Correlation between copy number variations of arm-level result and selected clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C12N50BM
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/C12N50BM
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 42 arm-level results and 15 clinical features across 421 patients, 42 significant findings detected with Q value < 0.25.

- 1q gain cnv correlated to 'EXTRATHYROIDAL.EXTENSION' and 'NEOPLASM.DISEASESTAGE'.

- 4p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 4q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 5p gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.

- 5q gain cnv correlated to 'DISTANT.METASTASIS', 'NUMBER.OF.LYMPH.NODES', and 'NEOPLASM.DISEASESTAGE'.

- 7p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

- 7q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

- 12p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 12q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 13q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 14q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 16p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

- 16q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

- 17p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 17q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 19p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 19q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 20p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

- 20q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES' and 'NEOPLASM.DISEASESTAGE'.

- 2p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 2q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 3q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 6q loss cnv correlated to 'Time to Death'.

- 9p loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.

- 9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.

- 10p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 10q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 11p loss cnv correlated to 'AGE' and 'NEOPLASM.DISEASESTAGE'.

- 11q loss cnv correlated to 'AGE' and 'NEOPLASM.DISEASESTAGE'.

- 13q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 19p loss cnv correlated to 'Time to Death'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 42 arm-level results and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 42 significant findings detected.

|  | Clinical Features | Time to Death | AGE | GENDER | HISTOLOGICAL TYPE | RADIATIONS RADIATION REGIMENINDICATION | RADIATIONEXPOSURE | DISTANT METASTASIS | EXTRATHYROIDAL EXTENSION | LYMPH NODE METASTASIS | COMPLETENESS OF RESECTION | NUMBER OF LYMPH NODES | TUMOR STAGECODE | NEOPLASM DISEASESTAGE | MULTIFOCALITY | TUMOR SIZE
| nCNV (%) | nWild-Type | logrank test | t-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 | Chi-square test | Fisher's exact test | t-test | t-test | Chi-square test | Fisher's exact test | t-test
5q gain | 0 (0%) | 410 | 0.00139 (0.738) | 0.008 (1.00) | 1 (1.00) | 0.25 (1.00) | 0.314 (1.00) | 1 (1.00) | 0.000218 (0.117) | 0.0351 (1.00) | 0.156 (1.00) | 0.828 (1.00) | 1.04e-21 (5.98e-19) |  | 1.68e-05 (0.00922) | 0.224 (1.00) | 0.057 (1.00)
1q gain | 0 (0%) | 403 | 0.0639 (1.00) | 0.00122 (0.655) | 0.416 (1.00) | 0.0941 (1.00) | 0.463 (1.00) | 1 (1.00) | 0.867 (1.00) | 4.34e-06 (0.0024) | 0.00641 (1.00) | 0.0201 (1.00) | 0.33 (1.00) |  | 3.37e-05 (0.0183) | 0.225 (1.00) | 0.0333 (1.00)
7p gain | 0 (0%) | 409 | 0.132 (1.00) | 0.0191 (1.00) | 0.738 (1.00) | 0.0947 (1.00) | 1 (1.00) | 1 (1.00) | 0.00238 (1.00) | 0.0206 (1.00) | 0.12 (1.00) | 0.309 (1.00) | 1.01e-21 (5.87e-19) |  | 1.05e-05 (0.00577) | 0.381 (1.00) | 0.269 (1.00)
7q gain | 0 (0%) | 407 | 0.151 (1.00) | 0.011 (1.00) | 0.533 (1.00) | 0.0565 (1.00) | 1 (1.00) | 1 (1.00) | 0.00406 (1.00) | 0.0414 (1.00) | 0.0171 (1.00) | 0.167 (1.00) | 1.01e-21 (5.87e-19) |  | 9.51e-05 (0.0515) | 0.413 (1.00) | 0.278 (1.00)
16p gain | 0 (0%) | 412 | 0.0515 (1.00) | 0.139 (1.00) | 0.12 (1.00) | 0.566 (1.00) | 1 (1.00) | 1 (1.00) | 0.0909 (1.00) | 0.0343 (1.00) | 0.0603 (1.00) | 0.148 (1.00) | 1.11e-21 (6.32e-19) |  | 3.53e-05 (0.0192) | 1 (1.00) | 0.567 (1.00)
16q gain | 0 (0%) | 414 | 0.0448 (1.00) | 0.0726 (1.00) | 0.199 (1.00) | 0.326 (1.00) | 1 (1.00) | 1 (1.00) | 0.0955 (1.00) | 0.0233 (1.00) | 0.24 (1.00) | 0.335 (1.00) | 1.13e-21 (6.43e-19) |  | 5.12e-07 (0.000284) | 0.704 (1.00) | 0.46 (1.00)
20p gain | 0 (0%) | 414 | 0.119 (1.00) | 0.0677 (1.00) | 0.684 (1.00) | 0.125 (1.00) | 1 (1.00) | 1 (1.00) | 0.00929 (1.00) | 0.0233 (1.00) | 0.24 (1.00) | 0.718 (1.00) | 1.13e-21 (6.43e-19) |  | 2.98e-07 (0.000166) | 0.704 (1.00) | 0.0763 (1.00)
20q gain | 0 (0%) | 414 | 0.119 (1.00) | 0.0677 (1.00) | 0.684 (1.00) | 0.125 (1.00) | 1 (1.00) | 1 (1.00) | 0.00929 (1.00) | 0.0233 (1.00) | 0.24 (1.00) | 0.718 (1.00) | 1.13e-21 (6.43e-19) |  | 2.98e-07 (0.000166) | 0.704 (1.00) | 0.0763 (1.00)
11p loss | 0 (0%) | 414 | 0.00162 (0.858) | 0.000427 (0.23) | 0.0132 (1.00) | 0.831 (1.00) | 0.212 (1.00) | 1 (1.00) | 0.0955 (1.00) | 0.548 (1.00) | 0.584 (1.00) | 0.493 (1.00) | 0.0855 (1.00) |  | 1.36e-06 (0.000752) | 0.704 (1.00) | 0.0337 (1.00)
11q loss | 0 (0%) | 412 | 0.00416 (1.00) | 7.15e-05 (0.0387) | 0.00132 (0.705) | 1 (1.00) | 0.265 (1.00) | 1 (1.00) | 0.0909 (1.00) | 0.8 (1.00) | 0.712 (1.00) | 0.603 (1.00) | 0.266 (1.00) |  | 2.97e-05 (0.0162) | 1 (1.00) | 0.0127 (1.00)
4p gain | 0 (0%) | 417 | 0.0044 (1.00) | 0.123 (1.00) | 1 (1.00) | 0.479 (1.00) | 0.127 (1.00) | 1 (1.00) | 0.105 (1.00) | 1 (1.00) | 0.307 (1.00) | 0.294 (1.00) | 1.13e-21 (6.43e-19) |  | 0.655 (1.00) | 0.324 (1.00) | 0.587 (1.00)
4q gain | 0 (0%) | 417 | 0.0044 (1.00) | 0.123 (1.00) | 1 (1.00) | 0.479 (1.00) | 0.127 (1.00) | 1 (1.00) | 0.105 (1.00) | 1 (1.00) | 0.307 (1.00) | 0.294 (1.00) | 1.13e-21 (6.43e-19) |  | 0.655 (1.00) | 0.324 (1.00) | 0.587 (1.00)
5p gain | 0 (0%) | 409 | 0.0193 (1.00) | 0.00308 (1.00) | 1 (1.00) | 0.345 (1.00) | 0.337 (1.00) | 1 (1.00) | 0.00238 (1.00) | 0.0514 (1.00) | 0.175 (1.00) | 0.844 (1.00) | 0.0605 (1.00) |  | 2.58e-05 (0.0141) | 0.381 (1.00) | 0.0293 (1.00)
12p gain | 0 (0%) | 412 | 0.623 (1.00) | 0.201 (1.00) | 0.459 (1.00) | 0.0899 (1.00) | 1 (1.00) | 1 (1.00) | 0.00137 (0.728) | 0.607 (1.00) | 0.0951 (1.00) | 0.603 (1.00) | 1.06e-21 (6.09e-19) |  | 0.0364 (1.00) | 0.19 (1.00) | 0.607 (1.00)
12q gain | 0 (0%) | 411 | 0.623 (1.00) | 0.16 (1.00) | 0.463 (1.00) | 0.0339 (1.00) | 1 (1.00) | 1 (1.00) | 0.00104 (0.556) | 0.506 (1.00) | 0.03 (1.00) | 0.515 (1.00) | 1.06e-21 (6.09e-19) |  | 0.0741 (1.00) | 0.346 (1.00) | 0.607 (1.00)
13q gain | 0 (0%) | 418 | 0.799 (1.00) | 0.267 (1.00) | 1 (1.00) | 0.233 (1.00) | 1 (1.00) | 1 (1.00) | 0.13 (1.00) | 1 (1.00) | 0.462 (1.00) | 1 (1.00) | 1.16e-21 (6.49e-19) |  | 0.047 (1.00) | 0.084 (1.00) | 0.378 (1.00)
14q gain | 0 (0%) | 413 | 0.617 (1.00) | 0.147 (1.00) | 0.686 (1.00) | 0.214 (1.00) | 1 (1.00) | 1 (1.00) | 0.0346 (1.00) | 1 (1.00) | 0.116 (1.00) | 0.55 (1.00) | 1.11e-21 (6.32e-19) |  | 0.0134 (1.00) | 0.146 (1.00) | 0.387 (1.00)
17p gain | 0 (0%) | 410 | 0.505 (1.00) | 0.245 (1.00) | 0.303 (1.00) | 0.25 (1.00) | 1 (1.00) | 1 (1.00) | 0.126 (1.00) | 0.677 (1.00) | 0.156 (1.00) | 0.555 (1.00) | 0.000126 (0.0683) |  | 0.00965 (1.00) | 0.546 (1.00) | 0.438 (1.00)
17q gain | 0 (0%) | 409 | 0.505 (1.00) | 0.388 (1.00) | 0.31 (1.00) | 0.345 (1.00) | 1 (1.00) | 1 (1.00) | 0.0704 (1.00) | 0.689 (1.00) | 0.12 (1.00) | 0.592 (1.00) | 1.57e-05 (0.00863) |  | 0.0205 (1.00) | 0.771 (1.00) | 0.648 (1.00)
19p gain | 0 (0%) | 417 | 0.771 (1.00) | 0.0671 (1.00) | 1 (1.00) | 0.117 (1.00) | 1 (1.00) | 1 (1.00) | 0.105 (1.00) | 1 (1.00) | 0.307 (1.00) | 0.294 (1.00) | 1.13e-21 (6.43e-19) |  | 0.655 (1.00) | 0.324 (1.00) | 0.305 (1.00)
19q gain | 0 (0%) | 416 | 0.0161 (1.00) | 0.0282 (1.00) | 0.605 (1.00) | 0.178 (1.00) | 0.156 (1.00) | 1 (1.00) | 0.0282 (1.00) | 1 (1.00) | 0.197 (1.00) | 0.364 (1.00) | 1.11e-21 (6.32e-19) |  | 0.378 (1.00) | 0.658 (1.00) | 0.193 (1.00)
2p loss | 0 (0%) | 414 | 0.853 (1.00) | 0.208 (1.00) | 0.684 (1.00) | 0.125 (1.00) | 1 (1.00) | 1 (1.00) | 0.0955 (1.00) | 0.308 (1.00) | 0.0752 (1.00) | 0.493 (1.00) | 1.06e-21 (6.09e-19) |  | 0.00524 (1.00) | 0.704 (1.00) | 0.682 (1.00)
2q loss | 0 (0%) | 415 | 0.853 (1.00) | 0.0423 (1.00) | 1 (1.00) | 0.0614 (1.00) | 1 (1.00) | 1 (1.00) | 0.188 (1.00) | 0.344 (1.00) | 0.123 (1.00) | 0.431 (1.00) | 1.08e-21 (6.2e-19) |  | 0.000937 (0.503) | 0.412 (1.00) | 0.716 (1.00)
3q loss | 0 (0%) | 418 | 0.901 (1.00) | 0.212 (1.00) | 1 (1.00) | 0.233 (1.00) | 1 (1.00) | 1 (1.00) | 0.13 (1.00) | 0.604 (1.00) | 0.462 (1.00) | 1 (1.00) | 1.16e-21 (6.49e-19) |  | 0.047 (1.00) | 0.584 (1.00) | 0.231 (1.00)
6q loss | 0 (0%) | 418 | 3.21e-05 (0.0175) | 0.184 (1.00) | 1 (1.00) | 0.233 (1.00) | 1 (1.00) | 0.0828 (1.00) | 0.13 (1.00) | 0.604 (1.00) | 0.462 (1.00) | 1 (1.00) |  |  | 0.047 (1.00) | 1 (1.00) | 0.225 (1.00)
9p loss | 0 (0%) | 413 | 0.8 (1.00) | 0.22 (1.00) | 0.425 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.398 (1.00) | 0.772 (1.00) | 0.83 (1.00) | 1 (1.00) | 0.336 (1.00) |  | 1.27e-07 (7.1e-05) | 1 (1.00) | 0.106 (1.00)
9q loss | 0 (0%) | 409 | 0.00198 (1.00) | 0.0112 (1.00) | 0.51 (1.00) | 0.749 (1.00) | 0.337 (1.00) | 0.409 (1.00) | 0.317 (1.00) | 0.0459 (1.00) | 0.72 (1.00) | 0.483 (1.00) | 0.991 (1.00) |  | 6.18e-17 (3.45e-14) | 1 (1.00) | 0.0479 (1.00)
10p loss | 0 (0%) | 416 | 0.879 (1.00) | 0.0227 (1.00) | 0.605 (1.00) | 0.585 (1.00) | 1 (1.00) | 1 (1.00) | 0.246 (1.00) | 1 (1.00) | 0.197 (1.00) | 1 (1.00) | 1.13e-21 (6.43e-19) |  | 0.00729 (1.00) | 0.658 (1.00) | 0.201 (1.00)
10q loss | 0 (0%) | 417 | 0.931 (1.00) | 0.0057 (1.00) | 0.268 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.369 (1.00) | 1 (1.00) | 0.307 (1.00) | 1 (1.00) | 1.16e-21 (6.49e-19) |  | 0.074 (1.00) | 0.324 (1.00) | 0.217 (1.00)
13q loss | 0 (0%) | 412 | 0.103 (1.00) | 0.0373 (1.00) | 0.241 (1.00) | 0.0899 (1.00) | 0.265 (1.00) | 0.00305 (1.00) | 0.0909 (1.00) | 0.607 (1.00) | 0.093 (1.00) | 0.461 (1.00) | 1.04e-21 (5.98e-19) |  | 0.231 (1.00) | 0.19 (1.00) | 0.642 (1.00)
19p loss | 0 (0%) | 418 | 5.48e-06 (0.00302) | 0.0819 (1.00) | 0.16 (1.00) | 0.653 (1.00) | 1 (1.00) | 0.122 (1.00) | 0.603 (1.00) | 0.604 (1.00) | 0.471 (1.00) | 1 (1.00) |  |  | 0.0664 (1.00) | 0.259 (1.00) |
11p gain | 0 (0%) | 417 | 0.618 (1.00) | 0.725 (1.00) | 1 (1.00) | 0.479 (1.00) | 1 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.416 (1.00) | 0.453 (1.00) | 1 (1.00) |  |  | 0.655 (1.00) | 0.634 (1.00) | 0.139 (1.00)
11q gain | 0 (0%) | 418 | 0.621 (1.00) | 0.736 (1.00) | 0.574 (1.00) | 0.653 (1.00) | 1 (1.00) | 1 (1.00) | 0.603 (1.00) | 0.604 (1.00) | 0.471 (1.00) | 1 (1.00) |  |  | 0.813 (1.00) | 0.259 (1.00) | 0.321 (1.00)
18p gain | 0 (0%) | 418 | 0.669 (1.00) | 0.876 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.603 (1.00) | 1 (1.00) | 0.471 (1.00) | 1 (1.00) |  |  | 0.813 (1.00) | 1 (1.00) | 0.327 (1.00)
18q gain | 0 (0%) | 418 | 0.669 (1.00) | 0.876 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.603 (1.00) | 1 (1.00) | 0.471 (1.00) | 1 (1.00) |  |  | 0.813 (1.00) | 1 (1.00) | 0.327 (1.00)
1p loss | 0 (0%) | 418 | 0.901 (1.00) | 0.192 (1.00) | 0.574 (1.00) | 0.233 (1.00) | 1 (1.00) | 1 (1.00) | 0.603 (1.00) | 0.604 (1.00) | 0.462 (1.00) | 1 (1.00) |  |  | 0.047 (1.00) | 1 (1.00) |
15q loss | 0 (0%) | 416 | 0.777 (1.00) | 0.769 (1.00) | 0.336 (1.00) | 0.0194 (1.00) | 1 (1.00) | 1 (1.00) | 0.0443 (1.00) | 1 (1.00) | 0.484 (1.00) | 1 (1.00) | 0.579 (1.00) |  | 0.0191 (1.00) | 1 (1.00) | 0.407 (1.00)
17p loss | 0 (0%) | 417 | 0.696 (1.00) | 0.556 (1.00) | 0.576 (1.00) | 0.479 (1.00) | 0.00594 (1.00) | 1 (1.00) | 0.369 (1.00) | 0.139 (1.00) | 0.539 (1.00) | 1 (1.00) | 0.379 (1.00) |  | 0.112 (1.00) | 0.634 (1.00) | 0.277 (1.00)
18p loss | 0 (0%) | 418 | 0.879 (1.00) | 0.939 (1.00) | 0.574 (1.00) | 0.653 (1.00) | 1 (1.00) | 1 (1.00) | 0.603 (1.00) | 0.604 (1.00) | 0.797 (1.00) | 1 (1.00) | 0.0277 (1.00) |  | 0.0664 (1.00) | 1 (1.00) | 0.389 (1.00)
18q loss | 0 (0%) | 418 | 0.879 (1.00) | 0.939 (1.00) | 0.574 (1.00) | 0.653 (1.00) | 1 (1.00) | 1 (1.00) | 0.603 (1.00) | 0.604 (1.00) | 0.797 (1.00) | 1 (1.00) | 0.0277 (1.00) |  | 0.0664 (1.00) | 1 (1.00) | 0.389 (1.00)
21q loss | 0 (0%) | 415 | 0.892 (1.00) | 0.00855 (1.00) | 0.647 (1.00) | 0.794 (1.00) | 1 (1.00) | 1 (1.00) | 0.474 (1.00) | 0.344 (1.00) | 0.647 (1.00) | 0.662 (1.00) | 0.994 (1.00) |  | 0.0204 (1.00) | 0.091 (1.00) | 0.985 (1.00)
22q loss | 0 (0%) | 367 | 0.339 (1.00) | 0.146 (1.00) | 0.738 (1.00) | 0.0216 (1.00) | 0.232 (1.00) | 0.708 (1.00) | 0.397 (1.00) | 0.175 (1.00) | 0.252 (1.00) | 0.899 (1.00) | 0.201 (1.00) |  | 0.281 (1.00) | 0.378 (1.00) | 0.783 (1.00)

'1q gain' versus 'EXTRATHYROIDAL.EXTENSION'

P value = 4.34e-06 (Fisher's exact test), Q value = 0.0024

Table S1. Gene #1: '1q gain' versus Clinical Feature #8: 'EXTRATHYROIDAL.EXTENSION'

nPatients | MINIMAL (T3) | MODERATE/ADVANCED (T4A) | NONE | VERY ADVANCED (T4B)
--- | --- | --- | --- | ---
ALL | 113 | 13 | 275 | 1
1Q GAIN CNV | 10 | 3 | 4 | 1
1Q GAIN WILD-TYPE | 103 | 10 | 271 | 0

Figure S1. Get High-res Image Gene #1: '1q gain' versus Clinical Feature #8: 'EXTRATHYROIDAL.EXTENSION'

'1q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.37e-05 (Chi-square test), Q value = 0.018

Table S2. Gene #1: '1q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
1Q GAIN CNV | 3 | 1 | 8 | 1 | 5 | 0
1Q GAIN WILD-TYPE | 234 | 43 | 86 | 1 | 31 | 5

Figure S2. Get High-res Image Gene #1: '1q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'4p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S3. Gene #2: '4p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
4P GAIN CNV | 4 | 0.0 (0.0)
4P GAIN WILD-TYPE | 324 | 3.6 (6.2)

Figure S3. Get High-res Image Gene #2: '4p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'4q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S4. Gene #3: '4q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
4Q GAIN CNV | 4 | 0.0 (0.0)
4Q GAIN WILD-TYPE | 324 | 3.6 (6.2)

Figure S4. Get High-res Image Gene #3: '4q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'5p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.58e-05 (Chi-square test), Q value = 0.014

Table S5. Gene #4: '5p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
5P GAIN CNV | 2 | 4 | 5 | 1 | 0 | 0
5P GAIN WILD-TYPE | 235 | 40 | 89 | 1 | 36 | 5

Figure S5. Get High-res Image Gene #4: '5p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'5q gain' versus 'DISTANT.METASTASIS'

P value = 0.000218 (Fisher's exact test), Q value = 0.12

Table S6. Gene #5: '5q gain' versus Clinical Feature #7: 'DISTANT.METASTASIS'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 235 | 8 | 177
5Q GAIN CNV | 0 | 0 | 11
5Q GAIN WILD-TYPE | 235 | 8 | 166

Figure S6. Get High-res Image Gene #5: '5q gain' versus Clinical Feature #7: 'DISTANT.METASTASIS'

'5q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.04e-21 (t-test), Q value = 6e-19

Table S7. Gene #5: '5q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
5Q GAIN CNV | 8 | 0.0 (0.0)
5Q GAIN WILD-TYPE | 320 | 3.6 (6.3)

Figure S7. Get High-res Image Gene #5: '5q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'5q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.68e-05 (Chi-square test), Q value = 0.0092

Table S8. Gene #5: '5q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
5Q GAIN CNV | 2 | 4 | 4 | 1 | 0 | 0
5Q GAIN WILD-TYPE | 235 | 40 | 90 | 1 | 36 | 5

Figure S8. Get High-res Image Gene #5: '5q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'7p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.01e-21 (t-test), Q value = 5.9e-19

Table S9. Gene #6: '7p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
7P GAIN CNV | 9 | 0.0 (0.0)
7P GAIN WILD-TYPE | 319 | 3.6 (6.3)

Figure S9. Get High-res Image Gene #6: '7p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'7p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.05e-05 (Chi-square test), Q value = 0.0058

Table S10. Gene #6: '7p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
7P GAIN CNV | 3 | 5 | 3 | 1 | 0 | 0
7P GAIN WILD-TYPE | 234 | 39 | 91 | 1 | 36 | 5

Figure S10. Get High-res Image Gene #6: '7p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'7q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.01e-21 (t-test), Q value = 5.9e-19

Table S11. Gene #7: '7q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
7Q GAIN CNV | 9 | 0.0 (0.0)
7Q GAIN WILD-TYPE | 319 | 3.6 (6.3)

Figure S11. Get High-res Image Gene #7: '7q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'7q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.51e-05 (Chi-square test), Q value = 0.051

Table S12. Gene #7: '7q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
7Q GAIN CNV | 4 | 5 | 4 | 1 | 0 | 0
7Q GAIN WILD-TYPE | 233 | 39 | 90 | 1 | 36 | 5

Figure S12. Get High-res Image Gene #7: '7q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'12p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.06e-21 (t-test), Q value = 6.1e-19

Table S13. Gene #10: '12p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
12P GAIN CNV | 7 | 0.0 (0.0)
12P GAIN WILD-TYPE | 321 | 3.6 (6.2)

Figure S13. Get High-res Image Gene #10: '12p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'12q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.06e-21 (t-test), Q value = 6.1e-19

Table S14. Gene #11: '12q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
12Q GAIN CNV | 7 | 0.0 (0.0)
12Q GAIN WILD-TYPE | 321 | 3.6 (6.2)

Figure S14. Get High-res Image Gene #11: '12q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'13q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.16e-21 (t-test), Q value = 6.5e-19

Table S15. Gene #12: '13q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
13Q GAIN CNV | 3 | 0.0 (0.0)
13Q GAIN WILD-TYPE | 325 | 3.6 (6.2)

Figure S15. Get High-res Image Gene #12: '13q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'14q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.11e-21 (t-test), Q value = 6.3e-19

Table S16. Gene #13: '14q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
14Q GAIN CNV | 5 | 0.0 (0.0)
14Q GAIN WILD-TYPE | 323 | 3.6 (6.2)

Figure S16. Get High-res Image Gene #13: '14q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'16p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.11e-21 (t-test), Q value = 6.3e-19

Table S17. Gene #14: '16p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
16P GAIN CNV | 5 | 0.0 (0.0)
16P GAIN WILD-TYPE | 323 | 3.6 (6.2)

Figure S17. Get High-res Image Gene #14: '16p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'16p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.53e-05 (Chi-square test), Q value = 0.019

Table S18. Gene #14: '16p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
16P GAIN CNV | 3 | 3 | 2 | 1 | 0 | 0
16P GAIN WILD-TYPE | 234 | 41 | 92 | 1 | 36 | 5

Figure S18. Get High-res Image Gene #14: '16p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'16q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S19. Gene #15: '16q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
16Q GAIN CNV | 4 | 0.0 (0.0)
16Q GAIN WILD-TYPE | 324 | 3.6 (6.2)

Figure S19. Get High-res Image Gene #15: '16q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'16q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.12e-07 (Chi-square test), Q value = 0.00028

Table S20. Gene #15: '16q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
16Q GAIN CNV | 2 | 3 | 1 | 1 | 0 | 0
16Q GAIN WILD-TYPE | 235 | 41 | 93 | 1 | 36 | 5

Figure S20. Get High-res Image Gene #15: '16q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'17p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000126 (t-test), Q value = 0.068

Table S21. Gene #16: '17p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
17P GAIN CNV | 8 | 0.5 (1.4)
17P GAIN WILD-TYPE | 320 | 3.6 (6.3)

Figure S21. Get High-res Image Gene #16: '17p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'17q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.57e-05 (t-test), Q value = 0.0086

Table S22. Gene #17: '17q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
17Q GAIN CNV | 9 | 0.4 (1.3)
17Q GAIN WILD-TYPE | 319 | 3.6 (6.3)

Figure S22. Get High-res Image Gene #17: '17q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'19p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S23. Gene #20: '19p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
19P GAIN CNV | 4 | 0.0 (0.0)
19P GAIN WILD-TYPE | 324 | 3.6 (6.2)

Figure S23. Get High-res Image Gene #20: '19p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'19q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.11e-21 (t-test), Q value = 6.3e-19

Table S24. Gene #21: '19q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
19Q GAIN CNV | 5 | 0.0 (0.0)
19Q GAIN WILD-TYPE | 323 | 3.6 (6.2)

Figure S24. Get High-res Image Gene #21: '19q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'20p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S25. Gene #22: '20p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
20P GAIN CNV | 4 | 0.0 (0.0)
20P GAIN WILD-TYPE | 324 | 3.6 (6.2)

Figure S25. Get High-res Image Gene #22: '20p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.98e-07 (Chi-square test), Q value = 0.00017

Table S26. Gene #22: '20p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
20P GAIN CNV | 1 | 3 | 2 | 1 | 0 | 0
20P GAIN WILD-TYPE | 236 | 41 | 92 | 1 | 36 | 5

Figure S26. Get High-res Image Gene #22: '20p gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'20q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S27. Gene #23: '20q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
20Q GAIN CNV | 4 | 0.0 (0.0)
20Q GAIN WILD-TYPE | 324 | 3.6 (6.2)

Figure S27. Get High-res Image Gene #23: '20q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'20q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.98e-07 (Chi-square test), Q value = 0.00017

Table S28. Gene #23: '20q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
20Q GAIN CNV | 1 | 3 | 2 | 1 | 0 | 0
20Q GAIN WILD-TYPE | 236 | 41 | 92 | 1 | 36 | 5

Figure S28. Get High-res Image Gene #23: '20q gain' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'2p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.06e-21 (t-test), Q value = 6.1e-19

Table S29. Gene #25: '2p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
2P LOSS CNV | 7 | 0.0 (0.0)
2P LOSS WILD-TYPE | 321 | 3.6 (6.2)

Figure S29. Get High-res Image Gene #25: '2p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'2q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.08e-21 (t-test), Q value = 6.2e-19

Table S30. Gene #26: '2q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
2Q LOSS CNV | 6 | 0.0 (0.0)
2Q LOSS WILD-TYPE | 322 | 3.6 (6.2)

Figure S30. Get High-res Image Gene #26: '2q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'3q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.16e-21 (t-test), Q value = 6.5e-19

Table S31. Gene #27: '3q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
3Q LOSS CNV | 3 | 0.0 (0.0)
3Q LOSS WILD-TYPE | 325 | 3.6 (6.2)

Figure S31. Get High-res Image Gene #27: '3q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'6q loss' versus 'Time to Death'

P value = 3.21e-05 (logrank test), Q value = 0.017

Table S32. Gene #28: '6q loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 416 | 10 | 0.0 - 147.4 (9.3)
6Q LOSS CNV | 3 | 1 | 1.6 - 33.5 (21.4)
6Q LOSS WILD-TYPE | 413 | 9 | 0.0 - 147.4 (9.3)

Figure S32. Get High-res Image Gene #28: '6q loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.27e-07 (Chi-square test), Q value = 7.1e-05

Table S33. Gene #29: '9p loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
9P LOSS CNV | 1 | 4 | 2 | 1 | 0 | 0
9P LOSS WILD-TYPE | 236 | 40 | 92 | 1 | 36 | 5

Figure S33. Get High-res Image Gene #29: '9p loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.18e-17 (Chi-square test), Q value = 3.4e-14

Table S34. Gene #30: '9q loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
9Q LOSS CNV | 1 | 5 | 2 | 2 | 2 | 0
9Q LOSS WILD-TYPE | 236 | 39 | 92 | 0 | 34 | 5

Figure S34. Get High-res Image Gene #30: '9q loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'10p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.13e-21 (t-test), Q value = 6.4e-19

Table S35. Gene #31: '10p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
10P LOSS CNV | 4 | 0.0 (0.0)
10P LOSS WILD-TYPE | 324 | 3.6 (6.2)

Figure S35. Get High-res Image Gene #31: '10p loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'10q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.16e-21 (t-test), Q value = 6.5e-19

Table S36. Gene #32: '10q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
10Q LOSS CNV | 3 | 0.0 (0.0)
10Q LOSS WILD-TYPE | 325 | 3.6 (6.2)

Figure S36. Get High-res Image Gene #32: '10q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'11p loss' versus 'AGE'

P value = 0.000427 (t-test), Q value = 0.23

Table S37. Gene #33: '11p loss' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 46.6 (15.6)
11P LOSS CNV | 7 | 68.1 (8.7)
11P LOSS WILD-TYPE | 414 | 46.2 (15.4)

Figure S37. Get High-res Image Gene #33: '11p loss' versus Clinical Feature #2: 'AGE'

'11p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.36e-06 (Chi-square test), Q value = 0.00075

Table S38. Gene #33: '11p loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
11P LOSS CNV | 1 | 1 | 4 | 1 | 0 | 0
11P LOSS WILD-TYPE | 236 | 43 | 90 | 1 | 36 | 5

Figure S38. Get High-res Image Gene #33: '11p loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'11q loss' versus 'AGE'

P value = 7.15e-05 (t-test), Q value = 0.039

Table S39. Gene #34: '11q loss' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 46.6 (15.6)
11Q LOSS CNV | 9 | 67.0 (8.9)
11Q LOSS WILD-TYPE | 412 | 46.1 (15.4)

Figure S39. Get High-res Image Gene #34: '11q loss' versus Clinical Feature #2: 'AGE'

'11q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.97e-05 (Chi-square test), Q value = 0.016

Table S40. Gene #34: '11q loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 237 | 44 | 94 | 2 | 36 | 5
11Q LOSS CNV | 1 | 2 | 4 | 1 | 1 | 0
11Q LOSS WILD-TYPE | 236 | 42 | 90 | 1 | 35 | 5

Figure S40. Get High-res Image Gene #34: '11q loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'13q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.04e-21 (t-test), Q value = 6e-19

Table S41. Gene #35: '13q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 328 | 3.5 (6.2)
13Q LOSS CNV | 8 | 0.0 (0.0)
13Q LOSS WILD-TYPE | 320 | 3.6 (6.3)

Figure S41. Get High-res Image Gene #35: '13q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'19p loss' versus 'Time to Death'

P value = 5.48e-06 (logrank test), Q value = 0.003

Table S42. Gene #40: '19p loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 416 | 10 | 0.0 - 147.4 (9.3)
19P LOSS CNV | 3 | 1 | 0.9 - 33.5 (15.8)
19P LOSS WILD-TYPE | 413 | 9 | 0.0 - 147.4 (9.3)

Figure S42. Get High-res Image Gene #40: '19p loss' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

- Mutation data file = broad_values_by_arm.mutsig.cluster.txt

- Clinical data file = THCA-TP.clin.merged.picked.txt

- Number of patients = 421

- Number of significantly arm-level cnvs = 42

- Number of selected clinical features = 15

- 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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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)
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