(primary solid tumor cohort)
This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 82 arm-level results and 14 clinical features across 370 patients, 6 significant findings detected with Q value < 0.25.
-
Amp Peak 17(10p15.1) cnv correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
Amp Peak 18(11q13.3) cnv correlated to 'AGE'.
-
Del Peak 13(5q22.1) cnv correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
Del Peak 24(10p15.3) cnv correlated to 'GENDER'.
-
Del Peak 29(12p13.2) cnv correlated to 'GENDER'.
-
Del Peak 50(22q13.32) cnv correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET |
COMPLETENESS OF RESECTION |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact 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 | t-test | Fisher's exact test | t-test | Fisher's exact test | |
Amp Peak 17(10p15 1) | 102 (28%) | 268 |
0.103 (1.00) |
0.712 (1.00) |
0.00701 (1.00) |
0.571 (1.00) |
0.253 (1.00) |
0.523 (1.00) |
0.0223 (1.00) |
0.947 (1.00) |
0.47 (1.00) |
0.608 (1.00) |
0.00144 (1.00) |
4.36e-06 (0.00499) |
0.779 (1.00) |
0.554 (1.00) |
Amp Peak 18(11q13 3) | 128 (35%) | 242 |
0.918 (1.00) |
0.000197 (0.225) |
0.188 (1.00) |
0.519 (1.00) |
0.518 (1.00) |
0.251 (1.00) |
0.79 (1.00) |
0.666 (1.00) |
0.239 (1.00) |
0.811 (1.00) |
0.799 (1.00) |
0.00396 (1.00) |
0.79 (1.00) |
0.43 (1.00) |
Del Peak 13(5q22 1) | 151 (41%) | 219 |
0.262 (1.00) |
0.00296 (1.00) |
0.75 (1.00) |
0.47 (1.00) |
0.171 (1.00) |
0.427 (1.00) |
0.188 (1.00) |
0.849 (1.00) |
0.295 (1.00) |
0.165 (1.00) |
0.014 (1.00) |
1.08e-05 (0.0124) |
0.179 (1.00) |
0.468 (1.00) |
Del Peak 24(10p15 3) | 87 (24%) | 283 |
0.154 (1.00) |
0.537 (1.00) |
7.03e-05 (0.0804) |
0.851 (1.00) |
0.455 (1.00) |
0.335 (1.00) |
0.599 (1.00) |
0.439 (1.00) |
0.73 (1.00) |
1 (1.00) |
0.591 (1.00) |
0.029 (1.00) |
0.575 (1.00) |
0.965 (1.00) |
Del Peak 29(12p13 2) | 105 (28%) | 265 |
0.282 (1.00) |
0.681 (1.00) |
0.000192 (0.219) |
0.826 (1.00) |
0.84 (1.00) |
0.908 (1.00) |
0.775 (1.00) |
0.109 (1.00) |
0.519 (1.00) |
0.805 (1.00) |
0.0607 (1.00) |
0.387 (1.00) |
0.103 (1.00) |
0.348 (1.00) |
Del Peak 50(22q13 32) | 178 (48%) | 192 |
0.337 (1.00) |
0.00462 (1.00) |
0.0761 (1.00) |
0.537 (1.00) |
0.158 (1.00) |
0.926 (1.00) |
0.495 (1.00) |
0.254 (1.00) |
0.346 (1.00) |
0.822 (1.00) |
0.961 (1.00) |
0.000137 (0.156) |
0.00771 (1.00) |
0.552 (1.00) |
Amp Peak 1(1p34 3) | 102 (28%) | 268 |
0.75 (1.00) |
0.0124 (1.00) |
1 (1.00) |
0.421 (1.00) |
0.665 (1.00) |
0.742 (1.00) |
0.25 (1.00) |
0.945 (1.00) |
0.66 (1.00) |
0.608 (1.00) |
0.858 (1.00) |
0.156 (1.00) |
0.584 (1.00) |
0.193 (1.00) |
Amp Peak 2(1p22 3) | 101 (27%) | 269 |
0.932 (1.00) |
0.000387 (0.441) |
1 (1.00) |
0.609 (1.00) |
0.132 (1.00) |
0.774 (1.00) |
0.0856 (1.00) |
0.727 (1.00) |
0.418 (1.00) |
0.443 (1.00) |
0.466 (1.00) |
0.485 (1.00) |
0.495 (1.00) |
0.61 (1.00) |
Amp Peak 3(1q21 3) | 265 (72%) | 105 |
0.374 (1.00) |
0.152 (1.00) |
0.0368 (1.00) |
0.311 (1.00) |
0.00731 (1.00) |
0.35 (1.00) |
0.889 (1.00) |
0.499 (1.00) |
0.957 (1.00) |
0.21 (1.00) |
0.615 (1.00) |
0.057 (1.00) |
0.186 (1.00) |
0.532 (1.00) |
Amp Peak 4(3q26 2) | 126 (34%) | 244 |
0.838 (1.00) |
0.568 (1.00) |
0.66 (1.00) |
0.726 (1.00) |
0.743 (1.00) |
0.738 (1.00) |
0.184 (1.00) |
0.398 (1.00) |
0.456 (1.00) |
0.472 (1.00) |
0.112 (1.00) |
0.0699 (1.00) |
0.183 (1.00) |
0.393 (1.00) |
Amp Peak 5(4q12) | 72 (19%) | 298 |
0.235 (1.00) |
0.00839 (1.00) |
0.513 (1.00) |
0.902 (1.00) |
0.28 (1.00) |
0.082 (1.00) |
0.352 (1.00) |
0.306 (1.00) |
0.434 (1.00) |
0.776 (1.00) |
0.709 (1.00) |
0.849 (1.00) |
0.233 (1.00) |
0.634 (1.00) |
Amp Peak 6(5p15 33) | 239 (65%) | 131 |
0.14 (1.00) |
0.00797 (1.00) |
0.0378 (1.00) |
0.0263 (1.00) |
0.0243 (1.00) |
0.304 (1.00) |
0.624 (1.00) |
0.776 (1.00) |
0.599 (1.00) |
0.471 (1.00) |
0.0221 (1.00) |
0.148 (1.00) |
0.455 (1.00) |
0.344 (1.00) |
Amp Peak 7(5p13 1) | 217 (59%) | 153 |
0.048 (1.00) |
0.0111 (1.00) |
0.0437 (1.00) |
0.867 (1.00) |
0.0845 (1.00) |
0.107 (1.00) |
0.317 (1.00) |
0.788 (1.00) |
0.228 (1.00) |
1 (1.00) |
0.0125 (1.00) |
0.172 (1.00) |
0.7 (1.00) |
0.118 (1.00) |
Amp Peak 8(5q35 1) | 86 (23%) | 284 |
0.102 (1.00) |
0.278 (1.00) |
0.0186 (1.00) |
0.971 (1.00) |
0.65 (1.00) |
0.242 (1.00) |
0.458 (1.00) |
0.693 (1.00) |
0.36 (1.00) |
0.426 (1.00) |
0.394 (1.00) |
0.108 (1.00) |
0.145 (1.00) |
0.59 (1.00) |
Amp Peak 9(6p21 1) | 136 (37%) | 234 |
0.681 (1.00) |
0.415 (1.00) |
0.516 (1.00) |
0.924 (1.00) |
0.507 (1.00) |
0.793 (1.00) |
0.377 (1.00) |
0.341 (1.00) |
0.535 (1.00) |
0.637 (1.00) |
0.838 (1.00) |
0.0557 (1.00) |
0.632 (1.00) |
0.249 (1.00) |
Amp Peak 10(7p21 1) | 203 (55%) | 167 |
0.85 (1.00) |
0.497 (1.00) |
0.346 (1.00) |
0.908 (1.00) |
0.31 (1.00) |
0.161 (1.00) |
0.0557 (1.00) |
0.26 (1.00) |
0.65 (1.00) |
1 (1.00) |
0.345 (1.00) |
0.214 (1.00) |
0.922 (1.00) |
0.302 (1.00) |
Amp Peak 11(7p11 2) | 196 (53%) | 174 |
0.221 (1.00) |
0.124 (1.00) |
0.403 (1.00) |
0.695 (1.00) |
0.316 (1.00) |
0.0858 (1.00) |
0.00852 (1.00) |
0.366 (1.00) |
0.298 (1.00) |
0.821 (1.00) |
0.236 (1.00) |
0.17 (1.00) |
0.185 (1.00) |
0.832 (1.00) |
Amp Peak 12(7q31 2) | 152 (41%) | 218 |
0.783 (1.00) |
0.0366 (1.00) |
0.751 (1.00) |
0.376 (1.00) |
0.318 (1.00) |
0.182 (1.00) |
0.268 (1.00) |
0.666 (1.00) |
0.455 (1.00) |
0.243 (1.00) |
0.271 (1.00) |
0.4 (1.00) |
0.835 (1.00) |
0.384 (1.00) |
Amp Peak 13(8p11 23) | 102 (28%) | 268 |
0.964 (1.00) |
0.0102 (1.00) |
0.128 (1.00) |
0.143 (1.00) |
0.234 (1.00) |
0.919 (1.00) |
0.978 (1.00) |
0.953 (1.00) |
0.884 (1.00) |
1 (1.00) |
0.839 (1.00) |
0.107 (1.00) |
0.298 (1.00) |
0.825 (1.00) |
Amp Peak 14(8p11 21) | 127 (34%) | 243 |
0.299 (1.00) |
0.0499 (1.00) |
0.00298 (1.00) |
0.869 (1.00) |
0.0143 (1.00) |
0.456 (1.00) |
0.215 (1.00) |
0.637 (1.00) |
0.371 (1.00) |
1 (1.00) |
0.649 (1.00) |
0.0304 (1.00) |
0.947 (1.00) |
0.909 (1.00) |
Amp Peak 15(8q11 1) | 172 (46%) | 198 |
0.635 (1.00) |
0.0217 (1.00) |
0.295 (1.00) |
0.913 (1.00) |
0.0393 (1.00) |
0.451 (1.00) |
0.375 (1.00) |
0.728 (1.00) |
0.599 (1.00) |
1 (1.00) |
0.809 (1.00) |
0.00386 (1.00) |
0.111 (1.00) |
0.582 (1.00) |
Amp Peak 16(8q24 21) | 234 (63%) | 136 |
0.304 (1.00) |
0.192 (1.00) |
0.746 (1.00) |
0.885 (1.00) |
0.013 (1.00) |
0.135 (1.00) |
0.507 (1.00) |
0.931 (1.00) |
0.775 (1.00) |
0.637 (1.00) |
0.527 (1.00) |
0.0121 (1.00) |
0.612 (1.00) |
0.515 (1.00) |
Amp Peak 19(12p12 1) | 127 (34%) | 243 |
0.0237 (1.00) |
0.384 (1.00) |
0.913 (1.00) |
0.821 (1.00) |
0.548 (1.00) |
0.235 (1.00) |
0.727 (1.00) |
0.845 (1.00) |
0.744 (1.00) |
0.631 (1.00) |
0.62 (1.00) |
0.106 (1.00) |
0.256 (1.00) |
0.0351 (1.00) |
Amp Peak 20(12q14 1) | 113 (31%) | 257 |
0.133 (1.00) |
0.115 (1.00) |
0.499 (1.00) |
0.558 (1.00) |
0.587 (1.00) |
0.197 (1.00) |
0.756 (1.00) |
0.333 (1.00) |
0.51 (1.00) |
1 (1.00) |
0.201 (1.00) |
0.233 (1.00) |
0.00345 (1.00) |
0.276 (1.00) |
Amp Peak 21(12q15) | 119 (32%) | 251 |
0.35 (1.00) |
0.51 (1.00) |
0.503 (1.00) |
0.321 (1.00) |
0.596 (1.00) |
0.464 (1.00) |
0.66 (1.00) |
0.679 (1.00) |
0.787 (1.00) |
0.808 (1.00) |
0.126 (1.00) |
0.17 (1.00) |
0.0183 (1.00) |
0.231 (1.00) |
Amp Peak 22(13q33 3) | 62 (17%) | 308 |
0.806 (1.00) |
0.503 (1.00) |
0.208 (1.00) |
0.875 (1.00) |
0.27 (1.00) |
0.542 (1.00) |
0.0942 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.221 (1.00) |
0.819 (1.00) |
0.696 (1.00) |
0.472 (1.00) |
|
Amp Peak 23(14q13 3) | 157 (42%) | 213 |
0.355 (1.00) |
0.565 (1.00) |
0.751 (1.00) |
0.538 (1.00) |
0.369 (1.00) |
0.964 (1.00) |
0.785 (1.00) |
0.161 (1.00) |
0.567 (1.00) |
0.643 (1.00) |
0.733 (1.00) |
0.248 (1.00) |
0.229 (1.00) |
0.804 (1.00) |
Amp Peak 24(17q12) | 164 (44%) | 206 |
0.82 (1.00) |
0.996 (1.00) |
0.916 (1.00) |
0.0981 (1.00) |
0.466 (1.00) |
0.708 (1.00) |
0.627 (1.00) |
0.348 (1.00) |
0.455 (1.00) |
0.0656 (1.00) |
0.00785 (1.00) |
0.439 (1.00) |
0.459 (1.00) |
0.013 (1.00) |
Amp Peak 25(17q23 1) | 177 (48%) | 193 |
0.479 (1.00) |
0.234 (1.00) |
0.601 (1.00) |
0.591 (1.00) |
0.127 (1.00) |
0.583 (1.00) |
0.537 (1.00) |
0.638 (1.00) |
0.529 (1.00) |
0.646 (1.00) |
0.0363 (1.00) |
0.225 (1.00) |
0.456 (1.00) |
0.0321 (1.00) |
Amp Peak 26(18q11 2) | 76 (21%) | 294 |
0.831 (1.00) |
0.718 (1.00) |
0.246 (1.00) |
0.752 (1.00) |
0.044 (1.00) |
1 (1.00) |
0.772 (1.00) |
0.352 (1.00) |
0.327 (1.00) |
0.391 (1.00) |
0.424 (1.00) |
0.114 (1.00) |
0.53 (1.00) |
0.585 (1.00) |
Amp Peak 27(19q12) | 102 (28%) | 268 |
0.87 (1.00) |
0.477 (1.00) |
0.0466 (1.00) |
0.259 (1.00) |
0.532 (1.00) |
0.329 (1.00) |
0.342 (1.00) |
0.976 (1.00) |
0.342 (1.00) |
0.302 (1.00) |
0.113 (1.00) |
0.54 (1.00) |
0.333 (1.00) |
0.585 (1.00) |
Amp Peak 28(20p11 21) | 137 (37%) | 233 |
0.492 (1.00) |
0.942 (1.00) |
0.914 (1.00) |
0.201 (1.00) |
0.238 (1.00) |
0.182 (1.00) |
0.085 (1.00) |
0.289 (1.00) |
0.0308 (1.00) |
0.636 (1.00) |
0.59 (1.00) |
0.0952 (1.00) |
0.213 (1.00) |
0.521 (1.00) |
Amp Peak 29(20q13 33) | 177 (48%) | 193 |
0.416 (1.00) |
0.229 (1.00) |
0.917 (1.00) |
0.274 (1.00) |
0.0615 (1.00) |
0.176 (1.00) |
0.44 (1.00) |
0.18 (1.00) |
0.0919 (1.00) |
0.5 (1.00) |
0.353 (1.00) |
0.202 (1.00) |
0.578 (1.00) |
0.95 (1.00) |
Amp Peak 30(22q11 22) | 61 (16%) | 309 |
0.3 (1.00) |
0.767 (1.00) |
0.209 (1.00) |
0.363 (1.00) |
0.583 (1.00) |
0.685 (1.00) |
0.0671 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.512 (1.00) |
0.695 (1.00) |
0.189 (1.00) |
1 (1.00) |
|
Amp Peak 31(Xq28) | 121 (33%) | 249 |
0.271 (1.00) |
0.367 (1.00) |
0.119 (1.00) |
0.288 (1.00) |
0.469 (1.00) |
0.657 (1.00) |
0.283 (1.00) |
0.4 (1.00) |
0.449 (1.00) |
0.81 (1.00) |
0.375 (1.00) |
0.0209 (1.00) |
0.759 (1.00) |
0.95 (1.00) |
Del Peak 1(1p36 13) | 85 (23%) | 285 |
0.0359 (1.00) |
0.327 (1.00) |
0.0632 (1.00) |
0.447 (1.00) |
0.612 (1.00) |
0.0516 (1.00) |
0.0347 (1.00) |
0.548 (1.00) |
0.0506 (1.00) |
0.421 (1.00) |
0.845 (1.00) |
0.197 (1.00) |
0.994 (1.00) |
0.251 (1.00) |
Del Peak 2(1p13 3) | 113 (31%) | 257 |
0.764 (1.00) |
0.185 (1.00) |
1 (1.00) |
0.615 (1.00) |
0.876 (1.00) |
0.206 (1.00) |
0.461 (1.00) |
0.265 (1.00) |
0.0685 (1.00) |
1 (1.00) |
0.919 (1.00) |
0.892 (1.00) |
0.927 (1.00) |
0.281 (1.00) |
Del Peak 3(1p13 1) | 109 (29%) | 261 |
0.425 (1.00) |
0.131 (1.00) |
0.909 (1.00) |
0.746 (1.00) |
0.762 (1.00) |
0.308 (1.00) |
0.548 (1.00) |
0.269 (1.00) |
0.0673 (1.00) |
1 (1.00) |
0.546 (1.00) |
0.631 (1.00) |
0.736 (1.00) |
0.51 (1.00) |
Del Peak 4(2q22 1) | 40 (11%) | 330 |
0.742 (1.00) |
0.832 (1.00) |
1 (1.00) |
0.901 (1.00) |
0.151 (1.00) |
0.312 (1.00) |
0.626 (1.00) |
0.381 (1.00) |
0.25 (1.00) |
1 (1.00) |
0.0456 (1.00) |
0.384 (1.00) |
0.612 (1.00) |
0.744 (1.00) |
Del Peak 5(2q37 3) | 57 (15%) | 313 |
0.252 (1.00) |
0.944 (1.00) |
0.112 (1.00) |
0.561 (1.00) |
0.0883 (1.00) |
0.836 (1.00) |
0.182 (1.00) |
0.195 (1.00) |
0.593 (1.00) |
0.0537 (1.00) |
0.913 (1.00) |
0.354 (1.00) |
0.385 (1.00) |
0.861 (1.00) |
Del Peak 6(3p21 31) | 180 (49%) | 190 |
0.645 (1.00) |
0.569 (1.00) |
0.835 (1.00) |
0.0638 (1.00) |
0.633 (1.00) |
0.00473 (1.00) |
0.0474 (1.00) |
0.537 (1.00) |
0.228 (1.00) |
0.254 (1.00) |
0.994 (1.00) |
0.0787 (1.00) |
0.000564 (0.642) |
0.912 (1.00) |
Del Peak 7(3q11 1) | 110 (30%) | 260 |
0.428 (1.00) |
0.202 (1.00) |
0.733 (1.00) |
0.0824 (1.00) |
0.963 (1.00) |
0.853 (1.00) |
0.566 (1.00) |
0.931 (1.00) |
0.673 (1.00) |
0.803 (1.00) |
0.43 (1.00) |
0.764 (1.00) |
0.0345 (1.00) |
0.755 (1.00) |
Del Peak 8(3q29) | 107 (29%) | 263 |
0.785 (1.00) |
0.418 (1.00) |
0.565 (1.00) |
0.367 (1.00) |
0.819 (1.00) |
0.442 (1.00) |
0.409 (1.00) |
0.73 (1.00) |
0.491 (1.00) |
0.454 (1.00) |
0.252 (1.00) |
0.79 (1.00) |
0.202 (1.00) |
0.354 (1.00) |
Del Peak 9(4p16 3) | 92 (25%) | 278 |
0.148 (1.00) |
0.0388 (1.00) |
0.809 (1.00) |
0.629 (1.00) |
0.489 (1.00) |
0.492 (1.00) |
0.774 (1.00) |
0.881 (1.00) |
0.667 (1.00) |
1 (1.00) |
0.0921 (1.00) |
0.00151 (1.00) |
0.0781 (1.00) |
0.839 (1.00) |
Del Peak 10(4q22 1) | 114 (31%) | 256 |
0.485 (1.00) |
0.689 (1.00) |
0.736 (1.00) |
0.187 (1.00) |
0.261 (1.00) |
0.761 (1.00) |
0.0275 (1.00) |
0.649 (1.00) |
0.0583 (1.00) |
0.455 (1.00) |
0.428 (1.00) |
0.0234 (1.00) |
0.328 (1.00) |
0.35 (1.00) |
Del Peak 11(4q35 1) | 137 (37%) | 233 |
0.898 (1.00) |
0.179 (1.00) |
0.131 (1.00) |
0.188 (1.00) |
0.164 (1.00) |
0.385 (1.00) |
0.139 (1.00) |
0.239 (1.00) |
0.302 (1.00) |
0.239 (1.00) |
0.443 (1.00) |
0.00035 (0.399) |
0.163 (1.00) |
0.842 (1.00) |
Del Peak 12(5q11 2) | 132 (36%) | 238 |
0.242 (1.00) |
0.0338 (1.00) |
1 (1.00) |
0.47 (1.00) |
0.175 (1.00) |
0.385 (1.00) |
0.0673 (1.00) |
0.371 (1.00) |
0.154 (1.00) |
0.348 (1.00) |
0.0299 (1.00) |
0.045 (1.00) |
0.442 (1.00) |
0.681 (1.00) |
Del Peak 14(6q12) | 128 (35%) | 242 |
0.12 (1.00) |
0.55 (1.00) |
0.584 (1.00) |
0.192 (1.00) |
0.313 (1.00) |
0.473 (1.00) |
0.0581 (1.00) |
0.366 (1.00) |
0.059 (1.00) |
0.339 (1.00) |
0.0125 (1.00) |
0.0511 (1.00) |
0.0815 (1.00) |
0.507 (1.00) |
Del Peak 15(6q22 31) | 184 (50%) | 186 |
0.647 (1.00) |
0.259 (1.00) |
0.602 (1.00) |
0.189 (1.00) |
0.838 (1.00) |
0.46 (1.00) |
0.784 (1.00) |
0.533 (1.00) |
0.389 (1.00) |
1 (1.00) |
0.069 (1.00) |
0.0996 (1.00) |
0.414 (1.00) |
0.791 (1.00) |
Del Peak 16(6q26) | 187 (51%) | 183 |
0.627 (1.00) |
0.15 (1.00) |
0.466 (1.00) |
0.271 (1.00) |
0.808 (1.00) |
0.818 (1.00) |
0.498 (1.00) |
0.11 (1.00) |
0.159 (1.00) |
1 (1.00) |
0.366 (1.00) |
0.196 (1.00) |
0.185 (1.00) |
0.736 (1.00) |
Del Peak 17(8p23 2) | 181 (49%) | 189 |
0.705 (1.00) |
0.274 (1.00) |
0.251 (1.00) |
0.0446 (1.00) |
0.00682 (1.00) |
0.455 (1.00) |
0.904 (1.00) |
0.46 (1.00) |
0.578 (1.00) |
0.362 (1.00) |
0.453 (1.00) |
0.0198 (1.00) |
0.357 (1.00) |
0.771 (1.00) |
Del Peak 18(8p12) | 161 (44%) | 209 |
0.718 (1.00) |
0.792 (1.00) |
0.172 (1.00) |
0.23 (1.00) |
0.0138 (1.00) |
0.833 (1.00) |
0.665 (1.00) |
0.323 (1.00) |
0.92 (1.00) |
0.82 (1.00) |
0.389 (1.00) |
0.137 (1.00) |
0.683 (1.00) |
0.207 (1.00) |
Del Peak 19(8p11 21) | 80 (22%) | 290 |
0.566 (1.00) |
0.964 (1.00) |
0.0112 (1.00) |
0.115 (1.00) |
0.0563 (1.00) |
0.689 (1.00) |
0.476 (1.00) |
0.903 (1.00) |
0.514 (1.00) |
0.4 (1.00) |
0.56 (1.00) |
0.979 (1.00) |
0.608 (1.00) |
0.0427 (1.00) |
Del Peak 20(8q11 21) | 43 (12%) | 327 |
0.557 (1.00) |
0.277 (1.00) |
0.328 (1.00) |
0.00456 (1.00) |
0.054 (1.00) |
0.185 (1.00) |
0.066 (1.00) |
0.946 (1.00) |
0.456 (1.00) |
1 (1.00) |
0.905 (1.00) |
0.91 (1.00) |
0.162 (1.00) |
0.212 (1.00) |
Del Peak 21(9p23) | 200 (54%) | 170 |
0.101 (1.00) |
0.17 (1.00) |
0.464 (1.00) |
0.614 (1.00) |
0.646 (1.00) |
0.851 (1.00) |
0.0167 (1.00) |
0.696 (1.00) |
0.34 (1.00) |
0.362 (1.00) |
0.986 (1.00) |
0.191 (1.00) |
0.317 (1.00) |
1 (1.00) |
Del Peak 22(9p21 3) | 206 (56%) | 164 |
0.499 (1.00) |
0.0748 (1.00) |
0.0595 (1.00) |
0.821 (1.00) |
0.496 (1.00) |
0.944 (1.00) |
0.0041 (1.00) |
0.602 (1.00) |
0.0933 (1.00) |
1 (1.00) |
0.506 (1.00) |
0.179 (1.00) |
0.224 (1.00) |
0.905 (1.00) |
Del Peak 23(9q21 11) | 181 (49%) | 189 |
0.276 (1.00) |
0.984 (1.00) |
0.754 (1.00) |
0.908 (1.00) |
0.0371 (1.00) |
0.447 (1.00) |
0.47 (1.00) |
0.815 (1.00) |
0.812 (1.00) |
0.107 (1.00) |
0.0696 (1.00) |
0.285 (1.00) |
0.614 (1.00) |
0.216 (1.00) |
Del Peak 25(10q26 3) | 98 (26%) | 272 |
0.537 (1.00) |
0.909 (1.00) |
0.0584 (1.00) |
0.236 (1.00) |
0.762 (1.00) |
0.0882 (1.00) |
0.372 (1.00) |
1 (1.00) |
0.202 (1.00) |
0.117 (1.00) |
0.0235 (1.00) |
0.217 (1.00) |
0.0781 (1.00) |
0.579 (1.00) |
Del Peak 26(11p15 5) | 98 (26%) | 272 |
0.592 (1.00) |
0.0913 (1.00) |
0.193 (1.00) |
0.318 (1.00) |
0.208 (1.00) |
0.925 (1.00) |
0.943 (1.00) |
0.0832 (1.00) |
0.572 (1.00) |
1 (1.00) |
0.119 (1.00) |
0.003 (1.00) |
0.148 (1.00) |
1 (1.00) |
Del Peak 27(11q23 2) | 82 (22%) | 288 |
0.85 (1.00) |
0.429 (1.00) |
0.454 (1.00) |
0.535 (1.00) |
0.753 (1.00) |
0.563 (1.00) |
0.317 (1.00) |
0.216 (1.00) |
0.462 (1.00) |
0.584 (1.00) |
0.308 (1.00) |
0.539 (1.00) |
0.201 (1.00) |
0.385 (1.00) |
Del Peak 28(11q25) | 79 (21%) | 291 |
0.235 (1.00) |
0.49 (1.00) |
0.203 (1.00) |
0.535 (1.00) |
0.914 (1.00) |
0.672 (1.00) |
0.193 (1.00) |
0.279 (1.00) |
0.45 (1.00) |
0.586 (1.00) |
0.331 (1.00) |
0.293 (1.00) |
0.186 (1.00) |
0.491 (1.00) |
Del Peak 30(12q12) | 70 (19%) | 300 |
0.253 (1.00) |
0.11 (1.00) |
0.0461 (1.00) |
0.693 (1.00) |
0.596 (1.00) |
0.413 (1.00) |
0.603 (1.00) |
0.0933 (1.00) |
0.648 (1.00) |
0.777 (1.00) |
0.125 (1.00) |
0.929 (1.00) |
0.322 (1.00) |
0.537 (1.00) |
Del Peak 31(12q24 33) | 90 (24%) | 280 |
0.521 (1.00) |
0.94 (1.00) |
0.0389 (1.00) |
0.392 (1.00) |
0.288 (1.00) |
0.0851 (1.00) |
0.928 (1.00) |
0.239 (1.00) |
0.789 (1.00) |
0.18 (1.00) |
0.489 (1.00) |
0.0348 (1.00) |
0.327 (1.00) |
0.702 (1.00) |
Del Peak 32(13q12 11) | 204 (55%) | 166 |
0.429 (1.00) |
0.152 (1.00) |
0.0156 (1.00) |
0.0252 (1.00) |
0.0577 (1.00) |
0.638 (1.00) |
0.916 (1.00) |
0.605 (1.00) |
0.715 (1.00) |
0.365 (1.00) |
0.000784 (0.889) |
0.00541 (1.00) |
0.326 (1.00) |
0.907 (1.00) |
Del Peak 33(13q12 13) | 205 (55%) | 165 |
0.525 (1.00) |
0.333 (1.00) |
0.0584 (1.00) |
0.0399 (1.00) |
0.0266 (1.00) |
0.744 (1.00) |
0.792 (1.00) |
0.605 (1.00) |
0.751 (1.00) |
0.171 (1.00) |
0.00548 (1.00) |
0.021 (1.00) |
0.322 (1.00) |
0.919 (1.00) |
Del Peak 34(13q14 2) | 197 (53%) | 173 |
0.864 (1.00) |
0.166 (1.00) |
0.532 (1.00) |
0.655 (1.00) |
0.156 (1.00) |
0.692 (1.00) |
1 (1.00) |
0.519 (1.00) |
0.919 (1.00) |
1 (1.00) |
0.139 (1.00) |
0.0165 (1.00) |
0.306 (1.00) |
0.896 (1.00) |
Del Peak 35(13q34) | 164 (44%) | 206 |
0.994 (1.00) |
0.0698 (1.00) |
0.916 (1.00) |
0.669 (1.00) |
0.301 (1.00) |
0.6 (1.00) |
0.943 (1.00) |
0.173 (1.00) |
0.624 (1.00) |
1 (1.00) |
0.21 (1.00) |
0.0332 (1.00) |
0.192 (1.00) |
0.296 (1.00) |
Del Peak 36(14q32 33) | 110 (30%) | 260 |
0.407 (1.00) |
0.942 (1.00) |
0.569 (1.00) |
0.786 (1.00) |
0.389 (1.00) |
0.401 (1.00) |
0.53 (1.00) |
0.728 (1.00) |
0.692 (1.00) |
0.618 (1.00) |
0.15 (1.00) |
0.258 (1.00) |
0.051 (1.00) |
0.104 (1.00) |
Del Peak 37(15q11 2) | 188 (51%) | 182 |
0.332 (1.00) |
0.0434 (1.00) |
0.0757 (1.00) |
0.241 (1.00) |
0.0444 (1.00) |
0.308 (1.00) |
0.956 (1.00) |
0.975 (1.00) |
0.728 (1.00) |
1 (1.00) |
0.916 (1.00) |
0.324 (1.00) |
0.355 (1.00) |
0.61 (1.00) |
Del Peak 38(16q23 1) | 126 (34%) | 244 |
0.997 (1.00) |
0.685 (1.00) |
1 (1.00) |
0.591 (1.00) |
0.797 (1.00) |
0.704 (1.00) |
0.567 (1.00) |
1 (1.00) |
0.788 (1.00) |
1 (1.00) |
0.591 (1.00) |
0.182 (1.00) |
0.857 (1.00) |
0.711 (1.00) |
Del Peak 39(16q24 3) | 138 (37%) | 232 |
0.669 (1.00) |
0.485 (1.00) |
0.829 (1.00) |
0.589 (1.00) |
0.818 (1.00) |
0.958 (1.00) |
0.197 (1.00) |
0.693 (1.00) |
0.665 (1.00) |
1 (1.00) |
0.36 (1.00) |
0.0414 (1.00) |
0.853 (1.00) |
0.878 (1.00) |
Del Peak 40(17p13 3) | 204 (55%) | 166 |
0.641 (1.00) |
0.132 (1.00) |
0.0595 (1.00) |
0.778 (1.00) |
0.0309 (1.00) |
0.286 (1.00) |
0.807 (1.00) |
0.879 (1.00) |
0.691 (1.00) |
0.365 (1.00) |
0.751 (1.00) |
0.196 (1.00) |
0.0206 (1.00) |
0.409 (1.00) |
Del Peak 41(18q21 32) | 190 (51%) | 180 |
0.218 (1.00) |
0.483 (1.00) |
0.0759 (1.00) |
0.301 (1.00) |
0.576 (1.00) |
0.286 (1.00) |
0.461 (1.00) |
0.09 (1.00) |
0.271 (1.00) |
1 (1.00) |
0.952 (1.00) |
0.561 (1.00) |
0.332 (1.00) |
0.0474 (1.00) |
Del Peak 42(18q23) | 184 (50%) | 186 |
0.297 (1.00) |
0.206 (1.00) |
0.061 (1.00) |
0.318 (1.00) |
0.384 (1.00) |
0.163 (1.00) |
0.283 (1.00) |
0.349 (1.00) |
0.0514 (1.00) |
1 (1.00) |
0.782 (1.00) |
0.488 (1.00) |
0.123 (1.00) |
0.0473 (1.00) |
Del Peak 43(19p13 3) | 201 (54%) | 169 |
0.0637 (1.00) |
0.164 (1.00) |
0.0033 (1.00) |
0.802 (1.00) |
0.422 (1.00) |
0.138 (1.00) |
0.0825 (1.00) |
0.312 (1.00) |
0.0132 (1.00) |
0.651 (1.00) |
0.461 (1.00) |
0.15 (1.00) |
0.175 (1.00) |
0.364 (1.00) |
Del Peak 44(19p13 2) | 196 (53%) | 174 |
0.323 (1.00) |
0.0224 (1.00) |
0.000567 (0.645) |
0.923 (1.00) |
0.56 (1.00) |
0.17 (1.00) |
0.0534 (1.00) |
0.09 (1.00) |
0.0228 (1.00) |
0.821 (1.00) |
0.501 (1.00) |
0.0252 (1.00) |
0.16 (1.00) |
0.588 (1.00) |
Del Peak 45(19p12) | 156 (42%) | 214 |
0.00559 (1.00) |
0.00527 (1.00) |
0.0268 (1.00) |
0.962 (1.00) |
0.536 (1.00) |
0.0201 (1.00) |
0.0197 (1.00) |
0.089 (1.00) |
0.000663 (0.754) |
0.819 (1.00) |
0.19 (1.00) |
0.143 (1.00) |
0.111 (1.00) |
0.883 (1.00) |
Del Peak 46(19q13 33) | 136 (37%) | 234 |
0.0294 (1.00) |
0.289 (1.00) |
0.589 (1.00) |
0.465 (1.00) |
0.454 (1.00) |
0.614 (1.00) |
0.631 (1.00) |
0.24 (1.00) |
0.241 (1.00) |
0.813 (1.00) |
0.731 (1.00) |
0.397 (1.00) |
0.665 (1.00) |
0.311 (1.00) |
Del Peak 47(20p13) | 93 (25%) | 277 |
0.681 (1.00) |
1 (1.00) |
0.117 (1.00) |
0.696 (1.00) |
0.211 (1.00) |
0.762 (1.00) |
0.1 (1.00) |
0.881 (1.00) |
0.188 (1.00) |
0.601 (1.00) |
0.259 (1.00) |
0.179 (1.00) |
0.0505 (1.00) |
0.815 (1.00) |
Del Peak 48(21q11 2) | 127 (34%) | 243 |
0.69 (1.00) |
0.274 (1.00) |
0.583 (1.00) |
0.751 (1.00) |
0.408 (1.00) |
0.506 (1.00) |
0.762 (1.00) |
0.909 (1.00) |
0.713 (1.00) |
0.336 (1.00) |
0.29 (1.00) |
0.0488 (1.00) |
0.0385 (1.00) |
0.836 (1.00) |
Del Peak 49(21q21 3) | 122 (33%) | 248 |
0.577 (1.00) |
0.666 (1.00) |
0.148 (1.00) |
0.535 (1.00) |
0.402 (1.00) |
0.57 (1.00) |
0.804 (1.00) |
0.475 (1.00) |
0.658 (1.00) |
0.327 (1.00) |
0.165 (1.00) |
0.00822 (1.00) |
0.26 (1.00) |
0.507 (1.00) |
Del Peak 51(Xp22 2) | 109 (29%) | 261 |
0.559 (1.00) |
0.384 (1.00) |
0.0514 (1.00) |
0.931 (1.00) |
0.61 (1.00) |
0.947 (1.00) |
0.541 (1.00) |
0.872 (1.00) |
0.918 (1.00) |
0.803 (1.00) |
0.947 (1.00) |
0.265 (1.00) |
0.148 (1.00) |
0.558 (1.00) |
P value = 4.36e-06 (Fisher's exact test), Q value = 0.005
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 125 | 94 | 84 | 54 |
AMP PEAK 17(10P15.1) MUTATED | 46 | 18 | 30 | 3 |
AMP PEAK 17(10P15.1) WILD-TYPE | 79 | 76 | 54 | 51 |
P value = 0.000197 (t-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 339 | 65.3 (9.8) |
AMP PEAK 18(11Q13.3) MUTATED | 119 | 62.6 (9.7) |
AMP PEAK 18(11Q13.3) WILD-TYPE | 220 | 66.7 (9.6) |
P value = 1.08e-05 (Fisher's exact test), Q value = 0.012
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 125 | 94 | 84 | 54 |
DEL PEAK 13(5Q22.1) MUTATED | 58 | 27 | 50 | 13 |
DEL PEAK 13(5Q22.1) WILD-TYPE | 67 | 67 | 34 | 41 |
P value = 7.03e-05 (Fisher's exact test), Q value = 0.08
nPatients | FEMALE | MALE |
---|---|---|
ALL | 203 | 167 |
DEL PEAK 24(10P15.3) MUTATED | 64 | 23 |
DEL PEAK 24(10P15.3) WILD-TYPE | 139 | 144 |
P value = 0.000192 (Fisher's exact test), Q value = 0.22
nPatients | FEMALE | MALE |
---|---|---|
ALL | 203 | 167 |
DEL PEAK 29(12P13.2) MUTATED | 74 | 31 |
DEL PEAK 29(12P13.2) WILD-TYPE | 129 | 136 |
P value = 0.000137 (Fisher's exact test), Q value = 0.16
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 125 | 94 | 84 | 54 |
DEL PEAK 50(22Q13.32) MUTATED | 67 | 34 | 54 | 18 |
DEL PEAK 50(22Q13.32) WILD-TYPE | 58 | 60 | 30 | 36 |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = LUAD-TP.clin.merged.picked.txt
-
Number of patients = 370
-
Number of significantly arm-level cnvs = 82
-
Number of selected clinical features = 14
-
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 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 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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.