Lung Adenocarcinoma: Correlation between copy number variations of arm-level result and selected clinical features
Maintained by TCGA GDAC Team
(Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction
This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Summary
Testing the association between copy number variation 79 arm-level results and 11 clinical features across 288 patients, 4 significant findings detected with Q value < 0.25.
-
4q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
-
8q gain cnv correlated to 'AGE'.
-
1q loss cnv correlated to 'Time to Death'.
-
8q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 4 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 |
NEOADJUVANT THERAPY |
||
| 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 | Fisher's exact test | |
| 4q gain | 8 (3%) | 280 |
0.621 (1.00) |
0.561 (1.00) |
0.148 (1.00) |
6.39e-05 (0.0527) |
0.0825 (1.00) |
0.364 (1.00) |
0.505 (1.00) |
0.644 (1.00) |
0.425 (1.00) |
1 (1.00) |
|
| 8q gain | 91 (32%) | 197 |
0.92 (1.00) |
0.000275 (0.227) |
0.446 (1.00) |
0.352 (1.00) |
0.635 (1.00) |
0.869 (1.00) |
0.478 (1.00) |
0.368 (1.00) |
0.535 (1.00) |
0.799 (1.00) |
0.598 (1.00) |
| 1q loss | 9 (3%) | 279 |
6.52e-05 (0.0537) |
0.667 (1.00) |
0.737 (1.00) |
0.621 (1.00) |
0.792 (1.00) |
0.0653 (1.00) |
1 (1.00) |
0.165 (1.00) |
0.113 (1.00) |
1 (1.00) |
|
| 8q loss | 10 (3%) | 278 |
0.18 (1.00) |
0.59 (1.00) |
1 (1.00) |
5.31e-05 (0.0439) |
0.677 (1.00) |
0.813 (1.00) |
0.123 (1.00) |
1 (1.00) |
1 (1.00) |
0.653 (1.00) |
|
| 1p gain | 38 (13%) | 250 |
0.931 (1.00) |
0.00292 (1.00) |
0.863 (1.00) |
0.53 (1.00) |
0.979 (1.00) |
0.694 (1.00) |
0.003 (1.00) |
0.739 (1.00) |
0.0025 (1.00) |
0.485 (1.00) |
0.813 (1.00) |
| 1q gain | 112 (39%) | 176 |
0.764 (1.00) |
0.49 (1.00) |
0.546 (1.00) |
0.604 (1.00) |
0.608 (1.00) |
0.634 (1.00) |
0.0358 (1.00) |
0.338 (1.00) |
0.0364 (1.00) |
0.629 (1.00) |
0.239 (1.00) |
| 2p gain | 36 (12%) | 252 |
0.134 (1.00) |
0.0658 (1.00) |
0.0308 (1.00) |
0.74 (1.00) |
0.782 (1.00) |
0.0694 (1.00) |
0.674 (1.00) |
0.0815 (1.00) |
0.117 (1.00) |
1 (1.00) |
0.805 (1.00) |
| 2q gain | 30 (10%) | 258 |
0.2 (1.00) |
0.235 (1.00) |
0.247 (1.00) |
0.224 (1.00) |
0.27 (1.00) |
0.962 (1.00) |
0.0969 (1.00) |
0.228 (1.00) |
0.704 (1.00) |
1 (1.00) |
|
| 3p gain | 9 (3%) | 279 |
0.122 (1.00) |
0.658 (1.00) |
0.737 (1.00) |
0.905 (1.00) |
0.0854 (1.00) |
0.623 (1.00) |
0.545 (1.00) |
0.426 (1.00) |
0.464 (1.00) |
0.631 (1.00) |
|
| 3q gain | 18 (6%) | 270 |
0.105 (1.00) |
0.677 (1.00) |
0.809 (1.00) |
0.98 (1.00) |
0.866 (1.00) |
0.292 (1.00) |
0.91 (1.00) |
0.549 (1.00) |
0.336 (1.00) |
0.494 (1.00) |
|
| 4p gain | 21 (7%) | 267 |
0.641 (1.00) |
0.0141 (1.00) |
0.364 (1.00) |
0.0606 (1.00) |
0.221 (1.00) |
0.896 (1.00) |
0.0902 (1.00) |
0.271 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 5p gain | 113 (39%) | 175 |
0.55 (1.00) |
0.154 (1.00) |
1 (1.00) |
0.691 (1.00) |
0.296 (1.00) |
0.495 (1.00) |
0.818 (1.00) |
0.628 (1.00) |
0.985 (1.00) |
0.0939 (1.00) |
0.616 (1.00) |
| 5q gain | 37 (13%) | 251 |
0.67 (1.00) |
0.754 (1.00) |
0.377 (1.00) |
0.82 (1.00) |
0.68 (1.00) |
0.604 (1.00) |
0.522 (1.00) |
0.78 (1.00) |
0.0798 (1.00) |
0.138 (1.00) |
|
| 6p gain | 39 (14%) | 249 |
0.903 (1.00) |
0.9 (1.00) |
0.605 (1.00) |
0.94 (1.00) |
0.695 (1.00) |
0.63 (1.00) |
0.248 (1.00) |
0.788 (1.00) |
0.814 (1.00) |
1 (1.00) |
0.633 (1.00) |
| 6q gain | 9 (3%) | 279 |
0.368 (1.00) |
0.315 (1.00) |
0.0419 (1.00) |
0.998 (1.00) |
1 (1.00) |
0.709 (1.00) |
0.545 (1.00) |
0.528 (1.00) |
1 (1.00) |
0.631 (1.00) |
|
| 7p gain | 99 (34%) | 189 |
0.239 (1.00) |
0.0556 (1.00) |
0.901 (1.00) |
0.225 (1.00) |
0.45 (1.00) |
0.162 (1.00) |
0.0165 (1.00) |
0.088 (1.00) |
0.0479 (1.00) |
0.618 (1.00) |
0.605 (1.00) |
| 7q gain | 70 (24%) | 218 |
0.907 (1.00) |
0.00547 (1.00) |
0.335 (1.00) |
0.92 (1.00) |
0.657 (1.00) |
0.366 (1.00) |
0.208 (1.00) |
0.055 (1.00) |
0.0384 (1.00) |
0.418 (1.00) |
0.445 (1.00) |
| 8p gain | 33 (11%) | 255 |
0.333 (1.00) |
0.000629 (0.517) |
0.194 (1.00) |
0.897 (1.00) |
0.681 (1.00) |
1 (1.00) |
0.255 (1.00) |
0.961 (1.00) |
0.466 (1.00) |
0.13 (1.00) |
|
| 9p gain | 5 (2%) | 283 |
0.212 (1.00) |
0.625 (1.00) |
0.183 (1.00) |
0.999 (1.00) |
0.441 (1.00) |
0.825 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 9q gain | 3 (1%) | 285 |
0.0592 (1.00) |
0.227 (1.00) |
1 (1.00) |
1 (1.00) |
0.709 (1.00) |
1 (1.00) |
0.63 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 10p gain | 31 (11%) | 257 |
0.951 (1.00) |
0.18 (1.00) |
0.182 (1.00) |
0.921 (1.00) |
0.277 (1.00) |
0.634 (1.00) |
0.173 (1.00) |
0.891 (1.00) |
0.522 (1.00) |
0.705 (1.00) |
1 (1.00) |
| 10q gain | 18 (6%) | 270 |
0.835 (1.00) |
0.623 (1.00) |
0.224 (1.00) |
0.131 (1.00) |
0.398 (1.00) |
0.227 (1.00) |
0.551 (1.00) |
0.32 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 11p gain | 23 (8%) | 265 |
0.739 (1.00) |
0.108 (1.00) |
0.383 (1.00) |
0.685 (1.00) |
0.712 (1.00) |
0.492 (1.00) |
1 (1.00) |
0.441 (1.00) |
1 (1.00) |
0.763 (1.00) |
|
| 11q gain | 33 (11%) | 255 |
0.379 (1.00) |
0.000795 (0.653) |
0.0939 (1.00) |
0.745 (1.00) |
0.791 (1.00) |
0.618 (1.00) |
0.579 (1.00) |
0.519 (1.00) |
0.155 (1.00) |
0.466 (1.00) |
0.798 (1.00) |
| 12p gain | 38 (13%) | 250 |
0.804 (1.00) |
0.00189 (1.00) |
0.727 (1.00) |
0.705 (1.00) |
0.147 (1.00) |
0.065 (1.00) |
1 (1.00) |
0.0281 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 12q gain | 31 (11%) | 257 |
0.756 (1.00) |
0.00105 (0.861) |
0.449 (1.00) |
0.765 (1.00) |
0.137 (1.00) |
0.123 (1.00) |
0.734 (1.00) |
0.0687 (1.00) |
0.705 (1.00) |
0.596 (1.00) |
|
| 13q gain | 15 (5%) | 273 |
0.575 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.981 (1.00) |
0.109 (1.00) |
0.453 (1.00) |
0.136 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.259 (1.00) |
|
| 14q gain | 32 (11%) | 256 |
0.297 (1.00) |
0.167 (1.00) |
0.191 (1.00) |
0.82 (1.00) |
0.049 (1.00) |
0.517 (1.00) |
0.338 (1.00) |
0.618 (1.00) |
0.723 (1.00) |
0.145 (1.00) |
0.798 (1.00) |
| 15q gain | 10 (3%) | 278 |
0.278 (1.00) |
0.38 (1.00) |
0.758 (1.00) |
0.0897 (1.00) |
0.678 (1.00) |
0.351 (1.00) |
0.442 (1.00) |
0.209 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 16p gain | 38 (13%) | 250 |
0.492 (1.00) |
0.23 (1.00) |
0.863 (1.00) |
0.332 (1.00) |
0.661 (1.00) |
0.435 (1.00) |
0.409 (1.00) |
0.522 (1.00) |
0.447 (1.00) |
0.725 (1.00) |
0.331 (1.00) |
| 16q gain | 26 (9%) | 262 |
0.662 (1.00) |
0.271 (1.00) |
0.416 (1.00) |
0.299 (1.00) |
0.473 (1.00) |
0.344 (1.00) |
0.517 (1.00) |
0.418 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.568 (1.00) |
| 17p gain | 17 (6%) | 271 |
0.503 (1.00) |
0.64 (1.00) |
0.32 (1.00) |
0.226 (1.00) |
0.08 (1.00) |
0.883 (1.00) |
0.599 (1.00) |
0.427 (1.00) |
0.459 (1.00) |
0.0187 (1.00) |
0.306 (1.00) |
| 17q gain | 48 (17%) | 240 |
0.205 (1.00) |
0.357 (1.00) |
1 (1.00) |
0.41 (1.00) |
0.242 (1.00) |
0.0299 (1.00) |
0.517 (1.00) |
0.0232 (1.00) |
0.027 (1.00) |
0.103 (1.00) |
0.271 (1.00) |
| 18p gain | 20 (7%) | 268 |
0.446 (1.00) |
0.202 (1.00) |
0.817 (1.00) |
0.338 (1.00) |
1 (1.00) |
1 (1.00) |
0.916 (1.00) |
0.927 (1.00) |
1 (1.00) |
0.522 (1.00) |
|
| 18q gain | 15 (5%) | 273 |
0.468 (1.00) |
0.235 (1.00) |
0.602 (1.00) |
0.108 (1.00) |
1 (1.00) |
0.867 (1.00) |
0.419 (1.00) |
0.715 (1.00) |
1 (1.00) |
0.259 (1.00) |
|
| 19p gain | 4 (1%) | 284 |
0.33 (1.00) |
0.135 (1.00) |
1 (1.00) |
0.993 (1.00) |
0.335 (1.00) |
0.336 (1.00) |
0.244 (1.00) |
0.163 (1.00) |
1 (1.00) |
0.112 (1.00) |
|
| 19q gain | 11 (4%) | 277 |
0.762 (1.00) |
0.925 (1.00) |
1 (1.00) |
0.993 (1.00) |
0.374 (1.00) |
0.832 (1.00) |
0.287 (1.00) |
0.703 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 20p gain | 40 (14%) | 248 |
0.7 (1.00) |
0.286 (1.00) |
0.865 (1.00) |
0.591 (1.00) |
0.749 (1.00) |
0.405 (1.00) |
0.455 (1.00) |
0.859 (1.00) |
0.193 (1.00) |
0.735 (1.00) |
0.0155 (1.00) |
| 20q gain | 47 (16%) | 241 |
0.583 (1.00) |
0.147 (1.00) |
0.337 (1.00) |
0.148 (1.00) |
0.735 (1.00) |
0.139 (1.00) |
0.922 (1.00) |
0.595 (1.00) |
0.81 (1.00) |
0.33 (1.00) |
0.0245 (1.00) |
| 21q gain | 26 (9%) | 262 |
0.492 (1.00) |
0.568 (1.00) |
0.148 (1.00) |
0.64 (1.00) |
0.626 (1.00) |
0.557 (1.00) |
0.418 (1.00) |
0.934 (1.00) |
1 (1.00) |
0.254 (1.00) |
|
| 22q gain | 14 (5%) | 274 |
0.23 (1.00) |
0.203 (1.00) |
1 (1.00) |
0.446 (1.00) |
0.0733 (1.00) |
0.0605 (1.00) |
0.611 (1.00) |
0.321 (1.00) |
1 (1.00) |
0.0457 (1.00) |
|
| Xq gain | 11 (4%) | 277 |
0.183 (1.00) |
0.264 (1.00) |
0.759 (1.00) |
0.465 (1.00) |
0.608 (1.00) |
0.832 (1.00) |
0.59 (1.00) |
0.606 (1.00) |
0.534 (1.00) |
0.383 (1.00) |
|
| 1p loss | 21 (7%) | 267 |
0.412 (1.00) |
0.993 (1.00) |
0.172 (1.00) |
0.924 (1.00) |
0.907 (1.00) |
0.692 (1.00) |
0.387 (1.00) |
0.0861 (1.00) |
0.151 (1.00) |
1 (1.00) |
|
| 2p loss | 3 (1%) | 285 |
1 (1.00) |
0.998 (1.00) |
1 (1.00) |
1 (1.00) |
0.63 (1.00) |
1 (1.00) |
1 (1.00) |
0.393 (1.00) |
|||
| 3p loss | 56 (19%) | 232 |
0.903 (1.00) |
0.64 (1.00) |
0.765 (1.00) |
0.0268 (1.00) |
0.891 (1.00) |
0.197 (1.00) |
0.379 (1.00) |
0.177 (1.00) |
0.00331 (1.00) |
0.771 (1.00) |
0.306 (1.00) |
| 3q loss | 30 (10%) | 258 |
0.831 (1.00) |
0.655 (1.00) |
0.441 (1.00) |
0.0583 (1.00) |
0.993 (1.00) |
0.331 (1.00) |
0.338 (1.00) |
0.683 (1.00) |
0.106 (1.00) |
1 (1.00) |
0.427 (1.00) |
| 4p loss | 26 (9%) | 262 |
0.471 (1.00) |
0.027 (1.00) |
0.102 (1.00) |
0.694 (1.00) |
0.661 (1.00) |
0.32 (1.00) |
0.265 (1.00) |
0.65 (1.00) |
0.479 (1.00) |
0.395 (1.00) |
0.568 (1.00) |
| 4q loss | 31 (11%) | 257 |
0.527 (1.00) |
0.0484 (1.00) |
0.0125 (1.00) |
0.946 (1.00) |
0.969 (1.00) |
0.155 (1.00) |
0.00814 (1.00) |
0.514 (1.00) |
0.0645 (1.00) |
0.134 (1.00) |
0.797 (1.00) |
| 5p loss | 8 (3%) | 280 |
0.938 (1.00) |
0.242 (1.00) |
0.148 (1.00) |
0.224 (1.00) |
0.751 (1.00) |
0.589 (1.00) |
0.505 (1.00) |
0.761 (1.00) |
1 (1.00) |
0.107 (1.00) |
|
| 5q loss | 39 (14%) | 249 |
0.552 (1.00) |
0.0683 (1.00) |
0.00181 (1.00) |
0.738 (1.00) |
0.0699 (1.00) |
0.876 (1.00) |
0.0709 (1.00) |
0.474 (1.00) |
0.377 (1.00) |
0.487 (1.00) |
0.154 (1.00) |
| 6p loss | 23 (8%) | 265 |
0.805 (1.00) |
0.169 (1.00) |
0.0791 (1.00) |
0.468 (1.00) |
0.664 (1.00) |
0.614 (1.00) |
0.173 (1.00) |
0.632 (1.00) |
0.655 (1.00) |
1 (1.00) |
|
| 6q loss | 63 (22%) | 225 |
0.776 (1.00) |
0.523 (1.00) |
0.393 (1.00) |
0.018 (1.00) |
0.503 (1.00) |
0.259 (1.00) |
0.346 (1.00) |
0.432 (1.00) |
0.429 (1.00) |
0.576 (1.00) |
1 (1.00) |
| 7p loss | 10 (3%) | 278 |
0.821 (1.00) |
0.232 (1.00) |
1 (1.00) |
0.435 (1.00) |
1 (1.00) |
0.282 (1.00) |
0.442 (1.00) |
0.254 (1.00) |
0.5 (1.00) |
1 (1.00) |
|
| 7q loss | 11 (4%) | 277 |
0.713 (1.00) |
0.19 (1.00) |
0.557 (1.00) |
0.0193 (1.00) |
0.894 (1.00) |
0.691 (1.00) |
1 (1.00) |
0.677 (1.00) |
0.534 (1.00) |
0.678 (1.00) |
|
| 8p loss | 75 (26%) | 213 |
0.616 (1.00) |
0.673 (1.00) |
0.893 (1.00) |
0.141 (1.00) |
0.0449 (1.00) |
0.0931 (1.00) |
0.91 (1.00) |
0.697 (1.00) |
0.898 (1.00) |
0.789 (1.00) |
1 (1.00) |
| 9p loss | 90 (31%) | 198 |
0.00693 (1.00) |
0.0587 (1.00) |
0.161 (1.00) |
0.897 (1.00) |
0.575 (1.00) |
0.181 (1.00) |
0.0267 (1.00) |
0.947 (1.00) |
0.0575 (1.00) |
1 (1.00) |
0.48 (1.00) |
| 9q loss | 75 (26%) | 213 |
0.313 (1.00) |
0.358 (1.00) |
0.893 (1.00) |
0.947 (1.00) |
0.288 (1.00) |
0.262 (1.00) |
0.19 (1.00) |
0.669 (1.00) |
0.369 (1.00) |
0.419 (1.00) |
0.853 (1.00) |
| 10p loss | 23 (8%) | 265 |
0.303 (1.00) |
0.626 (1.00) |
0.133 (1.00) |
0.327 (1.00) |
0.898 (1.00) |
0.483 (1.00) |
0.424 (1.00) |
0.892 (1.00) |
0.38 (1.00) |
1 (1.00) |
|
| 10q loss | 25 (9%) | 263 |
0.332 (1.00) |
0.175 (1.00) |
1 (1.00) |
0.00115 (0.942) |
0.321 (1.00) |
0.107 (1.00) |
1 (1.00) |
0.161 (1.00) |
0.389 (1.00) |
1 (1.00) |
|
| 11p loss | 22 (8%) | 266 |
0.193 (1.00) |
0.00271 (1.00) |
0.505 (1.00) |
0.401 (1.00) |
0.932 (1.00) |
0.0624 (1.00) |
0.0466 (1.00) |
0.0346 (1.00) |
1 (1.00) |
0.757 (1.00) |
|
| 11q loss | 16 (6%) | 272 |
0.12 (1.00) |
0.827 (1.00) |
1 (1.00) |
0.738 (1.00) |
0.471 (1.00) |
0.872 (1.00) |
0.876 (1.00) |
0.0514 (1.00) |
0.975 (1.00) |
0.285 (1.00) |
0.0784 (1.00) |
| 12p loss | 25 (9%) | 263 |
0.35 (1.00) |
0.774 (1.00) |
0.837 (1.00) |
0.561 (1.00) |
0.107 (1.00) |
0.612 (1.00) |
1 (1.00) |
0.307 (1.00) |
0.544 (1.00) |
0.674 (1.00) |
0.392 (1.00) |
| 12q loss | 18 (6%) | 270 |
0.0698 (1.00) |
0.871 (1.00) |
0.467 (1.00) |
0.0783 (1.00) |
0.481 (1.00) |
0.375 (1.00) |
0.365 (1.00) |
0.293 (1.00) |
0.618 (1.00) |
1 (1.00) |
|
| 13q loss | 66 (23%) | 222 |
0.142 (1.00) |
0.232 (1.00) |
0.326 (1.00) |
0.652 (1.00) |
0.384 (1.00) |
0.907 (1.00) |
0.138 (1.00) |
0.404 (1.00) |
0.391 (1.00) |
0.778 (1.00) |
0.442 (1.00) |
| 14q loss | 29 (10%) | 259 |
0.551 (1.00) |
0.869 (1.00) |
0.558 (1.00) |
0.654 (1.00) |
0.206 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.263 (1.00) |
0.878 (1.00) |
0.421 (1.00) |
0.174 (1.00) |
| 15q loss | 64 (22%) | 224 |
0.75 (1.00) |
0.0473 (1.00) |
0.394 (1.00) |
0.919 (1.00) |
0.0809 (1.00) |
0.775 (1.00) |
0.979 (1.00) |
0.934 (1.00) |
0.891 (1.00) |
0.775 (1.00) |
0.431 (1.00) |
| 16p loss | 24 (8%) | 264 |
0.701 (1.00) |
0.144 (1.00) |
0.402 (1.00) |
0.463 (1.00) |
0.939 (1.00) |
0.953 (1.00) |
0.00845 (1.00) |
0.0615 (1.00) |
0.203 (1.00) |
0.386 (1.00) |
|
| 16q loss | 42 (15%) | 246 |
0.167 (1.00) |
0.14 (1.00) |
0.617 (1.00) |
0.796 (1.00) |
0.152 (1.00) |
0.163 (1.00) |
0.435 (1.00) |
0.156 (1.00) |
0.146 (1.00) |
0.746 (1.00) |
1 (1.00) |
| 17p loss | 73 (25%) | 215 |
0.819 (1.00) |
0.651 (1.00) |
0.5 (1.00) |
0.137 (1.00) |
0.735 (1.00) |
0.572 (1.00) |
0.456 (1.00) |
0.913 (1.00) |
0.302 (1.00) |
0.173 (1.00) |
1 (1.00) |
| 17q loss | 11 (4%) | 277 |
0.223 (1.00) |
0.896 (1.00) |
1 (1.00) |
0.484 (1.00) |
0.543 (1.00) |
0.832 (1.00) |
0.36 (1.00) |
0.703 (1.00) |
1 (1.00) |
0.383 (1.00) |
|
| 18p loss | 46 (16%) | 242 |
0.496 (1.00) |
0.0428 (1.00) |
0.75 (1.00) |
0.0103 (1.00) |
0.299 (1.00) |
0.162 (1.00) |
0.39 (1.00) |
0.0386 (1.00) |
0.00453 (1.00) |
0.328 (1.00) |
0.657 (1.00) |
| 18q loss | 74 (26%) | 214 |
0.0211 (1.00) |
0.249 (1.00) |
1 (1.00) |
0.57 (1.00) |
0.477 (1.00) |
0.167 (1.00) |
0.34 (1.00) |
0.218 (1.00) |
0.0047 (1.00) |
0.173 (1.00) |
0.575 (1.00) |
| 19p loss | 79 (27%) | 209 |
0.0279 (1.00) |
0.367 (1.00) |
0.0117 (1.00) |
0.8 (1.00) |
0.531 (1.00) |
0.236 (1.00) |
0.0176 (1.00) |
0.0985 (1.00) |
0.162 (1.00) |
1 (1.00) |
0.358 (1.00) |
| 19q loss | 44 (15%) | 244 |
0.0904 (1.00) |
0.405 (1.00) |
0.412 (1.00) |
0.131 (1.00) |
0.27 (1.00) |
0.369 (1.00) |
0.0452 (1.00) |
0.307 (1.00) |
0.506 (1.00) |
1 (1.00) |
|
| 20p loss | 43 (15%) | 245 |
0.152 (1.00) |
0.401 (1.00) |
1 (1.00) |
0.304 (1.00) |
0.201 (1.00) |
0.042 (1.00) |
0.205 (1.00) |
0.0574 (1.00) |
1 (1.00) |
0.495 (1.00) |
|
| 20q loss | 15 (5%) | 273 |
0.379 (1.00) |
0.324 (1.00) |
1 (1.00) |
0.365 (1.00) |
0.864 (1.00) |
0.649 (1.00) |
0.326 (1.00) |
0.497 (1.00) |
1 (1.00) |
1 (1.00) |
|
| 21q loss | 42 (15%) | 246 |
0.841 (1.00) |
0.72 (1.00) |
0.0292 (1.00) |
0.0991 (1.00) |
0.571 (1.00) |
0.877 (1.00) |
0.728 (1.00) |
0.831 (1.00) |
0.768 (1.00) |
0.496 (1.00) |
1 (1.00) |
| 22q loss | 65 (23%) | 223 |
0.799 (1.00) |
0.224 (1.00) |
0.0902 (1.00) |
0.475 (1.00) |
0.801 (1.00) |
0.813 (1.00) |
0.92 (1.00) |
0.185 (1.00) |
0.991 (1.00) |
0.153 (1.00) |
1 (1.00) |
| Xq loss | 6 (2%) | 282 |
0.277 (1.00) |
0.326 (1.00) |
0.418 (1.00) |
0.00921 (1.00) |
0.349 (1.00) |
1 (1.00) |
1 (1.00) |
0.537 (1.00) |
0.0528 (1.00) |
1 (1.00) |
'4q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'
P value = 6.39e-05 (Chi-square test), Q value = 0.053
Table S1. Gene #8: '4q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
| nPatients | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | MUCINOUS (COLLOID) ADENOCARCINOMA |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 6 | 65 | 182 | 3 | 10 | 2 | 3 | 2 | 10 | 1 | 4 |
| 4Q GAIN MUTATED | 0 | 1 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| 4Q GAIN WILD-TYPE | 6 | 64 | 176 | 3 | 10 | 2 | 3 | 2 | 10 | 0 | 4 |
Figure S1. Get High-res Image Gene #8: '4q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
'8q gain mutation analysis' versus 'AGE'
P value = 0.000275 (t-test), Q value = 0.23
Table S2. Gene #16: '8q gain mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 257 | 65.4 (9.7) |
| 8Q GAIN MUTATED | 79 | 62.2 (9.1) |
| 8Q GAIN WILD-TYPE | 178 | 66.8 (9.6) |
Figure S2. Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #2: 'AGE'
'1q loss mutation analysis' versus 'Time to Death'
P value = 6.52e-05 (logrank test), Q value = 0.054
Table S3. Gene #42: '1q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 254 | 81 | 0.0 - 224.0 (13.4) |
| 1Q LOSS MUTATED | 7 | 4 | 0.1 - 21.5 (8.4) |
| 1Q LOSS WILD-TYPE | 247 | 77 | 0.0 - 224.0 (13.7) |
Figure S3. Get High-res Image Gene #42: '1q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'
'8q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'
P value = 5.31e-05 (Chi-square test), Q value = 0.044
Table S4. Gene #55: '8q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
| nPatients | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | MUCINOUS (COLLOID) ADENOCARCINOMA |
|---|---|---|---|---|---|---|---|---|---|---|---|
| ALL | 6 | 65 | 182 | 3 | 10 | 2 | 3 | 2 | 10 | 1 | 4 |
| 8Q LOSS MUTATED | 0 | 2 | 6 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 0 |
| 8Q LOSS WILD-TYPE | 6 | 63 | 176 | 3 | 10 | 2 | 2 | 2 | 10 | 0 | 4 |
Figure S4. Get High-res Image Gene #55: '8q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
Methods & Data
Input
-
Mutation data file = broad_values_by_arm.mutsig.cluster.txt
-
Clinical data file = LUAD.clin.merged.picked.txt
-
Number of patients = 288
-
Number of significantly arm-level cnvs = 79
-
Number of selected clinical features = 11
-
Exclude genes that fewer than K tumors have mutations, K = 3
Survival analysis
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
Student's t-test analysis
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
Fisher's exact test
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
Chi-square test
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
Q value calculation
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.
Download Results
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.
References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2012
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.