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 77 arm-level results and 5 clinical features across 410 patients, 53 significant findings detected with Q value < 0.25.

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

  • 5p gain cnv correlated to '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'.

  • 3p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 4p loss cnv correlated to 'AGE' and '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 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 7q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

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

  • 12p loss cnv correlated to 'AGE' and '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'.

  • 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 77 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 		NEOADJUVANT
THERAPY
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test
11p loss 45 (11%) 365 0.000516
(0.175) 		8.39e-07
(0.000303) 		6.58e-09
(2.45e-06) 		0.31
(1.00) 		0.0474
(1.00)
13q gain 22 (5%) 388 0.896
(1.00) 		0.000473
(0.161) 		1.86e-05
(0.00655) 		0.355
(1.00) 		0.127
(1.00)
18p gain 27 (7%) 383 0.138
(1.00) 		0.000731
(0.243) 		2.49e-07
(9.05e-05) 		0.67
(1.00) 		1
(1.00)
19p gain 27 (7%) 383 0.328
(1.00) 		4.62e-06
(0.00165) 		1.02e-05
(0.0036) 		0.0547
(1.00) 		1
(1.00)
19q gain 25 (6%) 385 0.00088
(0.292) 		9.93e-06
(0.00353) 		1.86e-08
(6.86e-06) 		0.382
(1.00) 		0.00341
(1.00)
3p loss 30 (7%) 380 0.096
(1.00) 		0.000727
(0.243) 		0.000105
(0.0362) 		1
(1.00) 		0.0277
(1.00)
4p loss 46 (11%) 364 0.0635
(1.00) 		0.000543
(0.183) 		2.66e-11
(1.01e-08) 		0.243
(1.00) 		1
(1.00)
7p loss 31 (8%) 379 0.514
(1.00) 		0.000621
(0.209) 		2.39e-05
(0.00835) 		0.842
(1.00) 		0.033
(1.00)
7q loss 27 (7%) 383 0.523
(1.00) 		9.24e-05
(0.0321) 		1.28e-10
(4.81e-08) 		0.834
(1.00) 		0.00991
(1.00)
9p loss 60 (15%) 350 0.619
(1.00) 		1.69e-06
(0.000607) 		3.27e-13
(1.25e-10) 		0.767
(1.00) 		0.016
(1.00)
9q loss 75 (18%) 335 0.291
(1.00) 		8.6e-09
(3.2e-06) 		1.05e-12
(3.98e-10) 		0.338
(1.00) 		0.145
(1.00)
11q loss 43 (10%) 367 0.0223
(1.00) 		0.000124
(0.0428) 		1.02e-05
(0.0036) 		0.229
(1.00) 		0.0655
(1.00)
12p loss 19 (5%) 391 0.178
(1.00) 		0.000702
(0.235) 		0.000233
(0.0796) 		1
(1.00) 		0.589
(1.00)
14q loss 32 (8%) 378 0.181
(1.00) 		0.000133
(0.0457) 		8.06e-08
(2.97e-05) 		1
(1.00) 		0.00573
(1.00)
15q loss 63 (15%) 347 0.585
(1.00) 		3.47e-06
(0.00124) 		9.94e-12
(3.77e-09) 		0.144
(1.00) 		0.211
(1.00)
16p loss 51 (12%) 359 0.13
(1.00) 		8.41e-06
(0.00299) 		6.93e-10
(2.6e-07) 		0.338
(1.00) 		0.057
(1.00)
16q loss 87 (21%) 323 0.06
(1.00) 		1.39e-07
(5.09e-05) 		3.53e-13
(1.35e-10) 		0.699
(1.00) 		0.0367
(1.00)
17p loss 75 (18%) 335 0.774
(1.00) 		8.69e-09
(3.22e-06) 		1.85e-17
(7.1e-15) 		0.891
(1.00) 		0.00195
(0.637)
17q loss 48 (12%) 362 0.418
(1.00) 		0.000547
(0.184) 		1.49e-07
(5.45e-05) 		0.188
(1.00) 		0.728
(1.00)
22q loss 64 (16%) 346 0.0971
(1.00) 		0.000486
(0.165) 		1.23e-06
(0.000444) 		0.56
(1.00) 		0.159
(1.00)
3q gain 56 (14%) 354 0.1
(1.00) 		0.031
(1.00) 		1.6e-07
(5.83e-05) 		0.281
(1.00) 		0.408
(1.00)
5p gain 32 (8%) 378 0.0111
(1.00) 		0.0313
(1.00) 		2.91e-07
(0.000106) 		0.697
(1.00) 		0.405
(1.00)
20p gain 42 (10%) 368 0.0663
(1.00) 		0.0178
(1.00) 		0.000145
(0.0499) 		0.295
(1.00) 		0.0599
(1.00)
20q gain 51 (12%) 359 0.453
(1.00) 		0.00381
(1.00) 		2.47e-09
(9.22e-07) 		0.0534
(1.00) 		0.057
(1.00)
4q loss 42 (10%) 368 0.0357
(1.00) 		0.00196
(0.637) 		1.24e-10
(4.67e-08) 		0.0794
(1.00) 		0.58
(1.00)
5p loss 20 (5%) 390 0.958
(1.00) 		0.208
(1.00) 		7.32e-07
(0.000265) 		1
(1.00) 		1
(1.00)
5q loss 35 (9%) 375 0.899
(1.00) 		0.00583
(1.00) 		4.88e-13
(1.86e-10) 		0.57
(1.00) 		0.105
(1.00)
8p loss 45 (11%) 365 0.941
(1.00) 		0.00617
(1.00) 		7.02e-19
(2.7e-16) 		1
(1.00) 		0.0101
(1.00)
8q loss 10 (2%) 400 1
(1.00) 		0.311
(1.00) 		3.24e-05
(0.0113) 		1
(1.00) 		0.282
(1.00)
18q loss 38 (9%) 372 0.784
(1.00) 		0.0019
(0.622) 		2.2e-05
(0.00772) 		0.279
(1.00) 		0.0488
(1.00)
19p loss 33 (8%) 377 0.195
(1.00) 		0.0266
(1.00) 		1.48e-08
(5.47e-06) 		1
(1.00) 		0.0345
(1.00)
19q loss 24 (6%) 386 0.515
(1.00) 		0.026
(1.00) 		5.68e-05
(0.0198) 		1
(1.00) 		0.634
(1.00)
1p gain 19 (5%) 391 0.302
(1.00) 		0.159
(1.00) 		0.452
(1.00) 		0.802
(1.00) 		0.279
(1.00)
1q gain 132 (32%) 278 0.6
(1.00) 		0.239
(1.00) 		0.0135
(1.00) 		0.91
(1.00) 		0.145
(1.00)
2p gain 57 (14%) 353 0.0532
(1.00) 		0.0159
(1.00) 		0.00154
(0.508) 		0.223
(1.00) 		0.253
(1.00)
2q gain 36 (9%) 374 0.0689
(1.00) 		0.373
(1.00) 		0.14
(1.00) 		0.455
(1.00) 		0.158
(1.00)
3p gain 27 (7%) 383 0.276
(1.00) 		0.208
(1.00) 		0.511
(1.00) 		0.295
(1.00) 		1
(1.00)
4p gain 7 (2%) 403 0.532
(1.00) 		0.0293
(1.00) 		0.077
(1.00) 		0.685
(1.00) 		0.377
(1.00)
4q gain 3 (1%) 407 0.54
(1.00) 		0.228
(1.00) 		0.464
(1.00) 		1
(1.00) 		0.574
(1.00)
5q gain 9 (2%) 401 0.346
(1.00) 		0.905
(1.00) 		0.101
(1.00) 		0.725
(1.00) 		0.0499
(1.00)
6p gain 32 (8%) 378 0.731
(1.00) 		0.488
(1.00) 		0.0103
(1.00) 		0.844
(1.00) 		0.289
(1.00)
6q gain 25 (6%) 385 0.466
(1.00) 		0.32
(1.00) 		0.0559
(1.00) 		0.382
(1.00) 		0.0971
(1.00)
7p gain 34 (8%) 376 0.114
(1.00) 		0.522
(1.00) 		0.192
(1.00) 		0.339
(1.00) 		0.681
(1.00)
7q gain 34 (8%) 376 0.00335
(1.00) 		0.94
(1.00) 		0.278
(1.00) 		0.339
(1.00) 		0.154
(1.00)
8p gain 68 (17%) 342 0.00293
(0.945) 		0.127
(1.00) 		0.297
(1.00) 		0.671
(1.00) 		1
(1.00)
8q gain 96 (23%) 314 0.00648
(1.00) 		0.942
(1.00) 		0.0737
(1.00) 		0.709
(1.00) 		0.0821
(1.00)
9p gain 11 (3%) 399 0.875
(1.00) 		0.64
(1.00) 		0.933
(1.00) 		0.186
(1.00) 		0.156
(1.00)
10p gain 79 (19%) 331 0.641
(1.00) 		0.668
(1.00) 		0.314
(1.00) 		0.893
(1.00) 		0.775
(1.00)
10q gain 73 (18%) 337 0.937
(1.00) 		0.863
(1.00) 		0.339
(1.00) 		0.89
(1.00) 		0.883
(1.00)
11p gain 6 (1%) 404 0.409
(1.00) 		0.383
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.00466
(1.00)
11q gain 10 (2%) 400 0.943
(1.00) 		0.571
(1.00) 		0.908
(1.00) 		1
(1.00) 		0.282
(1.00)
12p gain 31 (8%) 379 0.695
(1.00) 		0.95
(1.00) 		0.111
(1.00) 		1
(1.00) 		0.668
(1.00)
12q gain 24 (6%) 386 0.731
(1.00) 		0.339
(1.00) 		0.555
(1.00) 		1
(1.00) 		0.634
(1.00)
14q gain 13 (3%) 397 0.204
(1.00) 		0.704
(1.00) 		0.477
(1.00) 		0.0701
(1.00) 		0.746
(1.00)
15q gain 5 (1%) 405 0.0624
(1.00) 		0.457
(1.00) 		0.944
(1.00) 		0.182
(1.00) 		0.106
(1.00)
16p gain 11 (3%) 399 0.367
(1.00) 		0.0852
(1.00) 		0.278
(1.00) 		0.514
(1.00) 		1
(1.00)
16q gain 4 (1%) 406 0.604
(1.00) 		0.256
(1.00) 		0.745
(1.00) 		1
(1.00) 		1
(1.00)
17p gain 8 (2%) 402 0.00845
(1.00) 		0.531
(1.00) 		0.792
(1.00) 		0.274
(1.00) 		0.117
(1.00)
17q gain 16 (4%) 394 0.0421
(1.00) 		0.0835
(1.00) 		0.733
(1.00) 		0.168
(1.00) 		0.252
(1.00)
18q gain 14 (3%) 396 0.0107
(1.00) 		0.0793
(1.00) 		0.0517
(1.00) 		0.562
(1.00) 		0.0255
(1.00)
21q gain 15 (4%) 395 0.573
(1.00) 		0.0279
(1.00) 		0.00118
(0.39) 		0.783
(1.00) 		0.224
(1.00)
22q gain 7 (2%) 403 0.515
(1.00) 		0.115
(1.00) 		0.182
(1.00) 		1
(1.00) 		1
(1.00)
1p loss 13 (3%) 397 0.0681
(1.00) 		0.143
(1.00) 		0.132
(1.00) 		1
(1.00) 		0.53
(1.00)
1q loss 7 (2%) 403 0.0534
(1.00) 		0.369
(1.00) 		0.0143
(1.00) 		1
(1.00) 		0.684
(1.00)
2p loss 6 (1%) 404 0.349
(1.00) 		0.204
(1.00) 		0.148
(1.00) 		0.183
(1.00) 		0.344
(1.00)
2q loss 9 (2%) 401 0.468
(1.00) 		0.0675
(1.00) 		0.303
(1.00) 		0.063
(1.00) 		0.459
(1.00)
3q loss 11 (3%) 399 0.283
(1.00) 		0.138
(1.00) 		0.252
(1.00) 		0.514
(1.00) 		1
(1.00)
6p loss 7 (2%) 403 0.68
(1.00) 		0.0483
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.377
(1.00)
6q loss 11 (3%) 399 0.52
(1.00) 		0.246
(1.00) 		0.278
(1.00) 		0.339
(1.00) 		1
(1.00)
10p loss 21 (5%) 389 0.0138
(1.00) 		0.0362
(1.00) 		0.00581
(1.00) 		0.631
(1.00) 		0.197
(1.00)
10q loss 22 (5%) 388 0.212
(1.00) 		0.0485
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.458
(1.00)
12q loss 13 (3%) 397 0.881
(1.00) 		0.114
(1.00) 		0.00162
(0.532) 		1
(1.00) 		0.746
(1.00)
13q loss 40 (10%) 370 0.177
(1.00) 		0.00187
(0.612) 		0.0136
(1.00) 		0.595
(1.00) 		1
(1.00)
18p loss 24 (6%) 386 0.207
(1.00) 		0.108
(1.00) 		0.0138
(1.00) 		0.508
(1.00) 		0.224
(1.00)
20p loss 11 (3%) 399 0.207
(1.00) 		0.0622
(1.00) 		0.212
(1.00) 		0.113
(1.00) 		0.481
(1.00)
20q loss 5 (1%) 405 0.503
(1.00) 		0.48
(1.00) 		0.744
(1.00) 		0.656
(1.00) 		0.336
(1.00)
21q loss 22 (5%) 388 0.165
(1.00) 		0.426
(1.00) 		0.00287
(0.93) 		0.644
(1.00) 		0.804
(1.00)
'3q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.6e-07 (Chi-square test), Q value = 5.8e-05

Table S1.  Gene #6: '3q 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 306 3 8 2 7 17 67
3Q GAIN MUTATED 26 0 0 0 2 3 25
3Q GAIN WILD-TYPE 280 3 8 2 5 14 42

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

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

P value = 2.91e-07 (Chi-square test), Q value = 0.00011

Table S2.  Gene #9: '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 306 3 8 2 7 17 67
5P GAIN MUTATED 13 0 0 0 0 1 18
5P GAIN WILD-TYPE 293 3 8 2 7 16 49

Figure S2.  Get High-res Image Gene #9: '5p gain mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'13q gain mutation analysis' versus 'AGE'

P value = 0.000473 (t-test), Q value = 0.16

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

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
13Q GAIN MUTATED 22 68.9 (6.3)
13Q GAIN WILD-TYPE 387 63.1 (11.3)

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 = 1.86e-05 (Chi-square test), Q value = 0.0065

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 306 3 8 2 7 17 67
13Q GAIN MUTATED 8 0 0 0 0 1 13
13Q GAIN WILD-TYPE 298 3 8 2 7 16 54

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 = 0.000731 (t-test), Q value = 0.24

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

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
18P GAIN MUTATED 27 68.8 (7.5)
18P GAIN WILD-TYPE 382 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 = 2.49e-07 (Chi-square test), Q value = 9.1e-05

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 306 3 8 2 7 17 67
18P GAIN MUTATED 9 0 0 0 0 2 16
18P GAIN WILD-TYPE 297 3 8 2 7 15 51

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 = 4.62e-06 (t-test), Q value = 0.0017

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

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
19P GAIN MUTATED 27 72.2 (8.4)
19P GAIN WILD-TYPE 382 62.8 (11.0)

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 = 1.02e-05 (Chi-square test), Q value = 0.0036

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 306 3 8 2 7 17 67
19P GAIN MUTATED 11 0 0 0 0 1 15
19P GAIN WILD-TYPE 295 3 8 2 7 16 52

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 = 9.93e-06 (t-test), Q value = 0.0035

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

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
19Q GAIN MUTATED 25 71.2 (7.3)
19Q GAIN WILD-TYPE 384 62.9 (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 = 1.86e-08 (Chi-square test), Q value = 6.9e-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 306 3 8 2 7 17 67
19Q GAIN MUTATED 7 0 0 0 0 2 16
19Q GAIN WILD-TYPE 299 3 8 2 7 15 51

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 = 0.000145 (Chi-square test), Q value = 0.05

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 306 3 8 2 7 17 67
20P GAIN MUTATED 21 0 0 1 0 3 17
20P GAIN WILD-TYPE 285 3 8 1 7 14 50

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 = 2.47e-09 (Chi-square test), Q value = 9.2e-07

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 306 3 8 2 7 17 67
20Q GAIN MUTATED 21 0 0 1 1 3 25
20Q GAIN WILD-TYPE 285 3 8 1 6 14 42

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

'3p loss mutation analysis' versus 'AGE'

P value = 0.000727 (t-test), Q value = 0.24

Table S13.  Gene #43: '3p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
3P LOSS MUTATED 30 68.4 (7.4)
3P LOSS WILD-TYPE 379 63.0 (11.3)

Figure S13.  Get High-res Image Gene #43: '3p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 0.000105 (Chi-square test), Q value = 0.036

Table S14.  Gene #43: '3p 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 306 3 8 2 7 17 67
3P LOSS MUTATED 12 0 0 0 1 4 13
3P LOSS WILD-TYPE 294 3 8 2 6 13 54

Figure S14.  Get High-res Image Gene #43: '3p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'4p loss mutation analysis' versus 'AGE'

P value = 0.000543 (t-test), Q value = 0.18

Table S15.  Gene #45: '4p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
4P LOSS MUTATED 46 68.1 (8.9)
4P LOSS WILD-TYPE 363 62.8 (11.2)

Figure S15.  Get High-res Image Gene #45: '4p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 2.66e-11 (Chi-square test), Q value = 1e-08

Table S16.  Gene #45: '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 306 3 8 2 7 17 67
4P LOSS MUTATED 16 0 0 0 1 4 25
4P LOSS WILD-TYPE 290 3 8 2 6 13 42

Figure S16.  Get High-res Image Gene #45: '4p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 1.24e-10 (Chi-square test), Q value = 4.7e-08

Table S17.  Gene #46: '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 306 3 8 2 7 17 67
4Q LOSS MUTATED 14 0 0 0 1 4 23
4Q LOSS WILD-TYPE 292 3 8 2 6 13 44

Figure S17.  Get High-res Image Gene #46: '4q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 7.32e-07 (Chi-square test), Q value = 0.00027

Table S18.  Gene #47: '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 306 3 8 2 7 17 67
5P LOSS MUTATED 6 0 0 0 1 0 13
5P LOSS WILD-TYPE 300 3 8 2 6 17 54

Figure S18.  Get High-res Image Gene #47: '5p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 4.88e-13 (Chi-square test), Q value = 1.9e-10

Table S19.  Gene #48: '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 306 3 8 2 7 17 67
5Q LOSS MUTATED 10 0 0 0 1 1 23
5Q LOSS WILD-TYPE 296 3 8 2 6 16 44

Figure S19.  Get High-res Image Gene #48: '5q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7p loss mutation analysis' versus 'AGE'

P value = 0.000621 (t-test), Q value = 0.21

Table S20.  Gene #51: '7p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
7P LOSS MUTATED 31 70.0 (10.0)
7P LOSS WILD-TYPE 378 62.9 (11.0)

Figure S20.  Get High-res Image Gene #51: '7p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 2.39e-05 (Chi-square test), Q value = 0.0083

Table S21.  Gene #51: '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 306 3 8 2 7 17 67
7P LOSS MUTATED 14 0 0 0 0 1 16
7P LOSS WILD-TYPE 292 3 8 2 7 16 51

Figure S21.  Get High-res Image Gene #51: '7p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7q loss mutation analysis' versus 'AGE'

P value = 9.24e-05 (t-test), Q value = 0.032

Table S22.  Gene #52: '7q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
7Q LOSS MUTATED 27 69.9 (7.5)
7Q LOSS WILD-TYPE 382 63.0 (11.2)

Figure S22.  Get High-res Image Gene #52: '7q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.28e-10 (Chi-square test), Q value = 4.8e-08

Table S23.  Gene #52: '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 306 3 8 2 7 17 67
7Q LOSS MUTATED 6 0 0 0 1 2 18
7Q LOSS WILD-TYPE 300 3 8 2 6 15 49

Figure S23.  Get High-res Image Gene #52: '7q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 7.02e-19 (Chi-square test), Q value = 2.7e-16

Table S24.  Gene #53: '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 306 3 8 2 7 17 67
8P LOSS MUTATED 11 0 0 0 1 3 30
8P LOSS WILD-TYPE 295 3 8 2 6 14 37

Figure S24.  Get High-res Image Gene #53: '8p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 3.24e-05 (Chi-square test), Q value = 0.011

Table S25.  Gene #54: '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 306 3 8 2 7 17 67
8Q LOSS MUTATED 2 0 0 0 0 0 8
8Q LOSS WILD-TYPE 304 3 8 2 7 17 59

Figure S25.  Get High-res Image Gene #54: '8q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9p loss mutation analysis' versus 'AGE'

P value = 1.69e-06 (t-test), Q value = 0.00061

Table S26.  Gene #55: '9p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
9P LOSS MUTATED 60 69.2 (9.1)
9P LOSS WILD-TYPE 349 62.4 (11.1)

Figure S26.  Get High-res Image Gene #55: '9p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 3.27e-13 (Chi-square test), Q value = 1.3e-10

Table S27.  Gene #55: '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 306 3 8 2 7 17 67
9P LOSS MUTATED 23 0 0 0 2 4 31
9P LOSS WILD-TYPE 283 3 8 2 5 13 36

Figure S27.  Get High-res Image Gene #55: '9p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9q loss mutation analysis' versus 'AGE'

P value = 8.6e-09 (t-test), Q value = 3.2e-06

Table S28.  Gene #56: '9q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
9Q LOSS MUTATED 75 69.3 (8.7)
9Q LOSS WILD-TYPE 334 62.1 (11.2)

Figure S28.  Get High-res Image Gene #56: '9q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.05e-12 (Chi-square test), Q value = 4e-10

Table S29.  Gene #56: '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 306 3 8 2 7 17 67
9Q LOSS MUTATED 33 0 0 0 2 5 35
9Q LOSS WILD-TYPE 273 3 8 2 5 12 32

Figure S29.  Get High-res Image Gene #56: '9q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 0.000516 (logrank test), Q value = 0.18

Table S30.  Gene #59: '11p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 407 40 0.0 - 187.1 (17.2)
11P LOSS MUTATED 45 10 0.1 - 91.0 (12.4)
11P LOSS WILD-TYPE 362 30 0.0 - 187.1 (17.8)

Figure S30.  Get High-res Image Gene #59: '11p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'11p loss mutation analysis' versus 'AGE'

P value = 8.39e-07 (t-test), Q value = 3e-04

Table S31.  Gene #59: '11p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
11P LOSS MUTATED 45 70.1 (8.4)
11P LOSS WILD-TYPE 364 62.6 (11.1)

Figure S31.  Get High-res Image Gene #59: '11p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 6.58e-09 (Chi-square test), Q value = 2.5e-06

Table S32.  Gene #59: '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 306 3 8 2 7 17 67
11P LOSS MUTATED 18 0 0 0 0 5 22
11P LOSS WILD-TYPE 288 3 8 2 7 12 45

Figure S32.  Get High-res Image Gene #59: '11p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'11q loss mutation analysis' versus 'AGE'

P value = 0.000124 (t-test), Q value = 0.043

Table S33.  Gene #60: '11q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
11Q LOSS MUTATED 43 68.9 (9.0)
11Q LOSS WILD-TYPE 366 62.8 (11.2)

Figure S33.  Get High-res Image Gene #60: '11q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.02e-05 (Chi-square test), Q value = 0.0036

Table S34.  Gene #60: '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 306 3 8 2 7 17 67
11Q LOSS MUTATED 20 0 0 0 0 5 18
11Q LOSS WILD-TYPE 286 3 8 2 7 12 49

Figure S34.  Get High-res Image Gene #60: '11q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'12p loss mutation analysis' versus 'AGE'

P value = 0.000702 (t-test), Q value = 0.24

Table S35.  Gene #61: '12p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
12P LOSS MUTATED 19 68.3 (5.2)
12P LOSS WILD-TYPE 390 63.2 (11.3)

Figure S35.  Get High-res Image Gene #61: '12p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 0.000233 (Chi-square test), Q value = 0.08

Table S36.  Gene #61: '12p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 306 3 8 2 7 17 67
12P LOSS MUTATED 7 0 0 0 0 1 11
12P LOSS WILD-TYPE 299 3 8 2 7 16 56

Figure S36.  Get High-res Image Gene #61: '12p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'14q loss mutation analysis' versus 'AGE'

P value = 0.000133 (t-test), Q value = 0.046

Table S37.  Gene #64: '14q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
14Q LOSS MUTATED 32 69.2 (7.9)
14Q LOSS WILD-TYPE 377 62.9 (11.2)

Figure S37.  Get High-res Image Gene #64: '14q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 8.06e-08 (Chi-square test), Q value = 3e-05

Table S38.  Gene #64: '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 306 3 8 2 7 17 67
14Q LOSS MUTATED 11 0 0 0 0 4 17
14Q LOSS WILD-TYPE 295 3 8 2 7 13 50

Figure S38.  Get High-res Image Gene #64: '14q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'15q loss mutation analysis' versus 'AGE'

P value = 3.47e-06 (t-test), Q value = 0.0012

Table S39.  Gene #65: '15q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
15Q LOSS MUTATED 63 69.1 (9.7)
15Q LOSS WILD-TYPE 346 62.4 (11.1)

Figure S39.  Get High-res Image Gene #65: '15q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 9.94e-12 (Chi-square test), Q value = 3.8e-09

Table S40.  Gene #65: '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 306 3 8 2 7 17 67
15Q LOSS MUTATED 26 0 0 0 1 6 30
15Q LOSS WILD-TYPE 280 3 8 2 6 11 37

Figure S40.  Get High-res Image Gene #65: '15q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16p loss mutation analysis' versus 'AGE'

P value = 8.41e-06 (t-test), Q value = 0.003

Table S41.  Gene #66: '16p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
16P LOSS MUTATED 51 68.9 (8.4)
16P LOSS WILD-TYPE 358 62.6 (11.2)

Figure S41.  Get High-res Image Gene #66: '16p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 6.93e-10 (Chi-square test), Q value = 2.6e-07

Table S42.  Gene #66: '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 306 3 8 2 7 17 67
16P LOSS MUTATED 21 0 0 0 0 5 25
16P LOSS WILD-TYPE 285 3 8 2 7 12 42

Figure S42.  Get High-res Image Gene #66: '16p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16q loss mutation analysis' versus 'AGE'

P value = 1.39e-07 (t-test), Q value = 5.1e-05

Table S43.  Gene #67: '16q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
16Q LOSS MUTATED 87 68.2 (8.5)
16Q LOSS WILD-TYPE 322 62.1 (11.4)

Figure S43.  Get High-res Image Gene #67: '16q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 3.53e-13 (Chi-square test), Q value = 1.3e-10

Table S44.  Gene #67: '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 306 3 8 2 7 17 67
16Q LOSS MUTATED 43 0 0 0 0 5 39
16Q LOSS WILD-TYPE 263 3 8 2 7 12 28

Figure S44.  Get High-res Image Gene #67: '16q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17p loss mutation analysis' versus 'AGE'

P value = 8.69e-09 (t-test), Q value = 3.2e-06

Table S45.  Gene #68: '17p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
17P LOSS MUTATED 75 68.9 (7.9)
17P LOSS WILD-TYPE 334 62.2 (11.4)

Figure S45.  Get High-res Image Gene #68: '17p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.85e-17 (Chi-square test), Q value = 7.1e-15

Table S46.  Gene #68: '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 306 3 8 2 7 17 67
17P LOSS MUTATED 29 0 0 0 1 7 38
17P LOSS WILD-TYPE 277 3 8 2 6 10 29

Figure S46.  Get High-res Image Gene #68: '17p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17q loss mutation analysis' versus 'AGE'

P value = 0.000547 (t-test), Q value = 0.18

Table S47.  Gene #69: '17q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
17Q LOSS MUTATED 48 67.7 (8.4)
17Q LOSS WILD-TYPE 361 62.8 (11.3)

Figure S47.  Get High-res Image Gene #69: '17q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.49e-07 (Chi-square test), Q value = 5.4e-05

Table S48.  Gene #69: '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 306 3 8 2 7 17 67
17Q LOSS MUTATED 21 0 0 0 1 3 23
17Q LOSS WILD-TYPE 285 3 8 2 6 14 44

Figure S48.  Get High-res Image Gene #69: '17q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 2.2e-05 (Chi-square test), Q value = 0.0077

Table S49.  Gene #71: '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 306 3 8 2 7 17 67
18Q LOSS MUTATED 17 0 0 0 2 6 13
18Q LOSS WILD-TYPE 289 3 8 2 5 11 54

Figure S49.  Get High-res Image Gene #71: '18q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 1.48e-08 (Chi-square test), Q value = 5.5e-06

Table S50.  Gene #72: '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 306 3 8 2 7 17 67
19P LOSS MUTATED 11 0 0 0 0 4 18
19P LOSS WILD-TYPE 295 3 8 2 7 13 49

Figure S50.  Get High-res Image Gene #72: '19p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 5.68e-05 (Chi-square test), Q value = 0.02

Table S51.  Gene #73: '19q 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 306 3 8 2 7 17 67
19Q LOSS MUTATED 9 0 0 0 0 4 11
19Q LOSS WILD-TYPE 297 3 8 2 7 13 56

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

'22q loss mutation analysis' versus 'AGE'

P value = 0.000486 (t-test), Q value = 0.17

Table S52.  Gene #77: '22q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 409 63.4 (11.1)
22Q LOSS MUTATED 64 67.2 (8.8)
22Q LOSS WILD-TYPE 345 62.7 (11.4)

Figure S52.  Get High-res Image Gene #77: '22q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.23e-06 (Chi-square test), Q value = 0.00044

Table S53.  Gene #77: '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 306 3 8 2 7 17 67
22Q LOSS MUTATED 32 0 0 0 1 7 24
22Q LOSS WILD-TYPE 274 3 8 2 6 10 43

Figure S53.  Get High-res Image Gene #77: '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 = 410

  • Number of significantly arm-level cnvs = 77

  • 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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