Correlation between copy number variations of arm-level result and selected clinical features
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
04 October 2018  |  None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
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 72 arm-level events and 17 clinical features across 100 patients, 76 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'FIGO_GRADE' and 'YEARS_TO_BIRTH'.

  • 3p gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'YEARS_TO_BIRTH'.

  • 3q gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'YEARS_TO_BIRTH'.

  • 5p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 6p gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'YEARS_TO_BIRTH'.

  • 6q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 13q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 14q gain cnv correlated to 'PATHOLOGY_T_STAGE' and 'PATHOLOGY_N_STAGE'.

  • 17p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 18p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 19p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 20p gain cnv correlated to 'HISTOLOGICAL_TYPE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGIC_STAGE'.

  • 20q gain cnv correlated to 'HISTOLOGICAL_TYPE',  'KARNOFSKY_PERFORMANCE_SCORE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGIC_STAGE'.

  • 1q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'PATHOLOGY_T_STAGE'.

  • 4p loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP',  'HISTOLOGICAL_TYPE',  'FIGO_GRADE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGIC_STAGE'.

  • 4q loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP',  'HISTOLOGICAL_TYPE',  'FIGO_GRADE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGIC_STAGE'.

  • 5p loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP',  'FIGO_GRADE', and 'PATHOLOGY_N_STAGE'.

  • 5q loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP',  'FIGO_GRADE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGIC_STAGE'.

  • 8p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 9p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'PATHOLOGY_N_STAGE'.

  • 9q loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP',  'HISTOLOGICAL_TYPE',  'FIGO_GRADE', and 'PATHOLOGY_N_STAGE'.

  • 11q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 13q loss cnv correlated to 'FIGO_GRADE'.

  • 15q loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP',  'HISTOLOGICAL_TYPE',  'FIGO_GRADE',  'PATHOLOGY_N_STAGE', and 'YEARS_TO_BIRTH'.

  • 16p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 16q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 17p loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP',  'FIGO_GRADE', and 'PATHOLOGY_N_STAGE'.

  • 17q loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP' and 'FIGO_GRADE'.

  • 18p loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

  • 18q loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

  • 21q loss cnv correlated to 'HISTOLOGICAL_TYPE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.

  • 22q loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP',  'FIGO_GRADE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGIC_STAGE'.

  • xp loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'PATHOLOGIC_STAGE'.

  • xq loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'PATHOLOGIC_STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 72 arm-level events and 17 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 76 significant findings detected.

Clinical
Features 		DAYS
TO
DEATH
OR
LAST
FUP 		HISTOLOGICAL
TYPE 		FIGO
GRADE 		KARNOFSKY
PERFORMANCE
SCORE 		MSI PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGIC
STAGE 		YEARS
TO
BIRTH 		ETHNICITY RACE RADIATION
THERAPY 		DIABETES BMI NUMBER
PACK
YEARS
SMOKED 		SMOKER COUNTRY
OF
ORIGIN
nCNV (%) nWild-Type logrank test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
4p loss 12 (12%) 88 0.00446
(0.158) 		6e-05
(0.0147) 		0.0113
(0.205) 		0.937
(1.00) 		0.801
(1.00) 		0.0105
(0.205) 		0.0201
(0.277) 		0.011
(0.205) 		0.111
(0.592) 		1
(1.00) 		0.515
(1.00) 		0.54
(1.00) 		1
(1.00) 		0.189
(0.728) 		0.464
(1.00) 		0.14
(0.645)
4q loss 12 (12%) 88 0.00446
(0.158) 		4e-05
(0.0147) 		0.0114
(0.205) 		0.937
(1.00) 		0.799
(1.00) 		0.0102
(0.205) 		0.0195
(0.274) 		0.0115
(0.205) 		0.111
(0.592) 		1
(1.00) 		0.517
(1.00) 		0.54
(1.00) 		1
(1.00) 		0.186
(0.726) 		0.464
(1.00) 		0.138
(0.637)
15q loss 13 (13%) 87 0.00283
(0.141) 		0.00166
(0.115) 		0.00054
(0.0579) 		0.325
(0.909) 		0.68
(1.00) 		0.0469
(0.431) 		0.00504
(0.158) 		0.0264
(0.323) 		0.015
(0.242) 		0.557
(1.00) 		1
(1.00) 		0.54
(1.00) 		0.752
(1.00) 		0.275
(0.853) 		1
(1.00) 		0.453
(1.00)
20q gain 22 (22%) 78 0.63
(1.00) 		0.0113
(0.205) 		0.0176
(0.251) 		0.0105
(0.205) 		0.49
(1.00) 		0.00063
(0.0579) 		0.591
(1.00) 		0.00782
(0.195) 		0.0528
(0.455) 		1
(1.00) 		0.619
(1.00) 		0.806
(1.00) 		0.108
(0.592) 		0.245
(0.838) 		0.859
(1.00) 		1
(1.00) 		0.5
(1.00)
5q loss 11 (11%) 89 0.00149
(0.114) 		0.254
(0.842) 		0.00515
(0.158) 		0.096
(0.573) 		0.801
(1.00) 		0.113
(0.595) 		0.00304
(0.143) 		0.00935
(0.205) 		0.491
(1.00) 		0.557
(1.00) 		1
(1.00) 		1
(1.00) 		0.72
(1.00) 		0.158
(0.69) 		0.273
(0.853) 		0.19
(0.728)
9q loss 16 (16%) 84 0.0108
(0.205) 		2e-05
(0.0147) 		0.00206
(0.13) 		0.201
(0.75) 		0.804
(1.00) 		0.0721
(0.525) 		0.0102
(0.205) 		0.0252
(0.319) 		0.0338
(0.366) 		0.557
(1.00) 		0.475
(1.00) 		0.408
(1.00) 		0.219
(0.789) 		0.0432
(0.41) 		0.756
(1.00) 		0.939
(1.00)
22q loss 12 (12%) 88 0.000641
(0.0579) 		0.0507
(0.45) 		0.00287
(0.141) 		0.255
(0.842) 		1
(1.00) 		0.0145
(0.236) 		0.0975
(0.579) 		0.0122
(0.21) 		0.236
(0.825) 		1
(1.00) 		0.389
(0.973) 		0.337
(0.928) 		0.505
(1.00) 		0.244
(0.838) 		1
(1.00) 		0.842
(1.00)
20p gain 22 (22%) 78 0.598
(1.00) 		0.00169
(0.115) 		0.0848
(0.545) 		0.0596
(0.505) 		0.488
(1.00) 		0.00066
(0.0579) 		0.595
(1.00) 		0.0081
(0.198) 		0.0528
(0.455) 		1
(1.00) 		0.648
(1.00) 		1
(1.00) 		0.108
(0.592) 		0.243
(0.836) 		0.671
(1.00) 		0.561
(1.00) 		0.302
(0.881)
5p loss 9 (9%) 91 0.000208
(0.0299) 		0.253
(0.842) 		0.00488
(0.158) 		0.096
(0.573) 		0.805
(1.00) 		0.274
(0.853) 		0.00743
(0.193) 		0.0597
(0.505) 		0.5
(1.00) 		0.448
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.495
(1.00) 		0.205
(0.755) 		0.454
(1.00)
17p loss 13 (13%) 87 0.00283
(0.141) 		0.0165
(0.251) 		0.00234
(0.13) 		0.255
(0.842) 		0.679
(1.00) 		0.12
(0.606) 		0.00655
(0.188) 		0.073
(0.525) 		0.176
(0.716) 		0.505
(1.00) 		1
(1.00) 		1
(1.00) 		0.5
(1.00) 		0.169
(0.705) 		0.49
(1.00) 		0.725
(1.00)
21q loss 5 (5%) 95 0.779
(1.00) 		0.0114
(0.205) 		0.00695
(0.19) 		0.0137
(0.229) 		0.0331
(0.362) 		0.173
(0.71) 		1
(1.00) 		0.185
(0.726) 		0.627
(1.00) 		0.622
(1.00) 		0.389
(0.973) 		1
(1.00) 		0.341
(0.928)
1p gain 9 (9%) 91 0.661
(1.00) 		0.253
(0.842) 		0.00479
(0.158) 		0.539
(1.00) 		0.0917
(0.564) 		1
(1.00) 		0.105
(0.592) 		0.101
(0.579) 		0.00757
(0.193) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.439
(1.00) 		0.584
(1.00) 		1
(1.00) 		0.458
(1.00)
3p gain 10 (10%) 90 0.573
(1.00) 		0.00724
(0.193) 		0.141
(0.645) 		0.684
(1.00) 		1
(1.00) 		0.522
(1.00) 		0.0767
(0.526) 		0.00389
(0.158) 		1
(1.00) 		0.342
(0.928) 		0.177
(0.716) 		0.72
(1.00) 		0.0362
(0.375) 		1
(1.00) 		1
(1.00)
3q gain 16 (16%) 84 0.295
(0.865) 		0.00019
(0.0299) 		0.0221
(0.294) 		0.178
(0.716) 		1
(1.00) 		0.387
(0.972) 		0.0199
(0.277) 		0.137
(0.636) 		0.00461
(0.158) 		1
(1.00) 		0.476
(1.00) 		0.0828
(0.542) 		1
(1.00) 		0.0921
(0.564) 		0.516
(1.00) 		0.522
(1.00)
6p gain 10 (10%) 90 0.122
(0.608) 		6e-05
(0.0147) 		0.325
(0.909) 		1
(1.00) 		0.085
(0.545) 		0.0256
(0.32) 		0.258
(0.844) 		0.0138
(0.229) 		1
(1.00) 		1
(1.00) 		0.291
(0.862) 		0.273
(0.853) 		0.0389
(0.378) 		0.693
(1.00) 		0.636
(1.00)
14q gain 7 (7%) 93 0.129
(0.621) 		0.166
(0.7) 		1
(1.00) 		0.00381
(0.158) 		0.0115
(0.205) 		0.0382
(0.378) 		0.301
(0.881) 		0.505
(1.00) 		0.0605
(0.505) 		0.458
(1.00) 		1
(1.00) 		0.0493
(0.444) 		1
(1.00) 		0.0755
(0.525)
1q loss 3 (3%) 97 0.773
(1.00) 		0.011
(0.205) 		0.00513
(0.158) 		0.0669
(0.518) 		0.0346
(0.367) 		0.762
(1.00) 		0.172
(0.708) 		1
(1.00) 		1
(1.00) 		0.316
(0.905) 		1
(1.00) 		1
(1.00)
9p loss 14 (14%) 86 0.266
(0.85) 		6e-05
(0.0147) 		0.708
(1.00) 		0.805
(1.00) 		0.0325
(0.358) 		0.01
(0.205) 		0.125
(0.613) 		0.387
(0.972) 		0.505
(1.00) 		0.476
(1.00) 		0.136
(0.636) 		0.338
(0.928) 		0.0629
(0.512) 		0.732
(1.00) 		0.726
(1.00)
17q loss 8 (8%) 92 0.000675
(0.0579) 		0.463
(1.00) 		0.00219
(0.13) 		0.808
(1.00) 		0.158
(0.69) 		0.121
(0.606) 		0.137
(0.636) 		0.263
(0.846) 		0.448
(1.00) 		1
(1.00) 		0.295
(0.865) 		0.433
(1.00) 		0.0615
(0.509) 		0.676
(1.00) 		0.516
(1.00)
xp loss 19 (19%) 81 0.0325
(0.358) 		0.00022
(0.0299) 		0.189
(0.728) 		0.153
(0.681) 		0.681
(1.00) 		0.017
(0.251) 		0.539
(1.00) 		0.007
(0.19) 		0.123
(0.608) 		0.209
(0.762) 		1
(1.00) 		0.431
(1.00) 		0.0869
(0.551) 		0.0487
(0.444) 		0.552
(1.00) 		0.626
(1.00)
xq loss 19 (19%) 81 0.0325
(0.358) 		0.00022
(0.0299) 		0.19
(0.728) 		0.153
(0.681) 		0.68
(1.00) 		0.0166
(0.251) 		0.536
(1.00) 		0.00661
(0.188) 		0.123
(0.608) 		0.209
(0.762) 		1
(1.00) 		0.431
(1.00) 		0.0869
(0.551) 		0.0489
(0.444) 		0.552
(1.00) 		0.624
(1.00)
5p gain 5 (5%) 95 0.652
(1.00) 		0.0117
(0.205) 		0.352
(0.932) 		0.486
(1.00) 		0.0347
(0.367) 		0.266
(0.85) 		0.229
(0.803) 		1
(1.00) 		0.378
(0.968) 		0.317
(0.905) 		0.0702
(0.521) 		0.587
(1.00) 		0.796
(1.00)
6q gain 8 (8%) 92 0.0985
(0.579) 		0.00071
(0.0579) 		0.416
(1.00) 		0.646
(1.00) 		0.158
(0.69) 		0.105
(0.592) 		0.315
(0.905) 		0.0221
(0.294) 		1
(1.00) 		1
(1.00) 		0.0163
(0.251) 		0.433
(1.00) 		0.253
(0.842) 		1
(1.00) 		0.538
(1.00)
13q gain 6 (6%) 94 0.0446
(0.417) 		0.00512
(0.158) 		1
(1.00) 		0.164
(0.7) 		0.0675
(0.52) 		0.288
(0.862) 		0.286
(0.862) 		0.32
(0.909) 		1
(1.00) 		0.69
(1.00) 		0.178
(0.716) 		0.13
(0.626) 		1
(1.00) 		0.614
(1.00)
17p gain 7 (7%) 93 0.648
(1.00) 		0.00369
(0.158) 		0.461
(1.00) 		0.603
(1.00) 		0.29
(0.862) 		0.68
(1.00) 		1
(1.00) 		0.291
(0.862) 		1
(1.00) 		1
(1.00) 		0.815
(1.00) 		0.62
(1.00) 		0.823
(1.00)
18p gain 9 (9%) 91 0.606
(1.00) 		0.00226
(0.13) 		1
(1.00) 		0.134
(0.633) 		0.52
(1.00) 		0.176
(0.716) 		0.448
(1.00) 		0.448
(1.00) 		0.391
(0.975) 		1
(1.00) 		0.712
(1.00) 		0.484
(1.00) 		0.286
(0.862) 		0.428
(1.00) 		0.202
(0.75)
19p gain 7 (7%) 93 0.0745
(0.525) 		0.0107
(0.205) 		1
(1.00) 		0.164
(0.7) 		0.42
(1.00) 		0.484
(1.00) 		0.0515
(0.45) 		1
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.187
(0.726) 		0.776
(1.00) 		0.62
(1.00) 		1
(1.00)
8p loss 7 (7%) 93 0.643
(1.00) 		0.0109
(0.205) 		1
(1.00) 		0.225
(0.797) 		0.121
(0.606) 		0.656
(1.00) 		0.137
(0.636) 		0.32
(0.909) 		1
(1.00) 		0.696
(1.00) 		0.187
(0.726) 		0.101
(0.579) 		1
(1.00) 		1
(1.00)
11q loss 7 (7%) 93 0.116
(0.598) 		0.281
(0.862) 		0.438
(1.00) 		1
(1.00) 		0.0138
(0.229) 		0.0407
(0.389) 		0.1
(0.579) 		0.273
(0.853) 		0.387
(0.972) 		1
(1.00) 		1
(1.00) 		0.669
(1.00) 		0.0253
(0.319) 		0.661
(1.00) 		0.723
(1.00)
13q loss 10 (10%) 90 0.116
(0.598) 		0.0307
(0.353) 		0.00542
(0.162) 		0.255
(0.842) 		0.643
(1.00) 		1
(1.00) 		0.151
(0.676) 		0.0659
(0.514) 		0.352
(0.932) 		1
(1.00) 		1
(1.00) 		0.291
(0.862) 		1
(1.00) 		0.893
(1.00) 		0.693
(1.00) 		0.799
(1.00)
16p loss 6 (6%) 94 0.0446
(0.417) 		0.00516
(0.158) 		1
(1.00) 		0.377
(0.968) 		0.519
(1.00) 		0.495
(1.00) 		0.0377
(0.378) 		1
(1.00) 		1
(1.00) 		0.378
(0.968) 		0.671
(1.00) 		0.205
(0.755) 		0.62
(1.00) 		0.342
(0.928)
16q loss 7 (7%) 93 0.0908
(0.564) 		0.0107
(0.205) 		1
(1.00) 		0.461
(1.00) 		0.522
(1.00) 		0.657
(1.00) 		0.0601
(0.505) 		1
(1.00) 		1
(1.00) 		0.69
(1.00) 		0.669
(1.00) 		0.0697
(0.52) 		0.661
(1.00) 		0.277
(0.855)
18p loss 4 (4%) 96 0.00439
(0.158) 		0.26
(0.846) 		0.641
(1.00) 		0.196
(0.746) 		0.311
(0.9) 		0.0175
(0.251) 		1
(1.00) 		1
(1.00) 		0.627
(1.00) 		0.576
(1.00) 		0.123
(0.609) 		0.228
(0.803) 		0.744
(1.00)
18q loss 5 (5%) 95 0.0112
(0.205) 		0.0282
(0.332) 		0.643
(1.00) 		0.285
(0.862) 		0.404
(1.00) 		0.0452
(0.419) 		1
(1.00) 		1
(1.00) 		0.378
(0.968) 		0.317
(0.905) 		0.387
(0.972) 		0.0795
(0.526) 		0.742
(1.00)
1q gain 27 (27%) 73 0.866
(1.00) 		0.614
(1.00) 		0.0917
(0.564) 		0.146
(0.665) 		0.827
(1.00) 		0.922
(1.00) 		0.258
(0.844) 		0.656
(1.00) 		0.0621
(0.511) 		0.308
(0.892) 		0.353
(0.933) 		0.645
(1.00) 		1
(1.00) 		0.854
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
2p gain 15 (15%) 85 0.448
(1.00) 		0.0782
(0.526) 		0.271
(0.853) 		0.201
(0.75) 		0.803
(1.00) 		0.118
(0.601) 		0.475
(1.00) 		0.593
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.569
(1.00) 		0.758
(1.00) 		0.515
(1.00) 		0.743
(1.00) 		0.874
(1.00)
2q gain 14 (14%) 86 0.448
(1.00) 		0.158
(0.69) 		0.272
(0.853) 		0.545
(1.00) 		0.806
(1.00) 		0.0906
(0.564) 		0.431
(1.00) 		0.561
(1.00) 		0.263
(0.846) 		1
(1.00) 		0.476
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.321
(0.909) 		0.732
(1.00) 		0.703
(1.00)
7p gain 13 (13%) 87 0.496
(1.00) 		0.597
(1.00) 		0.496
(1.00) 		0.0369
(0.377) 		0.426
(1.00) 		0.575
(1.00) 		0.197
(0.746) 		0.186
(0.726) 		0.866
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.768
(1.00) 		0.752
(1.00) 		0.642
(1.00) 		0.49
(1.00) 		0.488
(1.00)
7q gain 14 (14%) 86 0.483
(1.00) 		0.624
(1.00) 		0.616
(1.00) 		0.0291
(0.339) 		0.429
(1.00) 		0.661
(1.00) 		0.201
(0.75) 		0.255
(0.842) 		0.588
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.569
(1.00) 		0.751
(1.00) 		0.445
(1.00) 		0.732
(1.00) 		0.41
(1.00)
8p gain 19 (19%) 81 0.559
(1.00) 		0.117
(0.599) 		0.29
(0.862) 		0.109
(0.592) 		0.781
(1.00) 		0.224
(0.797) 		0.672
(1.00) 		0.693
(1.00) 		0.202
(0.75) 		0.557
(1.00) 		1
(1.00) 		0.188
(0.728) 		1
(1.00) 		0.56
(1.00) 		0.49
(1.00) 		0.367
(0.965) 		0.242
(0.836)
8q gain 20 (20%) 80 0.572
(1.00) 		0.0644
(0.512) 		0.288
(0.862) 		0.109
(0.592) 		1
(1.00) 		0.313
(0.903) 		0.673
(1.00) 		0.76
(1.00) 		0.0934
(0.569) 		1
(1.00) 		1
(1.00) 		0.304
(0.885) 		0.787
(1.00) 		0.443
(1.00) 		0.49
(1.00) 		0.231
(0.807) 		0.196
(0.746)
10p gain 25 (25%) 75 0.855
(1.00) 		0.761
(1.00) 		0.862
(1.00) 		0.729
(1.00) 		0.226
(0.798) 		1
(1.00) 		0.647
(1.00) 		0.759
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.676
(1.00) 		0.648
(1.00) 		0.618
(1.00) 		0.717
(1.00) 		0.101
(0.579) 		0.147
(0.665) 		0.452
(1.00)
10q gain 24 (24%) 76 0.803
(1.00) 		0.758
(1.00) 		0.64
(1.00) 		0.729
(1.00) 		0.262
(0.846) 		0.918
(1.00) 		0.628
(1.00) 		0.685
(1.00) 		0.75
(1.00) 		1
(1.00) 		0.671
(1.00) 		0.816
(1.00) 		0.797
(1.00) 		0.854
(1.00) 		0.101
(0.579) 		0.245
(0.839) 		0.421
(1.00)
11p gain 3 (3%) 97 0.773
(1.00) 		0.169
(0.705) 		0.113
(0.595) 		1
(1.00) 		0.267
(0.85) 		0.0734
(0.525) 		1
(1.00) 		0.252
(0.842) 		1
(1.00) 		0.316
(0.905) 		1
(1.00) 		0.173
(0.709)
11q gain 4 (4%) 96 0.744
(1.00) 		0.107
(0.592) 		0.0176
(0.251) 		0.52
(1.00) 		0.0405
(0.389) 		0.0813
(0.535) 		1
(1.00) 		0.185
(0.726) 		0.127
(0.616) 		1
(1.00) 		0.272
(0.853) 		0.57
(1.00) 		0.111
(0.592)
12p gain 10 (10%) 90 0.589
(1.00) 		0.0309
(0.353) 		0.619
(1.00) 		0.0753
(0.525) 		0.495
(1.00) 		0.15
(0.676) 		0.436
(1.00) 		0.654
(1.00) 		1
(1.00) 		1
(1.00) 		0.291
(0.862) 		1
(1.00) 		0.664
(1.00) 		0.693
(1.00) 		0.223
(0.797)
12q gain 10 (10%) 90 0.589
(1.00) 		0.0324
(0.358) 		0.615
(1.00) 		0.0753
(0.525) 		0.495
(1.00) 		0.149
(0.675) 		0.431
(1.00) 		0.654
(1.00) 		1
(1.00) 		1
(1.00) 		0.291
(0.862) 		1
(1.00) 		0.668
(1.00) 		0.693
(1.00) 		0.225
(0.797)
16p gain 6 (6%) 94 0.61
(1.00) 		0.218
(0.787) 		1
(1.00) 		0.352
(0.932) 		0.375
(0.968) 		0.323
(0.909) 		0.0994
(0.579) 		0.884
(1.00) 		0.249
(0.841) 		1
(1.00) 		0.223
(0.796) 		0.671
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
16q gain 5 (5%) 95 0.652
(1.00) 		0.156
(0.689) 		0.352
(0.932) 		0.285
(0.862) 		0.256
(0.844) 		0.504
(1.00) 		0.558
(1.00) 		0.172
(0.708) 		0.378
(0.968) 		1
(1.00) 		0.725
(1.00) 		1
(1.00) 		0.793
(1.00)
17q gain 6 (6%) 94 0.668
(1.00) 		0.0515
(0.45) 		0.375
(0.968) 		0.523
(1.00) 		0.247
(0.841) 		0.571
(1.00) 		1
(1.00) 		0.237
(0.825) 		1
(1.00) 		1
(1.00) 		0.815
(1.00) 		1
(1.00) 		0.827
(1.00)
18q gain 7 (7%) 93 0.668
(1.00) 		0.167
(0.7) 		1
(1.00) 		0.162
(0.7) 		0.678
(1.00) 		0.0952
(0.573) 		0.239
(0.83) 		1
(1.00) 		0.292
(0.864) 		1
(1.00) 		0.404
(1.00) 		0.345
(0.928) 		0.661
(1.00) 		0.279
(0.861)
19q gain 8 (8%) 92 0.128
(0.619) 		0.0205
(0.278) 		1
(1.00) 		0.29
(0.862) 		0.424
(1.00) 		0.563
(1.00) 		0.075
(0.525) 		1
(1.00) 		1
(1.00) 		0.46
(1.00) 		0.101
(0.579) 		0.408
(1.00) 		0.661
(1.00) 		0.876
(1.00)
21q gain 6 (6%) 94 0.0754
(0.525) 		0.132
(0.631) 		0.441
(1.00) 		0.937
(1.00) 		1
(1.00) 		0.166
(0.7) 		0.494
(1.00) 		0.805
(1.00) 		1
(1.00) 		1
(1.00) 		0.69
(1.00) 		0.671
(1.00) 		0.306
(0.889) 		0.62
(1.00) 		1
(1.00)
22q gain 8 (8%) 92 0.585
(1.00) 		0.108
(0.592) 		1
(1.00) 		0.937
(1.00) 		0.429
(1.00) 		0.155
(0.689) 		0.259
(0.844) 		0.564
(1.00) 		0.283
(0.862) 		0.387
(0.972) 		1
(1.00) 		1
(1.00) 		0.433
(1.00) 		0.787
(1.00) 		0.347
(0.928) 		0.721
(1.00)
xp gain 8 (8%) 92 0.577
(1.00) 		0.73
(1.00) 		0.616
(1.00) 		0.862
(1.00) 		1
(1.00) 		0.375
(0.968) 		0.105
(0.592) 		0.133
(0.632) 		0.864
(1.00) 		0.387
(0.972) 		0.344
(0.928) 		0.46
(1.00) 		0.685
(1.00) 		0.0844
(0.545) 		0.382
(0.972) 		0.247
(0.841)
xq gain 8 (8%) 92 0.577
(1.00) 		0.729
(1.00) 		0.141
(0.645) 		0.275
(0.853) 		0.643
(1.00) 		0.379
(0.968) 		0.0652
(0.512) 		0.134
(0.633) 		0.356
(0.94) 		0.387
(0.972) 		0.293
(0.865) 		1
(1.00) 		0.685
(1.00) 		0.0832
(0.542) 		1
(1.00) 		0.363
(0.956)
yp gain 14 (14%) 86 0.464
(1.00) 		0.802
(1.00) 		1
(1.00) 		0.344
(0.928) 		1
(1.00) 		0.431
(1.00) 		0.525
(1.00) 		0.0725
(0.525) 		0.897
(1.00) 		0.448
(1.00) 		0.0759
(0.525) 		0.773
(1.00) 		0.534
(1.00) 		0.651
(1.00) 		1
(1.00) 		0.334
(0.922)
yq gain 14 (14%) 86 0.464
(1.00) 		0.799
(1.00) 		1
(1.00) 		0.344
(0.928) 		1
(1.00) 		0.425
(1.00) 		0.524
(1.00) 		0.0724
(0.525) 		0.897
(1.00) 		0.448
(1.00) 		0.0773
(0.526) 		0.773
(1.00) 		0.534
(1.00) 		0.652
(1.00) 		1
(1.00) 		0.33
(0.917)
1p loss 4 (4%) 96 0.712
(1.00) 		0.106
(0.592) 		0.0173
(0.251) 		0.118
(0.601) 		0.172
(0.708) 		0.555
(1.00) 		0.249
(0.841) 		0.184
(0.726) 		1
(1.00) 		0.322
(0.909) 		0.346
(0.928) 		1
(1.00) 		0.743
(1.00)
3p loss 6 (6%) 94 0.701
(1.00) 		0.0515
(0.45) 		0.539
(1.00) 		1
(1.00) 		0.566
(1.00) 		0.185
(0.726) 		0.494
(1.00) 		0.647
(1.00) 		1
(1.00) 		1
(1.00) 		0.652
(1.00) 		0.622
(1.00) 		0.933
(1.00) 		0.135
(0.634) 		0.505
(1.00)
7p loss 5 (5%) 95 0.0162
(0.251) 		0.0271
(0.324) 		0.642
(1.00) 		0.0384
(0.378) 		0.0352
(0.369) 		0.0916
(0.564) 		0.652
(1.00) 		1
(1.00) 		1
(1.00) 		0.064
(0.512) 		1
(1.00) 		0.78
(1.00) 		0.0795
(0.526) 		0.439
(1.00)
7q loss 5 (5%) 95 0.0162
(0.251) 		0.0273
(0.324) 		0.643
(1.00) 		0.0388
(0.378) 		0.0345
(0.367) 		0.0922
(0.564) 		0.652
(1.00) 		1
(1.00) 		1
(1.00) 		0.064
(0.512) 		1
(1.00) 		0.78
(1.00) 		0.0795
(0.526) 		0.437
(1.00)
8q loss 4 (4%) 96 0.712
(1.00) 		0.262
(0.846) 		0.4
(0.995) 		0.738
(1.00) 		0.379
(0.968) 		1
(1.00) 		1
(1.00) 		0.576
(1.00) 		0.0252
(0.319) 		0.57
(1.00) 		1
(1.00)
10p loss 5 (5%) 95 0.744
(1.00) 		0.0272
(0.324) 		0.945
(1.00) 		0.484
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.924
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.622
(1.00) 		0.534
(1.00) 		0.327
(0.915) 		0.332
(0.918)
10q loss 4 (4%) 96 0.744
(1.00) 		0.261
(0.846) 		0.0651
(0.512) 		0.212
(0.771) 		0.603
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.27
(0.853) 		1
(1.00) 		1
(1.00)
11p loss 8 (8%) 92 0.116
(0.598) 		0.206
(0.755) 		0.44
(1.00) 		0.096
(0.573) 		1
(1.00) 		0.0262
(0.323) 		0.0644
(0.512) 		0.167
(0.7) 		0.624
(1.00) 		0.387
(0.972) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0606
(0.505) 		1
(1.00) 		0.46
(1.00)
12p loss 4 (4%) 96 0.744
(1.00) 		0.107
(0.592) 		0.619
(1.00) 		0.506
(1.00) 		0.0226
(0.294) 		1
(1.00) 		0.185
(0.726) 		1
(1.00) 		1
(1.00) 		0.0688
(0.52) 		1
(1.00) 		0.744
(1.00)
12q loss 4 (4%) 96 0.744
(1.00) 		0.107
(0.592) 		0.619
(1.00) 		0.509
(1.00) 		0.0226
(0.294) 		1
(1.00) 		0.185
(0.726) 		1
(1.00) 		1
(1.00) 		0.0685
(0.52) 		1
(1.00) 		0.741
(1.00)
19p loss 6 (6%) 94 0.689
(1.00) 		0.216
(0.781) 		0.441
(1.00) 		0.325
(0.909) 		0.167
(0.7) 		0.423
(1.00) 		0.494
(1.00) 		0.513
(1.00) 		1
(1.00) 		0.378
(0.968) 		0.671
(1.00) 		0.544
(1.00) 		0.33
(0.917) 		0.273
(0.853)
19q loss 6 (6%) 94 0.668
(1.00) 		0.651
(1.00) 		0.412
(1.00) 		0.684
(1.00) 		0.164
(0.7) 		0.423
(1.00) 		0.496
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.223
(0.796) 		0.178
(0.716) 		0.206
(0.755) 		0.33
(0.917) 		0.416
(1.00)
yp loss 47 (47%) 53 0.0373
(0.377) 		0.126
(0.615) 		0.162
(0.7) 		0.846
(1.00) 		0.857
(1.00) 		0.0786
(0.526) 		1
(1.00) 		0.346
(0.928) 		0.753
(1.00) 		0.346
(0.928) 		0.113
(0.595) 		0.0696
(0.52) 		0.116
(0.598) 		0.369
(0.966) 		1
(1.00) 		1
(1.00) 		0.201
(0.75)
yq loss 47 (47%) 53 0.0373
(0.377) 		0.125
(0.613) 		0.162
(0.7) 		0.846
(1.00) 		0.857
(1.00) 		0.0785
(0.526) 		1
(1.00) 		0.346
(0.928) 		0.753
(1.00) 		0.346
(0.928) 		0.111
(0.592) 		0.0696
(0.52) 		0.116
(0.598) 		0.369
(0.966) 		1
(1.00) 		1
(1.00) 		0.2
(0.75)
'1p gain' versus 'FIGO_GRADE'

P value = 0.00479 (Fisher's exact test), Q value = 0.16

Table S1.  Gene #1: '1p gain' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
1P GAIN MUTATED 1 1 3
1P GAIN WILD-TYPE 31 33 4

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #3: 'FIGO_GRADE'

'1p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00757 (Wilcoxon-test), Q value = 0.19

Table S2.  Gene #1: '1p gain' versus Clinical Feature #9: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 100 63.6 (10.1)
1P GAIN MUTATED 9 72.8 (10.0)
1P GAIN WILD-TYPE 91 62.6 (9.6)

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #9: 'YEARS_TO_BIRTH'

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00724 (Fisher's exact test), Q value = 0.19

Table S3.  Gene #5: '3p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
3P GAIN MUTATED 1 4 0 5
3P GAIN WILD-TYPE 0 73 1 16

Figure S3.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'3p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00389 (Wilcoxon-test), Q value = 0.16

Table S4.  Gene #5: '3p gain' versus Clinical Feature #9: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 100 63.6 (10.1)
3P GAIN MUTATED 10 73.4 (10.4)
3P GAIN WILD-TYPE 90 62.5 (9.5)

Figure S4.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #9: 'YEARS_TO_BIRTH'

'3q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00019 (Fisher's exact test), Q value = 0.03

Table S5.  Gene #6: '3q gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
3Q GAIN MUTATED 1 6 0 9
3Q GAIN WILD-TYPE 0 71 1 12

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00461 (Wilcoxon-test), Q value = 0.16

Table S6.  Gene #6: '3q gain' versus Clinical Feature #9: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 100 63.6 (10.1)
3Q GAIN MUTATED 16 71.2 (10.3)
3Q GAIN WILD-TYPE 84 62.1 (9.4)

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #9: 'YEARS_TO_BIRTH'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0117 (Fisher's exact test), Q value = 0.2

Table S7.  Gene #7: '5p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
5P GAIN MUTATED 0 1 0 4
5P GAIN WILD-TYPE 1 76 1 17

Figure S7.  Get High-res Image Gene #7: '5p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'6p gain' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S8.  Gene #8: '6p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
6P GAIN MUTATED 1 2 0 7
6P GAIN WILD-TYPE 0 75 1 14

Figure S8.  Get High-res Image Gene #8: '6p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'6p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0138 (Wilcoxon-test), Q value = 0.23

Table S9.  Gene #8: '6p gain' versus Clinical Feature #9: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 100 63.6 (10.1)
6P GAIN MUTATED 10 71.6 (9.8)
6P GAIN WILD-TYPE 90 62.7 (9.7)

Figure S9.  Get High-res Image Gene #8: '6p gain' versus Clinical Feature #9: 'YEARS_TO_BIRTH'

'6q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00071 (Fisher's exact test), Q value = 0.058

Table S10.  Gene #9: '6q gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
6Q GAIN MUTATED 1 2 0 5
6Q GAIN WILD-TYPE 0 75 1 16

Figure S10.  Get High-res Image Gene #9: '6q gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00512 (Fisher's exact test), Q value = 0.16

Table S11.  Gene #20: '13q gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
13Q GAIN MUTATED 0 1 0 5
13Q GAIN WILD-TYPE 1 76 1 16

Figure S11.  Get High-res Image Gene #20: '13q gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00381 (Kruskal-Wallis (anova)), Q value = 0.16

Table S12.  Gene #21: '14q gain' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 78 11 10
14Q GAIN MUTATED 2 2 3
14Q GAIN WILD-TYPE 76 9 7

Figure S12.  Get High-res Image Gene #21: '14q gain' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

'14q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0115 (Kruskal-Wallis (anova)), Q value = 0.2

Table S13.  Gene #21: '14q gain' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 46 6 3
14Q GAIN MUTATED 1 2 1
14Q GAIN WILD-TYPE 45 4 2

Figure S13.  Get High-res Image Gene #21: '14q gain' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

'17p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00369 (Fisher's exact test), Q value = 0.16

Table S14.  Gene #24: '17p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
17P GAIN MUTATED 1 2 0 4
17P GAIN WILD-TYPE 0 75 1 17

Figure S14.  Get High-res Image Gene #24: '17p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00226 (Fisher's exact test), Q value = 0.13

Table S15.  Gene #26: '18p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
18P GAIN MUTATED 1 3 0 5
18P GAIN WILD-TYPE 0 74 1 16

Figure S15.  Get High-res Image Gene #26: '18p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0107 (Fisher's exact test), Q value = 0.2

Table S16.  Gene #28: '19p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
19P GAIN MUTATED 0 2 0 5
19P GAIN WILD-TYPE 1 75 1 16

Figure S16.  Get High-res Image Gene #28: '19p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00169 (Fisher's exact test), Q value = 0.11

Table S17.  Gene #30: '20p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
20P GAIN MUTATED 1 11 0 10
20P GAIN WILD-TYPE 0 66 1 11

Figure S17.  Get High-res Image Gene #30: '20p gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00066 (Wilcoxon-test), Q value = 0.058

Table S18.  Gene #30: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 78 11 10
20P GAIN MUTATED 11 5 6
20P GAIN WILD-TYPE 67 6 4

Figure S18.  Get High-res Image Gene #30: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

'20p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0081 (Fisher's exact test), Q value = 0.2

Table S19.  Gene #30: '20p gain' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV STAGE IVB
ALL 72 1 1 8 15 2 1
20P GAIN MUTATED 10 0 1 4 6 1 0
20P GAIN WILD-TYPE 62 1 0 4 9 1 1

Figure S19.  Get High-res Image Gene #30: '20p gain' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0113 (Fisher's exact test), Q value = 0.2

Table S20.  Gene #31: '20q gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
20Q GAIN MUTATED 0 12 0 10
20Q GAIN WILD-TYPE 1 65 1 11

Figure S20.  Get High-res Image Gene #31: '20q gain' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0105 (Wilcoxon-test), Q value = 0.2

Table S21.  Gene #31: '20q gain' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 58 91.9 (8.5)
20Q GAIN MUTATED 8 85.0 (9.3)
20Q GAIN WILD-TYPE 50 93.0 (7.9)

Figure S21.  Get High-res Image Gene #31: '20q gain' versus Clinical Feature #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'20q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00063 (Wilcoxon-test), Q value = 0.058

Table S22.  Gene #31: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 78 11 10
20Q GAIN MUTATED 11 5 6
20Q GAIN WILD-TYPE 67 6 4

Figure S22.  Get High-res Image Gene #31: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

'20q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00782 (Fisher's exact test), Q value = 0.2

Table S23.  Gene #31: '20q gain' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV STAGE IVB
ALL 72 1 1 8 15 2 1
20Q GAIN MUTATED 10 0 1 4 6 1 0
20Q GAIN WILD-TYPE 62 1 0 4 9 1 1

Figure S23.  Get High-res Image Gene #31: '20q gain' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

'1q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.011 (Fisher's exact test), Q value = 0.2

Table S24.  Gene #39: '1q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
1Q LOSS MUTATED 0 0 0 3
1Q LOSS WILD-TYPE 1 77 1 18

Figure S24.  Get High-res Image Gene #39: '1q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'1q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00513 (Wilcoxon-test), Q value = 0.16

Table S25.  Gene #39: '1q loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 78 11 10
1Q LOSS MUTATED 0 1 2
1Q LOSS WILD-TYPE 78 10 8

Figure S25.  Get High-res Image Gene #39: '1q loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00446 (logrank test), Q value = 0.16

Table S26.  Gene #41: '4p loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
4P LOSS MUTATED 12 2 5.4 - 23.4 (12.7)
4P LOSS WILD-TYPE 86 1 0.0 - 130.4 (11.5)

Figure S26.  Get High-res Image Gene #41: '4p loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S27.  Gene #41: '4p loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
4P LOSS MUTATED 1 3 0 8
4P LOSS WILD-TYPE 0 74 1 13

Figure S27.  Get High-res Image Gene #41: '4p loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'FIGO_GRADE'

P value = 0.0113 (Fisher's exact test), Q value = 0.2

Table S28.  Gene #41: '4p loss' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
4P LOSS MUTATED 1 0 2
4P LOSS WILD-TYPE 31 34 5

Figure S28.  Get High-res Image Gene #41: '4p loss' versus Clinical Feature #3: 'FIGO_GRADE'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0105 (Wilcoxon-test), Q value = 0.2

Table S29.  Gene #41: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 78 11 10
4P LOSS MUTATED 6 2 4
4P LOSS WILD-TYPE 72 9 6

Figure S29.  Get High-res Image Gene #41: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.011 (Fisher's exact test), Q value = 0.2

Table S30.  Gene #41: '4p loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV STAGE IVB
ALL 72 1 1 8 15 2 1
4P LOSS MUTATED 5 0 0 1 4 2 0
4P LOSS WILD-TYPE 67 1 1 7 11 0 1

Figure S30.  Get High-res Image Gene #41: '4p loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

'4q loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00446 (logrank test), Q value = 0.16

Table S31.  Gene #42: '4q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
4Q LOSS MUTATED 12 2 5.4 - 23.4 (12.7)
4Q LOSS WILD-TYPE 86 1 0.0 - 130.4 (11.5)

Figure S31.  Get High-res Image Gene #42: '4q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 4e-05 (Fisher's exact test), Q value = 0.015

Table S32.  Gene #42: '4q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
4Q LOSS MUTATED 1 3 0 8
4Q LOSS WILD-TYPE 0 74 1 13

Figure S32.  Get High-res Image Gene #42: '4q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'FIGO_GRADE'

P value = 0.0114 (Fisher's exact test), Q value = 0.2

Table S33.  Gene #42: '4q loss' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
4Q LOSS MUTATED 1 0 2
4Q LOSS WILD-TYPE 31 34 5

Figure S33.  Get High-res Image Gene #42: '4q loss' versus Clinical Feature #3: 'FIGO_GRADE'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0102 (Wilcoxon-test), Q value = 0.2

Table S34.  Gene #42: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 78 11 10
4Q LOSS MUTATED 6 2 4
4Q LOSS WILD-TYPE 72 9 6

Figure S34.  Get High-res Image Gene #42: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

'4q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0115 (Fisher's exact test), Q value = 0.2

Table S35.  Gene #42: '4q loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV STAGE IVB
ALL 72 1 1 8 15 2 1
4Q LOSS MUTATED 5 0 0 1 4 2 0
4Q LOSS WILD-TYPE 67 1 1 7 11 0 1

Figure S35.  Get High-res Image Gene #42: '4q loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

'5p loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.000208 (logrank test), Q value = 0.03

Table S36.  Gene #43: '5p loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
5P LOSS MUTATED 8 2 5.4 - 22.0 (10.7)
5P LOSS WILD-TYPE 90 1 0.0 - 130.4 (11.6)

Figure S36.  Get High-res Image Gene #43: '5p loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'5p loss' versus 'FIGO_GRADE'

P value = 0.00488 (Fisher's exact test), Q value = 0.16

Table S37.  Gene #43: '5p loss' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
5P LOSS MUTATED 1 1 3
5P LOSS WILD-TYPE 31 33 4

Figure S37.  Get High-res Image Gene #43: '5p loss' versus Clinical Feature #3: 'FIGO_GRADE'

'5p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00743 (Wilcoxon-test), Q value = 0.19

Table S38.  Gene #43: '5p loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 46 6 3
5P LOSS MUTATED 2 1 2
5P LOSS WILD-TYPE 44 5 1

Figure S38.  Get High-res Image Gene #43: '5p loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00149 (logrank test), Q value = 0.11

Table S39.  Gene #44: '5q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
5Q LOSS MUTATED 10 2 5.4 - 24.8 (11.6)
5Q LOSS WILD-TYPE 88 1 0.0 - 130.4 (11.6)

Figure S39.  Get High-res Image Gene #44: '5q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'5q loss' versus 'FIGO_GRADE'

P value = 0.00515 (Fisher's exact test), Q value = 0.16

Table S40.  Gene #44: '5q loss' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
5Q LOSS MUTATED 1 1 3
5Q LOSS WILD-TYPE 31 33 4

Figure S40.  Get High-res Image Gene #44: '5q loss' versus Clinical Feature #3: 'FIGO_GRADE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00304 (Wilcoxon-test), Q value = 0.14

Table S41.  Gene #44: '5q loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 46 6 3
5Q LOSS MUTATED 2 2 2
5Q LOSS WILD-TYPE 44 4 1

Figure S41.  Get High-res Image Gene #44: '5q loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00935 (Fisher's exact test), Q value = 0.2

Table S42.  Gene #44: '5q loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV STAGE IVB
ALL 72 1 1 8 15 2 1
5Q LOSS MUTATED 5 0 0 0 4 2 0
5Q LOSS WILD-TYPE 67 1 1 8 11 0 1

Figure S42.  Get High-res Image Gene #44: '5q loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0109 (Fisher's exact test), Q value = 0.2

Table S43.  Gene #47: '8p loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
8P LOSS MUTATED 0 2 0 5
8P LOSS WILD-TYPE 1 75 1 16

Figure S43.  Get High-res Image Gene #47: '8p loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S44.  Gene #49: '9p loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
9P LOSS MUTATED 1 4 0 9
9P LOSS WILD-TYPE 0 73 1 12

Figure S44.  Get High-res Image Gene #49: '9p loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.01 (Wilcoxon-test), Q value = 0.2

Table S45.  Gene #49: '9p loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 46 6 3
9P LOSS MUTATED 5 3 2
9P LOSS WILD-TYPE 41 3 1

Figure S45.  Get High-res Image Gene #49: '9p loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

'9q loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.0108 (logrank test), Q value = 0.2

Table S46.  Gene #50: '9q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
9Q LOSS MUTATED 15 2 6.0 - 24.8 (11.1)
9Q LOSS WILD-TYPE 83 1 0.0 - 130.4 (11.6)

Figure S46.  Get High-res Image Gene #50: '9q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.015

Table S47.  Gene #50: '9q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
9Q LOSS MUTATED 1 5 0 10
9Q LOSS WILD-TYPE 0 72 1 11

Figure S47.  Get High-res Image Gene #50: '9q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'FIGO_GRADE'

P value = 0.00206 (Fisher's exact test), Q value = 0.13

Table S48.  Gene #50: '9q loss' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
9Q LOSS MUTATED 0 1 3
9Q LOSS WILD-TYPE 32 33 4

Figure S48.  Get High-res Image Gene #50: '9q loss' versus Clinical Feature #3: 'FIGO_GRADE'

'9q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0102 (Wilcoxon-test), Q value = 0.2

Table S49.  Gene #50: '9q loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 46 6 3
9Q LOSS MUTATED 5 3 2
9Q LOSS WILD-TYPE 41 3 1

Figure S49.  Get High-res Image Gene #50: '9q loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

'11q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0138 (Wilcoxon-test), Q value = 0.23

Table S50.  Gene #54: '11q loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 78 11 10
11Q LOSS MUTATED 3 1 3
11Q LOSS WILD-TYPE 75 10 7

Figure S50.  Get High-res Image Gene #54: '11q loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'FIGO_GRADE'

P value = 0.00542 (Fisher's exact test), Q value = 0.16

Table S51.  Gene #57: '13q loss' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
13Q LOSS MUTATED 1 1 3
13Q LOSS WILD-TYPE 31 33 4

Figure S51.  Get High-res Image Gene #57: '13q loss' versus Clinical Feature #3: 'FIGO_GRADE'

'15q loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00283 (logrank test), Q value = 0.14

Table S52.  Gene #58: '15q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
15Q LOSS MUTATED 13 2 0.0 - 24.8 (10.3)
15Q LOSS WILD-TYPE 85 1 1.9 - 130.4 (11.6)

Figure S52.  Get High-res Image Gene #58: '15q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00166 (Fisher's exact test), Q value = 0.11

Table S53.  Gene #58: '15q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
15Q LOSS MUTATED 0 5 0 8
15Q LOSS WILD-TYPE 1 72 1 13

Figure S53.  Get High-res Image Gene #58: '15q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'FIGO_GRADE'

P value = 0.00054 (Fisher's exact test), Q value = 0.058

Table S54.  Gene #58: '15q loss' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
15Q LOSS MUTATED 0 0 3
15Q LOSS WILD-TYPE 32 34 4

Figure S54.  Get High-res Image Gene #58: '15q loss' versus Clinical Feature #3: 'FIGO_GRADE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00504 (Wilcoxon-test), Q value = 0.16

Table S55.  Gene #58: '15q loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 46 6 3
15Q LOSS MUTATED 2 3 1
15Q LOSS WILD-TYPE 44 3 2

Figure S55.  Get High-res Image Gene #58: '15q loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.015 (Wilcoxon-test), Q value = 0.24

Table S56.  Gene #58: '15q loss' versus Clinical Feature #9: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 100 63.6 (10.1)
15Q LOSS MUTATED 13 70.6 (9.7)
15Q LOSS WILD-TYPE 87 62.5 (9.7)

Figure S56.  Get High-res Image Gene #58: '15q loss' versus Clinical Feature #9: 'YEARS_TO_BIRTH'

'16p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00516 (Fisher's exact test), Q value = 0.16

Table S57.  Gene #59: '16p loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
16P LOSS MUTATED 0 1 0 5
16P LOSS WILD-TYPE 1 76 1 16

Figure S57.  Get High-res Image Gene #59: '16p loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'16q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0107 (Fisher's exact test), Q value = 0.2

Table S58.  Gene #60: '16q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
16Q LOSS MUTATED 0 2 0 5
16Q LOSS WILD-TYPE 1 75 1 16

Figure S58.  Get High-res Image Gene #60: '16q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00283 (logrank test), Q value = 0.14

Table S59.  Gene #61: '17p loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
17P LOSS MUTATED 12 2 5.4 - 24.8 (10.7)
17P LOSS WILD-TYPE 86 1 0.0 - 130.4 (11.6)

Figure S59.  Get High-res Image Gene #61: '17p loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'17p loss' versus 'FIGO_GRADE'

P value = 0.00234 (Fisher's exact test), Q value = 0.13

Table S60.  Gene #61: '17p loss' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
17P LOSS MUTATED 0 1 3
17P LOSS WILD-TYPE 32 33 4

Figure S60.  Get High-res Image Gene #61: '17p loss' versus Clinical Feature #3: 'FIGO_GRADE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00655 (Wilcoxon-test), Q value = 0.19

Table S61.  Gene #61: '17p loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 46 6 3
17P LOSS MUTATED 3 2 2
17P LOSS WILD-TYPE 43 4 1

Figure S61.  Get High-res Image Gene #61: '17p loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

'17q loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.000675 (logrank test), Q value = 0.058

Table S62.  Gene #62: '17q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
17Q LOSS MUTATED 8 2 6.7 - 24.8 (12.5)
17Q LOSS WILD-TYPE 90 1 0.0 - 130.4 (11.6)

Figure S62.  Get High-res Image Gene #62: '17q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'17q loss' versus 'FIGO_GRADE'

P value = 0.00219 (Fisher's exact test), Q value = 0.13

Table S63.  Gene #62: '17q loss' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
17Q LOSS MUTATED 0 1 3
17Q LOSS WILD-TYPE 32 33 4

Figure S63.  Get High-res Image Gene #62: '17q loss' versus Clinical Feature #3: 'FIGO_GRADE'

'18p loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00439 (logrank test), Q value = 0.16

Table S64.  Gene #63: '18p loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
18P LOSS MUTATED 4 1 5.4 - 13.9 (9.1)
18P LOSS WILD-TYPE 94 2 0.0 - 130.4 (11.6)

Figure S64.  Get High-res Image Gene #63: '18p loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'18q loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.0112 (logrank test), Q value = 0.2

Table S65.  Gene #64: '18q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
18Q LOSS MUTATED 5 1 5.4 - 13.9 (8.3)
18Q LOSS WILD-TYPE 93 2 0.0 - 130.4 (11.6)

Figure S65.  Get High-res Image Gene #64: '18q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0114 (Fisher's exact test), Q value = 0.2

Table S66.  Gene #67: '21q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
21Q LOSS MUTATED 0 1 0 4
21Q LOSS WILD-TYPE 1 76 1 17

Figure S66.  Get High-res Image Gene #67: '21q loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00695 (Wilcoxon-test), Q value = 0.19

Table S67.  Gene #67: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 78 11 10
21Q LOSS MUTATED 1 2 2
21Q LOSS WILD-TYPE 77 9 8

Figure S67.  Get High-res Image Gene #67: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0137 (Wilcoxon-test), Q value = 0.23

Table S68.  Gene #67: '21q loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

N0 N1 N2
ALL 46 6 3
21Q LOSS MUTATED 2 3 0
21Q LOSS WILD-TYPE 44 3 3

Figure S68.  Get High-res Image Gene #67: '21q loss' versus Clinical Feature #7: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.000641 (logrank test), Q value = 0.058

Table S69.  Gene #68: '22q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

nPatients nDeath Duration Range (Median), Month
ALL 99 3 0.0 - 130.4 (11.6)
22Q LOSS MUTATED 11 2 6.0 - 23.4 (10.3)
22Q LOSS WILD-TYPE 87 1 0.0 - 130.4 (11.6)

Figure S69.  Get High-res Image Gene #68: '22q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

'22q loss' versus 'FIGO_GRADE'

P value = 0.00287 (Fisher's exact test), Q value = 0.14

Table S70.  Gene #68: '22q loss' versus Clinical Feature #3: 'FIGO_GRADE'

nPatients FIGO GRADE 1 FIGO GRADE 2 FIGO GRADE 3
ALL 32 34 7
22Q LOSS MUTATED 0 2 3
22Q LOSS WILD-TYPE 32 32 4

Figure S70.  Get High-res Image Gene #68: '22q loss' versus Clinical Feature #3: 'FIGO_GRADE'

'22q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0145 (Wilcoxon-test), Q value = 0.24

Table S71.  Gene #68: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

T1 T2 T3
ALL 78 11 10
22Q LOSS MUTATED 6 4 2
22Q LOSS WILD-TYPE 72 7 8

Figure S71.  Get High-res Image Gene #68: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_T_STAGE'

'22q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0122 (Fisher's exact test), Q value = 0.21

Table S72.  Gene #68: '22q loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV STAGE IVB
ALL 72 1 1 8 15 2 1
22Q LOSS MUTATED 4 0 0 3 4 1 0
22Q LOSS WILD-TYPE 68 1 1 5 11 1 1

Figure S72.  Get High-res Image Gene #68: '22q loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

'xp loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00022 (Fisher's exact test), Q value = 0.03

Table S73.  Gene #69: 'xp loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
XP LOSS MUTATED 1 8 0 10
XP LOSS WILD-TYPE 0 69 1 11

Figure S73.  Get High-res Image Gene #69: 'xp loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'xp loss' versus 'PATHOLOGIC_STAGE'

P value = 0.007 (Fisher's exact test), Q value = 0.19

Table S74.  Gene #69: 'xp loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV STAGE IVB
ALL 72 1 1 8 15 2 1
XP LOSS MUTATED 9 0 1 3 4 2 0
XP LOSS WILD-TYPE 63 1 0 5 11 0 1

Figure S74.  Get High-res Image Gene #69: 'xp loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

'xq loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00022 (Fisher's exact test), Q value = 0.03

Table S75.  Gene #70: 'xq loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

nPatients CLEAR CELL CARCINOMA ENDOMETRIOID CARCINOMA MIXED CELL ADENOCARCINOMA SEROUS CARCINOMA
ALL 1 77 1 21
XQ LOSS MUTATED 1 8 0 10
XQ LOSS WILD-TYPE 0 69 1 11

Figure S75.  Get High-res Image Gene #70: 'xq loss' versus Clinical Feature #2: 'HISTOLOGICAL_TYPE'

'xq loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00661 (Fisher's exact test), Q value = 0.19

Table S76.  Gene #70: 'xq loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE III STAGE IV STAGE IVB
ALL 72 1 1 8 15 2 1
XQ LOSS MUTATED 9 0 1 3 4 2 0
XQ LOSS WILD-TYPE 63 1 0 5 11 0 1

Figure S76.  Get High-res Image Gene #70: 'xq loss' versus Clinical Feature #8: 'PATHOLOGIC_STAGE'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/dd472489-0497-4592-8e57-feebd57f430a/correlate_genomic_events_all/b25b700b-900d-4ef4-9d8a-8dba01dad061/call-preprocess_genomic_event/transformed.cor.cli.txt

  • Clinical data file = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/f48b4003-eaf7-47c4-8ca4-0ddbd4729902/normalize_clinical_cptac/0ea0fb0d-64a4-4204-8245-a79f52e6cd0a/call-normalize_clinical_cptac_task_1/CPTAC3-UCEC-TP.clin.merged.picked.txt

  • Number of patients = 100

  • Number of significantly arm-level cnvs = 72

  • Number of selected clinical features = 17

  • Exclude regions 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

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.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] 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)
[3] 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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