This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 81 arm-level events and 13 clinical features across 441 patients, 9 significant findings detected with Q value < 0.25.
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6p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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6q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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15q gain cnv correlated to 'RACE'.
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20q gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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5q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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8p loss cnv correlated to 'GENDER' and 'NUMBER_OF_LYMPH_NODES'.
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8q loss cnv correlated to 'PATHOLOGY_T_STAGE'.
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19p loss cnv correlated to 'HISTOLOGICAL_TYPE'.
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 |
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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
8p loss | 91 (21%) | 350 |
0.829 (1.00) |
0.676 (0.974) |
0.0313 (0.547) |
0.161 (0.732) |
0.0104 (0.324) |
0.644 (0.968) |
0.000856 (0.205) |
0.43 (0.92) |
0.0185 (0.424) |
0.253 (0.809) |
0.00113 (0.205) |
0.314 (0.866) |
0.223 (0.8) |
6p gain | 81 (18%) | 360 |
0.158 (0.732) |
0.456 (0.922) |
0.531 (0.932) |
0.172 (0.734) |
0.788 (0.988) |
1 (1.00) |
0.799 (0.988) |
0.517 (0.928) |
0.00117 (0.205) |
0.302 (0.852) |
0.908 (1.00) |
0.0382 (0.547) |
0.248 (0.809) |
6q gain | 66 (15%) | 375 |
0.0168 (0.403) |
0.771 (0.988) |
0.18 (0.737) |
0.175 (0.734) |
0.995 (1.00) |
0.413 (0.919) |
1 (1.00) |
0.862 (1.00) |
0.00164 (0.216) |
0.313 (0.866) |
0.868 (1.00) |
0.0166 (0.403) |
0.163 (0.732) |
15q gain | 39 (9%) | 402 |
0.0776 (0.621) |
0.624 (0.963) |
0.573 (0.94) |
0.785 (0.988) |
0.0726 (0.621) |
0.175 (0.734) |
0.601 (0.944) |
1 (1.00) |
0.539 (0.932) |
0.00331 (0.274) |
0.205 (0.771) |
0.00194 (0.227) |
1 (1.00) |
20q gain | 280 (63%) | 161 |
0.47 (0.922) |
0.414 (0.919) |
0.457 (0.922) |
0.159 (0.732) |
0.0893 (0.653) |
0.169 (0.734) |
0.00384 (0.274) |
0.233 (0.8) |
5e-05 (0.0526) |
0.3 (0.85) |
0.401 (0.919) |
0.744 (0.982) |
0.657 (0.969) |
5q loss | 108 (24%) | 333 |
0.0427 (0.547) |
0.24 (0.801) |
0.00945 (0.302) |
0.607 (0.95) |
0.0784 (0.621) |
0.382 (0.901) |
0.908 (1.00) |
1 (1.00) |
0.00012 (0.0632) |
0.424 (0.919) |
0.256 (0.811) |
0.114 (0.711) |
0.343 (0.881) |
8q loss | 37 (8%) | 404 |
0.859 (1.00) |
0.883 (1.00) |
0.186 (0.742) |
0.00161 (0.216) |
0.297 (0.847) |
0.734 (0.982) |
0.0728 (0.621) |
0.487 (0.923) |
0.235 (0.8) |
0.141 (0.732) |
0.0612 (0.592) |
0.0463 (0.554) |
1 (1.00) |
19p loss | 116 (26%) | 325 |
0.078 (0.621) |
0.234 (0.8) |
0.915 (1.00) |
0.936 (1.00) |
0.735 (0.982) |
0.521 (0.929) |
1 (1.00) |
0.774 (0.988) |
0.00045 (0.158) |
0.122 (0.725) |
0.343 (0.881) |
0.112 (0.711) |
1 (1.00) |
1p gain | 50 (11%) | 391 |
0.225 (0.8) |
0.447 (0.92) |
0.186 (0.742) |
0.203 (0.771) |
0.637 (0.965) |
0.23 (0.8) |
0.273 (0.835) |
0.23 (0.8) |
0.534 (0.932) |
0.382 (0.901) |
0.739 (0.982) |
0.873 (1.00) |
1 (1.00) |
1q gain | 105 (24%) | 336 |
0.576 (0.94) |
0.816 (0.996) |
0.514 (0.927) |
0.804 (0.988) |
0.0899 (0.653) |
0.502 (0.925) |
0.417 (0.919) |
0.137 (0.732) |
0.168 (0.734) |
0.351 (0.881) |
0.323 (0.873) |
0.221 (0.8) |
0.335 (0.879) |
2p gain | 78 (18%) | 363 |
0.32 (0.871) |
0.269 (0.835) |
0.679 (0.974) |
0.401 (0.919) |
0.407 (0.919) |
0.626 (0.963) |
0.796 (0.988) |
0.137 (0.732) |
0.0355 (0.547) |
0.299 (0.85) |
0.926 (1.00) |
0.26 (0.821) |
0.591 (0.944) |
2q gain | 66 (15%) | 375 |
0.88 (1.00) |
0.134 (0.732) |
0.269 (0.835) |
0.619 (0.962) |
0.442 (0.92) |
1 (1.00) |
0.781 (0.988) |
0.113 (0.711) |
0.146 (0.732) |
0.554 (0.938) |
0.93 (1.00) |
0.728 (0.982) |
1 (1.00) |
3p gain | 52 (12%) | 389 |
0.128 (0.732) |
0.886 (1.00) |
0.926 (1.00) |
0.921 (1.00) |
0.661 (0.971) |
0.56 (0.938) |
0.758 (0.988) |
0.56 (0.938) |
0.609 (0.952) |
1 (1.00) |
0.575 (0.94) |
0.405 (0.919) |
0.0889 (0.653) |
3q gain | 91 (21%) | 350 |
0.347 (0.881) |
0.573 (0.94) |
0.443 (0.92) |
0.371 (0.889) |
0.556 (0.938) |
0.479 (0.922) |
1 (1.00) |
0.44 (0.92) |
0.632 (0.965) |
0.652 (0.969) |
0.252 (0.809) |
0.201 (0.771) |
0.223 (0.8) |
4p gain | 21 (5%) | 420 |
0.731 (0.982) |
0.657 (0.969) |
0.0344 (0.547) |
0.287 (0.835) |
0.858 (1.00) |
1 (1.00) |
0.351 (0.881) |
0.759 (0.988) |
0.158 (0.732) |
0.368 (0.889) |
0.467 (0.922) |
1 (1.00) |
1 (1.00) |
4q gain | 16 (4%) | 425 |
0.75 (0.987) |
0.157 (0.732) |
0.342 (0.881) |
0.819 (0.997) |
0.639 (0.967) |
1 (1.00) |
0.435 (0.92) |
0.736 (0.982) |
0.0547 (0.576) |
0.711 (0.982) |
0.763 (0.988) |
1 (1.00) |
1 (1.00) |
5p gain | 100 (23%) | 341 |
0.776 (0.988) |
0.428 (0.92) |
0.874 (1.00) |
0.037 (0.547) |
0.778 (0.988) |
0.651 (0.969) |
0.906 (1.00) |
1 (1.00) |
0.00715 (0.279) |
0.981 (1.00) |
0.237 (0.8) |
0.838 (1.00) |
1 (1.00) |
5q gain | 43 (10%) | 398 |
0.625 (0.963) |
0.351 (0.881) |
0.501 (0.925) |
0.134 (0.732) |
0.761 (0.988) |
1 (1.00) |
0.504 (0.925) |
0.831 (1.00) |
0.0604 (0.592) |
0.813 (0.995) |
0.998 (1.00) |
0.939 (1.00) |
1 (1.00) |
7p gain | 202 (46%) | 239 |
0.922 (1.00) |
0.213 (0.791) |
0.778 (0.988) |
0.705 (0.982) |
0.464 (0.922) |
0.346 (0.881) |
0.111 (0.711) |
0.899 (1.00) |
0.0616 (0.592) |
0.673 (0.974) |
0.234 (0.8) |
0.307 (0.863) |
0.657 (0.969) |
7q gain | 171 (39%) | 270 |
0.687 (0.979) |
0.46 (0.922) |
0.739 (0.982) |
0.824 (1) |
0.452 (0.922) |
0.436 (0.92) |
0.154 (0.732) |
0.694 (0.982) |
0.205 (0.771) |
0.328 (0.875) |
0.31 (0.863) |
0.229 (0.8) |
0.364 (0.889) |
8p gain | 183 (41%) | 258 |
0.549 (0.938) |
0.0126 (0.357) |
0.572 (0.94) |
0.294 (0.844) |
0.539 (0.932) |
1 (1.00) |
0.00869 (0.302) |
0.796 (0.988) |
0.147 (0.732) |
0.0622 (0.592) |
0.494 (0.925) |
0.925 (1.00) |
1 (1.00) |
8q gain | 240 (54%) | 201 |
0.778 (0.988) |
0.028 (0.547) |
0.374 (0.89) |
0.285 (0.835) |
0.55 (0.938) |
0.452 (0.922) |
0.0739 (0.621) |
1 (1.00) |
0.463 (0.922) |
0.012 (0.35) |
0.764 (0.988) |
0.485 (0.923) |
0.386 (0.904) |
9p gain | 59 (13%) | 382 |
0.0368 (0.547) |
0.631 (0.965) |
0.988 (1.00) |
0.244 (0.801) |
0.959 (1.00) |
0.783 (0.988) |
0.773 (0.988) |
0.0626 (0.592) |
0.00584 (0.279) |
0.667 (0.973) |
0.888 (1.00) |
0.569 (0.94) |
0.135 (0.732) |
9q gain | 77 (17%) | 364 |
0.119 (0.721) |
0.229 (0.8) |
0.923 (1.00) |
0.331 (0.876) |
0.958 (1.00) |
0.627 (0.964) |
0.364 (0.889) |
0.0497 (0.557) |
0.0354 (0.547) |
0.417 (0.919) |
0.407 (0.919) |
1 (1.00) |
0.198 (0.771) |
10p gain | 98 (22%) | 343 |
0.324 (0.873) |
0.932 (1.00) |
0.655 (0.969) |
0.479 (0.922) |
0.724 (0.982) |
1 (1.00) |
0.551 (0.938) |
0.444 (0.92) |
0.308 (0.863) |
0.513 (0.927) |
0.78 (0.988) |
0.00636 (0.279) |
0.594 (0.944) |
10q gain | 67 (15%) | 374 |
0.739 (0.982) |
0.116 (0.714) |
0.106 (0.703) |
0.551 (0.938) |
0.2 (0.771) |
0.599 (0.944) |
0.583 (0.941) |
0.725 (0.982) |
0.425 (0.919) |
0.744 (0.982) |
0.949 (1.00) |
0.105 (0.701) |
1 (1.00) |
11p gain | 62 (14%) | 379 |
0.83 (1.00) |
0.386 (0.904) |
0.446 (0.92) |
0.248 (0.809) |
0.0706 (0.621) |
1 (1.00) |
1 (1.00) |
0.0996 (0.685) |
0.35 (0.881) |
0.423 (0.919) |
0.114 (0.711) |
0.0836 (0.63) |
0.497 (0.925) |
11q gain | 74 (17%) | 367 |
0.596 (0.944) |
0.565 (0.94) |
0.204 (0.771) |
0.633 (0.965) |
0.0353 (0.547) |
0.801 (0.988) |
0.356 (0.881) |
0.041 (0.547) |
0.121 (0.725) |
0.371 (0.889) |
0.198 (0.771) |
0.071 (0.621) |
0.549 (0.938) |
12p gain | 92 (21%) | 349 |
0.27 (0.835) |
0.397 (0.918) |
0.789 (0.988) |
0.0402 (0.547) |
0.283 (0.835) |
1 (1.00) |
0.714 (0.982) |
1 (1.00) |
0.437 (0.92) |
0.155 (0.732) |
0.534 (0.932) |
0.834 (1.00) |
0.3 (0.85) |
12q gain | 78 (18%) | 363 |
0.678 (0.974) |
0.0819 (0.625) |
0.755 (0.988) |
0.272 (0.835) |
0.0607 (0.592) |
0.804 (0.988) |
0.516 (0.928) |
0.623 (0.963) |
0.181 (0.737) |
0.653 (0.969) |
0.769 (0.988) |
0.103 (0.701) |
0.242 (0.801) |
13q gain | 153 (35%) | 288 |
0.278 (0.835) |
0.944 (1.00) |
0.734 (0.982) |
0.504 (0.925) |
0.707 (0.982) |
0.845 (1.00) |
0.175 (0.734) |
0.893 (1.00) |
0.214 (0.791) |
0.796 (0.988) |
0.34 (0.881) |
0.34 (0.881) |
0.661 (0.971) |
14q gain | 28 (6%) | 413 |
0.184 (0.742) |
0.617 (0.961) |
0.371 (0.889) |
0.875 (1.00) |
0.175 (0.734) |
0.0405 (0.547) |
0.423 (0.919) |
0.453 (0.922) |
0.473 (0.922) |
0.131 (0.732) |
0.0481 (0.557) |
0.409 (0.919) |
0.277 (0.835) |
16p gain | 58 (13%) | 383 |
0.129 (0.732) |
0.404 (0.919) |
0.0301 (0.547) |
0.526 (0.93) |
0.318 (0.867) |
0.239 (0.801) |
0.884 (1.00) |
0.56 (0.938) |
0.858 (1.00) |
0.115 (0.711) |
0.0603 (0.592) |
0.235 (0.8) |
0.506 (0.925) |
16q gain | 48 (11%) | 393 |
0.0394 (0.547) |
0.625 (0.963) |
0.17 (0.734) |
0.744 (0.982) |
0.425 (0.919) |
0.054 (0.576) |
0.752 (0.988) |
0.285 (0.835) |
0.241 (0.801) |
0.155 (0.732) |
0.0426 (0.547) |
0.173 (0.734) |
0.431 (0.92) |
17p gain | 29 (7%) | 412 |
0.346 (0.881) |
0.229 (0.8) |
0.0794 (0.621) |
0.642 (0.967) |
0.595 (0.944) |
0.0935 (0.66) |
0.69 (0.98) |
1 (1.00) |
0.0138 (0.381) |
0.0185 (0.424) |
0.784 (0.988) |
0.0568 (0.58) |
1 (1.00) |
17q gain | 64 (15%) | 377 |
0.51 (0.926) |
0.798 (0.988) |
0.157 (0.732) |
0.666 (0.973) |
0.469 (0.922) |
0.163 (0.732) |
0.324 (0.873) |
0.59 (0.944) |
0.128 (0.732) |
0.019 (0.425) |
0.945 (1.00) |
0.0437 (0.547) |
0.506 (0.925) |
18p gain | 85 (19%) | 356 |
0.0496 (0.557) |
0.0838 (0.63) |
0.555 (0.938) |
0.17 (0.734) |
0.356 (0.881) |
1 (1.00) |
0.103 (0.701) |
0.873 (1.00) |
0.0362 (0.547) |
0.733 (0.982) |
0.425 (0.919) |
0.31 (0.863) |
1 (1.00) |
18q gain | 55 (12%) | 386 |
0.288 (0.835) |
0.526 (0.93) |
0.353 (0.881) |
0.00916 (0.302) |
0.42 (0.919) |
0.767 (0.988) |
0.229 (0.8) |
0.44 (0.92) |
0.021 (0.461) |
0.804 (0.988) |
0.583 (0.941) |
0.536 (0.932) |
0.524 (0.929) |
19p gain | 53 (12%) | 388 |
0.348 (0.881) |
0.538 (0.932) |
0.726 (0.982) |
0.0806 (0.621) |
0.0649 (0.6) |
0.151 (0.732) |
1 (1.00) |
0.699 (0.982) |
0.287 (0.835) |
0.0808 (0.621) |
0.0258 (0.547) |
0.953 (1.00) |
1 (1.00) |
19q gain | 79 (18%) | 362 |
0.868 (1.00) |
0.738 (0.982) |
0.88 (1.00) |
0.18 (0.737) |
0.00469 (0.274) |
0.803 (0.988) |
0.606 (0.949) |
0.181 (0.737) |
0.726 (0.982) |
0.0916 (0.659) |
0.0151 (0.388) |
0.147 (0.732) |
0.595 (0.944) |
20p gain | 242 (55%) | 199 |
0.168 (0.734) |
0.415 (0.919) |
0.822 (0.999) |
0.375 (0.89) |
0.243 (0.801) |
0.253 (0.809) |
0.0363 (0.547) |
0.0553 (0.577) |
0.0432 (0.547) |
0.901 (1.00) |
0.421 (0.919) |
0.625 (0.963) |
0.656 (0.969) |
21q gain | 22 (5%) | 419 |
0.35 (0.881) |
0.807 (0.991) |
0.566 (0.94) |
0.332 (0.876) |
0.642 (0.967) |
1 (1.00) |
1 (1.00) |
0.548 (0.938) |
0.289 (0.835) |
0.779 (0.988) |
0.105 (0.701) |
0.815 (0.995) |
1 (1.00) |
22q gain | 32 (7%) | 409 |
0.47 (0.922) |
0.713 (0.982) |
0.289 (0.835) |
0.0526 (0.571) |
0.635 (0.965) |
1 (1.00) |
0.57 (0.94) |
0.634 (0.965) |
0.478 (0.922) |
0.962 (1.00) |
0.938 (1.00) |
0.508 (0.925) |
0.346 (0.881) |
xp gain | 51 (12%) | 390 |
0.624 (0.963) |
0.738 (0.982) |
0.0305 (0.547) |
0.392 (0.913) |
0.475 (0.922) |
0.767 (0.988) |
0.163 (0.732) |
1 (1.00) |
0.176 (0.734) |
0.785 (0.988) |
0.125 (0.732) |
0.0111 (0.335) |
1 (1.00) |
xq gain | 55 (12%) | 386 |
0.699 (0.982) |
0.978 (1.00) |
0.146 (0.732) |
0.517 (0.928) |
0.272 (0.835) |
0.4 (0.919) |
0.229 (0.8) |
0.441 (0.92) |
0.00343 (0.274) |
0.398 (0.918) |
0.0869 (0.645) |
0.0406 (0.547) |
0.488 (0.924) |
1p loss | 58 (13%) | 383 |
0.14 (0.732) |
0.872 (1.00) |
0.447 (0.92) |
0.222 (0.8) |
0.93 (1.00) |
0.0449 (0.547) |
1 (1.00) |
0.572 (0.94) |
0.0417 (0.547) |
0.00338 (0.274) |
0.73 (0.982) |
0.173 (0.734) |
1 (1.00) |
1q loss | 25 (6%) | 416 |
0.171 (0.734) |
0.997 (1.00) |
0.741 (0.982) |
0.542 (0.935) |
0.643 (0.968) |
0.063 (0.592) |
0.671 (0.974) |
1 (1.00) |
0.792 (0.988) |
0.0452 (0.547) |
0.42 (0.919) |
0.502 (0.925) |
1 (1.00) |
2p loss | 23 (5%) | 418 |
0.706 (0.982) |
0.549 (0.938) |
0.489 (0.924) |
0.579 (0.941) |
0.667 (0.973) |
0.385 (0.904) |
0.117 (0.718) |
0.411 (0.919) |
0.148 (0.732) |
0.109 (0.711) |
0.522 (0.929) |
0.572 (0.94) |
1 (1.00) |
2q loss | 30 (7%) | 411 |
0.957 (1.00) |
0.914 (1.00) |
0.782 (0.988) |
0.829 (1.00) |
0.367 (0.889) |
0.709 (0.982) |
1 (1.00) |
0.0808 (0.621) |
0.00665 (0.279) |
0.163 (0.732) |
0.489 (0.924) |
0.132 (0.732) |
1 (1.00) |
3p loss | 93 (21%) | 348 |
0.31 (0.863) |
0.537 (0.932) |
0.998 (1.00) |
0.868 (1.00) |
0.0162 (0.403) |
0.0995 (0.685) |
1 (1.00) |
1 (1.00) |
0.277 (0.835) |
0.359 (0.887) |
0.94 (1.00) |
0.879 (1.00) |
1 (1.00) |
3q loss | 56 (13%) | 385 |
0.95 (1.00) |
0.393 (0.913) |
0.651 (0.969) |
0.00705 (0.279) |
0.334 (0.877) |
0.0941 (0.66) |
0.768 (0.988) |
0.573 (0.94) |
0.138 (0.732) |
0.87 (1.00) |
0.791 (0.988) |
0.666 (0.973) |
0.497 (0.925) |
4p loss | 167 (38%) | 274 |
0.534 (0.932) |
0.397 (0.918) |
0.225 (0.8) |
0.0429 (0.547) |
0.389 (0.908) |
0.118 (0.718) |
0.759 (0.988) |
0.432 (0.92) |
0.18 (0.737) |
0.988 (1.00) |
0.203 (0.771) |
0.73 (0.982) |
1 (1.00) |
4q loss | 165 (37%) | 276 |
0.153 (0.732) |
0.135 (0.732) |
0.329 (0.876) |
0.13 (0.732) |
0.276 (0.835) |
0.243 (0.801) |
0.758 (0.988) |
0.793 (0.988) |
0.143 (0.732) |
0.873 (1.00) |
0.104 (0.701) |
0.856 (1.00) |
1 (1.00) |
5p loss | 63 (14%) | 378 |
0.00404 (0.274) |
0.122 (0.725) |
0.149 (0.732) |
0.176 (0.734) |
0.0943 (0.66) |
1 (1.00) |
0.777 (0.988) |
0.477 (0.922) |
0.0739 (0.621) |
0.783 (0.988) |
0.368 (0.889) |
0.0443 (0.547) |
1 (1.00) |
6p loss | 50 (11%) | 391 |
0.48 (0.922) |
0.998 (1.00) |
0.499 (0.925) |
0.345 (0.881) |
0.649 (0.969) |
0.76 (0.988) |
0.273 (0.835) |
1 (1.00) |
0.074 (0.621) |
0.504 (0.925) |
0.975 (1.00) |
0.79 (0.988) |
1 (1.00) |
6q loss | 69 (16%) | 372 |
0.325 (0.873) |
0.432 (0.92) |
0.594 (0.944) |
0.161 (0.732) |
0.414 (0.919) |
0.285 (0.835) |
0.22 (0.8) |
1 (1.00) |
0.0775 (0.621) |
0.707 (0.982) |
0.417 (0.919) |
0.508 (0.925) |
1 (1.00) |
7p loss | 17 (4%) | 424 |
0.695 (0.982) |
0.635 (0.965) |
0.728 (0.982) |
0.159 (0.732) |
0.0391 (0.547) |
1 (1.00) |
0.317 (0.867) |
0.318 (0.867) |
0.458 (0.922) |
0.925 (1.00) |
0.287 (0.835) |
0.158 (0.732) |
1 (1.00) |
7q loss | 29 (7%) | 412 |
0.678 (0.974) |
0.16 (0.732) |
0.221 (0.8) |
0.0147 (0.388) |
0.0361 (0.547) |
0.709 (0.982) |
0.69 (0.98) |
0.799 (0.988) |
0.212 (0.788) |
0.915 (1.00) |
0.474 (0.922) |
0.289 (0.835) |
1 (1.00) |
9p loss | 149 (34%) | 292 |
0.181 (0.737) |
0.092 (0.659) |
0.649 (0.969) |
0.834 (1.00) |
0.328 (0.875) |
0.694 (0.982) |
0.601 (0.944) |
0.788 (0.988) |
0.0391 (0.547) |
0.523 (0.929) |
0.185 (0.742) |
0.282 (0.835) |
0.661 (0.971) |
9q loss | 104 (24%) | 337 |
0.173 (0.734) |
0.414 (0.919) |
0.746 (0.983) |
0.606 (0.949) |
0.758 (0.988) |
1 (1.00) |
0.484 (0.923) |
0.765 (0.988) |
0.36 (0.887) |
0.82 (0.997) |
0.113 (0.711) |
0.182 (0.737) |
1 (1.00) |
10p loss | 64 (15%) | 377 |
0.191 (0.753) |
0.839 (1.00) |
0.206 (0.771) |
0.331 (0.876) |
0.0695 (0.621) |
0.599 (0.944) |
0.481 (0.922) |
0.111 (0.711) |
0.147 (0.732) |
0.574 (0.94) |
0.00717 (0.279) |
0.24 (0.801) |
0.524 (0.929) |
10q loss | 68 (15%) | 373 |
0.51 (0.926) |
0.0757 (0.621) |
0.282 (0.835) |
0.67 (0.974) |
0.0482 (0.557) |
0.433 (0.92) |
1 (1.00) |
0.482 (0.922) |
0.0674 (0.617) |
1 (1.00) |
0.0045 (0.274) |
0.325 (0.873) |
0.558 (0.938) |
11p loss | 64 (15%) | 377 |
0.206 (0.771) |
0.556 (0.938) |
0.236 (0.8) |
0.364 (0.889) |
0.28 (0.835) |
0.176 (0.734) |
0.673 (0.974) |
0.375 (0.89) |
0.00942 (0.302) |
0.371 (0.889) |
0.0486 (0.557) |
0.737 (0.982) |
0.524 (0.929) |
11q loss | 61 (14%) | 380 |
0.0799 (0.621) |
0.961 (1.00) |
0.203 (0.771) |
0.876 (1.00) |
0.0279 (0.547) |
0.573 (0.94) |
0.196 (0.766) |
0.857 (1.00) |
0.142 (0.732) |
0.536 (0.932) |
0.0146 (0.388) |
0.961 (1.00) |
0.524 (0.929) |
12p loss | 62 (14%) | 379 |
0.00636 (0.279) |
0.0649 (0.6) |
0.858 (1.00) |
0.272 (0.835) |
0.846 (1.00) |
1 (1.00) |
0.475 (0.922) |
0.857 (1.00) |
0.00641 (0.279) |
0.458 (0.922) |
0.44 (0.92) |
0.496 (0.925) |
0.479 (0.922) |
12q loss | 52 (12%) | 389 |
0.0284 (0.547) |
0.254 (0.809) |
0.904 (1.00) |
0.133 (0.732) |
0.461 (0.922) |
0.557 (0.938) |
0.538 (0.932) |
0.424 (0.919) |
0.0431 (0.547) |
0.449 (0.92) |
0.524 (0.929) |
0.46 (0.922) |
0.4 (0.919) |
13q loss | 37 (8%) | 404 |
0.502 (0.925) |
0.346 (0.881) |
0.733 (0.982) |
0.728 (0.982) |
0.738 (0.982) |
0.717 (0.982) |
0.592 (0.944) |
1 (1.00) |
0.58 (0.941) |
0.137 (0.732) |
0.629 (0.964) |
0.775 (0.988) |
0.368 (0.889) |
14q loss | 111 (25%) | 330 |
0.843 (1.00) |
0.6 (0.944) |
0.262 (0.822) |
0.326 (0.874) |
0.434 (0.92) |
0.0752 (0.621) |
0.732 (0.982) |
1 (1.00) |
0.287 (0.835) |
0.427 (0.92) |
0.556 (0.938) |
1 (1.00) |
0.333 (0.876) |
15q loss | 90 (20%) | 351 |
0.95 (1.00) |
0.499 (0.925) |
0.565 (0.94) |
0.0544 (0.576) |
0.829 (1.00) |
0.814 (0.995) |
0.712 (0.982) |
0.0561 (0.579) |
0.0337 (0.547) |
0.756 (0.988) |
0.482 (0.922) |
0.449 (0.92) |
0.293 (0.843) |
16p loss | 100 (23%) | 341 |
0.469 (0.922) |
0.0747 (0.621) |
0.681 (0.974) |
0.683 (0.974) |
0.706 (0.982) |
0.112 (0.711) |
0.636 (0.965) |
0.547 (0.938) |
0.00568 (0.279) |
0.597 (0.944) |
0.583 (0.941) |
0.368 (0.889) |
0.588 (0.944) |
16q loss | 114 (26%) | 327 |
0.281 (0.835) |
0.786 (0.988) |
0.207 (0.775) |
0.664 (0.973) |
0.903 (1.00) |
0.0325 (0.547) |
0.497 (0.925) |
0.0846 (0.632) |
0.00461 (0.274) |
0.7 (0.982) |
0.737 (0.982) |
0.628 (0.964) |
1 (1.00) |
17p loss | 164 (37%) | 277 |
0.802 (0.988) |
0.997 (1.00) |
0.673 (0.974) |
0.218 (0.8) |
0.74 (0.982) |
0.441 (0.92) |
0.051 (0.559) |
0.147 (0.732) |
0.00832 (0.302) |
0.191 (0.753) |
0.512 (0.927) |
0.472 (0.922) |
1 (1.00) |
17q loss | 74 (17%) | 367 |
0.915 (1.00) |
0.836 (1.00) |
0.695 (0.982) |
0.433 (0.92) |
0.27 (0.835) |
0.446 (0.92) |
0.895 (1.00) |
0.863 (1.00) |
0.147 (0.732) |
0.85 (1.00) |
0.253 (0.809) |
0.244 (0.801) |
0.589 (0.944) |
18p loss | 119 (27%) | 322 |
0.256 (0.811) |
0.854 (1.00) |
0.92 (1.00) |
0.309 (0.863) |
0.59 (0.944) |
0.676 (0.974) |
0.0337 (0.547) |
1 (1.00) |
0.814 (0.995) |
0.704 (0.982) |
0.235 (0.8) |
0.0389 (0.547) |
0.136 (0.732) |
18q loss | 154 (35%) | 287 |
0.848 (1.00) |
0.19 (0.753) |
0.761 (0.988) |
0.0092 (0.302) |
0.913 (1.00) |
1 (1.00) |
0.533 (0.932) |
0.506 (0.925) |
0.615 (0.96) |
0.939 (1.00) |
0.13 (0.732) |
0.641 (0.967) |
0.341 (0.881) |
19q loss | 86 (20%) | 355 |
0.73 (0.982) |
0.0697 (0.621) |
0.924 (1.00) |
0.974 (1.00) |
0.716 (0.982) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.00353 (0.274) |
0.113 (0.711) |
0.977 (1.00) |
0.416 (0.919) |
1 (1.00) |
20p loss | 22 (5%) | 419 |
0.356 (0.881) |
0.791 (0.988) |
0.236 (0.8) |
0.356 (0.881) |
0.464 (0.922) |
0.147 (0.732) |
0.174 (0.734) |
0.0346 (0.547) |
0.674 (0.974) |
0.566 (0.94) |
0.494 (0.925) |
0.295 (0.845) |
1 (1.00) |
21q loss | 181 (41%) | 260 |
0.701 (0.982) |
0.0947 (0.66) |
0.682 (0.974) |
0.578 (0.941) |
0.363 (0.889) |
0.249 (0.809) |
0.314 (0.866) |
0.157 (0.732) |
0.236 (0.8) |
0.654 (0.969) |
0.428 (0.92) |
0.582 (0.941) |
1 (1.00) |
22q loss | 146 (33%) | 295 |
0.38 (0.899) |
0.982 (1.00) |
0.556 (0.938) |
0.317 (0.867) |
0.256 (0.811) |
0.158 (0.732) |
0.527 (0.93) |
0.14 (0.732) |
0.274 (0.835) |
0.409 (0.919) |
0.0489 (0.557) |
0.582 (0.941) |
0.654 (0.969) |
xp loss | 61 (14%) | 380 |
0.162 (0.732) |
0.717 (0.982) |
0.218 (0.8) |
0.742 (0.982) |
0.676 (0.974) |
0.407 (0.919) |
0.0609 (0.592) |
0.467 (0.922) |
0.0749 (0.621) |
0.457 (0.922) |
0.731 (0.982) |
0.375 (0.89) |
0.146 (0.732) |
xq loss | 55 (12%) | 386 |
0.482 (0.922) |
0.682 (0.974) |
0.252 (0.809) |
0.472 (0.922) |
0.991 (1.00) |
0.153 (0.732) |
0.0505 (0.559) |
0.126 (0.732) |
0.82 (0.997) |
0.195 (0.766) |
0.69 (0.98) |
0.486 (0.923) |
0.479 (0.922) |
P value = 0.00117 (Fisher's exact test), Q value = 0.21
nPatients | STOMACH ADENOCARCINOMA, SIGNET RING TYPE | STOMACH, ADENOCARCINOMA, DIFFUSE TYPE | STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) | STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE | STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) | STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE | STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE |
---|---|---|---|---|---|---|---|
ALL | 13 | 72 | 163 | 21 | 82 | 8 | 79 |
6P GAIN MUTATED | 2 | 3 | 34 | 1 | 23 | 1 | 17 |
6P GAIN WILD-TYPE | 11 | 69 | 129 | 20 | 59 | 7 | 62 |
P value = 0.00164 (Fisher's exact test), Q value = 0.22
nPatients | STOMACH ADENOCARCINOMA, SIGNET RING TYPE | STOMACH, ADENOCARCINOMA, DIFFUSE TYPE | STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) | STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE | STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) | STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE | STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE |
---|---|---|---|---|---|---|---|
ALL | 13 | 72 | 163 | 21 | 82 | 8 | 79 |
6Q GAIN MUTATED | 2 | 2 | 30 | 0 | 19 | 1 | 12 |
6Q GAIN WILD-TYPE | 11 | 70 | 133 | 21 | 63 | 7 | 67 |
P value = 0.00194 (Fisher's exact test), Q value = 0.23
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|
ALL | 88 | 12 | 1 | 278 |
15Q GAIN MUTATED | 9 | 4 | 1 | 19 |
15Q GAIN WILD-TYPE | 79 | 8 | 0 | 259 |
P value = 5e-05 (Fisher's exact test), Q value = 0.053
nPatients | STOMACH ADENOCARCINOMA, SIGNET RING TYPE | STOMACH, ADENOCARCINOMA, DIFFUSE TYPE | STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) | STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE | STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) | STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE | STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE |
---|---|---|---|---|---|---|---|
ALL | 13 | 72 | 163 | 21 | 82 | 8 | 79 |
20Q GAIN MUTATED | 8 | 32 | 96 | 11 | 62 | 6 | 62 |
20Q GAIN WILD-TYPE | 5 | 40 | 67 | 10 | 20 | 2 | 17 |
P value = 0.00012 (Fisher's exact test), Q value = 0.063
nPatients | STOMACH ADENOCARCINOMA, SIGNET RING TYPE | STOMACH, ADENOCARCINOMA, DIFFUSE TYPE | STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) | STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE | STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) | STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE | STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE |
---|---|---|---|---|---|---|---|
ALL | 13 | 72 | 163 | 21 | 82 | 8 | 79 |
5Q LOSS MUTATED | 3 | 6 | 35 | 5 | 23 | 2 | 34 |
5Q LOSS WILD-TYPE | 10 | 66 | 128 | 16 | 59 | 6 | 45 |
P value = 0.000856 (Fisher's exact test), Q value = 0.21
nPatients | FEMALE | MALE |
---|---|---|
ALL | 158 | 283 |
8P LOSS MUTATED | 19 | 72 |
8P LOSS WILD-TYPE | 139 | 211 |
P value = 0.00113 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 391 | 5.6 (8.4) |
8P LOSS MUTATED | 83 | 8.2 (11.4) |
8P LOSS WILD-TYPE | 308 | 5.0 (7.3) |
P value = 0.00161 (Fisher's exact test), Q value = 0.22
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 23 | 93 | 196 | 119 |
8Q LOSS MUTATED | 2 | 6 | 26 | 2 |
8Q LOSS WILD-TYPE | 21 | 87 | 170 | 117 |
P value = 0.00045 (Fisher's exact test), Q value = 0.16
nPatients | STOMACH ADENOCARCINOMA, SIGNET RING TYPE | STOMACH, ADENOCARCINOMA, DIFFUSE TYPE | STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) | STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE | STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS) | STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE | STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE |
---|---|---|---|---|---|---|---|
ALL | 13 | 72 | 163 | 21 | 82 | 8 | 79 |
19P LOSS MUTATED | 2 | 10 | 40 | 1 | 31 | 4 | 28 |
19P LOSS WILD-TYPE | 11 | 62 | 123 | 20 | 51 | 4 | 51 |
-
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/STAD-TP/22533931/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STAD-TP/22507291/STAD-TP.merged_data.txt
-
Number of patients = 441
-
Number of significantly arm-level cnvs = 81
-
Number of selected clinical features = 13
-
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.