Correlation between copy number variations of arm-level result and selected clinical features
Lung Squamous Cell Carcinoma (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/C1MS3S6X
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 82 arm-level events and 15 clinical features across 501 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 82 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
KARNOFSKY
PERFORMANCE
SCORE
HISTOLOGICAL
TYPE
NUMBER
PACK
YEARS
SMOKED
YEAR
OF
TOBACCO
SMOKING
ONSET
RESIDUAL
TUMOR
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 Wilcoxon-test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 91 (18%) 410 0.531
(0.917)
0.865
(1.00)
0.0996
(0.709)
0.755
(0.962)
0.655
(0.945)
0.0313
(0.599)
0.792
(0.973)
0.262
(0.845)
0.858
(1.00)
0.0275
(0.57)
0.388
(0.883)
0.814
(0.981)
0.654
(0.945)
0.884
(1.00)
1
(1.00)
1q gain 202 (40%) 299 0.736
(0.954)
0.327
(0.855)
0.0342
(0.61)
0.0913
(0.705)
0.764
(0.962)
0.0451
(0.612)
0.213
(0.816)
0.882
(1.00)
0.448
(0.906)
0.00194
(0.271)
0.804
(0.981)
0.467
(0.906)
0.959
(1.00)
0.754
(0.962)
0.72
(0.954)
2p gain 223 (45%) 278 0.00708
(0.458)
0.696
(0.953)
0.315
(0.855)
0.139
(0.733)
0.204
(0.807)
1
(1.00)
0.00286
(0.271)
0.0773
(0.689)
0.135
(0.733)
0.0349
(0.61)
0.258
(0.845)
0.189
(0.802)
0.334
(0.855)
0.316
(0.855)
0.0827
(0.691)
2q gain 143 (29%) 358 0.0459
(0.612)
0.663
(0.945)
0.382
(0.883)
0.222
(0.836)
0.479
(0.906)
1
(1.00)
0.0425
(0.612)
0.264
(0.845)
0.11
(0.711)
0.0431
(0.612)
0.53
(0.917)
0.586
(0.927)
0.474
(0.906)
0.684
(0.951)
0.443
(0.906)
3p gain 108 (22%) 393 0.49
(0.909)
0.881
(1.00)
0.0932
(0.705)
0.849
(0.998)
0.52
(0.917)
0.356
(0.872)
0.0843
(0.691)
0.0512
(0.617)
0.897
(1.00)
0.54
(0.917)
0.768
(0.962)
0.292
(0.855)
0.319
(0.855)
0.565
(0.923)
1
(1.00)
3q gain 315 (63%) 186 0.79
(0.973)
0.73
(0.954)
0.138
(0.733)
0.321
(0.855)
0.863
(1.00)
0.0491
(0.613)
0.598
(0.929)
0.651
(0.945)
0.621
(0.939)
0.00309
(0.271)
0.423
(0.906)
0.333
(0.855)
0.97
(1.00)
0.346
(0.869)
1
(1.00)
4p gain 31 (6%) 470 0.328
(0.855)
0.808
(0.981)
0.541
(0.917)
0.661
(0.945)
0.827
(0.987)
1
(1.00)
0.0943
(0.705)
0.54
(0.917)
0.0206
(0.57)
1
(1.00)
0.995
(1.00)
0.729
(0.954)
0.677
(0.948)
0.462
(0.906)
1
(1.00)
4q gain 21 (4%) 480 0.345
(0.869)
0.0105
(0.521)
0.172
(0.769)
0.922
(1.00)
0.858
(1.00)
1
(1.00)
0.309
(0.855)
0.722
(0.954)
0.116
(0.731)
0.62
(0.939)
0.37
(0.883)
0.551
(0.917)
1
(1.00)
1
(1.00)
1
(1.00)
5p gain 309 (62%) 192 0.294
(0.855)
0.0833
(0.691)
0.49
(0.909)
0.509
(0.917)
0.161
(0.766)
0.715
(0.954)
0.53
(0.917)
0.653
(0.945)
0.773
(0.963)
0.333
(0.855)
0.0369
(0.612)
0.133
(0.733)
0.0275
(0.57)
0.204
(0.807)
0.267
(0.845)
5q gain 97 (19%) 404 0.381
(0.883)
0.237
(0.845)
0.981
(1.00)
0.497
(0.914)
0.923
(1.00)
1
(1.00)
0.442
(0.906)
0.204
(0.807)
0.396
(0.886)
0.727
(0.954)
0.173
(0.771)
0.0377
(0.612)
0.238
(0.845)
0.279
(0.853)
1
(1.00)
6p gain 108 (22%) 393 0.716
(0.954)
0.23
(0.84)
0.924
(1.00)
0.827
(0.987)
0.379
(0.883)
1
(1.00)
0.536
(0.917)
0.0454
(0.612)
0.136
(0.733)
0.166
(0.769)
0.856
(1.00)
0.0653
(0.679)
0.345
(0.869)
0.107
(0.711)
1
(1.00)
6q gain 92 (18%) 409 0.994
(1.00)
0.859
(1.00)
0.454
(0.906)
0.958
(1.00)
0.0721
(0.679)
0.612
(0.933)
0.694
(0.952)
0.0874
(0.702)
0.435
(0.906)
0.246
(0.845)
0.991
(1.00)
0.657
(0.945)
0.722
(0.954)
0.44
(0.906)
0.201
(0.807)
7p gain 238 (48%) 263 0.0263
(0.57)
0.0726
(0.679)
0.1
(0.709)
0.00256
(0.271)
0.576
(0.927)
0.715
(0.954)
0.126
(0.731)
0.884
(1.00)
0.159
(0.766)
0.38
(0.883)
0.138
(0.733)
0.166
(0.769)
0.848
(0.998)
0.0168
(0.569)
0.297
(0.855)
7q gain 220 (44%) 281 0.153
(0.76)
0.146
(0.747)
0.272
(0.845)
0.116
(0.731)
0.369
(0.883)
0.251
(0.845)
0.101
(0.709)
0.376
(0.883)
0.0873
(0.702)
0.544
(0.917)
0.191
(0.803)
0.12
(0.731)
0.72
(0.954)
0.00658
(0.45)
0.474
(0.906)
8p gain 129 (26%) 372 0.899
(1.00)
0.0263
(0.57)
0.0641
(0.679)
0.0517
(0.618)
0.658
(0.945)
0.0816
(0.691)
0.908
(1.00)
0.244
(0.845)
0.643
(0.945)
0.269
(0.845)
0.95
(1.00)
0.736
(0.954)
0.025
(0.57)
0.109
(0.711)
0.431
(0.906)
8q gain 256 (51%) 245 0.293
(0.855)
0.322
(0.855)
0.0222
(0.57)
0.18
(0.783)
0.377
(0.883)
0.123
(0.731)
0.839
(0.991)
0.464
(0.906)
0.0573
(0.656)
0.481
(0.906)
0.188
(0.802)
0.489
(0.909)
0.128
(0.731)
0.0606
(0.667)
0.724
(0.954)
9p gain 62 (12%) 439 0.587
(0.927)
0.347
(0.869)
0.0498
(0.613)
0.33
(0.855)
0.00443
(0.321)
1
(1.00)
0.759
(0.962)
0.658
(0.945)
0.918
(1.00)
0.273
(0.847)
0.426
(0.906)
0.947
(1.00)
0.667
(0.945)
0.303
(0.855)
0.228
(0.839)
9q gain 91 (18%) 410 0.914
(1.00)
0.628
(0.943)
0.181
(0.786)
0.541
(0.917)
0.0495
(0.613)
1
(1.00)
0.512
(0.917)
0.852
(1.00)
0.729
(0.954)
0.509
(0.917)
0.862
(1.00)
0.719
(0.954)
0.601
(0.929)
0.461
(0.906)
0.637
(0.945)
10p gain 78 (16%) 423 0.553
(0.917)
0.992
(1.00)
0.193
(0.803)
0.693
(0.952)
0.639
(0.945)
0.299
(0.855)
0.0239
(0.57)
0.839
(0.991)
0.671
(0.947)
0.902
(1.00)
0.0504
(0.614)
0.0155
(0.547)
0.321
(0.855)
0.0662
(0.679)
1
(1.00)
10q gain 44 (9%) 457 0.906
(1.00)
0.452
(0.906)
0.687
(0.951)
0.811
(0.981)
0.815
(0.981)
0.48
(0.906)
0.149
(0.751)
0.609
(0.932)
0.743
(0.959)
1
(1.00)
0.263
(0.845)
0.00878
(0.508)
0.771
(0.962)
0.132
(0.733)
0.591
(0.927)
11p gain 75 (15%) 426 0.58
(0.927)
0.269
(0.845)
0.721
(0.954)
0.864
(1.00)
0.148
(0.751)
0.602
(0.929)
0.253
(0.845)
0.832
(0.99)
0.00908
(0.508)
1
(1.00)
0.675
(0.948)
0.736
(0.954)
0.508
(0.917)
0.299
(0.855)
1
(1.00)
11q gain 89 (18%) 412 0.356
(0.872)
0.587
(0.927)
0.583
(0.927)
0.246
(0.845)
0.214
(0.816)
0.12
(0.731)
1
(1.00)
0.432
(0.906)
0.649
(0.945)
1
(1.00)
0.494
(0.91)
0.789
(0.973)
0.54
(0.917)
0.503
(0.917)
1
(1.00)
12p gain 226 (45%) 275 0.75
(0.962)
0.751
(0.962)
0.425
(0.906)
0.125
(0.731)
0.416
(0.906)
0.464
(0.906)
0.00295
(0.271)
0.659
(0.945)
0.0743
(0.679)
0.933
(1.00)
0.131
(0.733)
0.872
(1.00)
0.886
(1.00)
0.924
(1.00)
1
(1.00)
12q gain 151 (30%) 350 0.989
(1.00)
0.542
(0.917)
0.356
(0.872)
0.232
(0.841)
0.0987
(0.709)
1
(1.00)
0.00376
(0.308)
0.205
(0.809)
0.084
(0.691)
0.857
(1.00)
0.767
(0.962)
0.555
(0.917)
0.947
(1.00)
0.875
(1.00)
0.701
(0.954)
13q gain 39 (8%) 462 0.182
(0.787)
0.442
(0.906)
0.681
(0.949)
0.394
(0.886)
0.469
(0.906)
0.409
(0.897)
0.568
(0.927)
0.256
(0.845)
0.15
(0.751)
0.384
(0.883)
0.317
(0.855)
0.269
(0.845)
0.724
(0.954)
0.0383
(0.612)
1
(1.00)
14q gain 126 (25%) 375 0.0152
(0.547)
0.0834
(0.691)
0.17
(0.769)
0.128
(0.731)
0.276
(0.852)
1
(1.00)
0.814
(0.981)
0.74
(0.956)
0.989
(1.00)
1
(1.00)
0.469
(0.906)
0.514
(0.917)
0.608
(0.932)
0.521
(0.917)
0.0203
(0.57)
15q gain 107 (21%) 394 0.809
(0.981)
0.612
(0.933)
0.167
(0.769)
0.311
(0.855)
0.0971
(0.705)
0.201
(0.807)
0.172
(0.769)
0.861
(1.00)
0.132
(0.733)
0.537
(0.917)
0.316
(0.855)
0.268
(0.845)
0.787
(0.973)
0.8
(0.978)
0.687
(0.951)
16p gain 86 (17%) 415 0.889
(1.00)
0.544
(0.917)
0.678
(0.948)
0.726
(0.954)
0.395
(0.886)
1
(1.00)
0.177
(0.78)
0.691
(0.951)
0.872
(1.00)
0.193
(0.803)
0.118
(0.731)
0.753
(0.962)
0.936
(1.00)
0.479
(0.906)
1
(1.00)
16q gain 85 (17%) 416 0.748
(0.961)
0.294
(0.855)
0.225
(0.839)
0.501
(0.915)
0.725
(0.954)
0.36
(0.876)
0.0143
(0.547)
0.546
(0.917)
0.59
(0.927)
0.299
(0.855)
0.262
(0.845)
0.55
(0.917)
0.79
(0.973)
0.134
(0.733)
1
(1.00)
17p gain 65 (13%) 436 0.161
(0.766)
0.0662
(0.679)
0.769
(0.962)
0.456
(0.906)
0.966
(1.00)
1
(1.00)
0.45
(0.906)
0.675
(0.948)
0.598
(0.929)
0.518
(0.917)
0.124
(0.731)
0.011
(0.521)
0.332
(0.855)
0.918
(1.00)
0.326
(0.855)
17q gain 158 (32%) 343 0.952
(1.00)
0.0889
(0.705)
0.259
(0.845)
0.0149
(0.547)
0.0851
(0.693)
0.684
(0.951)
0.000962
(0.271)
0.529
(0.917)
0.0966
(0.705)
0.752
(0.962)
0.293
(0.855)
0.0464
(0.612)
0.624
(0.941)
0.166
(0.769)
0.249
(0.845)
18p gain 148 (30%) 353 0.581
(0.927)
0.15
(0.751)
0.44
(0.906)
0.544
(0.917)
0.167
(0.769)
0.679
(0.948)
0.264
(0.845)
0.0171
(0.569)
0.0202
(0.57)
0.769
(0.962)
0.701
(0.954)
0.334
(0.855)
0.234
(0.845)
0.0156
(0.547)
1
(1.00)
18q gain 102 (20%) 399 0.977
(1.00)
0.772
(0.962)
0.425
(0.906)
0.0803
(0.691)
0.556
(0.917)
0.354
(0.872)
0.448
(0.906)
0.104
(0.711)
0.0155
(0.547)
0.788
(0.973)
0.0392
(0.612)
0.471
(0.906)
0.353
(0.872)
0.02
(0.57)
0.667
(0.945)
19p gain 115 (23%) 386 0.121
(0.731)
0.809
(0.981)
0.59
(0.927)
0.464
(0.906)
0.405
(0.892)
1
(1.00)
0.546
(0.917)
0.167
(0.769)
0.293
(0.855)
0.139
(0.733)
0.722
(0.954)
0.0708
(0.679)
1
(1.00)
0.618
(0.938)
1
(1.00)
19q gain 163 (33%) 338 0.354
(0.872)
0.146
(0.747)
0.556
(0.917)
0.336
(0.857)
0.199
(0.807)
0.689
(0.951)
0.828
(0.987)
1
(1.00)
0.19
(0.803)
0.0691
(0.679)
0.133
(0.733)
0.00178
(0.271)
0.633
(0.943)
0.157
(0.763)
0.703
(0.954)
20p gain 263 (52%) 238 0.38
(0.883)
0.174
(0.771)
0.402
(0.886)
0.0902
(0.705)
0.578
(0.927)
0.128
(0.731)
0.00423
(0.321)
0.189
(0.802)
0.243
(0.845)
0.401
(0.886)
0.374
(0.883)
0.812
(0.981)
0.853
(1.00)
0.731
(0.954)
0.0693
(0.679)
20q gain 251 (50%) 250 0.6
(0.929)
0.372
(0.883)
0.467
(0.906)
0.252
(0.845)
0.154
(0.761)
0.122
(0.731)
0.0011
(0.271)
0.38
(0.883)
0.74
(0.956)
0.143
(0.745)
0.735
(0.954)
0.64
(0.945)
0.804
(0.981)
0.679
(0.948)
0.284
(0.855)
21q gain 57 (11%) 444 0.0441
(0.612)
0.322
(0.855)
0.152
(0.756)
0.0233
(0.57)
0.0316
(0.599)
1
(1.00)
0.263
(0.845)
0.0221
(0.57)
0.172
(0.769)
0.0283
(0.57)
0.833
(0.99)
0.461
(0.906)
0.0753
(0.679)
0.306
(0.855)
1
(1.00)
22q gain 222 (44%) 279 0.175
(0.774)
0.0337
(0.61)
0.0653
(0.679)
0.107
(0.711)
0.315
(0.855)
0.255
(0.845)
0.125
(0.731)
0.187
(0.801)
0.372
(0.883)
0.447
(0.906)
0.108
(0.711)
0.0322
(0.6)
0.442
(0.906)
0.117
(0.731)
1
(1.00)
xp gain 64 (13%) 437 0.783
(0.973)
0.453
(0.906)
0.64
(0.945)
0.323
(0.855)
0.913
(1.00)
1
(1.00)
0.88
(1.00)
0.517
(0.917)
0.964
(1.00)
0.0445
(0.612)
0.144
(0.745)
0.75
(0.962)
0.49
(0.909)
0.659
(0.945)
0.603
(0.929)
xq gain 79 (16%) 422 0.878
(1.00)
0.587
(0.927)
0.108
(0.711)
0.0154
(0.547)
0.594
(0.928)
0.319
(0.855)
0.402
(0.886)
0.84
(0.991)
0.564
(0.922)
0.819
(0.982)
0.905
(1.00)
0.554
(0.917)
0.688
(0.951)
0.319
(0.855)
0.361
(0.878)
1p loss 155 (31%) 346 0.694
(0.952)
0.0437
(0.612)
0.518
(0.917)
0.973
(1.00)
0.0235
(0.57)
0.445
(0.906)
0.0779
(0.69)
0.158
(0.763)
0.478
(0.906)
0.902
(1.00)
0.317
(0.855)
0.826
(0.987)
0.854
(1.00)
0.761
(0.962)
0.0569
(0.656)
1q loss 60 (12%) 441 0.248
(0.845)
0.632
(0.943)
0.0715
(0.679)
0.755
(0.962)
0.272
(0.845)
1
(1.00)
0.346
(0.869)
0.0743
(0.679)
0.371
(0.883)
0.376
(0.883)
0.324
(0.855)
0.492
(0.909)
0.0373
(0.612)
0.193
(0.803)
0.238
(0.845)
2p loss 24 (5%) 477 0.272
(0.845)
0.18
(0.783)
0.639
(0.945)
0.699
(0.954)
0.367
(0.883)
1
(1.00)
0.0927
(0.705)
0.71
(0.954)
0.763
(0.962)
0.667
(0.945)
0.245
(0.845)
0.49
(0.909)
1
(1.00)
0.796
(0.975)
0.352
(0.872)
2q loss 44 (9%) 457 0.388
(0.883)
0.196
(0.806)
0.708
(0.954)
0.33
(0.855)
0.121
(0.731)
0.47
(0.906)
0.37
(0.883)
1
(1.00)
0.771
(0.962)
0.808
(0.981)
0.0362
(0.612)
0.958
(1.00)
1
(1.00)
0.892
(1.00)
1
(1.00)
3p loss 310 (62%) 191 0.864
(1.00)
0.397
(0.886)
0.446
(0.906)
0.965
(1.00)
0.827
(0.987)
0.0476
(0.612)
0.347
(0.869)
0.449
(0.906)
0.236
(0.845)
0.885
(1.00)
0.588
(0.927)
0.963
(1.00)
0.24
(0.845)
0.382
(0.883)
0.479
(0.906)
3q loss 73 (15%) 428 0.668
(0.945)
0.155
(0.761)
0.366
(0.883)
0.107
(0.711)
0.504
(0.917)
0.604
(0.929)
0.665
(0.945)
0.839
(0.991)
0.474
(0.906)
0.381
(0.883)
0.0828
(0.691)
0.125
(0.731)
0.895
(1.00)
0.522
(0.917)
1
(1.00)
4p loss 315 (63%) 186 0.535
(0.917)
0.123
(0.731)
0.166
(0.769)
0.299
(0.855)
0.764
(0.962)
0.433
(0.906)
0.461
(0.906)
0.0676
(0.679)
0.74
(0.956)
0.0566
(0.656)
0.786
(0.973)
0.52
(0.917)
0.513
(0.917)
0.0836
(0.691)
1
(1.00)
4q loss 297 (59%) 204 0.547
(0.917)
0.357
(0.872)
0.134
(0.733)
0.2
(0.807)
0.57
(0.927)
0.451
(0.906)
0.917
(1.00)
0.135
(0.733)
0.542
(0.917)
0.169
(0.769)
0.186
(0.801)
0.983
(1.00)
0.529
(0.917)
0.59
(0.927)
0.731
(0.954)
5p loss 79 (16%) 422 0.156
(0.763)
0.643
(0.945)
0.534
(0.917)
0.28
(0.853)
0.269
(0.845)
0.602
(0.929)
0.263
(0.845)
0.314
(0.855)
0.421
(0.906)
0.49
(0.909)
0.0352
(0.61)
0.0446
(0.612)
0.124
(0.731)
0.928
(1.00)
0.109
(0.711)
5q loss 290 (58%) 211 0.481
(0.906)
0.588
(0.927)
0.72
(0.954)
0.464
(0.906)
0.341
(0.866)
0.247
(0.845)
0.68
(0.948)
0.304
(0.855)
0.364
(0.882)
0.473
(0.906)
0.419
(0.906)
0.0104
(0.521)
0.766
(0.962)
0.207
(0.809)
1
(1.00)
6p loss 114 (23%) 387 0.386
(0.883)
0.69
(0.951)
0.432
(0.906)
0.458
(0.906)
0.172
(0.769)
0.666
(0.945)
0.627
(0.943)
1
(1.00)
0.392
(0.885)
0.929
(1.00)
0.732
(0.954)
0.553
(0.917)
0.437
(0.906)
0.892
(1.00)
1
(1.00)
6q loss 114 (23%) 387 0.397
(0.886)
0.627
(0.943)
0.503
(0.917)
0.577
(0.927)
0.386
(0.883)
0.666
(0.945)
0.546
(0.917)
0.302
(0.855)
0.893
(1.00)
0.28
(0.853)
0.775
(0.965)
0.66
(0.945)
0.521
(0.917)
1
(1.00)
0.392
(0.885)
7p loss 60 (12%) 441 0.581
(0.927)
0.516
(0.917)
0.231
(0.841)
0.436
(0.906)
0.365
(0.882)
0.585
(0.927)
0.53
(0.917)
0.818
(0.982)
0.384
(0.883)
1
(1.00)
0.0756
(0.679)
0.819
(0.982)
0.0966
(0.705)
0.762
(0.962)
1
(1.00)
7q loss 50 (10%) 451 0.592
(0.927)
0.533
(0.917)
0.901
(1.00)
0.458
(0.906)
0.902
(1.00)
1
(1.00)
0.611
(0.933)
0.0444
(0.612)
0.256
(0.845)
1
(1.00)
0.0973
(0.705)
0.111
(0.715)
0.272
(0.845)
0.471
(0.906)
0.556
(0.917)
8p loss 243 (49%) 258 0.491
(0.909)
0.00308
(0.271)
0.543
(0.917)
0.392
(0.885)
0.658
(0.945)
0.451
(0.906)
0.31
(0.855)
0.0279
(0.57)
0.349
(0.87)
0.275
(0.85)
0.431
(0.906)
0.198
(0.807)
0.878
(1.00)
0.787
(0.973)
0.727
(0.954)
8q loss 54 (11%) 447 0.579
(0.927)
0.137
(0.733)
0.0795
(0.691)
0.24
(0.845)
0.605
(0.93)
0.561
(0.92)
0.249
(0.845)
0.0468
(0.612)
0.617
(0.938)
0.619
(0.938)
0.0936
(0.705)
0.00168
(0.271)
0.71
(0.954)
0.0415
(0.612)
0.556
(0.917)
9p loss 315 (63%) 186 0.955
(1.00)
0.616
(0.938)
0.339
(0.862)
0.739
(0.956)
0.216
(0.816)
0.716
(0.954)
0.674
(0.948)
1
(1.00)
0.319
(0.855)
0.0632
(0.679)
0.146
(0.747)
0.447
(0.906)
0.795
(0.975)
0.918
(1.00)
0.465
(0.906)
9q loss 247 (49%) 254 0.56
(0.92)
0.00119
(0.271)
0.542
(0.917)
0.198
(0.807)
0.747
(0.961)
0.271
(0.845)
0.919
(1.00)
0.041
(0.612)
0.95
(1.00)
0.0727
(0.679)
0.706
(0.954)
0.0202
(0.57)
0.353
(0.872)
0.56
(0.92)
0.067
(0.679)
10p loss 215 (43%) 286 0.38
(0.883)
0.699
(0.954)
0.534
(0.917)
0.942
(1.00)
0.809
(0.981)
0.142
(0.744)
0.472
(0.906)
0.77
(0.962)
0.941
(1.00)
0.899
(1.00)
0.332
(0.855)
0.227
(0.839)
0.31
(0.855)
0.416
(0.906)
0.733
(0.954)
10q loss 229 (46%) 272 0.169
(0.769)
0.106
(0.711)
0.323
(0.855)
0.298
(0.855)
0.919
(1.00)
0.133
(0.733)
0.306
(0.855)
0.305
(0.855)
0.314
(0.855)
0.793
(0.973)
0.878
(1.00)
0.194
(0.803)
0.259
(0.845)
0.291
(0.855)
1
(1.00)
11p loss 169 (34%) 332 0.811
(0.981)
0.139
(0.733)
0.47
(0.906)
0.479
(0.906)
0.317
(0.855)
0.24
(0.845)
0.332
(0.855)
0.878
(1.00)
0.228
(0.839)
0.428
(0.906)
0.208
(0.809)
0.476
(0.906)
0.968
(1.00)
0.241
(0.845)
0.718
(0.954)
11q loss 143 (29%) 358 0.713
(0.954)
0.0479
(0.612)
0.666
(0.945)
0.542
(0.917)
0.048
(0.612)
1
(1.00)
0.178
(0.78)
0.15
(0.751)
0.458
(0.906)
0.72
(0.954)
0.827
(0.987)
0.195
(0.803)
0.329
(0.855)
0.471
(0.906)
1
(1.00)
12p loss 39 (8%) 462 0.607
(0.932)
0.585
(0.927)
0.376
(0.883)
0.399
(0.886)
0.431
(0.906)
1
(1.00)
0.707
(0.954)
0.289
(0.855)
0.641
(0.945)
0.057
(0.656)
0.0197
(0.57)
0.364
(0.882)
1
(1.00)
0.192
(0.803)
1
(1.00)
12q loss 47 (9%) 454 0.765
(0.962)
0.732
(0.954)
0.285
(0.855)
0.688
(0.951)
0.652
(0.945)
1
(1.00)
0.6
(0.929)
0.452
(0.906)
0.699
(0.954)
0.0598
(0.667)
0.115
(0.731)
0.758
(0.962)
0.641
(0.945)
0.208
(0.809)
1
(1.00)
13q loss 311 (62%) 190 0.0907
(0.705)
0.511
(0.917)
0.17
(0.769)
0.278
(0.853)
0.386
(0.883)
0.432
(0.906)
0.834
(0.99)
0.879
(1.00)
0.451
(0.906)
0.00275
(0.271)
0.592
(0.927)
0.322
(0.855)
0.858
(1.00)
0.0607
(0.667)
0.023
(0.57)
14q loss 167 (33%) 334 0.0965
(0.705)
0.814
(0.981)
0.0926
(0.705)
0.0924
(0.705)
0.105
(0.711)
0.101
(0.709)
0.59
(0.927)
0.756
(0.962)
0.489
(0.909)
0.161
(0.766)
0.295
(0.855)
0.526
(0.917)
0.629
(0.943)
0.809
(0.981)
0.269
(0.845)
15q loss 141 (28%) 360 0.632
(0.943)
0.42
(0.906)
0.0824
(0.691)
0.421
(0.906)
0.118
(0.731)
0.397
(0.886)
0.573
(0.927)
0.251
(0.845)
0.0205
(0.57)
0.243
(0.845)
0.609
(0.932)
0.782
(0.972)
0.691
(0.951)
0.0975
(0.705)
1
(1.00)
16p loss 163 (33%) 338 0.441
(0.906)
0.917
(1.00)
0.0999
(0.709)
0.337
(0.857)
0.44
(0.906)
0.435
(0.906)
0.328
(0.855)
0.643
(0.945)
0.652
(0.945)
0.0698
(0.679)
0.243
(0.845)
0.835
(0.991)
0.144
(0.745)
0.0583
(0.658)
1
(1.00)
16q loss 184 (37%) 317 0.185
(0.8)
0.508
(0.917)
0.534
(0.917)
0.668
(0.945)
0.746
(0.961)
0.263
(0.845)
0.0909
(0.705)
0.651
(0.945)
0.45
(0.906)
0.16
(0.766)
0.043
(0.612)
0.877
(1.00)
0.483
(0.907)
0.263
(0.845)
0.717
(0.954)
17p loss 292 (58%) 209 0.496
(0.914)
0.117
(0.731)
0.919
(1.00)
0.499
(0.914)
0.0351
(0.61)
0.704
(0.954)
0.757
(0.962)
0.769
(0.962)
0.632
(0.943)
0.597
(0.929)
0.0483
(0.612)
0.307
(0.855)
0.332
(0.855)
0.389
(0.883)
1
(1.00)
17q loss 91 (18%) 410 0.126
(0.731)
0.0281
(0.57)
0.948
(1.00)
0.279
(0.853)
0.0394
(0.612)
0.621
(0.939)
0.29
(0.855)
0.575
(0.927)
0.157
(0.763)
0.202
(0.807)
0.0739
(0.679)
0.379
(0.883)
0.92
(1.00)
0.0704
(0.679)
0.663
(0.945)
18p loss 141 (28%) 360 0.815
(0.981)
0.598
(0.929)
0.0576
(0.656)
0.464
(0.906)
0.901
(1.00)
0.0228
(0.57)
0.311
(0.855)
0.245
(0.845)
0.862
(1.00)
0.848
(0.998)
0.79
(0.973)
0.729
(0.954)
0.834
(0.99)
0.586
(0.927)
0.69
(0.951)
18q loss 190 (38%) 311 0.388
(0.883)
0.4
(0.886)
0.0289
(0.574)
0.203
(0.807)
0.459
(0.906)
0.108
(0.711)
0.529
(0.917)
0.291
(0.855)
0.324
(0.855)
0.885
(1.00)
0.516
(0.917)
0.135
(0.733)
0.17
(0.769)
0.479
(0.906)
0.716
(0.954)
19p loss 162 (32%) 339 0.283
(0.855)
0.668
(0.945)
0.653
(0.945)
0.665
(0.945)
0.0276
(0.57)
0.223
(0.839)
0.327
(0.855)
0.212
(0.816)
0.214
(0.816)
0.593
(0.927)
0.474
(0.906)
0.327
(0.855)
0.552
(0.917)
0.839
(0.991)
1
(1.00)
19q loss 110 (22%) 391 0.529
(0.917)
0.0635
(0.679)
0.385
(0.883)
0.817
(0.982)
0.672
(0.948)
0.657
(0.945)
0.0658
(0.679)
0.0316
(0.599)
0.109
(0.711)
0.225
(0.839)
0.195
(0.803)
0.0119
(0.543)
0.758
(0.962)
0.846
(0.998)
1
(1.00)
20p loss 42 (8%) 459 0.635
(0.945)
0.715
(0.954)
0.883
(1.00)
0.343
(0.868)
0.592
(0.927)
1
(1.00)
0.359
(0.876)
1
(1.00)
0.231
(0.841)
1
(1.00)
0.332
(0.855)
0.428
(0.906)
0.711
(0.954)
0.885
(1.00)
1
(1.00)
20q loss 49 (10%) 452 0.862
(1.00)
0.499
(0.914)
0.509
(0.917)
0.106
(0.711)
0.654
(0.945)
1
(1.00)
1
(1.00)
0.632
(0.943)
0.542
(0.917)
0.587
(0.927)
0.415
(0.906)
0.784
(0.973)
0.42
(0.906)
1
(1.00)
0.556
(0.917)
21q loss 264 (53%) 237 0.513
(0.917)
0.0747
(0.679)
0.228
(0.839)
0.674
(0.948)
0.536
(0.917)
0.134
(0.733)
0.000493
(0.271)
0.464
(0.906)
0.255
(0.845)
0.535
(0.917)
0.792
(0.973)
0.207
(0.809)
0.88
(1.00)
0.399
(0.886)
0.285
(0.855)
22q loss 98 (20%) 403 0.431
(0.906)
0.00272
(0.271)
0.328
(0.855)
0.524
(0.917)
0.0244
(0.57)
0.625
(0.943)
0.798
(0.976)
0.00813
(0.5)
0.498
(0.914)
0.212
(0.816)
0.897
(1.00)
0.0108
(0.521)
0.485
(0.909)
0.215
(0.816)
0.64
(0.945)
xp loss 145 (29%) 356 0.335
(0.857)
0.228
(0.839)
0.561
(0.92)
0.295
(0.855)
0.265
(0.845)
0.679
(0.948)
0.653
(0.945)
0.872
(1.00)
0.397
(0.886)
1
(1.00)
0.591
(0.927)
0.935
(1.00)
0.266
(0.845)
0.593
(0.927)
0.449
(0.906)
xq loss 114 (23%) 387 0.257
(0.845)
0.472
(0.906)
0.491
(0.909)
0.0134
(0.547)
0.564
(0.922)
0.357
(0.872)
0.331
(0.855)
0.728
(0.954)
0.482
(0.906)
0.226
(0.839)
0.215
(0.816)
0.547
(0.917)
0.575
(0.927)
0.257
(0.845)
0.211
(0.816)
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/LUSC-TP/22533933/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUSC-TP/22506957/LUSC-TP.merged_data.txt

  • Number of patients = 501

  • Number of significantly arm-level cnvs = 82

  • 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.

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)