Correlation between copy number variations of arm-level result and selected clinical features
Bladder Urothelial Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1BP0165
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/C1BP0165
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 183 patients, 6 significant findings detected with Q value < 0.25.

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

  • 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 '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 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 6 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 24 (13%) 159 0.738
(1.00) 		0.937
(1.00) 		0.186
(1.00) 		0.705
(1.00) 		0.196
(1.00) 		0.835
(1.00) 		0.449
(1.00) 		0.444
(1.00) 		0.937
(1.00) 		0.000218
(0.19) 		0.2
(1.00)
9q gain 25 (14%) 158 0.166
(1.00) 		0.169
(1.00) 		0.0487
(1.00) 		0.408
(1.00) 		0.337
(1.00) 		0.0308
(1.00) 		0.457
(1.00) 		0.904
(1.00) 		0.0463
(1.00) 		0.558
(1.00) 		0.000247
(0.214)
15q gain 18 (10%) 165 0.666
(1.00) 		0.387
(1.00) 		0.823
(1.00) 		0.226
(1.00) 		0.0903
(1.00) 		0.0756
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.621
(1.00) 		0.753
(1.00) 		0.000256
(0.222)
19p gain 31 (17%) 152 0.815
(1.00) 		0.535
(1.00) 		0.709
(1.00) 		0.261
(1.00) 		0.0745
(1.00) 		0.634
(1.00) 		0.501
(1.00) 		0.685
(1.00) 		0.898
(1.00) 		0.569
(1.00) 		0.000256
(0.222)
xq gain 20 (11%) 163 0.393
(1.00) 		0.923
(1.00) 		0.455
(1.00) 		0.279
(1.00) 		0.832
(1.00) 		1
(1.00) 		1
(1.00) 		0.319
(1.00) 		0.364
(1.00) 		0.0163
(1.00) 		0.000237
(0.206)
3q loss 8 (4%) 175 0.838
(1.00) 		0.592
(1.00) 		0.582
(1.00) 		1
(1.00) 		0.576
(1.00) 		0.207
(1.00) 		0.417
(1.00) 		0.416
(1.00) 		2.54e-07
(0.000221) 		0.385
(1.00)
1p gain 45 (25%) 138 0.0411
(1.00) 		0.673
(1.00) 		0.64
(1.00) 		1
(1.00) 		0.0583
(1.00) 		1
(1.00) 		0.432
(1.00) 		0.418
(1.00) 		0.0924
(1.00) 		0.54
(1.00) 		0.417
(1.00)
1q gain 58 (32%) 125 0.0772
(1.00) 		0.638
(1.00) 		0.0591
(1.00) 		0.767
(1.00) 		0.042
(1.00) 		0.0777
(1.00) 		0.714
(1.00) 		0.776
(1.00) 		0.0592
(1.00) 		0.156
(1.00) 		0.119
(1.00)
2p gain 54 (30%) 129 0.648
(1.00) 		0.0161
(1.00) 		0.0298
(1.00) 		0.869
(1.00) 		0.00367
(1.00) 		0.777
(1.00) 		0.000709
(0.613) 		0.917
(1.00) 		0.101
(1.00) 		0.0816
(1.00) 		0.659
(1.00)
2q gain 25 (14%) 158 0.601
(1.00) 		0.596
(1.00) 		0.922
(1.00) 		0.421
(1.00) 		0.794
(1.00) 		0.176
(1.00) 		0.215
(1.00) 		0.0937
(1.00) 		0.924
(1.00) 		0.308
(1.00) 		0.303
(1.00)
3p gain 61 (33%) 122 0.629
(1.00) 		0.0574
(1.00) 		0.0218
(1.00) 		0.184
(1.00) 		0.0595
(1.00) 		1
(1.00) 		0.719
(1.00) 		0.00349
(1.00) 		0.234
(1.00) 		0.0723
(1.00) 		0.822
(1.00)
3q gain 80 (44%) 103 0.585
(1.00) 		0.188
(1.00) 		0.0333
(1.00) 		0.404
(1.00) 		0.00371
(1.00) 		0.555
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.491
(1.00) 		0.0314
(1.00) 		0.551
(1.00)
4p gain 17 (9%) 166 0.175
(1.00) 		0.865
(1.00) 		0.553
(1.00) 		0.12
(1.00) 		0.09
(1.00) 		0.334
(1.00) 		0.378
(1.00) 		0.535
(1.00) 		0.834
(1.00) 		0.571
(1.00) 		0.491
(1.00)
4q gain 11 (6%) 172 0.178
(1.00) 		0.818
(1.00) 		0.636
(1.00) 		0.493
(1.00) 		0.86
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.821
(1.00) 		0.294
(1.00) 		0.228
(1.00) 		0.83
(1.00)
5p gain 73 (40%) 110 0.729
(1.00) 		0.432
(1.00) 		0.523
(1.00) 		0.613
(1.00) 		0.534
(1.00) 		0.0236
(1.00) 		0.488
(1.00) 		0.549
(1.00) 		0.563
(1.00) 		0.177
(1.00) 		0.0412
(1.00)
6p gain 25 (14%) 158 0.854
(1.00) 		0.834
(1.00) 		0.873
(1.00) 		0.531
(1.00) 		0.473
(1.00) 		0.275
(1.00) 		0.626
(1.00) 		0.724
(1.00) 		0.111
(1.00) 		0.951
(1.00) 		0.976
(1.00)
6q gain 16 (9%) 167 0.327
(1.00) 		0.44
(1.00) 		0.801
(1.00) 		0.815
(1.00) 		0.066
(1.00) 		0.426
(1.00) 		0.365
(1.00) 		0.567
(1.00) 		0.0931
(1.00) 		0.772
(1.00) 		0.61
(1.00)
7p gain 75 (41%) 108 0.537
(1.00) 		0.0429
(1.00) 		0.141
(1.00) 		0.562
(1.00) 		0.106
(1.00) 		0.915
(1.00) 		0.731
(1.00) 		0.534
(1.00) 		0.933
(1.00) 		0.357
(1.00) 		0.059
(1.00)
7q gain 70 (38%) 113 0.949
(1.00) 		0.134
(1.00) 		0.417
(1.00) 		0.693
(1.00) 		0.00329
(1.00) 		0.206
(1.00) 		0.293
(1.00) 		0.287
(1.00) 		0.469
(1.00) 		0.261
(1.00) 		0.167
(1.00)
8p gain 35 (19%) 148 0.295
(1.00) 		0.459
(1.00) 		0.23
(1.00) 		0.501
(1.00) 		0.961
(1.00) 		0.714
(1.00) 		0.52
(1.00) 		0.888
(1.00) 		0.968
(1.00) 		0.116
(1.00) 		0.771
(1.00)
8q gain 84 (46%) 99 0.563
(1.00) 		0.46
(1.00) 		0.386
(1.00) 		0.849
(1.00) 		0.867
(1.00) 		0.919
(1.00) 		0.498
(1.00) 		0.499
(1.00) 		0.77
(1.00) 		0.159
(1.00) 		0.449
(1.00)
9p gain 31 (17%) 152 0.0106
(1.00) 		0.578
(1.00) 		0.561
(1.00) 		0.584
(1.00) 		0.232
(1.00) 		0.281
(1.00) 		0.501
(1.00) 		0.562
(1.00) 		0.0259
(1.00) 		0.596
(1.00) 		0.619
(1.00)
10p gain 48 (26%) 135 0.589
(1.00) 		0.839
(1.00) 		0.464
(1.00) 		0.942
(1.00) 		0.188
(1.00) 		0.374
(1.00) 		0.847
(1.00) 		0.4
(1.00) 		0.446
(1.00) 		0.523
(1.00) 		0.131
(1.00)
10q gain 15 (8%) 168 0.754
(1.00) 		0.217
(1.00) 		0.394
(1.00) 		0.498
(1.00) 		0.175
(1.00) 		0.864
(1.00) 		0.764
(1.00) 		0.904
(1.00) 		0.498
(1.00) 		0.318
(1.00) 		0.777
(1.00)
11p gain 18 (10%) 165 0.154
(1.00) 		0.966
(1.00) 		0.888
(1.00) 		0.718
(1.00) 		0.273
(1.00) 		0.678
(1.00) 		0.25
(1.00) 		0.662
(1.00) 		0.881
(1.00) 		0.375
(1.00) 		0.376
(1.00)
11q gain 24 (13%) 159 0.828
(1.00) 		0.115
(1.00) 		0.799
(1.00) 		0.748
(1.00) 		0.375
(1.00) 		0.51
(1.00) 		0.205
(1.00) 		0.949
(1.00) 		0.559
(1.00) 		0.581
(1.00) 		0.139
(1.00)
12p gain 56 (31%) 127 0.419
(1.00) 		0.0594
(1.00) 		0.438
(1.00) 		0.526
(1.00) 		0.567
(1.00) 		0.43
(1.00) 		0.467
(1.00) 		0.863
(1.00) 		0.147
(1.00) 		0.34
(1.00) 		0.443
(1.00)
12q gain 43 (23%) 140 0.483
(1.00) 		0.994
(1.00) 		0.284
(1.00) 		0.825
(1.00) 		0.585
(1.00) 		0.333
(1.00) 		1
(1.00) 		0.89
(1.00) 		0.039
(1.00) 		0.366
(1.00) 		0.577
(1.00)
13q gain 45 (25%) 138 0.839
(1.00) 		0.107
(1.00) 		0.109
(1.00) 		0.968
(1.00) 		0.011
(1.00) 		0.0264
(1.00) 		0.844
(1.00) 		0.354
(1.00) 		0.82
(1.00) 		0.441
(1.00) 		0.852
(1.00)
14q gain 33 (18%) 150 0.285
(1.00) 		0.314
(1.00) 		0.431
(1.00) 		0.37
(1.00) 		0.302
(1.00) 		0.112
(1.00) 		0.269
(1.00) 		0.745
(1.00) 		0.843
(1.00) 		0.202
(1.00) 		0.976
(1.00)
16p gain 29 (16%) 154 0.147
(1.00) 		0.397
(1.00) 		0.19
(1.00) 		0.0268
(1.00) 		0.429
(1.00) 		0.0363
(1.00) 		0.485
(1.00) 		0.822
(1.00) 		0.607
(1.00) 		0.725
(1.00) 		0.429
(1.00)
16q gain 36 (20%) 147 0.558
(1.00) 		0.952
(1.00) 		0.386
(1.00) 		0.0892
(1.00) 		0.129
(1.00) 		0.0858
(1.00) 		0.206
(1.00) 		0.907
(1.00) 		0.807
(1.00) 		0.33
(1.00) 		0.471
(1.00)
17p gain 27 (15%) 156 0.00144
(1.00) 		0.0565
(1.00) 		0.0283
(1.00) 		0.241
(1.00) 		0.437
(1.00) 		0.448
(1.00) 		0.631
(1.00) 		0.707
(1.00) 		0.526
(1.00) 		0.0263
(1.00) 		0.671
(1.00)
17q gain 65 (36%) 118 0.0866
(1.00) 		0.455
(1.00) 		0.0568
(1.00) 		0.251
(1.00) 		0.0184
(1.00) 		0.663
(1.00) 		0.376
(1.00) 		0.0758
(1.00) 		0.109
(1.00) 		0.593
(1.00) 		0.738
(1.00)
18p gain 54 (30%) 129 0.724
(1.00) 		0.823
(1.00) 		0.8
(1.00) 		0.198
(1.00) 		0.773
(1.00) 		0.184
(1.00) 		0.455
(1.00) 		0.0115
(1.00) 		0.591
(1.00) 		0.961
(1.00) 		0.471
(1.00)
18q gain 27 (15%) 156 0.14
(1.00) 		0.919
(1.00) 		0.803
(1.00) 		0.141
(1.00) 		0.93
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.00224
(1.00) 		0.517
(1.00) 		0.734
(1.00) 		0.429
(1.00)
19q gain 58 (32%) 125 0.549
(1.00) 		0.906
(1.00) 		0.0947
(1.00) 		0.0942
(1.00) 		0.131
(1.00) 		1
(1.00) 		0.589
(1.00) 		0.29
(1.00) 		0.25
(1.00) 		0.187
(1.00) 		0.539
(1.00)
20p gain 93 (51%) 90 0.0394
(1.00) 		0.275
(1.00) 		0.813
(1.00) 		0.977
(1.00) 		0.461
(1.00) 		0.532
(1.00) 		1
(1.00) 		0.401
(1.00) 		0.37
(1.00) 		0.155
(1.00) 		0.181
(1.00)
20q gain 106 (58%) 77 0.473
(1.00) 		0.804
(1.00) 		0.923
(1.00) 		0.355
(1.00) 		0.461
(1.00) 		0.84
(1.00) 		0.23
(1.00) 		0.463
(1.00) 		0.349
(1.00) 		0.965
(1.00) 		0.474
(1.00)
21q gain 59 (32%) 124 0.786
(1.00) 		0.0377
(1.00) 		0.292
(1.00) 		0.874
(1.00) 		0.0692
(1.00) 		0.713
(1.00) 		0.586
(1.00) 		0.75
(1.00) 		0.353
(1.00) 		0.53
(1.00) 		0.311
(1.00)
22q gain 29 (16%) 154 0.393
(1.00) 		0.948
(1.00) 		0.455
(1.00) 		0.776
(1.00) 		0.446
(1.00) 		0.361
(1.00) 		0.646
(1.00) 		0.322
(1.00) 		0.802
(1.00) 		0.203
(1.00) 		0.279
(1.00)
1p loss 11 (6%) 172 0.605
(1.00) 		0.281
(1.00) 		0.677
(1.00) 		0.327
(1.00) 		0.392
(1.00) 		0.295
(1.00) 		0.733
(1.00) 		0.0314
(1.00) 		0.927
(1.00) 		0.111
(1.00)
1q loss 15 (8%) 168 0.77
(1.00) 		0.893
(1.00) 		0.865
(1.00) 		0.324
(1.00) 		0.929
(1.00) 		0.736
(1.00) 		0.534
(1.00) 		0.303
(1.00) 		0.0121
(1.00) 		0.644
(1.00) 		0.267
(1.00)
2p loss 19 (10%) 164 0.939
(1.00) 		0.873
(1.00) 		0.492
(1.00) 		0.11
(1.00) 		0.182
(1.00) 		0.488
(1.00) 		0.0471
(1.00) 		0.897
(1.00) 		0.341
(1.00) 		0.149
(1.00) 		0.283
(1.00)
2q loss 41 (22%) 142 0.296
(1.00) 		0.605
(1.00) 		0.208
(1.00) 		0.967
(1.00) 		0.0345
(1.00) 		1
(1.00) 		0.839
(1.00) 		0.457
(1.00) 		0.861
(1.00) 		0.905
(1.00) 		0.669
(1.00)
3p loss 24 (13%) 159 0.735
(1.00) 		0.13
(1.00) 		0.768
(1.00) 		0.619
(1.00) 		0.513
(1.00) 		0.567
(1.00) 		0.138
(1.00) 		0.415
(1.00) 		0.411
(1.00) 		0.445
(1.00) 		0.719
(1.00)
4p loss 61 (33%) 122 0.157
(1.00) 		0.147
(1.00) 		0.505
(1.00) 		0.696
(1.00) 		0.306
(1.00) 		0.536
(1.00) 		0.857
(1.00) 		0.948
(1.00) 		0.231
(1.00) 		0.413
(1.00) 		0.525
(1.00)
4q loss 62 (34%) 121 0.515
(1.00) 		0.0684
(1.00) 		0.441
(1.00) 		0.322
(1.00) 		0.489
(1.00) 		0.451
(1.00) 		0.719
(1.00) 		0.742
(1.00) 		0.226
(1.00) 		0.529
(1.00) 		0.159
(1.00)
5p loss 29 (16%) 154 0.259
(1.00) 		0.0799
(1.00) 		0.419
(1.00) 		0.957
(1.00) 		0.309
(1.00) 		0.292
(1.00) 		0.244
(1.00) 		0.0829
(1.00) 		0.633
(1.00) 		0.4
(1.00) 		0.283
(1.00)
5q loss 66 (36%) 117 0.793
(1.00) 		0.223
(1.00) 		0.0414
(1.00) 		0.682
(1.00) 		0.02
(1.00) 		0.00574
(1.00) 		1
(1.00) 		0.0327
(1.00) 		0.728
(1.00) 		0.0704
(1.00) 		0.311
(1.00)
6p loss 45 (25%) 138 0.882
(1.00) 		0.562
(1.00) 		0.0588
(1.00) 		0.0299
(1.00) 		0.0536
(1.00) 		0.646
(1.00) 		0.554
(1.00) 		0.681
(1.00) 		0.976
(1.00) 		0.203
(1.00) 		0.279
(1.00)
6q loss 67 (37%) 116 0.603
(1.00) 		0.547
(1.00) 		0.0939
(1.00) 		0.561
(1.00) 		0.0459
(1.00) 		0.486
(1.00) 		0.482
(1.00) 		0.41
(1.00) 		0.723
(1.00) 		0.0424
(1.00) 		0.854
(1.00)
7p loss 7 (4%) 176 0.0237
(1.00) 		0.803
(1.00) 		0.812
(1.00) 		1
(1.00) 		0.26
(1.00) 		0.756
(1.00) 		0.682
(1.00) 		0.67
(1.00) 		0.473
(1.00) 		0.539
(1.00)
7q loss 9 (5%) 174 0.946
(1.00) 		0.593
(1.00) 		0.852
(1.00) 		0.894
(1.00) 		0.673
(1.00) 		0.625
(1.00) 		0.453
(1.00) 		0.00298
(1.00) 		0.704
(1.00)
8p loss 81 (44%) 102 0.814
(1.00) 		0.226
(1.00) 		0.0558
(1.00) 		0.683
(1.00) 		0.083
(1.00) 		0.000466
(0.404) 		0.732
(1.00) 		0.0383
(1.00) 		0.255
(1.00) 		0.855
(1.00) 		0.241
(1.00)
8q loss 17 (9%) 166 0.736
(1.00) 		0.0166
(1.00) 		0.364
(1.00) 		0.168
(1.00) 		0.362
(1.00) 		0.0767
(1.00) 		0.378
(1.00) 		0.978
(1.00) 		0.439
(1.00) 		0.283
(1.00)
9p loss 75 (41%) 108 0.784
(1.00) 		0.0709
(1.00) 		0.838
(1.00) 		0.888
(1.00) 		0.678
(1.00) 		0.958
(1.00) 		0.387
(1.00) 		0.949
(1.00) 		0.96
(1.00) 		0.488
(1.00) 		0.49
(1.00)
9q loss 70 (38%) 113 0.907
(1.00) 		0.114
(1.00) 		0.618
(1.00) 		0.342
(1.00) 		0.686
(1.00) 		0.838
(1.00) 		0.118
(1.00) 		0.744
(1.00) 		0.324
(1.00) 		0.818
(1.00) 		0.895
(1.00)
10p loss 36 (20%) 147 0.817
(1.00) 		0.868
(1.00) 		0.784
(1.00) 		0.386
(1.00) 		0.536
(1.00) 		0.24
(1.00) 		0.831
(1.00) 		0.0199
(1.00) 		0.252
(1.00) 		0.462
(1.00) 		0.473
(1.00)
10q loss 61 (33%) 122 0.419
(1.00) 		0.0231
(1.00) 		0.964
(1.00) 		0.948
(1.00) 		0.976
(1.00) 		0.467
(1.00) 		1
(1.00) 		0.0134
(1.00) 		0.812
(1.00) 		0.991
(1.00) 		0.608
(1.00)
11p loss 71 (39%) 112 0.586
(1.00) 		0.153
(1.00) 		0.0239
(1.00) 		0.749
(1.00) 		0.0842
(1.00) 		0.17
(1.00) 		0.601
(1.00) 		0.54
(1.00) 		0.694
(1.00) 		0.078
(1.00) 		0.81
(1.00)
11q loss 54 (30%) 129 0.477
(1.00) 		0.441
(1.00) 		0.457
(1.00) 		0.948
(1.00) 		0.166
(1.00) 		0.861
(1.00) 		0.581
(1.00) 		0.419
(1.00) 		0.146
(1.00) 		0.57
(1.00) 		0.263
(1.00)
12p loss 18 (10%) 165 0.325
(1.00) 		0.49
(1.00) 		0.194
(1.00) 		0.573
(1.00) 		0.0617
(1.00) 		0.226
(1.00) 		0.0467
(1.00) 		0.873
(1.00) 		0.0555
(1.00) 		0.277
(1.00) 		0.153
(1.00)
12q loss 21 (11%) 162 0.987
(1.00) 		0.24
(1.00) 		0.0134
(1.00) 		0.375
(1.00) 		0.00106
(0.918) 		0.218
(1.00) 		0.291
(1.00) 		0.993
(1.00) 		0.166
(1.00) 		0.196
(1.00) 		0.517
(1.00)
13q loss 40 (22%) 143 0.139
(1.00) 		0.509
(1.00) 		0.856
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.622
(1.00) 		0.302
(1.00) 		0.0072
(1.00) 		0.668
(1.00) 		0.85
(1.00) 		0.933
(1.00)
14q loss 49 (27%) 134 0.426
(1.00) 		0.156
(1.00) 		0.409
(1.00) 		1
(1.00) 		0.229
(1.00) 		0.947
(1.00) 		0.124
(1.00) 		0.544
(1.00) 		0.118
(1.00) 		0.412
(1.00) 		0.507
(1.00)
15q loss 58 (32%) 125 0.434
(1.00) 		0.347
(1.00) 		0.597
(1.00) 		0.459
(1.00) 		0.727
(1.00) 		0.0693
(1.00) 		0.857
(1.00) 		0.347
(1.00) 		0.233
(1.00) 		0.261
(1.00) 		0.417
(1.00)
16p loss 46 (25%) 137 0.373
(1.00) 		0.482
(1.00) 		0.144
(1.00) 		0.0471
(1.00) 		0.387
(1.00) 		0.0897
(1.00) 		0.847
(1.00) 		0.971
(1.00) 		0.622
(1.00) 		0.189
(1.00) 		0.573
(1.00)
16q loss 45 (25%) 138 0.944
(1.00) 		0.521
(1.00) 		0.386
(1.00) 		0.283
(1.00) 		0.226
(1.00) 		0.0107
(1.00) 		0.695
(1.00) 		0.531
(1.00) 		0.939
(1.00) 		0.442
(1.00) 		0.328
(1.00)
17p loss 78 (43%) 105 0.659
(1.00) 		0.334
(1.00) 		0.15
(1.00) 		0.696
(1.00) 		0.962
(1.00) 		0.841
(1.00) 		0.609
(1.00) 		0.451
(1.00) 		0.635
(1.00) 		0.454
(1.00) 		0.328
(1.00)
17q loss 22 (12%) 161 0.941
(1.00) 		0.319
(1.00) 		0.543
(1.00) 		0.199
(1.00) 		0.23
(1.00) 		0.17
(1.00) 		1
(1.00) 		0.839
(1.00) 		0.191
(1.00) 		0.667
(1.00) 		0.517
(1.00)
18p loss 41 (22%) 142 0.949
(1.00) 		0.945
(1.00) 		0.222
(1.00) 		0.194
(1.00) 		0.17
(1.00) 		0.16
(1.00) 		0.839
(1.00) 		0.103
(1.00) 		0.0965
(1.00) 		0.685
(1.00) 		0.175
(1.00)
18q loss 64 (35%) 119 0.2
(1.00) 		0.443
(1.00) 		0.618
(1.00) 		0.553
(1.00) 		0.727
(1.00) 		0.763
(1.00) 		0.372
(1.00) 		0.494
(1.00) 		0.595
(1.00) 		0.851
(1.00) 		0.822
(1.00)
19p loss 47 (26%) 136 0.0534
(1.00) 		0.312
(1.00) 		0.00536
(1.00) 		0.0471
(1.00) 		0.00687
(1.00) 		0.0267
(1.00) 		0.698
(1.00) 		0.472
(1.00) 		0.69
(1.00) 		0.775
(1.00) 		0.96
(1.00)
19q loss 26 (14%) 157 0.0213
(1.00) 		0.876
(1.00) 		0.757
(1.00) 		0.0498
(1.00) 		0.372
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.314
(1.00) 		0.294
(1.00) 		0.491
(1.00)
20p loss 12 (7%) 171 0.393
(1.00) 		0.904
(1.00) 		1
(1.00) 		1
(1.00) 		0.302
(1.00) 		0.562
(1.00) 		0.733
(1.00) 		0.2
(1.00) 		0.00967
(1.00) 		0.6
(1.00) 		0.385
(1.00)
20q loss 5 (3%) 178 0.854
(1.00) 		0.93
(1.00) 		0.0948
(1.00) 		0.361
(1.00) 		0.0413
(1.00) 		0.461
(1.00) 		0.601
(1.00) 		0.00157
(1.00) 		0.438
(1.00)
21q loss 27 (15%) 156 0.094
(1.00) 		0.0751
(1.00) 		0.608
(1.00) 		0.163
(1.00) 		0.0296
(1.00) 		0.661
(1.00) 		0.477
(1.00) 		0.127
(1.00) 		0.697
(1.00) 		0.766
(1.00) 		0.459
(1.00)
22q loss 66 (36%) 117 0.203
(1.00) 		0.238
(1.00) 		0.0974
(1.00) 		0.297
(1.00) 		0.193
(1.00) 		0.00841
(1.00) 		1
(1.00) 		0.0853
(1.00) 		0.827
(1.00) 		0.711
(1.00) 		0.71
(1.00)
xq loss 34 (19%) 149 0.559
(1.00) 		0.621
(1.00) 		0.451
(1.00) 		0.412
(1.00) 		0.435
(1.00) 		0.458
(1.00) 		0.662
(1.00) 		0.674
(1.00) 		0.473
(1.00) 		0.739
(1.00) 		0.971
(1.00)
'5q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000218 (t-test), Q value = 0.19

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

nPatients Mean (Std.Dev)
ALL 134 1.6 (3.4)
5Q GAIN MUTATED 18 0.3 (0.8)
5Q GAIN WILD-TYPE 116 1.8 (3.6)

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

'9q gain' versus 'GLEASON_SCORE'

P value = 0.000247 (t-test), Q value = 0.21

Table S2.  Gene #18: '9q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 39 6.4 (0.7)
9Q GAIN MUTATED 4 6.0 (0.0)
9Q GAIN WILD-TYPE 35 6.5 (0.7)

Figure S2.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'15q gain' versus 'GLEASON_SCORE'

P value = 0.000256 (t-test), Q value = 0.22

Table S3.  Gene #27: '15q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 39 6.4 (0.7)
15Q GAIN MUTATED 3 6.0 (0.0)
15Q GAIN WILD-TYPE 36 6.5 (0.7)

Figure S3.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'19p gain' versus 'GLEASON_SCORE'

P value = 0.000256 (t-test), Q value = 0.22

Table S4.  Gene #34: '19p gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 39 6.4 (0.7)
19P GAIN MUTATED 3 6.0 (0.0)
19P GAIN WILD-TYPE 36 6.5 (0.7)

Figure S4.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'xq gain' versus 'GLEASON_SCORE'

P value = 0.000237 (t-test), Q value = 0.21

Table S5.  Gene #40: 'xq gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 39 6.4 (0.7)
XQ GAIN MUTATED 5 6.0 (0.0)
XQ GAIN WILD-TYPE 34 6.5 (0.7)

Figure S5.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'3q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.54e-07 (t-test), Q value = 0.00022

Table S6.  Gene #46: '3q loss' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 134 1.6 (3.4)
3Q LOSS MUTATED 5 0.0 (0.0)
3Q LOSS WILD-TYPE 129 1.6 (3.4)

Figure S6.  Get High-res Image Gene #46: '3q loss' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

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

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

  • Number of patients = 183

  • 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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