Correlation between copy number variations of arm-level result and selected clinical features
Bladder Urothelial Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1G15Z41
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1G15Z41
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 10 clinical features across 152 patients, 2 significant findings detected with Q value < 0.25.

  • 5Q GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 3Q LOSS MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

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 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 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
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
5Q GAIN MUTATION ANALYSIS 22 (14%) 130 0.895
(1.00) 		0.751
(1.00) 		0.0506
(1.00) 		0.291
(1.00) 		0.0428
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.79
(1.00) 		0.937
(1.00) 		3.35e-05
(0.0265)
3Q LOSS MUTATION ANALYSIS 8 (5%) 144 0.0526
(1.00) 		0.691
(1.00) 		0.583
(1.00) 		0.87
(1.00) 		0.577
(1.00) 		0.219
(1.00) 		1
(1.00) 		0.0337
(1.00) 		0.493
(1.00) 		2.69e-06
(0.00213)
1P GAIN MUTATION ANALYSIS 39 (26%) 113 0.0142
(1.00) 		0.602
(1.00) 		0.739
(1.00) 		0.863
(1.00) 		0.134
(1.00) 		0.259
(1.00) 		0.388
(1.00) 		0.389
(1.00) 		0.0208
(1.00) 		0.572
(1.00)
1Q GAIN MUTATION ANALYSIS 50 (33%) 102 0.000594
(0.469) 		0.506
(1.00) 		0.0372
(1.00) 		0.292
(1.00) 		0.0127
(1.00) 		0.0371
(1.00) 		0.84
(1.00) 		0.768
(1.00) 		0.0212
(1.00) 		0.173
(1.00)
2P GAIN MUTATION ANALYSIS 44 (29%) 108 0.284
(1.00) 		0.066
(1.00) 		0.0353
(1.00) 		0.966
(1.00) 		0.00539
(1.00) 		0.666
(1.00) 		0.00278
(1.00) 		0.628
(1.00) 		0.566
(1.00) 		0.0894
(1.00)
2Q GAIN MUTATION ANALYSIS 21 (14%) 131 0.132
(1.00) 		0.936
(1.00) 		0.451
(1.00) 		0.0871
(1.00) 		0.683
(1.00) 		0.104
(1.00) 		1
(1.00) 		0.103
(1.00) 		0.663
(1.00) 		0.458
(1.00)
3P GAIN MUTATION ANALYSIS 53 (35%) 99 0.848
(1.00) 		0.0874
(1.00) 		0.208
(1.00) 		0.319
(1.00) 		0.467
(1.00) 		0.861
(1.00) 		1
(1.00) 		0.102
(1.00) 		0.701
(1.00) 		0.353
(1.00)
3Q GAIN MUTATION ANALYSIS 72 (47%) 80 0.12
(1.00) 		0.159
(1.00) 		0.102
(1.00) 		0.692
(1.00) 		0.0481
(1.00) 		0.754
(1.00) 		0.567
(1.00) 		0.497
(1.00) 		0.861
(1.00) 		0.162
(1.00)
4P GAIN MUTATION ANALYSIS 14 (9%) 138 0.0691
(1.00) 		0.903
(1.00) 		0.742
(1.00) 		0.2
(1.00) 		0.109
(1.00) 		0.16
(1.00) 		1
(1.00) 		0.729
(1.00) 		0.688
(1.00) 		0.78
(1.00)
4Q GAIN MUTATION ANALYSIS 8 (5%) 144 0.12
(1.00) 		0.571
(1.00) 		0.583
(1.00) 		0.76
(1.00) 		0.527
(1.00) 		0.358
(1.00) 		1
(1.00) 		0.781
(1.00) 		0.000329
(0.261)
5P GAIN MUTATION ANALYSIS 56 (37%) 96 0.647
(1.00) 		0.328
(1.00) 		0.716
(1.00) 		0.41
(1.00) 		0.054
(1.00) 		0.336
(1.00) 		0.114
(1.00) 		0.899
(1.00) 		0.984
(1.00) 		0.168
(1.00)
6P GAIN MUTATION ANALYSIS 23 (15%) 129 0.356
(1.00) 		0.874
(1.00) 		0.916
(1.00) 		0.57
(1.00) 		0.201
(1.00) 		0.445
(1.00) 		0.287
(1.00) 		0.502
(1.00) 		0.0692
(1.00) 		1
(1.00)
6Q GAIN MUTATION ANALYSIS 15 (10%) 137 0.863
(1.00) 		0.48
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.0178
(1.00) 		0.364
(1.00) 		0.122
(1.00) 		0.41
(1.00) 		0.119
(1.00) 		0.829
(1.00)
7P GAIN MUTATION ANALYSIS 60 (39%) 92 0.267
(1.00) 		0.0416
(1.00) 		0.118
(1.00) 		0.609
(1.00) 		0.267
(1.00) 		0.951
(1.00) 		0.846
(1.00) 		0.634
(1.00) 		0.644
(1.00) 		0.442
(1.00)
7Q GAIN MUTATION ANALYSIS 54 (36%) 98 0.594
(1.00) 		0.0676
(1.00) 		0.375
(1.00) 		0.782
(1.00) 		0.00881
(1.00) 		0.434
(1.00) 		0.234
(1.00) 		0.463
(1.00) 		0.17
(1.00) 		0.277
(1.00)
8P GAIN MUTATION ANALYSIS 32 (21%) 120 0.592
(1.00) 		0.549
(1.00) 		0.39
(1.00) 		0.151
(1.00) 		0.863
(1.00) 		0.605
(1.00) 		0.64
(1.00) 		0.656
(1.00) 		0.506
(1.00) 		0.00954
(1.00)
8Q GAIN MUTATION ANALYSIS 70 (46%) 82 0.326
(1.00) 		0.609
(1.00) 		0.334
(1.00) 		0.601
(1.00) 		0.888
(1.00) 		0.954
(1.00) 		0.186
(1.00) 		0.292
(1.00) 		0.454
(1.00) 		0.0839
(1.00)
9P GAIN MUTATION ANALYSIS 27 (18%) 125 0.00653
(1.00) 		0.233
(1.00) 		0.51
(1.00) 		0.619
(1.00) 		0.555
(1.00) 		0.335
(1.00) 		0.621
(1.00) 		0.379
(1.00) 		0.204
(1.00) 		0.775
(1.00)
9Q GAIN MUTATION ANALYSIS 21 (14%) 131 0.113
(1.00) 		0.171
(1.00) 		0.136
(1.00) 		1
(1.00) 		0.193
(1.00) 		0.0196
(1.00) 		0.585
(1.00) 		0.951
(1.00) 		0.236
(1.00) 		0.601
(1.00)
10P GAIN MUTATION ANALYSIS 39 (26%) 113 0.3
(1.00) 		0.854
(1.00) 		0.532
(1.00) 		0.67
(1.00) 		0.309
(1.00) 		0.259
(1.00) 		0.667
(1.00) 		0.58
(1.00) 		0.995
(1.00) 		0.45
(1.00)
10Q GAIN MUTATION ANALYSIS 12 (8%) 140 0.167
(1.00) 		0.321
(1.00) 		0.228
(1.00) 		0.25
(1.00) 		0.149
(1.00) 		0.848
(1.00) 		0.732
(1.00) 		0.311
(1.00) 		0.299
(1.00)
11P GAIN MUTATION ANALYSIS 12 (8%) 140 0.0152
(1.00) 		0.472
(1.00) 		0.94
(1.00) 		0.911
(1.00) 		0.462
(1.00) 		0.696
(1.00) 		0.296
(1.00) 		0.709
(1.00) 		0.752
(1.00) 		0.526
(1.00)
11Q GAIN MUTATION ANALYSIS 19 (12%) 133 0.978
(1.00) 		0.556
(1.00) 		0.93
(1.00) 		0.942
(1.00) 		0.168
(1.00) 		0.576
(1.00) 		0.566
(1.00) 		0.654
(1.00) 		0.646
(1.00) 		0.492
(1.00)
12P GAIN MUTATION ANALYSIS 45 (30%) 107 0.989
(1.00) 		0.0487
(1.00) 		0.474
(1.00) 		0.19
(1.00) 		0.822
(1.00) 		0.38
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.571
(1.00) 		0.648
(1.00)
12Q GAIN MUTATION ANALYSIS 37 (24%) 115 0.814
(1.00) 		0.844
(1.00) 		0.496
(1.00) 		0.504
(1.00) 		0.529
(1.00) 		0.201
(1.00) 		0.51
(1.00) 		0.874
(1.00) 		0.0926
(1.00) 		0.666
(1.00)
13Q GAIN MUTATION ANALYSIS 37 (24%) 115 0.883
(1.00) 		0.494
(1.00) 		0.311
(1.00) 		1
(1.00) 		0.185
(1.00) 		0.195
(1.00) 		0.375
(1.00) 		0.292
(1.00) 		0.252
(1.00) 		0.787
(1.00)
14Q GAIN MUTATION ANALYSIS 26 (17%) 126 0.535
(1.00) 		0.672
(1.00) 		0.751
(1.00) 		0.622
(1.00) 		0.291
(1.00) 		0.124
(1.00) 		0.623
(1.00) 		0.59
(1.00) 		0.577
(1.00) 		0.0742
(1.00)
15Q GAIN MUTATION ANALYSIS 15 (10%) 137 0.852
(1.00) 		0.452
(1.00) 		0.796
(1.00) 		0.86
(1.00) 		0.0936
(1.00) 		0.0743
(1.00) 		0.755
(1.00) 		0.349
(1.00) 		0.02
(1.00) 		0.898
(1.00)
16P GAIN MUTATION ANALYSIS 27 (18%) 125 0.0328
(1.00) 		0.399
(1.00) 		0.796
(1.00) 		0.0477
(1.00) 		0.331
(1.00) 		0.379
(1.00) 		0.804
(1.00) 		0.699
(1.00) 		0.437
(1.00) 		0.673
(1.00)
16Q GAIN MUTATION ANALYSIS 29 (19%) 123 0.262
(1.00) 		0.938
(1.00) 		0.362
(1.00) 		0.0637
(1.00) 		0.339
(1.00) 		0.316
(1.00) 		0.0542
(1.00) 		0.867
(1.00) 		0.71
(1.00) 		0.432
(1.00)
17P GAIN MUTATION ANALYSIS 21 (14%) 131 0.000681
(0.537) 		0.108
(1.00) 		0.0975
(1.00) 		0.514
(1.00) 		0.368
(1.00) 		0.373
(1.00) 		0.585
(1.00) 		0.569
(1.00) 		0.756
(1.00) 		0.0266
(1.00)
17Q GAIN MUTATION ANALYSIS 52 (34%) 100 0.0427
(1.00) 		0.245
(1.00) 		0.16
(1.00) 		0.558
(1.00) 		0.0289
(1.00) 		0.693
(1.00) 		0.549
(1.00) 		0.0277
(1.00) 		0.666
(1.00) 		0.74
(1.00)
18P GAIN MUTATION ANALYSIS 40 (26%) 112 0.831
(1.00) 		0.634
(1.00) 		1
(1.00) 		0.457
(1.00) 		0.387
(1.00) 		0.881
(1.00) 		1
(1.00) 		0.0334
(1.00) 		0.141
(1.00) 		0.748
(1.00)
18Q GAIN MUTATION ANALYSIS 18 (12%) 134 0.251
(1.00) 		0.853
(1.00) 		0.895
(1.00) 		0.168
(1.00) 		0.741
(1.00) 		0.706
(1.00) 		0.566
(1.00) 		0.00722
(1.00) 		0.303
(1.00) 		0.977
(1.00)
19P GAIN MUTATION ANALYSIS 30 (20%) 122 0.291
(1.00) 		0.545
(1.00) 		0.955
(1.00) 		0.376
(1.00) 		0.063
(1.00) 		0.688
(1.00) 		0.811
(1.00) 		0.707
(1.00) 		0.713
(1.00) 		0.479
(1.00)
19Q GAIN MUTATION ANALYSIS 52 (34%) 100 0.476
(1.00) 		0.96
(1.00) 		0.112
(1.00) 		0.101
(1.00) 		0.111
(1.00) 		0.552
(1.00) 		0.842
(1.00) 		0.0829
(1.00) 		0.169
(1.00) 		0.225
(1.00)
20P GAIN MUTATION ANALYSIS 81 (53%) 71 0.159
(1.00) 		0.409
(1.00) 		0.707
(1.00) 		0.796
(1.00) 		0.594
(1.00) 		0.49
(1.00) 		0.849
(1.00) 		0.579
(1.00) 		0.0528
(1.00) 		0.211
(1.00)
20Q GAIN MUTATION ANALYSIS 92 (61%) 60 0.988
(1.00) 		0.78
(1.00) 		0.918
(1.00) 		0.271
(1.00) 		0.608
(1.00) 		0.528
(1.00) 		0.33
(1.00) 		0.491
(1.00) 		0.0389
(1.00) 		0.762
(1.00)
21Q GAIN MUTATION ANALYSIS 51 (34%) 101 0.253
(1.00) 		0.0372
(1.00) 		0.387
(1.00) 		0.467
(1.00) 		0.252
(1.00) 		0.905
(1.00) 		0.428
(1.00) 		0.947
(1.00) 		0.131
(1.00) 		0.953
(1.00)
22Q GAIN MUTATION ANALYSIS 28 (18%) 124 0.379
(1.00) 		0.849
(1.00) 		0.661
(1.00) 		0.802
(1.00) 		0.902
(1.00) 		0.739
(1.00) 		1
(1.00) 		0.316
(1.00) 		0.831
(1.00) 		0.0204
(1.00)
XQ GAIN MUTATION ANALYSIS 20 (13%) 132 0.598
(1.00) 		0.87
(1.00) 		0.317
(1.00) 		0.26
(1.00) 		0.833
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.368
(1.00) 		0.633
(1.00) 		0.0118
(1.00)
1P LOSS MUTATION ANALYSIS 11 (7%) 141 0.796
(1.00) 		0.396
(1.00) 		0.504
(1.00) 		0.408
(1.00) 		0.347
(1.00) 		0.0491
(1.00) 		1
(1.00) 		0.0583
(1.00) 		0.909
(1.00)
1Q LOSS MUTATION ANALYSIS 12 (8%) 140 0.961
(1.00) 		0.36
(1.00) 		0.939
(1.00) 		0.408
(1.00) 		0.778
(1.00) 		1
(1.00) 		1
(1.00) 		0.19
(1.00) 		0.0118
(1.00) 		0.862
(1.00)
2P LOSS MUTATION ANALYSIS 15 (10%) 137 0.548
(1.00) 		0.709
(1.00) 		0.796
(1.00) 		0.459
(1.00) 		0.225
(1.00) 		0.567
(1.00) 		0.122
(1.00) 		0.535
(1.00) 		0.314
(1.00) 		0.441
(1.00)
2Q LOSS MUTATION ANALYSIS 33 (22%) 119 0.0644
(1.00) 		0.421
(1.00) 		0.38
(1.00) 		0.753
(1.00) 		0.0467
(1.00) 		0.933
(1.00) 		1
(1.00) 		0.41
(1.00) 		0.226
(1.00) 		0.611
(1.00)
3P LOSS MUTATION ANALYSIS 23 (15%) 129 0.444
(1.00) 		0.526
(1.00) 		0.94
(1.00) 		0.902
(1.00) 		0.465
(1.00) 		0.245
(1.00) 		0.0672
(1.00) 		0.98
(1.00) 		0.588
(1.00) 		0.482
(1.00)
4P LOSS MUTATION ANALYSIS 51 (34%) 101 0.0548
(1.00) 		0.0541
(1.00) 		0.243
(1.00) 		0.941
(1.00) 		0.229
(1.00) 		0.652
(1.00) 		0.84
(1.00) 		0.89
(1.00) 		0.187
(1.00) 		0.442
(1.00)
4Q LOSS MUTATION ANALYSIS 47 (31%) 105 0.484
(1.00) 		0.0121
(1.00) 		0.537
(1.00) 		0.635
(1.00) 		0.802
(1.00) 		0.852
(1.00) 		1
(1.00) 		0.636
(1.00) 		0.267
(1.00) 		0.456
(1.00)
5P LOSS MUTATION ANALYSIS 29 (19%) 123 0.0589
(1.00) 		0.0432
(1.00) 		0.715
(1.00) 		0.634
(1.00) 		0.424
(1.00) 		0.216
(1.00) 		0.629
(1.00) 		0.0367
(1.00) 		0.451
(1.00) 		0.528
(1.00)
5Q LOSS MUTATION ANALYSIS 57 (38%) 95 0.928
(1.00) 		0.0503
(1.00) 		0.0404
(1.00) 		0.212
(1.00) 		0.0481
(1.00) 		0.0126
(1.00) 		0.431
(1.00) 		0.0692
(1.00) 		0.853
(1.00) 		0.167
(1.00)
6P LOSS MUTATION ANALYSIS 38 (25%) 114 0.76
(1.00) 		0.287
(1.00) 		0.0123
(1.00) 		0.0659
(1.00) 		0.0206
(1.00) 		0.69
(1.00) 		0.664
(1.00) 		0.725
(1.00) 		0.915
(1.00) 		0.132
(1.00)
6Q LOSS MUTATION ANALYSIS 53 (35%) 99 0.963
(1.00) 		0.284
(1.00) 		0.0386
(1.00) 		0.431
(1.00) 		0.0179
(1.00) 		0.952
(1.00) 		1
(1.00) 		0.436
(1.00) 		0.511
(1.00) 		0.0158
(1.00)
7P LOSS MUTATION ANALYSIS 6 (4%) 146 0.101
(1.00) 		0.937
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.168
(1.00) 		0.736
(1.00) 		0.336
(1.00) 		0.869
(1.00) 		0.425
(1.00)
7Q LOSS MUTATION ANALYSIS 9 (6%) 143 0.893
(1.00) 		0.892
(1.00) 		0.76
(1.00) 		0.728
(1.00) 		0.823
(1.00) 		0.204
(1.00) 		0.116
(1.00) 		0.00535
(1.00) 		0.897
(1.00)
8P LOSS MUTATION ANALYSIS 62 (41%) 90 0.641
(1.00) 		0.298
(1.00) 		0.109
(1.00) 		0.333
(1.00) 		0.0846
(1.00) 		0.00115
(0.906) 		0.336
(1.00) 		0.113
(1.00) 		0.171
(1.00) 		0.582
(1.00)
8Q LOSS MUTATION ANALYSIS 13 (9%) 139 0.787
(1.00) 		0.0536
(1.00) 		0.308
(1.00) 		0.0683
(1.00) 		0.159
(1.00) 		0.0353
(1.00) 		0.508
(1.00) 		0.973
(1.00) 		0.356
(1.00)
9P LOSS MUTATION ANALYSIS 59 (39%) 93 0.383
(1.00) 		0.0176
(1.00) 		0.712
(1.00) 		1
(1.00) 		0.486
(1.00) 		0.904
(1.00) 		0.558
(1.00) 		0.792
(1.00) 		0.564
(1.00) 		0.474
(1.00)
9Q LOSS MUTATION ANALYSIS 56 (37%) 96 0.498
(1.00) 		0.131
(1.00) 		0.836
(1.00) 		0.68
(1.00) 		0.902
(1.00) 		0.738
(1.00) 		0.238
(1.00) 		0.865
(1.00) 		0.0978
(1.00) 		0.903
(1.00)
10P LOSS MUTATION ANALYSIS 30 (20%) 122 0.243
(1.00) 		0.769
(1.00) 		1
(1.00) 		0.619
(1.00) 		0.367
(1.00) 		0.256
(1.00) 		1
(1.00) 		0.0241
(1.00) 		0.231
(1.00) 		0.444
(1.00)
10Q LOSS MUTATION ANALYSIS 50 (33%) 102 0.349
(1.00) 		0.00451
(1.00) 		0.885
(1.00) 		0.537
(1.00) 		0.769
(1.00) 		0.544
(1.00) 		1
(1.00) 		0.0615
(1.00) 		0.88
(1.00) 		0.745
(1.00)
11P LOSS MUTATION ANALYSIS 59 (39%) 93 0.334
(1.00) 		0.0395
(1.00) 		0.0391
(1.00) 		0.612
(1.00) 		0.165
(1.00) 		0.125
(1.00) 		0.845
(1.00) 		0.244
(1.00) 		0.196
(1.00) 		0.168
(1.00)
11Q LOSS MUTATION ANALYSIS 43 (28%) 109 0.148
(1.00) 		0.967
(1.00) 		0.209
(1.00) 		0.243
(1.00) 		0.105
(1.00) 		0.626
(1.00) 		0.833
(1.00) 		0.685
(1.00) 		0.0188
(1.00) 		0.209
(1.00)
12P LOSS MUTATION ANALYSIS 15 (10%) 137 0.906
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.16
(1.00) 		0.834
(1.00) 		0.567
(1.00) 		0.122
(1.00) 		0.667
(1.00) 		0.136
(1.00) 		0.489
(1.00)
12Q LOSS MUTATION ANALYSIS 18 (12%) 134 0.688
(1.00) 		0.837
(1.00) 		0.25
(1.00) 		0.319
(1.00) 		0.00425
(1.00) 		0.372
(1.00) 		0.245
(1.00) 		0.579
(1.00) 		0.141
(1.00) 		0.243
(1.00)
13Q LOSS MUTATION ANALYSIS 34 (22%) 118 0.0805
(1.00) 		0.173
(1.00) 		0.946
(1.00) 		0.587
(1.00) 		0.938
(1.00) 		0.674
(1.00) 		0.0704
(1.00) 		0.0023
(1.00) 		0.52
(1.00) 		0.952
(1.00)
14Q LOSS MUTATION ANALYSIS 41 (27%) 111 0.245
(1.00) 		0.0742
(1.00) 		0.862
(1.00) 		0.93
(1.00) 		0.457
(1.00) 		0.884
(1.00) 		0.135
(1.00) 		0.869
(1.00) 		0.194
(1.00) 		0.551
(1.00)
15Q LOSS MUTATION ANALYSIS 48 (32%) 104 0.27
(1.00) 		0.0879
(1.00) 		0.921
(1.00) 		1
(1.00) 		0.591
(1.00) 		0.115
(1.00) 		0.413
(1.00) 		0.347
(1.00) 		0.977
(1.00) 		0.24
(1.00)
16P LOSS MUTATION ANALYSIS 38 (25%) 114 0.439
(1.00) 		0.14
(1.00) 		0.181
(1.00) 		0.0955
(1.00) 		0.443
(1.00) 		0.543
(1.00) 		1
(1.00) 		0.762
(1.00) 		0.746
(1.00) 		0.139
(1.00)
16Q LOSS MUTATION ANALYSIS 36 (24%) 116 0.801
(1.00) 		0.303
(1.00) 		0.607
(1.00) 		0.621
(1.00) 		0.211
(1.00) 		0.318
(1.00) 		0.369
(1.00) 		0.914
(1.00) 		0.673
(1.00) 		0.557
(1.00)
17P LOSS MUTATION ANALYSIS 64 (42%) 88 0.93
(1.00) 		0.15
(1.00) 		0.154
(1.00) 		0.971
(1.00) 		0.925
(1.00) 		0.863
(1.00) 		0.445
(1.00) 		0.462
(1.00) 		0.289
(1.00) 		0.479
(1.00)
17Q LOSS MUTATION ANALYSIS 19 (12%) 133 0.758
(1.00) 		0.642
(1.00) 		0.678
(1.00) 		0.236
(1.00) 		0.25
(1.00) 		0.0528
(1.00) 		1
(1.00) 		0.934
(1.00) 		0.49
(1.00) 		0.371
(1.00)
18P LOSS MUTATION ANALYSIS 39 (26%) 113 0.261
(1.00) 		0.525
(1.00) 		0.144
(1.00) 		0.161
(1.00) 		0.246
(1.00) 		0.277
(1.00) 		0.513
(1.00) 		0.189
(1.00) 		0.929
(1.00) 		0.834
(1.00)
18Q LOSS MUTATION ANALYSIS 60 (39%) 92 0.78
(1.00) 		0.211
(1.00) 		0.675
(1.00) 		0.29
(1.00) 		0.892
(1.00) 		0.784
(1.00) 		0.172
(1.00) 		0.815
(1.00) 		0.931
(1.00) 		0.626
(1.00)
19P LOSS MUTATION ANALYSIS 35 (23%) 117 0.0623
(1.00) 		0.0698
(1.00) 		0.016
(1.00) 		0.136
(1.00) 		0.000679
(0.536) 		0.0243
(1.00) 		1
(1.00) 		0.0246
(1.00) 		0.233
(1.00) 		0.701
(1.00)
19Q LOSS MUTATION ANALYSIS 19 (12%) 133 0.0291
(1.00) 		0.244
(1.00) 		0.708
(1.00) 		0.0737
(1.00) 		0.0801
(1.00) 		0.184
(1.00) 		0.566
(1.00) 		0.19
(1.00) 		0.926
(1.00) 		0.545
(1.00)
20P LOSS MUTATION ANALYSIS 12 (8%) 140 0.522
(1.00) 		0.695
(1.00) 		0.68
(1.00) 		1
(1.00) 		0.417
(1.00) 		0.547
(1.00) 		0.732
(1.00) 		0.0337
(1.00) 		0.0299
(1.00) 		0.869
(1.00)
20Q LOSS MUTATION ANALYSIS 5 (3%) 147 0.928
(1.00) 		0.997
(1.00) 		0.111
(1.00) 		0.371
(1.00) 		0.0425
(1.00) 		0.704
(1.00) 		0.339
(1.00) 		0.0033
(1.00) 		0.468
(1.00)
21Q LOSS MUTATION ANALYSIS 24 (16%) 128 0.154
(1.00) 		0.111
(1.00) 		0.516
(1.00) 		0.221
(1.00) 		0.0151
(1.00) 		0.925
(1.00) 		0.198
(1.00) 		0.0664
(1.00) 		0.592
(1.00) 		0.864
(1.00)
22Q LOSS MUTATION ANALYSIS 49 (32%) 103 0.32
(1.00) 		0.0601
(1.00) 		0.583
(1.00) 		0.968
(1.00) 		0.4
(1.00) 		0.0458
(1.00) 		0.842
(1.00) 		0.213
(1.00) 		0.139
(1.00) 		0.73
(1.00)
XQ LOSS MUTATION ANALYSIS 32 (21%) 120 0.586
(1.00) 		0.706
(1.00) 		0.0421
(1.00) 		0.0498
(1.00) 		0.332
(1.00) 		0.334
(1.00) 		0.349
(1.00) 		0.93
(1.00) 		0.694
(1.00) 		0.661
(1.00)
'5Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.35e-05 (t-test), Q value = 0.027

Table S1.  Gene #10: '5Q GAIN MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 108 1.7 (3.6)
5Q GAIN MUTATED 16 0.2 (0.4)
5Q GAIN WILD-TYPE 92 2.0 (3.9)

Figure S1.  Get High-res Image Gene #10: '5Q GAIN MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'3Q LOSS MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.69e-06 (t-test), Q value = 0.0021

Table S2.  Gene #46: '3Q LOSS MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 108 1.7 (3.6)
3Q LOSS MUTATED 5 0.0 (0.0)
3Q LOSS WILD-TYPE 103 1.8 (3.7)

Figure S2.  Get High-res Image Gene #46: '3Q LOSS MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

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

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

  • Number of patients = 152

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 10

  • 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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