Correlation between copy number variations of arm-level result and selected clinical features
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
16 April 2014 | analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C18914HD
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/C18914HD
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 69 arm-level events and 10 clinical features across 163 patients, 47 significant findings detected with Q value < 0.25.

- 1p gain cnv correlated to 'Time to Death'.

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

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

- 7p gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.

- 7q gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.

- 8q gain cnv correlated to 'Time to Death'.

- 17p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.M.STAGE'.

- 17q gain cnv correlated to 'PATHOLOGY.M.STAGE'.

- 3p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

- 3q loss cnv correlated to 'Time to Death'.

- 4p loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'GENDER'.

- 4q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

- 5p loss cnv correlated to 'Time to Death'.

- 5q loss cnv correlated to 'Time to Death'.

- 9p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

- 9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

- 11q loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

- 13q loss cnv correlated to 'Time to Death' and 'GENDER'.

- 15q loss cnv correlated to 'Time to Death'.

- 16p loss cnv correlated to 'Time to Death'.

- 16q loss cnv correlated to 'Time to Death'.

- 17p loss cnv correlated to 'Time to Death' and 'NEOPLASM.DISEASESTAGE'.

- 18p loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

- 18q loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

- 22q loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

- xq loss cnv correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 69 arm-level events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 47 significant findings detected.

|  | Clinical Features | Time to Death | AGE | NEOPLASM DISEASESTAGE | PATHOLOGY T STAGE | PATHOLOGY N STAGE | PATHOLOGY M STAGE | GENDER | KARNOFSKY PERFORMANCE SCORE | NUMBERPACKYEARSSMOKED | YEAROFTOBACCOSMOKINGONSET
| 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 | t-test | t-test | t-test
4p loss | 15 (9%) | 148 | 0.000358 (0.177) | 0.00867 (1.00) | 5.58e-05 (0.0283) | 1.58e-05 (0.00818) | 0.00898 (1.00) | 0.536 (1.00) | 4e-05 (0.0204) | 0.792 (1.00) |  |
1q gain | 13 (8%) | 150 | 3.52e-05 (0.018) | 0.666 (1.00) | 1.29e-05 (0.00671) | 3.26e-05 (0.0168) | 0.408 (1.00) | 0.133 (1.00) | 0.0629 (1.00) | 0.478 (1.00) |  |
11q loss | 14 (9%) | 149 | 2.48e-05 (0.0128) | 0.331 (1.00) | 0.000129 (0.0644) | 5.22e-05 (0.0266) | 0.0641 (1.00) | 0.0824 (1.00) | 0.36 (1.00) | 0.792 (1.00) |  |
18p loss | 26 (16%) | 137 | 5.21e-05 (0.0266) | 0.18 (1.00) | 7.2e-05 (0.0363) | 5.11e-06 (0.0027) | 0.0607 (1.00) | 0.0774 (1.00) | 0.063 (1.00) | 0.724 (1.00) |  |
18q loss | 28 (17%) | 135 | 5.21e-05 (0.0266) | 0.28 (1.00) | 8.45e-06 (0.00444) | 5.88e-06 (0.0031) | 0.029 (1.00) | 0.0938 (1.00) | 0.0442 (1.00) | 0.724 (1.00) |  |
xq loss | 20 (12%) | 143 | 6.67e-05 (0.0337) | 0.174 (1.00) | 0.000495 (0.243) | 0.000194 (0.0965) | 0.0526 (1.00) | 0.213 (1.00) | 0.0169 (1.00) | 0.469 (1.00) |  |
17p gain | 99 (61%) | 64 | 0.0569 (1.00) | 0.0561 (1.00) | 1.59e-05 (0.00826) | 0.000589 (0.289) | 0.215 (1.00) | 1.07e-05 (0.00561) | 0.0546 (1.00) | 0.254 (1.00) | 0.369 (1.00) |
3p loss | 14 (9%) | 149 | 0.0103 (1.00) | 0.177 (1.00) | 1.8e-05 (0.0093) | 0.000186 (0.0926) | 0.669 (1.00) | 0.11 (1.00) | 0.761 (1.00) | 0.792 (1.00) | 0.453 (1.00) |
4q loss | 16 (10%) | 147 | 0.0112 (1.00) | 0.0535 (1.00) | 0.000432 (0.213) | 0.000146 (0.073) | 0.0698 (1.00) | 0.165 (1.00) | 0.000894 (0.435) | 0.754 (1.00) |  |
9p loss | 21 (13%) | 142 | 0.00952 (1.00) | 0.561 (1.00) | 1.43e-05 (0.00744) | 8.13e-05 (0.0409) | 0.119 (1.00) | 0.034 (1.00) | 0.00886 (1.00) | 0.314 (1.00) |  |
9q loss | 23 (14%) | 140 | 0.00179 (0.862) | 0.587 (1.00) | 5.93e-05 (0.03) | 1.49e-05 (0.00777) | 0.0607 (1.00) | 0.24 (1.00) | 0.0248 (1.00) | 0.325 (1.00) |  |
13q loss | 16 (10%) | 147 | 1.05e-05 (0.00549) | 0.0404 (1.00) | 0.00285 (1.00) | 0.000696 (0.34) | 0.0444 (1.00) | 0.489 (1.00) | 0.000123 (0.0618) | 0.467 (1.00) |  |
17p loss | 8 (5%) | 155 | 4.03e-14 (2.16e-11) | 0.753 (1.00) | 0.000306 (0.152) | 0.00691 (1.00) | 0.00807 (1.00) | 0.0499 (1.00) | 0.0538 (1.00) | 0.478 (1.00) |  |
22q loss | 39 (24%) | 124 | 0.0393 (1.00) | 0.395 (1.00) | 2.02e-06 (0.00107) | 3.32e-06 (0.00176) | 0.0619 (1.00) | 0.185 (1.00) | 0.00138 (0.669) | 0.447 (1.00) |  |
1p gain | 4 (2%) | 159 | 7.98e-06 (0.0042) | 0.444 (1.00) | 0.0212 (1.00) | 0.0129 (1.00) | 0.0803 (1.00) | 0.18 (1.00) | 0.0816 (1.00) |  |  |
6q gain | 5 (3%) | 158 | 1.53e-09 (8.19e-07) | 0.166 (1.00) | 0.0285 (1.00) | 0.0441 (1.00) | 0.0803 (1.00) | 0.0127 (1.00) | 0.637 (1.00) | 0.548 (1.00) |  |
7p gain | 95 (58%) | 68 | 0.0607 (1.00) | 0.466 (1.00) | 0.000467 (0.23) | 0.0068 (1.00) | 0.662 (1.00) | 0.223 (1.00) | 0.123 (1.00) | 0.159 (1.00) | 0.354 (1.00) | 0.837 (1.00)
7q gain | 96 (59%) | 67 | 0.0546 (1.00) | 0.402 (1.00) | 0.000276 (0.137) | 0.00554 (1.00) | 0.54 (1.00) | 0.314 (1.00) | 0.118 (1.00) | 0.159 (1.00) | 0.354 (1.00) | 0.837 (1.00)
8q gain | 15 (9%) | 148 | 1.56e-06 (0.000828) | 0.789 (1.00) | 0.00568 (1.00) | 0.00185 (0.888) | 0.0444 (1.00) | 0.349 (1.00) | 0.0715 (1.00) | 0.566 (1.00) |  |
17q gain | 112 (69%) | 51 | 0.481 (1.00) | 0.124 (1.00) | 0.0431 (1.00) | 0.144 (1.00) | 0.443 (1.00) | 0.000504 (0.247) | 0.199 (1.00) | 0.667 (1.00) |  |
3q loss | 4 (2%) | 159 | 3.96e-11 (2.12e-08) | 0.21 (1.00) | 0.00511 (1.00) | 0.0129 (1.00) | 0.192 (1.00) | 0.18 (1.00) | 0.584 (1.00) |  |  |
5p loss | 7 (4%) | 156 | 1.91e-10 (1.02e-07) | 0.0911 (1.00) | 0.0161 (1.00) | 0.0045 (1.00) | 0.0396 (1.00) | 0.163 (1.00) | 0.0262 (1.00) |  |  |
5q loss | 7 (4%) | 156 | 8.61e-08 (4.58e-05) | 0.0351 (1.00) | 0.0272 (1.00) | 0.0045 (1.00) | 0.0152 (1.00) | 0.163 (1.00) | 0.0262 (1.00) |  |  |
15q loss | 18 (11%) | 145 | 2.65e-08 (1.41e-05) | 0.119 (1.00) | 0.00732 (1.00) | 0.00478 (1.00) | 0.112 (1.00) | 0.125 (1.00) | 0.178 (1.00) | 0.666 (1.00) |  |
16p loss | 4 (2%) | 159 | 3.35e-05 (0.0172) | 0.648 (1.00) | 0.13 (1.00) | 0.115 (1.00) |  | 1 (1.00) | 0.0816 (1.00) |  |  |
16q loss | 5 (3%) | 158 | 3.35e-05 (0.0172) | 0.316 (1.00) | 0.0748 (1.00) | 0.205 (1.00) | 0.273 (1.00) | 1 (1.00) | 0.161 (1.00) |  |  |
2p gain | 31 (19%) | 132 | 0.259 (1.00) | 0.34 (1.00) | 0.0987 (1.00) | 0.76 (1.00) | 0.669 (1.00) | 0.00328 (1.00) | 0.516 (1.00) | 0.534 (1.00) | 0.331 (1.00) | 0.477 (1.00)
2q gain | 33 (20%) | 130 | 0.392 (1.00) | 0.695 (1.00) | 0.0242 (1.00) | 0.799 (1.00) | 0.223 (1.00) | 0.00479 (1.00) | 0.4 (1.00) | 0.531 (1.00) | 0.331 (1.00) | 0.477 (1.00)
3p gain | 46 (28%) | 117 | 0.415 (1.00) | 0.763 (1.00) | 0.0508 (1.00) | 0.0326 (1.00) | 1 (1.00) | 0.381 (1.00) | 0.85 (1.00) | 0.0416 (1.00) | 0.368 (1.00) |
3q gain | 55 (34%) | 108 | 0.17 (1.00) | 0.464 (1.00) | 0.161 (1.00) | 0.0885 (1.00) | 1 (1.00) | 0.169 (1.00) | 0.718 (1.00) | 0.113 (1.00) | 0.357 (1.00) |
4p gain | 6 (4%) | 157 | 0.0202 (1.00) | 0.00484 (1.00) | 0.0433 (1.00) | 0.542 (1.00) | 0.501 (1.00) | 0.18 (1.00) | 0.669 (1.00) |  |  |
4q gain | 5 (3%) | 158 | 0.333 (1.00) | 0.0155 (1.00) | 0.259 (1.00) | 0.612 (1.00) | 0.167 (1.00) | 0.69 (1.00) | 1 (1.00) |  |  |
5p gain | 24 (15%) | 139 | 0.679 (1.00) | 0.893 (1.00) | 0.202 (1.00) | 0.137 (1.00) | 0.558 (1.00) | 0.385 (1.00) | 0.637 (1.00) | 0.401 (1.00) |  |
5q gain | 24 (15%) | 139 | 0.679 (1.00) | 0.422 (1.00) | 0.202 (1.00) | 0.327 (1.00) | 1 (1.00) | 0.385 (1.00) | 0.637 (1.00) | 0.401 (1.00) |  |
6p gain | 7 (4%) | 156 | 0.00143 (0.691) | 0.577 (1.00) | 0.00775 (1.00) | 0.0045 (1.00) | 0.277 (1.00) | 0.0257 (1.00) | 1 (1.00) | 0.548 (1.00) |  |
8p gain | 11 (7%) | 152 | 0.00353 (1.00) | 0.969 (1.00) | 0.165 (1.00) | 0.0845 (1.00) | 0.296 (1.00) | 0.848 (1.00) | 0.308 (1.00) |  |  |
9p gain | 3 (2%) | 160 | 0.107 (1.00) | 0.931 (1.00) | 0.0557 (1.00) | 0.0704 (1.00) |  | 0.627 (1.00) | 1 (1.00) |  |  |
10p gain | 5 (3%) | 158 | 0.465 (1.00) | 0.927 (1.00) | 0.162 (1.00) | 0.377 (1.00) |  | 0.321 (1.00) | 1 (1.00) |  |  |
10q gain | 5 (3%) | 158 | 0.465 (1.00) | 0.927 (1.00) | 0.162 (1.00) | 0.377 (1.00) |  | 0.321 (1.00) | 1 (1.00) |  |  |
11p gain | 8 (5%) | 155 | 0.0524 (1.00) | 0.638 (1.00) | 0.0363 (1.00) | 0.0404 (1.00) | 0.588 (1.00) | 0.0191 (1.00) | 0.698 (1.00) |  |  |
11q gain | 7 (4%) | 156 | 0.466 (1.00) | 0.449 (1.00) | 0.186 (1.00) | 0.0625 (1.00) | 0.738 (1.00) | 0.163 (1.00) | 0.199 (1.00) |  |  |
12p gain | 66 (40%) | 97 | 0.804 (1.00) | 0.681 (1.00) | 0.319 (1.00) | 0.601 (1.00) | 0.818 (1.00) | 0.126 (1.00) | 0.0233 (1.00) | 0.847 (1.00) | 0.29 (1.00) |
12q gain | 66 (40%) | 97 | 0.804 (1.00) | 0.681 (1.00) | 0.319 (1.00) | 0.601 (1.00) | 0.818 (1.00) | 0.126 (1.00) | 0.0233 (1.00) | 0.847 (1.00) | 0.29 (1.00) |
13q gain | 18 (11%) | 145 | 0.906 (1.00) | 0.762 (1.00) | 0.601 (1.00) | 0.804 (1.00) | 0.738 (1.00) | 1 (1.00) | 0.788 (1.00) | 0.153 (1.00) |  |
14q gain | 3 (2%) | 160 |  |  | 0.069 (1.00) | 0.0281 (1.00) |  | 0.627 (1.00) | 0.215 (1.00) |  |  |
15q gain | 4 (2%) | 159 | 0.478 (1.00) | 0.588 (1.00) | 0.486 (1.00) | 0.412 (1.00) |  | 0.69 (1.00) | 0.584 (1.00) |  |  |
16p gain | 86 (53%) | 77 | 0.785 (1.00) | 0.158 (1.00) | 0.792 (1.00) | 0.943 (1.00) | 1 (1.00) | 0.323 (1.00) | 0.01 (1.00) | 0.674 (1.00) | 0.369 (1.00) |
16q gain | 83 (51%) | 80 | 0.227 (1.00) | 0.353 (1.00) | 0.545 (1.00) | 0.513 (1.00) | 0.742 (1.00) | 0.081 (1.00) | 0.0597 (1.00) | 0.207 (1.00) | 0.369 (1.00) |
18p gain | 8 (5%) | 155 | 0.888 (1.00) | 0.903 (1.00) | 0.294 (1.00) | 0.545 (1.00) |  | 0.149 (1.00) | 1 (1.00) | 0.548 (1.00) |  |
18q gain | 5 (3%) | 158 | 0.355 (1.00) | 0.962 (1.00) | 0.59 (1.00) | 0.612 (1.00) |  | 0.419 (1.00) | 1 (1.00) |  |  |
19p gain | 3 (2%) | 160 | 0.626 (1.00) | 0.344 (1.00) | 0.481 (1.00) | 0.438 (1.00) | 1 (1.00) | 0.627 (1.00) | 1 (1.00) |  |  |
19q gain | 3 (2%) | 160 | 0.626 (1.00) | 0.344 (1.00) | 0.481 (1.00) | 0.438 (1.00) | 1 (1.00) | 0.627 (1.00) | 1 (1.00) |  |  |
20p gain | 55 (34%) | 108 | 0.635 (1.00) | 0.148 (1.00) | 0.51 (1.00) | 0.476 (1.00) | 0.787 (1.00) | 0.867 (1.00) | 0.594 (1.00) | 0.641 (1.00) |  |
20q gain | 57 (35%) | 106 | 0.38 (1.00) | 0.116 (1.00) | 0.224 (1.00) | 0.271 (1.00) | 0.512 (1.00) | 1 (1.00) | 0.591 (1.00) | 0.641 (1.00) |  |
21q gain | 9 (6%) | 154 | 0.011 (1.00) | 0.0647 (1.00) | 1 (1.00) | 1 (1.00) |  | 0.192 (1.00) | 1 (1.00) | 0.905 (1.00) |  |
xq gain | 51 (31%) | 112 | 0.577 (1.00) | 0.738 (1.00) | 0.00285 (1.00) | 0.00676 (1.00) | 0.608 (1.00) | 0.337 (1.00) | 0.065 (1.00) | 0.268 (1.00) | 0.373 (1.00) |
1p loss | 20 (12%) | 143 | 0.0379 (1.00) | 0.815 (1.00) | 0.0626 (1.00) | 0.124 (1.00) | 0.296 (1.00) | 0.915 (1.00) | 0.308 (1.00) | 0.13 (1.00) |  |
1q loss | 11 (7%) | 152 | 0.506 (1.00) | 0.333 (1.00) | 0.268 (1.00) | 0.577 (1.00) | 0.654 (1.00) | 0.467 (1.00) | 0.735 (1.00) | 0.314 (1.00) |  |
6p loss | 11 (7%) | 152 | 0.0121 (1.00) | 0.428 (1.00) | 0.0275 (1.00) | 0.0295 (1.00) | 0.0582 (1.00) | 0.833 (1.00) | 0.0886 (1.00) | 0.157 (1.00) |  |
6q loss | 15 (9%) | 148 | 0.206 (1.00) | 0.92 (1.00) | 0.0361 (1.00) | 0.0025 (1.00) | 0.169 (1.00) | 0.347 (1.00) | 0.015 (1.00) | 0.754 (1.00) |  |
8p loss | 6 (4%) | 157 | 0.00199 (0.95) | 0.534 (1.00) | 0.0505 (1.00) | 0.542 (1.00) | 0.0803 (1.00) | 0.0257 (1.00) | 0.366 (1.00) |  |  |
8q loss | 4 (2%) | 159 | 0.0317 (1.00) | 0.3 (1.00) | 0.0791 (1.00) | 0.412 (1.00) |  | 0.18 (1.00) | 0.584 (1.00) |  |  |
10p loss | 11 (7%) | 152 | 0.208 (1.00) | 0.87 (1.00) | 0.00632 (1.00) | 0.0109 (1.00) | 0.0556 (1.00) | 0.0872 (1.00) | 0.308 (1.00) | 0.44 (1.00) |  |
10q loss | 11 (7%) | 152 | 0.15 (1.00) | 0.442 (1.00) | 0.00231 (1.00) | 0.00535 (1.00) | 0.0248 (1.00) | 0.168 (1.00) | 0.308 (1.00) | 0.355 (1.00) |  |
11p loss | 10 (6%) | 153 | 0.000775 (0.378) | 0.105 (1.00) | 0.0256 (1.00) | 0.0541 (1.00) | 0.192 (1.00) | 0.467 (1.00) | 0.169 (1.00) |  |  |
14q loss | 31 (19%) | 132 | 0.0128 (1.00) | 0.991 (1.00) | 0.00198 (0.95) | 0.00514 (1.00) | 0.0776 (1.00) | 0.108 (1.00) | 0.0511 (1.00) | 0.448 (1.00) |  |
19p loss | 12 (7%) | 151 | 0.744 (1.00) | 0.171 (1.00) | 0.0381 (1.00) | 0.0367 (1.00) | 0.192 (1.00) | 0.263 (1.00) | 0.348 (1.00) | 0.754 (1.00) | 0.315 (1.00) |
19q loss | 11 (7%) | 152 | 0.000889 (0.433) | 0.948 (1.00) | 0.00135 (0.655) | 0.00197 (0.945) | 0.192 (1.00) | 0.134 (1.00) | 0.0886 (1.00) | 0.754 (1.00) |  |
21q loss | 31 (19%) | 132 | 0.577 (1.00) | 0.661 (1.00) | 0.0139 (1.00) | 0.00747 (1.00) | 0.872 (1.00) | 0.143 (1.00) | 0.129 (1.00) | 0.711 (1.00) | 0.332 (1.00) |

'1p gain' versus 'Time to Death'

P value = 7.98e-06 (logrank test), Q value = 0.0042

Table S1. Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
1P GAIN MUTATED | 3 | 1 | 2.0 - 7.9 (3.7)
1P GAIN WILD-TYPE | 147 | 16 | 0.0 - 194.8 (14.4)

Figure S1. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'Time to Death'

P value = 3.52e-05 (logrank test), Q value = 0.018

Table S2. Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
1Q GAIN MUTATED | 12 | 3 | 0.7 - 30.3 (3.8)
1Q GAIN WILD-TYPE | 138 | 14 | 0.0 - 194.8 (14.9)

Figure S2. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.29e-05 (Fisher's exact test), Q value = 0.0067

Table S3. Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
1Q GAIN MUTATED | 1 | 0 | 9 | 3
1Q GAIN WILD-TYPE | 94 | 11 | 28 | 7

Figure S3. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

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

P value = 3.26e-05 (Fisher's exact test), Q value = 0.017

Table S4. Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
1Q GAIN MUTATED | 2 | 0 | 11
1Q GAIN WILD-TYPE | 100 | 17 | 33

Figure S4. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'6q gain' versus 'Time to Death'

P value = 1.53e-09 (logrank test), Q value = 8.2e-07

Table S5. Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
6Q GAIN MUTATED | 5 | 3 | 1.9 - 13.6 (7.9)
6Q GAIN WILD-TYPE | 145 | 14 | 0.0 - 194.8 (14.6)

Figure S5. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000467 (Fisher's exact test), Q value = 0.23

Table S6. Gene #13: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
7P GAIN MUTATED | 66 | 4 | 12 | 6
7P GAIN WILD-TYPE | 29 | 7 | 25 | 4

Figure S6. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'7q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000276 (Fisher's exact test), Q value = 0.14

Table S7. Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
7Q GAIN MUTATED | 67 | 4 | 12 | 6
7Q GAIN WILD-TYPE | 28 | 7 | 25 | 4

Figure S7. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'8q gain' versus 'Time to Death'

P value = 1.56e-06 (logrank test), Q value = 0.00083

Table S8. Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
8Q GAIN MUTATED | 15 | 5 | 0.2 - 43.2 (6.6)
8Q GAIN WILD-TYPE | 135 | 12 | 0.0 - 194.8 (14.7)

Figure S8. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.59e-05 (Fisher's exact test), Q value = 0.0083

Table S9. Gene #29: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
17P GAIN MUTATED | 70 | 6 | 13 | 2
17P GAIN WILD-TYPE | 25 | 5 | 24 | 8

Figure S9. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'17p gain' versus 'PATHOLOGY.M.STAGE'

P value = 1.07e-05 (Fisher's exact test), Q value = 0.0056

Table S10. Gene #29: '17p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 62 | 6 | 82
17P GAIN MUTATED | 26 | 1 | 62
17P GAIN WILD-TYPE | 36 | 5 | 20

Figure S10. Get High-res Image Gene #29: '17p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'17q gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.000504 (Fisher's exact test), Q value = 0.25

Table S11. Gene #30: '17q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients | M0 | M1 | MX
--- | --- | --- | ---
ALL | 62 | 6 | 82
17Q GAIN MUTATED | 32 | 3 | 66
17Q GAIN WILD-TYPE | 30 | 3 | 16

Figure S11. Get High-res Image Gene #30: '17q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'3p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.8e-05 (Fisher's exact test), Q value = 0.0093

Table S12. Gene #41: '3p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
3P LOSS MUTATED | 1 | 1 | 9 | 3
3P LOSS WILD-TYPE | 94 | 10 | 28 | 7

Figure S12. Get High-res Image Gene #41: '3p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'3p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000186 (Fisher's exact test), Q value = 0.093

Table S13. Gene #41: '3p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
3P LOSS MUTATED | 2 | 2 | 10
3P LOSS WILD-TYPE | 100 | 15 | 34

Figure S13. Get High-res Image Gene #41: '3p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'3q loss' versus 'Time to Death'

P value = 3.96e-11 (logrank test), Q value = 2.1e-08

Table S14. Gene #42: '3q loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
3Q LOSS MUTATED | 4 | 3 | 3.7 - 21.6 (6.4)
3Q LOSS WILD-TYPE | 146 | 14 | 0.0 - 194.8 (14.3)

Figure S14. Get High-res Image Gene #42: '3q loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'Time to Death'

P value = 0.000358 (logrank test), Q value = 0.18

Table S15. Gene #43: '4p loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
4P LOSS MUTATED | 14 | 4 | 0.1 - 79.9 (5.1)
4P LOSS WILD-TYPE | 136 | 13 | 0.0 - 194.8 (14.9)

Figure S15. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.58e-05 (Fisher's exact test), Q value = 0.028

Table S16. Gene #43: '4p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
4P LOSS MUTATED | 2 | 1 | 11 | 1
4P LOSS WILD-TYPE | 93 | 10 | 26 | 9

Figure S16. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4p loss' versus 'PATHOLOGY.T.STAGE'

P value = 1.58e-05 (Fisher's exact test), Q value = 0.0082

Table S17. Gene #43: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
4P LOSS MUTATED | 2 | 1 | 12
4P LOSS WILD-TYPE | 100 | 16 | 32

Figure S17. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4p loss' versus 'GENDER'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S18. Gene #43: '4p loss' versus Clinical Feature #7: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 49 | 114
4P LOSS MUTATED | 12 | 3
4P LOSS WILD-TYPE | 37 | 111

Figure S18. Get High-res Image Gene #43: '4p loss' versus Clinical Feature #7: 'GENDER'

'4q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000432 (Fisher's exact test), Q value = 0.21

Table S19. Gene #44: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
4Q LOSS MUTATED | 3 | 1 | 10 | 2
4Q LOSS WILD-TYPE | 92 | 10 | 27 | 8

Figure S19. Get High-res Image Gene #44: '4q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4q loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000146 (Fisher's exact test), Q value = 0.073

Table S20. Gene #44: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
4Q LOSS MUTATED | 3 | 2 | 11
4Q LOSS WILD-TYPE | 99 | 15 | 33

Figure S20. Get High-res Image Gene #44: '4q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'5p loss' versus 'Time to Death'

P value = 1.91e-10 (logrank test), Q value = 1e-07

Table S21. Gene #45: '5p loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
5P LOSS MUTATED | 7 | 4 | 0.7 - 22.9 (6.6)
5P LOSS WILD-TYPE | 143 | 13 | 0.0 - 194.8 (14.4)

Figure S21. Get High-res Image Gene #45: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'Time to Death'

P value = 8.61e-08 (logrank test), Q value = 4.6e-05

Table S22. Gene #46: '5q loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
5Q LOSS MUTATED | 7 | 3 | 0.7 - 22.9 (3.7)
5Q LOSS WILD-TYPE | 143 | 14 | 0.0 - 194.8 (14.4)

Figure S22. Get High-res Image Gene #46: '5q loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.43e-05 (Fisher's exact test), Q value = 0.0074

Table S23. Gene #51: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
9P LOSS MUTATED | 4 | 0 | 10 | 5
9P LOSS WILD-TYPE | 91 | 11 | 27 | 5

Figure S23. Get High-res Image Gene #51: '9p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9p loss' versus 'PATHOLOGY.T.STAGE'

P value = 8.13e-05 (Fisher's exact test), Q value = 0.041

Table S24. Gene #51: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
9P LOSS MUTATED | 5 | 2 | 14
9P LOSS WILD-TYPE | 97 | 15 | 30

Figure S24. Get High-res Image Gene #51: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.93e-05 (Fisher's exact test), Q value = 0.03

Table S25. Gene #52: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
9Q LOSS MUTATED | 5 | 1 | 12 | 4
9Q LOSS WILD-TYPE | 90 | 10 | 25 | 6

Figure S25. Get High-res Image Gene #52: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9q loss' versus 'PATHOLOGY.T.STAGE'

P value = 1.49e-05 (Fisher's exact test), Q value = 0.0078

Table S26. Gene #52: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
9Q LOSS MUTATED | 6 | 1 | 16
9Q LOSS WILD-TYPE | 96 | 16 | 28

Figure S26. Get High-res Image Gene #52: '9q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'11q loss' versus 'Time to Death'

P value = 2.48e-05 (logrank test), Q value = 0.013

Table S27. Gene #56: '11q loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
11Q LOSS MUTATED | 13 | 5 | 0.1 - 123.6 (8.9)
11Q LOSS WILD-TYPE | 137 | 12 | 0.0 - 194.8 (14.6)

Figure S27. Get High-res Image Gene #56: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000129 (Fisher's exact test), Q value = 0.064

Table S28. Gene #56: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
11Q LOSS MUTATED | 2 | 1 | 7 | 4
11Q LOSS WILD-TYPE | 93 | 10 | 30 | 6

Figure S28. Get High-res Image Gene #56: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'11q loss' versus 'PATHOLOGY.T.STAGE'

P value = 5.22e-05 (Fisher's exact test), Q value = 0.027

Table S29. Gene #56: '11q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
11Q LOSS MUTATED | 2 | 1 | 11
11Q LOSS WILD-TYPE | 100 | 16 | 33

Figure S29. Get High-res Image Gene #56: '11q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'13q loss' versus 'Time to Death'

P value = 1.05e-05 (logrank test), Q value = 0.0055

Table S30. Gene #57: '13q loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
13Q LOSS MUTATED | 16 | 5 | 0.1 - 86.8 (3.4)
13Q LOSS WILD-TYPE | 134 | 12 | 0.0 - 194.8 (14.9)

Figure S30. Get High-res Image Gene #57: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'GENDER'

P value = 0.000123 (Fisher's exact test), Q value = 0.062

Table S31. Gene #57: '13q loss' versus Clinical Feature #7: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 49 | 114
13Q LOSS MUTATED | 12 | 4
13Q LOSS WILD-TYPE | 37 | 110

Figure S31. Get High-res Image Gene #57: '13q loss' versus Clinical Feature #7: 'GENDER'

'15q loss' versus 'Time to Death'

P value = 2.65e-08 (logrank test), Q value = 1.4e-05

Table S32. Gene #59: '15q loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
15Q LOSS MUTATED | 17 | 6 | 0.1 - 34.8 (6.8)
15Q LOSS WILD-TYPE | 133 | 11 | 0.0 - 194.8 (14.6)

Figure S32. Get High-res Image Gene #59: '15q loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'Time to Death'

P value = 3.35e-05 (logrank test), Q value = 0.017

Table S33. Gene #60: '16p loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
16P LOSS MUTATED | 3 | 2 | 0.7 - 21.6 (11.1)
16P LOSS WILD-TYPE | 147 | 15 | 0.0 - 194.8 (14.1)

Figure S33. Get High-res Image Gene #60: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'Time to Death'

P value = 3.35e-05 (logrank test), Q value = 0.017

Table S34. Gene #61: '16q loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
16Q LOSS MUTATED | 4 | 2 | 0.7 - 21.6 (7.0)
16Q LOSS WILD-TYPE | 146 | 15 | 0.0 - 194.8 (14.3)

Figure S34. Get High-res Image Gene #61: '16q loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'Time to Death'

P value = 4.03e-14 (logrank test), Q value = 2.2e-11

Table S35. Gene #62: '17p loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
17P LOSS MUTATED | 6 | 4 | 0.2 - 11.3 (6.8)
17P LOSS WILD-TYPE | 144 | 13 | 0.0 - 194.8 (14.6)

Figure S35. Get High-res Image Gene #62: '17p loss' versus Clinical Feature #1: 'Time to Death'

'17p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000306 (Fisher's exact test), Q value = 0.15

Table S36. Gene #62: '17p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
17P LOSS MUTATED | 1 | 1 | 2 | 4
17P LOSS WILD-TYPE | 94 | 10 | 35 | 6

Figure S36. Get High-res Image Gene #62: '17p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18p loss' versus 'Time to Death'

P value = 5.21e-05 (logrank test), Q value = 0.027

Table S37. Gene #63: '18p loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
18P LOSS MUTATED | 25 | 7 | 0.0 - 123.6 (7.6)
18P LOSS WILD-TYPE | 125 | 10 | 0.0 - 194.8 (15.1)

Figure S37. Get High-res Image Gene #63: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.2e-05 (Fisher's exact test), Q value = 0.036

Table S38. Gene #63: '18p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
18P LOSS MUTATED | 6 | 1 | 13 | 4
18P LOSS WILD-TYPE | 89 | 10 | 24 | 6

Figure S38. Get High-res Image Gene #63: '18p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18p loss' versus 'PATHOLOGY.T.STAGE'

P value = 5.11e-06 (Fisher's exact test), Q value = 0.0027

Table S39. Gene #63: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
18P LOSS MUTATED | 6 | 3 | 17
18P LOSS WILD-TYPE | 96 | 14 | 27

Figure S39. Get High-res Image Gene #63: '18p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'18q loss' versus 'Time to Death'

P value = 5.21e-05 (logrank test), Q value = 0.027

Table S40. Gene #64: '18q loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
18Q LOSS MUTATED | 26 | 7 | 0.0 - 123.6 (7.5)
18Q LOSS WILD-TYPE | 124 | 10 | 0.0 - 194.8 (15.7)

Figure S40. Get High-res Image Gene #64: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.45e-06 (Fisher's exact test), Q value = 0.0044

Table S41. Gene #64: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
18Q LOSS MUTATED | 6 | 1 | 15 | 4
18Q LOSS WILD-TYPE | 89 | 10 | 22 | 6

Figure S41. Get High-res Image Gene #64: '18q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'18q loss' versus 'PATHOLOGY.T.STAGE'

P value = 5.88e-06 (Fisher's exact test), Q value = 0.0031

Table S42. Gene #64: '18q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
18Q LOSS MUTATED | 7 | 3 | 18
18Q LOSS WILD-TYPE | 95 | 14 | 26

Figure S42. Get High-res Image Gene #64: '18q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'22q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.02e-06 (Fisher's exact test), Q value = 0.0011

Table S43. Gene #68: '22q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
22Q LOSS MUTATED | 10 | 3 | 19 | 5
22Q LOSS WILD-TYPE | 85 | 8 | 18 | 5

Figure S43. Get High-res Image Gene #68: '22q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'22q loss' versus 'PATHOLOGY.T.STAGE'

P value = 3.32e-06 (Fisher's exact test), Q value = 0.0018

Table S44. Gene #68: '22q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
22Q LOSS MUTATED | 13 | 3 | 23
22Q LOSS WILD-TYPE | 89 | 14 | 21

Figure S44. Get High-res Image Gene #68: '22q loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'xq loss' versus 'Time to Death'

P value = 6.67e-05 (logrank test), Q value = 0.034

Table S45. Gene #69: 'xq loss' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 150 | 17 | 0.0 - 194.8 (14.0)
XQ LOSS MUTATED | 19 | 6 | 0.1 - 79.9 (11.1)
XQ LOSS WILD-TYPE | 131 | 11 | 0.0 - 194.8 (14.4)

Figure S45. Get High-res Image Gene #69: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000495 (Fisher's exact test), Q value = 0.24

Table S46. Gene #69: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 95 | 11 | 37 | 10
XQ LOSS MUTATED | 4 | 1 | 10 | 3
XQ LOSS WILD-TYPE | 91 | 10 | 27 | 7

Figure S46. Get High-res Image Gene #69: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'xq loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000194 (Fisher's exact test), Q value = 0.097

Table S47. Gene #69: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients | T1 | T2 | T3+T4
--- | --- | --- | ---
ALL | 102 | 17 | 44
XQ LOSS MUTATED | 5 | 2 | 13
XQ LOSS WILD-TYPE | 97 | 15 | 31

Figure S47. Get High-res Image Gene #69: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

Methods & Data
Input

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

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

- Number of patients = 163

- Number of significantly arm-level cnvs = 69

- Number of selected clinical features = 10

- 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

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] 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] 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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