(primary solid tumor cohort)
This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.
Testing the association between copy number variation of 77 peak regions and 14 clinical features across 327 patients, 7 significant findings detected with Q value < 0.25.
-
Amp Peak 17(10p15.1) cnvs correlated to 'STOPPEDSMOKINGYEAR' and 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
Amp Peak 18(11q13.3) cnvs correlated to 'AGE'.
-
Del Peak 6(3p21.31) cnvs correlated to 'YEAROFTOBACCOSMOKINGONSET'.
-
Del Peak 13(5q34) cnvs correlated to 'STOPPEDSMOKINGYEAR' and 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
Del Peak 22(10p15.3) cnvs correlated to 'GENDER'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 77 regions and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 7 significant findings detected.
|
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | STOPPEDSMOKINGYEAR | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET | ||
| 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 | t-test | Fisher's exact test | t-test | |
| Amp Peak 17(10p15 1) | 91 (28%) | 236 |
0.125 (1.00) |
0.407 (1.00) |
0.0629 (1.00) |
0.571 (1.00) |
0.501 (1.00) |
0.707 (1.00) |
0.0131 (1.00) |
0.857 (1.00) |
0.48 (1.00) |
0.607 (1.00) |
0.0134 (1.00) |
0.000193 (0.207) |
3.65e-06 (0.00393) |
0.827 (1.00) |
| Del Peak 13(5q34) | 113 (35%) | 214 |
0.318 (1.00) |
0.000561 (0.599) |
0.293 (1.00) |
0.817 (1.00) |
0.234 (1.00) |
0.725 (1.00) |
0.167 (1.00) |
1 (1.00) |
0.133 (1.00) |
0.469 (1.00) |
0.152 (1.00) |
6.1e-05 (0.0654) |
5.82e-07 (0.000626) |
0.0154 (1.00) |
| Amp Peak 18(11q13 3) | 114 (35%) | 213 |
0.804 (1.00) |
2.74e-05 (0.0295) |
0.244 (1.00) |
0.519 (1.00) |
0.623 (1.00) |
0.695 (1.00) |
0.788 (1.00) |
0.536 (1.00) |
0.149 (1.00) |
0.81 (1.00) |
0.912 (1.00) |
0.0792 (1.00) |
0.0107 (1.00) |
0.576 (1.00) |
| Del Peak 6(3p21 31) | 163 (50%) | 164 |
0.57 (1.00) |
0.405 (1.00) |
0.579 (1.00) |
0.0638 (1.00) |
0.579 (1.00) |
0.00712 (1.00) |
0.031 (1.00) |
0.442 (1.00) |
0.14 (1.00) |
0.248 (1.00) |
0.743 (1.00) |
0.0233 (1.00) |
0.016 (1.00) |
5.07e-05 (0.0544) |
| Del Peak 22(10p15 3) | 81 (25%) | 246 |
0.154 (1.00) |
0.537 (1.00) |
5.81e-05 (0.0623) |
0.851 (1.00) |
0.463 (1.00) |
0.393 (1.00) |
0.662 (1.00) |
0.371 (1.00) |
0.83 (1.00) |
0.791 (1.00) |
0.539 (1.00) |
0.58 (1.00) |
0.00446 (1.00) |
0.751 (1.00) |
| Amp Peak 1(1p34 3) | 95 (29%) | 232 |
0.911 (1.00) |
0.00927 (1.00) |
0.808 (1.00) |
0.421 (1.00) |
0.498 (1.00) |
0.73 (1.00) |
0.219 (1.00) |
0.855 (1.00) |
0.583 (1.00) |
0.452 (1.00) |
0.888 (1.00) |
0.6 (1.00) |
0.0565 (1.00) |
0.802 (1.00) |
| Amp Peak 2(1p22 3) | 92 (28%) | 235 |
0.755 (1.00) |
0.00066 (0.703) |
1 (1.00) |
0.609 (1.00) |
0.12 (1.00) |
0.886 (1.00) |
0.0585 (1.00) |
0.432 (1.00) |
0.284 (1.00) |
0.454 (1.00) |
0.403 (1.00) |
0.388 (1.00) |
0.547 (1.00) |
0.444 (1.00) |
| Amp Peak 3(1q21 3) | 239 (73%) | 88 |
0.334 (1.00) |
0.282 (1.00) |
0.0601 (1.00) |
0.311 (1.00) |
0.0255 (1.00) |
0.696 (1.00) |
0.845 (1.00) |
0.852 (1.00) |
0.9 (1.00) |
0.3 (1.00) |
0.626 (1.00) |
0.57 (1.00) |
0.237 (1.00) |
0.295 (1.00) |
| Amp Peak 4(3q26 2) | 118 (36%) | 209 |
0.892 (1.00) |
0.444 (1.00) |
1 (1.00) |
0.726 (1.00) |
0.845 (1.00) |
0.755 (1.00) |
0.238 (1.00) |
0.384 (1.00) |
0.567 (1.00) |
0.344 (1.00) |
0.142 (1.00) |
0.0244 (1.00) |
0.0166 (1.00) |
0.0922 (1.00) |
| Amp Peak 5(4q12) | 66 (20%) | 261 |
0.225 (1.00) |
0.00981 (1.00) |
0.783 (1.00) |
0.902 (1.00) |
0.294 (1.00) |
0.0876 (1.00) |
0.439 (1.00) |
0.48 (1.00) |
0.596 (1.00) |
0.775 (1.00) |
0.987 (1.00) |
0.595 (1.00) |
0.965 (1.00) |
0.246 (1.00) |
| Amp Peak 6(5p15 33) | 215 (66%) | 112 |
0.194 (1.00) |
0.00449 (1.00) |
0.00995 (1.00) |
0.0263 (1.00) |
0.158 (1.00) |
0.127 (1.00) |
0.545 (1.00) |
0.451 (1.00) |
0.493 (1.00) |
0.47 (1.00) |
0.195 (1.00) |
0.0263 (1.00) |
0.139 (1.00) |
0.199 (1.00) |
| Amp Peak 7(5p13 1) | 193 (59%) | 134 |
0.111 (1.00) |
0.0121 (1.00) |
0.042 (1.00) |
0.867 (1.00) |
0.282 (1.00) |
0.178 (1.00) |
0.349 (1.00) |
0.824 (1.00) |
0.522 (1.00) |
1 (1.00) |
0.0358 (1.00) |
0.0251 (1.00) |
0.305 (1.00) |
0.557 (1.00) |
| Amp Peak 8(5q35 1) | 79 (24%) | 248 |
0.102 (1.00) |
0.29 (1.00) |
0.0273 (1.00) |
0.971 (1.00) |
0.506 (1.00) |
0.392 (1.00) |
0.586 (1.00) |
0.77 (1.00) |
0.64 (1.00) |
0.59 (1.00) |
0.553 (1.00) |
0.451 (1.00) |
0.061 (1.00) |
0.148 (1.00) |
| Amp Peak 9(6p25 3) | 130 (40%) | 197 |
0.519 (1.00) |
0.206 (1.00) |
0.427 (1.00) |
0.863 (1.00) |
0.444 (1.00) |
0.57 (1.00) |
0.0178 (1.00) |
0.331 (1.00) |
0.0943 (1.00) |
0.353 (1.00) |
0.527 (1.00) |
0.571 (1.00) |
0.0969 (1.00) |
0.407 (1.00) |
| Amp Peak 10(6p21 1) | 120 (37%) | 207 |
0.648 (1.00) |
0.417 (1.00) |
0.25 (1.00) |
0.924 (1.00) |
0.779 (1.00) |
0.524 (1.00) |
0.0973 (1.00) |
0.203 (1.00) |
0.541 (1.00) |
0.636 (1.00) |
0.786 (1.00) |
0.608 (1.00) |
0.0309 (1.00) |
0.624 (1.00) |
| Amp Peak 11(7p21 1) | 179 (55%) | 148 |
0.76 (1.00) |
0.337 (1.00) |
0.267 (1.00) |
0.908 (1.00) |
0.389 (1.00) |
0.179 (1.00) |
0.0526 (1.00) |
0.714 (1.00) |
0.281 (1.00) |
1 (1.00) |
0.641 (1.00) |
0.601 (1.00) |
0.0243 (1.00) |
0.682 (1.00) |
| Amp Peak 12(7p11 2) | 172 (53%) | 155 |
0.18 (1.00) |
0.113 (1.00) |
0.436 (1.00) |
0.695 (1.00) |
0.322 (1.00) |
0.129 (1.00) |
0.00712 (1.00) |
0.776 (1.00) |
0.158 (1.00) |
0.822 (1.00) |
0.606 (1.00) |
0.553 (1.00) |
0.0496 (1.00) |
0.101 (1.00) |
| Amp Peak 13(7q31 2) | 136 (42%) | 191 |
0.976 (1.00) |
0.0552 (1.00) |
0.737 (1.00) |
0.376 (1.00) |
0.555 (1.00) |
0.376 (1.00) |
0.186 (1.00) |
0.4 (1.00) |
0.353 (1.00) |
0.245 (1.00) |
0.429 (1.00) |
0.231 (1.00) |
0.313 (1.00) |
0.984 (1.00) |
| Amp Peak 14(8p11 21) | 100 (31%) | 227 |
0.83 (1.00) |
0.155 (1.00) |
0.0708 (1.00) |
0.143 (1.00) |
0.123 (1.00) |
0.78 (1.00) |
0.235 (1.00) |
0.285 (1.00) |
0.313 (1.00) |
0.626 (1.00) |
0.782 (1.00) |
0.23 (1.00) |
0.142 (1.00) |
0.653 (1.00) |
| Amp Peak 15(8q11 1) | 148 (45%) | 179 |
0.83 (1.00) |
0.0261 (1.00) |
0.657 (1.00) |
0.913 (1.00) |
0.16 (1.00) |
0.715 (1.00) |
0.343 (1.00) |
0.615 (1.00) |
0.505 (1.00) |
1 (1.00) |
0.297 (1.00) |
0.434 (1.00) |
0.0171 (1.00) |
0.116 (1.00) |
| Amp Peak 16(8q24 21) | 204 (62%) | 123 |
0.234 (1.00) |
0.0893 (1.00) |
0.647 (1.00) |
0.885 (1.00) |
0.0735 (1.00) |
0.457 (1.00) |
0.71 (1.00) |
0.836 (1.00) |
0.859 (1.00) |
0.635 (1.00) |
0.516 (1.00) |
0.588 (1.00) |
0.0509 (1.00) |
0.669 (1.00) |
| Amp Peak 19(12p12 1) | 118 (36%) | 209 |
0.0361 (1.00) |
0.3 (1.00) |
0.817 (1.00) |
0.821 (1.00) |
0.598 (1.00) |
0.56 (1.00) |
0.759 (1.00) |
0.382 (1.00) |
0.866 (1.00) |
0.811 (1.00) |
0.849 (1.00) |
0.241 (1.00) |
0.0886 (1.00) |
0.218 (1.00) |
| Amp Peak 20(12q14 1) | 106 (32%) | 221 |
0.188 (1.00) |
0.0744 (1.00) |
0.637 (1.00) |
0.558 (1.00) |
0.806 (1.00) |
0.567 (1.00) |
0.748 (1.00) |
0.445 (1.00) |
0.376 (1.00) |
1 (1.00) |
0.408 (1.00) |
0.000598 (0.638) |
0.0504 (1.00) |
0.00102 (1.00) |
| Amp Peak 21(12q15) | 109 (33%) | 218 |
0.449 (1.00) |
0.213 (1.00) |
0.725 (1.00) |
0.321 (1.00) |
0.828 (1.00) |
0.777 (1.00) |
0.532 (1.00) |
0.721 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.237 (1.00) |
0.026 (1.00) |
0.03 (1.00) |
0.00326 (1.00) |
| Amp Peak 22(13q33 3) | 54 (17%) | 273 |
0.896 (1.00) |
0.821 (1.00) |
0.134 (1.00) |
0.934 (1.00) |
0.423 (1.00) |
0.492 (1.00) |
0.634 (1.00) |
0.695 (1.00) |
1 (1.00) |
0.392 (1.00) |
0.845 (1.00) |
0.663 (1.00) |
0.967 (1.00) |
|
| Amp Peak 23(14q13 3) | 143 (44%) | 184 |
0.371 (1.00) |
0.669 (1.00) |
0.576 (1.00) |
0.538 (1.00) |
0.566 (1.00) |
0.726 (1.00) |
0.934 (1.00) |
0.176 (1.00) |
0.699 (1.00) |
0.49 (1.00) |
0.865 (1.00) |
0.0886 (1.00) |
0.278 (1.00) |
0.0797 (1.00) |
| Amp Peak 24(17q12) | 148 (45%) | 179 |
0.904 (1.00) |
0.879 (1.00) |
0.824 (1.00) |
0.0981 (1.00) |
0.592 (1.00) |
0.493 (1.00) |
0.523 (1.00) |
0.353 (1.00) |
0.551 (1.00) |
0.103 (1.00) |
0.0159 (1.00) |
0.0737 (1.00) |
0.224 (1.00) |
0.692 (1.00) |
| Amp Peak 25(17q23 1) | 160 (49%) | 167 |
0.561 (1.00) |
0.335 (1.00) |
0.657 (1.00) |
0.591 (1.00) |
0.177 (1.00) |
0.311 (1.00) |
0.401 (1.00) |
0.388 (1.00) |
0.612 (1.00) |
0.648 (1.00) |
0.0659 (1.00) |
0.0261 (1.00) |
0.133 (1.00) |
0.372 (1.00) |
| Amp Peak 26(18p11 32) | 86 (26%) | 241 |
0.172 (1.00) |
0.321 (1.00) |
0.802 (1.00) |
0.882 (1.00) |
0.58 (1.00) |
0.719 (1.00) |
0.362 (1.00) |
0.806 (1.00) |
0.951 (1.00) |
0.302 (1.00) |
0.178 (1.00) |
0.105 (1.00) |
0.379 (1.00) |
0.355 (1.00) |
| Amp Peak 27(18q11 2) | 70 (21%) | 257 |
0.972 (1.00) |
0.71 (1.00) |
0.417 (1.00) |
0.752 (1.00) |
0.0592 (1.00) |
0.906 (1.00) |
0.486 (1.00) |
0.188 (1.00) |
0.403 (1.00) |
0.267 (1.00) |
0.483 (1.00) |
0.657 (1.00) |
0.0966 (1.00) |
0.81 (1.00) |
| Amp Peak 28(19q12) | 91 (28%) | 236 |
0.706 (1.00) |
0.601 (1.00) |
0.107 (1.00) |
0.259 (1.00) |
0.409 (1.00) |
0.436 (1.00) |
0.66 (1.00) |
0.926 (1.00) |
0.57 (1.00) |
0.301 (1.00) |
0.435 (1.00) |
0.0137 (1.00) |
0.791 (1.00) |
0.278 (1.00) |
| Amp Peak 29(20q11 21) | 144 (44%) | 183 |
0.507 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.192 (1.00) |
0.407 (1.00) |
0.0173 (1.00) |
0.242 (1.00) |
0.0587 (1.00) |
0.216 (1.00) |
0.247 (1.00) |
0.00731 (1.00) |
0.687 (1.00) |
0.4 (1.00) |
0.176 (1.00) |
| Amp Peak 30(20q13 33) | 160 (49%) | 167 |
0.44 (1.00) |
0.42 (1.00) |
0.824 (1.00) |
0.274 (1.00) |
0.119 (1.00) |
0.128 (1.00) |
0.186 (1.00) |
0.0998 (1.00) |
0.0345 (1.00) |
0.492 (1.00) |
0.361 (1.00) |
0.119 (1.00) |
0.165 (1.00) |
0.866 (1.00) |
| Amp Peak 31(22q11 22) | 54 (17%) | 273 |
0.299 (1.00) |
0.489 (1.00) |
0.37 (1.00) |
0.424 (1.00) |
0.444 (1.00) |
0.435 (1.00) |
0.0457 (1.00) |
0.236 (1.00) |
1 (1.00) |
0.855 (1.00) |
0.621 (1.00) |
0.71 (1.00) |
0.574 (1.00) |
|
| Amp Peak 32(Xq28) | 113 (35%) | 214 |
0.195 (1.00) |
0.191 (1.00) |
0.199 (1.00) |
0.288 (1.00) |
0.382 (1.00) |
0.577 (1.00) |
0.33 (1.00) |
0.52 (1.00) |
0.46 (1.00) |
1 (1.00) |
0.273 (1.00) |
0.93 (1.00) |
0.0508 (1.00) |
0.937 (1.00) |
| Del Peak 1(1p36 13) | 77 (24%) | 250 |
0.0356 (1.00) |
0.598 (1.00) |
0.0676 (1.00) |
0.447 (1.00) |
0.668 (1.00) |
0.0926 (1.00) |
0.0712 (1.00) |
0.473 (1.00) |
0.0779 (1.00) |
0.586 (1.00) |
0.941 (1.00) |
0.682 (1.00) |
0.426 (1.00) |
0.75 (1.00) |
| Del Peak 2(1p13 1) | 98 (30%) | 229 |
0.67 (1.00) |
0.143 (1.00) |
0.467 (1.00) |
0.746 (1.00) |
0.653 (1.00) |
0.379 (1.00) |
0.542 (1.00) |
0.593 (1.00) |
0.119 (1.00) |
1 (1.00) |
0.412 (1.00) |
0.477 (1.00) |
0.812 (1.00) |
0.581 (1.00) |
| Del Peak 3(2q22 1) | 37 (11%) | 290 |
0.86 (1.00) |
0.591 (1.00) |
1 (1.00) |
0.901 (1.00) |
0.248 (1.00) |
0.181 (1.00) |
0.636 (1.00) |
0.261 (1.00) |
0.137 (1.00) |
1 (1.00) |
0.124 (1.00) |
0.0774 (1.00) |
0.0861 (1.00) |
0.579 (1.00) |
| Del Peak 4(2q37 3) | 54 (17%) | 273 |
0.397 (1.00) |
0.889 (1.00) |
0.0719 (1.00) |
0.561 (1.00) |
0.0994 (1.00) |
0.823 (1.00) |
0.074 (1.00) |
0.253 (1.00) |
0.55 (1.00) |
0.0549 (1.00) |
0.843 (1.00) |
0.846 (1.00) |
0.195 (1.00) |
0.403 (1.00) |
| Del Peak 5(3p26 3) | 152 (46%) | 175 |
0.984 (1.00) |
0.821 (1.00) |
0.221 (1.00) |
0.399 (1.00) |
0.705 (1.00) |
0.00213 (1.00) |
0.177 (1.00) |
0.0812 (1.00) |
0.0395 (1.00) |
0.166 (1.00) |
0.454 (1.00) |
0.0722 (1.00) |
0.0207 (1.00) |
0.00144 (1.00) |
| Del Peak 7(3q11 1) | 97 (30%) | 230 |
0.425 (1.00) |
0.107 (1.00) |
0.395 (1.00) |
0.0824 (1.00) |
0.959 (1.00) |
0.818 (1.00) |
0.868 (1.00) |
0.884 (1.00) |
0.559 (1.00) |
0.802 (1.00) |
0.137 (1.00) |
0.705 (1.00) |
0.871 (1.00) |
0.0159 (1.00) |
| Del Peak 8(3q29) | 95 (29%) | 232 |
0.759 (1.00) |
0.558 (1.00) |
0.808 (1.00) |
0.367 (1.00) |
0.587 (1.00) |
0.47 (1.00) |
0.134 (1.00) |
0.601 (1.00) |
0.121 (1.00) |
0.452 (1.00) |
0.189 (1.00) |
0.696 (1.00) |
0.686 (1.00) |
0.153 (1.00) |
| Del Peak 9(4p15 2) | 77 (24%) | 250 |
0.891 (1.00) |
0.143 (1.00) |
0.513 (1.00) |
0.871 (1.00) |
0.458 (1.00) |
0.66 (1.00) |
0.358 (1.00) |
1 (1.00) |
0.438 (1.00) |
0.274 (1.00) |
0.332 (1.00) |
0.00132 (1.00) |
0.0697 (1.00) |
0.191 (1.00) |
| Del Peak 10(4q22 1) | 100 (31%) | 227 |
0.462 (1.00) |
0.724 (1.00) |
0.718 (1.00) |
0.187 (1.00) |
0.484 (1.00) |
0.583 (1.00) |
0.0342 (1.00) |
0.34 (1.00) |
0.0327 (1.00) |
0.33 (1.00) |
0.902 (1.00) |
0.348 (1.00) |
0.0639 (1.00) |
0.337 (1.00) |
| Del Peak 11(4q35 1) | 120 (37%) | 207 |
0.756 (1.00) |
0.142 (1.00) |
0.206 (1.00) |
0.188 (1.00) |
0.0895 (1.00) |
0.189 (1.00) |
0.287 (1.00) |
0.194 (1.00) |
0.283 (1.00) |
0.234 (1.00) |
0.475 (1.00) |
0.0898 (1.00) |
0.00157 (1.00) |
0.194 (1.00) |
| Del Peak 12(5q11 2) | 116 (35%) | 211 |
0.298 (1.00) |
0.0338 (1.00) |
0.908 (1.00) |
0.47 (1.00) |
0.436 (1.00) |
0.309 (1.00) |
0.0283 (1.00) |
0.482 (1.00) |
0.11 (1.00) |
0.348 (1.00) |
0.123 (1.00) |
0.000494 (0.528) |
0.0889 (1.00) |
0.287 (1.00) |
| Del Peak 14(6q12) | 116 (35%) | 211 |
0.17 (1.00) |
0.776 (1.00) |
0.246 (1.00) |
0.192 (1.00) |
0.35 (1.00) |
0.711 (1.00) |
0.057 (1.00) |
0.443 (1.00) |
0.0498 (1.00) |
0.47 (1.00) |
0.0193 (1.00) |
0.495 (1.00) |
0.0226 (1.00) |
0.0978 (1.00) |
| Del Peak 15(6q22 31) | 168 (51%) | 159 |
0.456 (1.00) |
0.365 (1.00) |
1 (1.00) |
0.189 (1.00) |
0.908 (1.00) |
0.679 (1.00) |
0.725 (1.00) |
0.44 (1.00) |
0.414 (1.00) |
1 (1.00) |
0.19 (1.00) |
0.0869 (1.00) |
0.153 (1.00) |
0.452 (1.00) |
| Del Peak 16(6q26) | 171 (52%) | 156 |
0.524 (1.00) |
0.171 (1.00) |
0.74 (1.00) |
0.271 (1.00) |
0.868 (1.00) |
0.961 (1.00) |
0.465 (1.00) |
0.102 (1.00) |
0.156 (1.00) |
1 (1.00) |
0.726 (1.00) |
0.146 (1.00) |
0.372 (1.00) |
0.303 (1.00) |
| Del Peak 17(8p23 2) | 164 (50%) | 163 |
0.692 (1.00) |
0.293 (1.00) |
0.267 (1.00) |
0.0446 (1.00) |
0.0118 (1.00) |
0.382 (1.00) |
0.818 (1.00) |
0.939 (1.00) |
0.871 (1.00) |
0.49 (1.00) |
0.763 (1.00) |
0.874 (1.00) |
0.0411 (1.00) |
0.235 (1.00) |
| Del Peak 18(8p21 3) | 175 (54%) | 152 |
0.24 (1.00) |
0.978 (1.00) |
0.12 (1.00) |
0.0494 (1.00) |
0.0114 (1.00) |
0.586 (1.00) |
0.451 (1.00) |
0.319 (1.00) |
0.908 (1.00) |
0.646 (1.00) |
0.28 (1.00) |
0.289 (1.00) |
0.132 (1.00) |
0.495 (1.00) |
| Del Peak 19(9p23) | 180 (55%) | 147 |
0.0614 (1.00) |
0.0936 (1.00) |
0.739 (1.00) |
0.614 (1.00) |
0.75 (1.00) |
0.856 (1.00) |
0.0116 (1.00) |
0.714 (1.00) |
0.356 (1.00) |
0.488 (1.00) |
0.848 (1.00) |
0.0356 (1.00) |
0.0715 (1.00) |
0.277 (1.00) |
| Del Peak 20(9p21 3) | 187 (57%) | 140 |
0.374 (1.00) |
0.0327 (1.00) |
0.116 (1.00) |
0.821 (1.00) |
0.831 (1.00) |
0.941 (1.00) |
0.00282 (1.00) |
0.756 (1.00) |
0.0874 (1.00) |
1 (1.00) |
0.46 (1.00) |
0.00427 (1.00) |
0.152 (1.00) |
0.189 (1.00) |
| Del Peak 21(9q21 11) | 160 (49%) | 167 |
0.222 (1.00) |
0.714 (1.00) |
0.657 (1.00) |
0.908 (1.00) |
0.0471 (1.00) |
0.386 (1.00) |
0.385 (1.00) |
0.73 (1.00) |
0.43 (1.00) |
0.106 (1.00) |
0.0656 (1.00) |
0.901 (1.00) |
0.324 (1.00) |
0.769 (1.00) |
| Del Peak 23(10q26 3) | 90 (28%) | 237 |
0.665 (1.00) |
0.897 (1.00) |
0.0345 (1.00) |
0.236 (1.00) |
0.666 (1.00) |
0.0639 (1.00) |
0.455 (1.00) |
0.975 (1.00) |
0.198 (1.00) |
0.0755 (1.00) |
0.0269 (1.00) |
0.84 (1.00) |
0.0257 (1.00) |
0.0668 (1.00) |
| Del Peak 24(11p15 5) | 88 (27%) | 239 |
0.518 (1.00) |
0.0722 (1.00) |
0.318 (1.00) |
0.318 (1.00) |
0.287 (1.00) |
1 (1.00) |
1 (1.00) |
0.0614 (1.00) |
0.326 (1.00) |
1 (1.00) |
0.325 (1.00) |
0.715 (1.00) |
0.0149 (1.00) |
0.131 (1.00) |
| Del Peak 25(11q25) | 73 (22%) | 254 |
0.26 (1.00) |
0.523 (1.00) |
0.505 (1.00) |
0.535 (1.00) |
0.722 (1.00) |
0.742 (1.00) |
0.215 (1.00) |
0.441 (1.00) |
0.733 (1.00) |
0.582 (1.00) |
0.349 (1.00) |
0.901 (1.00) |
0.347 (1.00) |
0.152 (1.00) |
| Del Peak 26(12p13 2) | 91 (28%) | 236 |
0.282 (1.00) |
0.823 (1.00) |
0.00123 (1.00) |
0.788 (1.00) |
0.7 (1.00) |
0.825 (1.00) |
0.906 (1.00) |
0.351 (1.00) |
0.518 (1.00) |
0.8 (1.00) |
0.0141 (1.00) |
0.629 (1.00) |
0.299 (1.00) |
0.0522 (1.00) |
| Del Peak 27(12q12) | 60 (18%) | 267 |
0.23 (1.00) |
0.0859 (1.00) |
0.253 (1.00) |
0.693 (1.00) |
0.257 (1.00) |
0.481 (1.00) |
0.505 (1.00) |
0.137 (1.00) |
0.528 (1.00) |
1 (1.00) |
0.0574 (1.00) |
0.622 (1.00) |
0.954 (1.00) |
0.293 (1.00) |
| Del Peak 28(12q24 33) | 80 (24%) | 247 |
0.488 (1.00) |
0.83 (1.00) |
0.197 (1.00) |
0.392 (1.00) |
0.0851 (1.00) |
0.0665 (1.00) |
0.899 (1.00) |
0.413 (1.00) |
0.692 (1.00) |
0.178 (1.00) |
0.19 (1.00) |
0.861 (1.00) |
0.0154 (1.00) |
0.376 (1.00) |
| Del Peak 29(13q12 11) | 180 (55%) | 147 |
0.606 (1.00) |
0.131 (1.00) |
0.0105 (1.00) |
0.0252 (1.00) |
0.0261 (1.00) |
0.562 (1.00) |
0.987 (1.00) |
0.343 (1.00) |
0.839 (1.00) |
0.364 (1.00) |
0.0318 (1.00) |
0.206 (1.00) |
0.0135 (1.00) |
0.18 (1.00) |
| Del Peak 30(13q12 13) | 181 (55%) | 146 |
0.722 (1.00) |
0.31 (1.00) |
0.045 (1.00) |
0.0399 (1.00) |
0.0108 (1.00) |
0.724 (1.00) |
0.885 (1.00) |
0.343 (1.00) |
0.858 (1.00) |
0.17 (1.00) |
0.127 (1.00) |
0.658 (1.00) |
0.0552 (1.00) |
0.176 (1.00) |
| Del Peak 31(13q34) | 147 (45%) | 180 |
0.771 (1.00) |
0.103 (1.00) |
0.823 (1.00) |
0.669 (1.00) |
0.299 (1.00) |
0.636 (1.00) |
0.987 (1.00) |
0.119 (1.00) |
0.306 (1.00) |
1 (1.00) |
0.497 (1.00) |
0.275 (1.00) |
0.0822 (1.00) |
0.121 (1.00) |
| Del Peak 32(14q32 33) | 99 (30%) | 228 |
0.411 (1.00) |
0.958 (1.00) |
1 (1.00) |
0.786 (1.00) |
0.351 (1.00) |
0.402 (1.00) |
0.27 (1.00) |
0.524 (1.00) |
0.544 (1.00) |
0.622 (1.00) |
0.148 (1.00) |
0.905 (1.00) |
0.249 (1.00) |
0.0499 (1.00) |
| Del Peak 33(15q11 2) | 171 (52%) | 156 |
0.324 (1.00) |
0.0898 (1.00) |
0.0452 (1.00) |
0.241 (1.00) |
0.116 (1.00) |
0.246 (1.00) |
0.961 (1.00) |
0.979 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.373 (1.00) |
0.207 (1.00) |
0.254 (1.00) |
0.188 (1.00) |
| Del Peak 34(15q15 3) | 177 (54%) | 150 |
0.434 (1.00) |
0.129 (1.00) |
0.12 (1.00) |
0.241 (1.00) |
0.0183 (1.00) |
0.397 (1.00) |
0.987 (1.00) |
0.959 (1.00) |
0.898 (1.00) |
0.649 (1.00) |
0.801 (1.00) |
0.167 (1.00) |
0.114 (1.00) |
0.247 (1.00) |
| Del Peak 35(16q23 3) | 118 (36%) | 209 |
0.954 (1.00) |
0.769 (1.00) |
0.73 (1.00) |
0.622 (1.00) |
0.404 (1.00) |
0.503 (1.00) |
0.208 (1.00) |
0.709 (1.00) |
0.506 (1.00) |
1 (1.00) |
0.205 (1.00) |
0.318 (1.00) |
0.134 (1.00) |
0.87 (1.00) |
| Del Peak 36(17p13 3) | 188 (57%) | 139 |
0.642 (1.00) |
0.16 (1.00) |
0.179 (1.00) |
0.778 (1.00) |
0.0493 (1.00) |
0.237 (1.00) |
0.908 (1.00) |
0.706 (1.00) |
0.826 (1.00) |
0.253 (1.00) |
0.418 (1.00) |
0.482 (1.00) |
0.121 (1.00) |
0.00869 (1.00) |
| Del Peak 37(18q21 32) | 170 (52%) | 157 |
0.244 (1.00) |
0.34 (1.00) |
0.0952 (1.00) |
0.301 (1.00) |
0.703 (1.00) |
0.266 (1.00) |
0.169 (1.00) |
0.0699 (1.00) |
0.0458 (1.00) |
1 (1.00) |
0.494 (1.00) |
0.855 (1.00) |
0.25 (1.00) |
0.152 (1.00) |
| Del Peak 38(18q23) | 164 (50%) | 163 |
0.329 (1.00) |
0.12 (1.00) |
0.0758 (1.00) |
0.318 (1.00) |
0.41 (1.00) |
0.0738 (1.00) |
0.0645 (1.00) |
0.305 (1.00) |
0.00276 (1.00) |
1 (1.00) |
0.356 (1.00) |
0.419 (1.00) |
0.293 (1.00) |
0.0407 (1.00) |
| Del Peak 39(19p13 3) | 184 (56%) | 143 |
0.0489 (1.00) |
0.283 (1.00) |
0.00249 (1.00) |
0.802 (1.00) |
0.469 (1.00) |
0.241 (1.00) |
0.157 (1.00) |
0.463 (1.00) |
0.0174 (1.00) |
0.819 (1.00) |
0.501 (1.00) |
0.584 (1.00) |
0.152 (1.00) |
0.245 (1.00) |
| Del Peak 40(19p13 2) | 177 (54%) | 150 |
0.361 (1.00) |
0.0411 (1.00) |
0.00119 (1.00) |
0.923 (1.00) |
0.595 (1.00) |
0.264 (1.00) |
0.093 (1.00) |
0.139 (1.00) |
0.0306 (1.00) |
0.818 (1.00) |
0.459 (1.00) |
0.47 (1.00) |
0.0372 (1.00) |
0.228 (1.00) |
| Del Peak 41(19q11) | 95 (29%) | 232 |
0.00622 (1.00) |
0.0112 (1.00) |
1 (1.00) |
0.54 (1.00) |
0.849 (1.00) |
0.394 (1.00) |
0.086 (1.00) |
0.275 (1.00) |
0.00384 (1.00) |
0.803 (1.00) |
0.0588 (1.00) |
0.314 (1.00) |
0.00689 (1.00) |
0.0651 (1.00) |
| Del Peak 42(19q13 33) | 123 (38%) | 204 |
0.0384 (1.00) |
0.193 (1.00) |
0.359 (1.00) |
0.465 (1.00) |
0.187 (1.00) |
0.557 (1.00) |
0.591 (1.00) |
0.167 (1.00) |
0.146 (1.00) |
0.816 (1.00) |
0.45 (1.00) |
0.902 (1.00) |
0.258 (1.00) |
0.513 (1.00) |
| Del Peak 43(21q11 2) | 116 (35%) | 211 |
0.619 (1.00) |
0.0607 (1.00) |
0.908 (1.00) |
0.751 (1.00) |
0.391 (1.00) |
0.705 (1.00) |
0.916 (1.00) |
0.913 (1.00) |
0.78 (1.00) |
0.47 (1.00) |
0.133 (1.00) |
0.0502 (1.00) |
0.0158 (1.00) |
0.0131 (1.00) |
| Del Peak 44(22q13 32) | 160 (49%) | 167 |
0.475 (1.00) |
0.02 (1.00) |
0.223 (1.00) |
0.537 (1.00) |
0.362 (1.00) |
0.762 (1.00) |
0.677 (1.00) |
0.714 (1.00) |
0.721 (1.00) |
0.819 (1.00) |
0.502 (1.00) |
0.112 (1.00) |
0.00109 (1.00) |
0.00591 (1.00) |
| Del Peak 45(Xp22 2) | 96 (29%) | 231 |
0.56 (1.00) |
0.666 (1.00) |
0.039 (1.00) |
0.931 (1.00) |
0.653 (1.00) |
0.913 (1.00) |
0.428 (1.00) |
0.795 (1.00) |
0.894 (1.00) |
0.803 (1.00) |
0.64 (1.00) |
0.651 (1.00) |
0.624 (1.00) |
0.17 (1.00) |
P value = 0.000193 (t-test), Q value = 0.21
Table S1. Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #12: 'STOPPEDSMOKINGYEAR'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 164 | 1993.9 (13.8) |
| AMP PEAK 17(10P15.1) MUTATED | 47 | 1999.4 (10.4) |
| AMP PEAK 17(10P15.1) WILD-TYPE | 117 | 1991.6 (14.3) |
Figure S1. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #12: 'STOPPEDSMOKINGYEAR'
P value = 3.65e-06 (Fisher's exact test), Q value = 0.0039
Table S2. Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
| nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
|---|---|---|---|---|
| ALL | 110 | 86 | 72 | 46 |
| AMP PEAK 17(10P15.1) MUTATED | 42 | 16 | 26 | 2 |
| AMP PEAK 17(10P15.1) WILD-TYPE | 68 | 70 | 46 | 44 |
Figure S2. Get High-res Image Gene #17: 'Amp Peak 17(10p15.1) mutation analysis' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
P value = 2.74e-05 (t-test), Q value = 0.029
Table S3. Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 296 | 65.3 (9.8) |
| AMP PEAK 18(11Q13.3) MUTATED | 105 | 62.0 (9.7) |
| AMP PEAK 18(11Q13.3) WILD-TYPE | 191 | 67.0 (9.5) |
Figure S3. Get High-res Image Gene #18: 'Amp Peak 18(11q13.3) mutation analysis' versus Clinical Feature #2: 'AGE'
P value = 5.07e-05 (t-test), Q value = 0.054
Table S4. Gene #38: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #14: 'YEAROFTOBACCOSMOKINGONSET'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 163 | 1964.8 (13.0) |
| DEL PEAK 6(3P21.31) MUTATED | 81 | 1968.9 (13.1) |
| DEL PEAK 6(3P21.31) WILD-TYPE | 82 | 1960.8 (11.6) |
Figure S4. Get High-res Image Gene #38: 'Del Peak 6(3p21.31) mutation analysis' versus Clinical Feature #14: 'YEAROFTOBACCOSMOKINGONSET'
P value = 6.1e-05 (t-test), Q value = 0.065
Table S5. Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #12: 'STOPPEDSMOKINGYEAR'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 164 | 1993.9 (13.8) |
| DEL PEAK 13(5Q34) MUTATED | 49 | 1999.6 (10.1) |
| DEL PEAK 13(5Q34) WILD-TYPE | 115 | 1991.4 (14.4) |
Figure S5. Get High-res Image Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #12: 'STOPPEDSMOKINGYEAR'
P value = 5.82e-07 (Fisher's exact test), Q value = 0.00063
Table S6. Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
| nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
|---|---|---|---|---|
| ALL | 110 | 86 | 72 | 46 |
| DEL PEAK 13(5Q34) MUTATED | 44 | 16 | 41 | 9 |
| DEL PEAK 13(5Q34) WILD-TYPE | 66 | 70 | 31 | 37 |
Figure S6. Get High-res Image Gene #45: 'Del Peak 13(5q34) mutation analysis' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'
P value = 5.81e-05 (Fisher's exact test), Q value = 0.062
Table S7. Gene #54: 'Del Peak 22(10p15.3) mutation analysis' versus Clinical Feature #3: 'GENDER'
| nPatients | FEMALE | MALE |
|---|---|---|
| ALL | 148 | 179 |
| DEL PEAK 22(10P15.3) MUTATED | 21 | 60 |
| DEL PEAK 22(10P15.3) WILD-TYPE | 127 | 119 |
Figure S7. Get High-res Image Gene #54: 'Del Peak 22(10p15.3) mutation analysis' versus Clinical Feature #3: 'GENDER'
-
Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
-
Clinical data file = LUAD-TP.clin.merged.picked.txt
-
Number of patients = 327
-
Number of copy number variation regions = 77
-
Number of selected clinical features = 14
-
Exclude regions that fewer than K tumors have alterations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs 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 cnvs 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.