Correlation between copy number variations of arm-level result and selected clinical features
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1NC5Z6X
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Uterine Corpus Endometrioid Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1NC5Z6X
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 454 patients, 55 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'.

  • 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 'Time to Death',  'AGE', and 'HISTOLOGICAL.TYPE'.

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

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

  • 12q 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, 55 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
11p loss 0 (0%) 405 0.000531
(0.181) 		7.91e-05
(0.0279) 		5.69e-08
(2.16e-05) 		0.32
(1.00) 		0.541
(1.00)
11q loss 0 (0%) 413 0.000143
(0.0499) 		8.79e-05
(0.0309) 		3.51e-07
(0.000131) 		0.155
(1.00) 		0.0814
(1.00)
5p gain 0 (0%) 425 2.57e-05
(0.00932) 		0.108
(1.00) 		1.48e-06
(0.000547) 		0.674
(1.00) 		0.0573
(1.00)
13q gain 0 (0%) 434 0.399
(1.00) 		0.000471
(0.162) 		5.35e-06
(0.00197) 		0.618
(1.00) 		0.172
(1.00)
18p gain 0 (0%) 420 0.129
(1.00) 		0.000385
(0.133) 		6.24e-09
(2.37e-06) 		0.558
(1.00) 		0.0318
(1.00)
19p gain 0 (0%) 428 0.0734
(1.00) 		2.84e-05
(0.0103) 		0.000133
(0.0467) 		0.276
(1.00) 		0.0982
(1.00)
19q gain 0 (0%) 431 0.00816
(1.00) 		6.14e-06
(0.00225) 		2.49e-07
(9.31e-05) 		0.64
(1.00) 		0.18
(1.00)
8p loss 0 (0%) 410 0.351
(1.00) 		3.38e-05
(0.0121) 		3.51e-18
(1.38e-15) 		0.73
(1.00) 		0.594
(1.00)
9p loss 0 (0%) 387 0.696
(1.00) 		3.32e-06
(0.00122) 		5.64e-15
(2.2e-12) 		0.885
(1.00) 		0.177
(1.00)
9q loss 0 (0%) 371 0.211
(1.00) 		3.71e-10
(1.43e-07) 		1.73e-12
(6.7e-10) 		0.595
(1.00) 		0.67
(1.00)
14q loss 0 (0%) 416 0.342
(1.00) 		0.000169
(0.059) 		4.4e-09
(1.68e-06) 		0.853
(1.00) 		0.0762
(1.00)
15q loss 0 (0%) 385 0.619
(1.00) 		2.91e-05
(0.0105) 		7.77e-13
(3.03e-10) 		0.252
(1.00) 		0.919
(1.00)
16p loss 0 (0%) 395 0.0166
(1.00) 		3.3e-05
(0.0118) 		7.87e-10
(3.02e-07) 		0.76
(1.00) 		0.0339
(1.00)
16q loss 0 (0%) 357 0.0229
(1.00) 		9.45e-07
(0.00035) 		1.24e-15
(4.84e-13) 		0.261
(1.00) 		0.0416
(1.00)
17p loss 0 (0%) 364 0.124
(1.00) 		6.58e-07
(0.000245) 		8.68e-22
(3.42e-19) 		0.439
(1.00) 		0.126
(1.00)
17q loss 0 (0%) 393 0.815
(1.00) 		0.000264
(0.0914) 		9.97e-08
(3.75e-05) 		0.174
(1.00) 		0.207
(1.00)
22q loss 0 (0%) 378 0.00403
(1.00) 		0.000369
(0.128) 		5.95e-10
(2.29e-07) 		0.27
(1.00) 		0.67
(1.00)
17p gain 0 (0%) 448 0.000521
(0.178) 		0.762
(1.00) 		0.477
(1.00) 		0.367
(1.00) 		0.0755
(1.00)
20p gain 0 (0%) 398 0.0072
(1.00) 		0.00239
(0.787) 		6.56e-08
(2.47e-05) 		0.0187
(1.00) 		0.0744
(1.00)
20q gain 0 (0%) 388 0.0423
(1.00) 		0.00265
(0.868) 		8.67e-13
(3.37e-10) 		0.013
(1.00) 		0.0205
(1.00)
21q gain 0 (0%) 432 0.85
(1.00) 		0.00279
(0.911) 		7.27e-05
(0.0257) 		1
(1.00) 		0.773
(1.00)
3p loss 0 (0%) 427 0.122
(1.00) 		0.00974
(1.00) 		5.79e-05
(0.0206) 		0.829
(1.00) 		0.792
(1.00)
4p loss 0 (0%) 402 0.0411
(1.00) 		0.000759
(0.257) 		1.15e-12
(4.48e-10) 		0.196
(1.00) 		0.0746
(1.00)
4q loss 0 (0%) 405 0.0273
(1.00) 		0.00544
(1.00) 		1.3e-09
(5e-07) 		0.0318
(1.00) 		0.501
(1.00)
5p loss 0 (0%) 433 0.327
(1.00) 		0.911
(1.00) 		2.87e-05
(0.0104) 		0.807
(1.00) 		0.153
(1.00)
5q loss 0 (0%) 419 0.8
(1.00) 		0.0219
(1.00) 		6.11e-09
(2.33e-06) 		0.336
(1.00) 		0.187
(1.00)
7p loss 0 (0%) 429 0.352
(1.00) 		0.0113
(1.00) 		0.000262
(0.0911) 		1
(1.00) 		0.255
(1.00)
7q loss 0 (0%) 431 0.848
(1.00) 		0.00105
(0.355) 		6.37e-08
(2.41e-05) 		1
(1.00) 		0.287
(1.00)
8q loss 0 (0%) 447 0.689
(1.00) 		0.62
(1.00) 		1.53e-05
(0.00558) 		0.679
(1.00) 		0.228
(1.00)
12p loss 0 (0%) 433 0.422
(1.00) 		0.00817
(1.00) 		1.33e-06
(0.00049) 		0.633
(1.00) 		0.873
(1.00)
12q loss 0 (0%) 441 0.447
(1.00) 		0.0157
(1.00) 		0.000482
(0.165) 		1
(1.00) 		1
(1.00)
13q loss 0 (0%) 402 0.137
(1.00) 		0.00167
(0.559) 		0.000477
(0.163) 		0.52
(1.00) 		0.545
(1.00)
18q loss 0 (0%) 412 0.505
(1.00) 		0.0433
(1.00) 		7.98e-06
(0.00291) 		0.287
(1.00) 		0.16
(1.00)
19p loss 0 (0%) 424 0.345
(1.00) 		0.906
(1.00) 		1.44e-07
(5.39e-05) 		0.837
(1.00) 		0.124
(1.00)
19q loss 0 (0%) 430 0.572
(1.00) 		0.99
(1.00) 		3.61e-05
(0.0128) 		1
(1.00) 		0.0808
(1.00)
21q loss 0 (0%) 428 0.307
(1.00) 		0.469
(1.00) 		2.92e-05
(0.0105) 		0.375
(1.00) 		0.293
(1.00)
1p gain 0 (0%) 436 0.0642
(1.00) 		0.0394
(1.00) 		0.0272
(1.00) 		0.605
(1.00) 		0.85
(1.00)
1q gain 0 (0%) 323 0.56
(1.00) 		0.062
(1.00) 		0.000772
(0.261) 		0.496
(1.00) 		0.0784
(1.00)
2p gain 0 (0%) 406 0.0921
(1.00) 		0.0363
(1.00) 		0.0609
(1.00) 		0.509
(1.00) 		0.518
(1.00)
2q gain 0 (0%) 416 0.111
(1.00) 		0.187
(1.00) 		0.116
(1.00) 		0.463
(1.00) 		0.172
(1.00)
3p gain 0 (0%) 430 0.478
(1.00) 		0.428
(1.00) 		0.568
(1.00) 		0.0673
(1.00) 		0.361
(1.00)
3q gain 0 (0%) 411 0.0444
(1.00) 		0.176
(1.00) 		0.00168
(0.559) 		0.603
(1.00) 		0.0524
(1.00)
4p gain 0 (0%) 448 0.596
(1.00) 		0.00713
(1.00) 		0.00252
(0.829) 		1
(1.00) 		0.677
(1.00)
5q gain 0 (0%) 446 0.317
(1.00) 		0.919
(1.00) 		0.0128
(1.00) 		1
(1.00) 		0.0324
(1.00)
6p gain 0 (0%) 420 0.685
(1.00) 		0.283
(1.00) 		0.00418
(1.00) 		1
(1.00) 		0.733
(1.00)
6q gain 0 (0%) 425 0.975
(1.00) 		0.284
(1.00) 		0.0107
(1.00) 		0.534
(1.00) 		0.673
(1.00)
7p gain 0 (0%) 414 0.373
(1.00) 		0.738
(1.00) 		0.17
(1.00) 		0.102
(1.00) 		0.737
(1.00)
7q gain 0 (0%) 416 0.0264
(1.00) 		0.585
(1.00) 		0.886
(1.00) 		0.139
(1.00) 		0.48
(1.00)
8p gain 0 (0%) 374 0.0017
(0.564) 		0.314
(1.00) 		0.805
(1.00) 		0.589
(1.00) 		0.214
(1.00)
8q gain 0 (0%) 349 0.00798
(1.00) 		0.711
(1.00) 		0.0216
(1.00) 		0.715
(1.00) 		0.12
(1.00)
9p gain 0 (0%) 443 0.787
(1.00) 		0.774
(1.00) 		0.274
(1.00) 		0.0387
(1.00) 		0.0956
(1.00)
9q gain 0 (0%) 451 0.797
(1.00) 		0.775
(1.00) 		0.0495
(1.00) 		0.559
(1.00)
10p gain 0 (0%) 372 0.667
(1.00) 		0.548
(1.00) 		0.286
(1.00) 		0.894
(1.00) 		0.979
(1.00)
10q gain 0 (0%) 377 0.889
(1.00) 		0.718
(1.00) 		0.275
(1.00) 		1
(1.00) 		0.379
(1.00)
11p gain 0 (0%) 448 0.448
(1.00) 		0.48
(1.00) 		0.0423
(1.00) 		1
(1.00) 		0.0572
(1.00)
11q gain 0 (0%) 447 0.551
(1.00) 		0.526
(1.00) 		0.264
(1.00) 		1
(1.00) 		0.203
(1.00)
12p gain 0 (0%) 421 0.534
(1.00) 		0.702
(1.00) 		0.00923
(1.00) 		0.845
(1.00) 		0.498
(1.00)
12q gain 0 (0%) 428 0.801
(1.00) 		0.47
(1.00) 		0.455
(1.00) 		0.829
(1.00) 		0.317
(1.00)
14q gain 0 (0%) 437 0.2
(1.00) 		0.424
(1.00) 		0.0141
(1.00) 		0.0294
(1.00) 		0.919
(1.00)
15q gain 0 (0%) 449 0.00974
(1.00) 		0.503
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.0368
(1.00)
16p gain 0 (0%) 443 0.319
(1.00) 		0.131
(1.00) 		0.0191
(1.00) 		0.52
(1.00) 		0.553
(1.00)
16q gain 0 (0%) 450 0.671
(1.00) 		0.49
(1.00) 		0.644
(1.00) 		0.325
(1.00) 		0.0184
(1.00)
17q gain 0 (0%) 443 0.0904
(1.00) 		0.0815
(1.00) 		0.341
(1.00) 		0.739
(1.00) 		0.067
(1.00)
18q gain 0 (0%) 437 0.0121
(1.00) 		0.0375
(1.00) 		0.00139
(0.467) 		0.417
(1.00) 		0.391
(1.00)
22q gain 0 (0%) 447 0.507
(1.00) 		0.0248
(1.00) 		0.00622
(1.00) 		1
(1.00) 		0.367
(1.00)
Xq gain 0 (0%) 446 0.102
(1.00) 		0.167
(1.00) 		0.0128
(1.00) 		1
(1.00) 		0.496
(1.00)
1p loss 0 (0%) 443 0.344
(1.00) 		0.267
(1.00) 		0.0141
(1.00) 		0.314
(1.00) 		0.388
(1.00)
1q loss 0 (0%) 450 0.0124
(1.00) 		0.184
(1.00) 		0.0236
(1.00) 		0.325
(1.00) 		0.0787
(1.00)
2p loss 0 (0%) 448 0.532
(1.00) 		0.0731
(1.00) 		0.688
(1.00) 		0.186
(1.00) 		0.0526
(1.00)
2q loss 0 (0%) 447 0.344
(1.00) 		0.0313
(1.00) 		0.515
(1.00) 		0.111
(1.00) 		0.0946
(1.00)
3q loss 0 (0%) 442 0.223
(1.00) 		0.155
(1.00) 		0.0369
(1.00) 		0.523
(1.00) 		0.518
(1.00)
6p loss 0 (0%) 447 0.152
(1.00) 		0.173
(1.00) 		0.07
(1.00) 		0.426
(1.00) 		1
(1.00)
6q loss 0 (0%) 445 0.51
(1.00) 		0.188
(1.00) 		0.0322
(1.00) 		0.46
(1.00) 		1
(1.00)
10p loss 0 (0%) 437 0.0289
(1.00) 		0.0704
(1.00) 		0.00169
(0.561) 		1
(1.00) 		0.28
(1.00)
10q loss 0 (0%) 437 0.447
(1.00) 		0.0158
(1.00) 		0.0471
(1.00) 		0.788
(1.00) 		1
(1.00)
18p loss 0 (0%) 425 0.221
(1.00) 		0.119
(1.00) 		0.00125
(0.421) 		0.674
(1.00) 		0.0764
(1.00)
20p loss 0 (0%) 441 0.574
(1.00) 		0.0847
(1.00) 		0.0233
(1.00) 		0.218
(1.00) 		0.518
(1.00)
20q loss 0 (0%) 448 0.48
(1.00) 		0.244
(1.00) 		0.0144
(1.00) 		0.367
(1.00) 		1
(1.00)
Xq loss 0 (0%) 440 0.621
(1.00) 		0.105
(1.00) 		0.00858
(1.00) 		0.0753
(1.00) 		0.159
(1.00)
'5p gain' versus 'Time to Death'

P value = 2.57e-05 (logrank test), Q value = 0.0093

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

nPatients nDeath Duration Range (Median), Month
ALL 450 42 0.0 - 187.1 (15.5)
5P GAIN CNV 29 8 0.1 - 59.0 (10.9)
5P GAIN WILD-TYPE 421 34 0.0 - 187.1 (15.9)

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

'5p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.48e-06 (Fisher's exact test), Q value = 0.00055

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
5P GAIN CNV 11 1 17
5P GAIN WILD-TYPE 340 17 68

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

'13q gain' versus 'AGE'

P value = 0.000471 (t-test), Q value = 0.16

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

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
13Q GAIN CNV 20 69.3 (6.1)
13Q GAIN WILD-TYPE 433 63.4 (11.4)

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

'13q gain' versus 'HISTOLOGICAL.TYPE'

P value = 5.35e-06 (Fisher's exact test), Q value = 0.002

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
13Q GAIN CNV 6 1 13
13Q GAIN WILD-TYPE 345 17 72

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

'17p gain' versus 'Time to Death'

P value = 0.000521 (logrank test), Q value = 0.18

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

nPatients nDeath Duration Range (Median), Month
ALL 450 42 0.0 - 187.1 (15.5)
17P GAIN CNV 6 2 3.0 - 15.8 (12.1)
17P GAIN WILD-TYPE 444 40 0.0 - 187.1 (15.9)

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

'18p gain' versus 'AGE'

P value = 0.000385 (t-test), Q value = 0.13

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

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
18P GAIN CNV 34 69.7 (9.4)
18P GAIN WILD-TYPE 419 63.1 (11.2)

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

'18p gain' versus 'HISTOLOGICAL.TYPE'

P value = 6.24e-09 (Fisher's exact test), Q value = 2.4e-06

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
18P GAIN CNV 11 2 21
18P GAIN WILD-TYPE 340 16 64

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

'19p gain' versus 'AGE'

P value = 2.84e-05 (t-test), Q value = 0.01

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

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
19P GAIN CNV 26 70.9 (7.5)
19P GAIN WILD-TYPE 427 63.2 (11.3)

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

'19p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000133 (Fisher's exact test), Q value = 0.047

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
19P GAIN CNV 12 0 14
19P GAIN WILD-TYPE 339 18 71

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

'19q gain' versus 'AGE'

P value = 6.14e-06 (t-test), Q value = 0.0022

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

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
19Q GAIN CNV 23 72.3 (7.5)
19Q GAIN WILD-TYPE 430 63.2 (11.2)

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

'19q gain' versus 'HISTOLOGICAL.TYPE'

P value = 2.49e-07 (Fisher's exact test), Q value = 9.3e-05

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
19Q GAIN CNV 7 0 16
19Q GAIN WILD-TYPE 344 18 69

Figure S11.  Get High-res Image Gene #34: '19q gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 6.56e-08 (Fisher's exact test), Q value = 2.5e-05

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
20P GAIN CNV 26 3 27
20P GAIN WILD-TYPE 325 15 58

Figure S12.  Get High-res Image Gene #35: '20p gain' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 8.67e-13 (Fisher's exact test), Q value = 3.4e-10

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
20Q GAIN CNV 27 3 36
20Q GAIN WILD-TYPE 324 15 49

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

'21q gain' versus 'HISTOLOGICAL.TYPE'

P value = 7.27e-05 (Fisher's exact test), Q value = 0.026

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
21Q GAIN CNV 9 0 13
21Q GAIN WILD-TYPE 342 18 72

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

'3p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.79e-05 (Fisher's exact test), Q value = 0.021

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
3P LOSS CNV 11 3 13
3P LOSS WILD-TYPE 340 15 72

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

'4p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.15e-12 (Fisher's exact test), Q value = 4.5e-10

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
4P LOSS CNV 18 3 31
4P LOSS WILD-TYPE 333 15 54

Figure S16.  Get High-res Image Gene #46: '4p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'4q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.3e-09 (Fisher's exact test), Q value = 5e-07

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
4Q LOSS CNV 19 4 26
4Q LOSS WILD-TYPE 332 14 59

Figure S17.  Get High-res Image Gene #47: '4q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5p loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.87e-05 (Fisher's exact test), Q value = 0.01

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
5P LOSS CNV 8 0 13
5P LOSS WILD-TYPE 343 18 72

Figure S18.  Get High-res Image Gene #48: '5p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'5q loss' versus 'HISTOLOGICAL.TYPE'

P value = 6.11e-09 (Fisher's exact test), Q value = 2.3e-06

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
5Q LOSS CNV 12 1 22
5Q LOSS WILD-TYPE 339 17 63

Figure S19.  Get High-res Image Gene #49: '5q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7p loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000262 (Fisher's exact test), Q value = 0.091

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
7P LOSS CNV 11 1 13
7P LOSS WILD-TYPE 340 17 72

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

'7q loss' versus 'HISTOLOGICAL.TYPE'

P value = 6.37e-08 (Fisher's exact test), Q value = 2.4e-05

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
7Q LOSS CNV 6 1 16
7Q LOSS WILD-TYPE 345 17 69

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

'8p loss' versus 'AGE'

P value = 3.38e-05 (t-test), Q value = 0.012

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

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
8P LOSS CNV 44 68.6 (7.4)
8P LOSS WILD-TYPE 409 63.1 (11.5)

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

'8p loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.51e-18 (Fisher's exact test), Q value = 1.4e-15

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
8P LOSS CNV 9 2 33
8P LOSS WILD-TYPE 342 16 52

Figure S23.  Get High-res Image Gene #54: '8p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.53e-05 (Fisher's exact test), Q value = 0.0056

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
8Q LOSS CNV 0 0 7
8Q LOSS WILD-TYPE 351 18 78

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

'9p loss' versus 'AGE'

P value = 3.32e-06 (t-test), Q value = 0.0012

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

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
9P LOSS CNV 67 68.7 (8.8)
9P LOSS WILD-TYPE 386 62.8 (11.4)

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

'9p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.64e-15 (Fisher's exact test), Q value = 2.2e-12

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
9P LOSS CNV 25 4 38
9P LOSS WILD-TYPE 326 14 47

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

'9q loss' versus 'AGE'

P value = 3.71e-10 (t-test), Q value = 1.4e-07

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

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
9Q LOSS CNV 83 69.8 (8.7)
9Q LOSS WILD-TYPE 370 62.3 (11.3)

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

'9q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.73e-12 (Fisher's exact test), Q value = 6.7e-10

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
9Q LOSS CNV 38 5 40
9Q LOSS WILD-TYPE 313 13 45

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

'11p loss' versus 'Time to Death'

P value = 0.000531 (logrank test), Q value = 0.18

Table S29.  Gene #60: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 450 42 0.0 - 187.1 (15.5)
11P LOSS CNV 48 10 0.0 - 102.0 (12.1)
11P LOSS WILD-TYPE 402 32 0.0 - 187.1 (16.0)

Figure S29.  Get High-res Image Gene #60: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'AGE'

P value = 7.91e-05 (t-test), Q value = 0.028

Table S30.  Gene #60: '11p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
11P LOSS CNV 49 69.3 (9.8)
11P LOSS WILD-TYPE 404 63.0 (11.2)

Figure S30.  Get High-res Image Gene #60: '11p loss' versus Clinical Feature #2: 'AGE'

'11p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.69e-08 (Fisher's exact test), Q value = 2.2e-05

Table S31.  Gene #60: '11p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
11P LOSS CNV 21 4 24
11P LOSS WILD-TYPE 330 14 61

Figure S31.  Get High-res Image Gene #60: '11p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11q loss' versus 'Time to Death'

P value = 0.000143 (logrank test), Q value = 0.05

Table S32.  Gene #61: '11q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 450 42 0.0 - 187.1 (15.5)
11Q LOSS CNV 40 9 0.0 - 102.0 (11.6)
11Q LOSS WILD-TYPE 410 33 0.0 - 187.1 (16.0)

Figure S32.  Get High-res Image Gene #61: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'AGE'

P value = 8.79e-05 (t-test), Q value = 0.031

Table S33.  Gene #61: '11q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
11Q LOSS CNV 41 69.7 (9.4)
11Q LOSS WILD-TYPE 412 63.0 (11.2)

Figure S33.  Get High-res Image Gene #61: '11q loss' versus Clinical Feature #2: 'AGE'

'11q loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.51e-07 (Fisher's exact test), Q value = 0.00013

Table S34.  Gene #61: '11q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
11Q LOSS CNV 17 5 19
11Q LOSS WILD-TYPE 334 13 66

Figure S34.  Get High-res Image Gene #61: '11q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.33e-06 (Fisher's exact test), Q value = 0.00049

Table S35.  Gene #62: '12p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
12P LOSS CNV 6 1 14
12P LOSS WILD-TYPE 345 17 71

Figure S35.  Get High-res Image Gene #62: '12p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000482 (Fisher's exact test), Q value = 0.16

Table S36.  Gene #63: '12q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
12Q LOSS CNV 4 1 8
12Q LOSS WILD-TYPE 347 17 77

Figure S36.  Get High-res Image Gene #63: '12q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'13q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000477 (Fisher's exact test), Q value = 0.16

Table S37.  Gene #64: '13q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
13Q LOSS CNV 29 3 20
13Q LOSS WILD-TYPE 322 15 65

Figure S37.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'14q loss' versus 'AGE'

P value = 0.000169 (t-test), Q value = 0.059

Table S38.  Gene #65: '14q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
14Q LOSS CNV 38 69.2 (8.6)
14Q LOSS WILD-TYPE 415 63.1 (11.3)

Figure S38.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #2: 'AGE'

'14q loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.4e-09 (Fisher's exact test), Q value = 1.7e-06

Table S39.  Gene #65: '14q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
14Q LOSS CNV 13 3 22
14Q LOSS WILD-TYPE 338 15 63

Figure S39.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'15q loss' versus 'AGE'

P value = 2.91e-05 (t-test), Q value = 0.01

Table S40.  Gene #66: '15q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
15Q LOSS CNV 69 68.9 (10.7)
15Q LOSS WILD-TYPE 384 62.7 (11.1)

Figure S40.  Get High-res Image Gene #66: '15q loss' versus Clinical Feature #2: 'AGE'

'15q loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.77e-13 (Fisher's exact test), Q value = 3e-10

Table S41.  Gene #66: '15q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
15Q LOSS CNV 28 6 35
15Q LOSS WILD-TYPE 323 12 50

Figure S41.  Get High-res Image Gene #66: '15q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16p loss' versus 'AGE'

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

Table S42.  Gene #67: '16p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
16P LOSS CNV 59 69.0 (9.8)
16P LOSS WILD-TYPE 394 62.8 (11.2)

Figure S42.  Get High-res Image Gene #67: '16p loss' versus Clinical Feature #2: 'AGE'

'16p loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.87e-10 (Fisher's exact test), Q value = 3e-07

Table S43.  Gene #67: '16p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
16P LOSS CNV 25 5 29
16P LOSS WILD-TYPE 326 13 56

Figure S43.  Get High-res Image Gene #67: '16p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16q loss' versus 'AGE'

P value = 9.45e-07 (t-test), Q value = 0.00035

Table S44.  Gene #68: '16q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
16Q LOSS CNV 97 68.1 (9.4)
16Q LOSS WILD-TYPE 356 62.4 (11.4)

Figure S44.  Get High-res Image Gene #68: '16q loss' versus Clinical Feature #2: 'AGE'

'16q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.24e-15 (Fisher's exact test), Q value = 4.8e-13

Table S45.  Gene #68: '16q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
16Q LOSS CNV 44 6 47
16Q LOSS WILD-TYPE 307 12 38

Figure S45.  Get High-res Image Gene #68: '16q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17p loss' versus 'AGE'

P value = 6.58e-07 (t-test), Q value = 0.00024

Table S46.  Gene #69: '17p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
17P LOSS CNV 90 68.4 (9.4)
17P LOSS WILD-TYPE 363 62.4 (11.4)

Figure S46.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #2: 'AGE'

'17p loss' versus 'HISTOLOGICAL.TYPE'

P value = 8.68e-22 (Fisher's exact test), Q value = 3.4e-19

Table S47.  Gene #69: '17p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
17P LOSS CNV 33 7 50
17P LOSS WILD-TYPE 318 11 35

Figure S47.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17q loss' versus 'AGE'

P value = 0.000264 (t-test), Q value = 0.091

Table S48.  Gene #70: '17q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
17Q LOSS CNV 61 68.5 (10.5)
17Q LOSS WILD-TYPE 392 62.9 (11.2)

Figure S48.  Get High-res Image Gene #70: '17q loss' versus Clinical Feature #2: 'AGE'

'17q loss' versus 'HISTOLOGICAL.TYPE'

P value = 9.97e-08 (Fisher's exact test), Q value = 3.7e-05

Table S49.  Gene #70: '17q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
17Q LOSS CNV 29 5 27
17Q LOSS WILD-TYPE 322 13 58

Figure S49.  Get High-res Image Gene #70: '17q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'18q loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.98e-06 (Fisher's exact test), Q value = 0.0029

Table S50.  Gene #72: '18q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
18Q LOSS CNV 20 6 16
18Q LOSS WILD-TYPE 331 12 69

Figure S50.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.44e-07 (Fisher's exact test), Q value = 5.4e-05

Table S51.  Gene #73: '19p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
19P LOSS CNV 10 2 18
19P LOSS WILD-TYPE 341 16 67

Figure S51.  Get High-res Image Gene #73: '19p loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'19q loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.61e-05 (Fisher's exact test), Q value = 0.013

Table S52.  Gene #74: '19q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
19Q LOSS CNV 9 2 13
19Q LOSS WILD-TYPE 342 16 72

Figure S52.  Get High-res Image Gene #74: '19q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'21q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.92e-05 (Fisher's exact test), Q value = 0.01

Table S53.  Gene #77: '21q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
21Q LOSS CNV 10 3 13
21Q LOSS WILD-TYPE 341 15 72

Figure S53.  Get High-res Image Gene #77: '21q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'22q loss' versus 'AGE'

P value = 0.000369 (t-test), Q value = 0.13

Table S54.  Gene #78: '22q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 453 63.6 (11.2)
22Q LOSS CNV 76 67.3 (9.0)
22Q LOSS WILD-TYPE 377 62.9 (11.5)

Figure S54.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #2: 'AGE'

'22q loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.95e-10 (Fisher's exact test), Q value = 2.3e-07

Table S55.  Gene #78: '22q loss' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 351 18 85
22Q LOSS CNV 36 6 34
22Q LOSS WILD-TYPE 315 12 51

Figure S55.  Get High-res Image Gene #78: '22q loss' 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 = 454

  • 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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