) |
0.0596 (0.716) |
0.561 (0.996) |
0.545 (0.996) |
0.207 (0.881) |
0.489 (0.996) |
0.432 (0.996) |
0.539 (0.996) |
0.408 (0.996) |
-
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/READ-TP/22532765/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/READ-TP/22507018/READ-TP.merged_data.txt
-
Number of patients = 165
-
Number of significantly arm-level cnvs = 80
-
Number of selected clinical features = 11
-
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.