Correlation between copy number variations of arm-level result and selected clinical features
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 81 arm-level events and 15 clinical features across 184 patients, no significant finding detected with Q value < 0.25.

  • No arm-level cnvs related to clinical features.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 81 arm-level events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		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 Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
1p gain 18 (10%) 166 0.672
(1.00) 		0.184
(0.925) 		0.327
(1.00) 		0.526
(1.00) 		1
(1.00) 		0.111
(0.897) 		0.626
(1.00) 		0.764
(1.00) 		0.0619
(0.897) 		0.219
(0.947) 		0.558
(1.00) 		0.323
(1.00) 		0.757
(1.00) 		1
(1.00) 		0.363
(1.00)
1q gain 50 (27%) 134 0.677
(1.00) 		0.364
(1.00) 		0.0657
(0.897) 		0.376
(1.00) 		0.262
(0.979) 		0.116
(0.897) 		0.0694
(0.897) 		0.84
(1.00) 		0.371
(1.00) 		0.761
(1.00) 		0.732
(1.00) 		0.859
(1.00) 		0.437
(1.00) 		0.392
(1.00) 		0.602
(1.00)
2p gain 14 (8%) 170 0.352
(1.00) 		0.806
(1.00) 		0.459
(1.00) 		0.877
(1.00) 		0.76
(1.00) 		0.417
(1.00) 		0.0924
(0.897) 		0.756
(1.00) 		0.791
(1.00) 		0.773
(1.00) 		0.0666
(0.897) 		0.44
(1.00) 		0.311
(1.00) 		0.777
(1.00) 		1
(1.00)
2q gain 16 (9%) 168 0.196
(0.933) 		0.433
(1.00) 		0.512
(1.00) 		0.896
(1.00) 		1
(1.00) 		0.453
(1.00) 		0.0344
(0.865) 		0.558
(1.00) 		1
(1.00) 		0.359
(1.00) 		0.197
(0.933) 		0.357
(1.00) 		0.635
(1.00) 		0.796
(1.00) 		1
(1.00)
3p gain 10 (5%) 174 0.382
(1.00) 		0.585
(1.00) 		0.312
(1.00) 		0.463
(1.00) 		0.145
(0.916) 		0.339
(1.00) 		0.0239
(0.831) 		0.113
(0.897) 		1
(1.00) 		0.712
(1.00) 		0.421
(1.00) 		1
(1.00) 		1
(1.00)
3q gain 20 (11%) 164 0.00046
(0.28) 		0.933
(1.00) 		0.493
(1.00) 		1
(1.00) 		0.788
(1.00) 		0.0931
(0.897) 		0.0611
(0.897) 		0.00744
(0.558) 		0.857
(1.00) 		0.688
(1.00) 		0.221
(0.947) 		0.495
(1.00) 		0.172
(0.916) 		1
(1.00) 		1
(1.00)
4p gain 11 (6%) 173 0.122
(0.9) 		0.485
(1.00) 		0.182
(0.925) 		0.513
(1.00) 		0.469
(1.00) 		0.159
(0.916) 		0.548
(1.00) 		0.423
(1.00) 		0.00678
(0.558) 		1
(1.00) 		0.37
(1.00) 		1
(1.00) 		0.257
(0.975)
4q gain 8 (4%) 176 0.0768
(0.897) 		0.184
(0.925) 		0.0589
(0.897) 		0.25
(0.975) 		0.401
(1.00) 		0.0556
(0.897) 		1
(1.00) 		0.176
(0.919) 		0.0456
(0.897) 		0.816
(1.00) 		0.887
(1.00) 		1
(1.00) 		1
(1.00)
5p gain 28 (15%) 156 0.618
(1.00) 		0.847
(1.00) 		0.276
(0.996) 		0.405
(1.00) 		1
(1.00) 		1
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.0324
(0.865) 		0.507
(1.00) 		0.0482
(0.897) 		0.578
(1.00) 		0.625
(1.00) 		1
(1.00) 		0.54
(1.00)
5q gain 20 (11%) 164 0.293
(1.00) 		0.783
(1.00) 		0.116
(0.897) 		0.08
(0.897) 		0.57
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.567
(1.00) 		0.171
(0.916) 		0.381
(1.00) 		0.148
(0.916) 		0.823
(1.00) 		0.898
(1.00) 		0.556
(1.00) 		0.457
(1.00)
6p gain 7 (4%) 177 0.131
(0.9) 		0.939
(1.00) 		0.228
(0.947) 		1
(1.00) 		0.351
(1.00) 		0.109
(0.897) 		0.13
(0.9) 		1
(1.00) 		0.0795
(0.897) 		1
(1.00) 		0.387
(1.00) 		0.296
(1.00) 		1
(1.00)
6q gain 5 (3%) 179 0.467
(1.00) 		0.512
(1.00) 		0.27
(0.991) 		1
(1.00) 		0.311
(1.00) 		0.109
(0.897) 		0.38
(1.00) 		0.603
(1.00) 		0.255
(0.975) 		0.739
(1.00) 		0.898
(1.00) 		0.209
(0.947) 		1
(1.00)
7p gain 52 (28%) 132 0.548
(1.00) 		0.613
(1.00) 		0.316
(1.00) 		0.488
(1.00) 		0.58
(1.00) 		0.615
(1.00) 		0.324
(1.00) 		0.24
(0.957) 		0.0289
(0.865) 		0.133
(0.9) 		0.285
(1.00) 		0.102
(0.897) 		0.308
(1.00) 		0.52
(1.00) 		0.324
(1.00)
7q gain 48 (26%) 136 0.707
(1.00) 		0.833
(1.00) 		0.346
(1.00) 		0.433
(1.00) 		0.701
(1.00) 		0.599
(1.00) 		0.241
(0.957) 		0.423
(1.00) 		0.0327
(0.865) 		0.118
(0.9) 		0.179
(0.92) 		0.0645
(0.897) 		0.169
(0.916) 		0.275
(0.996) 		0.329
(1.00)
8p gain 26 (14%) 158 0.315
(1.00) 		0.827
(1.00) 		0.938
(1.00) 		0.942
(1.00) 		0.635
(1.00) 		1
(1.00) 		0.291
(1.00) 		0.0419
(0.897) 		1
(1.00) 		0.227
(0.947) 		0.764
(1.00) 		0.189
(0.932) 		0.915
(1.00) 		0.856
(1.00) 		0.147
(0.916)
8q gain 48 (26%) 136 0.527
(1.00) 		0.22
(0.947) 		0.742
(1.00) 		0.973
(1.00) 		0.57
(1.00) 		1
(1.00) 		0.241
(0.957) 		0.683
(1.00) 		0.263
(0.979) 		0.802
(1.00) 		0.553
(1.00) 		0.117
(0.897) 		0.714
(1.00) 		0.371
(1.00) 		0.0906
(0.897)
9p gain 8 (4%) 176 0.388
(1.00) 		0.0839
(0.897) 		0.793
(1.00) 		0.586
(1.00) 		0.688
(1.00) 		1
(1.00) 		0.297
(1.00) 		0.423
(1.00) 		0.0741
(0.897) 		0.53
(1.00) 		0.575
(1.00) 		1
(1.00) 		0.167
(0.916)
9q gain 12 (7%) 172 0.226
(0.947) 		0.31
(1.00) 		0.325
(1.00) 		0.252
(0.975) 		0.184
(0.925) 		1
(1.00) 		0.551
(1.00) 		0.475
(1.00) 		0.56
(1.00) 		0.128
(0.9) 		0.328
(1.00) 		1
(1.00) 		0.257
(0.975)
10p gain 10 (5%) 174 0.755
(1.00) 		0.527
(1.00) 		0.525
(1.00) 		0.644
(1.00) 		0.711
(1.00) 		0.298
(1.00) 		0.117
(0.897) 		1
(1.00) 		0.359
(1.00) 		0.369
(1.00) 		0.729
(1.00) 		0.00348
(0.544) 		1
(1.00)
10q gain 13 (7%) 171 0.167
(0.916) 		0.461
(1.00) 		0.661
(1.00) 		0.226
(0.947) 		0.514
(1.00) 		0.379
(1.00) 		0.0397
(0.894) 		0.518
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.462
(1.00) 		0.355
(1.00) 		0.127
(0.9) 		0.0106
(0.558) 		1
(1.00)
11p gain 13 (7%) 171 0.34
(1.00) 		0.498
(1.00) 		0.45
(1.00) 		0.508
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.0397
(0.894) 		0.732
(1.00) 		0.156
(0.916) 		0.0719
(0.897) 		0.622
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 15 (8%) 169 0.00975
(0.558) 		0.752
(1.00) 		0.56
(1.00) 		0.888
(1.00) 		0.764
(1.00) 		1
(1.00) 		0.0568
(0.897) 		0.522
(1.00) 		0.301
(1.00) 		0.2
(0.933) 		0.871
(1.00) 		0.779
(1.00) 		0.0488
(0.897)
12p gain 30 (16%) 154 0.917
(1.00) 		0.826
(1.00) 		0.122
(0.9) 		0.463
(1.00) 		1
(1.00) 		0.379
(1.00) 		0.167
(0.916) 		0.641
(1.00) 		0.0334
(0.865) 		0.823
(1.00) 		0.52
(1.00) 		0.0357
(0.865) 		0.0976
(0.897) 		0.669
(1.00) 		0.592
(1.00)
12q gain 22 (12%) 162 0.742
(1.00) 		0.242
(0.958) 		0.128
(0.9) 		0.607
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.109
(0.897) 		0.286
(1.00) 		0.0678
(0.897) 		0.0135
(0.607) 		0.0414
(0.897) 		0.849
(1.00) 		1
(1.00)
13q gain 29 (16%) 155 0.215
(0.947) 		0.445
(1.00) 		0.312
(1.00) 		0.704
(1.00) 		0.642
(1.00) 		0.55
(1.00) 		0.424
(1.00) 		0.229
(0.947) 		0.00448
(0.544) 		0.0359
(0.865) 		0.136
(0.9) 		0.962
(1.00) 		0.651
(1.00) 		1
(1.00)
14q gain 26 (14%) 158 0.37
(1.00) 		0.707
(1.00) 		0.7
(1.00) 		1
(1.00) 		0.473
(1.00) 		0.487
(1.00) 		0.527
(1.00) 		0.445
(1.00) 		0.891
(1.00) 		0.794
(1.00) 		0.909
(1.00) 		0.575
(1.00) 		0.37
(1.00) 		0.743
(1.00) 		0.52
(1.00)
15q gain 14 (8%) 170 0.962
(1.00) 		0.176
(0.919) 		0.206
(0.945) 		0.327
(1.00) 		0.115
(0.897) 		1
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.406
(1.00) 		0.61
(1.00) 		0.294
(1.00) 		0.0669
(0.897) 		0.763
(1.00) 		1
(1.00)
16p gain 22 (12%) 162 0.177
(0.919) 		0.074
(0.897) 		0.899
(1.00) 		0.939
(1.00) 		0.8
(1.00) 		0.453
(1.00) 		0.109
(0.897) 		1
(1.00) 		0.5
(1.00) 		0.719
(1.00) 		0.137
(0.9) 		0.082
(0.897) 		0.607
(1.00) 		0.471
(1.00) 		1
(1.00)
16q gain 23 (12%) 161 0.93
(1.00) 		0.166
(0.916) 		0.55
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.13
(0.9) 		0.0718
(0.897) 		0.79
(1.00) 		0.872
(1.00) 		0.719
(1.00) 		0.137
(0.9) 		0.416
(1.00) 		0.913
(1.00) 		0.491
(1.00) 		1
(1.00)
17p gain 9 (5%) 175 0.00328
(0.544) 		0.00839
(0.558) 		0.0424
(0.897) 		0.124
(0.9) 		0.351
(1.00) 		1
(1.00) 		0.733
(1.00) 		0.695
(1.00) 		0.00022
(0.267) 		1
(1.00) 		0.887
(1.00) 		0.38
(1.00) 		1
(1.00)
17q gain 17 (9%) 167 0.000883
(0.328) 		0.0177
(0.712) 		0.138
(0.9) 		0.71
(1.00) 		0.219
(0.947) 		0.298
(1.00) 		0.611
(1.00) 		0.0312
(0.865) 		0.0126
(0.6) 		0.412
(1.00) 		0.672
(1.00) 		0.909
(1.00) 		0.672
(1.00) 		0.481
(1.00) 		1
(1.00)
18p gain 28 (15%) 156 0.406
(1.00) 		0.0623
(0.897) 		1
(1.00) 		0.872
(1.00) 		1
(1.00) 		0.55
(1.00) 		0.153
(0.916) 		1
(1.00) 		0.0208
(0.765) 		0.32
(1.00) 		0.435
(1.00) 		0.721
(1.00) 		0.4
(1.00) 		0.649
(1.00) 		1
(1.00)
18q gain 12 (7%) 172 0.166
(0.916) 		0.877
(1.00) 		0.809
(1.00) 		0.63
(1.00) 		0.73
(1.00) 		1
(1.00) 		0.551
(1.00) 		1
(1.00) 		0.00702
(0.558) 		0.636
(1.00) 		0.787
(1.00) 		1
(1.00) 		1
(1.00)
19p gain 17 (9%) 167 0.066
(0.897) 		0.88
(1.00) 		0.43
(1.00) 		0.222
(0.947) 		1
(1.00) 		0.379
(1.00) 		0.0749
(0.897) 		1
(1.00) 		0.0994
(0.897) 		0.0879
(0.897) 		0.938
(1.00) 		0.181
(0.925) 		0.47
(1.00) 		1
(1.00) 		1
(1.00)
19q gain 28 (15%) 156 0.116
(0.897) 		0.858
(1.00) 		0.895
(1.00) 		0.504
(1.00) 		0.814
(1.00) 		0.58
(1.00) 		0.065
(0.897) 		0.474
(1.00) 		0.378
(1.00) 		0.121
(0.9) 		0.552
(1.00) 		0.33
(1.00) 		0.233
(0.95) 		0.146
(0.916) 		1
(1.00)
20p gain 34 (18%) 150 0.314
(1.00) 		0.0891
(0.897) 		0.566
(1.00) 		0.423
(1.00) 		1
(1.00) 		1
(1.00) 		0.253
(0.975) 		0.651
(1.00) 		0.0368
(0.865) 		0.75
(1.00) 		0.659
(1.00) 		0.315
(1.00) 		0.528
(1.00) 		0.305
(1.00) 		1
(1.00)
20q gain 45 (24%) 139 0.388
(1.00) 		0.211
(0.947) 		0.973
(1.00) 		0.734
(1.00) 		0.695
(1.00) 		1
(1.00) 		0.0849
(0.897) 		0.838
(1.00) 		0.137
(0.9) 		0.17
(0.916) 		0.459
(1.00) 		0.635
(1.00) 		0.539
(1.00) 		0.656
(1.00) 		1
(1.00)
22q gain 8 (4%) 176 0.0109
(0.558) 		0.0858
(0.897) 		1
(1.00) 		0.759
(1.00) 		0.446
(1.00) 		1
(1.00) 		0.143
(0.916) 		1
(1.00) 		0.0748
(0.897) 		1
(1.00) 		0.257
(0.975) 		0.298
(1.00) 		1
(1.00)
xp gain 8 (4%) 176 0.0107
(0.558) 		0.192
(0.932) 		0.498
(1.00) 		0.158
(0.916) 		0.672
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.679
(1.00) 		0.00362
(0.544) 		0.529
(1.00) 		0.871
(1.00) 		0.339
(1.00) 		1
(1.00)
xq gain 13 (7%) 171 0.0143
(0.622) 		0.729
(1.00) 		0.0676
(0.897) 		0.178
(0.92) 		1
(1.00) 		0.109
(0.897) 		0.571
(1.00) 		0.731
(1.00) 		0.0931
(0.897) 		0.475
(1.00) 		0.815
(1.00) 		0.528
(1.00) 		0.363
(1.00)
1p loss 36 (20%) 148 0.653
(1.00) 		0.192
(0.932) 		0.299
(1.00) 		0.822
(1.00) 		0.295
(1.00) 		0.581
(1.00) 		0.136
(0.9) 		0.829
(1.00) 		1
(1.00) 		0.225
(0.947) 		0.491
(1.00) 		0.617
(1.00) 		0.417
(1.00) 		0.565
(1.00) 		1
(1.00)
1q loss 8 (4%) 176 0.548
(1.00) 		0.0902
(0.897) 		0.161
(0.916) 		0.45
(1.00) 		1
(1.00) 		1
(1.00) 		0.297
(1.00) 		0.115
(0.897) 		0.452
(1.00) 		0.177
(0.919) 		0.815
(1.00) 		0.852
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 11 (6%) 173 0.166
(0.916) 		0.362
(1.00) 		0.168
(0.916) 		0.597
(1.00) 		0.469
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.00537
(0.544) 		0.458
(1.00) 		0.204
(0.944) 		0.305
(1.00) 		1
(1.00)
2q loss 5 (3%) 179 0.0879
(0.897) 		0.1
(0.897) 		0.0564
(0.897) 		0.2
(0.933) 		0.311
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0187
(0.712) 		1
(1.00) 		0.888
(1.00) 		1
(1.00) 		1
(1.00)
3p loss 36 (20%) 148 0.686
(1.00) 		0.677
(1.00) 		0.791
(1.00) 		0.758
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.0247
(0.831) 		0.377
(1.00) 		0.233
(0.95) 		0.563
(1.00) 		0.782
(1.00) 		0.92
(1.00) 		0.29
(1.00) 		0.631
(1.00) 		0.584
(1.00)
3q loss 19 (10%) 165 0.439
(1.00) 		0.933
(1.00) 		0.986
(1.00) 		0.598
(1.00) 		1
(1.00) 		1
(1.00) 		0.0933
(0.897) 		0.781
(1.00) 		0.19
(0.932) 		0.385
(1.00) 		0.11
(0.897) 		1
(1.00) 		0.975
(1.00) 		0.0278
(0.865) 		1
(1.00)
4p loss 25 (14%) 159 0.461
(1.00) 		0.889
(1.00) 		0.837
(1.00) 		0.756
(1.00) 		0.228
(0.947) 		1
(1.00) 		0.0297
(0.865) 		1
(1.00) 		0.306
(1.00) 		0.763
(1.00) 		0.646
(1.00) 		0.868
(1.00) 		0.172
(0.916) 		0.331
(1.00) 		0.52
(1.00)
4q loss 25 (14%) 159 0.583
(1.00) 		0.739
(1.00) 		0.837
(1.00) 		0.894
(1.00) 		0.228
(0.947) 		1
(1.00) 		0.00861
(0.558) 		1
(1.00) 		0.308
(1.00) 		0.32
(1.00) 		0.366
(1.00) 		0.868
(1.00) 		0.386
(1.00) 		0.327
(1.00) 		0.134
(0.9)
5p loss 9 (5%) 175 0.431
(1.00) 		0.596
(1.00) 		0.751
(1.00) 		1
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.205
(0.944) 		1
(1.00) 		0.477
(1.00) 		0.558
(1.00) 		0.531
(1.00) 		0.0887
(0.897) 		0.621
(1.00) 		0.198
(0.933)
5q loss 13 (7%) 171 0.581
(1.00) 		0.948
(1.00) 		0.523
(1.00) 		0.868
(1.00) 		0.115
(0.897) 		1
(1.00) 		0.775
(1.00) 		0.506
(1.00) 		0.108
(0.897) 		0.323
(1.00) 		0.659
(1.00) 		0.266
(0.988) 		0.0952
(0.897) 		0.256
(0.975) 		0.284
(1.00)
6p loss 64 (35%) 120 0.146
(0.916) 		0.285
(1.00) 		0.342
(1.00) 		0.904
(1.00) 		0.295
(1.00) 		0.171
(0.916) 		0.162
(0.916) 		0.852
(1.00) 		0.156
(0.916) 		0.193
(0.932) 		0.991
(1.00) 		0.618
(1.00) 		0.115
(0.897) 		1
(1.00) 		0.661
(1.00)
6q loss 83 (45%) 101 0.1
(0.897) 		0.235
(0.953) 		0.541
(1.00) 		0.48
(1.00) 		1
(1.00) 		1
(1.00) 		0.234
(0.95) 		1
(1.00) 		0.626
(1.00) 		0.186
(0.928) 		0.78
(1.00) 		0.813
(1.00) 		0.964
(1.00) 		0.595
(1.00) 		0.652
(1.00)
7p loss 3 (2%) 181 0.709
(1.00) 		0.269
(0.991) 		0.486
(1.00) 		0.476
(1.00) 		1
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.0644
(0.897) 		1
(1.00) 		0.829
(1.00) 		1
(1.00) 		0.103
(0.897)
7q loss 4 (2%) 180 0.564
(1.00) 		0.323
(1.00) 		0.612
(1.00) 		0.579
(1.00) 		1
(1.00) 		1
(1.00) 		0.329
(1.00) 		0.161
(0.916) 		1
(1.00) 		1
(1.00) 		0.832
(1.00) 		0.35
(1.00) 		0.103
(0.897)
8p loss 41 (22%) 143 0.885
(1.00) 		0.391
(1.00) 		0.324
(1.00) 		0.406
(1.00) 		0.109
(0.897) 		1
(1.00) 		0.722
(1.00) 		0.392
(1.00) 		0.158
(0.916) 		0.741
(1.00) 		0.945
(1.00) 		0.794
(1.00) 		0.0241
(0.831) 		0.901
(1.00) 		0.586
(1.00)
8q loss 16 (9%) 168 0.957
(1.00) 		0.793
(1.00) 		0.384
(1.00) 		0.734
(1.00) 		0.76
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.359
(1.00) 		0.0933
(0.897) 		0.655
(1.00) 		0.561
(1.00) 		0.893
(1.00) 		0.629
(1.00) 		1
(1.00)
9p loss 75 (41%) 109 0.159
(0.916) 		0.751
(1.00) 		0.00108
(0.328) 		0.0906
(0.897) 		0.401
(1.00) 		0.646
(1.00) 		1
(1.00) 		0.208
(0.947) 		0.109
(0.897) 		0.294
(1.00) 		0.366
(1.00) 		0.919
(1.00) 		0.714
(1.00) 		0.929
(1.00) 		1
(1.00)
9q loss 43 (23%) 141 0.628
(1.00) 		0.676
(1.00) 		0.332
(1.00) 		0.827
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.0338
(0.865) 		0.396
(1.00) 		0.599
(1.00) 		0.36
(1.00) 		0.795
(1.00) 		0.2
(0.933) 		0.128
(0.9) 		0.594
(1.00)
10p loss 36 (20%) 148 0.478
(1.00) 		0.787
(1.00) 		0.0433
(0.897) 		0.52
(1.00) 		0.297
(1.00) 		0.307
(1.00) 		1
(1.00) 		1
(1.00) 		0.217
(0.947) 		0.938
(1.00) 		0.417
(1.00) 		0.816
(1.00) 		0.589
(1.00) 		0.424
(1.00) 		1
(1.00)
10q loss 30 (16%) 154 0.786
(1.00) 		0.672
(1.00) 		0.114
(0.897) 		1
(1.00) 		0.498
(1.00) 		0.237
(0.955) 		1
(1.00) 		1
(1.00) 		0.0832
(0.897) 		0.222
(0.947) 		0.339
(1.00) 		0.807
(1.00) 		0.772
(1.00) 		0.753
(1.00) 		0.559
(1.00)
11p loss 17 (9%) 167 0.0513
(0.897) 		0.405
(1.00) 		0.347
(1.00) 		0.625
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.558
(1.00) 		0.552
(1.00) 		0.772
(1.00) 		0.778
(1.00) 		0.132
(0.9) 		0.275
(0.996) 		0.435
(1.00)
11q loss 16 (9%) 168 0.037
(0.865) 		0.269
(0.991) 		0.319
(1.00) 		0.734
(1.00) 		1
(1.00) 		1
(1.00) 		0.117
(0.897) 		0.756
(1.00) 		0.011
(0.558) 		0.911
(1.00) 		0.483
(1.00) 		0.215
(0.947) 		0.628
(1.00) 		0.412
(1.00)
12p loss 20 (11%) 164 0.607
(1.00) 		0.27
(0.991) 		0.549
(1.00) 		0.688
(1.00) 		1
(1.00) 		0.58
(1.00) 		0.163
(0.916) 		0.243
(0.958) 		0.0829
(0.897) 		0.133
(0.9) 		0.412
(1.00) 		0.733
(1.00) 		0.755
(1.00) 		0.0534
(0.897) 		1
(1.00)
12q loss 28 (15%) 156 0.703
(1.00) 		0.978
(1.00) 		0.621
(1.00) 		0.837
(1.00) 		0.819
(1.00) 		0.26
(0.977) 		0.839
(1.00) 		0.229
(0.947) 		0.453
(1.00) 		0.231
(0.95) 		0.696
(1.00) 		0.367
(1.00) 		0.781
(1.00) 		0.009
(0.558) 		1
(1.00)
13q loss 20 (11%) 164 0.111
(0.897) 		0.815
(1.00) 		0.172
(0.916) 		0.405
(1.00) 		0.198
(0.933) 		0.453
(1.00) 		1
(1.00) 		0.567
(1.00) 		1
(1.00) 		0.427
(1.00) 		0.862
(1.00) 		0.257
(0.975) 		0.227
(0.947) 		0.212
(0.947) 		0.5
(1.00)
14q loss 16 (9%) 168 0.928
(1.00) 		0.51
(1.00) 		0.475
(1.00) 		0.734
(1.00) 		0.764
(1.00) 		1
(1.00) 		0.794
(1.00) 		0.558
(1.00) 		0.5
(1.00) 		0.2
(0.933) 		0.612
(1.00) 		0.494
(1.00) 		0.362
(1.00) 		0.0128
(0.6) 		1
(1.00)
15q loss 30 (16%) 154 0.356
(1.00) 		0.38
(1.00) 		0.13
(0.9) 		0.812
(1.00) 		0.17
(0.916) 		1
(1.00) 		0.167
(0.916) 		0.812
(1.00) 		0.127
(0.9) 		0.637
(1.00) 		0.783
(1.00) 		0.752
(1.00) 		0.222
(0.947) 		0.082
(0.897) 		0.134
(0.9)
16p loss 11 (6%) 173 0.0097
(0.558) 		0.183
(0.925) 		0.0923
(0.897) 		0.214
(0.947) 		0.728
(1.00) 		1
(1.00) 		0.35
(1.00) 		0.475
(1.00) 		0.00164
(0.399) 		0.841
(1.00) 		0.53
(1.00) 		0.701
(1.00) 		0.228
(0.947)
16q loss 13 (7%) 171 0.139
(0.9) 		0.476
(1.00) 		0.193
(0.932) 		0.585
(1.00) 		1
(1.00) 		1
(1.00) 		0.389
(1.00) 		1
(1.00) 		0.005
(0.544) 		0.0667
(0.897) 		0.686
(1.00) 		0.254
(0.975) 		0.198
(0.933)
17p loss 80 (43%) 104 0.0151
(0.634) 		0.441
(1.00) 		0.19
(0.932) 		0.445
(1.00) 		0.507
(1.00) 		0.385
(1.00) 		0.553
(1.00) 		0.859
(1.00) 		0.105
(0.897) 		0.0563
(0.897) 		0.412
(1.00) 		0.0984
(0.897) 		0.951
(1.00) 		0.75
(1.00) 		1
(1.00)
17q loss 22 (12%) 162 0.632
(1.00) 		0.616
(1.00) 		0.829
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.55
(1.00) 		0.109
(0.897) 		0.596
(1.00) 		0.223
(0.947) 		0.0919
(0.897) 		0.911
(1.00) 		0.0187
(0.712) 		0.656
(1.00) 		1
(1.00) 		0.457
(1.00)
18p loss 55 (30%) 129 0.896
(1.00) 		0.0582
(0.897) 		0.415
(1.00) 		0.606
(1.00) 		0.856
(1.00) 		0.328
(1.00) 		0.258
(0.977) 		0.843
(1.00) 		0.678
(1.00) 		0.0636
(0.897) 		0.373
(1.00) 		0.865
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.176
(0.919)
18q loss 106 (58%) 78 0.14
(0.905) 		0.17
(0.916) 		0.00476
(0.544) 		0.167
(0.916) 		0.613
(1.00) 		0.154
(0.916) 		0.295
(1.00) 		1
(1.00) 		0.0924
(0.897) 		0.762
(1.00) 		0.991
(1.00) 		0.289
(1.00) 		0.279
(1.00) 		0.0502
(0.897) 		1
(1.00)
19p loss 19 (10%) 165 0.976
(1.00) 		0.376
(1.00) 		0.58
(1.00) 		0.721
(1.00) 		0.284
(1.00) 		0.52
(1.00) 		1
(1.00) 		0.77
(1.00) 		0.116
(0.897) 		0.747
(1.00) 		0.878
(1.00) 		0.632
(1.00) 		0.0816
(0.897) 		0.825
(1.00) 		0.435
(1.00)
19q loss 12 (7%) 172 0.91
(1.00) 		0.253
(0.975) 		0.714
(1.00) 		1
(1.00) 		1
(1.00) 		0.379
(1.00) 		1
(1.00) 		0.151
(0.916) 		1
(1.00) 		0.403
(1.00) 		0.331
(1.00) 		0.49
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.312
(1.00)
20p loss 20 (11%) 164 0.812
(1.00) 		0.376
(1.00) 		0.721
(1.00) 		0.568
(1.00) 		1
(1.00) 		0.453
(1.00) 		0.813
(1.00) 		0.405
(1.00) 		1
(1.00) 		0.806
(1.00) 		0.304
(1.00) 		0.284
(1.00) 		0.683
(1.00) 		0.192
(0.932) 		0.457
(1.00)
20q loss 5 (3%) 179 0.737
(1.00) 		0.233
(0.95) 		0.632
(1.00) 		0.662
(1.00) 		1
(1.00) 		1
(1.00) 		0.38
(1.00) 		0.271
(0.991) 		1
(1.00) 		0.572
(1.00) 		0.491
(1.00) 		0.461
(1.00) 		0.21
(0.947) 		0.136
(0.9)
21q loss 58 (32%) 126 0.496
(1.00) 		0.387
(1.00) 		0.0464
(0.897) 		0.0255
(0.831) 		0.0326
(0.865) 		0.398
(1.00) 		0.205
(0.944) 		0.564
(1.00) 		0.298
(1.00) 		0.466
(1.00) 		0.239
(0.957) 		0.254
(0.975) 		0.0471
(0.897) 		0.779
(1.00) 		0.156
(0.916)
22q loss 46 (25%) 138 0.542
(1.00) 		0.0743
(0.897) 		0.26
(0.977) 		0.562
(1.00) 		0.701
(1.00) 		1
(1.00) 		0.026
(0.831) 		0.407
(1.00) 		0.938
(1.00) 		0.757
(1.00) 		0.488
(1.00) 		0.799
(1.00) 		0.757
(1.00) 		0.914
(1.00) 		1
(1.00)
xp loss 27 (15%) 157 0.131
(0.9) 		0.57
(1.00) 		0.192
(0.932) 		0.439
(1.00) 		0.237
(0.955) 		1
(1.00) 		1
(1.00) 		0.609
(1.00) 		0.797
(1.00) 		0.476
(1.00) 		0.173
(0.916) 		0.275
(0.996) 		0.115
(0.897) 		0.652
(1.00) 		0.578
(1.00)
xq loss 18 (10%) 166 0.158
(0.916) 		0.778
(1.00) 		0.047
(0.897) 		0.283
(1.00) 		0.0867
(0.897) 		1
(1.00) 		0.329
(1.00) 		0.558
(1.00) 		0.261
(0.977) 		0.152
(0.916) 		0.223
(0.947) 		0.793
(1.00) 		0.0823
(0.897) 		0.415
(1.00) 		1
(1.00)
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/PAAD-TP/19783029/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PAAD-TP/19775410/PAAD-TP.merged_data.txt

  • Number of patients = 184

  • Number of significantly arm-level cnvs = 81

  • Number of selected clinical features = 15

  • 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.

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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