Correlation between copy number variations of arm-level result and selected clinical features
Bladder Urothelial Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1X34W16
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1X34W16
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 80 arm-level events and 11 clinical features across 195 patients, 8 significant findings detected with Q value < 0.25.

  • 5q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 8p gain cnv correlated to 'GLEASON_SCORE'.

  • 9q gain cnv correlated to 'GLEASON_SCORE'.

  • 15q gain cnv correlated to 'GLEASON_SCORE'.

  • 19p gain cnv correlated to 'GLEASON_SCORE'.

  • xq gain cnv correlated to 'GLEASON_SCORE'.

  • 3q loss cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.

  • 8p loss cnv correlated to 'PATHOLOGY.M.STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 8 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBERPACKYEARSSMOKED NUMBER
OF
LYMPH
NODES 		GLEASON
SCORE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test t-test t-test t-test
5q gain 26 (13%) 169 0.786
(1.00) 		0.813
(1.00) 		0.15
(1.00) 		0.625
(1.00) 		0.198
(1.00) 		0.843
(1.00) 		0.628
(1.00) 		0.441
(1.00) 		0.608
(1.00) 		0.00016
(0.139) 		0.257
(1.00)
8p gain 37 (19%) 158 0.376
(1.00) 		0.692
(1.00) 		0.196
(1.00) 		0.359
(1.00) 		0.741
(1.00) 		0.632
(1.00) 		0.525
(1.00) 		0.738
(1.00) 		0.336
(1.00) 		0.133
(1.00) 		0.000128
(0.112)
9q gain 26 (13%) 169 0.191
(1.00) 		0.149
(1.00) 		0.0528
(1.00) 		0.306
(1.00) 		0.373
(1.00) 		0.0319
(1.00) 		0.466
(1.00) 		0.983
(1.00) 		0.028
(1.00) 		0.62
(1.00) 		0.000134
(0.117)
15q gain 19 (10%) 176 0.774
(1.00) 		0.338
(1.00) 		0.893
(1.00) 		0.304
(1.00) 		0.127
(1.00) 		0.052
(1.00) 		1
(1.00) 		0.446
(1.00) 		0.68
(1.00) 		0.799
(1.00) 		0.000144
(0.126)
19p gain 38 (19%) 157 0.614
(1.00) 		0.351
(1.00) 		0.349
(1.00) 		0.371
(1.00) 		0.343
(1.00) 		0.59
(1.00) 		0.404
(1.00) 		0.989
(1.00) 		0.977
(1.00) 		0.587
(1.00) 		0.000134
(0.117)
xq gain 20 (10%) 175 0.317
(1.00) 		0.997
(1.00) 		0.372
(1.00) 		0.238
(1.00) 		0.84
(1.00) 		1
(1.00) 		1
(1.00) 		0.283
(1.00) 		0.409
(1.00) 		0.0219
(1.00) 		0.000134
(0.117)
3q loss 10 (5%) 185 0.921
(1.00) 		0.147
(1.00) 		1
(1.00) 		0.374
(1.00) 		0.499
(1.00) 		0.213
(1.00) 		0.71
(1.00) 		2.17e-06
(0.0019) 		0.379
(1.00) 		0.325
(1.00) 		0.384
(1.00)
8p loss 86 (44%) 109 0.948
(1.00) 		0.273
(1.00) 		0.0614
(1.00) 		0.492
(1.00) 		0.163
(1.00) 		0.000206
(0.179) 		0.74
(1.00) 		0.0484
(1.00) 		0.522
(1.00) 		0.712
(1.00) 		0.679
(1.00)
1p gain 45 (23%) 150 0.0301
(1.00) 		0.605
(1.00) 		0.645
(1.00) 		0.97
(1.00) 		0.0557
(1.00) 		0.715
(1.00) 		0.245
(1.00) 		0.483
(1.00) 		0.168
(1.00) 		0.454
(1.00) 		0.445
(1.00)
1q gain 62 (32%) 133 0.115
(1.00) 		0.782
(1.00) 		0.0724
(1.00) 		0.693
(1.00) 		0.0509
(1.00) 		0.0685
(1.00) 		0.478
(1.00) 		0.849
(1.00) 		0.0992
(1.00) 		0.167
(1.00) 		0.263
(1.00)
2p gain 58 (30%) 137 0.459
(1.00) 		0.00858
(1.00) 		0.0435
(1.00) 		0.925
(1.00) 		0.00363
(1.00) 		0.824
(1.00) 		0.000886
(0.769) 		0.989
(1.00) 		0.0765
(1.00) 		0.0896
(1.00) 		0.782
(1.00)
2q gain 25 (13%) 170 0.791
(1.00) 		0.507
(1.00) 		0.946
(1.00) 		0.552
(1.00) 		0.802
(1.00) 		0.205
(1.00) 		0.212
(1.00) 		0.163
(1.00) 		0.992
(1.00) 		0.275
(1.00) 		0.295
(1.00)
3p gain 66 (34%) 129 0.647
(1.00) 		0.119
(1.00) 		0.0268
(1.00) 		0.215
(1.00) 		0.0843
(1.00) 		0.959
(1.00) 		0.727
(1.00) 		0.0739
(1.00) 		0.266
(1.00) 		0.0958
(1.00) 		0.945
(1.00)
3q gain 84 (43%) 111 0.755
(1.00) 		0.0988
(1.00) 		0.0285
(1.00) 		0.549
(1.00) 		0.00448
(1.00) 		0.541
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.527
(1.00) 		0.0309
(1.00) 		0.469
(1.00)
4p gain 20 (10%) 175 0.178
(1.00) 		0.736
(1.00) 		0.55
(1.00) 		0.0815
(1.00) 		0.059
(1.00) 		0.149
(1.00) 		0.277
(1.00) 		0.631
(1.00) 		0.612
(1.00) 		0.43
(1.00) 		0.297
(1.00)
4q gain 12 (6%) 183 0.334
(1.00) 		0.86
(1.00) 		0.522
(1.00) 		0.301
(1.00) 		0.874
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.905
(1.00) 		0.336
(1.00) 		0.173
(1.00) 		0.811
(1.00)
5p gain 78 (40%) 117 0.81
(1.00) 		0.291
(1.00) 		0.704
(1.00) 		0.649
(1.00) 		0.834
(1.00) 		0.039
(1.00) 		0.736
(1.00) 		0.513
(1.00) 		0.353
(1.00) 		0.261
(1.00) 		0.0469
(1.00)
6p gain 27 (14%) 168 0.971
(1.00) 		0.708
(1.00) 		0.764
(1.00) 		0.671
(1.00) 		0.399
(1.00) 		0.439
(1.00) 		0.63
(1.00) 		0.743
(1.00) 		0.249
(1.00) 		0.969
(1.00) 		0.955
(1.00)
6q gain 17 (9%) 178 0.524
(1.00) 		0.391
(1.00) 		0.957
(1.00) 		0.822
(1.00) 		0.0996
(1.00) 		0.378
(1.00) 		0.251
(1.00) 		0.455
(1.00) 		0.109
(1.00) 		0.791
(1.00) 		0.603
(1.00)
7p gain 81 (42%) 114 0.821
(1.00) 		0.0792
(1.00) 		0.151
(1.00) 		0.479
(1.00) 		0.0422
(1.00) 		0.812
(1.00) 		0.738
(1.00) 		0.402
(1.00) 		0.718
(1.00) 		0.23
(1.00) 		0.0923
(1.00)
7q gain 73 (37%) 122 0.702
(1.00) 		0.239
(1.00) 		0.386
(1.00) 		0.549
(1.00) 		0.000988
(0.856) 		0.17
(1.00) 		0.308
(1.00) 		0.301
(1.00) 		0.538
(1.00) 		0.177
(1.00) 		0.129
(1.00)
8q gain 86 (44%) 109 0.659
(1.00) 		0.576
(1.00) 		0.22
(1.00) 		0.958
(1.00) 		0.661
(1.00) 		0.883
(1.00) 		0.74
(1.00) 		0.704
(1.00) 		0.65
(1.00) 		0.199
(1.00) 		0.0469
(1.00)
9p gain 32 (16%) 163 0.0155
(1.00) 		0.774
(1.00) 		0.466
(1.00) 		0.961
(1.00) 		0.287
(1.00) 		0.331
(1.00) 		0.504
(1.00) 		0.517
(1.00) 		0.00438
(1.00) 		0.749
(1.00) 		0.767
(1.00)
10p gain 54 (28%) 141 0.209
(1.00) 		0.94
(1.00) 		0.611
(1.00) 		0.923
(1.00) 		0.305
(1.00) 		0.237
(1.00) 		0.712
(1.00) 		0.306
(1.00) 		0.426
(1.00) 		0.6
(1.00) 		0.148
(1.00)
10q gain 17 (9%) 178 0.476
(1.00) 		0.315
(1.00) 		0.379
(1.00) 		0.545
(1.00) 		0.109
(1.00) 		0.654
(1.00) 		0.768
(1.00) 		0.786
(1.00) 		0.229
(1.00) 		0.341
(1.00) 		0.508
(1.00)
11p gain 19 (10%) 176 0.0125
(1.00) 		0.817
(1.00) 		0.83
(1.00) 		0.545
(1.00) 		0.0328
(1.00) 		0.539
(1.00) 		0.0477
(1.00) 		0.818
(1.00) 		0.812
(1.00) 		0.571
(1.00) 		0.373
(1.00)
11q gain 25 (13%) 170 0.287
(1.00) 		0.202
(1.00) 		0.766
(1.00) 		0.833
(1.00) 		0.0695
(1.00) 		0.414
(1.00) 		0.0457
(1.00) 		0.809
(1.00) 		0.899
(1.00) 		0.465
(1.00) 		0.139
(1.00)
12p gain 61 (31%) 134 0.523
(1.00) 		0.0468
(1.00) 		0.605
(1.00) 		0.595
(1.00) 		0.84
(1.00) 		0.466
(1.00) 		0.479
(1.00) 		0.916
(1.00) 		0.0865
(1.00) 		0.69
(1.00) 		0.53
(1.00)
12q gain 45 (23%) 150 0.419
(1.00) 		0.723
(1.00) 		0.24
(1.00) 		0.695
(1.00) 		0.46
(1.00) 		0.21
(1.00) 		0.698
(1.00) 		0.702
(1.00) 		0.0263
(1.00) 		0.339
(1.00) 		0.558
(1.00)
13q gain 47 (24%) 148 0.825
(1.00) 		0.266
(1.00) 		0.248
(1.00) 		1
(1.00) 		0.0478
(1.00) 		0.0298
(1.00) 		0.566
(1.00) 		0.566
(1.00) 		0.886
(1.00) 		0.483
(1.00) 		0.885
(1.00)
14q gain 36 (18%) 159 0.199
(1.00) 		0.287
(1.00) 		0.194
(1.00) 		0.147
(1.00) 		0.342
(1.00) 		0.0334
(1.00) 		0.201
(1.00) 		0.58
(1.00) 		0.646
(1.00) 		0.166
(1.00) 		0.909
(1.00)
16p gain 29 (15%) 166 0.0585
(1.00) 		0.609
(1.00) 		0.109
(1.00) 		0.0328
(1.00) 		0.246
(1.00) 		0.0275
(1.00) 		0.483
(1.00) 		0.861
(1.00) 		0.45
(1.00) 		0.885
(1.00) 		0.161
(1.00)
16q gain 37 (19%) 158 0.404
(1.00) 		0.691
(1.00) 		0.224
(1.00) 		0.0862
(1.00) 		0.0795
(1.00) 		0.068
(1.00) 		0.136
(1.00) 		0.905
(1.00) 		0.994
(1.00) 		0.384
(1.00) 		0.28
(1.00)
17p gain 29 (15%) 166 0.00222
(1.00) 		0.0346
(1.00) 		0.134
(1.00) 		0.353
(1.00) 		0.629
(1.00) 		0.464
(1.00) 		1
(1.00) 		0.247
(1.00) 		0.284
(1.00) 		0.0166
(1.00) 		0.824
(1.00)
17q gain 64 (33%) 131 0.0157
(1.00) 		0.443
(1.00) 		0.324
(1.00) 		0.458
(1.00) 		0.102
(1.00) 		0.726
(1.00) 		0.48
(1.00) 		0.105
(1.00) 		0.19
(1.00) 		0.861
(1.00) 		0.127
(1.00)
18p gain 56 (29%) 139 0.423
(1.00) 		0.83
(1.00) 		0.713
(1.00) 		0.181
(1.00) 		0.845
(1.00) 		0.101
(1.00) 		0.464
(1.00) 		0.00911
(1.00) 		0.641
(1.00) 		0.899
(1.00) 		0.366
(1.00)
18q gain 30 (15%) 165 0.07
(1.00) 		0.77
(1.00) 		0.743
(1.00) 		0.0622
(1.00) 		0.896
(1.00) 		0.395
(1.00) 		0.819
(1.00) 		0.00134
(1.00) 		0.611
(1.00) 		0.986
(1.00) 		0.295
(1.00)
19q gain 64 (33%) 131 0.425
(1.00) 		0.979
(1.00) 		0.0739
(1.00) 		0.102
(1.00) 		0.143
(1.00) 		0.837
(1.00) 		0.724
(1.00) 		0.222
(1.00) 		0.338
(1.00) 		0.16
(1.00) 		0.404
(1.00)
20p gain 99 (51%) 96 0.163
(1.00) 		0.499
(1.00) 		0.528
(1.00) 		0.937
(1.00) 		0.543
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.323
(1.00) 		0.164
(1.00) 		0.11
(1.00) 		0.148
(1.00)
20q gain 112 (57%) 83 0.561
(1.00) 		0.662
(1.00) 		0.853
(1.00) 		0.421
(1.00) 		0.566
(1.00) 		0.59
(1.00) 		0.405
(1.00) 		0.522
(1.00) 		0.357
(1.00) 		0.832
(1.00) 		0.426
(1.00)
21q gain 61 (31%) 134 0.788
(1.00) 		0.0214
(1.00) 		0.225
(1.00) 		0.739
(1.00) 		0.0424
(1.00) 		0.832
(1.00) 		0.591
(1.00) 		0.841
(1.00) 		0.238
(1.00) 		0.493
(1.00) 		0.333
(1.00)
22q gain 28 (14%) 167 0.969
(1.00) 		0.941
(1.00) 		0.309
(1.00) 		0.81
(1.00) 		0.511
(1.00) 		0.41
(1.00) 		0.48
(1.00) 		0.485
(1.00) 		0.863
(1.00) 		0.231
(1.00) 		0.295
(1.00)
1p loss 13 (7%) 182 0.434
(1.00) 		0.367
(1.00) 		0.682
(1.00) 		0.223
(1.00) 		0.422
(1.00) 		0.0186
(1.00) 		0.526
(1.00) 		0.905
(1.00) 		0.126
(1.00) 		0.944
(1.00) 		0.195
(1.00)
1q loss 15 (8%) 180 0.587
(1.00) 		0.711
(1.00) 		0.655
(1.00) 		0.232
(1.00) 		0.863
(1.00) 		0.73
(1.00) 		0.765
(1.00) 		0.229
(1.00) 		0.00172
(1.00) 		0.965
(1.00) 		0.331
(1.00)
2p loss 19 (10%) 176 0.992
(1.00) 		0.805
(1.00) 		0.518
(1.00) 		0.146
(1.00) 		0.205
(1.00) 		0.42
(1.00) 		0.0477
(1.00) 		0.837
(1.00) 		0.314
(1.00) 		0.188
(1.00) 		0.297
(1.00)
2q loss 44 (23%) 151 0.642
(1.00) 		0.478
(1.00) 		0.25
(1.00) 		0.807
(1.00) 		0.0484
(1.00) 		0.944
(1.00) 		0.692
(1.00) 		0.394
(1.00) 		0.514
(1.00) 		0.959
(1.00) 		0.777
(1.00)
3p loss 24 (12%) 171 0.577
(1.00) 		0.14
(1.00) 		0.788
(1.00) 		0.103
(1.00) 		0.492
(1.00) 		0.75
(1.00) 		0.132
(1.00) 		0.869
(1.00) 		0.544
(1.00) 		0.822
(1.00) 		0.708
(1.00)
4p loss 68 (35%) 127 0.367
(1.00) 		0.19
(1.00) 		0.373
(1.00) 		0.491
(1.00) 		0.144
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.801
(1.00) 		0.183
(1.00) 		0.316
(1.00) 		0.458
(1.00)
4q loss 68 (35%) 127 0.872
(1.00) 		0.0487
(1.00) 		0.434
(1.00) 		0.265
(1.00) 		0.216
(1.00) 		0.312
(1.00) 		0.486
(1.00) 		0.528
(1.00) 		0.356
(1.00) 		0.687
(1.00) 		0.0924
(1.00)
5p loss 31 (16%) 164 0.457
(1.00) 		0.0488
(1.00) 		0.639
(1.00) 		0.922
(1.00) 		0.486
(1.00) 		0.235
(1.00) 		0.362
(1.00) 		0.0506
(1.00) 		0.536
(1.00) 		0.453
(1.00) 		0.161
(1.00)
5q loss 72 (37%) 123 0.687
(1.00) 		0.377
(1.00) 		0.0113
(1.00) 		0.341
(1.00) 		0.00696
(1.00) 		0.00361
(1.00) 		1
(1.00) 		0.00813
(1.00) 		0.811
(1.00) 		0.0717
(1.00) 		0.518
(1.00)
6p loss 48 (25%) 147 0.765
(1.00) 		0.488
(1.00) 		0.0446
(1.00) 		0.0155
(1.00) 		0.0224
(1.00) 		0.688
(1.00) 		0.248
(1.00) 		0.563
(1.00) 		0.459
(1.00) 		0.208
(1.00) 		0.187
(1.00)
6q loss 72 (37%) 123 0.836
(1.00) 		0.729
(1.00) 		0.064
(1.00) 		0.263
(1.00) 		0.0222
(1.00) 		0.434
(1.00) 		0.302
(1.00) 		0.31
(1.00) 		0.953
(1.00) 		0.0288
(1.00) 		1
(1.00)
7p loss 8 (4%) 187 0.256
(1.00) 		0.416
(1.00) 		0.63
(1.00) 		0.782
(1.00) 		0.159
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.905
(1.00) 		0.708
(1.00) 		0.418
(1.00) 		0.528
(1.00)
7q loss 9 (5%) 186 0.964
(1.00) 		0.55
(1.00) 		0.786
(1.00) 		0.728
(1.00) 		0.679
(1.00) 		0.617
(1.00) 		0.457
(1.00) 		0.00367
(1.00) 		0.656
(1.00)
8q loss 19 (10%) 176 0.998
(1.00) 		0.368
(1.00) 		0.111
(1.00) 		0.0296
(1.00) 		0.14
(1.00) 		0.093
(1.00) 		0.575
(1.00) 		0.614
(1.00) 		0.988
(1.00) 		0.314
(1.00) 		0.297
(1.00)
9p loss 83 (43%) 112 0.998
(1.00) 		0.115
(1.00) 		0.773
(1.00) 		0.957
(1.00) 		0.899
(1.00) 		1
(1.00) 		0.502
(1.00) 		0.799
(1.00) 		0.706
(1.00) 		0.477
(1.00) 		0.526
(1.00)
9q loss 75 (38%) 120 0.876
(1.00) 		0.168
(1.00) 		0.832
(1.00) 		0.746
(1.00) 		0.813
(1.00) 		0.776
(1.00) 		0.305
(1.00) 		0.671
(1.00) 		0.388
(1.00) 		0.743
(1.00) 		0.946
(1.00)
10p loss 38 (19%) 157 0.719
(1.00) 		0.747
(1.00) 		0.831
(1.00) 		0.371
(1.00) 		0.55
(1.00) 		0.213
(1.00) 		0.677
(1.00) 		0.045
(1.00) 		0.166
(1.00) 		0.409
(1.00) 		0.653
(1.00)
10q loss 64 (33%) 131 0.593
(1.00) 		0.0835
(1.00) 		0.974
(1.00) 		0.927
(1.00) 		0.8
(1.00) 		0.4
(1.00) 		0.861
(1.00) 		0.0252
(1.00) 		0.879
(1.00) 		0.82
(1.00) 		0.585
(1.00)
11p loss 73 (37%) 122 0.511
(1.00) 		0.0402
(1.00) 		0.0158
(1.00) 		0.666
(1.00) 		0.0469
(1.00) 		0.113
(1.00) 		0.607
(1.00) 		0.521
(1.00) 		0.667
(1.00) 		0.0717
(1.00) 		0.764
(1.00)
11q loss 56 (29%) 139 0.59
(1.00) 		0.761
(1.00) 		0.521
(1.00) 		0.817
(1.00) 		0.149
(1.00) 		0.746
(1.00) 		0.714
(1.00) 		0.307
(1.00) 		0.234
(1.00) 		0.582
(1.00) 		0.19
(1.00)
12p loss 19 (10%) 176 0.377
(1.00) 		0.773
(1.00) 		0.363
(1.00) 		0.792
(1.00) 		0.0939
(1.00) 		0.201
(1.00) 		0.168
(1.00) 		0.94
(1.00) 		0.0625
(1.00) 		0.296
(1.00) 		0.161
(1.00)
12q loss 22 (11%) 173 0.915
(1.00) 		0.134
(1.00) 		0.0464
(1.00) 		0.663
(1.00) 		0.00237
(1.00) 		0.178
(1.00) 		0.603
(1.00) 		0.829
(1.00) 		0.178
(1.00) 		0.203
(1.00) 		0.513
(1.00)
13q loss 43 (22%) 152 0.13
(1.00) 		0.888
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.944
(1.00) 		0.745
(1.00) 		0.167
(1.00) 		0.0012
(1.00) 		0.598
(1.00) 		0.992
(1.00) 		0.953
(1.00)
14q loss 53 (27%) 142 0.597
(1.00) 		0.312
(1.00) 		0.268
(1.00) 		0.678
(1.00) 		0.145
(1.00) 		0.949
(1.00) 		0.14
(1.00) 		0.477
(1.00) 		0.144
(1.00) 		0.338
(1.00) 		0.481
(1.00)
15q loss 63 (32%) 132 0.807
(1.00) 		0.591
(1.00) 		0.23
(1.00) 		0.172
(1.00) 		0.641
(1.00) 		0.0528
(1.00) 		0.861
(1.00) 		0.161
(1.00) 		0.366
(1.00) 		0.343
(1.00) 		0.445
(1.00)
16p loss 52 (27%) 143 0.292
(1.00) 		0.664
(1.00) 		0.23
(1.00) 		0.0607
(1.00) 		0.657
(1.00) 		0.056
(1.00) 		0.852
(1.00) 		0.858
(1.00) 		0.699
(1.00) 		0.11
(1.00) 		0.359
(1.00)
16q loss 48 (25%) 147 0.979
(1.00) 		0.6
(1.00) 		0.742
(1.00) 		0.451
(1.00) 		0.354
(1.00) 		0.027
(1.00) 		0.337
(1.00) 		0.464
(1.00) 		0.699
(1.00) 		0.455
(1.00) 		0.282
(1.00)
17p loss 82 (42%) 113 0.834
(1.00) 		0.172
(1.00) 		0.367
(1.00) 		0.836
(1.00) 		0.889
(1.00) 		0.845
(1.00) 		1
(1.00) 		0.671
(1.00) 		0.341
(1.00) 		0.523
(1.00) 		0.316
(1.00)
17q loss 25 (13%) 170 0.396
(1.00) 		0.171
(1.00) 		0.652
(1.00) 		0.169
(1.00) 		0.419
(1.00) 		0.115
(1.00) 		0.628
(1.00) 		0.807
(1.00) 		0.436
(1.00) 		0.504
(1.00) 		0.513
(1.00)
18p loss 46 (24%) 149 0.922
(1.00) 		0.95
(1.00) 		0.216
(1.00) 		0.418
(1.00) 		0.369
(1.00) 		0.239
(1.00) 		0.558
(1.00) 		0.223
(1.00) 		0.191
(1.00) 		0.722
(1.00) 		0.187
(1.00)
18q loss 68 (35%) 127 0.279
(1.00) 		0.744
(1.00) 		0.682
(1.00) 		0.67
(1.00) 		0.952
(1.00) 		0.879
(1.00) 		0.296
(1.00) 		0.837
(1.00) 		0.686
(1.00) 		0.981
(1.00) 		0.782
(1.00)
19p loss 50 (26%) 145 0.0276
(1.00) 		0.191
(1.00) 		0.0277
(1.00) 		0.0542
(1.00) 		0.0785
(1.00) 		0.0173
(1.00) 		0.569
(1.00) 		0.5
(1.00) 		0.625
(1.00) 		0.893
(1.00) 		0.461
(1.00)
19q loss 30 (15%) 165 0.056
(1.00) 		0.762
(1.00) 		0.914
(1.00) 		0.0548
(1.00) 		0.719
(1.00) 		0.095
(1.00) 		1
(1.00) 		0.831
(1.00) 		0.569
(1.00) 		0.133
(1.00) 		0.908
(1.00)
20p loss 14 (7%) 181 0.779
(1.00) 		0.5
(1.00) 		0.758
(1.00) 		0.782
(1.00) 		0.399
(1.00) 		0.597
(1.00) 		1
(1.00) 		0.287
(1.00) 		0.00116
(1.00) 		0.748
(1.00) 		0.384
(1.00)
20q loss 5 (3%) 190 0.717
(1.00) 		0.961
(1.00) 		0.0903
(1.00) 		0.365
(1.00) 		0.0436
(1.00) 		0.455
(1.00) 		0.598
(1.00) 		0.00208
(1.00) 		0.422
(1.00)
21q loss 28 (14%) 167 0.0941
(1.00) 		0.0665
(1.00) 		0.714
(1.00) 		0.178
(1.00) 		0.0287
(1.00) 		0.55
(1.00) 		0.48
(1.00) 		0.117
(1.00) 		0.933
(1.00) 		0.842
(1.00) 		0.548
(1.00)
22q loss 73 (37%) 122 0.515
(1.00) 		0.352
(1.00) 		0.0405
(1.00) 		0.157
(1.00) 		0.141
(1.00) 		0.0177
(1.00) 		0.734
(1.00) 		0.0322
(1.00) 		0.479
(1.00) 		0.824
(1.00) 		0.499
(1.00)
xq loss 38 (19%) 157 0.634
(1.00) 		0.367
(1.00) 		0.505
(1.00) 		0.329
(1.00) 		0.686
(1.00) 		0.251
(1.00) 		0.404
(1.00) 		0.815
(1.00) 		0.747
(1.00) 		0.831
(1.00) 		0.7
(1.00)
'5q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.00016 (t-test), Q value = 0.14

Table S1.  Gene #10: '5q gain' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 145 1.5 (3.3)
5Q GAIN MUTATED 19 0.3 (0.7)
5Q GAIN WILD-TYPE 126 1.7 (3.5)

Figure S1.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'8p gain' versus 'GLEASON_SCORE'

P value = 0.000128 (t-test), Q value = 0.11

Table S2.  Gene #15: '8p gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 42 6.4 (0.7)
8P GAIN MUTATED 6 6.0 (0.0)
8P GAIN WILD-TYPE 36 6.5 (0.7)

Figure S2.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'9q gain' versus 'GLEASON_SCORE'

P value = 0.000134 (t-test), Q value = 0.12

Table S3.  Gene #18: '9q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 42 6.4 (0.7)
9Q GAIN MUTATED 5 6.0 (0.0)
9Q GAIN WILD-TYPE 37 6.5 (0.7)

Figure S3.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'15q gain' versus 'GLEASON_SCORE'

P value = 0.000144 (t-test), Q value = 0.13

Table S4.  Gene #27: '15q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 42 6.4 (0.7)
15Q GAIN MUTATED 3 6.0 (0.0)
15Q GAIN WILD-TYPE 39 6.5 (0.7)

Figure S4.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'19p gain' versus 'GLEASON_SCORE'

P value = 0.000134 (t-test), Q value = 0.12

Table S5.  Gene #34: '19p gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 42 6.4 (0.7)
19P GAIN MUTATED 5 6.0 (0.0)
19P GAIN WILD-TYPE 37 6.5 (0.7)

Figure S5.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'xq gain' versus 'GLEASON_SCORE'

P value = 0.000134 (t-test), Q value = 0.12

Table S6.  Gene #40: 'xq gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 42 6.4 (0.7)
XQ GAIN MUTATED 5 6.0 (0.0)
XQ GAIN WILD-TYPE 37 6.5 (0.7)

Figure S6.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'3q loss' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 2.17e-06 (t-test), Q value = 0.0019

Table S7.  Gene #46: '3q loss' versus Clinical Feature #8: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 54 78.7 (15.8)
3Q LOSS MUTATED 4 90.0 (0.0)
3Q LOSS WILD-TYPE 50 77.8 (16.1)

Figure S7.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #8: 'KARNOFSKY.PERFORMANCE.SCORE'

'8p loss' versus 'PATHOLOGY.M.STAGE'

P value = 0.000206 (Fisher's exact test), Q value = 0.18

Table S8.  Gene #55: '8p loss' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 103 5 86
8P LOSS MUTATED 32 4 49
8P LOSS WILD-TYPE 71 1 37

Figure S8.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = BLCA-TP.merged_data.txt

  • Number of patients = 195

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 11

  • 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

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

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] 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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