Correlation between copy number variations of arm-level result and selected clinical features
Bladder Urothelial Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1F76BHN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1F76BHN
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 82 arm-level events and 12 clinical features across 389 patients, 14 significant findings detected with Q value < 0.25.

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

  • 3q gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 7q gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 11q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 14q gain cnv correlated to 'RACE'.

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 3p loss cnv correlated to 'GENDER'.

  • 4p loss cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 5p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 5q loss cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 6q loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 15q loss cnv correlated to 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 14 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBER
PACK
YEARS
SMOKED 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nCNV (%) nWild-Type logrank 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 Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
3p gain 134 (34%) 255 0.376
(0.879) 		0.00241
(0.246) 		0.207
(0.744) 		0.24
(0.78) 		0.0472
(0.491) 		0.306
(0.843) 		0.114
(0.637) 		0.0409
(0.468) 		0.0569
(0.514) 		0.00071
(0.175) 		0.142
(0.665) 		1
(1.00)
6q loss 148 (38%) 241 0.644
(0.978) 		0.644
(0.978) 		0.00941
(0.329) 		0.379
(0.879) 		0.00314
(0.246) 		0.329
(0.851) 		0.286
(0.832) 		0.0811
(0.557) 		0.42
(0.908) 		0.0014
(0.246) 		0.0715
(0.529) 		0.0884
(0.562)
3q gain 169 (43%) 220 0.571
(0.969) 		0.00474
(0.277) 		0.147
(0.671) 		0.573
(0.969) 		0.0103
(0.329) 		0.329
(0.851) 		0.727
(0.978) 		0.0612
(0.521) 		0.456
(0.937) 		0.000379
(0.175) 		0.18
(0.703) 		1
(1.00)
7q gain 142 (37%) 247 0.43
(0.918) 		0.0461
(0.491) 		0.104
(0.59) 		0.0615
(0.521) 		0.0007
(0.175) 		0.732
(0.978) 		0.632
(0.978) 		0.253
(0.788) 		0.657
(0.978) 		0.183
(0.706) 		0.057
(0.514) 		1
(1.00)
11q gain 47 (12%) 342 0.0142
(0.364) 		0.0035
(0.246) 		0.0907
(0.562) 		0.552
(0.963) 		0.0167
(0.364) 		1
(1.00) 		0.0759
(0.549) 		0.951
(1.00) 		0.74
(0.978) 		0.166
(0.69) 		0.324
(0.851) 		1
(1.00)
14q gain 55 (14%) 334 0.0353
(0.451) 		0.413
(0.908) 		0.323
(0.851) 		0.0481
(0.491) 		0.922
(1.00) 		0.232
(0.77) 		0.013
(0.364) 		0.379
(0.879) 		0.519
(0.938) 		0.432
(0.919) 		0.00266
(0.246) 		0.361
(0.863)
21q gain 105 (27%) 284 0.348
(0.857) 		0.00319
(0.246) 		0.783
(0.985) 		0.542
(0.958) 		0.253
(0.788) 		1
(1.00) 		0.299
(0.839) 		0.413
(0.908) 		0.886
(1.00) 		0.249
(0.788) 		0.644
(0.978) 		1
(1.00)
3p loss 51 (13%) 338 0.507
(0.938) 		0.342
(0.851) 		0.493
(0.938) 		0.399
(0.902) 		0.638
(0.978) 		1
(1.00) 		0.00173
(0.246) 		0.648
(0.978) 		0.649
(0.978) 		0.588
(0.976) 		0.0597
(0.521) 		1
(1.00)
4p loss 136 (35%) 253 0.0496
(0.493) 		0.183
(0.706) 		0.00737
(0.315) 		0.148
(0.672) 		0.00044
(0.175) 		1
(1.00) 		0.628
(0.978) 		0.699
(0.978) 		0.415
(0.908) 		0.021
(0.377) 		0.00697
(0.315) 		0.725
(0.978)
5p loss 53 (14%) 336 0.599
(0.976) 		0.00334
(0.246) 		0.538
(0.957) 		0.71
(0.978) 		0.521
(0.939) 		0.159
(0.68) 		0.5
(0.938) 		0.72
(0.978) 		0.935
(1.00) 		0.497
(0.938) 		1
(1.00) 		1
(1.00)
5q loss 149 (38%) 240 0.143
(0.665) 		0.159
(0.68) 		0.0666
(0.521) 		0.302
(0.839) 		0.00282
(0.246) 		0.17
(0.69) 		0.812
(1.00) 		0.0517
(0.504) 		0.0329
(0.435) 		0.00707
(0.315) 		0.0139
(0.364) 		0.738
(0.978)
15q loss 134 (34%) 255 0.409
(0.908) 		0.299
(0.839) 		0.503
(0.938) 		0.117
(0.647) 		0.862
(1.00) 		1
(1.00) 		0.627
(0.978) 		0.0857
(0.562) 		0.304
(0.843) 		0.502
(0.938) 		0.00297
(0.246) 		0.284
(0.83)
1p gain 88 (23%) 301 0.94
(1.00) 		0.416
(0.908) 		0.62
(0.978) 		0.489
(0.938) 		0.0101
(0.329) 		0.69
(0.978) 		0.581
(0.974) 		0.5
(0.938) 		0.18
(0.703) 		0.342
(0.851) 		0.102
(0.584) 		1
(1.00)
1q gain 122 (31%) 267 0.771
(0.983) 		0.94
(1.00) 		0.145
(0.669) 		0.784
(0.985) 		0.0331
(0.435) 		0.173
(0.691) 		1
(1.00) 		0.541
(0.957) 		0.083
(0.557) 		0.0555
(0.514) 		0.248
(0.788) 		0.726
(0.978)
2p gain 104 (27%) 285 0.277
(0.82) 		0.126
(0.655) 		0.0917
(0.564) 		0.93
(1.00) 		0.0175
(0.364) 		0.464
(0.938) 		0.0127
(0.364) 		0.762
(0.981) 		0.146
(0.67) 		0.00548
(0.3) 		0.494
(0.938) 		0.7
(0.978)
2q gain 53 (14%) 336 0.276
(0.818) 		0.661
(0.978) 		0.645
(0.978) 		0.699
(0.978) 		0.817
(1.00) 		0.334
(0.851) 		0.312
(0.846) 		0.674
(0.978) 		0.792
(0.991) 		0.178
(0.699) 		0.954
(1.00) 		1
(1.00)
4p gain 35 (9%) 354 0.0394
(0.461) 		0.687
(0.978) 		0.354
(0.861) 		0.0448
(0.491) 		0.184
(0.706) 		0.607
(0.976) 		0.155
(0.675) 		0.6
(0.976) 		0.793
(0.991) 		0.196
(0.729) 		0.612
(0.978) 		0.534
(0.953)
4q gain 26 (7%) 363 0.207
(0.744) 		0.172
(0.691) 		0.269
(0.807) 		0.0261
(0.406) 		0.641
(0.978) 		1
(1.00) 		0.643
(0.978) 		0.424
(0.913) 		0.936
(1.00) 		0.299
(0.839) 		0.596
(0.976) 		0.436
(0.924)
5p gain 155 (40%) 234 0.814
(1.00) 		0.997
(1.00) 		0.601
(0.976) 		0.921
(1.00) 		0.716
(0.978) 		0.101
(0.582) 		0.638
(0.978) 		0.322
(0.851) 		0.876
(1.00) 		0.548
(0.961) 		0.126
(0.655) 		0.742
(0.978)
5q gain 51 (13%) 338 0.681
(0.978) 		0.083
(0.557) 		0.928
(1.00) 		0.567
(0.968) 		0.3
(0.839) 		0.602
(0.976) 		0.735
(0.978) 		0.984
(1.00) 		0.0938
(0.566) 		0.51
(0.938) 		0.602
(0.976) 		1
(1.00)
6p gain 74 (19%) 315 0.358
(0.863) 		0.0864
(0.562) 		0.515
(0.938) 		0.517
(0.938) 		0.292
(0.836) 		0.662
(0.978) 		0.38
(0.879) 		0.451
(0.935) 		0.0251
(0.398) 		0.568
(0.968) 		0.338
(0.851) 		0.679
(0.978)
6q gain 39 (10%) 350 0.203
(0.74) 		0.43
(0.918) 		0.876
(1.00) 		0.745
(0.978) 		0.14
(0.665) 		1
(1.00) 		0.126
(0.655) 		0.849
(1.00) 		0.204
(0.741) 		0.631
(0.978) 		0.265
(0.806) 		1
(1.00)
7p gain 162 (42%) 227 0.472
(0.938) 		0.0381
(0.459) 		0.0296
(0.434) 		0.0268
(0.406) 		0.0169
(0.364) 		1
(1.00) 		0.725
(0.978) 		0.205
(0.742) 		0.815
(1.00) 		0.335
(0.851) 		0.0936
(0.566) 		1
(1.00)
8p gain 85 (22%) 304 0.381
(0.88) 		0.428
(0.918) 		0.655
(0.978) 		0.755
(0.979) 		0.561
(0.967) 		1
(1.00) 		0.484
(0.938) 		0.231
(0.769) 		0.69
(0.978) 		0.0512
(0.504) 		0.87
(1.00) 		1
(1.00)
8q gain 193 (50%) 196 0.374
(0.879) 		0.603
(0.976) 		0.741
(0.978) 		0.978
(1.00) 		0.591
(0.976) 		1
(1.00) 		0.818
(1.00) 		0.239
(0.78) 		0.827
(1.00) 		0.209
(0.746) 		0.263
(0.805) 		0.741
(0.978)
9p gain 65 (17%) 324 0.045
(0.491) 		0.793
(0.991) 		0.958
(1.00) 		0.852
(1.00) 		0.154
(0.675) 		0.214
(0.753) 		0.643
(0.978) 		0.289
(0.834) 		0.376
(0.879) 		0.873
(1.00) 		0.0702
(0.527) 		0.645
(0.978)
9q gain 54 (14%) 335 0.49
(0.938) 		0.461
(0.938) 		0.266
(0.806) 		0.121
(0.655) 		0.565
(0.967) 		0.0193
(0.373) 		0.507
(0.938) 		1
(1.00) 		0.161
(0.685) 		0.219
(0.76) 		0.155
(0.675) 		0.341
(0.851)
10p gain 109 (28%) 280 0.194
(0.729) 		0.628
(0.978) 		0.495
(0.938) 		0.541
(0.957) 		0.0524
(0.506) 		1
(1.00) 		0.198
(0.732) 		0.139
(0.665) 		0.312
(0.846) 		0.133
(0.665) 		0.0908
(0.562) 		0.705
(0.978)
10q gain 41 (11%) 348 0.0833
(0.557) 		0.906
(1.00) 		0.0691
(0.527) 		0.41
(0.908) 		0.00886
(0.329) 		1
(1.00) 		1
(1.00) 		0.47
(0.938) 		0.49
(0.938) 		0.0568
(0.514) 		0.879
(1.00) 		0.582
(0.974)
11p gain 27 (7%) 362 0.00593
(0.307) 		0.803
(0.997) 		0.891
(1.00) 		0.747
(0.978) 		0.0405
(0.468) 		1
(1.00) 		0.0219
(0.378) 		0.618
(0.978) 		0.892
(1.00) 		0.981
(1.00) 		0.263
(0.805) 		0.507
(0.938)
12p gain 111 (29%) 278 0.844
(1.00) 		0.00821
(0.329) 		0.6
(0.976) 		0.572
(0.969) 		0.718
(0.978) 		0.726
(0.978) 		0.609
(0.976) 		0.464
(0.938) 		0.55
(0.962) 		0.514
(0.938) 		0.918
(1.00) 		0.714
(0.978)
12q gain 89 (23%) 300 0.666
(0.978) 		0.223
(0.766) 		0.338
(0.851) 		0.43
(0.918) 		0.478
(0.938) 		1
(1.00) 		0.491
(0.938) 		0.749
(0.978) 		0.58
(0.974) 		0.47
(0.938) 		0.822
(1.00) 		1
(1.00)
13q gain 95 (24%) 294 0.472
(0.938) 		0.261
(0.805) 		0.602
(0.976) 		0.707
(0.978) 		0.0179
(0.364) 		0.274
(0.816) 		0.504
(0.938) 		0.253
(0.788) 		0.956
(1.00) 		0.141
(0.665) 		0.216
(0.753) 		0.119
(0.655)
15q gain 33 (8%) 356 0.334
(0.851) 		0.195
(0.729) 		0.339
(0.851) 		0.0479
(0.491) 		0.355
(0.861) 		1
(1.00) 		1
(1.00) 		0.212
(0.75) 		0.731
(0.978) 		0.456
(0.937) 		0.86
(1.00) 		0.546
(0.961)
16p gain 68 (17%) 321 0.309
(0.846) 		0.292
(0.836) 		0.0673
(0.521) 		0.00996
(0.329) 		0.13
(0.662) 		0.098
(0.582) 		0.361
(0.863) 		0.421
(0.909) 		0.467
(0.938) 		0.202
(0.74) 		0.394
(0.901) 		1
(1.00)
16q gain 77 (20%) 312 0.393
(0.901) 		0.186
(0.708) 		0.236
(0.777) 		0.0701
(0.527) 		0.164
(0.69) 		0.0899
(0.562) 		0.0584
(0.517) 		0.721
(0.978) 		0.937
(1.00) 		0.752
(0.979) 		0.131
(0.662) 		1
(1.00)
17p gain 57 (15%) 332 0.251
(0.788) 		0.159
(0.68) 		0.878
(1.00) 		0.449
(0.934) 		0.564
(0.967) 		0.133
(0.665) 		1
(1.00) 		0.23
(0.769) 		0.252
(0.788) 		0.921
(1.00) 		0.136
(0.665) 		0.361
(0.863)
17q gain 131 (34%) 258 0.511
(0.938) 		0.202
(0.74) 		0.0714
(0.529) 		0.929
(1.00) 		0.0359
(0.452) 		0.5
(0.938) 		1
(1.00) 		0.0467
(0.491) 		0.309
(0.846) 		0.0376
(0.459) 		0.401
(0.904) 		0.0649
(0.521)
18p gain 108 (28%) 281 0.967
(1.00) 		0.607
(0.976) 		0.795
(0.991) 		0.693
(0.978) 		0.417
(0.908) 		0.257
(0.796) 		0.608
(0.976) 		0.025
(0.398) 		0.301
(0.839) 		0.773
(0.983) 		0.0391
(0.461) 		0.714
(0.978)
18q gain 59 (15%) 330 0.488
(0.938) 		0.331
(0.851) 		0.669
(0.978) 		0.534
(0.953) 		0.748
(0.978) 		1
(1.00) 		0.629
(0.978) 		0.117
(0.647) 		0.803
(0.997) 		0.661
(0.978) 		0.0205
(0.377) 		0.632
(0.978)
19p gain 81 (21%) 308 0.539
(0.957) 		0.963
(1.00) 		0.76
(0.981) 		0.781
(0.983) 		0.404
(0.906) 		0.451
(0.935) 		0.319
(0.851) 		0.68
(0.978) 		0.767
(0.981) 		0.101
(0.582) 		0.121
(0.655) 		0.692
(0.978)
19q gain 124 (32%) 265 0.142
(0.665) 		0.6
(0.976) 		0.346
(0.856) 		0.441
(0.927) 		0.145
(0.669) 		0.728
(0.978) 		1
(1.00) 		0.548
(0.961) 		0.168
(0.69) 		0.0153
(0.364) 		0.848
(1.00) 		1
(1.00)
20p gain 190 (49%) 199 0.483
(0.938) 		0.137
(0.665) 		0.371
(0.877) 		0.344
(0.854) 		0.0838
(0.557) 		0.192
(0.728) 		0.908
(1.00) 		0.269
(0.807) 		0.363
(0.863) 		0.181
(0.703) 		0.0164
(0.364) 		0.175
(0.696)
20q gain 217 (56%) 172 0.676
(0.978) 		0.24
(0.78) 		0.507
(0.938) 		0.549
(0.961) 		0.126
(0.655) 		0.75
(0.979) 		0.296
(0.839) 		0.723
(0.978) 		0.832
(1.00) 		0.317
(0.851) 		0.0569
(0.514) 		0.309
(0.846)
22q gain 46 (12%) 343 0.751
(0.979) 		0.755
(0.979) 		0.686
(0.978) 		0.733
(0.978) 		0.515
(0.938) 		0.364
(0.863) 		0.592
(0.976) 		0.686
(0.978) 		0.764
(0.981) 		0.141
(0.665) 		0.572
(0.969) 		0.605
(0.976)
xp gain 66 (17%) 323 0.955
(1.00) 		0.166
(0.69) 		0.8
(0.996) 		0.981
(1.00) 		0.564
(0.967) 		0.363
(0.863) 		0.441
(0.927) 		0.636
(0.978) 		0.357
(0.863) 		0.712
(0.978) 		0.485
(0.938) 		0.156
(0.675)
xq gain 46 (12%) 343 0.533
(0.953) 		0.0484
(0.491) 		0.929
(1.00) 		0.834
(1.00) 		0.418
(0.908) 		1
(1.00) 		0.476
(0.938) 		0.794
(0.991) 		0.64
(0.978) 		0.533
(0.953) 		0.716
(0.978) 		1
(1.00)
1p loss 32 (8%) 357 0.762
(0.981) 		0.98
(1.00) 		0.142
(0.665) 		0.126
(0.655) 		0.562
(0.967) 		0.534
(0.953) 		0.678
(0.978) 		0.953
(1.00) 		0.231
(0.769) 		0.682
(0.978) 		0.337
(0.851) 		1
(1.00)
1q loss 33 (8%) 356 0.725
(0.978) 		0.768
(0.981) 		0.0321
(0.435) 		0.129
(0.661) 		0.67
(0.978) 		1
(1.00) 		0.837
(1.00) 		0.957
(1.00) 		0.0363
(0.452) 		0.67
(0.978) 		0.744
(0.978) 		1
(1.00)
2p loss 43 (11%) 346 0.476
(0.938) 		0.886
(1.00) 		0.68
(0.978) 		0.828
(1.00) 		0.71
(0.978) 		0.355
(0.861) 		0.143
(0.665) 		0.169
(0.69) 		0.762
(0.981) 		0.858
(1.00) 		0.606
(0.976) 		1
(1.00)
2q loss 85 (22%) 304 0.578
(0.974) 		0.546
(0.961) 		0.878
(1.00) 		0.778
(0.983) 		0.254
(0.789) 		0.706
(0.978) 		1
(1.00) 		0.0382
(0.459) 		0.456
(0.937) 		0.22
(0.762) 		0.933
(1.00) 		1
(1.00)
3q loss 23 (6%) 366 0.846
(1.00) 		0.341
(0.851) 		0.247
(0.788) 		0.503
(0.938) 		0.727
(0.978) 		0.478
(0.938) 		0.331
(0.851) 		0.501
(0.938) 		0.339
(0.851) 		0.515
(0.938) 		0.806
(0.999) 		1
(1.00)
4q loss 129 (33%) 260 0.237
(0.777) 		0.0104
(0.329) 		0.101
(0.582) 		0.442
(0.927) 		0.0632
(0.521) 		1
(1.00) 		0.903
(1.00) 		0.318
(0.851) 		0.695
(0.978) 		0.273
(0.816) 		0.0926
(0.566) 		0.484
(0.938)
6p loss 94 (24%) 295 0.341
(0.851) 		0.675
(0.978) 		0.172
(0.691) 		0.0821
(0.557) 		0.025
(0.398) 		0.727
(0.978) 		0.226
(0.769) 		0.52
(0.938) 		0.766
(0.981) 		0.106
(0.599) 		0.374
(0.879) 		0.23
(0.769)
7p loss 20 (5%) 369 0.84
(1.00) 		0.82
(1.00) 		0.142
(0.665) 		0.3
(0.839) 		0.0199
(0.377) 		1
(1.00) 		0.306
(0.843) 		0.963
(1.00) 		0.64
(0.978) 		0.0817
(0.557) 		0.89
(1.00) 		1
(1.00)
7q loss 25 (6%) 364 0.695
(0.978) 		0.501
(0.938) 		0.317
(0.851) 		1
(1.00) 		0.248
(0.788) 		1
(1.00) 		0.345
(0.856) 		0.578
(0.974) 		0.0986
(0.582) 		0.397
(0.901) 		0.512
(0.938) 		0.123
(0.655)
8p loss 177 (46%) 212 0.69
(0.978) 		0.562
(0.967) 		0.0307
(0.435) 		0.599
(0.976) 		0.0676
(0.521) 		0.197
(0.731) 		1
(1.00) 		0.335
(0.851) 		0.231
(0.769) 		0.0293
(0.434) 		0.0792
(0.557) 		1
(1.00)
8q loss 34 (9%) 355 0.809
(1.00) 		0.338
(0.851) 		0.0728
(0.535) 		0.0181
(0.364) 		0.296
(0.839) 		0.232
(0.77) 		0.413
(0.908) 		0.658
(0.978) 		0.642
(0.978) 		0.0612
(0.521) 		0.525
(0.944) 		1
(1.00)
9p loss 164 (42%) 225 0.905
(1.00) 		0.0795
(0.557) 		0.221
(0.762) 		0.977
(1.00) 		0.236
(0.777) 		0.519
(0.938) 		0.561
(0.967) 		0.287
(0.832) 		0.247
(0.788) 		0.311
(0.846) 		0.953
(1.00) 		1
(1.00)
9q loss 160 (41%) 229 0.214
(0.753) 		0.447
(0.932) 		0.138
(0.665) 		0.432
(0.919) 		0.195
(0.729) 		0.516
(0.938) 		0.726
(0.978) 		0.65
(0.978) 		0.0657
(0.521) 		0.586
(0.976) 		0.452
(0.935) 		0.743
(0.978)
10p loss 71 (18%) 318 0.652
(0.978) 		0.755
(0.979) 		0.337
(0.851) 		0.757
(0.98) 		0.847
(1.00) 		0.377
(0.879) 		0.881
(1.00) 		0.476
(0.938) 		0.031
(0.435) 		0.712
(0.978) 		0.00639
(0.314) 		0.675
(0.978)
10q loss 121 (31%) 268 0.352
(0.861) 		0.0211
(0.377) 		0.484
(0.938) 		0.811
(1.00) 		0.865
(1.00) 		0.468
(0.938) 		1
(1.00) 		0.403
(0.906) 		0.824
(1.00) 		0.635
(0.978) 		0.17
(0.69) 		0.474
(0.938)
11p loss 169 (43%) 220 0.875
(1.00) 		0.0267
(0.406) 		0.0214
(0.377) 		0.968
(1.00) 		0.0494
(0.493) 		0.198
(0.732) 		0.907
(1.00) 		0.514
(0.938) 		0.562
(0.967) 		0.012
(0.359) 		0.0583
(0.517) 		0.506
(0.938)
11q loss 121 (31%) 268 0.87
(1.00) 		0.896
(1.00) 		0.888
(1.00) 		0.749
(0.978) 		0.582
(0.974) 		1
(1.00) 		0.263
(0.805) 		0.876
(1.00) 		0.891
(1.00) 		0.773
(0.983) 		0.151
(0.674) 		1
(1.00)
12p loss 51 (13%) 338 0.609
(0.976) 		0.976
(1.00) 		0.125
(0.655) 		0.17
(0.69) 		0.0562
(0.514) 		1
(1.00) 		1
(1.00) 		0.779
(0.983) 		0.488
(0.938) 		0.0192
(0.373) 		0.635
(0.978) 		0.351
(0.859)
12q loss 54 (14%) 335 0.983
(1.00) 		0.251
(0.788) 		0.0662
(0.521) 		0.607
(0.976) 		0.0249
(0.398) 		1
(1.00) 		0.616
(0.978) 		0.397
(0.901) 		0.91
(1.00) 		0.0136
(0.364) 		0.864
(1.00) 		1
(1.00)
13q loss 81 (21%) 308 0.778
(0.983) 		0.446
(0.931) 		0.793
(0.991) 		0.439
(0.927) 		0.376
(0.879) 		0.69
(0.978) 		0.477
(0.938) 		0.717
(0.978) 		0.877
(1.00) 		0.682
(0.978) 		0.0619
(0.521) 		0.0787
(0.557)
14q loss 115 (30%) 274 0.297
(0.839) 		0.0314
(0.435) 		0.397
(0.901) 		0.96
(1.00) 		0.00479
(0.277) 		0.726
(0.978) 		0.057
(0.514) 		0.23
(0.769) 		0.0455
(0.491) 		0.173
(0.691) 		0.919
(1.00) 		0.282
(0.828)
16p loss 100 (26%) 289 0.509
(0.938) 		0.701
(0.978) 		0.963
(1.00) 		0.107
(0.599) 		0.418
(0.908) 		0.69
(0.978) 		0.509
(0.938) 		0.573
(0.969) 		0.962
(1.00) 		0.939
(1.00) 		0.0104
(0.329) 		0.7
(0.978)
16q loss 95 (24%) 294 0.554
(0.964) 		0.276
(0.818) 		0.616
(0.978) 		0.941
(1.00) 		0.137
(0.665) 		0.69
(0.978) 		0.0807
(0.557) 		0.165
(0.69) 		0.834
(1.00) 		0.15
(0.674) 		0.0231
(0.392) 		0.0422
(0.477)
17p loss 168 (43%) 221 0.726
(0.978) 		0.0163
(0.364) 		0.687
(0.978) 		0.441
(0.927) 		0.168
(0.69) 		0.743
(0.978) 		0.351
(0.859) 		0.722
(0.978) 		0.811
(1.00) 		0.25
(0.788) 		0.976
(1.00) 		1
(1.00)
17q loss 42 (11%) 347 0.39
(0.898) 		0.268
(0.807) 		0.516
(0.938) 		0.0661
(0.521) 		0.139
(0.665) 		1
(1.00) 		0.265
(0.806) 		0.916
(1.00) 		0.491
(0.938) 		0.89
(1.00) 		0.404
(0.906) 		0.606
(0.976)
18p loss 97 (25%) 292 0.747
(0.978) 		0.936
(1.00) 		0.101
(0.582) 		0.917
(1.00) 		0.0329
(0.435) 		0.065
(0.521) 		0.35
(0.859) 		0.28
(0.824) 		0.406
(0.906) 		0.0999
(0.582) 		0.856
(1.00) 		0.46
(0.938)
18q loss 138 (35%) 251 0.176
(0.697) 		0.731
(0.978) 		0.719
(0.978) 		0.907
(1.00) 		0.363
(0.863) 		0.0949
(0.569) 		0.63
(0.978) 		0.951
(1.00) 		0.147
(0.671) 		0.317
(0.851) 		1
(1.00) 		0.288
(0.833)
19p loss 90 (23%) 299 0.0678
(0.521) 		0.0756
(0.549) 		0.0857
(0.562) 		0.0349
(0.451) 		0.0439
(0.491) 		0.124
(0.655) 		0.891
(1.00) 		0.29
(0.835) 		0.997
(1.00) 		0.405
(0.906) 		0.0896
(0.562) 		0.223
(0.766)
19q loss 54 (14%) 335 0.0659
(0.521) 		0.741
(0.978) 		0.938
(1.00) 		0.283
(0.83) 		0.608
(0.976) 		0.334
(0.851) 		1
(1.00) 		0.167
(0.69) 		0.23
(0.769) 		0.691
(0.978) 		0.647
(0.978) 		0.62
(0.978)
20p loss 32 (8%) 357 0.384
(0.885) 		0.656
(0.978) 		0.825
(1.00) 		0.215
(0.753) 		0.508
(0.938) 		1
(1.00) 		0.208
(0.745) 		0.778
(0.983) 		0.0903
(0.562) 		0.815
(1.00) 		0.247
(0.788) 		1
(1.00)
20q loss 13 (3%) 376 0.15
(0.674) 		0.56
(0.967) 		0.153
(0.674) 		0.211
(0.748) 		0.319
(0.851) 		1
(1.00) 		1
(1.00) 		0.162
(0.685) 		0.593
(0.976) 		0.321
(0.851) 		0.842
(1.00) 		1
(1.00)
21q loss 76 (20%) 313 0.128
(0.659) 		0.193
(0.729) 		0.776
(0.983) 		0.808
(1.00) 		0.00383
(0.251) 		0.687
(0.978) 		0.56
(0.967) 		0.413
(0.908) 		0.407
(0.907) 		0.711
(0.978) 		0.0608
(0.521) 		0.692
(0.978)
22q loss 152 (39%) 237 0.151
(0.674) 		0.122
(0.655) 		0.0164
(0.364) 		0.0893
(0.562) 		0.0113
(0.346) 		1
(1.00) 		0.906
(1.00) 		0.0884
(0.562) 		0.396
(0.901) 		0.0154
(0.364) 		0.0176
(0.364) 		0.0313
(0.435)
xp loss 67 (17%) 322 0.674
(0.978) 		0.443
(0.927) 		0.662
(0.978) 		0.906
(1.00) 		0.701
(0.978) 		0.662
(0.978) 		0.76
(0.981) 		0.184
(0.706) 		0.765
(0.981) 		0.894
(1.00) 		0.699
(0.978) 		0.659
(0.978)
xq loss 78 (20%) 311 0.513
(0.938) 		0.337
(0.851) 		0.739
(0.978) 		0.73
(0.978) 		0.796
(0.991) 		0.692
(0.978) 		0.774
(0.983) 		0.153
(0.674) 		0.42
(0.908) 		0.503
(0.938) 		0.777
(0.983) 		0.0787
(0.557)
'3p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00241 (Wilcoxon-test), Q value = 0.25

Table S1.  Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 388 67.8 (10.6)
3P GAIN MUTATED 133 70.1 (10.3)
3P GAIN WILD-TYPE 255 66.6 (10.6)

Figure S1.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00071 (Wilcoxon-test), Q value = 0.17

Table S2.  Gene #5: '3p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 284 2.0 (6.9)
3P GAIN MUTATED 93 3.5 (10.9)
3P GAIN WILD-TYPE 191 1.3 (3.5)

Figure S2.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'3q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000379 (Wilcoxon-test), Q value = 0.17

Table S3.  Gene #6: '3q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 284 2.0 (6.9)
3Q GAIN MUTATED 122 3.2 (9.7)
3Q GAIN WILD-TYPE 162 1.1 (3.3)

Figure S3.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 7e-04 (Fisher's exact test), Q value = 0.17

Table S4.  Gene #14: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
7Q GAIN MUTATED 73 17 31 8
7Q GAIN WILD-TYPE 151 25 44 0

Figure S4.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0035 (Wilcoxon-test), Q value = 0.25

Table S5.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 388 67.8 (10.6)
11Q GAIN MUTATED 47 71.9 (11.1)
11Q GAIN WILD-TYPE 341 67.2 (10.4)

Figure S5.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'RACE'

P value = 0.00266 (Fisher's exact test), Q value = 0.25

Table S6.  Gene #26: '14q gain' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 42 21 311
14Q GAIN MUTATED 0 5 45
14Q GAIN WILD-TYPE 42 16 266

Figure S6.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #11: 'RACE'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00319 (Wilcoxon-test), Q value = 0.25

Table S7.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 388 67.8 (10.6)
21Q GAIN MUTATED 105 70.5 (9.9)
21Q GAIN WILD-TYPE 283 66.8 (10.7)

Figure S7.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'GENDER'

P value = 0.00173 (Fisher's exact test), Q value = 0.25

Table S8.  Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 101 288
3P LOSS MUTATED 23 28
3P LOSS WILD-TYPE 78 260

Figure S8.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00044 (Fisher's exact test), Q value = 0.17

Table S9.  Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
4P LOSS MUTATED 61 20 37 1
4P LOSS WILD-TYPE 163 22 38 7

Figure S9.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00334 (Wilcoxon-test), Q value = 0.25

Table S10.  Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 388 67.8 (10.6)
5P LOSS MUTATED 53 71.8 (8.3)
5P LOSS WILD-TYPE 335 67.1 (10.8)

Figure S10.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00282 (Fisher's exact test), Q value = 0.25

Table S11.  Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
5Q LOSS MUTATED 68 18 36 6
5Q LOSS WILD-TYPE 156 24 39 2

Figure S11.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00314 (Fisher's exact test), Q value = 0.25

Table S12.  Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 224 42 75 8
6Q LOSS MUTATED 70 16 41 4
6Q LOSS WILD-TYPE 154 26 34 4

Figure S12.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0014 (Wilcoxon-test), Q value = 0.25

Table S13.  Gene #53: '6q loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 284 2.0 (6.9)
6Q LOSS MUTATED 111 2.4 (4.6)
6Q LOSS WILD-TYPE 173 1.8 (8.1)

Figure S13.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #10: 'NUMBER_OF_LYMPH_NODES'

'15q loss' versus 'RACE'

P value = 0.00297 (Fisher's exact test), Q value = 0.25

Table S14.  Gene #68: '15q loss' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 42 21 311
15Q LOSS MUTATED 6 4 116
15Q LOSS WILD-TYPE 36 17 195

Figure S14.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #11: 'RACE'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/15082909/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/15076720/BLCA-TP.merged_data.txt

  • Number of patients = 389

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 12

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)
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