Correlation between copy number variation genes (focal events) 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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1H131FF
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 83 focal events and 15 clinical features across 501 patients, 4 significant findings detected with Q value < 0.25.

  • amp_7p11.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_20q11.21 cnv correlated to 'GENDER'.

  • amp_xq28 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_2q22.1 cnv correlated to 'YEARS_TO_BIRTH'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 83 focal events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 4 significant findings 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
amp 7p11 2 256 (51%) 245 0.00234
(0.288)
0.471
(0.88)
0.0117
(0.4)
0.00034
(0.181)
0.158
(0.757)
0.451
(0.88)
0.221
(0.78)
0.662
(0.962)
0.632
(0.946)
0.178
(0.771)
0.312
(0.839)
0.514
(0.9)
0.634
(0.948)
0.0142
(0.4)
0.284
(0.825)
amp 20q11 21 306 (61%) 195 0.274
(0.823)
0.314
(0.839)
0.507
(0.897)
0.0961
(0.647)
0.0324
(0.482)
0.265
(0.822)
6.7e-05
(0.0834)
0.655
(0.961)
0.537
(0.909)
0.0351
(0.506)
0.958
(1.00)
0.319
(0.84)
0.792
(0.977)
0.923
(1.00)
0.153
(0.757)
amp xq28 124 (25%) 377 0.403
(0.88)
0.967
(1.00)
0.0392
(0.51)
0.00051
(0.181)
0.243
(0.809)
0.683
(0.962)
0.158
(0.757)
0.313
(0.839)
0.0612
(0.565)
1
(1.00)
0.61
(0.941)
0.155
(0.757)
0.853
(0.995)
0.615
(0.941)
0.206
(0.777)
del 2q22 1 131 (26%) 370 0.889
(0.997)
0.000582
(0.181)
0.0984
(0.652)
0.718
(0.962)
0.0463
(0.533)
0.684
(0.962)
0.131
(0.717)
0.865
(0.996)
0.813
(0.986)
0.439
(0.88)
0.994
(1.00)
0.0109
(0.4)
0.388
(0.877)
0.482
(0.885)
0.686
(0.962)
amp 1q21 2 258 (51%) 243 0.47
(0.88)
0.0906
(0.641)
0.154
(0.757)
0.0183
(0.411)
0.176
(0.77)
0.13
(0.717)
0.126
(0.717)
0.056
(0.556)
0.756
(0.969)
0.00929
(0.393)
0.873
(0.996)
0.441
(0.88)
0.711
(0.962)
0.625
(0.946)
0.724
(0.962)
amp 2p16 1 275 (55%) 226 0.0814
(0.623)
0.906
(1.00)
0.0959
(0.647)
0.0765
(0.611)
0.0771
(0.611)
1
(1.00)
0.00406
(0.288)
0.24
(0.809)
0.031
(0.482)
0.0221
(0.424)
0.156
(0.757)
0.186
(0.771)
0.536
(0.909)
0.198
(0.777)
0.0292
(0.482)
amp 2q31 2 172 (34%) 329 0.194
(0.777)
0.33
(0.844)
0.265
(0.822)
0.632
(0.946)
0.624
(0.946)
1
(1.00)
0.0243
(0.445)
0.759
(0.969)
0.626
(0.946)
0.313
(0.839)
0.0148
(0.4)
0.079
(0.619)
0.392
(0.878)
0.568
(0.927)
1
(1.00)
amp 3q26 33 452 (90%) 49 0.0869
(0.636)
0.601
(0.937)
0.241
(0.809)
0.817
(0.986)
0.964
(1.00)
1
(1.00)
0.039
(0.51)
0.142
(0.74)
0.0211
(0.411)
0.0211
(0.411)
0.565
(0.925)
0.626
(0.946)
0.8
(0.98)
0.0714
(0.585)
0.568
(0.927)
amp 4q12 119 (24%) 382 0.776
(0.973)
0.049
(0.55)
0.279
(0.823)
0.44
(0.88)
0.879
(0.996)
0.36
(0.865)
1
(1.00)
0.384
(0.873)
0.547
(0.911)
0.513
(0.9)
0.339
(0.849)
0.0311
(0.482)
0.979
(1.00)
0.487
(0.885)
0.207
(0.777)
amp 5p15 33 387 (77%) 114 0.315
(0.839)
0.582
(0.932)
0.0193
(0.411)
0.251
(0.809)
0.0177
(0.411)
0.655
(0.961)
0.331
(0.844)
0.49
(0.886)
0.13
(0.717)
0.523
(0.904)
0.468
(0.88)
0.667
(0.962)
0.857
(0.995)
0.204
(0.777)
0.685
(0.962)
amp 5p12 354 (71%) 147 0.761
(0.969)
0.323
(0.84)
0.109
(0.671)
0.211
(0.778)
0.261
(0.822)
1
(1.00)
0.00994
(0.393)
0.751
(0.969)
0.304
(0.837)
0.0688
(0.579)
0.17
(0.763)
0.231
(0.805)
0.37
(0.872)
0.211
(0.778)
1
(1.00)
amp 6p12 1 166 (33%) 335 0.388
(0.877)
0.181
(0.771)
0.409
(0.88)
0.0357
(0.506)
0.863
(0.995)
0.43
(0.88)
0.518
(0.904)
0.0429
(0.519)
0.879
(0.996)
0.341
(0.851)
0.926
(1.00)
0.303
(0.837)
0.795
(0.978)
0.336
(0.845)
0.723
(0.962)
amp 6q12 152 (30%) 349 0.582
(0.932)
0.154
(0.757)
0.794
(0.978)
0.647
(0.959)
0.814
(0.986)
0.681
(0.962)
0.183
(0.771)
0.522
(0.904)
0.541
(0.909)
0.492
(0.886)
0.489
(0.886)
0.0734
(0.598)
0.879
(0.996)
0.202
(0.777)
1
(1.00)
amp 7q21 2 264 (53%) 237 0.0199
(0.411)
0.337
(0.846)
0.383
(0.873)
0.0121
(0.4)
0.243
(0.809)
0.459
(0.88)
0.0141
(0.4)
0.663
(0.962)
0.262
(0.822)
0.214
(0.778)
0.52
(0.904)
0.483
(0.885)
0.497
(0.889)
0.316
(0.84)
0.502
(0.894)
amp 8p11 23 238 (48%) 263 0.0595
(0.556)
0.73
(0.962)
0.907
(1.00)
0.494
(0.886)
0.977
(1.00)
0.713
(0.962)
0.00303
(0.288)
0.77
(0.971)
0.228
(0.799)
0.343
(0.853)
0.665
(0.962)
0.531
(0.905)
0.0128
(0.4)
0.417
(0.88)
0.299
(0.837)
amp 8q24 21 352 (70%) 149 0.247
(0.809)
0.796
(0.978)
0.0244
(0.445)
0.0241
(0.445)
0.185
(0.771)
0.199
(0.777)
0.0743
(0.601)
0.874
(0.996)
0.0414
(0.51)
0.612
(0.941)
0.426
(0.88)
0.745
(0.969)
0.164
(0.757)
0.373
(0.873)
0.443
(0.88)
amp 9p13 3 136 (27%) 365 0.709
(0.962)
0.206
(0.777)
0.118
(0.705)
0.475
(0.88)
0.218
(0.778)
0.405
(0.88)
0.819
(0.986)
1
(1.00)
0.459
(0.88)
0.0911
(0.641)
0.807
(0.983)
0.537
(0.909)
0.187
(0.771)
0.552
(0.915)
1
(1.00)
amp 11q13 3 185 (37%) 316 0.89
(0.997)
0.73
(0.962)
0.559
(0.923)
0.458
(0.88)
0.654
(0.961)
0.435
(0.88)
0.17
(0.763)
0.879
(0.996)
0.553
(0.916)
0.758
(0.969)
0.773
(0.973)
0.573
(0.931)
0.801
(0.98)
0.486
(0.885)
1
(1.00)
amp 12p13 33 255 (51%) 246 0.585
(0.933)
0.83
(0.989)
0.13
(0.717)
0.0781
(0.615)
0.326
(0.841)
0.449
(0.88)
0.025
(0.445)
0.884
(0.997)
0.412
(0.88)
0.75
(0.969)
0.949
(1.00)
0.725
(0.962)
0.749
(0.969)
0.164
(0.757)
1
(1.00)
amp 12q15 178 (36%) 323 0.614
(0.941)
0.583
(0.932)
0.777
(0.973)
0.661
(0.962)
0.447
(0.88)
1
(1.00)
0.0889
(0.641)
0.54
(0.909)
0.109
(0.671)
0.812
(0.986)
0.675
(0.962)
0.887
(0.997)
1
(1.00)
0.583
(0.932)
0.471
(0.88)
amp 13q34 91 (18%) 410 0.815
(0.986)
0.163
(0.757)
0.654
(0.961)
0.0703
(0.582)
0.201
(0.777)
1
(1.00)
0.512
(0.9)
0.849
(0.995)
0.582
(0.932)
0.0461
(0.533)
0.414
(0.88)
0.591
(0.937)
0.484
(0.885)
0.732
(0.962)
1
(1.00)
amp 14q13 3 159 (32%) 342 0.0412
(0.51)
0.0083
(0.393)
0.157
(0.757)
0.357
(0.865)
0.174
(0.77)
1
(1.00)
0.913
(1.00)
0.876
(0.996)
0.583
(0.932)
0.862
(0.995)
0.423
(0.88)
0.514
(0.9)
0.493
(0.886)
0.957
(1.00)
0.00956
(0.393)
amp 14q32 33 158 (32%) 343 0.0404
(0.51)
0.262
(0.822)
0.22
(0.778)
0.0201
(0.411)
0.798
(0.979)
0.686
(0.962)
0.324
(0.84)
0.53
(0.905)
0.766
(0.969)
0.751
(0.969)
0.458
(0.88)
0.733
(0.962)
0.819
(0.986)
0.751
(0.969)
0.05
(0.551)
amp 15q26 3 179 (36%) 322 0.763
(0.969)
0.254
(0.812)
0.764
(0.969)
0.279
(0.823)
0.0939
(0.646)
1
(1.00)
0.524
(0.904)
1
(1.00)
0.202
(0.777)
0.462
(0.88)
0.725
(0.962)
0.852
(0.995)
0.294
(0.834)
0.406
(0.88)
0.718
(0.962)
amp 17q25 1 236 (47%) 265 0.759
(0.969)
0.137
(0.73)
0.067
(0.579)
0.00344
(0.288)
0.00271
(0.288)
0.267
(0.822)
0.00215
(0.288)
0.0402
(0.51)
0.312
(0.839)
0.391
(0.877)
0.779
(0.973)
0.00594
(0.352)
0.631
(0.946)
0.548
(0.911)
0.735
(0.962)
amp 18p11 32 179 (36%) 322 0.829
(0.989)
0.0812
(0.623)
0.8
(0.98)
0.255
(0.812)
0.397
(0.88)
1
(1.00)
0.288
(0.829)
0.17
(0.763)
0.00521
(0.325)
0.842
(0.992)
0.732
(0.962)
0.135
(0.726)
0.333
(0.845)
0.105
(0.67)
0.718
(0.962)
amp 18q11 2 151 (30%) 350 0.69
(0.962)
0.322
(0.84)
0.706
(0.962)
0.154
(0.757)
0.0146
(0.4)
0.681
(0.962)
1
(1.00)
0.00656
(0.371)
0.0361
(0.506)
0.855
(0.995)
0.833
(0.99)
0.83
(0.989)
0.645
(0.959)
0.349
(0.861)
1
(1.00)
amp 19q12 225 (45%) 276 0.199
(0.777)
0.534
(0.908)
0.0591
(0.556)
0.464
(0.88)
0.0146
(0.4)
0.707
(0.962)
0.306
(0.837)
0.304
(0.837)
0.766
(0.969)
0.497
(0.889)
0.251
(0.809)
0.0526
(0.555)
0.707
(0.962)
0.647
(0.959)
1
(1.00)
amp 19q13 2 234 (47%) 267 0.193
(0.777)
0.587
(0.935)
0.467
(0.88)
0.156
(0.757)
0.115
(0.693)
1
(1.00)
0.0188
(0.411)
0.884
(0.997)
0.367
(0.868)
0.125
(0.717)
0.0566
(0.556)
0.00948
(0.393)
0.986
(1.00)
0.854
(0.995)
0.736
(0.962)
amp 20p12 2 280 (56%) 221 0.043
(0.519)
0.181
(0.771)
0.274
(0.823)
0.0321
(0.482)
0.856
(0.995)
0.247
(0.809)
0.00293
(0.288)
0.658
(0.962)
0.0188
(0.411)
0.626
(0.946)
0.555
(0.919)
0.54
(0.909)
0.721
(0.962)
0.731
(0.962)
0.0769
(0.611)
amp 22q11 21 256 (51%) 245 0.0999
(0.658)
0.206
(0.777)
0.0284
(0.477)
0.0891
(0.641)
0.162
(0.757)
0.457
(0.88)
0.103
(0.668)
0.383
(0.873)
0.914
(1.00)
0.18
(0.771)
0.175
(0.77)
0.0303
(0.482)
0.0704
(0.582)
0.0871
(0.636)
1
(1.00)
del 1p36 11 228 (46%) 273 0.353
(0.862)
0.00768
(0.393)
0.251
(0.809)
0.468
(0.88)
0.206
(0.777)
1
(1.00)
0.0409
(0.51)
0.0122
(0.4)
0.305
(0.837)
0.377
(0.873)
0.859
(0.995)
0.0544
(0.555)
0.911
(1.00)
0.961
(1.00)
0.475
(0.88)
del 1p13 1 221 (44%) 280 0.451
(0.88)
0.00125
(0.288)
0.211
(0.778)
0.897
(0.999)
0.0325
(0.482)
0.461
(0.88)
0.305
(0.837)
0.461
(0.88)
0.892
(0.997)
0.931
(1.00)
0.294
(0.834)
0.0209
(0.411)
0.719
(0.962)
0.374
(0.873)
0.0837
(0.628)
del 2p25 3 50 (10%) 451 0.974
(1.00)
0.0931
(0.646)
0.238
(0.809)
0.0407
(0.51)
0.112
(0.683)
0.544
(0.91)
0.31
(0.839)
0.803
(0.98)
0.194
(0.777)
0.17
(0.763)
0.474
(0.88)
0.76
(0.969)
0.874
(0.996)
0.0583
(0.556)
0.543
(0.91)
del 2q37 1 159 (32%) 342 0.706
(0.962)
0.00419
(0.288)
0.88
(0.996)
0.959
(1.00)
0.204
(0.777)
0.445
(0.88)
0.444
(0.88)
0.435
(0.88)
0.3
(0.837)
0.821
(0.987)
0.6
(0.937)
0.0204
(0.411)
0.529
(0.905)
0.915
(1.00)
0.712
(0.962)
del 3p25 3 398 (79%) 103 0.877
(0.996)
0.406
(0.88)
0.84
(0.992)
0.723
(0.962)
0.408
(0.88)
1
(1.00)
0.801
(0.98)
0.857
(0.995)
0.27
(0.823)
0.0367
(0.508)
0.379
(0.873)
0.529
(0.905)
0.564
(0.924)
0.47
(0.88)
0.683
(0.962)
del 3p13 434 (87%) 67 0.756
(0.969)
0.513
(0.9)
0.411
(0.88)
0.649
(0.96)
0.906
(1.00)
0.6
(0.937)
0.654
(0.961)
1
(1.00)
0.325
(0.84)
0.0477
(0.54)
0.621
(0.946)
0.61
(0.941)
0.189
(0.774)
0.0463
(0.533)
0.605
(0.937)
del 3p12 3 427 (85%) 74 0.494
(0.886)
0.464
(0.88)
0.652
(0.961)
0.421
(0.88)
0.785
(0.976)
0.601
(0.937)
0.667
(0.962)
0.832
(0.99)
0.172
(0.77)
0.0908
(0.641)
0.686
(0.962)
0.854
(0.995)
0.273
(0.823)
0.105
(0.67)
0.616
(0.941)
del 3p12 3 421 (84%) 80 0.701
(0.962)
0.401
(0.88)
0.672
(0.962)
0.289
(0.831)
0.561
(0.924)
0.606
(0.937)
0.781
(0.973)
1
(1.00)
0.285
(0.825)
0.131
(0.717)
0.841
(0.992)
0.828
(0.989)
0.383
(0.873)
0.118
(0.704)
0.362
(0.865)
del 3q11 1 79 (16%) 422 0.0379
(0.51)
0.753
(0.969)
0.558
(0.923)
0.576
(0.931)
0.723
(0.962)
0.278
(0.823)
1
(1.00)
0.109
(0.671)
0.864
(0.995)
0.164
(0.757)
0.129
(0.717)
0.469
(0.88)
0.785
(0.976)
0.922
(1.00)
0.0305
(0.482)
del 4p15 2 316 (63%) 185 0.528
(0.905)
0.0874
(0.636)
0.38
(0.873)
0.204
(0.777)
0.664
(0.962)
0.714
(0.962)
0.207
(0.777)
0.0685
(0.579)
0.819
(0.986)
0.281
(0.824)
0.876
(0.996)
0.248
(0.809)
0.575
(0.931)
0.086
(0.636)
1
(1.00)
del 4q22 1 285 (57%) 216 0.593
(0.937)
0.276
(0.823)
0.0166
(0.411)
0.0939
(0.646)
0.595
(0.937)
0.248
(0.809)
0.306
(0.837)
0.46
(0.88)
0.862
(0.995)
0.418
(0.88)
0.068
(0.579)
0.926
(1.00)
0.541
(0.909)
0.197
(0.777)
0.736
(0.962)
del 4q32 3 329 (66%) 172 0.729
(0.962)
0.154
(0.757)
0.0155
(0.403)
0.0247
(0.445)
0.423
(0.88)
0.242
(0.809)
0.336
(0.845)
0.76
(0.969)
0.92
(1.00)
0.0274
(0.474)
0.105
(0.67)
0.674
(0.962)
0.526
(0.905)
0.356
(0.865)
1
(1.00)
del 4q35 2 331 (66%) 170 0.484
(0.885)
0.469
(0.88)
0.0255
(0.447)
0.147
(0.757)
0.164
(0.757)
0.237
(0.809)
0.668
(0.962)
0.759
(0.969)
0.283
(0.824)
0.0804
(0.623)
0.0591
(0.556)
0.946
(1.00)
0.668
(0.962)
0.242
(0.809)
1
(1.00)
del 5q12 1 369 (74%) 132 0.794
(0.978)
0.912
(1.00)
0.435
(0.88)
0.216
(0.778)
0.384
(0.873)
0.197
(0.777)
0.0828
(0.628)
1
(1.00)
0.847
(0.995)
0.182
(0.771)
0.466
(0.88)
0.129
(0.717)
0.434
(0.88)
0.0596
(0.556)
1
(1.00)
del 5q31 1 386 (77%) 115 0.818
(0.986)
0.212
(0.778)
0.108
(0.671)
0.647
(0.959)
0.702
(0.962)
0.359
(0.865)
0.468
(0.88)
0.862
(0.995)
0.744
(0.969)
0.218
(0.778)
0.891
(0.997)
0.0662
(0.579)
0.485
(0.885)
0.0897
(0.641)
1
(1.00)
del 6p25 3 134 (27%) 367 0.277
(0.823)
0.201
(0.777)
0.278
(0.823)
0.911
(1.00)
0.441
(0.88)
0.4
(0.88)
0.135
(0.726)
0.14
(0.738)
0.579
(0.932)
0.89
(0.997)
0.816
(0.986)
0.782
(0.973)
0.216
(0.778)
0.503
(0.894)
0.219
(0.778)
del 6q26 135 (27%) 366 0.272
(0.823)
0.547
(0.911)
0.881
(0.996)
0.763
(0.969)
0.725
(0.962)
0.679
(0.962)
0.731
(0.962)
0.41
(0.88)
0.889
(0.997)
0.616
(0.941)
0.421
(0.88)
0.214
(0.778)
0.362
(0.865)
0.948
(1.00)
1
(1.00)
del 7q11 22 48 (10%) 453 0.492
(0.886)
0.521
(0.904)
0.461
(0.88)
0.872
(0.996)
0.965
(1.00)
1
(1.00)
0.605
(0.937)
0.804
(0.98)
0.169
(0.763)
1
(1.00)
0.896
(0.999)
0.855
(0.995)
0.201
(0.777)
1
(1.00)
1
(1.00)
del 7q36 3 104 (21%) 397 0.778
(0.973)
0.126
(0.717)
0.215
(0.778)
0.435
(0.88)
0.56
(0.923)
0.354
(0.862)
1
(1.00)
0.205
(0.777)
0.246
(0.809)
0.742
(0.967)
0.434
(0.88)
0.0115
(0.4)
0.471
(0.88)
0.614
(0.941)
0.667
(0.962)
del 8p23 2 341 (68%) 160 0.625
(0.946)
0.00854
(0.393)
0.531
(0.905)
0.702
(0.962)
0.204
(0.777)
0.204
(0.777)
0.328
(0.842)
0.353
(0.862)
0.322
(0.84)
0.295
(0.834)
0.597
(0.937)
0.639
(0.952)
0.603
(0.937)
0.705
(0.962)
1
(1.00)
del 9p23 332 (66%) 169 0.849
(0.995)
0.604
(0.937)
0.511
(0.9)
0.502
(0.894)
0.346
(0.856)
0.43
(0.88)
0.197
(0.777)
0.359
(0.865)
0.54
(0.909)
0.0358
(0.506)
0.319
(0.84)
0.575
(0.931)
0.924
(1.00)
0.304
(0.837)
0.448
(0.88)
del 9p21 3 388 (77%) 113 0.591
(0.937)
0.686
(0.962)
0.209
(0.778)
0.917
(1.00)
0.0151
(0.4)
1
(1.00)
0.0678
(0.579)
0.863
(0.995)
0.778
(0.973)
0.00407
(0.288)
0.436
(0.88)
0.942
(1.00)
0.345
(0.856)
0.802
(0.98)
0.4
(0.88)
del 9p21 1 326 (65%) 175 0.871
(0.996)
0.318
(0.84)
0.0525
(0.555)
0.163
(0.757)
0.308
(0.837)
0.259
(0.822)
0.915
(1.00)
0.358
(0.865)
0.238
(0.809)
0.0159
(0.403)
0.147
(0.757)
0.593
(0.937)
0.72
(0.962)
0.296
(0.834)
0.278
(0.823)
del 9q21 11 251 (50%) 250 0.375
(0.873)
0.00367
(0.288)
0.901
(1.00)
0.264
(0.822)
0.829
(0.989)
0.722
(0.962)
0.185
(0.771)
0.0186
(0.411)
0.791
(0.977)
0.0589
(0.556)
0.88
(0.996)
0.129
(0.717)
0.134
(0.726)
0.631
(0.946)
0.067
(0.579)
del 10p15 3 228 (46%) 273 0.259
(0.822)
0.482
(0.885)
0.442
(0.88)
0.365
(0.865)
0.892
(0.997)
0.13
(0.717)
0.683
(0.962)
0.77
(0.971)
0.477
(0.882)
0.791
(0.977)
0.185
(0.771)
0.343
(0.853)
0.597
(0.937)
0.372
(0.873)
0.735
(0.962)
del 10p15 1 211 (42%) 290 0.195
(0.777)
0.671
(0.962)
0.819
(0.986)
0.297
(0.834)
1
(1.00)
0.247
(0.809)
0.471
(0.88)
0.464
(0.88)
0.329
(0.842)
0.929
(1.00)
0.213
(0.778)
0.22
(0.778)
0.782
(0.973)
0.504
(0.894)
1
(1.00)
del 10q23 31 268 (53%) 233 0.29
(0.833)
0.939
(1.00)
0.734
(0.962)
0.379
(0.873)
0.732
(0.962)
0.053
(0.555)
0.0835
(0.628)
1
(1.00)
0.219
(0.778)
0.629
(0.946)
0.598
(0.937)
0.72
(0.962)
0.84
(0.992)
0.457
(0.88)
1
(1.00)
del 11p15 5 245 (49%) 256 0.365
(0.865)
0.23
(0.804)
0.545
(0.911)
0.0675
(0.579)
0.707
(0.962)
0.723
(0.962)
0.187
(0.771)
0.383
(0.873)
0.0932
(0.646)
0.966
(1.00)
0.523
(0.904)
0.989
(1.00)
0.889
(0.997)
0.179
(0.771)
0.293
(0.834)
del 11q22 1 163 (33%) 338 0.9
(1.00)
0.927
(1.00)
0.272
(0.823)
0.313
(0.839)
0.0557
(0.556)
1
(1.00)
0.385
(0.873)
0.28
(0.823)
0.168
(0.763)
0.791
(0.977)
0.592
(0.937)
0.839
(0.992)
0.728
(0.962)
0.838
(0.992)
0.723
(0.962)
del 11q25 184 (37%) 317 0.822
(0.987)
0.46
(0.88)
0.474
(0.88)
0.274
(0.823)
0.0474
(0.54)
1
(1.00)
0.113
(0.685)
0.765
(0.969)
0.068
(0.579)
0.455
(0.88)
0.293
(0.834)
0.567
(0.927)
0.562
(0.924)
0.812
(0.986)
0.715
(0.962)
del 12q24 31 86 (17%) 415 0.328
(0.842)
0.509
(0.9)
0.216
(0.778)
0.38
(0.873)
0.544
(0.91)
1
(1.00)
0.177
(0.77)
0.0516
(0.555)
0.176
(0.77)
0.756
(0.969)
0.103
(0.668)
0.44
(0.88)
0.404
(0.88)
0.0496
(0.551)
0.361
(0.865)
del 13q12 11 331 (66%) 170 0.706
(0.962)
0.584
(0.933)
0.0438
(0.524)
0.143
(0.741)
0.751
(0.969)
0.691
(0.962)
0.914
(1.00)
1
(1.00)
0.959
(1.00)
0.176
(0.77)
0.869
(0.996)
0.0516
(0.555)
0.636
(0.95)
0.448
(0.88)
0.159
(0.757)
del 13q14 2 344 (69%) 157 0.354
(0.862)
0.829
(0.989)
0.458
(0.88)
0.726
(0.962)
0.842
(0.992)
0.439
(0.88)
0.324
(0.84)
0.527
(0.905)
0.911
(1.00)
0.0389
(0.51)
0.462
(0.88)
0.692
(0.962)
0.737
(0.962)
0.334
(0.845)
0.0543
(0.555)
del 14q11 2 175 (35%) 326 0.0683
(0.579)
0.365
(0.865)
0.254
(0.812)
0.239
(0.809)
0.928
(1.00)
0.101
(0.663)
0.831
(0.989)
0.44
(0.88)
0.696
(0.962)
0.14
(0.737)
0.47
(0.88)
0.915
(1.00)
0.875
(0.996)
0.598
(0.937)
0.717
(0.962)
del 15q11 2 167 (33%) 334 0.326
(0.841)
0.131
(0.717)
0.021
(0.411)
0.341
(0.851)
0.00869
(0.393)
0.689
(0.962)
0.161
(0.757)
0.434
(0.88)
0.0179
(0.411)
0.397
(0.88)
0.503
(0.894)
0.666
(0.962)
0.664
(0.962)
0.197
(0.777)
1
(1.00)
del 15q21 1 169 (34%) 332 0.385
(0.873)
0.137
(0.73)
0.0307
(0.482)
0.627
(0.946)
0.0149
(0.4)
0.688
(0.962)
0.389
(0.877)
0.163
(0.757)
0.0101
(0.393)
0.156
(0.757)
0.622
(0.946)
0.487
(0.885)
0.78
(0.973)
0.0815
(0.623)
0.716
(0.962)
del 16p13 3 187 (37%) 314 0.407
(0.88)
0.154
(0.757)
0.124
(0.717)
0.12
(0.706)
0.396
(0.88)
0.715
(0.962)
0.6
(0.937)
0.88
(0.996)
0.936
(1.00)
0.295
(0.834)
0.364
(0.865)
0.445
(0.88)
0.0565
(0.556)
0.318
(0.84)
1
(1.00)
del 16q23 1 210 (42%) 291 0.188
(0.771)
0.964
(1.00)
0.451
(0.88)
0.188
(0.771)
0.872
(0.996)
0.704
(0.962)
0.123
(0.717)
0.14
(0.737)
0.113
(0.685)
0.119
(0.705)
0.0325
(0.482)
0.304
(0.837)
0.922
(1.00)
0.487
(0.885)
0.475
(0.88)
del 17p11 2 272 (54%) 229 0.732
(0.962)
0.276
(0.823)
0.984
(1.00)
0.626
(0.946)
0.458
(0.88)
0.46
(0.88)
0.262
(0.822)
0.662
(0.962)
0.243
(0.809)
0.419
(0.88)
0.0123
(0.4)
0.218
(0.778)
0.606
(0.937)
0.926
(1.00)
1
(1.00)
del 17q11 2 132 (26%) 369 0.442
(0.88)
0.039
(0.51)
0.128
(0.717)
0.285
(0.825)
0.00355
(0.288)
0.379
(0.873)
0.563
(0.924)
0.407
(0.88)
0.722
(0.962)
0.267
(0.822)
0.373
(0.873)
0.25
(0.809)
0.441
(0.88)
0.137
(0.731)
0.451
(0.88)
del 17q25 3 102 (20%) 399 0.232
(0.806)
0.108
(0.671)
0.484
(0.885)
0.165
(0.758)
0.124
(0.717)
0.353
(0.862)
0.311
(0.839)
0.27
(0.823)
0.156
(0.757)
0.852
(0.995)
0.762
(0.969)
0.0452
(0.533)
0.631
(0.946)
0.332
(0.845)
0.379
(0.873)
del 18q23 234 (47%) 267 0.756
(0.969)
0.0539
(0.555)
0.16
(0.757)
0.149
(0.757)
0.531
(0.905)
0.264
(0.822)
0.00301
(0.288)
1
(1.00)
0.456
(0.88)
0.967
(1.00)
0.836
(0.992)
0.152
(0.757)
0.353
(0.862)
0.859
(0.995)
0.477
(0.882)
del 19p13 3 236 (47%) 265 0.504
(0.894)
0.91
(1.00)
0.662
(0.962)
0.903
(1.00)
0.098
(0.652)
1
(1.00)
0.308
(0.837)
0.465
(0.88)
0.173
(0.77)
0.966
(1.00)
0.336
(0.845)
0.524
(0.904)
0.889
(0.997)
0.0959
(0.647)
0.724
(0.962)
del 19q13 32 149 (30%) 352 0.992
(1.00)
0.176
(0.77)
0.787
(0.976)
0.912
(1.00)
0.681
(0.962)
1
(1.00)
0.0951
(0.647)
0.0544
(0.555)
0.582
(0.932)
0.182
(0.771)
0.894
(0.998)
0.0574
(0.556)
0.249
(0.809)
0.753
(0.969)
1
(1.00)
del 21q11 2 244 (49%) 257 0.213
(0.778)
0.447
(0.88)
0.243
(0.809)
0.987
(1.00)
0.632
(0.946)
0.449
(0.88)
0.0143
(0.4)
0.464
(0.88)
0.324
(0.84)
0.572
(0.931)
0.823
(0.987)
0.582
(0.932)
0.596
(0.937)
0.702
(0.962)
0.156
(0.757)
del 21q22 3 281 (56%) 220 0.442
(0.88)
0.282
(0.824)
0.362
(0.865)
0.537
(0.909)
0.836
(0.992)
0.247
(0.809)
0.00283
(0.288)
0.884
(0.997)
0.252
(0.812)
0.662
(0.962)
0.856
(0.995)
0.377
(0.873)
0.986
(1.00)
0.238
(0.809)
0.301
(0.837)
del 22q11 21 95 (19%) 406 0.297
(0.834)
0.0044
(0.288)
0.517
(0.903)
0.855
(0.995)
0.472
(0.88)
0.616
(0.941)
0.897
(0.999)
0.0627
(0.57)
0.573
(0.931)
0.319
(0.84)
0.791
(0.977)
0.0706
(0.582)
0.35
(0.862)
0.522
(0.904)
1
(1.00)
del 22q13 32 127 (25%) 374 0.976
(1.00)
0.0279
(0.476)
0.391
(0.877)
0.431
(0.88)
0.281
(0.824)
1
(1.00)
0.484
(0.885)
0.0619
(0.567)
0.237
(0.809)
0.107
(0.671)
0.39
(0.877)
0.104
(0.67)
0.806
(0.982)
0.771
(0.971)
0.686
(0.962)
del xp22 2 155 (31%) 346 0.508
(0.898)
0.69
(0.962)
0.00815
(0.393)
0.284
(0.825)
0.0661
(0.579)
0.443
(0.88)
0.271
(0.823)
0.639
(0.952)
0.183
(0.771)
0.711
(0.962)
0.693
(0.962)
0.572
(0.931)
0.649
(0.96)
0.433
(0.88)
0.444
(0.88)
del xp21 1 151 (30%) 350 0.444
(0.88)
0.0845
(0.63)
0.393
(0.878)
0.606
(0.937)
0.142
(0.74)
0.68
(0.962)
0.825
(0.989)
0.752
(0.969)
0.322
(0.84)
0.454
(0.88)
0.78
(0.973)
0.952
(1.00)
0.492
(0.886)
0.652
(0.961)
0.449
(0.88)
del xp11 3 149 (30%) 352 0.726
(0.962)
0.605
(0.937)
0.467
(0.88)
0.266
(0.822)
0.335
(0.845)
0.68
(0.962)
1
(1.00)
0.874
(0.996)
0.247
(0.809)
0.769
(0.971)
0.935
(1.00)
0.279
(0.823)
0.53
(0.905)
0.786
(0.976)
0.688
(0.962)
del xq22 3 114 (23%) 387 0.547
(0.911)
0.307
(0.837)
0.78
(0.973)
0.237
(0.809)
0.439
(0.88)
1
(1.00)
0.224
(0.787)
1
(1.00)
0.265
(0.822)
0.109
(0.671)
0.0349
(0.506)
0.412
(0.88)
0.0598
(0.556)
0.0978
(0.652)
0.364
(0.865)
'amp_7p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00034 (Fisher's exact test), Q value = 0.18

Table S1.  Gene #10: 'amp_7p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 112 294 71 24
AMP PEAK 10(7P11.2) MUTATED 39 171 36 10
AMP PEAK 10(7P11.2) WILD-TYPE 73 123 35 14

Figure S1.  Get High-res Image Gene #10: 'amp_7p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_20q11.21' versus 'GENDER'

P value = 6.7e-05 (Fisher's exact test), Q value = 0.083

Table S2.  Gene #28: 'amp_20q11.21' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 130 371
AMP PEAK 28(20Q11.21) MUTATED 60 246
AMP PEAK 28(20Q11.21) WILD-TYPE 70 125

Figure S2.  Get High-res Image Gene #28: 'amp_20q11.21' versus Clinical Feature #7: 'GENDER'

'amp_xq28' versus 'PATHOLOGY_T_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.18

Table S3.  Gene #30: 'amp_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 112 294 71 24
AMP PEAK 30(XQ28) MUTATED 13 78 23 10
AMP PEAK 30(XQ28) WILD-TYPE 99 216 48 14

Figure S3.  Get High-res Image Gene #30: 'amp_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.000582 (Wilcoxon-test), Q value = 0.18

Table S4.  Gene #34: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 491 67.3 (8.6)
DEL PEAK 4(2Q22.1) MUTATED 129 65.3 (8.1)
DEL PEAK 4(2Q22.1) WILD-TYPE 362 68.0 (8.7)

Figure S4.  Get High-res Image Gene #34: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

Methods & Data
Input
  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/22533935/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 focal cnvs = 83

  • Number of selected clinical features = 15

  • Exclude genes 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)