Uterine Corpus Endometrioid Carcinoma: Correlation between copy number variations of arm-level result and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 79 arm-level results and 4 clinical features across 443 patients, 50 significant findings detected with Q value < 0.25.

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

  • 13q gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 17p gain cnv correlated to 'Time to Death'.

  • 18p gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 19p gain cnv correlated to 'AGE'.

  • 19q gain cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 20p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

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

  • 4q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 5p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 5q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

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

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

  • 8q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 9p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 9q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

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

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

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

  • 13q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 14q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 15q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 16p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 16q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 17p loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 17q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • 18q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 19p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

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

  • 22q loss cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 4 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 50 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test
11p loss 46 (10%) 397 0.000549
(0.149) 		0.000217
(0.0601) 		1.1e-06
(0.000327) 		0.398
(1.00)
11q loss 39 (9%) 404 0.000244
(0.0675) 		0.000109
(0.0305) 		1.87e-05
(0.00542) 		0.203
(1.00)
5p gain 29 (7%) 414 3.3e-05
(0.00955) 		0.0978
(1.00) 		2.21e-06
(0.000656) 		0.537
(1.00)
13q gain 19 (4%) 424 0.449
(1.00) 		0.000758
(0.203) 		5.68e-05
(0.0162) 		0.609
(1.00)
18p gain 31 (7%) 412 0.0887
(1.00) 		0.000157
(0.0438) 		5.47e-07
(0.000164) 		0.688
(1.00)
19q gain 22 (5%) 421 0.00791
(1.00) 		1.06e-05
(0.00308) 		2.71e-07
(8.18e-05) 		0.815
(1.00)
7q loss 23 (5%) 420 0.829
(1.00) 		0.000873
(0.233) 		3.27e-08
(9.98e-06) 		1
(1.00)
8p loss 41 (9%) 402 0.524
(1.00) 		7.71e-05
(0.0217) 		7.21e-19
(2.27e-16) 		0.592
(1.00)
9p loss 64 (14%) 379 0.838
(1.00) 		1.07e-06
(0.000319) 		4.11e-14
(1.29e-11) 		1
(1.00)
9q loss 81 (18%) 362 0.181
(1.00) 		1.23e-10
(3.8e-08) 		1.08e-11
(3.36e-09) 		0.422
(1.00)
14q loss 36 (8%) 407 0.241
(1.00) 		0.000469
(0.129) 		6.99e-09
(2.14e-06) 		1
(1.00)
15q loss 63 (14%) 380 0.682
(1.00) 		3.87e-05
(0.0111) 		3.42e-10
(1.06e-07) 		0.299
(1.00)
16p loss 56 (13%) 387 0.0291
(1.00) 		5.76e-05
(0.0164) 		6.56e-08
(1.99e-05) 		0.642
(1.00)
16q loss 92 (21%) 351 0.033
(1.00) 		4.55e-06
(0.00134) 		6.92e-14
(2.17e-11) 		0.253
(1.00)
17p loss 86 (19%) 357 0.173
(1.00) 		1.23e-06
(0.000366) 		2.25e-20
(7.1e-18) 		0.36
(1.00)
17q loss 57 (13%) 386 0.993
(1.00) 		0.000536
(0.146) 		3.72e-05
(0.0107) 		0.124
(1.00)
22q loss 73 (16%) 370 0.00829
(1.00) 		0.000178
(0.0495) 		4.89e-08
(1.49e-05) 		0.328
(1.00)
17p gain 6 (1%) 437 0.000609
(0.165) 		0.78
(1.00) 		0.965
(1.00) 		0.371
(1.00)
19p gain 25 (6%) 418 0.0523
(1.00) 		4.47e-05
(0.0128) 		0.000997
(0.265) 		0.176
(1.00)
20p gain 52 (12%) 391 0.0125
(1.00) 		0.00498
(1.00) 		5.04e-06
(0.00148) 		0.0151
(1.00)
20q gain 60 (14%) 383 0.0629
(1.00) 		0.00277
(0.712) 		3.97e-10
(1.22e-07) 		0.0152
(1.00)
4p loss 48 (11%) 395 0.0509
(1.00) 		0.00104
(0.276) 		8.23e-11
(2.56e-08) 		0.318
(1.00)
4q loss 45 (10%) 398 0.0329
(1.00) 		0.00604
(1.00) 		4.42e-07
(0.000133) 		0.0609
(1.00)
5p loss 20 (5%) 423 0.442
(1.00) 		0.758
(1.00) 		7.02e-05
(0.0199) 		0.622
(1.00)
5q loss 35 (8%) 408 0.932
(1.00) 		0.0187
(1.00) 		4.45e-10
(1.37e-07) 		0.341
(1.00)
8q loss 7 (2%) 436 0.701
(1.00) 		0.602
(1.00) 		9.25e-06
(0.0027) 		0.68
(1.00)
12p loss 18 (4%) 425 0.186
(1.00) 		0.00152
(0.397) 		0.000303
(0.0832) 		0.603
(1.00)
13q loss 51 (12%) 392 0.0936
(1.00) 		0.00269
(0.695) 		0.000641
(0.173) 		0.518
(1.00)
18q loss 41 (9%) 402 0.521
(1.00) 		0.0464
(1.00) 		0.000101
(0.0285) 		0.285
(1.00)
19p loss 28 (6%) 415 0.316
(1.00) 		0.985
(1.00) 		5.48e-06
(0.00161) 		1
(1.00)
21q loss 25 (6%) 418 0.227
(1.00) 		0.344
(1.00) 		0.0007
(0.188) 		0.268
(1.00)
1p gain 16 (4%) 427 0.0386
(1.00) 		0.111
(1.00) 		0.0832
(1.00) 		0.412
(1.00)
1q gain 128 (29%) 315 0.564
(1.00) 		0.0689
(1.00) 		0.0143
(1.00) 		0.569
(1.00)
2p gain 46 (10%) 397 0.0912
(1.00) 		0.028
(1.00) 		0.208
(1.00) 		0.613
(1.00)
2q gain 36 (8%) 407 0.102
(1.00) 		0.158
(1.00) 		0.172
(1.00) 		0.573
(1.00)
3p gain 24 (5%) 419 0.491
(1.00) 		0.403
(1.00) 		0.721
(1.00) 		0.0661
(1.00)
3q gain 43 (10%) 400 0.0485
(1.00) 		0.156
(1.00) 		0.00217
(0.561) 		0.601
(1.00)
4p gain 5 (1%) 438 0.6
(1.00) 		0.024
(1.00) 		0.0345
(1.00) 		0.639
(1.00)
5q gain 8 (2%) 435 0.329
(1.00) 		0.935
(1.00) 		0.0746
(1.00) 		1
(1.00)
6p gain 33 (7%) 410 0.691
(1.00) 		0.392
(1.00) 		0.0356
(1.00) 		1
(1.00)
6q gain 28 (6%) 415 0.978
(1.00) 		0.4
(1.00) 		0.0813
(1.00) 		0.525
(1.00)
7p gain 39 (9%) 404 0.303
(1.00) 		0.625
(1.00) 		0.17
(1.00) 		0.1
(1.00)
7q gain 37 (8%) 406 0.016
(1.00) 		0.692
(1.00) 		0.414
(1.00) 		0.138
(1.00)
8p gain 78 (18%) 365 0.00114
(0.3) 		0.444
(1.00) 		0.418
(1.00) 		0.587
(1.00)
8q gain 102 (23%) 341 0.00639
(1.00) 		0.96
(1.00) 		0.0545
(1.00) 		0.714
(1.00)
9p gain 11 (2%) 432 0.776
(1.00) 		0.79
(1.00) 		0.923
(1.00) 		0.039
(1.00)
9q gain 3 (1%) 440 0.796
(1.00) 		0.788
(1.00) 		0.269
(1.00) 		0.557
(1.00)
10p gain 82 (19%) 361 0.681
(1.00) 		0.491
(1.00) 		0.224
(1.00) 		0.895
(1.00)
10q gain 77 (17%) 366 0.87
(1.00) 		0.657
(1.00) 		0.239
(1.00) 		1
(1.00)
11p gain 5 (1%) 438 0.444
(1.00) 		0.642
(1.00) 		0.382
(1.00) 		0.639
(1.00)
11q gain 6 (1%) 437 0.563
(1.00) 		0.697
(1.00) 		0.965
(1.00) 		1
(1.00)
12p gain 33 (7%) 410 0.581
(1.00) 		0.667
(1.00) 		0.0427
(1.00) 		0.844
(1.00)
12q gain 26 (6%) 417 0.724
(1.00) 		0.496
(1.00) 		0.847
(1.00) 		1
(1.00)
14q gain 16 (4%) 427 0.198
(1.00) 		0.621
(1.00) 		0.2
(1.00) 		0.0477
(1.00)
15q gain 5 (1%) 438 0.0106
(1.00) 		0.51
(1.00) 		0.998
(1.00) 		0.328
(1.00)
16p gain 11 (2%) 432 0.315
(1.00) 		0.123
(1.00) 		0.0903
(1.00) 		0.517
(1.00)
16q gain 4 (1%) 439 0.664
(1.00) 		0.476
(1.00) 		0.998
(1.00) 		0.321
(1.00)
17q gain 10 (2%) 433 0.0812
(1.00) 		0.16
(1.00) 		0.938
(1.00) 		0.496
(1.00)
18q gain 15 (3%) 428 0.00363
(0.93) 		0.0425
(1.00) 		0.127
(1.00) 		0.569
(1.00)
21q gain 20 (5%) 423 0.841
(1.00) 		0.00819
(1.00) 		0.002
(0.521) 		1
(1.00)
22q gain 6 (1%) 437 0.519
(1.00) 		0.0179
(1.00) 		0.117
(1.00) 		1
(1.00)
Xq gain 7 (2%) 436 0.0842
(1.00) 		0.338
(1.00) 		0.249
(1.00) 		1
(1.00)
1p loss 11 (2%) 432 0.272
(1.00) 		0.255
(1.00) 		0.146
(1.00) 		0.318
(1.00)
1q loss 4 (1%) 439 0.0135
(1.00) 		0.18
(1.00) 		0.221
(1.00) 		0.321
(1.00)
2p loss 6 (1%) 437 0.528
(1.00) 		0.0696
(1.00) 		0.111
(1.00) 		0.185
(1.00)
2q loss 7 (2%) 436 0.353
(1.00) 		0.0298
(1.00) 		0.165
(1.00) 		0.108
(1.00)
3p loss 26 (6%) 417 0.123
(1.00) 		0.0171
(1.00) 		0.00146
(0.384) 		0.828
(1.00)
3q loss 12 (3%) 431 0.237
(1.00) 		0.143
(1.00) 		0.155
(1.00) 		0.524
(1.00)
6p loss 7 (2%) 436 0.207
(1.00) 		0.167
(1.00) 		0.249
(1.00) 		0.433
(1.00)
6q loss 9 (2%) 434 0.666
(1.00) 		0.178
(1.00) 		0.154
(1.00) 		0.462
(1.00)
7p loss 25 (6%) 418 0.37
(1.00) 		0.00998
(1.00) 		0.00112
(0.296) 		1
(1.00)
10p loss 17 (4%) 426 0.0183
(1.00) 		0.0629
(1.00) 		0.00447
(1.00) 		1
(1.00)
10q loss 16 (4%) 427 0.371
(1.00) 		0.0299
(1.00) 		0.24
(1.00) 		0.786
(1.00)
12q loss 12 (3%) 431 0.452
(1.00) 		0.0247
(1.00) 		0.0169
(1.00) 		1
(1.00)
18p loss 28 (6%) 415 0.234
(1.00) 		0.133
(1.00) 		0.00573
(1.00) 		0.672
(1.00)
19q loss 21 (5%) 422 0.529
(1.00) 		0.789
(1.00) 		0.0102
(1.00) 		0.808
(1.00)
20p loss 13 (3%) 430 0.639
(1.00) 		0.0778
(1.00) 		0.196
(1.00) 		0.223
(1.00)
20q loss 6 (1%) 437 0.476
(1.00) 		0.234
(1.00) 		0.0348
(1.00) 		0.371
(1.00)
Xq loss 12 (3%) 431 0.516
(1.00) 		0.293
(1.00) 		0.117
(1.00) 		0.119
(1.00)
'5p gain mutation analysis' versus 'Time to Death'

P value = 3.3e-05 (logrank test), Q value = 0.0096

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

nPatients nDeath Duration Range (Median), Month
ALL 438 41 0.0 - 187.1 (15.8)
5P GAIN MUTATED 28 8 0.1 - 59.0 (11.1)
5P GAIN WILD-TYPE 410 33 0.0 - 187.1 (16.1)

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

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

P value = 2.21e-06 (Chi-square test), Q value = 0.00066

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

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
5P GAIN MUTATED 11 0 0 0 0 1 17
5P GAIN WILD-TYPE 316 3 8 2 7 17 61

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

'13q gain mutation analysis' versus 'AGE'

P value = 0.000758 (t-test), Q value = 0.2

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

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
13Q GAIN MUTATED 19 69.3 (6.3)
13Q GAIN WILD-TYPE 423 63.3 (11.4)

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

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

P value = 5.68e-05 (Chi-square test), Q value = 0.016

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 327 3 8 2 7 18 78
13Q GAIN MUTATED 6 0 0 0 0 1 12
13Q GAIN WILD-TYPE 321 3 8 2 7 17 66

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

'17p gain mutation analysis' versus 'Time to Death'

P value = 0.000609 (logrank test), Q value = 0.16

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

nPatients nDeath Duration Range (Median), Month
ALL 438 41 0.0 - 187.1 (15.8)
17P GAIN MUTATED 6 2 3.0 - 15.8 (12.1)
17P GAIN WILD-TYPE 432 39 0.0 - 187.1 (16.1)

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

'18p gain mutation analysis' versus 'AGE'

P value = 0.000157 (t-test), Q value = 0.044

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

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
18P GAIN MUTATED 31 70.2 (9.0)
18P GAIN WILD-TYPE 411 63.0 (11.2)

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

'18p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.47e-07 (Chi-square test), Q value = 0.00016

Table S7.  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 327 3 8 2 7 18 78
18P GAIN MUTATED 11 0 0 0 0 2 18
18P GAIN WILD-TYPE 316 3 8 2 7 16 60

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

'19p gain mutation analysis' versus 'AGE'

P value = 4.47e-05 (t-test), Q value = 0.013

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

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
19P GAIN MUTATED 25 70.9 (7.7)
19P GAIN WILD-TYPE 417 63.1 (11.3)

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

'19q gain mutation analysis' versus 'AGE'

P value = 1.06e-05 (t-test), Q value = 0.0031

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

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
19Q GAIN MUTATED 22 72.4 (7.6)
19Q GAIN WILD-TYPE 420 63.1 (11.2)

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 = 2.71e-07 (Chi-square test), Q value = 8.2e-05

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 327 3 8 2 7 18 78
19Q GAIN MUTATED 7 0 0 0 0 0 15
19Q GAIN WILD-TYPE 320 3 8 2 7 18 63

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 = 5.04e-06 (Chi-square test), Q value = 0.0015

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 327 3 8 2 7 18 78
20P GAIN MUTATED 25 0 0 1 0 3 23
20P GAIN WILD-TYPE 302 3 8 1 7 15 55

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 = 3.97e-10 (Chi-square test), Q value = 1.2e-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 327 3 8 2 7 18 78
20Q GAIN MUTATED 26 0 0 1 0 3 30
20Q GAIN WILD-TYPE 301 3 8 1 7 15 48

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

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

P value = 8.23e-11 (Chi-square test), Q value = 2.6e-08

Table S13.  Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
4P LOSS MUTATED 17 0 0 0 1 3 27
4P LOSS WILD-TYPE 310 3 8 2 6 15 51

Figure S13.  Get High-res Image Gene #46: '4p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 4.42e-07 (Chi-square test), Q value = 0.00013

Table S14.  Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
4Q LOSS MUTATED 18 0 0 0 1 4 22
4Q LOSS WILD-TYPE 309 3 8 2 6 14 56

Figure S14.  Get High-res Image Gene #47: '4q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 7.02e-05 (Chi-square test), Q value = 0.02

Table S15.  Gene #48: '5p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
5P LOSS MUTATED 7 0 0 0 1 0 12
5P LOSS WILD-TYPE 320 3 8 2 6 18 66

Figure S15.  Get High-res Image Gene #48: '5p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 4.45e-10 (Chi-square test), Q value = 1.4e-07

Table S16.  Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
5Q LOSS MUTATED 11 0 0 0 1 1 22
5Q LOSS WILD-TYPE 316 3 8 2 6 17 56

Figure S16.  Get High-res Image Gene #49: '5q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'7q loss mutation analysis' versus 'AGE'

P value = 0.000873 (t-test), Q value = 0.23

Table S17.  Gene #53: '7q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
7Q LOSS MUTATED 23 69.0 (7.0)
7Q LOSS WILD-TYPE 419 63.2 (11.4)

Figure S17.  Get High-res Image Gene #53: '7q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 3.27e-08 (Chi-square test), Q value = 1e-05

Table S18.  Gene #53: '7q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
7Q LOSS MUTATED 6 0 0 0 0 1 16
7Q LOSS WILD-TYPE 321 3 8 2 7 17 62

Figure S18.  Get High-res Image Gene #53: '7q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'8p loss mutation analysis' versus 'AGE'

P value = 7.71e-05 (t-test), Q value = 0.022

Table S19.  Gene #54: '8p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
8P LOSS MUTATED 41 68.3 (7.0)
8P LOSS WILD-TYPE 401 63.0 (11.5)

Figure S19.  Get High-res Image Gene #54: '8p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 7.21e-19 (Chi-square test), Q value = 2.3e-16

Table S20.  Gene #54: '8p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
8P LOSS MUTATED 9 0 0 0 0 2 30
8P LOSS WILD-TYPE 318 3 8 2 7 16 48

Figure S20.  Get High-res Image Gene #54: '8p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 9.25e-06 (Chi-square test), Q value = 0.0027

Table S21.  Gene #55: '8q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
8Q LOSS MUTATED 0 0 0 0 0 0 7
8Q LOSS WILD-TYPE 327 3 8 2 7 18 71

Figure S21.  Get High-res Image Gene #55: '8q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9p loss mutation analysis' versus 'AGE'

P value = 1.07e-06 (t-test), Q value = 0.00032

Table S22.  Gene #56: '9p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
9P LOSS MUTATED 64 69.1 (8.8)
9P LOSS WILD-TYPE 378 62.6 (11.4)

Figure S22.  Get High-res Image Gene #56: '9p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 4.11e-14 (Chi-square test), Q value = 1.3e-11

Table S23.  Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
9P LOSS MUTATED 24 0 0 0 1 4 35
9P LOSS WILD-TYPE 303 3 8 2 6 14 43

Figure S23.  Get High-res Image Gene #56: '9p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'9q loss mutation analysis' versus 'AGE'

P value = 1.23e-10 (t-test), Q value = 3.8e-08

Table S24.  Gene #57: '9q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
9Q LOSS MUTATED 81 69.9 (8.6)
9Q LOSS WILD-TYPE 361 62.1 (11.3)

Figure S24.  Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.08e-11 (Chi-square test), Q value = 3.4e-09

Table S25.  Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
9Q LOSS MUTATED 37 0 0 0 1 5 38
9Q LOSS WILD-TYPE 290 3 8 2 6 13 40

Figure S25.  Get High-res Image Gene #57: '9q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 0.000549 (logrank test), Q value = 0.15

Table S26.  Gene #60: '11p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 438 41 0.0 - 187.1 (15.8)
11P LOSS MUTATED 44 9 0.0 - 91.0 (12.1)
11P LOSS WILD-TYPE 394 32 0.0 - 187.1 (16.2)

Figure S26.  Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'11p loss mutation analysis' versus 'AGE'

P value = 0.000217 (t-test), Q value = 0.06

Table S27.  Gene #60: '11p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
11P LOSS MUTATED 46 68.8 (9.5)
11P LOSS WILD-TYPE 396 62.9 (11.3)

Figure S27.  Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.1e-06 (Chi-square test), Q value = 0.00033

Table S28.  Gene #60: '11p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
11P LOSS MUTATED 20 0 0 0 0 4 22
11P LOSS WILD-TYPE 307 3 8 2 7 14 56

Figure S28.  Get High-res Image Gene #60: '11p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 0.000244 (logrank test), Q value = 0.067

Table S29.  Gene #61: '11q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 438 41 0.0 - 187.1 (15.8)
11Q LOSS MUTATED 37 8 0.0 - 91.0 (11.8)
11Q LOSS WILD-TYPE 401 33 0.0 - 187.1 (16.1)

Figure S29.  Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'11q loss mutation analysis' versus 'AGE'

P value = 0.000109 (t-test), Q value = 0.031

Table S30.  Gene #61: '11q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
11Q LOSS MUTATED 39 69.7 (9.3)
11Q LOSS WILD-TYPE 403 62.9 (11.2)

Figure S30.  Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 1.87e-05 (Chi-square test), Q value = 0.0054

Table S31.  Gene #61: '11q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
11Q LOSS MUTATED 17 0 0 0 0 5 17
11Q LOSS WILD-TYPE 310 3 8 2 7 13 61

Figure S31.  Get High-res Image Gene #61: '11q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 0.000303 (Chi-square test), Q value = 0.083

Table S32.  Gene #62: '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 327 3 8 2 7 18 78
12P LOSS MUTATED 6 0 0 0 0 1 11
12P LOSS WILD-TYPE 321 3 8 2 7 17 67

Figure S32.  Get High-res Image Gene #62: '12p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 0.000641 (Chi-square test), Q value = 0.17

Table S33.  Gene #64: '13q 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 327 3 8 2 7 18 78
13Q LOSS MUTATED 26 0 0 0 2 3 20
13Q LOSS WILD-TYPE 301 3 8 2 5 15 58

Figure S33.  Get High-res Image Gene #64: '13q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'14q loss mutation analysis' versus 'AGE'

P value = 0.000469 (t-test), Q value = 0.13

Table S34.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
14Q LOSS MUTATED 36 68.7 (8.3)
14Q LOSS WILD-TYPE 406 63.1 (11.4)

Figure S34.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 6.99e-09 (Chi-square test), Q value = 2.1e-06

Table S35.  Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
14Q LOSS MUTATED 12 0 0 0 0 3 21
14Q LOSS WILD-TYPE 315 3 8 2 7 15 57

Figure S35.  Get High-res Image Gene #65: '14q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'15q loss mutation analysis' versus 'AGE'

P value = 3.87e-05 (t-test), Q value = 0.011

Table S36.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
15Q LOSS MUTATED 63 69.0 (10.7)
15Q LOSS WILD-TYPE 379 62.6 (11.1)

Figure S36.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 3.42e-10 (Chi-square test), Q value = 1.1e-07

Table S37.  Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
15Q LOSS MUTATED 26 0 0 0 1 6 30
15Q LOSS WILD-TYPE 301 3 8 2 6 12 48

Figure S37.  Get High-res Image Gene #66: '15q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16p loss mutation analysis' versus 'AGE'

P value = 5.76e-05 (t-test), Q value = 0.016

Table S38.  Gene #67: '16p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
16P LOSS MUTATED 56 68.9 (9.8)
16P LOSS WILD-TYPE 386 62.8 (11.2)

Figure S38.  Get High-res Image Gene #67: '16p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 6.56e-08 (Chi-square test), Q value = 2e-05

Table S39.  Gene #67: '16p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
16P LOSS MUTATED 25 0 0 0 0 5 26
16P LOSS WILD-TYPE 302 3 8 2 7 13 52

Figure S39.  Get High-res Image Gene #67: '16p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'16q loss mutation analysis' versus 'AGE'

P value = 4.55e-06 (t-test), Q value = 0.0013

Table S40.  Gene #68: '16q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
16Q LOSS MUTATED 92 67.8 (9.3)
16Q LOSS WILD-TYPE 350 62.4 (11.5)

Figure S40.  Get High-res Image Gene #68: '16q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 6.92e-14 (Chi-square test), Q value = 2.2e-11

Table S41.  Gene #68: '16q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
16Q LOSS MUTATED 42 0 0 0 1 6 43
16Q LOSS WILD-TYPE 285 3 8 2 6 12 35

Figure S41.  Get High-res Image Gene #68: '16q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17p loss mutation analysis' versus 'AGE'

P value = 1.23e-06 (t-test), Q value = 0.00037

Table S42.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
17P LOSS MUTATED 86 68.4 (9.5)
17P LOSS WILD-TYPE 356 62.4 (11.3)

Figure S42.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 2.25e-20 (Chi-square test), Q value = 7.1e-18

Table S43.  Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
17P LOSS MUTATED 32 0 0 0 1 7 46
17P LOSS WILD-TYPE 295 3 8 2 6 11 32

Figure S43.  Get High-res Image Gene #69: '17p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'17q loss mutation analysis' versus 'AGE'

P value = 0.000536 (t-test), Q value = 0.15

Table S44.  Gene #70: '17q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
17Q LOSS MUTATED 57 68.4 (10.8)
17Q LOSS WILD-TYPE 385 62.8 (11.1)

Figure S44.  Get High-res Image Gene #70: '17q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 3.72e-05 (Chi-square test), Q value = 0.011

Table S45.  Gene #70: '17q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
17Q LOSS MUTATED 28 0 0 0 1 5 23
17Q LOSS WILD-TYPE 299 3 8 2 6 13 55

Figure S45.  Get High-res Image Gene #70: '17q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 0.000101 (Chi-square test), Q value = 0.028

Table S46.  Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
18Q LOSS MUTATED 19 0 0 0 1 6 15
18Q LOSS WILD-TYPE 308 3 8 2 6 12 63

Figure S46.  Get High-res Image Gene #72: '18q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 5.48e-06 (Chi-square test), Q value = 0.0016

Table S47.  Gene #73: '19p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
19P LOSS MUTATED 10 0 0 0 0 2 16
19P LOSS WILD-TYPE 317 3 8 2 7 16 62

Figure S47.  Get High-res Image Gene #73: '19p loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

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

P value = 7e-04 (Chi-square test), Q value = 0.19

Table S48.  Gene #77: '21q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
21Q LOSS MUTATED 10 0 0 0 0 3 12
21Q LOSS WILD-TYPE 317 3 8 2 7 15 66

Figure S48.  Get High-res Image Gene #77: '21q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

'22q loss mutation analysis' versus 'AGE'

P value = 0.000178 (t-test), Q value = 0.049

Table S49.  Gene #78: '22q loss mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 442 63.5 (11.2)
22Q LOSS MUTATED 73 67.5 (9.1)
22Q LOSS WILD-TYPE 369 62.8 (11.5)

Figure S49.  Get High-res Image Gene #78: '22q loss mutation analysis' versus Clinical Feature #2: 'AGE'

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

P value = 4.89e-08 (Chi-square test), Q value = 1.5e-05

Table S50.  Gene #78: '22q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

nPatients ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) MIXED SEROUS AND ENDOMETRIOID SEROUS ENDOMETRIAL ADENOCARCINOMA
ALL 327 3 8 2 7 18 78
22Q LOSS MUTATED 35 0 0 0 1 6 31
22Q LOSS WILD-TYPE 292 3 8 2 6 12 47

Figure S50.  Get High-res Image Gene #78: '22q loss mutation analysis' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Clinical data file = UCEC-TP.clin.merged.picked.txt

  • Number of patients = 443

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 4

  • 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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