Correlation between copy number variations of arm-level result and selected clinical features
Testicular Germ Cell Tumors (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/C1V12485
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 75 arm-level events and 10 clinical features across 134 patients, 14 significant findings detected with Q value < 0.25.

  • 7q gain cnv correlated to 'ETHNICITY'.

  • 10p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 10q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 15q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 19p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 19q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 20p gain cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 10p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 10q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 14q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 19p loss cnv correlated to 'PATHOLOGIC_STAGE'.

  • 19q loss cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE', and 'RADIATION_THERAPY'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 75 arm-level events and 10 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
PATHOLOGIC
STAGE
PATHOLOGY
T
STAGE
PATHOLOGY
N
STAGE
PATHOLOGY
M
STAGE
RADIATION
THERAPY
KARNOFSKY
PERFORMANCE
SCORE
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 Fisher's exact test Fisher's exact test
19q loss 42 (31%) 92 0.618
(1.00)
0.00175
(0.136)
0.00033
(0.0825)
0.147
(0.909)
0.105
(0.796)
0.596
(1.00)
0.000193
(0.0788)
0.278
(1.00)
1
(1.00)
0.751
(1.00)
7q gain 95 (71%) 39 0.933
(1.00)
0.825
(1.00)
0.462
(1.00)
0.0299
(0.582)
0.738
(1.00)
1
(1.00)
0.795
(1.00)
0.626
(1.00)
1
(1.00)
0.00441
(0.236)
10p gain 6 (4%) 128 0.723
(1.00)
0.000592
(0.0942)
0.948
(1.00)
0.173
(0.973)
1
(1.00)
0.586
(1.00)
0.596
(1.00)
0.339
(1.00)
1
(1.00)
10q gain 10 (7%) 124 0.637
(1.00)
0.00429
(0.236)
0.995
(1.00)
0.573
(1.00)
1
(1.00)
1
(1.00)
0.635
(1.00)
0.638
(1.00)
0.528
(1.00)
1
(1.00)
15q gain 48 (36%) 86 0.995
(1.00)
0.00021
(0.0788)
0.236
(1.00)
0.95
(1.00)
1
(1.00)
0.295
(1.00)
0.808
(1.00)
0.413
(1.00)
1
(1.00)
0.535
(1.00)
19p gain 34 (25%) 100 0.325
(1.00)
0.00146
(0.136)
0.0849
(0.77)
0.316
(1.00)
0.668
(1.00)
0.571
(1.00)
0.169
(0.965)
0.575
(1.00)
1
(1.00)
0.176
(0.973)
19q gain 27 (20%) 107 0.403
(1.00)
0.00104
(0.116)
0.14
(0.886)
0.278
(1.00)
1
(1.00)
0.582
(1.00)
0.0334
(0.611)
0.483
(1.00)
1
(1.00)
0.0666
(0.725)
20p gain 31 (23%) 103 0.365
(1.00)
0.908
(1.00)
0.0939
(0.77)
0.00322
(0.201)
0.426
(1.00)
0.207
(0.978)
0.402
(1.00)
0.55
(1.00)
0.839
(1.00)
1
(1.00)
10p loss 68 (51%) 66 0.464
(1.00)
0.00109
(0.116)
0.11
(0.804)
0.353
(1.00)
0.0575
(0.695)
0.619
(1.00)
0.031
(0.582)
0.0547
(0.686)
0.0888
(0.77)
1
(1.00)
10q loss 62 (46%) 72 0.289
(1.00)
0.00201
(0.137)
0.0719
(0.733)
0.295
(1.00)
0.0303
(0.582)
0.328
(1.00)
0.0304
(0.582)
0.011
(0.436)
0.535
(1.00)
0.0353
(0.63)
14q loss 17 (13%) 117 0.606
(1.00)
0.000628
(0.0942)
0.195
(0.973)
0.467
(1.00)
0.0623
(0.725)
0.374
(1.00)
0.307
(1.00)
0.903
(1.00)
0.77
(1.00)
0.627
(1.00)
19p loss 39 (29%) 95 0.549
(1.00)
0.0192
(0.558)
0.00182
(0.136)
0.1
(0.788)
0.0549
(0.686)
0.583
(1.00)
0.00747
(0.311)
0.491
(1.00)
1
(1.00)
1
(1.00)
1p gain 32 (24%) 102 0.824
(1.00)
0.0543
(0.686)
0.342
(1.00)
0.0563
(0.693)
0.187
(0.973)
1
(1.00)
0.158
(0.939)
0.895
(1.00)
0.717
(1.00)
0.495
(1.00)
1q gain 54 (40%) 80 0.774
(1.00)
0.381
(1.00)
0.429
(1.00)
0.0385
(0.656)
0.344
(1.00)
0.638
(1.00)
0.474
(1.00)
0.251
(1.00)
0.516
(1.00)
0.0269
(0.577)
2p gain 40 (30%) 94 0.865
(1.00)
0.915
(1.00)
0.946
(1.00)
0.455
(1.00)
0.517
(1.00)
1
(1.00)
0.797
(1.00)
0.0869
(0.77)
0.399
(1.00)
1
(1.00)
2q gain 38 (28%) 96 0.697
(1.00)
0.432
(1.00)
0.937
(1.00)
0.525
(1.00)
0.738
(1.00)
1
(1.00)
0.294
(1.00)
0.352
(1.00)
0.385
(1.00)
0.73
(1.00)
3p gain 22 (16%) 112 0.464
(1.00)
0.342
(1.00)
0.909
(1.00)
0.467
(1.00)
1
(1.00)
0.131
(0.869)
0.197
(0.974)
0.422
(1.00)
0.792
(1.00)
0.411
(1.00)
3q gain 31 (23%) 103 0.942
(1.00)
0.994
(1.00)
0.426
(1.00)
0.0466
(0.675)
0.481
(1.00)
0.221
(0.993)
0.781
(1.00)
0.408
(1.00)
0.836
(1.00)
0.725
(1.00)
4p gain 3 (2%) 131 0.818
(1.00)
0.609
(1.00)
0.855
(1.00)
0.368
(1.00)
1
(1.00)
1
(1.00)
0.652
(1.00)
0.216
(0.978)
1
(1.00)
5p gain 6 (4%) 128 0.714
(1.00)
0.0197
(0.558)
0.405
(1.00)
0.411
(1.00)
0.533
(1.00)
1
(1.00)
0.589
(1.00)
0.0144
(0.535)
1
(1.00)
0.467
(1.00)
5q gain 3 (2%) 131 0.821
(1.00)
0.101
(0.788)
0.124
(0.844)
1
(1.00)
1
(1.00)
1
(1.00)
0.267
(1.00)
6p gain 21 (16%) 113 0.341
(1.00)
0.353
(1.00)
0.616
(1.00)
0.546
(1.00)
1
(1.00)
0.526
(1.00)
0.194
(0.973)
0.749
(1.00)
0.461
(1.00)
0.411
(1.00)
6q gain 17 (13%) 117 0.505
(1.00)
0.623
(1.00)
0.264
(1.00)
0.325
(1.00)
0.643
(1.00)
0.465
(1.00)
0.073
(0.733)
0.872
(1.00)
0.545
(1.00)
0.37
(1.00)
7p gain 111 (83%) 23 0.727
(1.00)
1
(1.00)
0.712
(1.00)
1
(1.00)
1
(1.00)
0.526
(1.00)
1
(1.00)
0.476
(1.00)
0.807
(1.00)
0.0257
(0.577)
8p gain 102 (76%) 32 0.26
(1.00)
0.466
(1.00)
0.554
(1.00)
0.939
(1.00)
1
(1.00)
0.0361
(0.63)
0.404
(1.00)
0.37
(1.00)
0.841
(1.00)
0.732
(1.00)
8q gain 104 (78%) 30 0.271
(1.00)
0.23
(1.00)
0.24
(1.00)
0.552
(1.00)
1
(1.00)
0.0288
(0.582)
0.0437
(0.675)
0.173
(0.973)
0.702
(1.00)
0.278
(1.00)
9p gain 14 (10%) 120 0.408
(1.00)
0.546
(1.00)
0.54
(1.00)
0.336
(1.00)
1
(1.00)
0.698
(1.00)
0.402
(1.00)
1
(1.00)
0.0945
(0.77)
9q gain 15 (11%) 119 0.385
(1.00)
0.285
(1.00)
0.199
(0.974)
0.8
(1.00)
1
(1.00)
0.35
(1.00)
1
(1.00)
0.645
(1.00)
0.327
(1.00)
1
(1.00)
11p gain 8 (6%) 126 0.471
(1.00)
0.557
(1.00)
0.18
(0.973)
0.497
(1.00)
0.533
(1.00)
1
(1.00)
0.354
(1.00)
0.821
(1.00)
1
(1.00)
1
(1.00)
11q gain 3 (2%) 131 0.528
(1.00)
0.662
(1.00)
0.411
(1.00)
0.62
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
12p gain 130 (97%) 4 0.754
(1.00)
0.969
(1.00)
0.195
(0.973)
0.709
(1.00)
1
(1.00)
0.504
(1.00)
0.122
(0.844)
1
(1.00)
1
(1.00)
12q gain 91 (68%) 43 0.559
(1.00)
0.0477
(0.675)
0.21
(0.978)
0.554
(1.00)
0.738
(1.00)
1
(1.00)
0.124
(0.844)
0.923
(1.00)
0.569
(1.00)
0.339
(1.00)
14q gain 45 (34%) 89 0.392
(1.00)
0.0993
(0.788)
0.183
(0.973)
0.948
(1.00)
0.307
(1.00)
1
(1.00)
0.206
(0.978)
0.125
(0.844)
1
(1.00)
0.212
(0.978)
16p gain 14 (10%) 120 0.178
(0.973)
0.713
(1.00)
0.759
(1.00)
0.142
(0.886)
0.643
(1.00)
0.35
(1.00)
1
(1.00)
0.906
(1.00)
0.697
(1.00)
0.0945
(0.77)
16q gain 14 (10%) 120 0.202
(0.978)
0.357
(1.00)
0.759
(1.00)
0.212
(0.978)
0.643
(1.00)
0.35
(1.00)
1
(1.00)
0.906
(1.00)
0.695
(1.00)
0.0945
(0.77)
17p gain 32 (24%) 102 0.435
(1.00)
0.204
(0.978)
0.0927
(0.77)
0.166
(0.96)
0.513
(1.00)
0.278
(1.00)
0.025
(0.577)
0.227
(1.00)
0.603
(1.00)
0.729
(1.00)
17q gain 42 (31%) 92 0.118
(0.836)
0.228
(1.00)
0.239
(1.00)
0.393
(1.00)
1
(1.00)
0.592
(1.00)
0.0748
(0.739)
0.373
(1.00)
0.304
(1.00)
0.751
(1.00)
18p gain 4 (3%) 130 0.78
(1.00)
0.794
(1.00)
0.44
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.398
(1.00)
0.13
(0.868)
1
(1.00)
20q gain 34 (25%) 100 0.44
(1.00)
0.967
(1.00)
0.015
(0.535)
0.0186
(0.558)
0.712
(1.00)
0.235
(1.00)
0.277
(1.00)
0.452
(1.00)
0.608
(1.00)
0.291
(1.00)
21q gain 113 (84%) 21 0.109
(0.804)
0.0417
(0.672)
0.498
(1.00)
0.305
(1.00)
0.713
(1.00)
0.486
(1.00)
1
(1.00)
0.936
(1.00)
0.322
(1.00)
1
(1.00)
22q gain 36 (27%) 98 0.311
(1.00)
0.0682
(0.731)
0.333
(1.00)
0.3
(1.00)
0.432
(1.00)
0.573
(1.00)
0.00619
(0.29)
0.483
(1.00)
0.619
(1.00)
1
(1.00)
xp gain 18 (13%) 116 0.371
(1.00)
0.158
(0.939)
0.692
(1.00)
0.609
(1.00)
0.185
(0.973)
0.108
(0.804)
0.073
(0.733)
0.0801
(0.77)
1
(1.00)
0.688
(1.00)
xq gain 18 (13%) 116 0.371
(1.00)
0.0926
(0.77)
0.578
(1.00)
0.384
(1.00)
0.0979
(0.788)
0.486
(1.00)
0.073
(0.733)
0.133
(0.875)
1
(1.00)
0.688
(1.00)
1p loss 19 (14%) 115 0.00522
(0.261)
0.75
(1.00)
0.841
(1.00)
0.692
(1.00)
0.668
(1.00)
1
(1.00)
1
(1.00)
0.0212
(0.567)
0.272
(1.00)
1
(1.00)
1q loss 9 (7%) 125 0.0533
(0.686)
0.673
(1.00)
0.89
(1.00)
0.295
(1.00)
0.322
(1.00)
1
(1.00)
0.635
(1.00)
0.091
(0.77)
0.0634
(0.725)
1
(1.00)
2p loss 4 (3%) 130 0.754
(1.00)
0.395
(1.00)
1
(1.00)
0.19
(0.973)
1
(1.00)
0.504
(1.00)
0.694
(1.00)
1
(1.00)
0.34
(1.00)
2q loss 5 (4%) 129 0.723
(1.00)
0.655
(1.00)
0.403
(1.00)
0.721
(1.00)
1
(1.00)
1
(1.00)
0.937
(1.00)
1
(1.00)
0.407
(1.00)
3p loss 31 (23%) 103 0.815
(1.00)
0.0397
(0.661)
0.19
(0.973)
0.491
(1.00)
0.712
(1.00)
0.578
(1.00)
1
(1.00)
0.291
(1.00)
0.174
(0.973)
1
(1.00)
3q loss 23 (17%) 111 0.318
(1.00)
0.11
(0.804)
0.539
(1.00)
0.617
(1.00)
0.268
(1.00)
1
(1.00)
0.762
(1.00)
0.139
(0.886)
0.292
(1.00)
1
(1.00)
4p loss 86 (64%) 48 0.215
(0.978)
0.0816
(0.77)
0.752
(1.00)
0.103
(0.79)
0.334
(1.00)
1
(1.00)
0.808
(1.00)
0.463
(1.00)
0.87
(1.00)
0.751
(1.00)
4q loss 100 (75%) 34 0.313
(1.00)
0.152
(0.926)
0.346
(1.00)
0.0476
(0.675)
0.0259
(0.577)
1
(1.00)
0.41
(1.00)
0.364
(1.00)
0.103
(0.79)
0.732
(1.00)
5p loss 93 (69%) 41 0.951
(1.00)
0.75
(1.00)
0.453
(1.00)
0.0167
(0.552)
1
(1.00)
0.583
(1.00)
0.119
(0.836)
0.271
(1.00)
0.646
(1.00)
0.752
(1.00)
5q loss 91 (68%) 43 0.997
(1.00)
0.744
(1.00)
0.0548
(0.686)
0.00721
(0.311)
0.334
(1.00)
0.596
(1.00)
0.0201
(0.558)
0.196
(0.973)
0.565
(1.00)
1
(1.00)
6p loss 11 (8%) 123 0.616
(1.00)
0.0421
(0.672)
0.876
(1.00)
0.856
(1.00)
0.322
(1.00)
1
(1.00)
1
(1.00)
0.338
(1.00)
0.6
(1.00)
1
(1.00)
6q loss 14 (10%) 120 0.416
(1.00)
0.0825
(0.77)
0.382
(1.00)
0.693
(1.00)
1
(1.00)
0.325
(1.00)
0.698
(1.00)
0.866
(1.00)
0.667
(1.00)
1
(1.00)
7q loss 3 (2%) 131 0.777
(1.00)
0.351
(1.00)
0.854
(1.00)
0.369
(1.00)
1
(1.00)
1
(1.00)
0.652
(1.00)
1
(1.00)
0.267
(1.00)
8p loss 10 (7%) 124 0.438
(1.00)
0.632
(1.00)
0.0466
(0.675)
0.576
(1.00)
0.119
(0.836)
0.0169
(0.552)
1
(1.00)
0.236
(1.00)
0.529
(1.00)
1
(1.00)
8q loss 4 (3%) 130 0.514
(1.00)
0.844
(1.00)
0.0664
(0.725)
0.0733
(0.733)
0.0664
(0.725)
1
(1.00)
0.214
(0.978)
1
(1.00)
9p loss 56 (42%) 78 0.809
(1.00)
0.406
(1.00)
0.252
(1.00)
0.589
(1.00)
1
(1.00)
0.308
(1.00)
0.0535
(0.686)
0.734
(1.00)
0.524
(1.00)
0.557
(1.00)
9q loss 50 (37%) 84 0.698
(1.00)
0.65
(1.00)
0.452
(1.00)
0.906
(1.00)
1
(1.00)
0.633
(1.00)
0.625
(1.00)
0.541
(1.00)
0.769
(1.00)
0.37
(1.00)
11p loss 90 (67%) 44 0.595
(1.00)
0.189
(0.973)
0.958
(1.00)
0.562
(1.00)
0.307
(1.00)
1
(1.00)
0.206
(0.978)
0.77
(1.00)
1
(1.00)
1
(1.00)
11q loss 106 (79%) 28 0.191
(0.973)
0.372
(1.00)
0.852
(1.00)
0.581
(1.00)
0.0523
(0.686)
0.582
(1.00)
0.0454
(0.675)
0.0912
(0.77)
0.0852
(0.77)
0.696
(1.00)
13q loss 104 (78%) 30 0.336
(1.00)
0.31
(1.00)
0.885
(1.00)
0.137
(0.883)
0.26
(1.00)
1
(1.00)
0.158
(0.939)
0.805
(1.00)
0.377
(1.00)
1
(1.00)
15q loss 22 (16%) 112 0.71
(1.00)
0.214
(0.978)
0.0667
(0.725)
0.722
(1.00)
0.455
(1.00)
0.119
(0.836)
0.0237
(0.577)
0.652
(1.00)
0.346
(1.00)
0.688
(1.00)
16p loss 43 (32%) 91 0.44
(1.00)
0.981
(1.00)
0.561
(1.00)
0.501
(1.00)
0.721
(1.00)
0.305
(1.00)
0.804
(1.00)
0.476
(1.00)
0.863
(1.00)
1
(1.00)
16q loss 46 (34%) 88 0.212
(0.978)
0.894
(1.00)
0.622
(1.00)
0.261
(1.00)
1
(1.00)
0.297
(1.00)
0.452
(1.00)
0.592
(1.00)
0.672
(1.00)
1
(1.00)
17p loss 35 (26%) 99 0.989
(1.00)
0.166
(0.96)
0.83
(1.00)
0.742
(1.00)
0.693
(1.00)
0.571
(1.00)
0.0263
(0.577)
0.637
(1.00)
0.25
(1.00)
0.296
(1.00)
17q loss 17 (13%) 117 0.51
(1.00)
0.141
(0.886)
0.686
(1.00)
0.463
(1.00)
0.643
(1.00)
1
(1.00)
0.0221
(0.572)
0.855
(1.00)
0.768
(1.00)
1
(1.00)
18p loss 106 (79%) 28 0.373
(1.00)
0.346
(1.00)
0.785
(1.00)
0.229
(1.00)
0.26
(1.00)
1
(1.00)
1
(1.00)
0.643
(1.00)
0.674
(1.00)
1
(1.00)
18q loss 110 (82%) 24 0.411
(1.00)
0.159
(0.939)
0.625
(1.00)
0.0929
(0.77)
0.432
(1.00)
0.564
(1.00)
0.764
(1.00)
0.349
(1.00)
0.644
(1.00)
1
(1.00)
20p loss 27 (20%) 107 0.291
(1.00)
0.951
(1.00)
0.309
(1.00)
0.701
(1.00)
0.135
(0.882)
0.194
(0.973)
0.243
(1.00)
0.836
(1.00)
0.572
(1.00)
0.716
(1.00)
20q loss 14 (10%) 120 0.424
(1.00)
0.449
(1.00)
0.458
(1.00)
0.334
(1.00)
0.605
(1.00)
0.398
(1.00)
1
(1.00)
0.662
(1.00)
1
(1.00)
0.627
(1.00)
22q loss 36 (27%) 98 0.728
(1.00)
0.769
(1.00)
0.15
(0.922)
0.165
(0.96)
0.738
(1.00)
0.293
(1.00)
0.062
(0.725)
0.275
(1.00)
0.456
(1.00)
0.732
(1.00)
xp loss 23 (17%) 111 0.329
(1.00)
0.732
(1.00)
0.375
(1.00)
0.618
(1.00)
0.185
(0.973)
1
(1.00)
1
(1.00)
0.308
(1.00)
0.808
(1.00)
0.429
(1.00)
xq loss 23 (17%) 111 0.329
(1.00)
0.922
(1.00)
0.5
(1.00)
0.405
(1.00)
0.18
(0.973)
0.526
(1.00)
1
(1.00)
0.434
(1.00)
0.808
(1.00)
0.429
(1.00)
'7q gain' versus 'ETHNICITY'

P value = 0.00441 (Fisher's exact test), Q value = 0.24

Table S1.  Gene #13: '7q gain' versus Clinical Feature #10: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 12 111
7Q GAIN MUTATED 4 84
7Q GAIN WILD-TYPE 8 27

Figure S1.  Get High-res Image Gene #13: '7q gain' versus Clinical Feature #10: 'ETHNICITY'

'10p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000592 (Wilcoxon-test), Q value = 0.094

Table S2.  Gene #18: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
10P GAIN MUTATED 6 48.3 (10.7)
10P GAIN WILD-TYPE 128 31.2 (8.5)

Figure S2.  Get High-res Image Gene #18: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00429 (Wilcoxon-test), Q value = 0.24

Table S3.  Gene #19: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
10Q GAIN MUTATED 10 41.6 (12.2)
10Q GAIN WILD-TYPE 124 31.2 (8.6)

Figure S3.  Get High-res Image Gene #19: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00021 (Wilcoxon-test), Q value = 0.079

Table S4.  Gene #25: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
15Q GAIN MUTATED 48 35.9 (10.1)
15Q GAIN WILD-TYPE 86 29.8 (8.1)

Figure S4.  Get High-res Image Gene #25: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00146 (Wilcoxon-test), Q value = 0.14

Table S5.  Gene #31: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
19P GAIN MUTATED 34 35.6 (8.4)
19P GAIN WILD-TYPE 100 30.8 (9.3)

Figure S5.  Get High-res Image Gene #31: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00104 (Wilcoxon-test), Q value = 0.12

Table S6.  Gene #32: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
19Q GAIN MUTATED 27 36.3 (8.3)
19Q GAIN WILD-TYPE 107 30.9 (9.3)

Figure S6.  Get High-res Image Gene #32: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00322 (Fisher's exact test), Q value = 0.2

Table S7.  Gene #33: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3
ALL 76 51 6
20P GAIN MUTATED 10 18 3
20P GAIN WILD-TYPE 66 33 3

Figure S7.  Get High-res Image Gene #33: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00109 (Wilcoxon-test), Q value = 0.12

Table S8.  Gene #56: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
10P LOSS MUTATED 68 29.6 (8.6)
10P LOSS WILD-TYPE 66 34.4 (9.4)

Figure S8.  Get High-res Image Gene #56: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00201 (Wilcoxon-test), Q value = 0.14

Table S9.  Gene #57: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
10Q LOSS MUTATED 62 29.6 (8.9)
10Q LOSS WILD-TYPE 72 34.1 (9.2)

Figure S9.  Get High-res Image Gene #57: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000628 (Wilcoxon-test), Q value = 0.094

Table S10.  Gene #61: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
14Q LOSS MUTATED 17 25.4 (5.7)
14Q LOSS WILD-TYPE 117 32.9 (9.4)

Figure S10.  Get High-res Image Gene #61: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00182 (Fisher's exact test), Q value = 0.14

Table S11.  Gene #69: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
ALL 46 18 26 11 4 6 1 1 2 1 6 5
19P LOSS MUTATED 15 2 2 3 3 4 0 0 0 0 4 3
19P LOSS WILD-TYPE 31 16 24 8 1 2 1 1 2 1 2 2

Figure S11.  Get High-res Image Gene #69: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00175 (Wilcoxon-test), Q value = 0.14

Table S12.  Gene #70: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
19Q LOSS MUTATED 42 29.0 (10.1)
19Q LOSS WILD-TYPE 92 33.4 (8.6)

Figure S12.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00033 (Fisher's exact test), Q value = 0.082

Table S13.  Gene #70: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients IS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
ALL 46 18 26 11 4 6 1 1 2 1 6 5
19Q LOSS MUTATED 16 2 2 3 4 4 0 0 1 0 4 3
19Q LOSS WILD-TYPE 30 16 24 8 0 2 1 1 1 1 2 2

Figure S13.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q loss' versus 'RADIATION_THERAPY'

P value = 0.000193 (Fisher's exact test), Q value = 0.079

Table S14.  Gene #70: '19q loss' versus Clinical Feature #7: 'RADIATION_THERAPY'

nPatients NO YES
ALL 111 21
19Q LOSS MUTATED 42 0
19Q LOSS WILD-TYPE 69 21

Figure S14.  Get High-res Image Gene #70: '19q loss' versus Clinical Feature #7: 'RADIATION_THERAPY'

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/TGCT-TP/22533661/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/TGCT-TP/22507091/TGCT-TP.merged_data.txt

  • Number of patients = 134

  • Number of significantly arm-level cnvs = 75

  • 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

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)