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 422 patients, 48 significant findings detected with Q value < 0.25.

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

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

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

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

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

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

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

- 1q loss cnv correlated to 'Time to Death'.

- 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'.

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

- 7q loss cnv correlated to 'AGE' and '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'.

- 10p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

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

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

- 14q loss cnv correlated to '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, 48 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
5p gain | 29 (7%) | 393 | 0.000126 (0.0451) | 0.157 (1.00) | 1.86e-06 (0.000694) | 0.836 (1.00) | 0.262 (1.00)
13q gain | 19 (5%) | 403 | 0.456 (1.00) | 0.000621 (0.217) | 5.06e-05 (0.0183) | 0.615 (1.00) | 0.0981 (1.00)
18p gain | 30 (7%) | 392 | 0.0827 (1.00) | 0.000242 (0.086) | 2.41e-06 (0.000897) | 0.685 (1.00) | 0.826 (1.00)
19p gain | 25 (6%) | 397 | 0.182 (1.00) | 3.51e-05 (0.0127) | 9.68e-05 (0.0348) | 0.269 (1.00) | 0.811 (1.00)
19q gain | 22 (5%) | 400 | 0.0481 (1.00) | 8.27e-06 (0.00304) | 6.99e-09 (2.7e-06) | 0.637 (1.00) | 0.0379 (1.00)
7q loss | 23 (5%) | 399 | 0.838 (1.00) | 0.000703 (0.245) | 2.71e-08 (1.03e-05) | 1 (1.00) | 0.0441 (1.00)
8p loss | 40 (9%) | 382 | 0.509 (1.00) | 3.22e-05 (0.0117) | 4.37e-18 (1.72e-15) | 0.592 (1.00) | 0.00328 (1.00)
9p loss | 58 (14%) | 364 | 0.87 (1.00) | 1.72e-06 (0.000646) | 1.57e-14 (6.15e-12) | 1 (1.00) | 0.00278 (0.92)
9q loss | 73 (17%) | 349 | 0.297 (1.00) | 7.42e-10 (2.88e-07) | 1.66e-12 (6.5e-10) | 0.49 (1.00) | 0.235 (1.00)
11p loss | 43 (10%) | 379 | 0.00284 (0.933) | 0.000576 (0.203) | 6.27e-06 (0.00231) | 0.489 (1.00) | 0.133 (1.00)
11q loss | 37 (9%) | 385 | 0.00167 (0.56) | 0.000394 (0.139) | 2.16e-05 (0.00787) | 0.264 (1.00) | 0.16 (1.00)
15q loss | 59 (14%) | 363 | 0.653 (1.00) | 3.01e-06 (0.00112) | 8.06e-09 (3.1e-06) | 0.364 (1.00) | 0.258 (1.00)
16p loss | 54 (13%) | 368 | 0.0268 (1.00) | 9.01e-06 (0.0033) | 1e-08 (3.84e-06) | 0.434 (1.00) | 0.237 (1.00)
16q loss | 86 (20%) | 336 | 0.0651 (1.00) | 9.45e-07 (0.000355) | 3.64e-15 (1.43e-12) | 0.242 (1.00) | 0.0352 (1.00)
17p loss | 80 (19%) | 342 | 0.254 (1.00) | 8.24e-08 (3.14e-05) | 6.84e-22 (2.7e-19) | 0.503 (1.00) | 0.0095 (1.00)
17q loss | 54 (13%) | 368 | 0.943 (1.00) | 0.000131 (0.0468) | 7.18e-07 (0.000271) | 0.272 (1.00) | 0.612 (1.00)
22q loss | 66 (16%) | 356 | 0.0214 (1.00) | 0.000604 (0.212) | 1.9e-08 (7.27e-06) | 0.385 (1.00) | 0.276 (1.00)
20p gain | 48 (11%) | 374 | 0.0288 (1.00) | 0.00274 (0.911) | 2.33e-06 (0.000871) | 0.021 (1.00) | 0.0756 (1.00)
20q gain | 57 (14%) | 365 | 0.11 (1.00) | 0.000939 (0.322) | 2.15e-11 (8.4e-09) | 0.0203 (1.00) | 0.136 (1.00)
1q loss | 5 (1%) | 417 | 0.000191 (0.0682) | 0.48 (1.00) | 0.101 (1.00) | 0.33 (1.00) | 1 (1.00)
4p loss | 45 (11%) | 377 | 0.0432 (1.00) | 0.00279 (0.92) | 7.43e-10 (2.88e-07) | 0.232 (1.00) | 0.583 (1.00)
4q loss | 43 (10%) | 379 | 0.0285 (1.00) | 0.0102 (1.00) | 6.41e-07 (0.000243) | 0.0356 (1.00) | 1 (1.00)
5p loss | 18 (4%) | 404 | 0.5 (1.00) | 0.164 (1.00) | 5.84e-06 (0.00216) | 0.799 (1.00) | 0.781 (1.00)
5q loss | 32 (8%) | 390 | 0.951 (1.00) | 0.000973 (0.333) | 1.82e-10 (7.08e-08) | 0.43 (1.00) | 0.0891 (1.00)
7p loss | 26 (6%) | 396 | 0.458 (1.00) | 0.00406 (1.00) | 0.000237 (0.0845) | 0.827 (1.00) | 0.0566 (1.00)
8q loss | 7 (2%) | 415 | 0.694 (1.00) | 0.583 (1.00) | 8.5e-06 (0.00312) | 0.444 (1.00) | 0.683 (1.00)
10p loss | 17 (4%) | 405 | 0.013 (1.00) | 0.057 (1.00) | 0.000416 (0.147) | 1 (1.00) | 1 (1.00)
14q loss | 34 (8%) | 388 | 0.208 (1.00) | 0.00113 (0.386) | 1.62e-07 (6.17e-05) | 0.849 (1.00) | 0.063 (1.00)
18q loss | 37 (9%) | 385 | 0.888 (1.00) | 0.0152 (1.00) | 2.42e-05 (0.0088) | 0.264 (1.00) | 0.431 (1.00)
19p loss | 28 (7%) | 394 | 0.376 (1.00) | 0.449 (1.00) | 8.55e-07 (0.000323) | 0.836 (1.00) | 0.651 (1.00)
21q loss | 25 (6%) | 397 | 0.218 (1.00) | 0.316 (1.00) | 0.000616 (0.216) | 0.373 (1.00) | 0.472 (1.00)
1p gain | 13 (3%) | 409 | 0.424 (1.00) | 0.631 (1.00) | 0.241 (1.00) | 0.762 (1.00) | 1 (1.00)
1q gain | 122 (29%) | 300 | 0.718 (1.00) | 0.125 (1.00) | 0.0146 (1.00) | 0.643 (1.00) | 0.216 (1.00)
2p gain | 45 (11%) | 377 | 0.0879 (1.00) | 0.0455 (1.00) | 0.278 (1.00) | 0.61 (1.00) | 0.278 (1.00)
2q gain | 35 (8%) | 387 | 0.0995 (1.00) | 0.256 (1.00) | 0.244 (1.00) | 0.569 (1.00) | 0.314 (1.00)
3p gain | 25 (6%) | 397 | 0.169 (1.00) | 0.39 (1.00) | 0.604 (1.00) | 0.119 (1.00) | 1 (1.00)
3q gain | 42 (10%) | 380 | 0.0437 (1.00) | 0.205 (1.00) | 0.00134 (0.451) | 0.598 (1.00) | 0.187 (1.00)
4p gain | 5 (1%) | 417 | 0.604 (1.00) | 0.0225 (1.00) | 0.0334 (1.00) | 0.648 (1.00) | 1 (1.00)
5q gain | 8 (2%) | 414 | 0.32 (1.00) | 0.952 (1.00) | 0.0724 (1.00) | 1 (1.00) | 0.0245 (1.00)
6p gain | 33 (8%) | 389 | 0.717 (1.00) | 0.325 (1.00) | 0.00911 (1.00) | 0.845 (1.00) | 0.291 (1.00)
6q gain | 28 (7%) | 394 | 0.991 (1.00) | 0.337 (1.00) | 0.0226 (1.00) | 0.398 (1.00) | 0.0713 (1.00)
7p gain | 36 (9%) | 386 | 0.0742 (1.00) | 0.953 (1.00) | 0.127 (1.00) | 0.263 (1.00) | 0.314 (1.00)
7q gain | 35 (8%) | 387 | 0.00257 (0.857) | 0.685 (1.00) | 0.271 (1.00) | 0.342 (1.00) | 0.156 (1.00)
8p gain | 73 (17%) | 349 | 0.000901 (0.311) | 0.288 (1.00) | 0.436 (1.00) | 0.49 (1.00) | 1 (1.00)
8q gain | 96 (23%) | 326 | 0.00521 (1.00) | 0.903 (1.00) | 0.089 (1.00) | 0.707 (1.00) | 0.0589 (1.00)
9p gain | 13 (3%) | 409 | 0.794 (1.00) | 0.899 (1.00) | 0.525 (1.00) | 0.0119 (1.00) | 0.532 (1.00)
9q gain | 3 (1%) | 419 | 0.794 (1.00) | 0.803 (1.00) | 0.262 (1.00) | 0.556 (1.00) | 0.573 (1.00)
10p gain | 80 (19%) | 342 | 0.701 (1.00) | 0.598 (1.00) | 0.126 (1.00) | 1 (1.00) | 0.773 (1.00)
10q gain | 77 (18%) | 345 | 0.922 (1.00) | 0.699 (1.00) | 0.291 (1.00) | 0.892 (1.00) | 0.771 (1.00)
11p gain | 5 (1%) | 417 | 0.447 (1.00) | 0.627 (1.00) | 0.377 (1.00) | 0.648 (1.00) | 0.000844 (0.292)
11q gain | 6 (1%) | 416 | 0.56 (1.00) | 0.676 (1.00) | 0.963 (1.00) | 1 (1.00) | 0.0347 (1.00)
12p gain | 31 (7%) | 391 | 0.599 (1.00) | 0.96 (1.00) | 0.183 (1.00) | 1 (1.00) | 0.523 (1.00)
12q gain | 26 (6%) | 396 | 0.709 (1.00) | 0.524 (1.00) | 0.836 (1.00) | 1 (1.00) | 0.815 (1.00)
14q gain | 15 (4%) | 407 | 0.203 (1.00) | 0.799 (1.00) | 0.397 (1.00) | 0.0448 (1.00) | 0.769 (1.00)
15q gain | 5 (1%) | 417 | 0.0118 (1.00) | 0.518 (1.00) | 0.998 (1.00) | 0.33 (1.00) | 0.0986 (1.00)
16p gain | 9 (2%) | 413 | 0.33 (1.00) | 0.228 (1.00) | 0.15 (1.00) | 0.727 (1.00) | 0.233 (1.00)
16q gain | 3 (1%) | 419 | 0.686 (1.00) | 0.556 (1.00) | 0.994 (1.00) | 0.556 (1.00) | 0.573 (1.00)
17p gain | 5 (1%) | 417 | 0.0844 (1.00) | 0.793 (1.00) | 0.998 (1.00) | 0.176 (1.00) | 0.0986 (1.00)
17q gain | 10 (2%) | 412 | 0.0814 (1.00) | 0.15 (1.00) | 0.935 (1.00) | 0.508 (1.00) | 0.271 (1.00)
18q gain | 15 (4%) | 407 | 0.00752 (1.00) | 0.0659 (1.00) | 0.121 (1.00) | 1 (1.00) | 0.131 (1.00)
21q gain | 17 (4%) | 405 | 0.81 (1.00) | 0.0168 (1.00) | 0.00161 (0.541) | 1 (1.00) | 0.579 (1.00)
22q gain | 6 (1%) | 416 | 0.521 (1.00) | 0.0165 (1.00) | 0.114 (1.00) | 1 (1.00) | 0.639 (1.00)
Xq gain | 7 (2%) | 415 | 0.0812 (1.00) | 0.322 (1.00) | 0.245 (1.00) | 1 (1.00) | 1 (1.00)
1p loss | 12 (3%) | 410 | 0.0641 (1.00) | 0.431 (1.00) | 0.0794 (1.00) | 0.527 (1.00) | 1 (1.00)
2p loss | 6 (1%) | 416 | 0.531 (1.00) | 0.0661 (1.00) | 0.131 (1.00) | 0.183 (1.00) | 1 (1.00)
2q loss | 8 (2%) | 414 | 0.397 (1.00) | 0.0443 (1.00) | 0.238 (1.00) | 0.0624 (1.00) | 0.686 (1.00)
3p loss | 26 (6%) | 396 | 0.116 (1.00) | 0.0142 (1.00) | 0.0013 (0.438) | 0.827 (1.00) | 0.0566 (1.00)
3q loss | 12 (3%) | 410 | 0.231 (1.00) | 0.131 (1.00) | 0.15 (1.00) | 0.357 (1.00) | 0.179 (1.00)
6p loss | 6 (1%) | 416 | 0.188 (1.00) | 0.239 (1.00) | 0.114 (1.00) | 0.0776 (1.00) | 0.639 (1.00)
6q loss | 10 (2%) | 412 | 0.583 (1.00) | 0.133 (1.00) | 0.0429 (1.00) | 0.297 (1.00) | 0.713 (1.00)
10q loss | 16 (4%) | 406 | 0.327 (1.00) | 0.0281 (1.00) | 0.0776 (1.00) | 0.785 (1.00) | 0.377 (1.00)
12p loss | 19 (5%) | 403 | 0.184 (1.00) | 0.000928 (0.319) | 0.000743 (0.258) | 0.802 (1.00) | 0.429 (1.00)
12q loss | 12 (3%) | 410 | 0.442 (1.00) | 0.026 (1.00) | 0.113 (1.00) | 1 (1.00) | 0.5 (1.00)
13q loss | 46 (11%) | 376 | 0.207 (1.00) | 0.00683 (1.00) | 0.00107 (0.364) | 0.502 (1.00) | 1 (1.00)
18p loss | 26 (6%) | 396 | 0.54 (1.00) | 0.0198 (1.00) | 0.0018 (0.6) | 0.512 (1.00) | 0.242 (1.00)
19q loss | 21 (5%) | 401 | 0.612 (1.00) | 0.632 (1.00) | 0.0012 (0.406) | 0.812 (1.00) | 0.613 (1.00)
20p loss | 12 (3%) | 410 | 0.212 (1.00) | 0.144 (1.00) | 0.113 (1.00) | 0.203 (1.00) | 1 (1.00)
20q loss | 6 (1%) | 416 | 0.478 (1.00) | 0.224 (1.00) | 0.0328 (1.00) | 0.38 (1.00) | 1 (1.00)
Xq loss | 12 (3%) | 410 | 0.51 (1.00) | 0.281 (1.00) | 0.113 (1.00) | 0.115 (1.00) | 0.5 (1.00)

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

P value = 0.000126 (logrank test), Q value = 0.045

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

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 418 | 40 | 0.0 - 187.1 (16.6)
5P GAIN MUTATED | 29 | 8 | 0.1 - 85.5 (11.3)
5P GAIN WILD-TYPE | 389 | 32 | 0.0 - 187.1 (16.8)

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 = 1.86e-06 (Chi-square test), Q value = 0.00069

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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
5P GAIN MUTATED | 11 | 0 | 0 | 0 | 0 | 1 | 17
5P GAIN WILD-TYPE | 300 | 3 | 8 | 2 | 7 | 16 | 57

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

'13q gain mutation analysis' versus 'AGE'

P value = 0.000621 (t-test), Q value = 0.22

Table S3. Gene #24: '13q gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
13Q GAIN MUTATED | 19 | 69.3 (6.3)
13Q GAIN WILD-TYPE | 402 | 63.2 (11.2)

Figure S3. Get High-res Image Gene #24: '13q gain mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 5.06e-05 (Chi-square test), Q value = 0.018

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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
13Q GAIN MUTATED | 6 | 0 | 0 | 0 | 0 | 1 | 12
13Q GAIN WILD-TYPE | 305 | 3 | 8 | 2 | 7 | 16 | 62

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

'18p gain mutation analysis' versus 'AGE'

P value = 0.000242 (t-test), Q value = 0.086

Table S5. Gene #31: '18p gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
18P GAIN MUTATED | 30 | 69.5 (8.3)
18P GAIN WILD-TYPE | 391 | 63.0 (11.2)

Figure S5. Get High-res Image Gene #31: '18p gain mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 2.41e-06 (Chi-square test), Q value = 9e-04

Table S6. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
18P GAIN MUTATED | 11 | 0 | 0 | 0 | 0 | 2 | 17
18P GAIN WILD-TYPE | 300 | 3 | 8 | 2 | 7 | 15 | 57

Figure S6. Get High-res Image Gene #31: '18p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19p gain mutation analysis' versus 'AGE'

P value = 3.51e-05 (t-test), Q value = 0.013

Table S7. Gene #33: '19p gain mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
19P GAIN MUTATED | 25 | 70.4 (7.2)
19P GAIN WILD-TYPE | 396 | 63.0 (11.2)

Figure S7. Get High-res Image Gene #33: '19p gain mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 9.68e-05 (Chi-square test), Q value = 0.035

Table S8. Gene #33: '19p 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
19P GAIN MUTATED | 11 | 0 | 0 | 0 | 0 | 0 | 14
19P GAIN WILD-TYPE | 300 | 3 | 8 | 2 | 7 | 17 | 60

Figure S8. Get High-res Image Gene #33: '19p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19q gain mutation analysis' versus 'AGE'

P value = 8.27e-06 (t-test), Q value = 0.003

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

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
19Q GAIN MUTATED | 22 | 71.9 (7.2)
19Q GAIN WILD-TYPE | 399 | 63.0 (11.1)

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

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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
19Q GAIN MUTATED | 6 | 0 | 0 | 0 | 0 | 0 | 16
19Q GAIN WILD-TYPE | 305 | 3 | 8 | 2 | 7 | 17 | 58

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 = 2.33e-06 (Chi-square test), Q value = 0.00087

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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
20P GAIN MUTATED | 22 | 0 | 0 | 1 | 0 | 3 | 22
20P GAIN WILD-TYPE | 289 | 3 | 8 | 1 | 7 | 14 | 52

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 = 2.15e-11 (Chi-square test), Q value = 8.4e-09

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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
20Q GAIN MUTATED | 23 | 0 | 0 | 1 | 0 | 3 | 30
20Q GAIN WILD-TYPE | 288 | 3 | 8 | 1 | 7 | 14 | 44

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

'1q loss mutation analysis' versus 'Time to Death'

P value = 0.000191 (logrank test), Q value = 0.068

Table S13. Gene #41: '1q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 418 | 40 | 0.0 - 187.1 (16.6)
1Q LOSS MUTATED | 5 | 3 | 4.8 - 76.8 (12.4)
1Q LOSS WILD-TYPE | 413 | 37 | 0.0 - 187.1 (16.6)

Figure S13. Get High-res Image Gene #41: '1q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

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

P value = 7.43e-10 (Chi-square test), Q value = 2.9e-07

Table S14. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
4P LOSS MUTATED | 16 | 0 | 0 | 0 | 1 | 3 | 25
4P LOSS WILD-TYPE | 295 | 3 | 8 | 2 | 6 | 14 | 49

Figure S14. 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 = 6.41e-07 (Chi-square test), Q value = 0.00024

Table S15. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
4Q LOSS MUTATED | 17 | 0 | 0 | 0 | 1 | 4 | 21
4Q LOSS WILD-TYPE | 294 | 3 | 8 | 2 | 6 | 13 | 53

Figure S15. 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 = 5.84e-06 (Chi-square test), Q value = 0.0022

Table S16. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
5P LOSS MUTATED | 5 | 0 | 0 | 0 | 1 | 0 | 12
5P LOSS WILD-TYPE | 306 | 3 | 8 | 2 | 6 | 17 | 62

Figure S16. 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 = 1.82e-10 (Chi-square test), Q value = 7.1e-08

Table S17. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
5Q LOSS MUTATED | 9 | 0 | 0 | 0 | 1 | 1 | 21
5Q LOSS WILD-TYPE | 302 | 3 | 8 | 2 | 6 | 16 | 53

Figure S17. Get High-res Image Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 0.000237 (Chi-square test), Q value = 0.084

Table S18. Gene #52: '7p 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
7P LOSS MUTATED | 11 | 0 | 0 | 0 | 0 | 1 | 14
7P LOSS WILD-TYPE | 300 | 3 | 8 | 2 | 7 | 16 | 60

Figure S18. Get High-res Image Gene #52: '7p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7q loss mutation analysis' versus 'AGE'

P value = 0.000703 (t-test), Q value = 0.24

Table S19. Gene #53: '7q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
7Q LOSS MUTATED | 23 | 69.0 (7.0)
7Q LOSS WILD-TYPE | 398 | 63.1 (11.2)

Figure S19. Get High-res Image Gene #53: '7q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 2.71e-08 (Chi-square test), Q value = 1e-05

Table S20. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
7Q LOSS MUTATED | 6 | 0 | 0 | 0 | 0 | 1 | 16
7Q LOSS WILD-TYPE | 305 | 3 | 8 | 2 | 7 | 16 | 58

Figure S20. Get High-res Image Gene #53: '7q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8p loss mutation analysis' versus 'AGE'

P value = 3.22e-05 (t-test), Q value = 0.012

Table S21. Gene #54: '8p loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
8P LOSS MUTATED | 40 | 68.5 (7.0)
8P LOSS WILD-TYPE | 381 | 62.9 (11.3)

Figure S21. Get High-res Image Gene #54: '8p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 4.37e-18 (Chi-square test), Q value = 1.7e-15

Table S22. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
8P LOSS MUTATED | 9 | 0 | 0 | 0 | 0 | 2 | 29
8P LOSS WILD-TYPE | 302 | 3 | 8 | 2 | 7 | 15 | 45

Figure S22. 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 = 8.5e-06 (Chi-square test), Q value = 0.0031

Table S23. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
8Q LOSS MUTATED | 0 | 0 | 0 | 0 | 0 | 0 | 7
8Q LOSS WILD-TYPE | 311 | 3 | 8 | 2 | 7 | 17 | 67

Figure S23. Get High-res Image Gene #55: '8q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9p loss mutation analysis' versus 'AGE'

P value = 1.72e-06 (t-test), Q value = 0.00065

Table S24. Gene #56: '9p loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
9P LOSS MUTATED | 58 | 68.9 (8.3)
9P LOSS WILD-TYPE | 363 | 62.6 (11.3)

Figure S24. Get High-res Image Gene #56: '9p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.57e-14 (Chi-square test), Q value = 6.2e-12

Table S25. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
9P LOSS MUTATED | 20 | 0 | 0 | 0 | 1 | 4 | 33
9P LOSS WILD-TYPE | 291 | 3 | 8 | 2 | 6 | 13 | 41

Figure S25. Get High-res Image Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9q loss mutation analysis' versus 'AGE'

P value = 7.42e-10 (t-test), Q value = 2.9e-07

Table S26. Gene #57: '9q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
9Q LOSS MUTATED | 73 | 69.6 (8.2)
9Q LOSS WILD-TYPE | 348 | 62.1 (11.2)

Figure S26. Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.66e-12 (Chi-square test), Q value = 6.5e-10

Table S27. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
9Q LOSS MUTATED | 31 | 0 | 0 | 0 | 1 | 5 | 36
9Q LOSS WILD-TYPE | 280 | 3 | 8 | 2 | 6 | 12 | 38

Figure S27. Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'10p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000416 (Chi-square test), Q value = 0.15

Table S28. Gene #58: '10p 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
10P LOSS MUTATED | 5 | 0 | 0 | 0 | 1 | 1 | 10
10P LOSS WILD-TYPE | 306 | 3 | 8 | 2 | 6 | 16 | 64

Figure S28. Get High-res Image Gene #58: '10p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11p loss mutation analysis' versus 'AGE'

P value = 0.000576 (t-test), Q value = 0.2

Table S29. Gene #60: '11p loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
11P LOSS MUTATED | 43 | 68.2 (8.8)
11P LOSS WILD-TYPE | 378 | 62.9 (11.2)

Figure S29. Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 6.27e-06 (Chi-square test), Q value = 0.0023

Table S30. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
11P LOSS MUTATED | 19 | 0 | 0 | 0 | 0 | 4 | 20
11P LOSS WILD-TYPE | 292 | 3 | 8 | 2 | 7 | 13 | 54

Figure S30. Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11q loss mutation analysis' versus 'AGE'

P value = 0.000394 (t-test), Q value = 0.14

Table S31. Gene #61: '11q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
11Q LOSS MUTATED | 37 | 68.7 (8.6)
11Q LOSS WILD-TYPE | 384 | 62.9 (11.2)

Figure S31. Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 2.16e-05 (Chi-square test), Q value = 0.0079

Table S32. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
11Q LOSS MUTATED | 16 | 0 | 0 | 0 | 0 | 5 | 16
11Q LOSS WILD-TYPE | 295 | 3 | 8 | 2 | 7 | 12 | 58

Figure S32. Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 1.62e-07 (Chi-square test), Q value = 6.2e-05

Table S33. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
14Q LOSS MUTATED | 12 | 0 | 0 | 0 | 0 | 3 | 19
14Q LOSS WILD-TYPE | 299 | 3 | 8 | 2 | 7 | 14 | 55

Figure S33. Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'15q loss mutation analysis' versus 'AGE'

P value = 3.01e-06 (t-test), Q value = 0.0011

Table S34. Gene #66: '15q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
15Q LOSS MUTATED | 59 | 69.3 (9.5)
15Q LOSS WILD-TYPE | 362 | 62.5 (11.1)

Figure S34. Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 8.06e-09 (Chi-square test), Q value = 3.1e-06

Table S35. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
15Q LOSS MUTATED | 25 | 0 | 0 | 0 | 1 | 6 | 27
15Q LOSS WILD-TYPE | 286 | 3 | 8 | 2 | 6 | 11 | 47

Figure S35. Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16p loss mutation analysis' versus 'AGE'

P value = 9.01e-06 (t-test), Q value = 0.0033

Table S36. Gene #67: '16p loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
16P LOSS MUTATED | 54 | 68.8 (8.5)
16P LOSS WILD-TYPE | 367 | 62.6 (11.2)

Figure S36. Get High-res Image Gene #67: '16p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1e-08 (Chi-square test), Q value = 3.8e-06

Table S37. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
16P LOSS MUTATED | 23 | 0 | 0 | 0 | 0 | 5 | 26
16P LOSS WILD-TYPE | 288 | 3 | 8 | 2 | 7 | 12 | 48

Figure S37. Get High-res Image Gene #67: '16p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16q loss mutation analysis' versus 'AGE'

P value = 9.45e-07 (t-test), Q value = 0.00036

Table S38. Gene #68: '16q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
16Q LOSS MUTATED | 86 | 67.8 (8.3)
16Q LOSS WILD-TYPE | 335 | 62.3 (11.5)

Figure S38. Get High-res Image Gene #68: '16q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 3.64e-15 (Chi-square test), Q value = 1.4e-12

Table S39. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
16Q LOSS MUTATED | 37 | 0 | 0 | 0 | 1 | 6 | 42
16Q LOSS WILD-TYPE | 274 | 3 | 8 | 2 | 6 | 11 | 32

Figure S39. Get High-res Image Gene #68: '16q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17p loss mutation analysis' versus 'AGE'

P value = 8.24e-08 (t-test), Q value = 3.1e-05

Table S40. Gene #69: '17p loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
17P LOSS MUTATED | 80 | 68.4 (8.2)
17P LOSS WILD-TYPE | 341 | 62.3 (11.4)

Figure S40. Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 6.84e-22 (Chi-square test), Q value = 2.7e-19

Table S41. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
17P LOSS MUTATED | 27 | 0 | 0 | 0 | 1 | 8 | 44
17P LOSS WILD-TYPE | 284 | 3 | 8 | 2 | 6 | 9 | 30

Figure S41. Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17q loss mutation analysis' versus 'AGE'

P value = 0.000131 (t-test), Q value = 0.047

Table S42. Gene #70: '17q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
17Q LOSS MUTATED | 54 | 68.2 (9.1)
17Q LOSS WILD-TYPE | 367 | 62.7 (11.2)

Figure S42. Get High-res Image Gene #70: '17q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 7.18e-07 (Chi-square test), Q value = 0.00027

Table S43. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
17Q LOSS MUTATED | 24 | 0 | 0 | 0 | 1 | 6 | 23
17Q LOSS WILD-TYPE | 287 | 3 | 8 | 2 | 6 | 11 | 51

Figure S43. 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 = 2.42e-05 (Chi-square test), Q value = 0.0088

Table S44. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
18Q LOSS MUTATED | 16 | 0 | 0 | 0 | 1 | 6 | 14
18Q LOSS WILD-TYPE | 295 | 3 | 8 | 2 | 6 | 11 | 60

Figure S44. 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 = 8.55e-07 (Chi-square test), Q value = 0.00032

Table S45. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
19P LOSS MUTATED | 9 | 0 | 0 | 0 | 0 | 3 | 16
19P LOSS WILD-TYPE | 302 | 3 | 8 | 2 | 7 | 14 | 58

Figure S45. 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 = 0.000616 (Chi-square test), Q value = 0.22

Table S46. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
21Q LOSS MUTATED | 10 | 0 | 0 | 0 | 0 | 3 | 12
21Q LOSS WILD-TYPE | 301 | 3 | 8 | 2 | 7 | 14 | 62

Figure S46. Get High-res Image Gene #77: '21q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'22q loss mutation analysis' versus 'AGE'

P value = 0.000604 (t-test), Q value = 0.21

Table S47. Gene #78: '22q loss mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 421 | 63.4 (11.1)
22Q LOSS MUTATED | 66 | 67.1 (8.6)
22Q LOSS WILD-TYPE | 355 | 62.8 (11.4)

Figure S47. Get High-res Image Gene #78: '22q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.9e-08 (Chi-square test), Q value = 7.3e-06

Table S48. 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 | 311 | 3 | 8 | 2 | 7 | 17 | 74
22Q LOSS MUTATED | 30 | 0 | 0 | 0 | 1 | 6 | 29
22Q LOSS WILD-TYPE | 281 | 3 | 8 | 2 | 6 | 11 | 45

Figure S48. 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 = 422

- 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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