Correlation between copy number variations of arm-level result and selected clinical features
Testicular Germ Cell Tumors (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1BZ65C3
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1BZ65C3
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 74 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'.

  • 15q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 19p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 19q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 22q gain cnv correlated to 'RADIATION_THERAPY'.

  • 1p loss cnv correlated to 'Time to Death'.

  • 10p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 10q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 14q loss cnv correlated to 'YEARS_TO_BIRTH'.

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

  • 22q loss cnv correlated to 'RADIATION_THERAPY'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 74 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 0.617
(1.00) 		0.00175
(0.118) 		0.00018
(0.0778) 		0.149
(0.89) 		0.105
(0.833) 		0.596
(1.00) 		0.000356
(0.082) 		0.329
(0.958) 		1
(1.00) 		0.751
(1.00)
7q gain 97 (72%) 37 0.956
(1.00) 		0.909
(1.00) 		0.314
(0.958) 		0.0674
(0.723) 		1
(1.00) 		1
(1.00) 		0.417
(0.99) 		0.545
(1.00) 		0.856
(1.00) 		0.00281
(0.16)
10p gain 6 (4%) 128 0.74
(1.00) 		0.000592
(0.082) 		0.949
(1.00) 		0.171
(0.924) 		1
(1.00) 		1
(1.00) 		0.558
(1.00) 		0.337
(0.958) 		1
(1.00)
15q gain 48 (36%) 86 0.988
(1.00) 		0.00021
(0.0778) 		0.182
(0.926) 		0.951
(1.00) 		1
(1.00) 		0.295
(0.958) 		1
(1.00) 		0.329
(0.958) 		1
(1.00) 		0.535
(1.00)
19p gain 33 (25%) 101 0.338
(0.958) 		0.000665
(0.082) 		0.116
(0.833) 		0.395
(0.987) 		0.668
(1.00) 		0.571
(1.00) 		0.242
(0.958) 		0.64
(1.00) 		1
(1.00) 		0.176
(0.926)
19q gain 27 (20%) 107 0.406
(0.987) 		0.00104
(0.0973) 		0.126
(0.863) 		0.28
(0.958) 		1
(1.00) 		0.582
(1.00) 		0.0558
(0.677) 		0.394
(0.987) 		1
(1.00) 		0.0666
(0.723)
22q gain 35 (26%) 99 0.32
(0.958) 		0.0541
(0.677) 		0.394
(0.987) 		0.167
(0.915) 		0.426
(0.99) 		0.573
(1.00) 		0.00118
(0.0973) 		0.864
(1.00) 		0.715
(1.00) 		1
(1.00)
1p loss 17 (13%) 117 0.0037
(0.195) 		0.728
(1.00) 		0.896
(1.00) 		0.359
(0.979) 		0.671
(1.00) 		1
(1.00) 		1
(1.00) 		0.0488
(0.677) 		0.227
(0.958) 		1
(1.00)
10p loss 68 (51%) 66 0.457
(1.00) 		0.00109
(0.0973) 		0.0718
(0.728) 		0.356
(0.979) 		0.0575
(0.686) 		0.619
(1.00) 		0.0249
(0.624) 		0.0766
(0.736) 		0.0866
(0.789) 		1
(1.00)
10q loss 63 (47%) 71 0.291
(0.958) 		0.00254
(0.157) 		0.0466
(0.677) 		0.39
(0.987) 		0.0303
(0.624) 		0.334
(0.958) 		0.0234
(0.624) 		0.0294
(0.624) 		0.7
(1.00) 		0.0331
(0.628)
14q loss 17 (13%) 117 0.598
(1.00) 		0.000628
(0.082) 		0.207
(0.953) 		0.464
(1.00) 		0.0623
(0.709) 		0.374
(0.987) 		0.465
(1.00) 		0.942
(1.00) 		0.769
(1.00) 		0.627
(1.00)
22q loss 38 (28%) 96 0.715
(1.00) 		0.489
(1.00) 		0.0297
(0.624) 		0.062
(0.709) 		0.509
(1.00) 		0.307
(0.958) 		0.00165
(0.118) 		0.0441
(0.677) 		0.226
(0.958) 		0.736
(1.00)
1p gain 32 (24%) 102 0.836
(1.00) 		0.116
(0.833) 		0.383
(0.987) 		0.0553
(0.677) 		0.187
(0.926) 		1
(1.00) 		0.159
(0.907) 		0.514
(1.00) 		0.716
(1.00) 		0.495
(1.00)
1q gain 55 (41%) 79 0.777
(1.00) 		0.333
(0.958) 		0.267
(0.958) 		0.0251
(0.624) 		0.362
(0.979) 		0.634
(1.00) 		0.617
(1.00) 		0.416
(0.99) 		0.52
(1.00) 		0.0278
(0.624)
2p gain 39 (29%) 95 0.884
(1.00) 		0.825
(1.00) 		0.984
(1.00) 		0.449
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.792
(1.00) 		0.0592
(0.696) 		0.861
(1.00) 		1
(1.00)
2q gain 38 (28%) 96 0.695
(1.00) 		0.228
(0.958) 		0.993
(1.00) 		0.421
(0.99) 		0.735
(1.00) 		1
(1.00) 		0.408
(0.987) 		0.393
(0.987) 		0.856
(1.00) 		0.512
(1.00)
3p gain 23 (17%) 111 0.456
(1.00) 		0.285
(0.958) 		0.924
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.131
(0.863) 		0.194
(0.926) 		0.379
(0.987) 		0.64
(1.00) 		0.429
(0.99)
3q gain 32 (24%) 102 0.946
(1.00) 		0.915
(1.00) 		0.487
(1.00) 		0.0383
(0.677) 		0.481
(1.00) 		0.221
(0.958) 		0.56
(1.00) 		0.469
(1.00) 		0.839
(1.00) 		1
(1.00)
4p gain 3 (2%) 131 0.814
(1.00) 		0.609
(1.00) 		0.857
(1.00) 		0.365
(0.979) 		1
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.216
(0.958) 		1
(1.00)
5p gain 6 (4%) 128 0.709
(1.00) 		0.0197
(0.609) 		0.435
(0.995) 		0.412
(0.987) 		0.533
(1.00) 		1
(1.00) 		0.591
(1.00) 		0.016
(0.539) 		1
(1.00) 		0.467
(1.00)
5q gain 3 (2%) 131 0.818
(1.00) 		0.101
(0.829) 		0.123
(0.853) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.267
(0.958)
6p gain 21 (16%) 113 0.335
(0.958) 		0.353
(0.979) 		0.66
(1.00) 		0.541
(1.00) 		1
(1.00) 		0.526
(1.00) 		0.309
(0.958) 		0.505
(1.00) 		0.463
(1.00) 		0.411
(0.987)
6q gain 17 (13%) 117 0.496
(1.00) 		0.623
(1.00) 		0.259
(0.958) 		0.326
(0.958) 		0.643
(1.00) 		0.465
(1.00) 		0.0747
(0.728) 		0.922
(1.00) 		0.543
(1.00) 		0.37
(0.986)
7p gain 111 (83%) 23 0.745
(1.00) 		1
(1.00) 		0.682
(1.00) 		1
(1.00) 		1
(1.00) 		0.526
(1.00) 		1
(1.00) 		0.703
(1.00) 		0.806
(1.00) 		0.0257
(0.624)
8p gain 102 (76%) 32 0.273
(0.958) 		0.466
(1.00) 		0.695
(1.00) 		0.939
(1.00) 		1
(1.00) 		0.0361
(0.668) 		0.159
(0.907) 		0.306
(0.958) 		0.84
(1.00) 		0.732
(1.00)
8q gain 104 (78%) 30 0.269
(0.958) 		0.23
(0.958) 		0.386
(0.987) 		0.555
(1.00) 		1
(1.00) 		0.0288
(0.624) 		0.0732
(0.728) 		0.203
(0.953) 		0.702
(1.00) 		0.278
(0.958)
9p gain 14 (10%) 120 0.403
(0.987) 		0.546
(1.00) 		0.593
(1.00) 		0.336
(0.958) 		1
(1.00) 		0.692
(1.00) 		0.428
(0.99) 		1
(1.00) 		0.0945
(0.813)
9q gain 15 (11%) 119 0.379
(0.987) 		0.285
(0.958) 		0.23
(0.958) 		0.802
(1.00) 		1
(1.00) 		0.35
(0.978) 		1
(1.00) 		0.692
(1.00) 		0.325
(0.958) 		1
(1.00)
10q gain 8 (6%) 126 0.673
(1.00) 		0.00749
(0.292) 		0.928
(1.00) 		0.202
(0.953) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.627
(1.00) 		1
(1.00) 		0.522
(1.00)
11p gain 9 (7%) 125 0.455
(1.00) 		0.673
(1.00) 		0.325
(0.958) 		0.664
(1.00) 		1
(1.00) 		1
(1.00) 		0.355
(0.979) 		0.784
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 4 (3%) 130 0.512
(1.00) 		0.671
(1.00) 		0.148
(0.89) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0937
(0.813) 		1
(1.00) 		1
(1.00)
12p gain 130 (97%) 4 0.75
(1.00) 		0.969
(1.00) 		0.194
(0.926) 		0.709
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.116
(0.833) 		1
(1.00) 		1
(1.00)
12q gain 91 (68%) 43 0.533
(1.00) 		0.0477
(0.677) 		0.246
(0.958) 		0.554
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.111
(0.833) 		0.864
(1.00) 		0.568
(1.00) 		0.339
(0.958)
14q gain 45 (34%) 89 0.382
(0.987) 		0.0993
(0.828) 		0.173
(0.925) 		0.95
(1.00) 		0.307
(0.958) 		1
(1.00) 		0.113
(0.833) 		0.0859
(0.789) 		1
(1.00) 		0.212
(0.958)
16p gain 13 (10%) 121 0.157
(0.907) 		0.57
(1.00) 		0.672
(1.00) 		0.0874
(0.789) 		0.643
(1.00) 		0.325
(0.958) 		0.69
(1.00) 		0.622
(1.00) 		0.668
(1.00) 		0.292
(0.958)
16q gain 13 (10%) 121 0.182
(0.926) 		0.254
(0.958) 		0.674
(1.00) 		0.165
(0.915) 		0.643
(1.00) 		0.325
(0.958) 		0.69
(1.00) 		0.622
(1.00) 		0.666
(1.00) 		0.292
(0.958)
17p gain 32 (24%) 102 0.457
(1.00) 		0.204
(0.953) 		0.131
(0.863) 		0.165
(0.915) 		0.513
(1.00) 		0.278
(0.958) 		0.0417
(0.677) 		0.189
(0.926) 		0.603
(1.00) 		0.729
(1.00)
17q gain 43 (32%) 91 0.129
(0.863) 		0.334
(0.958) 		0.265
(0.958) 		0.335
(0.958) 		1
(1.00) 		0.596
(1.00) 		0.0328
(0.628) 		0.41
(0.987) 		0.312
(0.958) 		0.749
(1.00)
18p gain 4 (3%) 130 0.805
(1.00) 		0.794
(1.00) 		0.362
(0.979) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.38
(0.987) 		0.131
(0.863) 		1
(1.00)
20p gain 30 (22%) 104 0.922
(1.00) 		0.636
(1.00) 		0.139
(0.865) 		0.00654
(0.288) 		0.426
(0.99) 		0.194
(0.926) 		0.24
(0.958) 		0.325
(0.958) 		0.837
(1.00) 		1
(1.00)
20q gain 33 (25%) 101 0.983
(1.00) 		0.7
(1.00) 		0.0531
(0.677) 		0.0287
(0.624) 		0.712
(1.00) 		0.221
(0.958) 		0.155
(0.907) 		0.256
(0.958) 		0.606
(1.00) 		0.294
(0.958)
21q gain 113 (84%) 21 0.108
(0.833) 		0.0417
(0.677) 		0.464
(1.00) 		0.304
(0.958) 		0.713
(1.00) 		0.486
(1.00) 		1
(1.00) 		0.884
(1.00) 		0.323
(0.958) 		1
(1.00)
xp gain 18 (13%) 116 0.365
(0.979) 		0.158
(0.907) 		0.713
(1.00) 		0.612
(1.00) 		0.185
(0.926) 		0.108
(0.833) 		0.0747
(0.728) 		0.147
(0.89) 		1
(1.00) 		0.688
(1.00)
xq gain 18 (13%) 116 0.365
(0.979) 		0.0926
(0.813) 		0.605
(1.00) 		0.383
(0.987) 		0.0979
(0.828) 		0.486
(1.00) 		0.0747
(0.728) 		0.235
(0.958) 		1
(1.00) 		0.688
(1.00)
1q loss 8 (6%) 126 0.0522
(0.677) 		0.52
(1.00) 		0.902
(1.00) 		0.149
(0.89) 		0.576
(1.00) 		1
(1.00) 		0.335
(0.958) 		0.138
(0.865) 		0.0499
(0.677) 		1
(1.00)
2p loss 5 (4%) 129 0.74
(1.00) 		0.747
(1.00) 		0.262
(0.958) 		0.265
(0.958) 		1
(1.00) 		1
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.407
(0.987)
2q loss 6 (4%) 128 0.689
(1.00) 		0.996
(1.00) 		0.0995
(0.828) 		0.547
(1.00) 		0.119
(0.833) 		1
(1.00) 		0.591
(1.00) 		0.655
(1.00) 		1
(1.00) 		0.467
(1.00)
3p loss 30 (22%) 104 0.832
(1.00) 		0.0502
(0.677) 		0.388
(0.987) 		0.588
(1.00) 		0.712
(1.00) 		0.578
(1.00) 		1
(1.00) 		0.453
(1.00) 		0.165
(0.915) 		0.725
(1.00)
3q loss 22 (16%) 112 0.336
(0.958) 		0.137
(0.865) 		0.572
(1.00) 		0.554
(1.00) 		0.268
(0.958) 		1
(1.00) 		1
(1.00) 		0.254
(0.958) 		0.273
(0.958) 		1
(1.00)
4p loss 84 (63%) 50 0.205
(0.953) 		0.186
(0.926) 		0.337
(0.958) 		0.147
(0.89) 		0.334
(0.958) 		1
(1.00) 		1
(1.00) 		0.326
(0.958) 		0.876
(1.00) 		0.757
(1.00)
4q loss 99 (74%) 35 0.306
(0.958) 		0.193
(0.926) 		0.34
(0.958) 		0.0507
(0.677) 		0.0259
(0.624) 		1
(1.00) 		0.572
(1.00) 		0.411
(0.987) 		0.115
(0.833) 		0.73
(1.00)
5p loss 93 (69%) 41 0.966
(1.00) 		0.75
(1.00) 		0.394
(0.987) 		0.0154
(0.539) 		1
(1.00) 		0.583
(1.00) 		0.179
(0.926) 		0.322
(0.958) 		0.647
(1.00) 		0.752
(1.00)
5q loss 91 (68%) 43 0.981
(1.00) 		0.744
(1.00) 		0.0449
(0.677) 		0.00701
(0.288) 		0.334
(0.958) 		0.596
(1.00) 		0.0328
(0.628) 		0.239
(0.958) 		0.566
(1.00) 		1
(1.00)
6p loss 11 (8%) 123 0.61
(1.00) 		0.0421
(0.677) 		0.871
(1.00) 		0.856
(1.00) 		0.322
(0.958) 		1
(1.00) 		1
(1.00) 		0.316
(0.958) 		0.604
(1.00) 		1
(1.00)
6q loss 14 (10%) 120 0.411
(0.987) 		0.0825
(0.773) 		0.402
(0.987) 		0.691
(1.00) 		1
(1.00) 		0.325
(0.958) 		0.692
(1.00) 		0.823
(1.00) 		0.669
(1.00) 		1
(1.00)
8p loss 10 (7%) 124 0.455
(1.00) 		0.632
(1.00) 		0.0555
(0.677) 		0.573
(1.00) 		0.119
(0.833) 		0.0169
(0.545) 		0.355
(0.979) 		0.108
(0.833) 		0.527
(1.00) 		1
(1.00)
8q loss 4 (3%) 130 0.512
(1.00) 		0.844
(1.00) 		0.0653
(0.723) 		0.0746
(0.728) 		0.0664
(0.723) 		1
(1.00) 		0.216
(0.958) 		1
(1.00)
9p loss 56 (42%) 78 0.791
(1.00) 		0.406
(0.987) 		0.304
(0.958) 		0.59
(1.00) 		1
(1.00) 		0.308
(0.958) 		0.132
(0.863) 		0.896
(1.00) 		0.524
(1.00) 		0.557
(1.00)
9q loss 50 (37%) 84 0.693
(1.00) 		0.65
(1.00) 		0.491
(1.00) 		0.906
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.612
(1.00) 		0.708
(1.00) 		0.768
(1.00) 		0.37
(0.986)
11p loss 89 (66%) 45 0.567
(1.00) 		0.169
(0.917) 		0.955
(1.00) 		0.508
(1.00) 		0.189
(0.926) 		1
(1.00) 		0.114
(0.833) 		0.864
(1.00) 		1
(1.00) 		0.753
(1.00)
11q loss 105 (78%) 29 0.18
(0.926) 		0.587
(1.00) 		0.764
(1.00) 		0.511
(1.00) 		0.0523
(0.677) 		1
(1.00) 		0.0718
(0.728) 		0.107
(0.833) 		0.133
(0.863) 		0.701
(1.00)
13q loss 104 (78%) 30 0.324
(0.958) 		0.31
(0.958) 		0.879
(1.00) 		0.134
(0.863) 		0.26
(0.958) 		1
(1.00) 		0.24
(0.958) 		0.946
(1.00) 		0.379
(0.987) 		1
(1.00)
15q loss 22 (16%) 112 0.694
(1.00) 		0.214
(0.958) 		0.111
(0.833) 		0.722
(1.00) 		0.455
(1.00) 		0.119
(0.833) 		0.0422
(0.677) 		0.711
(1.00) 		0.346
(0.97) 		0.688
(1.00)
16p loss 43 (32%) 91 0.469
(1.00) 		0.981
(1.00) 		0.635
(1.00) 		0.5
(1.00) 		0.721
(1.00) 		0.305
(0.958) 		0.423
(0.99) 		0.429
(0.99) 		0.865
(1.00) 		1
(1.00)
16q loss 46 (34%) 88 0.229
(0.958) 		0.894
(1.00) 		0.683
(1.00) 		0.26
(0.958) 		1
(1.00) 		0.297
(0.958) 		0.794
(1.00) 		0.553
(1.00) 		0.671
(1.00) 		1
(1.00)
17p loss 35 (26%) 99 0.969
(1.00) 		0.166
(0.915) 		0.846
(1.00) 		0.742
(1.00) 		0.693
(1.00) 		0.571
(1.00) 		0.0824
(0.773) 		0.548
(1.00) 		0.246
(0.958) 		0.296
(0.958)
17q loss 15 (11%) 119 0.55
(1.00) 		0.288
(0.958) 		0.58
(1.00) 		0.546
(1.00) 		0.605
(1.00) 		1
(1.00) 		0.0244
(0.624) 		0.858
(1.00) 		0.722
(1.00) 		1
(1.00)
18p loss 104 (78%) 30 0.364
(0.979) 		0.272
(0.958) 		0.859
(1.00) 		0.237
(0.958) 		0.26
(0.958) 		1
(1.00) 		0.771
(1.00) 		0.551
(1.00) 		0.474
(1.00) 		0.732
(1.00)
18q loss 110 (82%) 24 0.401
(0.987) 		0.159
(0.907) 		0.622
(1.00) 		0.0927
(0.813) 		0.432
(0.994) 		0.564
(1.00) 		1
(1.00) 		0.392
(0.987) 		0.642
(1.00) 		1
(1.00)
19p loss 40 (30%) 94 0.566
(1.00) 		0.0124
(0.458) 		0.00575
(0.284) 		0.174
(0.925) 		0.0549
(0.677) 		0.583
(1.00) 		0.00696
(0.288) 		0.561
(1.00) 		1
(1.00) 		1
(1.00)
20p loss 28 (21%) 106 0.863
(1.00) 		0.671
(1.00) 		0.247
(0.958) 		0.544
(1.00) 		0.135
(0.863) 		0.207
(0.953) 		0.245
(0.958) 		0.72
(1.00) 		0.58
(1.00) 		0.725
(1.00)
20q loss 15 (11%) 119 0.78
(1.00) 		0.228
(0.958) 		0.436
(0.995) 		0.243
(0.958) 		0.605
(1.00) 		0.421
(0.99) 		1
(1.00) 		0.488
(1.00) 		1
(1.00) 		0.64
(1.00)
xp loss 23 (17%) 111 0.329
(0.958) 		0.732
(1.00) 		0.211
(0.958) 		0.621
(1.00) 		0.185
(0.926) 		1
(1.00) 		1
(1.00) 		0.272
(0.958) 		0.809
(1.00) 		0.429
(0.99)
xq loss 23 (17%) 111 0.329
(0.958) 		0.922
(1.00) 		0.298
(0.958) 		0.405
(0.987) 		0.18
(0.926) 		0.526
(1.00) 		1
(1.00) 		0.391
(0.987) 		0.806
(1.00) 		0.429
(0.99)
'7q gain' versus 'ETHNICITY'

P value = 0.00281 (Fisher's exact test), Q value = 0.16

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 86
7Q GAIN WILD-TYPE 8 25

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 = 0.082

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'

'15q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00021 (Wilcoxon-test), Q value = 0.078

Table S3.  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 S3.  Get High-res Image Gene #25: '15q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000665 (Wilcoxon-test), Q value = 0.082

Table S4.  Gene #31: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
19P GAIN MUTATED 33 35.9 (8.3)
19P GAIN WILD-TYPE 101 30.7 (9.3)

Figure S4.  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 = 0.097

Table S5.  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 S5.  Get High-res Image Gene #32: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'RADIATION_THERAPY'

P value = 0.00118 (Fisher's exact test), Q value = 0.097

Table S6.  Gene #36: '22q gain' versus Clinical Feature #7: 'RADIATION_THERAPY'

nPatients NO YES
ALL 110 19
22Q GAIN MUTATED 22 11
22Q GAIN WILD-TYPE 88 8

Figure S6.  Get High-res Image Gene #36: '22q gain' versus Clinical Feature #7: 'RADIATION_THERAPY'

'1p loss' versus 'Time to Death'

P value = 0.0037 (logrank test), Q value = 0.2

Table S7.  Gene #39: '1p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 134 4 0.1 - 244.5 (41.5)
1P LOSS MUTATED 17 2 0.6 - 199.2 (34.2)
1P LOSS WILD-TYPE 117 2 0.1 - 244.5 (41.7)

Figure S7.  Get High-res Image Gene #39: '1p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00109 (Wilcoxon-test), Q value = 0.097

Table S8.  Gene #55: '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 #55: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00254 (Wilcoxon-test), Q value = 0.16

Table S9.  Gene #56: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 134 32.0 (9.3)
10Q LOSS MUTATED 63 29.6 (8.8)
10Q LOSS WILD-TYPE 71 34.1 (9.3)

Figure S9.  Get High-res Image Gene #56: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000628 (Wilcoxon-test), Q value = 0.082

Table S10.  Gene #60: '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 #60: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00175 (Wilcoxon-test), Q value = 0.12

Table S11.  Gene #69: '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 S11.  Get High-res Image Gene #69: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00018 (Fisher's exact test), Q value = 0.078

Table S12.  Gene #69: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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

Figure S12.  Get High-res Image Gene #69: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q loss' versus 'RADIATION_THERAPY'

P value = 0.000356 (Fisher's exact test), Q value = 0.082

Table S13.  Gene #69: '19q loss' versus Clinical Feature #7: 'RADIATION_THERAPY'

nPatients NO YES
ALL 110 19
19Q LOSS MUTATED 42 0
19Q LOSS WILD-TYPE 68 19

Figure S13.  Get High-res Image Gene #69: '19q loss' versus Clinical Feature #7: 'RADIATION_THERAPY'

'22q loss' versus 'RADIATION_THERAPY'

P value = 0.00165 (Fisher's exact test), Q value = 0.12

Table S14.  Gene #72: '22q loss' versus Clinical Feature #7: 'RADIATION_THERAPY'

nPatients NO YES
ALL 110 19
22Q LOSS MUTATED 36 0
22Q LOSS WILD-TYPE 74 19

Figure S14.  Get High-res Image Gene #72: '22q 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/19781848/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/TGCT-TP/19775566/TGCT-TP.merged_data.txt

  • Number of patients = 134

  • Number of significantly arm-level cnvs = 74

  • 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)
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