This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 82 arm-level events and 13 clinical features across 408 patients, 22 significant findings detected with Q value < 0.25.
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2p gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
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3p gain cnv correlated to 'YEARS_TO_BIRTH' and 'NUMBER_OF_LYMPH_NODES'.
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3q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
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10q gain cnv correlated to 'PATHOLOGY_N_STAGE'.
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11q gain cnv correlated to 'YEARS_TO_BIRTH'.
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14q gain cnv correlated to 'RACE'.
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21q gain cnv correlated to 'YEARS_TO_BIRTH'.
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3p loss cnv correlated to 'GENDER'.
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4p loss cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', and 'RACE'.
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4q loss cnv correlated to 'YEARS_TO_BIRTH'.
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5p loss cnv correlated to 'YEARS_TO_BIRTH'.
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6q loss cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
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8q loss cnv correlated to 'PATHOLOGY_T_STAGE'.
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11p loss cnv correlated to 'YEARS_TO_BIRTH'.
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15q loss cnv correlated to 'RACE'.
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16p loss cnv correlated to 'RACE'.
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21q loss cnv correlated to 'PATHOLOGY_N_STAGE'.
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 |
NUMBER PACK YEARS SMOKED |
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 | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
3q gain | 179 (44%) | 229 |
0.759 (1.00) |
0.00226 (0.172) |
0.0183 (0.383) |
0.361 (0.876) |
0.00154 (0.172) |
0.217 (0.798) |
0.91 (1.00) |
1 (1.00) |
0.133 (0.671) |
0.207 (0.795) |
6.11e-05 (0.0652) |
0.0892 (0.565) |
1 (1.00) |
4p loss | 144 (35%) | 264 |
0.0637 (0.503) |
0.189 (0.766) |
0.00468 (0.243) |
0.0913 (0.565) |
0.0011 (0.172) |
0.742 (1.00) |
0.725 (1.00) |
0.811 (1.00) |
0.818 (1.00) |
0.111 (0.625) |
0.0149 (0.383) |
0.00336 (0.225) |
0.504 (0.972) |
3p gain | 143 (35%) | 265 |
0.418 (0.941) |
0.00152 (0.172) |
0.0556 (0.494) |
0.0856 (0.554) |
0.0162 (0.383) |
0.19 (0.766) |
0.157 (0.711) |
0.632 (1.00) |
0.0624 (0.503) |
0.0276 (0.427) |
0.000186 (0.0991) |
0.0912 (0.565) |
1 (1.00) |
2p gain | 111 (27%) | 297 |
0.713 (1.00) |
0.111 (0.625) |
0.0522 (0.492) |
0.84 (1.00) |
0.012 (0.352) |
0.173 (0.741) |
0.016 (0.383) |
1 (1.00) |
0.976 (1.00) |
0.0672 (0.51) |
0.0019 (0.172) |
0.439 (0.952) |
0.702 (1.00) |
10q gain | 44 (11%) | 364 |
0.0929 (0.565) |
0.583 (1.00) |
0.037 (0.45) |
0.366 (0.88) |
0.0017 (0.172) |
1 (1.00) |
0.717 (1.00) |
0.709 (1.00) |
0.8 (1.00) |
0.535 (0.98) |
0.0311 (0.433) |
0.835 (1.00) |
0.598 (1.00) |
11q gain | 47 (12%) | 361 |
0.0114 (0.348) |
0.00388 (0.24) |
0.0486 (0.489) |
0.644 (1.00) |
0.0193 (0.388) |
0.296 (0.857) |
0.0768 (0.538) |
0.711 (1.00) |
0.646 (1.00) |
0.77 (1.00) |
0.0696 (0.522) |
0.339 (0.86) |
1 (1.00) |
14q gain | 57 (14%) | 351 |
0.0403 (0.462) |
0.696 (1.00) |
0.391 (0.91) |
0.0534 (0.492) |
0.76 (1.00) |
0.275 (0.849) |
0.0337 (0.443) |
1 (1.00) |
0.528 (0.978) |
0.702 (1.00) |
0.344 (0.864) |
0.00338 (0.225) |
0.348 (0.864) |
21q gain | 116 (28%) | 292 |
0.493 (0.971) |
0.000403 (0.125) |
0.497 (0.971) |
0.411 (0.932) |
0.313 (0.857) |
1 (1.00) |
0.212 (0.798) |
0.609 (1.00) |
0.406 (0.927) |
0.854 (1.00) |
0.29 (0.857) |
0.507 (0.972) |
1 (1.00) |
3p loss | 51 (12%) | 357 |
0.461 (0.965) |
0.331 (0.857) |
0.668 (1.00) |
0.454 (0.963) |
0.542 (0.982) |
1 (1.00) |
0.00193 (0.172) |
1 (1.00) |
0.778 (1.00) |
0.367 (0.88) |
0.599 (1.00) |
0.0611 (0.503) |
1 (1.00) |
4q loss | 136 (33%) | 272 |
0.42 (0.941) |
0.00194 (0.172) |
0.0312 (0.433) |
0.293 (0.857) |
0.0654 (0.509) |
0.733 (1.00) |
0.633 (1.00) |
0.625 (1.00) |
0.495 (0.971) |
0.981 (1.00) |
0.237 (0.805) |
0.0221 (0.399) |
0.483 (0.971) |
5p loss | 54 (13%) | 354 |
0.699 (1.00) |
0.0022 (0.172) |
0.686 (1.00) |
0.686 (1.00) |
0.226 (0.801) |
0.0545 (0.492) |
0.618 (1.00) |
1 (1.00) |
0.613 (1.00) |
0.723 (1.00) |
0.431 (0.946) |
0.676 (1.00) |
1 (1.00) |
6q loss | 159 (39%) | 249 |
0.774 (1.00) |
0.845 (1.00) |
0.0105 (0.335) |
0.317 (0.857) |
0.00765 (0.314) |
0.542 (0.982) |
0.645 (1.00) |
0.241 (0.808) |
0.0212 (0.39) |
0.872 (1.00) |
0.00415 (0.24) |
0.0386 (0.452) |
0.0307 (0.433) |
8q loss | 38 (9%) | 370 |
0.712 (1.00) |
0.599 (1.00) |
0.234 (0.805) |
0.00428 (0.24) |
0.277 (0.851) |
0.253 (0.813) |
0.248 (0.812) |
0.24 (0.806) |
0.915 (1.00) |
0.94 (1.00) |
0.0668 (0.51) |
0.629 (1.00) |
1 (1.00) |
11p loss | 178 (44%) | 230 |
0.587 (1.00) |
0.00513 (0.249) |
0.0861 (0.554) |
0.947 (1.00) |
0.106 (0.613) |
0.356 (0.869) |
0.91 (1.00) |
0.644 (1.00) |
0.561 (0.997) |
0.397 (0.918) |
0.0407 (0.462) |
0.085 (0.554) |
0.506 (0.972) |
15q loss | 144 (35%) | 264 |
0.473 (0.971) |
0.276 (0.849) |
0.389 (0.908) |
0.122 (0.642) |
0.988 (1.00) |
0.5 (0.971) |
0.347 (0.864) |
0.228 (0.801) |
0.0896 (0.565) |
0.332 (0.857) |
0.523 (0.978) |
0.00114 (0.172) |
0.289 (0.857) |
16p loss | 110 (27%) | 298 |
0.189 (0.766) |
0.923 (1.00) |
0.636 (1.00) |
0.0345 (0.449) |
0.461 (0.965) |
1 (1.00) |
0.704 (1.00) |
0.117 (0.635) |
0.426 (0.943) |
0.579 (1.00) |
0.786 (1.00) |
0.00479 (0.243) |
0.706 (1.00) |
21q loss | 79 (19%) | 329 |
0.735 (1.00) |
0.119 (0.635) |
0.748 (1.00) |
0.642 (1.00) |
0.00047 (0.125) |
1 (1.00) |
0.776 (1.00) |
0.776 (1.00) |
0.521 (0.978) |
0.878 (1.00) |
0.563 (0.999) |
0.0515 (0.492) |
0.683 (1.00) |
1p gain | 89 (22%) | 319 |
0.378 (0.894) |
0.324 (0.857) |
0.275 (0.849) |
0.479 (0.971) |
0.0408 (0.462) |
0.464 (0.965) |
0.683 (1.00) |
0.586 (1.00) |
0.589 (1.00) |
0.166 (0.724) |
0.222 (0.801) |
0.115 (0.63) |
1 (1.00) |
1q gain | 126 (31%) | 282 |
0.553 (0.99) |
0.746 (1.00) |
0.0523 (0.492) |
0.677 (1.00) |
0.0175 (0.383) |
0.316 (0.857) |
1 (1.00) |
0.323 (0.857) |
0.269 (0.848) |
0.0809 (0.546) |
0.0299 (0.433) |
0.321 (0.857) |
0.728 (1.00) |
2q gain | 55 (13%) | 353 |
0.86 (1.00) |
0.839 (1.00) |
0.707 (1.00) |
0.691 (1.00) |
0.761 (1.00) |
1 (1.00) |
0.251 (0.812) |
0.497 (0.971) |
0.808 (1.00) |
0.697 (1.00) |
0.13 (0.664) |
0.955 (1.00) |
1 (1.00) |
4p gain | 38 (9%) | 370 |
0.038 (0.45) |
0.599 (1.00) |
0.367 (0.88) |
0.0943 (0.565) |
0.156 (0.711) |
0.368 (0.88) |
0.124 (0.653) |
1 (1.00) |
0.31 (0.857) |
0.778 (1.00) |
0.233 (0.805) |
0.7 (1.00) |
0.565 (0.999) |
4q gain | 26 (6%) | 382 |
0.071 (0.522) |
0.0752 (0.535) |
0.115 (0.63) |
0.019 (0.388) |
0.6 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.603 (1.00) |
0.98 (1.00) |
0.288 (0.857) |
0.593 (1.00) |
0.421 (0.941) |
5p gain | 166 (41%) | 242 |
0.925 (1.00) |
0.926 (1.00) |
0.725 (1.00) |
0.925 (1.00) |
0.313 (0.857) |
0.0592 (0.503) |
0.647 (1.00) |
1 (1.00) |
0.417 (0.941) |
0.885 (1.00) |
0.422 (0.941) |
0.0377 (0.45) |
0.741 (1.00) |
5q gain | 51 (12%) | 357 |
0.795 (1.00) |
0.222 (0.801) |
0.217 (0.798) |
0.68 (1.00) |
0.323 (0.857) |
0.604 (1.00) |
0.865 (1.00) |
0.491 (0.971) |
0.923 (1.00) |
0.0839 (0.554) |
0.405 (0.926) |
0.461 (0.965) |
1 (1.00) |
6p gain | 73 (18%) | 335 |
0.921 (1.00) |
0.0763 (0.538) |
0.237 (0.805) |
0.772 (1.00) |
0.352 (0.868) |
0.668 (1.00) |
0.144 (0.694) |
0.355 (0.869) |
0.653 (1.00) |
0.0231 (0.403) |
0.653 (1.00) |
0.105 (0.607) |
1 (1.00) |
6q gain | 39 (10%) | 369 |
0.333 (0.857) |
0.306 (0.857) |
0.292 (0.857) |
0.839 (1.00) |
0.159 (0.711) |
1 (1.00) |
0.127 (0.655) |
0.0267 (0.424) |
0.497 (0.971) |
0.141 (0.693) |
0.833 (1.00) |
0.319 (0.857) |
1 (1.00) |
7p gain | 171 (42%) | 237 |
0.698 (1.00) |
0.062 (0.503) |
0.0334 (0.443) |
0.0536 (0.492) |
0.0151 (0.383) |
0.759 (1.00) |
1 (1.00) |
0.162 (0.718) |
0.0837 (0.554) |
0.906 (1.00) |
0.311 (0.857) |
0.066 (0.51) |
1 (1.00) |
7q gain | 148 (36%) | 260 |
0.581 (1.00) |
0.0165 (0.383) |
0.159 (0.711) |
0.236 (0.805) |
0.00861 (0.314) |
0.51 (0.973) |
0.483 (0.971) |
0.637 (1.00) |
0.314 (0.857) |
0.959 (1.00) |
0.177 (0.746) |
0.0708 (0.522) |
1 (1.00) |
8p gain | 90 (22%) | 318 |
0.356 (0.869) |
0.638 (1.00) |
0.467 (0.965) |
0.701 (1.00) |
0.577 (1.00) |
0.734 (1.00) |
0.786 (1.00) |
0.784 (1.00) |
0.491 (0.971) |
0.593 (1.00) |
0.101 (0.593) |
0.626 (1.00) |
1 (1.00) |
8q gain | 200 (49%) | 208 |
0.546 (0.986) |
0.504 (0.972) |
0.928 (1.00) |
0.771 (1.00) |
0.716 (1.00) |
0.767 (1.00) |
0.822 (1.00) |
0.364 (0.88) |
0.135 (0.674) |
0.966 (1.00) |
0.117 (0.635) |
0.547 (0.986) |
0.74 (1.00) |
9p gain | 69 (17%) | 339 |
0.0675 (0.51) |
0.991 (1.00) |
0.595 (1.00) |
1 (1.00) |
0.434 (0.946) |
0.399 (0.918) |
0.453 (0.963) |
0.752 (1.00) |
0.227 (0.801) |
0.47 (0.968) |
0.878 (1.00) |
0.0643 (0.504) |
0.649 (1.00) |
9q gain | 56 (14%) | 352 |
0.242 (0.808) |
0.27 (0.848) |
0.221 (0.801) |
0.403 (0.925) |
0.771 (1.00) |
0.0376 (0.45) |
0.744 (1.00) |
0.492 (0.971) |
0.76 (1.00) |
0.208 (0.795) |
0.25 (0.812) |
0.156 (0.711) |
0.339 (0.86) |
10p gain | 117 (29%) | 291 |
0.249 (0.812) |
0.542 (0.982) |
0.42 (0.941) |
0.916 (1.00) |
0.0437 (0.47) |
1 (1.00) |
0.0622 (0.503) |
0.609 (1.00) |
0.151 (0.711) |
0.21 (0.797) |
0.0919 (0.565) |
0.0727 (0.527) |
0.709 (1.00) |
11p gain | 29 (7%) | 379 |
0.0496 (0.492) |
0.843 (1.00) |
0.739 (1.00) |
0.603 (1.00) |
0.0378 (0.45) |
0.435 (0.946) |
0.0143 (0.383) |
1 (1.00) |
0.575 (1.00) |
0.922 (1.00) |
0.547 (0.986) |
0.216 (0.798) |
0.516 (0.978) |
12p gain | 116 (28%) | 292 |
0.535 (0.98) |
0.00896 (0.314) |
0.348 (0.864) |
0.57 (1.00) |
0.715 (1.00) |
1 (1.00) |
0.709 (1.00) |
0.803 (1.00) |
0.521 (0.978) |
0.965 (1.00) |
0.904 (1.00) |
0.826 (1.00) |
0.715 (1.00) |
12q gain | 91 (22%) | 317 |
0.676 (1.00) |
0.271 (0.848) |
0.205 (0.795) |
0.554 (0.99) |
0.983 (1.00) |
1 (1.00) |
0.59 (1.00) |
0.792 (1.00) |
0.745 (1.00) |
0.955 (1.00) |
0.852 (1.00) |
0.825 (1.00) |
1 (1.00) |
13q gain | 100 (25%) | 308 |
0.669 (1.00) |
0.565 (0.999) |
0.518 (0.978) |
0.83 (1.00) |
0.017 (0.383) |
0.143 (0.694) |
0.435 (0.946) |
0.793 (1.00) |
0.345 (0.864) |
0.835 (1.00) |
0.0862 (0.554) |
0.166 (0.724) |
0.119 (0.635) |
15q gain | 35 (9%) | 373 |
0.53 (0.98) |
0.283 (0.857) |
0.203 (0.794) |
0.0258 (0.424) |
0.348 (0.864) |
1 (1.00) |
0.841 (1.00) |
0.227 (0.801) |
0.0952 (0.567) |
0.835 (1.00) |
0.328 (0.857) |
0.87 (1.00) |
0.553 (0.99) |
16p gain | 75 (18%) | 333 |
0.176 (0.743) |
0.298 (0.857) |
0.0837 (0.554) |
0.00835 (0.314) |
0.104 (0.603) |
0.232 (0.805) |
0.561 (0.997) |
1 (1.00) |
0.46 (0.965) |
0.851 (1.00) |
0.118 (0.635) |
0.287 (0.857) |
1 (1.00) |
16q gain | 82 (20%) | 326 |
0.656 (1.00) |
0.138 (0.686) |
0.33 (0.857) |
0.0564 (0.497) |
0.363 (0.879) |
0.232 (0.805) |
0.328 (0.857) |
1 (1.00) |
0.476 (0.971) |
0.741 (1.00) |
0.817 (1.00) |
0.189 (0.766) |
0.694 (1.00) |
17p gain | 56 (14%) | 352 |
0.494 (0.971) |
0.156 (0.711) |
0.289 (0.857) |
0.723 (1.00) |
0.451 (0.963) |
0.195 (0.772) |
0.872 (1.00) |
1 (1.00) |
0.318 (0.857) |
0.178 (0.746) |
0.744 (1.00) |
0.446 (0.956) |
0.339 (0.86) |
17q gain | 135 (33%) | 273 |
0.308 (0.857) |
0.129 (0.664) |
0.0792 (0.545) |
0.73 (1.00) |
0.0459 (0.485) |
0.739 (1.00) |
0.905 (1.00) |
0.228 (0.801) |
0.0989 (0.586) |
0.207 (0.795) |
0.0849 (0.554) |
0.332 (0.857) |
0.0636 (0.503) |
18p gain | 116 (28%) | 292 |
0.868 (1.00) |
0.516 (0.978) |
0.633 (1.00) |
0.604 (1.00) |
0.255 (0.814) |
0.467 (0.965) |
0.534 (0.98) |
0.61 (1.00) |
0.044 (0.47) |
0.163 (0.722) |
0.933 (1.00) |
0.0249 (0.424) |
0.719 (1.00) |
18q gain | 61 (15%) | 347 |
0.431 (0.946) |
0.413 (0.935) |
0.639 (1.00) |
0.849 (1.00) |
0.628 (1.00) |
1 (1.00) |
1 (1.00) |
0.751 (1.00) |
0.144 (0.694) |
0.491 (0.971) |
0.333 (0.857) |
0.0206 (0.39) |
0.63 (1.00) |
19p gain | 87 (21%) | 321 |
0.751 (1.00) |
0.629 (1.00) |
0.936 (1.00) |
0.714 (1.00) |
0.27 (0.848) |
0.711 (1.00) |
0.217 (0.798) |
0.572 (1.00) |
0.872 (1.00) |
0.96 (1.00) |
0.184 (0.758) |
0.224 (0.801) |
0.691 (1.00) |
19q gain | 132 (32%) | 276 |
0.467 (0.965) |
0.484 (0.971) |
0.189 (0.766) |
0.352 (0.868) |
0.159 (0.711) |
0.342 (0.864) |
0.905 (1.00) |
0.329 (0.857) |
1 (1.00) |
0.285 (0.857) |
0.0167 (0.383) |
0.566 (1) |
1 (1.00) |
20p gain | 201 (49%) | 207 |
0.435 (0.946) |
0.0912 (0.565) |
0.334 (0.857) |
0.386 (0.907) |
0.0474 (0.486) |
0.12 (0.636) |
1 (1.00) |
0.108 (0.621) |
0.264 (0.837) |
0.647 (1.00) |
0.111 (0.625) |
0.00794 (0.314) |
0.175 (0.743) |
20q gain | 230 (56%) | 178 |
0.771 (1.00) |
0.169 (0.731) |
0.484 (0.971) |
0.496 (0.971) |
0.0544 (0.492) |
0.547 (0.986) |
0.213 (0.798) |
0.648 (1.00) |
0.749 (1.00) |
0.988 (1.00) |
0.159 (0.711) |
0.0422 (0.469) |
0.191 (0.768) |
22q gain | 48 (12%) | 360 |
0.756 (1.00) |
0.687 (1.00) |
0.234 (0.805) |
0.295 (0.857) |
0.463 (0.965) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.747 (1.00) |
0.392 (0.91) |
0.203 (0.794) |
0.651 (1.00) |
0.606 (1.00) |
xp gain | 65 (16%) | 343 |
0.806 (1.00) |
0.514 (0.977) |
0.685 (1.00) |
0.842 (1.00) |
0.769 (1.00) |
0.366 (0.88) |
0.542 (0.982) |
0.0543 (0.492) |
0.582 (1.00) |
0.256 (0.815) |
0.726 (1.00) |
0.58 (1.00) |
0.14 (0.692) |
xq gain | 45 (11%) | 363 |
0.859 (1.00) |
0.315 (0.857) |
0.645 (1.00) |
0.854 (1.00) |
0.4 (0.918) |
0.606 (1.00) |
1 (1.00) |
0.147 (0.702) |
0.622 (1.00) |
0.171 (0.736) |
0.126 (0.655) |
0.844 (1.00) |
1 (1.00) |
1p loss | 31 (8%) | 377 |
0.655 (1.00) |
0.956 (1.00) |
0.269 (0.848) |
0.0928 (0.565) |
0.275 (0.849) |
0.131 (0.664) |
0.524 (0.978) |
0.67 (1.00) |
0.712 (1.00) |
0.395 (0.916) |
0.527 (0.978) |
0.333 (0.857) |
1 (1.00) |
1q loss | 31 (8%) | 377 |
0.663 (1.00) |
0.866 (1.00) |
0.0472 (0.486) |
0.0805 (0.546) |
0.669 (1.00) |
0.526 (0.978) |
0.676 (1.00) |
0.387 (0.907) |
1 (1.00) |
0.0635 (0.503) |
0.7 (1.00) |
0.677 (1.00) |
1 (1.00) |
2p loss | 45 (11%) | 363 |
0.846 (1.00) |
0.874 (1.00) |
0.922 (1.00) |
0.812 (1.00) |
0.848 (1.00) |
0.623 (1.00) |
0.593 (1.00) |
0.251 (0.812) |
0.061 (0.503) |
0.845 (1.00) |
0.85 (1.00) |
0.617 (1.00) |
1 (1.00) |
2q loss | 92 (23%) | 316 |
0.425 (0.943) |
0.662 (1.00) |
0.858 (1.00) |
0.78 (1.00) |
0.285 (0.857) |
0.467 (0.965) |
0.686 (1.00) |
0.408 (0.927) |
0.0599 (0.503) |
0.868 (1.00) |
0.157 (0.711) |
1 (1.00) |
1 (1.00) |
3q loss | 23 (6%) | 385 |
0.874 (1.00) |
0.387 (0.907) |
0.85 (1.00) |
0.627 (1.00) |
0.683 (1.00) |
0.467 (0.965) |
0.336 (0.858) |
1 (1.00) |
0.665 (1.00) |
0.586 (1.00) |
0.442 (0.952) |
0.453 (0.963) |
1 (1.00) |
5q loss | 160 (39%) | 248 |
0.436 (0.946) |
0.037 (0.45) |
0.0524 (0.492) |
0.297 (0.857) |
0.00892 (0.314) |
0.0591 (0.503) |
0.908 (1.00) |
1 (1.00) |
0.0209 (0.39) |
0.0588 (0.503) |
0.00948 (0.316) |
0.0313 (0.433) |
0.743 (1.00) |
6p loss | 103 (25%) | 305 |
0.0472 (0.486) |
0.924 (1.00) |
0.521 (0.978) |
0.147 (0.702) |
0.0331 (0.443) |
1 (1.00) |
0.198 (0.779) |
0.793 (1.00) |
0.306 (0.857) |
0.67 (1.00) |
0.218 (0.798) |
0.312 (0.857) |
0.0521 (0.492) |
7p loss | 20 (5%) | 388 |
0.793 (1.00) |
0.774 (1.00) |
0.572 (1.00) |
0.378 (0.894) |
0.021 (0.39) |
1 (1.00) |
0.305 (0.857) |
0.239 (0.806) |
0.928 (1.00) |
0.982 (1.00) |
0.0746 (0.534) |
0.889 (1.00) |
1 (1.00) |
7q loss | 28 (7%) | 380 |
0.856 (1.00) |
0.502 (0.972) |
1 (1.00) |
0.854 (1.00) |
0.32 (0.857) |
1 (1.00) |
0.182 (0.757) |
1 (1.00) |
0.482 (0.971) |
0.134 (0.673) |
0.77 (1.00) |
0.916 (1.00) |
0.13 (0.664) |
8p loss | 188 (46%) | 220 |
0.639 (1.00) |
0.299 (0.857) |
0.0122 (0.352) |
0.5 (0.971) |
0.0375 (0.45) |
0.352 (0.868) |
0.499 (0.971) |
0.49 (0.971) |
0.248 (0.812) |
0.334 (0.857) |
0.0371 (0.45) |
0.0294 (0.433) |
1 (1.00) |
9p loss | 174 (43%) | 234 |
0.902 (1.00) |
0.0262 (0.424) |
0.186 (0.764) |
0.929 (1.00) |
0.485 (0.971) |
0.76 (1.00) |
0.734 (1.00) |
0.644 (1.00) |
0.164 (0.722) |
0.375 (0.892) |
0.633 (1.00) |
0.852 (1.00) |
1 (1.00) |
9q loss | 169 (41%) | 239 |
0.573 (1.00) |
0.249 (0.812) |
0.505 (0.972) |
0.773 (1.00) |
0.442 (0.952) |
0.757 (1.00) |
0.82 (1.00) |
0.491 (0.971) |
0.422 (0.941) |
0.0905 (0.565) |
0.935 (1.00) |
0.333 (0.857) |
0.743 (1.00) |
10p loss | 73 (18%) | 335 |
0.695 (1.00) |
0.885 (1.00) |
0.798 (1.00) |
0.779 (1.00) |
0.739 (1.00) |
0.399 (0.918) |
0.771 (1.00) |
0.231 (0.805) |
0.305 (0.857) |
0.0183 (0.383) |
0.683 (1.00) |
0.00799 (0.314) |
0.667 (1.00) |
10q loss | 129 (32%) | 279 |
0.235 (0.805) |
0.0177 (0.383) |
0.631 (1.00) |
0.895 (1.00) |
0.528 (0.978) |
0.303 (0.857) |
0.904 (1.00) |
0.215 (0.798) |
0.508 (0.972) |
0.759 (1.00) |
0.597 (1.00) |
0.158 (0.711) |
0.475 (0.971) |
11q loss | 129 (32%) | 279 |
0.83 (1.00) |
0.306 (0.857) |
0.831 (1.00) |
0.688 (1.00) |
0.508 (0.972) |
1 (1.00) |
0.334 (0.857) |
0.219 (0.801) |
0.992 (1.00) |
0.81 (1.00) |
0.986 (1.00) |
0.251 (0.812) |
1 (1.00) |
12p loss | 54 (13%) | 354 |
0.54 (0.982) |
0.854 (1.00) |
0.496 (0.971) |
0.153 (0.711) |
0.142 (0.694) |
1 (1.00) |
0.618 (1.00) |
0.734 (1.00) |
0.743 (1.00) |
0.224 (0.801) |
0.0486 (0.489) |
0.555 (0.991) |
0.348 (0.864) |
12q loss | 58 (14%) | 350 |
0.914 (1.00) |
0.192 (0.768) |
0.246 (0.812) |
0.382 (0.902) |
0.0569 (0.497) |
1 (1.00) |
1 (1.00) |
0.173 (0.741) |
0.316 (0.857) |
0.55 (0.989) |
0.0297 (0.433) |
0.763 (1.00) |
1 (1.00) |
13q loss | 85 (21%) | 323 |
0.716 (1.00) |
0.286 (0.857) |
0.679 (1.00) |
0.522 (0.978) |
0.425 (0.943) |
0.698 (1.00) |
0.407 (0.927) |
0.577 (1.00) |
0.905 (1.00) |
0.977 (1.00) |
0.696 (1.00) |
0.0741 (0.534) |
0.0777 (0.538) |
14q loss | 121 (30%) | 287 |
0.152 (0.711) |
0.0421 (0.469) |
0.61 (1.00) |
0.772 (1.00) |
0.00912 (0.314) |
1 (1.00) |
0.11 (0.625) |
0.208 (0.795) |
0.322 (0.857) |
0.0933 (0.565) |
0.104 (0.603) |
0.809 (1.00) |
0.283 (0.857) |
16q loss | 107 (26%) | 301 |
0.388 (0.907) |
0.461 (0.965) |
0.535 (0.98) |
0.726 (1.00) |
0.134 (0.673) |
1 (1.00) |
0.522 (0.978) |
0.305 (0.857) |
0.217 (0.798) |
0.952 (1.00) |
0.174 (0.742) |
0.0317 (0.433) |
0.0543 (0.492) |
17p loss | 182 (45%) | 226 |
0.323 (0.857) |
0.00847 (0.314) |
0.462 (0.965) |
0.301 (0.857) |
0.302 (0.857) |
0.531 (0.98) |
0.498 (0.971) |
0.819 (1.00) |
1 (1.00) |
0.687 (1.00) |
0.253 (0.813) |
0.619 (1.00) |
1 (1.00) |
17q loss | 46 (11%) | 362 |
0.311 (0.857) |
0.642 (1.00) |
0.939 (1.00) |
0.0703 (0.522) |
0.147 (0.702) |
1 (1.00) |
0.291 (0.857) |
0.49 (0.971) |
0.718 (1.00) |
0.794 (1.00) |
0.966 (1.00) |
0.18 (0.752) |
0.606 (1.00) |
18p loss | 98 (24%) | 310 |
0.856 (1.00) |
0.923 (1.00) |
0.0441 (0.47) |
0.778 (1.00) |
0.0277 (0.427) |
0.296 (0.857) |
0.429 (0.946) |
1 (1.00) |
0.149 (0.704) |
0.449 (0.96) |
0.0627 (0.503) |
0.856 (1.00) |
0.445 (0.956) |
18q loss | 146 (36%) | 262 |
0.346 (0.864) |
0.689 (1.00) |
0.624 (1.00) |
0.798 (1.00) |
0.255 (0.814) |
0.334 (0.857) |
0.291 (0.857) |
0.349 (0.864) |
0.782 (1.00) |
0.183 (0.758) |
0.158 (0.711) |
0.953 (1.00) |
0.289 (0.857) |
19p loss | 95 (23%) | 313 |
0.194 (0.77) |
0.0809 (0.546) |
0.0429 (0.47) |
0.0227 (0.403) |
0.0168 (0.383) |
0.232 (0.805) |
0.791 (1.00) |
0.0553 (0.494) |
0.194 (0.77) |
0.901 (1.00) |
0.463 (0.965) |
0.0725 (0.527) |
0.224 (0.801) |
19q loss | 59 (14%) | 349 |
0.113 (0.629) |
0.642 (1.00) |
0.814 (1.00) |
0.238 (0.805) |
0.654 (1.00) |
0.361 (0.876) |
0.874 (1.00) |
0.332 (0.857) |
0.125 (0.654) |
0.36 (0.876) |
0.492 (0.971) |
0.532 (0.98) |
0.625 (1.00) |
20p loss | 32 (8%) | 376 |
0.514 (0.977) |
0.985 (1.00) |
0.808 (1.00) |
0.758 (1.00) |
0.433 (0.946) |
1 (1.00) |
0.209 (0.795) |
0.649 (1.00) |
0.978 (1.00) |
0.02 (0.39) |
0.5 (0.971) |
0.243 (0.811) |
1 (1.00) |
20q loss | 15 (4%) | 393 |
0.273 (0.849) |
0.85 (1.00) |
0.325 (0.857) |
0.483 (0.971) |
0.113 (0.629) |
1 (1.00) |
0.372 (0.887) |
1 (1.00) |
0.192 (0.768) |
0.982 (1.00) |
0.442 (0.952) |
1 (1.00) |
1 (1.00) |
22q loss | 160 (39%) | 248 |
0.315 (0.857) |
0.169 (0.731) |
0.0261 (0.424) |
0.0942 (0.565) |
0.013 (0.364) |
1 (1.00) |
1 (1.00) |
0.245 (0.812) |
0.114 (0.63) |
0.433 (0.946) |
0.0256 (0.424) |
0.0107 (0.335) |
0.0315 (0.433) |
xp loss | 73 (18%) | 335 |
0.538 (0.982) |
0.63 (1.00) |
0.715 (1.00) |
0.851 (1.00) |
0.662 (1.00) |
1 (1.00) |
0.561 (0.997) |
0.377 (0.894) |
0.205 (0.795) |
0.831 (1.00) |
0.991 (1.00) |
0.737 (1.00) |
0.663 (1.00) |
xq loss | 83 (20%) | 325 |
0.764 (1.00) |
0.509 (0.972) |
0.758 (1.00) |
0.84 (1.00) |
0.823 (1.00) |
1 (1.00) |
0.677 (1.00) |
0.572 (1.00) |
0.216 (0.798) |
0.623 (1.00) |
0.831 (1.00) |
0.78 (1.00) |
0.0777 (0.538) |
P value = 0.0019 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 297 | 2.1 (7.0) |
2P GAIN MUTATED | 79 | 2.7 (5.2) |
2P GAIN WILD-TYPE | 218 | 1.9 (7.6) |
P value = 0.00152 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
3P GAIN MUTATED | 142 | 70.4 (10.0) |
3P GAIN WILD-TYPE | 265 | 66.9 (10.8) |
P value = 0.000186 (Wilcoxon-test), Q value = 0.099
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 297 | 2.1 (7.0) |
3P GAIN MUTATED | 99 | 3.7 (11.0) |
3P GAIN WILD-TYPE | 198 | 1.3 (3.4) |
P value = 0.00226 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
3Q GAIN MUTATED | 178 | 70.0 (10.2) |
3Q GAIN WILD-TYPE | 229 | 66.6 (10.7) |
P value = 0.00154 (Fisher's exact test), Q value = 0.17
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
3Q GAIN MUTATED | 83 | 24 | 44 | 4 |
3Q GAIN WILD-TYPE | 153 | 23 | 31 | 4 |
P value = 6.11e-05 (Wilcoxon-test), Q value = 0.065
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 297 | 2.1 (7.0) |
3Q GAIN MUTATED | 130 | 3.4 (9.8) |
3Q GAIN WILD-TYPE | 167 | 1.1 (3.2) |
P value = 0.0017 (Fisher's exact test), Q value = 0.17
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
10Q GAIN MUTATED | 17 | 12 | 10 | 2 |
10Q GAIN WILD-TYPE | 219 | 35 | 65 | 6 |
P value = 0.00388 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
11Q GAIN MUTATED | 47 | 72.1 (10.9) |
11Q GAIN WILD-TYPE | 360 | 67.6 (10.5) |
P value = 0.00338 (Fisher's exact test), Q value = 0.23
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 43 | 22 | 327 |
14Q GAIN MUTATED | 0 | 5 | 46 |
14Q GAIN WILD-TYPE | 43 | 17 | 281 |
P value = 0.000403 (Wilcoxon-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
21Q GAIN MUTATED | 116 | 71.2 (9.7) |
21Q GAIN WILD-TYPE | 291 | 66.9 (10.7) |
P value = 0.00193 (Fisher's exact test), Q value = 0.17
nPatients | FEMALE | MALE |
---|---|---|
ALL | 107 | 301 |
3P LOSS MUTATED | 23 | 28 |
3P LOSS WILD-TYPE | 84 | 273 |
P value = 0.00468 (Fisher's exact test), Q value = 0.24
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 2 | 129 | 140 | 135 |
4P LOSS MUTATED | 0 | 36 | 45 | 63 |
4P LOSS WILD-TYPE | 2 | 93 | 95 | 72 |
P value = 0.0011 (Fisher's exact test), Q value = 0.17
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
4P LOSS MUTATED | 65 | 23 | 36 | 2 |
4P LOSS WILD-TYPE | 171 | 24 | 39 | 6 |
P value = 0.00336 (Fisher's exact test), Q value = 0.23
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 43 | 22 | 327 |
4P LOSS MUTATED | 9 | 14 | 116 |
4P LOSS WILD-TYPE | 34 | 8 | 211 |
P value = 0.00194 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
4Q LOSS MUTATED | 136 | 70.5 (9.4) |
4Q LOSS WILD-TYPE | 271 | 66.9 (11.0) |
P value = 0.0022 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
5P LOSS MUTATED | 54 | 72.2 (8.3) |
5P LOSS WILD-TYPE | 353 | 67.5 (10.8) |
P value = 0.00415 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 297 | 2.1 (7.0) |
6Q LOSS MUTATED | 123 | 2.5 (5.2) |
6Q LOSS WILD-TYPE | 174 | 1.8 (8.0) |
P value = 0.00428 (Fisher's exact test), Q value = 0.24
nPatients | T0+T1+T2 | T3 | T4 |
---|---|---|---|
ALL | 123 | 195 | 58 |
8Q LOSS MUTATED | 6 | 16 | 12 |
8Q LOSS WILD-TYPE | 117 | 179 | 46 |
P value = 0.00513 (Wilcoxon-test), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 68.1 (10.6) |
11P LOSS MUTATED | 177 | 69.8 (10.4) |
11P LOSS WILD-TYPE | 230 | 66.8 (10.6) |
P value = 0.00114 (Fisher's exact test), Q value = 0.17
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 43 | 22 | 327 |
15Q LOSS MUTATED | 6 | 4 | 126 |
15Q LOSS WILD-TYPE | 37 | 18 | 201 |
P value = 0.00479 (Fisher's exact test), Q value = 0.24
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 43 | 22 | 327 |
16P LOSS MUTATED | 4 | 3 | 98 |
16P LOSS WILD-TYPE | 39 | 19 | 229 |
P value = 0.00047 (Fisher's exact test), Q value = 0.13
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 236 | 47 | 75 | 8 |
21Q LOSS MUTATED | 42 | 20 | 10 | 0 |
21Q LOSS WILD-TYPE | 194 | 27 | 65 | 8 |
-
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/BLCA-TP/22507732/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/22506467/BLCA-TP.merged_data.txt
-
Number of patients = 408
-
Number of significantly arm-level cnvs = 82
-
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.