Correlation between copy number variations of arm-level result and selected clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C14B2ZSD
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C14B2ZSD
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 57 arm-level events and 15 clinical features across 482 patients, 56 significant findings detected with Q value < 0.25.

- 1q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

- 3p gain cnv correlated to '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 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

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

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

- 8q gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.

- 9q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 11p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 11q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 12p gain cnv correlated to 'PATHOLOGY.M.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

- 12q gain cnv correlated to 'PATHOLOGY.M.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

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

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

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

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

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

- 18p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 18q 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 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

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

- 21q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- xq gain cnv correlated to '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'.

- 8p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 8q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

- 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 'NEOPLASM.DISEASESTAGE'.

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

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

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

- xq loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 57 arm-level events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 56 significant findings detected.

|  | Clinical Features | Time to Death | AGE | NEOPLASM DISEASESTAGE | PATHOLOGY T STAGE | PATHOLOGY N STAGE | PATHOLOGY M STAGE | GENDER | HISTOLOGICAL TYPE | RADIATIONS RADIATION REGIMENINDICATION | RADIATIONEXPOSURE | EXTRATHYROIDAL EXTENSION | COMPLETENESS OF RESECTION | NUMBER OF LYMPH NODES | MULTIFOCALITY | TUMOR SIZE
| nCNV (%) | nWild-Type | logrank 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | Fisher's exact test | t-test
5q gain | 15 (3%) | 467 | 0.0205 (1.00) | 0.0105 (1.00) | 5.04e-05 (0.0405) | 0.66 (1.00) | 0.0108 (1.00) | 1.13e-05 (0.00912) | 0.557 (1.00) | 0.0277 (1.00) | 0.362 (1.00) | 1 (1.00) | 0.0354 (1.00) | 0.539 (1.00) | 1.41e-25 (1.19e-22) | 0.608 (1.00) | 0.152 (1.00)
20p gain | 12 (2%) | 470 | 0.34 (1.00) | 0.094 (1.00) | 5.17e-05 (0.0415) | 0.57 (1.00) | 0.0678 (1.00) | 0.000161 (0.128) | 0.528 (1.00) | 0.00457 (1.00) | 1 (1.00) | 1 (1.00) | 0.0245 (1.00) | 0.854 (1.00) | 1.51e-25 (1.27e-22) | 1 (1.00) | 0.133 (1.00)
20q gain | 12 (2%) | 470 | 0.34 (1.00) | 0.094 (1.00) | 5.17e-05 (0.0415) | 0.57 (1.00) | 0.0678 (1.00) | 0.000161 (0.128) | 0.528 (1.00) | 0.00457 (1.00) | 1 (1.00) | 1 (1.00) | 0.0245 (1.00) | 0.854 (1.00) | 1.51e-25 (1.27e-22) | 1 (1.00) | 0.133 (1.00)
1q gain | 23 (5%) | 459 | 0.165 (1.00) | 0.00069 (0.542) | 7.73e-06 (0.00626) | 0.000214 (0.169) | 0.002 (1.00) | 0.692 (1.00) | 0.343 (1.00) | 0.0261 (1.00) | 0.501 (1.00) | 0.586 (1.00) | 0.000325 (0.257) | 0.0237 (1.00) | 0.549 (1.00) | 0.0545 (1.00) | 0.0539 (1.00)
7p gain | 16 (3%) | 466 | 0.362 (1.00) | 0.0441 (1.00) | 3.58e-05 (0.0289) | 0.851 (1.00) | 0.0057 (1.00) | 0.00153 (1.00) | 1 (1.00) | 0.0112 (1.00) | 1 (1.00) | 1 (1.00) | 0.0132 (1.00) | 0.539 (1.00) | 1.38e-25 (1.16e-22) | 0.803 (1.00) | 0.65 (1.00)
7q gain | 18 (4%) | 464 | 0.376 (1.00) | 0.0306 (1.00) | 0.000194 (0.154) | 0.942 (1.00) | 0.0057 (1.00) | 0.00289 (1.00) | 0.791 (1.00) | 0.00773 (1.00) | 1 (1.00) | 1 (1.00) | 0.0253 (1.00) | 0.251 (1.00) | 1.38e-25 (1.16e-22) | 0.812 (1.00) | 0.6 (1.00)
12p gain | 13 (3%) | 469 | 0.517 (1.00) | 0.16 (1.00) | 0.0308 (1.00) | 1 (1.00) | 0.00359 (1.00) | 7.1e-05 (0.0568) | 1 (1.00) | 0.00971 (1.00) | 1 (1.00) | 1 (1.00) | 0.268 (1.00) | 0.304 (1.00) | 1.44e-25 (1.22e-22) | 0.587 (1.00) | 0.919 (1.00)
12q gain | 14 (3%) | 468 | 0.517 (1.00) | 0.136 (1.00) | 0.0535 (1.00) | 0.969 (1.00) | 0.00359 (1.00) | 2.71e-05 (0.0219) | 1 (1.00) | 0.00394 (1.00) | 1 (1.00) | 1 (1.00) | 0.244 (1.00) | 0.261 (1.00) | 1.44e-25 (1.22e-22) | 0.792 (1.00) | 0.919 (1.00)
16q gain | 12 (2%) | 470 | 0.216 (1.00) | 0.106 (1.00) | 6.71e-05 (0.0537) | 0.757 (1.00) | 0.0678 (1.00) | 0.00297 (1.00) | 1 (1.00) | 0.0233 (1.00) | 1 (1.00) | 1 (1.00) | 0.0245 (1.00) | 0.359 (1.00) | 1.51e-25 (1.27e-22) | 1 (1.00) | 0.681 (1.00)
17p gain | 16 (3%) | 466 | 0.418 (1.00) | 0.103 (1.00) | 3.58e-05 (0.0289) | 0.851 (1.00) | 0.036 (1.00) | 0.00789 (1.00) | 1 (1.00) | 0.0448 (1.00) | 1 (1.00) | 1 (1.00) | 0.767 (1.00) | 0.321 (1.00) | 1.42e-06 (0.00115) | 1 (1.00) | 0.41 (1.00)
17q gain | 17 (4%) | 465 | 0.418 (1.00) | 0.168 (1.00) | 9.64e-05 (0.0768) | 0.864 (1.00) | 0.0206 (1.00) | 0.00594 (1.00) | 1 (1.00) | 0.0711 (1.00) | 1 (1.00) | 1 (1.00) | 0.695 (1.00) | 0.352 (1.00) | 1.97e-07 (0.000161) | 0.806 (1.00) | 0.587 (1.00)
11q loss | 9 (2%) | 473 | 0.00286 (1.00) | 9.41e-05 (0.0751) | 5.89e-06 (0.00478) | 0.207 (1.00) | 0.503 (1.00) | 0.121 (1.00) | 0.00179 (1.00) | 1 (1.00) | 0.235 (1.00) | 1 (1.00) | 0.797 (1.00) | 0.507 (1.00) | 0.251 (1.00) | 1 (1.00) | 0.0135 (1.00)
xq loss | 3 (1%) | 479 | 0.752 (1.00) | 0.181 (1.00) | 9.08e-05 (0.0725) | 0.223 (1.00) | 0.248 (1.00) | 0.135 (1.00) | 0.174 (1.00) | 0.647 (1.00) | 1 (1.00) | 1 (1.00) | 0.609 (1.00) | 1 (1.00) | 1.69e-25 (1.39e-22) | 1 (1.00) |
3p gain | 3 (1%) | 479 | 0.0123 (1.00) | 0.0169 (1.00) | 4.31e-05 (0.0347) | 0.12 (1.00) | 1 (1.00) | 0.0114 (1.00) | 0.569 (1.00) | 0.234 (1.00) | 1 (1.00) | 1 (1.00) | 0.609 (1.00) | 0.0229 (1.00) |  | 1 (1.00) | 0.628 (1.00)
4p gain | 5 (1%) | 477 | 0.0265 (1.00) | 0.0542 (1.00) | 0.36 (1.00) | 0.704 (1.00) | 0.0611 (1.00) | 0.0295 (1.00) | 1 (1.00) | 0.187 (1.00) | 0.138 (1.00) | 1 (1.00) | 1 (1.00) | 0.385 (1.00) | 1.62e-25 (1.35e-22) | 0.186 (1.00) | 0.304 (1.00)
4q gain | 5 (1%) | 477 | 0.0265 (1.00) | 0.0542 (1.00) | 0.36 (1.00) | 0.704 (1.00) | 0.0611 (1.00) | 0.0295 (1.00) | 1 (1.00) | 0.187 (1.00) | 0.138 (1.00) | 1 (1.00) | 1 (1.00) | 0.385 (1.00) | 1.62e-25 (1.35e-22) | 0.186 (1.00) | 0.304 (1.00)
5p gain | 18 (4%) | 464 | 0.0822 (1.00) | 0.000966 (0.757) | 0.00021 (0.166) | 0.509 (1.00) | 0.172 (1.00) | 0.000431 (0.34) | 0.586 (1.00) | 0.0934 (1.00) | 0.417 (1.00) | 1 (1.00) | 0.0342 (1.00) | 0.558 (1.00) | 0.012 (1.00) | 1 (1.00) | 0.106 (1.00)
8q gain | 7 (1%) | 475 | 0.109 (1.00) | 0.37 (1.00) | 2.38e-06 (0.00193) | 0.41 (1.00) | 1 (1.00) | 0.0966 (1.00) | 0.681 (1.00) | 0.823 (1.00) | 1 (1.00) | 1 (1.00) | 0.00834 (1.00) | 0.38 (1.00) | 0.00203 (1.00) | 0.13 (1.00) | 0.281 (1.00)
9q gain | 4 (1%) | 478 | 0.697 (1.00) | 0.0155 (1.00) | 0.0694 (1.00) | 0.629 (1.00) | 0.623 (1.00) | 1 (1.00) | 0.288 (1.00) | 0.465 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.000162 (0.129) | 0.34 (1.00) | 0.00993 (1.00)
11p gain | 6 (1%) | 476 | 0.558 (1.00) | 0.777 (1.00) | 0.938 (1.00) | 0.762 (1.00) | 0.123 (1.00) | 0.19 (1.00) | 0.194 (1.00) | 0.257 (1.00) | 1 (1.00) | 1 (1.00) | 0.354 (1.00) | 0.455 (1.00) | 1.66e-25 (1.37e-22) | 0.224 (1.00) | 0.563 (1.00)
11q gain | 5 (1%) | 477 | 0.561 (1.00) | 0.808 (1.00) | 0.962 (1.00) | 0.892 (1.00) | 0.248 (1.00) | 0.249 (1.00) | 0.612 (1.00) | 0.571 (1.00) | 1 (1.00) | 1 (1.00) | 0.443 (1.00) | 0.385 (1.00) | 1.69e-25 (1.39e-22) | 0.0648 (1.00) | 0.829 (1.00)
13q gain | 5 (1%) | 477 | 0.73 (1.00) | 0.166 (1.00) | 0.0178 (1.00) | 0.704 (1.00) | 0.123 (1.00) | 0.249 (1.00) | 1 (1.00) | 0.187 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1.66e-25 (1.37e-22) | 0.666 (1.00) | 0.655 (1.00)
16p gain | 14 (3%) | 468 | 0.224 (1.00) | 0.158 (1.00) | 0.000481 (0.379) | 0.819 (1.00) | 0.0371 (1.00) | 0.00535 (1.00) | 1 (1.00) | 0.0825 (1.00) | 1 (1.00) | 1 (1.00) | 0.0366 (1.00) | 0.161 (1.00) | 1.48e-25 (1.24e-22) | 1 (1.00) | 0.69 (1.00)
18p gain | 6 (1%) | 476 | 0.616 (1.00) | 0.743 (1.00) | 0.938 (1.00) | 0.762 (1.00) | 0.0611 (1.00) | 0.476 (1.00) | 0.659 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.385 (1.00) | 1.66e-25 (1.37e-22) | 0.691 (1.00) | 0.61 (1.00)
18q gain | 6 (1%) | 476 | 0.616 (1.00) | 0.743 (1.00) | 0.938 (1.00) | 0.762 (1.00) | 0.0611 (1.00) | 0.476 (1.00) | 0.659 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.385 (1.00) | 1.66e-25 (1.37e-22) | 0.691 (1.00) | 0.61 (1.00)
19p gain | 8 (2%) | 474 | 0.733 (1.00) | 0.0784 (1.00) | 0.871 (1.00) | 0.613 (1.00) | 0.0302 (1.00) | 0.00251 (1.00) | 0.218 (1.00) | 0.00911 (1.00) | 1 (1.00) | 1 (1.00) | 0.594 (1.00) | 0.448 (1.00) | 1.55e-25 (1.29e-22) | 0.152 (1.00) | 0.219 (1.00)
19q gain | 10 (2%) | 472 | 0.0339 (1.00) | 0.0278 (1.00) | 0.753 (1.00) | 0.329 (1.00) | 0.0149 (1.00) | 0.00111 (0.867) | 0.139 (1.00) | 0.00576 (1.00) | 0.257 (1.00) | 1 (1.00) | 0.516 (1.00) | 0.681 (1.00) | 1.51e-25 (1.27e-22) | 0.524 (1.00) | 0.145 (1.00)
21q gain | 5 (1%) | 477 | 0.616 (1.00) | 0.0433 (1.00) | 0.765 (1.00) | 0.561 (1.00) | 0.248 (1.00) | 0.689 (1.00) | 0.612 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.639 (1.00) | 0.31 (1.00) | 1.69e-25 (1.39e-22) | 0.0648 (1.00) | 0.314 (1.00)
xq gain | 8 (2%) | 474 | 0.0775 (1.00) | 0.0531 (1.00) | 7.36e-07 (0.000599) | 0.557 (1.00) | 0.449 (1.00) | 0.00251 (1.00) | 0.688 (1.00) | 0.255 (1.00) | 1 (1.00) | 0.281 (1.00) | 0.0205 (1.00) | 0.154 (1.00) | 0.805 (1.00) | 0.152 (1.00) | 0.472 (1.00)
2p loss | 10 (2%) | 472 | 0.719 (1.00) | 0.281 (1.00) | 0.00344 (1.00) | 0.697 (1.00) | 0.00732 (1.00) | 0.0136 (1.00) | 0.73 (1.00) | 0.00576 (1.00) | 1 (1.00) | 1 (1.00) | 0.142 (1.00) | 0.551 (1.00) | 1.48e-25 (1.24e-22) | 1 (1.00) | 0.696 (1.00)
2q loss | 10 (2%) | 472 | 0.575 (1.00) | 0.256 (1.00) | 0.00344 (1.00) | 0.823 (1.00) | 0.0149 (1.00) | 0.0136 (1.00) | 0.73 (1.00) | 0.00576 (1.00) | 1 (1.00) | 1 (1.00) | 0.142 (1.00) | 0.551 (1.00) | 1.51e-25 (1.27e-22) | 1 (1.00) | 0.48 (1.00)
3q loss | 4 (1%) | 478 | 0.597 (1.00) | 0.645 (1.00) | 0.204 (1.00) | 0.629 (1.00) | 0.248 (1.00) | 0.107 (1.00) | 1 (1.00) | 0.465 (1.00) | 1 (1.00) | 1 (1.00) | 0.639 (1.00) | 1 (1.00) | 1.69e-25 (1.39e-22) | 1 (1.00) | 0.101 (1.00)
8p loss | 4 (1%) | 478 | 0.871 (1.00) | 0.983 (1.00) | 0.191 (1.00) | 1 (1.00) | 0.248 (1.00) | 0.374 (1.00) | 0.0592 (1.00) | 0.465 (1.00) | 1 (1.00) | 1 (1.00) | 0.639 (1.00) | 1 (1.00) | 1.66e-25 (1.37e-22) | 1 (1.00) | 0.89 (1.00)
8q loss | 4 (1%) | 478 | 0.871 (1.00) | 0.983 (1.00) | 0.191 (1.00) | 1 (1.00) | 0.248 (1.00) | 0.374 (1.00) | 0.0592 (1.00) | 0.465 (1.00) | 1 (1.00) | 1 (1.00) | 0.639 (1.00) | 1 (1.00) | 1.66e-25 (1.37e-22) | 1 (1.00) | 0.89 (1.00)
9q loss | 22 (5%) | 460 | 0.0297 (1.00) | 0.0219 (1.00) | 1.38e-09 (1.13e-06) | 0.19 (1.00) | 0.64 (1.00) | 0.0152 (1.00) | 0.323 (1.00) | 0.712 (1.00) | 0.485 (1.00) | 0.586 (1.00) | 0.0674 (1.00) | 0.568 (1.00) | 0.235 (1.00) | 0.666 (1.00) | 0.112 (1.00)
10p loss | 7 (1%) | 475 | 0.587 (1.00) | 0.332 (1.00) | 0.106 (1.00) | 0.261 (1.00) | 0.0302 (1.00) | 0.0966 (1.00) | 0.389 (1.00) | 0.396 (1.00) | 1 (1.00) | 1 (1.00) | 0.753 (1.00) | 1 (1.00) | 1.62e-25 (1.35e-22) | 0.709 (1.00) | 0.051 (1.00)
10q loss | 6 (1%) | 476 | 0.648 (1.00) | 0.337 (1.00) | 0.46 (1.00) | 0.329 (1.00) | 0.0611 (1.00) | 0.19 (1.00) | 0.194 (1.00) | 0.786 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1.66e-25 (1.37e-22) | 0.422 (1.00) | 0.0462 (1.00)
11p loss | 7 (1%) | 475 | 0.00137 (1.00) | 0.000519 (0.408) | 1.61e-07 (0.000131) | 0.229 (1.00) | 0.449 (1.00) | 0.0966 (1.00) | 0.0162 (1.00) | 0.823 (1.00) | 0.188 (1.00) | 1 (1.00) | 0.544 (1.00) | 0.52 (1.00) | 0.0801 (1.00) | 0.709 (1.00) | 0.0355 (1.00)
13q loss | 14 (3%) | 468 | 0.383 (1.00) | 0.0466 (1.00) | 0.607 (1.00) | 0.592 (1.00) | 0.0108 (1.00) | 0.366 (1.00) | 0.538 (1.00) | 0.471 (1.00) | 0.342 (1.00) | 0.000726 (0.57) | 0.627 (1.00) | 0.671 (1.00) | 9.97e-15 (8.16e-12) | 0.792 (1.00) | 0.153 (1.00)
17q loss | 4 (1%) | 478 | 0.805 (1.00) | 0.369 (1.00) | 0.795 (1.00) | 0.629 (1.00) | 0.123 (1.00) | 0.374 (1.00) | 1 (1.00) | 0.465 (1.00) | 0.112 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1.69e-25 (1.39e-22) | 1 (1.00) | 0.485 (1.00)
1p gain | 3 (1%) | 479 | 0.919 (1.00) | 0.304 (1.00) | 0.0193 (1.00) | 1 (1.00) | 0.623 (1.00) | 0.135 (1.00) | 1 (1.00) | 0.344 (1.00) | 1 (1.00) | 0.0787 (1.00) | 1 (1.00) | 0.232 (1.00) | 0.15 (1.00) | 1 (1.00) |
8p gain | 6 (1%) | 476 | 0.627 (1.00) | 0.634 (1.00) | 0.938 (1.00) | 0.906 (1.00) | 0.623 (1.00) | 0.19 (1.00) | 1 (1.00) | 0.786 (1.00) | 1 (1.00) | 1 (1.00) | 0.354 (1.00) | 0.455 (1.00) | 0.00203 (1.00) | 0.224 (1.00) | 0.425 (1.00)
9p gain | 3 (1%) | 479 | 0.702 (1.00) | 0.0789 (1.00) | 0.0443 (1.00) | 0.806 (1.00) | 0.248 (1.00) | 0.608 (1.00) | 1 (1.00) | 0.234 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) |  | 0.598 (1.00) | 0.0613 (1.00)
14q gain | 11 (2%) | 471 | 0.535 (1.00) | 0.029 (1.00) | 0.00241 (1.00) | 0.38 (1.00) | 0.0678 (1.00) | 0.0348 (1.00) | 0.302 (1.00) | 0.0638 (1.00) | 1 (1.00) | 1 (1.00) | 0.825 (1.00) | 0.49 (1.00) | 0.0173 (1.00) | 0.123 (1.00) | 0.312 (1.00)
1p loss | 4 (1%) | 478 | 0.601 (1.00) | 0.604 (1.00) | 0.204 (1.00) | 0.629 (1.00) | 0.248 (1.00) | 0.374 (1.00) | 0.578 (1.00) | 0.465 (1.00) | 1 (1.00) | 1 (1.00) | 0.639 (1.00) | 1 (1.00) |  | 0.628 (1.00) | 0.177 (1.00)
1q loss | 3 (1%) | 479 | 0.604 (1.00) | 0.871 (1.00) | 0.805 (1.00) | 0.806 (1.00) | 0.499 (1.00) | 0.135 (1.00) | 0.569 (1.00) | 0.234 (1.00) | 1 (1.00) | 1 (1.00) | 0.609 (1.00) | 1 (1.00) |  | 1 (1.00) | 0.177 (1.00)
3p loss | 3 (1%) | 479 | 0.661 (1.00) | 0.67 (1.00) | 0.805 (1.00) | 0.806 (1.00) | 0.499 (1.00) | 0.135 (1.00) | 1 (1.00) | 0.647 (1.00) | 1 (1.00) | 1 (1.00) | 0.609 (1.00) | 1 (1.00) |  | 0.598 (1.00) | 0.0828 (1.00)
6p loss | 4 (1%) | 478 | 0.633 (1.00) | 0.42 (1.00) | 0.805 (1.00) | 1 (1.00) | 1 (1.00) | 0.107 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.639 (1.00) | 0.543 (1.00) |  | 1 (1.00) | 0.0252 (1.00)
6q loss | 7 (1%) | 475 | 0.00836 (1.00) | 0.123 (1.00) | 0.37 (1.00) | 0.79 (1.00) | 0.372 (1.00) | 0.00974 (1.00) | 0.389 (1.00) | 0.823 (1.00) | 0.188 (1.00) | 0.219 (1.00) | 0.384 (1.00) | 0.748 (1.00) | 0.00203 (1.00) | 0.459 (1.00) | 0.0166 (1.00)
9p loss | 18 (4%) | 464 | 0.419 (1.00) | 0.203 (1.00) | 0.00279 (1.00) | 0.342 (1.00) | 1 (1.00) | 0.0259 (1.00) | 0.275 (1.00) | 0.719 (1.00) | 1 (1.00) | 1 (1.00) | 0.695 (1.00) | 0.65 (1.00) | 0.007 (1.00) | 0.633 (1.00) | 0.186 (1.00)
15q loss | 8 (2%) | 474 | 0.559 (1.00) | 0.707 (1.00) | 0.221 (1.00) | 0.724 (1.00) | 0.122 (1.00) | 0.0622 (1.00) | 0.688 (1.00) | 0.054 (1.00) | 1 (1.00) | 1 (1.00) | 0.594 (1.00) | 0.786 (1.00) | 0.386 (1.00) | 0.731 (1.00) | 0.0858 (1.00)
17p loss | 7 (1%) | 475 | 0.588 (1.00) | 0.682 (1.00) | 0.527 (1.00) | 0.14 (1.00) | 0.449 (1.00) | 0.343 (1.00) | 0.681 (1.00) | 0.155 (1.00) | 0.0152 (1.00) | 0.251 (1.00) | 0.246 (1.00) | 0.748 (1.00) | 0.929 (1.00) | 1 (1.00) | 0.0925 (1.00)
18p loss | 4 (1%) | 478 | 0.758 (1.00) | 0.544 (1.00) | 0.191 (1.00) | 0.345 (1.00) | 1 (1.00) | 0.374 (1.00) | 1 (1.00) | 0.465 (1.00) | 1 (1.00) | 1 (1.00) | 0.639 (1.00) | 1 (1.00) | 0.00203 (1.00) | 0.628 (1.00) | 0.233 (1.00)
18q loss | 4 (1%) | 478 | 0.758 (1.00) | 0.544 (1.00) | 0.191 (1.00) | 0.345 (1.00) | 1 (1.00) | 0.374 (1.00) | 1 (1.00) | 0.465 (1.00) | 1 (1.00) | 1 (1.00) | 0.639 (1.00) | 1 (1.00) | 0.00203 (1.00) | 0.628 (1.00) | 0.233 (1.00)
19p loss | 5 (1%) | 477 | 0.13 (1.00) | 0.52 (1.00) | 0.315 (1.00) | 1 (1.00) | 1 (1.00) | 0.689 (1.00) | 0.612 (1.00) | 1 (1.00) | 1 (1.00) | 0.0141 (1.00) | 1 (1.00) | 0.625 (1.00) |  | 0.38 (1.00) | 0.0195 (1.00)
21q loss | 8 (2%) | 474 | 0.847 (1.00) | 0.0972 (1.00) | 0.00902 (1.00) | 0.176 (1.00) | 0.724 (1.00) | 0.773 (1.00) | 0.443 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) | 0.215 (1.00) | 1 (1.00) | 0.98 (1.00) | 0.152 (1.00) | 0.671 (1.00)
22q loss | 84 (17%) | 398 | 0.492 (1.00) | 0.898 (1.00) | 0.696 (1.00) | 0.526 (1.00) | 0.315 (1.00) | 0.578 (1.00) | 0.497 (1.00) | 0.273 (1.00) | 0.481 (1.00) | 0.333 (1.00) | 0.306 (1.00) | 0.492 (1.00) | 0.306 (1.00) | 0.225 (1.00) | 0.861 (1.00)

'1q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.73e-06 (Chi-square test), Q value = 0.0063

Table S1. Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
1Q GAIN MUTATED | 6 | 0 | 9 | 1 | 7 | 0
1Q GAIN WILD-TYPE | 267 | 50 | 97 | 1 | 36 | 6

Figure S1. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'1q gain' versus 'PATHOLOGY.T.STAGE'

P value = 0.000214 (Fisher's exact test), Q value = 0.17

Table S2. Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 139 | 160 | 160 | 21
1Q GAIN MUTATED | 2 | 3 | 14 | 4
1Q GAIN WILD-TYPE | 137 | 157 | 146 | 17

Figure S2. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'3p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.31e-05 (Chi-square test), Q value = 0.035

Table S3. Gene #3: '3p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
3P GAIN MUTATED | 1 | 1 | 0 | 0 | 0 | 1
3P GAIN WILD-TYPE | 272 | 49 | 106 | 2 | 43 | 5

Figure S3. Get High-res Image Gene #3: '3p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.62e-25 (t-test), Q value = 1.3e-22

Table S4. Gene #4: '4p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
4P GAIN MUTATED | 5 | 0.0 (0.0)
4P GAIN WILD-TYPE | 378 | 3.6 (6.2)

Figure S4. Get High-res Image Gene #4: '4p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.62e-25 (t-test), Q value = 1.3e-22

Table S5. Gene #5: '4q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
4Q GAIN MUTATED | 5 | 0.0 (0.0)
4Q GAIN WILD-TYPE | 378 | 3.6 (6.2)

Figure S5. Get High-res Image Gene #5: '4q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'5p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00021 (Chi-square test), Q value = 0.17

Table S6. Gene #6: '5p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
5P GAIN MUTATED | 4 | 5 | 7 | 1 | 1 | 0
5P GAIN WILD-TYPE | 269 | 45 | 99 | 1 | 42 | 6

Figure S6. Get High-res Image Gene #6: '5p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'5q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.04e-05 (Chi-square test), Q value = 0.041

Table S7. Gene #7: '5q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
5Q GAIN MUTATED | 4 | 5 | 5 | 1 | 0 | 0
5Q GAIN WILD-TYPE | 269 | 45 | 101 | 1 | 43 | 6

Figure S7. Get High-res Image Gene #7: '5q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'5q gain' versus 'PATHOLOGY.M.STAGE'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0091

Table S8. Gene #7: '5q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 264 | 9 | 208
5Q GAIN MUTATED | 0 | 0 | 15
5Q GAIN WILD-TYPE | 264 | 9 | 193

Figure S8. Get High-res Image Gene #7: '5q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 1.41e-25 (t-test), Q value = 1.2e-22

Table S9. Gene #7: '5q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
5Q GAIN MUTATED | 11 | 0.0 (0.0)
5Q GAIN WILD-TYPE | 372 | 3.7 (6.3)

Figure S9. Get High-res Image Gene #7: '5q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'7p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.58e-05 (Chi-square test), Q value = 0.029

Table S10. Gene #8: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
7P GAIN MUTATED | 6 | 6 | 3 | 1 | 0 | 0
7P GAIN WILD-TYPE | 267 | 44 | 103 | 1 | 43 | 6

Figure S10. Get High-res Image Gene #8: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.38e-25 (t-test), Q value = 1.2e-22

Table S11. Gene #8: '7p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
7P GAIN MUTATED | 12 | 0.0 (0.0)
7P GAIN WILD-TYPE | 371 | 3.7 (6.3)

Figure S11. Get High-res Image Gene #8: '7p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'7q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000194 (Chi-square test), Q value = 0.15

Table S12. Gene #9: '7q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
7Q GAIN MUTATED | 7 | 6 | 4 | 1 | 0 | 0
7Q GAIN WILD-TYPE | 266 | 44 | 102 | 1 | 43 | 6

Figure S12. Get High-res Image Gene #9: '7q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.38e-25 (t-test), Q value = 1.2e-22

Table S13. Gene #9: '7q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
7Q GAIN MUTATED | 12 | 0.0 (0.0)
7Q GAIN WILD-TYPE | 371 | 3.7 (6.3)

Figure S13. Get High-res Image Gene #9: '7q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.38e-06 (Chi-square test), Q value = 0.0019

Table S14. Gene #11: '8q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
8Q GAIN MUTATED | 3 | 1 | 2 | 1 | 0 | 0
8Q GAIN WILD-TYPE | 270 | 49 | 104 | 1 | 43 | 6

Figure S14. Get High-res Image Gene #11: '8q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000162 (t-test), Q value = 0.13

Table S15. Gene #13: '9q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
9Q GAIN MUTATED | 3 | 0.3 (0.6)
9Q GAIN WILD-TYPE | 380 | 3.6 (6.2)

Figure S15. Get High-res Image Gene #13: '9q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
11P GAIN MUTATED | 4 | 0.0 (0.0)
11P GAIN WILD-TYPE | 379 | 3.6 (6.2)

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

'11q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.69e-25 (t-test), Q value = 1.4e-22

Table S17. Gene #15: '11q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
11Q GAIN MUTATED | 3 | 0.0 (0.0)
11Q GAIN WILD-TYPE | 380 | 3.6 (6.2)

Figure S17. Get High-res Image Gene #15: '11q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'12p gain' versus 'PATHOLOGY.M.STAGE'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.057

Table S18. Gene #16: '12p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 264 | 9 | 208
12P GAIN MUTATED | 0 | 0 | 13
12P GAIN WILD-TYPE | 264 | 9 | 195

Figure S18. Get High-res Image Gene #16: '12p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 1.44e-25 (t-test), Q value = 1.2e-22

Table S19. Gene #16: '12p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
12P GAIN MUTATED | 10 | 0.0 (0.0)
12P GAIN WILD-TYPE | 373 | 3.7 (6.3)

Figure S19. Get High-res Image Gene #16: '12p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'12q gain' versus 'PATHOLOGY.M.STAGE'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.022

Table S20. Gene #17: '12q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 264 | 9 | 208
12Q GAIN MUTATED | 0 | 0 | 14
12Q GAIN WILD-TYPE | 264 | 9 | 194

Figure S20. Get High-res Image Gene #17: '12q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 1.44e-25 (t-test), Q value = 1.2e-22

Table S21. Gene #17: '12q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
12Q GAIN MUTATED | 10 | 0.0 (0.0)
12Q GAIN WILD-TYPE | 373 | 3.7 (6.3)

Figure S21. Get High-res Image Gene #17: '12q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S22. Gene #18: '13q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
13Q GAIN MUTATED | 4 | 0.0 (0.0)
13Q GAIN WILD-TYPE | 379 | 3.6 (6.2)

Figure S22. Get High-res Image Gene #18: '13q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.48e-25 (t-test), Q value = 1.2e-22

Table S23. Gene #20: '16p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
16P GAIN MUTATED | 9 | 0.0 (0.0)
16P GAIN WILD-TYPE | 374 | 3.6 (6.3)

Figure S23. Get High-res Image Gene #20: '16p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'16q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.71e-05 (Chi-square test), Q value = 0.054

Table S24. Gene #21: '16q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
16Q GAIN MUTATED | 5 | 4 | 2 | 1 | 0 | 0
16Q GAIN WILD-TYPE | 268 | 46 | 104 | 1 | 43 | 6

Figure S24. Get High-res Image Gene #21: '16q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.51e-25 (t-test), Q value = 1.3e-22

Table S25. Gene #21: '16q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
16Q GAIN MUTATED | 8 | 0.0 (0.0)
16Q GAIN WILD-TYPE | 375 | 3.6 (6.3)

Figure S25. Get High-res Image Gene #21: '16q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'17p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.58e-05 (Chi-square test), Q value = 0.029

Table S26. Gene #22: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
17P GAIN MUTATED | 6 | 6 | 3 | 1 | 0 | 0
17P GAIN WILD-TYPE | 267 | 44 | 103 | 1 | 43 | 6

Figure S26. Get High-res Image Gene #22: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.42e-06 (t-test), Q value = 0.0012

Table S27. Gene #22: '17p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
17P GAIN MUTATED | 12 | 0.6 (1.4)
17P GAIN WILD-TYPE | 371 | 3.7 (6.3)

Figure S27. Get High-res Image Gene #22: '17p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'17q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.64e-05 (Chi-square test), Q value = 0.077

Table S28. Gene #23: '17q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
17Q GAIN MUTATED | 7 | 6 | 3 | 1 | 0 | 0
17Q GAIN WILD-TYPE | 266 | 44 | 103 | 1 | 43 | 6

Figure S28. Get High-res Image Gene #23: '17q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.97e-07 (t-test), Q value = 0.00016

Table S29. Gene #23: '17q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
17Q GAIN MUTATED | 13 | 0.5 (1.3)
17Q GAIN WILD-TYPE | 370 | 3.7 (6.3)

Figure S29. Get High-res Image Gene #23: '17q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'18p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S30. Gene #24: '18p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
18P GAIN MUTATED | 4 | 0.0 (0.0)
18P GAIN WILD-TYPE | 379 | 3.6 (6.2)

Figure S30. Get High-res Image Gene #24: '18p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'18q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S31. Gene #25: '18q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
18Q GAIN MUTATED | 4 | 0.0 (0.0)
18Q GAIN WILD-TYPE | 379 | 3.6 (6.2)

Figure S31. Get High-res Image Gene #25: '18q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.55e-25 (t-test), Q value = 1.3e-22

Table S32. Gene #26: '19p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
19P GAIN MUTATED | 7 | 0.0 (0.0)
19P GAIN WILD-TYPE | 376 | 3.6 (6.3)

Figure S32. Get High-res Image Gene #26: '19p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.51e-25 (t-test), Q value = 1.3e-22

Table S33. Gene #27: '19q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
19Q GAIN MUTATED | 8 | 0.0 (0.0)
19Q GAIN WILD-TYPE | 375 | 3.6 (6.3)

Figure S33. Get High-res Image Gene #27: '19q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.17e-05 (Chi-square test), Q value = 0.041

Table S34. Gene #28: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
20P GAIN MUTATED | 4 | 4 | 3 | 1 | 0 | 0
20P GAIN WILD-TYPE | 269 | 46 | 103 | 1 | 43 | 6

Figure S34. Get High-res Image Gene #28: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.000161 (Fisher's exact test), Q value = 0.13

Table S35. Gene #28: '20p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 264 | 9 | 208
20P GAIN MUTATED | 0 | 0 | 12
20P GAIN WILD-TYPE | 264 | 9 | 196

Figure S35. Get High-res Image Gene #28: '20p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 1.51e-25 (t-test), Q value = 1.3e-22

Table S36. Gene #28: '20p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
20P GAIN MUTATED | 8 | 0.0 (0.0)
20P GAIN WILD-TYPE | 375 | 3.6 (6.3)

Figure S36. Get High-res Image Gene #28: '20p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'20q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.17e-05 (Chi-square test), Q value = 0.041

Table S37. Gene #29: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
20Q GAIN MUTATED | 4 | 4 | 3 | 1 | 0 | 0
20Q GAIN WILD-TYPE | 269 | 46 | 103 | 1 | 43 | 6

Figure S37. Get High-res Image Gene #29: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20q gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.000161 (Fisher's exact test), Q value = 0.13

Table S38. Gene #29: '20q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 264 | 9 | 208
20Q GAIN MUTATED | 0 | 0 | 12
20Q GAIN WILD-TYPE | 264 | 9 | 196

Figure S38. Get High-res Image Gene #29: '20q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

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

P value = 1.51e-25 (t-test), Q value = 1.3e-22

Table S39. Gene #29: '20q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
20Q GAIN MUTATED | 8 | 0.0 (0.0)
20Q GAIN WILD-TYPE | 375 | 3.6 (6.3)

Figure S39. Get High-res Image Gene #29: '20q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'21q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.69e-25 (t-test), Q value = 1.4e-22

Table S40. Gene #30: '21q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
21Q GAIN MUTATED | 3 | 0.0 (0.0)
21Q GAIN WILD-TYPE | 380 | 3.6 (6.2)

Figure S40. Get High-res Image Gene #30: '21q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'xq gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.36e-07 (Chi-square test), Q value = 6e-04

Table S41. Gene #31: 'xq gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
XQ GAIN MUTATED | 2 | 3 | 2 | 1 | 0 | 0
XQ GAIN WILD-TYPE | 271 | 47 | 104 | 1 | 43 | 6

Figure S41. Get High-res Image Gene #31: 'xq gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.48e-25 (t-test), Q value = 1.2e-22

Table S42. Gene #34: '2p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
2P LOSS MUTATED | 9 | 0.0 (0.0)
2P LOSS WILD-TYPE | 374 | 3.6 (6.3)

Figure S42. Get High-res Image Gene #34: '2p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.51e-25 (t-test), Q value = 1.3e-22

Table S43. Gene #35: '2q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
2Q LOSS MUTATED | 8 | 0.0 (0.0)
2Q LOSS WILD-TYPE | 375 | 3.6 (6.3)

Figure S43. Get High-res Image Gene #35: '2q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.69e-25 (t-test), Q value = 1.4e-22

Table S44. Gene #37: '3q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
3Q LOSS MUTATED | 3 | 0.0 (0.0)
3Q LOSS WILD-TYPE | 380 | 3.6 (6.2)

Figure S44. Get High-res Image Gene #37: '3q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S45. Gene #40: '8p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
8P LOSS MUTATED | 4 | 0.0 (0.0)
8P LOSS WILD-TYPE | 379 | 3.6 (6.2)

Figure S45. Get High-res Image Gene #40: '8p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S46. Gene #41: '8q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
8Q LOSS MUTATED | 4 | 0.0 (0.0)
8Q LOSS WILD-TYPE | 379 | 3.6 (6.2)

Figure S46. Get High-res Image Gene #41: '8q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.38e-09 (Chi-square test), Q value = 1.1e-06

Table S47. Gene #43: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
9Q LOSS MUTATED | 8 | 5 | 3 | 2 | 3 | 1
9Q LOSS WILD-TYPE | 265 | 45 | 103 | 0 | 40 | 5

Figure S47. Get High-res Image Gene #43: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.62e-25 (t-test), Q value = 1.3e-22

Table S48. Gene #44: '10p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
10P LOSS MUTATED | 5 | 0.0 (0.0)
10P LOSS WILD-TYPE | 378 | 3.6 (6.2)

Figure S48. Get High-res Image Gene #44: '10p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S49. Gene #45: '10q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
10Q LOSS MUTATED | 4 | 0.0 (0.0)
10Q LOSS WILD-TYPE | 379 | 3.6 (6.2)

Figure S49. Get High-res Image Gene #45: '10q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.61e-07 (Chi-square test), Q value = 0.00013

Table S50. Gene #46: '11p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
11P LOSS MUTATED | 1 | 1 | 4 | 1 | 0 | 0
11P LOSS WILD-TYPE | 272 | 49 | 102 | 1 | 43 | 6

Figure S50. Get High-res Image Gene #46: '11p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'11q loss' versus 'AGE'

P value = 9.41e-05 (t-test), Q value = 0.075

Table S51. Gene #47: '11q loss' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 482 | 47.1 (15.6)
11Q LOSS MUTATED | 9 | 67.0 (8.9)
11Q LOSS WILD-TYPE | 473 | 46.7 (15.5)

Figure S51. Get High-res Image Gene #47: '11q loss' versus Clinical Feature #2: 'AGE'

'11q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.89e-06 (Chi-square test), Q value = 0.0048

Table S52. Gene #47: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
11Q LOSS MUTATED | 1 | 2 | 4 | 1 | 1 | 0
11Q LOSS WILD-TYPE | 272 | 48 | 102 | 1 | 42 | 6

Figure S52. Get High-res Image Gene #47: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 9.97e-15 (t-test), Q value = 8.2e-12

Table S53. Gene #48: '13q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
13Q LOSS MUTATED | 10 | 0.2 (0.6)
13Q LOSS WILD-TYPE | 373 | 3.7 (6.3)

Figure S53. Get High-res Image Gene #48: '13q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.69e-25 (t-test), Q value = 1.4e-22

Table S54. Gene #51: '17q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
17Q LOSS MUTATED | 3 | 0.0 (0.0)
17Q LOSS WILD-TYPE | 380 | 3.6 (6.2)

Figure S54. Get High-res Image Gene #51: '17q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'xq loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.08e-05 (Chi-square test), Q value = 0.073

Table S55. Gene #57: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC
--- | --- | --- | --- | --- | --- | ---
ALL | 273 | 50 | 106 | 2 | 43 | 6
XQ LOSS MUTATED | 0 | 3 | 0 | 0 | 0 | 0
XQ LOSS WILD-TYPE | 273 | 47 | 106 | 2 | 43 | 6

Figure S55. Get High-res Image Gene #57: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'xq loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.69e-25 (t-test), Q value = 1.4e-22

Table S56. Gene #57: 'xq loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 383 | 3.6 (6.2)
XQ LOSS MUTATED | 3 | 0.0 (0.0)
XQ LOSS WILD-TYPE | 380 | 3.6 (6.2)

Figure S56. Get High-res Image Gene #57: 'xq loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

- Copy number data file = transformed.cor.cli.txt

- Clinical data file = THCA-TP.merged_data.txt

- Number of patients = 482

- Number of significantly arm-level cnvs = 57

- Number of selected clinical features = 15

- Exclude regions 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

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

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

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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- 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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[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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