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 14 clinical features across 522 patients, 11 significant findings detected with Q value < 0.25.
-
1q gain cnv correlated to 'RACE'.
-
3q gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.
-
6q gain cnv correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
-
7p gain cnv correlated to 'Time to Death'.
-
18p gain cnv correlated to 'GENDER'.
-
18q gain cnv correlated to 'GENDER'.
-
1q loss cnv correlated to 'RADIATION_THERAPY'.
-
9p loss cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
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11q loss cnv correlated to 'GENDER', 'RADIATION_THERAPY', and 'NUMBER_OF_LYMPH_NODES'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
NUMBER PACK YEARS SMOKED |
YEAR OF TOBACCO SMOKING ONSET |
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 | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
11q loss | 172 (33%) | 350 |
0.889 (1.00) |
0.0238 (0.464) |
0.117 (0.676) |
0.913 (1.00) |
0.00682 (0.362) |
1 (1.00) |
0.000329 (0.0755) |
0.000906 (0.116) |
0.119 (0.676) |
0.439 (0.958) |
0.183 (0.768) |
0.00032 (0.0755) |
0.0434 (0.532) |
0.197 (0.773) |
1q gain | 121 (23%) | 401 |
0.657 (1.00) |
0.275 (0.861) |
0.622 (1.00) |
0.16 (0.749) |
0.158 (0.749) |
1 (1.00) |
0.242 (0.812) |
0.0543 (0.567) |
0.00451 (0.31) |
0.587 (1.00) |
0.357 (0.927) |
0.491 (0.96) |
0.00102 (0.117) |
0.635 (1.00) |
3q gain | 254 (49%) | 268 |
0.661 (1.00) |
0.204 (0.786) |
0.755 (1.00) |
0.899 (1.00) |
0.00725 (0.362) |
0.468 (0.96) |
0.0485 (0.546) |
0.315 (0.89) |
1 (1.00) |
0.879 (1.00) |
0.806 (1.00) |
0.00193 (0.201) |
1 (1.00) |
0.842 (1.00) |
6q gain | 63 (12%) | 459 |
0.414 (0.951) |
0.041 (0.513) |
0.3 (0.87) |
0.478 (0.96) |
0.27 (0.861) |
1 (1.00) |
0.65 (1.00) |
0.179 (0.768) |
0.425 (0.957) |
0.0599 (0.6) |
0.000772 (0.111) |
0.101 (0.637) |
0.218 (0.803) |
0.0256 (0.464) |
7p gain | 183 (35%) | 339 |
0.000199 (0.0755) |
0.997 (1.00) |
0.927 (1.00) |
0.38 (0.936) |
0.833 (1.00) |
1 (1.00) |
0.68 (1.00) |
0.392 (0.937) |
0.293 (0.869) |
0.0273 (0.464) |
0.449 (0.96) |
0.574 (1.00) |
0.367 (0.935) |
1 (1.00) |
18p gain | 123 (24%) | 399 |
0.206 (0.786) |
0.149 (0.736) |
0.142 (0.725) |
0.0807 (0.607) |
0.0652 (0.607) |
0.2 (0.784) |
0.000172 (0.0755) |
0.631 (1.00) |
1 (1.00) |
0.276 (0.861) |
0.503 (0.96) |
0.195 (0.771) |
0.494 (0.96) |
0.476 (0.96) |
18q gain | 53 (10%) | 469 |
0.838 (1.00) |
0.954 (1.00) |
0.226 (0.803) |
0.672 (1.00) |
0.622 (1.00) |
0.0895 (0.61) |
0.000462 (0.0818) |
0.868 (1.00) |
0.342 (0.911) |
0.913 (1.00) |
0.864 (1.00) |
0.963 (1.00) |
0.692 (1.00) |
1 (1.00) |
1q loss | 39 (7%) | 483 |
0.0205 (0.464) |
0.275 (0.861) |
0.655 (1.00) |
0.475 (0.96) |
0.932 (1.00) |
1 (1.00) |
0.708 (1.00) |
0.000499 (0.0818) |
1 (1.00) |
0.822 (1.00) |
0.373 (0.935) |
0.878 (1.00) |
0.133 (0.695) |
0.711 (1.00) |
9p loss | 186 (36%) | 336 |
0.569 (1.00) |
0.967 (1.00) |
0.845 (1.00) |
0.741 (1.00) |
0.897 (1.00) |
0.358 (0.927) |
0.18 (0.768) |
0.916 (1.00) |
1 (1.00) |
1.09e-05 (0.0125) |
0.343 (0.911) |
0.764 (1.00) |
0.0543 (0.567) |
0.673 (1.00) |
1p gain | 70 (13%) | 452 |
0.161 (0.749) |
0.79 (1.00) |
0.588 (1.00) |
0.525 (0.976) |
0.183 (0.768) |
1 (1.00) |
0.886 (1.00) |
0.108 (0.651) |
0.00486 (0.31) |
0.23 (0.803) |
0.582 (1.00) |
0.202 (0.785) |
0.0475 (0.541) |
0.378 (0.936) |
2p gain | 97 (19%) | 425 |
0.601 (1.00) |
0.418 (0.951) |
0.984 (1.00) |
0.577 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.0223 (0.464) |
0.35 (0.917) |
0.514 (0.965) |
0.00484 (0.31) |
0.478 (0.96) |
0.853 (1.00) |
0.0834 (0.607) |
1 (1.00) |
2q gain | 74 (14%) | 448 |
0.493 (0.96) |
0.62 (1.00) |
0.856 (1.00) |
0.954 (1.00) |
0.19 (0.769) |
1 (1.00) |
0.119 (0.676) |
0.557 (1.00) |
0.461 (0.96) |
0.0503 (0.555) |
0.756 (1.00) |
0.529 (0.978) |
0.237 (0.809) |
0.774 (1.00) |
3p gain | 81 (16%) | 441 |
0.932 (1.00) |
0.223 (0.803) |
0.5 (0.96) |
0.372 (0.935) |
0.299 (0.87) |
0.116 (0.676) |
0.785 (1.00) |
0.67 (1.00) |
1 (1.00) |
0.896 (1.00) |
0.0892 (0.61) |
0.126 (0.686) |
0.858 (1.00) |
1 (1.00) |
4p gain | 41 (8%) | 481 |
0.443 (0.958) |
0.0237 (0.464) |
0.387 (0.937) |
0.166 (0.754) |
0.437 (0.958) |
1 (1.00) |
0.855 (1.00) |
0.696 (1.00) |
1 (1.00) |
0.97 (1.00) |
0.378 (0.936) |
0.522 (0.975) |
0.0405 (0.513) |
0.118 (0.676) |
4q gain | 37 (7%) | 485 |
0.221 (0.803) |
0.327 (0.897) |
0.0117 (0.426) |
0.373 (0.935) |
0.176 (0.768) |
1 (1.00) |
0.848 (1.00) |
0.676 (1.00) |
0.558 (1.00) |
0.748 (1.00) |
0.874 (1.00) |
0.546 (0.993) |
0.07 (0.607) |
0.0912 (0.614) |
5p gain | 201 (39%) | 321 |
0.819 (1.00) |
0.102 (0.637) |
0.144 (0.731) |
0.786 (1.00) |
0.0186 (0.464) |
0.374 (0.935) |
0.187 (0.769) |
0.0817 (0.607) |
0.189 (0.769) |
0.146 (0.733) |
0.853 (1.00) |
0.0229 (0.464) |
0.278 (0.861) |
0.0606 (0.6) |
5q gain | 68 (13%) | 454 |
0.911 (1.00) |
0.223 (0.803) |
0.145 (0.731) |
0.288 (0.861) |
0.124 (0.686) |
1 (1.00) |
0.143 (0.729) |
0.0277 (0.464) |
0.0744 (0.607) |
0.775 (1.00) |
0.497 (0.96) |
0.0101 (0.414) |
0.832 (1.00) |
0.0669 (0.607) |
6p gain | 83 (16%) | 439 |
0.372 (0.935) |
0.0803 (0.607) |
0.654 (1.00) |
0.402 (0.943) |
0.869 (1.00) |
1 (1.00) |
0.42 (0.952) |
0.785 (1.00) |
0.718 (1.00) |
0.488 (0.96) |
0.0692 (0.607) |
0.393 (0.937) |
0.0236 (0.464) |
1 (1.00) |
7q gain | 129 (25%) | 393 |
0.0449 (0.532) |
0.0868 (0.61) |
0.853 (1.00) |
0.808 (1.00) |
0.618 (1.00) |
1 (1.00) |
0.819 (1.00) |
0.811 (1.00) |
0.345 (0.911) |
0.0939 (0.623) |
0.429 (0.957) |
0.709 (1.00) |
0.303 (0.875) |
0.485 (0.96) |
8p gain | 155 (30%) | 367 |
0.331 (0.902) |
0.935 (1.00) |
0.96 (1.00) |
0.271 (0.861) |
0.372 (0.935) |
1 (1.00) |
0.0403 (0.513) |
0.513 (0.965) |
0.101 (0.637) |
0.564 (1.00) |
0.938 (1.00) |
0.858 (1.00) |
0.287 (0.861) |
0.827 (1.00) |
8q gain | 310 (59%) | 212 |
0.342 (0.911) |
0.61 (1.00) |
0.305 (0.878) |
0.615 (1.00) |
0.357 (0.927) |
0.389 (0.937) |
0.615 (1.00) |
0.0308 (0.464) |
1 (1.00) |
0.915 (1.00) |
0.269 (0.861) |
0.152 (0.739) |
0.606 (1.00) |
0.309 (0.883) |
9p gain | 102 (20%) | 420 |
0.465 (0.96) |
0.127 (0.686) |
0.664 (1.00) |
0.61 (1.00) |
0.246 (0.815) |
1 (1.00) |
0.0183 (0.464) |
0.53 (0.978) |
0.755 (1.00) |
0.0137 (0.426) |
0.224 (0.803) |
0.584 (1.00) |
0.606 (1.00) |
0.449 (0.96) |
9q gain | 139 (27%) | 383 |
0.456 (0.96) |
0.041 (0.513) |
0.237 (0.809) |
0.149 (0.736) |
0.561 (1.00) |
1 (1.00) |
0.434 (0.957) |
0.734 (1.00) |
0.801 (1.00) |
0.481 (0.96) |
0.836 (1.00) |
0.714 (1.00) |
0.928 (1.00) |
0.173 (0.766) |
10p gain | 40 (8%) | 482 |
0.214 (0.801) |
0.777 (1.00) |
0.909 (1.00) |
0.787 (1.00) |
0.225 (0.803) |
1 (1.00) |
0.855 (1.00) |
0.851 (1.00) |
0.586 (1.00) |
0.272 (0.861) |
0.91 (1.00) |
0.0601 (0.6) |
0.927 (1.00) |
0.712 (1.00) |
10q gain | 34 (7%) | 488 |
0.44 (0.958) |
0.689 (1.00) |
0.681 (1.00) |
0.89 (1.00) |
0.766 (1.00) |
1 (1.00) |
0.841 (1.00) |
0.682 (1.00) |
1 (1.00) |
0.634 (1.00) |
0.414 (0.951) |
0.834 (1.00) |
0.17 (0.761) |
0.694 (1.00) |
11p gain | 66 (13%) | 456 |
0.385 (0.936) |
0.504 (0.96) |
0.182 (0.768) |
0.225 (0.803) |
0.0722 (0.607) |
1 (1.00) |
0.766 (1.00) |
0.455 (0.96) |
0.67 (1.00) |
0.58 (1.00) |
0.195 (0.771) |
0.125 (0.686) |
0.0771 (0.607) |
1 (1.00) |
11q gain | 71 (14%) | 451 |
0.953 (1.00) |
0.586 (1.00) |
0.283 (0.861) |
0.536 (0.985) |
0.0592 (0.6) |
1 (1.00) |
0.252 (0.82) |
0.19 (0.769) |
0.458 (0.96) |
0.391 (0.937) |
0.504 (0.96) |
0.0134 (0.426) |
0.649 (1.00) |
1 (1.00) |
12p gain | 148 (28%) | 374 |
0.701 (1.00) |
0.966 (1.00) |
0.953 (1.00) |
0.909 (1.00) |
0.915 (1.00) |
1 (1.00) |
0.229 (0.803) |
1 (1.00) |
0.808 (1.00) |
0.173 (0.766) |
0.623 (1.00) |
0.99 (1.00) |
0.184 (0.768) |
0.657 (1.00) |
12q gain | 89 (17%) | 433 |
0.81 (1.00) |
0.102 (0.637) |
0.705 (1.00) |
0.869 (1.00) |
0.497 (0.96) |
1 (1.00) |
0.896 (1.00) |
0.602 (1.00) |
1 (1.00) |
0.128 (0.686) |
0.603 (1.00) |
0.336 (0.911) |
0.968 (1.00) |
0.789 (1.00) |
13q gain | 57 (11%) | 465 |
0.344 (0.911) |
0.0567 (0.581) |
0.337 (0.911) |
0.285 (0.861) |
0.954 (1.00) |
1 (1.00) |
0.874 (1.00) |
0.74 (1.00) |
1 (1.00) |
0.889 (1.00) |
0.117 (0.676) |
0.925 (1.00) |
0.603 (1.00) |
0.512 (0.965) |
14q gain | 151 (29%) | 371 |
0.0262 (0.464) |
0.744 (1.00) |
0.917 (1.00) |
0.856 (1.00) |
0.849 (1.00) |
1 (1.00) |
0.329 (0.899) |
0.15 (0.736) |
0.0701 (0.607) |
0.205 (0.786) |
0.726 (1.00) |
0.845 (1.00) |
0.0701 (0.607) |
0.657 (1.00) |
15q gain | 72 (14%) | 450 |
0.497 (0.96) |
0.429 (0.957) |
0.866 (1.00) |
0.0221 (0.464) |
0.747 (1.00) |
1 (1.00) |
0.474 (0.96) |
1 (1.00) |
0.687 (1.00) |
0.465 (0.96) |
0.202 (0.785) |
0.384 (0.936) |
0.872 (1.00) |
0.232 (0.809) |
16p gain | 107 (20%) | 415 |
0.243 (0.812) |
0.443 (0.958) |
0.743 (1.00) |
0.859 (1.00) |
0.432 (0.957) |
1 (1.00) |
0.543 (0.991) |
0.32 (0.891) |
1 (1.00) |
0.202 (0.785) |
0.972 (1.00) |
0.0889 (0.61) |
0.116 (0.676) |
0.316 (0.89) |
16q gain | 107 (20%) | 415 |
0.139 (0.717) |
0.492 (0.96) |
0.615 (1.00) |
0.889 (1.00) |
0.854 (1.00) |
1 (1.00) |
0.625 (1.00) |
0.45 (0.96) |
1 (1.00) |
0.684 (1.00) |
0.981 (1.00) |
0.612 (1.00) |
0.205 (0.786) |
0.321 (0.891) |
17p gain | 67 (13%) | 455 |
0.647 (1.00) |
0.514 (0.965) |
0.107 (0.647) |
0.0309 (0.464) |
0.593 (1.00) |
1 (1.00) |
0.301 (0.871) |
1 (1.00) |
0.0722 (0.607) |
0.819 (1.00) |
0.492 (0.96) |
0.34 (0.911) |
0.753 (1.00) |
0.0361 (0.511) |
17q gain | 87 (17%) | 435 |
0.297 (0.869) |
0.663 (1.00) |
0.0738 (0.607) |
0.0126 (0.426) |
0.372 (0.935) |
0.189 (0.769) |
0.428 (0.957) |
0.685 (1.00) |
0.168 (0.76) |
0.114 (0.676) |
0.903 (1.00) |
0.888 (1.00) |
0.735 (1.00) |
0.0275 (0.464) |
19p gain | 56 (11%) | 466 |
0.583 (1.00) |
0.224 (0.803) |
0.608 (1.00) |
0.316 (0.89) |
0.165 (0.754) |
1 (1.00) |
0.15 (0.736) |
0.195 (0.771) |
0.369 (0.935) |
0.0827 (0.607) |
0.492 (0.96) |
0.0441 (0.532) |
0.761 (1.00) |
0.756 (1.00) |
19q gain | 78 (15%) | 444 |
0.378 (0.936) |
0.566 (1.00) |
0.96 (1.00) |
0.926 (1.00) |
0.442 (0.958) |
1 (1.00) |
0.0708 (0.607) |
0.777 (1.00) |
0.297 (0.869) |
0.326 (0.897) |
0.748 (1.00) |
0.0914 (0.614) |
0.179 (0.768) |
0.782 (1.00) |
20p gain | 190 (36%) | 332 |
0.8 (1.00) |
0.947 (1.00) |
0.479 (0.96) |
0.377 (0.936) |
0.103 (0.637) |
1 (1.00) |
0.918 (1.00) |
0.835 (1.00) |
1 (1.00) |
0.486 (0.96) |
0.61 (1.00) |
0.483 (0.96) |
0.726 (1.00) |
0.294 (0.869) |
20q gain | 201 (39%) | 321 |
0.838 (1.00) |
0.603 (1.00) |
0.41 (0.951) |
0.253 (0.82) |
0.738 (1.00) |
1 (1.00) |
0.919 (1.00) |
0.757 (1.00) |
0.844 (1.00) |
0.669 (1.00) |
0.237 (0.809) |
0.857 (1.00) |
0.444 (0.958) |
0.68 (1.00) |
21q gain | 35 (7%) | 487 |
0.798 (1.00) |
0.646 (1.00) |
0.0403 (0.513) |
0.466 (0.96) |
0.337 (0.911) |
1 (1.00) |
0.031 (0.464) |
1 (1.00) |
0.0113 (0.426) |
0.398 (0.939) |
0.767 (1.00) |
0.57 (1.00) |
0.453 (0.96) |
0.0832 (0.607) |
22q gain | 112 (21%) | 410 |
0.084 (0.607) |
0.944 (1.00) |
0.985 (1.00) |
0.723 (1.00) |
0.838 (1.00) |
1 (1.00) |
0.185 (0.768) |
0.804 (1.00) |
0.25 (0.82) |
0.0198 (0.464) |
0.153 (0.739) |
0.789 (1.00) |
0.414 (0.951) |
0.138 (0.715) |
xp gain | 53 (10%) | 469 |
0.503 (0.96) |
0.62 (1.00) |
0.692 (1.00) |
0.286 (0.861) |
0.405 (0.948) |
1 (1.00) |
0.252 (0.82) |
0.624 (1.00) |
0.648 (1.00) |
0.283 (0.861) |
0.0288 (0.464) |
0.173 (0.766) |
0.585 (1.00) |
1 (1.00) |
xq gain | 95 (18%) | 427 |
0.375 (0.936) |
0.235 (0.809) |
0.648 (1.00) |
0.0885 (0.61) |
0.492 (0.96) |
1 (1.00) |
0.443 (0.958) |
0.433 (0.957) |
0.752 (1.00) |
0.9 (1.00) |
0.48 (0.96) |
0.13 (0.687) |
0.251 (0.82) |
0.798 (1.00) |
1p loss | 58 (11%) | 464 |
0.0987 (0.637) |
0.00884 (0.39) |
0.7 (1.00) |
0.867 (1.00) |
0.928 (1.00) |
1 (1.00) |
0.753 (1.00) |
0.0753 (0.607) |
1 (1.00) |
0.00457 (0.31) |
0.602 (1.00) |
0.438 (0.958) |
0.586 (1.00) |
1 (1.00) |
2p loss | 33 (6%) | 489 |
0.639 (1.00) |
0.975 (1.00) |
0.363 (0.935) |
0.503 (0.96) |
0.272 (0.861) |
1 (1.00) |
0.0234 (0.464) |
0.847 (1.00) |
1 (1.00) |
0.212 (0.8) |
0.781 (1.00) |
0.315 (0.89) |
0.655 (1.00) |
0.0756 (0.607) |
2q loss | 46 (9%) | 476 |
0.659 (1.00) |
0.938 (1.00) |
0.0411 (0.513) |
0.433 (0.957) |
0.0818 (0.607) |
1 (1.00) |
0.0135 (0.426) |
0.868 (1.00) |
0.288 (0.861) |
0.285 (0.861) |
0.395 (0.937) |
0.973 (1.00) |
0.177 (0.768) |
0.274 (0.861) |
3p loss | 297 (57%) | 225 |
0.068 (0.607) |
0.879 (1.00) |
0.482 (0.96) |
0.0783 (0.607) |
0.344 (0.911) |
0.416 (0.951) |
0.00712 (0.362) |
0.839 (1.00) |
0.419 (0.952) |
0.00536 (0.317) |
0.027 (0.464) |
0.655 (1.00) |
0.00384 (0.31) |
0.686 (1.00) |
3q loss | 61 (12%) | 461 |
0.0211 (0.464) |
0.476 (0.96) |
0.195 (0.771) |
0.173 (0.766) |
0.3 (0.87) |
1 (1.00) |
0.357 (0.927) |
0.432 (0.957) |
0.661 (1.00) |
0.0944 (0.623) |
0.534 (0.984) |
0.152 (0.739) |
0.246 (0.815) |
0.757 (1.00) |
4p loss | 194 (37%) | 328 |
0.785 (1.00) |
0.482 (0.96) |
0.413 (0.951) |
0.0811 (0.607) |
0.464 (0.96) |
0.326 (0.897) |
0.154 (0.741) |
0.535 (0.984) |
0.693 (1.00) |
0.0709 (0.607) |
0.287 (0.861) |
0.216 (0.803) |
0.0497 (0.554) |
0.678 (1.00) |
4q loss | 151 (29%) | 371 |
0.584 (1.00) |
0.842 (1.00) |
0.102 (0.637) |
0.129 (0.686) |
0.179 (0.768) |
0.237 (0.809) |
0.663 (1.00) |
0.229 (0.803) |
0.811 (1.00) |
0.295 (0.869) |
0.429 (0.957) |
0.154 (0.741) |
0.0448 (0.532) |
0.512 (0.965) |
5p loss | 51 (10%) | 471 |
0.957 (1.00) |
0.234 (0.809) |
0.928 (1.00) |
0.437 (0.958) |
0.751 (1.00) |
1 (1.00) |
0.739 (1.00) |
0.867 (1.00) |
0.327 (0.897) |
0.697 (1.00) |
0.631 (1.00) |
0.893 (1.00) |
0.434 (0.957) |
0.474 (0.96) |
5q loss | 164 (31%) | 358 |
0.264 (0.852) |
0.446 (0.96) |
0.717 (1.00) |
0.112 (0.666) |
0.657 (1.00) |
1 (1.00) |
0.338 (0.911) |
1 (1.00) |
0.665 (1.00) |
0.0514 (0.562) |
0.995 (1.00) |
0.593 (1.00) |
0.0536 (0.567) |
1 (1.00) |
6p loss | 68 (13%) | 454 |
0.349 (0.917) |
0.607 (1.00) |
0.428 (0.957) |
0.571 (1.00) |
0.552 (1.00) |
1 (1.00) |
0.242 (0.812) |
0.766 (1.00) |
1 (1.00) |
0.24 (0.812) |
0.372 (0.935) |
0.882 (1.00) |
0.0945 (0.623) |
0.0306 (0.464) |
6q loss | 68 (13%) | 454 |
0.394 (0.937) |
0.972 (1.00) |
0.753 (1.00) |
0.676 (1.00) |
0.798 (1.00) |
1 (1.00) |
0.078 (0.607) |
0.882 (1.00) |
1 (1.00) |
0.862 (1.00) |
0.802 (1.00) |
0.858 (1.00) |
0.106 (0.645) |
0.554 (1.00) |
7p loss | 29 (6%) | 493 |
0.937 (1.00) |
0.94 (1.00) |
0.159 (0.749) |
0.722 (1.00) |
0.103 (0.637) |
0.0526 (0.567) |
0.666 (1.00) |
0.823 (1.00) |
0.472 (0.96) |
0.753 (1.00) |
0.36 (0.931) |
0.417 (0.951) |
1 (1.00) |
1 (1.00) |
7q loss | 40 (8%) | 482 |
0.187 (0.769) |
0.104 (0.639) |
0.87 (1.00) |
0.109 (0.654) |
0.128 (0.686) |
1 (1.00) |
0.71 (1.00) |
0.572 (1.00) |
0.238 (0.809) |
0.928 (1.00) |
0.072 (0.607) |
0.724 (1.00) |
1 (1.00) |
0.711 (1.00) |
8p loss | 187 (36%) | 335 |
0.0121 (0.426) |
0.389 (0.937) |
0.591 (1.00) |
0.161 (0.749) |
0.57 (1.00) |
0.384 (0.936) |
0.0798 (0.607) |
0.834 (1.00) |
0.683 (1.00) |
0.862 (1.00) |
0.411 (0.951) |
0.319 (0.891) |
0.296 (0.869) |
0.529 (0.978) |
8q loss | 30 (6%) | 492 |
0.271 (0.861) |
0.716 (1.00) |
0.972 (1.00) |
0.679 (1.00) |
0.866 (1.00) |
1 (1.00) |
0.832 (1.00) |
0.381 (0.936) |
0.482 (0.96) |
0.0844 (0.607) |
0.349 (0.917) |
0.39 (0.937) |
0.891 (1.00) |
0.663 (1.00) |
9q loss | 87 (17%) | 435 |
0.806 (1.00) |
0.834 (1.00) |
0.459 (0.96) |
0.397 (0.939) |
0.585 (1.00) |
0.184 (0.768) |
0.792 (1.00) |
1 (1.00) |
0.485 (0.96) |
0.0463 (0.541) |
0.454 (0.96) |
0.399 (0.939) |
0.0864 (0.61) |
0.159 (0.749) |
10p loss | 156 (30%) | 366 |
0.0311 (0.464) |
0.718 (1.00) |
0.37 (0.935) |
0.063 (0.607) |
0.61 (1.00) |
1 (1.00) |
0.0401 (0.513) |
0.745 (1.00) |
0.0476 (0.541) |
0.663 (1.00) |
0.888 (1.00) |
0.667 (1.00) |
0.0727 (0.607) |
0.829 (1.00) |
10q loss | 113 (22%) | 409 |
0.502 (0.96) |
0.851 (1.00) |
0.584 (1.00) |
0.17 (0.761) |
0.127 (0.686) |
1 (1.00) |
0.0304 (0.464) |
0.277 (0.861) |
0.313 (0.89) |
0.453 (0.96) |
0.381 (0.936) |
0.811 (1.00) |
0.219 (0.803) |
0.47 (0.96) |
11p loss | 141 (27%) | 381 |
0.515 (0.965) |
0.541 (0.99) |
0.00924 (0.393) |
0.823 (1.00) |
0.039 (0.513) |
1 (1.00) |
0.317 (0.891) |
0.069 (0.607) |
0.0397 (0.513) |
0.459 (0.96) |
0.838 (1.00) |
0.0185 (0.464) |
0.0961 (0.63) |
0.166 (0.754) |
12p loss | 37 (7%) | 485 |
0.026 (0.464) |
0.0717 (0.607) |
0.471 (0.96) |
0.554 (1.00) |
0.382 (0.936) |
1 (1.00) |
0.701 (1.00) |
0.118 (0.676) |
1 (1.00) |
0.341 (0.911) |
0.0467 (0.541) |
0.552 (1.00) |
0.505 (0.96) |
0.415 (0.951) |
12q loss | 33 (6%) | 489 |
0.764 (1.00) |
0.252 (0.82) |
0.925 (1.00) |
0.388 (0.937) |
0.638 (1.00) |
1 (1.00) |
0.841 (1.00) |
0.194 (0.771) |
0.514 (0.965) |
0.322 (0.891) |
0.249 (0.82) |
0.194 (0.771) |
0.283 (0.861) |
0.0756 (0.607) |
13q loss | 167 (32%) | 355 |
0.836 (1.00) |
0.73 (1.00) |
0.322 (0.891) |
0.925 (1.00) |
0.838 (1.00) |
0.311 (0.885) |
0.459 (0.96) |
1 (1.00) |
0.529 (0.978) |
0.513 (0.965) |
0.322 (0.891) |
0.283 (0.861) |
0.0376 (0.513) |
0.192 (0.771) |
14q loss | 58 (11%) | 464 |
0.928 (1.00) |
0.887 (1.00) |
0.344 (0.911) |
0.766 (1.00) |
0.859 (1.00) |
1 (1.00) |
0.0856 (0.61) |
0.0262 (0.464) |
0.191 (0.77) |
0.792 (1.00) |
0.793 (1.00) |
0.185 (0.768) |
0.449 (0.96) |
1 (1.00) |
15q loss | 103 (20%) | 419 |
0.12 (0.677) |
0.236 (0.809) |
0.71 (1.00) |
0.469 (0.96) |
0.297 (0.869) |
1 (1.00) |
1 (1.00) |
0.528 (0.978) |
0.0673 (0.607) |
0.956 (1.00) |
0.485 (0.96) |
0.368 (0.935) |
0.385 (0.936) |
0.132 (0.692) |
16p loss | 63 (12%) | 459 |
0.296 (0.869) |
0.0297 (0.464) |
0.944 (1.00) |
0.014 (0.426) |
0.0336 (0.488) |
1 (1.00) |
0.545 (0.993) |
0.539 (0.988) |
0.427 (0.957) |
0.746 (1.00) |
0.596 (1.00) |
0.0276 (0.464) |
0.616 (1.00) |
0.121 (0.681) |
16q loss | 81 (16%) | 441 |
0.433 (0.957) |
0.0879 (0.61) |
0.852 (1.00) |
0.214 (0.801) |
0.1 (0.637) |
1 (1.00) |
0.221 (0.803) |
0.491 (0.96) |
0.102 (0.637) |
0.928 (1.00) |
0.227 (0.803) |
0.13 (0.687) |
0.768 (1.00) |
0.585 (1.00) |
17p loss | 107 (20%) | 415 |
0.331 (0.902) |
0.227 (0.803) |
0.0898 (0.61) |
0.412 (0.951) |
0.654 (1.00) |
0.184 (0.768) |
0.715 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.429 (0.957) |
0.821 (1.00) |
0.522 (0.975) |
0.411 (0.951) |
0.0841 (0.607) |
17q loss | 34 (7%) | 488 |
0.912 (1.00) |
0.633 (1.00) |
0.644 (1.00) |
0.403 (0.943) |
0.448 (0.96) |
1 (1.00) |
0.841 (1.00) |
0.572 (1.00) |
0.524 (0.976) |
0.848 (1.00) |
0.624 (1.00) |
0.928 (1.00) |
0.735 (1.00) |
0.227 (0.803) |
18p loss | 104 (20%) | 418 |
0.128 (0.686) |
0.835 (1.00) |
0.906 (1.00) |
0.948 (1.00) |
0.75 (1.00) |
1 (1.00) |
0.0842 (0.607) |
0.798 (1.00) |
0.163 (0.75) |
0.779 (1.00) |
0.695 (1.00) |
0.875 (1.00) |
0.21 (0.8) |
0.0203 (0.464) |
18q loss | 211 (40%) | 311 |
0.0737 (0.607) |
0.101 (0.637) |
0.959 (1.00) |
0.968 (1.00) |
0.394 (0.937) |
1 (1.00) |
0.616 (1.00) |
0.757 (1.00) |
0.0325 (0.479) |
0.238 (0.809) |
0.0263 (0.464) |
0.139 (0.717) |
0.0173 (0.464) |
0.308 (0.883) |
19p loss | 98 (19%) | 424 |
0.00853 (0.39) |
0.148 (0.736) |
0.068 (0.607) |
0.163 (0.75) |
0.0778 (0.607) |
1 (1.00) |
0.129 (0.687) |
0.25 (0.82) |
0.367 (0.935) |
0.486 (0.96) |
0.0178 (0.464) |
0.484 (0.96) |
0.178 (0.768) |
0.128 (0.686) |
19q loss | 86 (16%) | 436 |
0.0688 (0.607) |
0.064 (0.607) |
0.00774 (0.37) |
0.0285 (0.464) |
0.453 (0.96) |
1 (1.00) |
0.351 (0.918) |
0.181 (0.768) |
1 (1.00) |
0.667 (1.00) |
0.0268 (0.464) |
0.87 (1.00) |
0.0352 (0.506) |
0.409 (0.951) |
20p loss | 47 (9%) | 475 |
0.785 (1.00) |
0.79 (1.00) |
0.51 (0.965) |
0.964 (1.00) |
0.288 (0.861) |
1 (1.00) |
1 (1.00) |
0.158 (0.749) |
0.646 (1.00) |
0.371 (0.935) |
0.929 (1.00) |
0.155 (0.743) |
0.756 (1.00) |
1 (1.00) |
20q loss | 28 (5%) | 494 |
0.211 (0.8) |
0.567 (1.00) |
0.122 (0.683) |
0.288 (0.861) |
0.925 (1.00) |
1 (1.00) |
0.662 (1.00) |
0.501 (0.96) |
0.46 (0.96) |
0.031 (0.464) |
0.00552 (0.317) |
0.214 (0.801) |
0.872 (1.00) |
1 (1.00) |
21q loss | 184 (35%) | 338 |
0.28 (0.861) |
0.953 (1.00) |
0.852 (1.00) |
0.0564 (0.581) |
0.28 (0.861) |
1 (1.00) |
0.68 (1.00) |
0.289 (0.861) |
0.836 (1.00) |
0.00482 (0.31) |
0.698 (1.00) |
0.542 (0.991) |
0.00446 (0.31) |
0.833 (1.00) |
22q loss | 75 (14%) | 447 |
0.672 (1.00) |
0.931 (1.00) |
0.577 (1.00) |
0.271 (0.861) |
0.495 (0.96) |
1 (1.00) |
0.204 (0.786) |
0.889 (1.00) |
0.459 (0.96) |
0.839 (1.00) |
0.263 (0.851) |
0.221 (0.803) |
0.148 (0.736) |
0.244 (0.815) |
xp loss | 134 (26%) | 388 |
0.0368 (0.513) |
0.805 (1.00) |
0.399 (0.939) |
0.0141 (0.426) |
0.575 (1.00) |
0.242 (0.812) |
0.309 (0.883) |
0.563 (1.00) |
0.22 (0.803) |
0.0131 (0.426) |
0.968 (1.00) |
0.0171 (0.464) |
0.438 (0.958) |
0.819 (1.00) |
xq loss | 83 (16%) | 439 |
0.182 (0.768) |
0.39 (0.937) |
0.0534 (0.567) |
0.0438 (0.532) |
0.224 (0.803) |
0.163 (0.75) |
0.5 (0.96) |
0.483 (0.96) |
0.109 (0.654) |
0.0846 (0.607) |
0.773 (1.00) |
0.0155 (0.457) |
0.964 (1.00) |
0.782 (1.00) |
P value = 0.00102 (Fisher's exact test), Q value = 0.12
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 48 | 446 |
1Q GAIN MUTATED | 0 | 0 | 21 | 95 |
1Q GAIN WILD-TYPE | 2 | 11 | 27 | 351 |
P value = 0.00193 (Wilcoxon-test), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 2.2 (4.3) |
3Q GAIN MUTATED | 205 | 2.7 (5.3) |
3Q GAIN WILD-TYPE | 203 | 1.7 (2.8) |
P value = 0.000772 (Wilcoxon-test), Q value = 0.11
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 277 | 1967.4 (12.8) |
6Q GAIN MUTATED | 25 | 1975.2 (11.2) |
6Q GAIN WILD-TYPE | 252 | 1966.6 (12.7) |
P value = 0.000199 (logrank test), Q value = 0.075
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 521 | 218 | 0.1 - 211.0 (20.9) |
7P GAIN MUTATED | 182 | 98 | 0.1 - 153.9 (18.8) |
7P GAIN WILD-TYPE | 339 | 120 | 0.1 - 211.0 (21.6) |
P value = 0.000172 (Fisher's exact test), Q value = 0.075
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
18P GAIN MUTATED | 17 | 106 |
18P GAIN WILD-TYPE | 123 | 276 |
P value = 0.000462 (Fisher's exact test), Q value = 0.082
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
18Q GAIN MUTATED | 4 | 49 |
18Q GAIN WILD-TYPE | 136 | 333 |
P value = 0.000499 (Fisher's exact test), Q value = 0.082
nPatients | NO | YES |
---|---|---|
ALL | 151 | 283 |
1Q LOSS MUTATED | 21 | 12 |
1Q LOSS WILD-TYPE | 130 | 271 |
P value = 1.09e-05 (Wilcoxon-test), Q value = 0.013
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 293 | 45.9 (35.3) |
9P LOSS MUTATED | 114 | 53.2 (30.6) |
9P LOSS WILD-TYPE | 179 | 41.2 (37.4) |
P value = 0.000329 (Fisher's exact test), Q value = 0.075
nPatients | FEMALE | MALE |
---|---|---|
ALL | 140 | 382 |
11Q LOSS MUTATED | 29 | 143 |
11Q LOSS WILD-TYPE | 111 | 239 |
P value = 0.000906 (Fisher's exact test), Q value = 0.12
nPatients | NO | YES |
---|---|---|
ALL | 151 | 283 |
11Q LOSS MUTATED | 35 | 111 |
11Q LOSS WILD-TYPE | 116 | 172 |
P value = 0.00032 (Wilcoxon-test), Q value = 0.075
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 408 | 2.2 (4.3) |
11Q LOSS MUTATED | 128 | 3.0 (4.9) |
11Q LOSS WILD-TYPE | 280 | 1.9 (4.0) |
-
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/HNSC-TP/19781934/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/19775211/HNSC-TP.merged_data.txt
-
Number of patients = 522
-
Number of significantly arm-level cnvs = 82
-
Number of selected clinical features = 14
-
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.