This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 73 focal events and 12 clinical features across 404 patients, 4 significant findings detected with Q value < 0.25.
-
amp_18p11.31 cnv correlated to 'GENDER'.
-
del_3p24.1 cnv correlated to 'Time to Death'.
-
del_3p12.1 cnv correlated to 'Time to Death'.
-
del_11q23.1 cnv correlated to 'GENDER'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | YEAROFTOBACCOSMOKINGONSET |
NUMBER OF LYMPH NODES |
||
nCNV (%) | nWild-Type | logrank test | t-test | Chi-square 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 | t-test | t-test | t-test | |
amp 18p11 31 | 119 (29%) | 285 |
0.105 (1.00) |
0.0667 (1.00) |
0.0883 (1.00) |
0.0923 (1.00) |
0.266 (1.00) |
0.29 (1.00) |
0.000183 (0.159) |
1 (1.00) |
0.584 (1.00) |
0.0472 (1.00) |
0.344 (1.00) |
0.945 (1.00) |
del 3p24 1 | 293 (73%) | 111 |
5.84e-05 (0.0511) |
0.644 (1.00) |
0.162 (1.00) |
0.00769 (1.00) |
0.0363 (1.00) |
0.241 (1.00) |
0.00442 (1.00) |
0.00684 (1.00) |
0.889 (1.00) |
0.000553 (0.482) |
0.459 (1.00) |
0.00166 (1.00) |
del 3p12 1 | 274 (68%) | 130 |
9.41e-05 (0.0822) |
0.697 (1.00) |
0.136 (1.00) |
0.259 (1.00) |
0.0726 (1.00) |
0.703 (1.00) |
0.0136 (1.00) |
0.119 (1.00) |
0.421 (1.00) |
0.0757 (1.00) |
0.778 (1.00) |
0.0112 (1.00) |
del 11q23 1 | 188 (47%) | 216 |
0.411 (1.00) |
0.139 (1.00) |
0.945 (1.00) |
0.947 (1.00) |
0.0111 (1.00) |
0.468 (1.00) |
7.13e-05 (0.0624) |
0.548 (1.00) |
0.132 (1.00) |
0.0816 (1.00) |
0.518 (1.00) |
0.024 (1.00) |
amp 2q11 2 | 84 (21%) | 320 |
0.303 (1.00) |
0.93 (1.00) |
0.0583 (1.00) |
0.000709 (0.617) |
0.294 (1.00) |
0.632 (1.00) |
0.282 (1.00) |
0.486 (1.00) |
0.644 (1.00) |
0.21 (1.00) |
0.595 (1.00) |
0.501 (1.00) |
amp 2q31 2 | 88 (22%) | 316 |
0.155 (1.00) |
0.776 (1.00) |
0.382 (1.00) |
0.181 (1.00) |
0.203 (1.00) |
0.0379 (1.00) |
0.288 (1.00) |
1 (1.00) |
1 (1.00) |
0.233 (1.00) |
0.583 (1.00) |
0.139 (1.00) |
amp 3q26 33 | 300 (74%) | 104 |
0.072 (1.00) |
0.152 (1.00) |
0.075 (1.00) |
0.478 (1.00) |
0.0985 (1.00) |
0.685 (1.00) |
0.00364 (1.00) |
0.197 (1.00) |
0.391 (1.00) |
0.0219 (1.00) |
0.029 (1.00) |
0.0424 (1.00) |
amp 5p15 33 | 183 (45%) | 221 |
0.979 (1.00) |
0.0451 (1.00) |
0.627 (1.00) |
0.474 (1.00) |
0.176 (1.00) |
0.276 (1.00) |
0.0365 (1.00) |
0.681 (1.00) |
0.131 (1.00) |
0.999 (1.00) |
0.257 (1.00) |
0.578 (1.00) |
amp 5p12 | 158 (39%) | 246 |
0.76 (1.00) |
0.046 (1.00) |
0.883 (1.00) |
0.579 (1.00) |
0.461 (1.00) |
0.269 (1.00) |
0.176 (1.00) |
0.641 (1.00) |
0.0211 (1.00) |
0.451 (1.00) |
0.711 (1.00) |
0.722 (1.00) |
amp 6p12 1 | 80 (20%) | 324 |
0.824 (1.00) |
0.232 (1.00) |
0.975 (1.00) |
0.282 (1.00) |
0.836 (1.00) |
0.635 (1.00) |
1 (1.00) |
1 (1.00) |
0.159 (1.00) |
0.788 (1.00) |
0.435 (1.00) |
0.477 (1.00) |
amp 6q12 | 73 (18%) | 331 |
0.713 (1.00) |
0.72 (1.00) |
0.948 (1.00) |
0.526 (1.00) |
0.963 (1.00) |
1 (1.00) |
0.255 (1.00) |
0.67 (1.00) |
0.103 (1.00) |
0.602 (1.00) |
0.0471 (1.00) |
0.979 (1.00) |
amp 7p11 2 | 172 (43%) | 232 |
0.00598 (1.00) |
0.306 (1.00) |
0.818 (1.00) |
0.0867 (1.00) |
0.831 (1.00) |
0.468 (1.00) |
0.912 (1.00) |
0.0207 (1.00) |
0.8 (1.00) |
0.848 (1.00) |
0.22 (1.00) |
0.5 (1.00) |
amp 7q21 3 | 139 (34%) | 265 |
0.00241 (1.00) |
0.56 (1.00) |
0.732 (1.00) |
0.0793 (1.00) |
0.386 (1.00) |
0.241 (1.00) |
0.418 (1.00) |
0.0471 (1.00) |
0.235 (1.00) |
0.155 (1.00) |
0.772 (1.00) |
0.502 (1.00) |
amp 8p11 23 | 125 (31%) | 279 |
0.26 (1.00) |
0.445 (1.00) |
0.0659 (1.00) |
0.0965 (1.00) |
0.377 (1.00) |
0.84 (1.00) |
0.905 (1.00) |
0.17 (1.00) |
0.499 (1.00) |
0.456 (1.00) |
0.691 (1.00) |
0.851 (1.00) |
amp 8q11 21 | 234 (58%) | 170 |
0.915 (1.00) |
0.868 (1.00) |
0.116 (1.00) |
0.345 (1.00) |
0.298 (1.00) |
0.359 (1.00) |
0.911 (1.00) |
0.826 (1.00) |
0.704 (1.00) |
0.807 (1.00) |
0.103 (1.00) |
0.229 (1.00) |
amp 8q24 21 | 294 (73%) | 110 |
0.14 (1.00) |
0.485 (1.00) |
0.511 (1.00) |
0.406 (1.00) |
0.00969 (1.00) |
0.544 (1.00) |
0.902 (1.00) |
0.757 (1.00) |
0.778 (1.00) |
0.687 (1.00) |
0.00959 (1.00) |
0.33 (1.00) |
amp 9p24 1 | 101 (25%) | 303 |
0.705 (1.00) |
0.105 (1.00) |
0.507 (1.00) |
0.593 (1.00) |
0.285 (1.00) |
0.408 (1.00) |
0.00335 (1.00) |
1 (1.00) |
0.111 (1.00) |
0.00922 (1.00) |
0.534 (1.00) |
0.41 (1.00) |
amp 9p23 | 99 (25%) | 305 |
0.966 (1.00) |
0.212 (1.00) |
0.455 (1.00) |
0.857 (1.00) |
0.173 (1.00) |
0.4 (1.00) |
0.0209 (1.00) |
1 (1.00) |
0.383 (1.00) |
0.00829 (1.00) |
0.52 (1.00) |
0.573 (1.00) |
amp 9p13 3 | 112 (28%) | 292 |
0.713 (1.00) |
0.439 (1.00) |
0.149 (1.00) |
0.996 (1.00) |
0.455 (1.00) |
0.844 (1.00) |
0.269 (1.00) |
0.763 (1.00) |
0.675 (1.00) |
0.478 (1.00) |
0.317 (1.00) |
0.529 (1.00) |
amp 9q34 3 | 136 (34%) | 268 |
0.517 (1.00) |
0.0521 (1.00) |
0.0634 (1.00) |
0.0183 (1.00) |
0.211 (1.00) |
0.845 (1.00) |
0.907 (1.00) |
1 (1.00) |
0.511 (1.00) |
0.445 (1.00) |
0.823 (1.00) |
0.568 (1.00) |
amp 11p13 | 84 (21%) | 320 |
0.418 (1.00) |
0.206 (1.00) |
0.213 (1.00) |
0.763 (1.00) |
0.281 (1.00) |
0.673 (1.00) |
0.591 (1.00) |
1 (1.00) |
1 (1.00) |
0.000667 (0.581) |
0.451 (1.00) |
0.261 (1.00) |
amp 11q13 3 | 183 (45%) | 221 |
0.0264 (1.00) |
0.601 (1.00) |
0.536 (1.00) |
0.564 (1.00) |
0.303 (1.00) |
0.0996 (1.00) |
0.583 (1.00) |
0.0342 (1.00) |
0.131 (1.00) |
0.0701 (1.00) |
0.716 (1.00) |
0.0549 (1.00) |
amp 12p13 33 | 127 (31%) | 277 |
0.542 (1.00) |
0.413 (1.00) |
0.974 (1.00) |
0.943 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.478 (1.00) |
0.774 (1.00) |
1 (1.00) |
0.455 (1.00) |
0.228 (1.00) |
0.746 (1.00) |
amp 12q15 | 79 (20%) | 325 |
0.717 (1.00) |
0.128 (1.00) |
0.256 (1.00) |
0.754 (1.00) |
0.249 (1.00) |
0.807 (1.00) |
0.782 (1.00) |
0.68 (1.00) |
0.27 (1.00) |
0.154 (1.00) |
0.382 (1.00) |
0.595 (1.00) |
amp 13q22 1 | 88 (22%) | 316 |
0.0452 (1.00) |
0.0621 (1.00) |
0.814 (1.00) |
0.392 (1.00) |
0.591 (1.00) |
0.49 (1.00) |
0.426 (1.00) |
0.489 (1.00) |
0.171 (1.00) |
0.445 (1.00) |
0.097 (1.00) |
0.645 (1.00) |
amp 13q34 | 82 (20%) | 322 |
0.12 (1.00) |
0.124 (1.00) |
0.114 (1.00) |
0.157 (1.00) |
0.144 (1.00) |
0.655 (1.00) |
0.274 (1.00) |
0.485 (1.00) |
0.353 (1.00) |
0.309 (1.00) |
0.185 (1.00) |
0.397 (1.00) |
amp 15q26 3 | 86 (21%) | 318 |
0.00901 (1.00) |
0.986 (1.00) |
0.954 (1.00) |
0.201 (1.00) |
0.974 (1.00) |
0.828 (1.00) |
0.788 (1.00) |
1 (1.00) |
1 (1.00) |
0.442 (1.00) |
0.451 (1.00) |
0.342 (1.00) |
amp 17q12 | 65 (16%) | 339 |
0.277 (1.00) |
0.0876 (1.00) |
0.639 (1.00) |
0.559 (1.00) |
0.679 (1.00) |
1 (1.00) |
0.298 (1.00) |
0.143 (1.00) |
0.866 (1.00) |
0.238 (1.00) |
0.156 (1.00) |
0.185 (1.00) |
amp 18q11 2 | 80 (20%) | 324 |
0.933 (1.00) |
0.013 (1.00) |
0.392 (1.00) |
0.63 (1.00) |
0.418 (1.00) |
0.619 (1.00) |
0.055 (1.00) |
0.275 (1.00) |
0.753 (1.00) |
0.159 (1.00) |
0.987 (1.00) |
0.423 (1.00) |
amp 20p12 2 | 148 (37%) | 256 |
0.963 (1.00) |
0.925 (1.00) |
0.923 (1.00) |
0.952 (1.00) |
0.41 (1.00) |
0.263 (1.00) |
0.57 (1.00) |
1 (1.00) |
0.3 (1.00) |
0.327 (1.00) |
0.463 (1.00) |
0.993 (1.00) |
amp 20q11 22 | 177 (44%) | 227 |
0.849 (1.00) |
0.372 (1.00) |
0.464 (1.00) |
0.36 (1.00) |
0.877 (1.00) |
0.206 (1.00) |
0.74 (1.00) |
0.313 (1.00) |
0.312 (1.00) |
0.7 (1.00) |
0.0755 (1.00) |
0.299 (1.00) |
amp xq28 | 115 (28%) | 289 |
0.286 (1.00) |
0.739 (1.00) |
0.83 (1.00) |
0.0704 (1.00) |
0.199 (1.00) |
0.205 (1.00) |
0.903 (1.00) |
0.77 (1.00) |
0.0727 (1.00) |
0.311 (1.00) |
0.882 (1.00) |
0.505 (1.00) |
del 1p36 21 | 77 (19%) | 327 |
0.256 (1.00) |
0.0454 (1.00) |
0.324 (1.00) |
0.567 (1.00) |
0.759 (1.00) |
0.615 (1.00) |
0.266 (1.00) |
0.184 (1.00) |
0.0369 (1.00) |
0.00926 (1.00) |
0.141 (1.00) |
0.0962 (1.00) |
del 1p13 2 | 102 (25%) | 302 |
0.223 (1.00) |
0.0571 (1.00) |
0.822 (1.00) |
0.763 (1.00) |
0.95 (1.00) |
0.515 (1.00) |
0.899 (1.00) |
0.382 (1.00) |
0.471 (1.00) |
0.0293 (1.00) |
0.592 (1.00) |
0.962 (1.00) |
del 1q44 | 37 (9%) | 367 |
0.296 (1.00) |
0.266 (1.00) |
0.708 (1.00) |
0.686 (1.00) |
0.901 (1.00) |
1 (1.00) |
0.573 (1.00) |
1 (1.00) |
1 (1.00) |
0.733 (1.00) |
0.11 (1.00) |
0.0407 (1.00) |
del 2q21 2 | 54 (13%) | 350 |
0.798 (1.00) |
0.283 (1.00) |
0.803 (1.00) |
0.639 (1.00) |
0.158 (1.00) |
1 (1.00) |
0.00918 (1.00) |
1 (1.00) |
0.268 (1.00) |
0.761 (1.00) |
0.485 (1.00) |
0.00744 (1.00) |
del 2q22 1 | 85 (21%) | 319 |
0.463 (1.00) |
0.245 (1.00) |
0.348 (1.00) |
0.128 (1.00) |
0.539 (1.00) |
0.204 (1.00) |
0.139 (1.00) |
0.487 (1.00) |
0.879 (1.00) |
0.332 (1.00) |
0.564 (1.00) |
0.89 (1.00) |
del 2q36 2 | 121 (30%) | 283 |
0.0973 (1.00) |
0.682 (1.00) |
0.069 (1.00) |
0.00142 (1.00) |
0.699 (1.00) |
0.69 (1.00) |
0.472 (1.00) |
0.771 (1.00) |
0.497 (1.00) |
0.0734 (1.00) |
0.503 (1.00) |
0.728 (1.00) |
del 4p15 2 | 169 (42%) | 235 |
0.115 (1.00) |
0.361 (1.00) |
0.825 (1.00) |
0.526 (1.00) |
0.579 (1.00) |
0.266 (1.00) |
0.0592 (1.00) |
0.825 (1.00) |
0.525 (1.00) |
0.163 (1.00) |
0.626 (1.00) |
0.0513 (1.00) |
del 4q22 1 | 129 (32%) | 275 |
0.838 (1.00) |
0.995 (1.00) |
0.281 (1.00) |
0.664 (1.00) |
0.629 (1.00) |
0.426 (1.00) |
0.724 (1.00) |
0.775 (1.00) |
0.687 (1.00) |
0.384 (1.00) |
0.125 (1.00) |
0.12 (1.00) |
del 4q35 2 | 164 (41%) | 240 |
0.563 (1.00) |
0.847 (1.00) |
0.0548 (1.00) |
0.0313 (1.00) |
0.635 (1.00) |
0.459 (1.00) |
0.145 (1.00) |
0.408 (1.00) |
1 (1.00) |
0.866 (1.00) |
0.0974 (1.00) |
0.0991 (1.00) |
del 5q11 2 | 165 (41%) | 239 |
0.58 (1.00) |
0.189 (1.00) |
0.542 (1.00) |
0.0114 (1.00) |
0.0741 (1.00) |
0.346 (1.00) |
0.0733 (1.00) |
0.217 (1.00) |
0.252 (1.00) |
0.00526 (1.00) |
0.904 (1.00) |
0.0898 (1.00) |
del 5q15 | 174 (43%) | 230 |
0.494 (1.00) |
0.187 (1.00) |
0.513 (1.00) |
0.0125 (1.00) |
0.505 (1.00) |
0.578 (1.00) |
0.149 (1.00) |
0.155 (1.00) |
0.315 (1.00) |
0.00808 (1.00) |
0.957 (1.00) |
0.285 (1.00) |
del 5q35 3 | 155 (38%) | 249 |
0.782 (1.00) |
0.305 (1.00) |
0.406 (1.00) |
0.0381 (1.00) |
0.165 (1.00) |
1 (1.00) |
0.175 (1.00) |
0.288 (1.00) |
0.368 (1.00) |
0.0871 (1.00) |
0.869 (1.00) |
0.877 (1.00) |
del 6p25 3 | 76 (19%) | 328 |
0.181 (1.00) |
0.39 (1.00) |
0.183 (1.00) |
0.0764 (1.00) |
0.472 (1.00) |
1 (1.00) |
0.122 (1.00) |
1 (1.00) |
0.521 (1.00) |
0.698 (1.00) |
0.144 (1.00) |
0.467 (1.00) |
del 7q31 1 | 65 (16%) | 339 |
0.86 (1.00) |
0.103 (1.00) |
0.652 (1.00) |
0.892 (1.00) |
0.0928 (1.00) |
0.811 (1.00) |
0.882 (1.00) |
1 (1.00) |
0.494 (1.00) |
0.106 (1.00) |
0.0704 (1.00) |
0.579 (1.00) |
del 7q36 1 | 103 (25%) | 301 |
0.0413 (1.00) |
0.865 (1.00) |
0.748 (1.00) |
0.95 (1.00) |
0.343 (1.00) |
0.525 (1.00) |
0.103 (1.00) |
1 (1.00) |
0.776 (1.00) |
0.237 (1.00) |
0.16 (1.00) |
0.366 (1.00) |
del 8p23 2 | 234 (58%) | 170 |
0.00179 (1.00) |
0.021 (1.00) |
0.936 (1.00) |
0.556 (1.00) |
0.429 (1.00) |
0.194 (1.00) |
0.436 (1.00) |
0.0396 (1.00) |
0.8 (1.00) |
0.0991 (1.00) |
0.945 (1.00) |
0.212 (1.00) |
del 9p23 | 181 (45%) | 223 |
0.415 (1.00) |
0.22 (1.00) |
0.525 (1.00) |
0.842 (1.00) |
0.491 (1.00) |
0.713 (1.00) |
0.15 (1.00) |
0.231 (1.00) |
0.801 (1.00) |
0.0239 (1.00) |
0.773 (1.00) |
0.2 (1.00) |
del 9p21 3 | 231 (57%) | 173 |
0.0102 (1.00) |
0.522 (1.00) |
0.357 (1.00) |
0.531 (1.00) |
0.601 (1.00) |
0.282 (1.00) |
0.58 (1.00) |
0.0882 (1.00) |
0.613 (1.00) |
0.144 (1.00) |
0.422 (1.00) |
0.193 (1.00) |
del 9q21 11 | 71 (18%) | 333 |
0.161 (1.00) |
0.854 (1.00) |
0.648 (1.00) |
0.565 (1.00) |
0.561 (1.00) |
0.633 (1.00) |
0.564 (1.00) |
0.667 (1.00) |
0.324 (1.00) |
0.119 (1.00) |
0.551 (1.00) |
0.271 (1.00) |
del 9q34 3 | 60 (15%) | 344 |
0.742 (1.00) |
0.546 (1.00) |
0.879 (1.00) |
0.681 (1.00) |
0.932 (1.00) |
0.579 (1.00) |
0.44 (1.00) |
0.658 (1.00) |
1 (1.00) |
0.109 (1.00) |
0.922 (1.00) |
0.477 (1.00) |
del 10p15 3 | 133 (33%) | 271 |
0.0158 (1.00) |
0.71 (1.00) |
0.259 (1.00) |
0.135 (1.00) |
0.0348 (1.00) |
0.334 (1.00) |
0.484 (1.00) |
0.184 (1.00) |
0.185 (1.00) |
0.656 (1.00) |
0.79 (1.00) |
0.0732 (1.00) |
del 10p11 21 | 125 (31%) | 279 |
0.0757 (1.00) |
0.281 (1.00) |
0.598 (1.00) |
0.26 (1.00) |
0.42 (1.00) |
0.842 (1.00) |
0.405 (1.00) |
0.334 (1.00) |
0.0793 (1.00) |
0.272 (1.00) |
0.343 (1.00) |
0.721 (1.00) |
del 10q23 31 | 98 (24%) | 306 |
0.175 (1.00) |
0.568 (1.00) |
0.518 (1.00) |
0.547 (1.00) |
0.891 (1.00) |
0.831 (1.00) |
0.125 (1.00) |
1 (1.00) |
0.464 (1.00) |
0.162 (1.00) |
0.0251 (1.00) |
0.35 (1.00) |
del 11p15 5 | 125 (31%) | 279 |
0.024 (1.00) |
0.752 (1.00) |
0.114 (1.00) |
0.885 (1.00) |
0.0493 (1.00) |
0.312 (1.00) |
0.405 (1.00) |
0.572 (1.00) |
0.893 (1.00) |
0.659 (1.00) |
0.962 (1.00) |
0.261 (1.00) |
del 12q24 33 | 49 (12%) | 355 |
0.729 (1.00) |
0.852 (1.00) |
0.725 (1.00) |
0.267 (1.00) |
0.638 (1.00) |
0.279 (1.00) |
1 (1.00) |
1 (1.00) |
0.849 (1.00) |
0.704 (1.00) |
0.691 (1.00) |
0.646 (1.00) |
del 13q12 11 | 173 (43%) | 231 |
0.315 (1.00) |
0.985 (1.00) |
0.0739 (1.00) |
0.295 (1.00) |
0.0107 (1.00) |
0.579 (1.00) |
0.0593 (1.00) |
0.156 (1.00) |
0.801 (1.00) |
0.0626 (1.00) |
0.958 (1.00) |
0.0266 (1.00) |
del 13q14 2 | 165 (41%) | 239 |
0.467 (1.00) |
0.411 (1.00) |
0.398 (1.00) |
0.415 (1.00) |
0.183 (1.00) |
0.853 (1.00) |
0.117 (1.00) |
0.523 (1.00) |
0.702 (1.00) |
0.125 (1.00) |
0.901 (1.00) |
0.264 (1.00) |
del 14q11 2 | 51 (13%) | 353 |
0.088 (1.00) |
0.296 (1.00) |
0.274 (1.00) |
0.0425 (1.00) |
0.948 (1.00) |
0.758 (1.00) |
0.413 (1.00) |
1 (1.00) |
0.707 (1.00) |
0.0205 (1.00) |
0.326 (1.00) |
0.0365 (1.00) |
del 14q32 32 | 53 (13%) | 351 |
0.537 (1.00) |
0.196 (1.00) |
0.48 (1.00) |
0.0337 (1.00) |
0.752 (1.00) |
0.723 (1.00) |
0.104 (1.00) |
1 (1.00) |
0.0951 (1.00) |
0.434 (1.00) |
0.433 (1.00) |
0.197 (1.00) |
del 15q15 1 | 93 (23%) | 311 |
0.32 (1.00) |
0.417 (1.00) |
0.613 (1.00) |
0.173 (1.00) |
0.657 (1.00) |
0.153 (1.00) |
0.516 (1.00) |
0.1 (1.00) |
0.297 (1.00) |
0.691 (1.00) |
0.675 (1.00) |
0.199 (1.00) |
del 16q23 3 | 80 (20%) | 324 |
0.298 (1.00) |
0.114 (1.00) |
0.122 (1.00) |
0.202 (1.00) |
0.0928 (1.00) |
0.32 (1.00) |
0.491 (1.00) |
0.471 (1.00) |
0.876 (1.00) |
0.568 (1.00) |
0.35 (1.00) |
0.885 (1.00) |
del 17q25 3 | 56 (14%) | 348 |
0.692 (1.00) |
0.702 (1.00) |
0.629 (1.00) |
0.13 (1.00) |
0.29 (1.00) |
0.219 (1.00) |
0.426 (1.00) |
0.114 (1.00) |
0.278 (1.00) |
0.766 (1.00) |
0.843 (1.00) |
0.963 (1.00) |
del 18q21 2 | 211 (52%) | 193 |
0.0646 (1.00) |
0.323 (1.00) |
0.653 (1.00) |
0.557 (1.00) |
0.443 (1.00) |
0.856 (1.00) |
0.037 (1.00) |
0.431 (1.00) |
0.707 (1.00) |
0.000913 (0.793) |
0.12 (1.00) |
0.0313 (1.00) |
del 18q23 | 225 (56%) | 179 |
0.029 (1.00) |
0.0743 (1.00) |
0.876 (1.00) |
0.253 (1.00) |
0.628 (1.00) |
0.718 (1.00) |
0.0979 (1.00) |
0.0922 (1.00) |
0.705 (1.00) |
0.00601 (1.00) |
0.0208 (1.00) |
0.0167 (1.00) |
del 19p13 3 | 134 (33%) | 270 |
0.00751 (1.00) |
0.325 (1.00) |
0.513 (1.00) |
0.849 (1.00) |
0.373 (1.00) |
0.703 (1.00) |
0.484 (1.00) |
0.184 (1.00) |
0.351 (1.00) |
0.259 (1.00) |
0.16 (1.00) |
0.225 (1.00) |
del 19q13 43 | 77 (19%) | 327 |
0.0931 (1.00) |
0.323 (1.00) |
0.418 (1.00) |
0.0724 (1.00) |
0.635 (1.00) |
0.613 (1.00) |
0.889 (1.00) |
1 (1.00) |
0.526 (1.00) |
0.799 (1.00) |
0.0303 (1.00) |
0.167 (1.00) |
del 21q22 3 | 161 (40%) | 243 |
0.603 (1.00) |
0.54 (1.00) |
0.764 (1.00) |
0.104 (1.00) |
0.443 (1.00) |
0.0944 (1.00) |
0.823 (1.00) |
0.519 (1.00) |
0.442 (1.00) |
0.457 (1.00) |
0.413 (1.00) |
0.558 (1.00) |
del 22q13 31 | 72 (18%) | 332 |
0.447 (1.00) |
0.337 (1.00) |
0.726 (1.00) |
0.406 (1.00) |
0.378 (1.00) |
0.461 (1.00) |
0.25 (1.00) |
0.668 (1.00) |
0.25 (1.00) |
0.652 (1.00) |
0.541 (1.00) |
0.294 (1.00) |
del xp22 2 | 115 (28%) | 289 |
0.00736 (1.00) |
0.291 (1.00) |
0.571 (1.00) |
0.00595 (1.00) |
0.0248 (1.00) |
1 (1.00) |
0.394 (1.00) |
1 (1.00) |
0.0727 (1.00) |
0.0825 (1.00) |
0.691 (1.00) |
0.0188 (1.00) |
del xp21 3 | 119 (29%) | 285 |
0.0689 (1.00) |
0.594 (1.00) |
0.584 (1.00) |
0.0325 (1.00) |
0.0192 (1.00) |
1 (1.00) |
0.631 (1.00) |
1 (1.00) |
0.0738 (1.00) |
0.123 (1.00) |
0.692 (1.00) |
0.0803 (1.00) |
del xq21 33 | 60 (15%) | 344 |
0.866 (1.00) |
0.926 (1.00) |
0.44 (1.00) |
0.71 (1.00) |
0.156 (1.00) |
1 (1.00) |
0.759 (1.00) |
0.336 (1.00) |
0.601 (1.00) |
0.945 (1.00) |
0.429 (1.00) |
0.123 (1.00) |
P value = 0.000183 (Fisher's exact test), Q value = 0.16
nPatients | FEMALE | MALE |
---|---|---|
ALL | 116 | 288 |
AMP PEAK 25(18P11.31) MUTATED | 19 | 100 |
AMP PEAK 25(18P11.31) WILD-TYPE | 97 | 188 |
P value = 5.84e-05 (logrank test), Q value = 0.051
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 399 | 152 | 0.1 - 211.0 (16.1) |
DEL PEAK 7(3P24.1) MUTATED | 289 | 127 | 0.1 - 211.0 (15.8) |
DEL PEAK 7(3P24.1) WILD-TYPE | 110 | 25 | 0.1 - 169.4 (21.0) |
P value = 9.41e-05 (logrank test), Q value = 0.082
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 399 | 152 | 0.1 - 211.0 (16.1) |
DEL PEAK 8(3P12.1) MUTATED | 271 | 121 | 0.1 - 211.0 (15.2) |
DEL PEAK 8(3P12.1) WILD-TYPE | 128 | 31 | 0.1 - 169.4 (19.8) |
P value = 7.13e-05 (Fisher's exact test), Q value = 0.062
nPatients | FEMALE | MALE |
---|---|---|
ALL | 116 | 288 |
DEL PEAK 27(11Q23.1) MUTATED | 36 | 152 |
DEL PEAK 27(11Q23.1) WILD-TYPE | 80 | 136 |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = HNSC-TP.merged_data.txt
-
Number of patients = 404
-
Number of significantly focal cnvs = 73
-
Number of selected clinical features = 12
-
Exclude genes 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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' 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.