Uterine Corpus Endometrioid Carcinoma: Correlation between copy number variations of arm-level result and selected clinical features
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/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 447 patients, 53 significant findings detected with Q value < 0.25.

  • 3q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

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

  • 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' 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'.

  • 21q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 3p loss 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'.

  • 7p 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 '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'.

  • 19q 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, 53 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test
11q loss 39 (9%) 408 0.000215
(0.075) 		0.00012
(0.0424) 		8.75e-07
(0.000327) 		0.205
(1.00) 		0.0705
(1.00)
5p gain 29 (6%) 418 2.85e-05
(0.0103) 		0.102
(1.00) 		7.3e-07
(0.000274) 		0.675
(1.00) 		0.0603
(1.00)
18p gain 32 (7%) 415 0.0966
(1.00) 		0.000394
(0.136) 		2.78e-08
(1.06e-05) 		0.689
(1.00) 		0.024
(1.00)
19p gain 25 (6%) 422 0.0523
(1.00) 		4.84e-05
(0.0174) 		0.000217
(0.0757) 		0.175
(1.00) 		0.0904
(1.00)
19q gain 22 (5%) 425 0.00798
(1.00) 		1.14e-05
(0.00413) 		4.97e-07
(0.000187) 		0.814
(1.00) 		0.169
(1.00)
8p loss 41 (9%) 406 0.513
(1.00) 		8.76e-05
(0.0312) 		8.24e-17
(3.24e-14) 		0.591
(1.00) 		0.49
(1.00)
9p loss 65 (15%) 382 0.85
(1.00) 		2.7e-06
(0.000996) 		1.1e-14
(4.32e-12) 		1
(1.00) 		0.291
(1.00)
9q loss 82 (18%) 365 0.186
(1.00) 		4.23e-10
(1.63e-07) 		4.82e-13
(1.88e-10) 		0.423
(1.00) 		0.669
(1.00)
11p loss 47 (11%) 400 0.000924
(0.314) 		0.000108
(0.0383) 		2.01e-07
(7.57e-05) 		0.399
(1.00) 		0.529
(1.00)
14q loss 37 (8%) 410 0.284
(1.00) 		0.000234
(0.0813) 		4.84e-09
(1.85e-06) 		1
(1.00) 		0.0805
(1.00)
15q loss 65 (15%) 382 0.757
(1.00) 		3.28e-05
(0.0118) 		2.38e-11
(9.22e-09) 		0.241
(1.00) 		0.833
(1.00)
16p loss 56 (13%) 391 0.0279
(1.00) 		6.56e-05
(0.0235) 		7.49e-09
(2.86e-06) 		0.643
(1.00) 		0.0317
(1.00)
16q loss 93 (21%) 354 0.0373
(1.00) 		2.36e-06
(0.000874) 		2.22e-14
(8.67e-12) 		0.254
(1.00) 		0.0513
(1.00)
17p loss 86 (19%) 361 0.163
(1.00) 		1.53e-06
(0.000571) 		1.9e-20
(7.5e-18) 		0.431
(1.00) 		0.167
(1.00)
17q loss 57 (13%) 390 0.977
(1.00) 		0.000598
(0.205) 		2.12e-06
(0.000786) 		0.162
(1.00) 		0.288
(1.00)
22q loss 73 (16%) 374 0.00769
(1.00) 		0.000208
(0.0729) 		2.79e-09
(1.07e-06) 		0.33
(1.00) 		0.847
(1.00)
3q gain 43 (10%) 404 0.0467
(1.00) 		0.163
(1.00) 		0.000664
(0.227) 		0.602
(1.00) 		0.0542
(1.00)
13q gain 19 (4%) 428 0.447
(1.00) 		0.000813
(0.277) 		9.07e-06
(0.00333) 		0.456
(1.00) 		0.353
(1.00)
17p gain 6 (1%) 441 0.00055
(0.189) 		0.773
(1.00) 		0.458
(1.00) 		0.369
(1.00) 		0.0754
(1.00)
20p gain 52 (12%) 395 0.0121
(1.00) 		0.00541
(1.00) 		1.84e-06
(0.000683) 		0.0154
(1.00) 		0.0689
(1.00)
20q gain 61 (14%) 386 0.0683
(1.00) 		0.0043
(1.00) 		1.14e-10
(4.43e-08) 		0.0154
(1.00) 		0.0251
(1.00)
21q gain 20 (4%) 427 0.838
(1.00) 		0.00859
(1.00) 		0.000426
(0.147) 		1
(1.00) 		0.934
(1.00)
3p loss 26 (6%) 421 0.118
(1.00) 		0.0183
(1.00) 		8.24e-05
(0.0294) 		0.828
(1.00) 		0.82
(1.00)
4p loss 49 (11%) 398 0.054
(1.00) 		0.00183
(0.609) 		1.18e-11
(4.6e-09) 		0.32
(1.00) 		0.0467
(1.00)
4q loss 46 (10%) 401 0.0356
(1.00) 		0.00949
(1.00) 		1.39e-08
(5.3e-06) 		0.0609
(1.00) 		0.602
(1.00)
5p loss 21 (5%) 426 0.424
(1.00) 		0.89
(1.00) 		1.77e-05
(0.00642) 		0.807
(1.00) 		0.152
(1.00)
5q loss 35 (8%) 412 0.94
(1.00) 		0.0199
(1.00) 		1.49e-09
(5.72e-07) 		0.338
(1.00) 		0.187
(1.00)
7p loss 25 (6%) 422 0.36
(1.00) 		0.0105
(1.00) 		0.000117
(0.0416) 		1
(1.00) 		0.268
(1.00)
7q loss 23 (5%) 424 0.839
(1.00) 		0.000941
(0.319) 		3.73e-08
(1.41e-05) 		1
(1.00) 		0.286
(1.00)
8q loss 7 (2%) 440 0.694
(1.00) 		0.609
(1.00) 		7.65e-06
(0.00281) 		0.68
(1.00) 		0.229
(1.00)
12p loss 19 (4%) 428 0.178
(1.00) 		0.00777
(1.00) 		9.07e-06
(0.00333) 		0.608
(1.00) 		0.929
(1.00)
13q loss 52 (12%) 395 0.114
(1.00) 		0.00144
(0.482) 		0.000175
(0.0614) 		0.519
(1.00) 		0.553
(1.00)
18q loss 41 (9%) 406 0.514
(1.00) 		0.0492
(1.00) 		1.04e-05
(0.0038) 		0.287
(1.00) 		0.323
(1.00)
19p loss 29 (6%) 418 0.34
(1.00) 		0.861
(1.00) 		1.97e-07
(7.44e-05) 		1
(1.00) 		0.112
(1.00)
19q loss 22 (5%) 425 0.563
(1.00) 		0.673
(1.00) 		0.000203
(0.0714) 		0.814
(1.00) 		0.103
(1.00)
21q loss 26 (6%) 421 0.248
(1.00) 		0.449
(1.00) 		1.22e-05
(0.00442) 		0.376
(1.00) 		0.281
(1.00)
1p gain 17 (4%) 430 0.0625
(1.00) 		0.0554
(1.00) 		0.0529
(1.00) 		0.417
(1.00) 		0.849
(1.00)
1q gain 129 (29%) 318 0.575
(1.00) 		0.0491
(1.00) 		0.00106
(0.356) 		0.569
(1.00) 		0.0897
(1.00)
2p gain 47 (11%) 400 0.0961
(1.00) 		0.0406
(1.00) 		0.0822
(1.00) 		0.614
(1.00) 		0.64
(1.00)
2q gain 37 (8%) 410 0.114
(1.00) 		0.208
(1.00) 		0.14
(1.00) 		0.574
(1.00) 		0.26
(1.00)
3p gain 24 (5%) 423 0.487
(1.00) 		0.413
(1.00) 		0.557
(1.00) 		0.0666
(1.00) 		0.377
(1.00)
4p gain 5 (1%) 442 0.594
(1.00) 		0.0246
(1.00) 		0.00913
(1.00) 		0.637
(1.00) 		1
(1.00)
5q gain 8 (2%) 439 0.322
(1.00) 		0.929
(1.00) 		0.0109
(1.00) 		1
(1.00) 		0.0374
(1.00)
6p gain 33 (7%) 414 0.682
(1.00) 		0.404
(1.00) 		0.00566
(1.00) 		1
(1.00) 		0.742
(1.00)
6q gain 28 (6%) 419 0.971
(1.00) 		0.411
(1.00) 		0.0158
(1.00) 		0.523
(1.00) 		0.612
(1.00)
7p gain 40 (9%) 407 0.322
(1.00) 		0.714
(1.00) 		0.103
(1.00) 		0.102
(1.00) 		0.757
(1.00)
7q gain 38 (9%) 409 0.0185
(1.00) 		0.606
(1.00) 		0.883
(1.00) 		0.138
(1.00) 		0.48
(1.00)
8p gain 79 (18%) 368 0.00123
(0.414) 		0.383
(1.00) 		0.723
(1.00) 		0.588
(1.00) 		0.2
(1.00)
8q gain 103 (23%) 344 0.00652
(1.00) 		0.871
(1.00) 		0.0111
(1.00) 		0.714
(1.00) 		0.112
(1.00)
9p gain 11 (2%) 436 0.793
(1.00) 		0.784
(1.00) 		0.21
(1.00) 		0.0388
(1.00) 		0.11
(1.00)
9q gain 3 (1%) 444 0.797
(1.00) 		0.783
(1.00) 		0.0473
(1.00) 		0.558
(1.00)
10p gain 82 (18%) 365 0.701
(1.00) 		0.513
(1.00) 		0.427
(1.00) 		0.894
(1.00) 		0.989
(1.00)
10q gain 77 (17%) 370 0.848
(1.00) 		0.681
(1.00) 		0.41
(1.00) 		1
(1.00) 		0.413
(1.00)
11p gain 5 (1%) 442 0.446
(1.00) 		0.648
(1.00) 		0.0782
(1.00) 		0.637
(1.00) 		0.43
(1.00)
11q gain 6 (1%) 441 0.556
(1.00) 		0.705
(1.00) 		0.458
(1.00) 		1
(1.00) 		0.528
(1.00)
12p gain 33 (7%) 414 0.586
(1.00) 		0.68
(1.00) 		0.00667
(1.00) 		0.845
(1.00) 		0.513
(1.00)
12q gain 26 (6%) 421 0.719
(1.00) 		0.485
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.344
(1.00)
14q gain 16 (4%) 431 0.198
(1.00) 		0.634
(1.00) 		0.0428
(1.00) 		0.0476
(1.00) 		0.916
(1.00)
15q gain 5 (1%) 442 0.0101
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.0365
(1.00)
16p gain 11 (2%) 436 0.317
(1.00) 		0.126
(1.00) 		0.0168
(1.00) 		0.519
(1.00) 		0.553
(1.00)
16q gain 4 (1%) 443 0.67
(1.00) 		0.482
(1.00) 		0.626
(1.00) 		0.323
(1.00) 		0.0288
(1.00)
17q gain 10 (2%) 437 0.0784
(1.00) 		0.163
(1.00) 		0.605
(1.00) 		0.493
(1.00) 		0.0477
(1.00)
18q gain 16 (4%) 431 0.00527
(1.00) 		0.0679
(1.00) 		0.0033
(1.00) 		0.413
(1.00) 		0.353
(1.00)
22q gain 6 (1%) 441 0.521
(1.00) 		0.0184
(1.00) 		0.0305
(1.00) 		1
(1.00) 		0.299
(1.00)
Xq gain 7 (2%) 440 0.0893
(1.00) 		0.343
(1.00) 		0.0641
(1.00) 		1
(1.00) 		0.434
(1.00)
1p loss 11 (2%) 436 0.266
(1.00) 		0.26
(1.00) 		0.013
(1.00) 		0.316
(1.00) 		0.443
(1.00)
1q loss 4 (1%) 443 0.0129
(1.00) 		0.182
(1.00) 		0.0224
(1.00) 		0.323
(1.00) 		0.101
(1.00)
2p loss 6 (1%) 441 0.53
(1.00) 		0.071
(1.00) 		0.686
(1.00) 		0.186
(1.00) 		0.0522
(1.00)
2q loss 7 (2%) 440 0.348
(1.00) 		0.0304
(1.00) 		0.52
(1.00) 		0.109
(1.00) 		0.0943
(1.00)
3q loss 12 (3%) 435 0.228
(1.00) 		0.147
(1.00) 		0.0254
(1.00) 		0.523
(1.00) 		0.519
(1.00)
6p loss 7 (2%) 440 0.208
(1.00) 		0.169
(1.00) 		0.0641
(1.00) 		0.43
(1.00) 		1
(1.00)
6q loss 9 (2%) 438 0.671
(1.00) 		0.182
(1.00) 		0.0197
(1.00) 		0.461
(1.00) 		1
(1.00)
10p loss 17 (4%) 430 0.0173
(1.00) 		0.0658
(1.00) 		0.000964
(0.326) 		1
(1.00) 		0.279
(1.00)
10q loss 16 (4%) 431 0.364
(1.00) 		0.0313
(1.00) 		0.0606
(1.00) 		0.787
(1.00) 		0.897
(1.00)
12q loss 12 (3%) 435 0.454
(1.00) 		0.0255
(1.00) 		0.00159
(0.531) 		1
(1.00) 		1
(1.00)
18p loss 28 (6%) 419 0.227
(1.00) 		0.138
(1.00) 		0.00159
(0.531) 		0.673
(1.00) 		0.127
(1.00)
20p loss 13 (3%) 434 0.647
(1.00) 		0.0805
(1.00) 		0.0143
(1.00) 		0.22
(1.00) 		0.519
(1.00)
20q loss 6 (1%) 441 0.479
(1.00) 		0.238
(1.00) 		0.0138
(1.00) 		0.369
(1.00) 		1
(1.00)
Xq loss 13 (3%) 434 0.628
(1.00) 		0.164
(1.00) 		0.0143
(1.00) 		0.12
(1.00) 		0.127
(1.00)
'3q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000664 (Fisher's exact test), Q value = 0.23

Table S1.  Gene #6: '3q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
3Q GAIN MUTATED 24 2 17
3Q GAIN WILD-TYPE 326 16 62

Figure S1.  Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 2.85e-05 (logrank test), Q value = 0.01

Table S2.  Gene #8: '5p gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 442 41 0.0 - 187.1 (15.9)
5P GAIN MUTATED 28 8 0.1 - 59.0 (11.1)
5P GAIN WILD-TYPE 414 33 0.0 - 187.1 (16.2)

Figure S2.  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 = 7.3e-07 (Fisher's exact test), Q value = 0.00027

Table S3.  Gene #8: '5p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
5P GAIN MUTATED 11 1 17
5P GAIN WILD-TYPE 339 17 62

Figure S3.  Get High-res Image Gene #8: '5p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 9.07e-06 (Fisher's exact test), Q value = 0.0033

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
13Q GAIN MUTATED 6 1 12
13Q GAIN WILD-TYPE 344 17 67

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 = 0.00055 (logrank test), Q value = 0.19

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

nPatients nDeath Duration Range (Median), Month
ALL 442 41 0.0 - 187.1 (15.9)
17P GAIN MUTATED 6 2 3.0 - 15.8 (12.1)
17P GAIN WILD-TYPE 436 39 0.0 - 187.1 (16.2)

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

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

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
18P GAIN MUTATED 32 69.8 (9.2)
18P GAIN WILD-TYPE 414 63.1 (11.3)

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 = 2.78e-08 (Fisher's exact test), Q value = 1.1e-05

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
18P GAIN MUTATED 11 2 19
18P GAIN WILD-TYPE 339 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 = 4.84e-05 (t-test), Q value = 0.017

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

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
19P GAIN MUTATED 25 70.9 (7.7)
19P GAIN WILD-TYPE 421 63.1 (11.3)

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

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

P value = 0.000217 (Fisher's exact test), Q value = 0.076

Table S9.  Gene #33: '19p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
19P GAIN MUTATED 12 0 13
19P GAIN WILD-TYPE 338 18 66

Figure S9.  Get High-res Image Gene #33: '19p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19q gain mutation analysis' versus 'AGE'

P value = 1.14e-05 (t-test), Q value = 0.0041

Table S10.  Gene #34: '19q gain mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
19Q GAIN MUTATED 22 72.4 (7.6)
19Q GAIN WILD-TYPE 424 63.1 (11.2)

Figure S10.  Get High-res Image Gene #34: '19q gain mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 4.97e-07 (Fisher's exact test), Q value = 0.00019

Table S11.  Gene #34: '19q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
19Q GAIN MUTATED 7 0 15
19Q GAIN WILD-TYPE 343 18 64

Figure S11.  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 = 1.84e-06 (Fisher's exact test), Q value = 0.00068

Table S12.  Gene #35: '20p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
20P GAIN MUTATED 26 3 23
20P GAIN WILD-TYPE 324 15 56

Figure S12.  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 = 1.14e-10 (Fisher's exact test), Q value = 4.4e-08

Table S13.  Gene #36: '20q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
20Q GAIN MUTATED 27 3 31
20Q GAIN WILD-TYPE 323 15 48

Figure S13.  Get High-res Image Gene #36: '20q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 0.000426 (Fisher's exact test), Q value = 0.15

Table S14.  Gene #37: '21q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
21Q GAIN MUTATED 9 0 11
21Q GAIN WILD-TYPE 341 18 68

Figure S14.  Get High-res Image Gene #37: '21q gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'3p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.24e-05 (Fisher's exact test), Q value = 0.029

Table S15.  Gene #44: '3p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
3P LOSS MUTATED 11 3 12
3P LOSS WILD-TYPE 339 15 67

Figure S15.  Get High-res Image Gene #44: '3p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 1.18e-11 (Fisher's exact test), Q value = 4.6e-09

Table S16.  Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
4P LOSS MUTATED 18 3 28
4P LOSS WILD-TYPE 332 15 51

Figure S16.  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 = 1.39e-08 (Fisher's exact test), Q value = 5.3e-06

Table S17.  Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
4Q LOSS MUTATED 19 4 23
4Q LOSS WILD-TYPE 331 14 56

Figure S17.  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 = 1.77e-05 (Fisher's exact test), Q value = 0.0064

Table S18.  Gene #48: '5p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
5P LOSS MUTATED 8 0 13
5P LOSS WILD-TYPE 342 18 66

Figure S18.  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 = 1.49e-09 (Fisher's exact test), Q value = 5.7e-07

Table S19.  Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
5Q LOSS MUTATED 12 1 22
5Q LOSS WILD-TYPE 338 17 57

Figure S19.  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 = 0.000117 (Fisher's exact test), Q value = 0.042

Table S20.  Gene #52: '7p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
7P LOSS MUTATED 11 1 13
7P LOSS WILD-TYPE 339 17 66

Figure S20.  Get High-res Image Gene #52: '7p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 3.73e-08 (Fisher's exact test), Q value = 1.4e-05

Table S21.  Gene #53: '7q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
7Q LOSS MUTATED 6 1 16
7Q LOSS WILD-TYPE 344 17 63

Figure S21.  Get High-res Image Gene #53: '7q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8p loss mutation analysis' versus 'AGE'

P value = 8.76e-05 (t-test), Q value = 0.031

Table S22.  Gene #54: '8p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
8P LOSS MUTATED 41 68.3 (7.0)
8P LOSS WILD-TYPE 405 63.1 (11.5)

Figure S22.  Get High-res Image Gene #54: '8p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 8.24e-17 (Fisher's exact test), Q value = 3.2e-14

Table S23.  Gene #54: '8p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
8P LOSS MUTATED 9 2 30
8P LOSS WILD-TYPE 341 16 49

Figure S23.  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 = 7.65e-06 (Fisher's exact test), Q value = 0.0028

Table S24.  Gene #55: '8q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
8Q LOSS MUTATED 0 0 7
8Q LOSS WILD-TYPE 350 18 72

Figure S24.  Get High-res Image Gene #55: '8q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9p loss mutation analysis' versus 'AGE'

P value = 2.7e-06 (t-test), Q value = 0.001

Table S25.  Gene #56: '9p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
9P LOSS MUTATED 65 68.9 (8.9)
9P LOSS WILD-TYPE 381 62.7 (11.4)

Figure S25.  Get High-res Image Gene #56: '9p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.1e-14 (Fisher's exact test), Q value = 4.3e-12

Table S26.  Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
9P LOSS MUTATED 25 4 36
9P LOSS WILD-TYPE 325 14 43

Figure S26.  Get High-res Image Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9q loss mutation analysis' versus 'AGE'

P value = 4.23e-10 (t-test), Q value = 1.6e-07

Table S27.  Gene #57: '9q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
9Q LOSS MUTATED 82 69.7 (8.7)
9Q LOSS WILD-TYPE 364 62.2 (11.3)

Figure S27.  Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 4.82e-13 (Fisher's exact test), Q value = 1.9e-10

Table S28.  Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
9Q LOSS MUTATED 38 5 39
9Q LOSS WILD-TYPE 312 13 40

Figure S28.  Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11p loss mutation analysis' versus 'AGE'

P value = 0.000108 (t-test), Q value = 0.038

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

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
11P LOSS MUTATED 47 69.2 (9.7)
11P LOSS WILD-TYPE 399 62.9 (11.3)

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 = 2.01e-07 (Fisher's exact test), Q value = 7.6e-05

Table S30.  Gene #60: '11p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
11P LOSS MUTATED 21 4 22
11P LOSS WILD-TYPE 329 14 57

Figure S30.  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 = 0.000215 (logrank test), Q value = 0.075

Table S31.  Gene #61: '11q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 442 41 0.0 - 187.1 (15.9)
11Q LOSS MUTATED 37 8 0.0 - 91.0 (11.8)
11Q LOSS WILD-TYPE 405 33 0.0 - 187.1 (16.3)

Figure S31.  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 = 0.00012 (t-test), Q value = 0.042

Table S32.  Gene #61: '11q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
11Q LOSS MUTATED 39 69.7 (9.3)
11Q LOSS WILD-TYPE 407 63.0 (11.3)

Figure S32.  Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 8.75e-07 (Fisher's exact test), Q value = 0.00033

Table S33.  Gene #61: '11q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
11Q LOSS MUTATED 17 5 17
11Q LOSS WILD-TYPE 333 13 62

Figure S33.  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 = 9.07e-06 (Fisher's exact test), Q value = 0.0033

Table S34.  Gene #62: '12p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
12P LOSS MUTATED 6 1 12
12P LOSS WILD-TYPE 344 17 67

Figure S34.  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 = 0.000175 (Fisher's exact test), Q value = 0.061

Table S35.  Gene #64: '13q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
13Q LOSS MUTATED 29 3 20
13Q LOSS WILD-TYPE 321 15 59

Figure S35.  Get High-res Image Gene #64: '13q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'14q loss mutation analysis' versus 'AGE'

P value = 0.000234 (t-test), Q value = 0.081

Table S36.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
14Q LOSS MUTATED 37 69.2 (8.7)
14Q LOSS WILD-TYPE 409 63.1 (11.3)

Figure S36.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 4.84e-09 (Fisher's exact test), Q value = 1.9e-06

Table S37.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
14Q LOSS MUTATED 13 3 21
14Q LOSS WILD-TYPE 337 15 58

Figure S37.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'15q loss mutation analysis' versus 'AGE'

P value = 3.28e-05 (t-test), Q value = 0.012

Table S38.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
15Q LOSS MUTATED 65 69.0 (10.8)
15Q LOSS WILD-TYPE 381 62.6 (11.1)

Figure S38.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 2.38e-11 (Fisher's exact test), Q value = 9.2e-09

Table S39.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
15Q LOSS MUTATED 28 6 31
15Q LOSS WILD-TYPE 322 12 48

Figure S39.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16p loss mutation analysis' versus 'AGE'

P value = 6.56e-05 (t-test), Q value = 0.023

Table S40.  Gene #67: '16p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
16P LOSS MUTATED 56 68.9 (9.8)
16P LOSS WILD-TYPE 390 62.8 (11.3)

Figure S40.  Get High-res Image Gene #67: '16p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 7.49e-09 (Fisher's exact test), Q value = 2.9e-06

Table S41.  Gene #67: '16p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
16P LOSS MUTATED 25 5 26
16P LOSS WILD-TYPE 325 13 53

Figure S41.  Get High-res Image Gene #67: '16p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16q loss mutation analysis' versus 'AGE'

P value = 2.36e-06 (t-test), Q value = 0.00087

Table S42.  Gene #68: '16q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
16Q LOSS MUTATED 93 68.0 (9.4)
16Q LOSS WILD-TYPE 353 62.4 (11.4)

Figure S42.  Get High-res Image Gene #68: '16q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 2.22e-14 (Fisher's exact test), Q value = 8.7e-12

Table S43.  Gene #68: '16q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
16Q LOSS MUTATED 44 6 43
16Q LOSS WILD-TYPE 306 12 36

Figure S43.  Get High-res Image Gene #68: '16q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17p loss mutation analysis' versus 'AGE'

P value = 1.53e-06 (t-test), Q value = 0.00057

Table S44.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
17P LOSS MUTATED 86 68.4 (9.5)
17P LOSS WILD-TYPE 360 62.4 (11.3)

Figure S44.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.9e-20 (Fisher's exact test), Q value = 7.5e-18

Table S45.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
17P LOSS MUTATED 33 7 46
17P LOSS WILD-TYPE 317 11 33

Figure S45.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17q loss mutation analysis' versus 'AGE'

P value = 0.000598 (t-test), Q value = 0.21

Table S46.  Gene #70: '17q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
17Q LOSS MUTATED 57 68.4 (10.8)
17Q LOSS WILD-TYPE 389 62.9 (11.2)

Figure S46.  Get High-res Image Gene #70: '17q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 2.12e-06 (Fisher's exact test), Q value = 0.00079

Table S47.  Gene #70: '17q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
17Q LOSS MUTATED 29 5 23
17Q LOSS WILD-TYPE 321 13 56

Figure S47.  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 = 1.04e-05 (Fisher's exact test), Q value = 0.0038

Table S48.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
18Q LOSS MUTATED 20 6 15
18Q LOSS WILD-TYPE 330 12 64

Figure S48.  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 = 1.97e-07 (Fisher's exact test), Q value = 7.4e-05

Table S49.  Gene #73: '19p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
19P LOSS MUTATED 10 2 17
19P LOSS WILD-TYPE 340 16 62

Figure S49.  Get High-res Image Gene #73: '19p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 0.000203 (Fisher's exact test), Q value = 0.071

Table S50.  Gene #74: '19q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
19Q LOSS MUTATED 9 2 11
19Q LOSS WILD-TYPE 341 16 68

Figure S50.  Get High-res Image Gene #74: '19q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 1.22e-05 (Fisher's exact test), Q value = 0.0044

Table S51.  Gene #77: '21q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
21Q LOSS MUTATED 10 3 13
21Q LOSS WILD-TYPE 340 15 66

Figure S51.  Get High-res Image Gene #77: '21q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'22q loss mutation analysis' versus 'AGE'

P value = 0.000208 (t-test), Q value = 0.073

Table S52.  Gene #78: '22q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 446 63.6 (11.3)
22Q LOSS MUTATED 73 67.5 (9.1)
22Q LOSS WILD-TYPE 373 62.8 (11.5)

Figure S52.  Get High-res Image Gene #78: '22q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 2.79e-09 (Fisher's exact test), Q value = 1.1e-06

Table S53.  Gene #78: '22q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 350 18 79
22Q LOSS MUTATED 36 6 31
22Q LOSS WILD-TYPE 314 12 48

Figure S53.  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-TP.clin.merged.picked.txt

  • Number of patients = 447

  • 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

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] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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