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 15 clinical features across 515 patients, 5 significant findings detected with Q value < 0.25.
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1p gain cnv correlated to 'PATHOLOGY_N_STAGE'.
-
7p gain cnv correlated to 'PATHOLOGY_N_STAGE'.
-
17p gain cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
-
20q gain cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.
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5q loss cnv correlated to 'YEARS_TO_BIRTH'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBER PACK YEARS SMOKED |
YEAR OF TOBACCO SMOKING ONSET |
COMPLETENESS OF RESECTION |
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 | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
1p gain | 150 (29%) | 365 |
0.588 (0.969) |
0.0115 (0.341) |
0.162 (0.734) |
0.61 (0.969) |
0.00079 (0.194) |
0.822 (1.00) |
0.698 (0.977) |
0.408 (0.875) |
0.765 (0.991) |
0.807 (1.00) |
0.545 (0.961) |
0.598 (0.969) |
0.928 (1.00) |
0.092 (0.636) |
0.679 (0.974) |
7p gain | 258 (50%) | 257 |
0.132 (0.691) |
0.0388 (0.529) |
0.193 (0.756) |
0.221 (0.77) |
0.00076 (0.194) |
0.301 (0.826) |
0.724 (0.977) |
0.217 (0.77) |
0.0444 (0.529) |
0.514 (0.942) |
0.0217 (0.403) |
0.51 (0.941) |
0.723 (0.977) |
0.407 (0.875) |
0.721 (0.977) |
17p gain | 83 (16%) | 432 |
0.463 (0.908) |
0.0205 (0.393) |
0.133 (0.691) |
0.269 (0.813) |
0.131 (0.691) |
0.175 (0.743) |
0.0925 (0.636) |
0.927 (1.00) |
0.588 (0.969) |
0.0605 (0.556) |
2.41e-05 (0.0297) |
0.544 (0.961) |
0.198 (0.756) |
0.0785 (0.611) |
0.604 (0.969) |
20q gain | 191 (37%) | 324 |
0.537 (0.956) |
0.107 (0.665) |
0.368 (0.868) |
0.229 (0.77) |
0.23 (0.77) |
0.663 (0.974) |
0.315 (0.843) |
0.157 (0.725) |
0.156 (0.725) |
0.252 (0.788) |
0.000132 (0.0813) |
0.731 (0.982) |
0.857 (1.00) |
0.171 (0.743) |
0.716 (0.977) |
5q loss | 152 (30%) | 363 |
0.0534 (0.555) |
0.000456 (0.187) |
0.604 (0.969) |
0.811 (1.00) |
0.458 (0.902) |
0.654 (0.974) |
0.0202 (0.393) |
0.475 (0.913) |
0.32 (0.846) |
0.338 (0.855) |
0.00718 (0.324) |
0.388 (0.874) |
0.513 (0.942) |
0.175 (0.743) |
0.0312 (0.455) |
1q gain | 309 (60%) | 206 |
0.564 (0.967) |
0.172 (0.743) |
0.717 (0.977) |
0.757 (0.989) |
0.239 (0.776) |
0.679 (0.974) |
0.241 (0.776) |
0.931 (1.00) |
0.191 (0.756) |
0.5 (0.931) |
0.351 (0.861) |
0.463 (0.908) |
0.652 (0.974) |
0.918 (1.00) |
0.124 (0.679) |
2p gain | 153 (30%) | 362 |
0.826 (1.00) |
0.176 (0.743) |
0.754 (0.989) |
0.851 (1.00) |
0.454 (0.901) |
0.261 (0.802) |
0.562 (0.966) |
0.855 (1.00) |
0.571 (0.969) |
0.634 (0.974) |
0.0159 (0.377) |
0.509 (0.941) |
0.168 (0.743) |
0.273 (0.813) |
0.0212 (0.402) |
2q gain | 141 (27%) | 374 |
0.746 (0.989) |
0.75 (0.989) |
0.522 (0.946) |
0.995 (1.00) |
0.585 (0.969) |
0.364 (0.864) |
0.921 (1.00) |
0.401 (0.874) |
0.693 (0.977) |
0.808 (1.00) |
0.018 (0.389) |
0.423 (0.881) |
0.58 (0.969) |
0.852 (1.00) |
0.0805 (0.611) |
3p gain | 40 (8%) | 475 |
0.955 (1.00) |
0.175 (0.743) |
0.609 (0.969) |
0.289 (0.819) |
0.0589 (0.555) |
1 (1.00) |
0.51 (0.941) |
0.145 (0.719) |
0.765 (0.991) |
0.218 (0.77) |
0.222 (0.77) |
0.183 (0.748) |
0.048 (0.529) |
0.76 (0.99) |
0.0892 (0.636) |
3q gain | 88 (17%) | 427 |
0.4 (0.874) |
0.952 (1.00) |
0.536 (0.955) |
0.853 (1.00) |
0.531 (0.952) |
1 (1.00) |
0.816 (1.00) |
0.722 (0.977) |
0.741 (0.989) |
0.769 (0.993) |
0.112 (0.669) |
0.764 (0.991) |
0.117 (0.671) |
0.736 (0.987) |
0.0982 (0.653) |
4p gain | 77 (15%) | 438 |
0.61 (0.969) |
0.0166 (0.378) |
0.0797 (0.611) |
0.302 (0.826) |
1 (1.00) |
0.0426 (0.529) |
0.902 (1.00) |
0.692 (0.977) |
0.475 (0.913) |
0.754 (0.989) |
0.0219 (0.403) |
0.934 (1.00) |
0.93 (1.00) |
0.212 (0.77) |
1 (1.00) |
4q gain | 44 (9%) | 471 |
0.526 (0.95) |
0.639 (0.974) |
0.116 (0.671) |
0.346 (0.858) |
0.648 (0.974) |
0.488 (0.927) |
0.64 (0.974) |
0.776 (0.996) |
0.562 (0.966) |
1 (1.00) |
0.0105 (0.341) |
0.873 (1.00) |
0.921 (1.00) |
0.225 (0.77) |
1 (1.00) |
5p gain | 270 (52%) | 245 |
0.822 (1.00) |
0.0473 (0.529) |
0.376 (0.871) |
0.6 (0.969) |
0.566 (0.968) |
1 (1.00) |
0.25 (0.787) |
0.0946 (0.636) |
0.412 (0.878) |
0.264 (0.807) |
0.00293 (0.278) |
0.495 (0.927) |
0.973 (1.00) |
0.867 (1.00) |
0.71 (0.977) |
5q gain | 125 (24%) | 390 |
0.701 (0.977) |
0.651 (0.974) |
0.836 (1.00) |
0.963 (1.00) |
0.578 (0.969) |
0.635 (0.974) |
0.0995 (0.655) |
0.187 (0.756) |
0.401 (0.874) |
0.19 (0.756) |
0.561 (0.966) |
0.683 (0.974) |
0.568 (0.968) |
0.739 (0.989) |
1 (1.00) |
6p gain | 143 (28%) | 372 |
0.0791 (0.611) |
0.908 (1.00) |
0.4 (0.874) |
0.533 (0.952) |
0.694 (0.977) |
0.107 (0.665) |
0.43 (0.885) |
0.206 (0.767) |
0.552 (0.966) |
0.807 (1.00) |
0.234 (0.77) |
0.527 (0.95) |
0.68 (0.974) |
0.0194 (0.393) |
0.112 (0.669) |
6q gain | 61 (12%) | 454 |
0.691 (0.977) |
0.617 (0.973) |
0.826 (1.00) |
0.906 (1.00) |
0.806 (1.00) |
0.517 (0.942) |
0.785 (0.996) |
0.814 (1.00) |
0.957 (1.00) |
0.494 (0.927) |
0.977 (1.00) |
0.645 (0.974) |
0.767 (0.991) |
0.878 (1.00) |
0.223 (0.77) |
7q gain | 211 (41%) | 304 |
0.428 (0.884) |
0.00728 (0.324) |
0.0833 (0.621) |
0.876 (1.00) |
0.00491 (0.324) |
0.0916 (0.636) |
0.929 (1.00) |
0.558 (0.966) |
0.0688 (0.583) |
0.173 (0.743) |
0.223 (0.77) |
0.873 (1.00) |
0.374 (0.871) |
0.89 (1.00) |
0.704 (0.977) |
8p gain | 129 (25%) | 386 |
0.783 (0.996) |
0.157 (0.725) |
0.855 (1.00) |
0.219 (0.77) |
0.684 (0.974) |
0.483 (0.924) |
0.0107 (0.341) |
0.198 (0.756) |
0.766 (0.991) |
0.196 (0.756) |
0.75 (0.989) |
0.505 (0.936) |
0.214 (0.77) |
0.212 (0.77) |
0.199 (0.756) |
8q gain | 243 (47%) | 272 |
0.0151 (0.372) |
0.0317 (0.455) |
0.831 (1.00) |
0.304 (0.827) |
0.333 (0.855) |
0.679 (0.974) |
0.426 (0.883) |
0.727 (0.978) |
0.00416 (0.324) |
0.38 (0.874) |
0.999 (1.00) |
0.139 (0.707) |
0.402 (0.874) |
0.0119 (0.341) |
1 (1.00) |
9p gain | 45 (9%) | 470 |
0.725 (0.977) |
0.177 (0.743) |
0.874 (1.00) |
0.448 (0.9) |
0.587 (0.969) |
0.488 (0.927) |
0.159 (0.725) |
0.465 (0.908) |
0.306 (0.832) |
0.416 (0.879) |
0.827 (1.00) |
0.623 (0.974) |
0.478 (0.917) |
0.235 (0.772) |
1 (1.00) |
9q gain | 32 (6%) | 483 |
0.494 (0.927) |
0.289 (0.819) |
0.45 (0.9) |
0.865 (1.00) |
1 (1.00) |
0.0855 (0.622) |
0.584 (0.969) |
0.746 (0.989) |
0.676 (0.974) |
0.38 (0.874) |
0.95 (1.00) |
0.609 (0.969) |
0.709 (0.977) |
0.289 (0.819) |
1 (1.00) |
10p gain | 111 (22%) | 404 |
0.998 (1.00) |
0.0433 (0.529) |
0.854 (1.00) |
0.0424 (0.529) |
0.0801 (0.611) |
0.622 (0.974) |
0.00515 (0.324) |
0.803 (1.00) |
0.802 (1.00) |
0.589 (0.969) |
0.228 (0.77) |
0.487 (0.927) |
0.319 (0.844) |
0.0707 (0.588) |
0.624 (0.974) |
10q gain | 77 (15%) | 438 |
0.886 (1.00) |
0.219 (0.77) |
0.513 (0.942) |
0.024 (0.418) |
0.0973 (0.651) |
0.277 (0.818) |
0.00294 (0.278) |
0.349 (0.859) |
0.711 (0.977) |
1 (1.00) |
0.666 (0.974) |
0.91 (1.00) |
0.872 (1.00) |
0.091 (0.636) |
1 (1.00) |
11p gain | 94 (18%) | 421 |
0.0656 (0.58) |
0.276 (0.816) |
0.495 (0.927) |
0.225 (0.77) |
0.128 (0.691) |
0.784 (0.996) |
0.0863 (0.624) |
0.938 (1.00) |
0.343 (0.857) |
0.779 (0.996) |
0.0124 (0.346) |
0.292 (0.819) |
0.948 (1.00) |
0.951 (1.00) |
1 (1.00) |
11q gain | 114 (22%) | 401 |
0.337 (0.855) |
0.0462 (0.529) |
0.479 (0.918) |
0.85 (1.00) |
0.444 (0.897) |
0.0696 (0.583) |
0.137 (0.702) |
0.385 (0.874) |
0.106 (0.665) |
0.431 (0.885) |
0.048 (0.529) |
0.249 (0.787) |
0.958 (1.00) |
0.226 (0.77) |
0.659 (0.974) |
12p gain | 137 (27%) | 378 |
0.137 (0.702) |
0.0679 (0.58) |
0.0427 (0.529) |
0.785 (0.996) |
0.234 (0.77) |
0.155 (0.725) |
0.231 (0.77) |
0.839 (1.00) |
0.67 (0.974) |
1 (1.00) |
0.153 (0.725) |
0.13 (0.691) |
0.721 (0.977) |
0.541 (0.96) |
0.683 (0.974) |
12q gain | 130 (25%) | 385 |
0.205 (0.767) |
0.208 (0.767) |
0.233 (0.77) |
0.594 (0.969) |
0.272 (0.813) |
0.232 (0.77) |
0.416 (0.879) |
0.829 (1.00) |
0.581 (0.969) |
0.798 (0.999) |
0.676 (0.974) |
0.0145 (0.372) |
0.707 (0.977) |
0.598 (0.969) |
0.671 (0.974) |
13q gain | 44 (9%) | 471 |
0.907 (1.00) |
0.579 (0.969) |
0.015 (0.372) |
0.345 (0.858) |
0.475 (0.913) |
0.00796 (0.326) |
1 (1.00) |
0.902 (1.00) |
0.97 (1.00) |
0.698 (0.977) |
0.24 (0.776) |
0.217 (0.77) |
0.225 (0.77) |
1 (1.00) |
0.421 (0.879) |
14q gain | 130 (25%) | 385 |
0.621 (0.974) |
0.41 (0.877) |
0.746 (0.989) |
0.858 (1.00) |
0.385 (0.874) |
0.449 (0.9) |
0.188 (0.756) |
0.0941 (0.636) |
0.497 (0.929) |
0.123 (0.679) |
0.347 (0.858) |
0.201 (0.76) |
0.268 (0.813) |
0.631 (0.974) |
1 (1.00) |
15q gain | 38 (7%) | 477 |
0.00153 (0.27) |
0.53 (0.952) |
0.0265 (0.429) |
0.386 (0.874) |
0.0163 (0.377) |
0.475 (0.913) |
0.312 (0.843) |
0.945 (1.00) |
0.0566 (0.555) |
0.662 (0.974) |
0.42 (0.879) |
0.832 (1.00) |
0.563 (0.966) |
0.504 (0.936) |
1 (1.00) |
16p gain | 131 (25%) | 384 |
0.825 (1.00) |
0.547 (0.963) |
0.359 (0.862) |
0.466 (0.908) |
0.988 (1.00) |
0.0944 (0.636) |
1 (1.00) |
0.156 (0.725) |
0.0661 (0.58) |
0.615 (0.972) |
0.345 (0.858) |
0.991 (1.00) |
0.961 (1.00) |
0.281 (0.819) |
0.197 (0.756) |
16q gain | 99 (19%) | 416 |
0.886 (1.00) |
0.248 (0.787) |
0.399 (0.874) |
0.393 (0.874) |
0.986 (1.00) |
0.599 (0.969) |
0.575 (0.969) |
0.793 (0.999) |
0.0543 (0.555) |
0.779 (0.996) |
0.166 (0.743) |
0.333 (0.855) |
0.6 (0.969) |
0.271 (0.813) |
0.353 (0.861) |
17q gain | 191 (37%) | 324 |
0.834 (1.00) |
0.0641 (0.576) |
0.201 (0.76) |
0.456 (0.901) |
0.196 (0.756) |
0.204 (0.767) |
0.784 (0.996) |
0.434 (0.887) |
0.193 (0.756) |
0.646 (0.974) |
0.00413 (0.324) |
0.547 (0.963) |
0.0186 (0.393) |
0.0449 (0.529) |
0.702 (0.977) |
18p gain | 91 (18%) | 424 |
0.082 (0.619) |
0.364 (0.864) |
0.347 (0.858) |
0.798 (0.999) |
0.985 (1.00) |
0.592 (0.969) |
0.299 (0.825) |
0.123 (0.679) |
0.68 (0.974) |
1 (1.00) |
0.00225 (0.278) |
0.646 (0.974) |
0.596 (0.969) |
0.0457 (0.529) |
0.36 (0.862) |
18q gain | 69 (13%) | 446 |
0.834 (1.00) |
0.0587 (0.555) |
0.337 (0.855) |
0.612 (0.97) |
0.981 (1.00) |
0.554 (0.966) |
0.154 (0.725) |
0.0634 (0.573) |
0.454 (0.901) |
1 (1.00) |
0.00698 (0.324) |
0.337 (0.855) |
0.0666 (0.58) |
0.109 (0.666) |
0.6 (0.969) |
19p gain | 30 (6%) | 485 |
0.696 (0.977) |
0.92 (1.00) |
0.532 (0.952) |
0.178 (0.747) |
0.5 (0.931) |
0.229 (0.77) |
0.265 (0.807) |
0.973 (1.00) |
0.00617 (0.324) |
0.349 (0.859) |
0.0693 (0.583) |
0.834 (1.00) |
0.447 (0.9) |
1 (1.00) |
0.374 (0.871) |
19q gain | 75 (15%) | 440 |
0.319 (0.844) |
0.799 (1) |
0.426 (0.883) |
0.238 (0.776) |
0.394 (0.874) |
0.392 (0.874) |
0.046 (0.529) |
0.134 (0.696) |
0.061 (0.556) |
0.753 (0.989) |
0.142 (0.712) |
0.976 (1.00) |
0.84 (1.00) |
0.709 (0.977) |
0.295 (0.819) |
20p gain | 172 (33%) | 343 |
0.231 (0.77) |
0.176 (0.743) |
0.659 (0.974) |
0.336 (0.855) |
0.142 (0.712) |
1 (1.00) |
0.512 (0.942) |
0.394 (0.874) |
0.138 (0.702) |
1 (1.00) |
0.00682 (0.324) |
0.181 (0.747) |
0.354 (0.861) |
0.0543 (0.555) |
0.101 (0.661) |
21q gain | 96 (19%) | 419 |
0.18 (0.747) |
0.303 (0.827) |
0.156 (0.725) |
0.551 (0.966) |
0.0731 (0.596) |
1 (1.00) |
0.0311 (0.455) |
0.706 (0.977) |
0.54 (0.96) |
1 (1.00) |
0.116 (0.671) |
0.282 (0.819) |
1 (1.00) |
0.389 (0.874) |
0.358 (0.862) |
22q gain | 62 (12%) | 453 |
0.174 (0.743) |
0.0371 (0.512) |
0.671 (0.974) |
0.343 (0.857) |
0.456 (0.901) |
0.752 (0.989) |
0.135 (0.698) |
0.573 (0.969) |
0.327 (0.855) |
0.494 (0.927) |
0.368 (0.868) |
0.157 (0.725) |
0.358 (0.862) |
0.604 (0.969) |
0.58 (0.969) |
xp gain | 51 (10%) | 464 |
0.259 (0.799) |
0.939 (1.00) |
0.0131 (0.35) |
0.078 (0.611) |
0.106 (0.665) |
0.0068 (0.324) |
0.376 (0.871) |
0.27 (0.813) |
0.869 (1.00) |
0.0467 (0.529) |
0.0046 (0.324) |
0.108 (0.665) |
0.394 (0.874) |
0.835 (1.00) |
1 (1.00) |
xq gain | 83 (16%) | 432 |
0.606 (0.969) |
0.919 (1.00) |
0.318 (0.844) |
0.392 (0.874) |
0.936 (1.00) |
0.0475 (0.529) |
0.337 (0.855) |
0.42 (0.879) |
0.217 (0.77) |
1 (1.00) |
0.0246 (0.418) |
0.207 (0.767) |
0.915 (1.00) |
0.894 (1.00) |
0.6 (0.969) |
1p loss | 82 (16%) | 433 |
0.229 (0.77) |
0.89 (1.00) |
0.0434 (0.529) |
0.0878 (0.632) |
0.00821 (0.326) |
1 (1.00) |
0.399 (0.874) |
0.611 (0.969) |
0.65 (0.974) |
0.356 (0.861) |
0.977 (1.00) |
0.783 (0.996) |
0.473 (0.913) |
0.844 (1.00) |
0.288 (0.819) |
1q loss | 33 (6%) | 482 |
0.258 (0.799) |
0.859 (1.00) |
0.697 (0.977) |
0.986 (1.00) |
0.292 (0.819) |
1 (1.00) |
0.858 (1.00) |
0.412 (0.878) |
0.573 (0.969) |
0.145 (0.717) |
0.528 (0.95) |
0.601 (0.969) |
1 (1.00) |
1 (1.00) |
0.0733 (0.596) |
2p loss | 28 (5%) | 487 |
0.805 (1.00) |
0.0678 (0.58) |
0.559 (0.966) |
0.516 (0.942) |
0.467 (0.909) |
1 (1.00) |
0.25 (0.787) |
0.59 (0.969) |
0.606 (0.969) |
1 (1.00) |
0.195 (0.756) |
0.456 (0.901) |
0.712 (0.977) |
0.473 (0.913) |
0.311 (0.842) |
2q loss | 29 (6%) | 486 |
0.123 (0.679) |
0.0922 (0.636) |
0.591 (0.969) |
0.835 (1.00) |
0.706 (0.977) |
1 (1.00) |
0.444 (0.897) |
0.285 (0.819) |
0.189 (0.756) |
0.623 (0.974) |
0.0479 (0.529) |
0.194 (0.756) |
1 (1.00) |
0.423 (0.881) |
0.324 (0.85) |
3p loss | 212 (41%) | 303 |
0.779 (0.996) |
0.129 (0.691) |
0.665 (0.974) |
0.0318 (0.455) |
0.376 (0.871) |
1 (1.00) |
1 (1.00) |
0.562 (0.966) |
0.115 (0.671) |
1 (1.00) |
0.191 (0.756) |
0.0419 (0.529) |
0.107 (0.665) |
0.959 (1.00) |
0.704 (0.977) |
3q loss | 146 (28%) | 369 |
0.174 (0.743) |
0.0575 (0.555) |
0.315 (0.843) |
0.776 (0.996) |
0.0455 (0.529) |
0.653 (0.974) |
0.696 (0.977) |
0.417 (0.879) |
0.453 (0.901) |
1 (1.00) |
0.0466 (0.529) |
0.0113 (0.341) |
0.358 (0.862) |
0.699 (0.977) |
0.109 (0.666) |
4p loss | 123 (24%) | 392 |
0.324 (0.85) |
0.157 (0.725) |
0.424 (0.882) |
0.984 (1.00) |
0.216 (0.77) |
1 (1.00) |
0.757 (0.989) |
0.372 (0.871) |
0.276 (0.816) |
0.301 (0.826) |
0.386 (0.874) |
0.0719 (0.593) |
0.557 (0.966) |
0.636 (0.974) |
1 (1.00) |
4q loss | 140 (27%) | 375 |
0.88 (1.00) |
0.103 (0.665) |
0.313 (0.843) |
0.984 (1.00) |
0.00738 (0.324) |
0.64 (0.974) |
0.921 (1.00) |
0.223 (0.77) |
0.315 (0.843) |
0.616 (0.973) |
0.575 (0.969) |
0.132 (0.691) |
0.406 (0.875) |
0.779 (0.996) |
1 (1.00) |
5p loss | 52 (10%) | 463 |
0.112 (0.669) |
0.0562 (0.555) |
0.558 (0.966) |
0.675 (0.974) |
0.36 (0.862) |
1 (1.00) |
0.0564 (0.555) |
0.841 (1.00) |
0.409 (0.875) |
0.711 (0.977) |
0.643 (0.974) |
0.0193 (0.393) |
1 (1.00) |
0.339 (0.855) |
0.169 (0.743) |
6p loss | 106 (21%) | 409 |
0.12 (0.677) |
0.329 (0.855) |
0.257 (0.799) |
0.0846 (0.622) |
0.297 (0.824) |
0.797 (0.999) |
1 (1.00) |
0.899 (1.00) |
0.796 (0.999) |
0.406 (0.875) |
0.0162 (0.377) |
0.211 (0.77) |
0.935 (1.00) |
1 (1.00) |
0.639 (0.974) |
6q loss | 216 (42%) | 299 |
0.757 (0.989) |
0.158 (0.725) |
0.714 (0.977) |
0.52 (0.944) |
0.714 (0.977) |
1 (1.00) |
0.591 (0.969) |
0.745 (0.989) |
0.889 (1.00) |
0.37 (0.868) |
0.159 (0.725) |
0.0675 (0.58) |
0.673 (0.974) |
0.94 (1.00) |
1 (1.00) |
7p loss | 39 (8%) | 476 |
0.45 (0.9) |
0.339 (0.855) |
0.954 (1.00) |
0.882 (1.00) |
0.907 (1.00) |
0.712 (0.977) |
0.243 (0.777) |
0.224 (0.77) |
0.87 (1.00) |
0.668 (0.974) |
0.194 (0.756) |
0.118 (0.671) |
0.695 (0.977) |
0.63 (0.974) |
0.465 (0.908) |
7q loss | 47 (9%) | 468 |
0.299 (0.825) |
0.756 (0.989) |
0.392 (0.874) |
0.841 (1.00) |
0.434 (0.887) |
0.0922 (0.636) |
0.878 (1.00) |
0.165 (0.743) |
0.867 (1.00) |
0.243 (0.777) |
0.824 (1.00) |
0.144 (0.716) |
1 (1.00) |
0.232 (0.77) |
0.506 (0.937) |
8p loss | 202 (39%) | 313 |
0.66 (0.974) |
0.865 (1.00) |
0.368 (0.868) |
0.635 (0.974) |
0.848 (1.00) |
0.394 (0.874) |
0.0302 (0.455) |
0.631 (0.974) |
0.024 (0.418) |
0.173 (0.743) |
0.608 (0.969) |
0.929 (1.00) |
0.152 (0.725) |
0.591 (0.969) |
0.12 (0.677) |
8q loss | 60 (12%) | 455 |
0.978 (1.00) |
0.694 (0.977) |
0.408 (0.875) |
0.335 (0.855) |
0.414 (0.879) |
0.753 (0.989) |
0.492 (0.927) |
0.58 (0.969) |
0.126 (0.689) |
0.494 (0.927) |
0.99 (1.00) |
0.366 (0.867) |
0.703 (0.977) |
0.19 (0.756) |
0.589 (0.969) |
9p loss | 270 (52%) | 245 |
0.146 (0.72) |
0.29 (0.819) |
0.489 (0.927) |
0.664 (0.974) |
0.032 (0.455) |
0.838 (1.00) |
0.0773 (0.611) |
0.28 (0.819) |
0.763 (0.991) |
0.663 (0.974) |
0.756 (0.989) |
0.957 (1.00) |
0.949 (1.00) |
0.416 (0.879) |
1 (1.00) |
9q loss | 254 (49%) | 261 |
0.649 (0.974) |
0.672 (0.974) |
0.839 (1.00) |
0.453 (0.901) |
0.28 (0.819) |
0.682 (0.974) |
0.93 (1.00) |
0.643 (0.974) |
0.53 (0.952) |
0.658 (0.974) |
0.231 (0.77) |
0.59 (0.969) |
1 (1.00) |
0.466 (0.908) |
0.724 (0.977) |
10p loss | 114 (22%) | 401 |
0.229 (0.77) |
0.836 (1.00) |
0.926 (1.00) |
0.224 (0.77) |
0.621 (0.974) |
1 (1.00) |
0.00566 (0.324) |
0.869 (1.00) |
0.03 (0.455) |
0.188 (0.756) |
0.986 (1.00) |
0.788 (0.999) |
0.69 (0.977) |
0.0466 (0.529) |
0.204 (0.767) |
10q loss | 136 (26%) | 379 |
0.14 (0.707) |
0.273 (0.813) |
0.659 (0.974) |
0.115 (0.671) |
0.604 (0.969) |
0.251 (0.787) |
0.0449 (0.529) |
0.675 (0.974) |
0.0253 (0.418) |
0.0805 (0.611) |
0.345 (0.858) |
0.577 (0.969) |
0.389 (0.874) |
0.117 (0.671) |
0.0831 (0.621) |
11p loss | 116 (23%) | 399 |
0.678 (0.974) |
0.018 (0.389) |
0.0851 (0.622) |
0.26 (0.799) |
0.211 (0.77) |
0.471 (0.913) |
0.00209 (0.278) |
0.195 (0.756) |
0.283 (0.819) |
0.436 (0.888) |
0.867 (1.00) |
0.0527 (0.555) |
0.281 (0.819) |
0.388 (0.874) |
0.00989 (0.341) |
11q loss | 91 (18%) | 424 |
0.741 (0.989) |
0.355 (0.861) |
0.26 (0.799) |
0.734 (0.985) |
0.971 (1.00) |
0.797 (0.999) |
0.00781 (0.326) |
0.655 (0.974) |
0.587 (0.969) |
0.557 (0.966) |
0.882 (1.00) |
0.239 (0.776) |
0.419 (0.879) |
0.573 (0.969) |
0.618 (0.973) |
12p loss | 114 (22%) | 401 |
0.435 (0.887) |
0.0843 (0.622) |
0.736 (0.987) |
0.858 (1.00) |
0.846 (1.00) |
0.438 (0.89) |
0.00286 (0.278) |
0.006 (0.324) |
0.661 (0.974) |
1 (1.00) |
0.0649 (0.578) |
0.562 (0.966) |
0.791 (0.999) |
0.319 (0.844) |
0.684 (0.974) |
12q loss | 102 (20%) | 413 |
0.283 (0.819) |
0.162 (0.734) |
0.791 (0.999) |
0.753 (0.989) |
0.709 (0.977) |
0.781 (0.996) |
0.00564 (0.324) |
0.24 (0.776) |
0.498 (0.929) |
0.399 (0.874) |
0.00963 (0.341) |
0.439 (0.892) |
0.739 (0.989) |
0.253 (0.789) |
0.65 (0.974) |
13q loss | 257 (50%) | 258 |
0.704 (0.977) |
0.127 (0.69) |
0.665 (0.974) |
0.517 (0.942) |
0.316 (0.844) |
0.302 (0.826) |
0.659 (0.974) |
0.656 (0.974) |
0.702 (0.977) |
0.657 (0.974) |
0.092 (0.636) |
0.168 (0.743) |
0.796 (0.999) |
0.325 (0.85) |
0.45 (0.9) |
14q loss | 114 (22%) | 401 |
0.783 (0.996) |
0.0517 (0.555) |
0.556 (0.966) |
0.295 (0.819) |
0.0278 (0.432) |
0.81 (1.00) |
0.338 (0.855) |
0.174 (0.743) |
0.862 (1.00) |
1 (1.00) |
0.249 (0.787) |
0.541 (0.96) |
0.185 (0.756) |
0.0566 (0.555) |
0.671 (0.974) |
15q loss | 241 (47%) | 274 |
0.42 (0.879) |
0.00152 (0.27) |
0.86 (1.00) |
0.879 (1.00) |
0.804 (1.00) |
0.679 (0.974) |
0.288 (0.819) |
0.43 (0.885) |
0.0179 (0.389) |
0.377 (0.871) |
0.592 (0.969) |
0.291 (0.819) |
0.925 (1.00) |
0.715 (0.977) |
1 (1.00) |
16p loss | 117 (23%) | 398 |
0.352 (0.861) |
0.526 (0.95) |
0.0736 (0.596) |
0.387 (0.874) |
0.13 (0.691) |
0.471 (0.913) |
0.399 (0.874) |
0.601 (0.969) |
0.694 (0.977) |
1 (1.00) |
0.713 (0.977) |
0.626 (0.974) |
0.753 (0.989) |
1 (1.00) |
0.053 (0.555) |
16q loss | 144 (28%) | 371 |
0.824 (1.00) |
0.362 (0.864) |
0.673 (0.974) |
0.986 (1.00) |
0.403 (0.875) |
1 (1.00) |
0.491 (0.927) |
0.322 (0.849) |
0.607 (0.969) |
0.807 (1.00) |
0.674 (0.974) |
0.777 (0.996) |
0.434 (0.887) |
0.941 (1.00) |
0.0204 (0.393) |
17p loss | 216 (42%) | 299 |
0.628 (0.974) |
0.216 (0.77) |
0.294 (0.819) |
0.395 (0.874) |
0.783 (0.996) |
0.676 (0.974) |
0.0605 (0.556) |
0.533 (0.952) |
0.18 (0.747) |
0.113 (0.671) |
0.013 (0.35) |
0.0252 (0.418) |
0.725 (0.977) |
0.906 (1.00) |
0.0203 (0.393) |
17q loss | 57 (11%) | 458 |
0.294 (0.819) |
0.996 (1.00) |
0.0551 (0.555) |
0.0272 (0.429) |
0.253 (0.789) |
1 (1.00) |
0.328 (0.855) |
0.111 (0.669) |
0.919 (1.00) |
1 (1.00) |
0.229 (0.77) |
0.0242 (0.418) |
0.856 (1.00) |
0.795 (0.999) |
0.182 (0.748) |
18p loss | 177 (34%) | 338 |
0.407 (0.875) |
0.107 (0.665) |
0.0119 (0.341) |
0.385 (0.874) |
0.102 (0.665) |
0.118 (0.671) |
0.0255 (0.418) |
0.975 (1.00) |
0.556 (0.966) |
0.356 (0.861) |
0.0767 (0.611) |
0.0108 (0.341) |
0.107 (0.665) |
0.168 (0.743) |
1 (1.00) |
18q loss | 212 (41%) | 303 |
0.0236 (0.418) |
0.418 (0.879) |
0.00945 (0.341) |
0.342 (0.857) |
0.0534 (0.555) |
0.206 (0.767) |
0.0595 (0.555) |
0.875 (1.00) |
0.651 (0.974) |
0.265 (0.807) |
0.158 (0.725) |
0.177 (0.743) |
0.0109 (0.341) |
0.845 (1.00) |
1 (1.00) |
19p loss | 247 (48%) | 268 |
0.0764 (0.611) |
0.0502 (0.546) |
0.545 (0.961) |
0.515 (0.942) |
0.292 (0.819) |
0.408 (0.875) |
0.027 (0.429) |
0.527 (0.95) |
0.818 (1.00) |
0.382 (0.874) |
0.725 (0.977) |
0.374 (0.871) |
0.107 (0.665) |
0.809 (1.00) |
1 (1.00) |
19q loss | 160 (31%) | 355 |
0.241 (0.776) |
0.117 (0.671) |
0.271 (0.813) |
0.381 (0.874) |
0.341 (0.857) |
0.271 (0.813) |
0.567 (0.968) |
0.57 (0.969) |
0.362 (0.864) |
0.631 (0.974) |
0.765 (0.991) |
0.803 (1.00) |
0.198 (0.756) |
0.398 (0.874) |
1 (1.00) |
20p loss | 113 (22%) | 402 |
0.181 (0.747) |
0.369 (0.868) |
0.133 (0.691) |
0.284 (0.819) |
0.0592 (0.555) |
1 (1.00) |
0.456 (0.901) |
0.171 (0.743) |
0.292 (0.819) |
0.791 (0.999) |
0.094 (0.636) |
0.518 (0.942) |
0.815 (1.00) |
0.294 (0.819) |
1 (1.00) |
20q loss | 69 (13%) | 446 |
0.638 (0.974) |
0.61 (0.969) |
0.332 (0.855) |
0.409 (0.875) |
0.319 (0.844) |
1 (1.00) |
1 (1.00) |
0.0482 (0.529) |
0.0996 (0.655) |
1 (1.00) |
0.466 (0.908) |
0.66 (0.974) |
0.683 (0.974) |
0.149 (0.725) |
0.23 (0.77) |
21q loss | 167 (32%) | 348 |
0.927 (1.00) |
0.153 (0.725) |
0.777 (0.996) |
0.548 (0.963) |
0.959 (1.00) |
0.665 (0.974) |
0.132 (0.691) |
0.914 (1.00) |
0.0088 (0.338) |
0.057 (0.555) |
0.755 (0.989) |
0.0322 (0.455) |
0.557 (0.966) |
0.189 (0.756) |
1 (1.00) |
22q loss | 217 (42%) | 298 |
0.614 (0.972) |
0.00272 (0.278) |
0.847 (1.00) |
0.918 (1.00) |
0.843 (1.00) |
1 (1.00) |
0.245 (0.781) |
0.0348 (0.486) |
0.292 (0.819) |
1 (1.00) |
0.973 (1.00) |
0.0139 (0.365) |
0.817 (1.00) |
0.276 (0.816) |
1 (1.00) |
xp loss | 104 (20%) | 411 |
0.632 (0.974) |
0.977 (1.00) |
0.488 (0.927) |
0.794 (0.999) |
0.242 (0.777) |
0.441 (0.894) |
0.155 (0.725) |
0.75 (0.989) |
0.715 (0.977) |
1 (1.00) |
0.116 (0.671) |
0.123 (0.679) |
0.759 (0.99) |
0.43 (0.885) |
0.353 (0.861) |
xq loss | 62 (12%) | 453 |
0.497 (0.929) |
0.334 (0.855) |
0.33 (0.855) |
0.877 (1.00) |
0.723 (0.977) |
0.225 (0.77) |
0.0582 (0.555) |
0.891 (1.00) |
0.11 (0.669) |
0.159 (0.725) |
0.207 (0.767) |
0.14 (0.707) |
0.723 (0.977) |
0.159 (0.725) |
1 (1.00) |
P value = 0.00079 (Fisher's exact test), Q value = 0.19
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 332 | 96 | 76 |
1P GAIN MUTATED | 88 | 43 | 16 |
1P GAIN WILD-TYPE | 244 | 53 | 60 |
P value = 0.00076 (Fisher's exact test), Q value = 0.19
nPatients | N0 | N1 | N2+N3 |
---|---|---|---|
ALL | 332 | 96 | 76 |
7P GAIN MUTATED | 153 | 46 | 53 |
7P GAIN WILD-TYPE | 179 | 50 | 23 |
P value = 2.41e-05 (Wilcoxon-test), Q value = 0.03
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 355 | 41.6 (27.3) |
17P GAIN MUTATED | 56 | 55.3 (30.8) |
17P GAIN WILD-TYPE | 299 | 39.0 (25.9) |
P value = 0.000132 (Wilcoxon-test), Q value = 0.081
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 355 | 41.6 (27.3) |
20Q GAIN MUTATED | 142 | 47.5 (27.9) |
20Q GAIN WILD-TYPE | 213 | 37.7 (26.2) |
P value = 0.000456 (Wilcoxon-test), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 484 | 65.2 (10.0) |
5Q LOSS MUTATED | 145 | 62.7 (10.0) |
5Q LOSS WILD-TYPE | 339 | 66.3 (9.8) |
-
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/LUAD-TP/15092515/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/15084450/LUAD-TP.merged_data.txt
-
Number of patients = 515
-
Number of significantly arm-level cnvs = 82
-
Number of selected clinical features = 15
-
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.