Correlation between copy number variations of arm-level result and selected clinical features
Lung Adenocarcinoma (MOLECULAR_NONSMOKER)
07 February 2013
|
awg_luad__2013_02_07
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as
Broad Institute TCGA Genome Data Analysis Center
(2013):
Correlation between copy number variations of arm-level result and selected clinical features.
Broad Institute of MIT and Harvard.
doi:10.7908/C1KS6PPS
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 68 arm-level results and 14 clinical features across 80 patients, 2 significant findings detected with Q value < 0.25.
-
3p loss cnv correlated to 'NUMBERPACKYEARSSMOKED'.
-
4p 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 68 arm-level results and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 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 | |
| 3p loss | 10 (12%) | 70 |
0.784 (1.00) |
0.591 (1.00) |
1 (1.00) |
0.87 (1.00) |
0.186 (1.00) |
0.894 (1.00) |
0.815 (1.00) |
1 (1.00) |
0.497 (1.00) |
0.000136 (0.11) |
0.0778 (1.00) |
0.81 (1.00) |
0.46 (1.00) |
|
| 4p loss | 4 (5%) | 76 |
0.631 (1.00) |
0.00895 (1.00) |
1 (1.00) |
0.000293 (0.238) |
0.758 (1.00) |
1 (1.00) |
0.322 (1.00) |
1 (1.00) |
1 (1.00) |
0.193 (1.00) |
0.108 (1.00) |
|||
| 1p gain | 10 (12%) | 70 |
0.683 (1.00) |
0.0939 (1.00) |
1 (1.00) |
0.413 (1.00) |
0.213 (1.00) |
0.7 (1.00) |
1 (1.00) |
0.534 (1.00) |
0.497 (1.00) |
0.665 (1.00) |
0.916 (1.00) |
0.9 (1.00) |
||
| 1q gain | 25 (31%) | 55 |
0.544 (1.00) |
0.131 (1.00) |
0.33 (1.00) |
0.711 (1.00) |
0.682 (1.00) |
0.202 (1.00) |
0.803 (1.00) |
0.583 (1.00) |
0.173 (1.00) |
0.78 (1.00) |
0.674 (1.00) |
1 (1.00) |
0.683 (1.00) |
|
| 2p gain | 7 (9%) | 73 |
0.0305 (1.00) |
0.354 (1.00) |
0.038 (1.00) |
0.938 (1.00) |
0.156 (1.00) |
0.392 (1.00) |
0.285 (1.00) |
0.0536 (1.00) |
0.0583 (1.00) |
0.263 (1.00) |
0.248 (1.00) |
0.0206 (1.00) |
0.975 (1.00) |
|
| 2q gain | 6 (8%) | 74 |
0.0313 (1.00) |
0.857 (1.00) |
0.0782 (1.00) |
0.896 (1.00) |
0.106 (1.00) |
0.715 (1.00) |
0.228 (1.00) |
0.0629 (1.00) |
0.33 (1.00) |
0.361 (1.00) |
0.571 (1.00) |
0.0367 (1.00) |
0.466 (1.00) |
|
| 3q gain | 4 (5%) | 76 |
0.767 (1.00) |
0.507 (1.00) |
0.0293 (1.00) |
0.669 (1.00) |
0.055 (1.00) |
0.625 (1.00) |
1 (1.00) |
0.303 (1.00) |
0.231 (1.00) |
1 (1.00) |
||||
| 4p gain | 5 (6%) | 75 |
0.848 (1.00) |
0.0528 (1.00) |
0.646 (1.00) |
0.992 (1.00) |
1 (1.00) |
0.142 (1.00) |
0.209 (1.00) |
0.359 (1.00) |
0.282 (1.00) |
0.872 (1.00) |
0.824 (1.00) |
0.166 (1.00) |
0.173 (1.00) |
|
| 5p gain | 26 (32%) | 54 |
0.181 (1.00) |
0.302 (1.00) |
0.81 (1.00) |
0.626 (1.00) |
0.388 (1.00) |
0.615 (1.00) |
1 (1.00) |
0.754 (1.00) |
0.0363 (1.00) |
0.0567 (1.00) |
0.304 (1.00) |
0.858 (1.00) |
0.589 (1.00) |
|
| 5q gain | 16 (20%) | 64 |
0.149 (1.00) |
0.435 (1.00) |
1 (1.00) |
0.805 (1.00) |
0.916 (1.00) |
0.844 (1.00) |
0.525 (1.00) |
0.677 (1.00) |
0.26 (1.00) |
0.845 (1.00) |
0.578 (1.00) |
0.362 (1.00) |
0.719 (1.00) |
|
| 6p gain | 9 (11%) | 71 |
0.704 (1.00) |
0.615 (1.00) |
0.726 (1.00) |
0.233 (1.00) |
0.0931 (1.00) |
0.46 (1.00) |
0.492 (1.00) |
0.657 (1.00) |
0.458 (1.00) |
0.626 (1.00) |
0.81 (1.00) |
0.00338 (1.00) |
0.0997 (1.00) |
|
| 6q gain | 3 (4%) | 77 |
0.0324 (1.00) |
0.832 (1.00) |
0.258 (1.00) |
0.116 (1.00) |
0.339 (1.00) |
1 (1.00) |
1 (1.00) |
0.812 (1.00) |
1 (1.00) |
0.436 (1.00) |
||||
| 7p gain | 34 (42%) | 46 |
0.397 (1.00) |
0.336 (1.00) |
1 (1.00) |
0.345 (1.00) |
0.848 (1.00) |
0.0726 (1.00) |
0.354 (1.00) |
0.256 (1.00) |
0.646 (1.00) |
0.679 (1.00) |
0.662 (1.00) |
0.755 (1.00) |
0.466 (1.00) |
|
| 7q gain | 25 (31%) | 55 |
0.592 (1.00) |
0.0497 (1.00) |
1 (1.00) |
0.097 (1.00) |
0.682 (1.00) |
0.253 (1.00) |
0.0749 (1.00) |
0.342 (1.00) |
0.173 (1.00) |
0.799 (1.00) |
0.884 (1.00) |
0.527 (1.00) |
0.429 (1.00) |
|
| 8p gain | 9 (11%) | 71 |
0.533 (1.00) |
0.0148 (1.00) |
0.726 (1.00) |
0.584 (1.00) |
1 (1.00) |
0.277 (1.00) |
0.0586 (1.00) |
0.122 (1.00) |
0.0947 (1.00) |
0.254 (1.00) |
0.0594 (1.00) |
0.129 (1.00) |
0.155 (1.00) |
|
| 8q gain | 18 (22%) | 62 |
0.907 (1.00) |
0.123 (1.00) |
0.183 (1.00) |
0.565 (1.00) |
0.586 (1.00) |
0.418 (1.00) |
0.0408 (1.00) |
0.454 (1.00) |
0.313 (1.00) |
0.392 (1.00) |
0.24 (1.00) |
0.567 (1.00) |
0.0699 (1.00) |
|
| 10p gain | 6 (8%) | 74 |
0.885 (1.00) |
0.626 (1.00) |
0.0782 (1.00) |
0.0858 (1.00) |
0.145 (1.00) |
1 (1.00) |
0.702 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.106 (1.00) |
0.0568 (1.00) |
0.000882 (0.716) |
0.447 (1.00) |
|
| 10q gain | 6 (8%) | 74 |
0.899 (1.00) |
0.574 (1.00) |
0.0782 (1.00) |
0.327 (1.00) |
0.0122 (1.00) |
1 (1.00) |
0.702 (1.00) |
0.319 (1.00) |
1 (1.00) |
0.085 (1.00) |
0.0512 (1.00) |
0.000882 (0.716) |
0.405 (1.00) |
|
| 11p gain | 10 (12%) | 70 |
0.149 (1.00) |
0.0278 (1.00) |
1 (1.00) |
0.598 (1.00) |
0.875 (1.00) |
1 (1.00) |
0.575 (1.00) |
0.348 (1.00) |
1 (1.00) |
0.968 (1.00) |
0.412 (1.00) |
0.34 (1.00) |
0.515 (1.00) |
|
| 11q gain | 11 (14%) | 69 |
0.217 (1.00) |
0.0414 (1.00) |
0.514 (1.00) |
0.594 (1.00) |
0.779 (1.00) |
0.554 (1.00) |
0.611 (1.00) |
0.479 (1.00) |
0.533 (1.00) |
0.273 (1.00) |
0.123 (1.00) |
0.071 (1.00) |
0.741 (1.00) |
|
| 12p gain | 6 (8%) | 74 |
0.962 (1.00) |
0.54 (1.00) |
0.695 (1.00) |
0.779 (1.00) |
0.706 (1.00) |
0.0353 (1.00) |
0.143 (1.00) |
0.0369 (1.00) |
1 (1.00) |
0.35 (1.00) |
0.518 (1.00) |
0.312 (1.00) |
||
| 12q gain | 3 (4%) | 77 |
0.963 (1.00) |
0.749 (1.00) |
0.572 (1.00) |
0.97 (1.00) |
0.482 (1.00) |
0.048 (1.00) |
0.55 (1.00) |
0.0322 (1.00) |
1 (1.00) |
0.318 (1.00) |
||||
| 13q gain | 3 (4%) | 77 |
0.485 (1.00) |
0.0728 (1.00) |
0.888 (1.00) |
0.482 (1.00) |
0.31 (1.00) |
0.224 (1.00) |
0.0453 (1.00) |
0.178 (1.00) |
0.436 (1.00) |
|||||
| 14q gain | 7 (9%) | 73 |
0.437 (1.00) |
0.318 (1.00) |
0.229 (1.00) |
0.0182 (1.00) |
0.611 (1.00) |
0.325 (1.00) |
0.143 (1.00) |
0.55 (1.00) |
1 (1.00) |
0.9 (1.00) |
0.893 (1.00) |
|||
| 15q gain | 6 (8%) | 74 |
0.169 (1.00) |
0.458 (1.00) |
1 (1.00) |
0.135 (1.00) |
0.496 (1.00) |
0.817 (1.00) |
1 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.00643 (1.00) |
0.785 (1.00) |
|||
| 16p gain | 12 (15%) | 68 |
0.578 (1.00) |
0.235 (1.00) |
0.753 (1.00) |
0.789 (1.00) |
0.253 (1.00) |
0.73 (1.00) |
0.452 (1.00) |
0.803 (1.00) |
0.16 (1.00) |
0.652 (1.00) |
0.797 (1.00) |
0.768 (1.00) |
0.455 (1.00) |
|
| 16q gain | 9 (11%) | 71 |
0.753 (1.00) |
0.453 (1.00) |
0.484 (1.00) |
0.606 (1.00) |
0.478 (1.00) |
0.875 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.569 (1.00) |
0.831 (1.00) |
0.955 (1.00) |
0.719 (1.00) |
|
| 17p gain | 6 (8%) | 74 |
0.739 (1.00) |
0.682 (1.00) |
0.393 (1.00) |
0.988 (1.00) |
0.145 (1.00) |
0.506 (1.00) |
0.335 (1.00) |
0.266 (1.00) |
0.0427 (1.00) |
0.261 (1.00) |
0.836 (1.00) |
0.603 (1.00) |
0.945 (1.00) |
|
| 17q gain | 14 (18%) | 66 |
0.498 (1.00) |
0.925 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.473 (1.00) |
0.538 (1.00) |
0.246 (1.00) |
0.219 (1.00) |
0.0353 (1.00) |
0.375 (1.00) |
0.526 (1.00) |
0.802 (1.00) |
0.762 (1.00) |
|
| 18p gain | 5 (6%) | 75 |
0.668 (1.00) |
0.314 (1.00) |
1 (1.00) |
0.992 (1.00) |
0.819 (1.00) |
0.262 (1.00) |
1 (1.00) |
0.606 (1.00) |
0.282 (1.00) |
0.984 (1.00) |
0.255 (1.00) |
0.659 (1.00) |
0.472 (1.00) |
|
| 19p gain | 4 (5%) | 76 |
0.704 (1.00) |
0.972 (1.00) |
1 (1.00) |
0.927 (1.00) |
0.758 (1.00) |
0.217 (1.00) |
1 (1.00) |
1 (1.00) |
0.231 (1.00) |
1 (1.00) |
||||
| 19q gain | 4 (5%) | 76 |
0.236 (1.00) |
0.91 (1.00) |
0.307 (1.00) |
0.927 (1.00) |
0.758 (1.00) |
0.217 (1.00) |
1 (1.00) |
1 (1.00) |
0.231 (1.00) |
0.157 (1.00) |
0.246 (1.00) |
0.273 (1.00) |
0.658 (1.00) |
|
| 20p gain | 10 (12%) | 70 |
0.44 (1.00) |
0.483 (1.00) |
0.505 (1.00) |
0.598 (1.00) |
0.0931 (1.00) |
0.46 (1.00) |
0.346 (1.00) |
0.436 (1.00) |
1 (1.00) |
0.355 (1.00) |
0.989 (1.00) |
0.0179 (1.00) |
0.0556 (1.00) |
|
| 20q gain | 11 (14%) | 69 |
0.512 (1.00) |
0.346 (1.00) |
0.338 (1.00) |
0.332 (1.00) |
0.213 (1.00) |
0.303 (1.00) |
0.492 (1.00) |
0.341 (1.00) |
1 (1.00) |
0.208 (1.00) |
0.633 (1.00) |
0.00656 (1.00) |
0.339 (1.00) |
|
| 21q gain | 10 (12%) | 70 |
0.4 (1.00) |
0.564 (1.00) |
0.177 (1.00) |
0.176 (1.00) |
0.489 (1.00) |
0.894 (1.00) |
0.537 (1.00) |
0.484 (1.00) |
0.497 (1.00) |
0.0923 (1.00) |
||||
| 22q gain | 7 (9%) | 73 |
0.795 (1.00) |
0.135 (1.00) |
1 (1.00) |
0.0662 (1.00) |
0.859 (1.00) |
0.0183 (1.00) |
0.735 (1.00) |
0.225 (1.00) |
1 (1.00) |
0.561 (1.00) |
0.84 (1.00) |
0.946 (1.00) |
0.729 (1.00) |
|
| Xq gain | 5 (6%) | 75 |
0.448 (1.00) |
0.354 (1.00) |
1 (1.00) |
0.321 (1.00) |
0.819 (1.00) |
0.666 (1.00) |
0.658 (1.00) |
0.712 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.425 (1.00) |
0.182 (1.00) |
0.807 (1.00) |
|
| 1p loss | 6 (8%) | 74 |
0.299 (1.00) |
0.89 (1.00) |
0.0782 (1.00) |
0.327 (1.00) |
1 (1.00) |
0.506 (1.00) |
0.702 (1.00) |
0.887 (1.00) |
0.33 (1.00) |
0.161 (1.00) |
||||
| 3q loss | 7 (9%) | 73 |
0.899 (1.00) |
0.95 (1.00) |
0.229 (1.00) |
0.938 (1.00) |
0.522 (1.00) |
0.466 (1.00) |
1 (1.00) |
0.566 (1.00) |
0.375 (1.00) |
0.501 (1.00) |
1 (1.00) |
|||
| 4q loss | 4 (5%) | 76 |
0.925 (1.00) |
0.107 (1.00) |
1 (1.00) |
0.236 (1.00) |
1 (1.00) |
0.304 (1.00) |
0.322 (1.00) |
0.502 (1.00) |
1 (1.00) |
0.0735 (1.00) |
||||
| 5q loss | 9 (11%) | 71 |
0.578 (1.00) |
0.195 (1.00) |
0.159 (1.00) |
0.0462 (1.00) |
0.685 (1.00) |
0.887 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.57 (1.00) |
0.203 (1.00) |
0.149 (1.00) |
0.272 (1.00) |
|
| 6p loss | 7 (9%) | 73 |
0.689 (1.00) |
0.29 (1.00) |
0.451 (1.00) |
0.888 (1.00) |
0.057 (1.00) |
0.848 (1.00) |
0.547 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.847 (1.00) |
0.459 (1.00) |
0.15 (1.00) |
0.711 (1.00) |
|
| 6q loss | 16 (20%) | 64 |
0.431 (1.00) |
0.389 (1.00) |
1 (1.00) |
0.539 (1.00) |
0.0502 (1.00) |
0.921 (1.00) |
0.086 (1.00) |
0.379 (1.00) |
0.26 (1.00) |
0.353 (1.00) |
0.0474 (1.00) |
0.179 (1.00) |
0.477 (1.00) |
|
| 7p loss | 3 (4%) | 77 |
0.749 (1.00) |
0.572 (1.00) |
0.999 (1.00) |
0.339 (1.00) |
0.758 (1.00) |
0.55 (1.00) |
1 (1.00) |
1 (1.00) |
0.185 (1.00) |
|||||
| 7q loss | 4 (5%) | 76 |
0.783 (1.00) |
0.503 (1.00) |
1 (1.00) |
0.236 (1.00) |
0.758 (1.00) |
0.625 (1.00) |
0.322 (1.00) |
1 (1.00) |
1 (1.00) |
0.401 (1.00) |
||||
| 8p loss | 23 (29%) | 57 |
0.868 (1.00) |
0.0473 (1.00) |
1 (1.00) |
0.706 (1.00) |
0.88 (1.00) |
0.355 (1.00) |
1 (1.00) |
0.716 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.0919 (1.00) |
0.472 (1.00) |
0.584 (1.00) |
|
| 8q loss | 5 (6%) | 75 |
0.634 (1.00) |
0.143 (1.00) |
1 (1.00) |
0.00377 (1.00) |
0.305 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.275 (1.00) |
||||
| 9p loss | 24 (30%) | 56 |
0.269 (1.00) |
0.544 (1.00) |
0.806 (1.00) |
0.0218 (1.00) |
0.599 (1.00) |
1 (1.00) |
0.268 (1.00) |
0.806 (1.00) |
0.633 (1.00) |
0.662 (1.00) |
0.817 (1.00) |
0.51 (1.00) |
0.189 (1.00) |
|
| 9q loss | 20 (25%) | 60 |
0.227 (1.00) |
0.665 (1.00) |
1 (1.00) |
0.0752 (1.00) |
0.933 (1.00) |
0.745 (1.00) |
0.245 (1.00) |
0.436 (1.00) |
0.594 (1.00) |
0.967 (1.00) |
0.679 (1.00) |
0.574 (1.00) |
0.221 (1.00) |
|
| 10p loss | 5 (6%) | 75 |
0.486 (1.00) |
0.932 (1.00) |
0.0686 (1.00) |
0.0109 (1.00) |
0.819 (1.00) |
0.666 (1.00) |
1 (1.00) |
0.77 (1.00) |
1 (1.00) |
0.347 (1.00) |
||||
| 10q loss | 7 (9%) | 73 |
0.332 (1.00) |
0.268 (1.00) |
0.0185 (1.00) |
0.0752 (1.00) |
0.859 (1.00) |
0.466 (1.00) |
0.735 (1.00) |
0.425 (1.00) |
1 (1.00) |
0.624 (1.00) |
0.704 (1.00) |
|||
| 12p loss | 6 (8%) | 74 |
0.0913 (1.00) |
0.308 (1.00) |
1 (1.00) |
0.988 (1.00) |
1 (1.00) |
0.246 (1.00) |
0.507 (1.00) |
0.403 (1.00) |
0.33 (1.00) |
0.231 (1.00) |
0.786 (1.00) |
0.148 (1.00) |
||
| 12q loss | 4 (5%) | 76 |
0.591 (1.00) |
0.524 (1.00) |
1 (1.00) |
0.97 (1.00) |
0.443 (1.00) |
0.806 (1.00) |
0.658 (1.00) |
0.712 (1.00) |
1 (1.00) |
0.337 (1.00) |
0.884 (1.00) |
|||
| 13q loss | 16 (20%) | 64 |
0.0728 (1.00) |
0.82 (1.00) |
0.401 (1.00) |
0.0999 (1.00) |
0.918 (1.00) |
0.423 (1.00) |
0.147 (1.00) |
0.401 (1.00) |
1 (1.00) |
0.956 (1.00) |
0.258 (1.00) |
0.781 (1.00) |
0.591 (1.00) |
|
| 14q loss | 4 (5%) | 76 |
0.404 (1.00) |
0.274 (1.00) |
1 (1.00) |
0.00496 (1.00) |
0.313 (1.00) |
1 (1.00) |
0.209 (1.00) |
0.21 (1.00) |
0.231 (1.00) |
0.502 (1.00) |
0.795 (1.00) |
0.884 (1.00) |
||
| 15q loss | 14 (18%) | 66 |
0.211 (1.00) |
0.407 (1.00) |
0.373 (1.00) |
0.388 (1.00) |
0.918 (1.00) |
0.826 (1.00) |
0.632 (1.00) |
0.781 (1.00) |
0.209 (1.00) |
0.0915 (1.00) |
0.725 (1.00) |
0.32 (1.00) |
0.00415 (1.00) |
|
| 16p loss | 5 (6%) | 75 |
0.778 (1.00) |
0.0193 (1.00) |
0.388 (1.00) |
0.168 (1.00) |
1 (1.00) |
0.806 (1.00) |
0.178 (1.00) |
0.194 (1.00) |
1 (1.00) |
0.716 (1.00) |
||||
| 16q loss | 6 (8%) | 74 |
0.738 (1.00) |
0.0729 (1.00) |
0.233 (1.00) |
0.361 (1.00) |
1 (1.00) |
0.666 (1.00) |
0.335 (1.00) |
0.128 (1.00) |
1 (1.00) |
0.701 (1.00) |
||||
| 17p loss | 24 (30%) | 56 |
0.448 (1.00) |
0.751 (1.00) |
1 (1.00) |
0.118 (1.00) |
0.828 (1.00) |
1 (1.00) |
0.896 (1.00) |
0.953 (1.00) |
0.315 (1.00) |
0.0457 (1.00) |
0.0821 (1.00) |
0.205 (1.00) |
0.716 (1.00) |
|
| 17q loss | 4 (5%) | 76 |
0.0894 (1.00) |
0.133 (1.00) |
0.0109 (1.00) |
1 (1.00) |
0.217 (1.00) |
0.658 (1.00) |
0.425 (1.00) |
1 (1.00) |
1 (1.00) |
|||||
| 18p loss | 15 (19%) | 65 |
0.819 (1.00) |
0.976 (1.00) |
1 (1.00) |
0.175 (1.00) |
0.0685 (1.00) |
0.709 (1.00) |
0.767 (1.00) |
0.506 (1.00) |
0.578 (1.00) |
0.0435 (1.00) |
0.814 (1.00) |
0.944 (1.00) |
0.149 (1.00) |
|
| 18q loss | 24 (30%) | 56 |
0.741 (1.00) |
0.42 (1.00) |
0.219 (1.00) |
0.143 (1.00) |
0.157 (1.00) |
0.825 (1.00) |
0.538 (1.00) |
0.822 (1.00) |
0.315 (1.00) |
0.722 (1.00) |
0.382 (1.00) |
0.41 (1.00) |
0.791 (1.00) |
|
| 19p loss | 16 (20%) | 64 |
0.568 (1.00) |
0.881 (1.00) |
0.0923 (1.00) |
0.000311 (0.253) |
0.385 (1.00) |
0.772 (1.00) |
1 (1.00) |
1 (1.00) |
0.577 (1.00) |
0.743 (1.00) |
0.61 (1.00) |
0.404 (1.00) |
0.592 (1.00) |
|
| 19q loss | 8 (10%) | 72 |
0.655 (1.00) |
0.709 (1.00) |
1 (1.00) |
0.11 (1.00) |
0.763 (1.00) |
0.325 (1.00) |
0.111 (1.00) |
0.688 (1.00) |
1 (1.00) |
0.999 (1.00) |
0.256 (1.00) |
0.907 (1.00) |
0.452 (1.00) |
|
| 20p loss | 13 (16%) | 67 |
0.647 (1.00) |
0.942 (1.00) |
0.77 (1.00) |
0.306 (1.00) |
0.195 (1.00) |
0.104 (1.00) |
0.859 (1.00) |
0.679 (1.00) |
0.586 (1.00) |
0.812 (1.00) |
0.254 (1.00) |
|||
| 20q loss | 5 (6%) | 75 |
0.0221 (1.00) |
0.0503 (1.00) |
0.646 (1.00) |
0.00377 (1.00) |
0.819 (1.00) |
0.182 (1.00) |
0.677 (1.00) |
0.685 (1.00) |
1 (1.00) |
0.315 (1.00) |
||||
| 21q loss | 9 (11%) | 71 |
0.797 (1.00) |
0.188 (1.00) |
0.484 (1.00) |
0.165 (1.00) |
0.174 (1.00) |
0.46 (1.00) |
0.804 (1.00) |
0.934 (1.00) |
0.458 (1.00) |
0.137 (1.00) |
0.561 (1.00) |
0.277 (1.00) |
0.293 (1.00) |
|
| 22q loss | 12 (15%) | 68 |
0.886 (1.00) |
0.205 (1.00) |
0.753 (1.00) |
0.79 (1.00) |
0.902 (1.00) |
0.393 (1.00) |
0.594 (1.00) |
0.304 (1.00) |
0.566 (1.00) |
0.425 (1.00) |
0.523 (1.00) |
0.922 (1.00) |
0.712 (1.00) |
'3p loss mutation analysis' versus 'NUMBERPACKYEARSSMOKED'
P value = 0.000136 (t-test), Q value = 0.11
Table S1. Gene #37: '3p loss mutation analysis' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 40 | 33.0 (31.8) |
| 3P LOSS MUTATED | 4 | 6.8 (6.9) |
| 3P LOSS WILD-TYPE | 36 | 35.9 (32.2) |
Figure S1. Get High-res Image Gene #37: '3p loss mutation analysis' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'
'4p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'
P value = 0.000293 (Chi-square test), Q value = 0.24
Table S2. Gene #39: '4p 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 MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | MUCINOUS (COLLOID) ADENOCARCINOMA |
|---|---|---|---|---|---|---|---|---|---|
| ALL | 3 | 18 | 46 | 3 | 4 | 1 | 1 | 2 | 2 |
| 4P LOSS MUTATED | 0 | 0 | 2 | 0 | 0 | 0 | 1 | 0 | 1 |
| 4P LOSS WILD-TYPE | 3 | 18 | 44 | 3 | 4 | 1 | 0 | 2 | 1 |
Figure S2. Get High-res Image Gene #39: '4p 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 = MOLECULAR_NONSMOKER.clin.merged.picked.txt
-
Number of patients = 80
-
Number of significantly arm-level cnvs = 68
-
Number of selected clinical features = 14
-
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 © 2013
Broad Institute TCGA GDAC as part of the TCGA Research Network.
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