Uterine Corpus Endometrioid Carcinoma: Correlation between copy number variations of arm-level result and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 79 arm-level results and 5 clinical features across 443 patients, 49 significant findings detected with Q value < 0.25.

- 5p gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL.TYPE'.

- 11p gain cnv correlated to 'NEOADJUVANT.THERAPY'.

- 13q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

- 17p gain cnv correlated to 'Time to Death'.

- 18p gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 19p gain cnv correlated to 'AGE'.

- 19q gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 20p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

- 20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

- 4p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 4q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 5p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 5q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 7q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 8p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 8q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 9p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 9q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 11p loss cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.

- 11q loss cnv correlated to 'Time to Death', 'AGE', and 'HISTOLOGICAL.TYPE'.

- 12p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 13q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 14q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 15q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 16p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 16q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 17p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 17q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

- 18q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 19p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 21q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

- 22q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 49 significant findings detected.

|  | Clinical Features | Time to Death | AGE | HISTOLOGICAL TYPE | RADIATIONS RADIATION REGIMENINDICATION | NEOADJUVANT THERAPY
| nCNV (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test
11p loss | 46 (10%) | 397 | 0.000549 (0.193) | 0.000217 (0.0772) | 1.1e-06 (0.000414) | 0.398 (1.00) | 0.144 (1.00)
11q loss | 39 (9%) | 404 | 0.000244 (0.0868) | 0.000109 (0.0391) | 1.87e-05 (0.0069) | 0.203 (1.00) | 0.166 (1.00)
5p gain | 29 (7%) | 414 | 3.3e-05 (0.0122) | 0.0978 (1.00) | 2.21e-06 (0.00083) | 0.537 (1.00) | 0.176 (1.00)
18p gain | 31 (7%) | 412 | 0.0887 (1.00) | 0.000157 (0.0562) | 5.47e-07 (0.000207) | 0.688 (1.00) | 0.827 (1.00)
19q gain | 22 (5%) | 421 | 0.00791 (1.00) | 1.06e-05 (0.00392) | 2.71e-07 (0.000103) | 0.815 (1.00) | 0.0201 (1.00)
8p loss | 41 (9%) | 402 | 0.524 (1.00) | 7.71e-05 (0.0278) | 7.21e-19 (2.84e-16) | 0.592 (1.00) | 0.00315 (1.00)
9p loss | 64 (14%) | 379 | 0.838 (1.00) | 1.07e-06 (0.000404) | 4.11e-14 (1.61e-11) | 1 (1.00) | 0.00377 (1.00)
9q loss | 81 (18%) | 362 | 0.181 (1.00) | 1.23e-10 (4.77e-08) | 1.08e-11 (4.21e-09) | 0.422 (1.00) | 0.311 (1.00)
14q loss | 36 (8%) | 407 | 0.241 (1.00) | 0.000469 (0.166) | 6.99e-09 (2.69e-06) | 1 (1.00) | 0.0387 (1.00)
15q loss | 63 (14%) | 380 | 0.682 (1.00) | 3.87e-05 (0.0142) | 3.42e-10 (1.33e-07) | 0.299 (1.00) | 0.339 (1.00)
16p loss | 56 (13%) | 387 | 0.0291 (1.00) | 5.76e-05 (0.0209) | 6.56e-08 (2.51e-05) | 0.642 (1.00) | 0.13 (1.00)
16q loss | 92 (21%) | 351 | 0.033 (1.00) | 4.55e-06 (0.0017) | 6.92e-14 (2.71e-11) | 0.253 (1.00) | 0.0278 (1.00)
17p loss | 86 (19%) | 357 | 0.173 (1.00) | 1.23e-06 (0.000463) | 2.25e-20 (8.87e-18) | 0.36 (1.00) | 0.0105 (1.00)
17q loss | 57 (13%) | 386 | 0.993 (1.00) | 0.000536 (0.189) | 3.72e-05 (0.0137) | 0.124 (1.00) | 0.619 (1.00)
22q loss | 73 (16%) | 370 | 0.00829 (1.00) | 0.000178 (0.0635) | 4.89e-08 (1.87e-05) | 0.328 (1.00) | 0.292 (1.00)
11p gain | 5 (1%) | 438 | 0.444 (1.00) | 0.642 (1.00) | 0.382 (1.00) | 0.639 (1.00) | 0.000695 (0.242)
13q gain | 19 (4%) | 424 | 0.449 (1.00) | 0.000758 (0.262) | 5.68e-05 (0.0207) | 0.609 (1.00) | 0.0923 (1.00)
17p gain | 6 (1%) | 437 | 0.000609 (0.213) | 0.78 (1.00) | 0.965 (1.00) | 0.371 (1.00) | 0.148 (1.00)
19p gain | 25 (6%) | 418 | 0.0523 (1.00) | 4.47e-05 (0.0163) | 0.000997 (0.343) | 0.176 (1.00) | 0.811 (1.00)
20p gain | 52 (12%) | 391 | 0.0125 (1.00) | 0.00498 (1.00) | 5.04e-06 (0.00188) | 0.0151 (1.00) | 0.118 (1.00)
20q gain | 60 (14%) | 383 | 0.0629 (1.00) | 0.00277 (0.928) | 3.97e-10 (1.54e-07) | 0.0152 (1.00) | 0.141 (1.00)
4p loss | 48 (11%) | 395 | 0.0509 (1.00) | 0.00104 (0.358) | 8.23e-11 (3.21e-08) | 0.318 (1.00) | 0.721 (1.00)
4q loss | 45 (10%) | 398 | 0.0329 (1.00) | 0.00604 (1.00) | 4.42e-07 (0.000168) | 0.0609 (1.00) | 0.855 (1.00)
5p loss | 20 (5%) | 423 | 0.442 (1.00) | 0.758 (1.00) | 7.02e-05 (0.0254) | 0.622 (1.00) | 0.59 (1.00)
5q loss | 35 (8%) | 408 | 0.932 (1.00) | 0.0187 (1.00) | 4.45e-10 (1.72e-07) | 0.341 (1.00) | 0.0621 (1.00)
7q loss | 23 (5%) | 420 | 0.829 (1.00) | 0.000873 (0.301) | 3.27e-08 (1.26e-05) | 1 (1.00) | 0.0397 (1.00)
8q loss | 7 (2%) | 436 | 0.701 (1.00) | 0.602 (1.00) | 9.25e-06 (0.00343) | 0.68 (1.00) | 0.672 (1.00)
12p loss | 18 (4%) | 425 | 0.186 (1.00) | 0.00152 (0.515) | 0.000303 (0.107) | 0.603 (1.00) | 0.777 (1.00)
13q loss | 51 (12%) | 392 | 0.0936 (1.00) | 0.00269 (0.905) | 0.000641 (0.224) | 0.518 (1.00) | 1 (1.00)
18q loss | 41 (9%) | 402 | 0.521 (1.00) | 0.0464 (1.00) | 0.000101 (0.0365) | 0.285 (1.00) | 0.44 (1.00)
19p loss | 28 (6%) | 415 | 0.316 (1.00) | 0.985 (1.00) | 5.48e-06 (0.00204) | 1 (1.00) | 0.499 (1.00)
21q loss | 25 (6%) | 418 | 0.227 (1.00) | 0.344 (1.00) | 0.0007 (0.243) | 0.268 (1.00) | 0.334 (1.00)
1p gain | 16 (4%) | 427 | 0.0386 (1.00) | 0.111 (1.00) | 0.0832 (1.00) | 0.412 (1.00) | 1 (1.00)
1q gain | 128 (29%) | 315 | 0.564 (1.00) | 0.0689 (1.00) | 0.0143 (1.00) | 0.569 (1.00) | 0.218 (1.00)
2p gain | 46 (10%) | 397 | 0.0912 (1.00) | 0.028 (1.00) | 0.208 (1.00) | 0.613 (1.00) | 0.273 (1.00)
2q gain | 36 (8%) | 407 | 0.102 (1.00) | 0.158 (1.00) | 0.172 (1.00) | 0.573 (1.00) | 0.311 (1.00)
3p gain | 24 (5%) | 419 | 0.491 (1.00) | 0.403 (1.00) | 0.721 (1.00) | 0.0661 (1.00) | 0.81 (1.00)
3q gain | 43 (10%) | 400 | 0.0485 (1.00) | 0.156 (1.00) | 0.00217 (0.731) | 0.601 (1.00) | 0.185 (1.00)
4p gain | 5 (1%) | 438 | 0.6 (1.00) | 0.024 (1.00) | 0.0345 (1.00) | 0.639 (1.00) | 1 (1.00)
5q gain | 8 (2%) | 435 | 0.329 (1.00) | 0.935 (1.00) | 0.0746 (1.00) | 1 (1.00) | 0.0207 (1.00)
6p gain | 33 (7%) | 410 | 0.691 (1.00) | 0.392 (1.00) | 0.0356 (1.00) | 1 (1.00) | 0.201 (1.00)
6q gain | 28 (6%) | 415 | 0.978 (1.00) | 0.4 (1.00) | 0.0813 (1.00) | 0.525 (1.00) | 0.0634 (1.00)
7p gain | 39 (9%) | 404 | 0.303 (1.00) | 0.625 (1.00) | 0.17 (1.00) | 0.1 (1.00) | 0.436 (1.00)
7q gain | 37 (8%) | 406 | 0.016 (1.00) | 0.692 (1.00) | 0.414 (1.00) | 0.138 (1.00) | 0.158 (1.00)
8p gain | 78 (18%) | 365 | 0.00114 (0.388) | 0.444 (1.00) | 0.418 (1.00) | 0.587 (1.00) | 0.884 (1.00)
8q gain | 102 (23%) | 341 | 0.00639 (1.00) | 0.96 (1.00) | 0.0545 (1.00) | 0.714 (1.00) | 0.0462 (1.00)
9p gain | 11 (2%) | 432 | 0.776 (1.00) | 0.79 (1.00) | 0.923 (1.00) | 0.039 (1.00) | 0.299 (1.00)
9q gain | 3 (1%) | 440 | 0.796 (1.00) | 0.788 (1.00) | 0.269 (1.00) | 0.557 (1.00) | 0.557 (1.00)
10p gain | 82 (19%) | 361 | 0.681 (1.00) | 0.491 (1.00) | 0.224 (1.00) | 0.895 (1.00) | 0.667 (1.00)
10q gain | 77 (17%) | 366 | 0.87 (1.00) | 0.657 (1.00) | 0.239 (1.00) | 1 (1.00) | 0.658 (1.00)
11q gain | 6 (1%) | 437 | 0.563 (1.00) | 0.697 (1.00) | 0.965 (1.00) | 1 (1.00) | 0.0302 (1.00)
12p gain | 33 (7%) | 410 | 0.581 (1.00) | 0.667 (1.00) | 0.0427 (1.00) | 0.844 (1.00) | 0.671 (1.00)
12q gain | 26 (6%) | 417 | 0.724 (1.00) | 0.496 (1.00) | 0.847 (1.00) | 1 (1.00) | 0.641 (1.00)
14q gain | 16 (4%) | 427 | 0.198 (1.00) | 0.621 (1.00) | 0.2 (1.00) | 0.0477 (1.00) | 1 (1.00)
15q gain | 5 (1%) | 438 | 0.0106 (1.00) | 0.51 (1.00) | 0.998 (1.00) | 0.328 (1.00) | 0.0891 (1.00)
16p gain | 11 (2%) | 432 | 0.315 (1.00) | 0.123 (1.00) | 0.0903 (1.00) | 0.517 (1.00) | 0.299 (1.00)
16q gain | 4 (1%) | 439 | 0.664 (1.00) | 0.476 (1.00) | 0.998 (1.00) | 0.321 (1.00) | 1 (1.00)
17q gain | 10 (2%) | 433 | 0.0812 (1.00) | 0.16 (1.00) | 0.938 (1.00) | 0.496 (1.00) | 0.257 (1.00)
18q gain | 15 (3%) | 428 | 0.00363 (1.00) | 0.0425 (1.00) | 0.127 (1.00) | 0.569 (1.00) | 0.0272 (1.00)
21q gain | 20 (5%) | 423 | 0.841 (1.00) | 0.00819 (1.00) | 0.002 (0.677) | 1 (1.00) | 0.59 (1.00)
22q gain | 6 (1%) | 437 | 0.519 (1.00) | 0.0179 (1.00) | 0.117 (1.00) | 1 (1.00) | 0.631 (1.00)
Xq gain | 7 (2%) | 436 | 0.0842 (1.00) | 0.338 (1.00) | 0.249 (1.00) | 1 (1.00) | 1 (1.00)
1p loss | 11 (2%) | 432 | 0.272 (1.00) | 0.255 (1.00) | 0.146 (1.00) | 0.318 (1.00) | 0.727 (1.00)
1q loss | 4 (1%) | 439 | 0.0135 (1.00) | 0.18 (1.00) | 0.221 (1.00) | 0.321 (1.00) | 1 (1.00)
2p loss | 6 (1%) | 437 | 0.528 (1.00) | 0.0696 (1.00) | 0.111 (1.00) | 0.185 (1.00) | 1 (1.00)
2q loss | 7 (2%) | 436 | 0.353 (1.00) | 0.0298 (1.00) | 0.165 (1.00) | 0.108 (1.00) | 1 (1.00)
3p loss | 26 (6%) | 417 | 0.123 (1.00) | 0.0171 (1.00) | 0.00146 (0.498) | 0.828 (1.00) | 0.0308 (1.00)
3q loss | 12 (3%) | 431 | 0.237 (1.00) | 0.143 (1.00) | 0.155 (1.00) | 0.524 (1.00) | 0.166 (1.00)
6p loss | 7 (2%) | 436 | 0.207 (1.00) | 0.167 (1.00) | 0.249 (1.00) | 0.433 (1.00) | 1 (1.00)
6q loss | 9 (2%) | 434 | 0.666 (1.00) | 0.178 (1.00) | 0.154 (1.00) | 0.462 (1.00) | 1 (1.00)
7p loss | 25 (6%) | 418 | 0.37 (1.00) | 0.00998 (1.00) | 0.00112 (0.383) | 1 (1.00) | 0.0555 (1.00)
10p loss | 17 (4%) | 426 | 0.0183 (1.00) | 0.0629 (1.00) | 0.00447 (1.00) | 1 (1.00) | 1 (1.00)
10q loss | 16 (4%) | 427 | 0.371 (1.00) | 0.0299 (1.00) | 0.24 (1.00) | 0.786 (1.00) | 0.379 (1.00)
12q loss | 12 (3%) | 431 | 0.452 (1.00) | 0.0247 (1.00) | 0.0169 (1.00) | 1 (1.00) | 1 (1.00)
18p loss | 28 (6%) | 415 | 0.234 (1.00) | 0.133 (1.00) | 0.00573 (1.00) | 0.672 (1.00) | 0.165 (1.00)
19q loss | 21 (5%) | 422 | 0.529 (1.00) | 0.789 (1.00) | 0.0102 (1.00) | 0.808 (1.00) | 0.601 (1.00)
20p loss | 13 (3%) | 430 | 0.639 (1.00) | 0.0778 (1.00) | 0.196 (1.00) | 0.223 (1.00) | 1 (1.00)
20q loss | 6 (1%) | 437 | 0.476 (1.00) | 0.234 (1.00) | 0.0348 (1.00) | 0.371 (1.00) | 1 (1.00)
Xq loss | 12 (3%) | 431 | 0.516 (1.00) | 0.293 (1.00) | 0.117 (1.00) | 0.119 (1.00) | 0.49 (1.00)

'5p gain mutation analysis' versus 'Time to Death'

P value = 3.3e-05 (logrank test), Q value = 0.012

Table S1. Gene #8: '5p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 438 | 41 | 0.0 - 187.1 (15.8)
5P GAIN MUTATED | 28 | 8 | 0.1 - 59.0 (11.1)
5P GAIN WILD-TYPE | 410 | 33 | 0.0 - 187.1 (16.1)

Figure S1. Get High-res Image Gene #8: '5p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'5p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.21e-06 (Chi-square test), Q value = 0.00083

Table S2. Gene #8: '5p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
5P GAIN MUTATED | 11 | 0 | 0 | 0 | 0 | 1 | 17
5P GAIN WILD-TYPE | 316 | 3 | 8 | 2 | 7 | 17 | 61

Figure S2. Get High-res Image Gene #8: '5p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11p gain mutation analysis' versus 'NEOADJUVANT.THERAPY'

P value = 0.000695 (Fisher's exact test), Q value = 0.24

Table S3. Gene #20: '11p gain mutation analysis' versus Clinical Feature #5: 'NEOADJUVANT.THERAPY'

nPatients | NO | YES
--- | --- | ---
ALL | 105 | 338
11P GAIN MUTATED | 5 | 0
11P GAIN WILD-TYPE | 100 | 338

Figure S3. Get High-res Image Gene #20: '11p gain mutation analysis' versus Clinical Feature #5: 'NEOADJUVANT.THERAPY'

'13q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.68e-05 (Chi-square test), Q value = 0.021

Table S4. Gene #24: '13q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
13Q GAIN MUTATED | 6 | 0 | 0 | 0 | 0 | 1 | 12
13Q GAIN WILD-TYPE | 321 | 3 | 8 | 2 | 7 | 17 | 66

Figure S4. Get High-res Image Gene #24: '13q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17p gain mutation analysis' versus 'Time to Death'

P value = 0.000609 (logrank test), Q value = 0.21

Table S5. Gene #29: '17p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 438 | 41 | 0.0 - 187.1 (15.8)
17P GAIN MUTATED | 6 | 2 | 3.0 - 15.8 (12.1)
17P GAIN WILD-TYPE | 432 | 39 | 0.0 - 187.1 (16.1)

Figure S5. Get High-res Image Gene #29: '17p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'18p gain mutation analysis' versus 'AGE'

P value = 0.000157 (t-test), Q value = 0.056

Table S6. Gene #31: '18p gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
18P GAIN MUTATED | 31 | 70.2 (9.0)
18P GAIN WILD-TYPE | 411 | 63.0 (11.2)

Figure S6. Get High-res Image Gene #31: '18p gain mutation analysis' versus Clinical Feature #2: 'AGE'

'18p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.47e-07 (Chi-square test), Q value = 0.00021

Table S7. Gene #31: '18p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
18P GAIN MUTATED | 11 | 0 | 0 | 0 | 0 | 2 | 18
18P GAIN WILD-TYPE | 316 | 3 | 8 | 2 | 7 | 16 | 60

Figure S7. Get High-res Image Gene #31: '18p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19p gain mutation analysis' versus 'AGE'

P value = 4.47e-05 (t-test), Q value = 0.016

Table S8. Gene #33: '19p gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
19P GAIN MUTATED | 25 | 70.9 (7.7)
19P GAIN WILD-TYPE | 417 | 63.1 (11.3)

Figure S8. Get High-res Image Gene #33: '19p gain mutation analysis' versus Clinical Feature #2: 'AGE'

'19q gain mutation analysis' versus 'AGE'

P value = 1.06e-05 (t-test), Q value = 0.0039

Table S9. Gene #34: '19q gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
19Q GAIN MUTATED | 22 | 72.4 (7.6)
19Q GAIN WILD-TYPE | 420 | 63.1 (11.2)

Figure S9. Get High-res Image Gene #34: '19q gain mutation analysis' versus Clinical Feature #2: 'AGE'

'19q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.71e-07 (Chi-square test), Q value = 1e-04

Table S10. Gene #34: '19q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
19Q GAIN MUTATED | 7 | 0 | 0 | 0 | 0 | 0 | 15
19Q GAIN WILD-TYPE | 320 | 3 | 8 | 2 | 7 | 18 | 63

Figure S10. Get High-res Image Gene #34: '19q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'20p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.04e-06 (Chi-square test), Q value = 0.0019

Table S11. Gene #35: '20p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
20P GAIN MUTATED | 25 | 0 | 0 | 1 | 0 | 3 | 23
20P GAIN WILD-TYPE | 302 | 3 | 8 | 1 | 7 | 15 | 55

Figure S11. Get High-res Image Gene #35: '20p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'20q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.97e-10 (Chi-square test), Q value = 1.5e-07

Table S12. Gene #36: '20q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
20Q GAIN MUTATED | 26 | 0 | 0 | 1 | 0 | 3 | 30
20Q GAIN WILD-TYPE | 301 | 3 | 8 | 1 | 7 | 15 | 48

Figure S12. Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'4p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.23e-11 (Chi-square test), Q value = 3.2e-08

Table S13. Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
4P LOSS MUTATED | 17 | 0 | 0 | 0 | 1 | 3 | 27
4P LOSS WILD-TYPE | 310 | 3 | 8 | 2 | 6 | 15 | 51

Figure S13. Get High-res Image Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'4q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.42e-07 (Chi-square test), Q value = 0.00017

Table S14. Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
4Q LOSS MUTATED | 18 | 0 | 0 | 0 | 1 | 4 | 22
4Q LOSS WILD-TYPE | 309 | 3 | 8 | 2 | 6 | 14 | 56

Figure S14. Get High-res Image Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.02e-05 (Chi-square test), Q value = 0.025

Table S15. Gene #48: '5p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
5P LOSS MUTATED | 7 | 0 | 0 | 0 | 1 | 0 | 12
5P LOSS WILD-TYPE | 320 | 3 | 8 | 2 | 6 | 18 | 66

Figure S15. Get High-res Image Gene #48: '5p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.45e-10 (Chi-square test), Q value = 1.7e-07

Table S16. Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
5Q LOSS MUTATED | 11 | 0 | 0 | 0 | 1 | 1 | 22
5Q LOSS WILD-TYPE | 316 | 3 | 8 | 2 | 6 | 17 | 56

Figure S16. Get High-res Image Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.27e-08 (Chi-square test), Q value = 1.3e-05

Table S17. Gene #53: '7q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
7Q LOSS MUTATED | 6 | 0 | 0 | 0 | 0 | 1 | 16
7Q LOSS WILD-TYPE | 321 | 3 | 8 | 2 | 7 | 17 | 62

Figure S17. Get High-res Image Gene #53: '7q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8p loss mutation analysis' versus 'AGE'

P value = 7.71e-05 (t-test), Q value = 0.028

Table S18. Gene #54: '8p loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
8P LOSS MUTATED | 41 | 68.3 (7.0)
8P LOSS WILD-TYPE | 401 | 63.0 (11.5)

Figure S18. Get High-res Image Gene #54: '8p loss mutation analysis' versus Clinical Feature #2: 'AGE'

'8p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.21e-19 (Chi-square test), Q value = 2.8e-16

Table S19. Gene #54: '8p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
8P LOSS MUTATED | 9 | 0 | 0 | 0 | 0 | 2 | 30
8P LOSS WILD-TYPE | 318 | 3 | 8 | 2 | 7 | 16 | 48

Figure S19. Get High-res Image Gene #54: '8p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.25e-06 (Chi-square test), Q value = 0.0034

Table S20. Gene #55: '8q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
8Q LOSS MUTATED | 0 | 0 | 0 | 0 | 0 | 0 | 7
8Q LOSS WILD-TYPE | 327 | 3 | 8 | 2 | 7 | 18 | 71

Figure S20. Get High-res Image Gene #55: '8q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9p loss mutation analysis' versus 'AGE'

P value = 1.07e-06 (t-test), Q value = 4e-04

Table S21. Gene #56: '9p loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
9P LOSS MUTATED | 64 | 69.1 (8.8)
9P LOSS WILD-TYPE | 378 | 62.6 (11.4)

Figure S21. Get High-res Image Gene #56: '9p loss mutation analysis' versus Clinical Feature #2: 'AGE'

'9p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.11e-14 (Chi-square test), Q value = 1.6e-11

Table S22. Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
9P LOSS MUTATED | 24 | 0 | 0 | 0 | 1 | 4 | 35
9P LOSS WILD-TYPE | 303 | 3 | 8 | 2 | 6 | 14 | 43

Figure S22. Get High-res Image Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9q loss mutation analysis' versus 'AGE'

P value = 1.23e-10 (t-test), Q value = 4.8e-08

Table S23. Gene #57: '9q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
9Q LOSS MUTATED | 81 | 69.9 (8.6)
9Q LOSS WILD-TYPE | 361 | 62.1 (11.3)

Figure S23. Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #2: 'AGE'

'9q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.08e-11 (Chi-square test), Q value = 4.2e-09

Table S24. Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
9Q LOSS MUTATED | 37 | 0 | 0 | 0 | 1 | 5 | 38
9Q LOSS WILD-TYPE | 290 | 3 | 8 | 2 | 6 | 13 | 40

Figure S24. Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11p loss mutation analysis' versus 'Time to Death'

P value = 0.000549 (logrank test), Q value = 0.19

Table S25. Gene #60: '11p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 438 | 41 | 0.0 - 187.1 (15.8)
11P LOSS MUTATED | 44 | 9 | 0.0 - 91.0 (12.1)
11P LOSS WILD-TYPE | 394 | 32 | 0.0 - 187.1 (16.2)

Figure S25. Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'11p loss mutation analysis' versus 'AGE'

P value = 0.000217 (t-test), Q value = 0.077

Table S26. Gene #60: '11p loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
11P LOSS MUTATED | 46 | 68.8 (9.5)
11P LOSS WILD-TYPE | 396 | 62.9 (11.3)

Figure S26. Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #2: 'AGE'

'11p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.1e-06 (Chi-square test), Q value = 0.00041

Table S27. Gene #60: '11p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
11P LOSS MUTATED | 20 | 0 | 0 | 0 | 0 | 4 | 22
11P LOSS WILD-TYPE | 307 | 3 | 8 | 2 | 7 | 14 | 56

Figure S27. Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11q loss mutation analysis' versus 'Time to Death'

P value = 0.000244 (logrank test), Q value = 0.087

Table S28. Gene #61: '11q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 438 | 41 | 0.0 - 187.1 (15.8)
11Q LOSS MUTATED | 37 | 8 | 0.0 - 91.0 (11.8)
11Q LOSS WILD-TYPE | 401 | 33 | 0.0 - 187.1 (16.1)

Figure S28. Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'11q loss mutation analysis' versus 'AGE'

P value = 0.000109 (t-test), Q value = 0.039

Table S29. Gene #61: '11q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
11Q LOSS MUTATED | 39 | 69.7 (9.3)
11Q LOSS WILD-TYPE | 403 | 62.9 (11.2)

Figure S29. Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #2: 'AGE'

'11q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.87e-05 (Chi-square test), Q value = 0.0069

Table S30. Gene #61: '11q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
11Q LOSS MUTATED | 17 | 0 | 0 | 0 | 0 | 5 | 17
11Q LOSS WILD-TYPE | 310 | 3 | 8 | 2 | 7 | 13 | 61

Figure S30. Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000303 (Chi-square test), Q value = 0.11

Table S31. Gene #62: '12p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
12P LOSS MUTATED | 6 | 0 | 0 | 0 | 0 | 1 | 11
12P LOSS WILD-TYPE | 321 | 3 | 8 | 2 | 7 | 17 | 67

Figure S31. Get High-res Image Gene #62: '12p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'13q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000641 (Chi-square test), Q value = 0.22

Table S32. Gene #64: '13q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
13Q LOSS MUTATED | 26 | 0 | 0 | 0 | 2 | 3 | 20
13Q LOSS WILD-TYPE | 301 | 3 | 8 | 2 | 5 | 15 | 58

Figure S32. Get High-res Image Gene #64: '13q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'14q loss mutation analysis' versus 'AGE'

P value = 0.000469 (t-test), Q value = 0.17

Table S33. Gene #65: '14q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
14Q LOSS MUTATED | 36 | 68.7 (8.3)
14Q LOSS WILD-TYPE | 406 | 63.1 (11.4)

Figure S33. Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #2: 'AGE'

'14q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.99e-09 (Chi-square test), Q value = 2.7e-06

Table S34. Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
14Q LOSS MUTATED | 12 | 0 | 0 | 0 | 0 | 3 | 21
14Q LOSS WILD-TYPE | 315 | 3 | 8 | 2 | 7 | 15 | 57

Figure S34. Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'15q loss mutation analysis' versus 'AGE'

P value = 3.87e-05 (t-test), Q value = 0.014

Table S35. Gene #66: '15q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
15Q LOSS MUTATED | 63 | 69.0 (10.7)
15Q LOSS WILD-TYPE | 379 | 62.6 (11.1)

Figure S35. Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #2: 'AGE'

'15q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.42e-10 (Chi-square test), Q value = 1.3e-07

Table S36. Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
15Q LOSS MUTATED | 26 | 0 | 0 | 0 | 1 | 6 | 30
15Q LOSS WILD-TYPE | 301 | 3 | 8 | 2 | 6 | 12 | 48

Figure S36. Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16p loss mutation analysis' versus 'AGE'

P value = 5.76e-05 (t-test), Q value = 0.021

Table S37. Gene #67: '16p loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
16P LOSS MUTATED | 56 | 68.9 (9.8)
16P LOSS WILD-TYPE | 386 | 62.8 (11.2)

Figure S37. Get High-res Image Gene #67: '16p loss mutation analysis' versus Clinical Feature #2: 'AGE'

'16p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.56e-08 (Chi-square test), Q value = 2.5e-05

Table S38. Gene #67: '16p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
16P LOSS MUTATED | 25 | 0 | 0 | 0 | 0 | 5 | 26
16P LOSS WILD-TYPE | 302 | 3 | 8 | 2 | 7 | 13 | 52

Figure S38. Get High-res Image Gene #67: '16p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16q loss mutation analysis' versus 'AGE'

P value = 4.55e-06 (t-test), Q value = 0.0017

Table S39. Gene #68: '16q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
16Q LOSS MUTATED | 92 | 67.8 (9.3)
16Q LOSS WILD-TYPE | 350 | 62.4 (11.5)

Figure S39. Get High-res Image Gene #68: '16q loss mutation analysis' versus Clinical Feature #2: 'AGE'

'16q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.92e-14 (Chi-square test), Q value = 2.7e-11

Table S40. Gene #68: '16q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
16Q LOSS MUTATED | 42 | 0 | 0 | 0 | 1 | 6 | 43
16Q LOSS WILD-TYPE | 285 | 3 | 8 | 2 | 6 | 12 | 35

Figure S40. Get High-res Image Gene #68: '16q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17p loss mutation analysis' versus 'AGE'

P value = 1.23e-06 (t-test), Q value = 0.00046

Table S41. Gene #69: '17p loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
17P LOSS MUTATED | 86 | 68.4 (9.5)
17P LOSS WILD-TYPE | 356 | 62.4 (11.3)

Figure S41. Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #2: 'AGE'

'17p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.25e-20 (Chi-square test), Q value = 8.9e-18

Table S42. Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
17P LOSS MUTATED | 32 | 0 | 0 | 0 | 1 | 7 | 46
17P LOSS WILD-TYPE | 295 | 3 | 8 | 2 | 6 | 11 | 32

Figure S42. Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17q loss mutation analysis' versus 'AGE'

P value = 0.000536 (t-test), Q value = 0.19

Table S43. Gene #70: '17q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
17Q LOSS MUTATED | 57 | 68.4 (10.8)
17Q LOSS WILD-TYPE | 385 | 62.8 (11.1)

Figure S43. Get High-res Image Gene #70: '17q loss mutation analysis' versus Clinical Feature #2: 'AGE'

'17q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.72e-05 (Chi-square test), Q value = 0.014

Table S44. Gene #70: '17q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
17Q LOSS MUTATED | 28 | 0 | 0 | 0 | 1 | 5 | 23
17Q LOSS WILD-TYPE | 299 | 3 | 8 | 2 | 6 | 13 | 55

Figure S44. Get High-res Image Gene #70: '17q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'18q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000101 (Chi-square test), Q value = 0.036

Table S45. Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
18Q LOSS MUTATED | 19 | 0 | 0 | 0 | 1 | 6 | 15
18Q LOSS WILD-TYPE | 308 | 3 | 8 | 2 | 6 | 12 | 63

Figure S45. Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.48e-06 (Chi-square test), Q value = 0.002

Table S46. Gene #73: '19p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
19P LOSS MUTATED | 10 | 0 | 0 | 0 | 0 | 2 | 16
19P LOSS WILD-TYPE | 317 | 3 | 8 | 2 | 7 | 16 | 62

Figure S46. Get High-res Image Gene #73: '19p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'21q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7e-04 (Chi-square test), Q value = 0.24

Table S47. Gene #77: '21q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
21Q LOSS MUTATED | 10 | 0 | 0 | 0 | 0 | 3 | 12
21Q LOSS WILD-TYPE | 317 | 3 | 8 | 2 | 7 | 15 | 66

Figure S47. Get High-res Image Gene #77: '21q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'22q loss mutation analysis' versus 'AGE'

P value = 0.000178 (t-test), Q value = 0.064

Table S48. Gene #78: '22q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 442 | 63.5 (11.2)
22Q LOSS MUTATED | 73 | 67.5 (9.1)
22Q LOSS WILD-TYPE | 369 | 62.8 (11.5)

Figure S48. Get High-res Image Gene #78: '22q loss mutation analysis' versus Clinical Feature #2: 'AGE'

'22q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.89e-08 (Chi-square test), Q value = 1.9e-05

Table S49. Gene #78: '22q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA
--- | --- | --- | --- | --- | --- | --- | ---
ALL | 327 | 3 | 8 | 2 | 7 | 18 | 78
22Q LOSS MUTATED | 35 | 0 | 0 | 0 | 1 | 6 | 31
22Q LOSS WILD-TYPE | 292 | 3 | 8 | 2 | 6 | 12 | 47

Figure S49. Get High-res Image Gene #78: '22q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

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

- Clinical data file = UCEC.clin.merged.picked.txt

- Number of patients = 443

- Number of significantly arm-level cnvs = 79

- Number of selected clinical features = 5

- 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

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

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] 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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