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.

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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