Correlation between copy number variations of arm-level result and selected clinical features
Bladder Urothelial Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1319V6S
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 13 clinical features across 408 patients, 22 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

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

  • 3q gain cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 10q 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 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'RACE'.

  • 4q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 5p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 6q loss cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 8q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 11p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 15q loss cnv correlated to 'RACE'.

  • 16p loss cnv correlated to 'RACE'.

  • 21q loss cnv correlated to 'PATHOLOGY_N_STAGE'.

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 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 22 significant findings detected.

Clinical
Features
Time
to
Death
YEARS
TO
BIRTH
PATHOLOGIC
STAGE
PATHOLOGY
T
STAGE
PATHOLOGY
N
STAGE
PATHOLOGY
M
STAGE
GENDER RADIATION
THERAPY
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 Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
3q gain 179 (44%) 229 0.759
(1.00)
0.00226
(0.172)
0.0183
(0.383)
0.361
(0.876)
0.00154
(0.172)
0.217
(0.798)
0.91
(1.00)
1
(1.00)
0.133
(0.671)
0.207
(0.795)
6.11e-05
(0.0652)
0.0892
(0.565)
1
(1.00)
4p loss 144 (35%) 264 0.0637
(0.503)
0.189
(0.766)
0.00468
(0.243)
0.0913
(0.565)
0.0011
(0.172)
0.742
(1.00)
0.725
(1.00)
0.811
(1.00)
0.818
(1.00)
0.111
(0.625)
0.0149
(0.383)
0.00336
(0.225)
0.504
(0.972)
3p gain 143 (35%) 265 0.418
(0.941)
0.00152
(0.172)
0.0556
(0.494)
0.0856
(0.554)
0.0162
(0.383)
0.19
(0.766)
0.157
(0.711)
0.632
(1.00)
0.0624
(0.503)
0.0276
(0.427)
0.000186
(0.0991)
0.0912
(0.565)
1
(1.00)
2p gain 111 (27%) 297 0.713
(1.00)
0.111
(0.625)
0.0522
(0.492)
0.84
(1.00)
0.012
(0.352)
0.173
(0.741)
0.016
(0.383)
1
(1.00)
0.976
(1.00)
0.0672
(0.51)
0.0019
(0.172)
0.439
(0.952)
0.702
(1.00)
10q gain 44 (11%) 364 0.0929
(0.565)
0.583
(1.00)
0.037
(0.45)
0.366
(0.88)
0.0017
(0.172)
1
(1.00)
0.717
(1.00)
0.709
(1.00)
0.8
(1.00)
0.535
(0.98)
0.0311
(0.433)
0.835
(1.00)
0.598
(1.00)
11q gain 47 (12%) 361 0.0114
(0.348)
0.00388
(0.24)
0.0486
(0.489)
0.644
(1.00)
0.0193
(0.388)
0.296
(0.857)
0.0768
(0.538)
0.711
(1.00)
0.646
(1.00)
0.77
(1.00)
0.0696
(0.522)
0.339
(0.86)
1
(1.00)
14q gain 57 (14%) 351 0.0403
(0.462)
0.696
(1.00)
0.391
(0.91)
0.0534
(0.492)
0.76
(1.00)
0.275
(0.849)
0.0337
(0.443)
1
(1.00)
0.528
(0.978)
0.702
(1.00)
0.344
(0.864)
0.00338
(0.225)
0.348
(0.864)
21q gain 116 (28%) 292 0.493
(0.971)
0.000403
(0.125)
0.497
(0.971)
0.411
(0.932)
0.313
(0.857)
1
(1.00)
0.212
(0.798)
0.609
(1.00)
0.406
(0.927)
0.854
(1.00)
0.29
(0.857)
0.507
(0.972)
1
(1.00)
3p loss 51 (12%) 357 0.461
(0.965)
0.331
(0.857)
0.668
(1.00)
0.454
(0.963)
0.542
(0.982)
1
(1.00)
0.00193
(0.172)
1
(1.00)
0.778
(1.00)
0.367
(0.88)
0.599
(1.00)
0.0611
(0.503)
1
(1.00)
4q loss 136 (33%) 272 0.42
(0.941)
0.00194
(0.172)
0.0312
(0.433)
0.293
(0.857)
0.0654
(0.509)
0.733
(1.00)
0.633
(1.00)
0.625
(1.00)
0.495
(0.971)
0.981
(1.00)
0.237
(0.805)
0.0221
(0.399)
0.483
(0.971)
5p loss 54 (13%) 354 0.699
(1.00)
0.0022
(0.172)
0.686
(1.00)
0.686
(1.00)
0.226
(0.801)
0.0545
(0.492)
0.618
(1.00)
1
(1.00)
0.613
(1.00)
0.723
(1.00)
0.431
(0.946)
0.676
(1.00)
1
(1.00)
6q loss 159 (39%) 249 0.774
(1.00)
0.845
(1.00)
0.0105
(0.335)
0.317
(0.857)
0.00765
(0.314)
0.542
(0.982)
0.645
(1.00)
0.241
(0.808)
0.0212
(0.39)
0.872
(1.00)
0.00415
(0.24)
0.0386
(0.452)
0.0307
(0.433)
8q loss 38 (9%) 370 0.712
(1.00)
0.599
(1.00)
0.234
(0.805)
0.00428
(0.24)
0.277
(0.851)
0.253
(0.813)
0.248
(0.812)
0.24
(0.806)
0.915
(1.00)
0.94
(1.00)
0.0668
(0.51)
0.629
(1.00)
1
(1.00)
11p loss 178 (44%) 230 0.587
(1.00)
0.00513
(0.249)
0.0861
(0.554)
0.947
(1.00)
0.106
(0.613)
0.356
(0.869)
0.91
(1.00)
0.644
(1.00)
0.561
(0.997)
0.397
(0.918)
0.0407
(0.462)
0.085
(0.554)
0.506
(0.972)
15q loss 144 (35%) 264 0.473
(0.971)
0.276
(0.849)
0.389
(0.908)
0.122
(0.642)
0.988
(1.00)
0.5
(0.971)
0.347
(0.864)
0.228
(0.801)
0.0896
(0.565)
0.332
(0.857)
0.523
(0.978)
0.00114
(0.172)
0.289
(0.857)
16p loss 110 (27%) 298 0.189
(0.766)
0.923
(1.00)
0.636
(1.00)
0.0345
(0.449)
0.461
(0.965)
1
(1.00)
0.704
(1.00)
0.117
(0.635)
0.426
(0.943)
0.579
(1.00)
0.786
(1.00)
0.00479
(0.243)
0.706
(1.00)
21q loss 79 (19%) 329 0.735
(1.00)
0.119
(0.635)
0.748
(1.00)
0.642
(1.00)
0.00047
(0.125)
1
(1.00)
0.776
(1.00)
0.776
(1.00)
0.521
(0.978)
0.878
(1.00)
0.563
(0.999)
0.0515
(0.492)
0.683
(1.00)
1p gain 89 (22%) 319 0.378
(0.894)
0.324
(0.857)
0.275
(0.849)
0.479
(0.971)
0.0408
(0.462)
0.464
(0.965)
0.683
(1.00)
0.586
(1.00)
0.589
(1.00)
0.166
(0.724)
0.222
(0.801)
0.115
(0.63)
1
(1.00)
1q gain 126 (31%) 282 0.553
(0.99)
0.746
(1.00)
0.0523
(0.492)
0.677
(1.00)
0.0175
(0.383)
0.316
(0.857)
1
(1.00)
0.323
(0.857)
0.269
(0.848)
0.0809
(0.546)
0.0299
(0.433)
0.321
(0.857)
0.728
(1.00)
2q gain 55 (13%) 353 0.86
(1.00)
0.839
(1.00)
0.707
(1.00)
0.691
(1.00)
0.761
(1.00)
1
(1.00)
0.251
(0.812)
0.497
(0.971)
0.808
(1.00)
0.697
(1.00)
0.13
(0.664)
0.955
(1.00)
1
(1.00)
4p gain 38 (9%) 370 0.038
(0.45)
0.599
(1.00)
0.367
(0.88)
0.0943
(0.565)
0.156
(0.711)
0.368
(0.88)
0.124
(0.653)
1
(1.00)
0.31
(0.857)
0.778
(1.00)
0.233
(0.805)
0.7
(1.00)
0.565
(0.999)
4q gain 26 (6%) 382 0.071
(0.522)
0.0752
(0.535)
0.115
(0.63)
0.019
(0.388)
0.6
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.603
(1.00)
0.98
(1.00)
0.288
(0.857)
0.593
(1.00)
0.421
(0.941)
5p gain 166 (41%) 242 0.925
(1.00)
0.926
(1.00)
0.725
(1.00)
0.925
(1.00)
0.313
(0.857)
0.0592
(0.503)
0.647
(1.00)
1
(1.00)
0.417
(0.941)
0.885
(1.00)
0.422
(0.941)
0.0377
(0.45)
0.741
(1.00)
5q gain 51 (12%) 357 0.795
(1.00)
0.222
(0.801)
0.217
(0.798)
0.68
(1.00)
0.323
(0.857)
0.604
(1.00)
0.865
(1.00)
0.491
(0.971)
0.923
(1.00)
0.0839
(0.554)
0.405
(0.926)
0.461
(0.965)
1
(1.00)
6p gain 73 (18%) 335 0.921
(1.00)
0.0763
(0.538)
0.237
(0.805)
0.772
(1.00)
0.352
(0.868)
0.668
(1.00)
0.144
(0.694)
0.355
(0.869)
0.653
(1.00)
0.0231
(0.403)
0.653
(1.00)
0.105
(0.607)
1
(1.00)
6q gain 39 (10%) 369 0.333
(0.857)
0.306
(0.857)
0.292
(0.857)
0.839
(1.00)
0.159
(0.711)
1
(1.00)
0.127
(0.655)
0.0267
(0.424)
0.497
(0.971)
0.141
(0.693)
0.833
(1.00)
0.319
(0.857)
1
(1.00)
7p gain 171 (42%) 237 0.698
(1.00)
0.062
(0.503)
0.0334
(0.443)
0.0536
(0.492)
0.0151
(0.383)
0.759
(1.00)
1
(1.00)
0.162
(0.718)
0.0837
(0.554)
0.906
(1.00)
0.311
(0.857)
0.066
(0.51)
1
(1.00)
7q gain 148 (36%) 260 0.581
(1.00)
0.0165
(0.383)
0.159
(0.711)
0.236
(0.805)
0.00861
(0.314)
0.51
(0.973)
0.483
(0.971)
0.637
(1.00)
0.314
(0.857)
0.959
(1.00)
0.177
(0.746)
0.0708
(0.522)
1
(1.00)
8p gain 90 (22%) 318 0.356
(0.869)
0.638
(1.00)
0.467
(0.965)
0.701
(1.00)
0.577
(1.00)
0.734
(1.00)
0.786
(1.00)
0.784
(1.00)
0.491
(0.971)
0.593
(1.00)
0.101
(0.593)
0.626
(1.00)
1
(1.00)
8q gain 200 (49%) 208 0.546
(0.986)
0.504
(0.972)
0.928
(1.00)
0.771
(1.00)
0.716
(1.00)
0.767
(1.00)
0.822
(1.00)
0.364
(0.88)
0.135
(0.674)
0.966
(1.00)
0.117
(0.635)
0.547
(0.986)
0.74
(1.00)
9p gain 69 (17%) 339 0.0675
(0.51)
0.991
(1.00)
0.595
(1.00)
1
(1.00)
0.434
(0.946)
0.399
(0.918)
0.453
(0.963)
0.752
(1.00)
0.227
(0.801)
0.47
(0.968)
0.878
(1.00)
0.0643
(0.504)
0.649
(1.00)
9q gain 56 (14%) 352 0.242
(0.808)
0.27
(0.848)
0.221
(0.801)
0.403
(0.925)
0.771
(1.00)
0.0376
(0.45)
0.744
(1.00)
0.492
(0.971)
0.76
(1.00)
0.208
(0.795)
0.25
(0.812)
0.156
(0.711)
0.339
(0.86)
10p gain 117 (29%) 291 0.249
(0.812)
0.542
(0.982)
0.42
(0.941)
0.916
(1.00)
0.0437
(0.47)
1
(1.00)
0.0622
(0.503)
0.609
(1.00)
0.151
(0.711)
0.21
(0.797)
0.0919
(0.565)
0.0727
(0.527)
0.709
(1.00)
11p gain 29 (7%) 379 0.0496
(0.492)
0.843
(1.00)
0.739
(1.00)
0.603
(1.00)
0.0378
(0.45)
0.435
(0.946)
0.0143
(0.383)
1
(1.00)
0.575
(1.00)
0.922
(1.00)
0.547
(0.986)
0.216
(0.798)
0.516
(0.978)
12p gain 116 (28%) 292 0.535
(0.98)
0.00896
(0.314)
0.348
(0.864)
0.57
(1.00)
0.715
(1.00)
1
(1.00)
0.709
(1.00)
0.803
(1.00)
0.521
(0.978)
0.965
(1.00)
0.904
(1.00)
0.826
(1.00)
0.715
(1.00)
12q gain 91 (22%) 317 0.676
(1.00)
0.271
(0.848)
0.205
(0.795)
0.554
(0.99)
0.983
(1.00)
1
(1.00)
0.59
(1.00)
0.792
(1.00)
0.745
(1.00)
0.955
(1.00)
0.852
(1.00)
0.825
(1.00)
1
(1.00)
13q gain 100 (25%) 308 0.669
(1.00)
0.565
(0.999)
0.518
(0.978)
0.83
(1.00)
0.017
(0.383)
0.143
(0.694)
0.435
(0.946)
0.793
(1.00)
0.345
(0.864)
0.835
(1.00)
0.0862
(0.554)
0.166
(0.724)
0.119
(0.635)
15q gain 35 (9%) 373 0.53
(0.98)
0.283
(0.857)
0.203
(0.794)
0.0258
(0.424)
0.348
(0.864)
1
(1.00)
0.841
(1.00)
0.227
(0.801)
0.0952
(0.567)
0.835
(1.00)
0.328
(0.857)
0.87
(1.00)
0.553
(0.99)
16p gain 75 (18%) 333 0.176
(0.743)
0.298
(0.857)
0.0837
(0.554)
0.00835
(0.314)
0.104
(0.603)
0.232
(0.805)
0.561
(0.997)
1
(1.00)
0.46
(0.965)
0.851
(1.00)
0.118
(0.635)
0.287
(0.857)
1
(1.00)
16q gain 82 (20%) 326 0.656
(1.00)
0.138
(0.686)
0.33
(0.857)
0.0564
(0.497)
0.363
(0.879)
0.232
(0.805)
0.328
(0.857)
1
(1.00)
0.476
(0.971)
0.741
(1.00)
0.817
(1.00)
0.189
(0.766)
0.694
(1.00)
17p gain 56 (14%) 352 0.494
(0.971)
0.156
(0.711)
0.289
(0.857)
0.723
(1.00)
0.451
(0.963)
0.195
(0.772)
0.872
(1.00)
1
(1.00)
0.318
(0.857)
0.178
(0.746)
0.744
(1.00)
0.446
(0.956)
0.339
(0.86)
17q gain 135 (33%) 273 0.308
(0.857)
0.129
(0.664)
0.0792
(0.545)
0.73
(1.00)
0.0459
(0.485)
0.739
(1.00)
0.905
(1.00)
0.228
(0.801)
0.0989
(0.586)
0.207
(0.795)
0.0849
(0.554)
0.332
(0.857)
0.0636
(0.503)
18p gain 116 (28%) 292 0.868
(1.00)
0.516
(0.978)
0.633
(1.00)
0.604
(1.00)
0.255
(0.814)
0.467
(0.965)
0.534
(0.98)
0.61
(1.00)
0.044
(0.47)
0.163
(0.722)
0.933
(1.00)
0.0249
(0.424)
0.719
(1.00)
18q gain 61 (15%) 347 0.431
(0.946)
0.413
(0.935)
0.639
(1.00)
0.849
(1.00)
0.628
(1.00)
1
(1.00)
1
(1.00)
0.751
(1.00)
0.144
(0.694)
0.491
(0.971)
0.333
(0.857)
0.0206
(0.39)
0.63
(1.00)
19p gain 87 (21%) 321 0.751
(1.00)
0.629
(1.00)
0.936
(1.00)
0.714
(1.00)
0.27
(0.848)
0.711
(1.00)
0.217
(0.798)
0.572
(1.00)
0.872
(1.00)
0.96
(1.00)
0.184
(0.758)
0.224
(0.801)
0.691
(1.00)
19q gain 132 (32%) 276 0.467
(0.965)
0.484
(0.971)
0.189
(0.766)
0.352
(0.868)
0.159
(0.711)
0.342
(0.864)
0.905
(1.00)
0.329
(0.857)
1
(1.00)
0.285
(0.857)
0.0167
(0.383)
0.566
(1)
1
(1.00)
20p gain 201 (49%) 207 0.435
(0.946)
0.0912
(0.565)
0.334
(0.857)
0.386
(0.907)
0.0474
(0.486)
0.12
(0.636)
1
(1.00)
0.108
(0.621)
0.264
(0.837)
0.647
(1.00)
0.111
(0.625)
0.00794
(0.314)
0.175
(0.743)
20q gain 230 (56%) 178 0.771
(1.00)
0.169
(0.731)
0.484
(0.971)
0.496
(0.971)
0.0544
(0.492)
0.547
(0.986)
0.213
(0.798)
0.648
(1.00)
0.749
(1.00)
0.988
(1.00)
0.159
(0.711)
0.0422
(0.469)
0.191
(0.768)
22q gain 48 (12%) 360 0.756
(1.00)
0.687
(1.00)
0.234
(0.805)
0.295
(0.857)
0.463
(0.965)
1
(1.00)
1
(1.00)
1
(1.00)
0.747
(1.00)
0.392
(0.91)
0.203
(0.794)
0.651
(1.00)
0.606
(1.00)
xp gain 65 (16%) 343 0.806
(1.00)
0.514
(0.977)
0.685
(1.00)
0.842
(1.00)
0.769
(1.00)
0.366
(0.88)
0.542
(0.982)
0.0543
(0.492)
0.582
(1.00)
0.256
(0.815)
0.726
(1.00)
0.58
(1.00)
0.14
(0.692)
xq gain 45 (11%) 363 0.859
(1.00)
0.315
(0.857)
0.645
(1.00)
0.854
(1.00)
0.4
(0.918)
0.606
(1.00)
1
(1.00)
0.147
(0.702)
0.622
(1.00)
0.171
(0.736)
0.126
(0.655)
0.844
(1.00)
1
(1.00)
1p loss 31 (8%) 377 0.655
(1.00)
0.956
(1.00)
0.269
(0.848)
0.0928
(0.565)
0.275
(0.849)
0.131
(0.664)
0.524
(0.978)
0.67
(1.00)
0.712
(1.00)
0.395
(0.916)
0.527
(0.978)
0.333
(0.857)
1
(1.00)
1q loss 31 (8%) 377 0.663
(1.00)
0.866
(1.00)
0.0472
(0.486)
0.0805
(0.546)
0.669
(1.00)
0.526
(0.978)
0.676
(1.00)
0.387
(0.907)
1
(1.00)
0.0635
(0.503)
0.7
(1.00)
0.677
(1.00)
1
(1.00)
2p loss 45 (11%) 363 0.846
(1.00)
0.874
(1.00)
0.922
(1.00)
0.812
(1.00)
0.848
(1.00)
0.623
(1.00)
0.593
(1.00)
0.251
(0.812)
0.061
(0.503)
0.845
(1.00)
0.85
(1.00)
0.617
(1.00)
1
(1.00)
2q loss 92 (23%) 316 0.425
(0.943)
0.662
(1.00)
0.858
(1.00)
0.78
(1.00)
0.285
(0.857)
0.467
(0.965)
0.686
(1.00)
0.408
(0.927)
0.0599
(0.503)
0.868
(1.00)
0.157
(0.711)
1
(1.00)
1
(1.00)
3q loss 23 (6%) 385 0.874
(1.00)
0.387
(0.907)
0.85
(1.00)
0.627
(1.00)
0.683
(1.00)
0.467
(0.965)
0.336
(0.858)
1
(1.00)
0.665
(1.00)
0.586
(1.00)
0.442
(0.952)
0.453
(0.963)
1
(1.00)
5q loss 160 (39%) 248 0.436
(0.946)
0.037
(0.45)
0.0524
(0.492)
0.297
(0.857)
0.00892
(0.314)
0.0591
(0.503)
0.908
(1.00)
1
(1.00)
0.0209
(0.39)
0.0588
(0.503)
0.00948
(0.316)
0.0313
(0.433)
0.743
(1.00)
6p loss 103 (25%) 305 0.0472
(0.486)
0.924
(1.00)
0.521
(0.978)
0.147
(0.702)
0.0331
(0.443)
1
(1.00)
0.198
(0.779)
0.793
(1.00)
0.306
(0.857)
0.67
(1.00)
0.218
(0.798)
0.312
(0.857)
0.0521
(0.492)
7p loss 20 (5%) 388 0.793
(1.00)
0.774
(1.00)
0.572
(1.00)
0.378
(0.894)
0.021
(0.39)
1
(1.00)
0.305
(0.857)
0.239
(0.806)
0.928
(1.00)
0.982
(1.00)
0.0746
(0.534)
0.889
(1.00)
1
(1.00)
7q loss 28 (7%) 380 0.856
(1.00)
0.502
(0.972)
1
(1.00)
0.854
(1.00)
0.32
(0.857)
1
(1.00)
0.182
(0.757)
1
(1.00)
0.482
(0.971)
0.134
(0.673)
0.77
(1.00)
0.916
(1.00)
0.13
(0.664)
8p loss 188 (46%) 220 0.639
(1.00)
0.299
(0.857)
0.0122
(0.352)
0.5
(0.971)
0.0375
(0.45)
0.352
(0.868)
0.499
(0.971)
0.49
(0.971)
0.248
(0.812)
0.334
(0.857)
0.0371
(0.45)
0.0294
(0.433)
1
(1.00)
9p loss 174 (43%) 234 0.902
(1.00)
0.0262
(0.424)
0.186
(0.764)
0.929
(1.00)
0.485
(0.971)
0.76
(1.00)
0.734
(1.00)
0.644
(1.00)
0.164
(0.722)
0.375
(0.892)
0.633
(1.00)
0.852
(1.00)
1
(1.00)
9q loss 169 (41%) 239 0.573
(1.00)
0.249
(0.812)
0.505
(0.972)
0.773
(1.00)
0.442
(0.952)
0.757
(1.00)
0.82
(1.00)
0.491
(0.971)
0.422
(0.941)
0.0905
(0.565)
0.935
(1.00)
0.333
(0.857)
0.743
(1.00)
10p loss 73 (18%) 335 0.695
(1.00)
0.885
(1.00)
0.798
(1.00)
0.779
(1.00)
0.739
(1.00)
0.399
(0.918)
0.771
(1.00)
0.231
(0.805)
0.305
(0.857)
0.0183
(0.383)
0.683
(1.00)
0.00799
(0.314)
0.667
(1.00)
10q loss 129 (32%) 279 0.235
(0.805)
0.0177
(0.383)
0.631
(1.00)
0.895
(1.00)
0.528
(0.978)
0.303
(0.857)
0.904
(1.00)
0.215
(0.798)
0.508
(0.972)
0.759
(1.00)
0.597
(1.00)
0.158
(0.711)
0.475
(0.971)
11q loss 129 (32%) 279 0.83
(1.00)
0.306
(0.857)
0.831
(1.00)
0.688
(1.00)
0.508
(0.972)
1
(1.00)
0.334
(0.857)
0.219
(0.801)
0.992
(1.00)
0.81
(1.00)
0.986
(1.00)
0.251
(0.812)
1
(1.00)
12p loss 54 (13%) 354 0.54
(0.982)
0.854
(1.00)
0.496
(0.971)
0.153
(0.711)
0.142
(0.694)
1
(1.00)
0.618
(1.00)
0.734
(1.00)
0.743
(1.00)
0.224
(0.801)
0.0486
(0.489)
0.555
(0.991)
0.348
(0.864)
12q loss 58 (14%) 350 0.914
(1.00)
0.192
(0.768)
0.246
(0.812)
0.382
(0.902)
0.0569
(0.497)
1
(1.00)
1
(1.00)
0.173
(0.741)
0.316
(0.857)
0.55
(0.989)
0.0297
(0.433)
0.763
(1.00)
1
(1.00)
13q loss 85 (21%) 323 0.716
(1.00)
0.286
(0.857)
0.679
(1.00)
0.522
(0.978)
0.425
(0.943)
0.698
(1.00)
0.407
(0.927)
0.577
(1.00)
0.905
(1.00)
0.977
(1.00)
0.696
(1.00)
0.0741
(0.534)
0.0777
(0.538)
14q loss 121 (30%) 287 0.152
(0.711)
0.0421
(0.469)
0.61
(1.00)
0.772
(1.00)
0.00912
(0.314)
1
(1.00)
0.11
(0.625)
0.208
(0.795)
0.322
(0.857)
0.0933
(0.565)
0.104
(0.603)
0.809
(1.00)
0.283
(0.857)
16q loss 107 (26%) 301 0.388
(0.907)
0.461
(0.965)
0.535
(0.98)
0.726
(1.00)
0.134
(0.673)
1
(1.00)
0.522
(0.978)
0.305
(0.857)
0.217
(0.798)
0.952
(1.00)
0.174
(0.742)
0.0317
(0.433)
0.0543
(0.492)
17p loss 182 (45%) 226 0.323
(0.857)
0.00847
(0.314)
0.462
(0.965)
0.301
(0.857)
0.302
(0.857)
0.531
(0.98)
0.498
(0.971)
0.819
(1.00)
1
(1.00)
0.687
(1.00)
0.253
(0.813)
0.619
(1.00)
1
(1.00)
17q loss 46 (11%) 362 0.311
(0.857)
0.642
(1.00)
0.939
(1.00)
0.0703
(0.522)
0.147
(0.702)
1
(1.00)
0.291
(0.857)
0.49
(0.971)
0.718
(1.00)
0.794
(1.00)
0.966
(1.00)
0.18
(0.752)
0.606
(1.00)
18p loss 98 (24%) 310 0.856
(1.00)
0.923
(1.00)
0.0441
(0.47)
0.778
(1.00)
0.0277
(0.427)
0.296
(0.857)
0.429
(0.946)
1
(1.00)
0.149
(0.704)
0.449
(0.96)
0.0627
(0.503)
0.856
(1.00)
0.445
(0.956)
18q loss 146 (36%) 262 0.346
(0.864)
0.689
(1.00)
0.624
(1.00)
0.798
(1.00)
0.255
(0.814)
0.334
(0.857)
0.291
(0.857)
0.349
(0.864)
0.782
(1.00)
0.183
(0.758)
0.158
(0.711)
0.953
(1.00)
0.289
(0.857)
19p loss 95 (23%) 313 0.194
(0.77)
0.0809
(0.546)
0.0429
(0.47)
0.0227
(0.403)
0.0168
(0.383)
0.232
(0.805)
0.791
(1.00)
0.0553
(0.494)
0.194
(0.77)
0.901
(1.00)
0.463
(0.965)
0.0725
(0.527)
0.224
(0.801)
19q loss 59 (14%) 349 0.113
(0.629)
0.642
(1.00)
0.814
(1.00)
0.238
(0.805)
0.654
(1.00)
0.361
(0.876)
0.874
(1.00)
0.332
(0.857)
0.125
(0.654)
0.36
(0.876)
0.492
(0.971)
0.532
(0.98)
0.625
(1.00)
20p loss 32 (8%) 376 0.514
(0.977)
0.985
(1.00)
0.808
(1.00)
0.758
(1.00)
0.433
(0.946)
1
(1.00)
0.209
(0.795)
0.649
(1.00)
0.978
(1.00)
0.02
(0.39)
0.5
(0.971)
0.243
(0.811)
1
(1.00)
20q loss 15 (4%) 393 0.273
(0.849)
0.85
(1.00)
0.325
(0.857)
0.483
(0.971)
0.113
(0.629)
1
(1.00)
0.372
(0.887)
1
(1.00)
0.192
(0.768)
0.982
(1.00)
0.442
(0.952)
1
(1.00)
1
(1.00)
22q loss 160 (39%) 248 0.315
(0.857)
0.169
(0.731)
0.0261
(0.424)
0.0942
(0.565)
0.013
(0.364)
1
(1.00)
1
(1.00)
0.245
(0.812)
0.114
(0.63)
0.433
(0.946)
0.0256
(0.424)
0.0107
(0.335)
0.0315
(0.433)
xp loss 73 (18%) 335 0.538
(0.982)
0.63
(1.00)
0.715
(1.00)
0.851
(1.00)
0.662
(1.00)
1
(1.00)
0.561
(0.997)
0.377
(0.894)
0.205
(0.795)
0.831
(1.00)
0.991
(1.00)
0.737
(1.00)
0.663
(1.00)
xq loss 83 (20%) 325 0.764
(1.00)
0.509
(0.972)
0.758
(1.00)
0.84
(1.00)
0.823
(1.00)
1
(1.00)
0.677
(1.00)
0.572
(1.00)
0.216
(0.798)
0.623
(1.00)
0.831
(1.00)
0.78
(1.00)
0.0777
(0.538)
'2p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0019 (Wilcoxon-test), Q value = 0.17

Table S1.  Gene #3: '2p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
2P GAIN MUTATED 79 2.7 (5.2)
2P GAIN WILD-TYPE 218 1.9 (7.6)

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'3p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00152 (Wilcoxon-test), Q value = 0.17

Table S2.  Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
3P GAIN MUTATED 142 70.4 (10.0)
3P GAIN WILD-TYPE 265 66.9 (10.8)

Figure S2.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000186 (Wilcoxon-test), Q value = 0.099

Table S3.  Gene #5: '3p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
3P GAIN MUTATED 99 3.7 (11.0)
3P GAIN WILD-TYPE 198 1.3 (3.4)

Figure S3.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00226 (Wilcoxon-test), Q value = 0.17

Table S4.  Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
3Q GAIN MUTATED 178 70.0 (10.2)
3Q GAIN WILD-TYPE 229 66.6 (10.7)

Figure S4.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00154 (Fisher's exact test), Q value = 0.17

Table S5.  Gene #6: '3q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
3Q GAIN MUTATED 83 24 44 4
3Q GAIN WILD-TYPE 153 23 31 4

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'3q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 6.11e-05 (Wilcoxon-test), Q value = 0.065

Table S6.  Gene #6: '3q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
3Q GAIN MUTATED 130 3.4 (9.8)
3Q GAIN WILD-TYPE 167 1.1 (3.2)

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'10q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0017 (Fisher's exact test), Q value = 0.17

Table S7.  Gene #20: '10q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
10Q GAIN MUTATED 17 12 10 2
10Q GAIN WILD-TYPE 219 35 65 6

Figure S7.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00388 (Wilcoxon-test), Q value = 0.24

Table S8.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
11Q GAIN MUTATED 47 72.1 (10.9)
11Q GAIN WILD-TYPE 360 67.6 (10.5)

Figure S8.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'RACE'

P value = 0.00338 (Fisher's exact test), Q value = 0.23

Table S9.  Gene #26: '14q gain' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 43 22 327
14Q GAIN MUTATED 0 5 46
14Q GAIN WILD-TYPE 43 17 281

Figure S9.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #12: 'RACE'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000403 (Wilcoxon-test), Q value = 0.13

Table S10.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
21Q GAIN MUTATED 116 71.2 (9.7)
21Q GAIN WILD-TYPE 291 66.9 (10.7)

Figure S10.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'GENDER'

P value = 0.00193 (Fisher's exact test), Q value = 0.17

Table S11.  Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 107 301
3P LOSS MUTATED 23 28
3P LOSS WILD-TYPE 84 273

Figure S11.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #7: 'GENDER'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00468 (Fisher's exact test), Q value = 0.24

Table S12.  Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 2 129 140 135
4P LOSS MUTATED 0 36 45 63
4P LOSS WILD-TYPE 2 93 95 72

Figure S12.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0011 (Fisher's exact test), Q value = 0.17

Table S13.  Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
4P LOSS MUTATED 65 23 36 2
4P LOSS WILD-TYPE 171 24 39 6

Figure S13.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'RACE'

P value = 0.00336 (Fisher's exact test), Q value = 0.23

Table S14.  Gene #48: '4p loss' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 43 22 327
4P LOSS MUTATED 9 14 116
4P LOSS WILD-TYPE 34 8 211

Figure S14.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #12: 'RACE'

'4q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00194 (Wilcoxon-test), Q value = 0.17

Table S15.  Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
4Q LOSS MUTATED 136 70.5 (9.4)
4Q LOSS WILD-TYPE 271 66.9 (11.0)

Figure S15.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0022 (Wilcoxon-test), Q value = 0.17

Table S16.  Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
5P LOSS MUTATED 54 72.2 (8.3)
5P LOSS WILD-TYPE 353 67.5 (10.8)

Figure S16.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00415 (Wilcoxon-test), Q value = 0.24

Table S17.  Gene #53: '6q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 297 2.1 (7.0)
6Q LOSS MUTATED 123 2.5 (5.2)
6Q LOSS WILD-TYPE 174 1.8 (8.0)

Figure S17.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00428 (Fisher's exact test), Q value = 0.24

Table S18.  Gene #57: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1+T2 T3 T4
ALL 123 195 58
8Q LOSS MUTATED 6 16 12
8Q LOSS WILD-TYPE 117 179 46

Figure S18.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00513 (Wilcoxon-test), Q value = 0.25

Table S19.  Gene #62: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 407 68.1 (10.6)
11P LOSS MUTATED 177 69.8 (10.4)
11P LOSS WILD-TYPE 230 66.8 (10.6)

Figure S19.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q loss' versus 'RACE'

P value = 0.00114 (Fisher's exact test), Q value = 0.17

Table S20.  Gene #68: '15q loss' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 43 22 327
15Q LOSS MUTATED 6 4 126
15Q LOSS WILD-TYPE 37 18 201

Figure S20.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #12: 'RACE'

'16p loss' versus 'RACE'

P value = 0.00479 (Fisher's exact test), Q value = 0.24

Table S21.  Gene #69: '16p loss' versus Clinical Feature #12: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 43 22 327
16P LOSS MUTATED 4 3 98
16P LOSS WILD-TYPE 39 19 229

Figure S21.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #12: 'RACE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00047 (Fisher's exact test), Q value = 0.13

Table S22.  Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 236 47 75 8
21Q LOSS MUTATED 42 20 10 0
21Q LOSS WILD-TYPE 194 27 65 8

Figure S22.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

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/22507732/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BLCA-TP/22506467/BLCA-TP.merged_data.txt

  • Number of patients = 408

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 13

  • 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)
[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)