Correlation between copy number variations of arm-level result and selected clinical features
Lung Squamous Cell Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1X34VF5
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Lung Squamous Cell Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1X34VF5
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 79 arm-level results and 14 clinical features across 325 patients, 11 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 2q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 11p gain cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.

  • 17p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 19p gain cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE' and 'HISTOLOGICAL.TYPE'.

  • 21q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 12p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 12q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 16q loss cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.

  • Xq loss cnv correlated to 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level results and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 11 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED TOBACCOSMOKINGHISTORYINDICATOR YEAROFTOBACCOSMOKINGONSET COMPLETENESS
OF
RESECTION
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test Fisher's exact test t-test Fisher's exact test
19p gain 0 (0%) 292 0.438
(1.00) 		0.227
(1.00) 		0.675
(1.00) 		1.77e-06
(0.00192) 		5.63e-06
(0.0061) 		0.634
(1.00) 		0.378
(1.00) 		0.566
(1.00) 		0.63
(1.00) 		0.309
(1.00) 		0.592
(1.00) 		0.656
(1.00) 		0.83
(1.00) 		0.89
(1.00)
1p gain 0 (0%) 302 0.858
(1.00) 		0.853
(1.00) 		0.0489
(1.00) 		2.88e-08
(3.14e-05) 		0.0379
(1.00) 		1
(1.00) 		0.0321
(1.00) 		0.017
(1.00) 		0.56
(1.00) 		0.566
(1.00) 		0.368
(1.00) 		0.415
(1.00) 		0.602
(1.00)
2q gain 0 (0%) 289 0.198
(1.00) 		0.474
(1.00) 		0.425
(1.00) 		0.903
(1.00) 		8.58e-05
(0.0926) 		0.208
(1.00) 		0.486
(1.00) 		0.168
(1.00) 		0.00299
(1.00) 		0.11
(1.00) 		0.13
(1.00) 		0.938
(1.00) 		0.295
(1.00) 		1
(1.00)
11p gain 0 (0%) 305 0.902
(1.00) 		0.32
(1.00) 		0.426
(1.00) 		2e-06
(0.00217) 		0.954
(1.00) 		0.0123
(1.00) 		0.324
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.508
(1.00) 		0.148
(1.00) 		0.851
(1.00) 		0.541
(1.00) 		0.785
(1.00)
17p gain 0 (0%) 316 0.346
(1.00) 		0.839
(1.00) 		0.118
(1.00) 		3.79e-07
(0.000412) 		0.55
(1.00) 		0.419
(1.00) 		0.294
(1.00) 		0.095
(1.00) 		1
(1.00) 		0.948
(1.00) 		0.143
(1.00) 		0.0232
(1.00) 		0.5
(1.00)
21q gain 0 (0%) 307 0.268
(1.00) 		0.682
(1.00) 		1
(1.00) 		0.949
(1.00) 		5.96e-05
(0.0645) 		0.239
(1.00) 		0.249
(1.00) 		0.72
(1.00) 		0.191
(1.00) 		0.471
(1.00) 		0.865
(1.00) 		0.488
(1.00) 		0.631
(1.00) 		0.0937
(1.00)
12p loss 0 (0%) 321 0.51
(1.00) 		0.0145
(1.00) 		0.27
(1.00) 		1.32e-16
(1.44e-13) 		0.532
(1.00) 		1
(1.00) 		0.364
(1.00) 		0.549
(1.00) 		1
(1.00) 		0.256
(1.00) 		0.339
(1.00) 		1
(1.00)
12q loss 0 (0%) 321 0.864
(1.00) 		0.185
(1.00) 		0.27
(1.00) 		1.32e-16
(1.44e-13) 		0.185
(1.00) 		0.543
(1.00) 		0.364
(1.00) 		0.35
(1.00) 		1
(1.00) 		0.195
(1.00) 		0.327
(1.00) 		1
(1.00)
16q loss 0 (0%) 265 0.133
(1.00) 		0.164
(1.00) 		0.141
(1.00) 		1.77e-06
(0.00192) 		0.674
(1.00) 		0.8
(1.00) 		0.434
(1.00) 		0.138
(1.00) 		0.792
(1.00) 		0.433
(1.00) 		0.0755
(1.00) 		0.299
(1.00) 		0.59
(1.00) 		0.251
(1.00)
Xq loss 0 (0%) 312 0.884
(1.00) 		0.284
(1.00) 		0.329
(1.00) 		0.949
(1.00) 		6.63e-05
(0.0716) 		0.729
(1.00) 		0.15
(1.00) 		1
(1.00) 		0.449
(1.00) 		1
(1.00) 		0.681
(1.00) 		1
(1.00) 		0.788
(1.00) 		1
(1.00)
1q gain 0 (0%) 256 0.386
(1.00) 		0.468
(1.00) 		0.878
(1.00) 		0.358
(1.00) 		0.00453
(1.00) 		0.182
(1.00) 		0.832
(1.00) 		0.267
(1.00) 		0.452
(1.00) 		1
(1.00) 		0.259
(1.00) 		1
(1.00) 		0.52
(1.00) 		0.558
(1.00)
2p gain 0 (0%) 249 0.515
(1.00) 		0.875
(1.00) 		0.0706
(1.00) 		0.126
(1.00) 		0.0106
(1.00) 		0.125
(1.00) 		0.14
(1.00) 		0.173
(1.00) 		0.103
(1.00) 		0.137
(1.00) 		0.021
(1.00) 		0.726
(1.00) 		0.0201
(1.00) 		0.789
(1.00)
3p gain 0 (0%) 291 0.495
(1.00) 		0.127
(1.00) 		0.0609
(1.00) 		0.197
(1.00) 		0.977
(1.00) 		0.0403
(1.00) 		0.796
(1.00) 		0.498
(1.00) 		0.52
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.0688
(1.00) 		0.0561
(1.00) 		0.791
(1.00)
3q gain 0 (0%) 178 0.876
(1.00) 		0.211
(1.00) 		0.899
(1.00) 		0.248
(1.00) 		0.352
(1.00) 		0.373
(1.00) 		0.871
(1.00) 		0.437
(1.00) 		0.669
(1.00) 		0.554
(1.00) 		0.771
(1.00) 		0.0417
(1.00) 		0.0246
(1.00) 		0.878
(1.00)
4p gain 0 (0%) 311 0.33
(1.00) 		0.636
(1.00) 		0.0248
(1.00) 		0.712
(1.00) 		0.763
(1.00) 		0.131
(1.00) 		1
(1.00) 		0.692
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.354
(1.00) 		0.758
(1.00) 		0.404
(1.00) 		0.199
(1.00)
4q gain 0 (0%) 319 0.922
(1.00) 		0.14
(1.00) 		0.344
(1.00) 		0.188
(1.00) 		0.306
(1.00) 		0.663
(1.00) 		1
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.154
(1.00) 		0.122
(1.00) 		1
(1.00)
5p gain 0 (0%) 173 0.411
(1.00) 		0.0716
(1.00) 		0.525
(1.00) 		0.809
(1.00) 		0.328
(1.00) 		0.0376
(1.00) 		0.382
(1.00) 		0.63
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.489
(1.00) 		0.0412
(1.00) 		0.815
(1.00) 		0.0193
(1.00)
5q gain 0 (0%) 291 0.862
(1.00) 		0.286
(1.00) 		0.839
(1.00) 		0.453
(1.00) 		0.977
(1.00) 		0.933
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.598
(1.00) 		0.323
(1.00) 		0.906
(1.00) 		0.638
(1.00) 		0.295
(1.00) 		0.791
(1.00)
6p gain 0 (0%) 294 0.885
(1.00) 		0.327
(1.00) 		1
(1.00) 		0.286
(1.00) 		0.0337
(1.00) 		0.111
(1.00) 		0.657
(1.00) 		0.395
(1.00) 		0.123
(1.00) 		0.283
(1.00) 		0.416
(1.00) 		0.603
(1.00) 		0.013
(1.00) 		0.203
(1.00)
6q gain 0 (0%) 307 0.638
(1.00) 		0.43
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.00148
(1.00) 		0.646
(1.00) 		1
(1.00) 		0.75
(1.00) 		0.959
(1.00) 		0.471
(1.00) 		0.288
(1.00) 		0.71
(1.00) 		0.186
(1.00) 		0.125
(1.00)
7p gain 0 (0%) 235 0.228
(1.00) 		0.158
(1.00) 		0.478
(1.00) 		0.807
(1.00) 		0.379
(1.00) 		0.00393
(1.00) 		0.742
(1.00) 		0.326
(1.00) 		0.448
(1.00) 		0.734
(1.00) 		0.0605
(1.00) 		0.427
(1.00) 		0.355
(1.00) 		0.5
(1.00)
7q gain 0 (0%) 240 0.5
(1.00) 		0.393
(1.00) 		0.314
(1.00) 		0.355
(1.00) 		0.469
(1.00) 		0.00914
(1.00) 		0.721
(1.00) 		0.12
(1.00) 		0.323
(1.00) 		0.734
(1.00) 		0.772
(1.00) 		0.786
(1.00) 		0.52
(1.00) 		0.458
(1.00)
8p gain 0 (0%) 280 0.887
(1.00) 		0.255
(1.00) 		0.855
(1.00) 		0.00638
(1.00) 		0.0959
(1.00) 		0.598
(1.00) 		0.404
(1.00) 		0.0312
(1.00) 		0.191
(1.00) 		0.184
(1.00) 		0.677
(1.00) 		0.708
(1.00) 		0.615
(1.00) 		0.291
(1.00)
8q gain 0 (0%) 230 0.323
(1.00) 		0.301
(1.00) 		0.781
(1.00) 		0.209
(1.00) 		0.869
(1.00) 		0.209
(1.00) 		0.715
(1.00) 		0.0377
(1.00) 		0.0943
(1.00) 		0.309
(1.00) 		0.284
(1.00) 		0.273
(1.00) 		0.262
(1.00) 		0.19
(1.00)
9p gain 0 (0%) 306 0.214
(1.00) 		0.72
(1.00) 		0.279
(1.00) 		0.00127
(1.00) 		0.532
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.795
(1.00) 		1
(1.00) 		0.928
(1.00) 		0.879
(1.00) 		0.882
(1.00) 		0.525
(1.00)
9q gain 0 (0%) 297 0.198
(1.00) 		0.402
(1.00) 		0.657
(1.00) 		0.537
(1.00) 		0.423
(1.00) 		0.382
(1.00) 		0.837
(1.00) 		0.177
(1.00) 		0.725
(1.00) 		0.608
(1.00) 		0.666
(1.00) 		0.619
(1.00) 		0.74
(1.00) 		1
(1.00)
10p gain 0 (0%) 308 0.981
(1.00) 		0.746
(1.00) 		1
(1.00) 		0.936
(1.00) 		0.966
(1.00) 		0.57
(1.00) 		0.0693
(1.00) 		0.231
(1.00) 		0.03
(1.00) 		0.451
(1.00) 		0.179
(1.00) 		0.235
(1.00) 		0.327
(1.00) 		0.223
(1.00)
10q gain 0 (0%) 318 0.571
(1.00) 		0.699
(1.00) 		1
(1.00) 		0.994
(1.00) 		0.387
(1.00) 		0.419
(1.00) 		1
(1.00) 		0.327
(1.00) 		0.216
(1.00) 		0.582
(1.00) 		0.0471
(1.00) 		0.771
(1.00) 		1
(1.00)
11q gain 0 (0%) 303 0.735
(1.00) 		0.588
(1.00) 		0.216
(1.00) 		0.521
(1.00) 		0.932
(1.00) 		0.0512
(1.00) 		0.217
(1.00) 		0.776
(1.00) 		0.123
(1.00) 		0.543
(1.00) 		0.562
(1.00) 		0.478
(1.00) 		0.987
(1.00) 		1
(1.00)
12p gain 0 (0%) 235 0.868
(1.00) 		0.939
(1.00) 		0.00437
(1.00) 		0.0774
(1.00) 		0.884
(1.00) 		0.149
(1.00) 		0.804
(1.00) 		0.862
(1.00) 		0.903
(1.00) 		0.505
(1.00) 		0.965
(1.00) 		0.404
(1.00) 		0.404
(1.00) 		0.698
(1.00)
12q gain 0 (0%) 284 0.569
(1.00) 		0.872
(1.00) 		0.0122
(1.00) 		0.378
(1.00) 		0.978
(1.00) 		0.275
(1.00) 		0.0891
(1.00) 		0.304
(1.00) 		0.201
(1.00) 		0.636
(1.00) 		0.48
(1.00) 		0.343
(1.00) 		0.987
(1.00) 		0.61
(1.00)
13q gain 0 (0%) 317 0.275
(1.00) 		0.937
(1.00) 		0.685
(1.00) 		0.992
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.566
(1.00) 		0.123
(1.00) 		0.681
(1.00) 		1
(1.00)
14q gain 0 (0%) 294 0.0308
(1.00) 		0.0644
(1.00) 		0.83
(1.00) 		0.858
(1.00) 		0.974
(1.00) 		0.492
(1.00) 		0.338
(1.00) 		0.552
(1.00) 		0.756
(1.00) 		1
(1.00) 		0.612
(1.00) 		0.245
(1.00) 		0.752
(1.00) 		0.382
(1.00)
15q gain 0 (0%) 295 0.68
(1.00) 		0.97
(1.00) 		1
(1.00) 		0.389
(1.00) 		0.482
(1.00) 		0.642
(1.00) 		0.412
(1.00) 		0.834
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.0237
(1.00) 		0.365
(1.00) 		0.499
(1.00)
16p gain 0 (0%) 310 0.779
(1.00) 		0.311
(1.00) 		0.371
(1.00) 		0.0681
(1.00) 		0.799
(1.00) 		0.0156
(1.00) 		0.678
(1.00) 		1
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.806
(1.00) 		0.437
(1.00) 		0.121
(1.00) 		1
(1.00)
16q gain 0 (0%) 306 0.856
(1.00) 		0.109
(1.00) 		0.175
(1.00) 		0.366
(1.00) 		0.958
(1.00) 		0.00407
(1.00) 		0.228
(1.00) 		0.292
(1.00) 		0.153
(1.00) 		1
(1.00) 		0.94
(1.00) 		0.922
(1.00) 		0.0125
(1.00) 		0.802
(1.00)
17q gain 0 (0%) 290 0.704
(1.00) 		0.383
(1.00) 		0.0421
(1.00) 		0.12
(1.00) 		0.609
(1.00) 		0.477
(1.00) 		0.0206
(1.00) 		0.168
(1.00) 		0.0505
(1.00) 		0.336
(1.00) 		0.791
(1.00) 		0.567
(1.00) 		0.0558
(1.00) 		0.0641
(1.00)
18p gain 0 (0%) 271 0.329
(1.00) 		0.149
(1.00) 		0.233
(1.00) 		0.198
(1.00) 		0.858
(1.00) 		0.331
(1.00) 		0.0336
(1.00) 		0.0714
(1.00) 		0.268
(1.00) 		1
(1.00) 		0.642
(1.00) 		0.158
(1.00) 		0.646
(1.00) 		0.607
(1.00)
18q gain 0 (0%) 286 0.648
(1.00) 		0.248
(1.00) 		0.697
(1.00) 		0.378
(1.00) 		0.69
(1.00) 		0.452
(1.00) 		0.329
(1.00) 		0.283
(1.00) 		0.925
(1.00) 		0.628
(1.00) 		0.163
(1.00) 		0.696
(1.00) 		0.242
(1.00) 		0.914
(1.00)
19q gain 0 (0%) 279 0.667
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.139
(1.00) 		0.000565
(0.609) 		0.854
(1.00) 		0.112
(1.00) 		0.0747
(1.00) 		0.0574
(1.00) 		0.659
(1.00) 		0.879
(1.00) 		0.863
(1.00) 		0.162
(1.00) 		0.86
(1.00)
20p gain 0 (0%) 234 0.765
(1.00) 		0.0637
(1.00) 		0.0231
(1.00) 		0.279
(1.00) 		0.173
(1.00) 		0.942
(1.00) 		0.622
(1.00) 		0.0408
(1.00) 		0.152
(1.00) 		0.19
(1.00) 		0.741
(1.00) 		0.779
(1.00) 		0.198
(1.00) 		0.297
(1.00)
20q gain 0 (0%) 245 0.673
(1.00) 		0.266
(1.00) 		0.139
(1.00) 		0.77
(1.00) 		0.0985
(1.00) 		0.97
(1.00) 		0.501
(1.00) 		0.0805
(1.00) 		0.13
(1.00) 		0.147
(1.00) 		0.658
(1.00) 		0.661
(1.00) 		0.572
(1.00) 		0.253
(1.00)
22q gain 0 (0%) 248 0.0826
(1.00) 		0.361
(1.00) 		0.458
(1.00) 		0.782
(1.00) 		0.906
(1.00) 		0.204
(1.00) 		0.53
(1.00) 		1
(1.00) 		0.113
(1.00) 		0.726
(1.00) 		0.938
(1.00) 		0.328
(1.00) 		0.604
(1.00) 		0.372
(1.00)
Xq gain 0 (0%) 316 0.881
(1.00) 		0.287
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.99
(1.00) 		0.483
(1.00) 		0.89
(1.00) 		0.642
(1.00) 		0.694
(1.00) 		1
(1.00) 		0.563
(1.00) 		1
(1.00) 		0.964
(1.00) 		1
(1.00)
1p loss 0 (0%) 277 0.622
(1.00) 		0.793
(1.00) 		0.0021
(1.00) 		0.45
(1.00) 		0.119
(1.00) 		0.4
(1.00) 		0.333
(1.00) 		0.359
(1.00) 		0.195
(1.00) 		0.212
(1.00) 		0.592
(1.00) 		0.664
(1.00) 		0.546
(1.00) 		0.574
(1.00)
1q loss 0 (0%) 318 0.775
(1.00) 		0.0214
(1.00) 		0.683
(1.00) 		0.994
(1.00) 		0.294
(1.00) 		0.419
(1.00) 		0.549
(1.00) 		0.165
(1.00) 		0.216
(1.00) 		0.257
(1.00) 		0.539
(1.00) 		0.187
(1.00) 		0.119
(1.00)
2q loss 0 (0%) 317 0.0784
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.992
(1.00) 		0.607
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.112
(1.00) 		0.0353
(1.00) 		0.731
(1.00) 		1
(1.00)
3p loss 0 (0%) 184 0.885
(1.00) 		0.345
(1.00) 		0.799
(1.00) 		0.138
(1.00) 		0.406
(1.00) 		0.961
(1.00) 		0.916
(1.00) 		0.701
(1.00) 		0.967
(1.00) 		0.541
(1.00) 		0.557
(1.00) 		0.593
(1.00) 		0.396
(1.00) 		0.936
(1.00)
3q loss 0 (0%) 301 0.0955
(1.00) 		0.336
(1.00) 		0.808
(1.00) 		0.65
(1.00) 		0.0101
(1.00) 		0.488
(1.00) 		0.0374
(1.00) 		0.307
(1.00) 		0.0914
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.864
(1.00) 		0.0536
(1.00) 		0.0415
(1.00)
4p loss 0 (0%) 187 0.108
(1.00) 		0.863
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.406
(1.00) 		0.356
(1.00) 		0.318
(1.00) 		0.248
(1.00) 		0.0568
(1.00) 		1
(1.00) 		0.567
(1.00) 		0.87
(1.00) 		0.293
(1.00) 		0.66
(1.00)
4q loss 0 (0%) 206 0.0759
(1.00) 		0.507
(1.00) 		0.148
(1.00) 		0.138
(1.00) 		0.235
(1.00) 		0.525
(1.00) 		0.891
(1.00) 		0.322
(1.00) 		0.256
(1.00) 		0.539
(1.00) 		0.569
(1.00) 		0.624
(1.00) 		0.685
(1.00) 		0.868
(1.00)
5p loss 0 (0%) 303 0.0876
(1.00) 		0.238
(1.00) 		0.613
(1.00) 		0.491
(1.00) 		0.00604
(1.00) 		0.318
(1.00) 		0.36
(1.00) 		0.336
(1.00) 		0.879
(1.00) 		0.166
(1.00) 		0.992
(1.00) 		0.596
(1.00) 		0.174
(1.00) 		0.19
(1.00)
5q loss 0 (0%) 208 0.261
(1.00) 		0.723
(1.00) 		0.691
(1.00) 		0.684
(1.00) 		0.235
(1.00) 		0.0207
(1.00) 		0.245
(1.00) 		0.558
(1.00) 		0.0379
(1.00) 		0.533
(1.00) 		0.555
(1.00) 		0.253
(1.00) 		0.0221
(1.00) 		0.231
(1.00)
6p loss 0 (0%) 292 0.922
(1.00) 		0.44
(1.00) 		0.0897
(1.00) 		0.818
(1.00) 		0.0188
(1.00) 		0.0775
(1.00) 		0.254
(1.00) 		0.701
(1.00) 		0.138
(1.00) 		0.611
(1.00) 		0.821
(1.00) 		0.542
(1.00) 		0.923
(1.00) 		0.277
(1.00)
6q loss 0 (0%) 291 0.55
(1.00) 		0.647
(1.00) 		0.839
(1.00) 		0.789
(1.00) 		0.0227
(1.00) 		0.0294
(1.00) 		0.569
(1.00) 		0.712
(1.00) 		0.182
(1.00) 		0.613
(1.00) 		0.259
(1.00) 		0.624
(1.00) 		0.283
(1.00) 		0.114
(1.00)
7p loss 0 (0%) 305 0.739
(1.00) 		0.467
(1.00) 		0.792
(1.00) 		0.796
(1.00) 		0.954
(1.00) 		0.294
(1.00) 		0.214
(1.00) 		1
(1.00) 		0.547
(1.00) 		0.508
(1.00) 		0.103
(1.00) 		0.421
(1.00) 		0.394
(1.00) 		0.0477
(1.00)
7q loss 0 (0%) 315 0.485
(1.00) 		0.818
(1.00) 		0.462
(1.00) 		0.988
(1.00) 		0.124
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.923
(1.00) 		0.295
(1.00) 		0.165
(1.00) 		0.386
(1.00) 		0.596
(1.00) 		0.23
(1.00)
8p loss 0 (0%) 230 0.382
(1.00) 		0.0983
(1.00) 		0.578
(1.00) 		0.519
(1.00) 		0.869
(1.00) 		0.134
(1.00) 		0.692
(1.00) 		0.36
(1.00) 		0.634
(1.00) 		0.186
(1.00) 		0.0531
(1.00) 		0.0366
(1.00) 		0.35
(1.00) 		0.843
(1.00)
8q loss 0 (0%) 316 0.849
(1.00) 		0.863
(1.00) 		0.457
(1.00) 		0.463
(1.00) 		0.464
(1.00) 		0.516
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.801
(1.00) 		0.405
(1.00) 		0.0476
(1.00) 		0.548
(1.00)
9p loss 0 (0%) 191 0.763
(1.00) 		0.374
(1.00) 		0.44
(1.00) 		0.3
(1.00) 		0.404
(1.00) 		0.854
(1.00) 		0.482
(1.00) 		0.654
(1.00) 		0.752
(1.00) 		0.766
(1.00) 		0.108
(1.00) 		0.736
(1.00) 		0.312
(1.00) 		0.292
(1.00)
9q loss 0 (0%) 241 0.928
(1.00) 		0.00442
(1.00) 		0.772
(1.00) 		0.768
(1.00) 		0.16
(1.00) 		0.204
(1.00) 		0.713
(1.00) 		0.173
(1.00) 		0.717
(1.00) 		1
(1.00) 		0.663
(1.00) 		0.609
(1.00) 		0.0714
(1.00) 		0.593
(1.00)
10p loss 0 (0%) 254 0.431
(1.00) 		0.592
(1.00) 		0.222
(1.00) 		0.963
(1.00) 		0.363
(1.00) 		0.797
(1.00) 		0.327
(1.00) 		0.441
(1.00) 		0.327
(1.00) 		0.13
(1.00) 		0.929
(1.00) 		0.421
(1.00) 		0.556
(1.00) 		0.605
(1.00)
10q loss 0 (0%) 255 0.378
(1.00) 		0.998
(1.00) 		0.878
(1.00) 		0.832
(1.00) 		0.353
(1.00) 		0.98
(1.00) 		0.877
(1.00) 		0.211
(1.00) 		0.339
(1.00) 		0.13
(1.00) 		0.186
(1.00) 		0.734
(1.00) 		0.0797
(1.00) 		0.582
(1.00)
11p loss 0 (0%) 278 0.406
(1.00) 		0.609
(1.00) 		0.857
(1.00) 		0.712
(1.00) 		0.18
(1.00) 		0.674
(1.00) 		0.431
(1.00) 		0.404
(1.00) 		0.846
(1.00) 		0.202
(1.00) 		0.358
(1.00) 		0.548
(1.00) 		0.963
(1.00) 		0.715
(1.00)
11q loss 0 (0%) 297 0.626
(1.00) 		0.13
(1.00) 		0.496
(1.00) 		0.963
(1.00) 		0.914
(1.00) 		0.511
(1.00) 		0.0796
(1.00) 		0.812
(1.00) 		0.485
(1.00) 		0.243
(1.00) 		0.883
(1.00) 		0.803
(1.00) 		0.937
(1.00) 		0.319
(1.00)
13q loss 0 (0%) 203 0.0324
(1.00) 		0.485
(1.00) 		0.694
(1.00) 		0.0744
(1.00) 		0.34
(1.00) 		0.958
(1.00) 		0.116
(1.00) 		0.417
(1.00) 		0.0154
(1.00) 		0.753
(1.00) 		0.727
(1.00) 		0.261
(1.00) 		0.00734
(1.00) 		0.686
(1.00)
14q loss 0 (0%) 265 0.195
(1.00) 		0.211
(1.00) 		0.0719
(1.00) 		0.227
(1.00) 		0.167
(1.00) 		0.0193
(1.00) 		0.159
(1.00) 		0.433
(1.00) 		0.434
(1.00) 		0.433
(1.00) 		0.758
(1.00) 		0.427
(1.00) 		0.19
(1.00) 		0.904
(1.00)
15q loss 0 (0%) 287 0.685
(1.00) 		0.445
(1.00) 		0.0469
(1.00) 		0.836
(1.00) 		0.0678
(1.00) 		0.031
(1.00) 		0.223
(1.00) 		0.462
(1.00) 		0.0532
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.135
(1.00) 		0.834
(1.00) 		0.506
(1.00)
16p loss 0 (0%) 277 0.188
(1.00) 		0.754
(1.00) 		0.858
(1.00) 		0.453
(1.00) 		0.775
(1.00) 		0.75
(1.00) 		0.561
(1.00) 		0.789
(1.00) 		0.914
(1.00) 		1
(1.00) 		0.319
(1.00) 		0.931
(1.00) 		0.684
(1.00) 		0.865
(1.00)
17p loss 0 (0%) 210 0.203
(1.00) 		0.875
(1.00) 		0.354
(1.00) 		0.0135
(1.00) 		0.542
(1.00) 		0.346
(1.00) 		0.196
(1.00) 		0.315
(1.00) 		0.942
(1.00) 		0.528
(1.00) 		0.361
(1.00) 		0.28
(1.00) 		0.759
(1.00) 		0.948
(1.00)
17q loss 0 (0%) 306 0.791
(1.00) 		0.76
(1.00) 		0.0317
(1.00) 		0.453
(1.00) 		0.958
(1.00) 		0.473
(1.00) 		0.74
(1.00) 		0.117
(1.00) 		0.296
(1.00) 		0.49
(1.00) 		0.332
(1.00) 		0.516
(1.00) 		0.136
(1.00) 		0.051
(1.00)
18p loss 0 (0%) 292 0.599
(1.00) 		0.378
(1.00) 		0.675
(1.00) 		0.753
(1.00) 		0.884
(1.00) 		0.952
(1.00) 		0.392
(1.00) 		0.27
(1.00) 		0.345
(1.00) 		0.611
(1.00) 		0.0936
(1.00) 		0.871
(1.00) 		0.23
(1.00) 		0.599
(1.00)
18q loss 0 (0%) 262 0.351
(1.00) 		0.115
(1.00) 		0.203
(1.00) 		0.963
(1.00) 		0.313
(1.00) 		0.482
(1.00) 		0.802
(1.00) 		0.224
(1.00) 		0.905
(1.00) 		0.698
(1.00) 		0.219
(1.00) 		0.319
(1.00) 		0.29
(1.00) 		0.412
(1.00)
19p loss 0 (0%) 272 0.0716
(1.00) 		0.818
(1.00) 		0.864
(1.00) 		0.118
(1.00) 		0.142
(1.00) 		0.377
(1.00) 		0.0954
(1.00) 		0.158
(1.00) 		0.172
(1.00) 		0.0204
(1.00) 		0.961
(1.00) 		0.146
(1.00) 		0.111
(1.00) 		0.411
(1.00)
19q loss 0 (0%) 289 0.572
(1.00) 		0.197
(1.00) 		0.839
(1.00) 		0.26
(1.00) 		0.00187
(1.00) 		0.566
(1.00) 		0.248
(1.00) 		0.595
(1.00) 		0.882
(1.00) 		0.11
(1.00) 		0.156
(1.00) 		0.261
(1.00) 		0.035
(1.00) 		0.0086
(1.00)
20p loss 0 (0%) 309 0.06
(1.00) 		0.868
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.387
(1.00) 		0.524
(1.00) 		0.72
(1.00) 		0.0663
(1.00) 		1
(1.00) 		0.909
(1.00) 		0.795
(1.00) 		0.705
(1.00) 		0.728
(1.00)
20q loss 0 (0%) 308 0.376
(1.00) 		0.907
(1.00) 		0.575
(1.00) 		0.966
(1.00) 		0.945
(1.00) 		0.406
(1.00) 		0.735
(1.00) 		0.839
(1.00) 		1
(1.00) 		0.12
(1.00) 		0.89
(1.00) 		0.178
(1.00) 		0.19
(1.00)
21q loss 0 (0%) 226 0.454
(1.00) 		0.314
(1.00) 		0.0125
(1.00) 		0.564
(1.00) 		0.53
(1.00) 		0.504
(1.00) 		0.719
(1.00) 		0.29
(1.00) 		0.1
(1.00) 		0.741
(1.00) 		0.253
(1.00) 		0.945
(1.00) 		0.374
(1.00) 		0.729
(1.00)
22q loss 0 (0%) 292 0.648
(1.00) 		0.126
(1.00) 		0.0605
(1.00) 		0.327
(1.00) 		0.00119
(1.00) 		0.235
(1.00) 		0.000422
(0.455) 		0.282
(1.00) 		0.00292
(1.00) 		1
(1.00) 		0.715
(1.00) 		0.402
(1.00) 		0.0836
(1.00) 		0.184
(1.00)
'1p gain' versus 'HISTOLOGICAL.TYPE'

P value = 2.88e-08 (Chi-square test), Q value = 3.1e-05

Table S1.  Gene #1: '1p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients LUNG BASALOID SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARICNOMA LUNG SMALL CELL SQUAMOUS CELL CARCINOMA LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
ALL 7 1 1 1 315
1P GAIN CNV 4 0 0 1 18
1P GAIN WILD-TYPE 3 1 1 0 297

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'2q gain' versus 'HISTOLOGICAL.TYPE'

P value = 8.58e-05 (Chi-square test), Q value = 0.093

Table S2.  Gene #4: '2q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients LUNG BASALOID SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARICNOMA LUNG SMALL CELL SQUAMOUS CELL CARCINOMA LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
ALL 7 1 1 1 315
2Q GAIN CNV 4 1 0 0 31
2Q GAIN WILD-TYPE 3 0 1 1 284

Figure S2.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'11p gain' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 2e-06 (t-test), Q value = 0.0022

Table S3.  Gene #21: '11p gain' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 54 28.5 (39.7)
11P GAIN CNV 4 0.0 (0.0)
11P GAIN WILD-TYPE 50 30.8 (40.4)

Figure S3.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

'17p gain' versus 'HISTOLOGICAL.TYPE'

P value = 3.79e-07 (Chi-square test), Q value = 0.00041

Table S4.  Gene #30: '17p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients LUNG BASALOID SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARICNOMA LUNG SMALL CELL SQUAMOUS CELL CARCINOMA LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
ALL 7 1 1 1 315
17P GAIN CNV 0 1 0 0 8
17P GAIN WILD-TYPE 7 0 1 1 307

Figure S4.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'19p gain' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 1.77e-06 (t-test), Q value = 0.0019

Table S5.  Gene #34: '19p gain' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 54 28.5 (39.7)
19P GAIN CNV 6 0.0 (0.0)
19P GAIN WILD-TYPE 48 32.1 (40.7)

Figure S5.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

'19p gain' versus 'HISTOLOGICAL.TYPE'

P value = 5.63e-06 (Chi-square test), Q value = 0.0061

Table S6.  Gene #34: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients LUNG BASALOID SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARICNOMA LUNG SMALL CELL SQUAMOUS CELL CARCINOMA LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
ALL 7 1 1 1 315
19P GAIN CNV 5 0 0 0 28
19P GAIN WILD-TYPE 2 1 1 1 287

Figure S6.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'21q gain' versus 'HISTOLOGICAL.TYPE'

P value = 5.96e-05 (Chi-square test), Q value = 0.064

Table S7.  Gene #38: '21q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients LUNG BASALOID SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARICNOMA LUNG SMALL CELL SQUAMOUS CELL CARCINOMA LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
ALL 7 1 1 1 315
21Q GAIN CNV 2 0 0 1 15
21Q GAIN WILD-TYPE 5 1 1 0 300

Figure S7.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'12p loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.32e-16 (Chi-square test), Q value = 1.4e-13

Table S8.  Gene #62: '12p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients LUNG BASALOID SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARICNOMA LUNG SMALL CELL SQUAMOUS CELL CARCINOMA LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
ALL 7 1 1 1 315
12P LOSS CNV 0 0 0 1 3
12P LOSS WILD-TYPE 7 1 1 0 312

Figure S8.  Get High-res Image Gene #62: '12p loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'12q loss' versus 'HISTOLOGICAL.TYPE'

P value = 1.32e-16 (Chi-square test), Q value = 1.4e-13

Table S9.  Gene #63: '12q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients LUNG BASALOID SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARICNOMA LUNG SMALL CELL SQUAMOUS CELL CARCINOMA LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
ALL 7 1 1 1 315
12Q LOSS CNV 0 0 0 1 3
12Q LOSS WILD-TYPE 7 1 1 0 312

Figure S9.  Get High-res Image Gene #63: '12q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'16q loss' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 1.77e-06 (t-test), Q value = 0.0019

Table S10.  Gene #68: '16q loss' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 54 28.5 (39.7)
16Q LOSS CNV 6 0.0 (0.0)
16Q LOSS WILD-TYPE 48 32.1 (40.7)

Figure S10.  Get High-res Image Gene #68: '16q loss' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

'Xq loss' versus 'HISTOLOGICAL.TYPE'

P value = 6.63e-05 (Chi-square test), Q value = 0.072

Table S11.  Gene #79: 'Xq loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients LUNG BASALOID SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARCINOMA LUNG PAPILLARY SQUAMOUS CELL CARICNOMA LUNG SMALL CELL SQUAMOUS CELL CARCINOMA LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
ALL 7 1 1 1 315
XQ LOSS CNV 0 0 0 1 12
XQ LOSS WILD-TYPE 7 1 1 0 303

Figure S11.  Get High-res Image Gene #79: 'Xq loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Clinical data file = LUSC-TP.clin.merged.picked.txt

  • Number of patients = 325

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 14

  • 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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] 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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