Lung Squamous Cell Carcinoma: Correlation between copy number variations of arm-level result and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
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 11 clinical features across 307 patients, 13 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'.

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

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

  • 17q 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 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 13 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 		NEOADJUVANT
THERAPY
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 Fisher's exact test
19p gain 31 (10%) 276 0.542
(1.00) 		0.414
(1.00) 		0.829
(1.00) 		7.92e-06
(0.00673) 		5.05e-06
(0.0043) 		0.699
(1.00) 		0.391
(1.00) 		0.667
(1.00) 		0.588
(1.00) 		0.307
(1.00) 		1
(1.00)
1p gain 20 (7%) 287 0.875
(1.00) 		0.592
(1.00) 		0.185
(1.00) 		4.27e-06
(0.00364) 		0.108
(1.00) 		0.83
(1.00) 		0.306
(1.00) 		0.244
(1.00) 		0.529
(1.00) 		0.418
(1.00)
2q gain 32 (10%) 275 0.222
(1.00) 		0.838
(1.00) 		1
(1.00) 		0.95
(1.00) 		3.55e-05
(0.03) 		0.222
(1.00) 		0.59
(1.00) 		0.31
(1.00) 		0.00867
(1.00) 		0.0952
(1.00) 		0.523
(1.00)
11p gain 17 (6%) 290 0.979
(1.00) 		0.484
(1.00) 		0.255
(1.00) 		8.74e-06
(0.00741) 		0.962
(1.00) 		0.00195
(1.00) 		0.439
(1.00) 		1
(1.00) 		0.584
(1.00) 		0.471
(1.00) 		0.668
(1.00)
17p gain 7 (2%) 300 0.369
(1.00) 		0.283
(1.00) 		0.196
(1.00) 		9.6e-09
(8.19e-06) 		0.249
(1.00) 		0.367
(1.00) 		0.524
(1.00) 		0.0542
(1.00) 		1
(1.00) 		1
(1.00)
21q gain 18 (6%) 289 0.26
(1.00) 		0.65
(1.00) 		1
(1.00) 		0.996
(1.00) 		0.000122
(0.103) 		0.285
(1.00) 		0.26
(1.00) 		0.711
(1.00) 		0.188
(1.00) 		0.491
(1.00) 		0.0189
(1.00)
12p loss 5 (2%) 302 0.529
(1.00) 		0.00239
(1.00) 		0.608
(1.00) 		2.07e-12
(1.77e-09) 		0.162
(1.00) 		0.791
(1.00) 		0.411
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.393
(1.00)
12q loss 4 (1%) 303 0.882
(1.00) 		0.2
(1.00) 		0.279
(1.00) 		1.19e-15
(1.01e-12) 		0.186
(1.00) 		0.555
(1.00) 		0.344
(1.00) 		0.292
(1.00) 		1
(1.00) 		0.329
(1.00)
16p loss 45 (15%) 262 0.221
(1.00) 		0.374
(1.00) 		0.856
(1.00) 		8.74e-06
(0.00741) 		0.777
(1.00) 		0.84
(1.00) 		0.685
(1.00) 		0.884
(1.00) 		0.952
(1.00) 		1
(1.00) 		0.278
(1.00)
16q loss 57 (19%) 250 0.123
(1.00) 		0.0648
(1.00) 		0.182
(1.00) 		7.92e-06
(0.00673) 		0.67
(1.00) 		0.775
(1.00) 		0.352
(1.00) 		0.316
(1.00) 		0.685
(1.00) 		0.434
(1.00) 		0.62
(1.00)
17q loss 19 (6%) 288 0.576
(1.00) 		0.225
(1.00) 		0.11
(1.00) 		8.74e-06
(0.00741) 		0.954
(1.00) 		0.438
(1.00) 		0.784
(1.00) 		0.0763
(1.00) 		0.26
(1.00) 		0.511
(1.00) 		0.697
(1.00)
Xq loss 12 (4%) 295 0.759
(1.00) 		0.125
(1.00) 		0.518
(1.00) 		5.07e-05
(0.0428) 		0.835
(1.00) 		0.109
(1.00) 		1
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.0188
(1.00)
1q gain 64 (21%) 243 0.611
(1.00) 		0.788
(1.00) 		1
(1.00) 		0.446
(1.00) 		0.00379
(1.00) 		0.158
(1.00) 		0.772
(1.00) 		0.164
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.471
(1.00)
2p gain 73 (24%) 234 0.592
(1.00) 		0.73
(1.00) 		0.0688
(1.00) 		0.198
(1.00) 		0.0121
(1.00) 		0.133
(1.00) 		0.121
(1.00) 		0.138
(1.00) 		0.121
(1.00) 		0.14
(1.00) 		0.171
(1.00)
3p gain 33 (11%) 274 0.415
(1.00) 		0.0512
(1.00) 		0.147
(1.00) 		0.264
(1.00) 		0.978
(1.00) 		0.0552
(1.00) 		0.911
(1.00) 		0.476
(1.00) 		0.502
(1.00) 		1
(1.00) 		0.753
(1.00)
3q gain 136 (44%) 171 0.662
(1.00) 		0.184
(1.00) 		0.897
(1.00) 		0.232
(1.00) 		0.345
(1.00) 		0.584
(1.00) 		0.905
(1.00) 		0.409
(1.00) 		0.688
(1.00) 		1
(1.00) 		0.0761
(1.00)
4p gain 11 (4%) 296 0.964
(1.00) 		0.628
(1.00) 		0.0726
(1.00) 		0.796
(1.00) 		0.65
(1.00) 		0.0421
(1.00) 		0.833
(1.00) 		1
(1.00) 		0.683
(1.00) 		1
(1.00) 		0.608
(1.00)
4q gain 5 (2%) 302 0.54
(1.00) 		0.501
(1.00) 		0.332
(1.00) 		0.126
(1.00) 		0.0339
(1.00) 		0.791
(1.00) 		1
(1.00) 		0.118
(1.00) 		1
(1.00) 		1
(1.00)
5p gain 141 (46%) 166 0.482
(1.00) 		0.0936
(1.00) 		0.362
(1.00) 		0.693
(1.00) 		0.315
(1.00) 		0.0499
(1.00) 		0.558
(1.00) 		0.358
(1.00) 		0.695
(1.00) 		1
(1.00) 		0.846
(1.00)
5q gain 32 (10%) 275 0.795
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.523
(1.00) 		0.977
(1.00) 		0.929
(1.00) 		0.452
(1.00) 		0.383
(1.00) 		0.368
(1.00) 		0.321
(1.00) 		1
(1.00)
6p gain 29 (9%) 278 0.746
(1.00) 		0.226
(1.00) 		0.826
(1.00) 		0.225
(1.00) 		0.0325
(1.00) 		0.106
(1.00) 		0.919
(1.00) 		0.291
(1.00) 		0.176
(1.00) 		0.279
(1.00) 		1
(1.00)
6q gain 16 (5%) 291 0.786
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.428
(1.00) 		0.000901
(0.757) 		0.623
(1.00) 		0.667
(1.00) 		1
(1.00) 		0.953
(1.00) 		0.451
(1.00) 		0.654
(1.00)
7p gain 84 (27%) 223 0.3
(1.00) 		0.445
(1.00) 		0.663
(1.00) 		0.619
(1.00) 		0.74
(1.00) 		0.0109
(1.00) 		0.736
(1.00) 		0.324
(1.00) 		0.451
(1.00) 		0.733
(1.00) 		0.664
(1.00)
7q gain 81 (26%) 226 0.45
(1.00) 		0.695
(1.00) 		0.381
(1.00) 		0.333
(1.00) 		0.474
(1.00) 		0.0251
(1.00) 		0.759
(1.00) 		0.188
(1.00) 		0.323
(1.00) 		0.734
(1.00) 		0.828
(1.00)
8p gain 43 (14%) 264 0.888
(1.00) 		0.456
(1.00) 		0.851
(1.00) 		0.0117
(1.00) 		0.1
(1.00) 		0.549
(1.00) 		0.707
(1.00) 		0.0987
(1.00) 		0.248
(1.00) 		0.189
(1.00) 		0.153
(1.00)
8q gain 85 (28%) 222 0.365
(1.00) 		0.543
(1.00) 		0.564
(1.00) 		0.193
(1.00) 		0.884
(1.00) 		0.116
(1.00) 		0.732
(1.00) 		0.0843
(1.00) 		0.0469
(1.00) 		0.185
(1.00) 		0.389
(1.00)
9p gain 19 (6%) 288 0.21
(1.00) 		0.688
(1.00) 		0.285
(1.00) 		0.00217
(1.00) 		0.569
(1.00) 		0.685
(1.00) 		1
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.697
(1.00)
9q gain 28 (9%) 279 0.189
(1.00) 		0.372
(1.00) 		0.822
(1.00) 		0.602
(1.00) 		0.471
(1.00) 		0.428
(1.00) 		0.779
(1.00) 		0.214
(1.00) 		0.653
(1.00) 		0.607
(1.00) 		0.319
(1.00)
10p gain 15 (5%) 292 0.815
(1.00) 		0.977
(1.00) 		0.767
(1.00) 		0.852
(1.00) 		0.97
(1.00) 		0.351
(1.00) 		0.0949
(1.00) 		0.132
(1.00) 		0.0183
(1.00) 		0.429
(1.00) 		0.159
(1.00)
10q gain 6 (2%) 301 0.353
(1.00) 		0.723
(1.00) 		1
(1.00) 		0.995
(1.00) 		0.494
(1.00) 		0.463
(1.00) 		1
(1.00) 		0.521
(1.00) 		0.198
(1.00) 		0.102
(1.00)
11q gain 20 (7%) 287 0.713
(1.00) 		0.923
(1.00) 		0.302
(1.00) 		0.452
(1.00) 		0.923
(1.00) 		0.0294
(1.00) 		0.233
(1.00) 		0.531
(1.00) 		0.106
(1.00) 		0.529
(1.00) 		0.418
(1.00)
12p gain 85 (28%) 222 0.805
(1.00) 		0.795
(1.00) 		0.00865
(1.00) 		0.368
(1.00) 		0.884
(1.00) 		0.0819
(1.00) 		0.76
(1.00) 		0.733
(1.00) 		0.861
(1.00) 		0.504
(1.00) 		0.197
(1.00)
12q gain 38 (12%) 269 0.626
(1.00) 		0.512
(1.00) 		0.0737
(1.00) 		0.958
(1.00) 		0.978
(1.00) 		0.129
(1.00) 		0.156
(1.00) 		0.224
(1.00) 		0.227
(1.00) 		1
(1.00) 		0.148
(1.00)
13q gain 6 (2%) 301 0.0979
(1.00) 		0.587
(1.00) 		1
(1.00) 		0.995
(1.00) 		0.151
(1.00) 		1
(1.00) 		0.47
(1.00) 		0.761
(1.00) 		1
(1.00) 		1
(1.00)
14q gain 31 (10%) 276 0.0642
(1.00) 		0.0918
(1.00) 		0.517
(1.00) 		0.937
(1.00) 		0.976
(1.00) 		0.323
(1.00) 		0.696
(1.00) 		0.667
(1.00) 		0.939
(1.00) 		1
(1.00) 		0.192
(1.00)
15q gain 27 (9%) 280 0.684
(1.00) 		0.808
(1.00) 		1
(1.00) 		0.365
(1.00) 		0.44
(1.00) 		0.676
(1.00) 		0.236
(1.00) 		0.649
(1.00) 		0.411
(1.00) 		1
(1.00) 		0.73
(1.00)
16p gain 14 (5%) 293 0.203
(1.00) 		0.217
(1.00) 		0.533
(1.00) 		0.0584
(1.00) 		0.793
(1.00) 		0.0266
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.431
(1.00) 		1
(1.00) 		0.377
(1.00)
16q gain 18 (6%) 289 0.622
(1.00) 		0.0661
(1.00) 		0.173
(1.00) 		0.305
(1.00) 		0.958
(1.00) 		0.00784
(1.00) 		0.149
(1.00) 		0.267
(1.00) 		0.083
(1.00) 		1
(1.00) 		0.682
(1.00)
17q gain 33 (11%) 274 0.513
(1.00) 		0.283
(1.00) 		0.0595
(1.00) 		0.326
(1.00) 		0.608
(1.00) 		0.616
(1.00) 		0.0203
(1.00) 		0.223
(1.00) 		0.0985
(1.00) 		0.335
(1.00) 		0.753
(1.00)
18p gain 50 (16%) 257 0.162
(1.00) 		0.122
(1.00) 		0.217
(1.00) 		0.396
(1.00) 		0.851
(1.00) 		0.22
(1.00) 		0.0244
(1.00) 		0.161
(1.00) 		0.242
(1.00) 		0.696
(1.00) 		0.441
(1.00)
18q gain 36 (12%) 271 0.385
(1.00) 		0.406
(1.00) 		0.546
(1.00) 		0.639
(1.00) 		0.674
(1.00) 		0.309
(1.00) 		0.0983
(1.00) 		0.515
(1.00) 		0.824
(1.00) 		0.625
(1.00) 		0.359
(1.00)
19q gain 45 (15%) 262 0.755
(1.00) 		0.769
(1.00) 		1
(1.00) 		0.183
(1.00) 		0.000827
(0.696) 		0.915
(1.00) 		0.144
(1.00) 		0.109
(1.00) 		0.0725
(1.00) 		0.667
(1.00) 		0.404
(1.00)
20p gain 86 (28%) 221 0.812
(1.00) 		0.0757
(1.00) 		0.042
(1.00) 		0.19
(1.00) 		0.173
(1.00) 		0.953
(1.00) 		0.74
(1.00) 		0.0843
(1.00) 		0.186
(1.00) 		0.19
(1.00) 		0.67
(1.00)
20q gain 74 (24%) 233 0.714
(1.00) 		0.209
(1.00) 		0.129
(1.00) 		0.764
(1.00) 		0.0135
(1.00) 		0.891
(1.00) 		0.529
(1.00) 		0.064
(1.00) 		0.105
(1.00) 		0.142
(1.00) 		0.82
(1.00)
22q gain 72 (23%) 235 0.0866
(1.00) 		0.359
(1.00) 		0.285
(1.00) 		0.674
(1.00) 		0.906
(1.00) 		0.134
(1.00) 		0.665
(1.00) 		0.844
(1.00) 		0.39
(1.00) 		0.724
(1.00) 		0.821
(1.00)
Xq gain 9 (3%) 298 0.903
(1.00) 		0.272
(1.00) 		1
(1.00) 		0.952
(1.00) 		0.989
(1.00) 		0.458
(1.00) 		0.897
(1.00) 		0.617
(1.00) 		0.593
(1.00) 		1
(1.00) 		0.205
(1.00)
1p loss 46 (15%) 261 0.532
(1.00) 		0.702
(1.00) 		0.00311
(1.00) 		0.541
(1.00) 		0.122
(1.00) 		0.302
(1.00) 		0.494
(1.00) 		0.216
(1.00) 		0.37
(1.00) 		0.218
(1.00) 		1
(1.00)
1q loss 9 (3%) 298 0.701
(1.00) 		0.258
(1.00) 		0.455
(1.00) 		0.989
(1.00) 		0.349
(1.00) 		0.699
(1.00) 		0.617
(1.00) 		0.916
(1.00) 		0.283
(1.00) 		1
(1.00)
2q loss 8 (3%) 299 0.0522
(1.00) 		0.0748
(1.00) 		1
(1.00) 		0.991
(1.00) 		0.535
(1.00) 		0.66
(1.00) 		1
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.552
(1.00)
3p loss 136 (44%) 171 0.383
(1.00) 		0.141
(1.00) 		0.897
(1.00) 		0.116
(1.00) 		0.404
(1.00) 		0.985
(1.00) 		0.918
(1.00) 		0.883
(1.00) 		0.949
(1.00) 		0.546
(1.00) 		0.242
(1.00)
3q loss 27 (9%) 280 0.593
(1.00) 		0.273
(1.00) 		1
(1.00) 		0.745
(1.00) 		0.024
(1.00) 		0.445
(1.00) 		0.0973
(1.00) 		0.214
(1.00) 		0.18
(1.00) 		0.607
(1.00) 		0.303
(1.00)
4p loss 130 (42%) 177 0.152
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.227
(1.00) 		0.406
(1.00) 		0.389
(1.00) 		0.322
(1.00) 		0.257
(1.00) 		0.054
(1.00) 		1
(1.00) 		0.326
(1.00)
4q loss 112 (36%) 195 0.118
(1.00) 		0.619
(1.00) 		0.137
(1.00) 		0.0968
(1.00) 		0.235
(1.00) 		0.57
(1.00) 		0.859
(1.00) 		0.204
(1.00) 		0.156
(1.00) 		0.538
(1.00) 		0.223
(1.00)
5p loss 19 (6%) 288 0.0297
(1.00) 		0.301
(1.00) 		0.42
(1.00) 		0.787
(1.00) 		0.00336
(1.00) 		0.184
(1.00) 		0.376
(1.00) 		0.737
(1.00) 		0.503
(1.00) 		0.143
(1.00) 		0.0915
(1.00)
5q loss 112 (36%) 195 0.148
(1.00) 		0.838
(1.00) 		0.591
(1.00) 		0.285
(1.00) 		0.235
(1.00) 		0.0229
(1.00) 		0.33
(1.00) 		0.28
(1.00) 		0.00761
(1.00) 		0.538
(1.00) 		0.551
(1.00)
6p loss 33 (11%) 274 0.446
(1.00) 		0.416
(1.00) 		0.147
(1.00) 		0.939
(1.00) 		0.0267
(1.00) 		0.0428
(1.00) 		0.375
(1.00) 		0.692
(1.00) 		0.0886
(1.00) 		0.615
(1.00) 		0.533
(1.00)
6q loss 35 (11%) 272 0.86
(1.00) 		0.65
(1.00) 		0.687
(1.00) 		0.696
(1.00) 		0.0374
(1.00) 		0.0904
(1.00) 		0.254
(1.00) 		0.712
(1.00) 		0.278
(1.00) 		0.621
(1.00) 		0.552
(1.00)
7p loss 19 (6%) 288 0.73
(1.00) 		0.503
(1.00) 		0.789
(1.00) 		0.861
(1.00) 		0.954
(1.00) 		0.33
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.587
(1.00) 		0.511
(1.00) 		1
(1.00)
7q loss 11 (4%) 296 0.637
(1.00) 		0.936
(1.00) 		0.734
(1.00) 		0.984
(1.00) 		0.0893
(1.00) 		0.479
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.335
(1.00) 		0.608
(1.00)
8p loss 93 (30%) 214 0.521
(1.00) 		0.227
(1.00) 		0.573
(1.00) 		0.436
(1.00) 		0.856
(1.00) 		0.184
(1.00) 		0.719
(1.00) 		0.316
(1.00) 		0.696
(1.00) 		0.183
(1.00) 		0.529
(1.00)
8q loss 9 (3%) 298 0.489
(1.00) 		0.672
(1.00) 		0.455
(1.00) 		0.428
(1.00) 		0.506
(1.00) 		0.764
(1.00) 		0.797
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.205
(1.00)
9p loss 125 (41%) 182 0.62
(1.00) 		0.294
(1.00) 		0.358
(1.00) 		0.0888
(1.00) 		0.402
(1.00) 		0.788
(1.00) 		0.466
(1.00) 		0.68
(1.00) 		0.669
(1.00) 		0.763
(1.00) 		0.554
(1.00)
9q loss 78 (25%) 229 0.986
(1.00) 		0.00378
(1.00) 		0.552
(1.00) 		0.527
(1.00) 		0.154
(1.00) 		0.357
(1.00) 		0.624
(1.00) 		0.57
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.823
(1.00)
10p loss 66 (21%) 241 0.501
(1.00) 		0.767
(1.00) 		0.208
(1.00) 		0.896
(1.00) 		0.352
(1.00) 		0.708
(1.00) 		0.165
(1.00) 		0.374
(1.00) 		0.158
(1.00) 		0.129
(1.00) 		0.643
(1.00)
10q loss 66 (21%) 241 0.428
(1.00) 		0.818
(1.00) 		0.754
(1.00) 		0.708
(1.00) 		0.353
(1.00) 		0.899
(1.00) 		0.596
(1.00) 		0.403
(1.00) 		0.132
(1.00) 		0.129
(1.00) 		0.35
(1.00)
11p loss 47 (15%) 260 0.385
(1.00) 		0.428
(1.00) 		0.721
(1.00) 		0.62
(1.00) 		0.206
(1.00) 		0.587
(1.00) 		0.492
(1.00) 		0.336
(1.00) 		0.825
(1.00) 		0.384
(1.00) 		0.786
(1.00)
11q loss 30 (10%) 277 0.818
(1.00) 		0.0342
(1.00) 		0.516
(1.00) 		0.915
(1.00) 		0.891
(1.00) 		0.584
(1.00) 		0.239
(1.00) 		0.813
(1.00) 		0.676
(1.00) 		0.293
(1.00) 		0.0925
(1.00)
13q loss 116 (38%) 191 0.0143
(1.00) 		0.712
(1.00) 		0.503
(1.00) 		0.135
(1.00) 		0.337
(1.00) 		0.977
(1.00) 		0.133
(1.00) 		0.396
(1.00) 		0.0227
(1.00) 		0.753
(1.00) 		0.426
(1.00)
14q loss 54 (18%) 253 0.132
(1.00) 		0.123
(1.00) 		0.0256
(1.00) 		0.316
(1.00) 		0.157
(1.00) 		0.0252
(1.00) 		0.179
(1.00) 		0.653
(1.00) 		0.451
(1.00) 		0.416
(1.00) 		1
(1.00)
15q loss 36 (12%) 271 0.787
(1.00) 		0.367
(1.00) 		0.0704
(1.00) 		0.446
(1.00) 		0.0684
(1.00) 		0.0953
(1.00) 		0.0264
(1.00) 		0.604
(1.00) 		0.00948
(1.00) 		1
(1.00) 		1
(1.00)
17p loss 111 (36%) 196 0.334
(1.00) 		0.794
(1.00) 		0.59
(1.00) 		0.0191
(1.00) 		0.552
(1.00) 		0.425
(1.00) 		0.193
(1.00) 		0.469
(1.00) 		0.941
(1.00) 		0.534
(1.00) 		0.841
(1.00)
18p loss 30 (10%) 277 0.385
(1.00) 		0.843
(1.00) 		0.516
(1.00) 		0.618
(1.00) 		0.891
(1.00) 		0.824
(1.00) 		0.196
(1.00) 		0.358
(1.00) 		0.171
(1.00) 		0.609
(1.00) 		0.752
(1.00)
18q loss 60 (20%) 247 0.674
(1.00) 		0.0629
(1.00) 		0.0721
(1.00) 		0.527
(1.00) 		0.317
(1.00) 		0.294
(1.00) 		0.853
(1.00) 		0.412
(1.00) 		0.923
(1.00) 		0.698
(1.00) 		1
(1.00)
19p loss 50 (16%) 257 0.0635
(1.00) 		0.964
(1.00) 		1
(1.00) 		0.0806
(1.00) 		0.141
(1.00) 		0.432
(1.00) 		0.133
(1.00) 		0.359
(1.00) 		0.202
(1.00) 		0.0202
(1.00) 		0.286
(1.00)
19q loss 33 (11%) 274 0.445
(1.00) 		0.305
(1.00) 		0.836
(1.00) 		0.405
(1.00) 		0.00148
(1.00) 		0.769
(1.00) 		0.317
(1.00) 		0.683
(1.00) 		0.826
(1.00) 		0.103
(1.00) 		1
(1.00)
20p loss 15 (5%) 292 0.0775
(1.00) 		0.684
(1.00) 		0.767
(1.00) 		0.97
(1.00) 		0.683
(1.00) 		0.434
(1.00) 		0.698
(1.00) 		0.0894
(1.00) 		1
(1.00) 		1
(1.00)
20q loss 16 (5%) 291 0.378
(1.00) 		0.695
(1.00) 		0.77
(1.00) 		0.967
(1.00) 		0.861
(1.00) 		0.426
(1.00) 		0.711
(1.00) 		0.693
(1.00) 		1
(1.00) 		1
(1.00)
21q loss 97 (32%) 210 0.424
(1.00) 		0.326
(1.00) 		0.0115
(1.00) 		0.747
(1.00) 		0.538
(1.00) 		0.534
(1.00) 		0.806
(1.00) 		0.107
(1.00) 		0.215
(1.00) 		0.747
(1.00) 		0.409
(1.00)
22q loss 32 (10%) 275 0.657
(1.00) 		0.152
(1.00) 		0.0563
(1.00) 		0.275
(1.00) 		0.00151
(1.00) 		0.268
(1.00) 		0.000381
(0.321) 		0.397
(1.00) 		0.00277
(1.00) 		1
(1.00) 		0.523
(1.00)
'1p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.27e-06 (Chi-square test), Q value = 0.0036

Table S1.  Gene #1: '1p gain mutation analysis' 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 1 297
1P GAIN MUTATED 4 0 0 0 16
1P GAIN WILD-TYPE 3 1 1 1 281

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

'2q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.55e-05 (Chi-square test), Q value = 0.03

Table S2.  Gene #4: '2q gain mutation analysis' 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 1 297
2Q GAIN MUTATED 4 1 0 0 27
2Q GAIN WILD-TYPE 3 0 1 1 270

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

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

P value = 8.74e-06 (t-test), Q value = 0.0074

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

nPatients Mean (Std.Dev)
ALL 52 26.5 (39.1)
11P GAIN MUTATED 4 0.0 (0.0)
11P GAIN WILD-TYPE 48 28.8 (39.9)

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

'17p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.6e-09 (Chi-square test), Q value = 8.2e-06

Table S4.  Gene #30: '17p gain mutation analysis' 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 1 297
17P GAIN MUTATED 0 1 0 0 6
17P GAIN WILD-TYPE 7 0 1 1 291

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

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

P value = 7.92e-06 (t-test), Q value = 0.0067

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

nPatients Mean (Std.Dev)
ALL 52 26.5 (39.1)
19P GAIN MUTATED 6 0.0 (0.0)
19P GAIN WILD-TYPE 46 30.0 (40.3)

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

'19p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.05e-06 (Chi-square test), Q value = 0.0043

Table S6.  Gene #34: '19p gain mutation analysis' 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 1 297
19P GAIN MUTATED 5 0 0 0 26
19P GAIN WILD-TYPE 2 1 1 1 271

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

'21q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000122 (Chi-square test), Q value = 0.1

Table S7.  Gene #38: '21q gain mutation analysis' 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 1 297
21Q GAIN MUTATED 2 0 0 1 15
21Q GAIN WILD-TYPE 5 1 1 0 282

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

'12p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.07e-12 (Chi-square test), Q value = 1.8e-09

Table S8.  Gene #62: '12p loss mutation analysis' 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 1 297
12P LOSS MUTATED 0 0 0 1 4
12P LOSS WILD-TYPE 7 1 1 0 293

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

'12q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.19e-15 (Chi-square test), Q value = 1e-12

Table S9.  Gene #63: '12q loss mutation analysis' 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 1 297
12Q LOSS MUTATED 0 0 0 1 3
12Q LOSS WILD-TYPE 7 1 1 0 294

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

'16p loss mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 8.74e-06 (t-test), Q value = 0.0074

Table S10.  Gene #67: '16p loss mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 52 26.5 (39.1)
16P LOSS MUTATED 4 0.0 (0.0)
16P LOSS WILD-TYPE 48 28.8 (39.9)

Figure S10.  Get High-res Image Gene #67: '16p loss mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

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

P value = 7.92e-06 (t-test), Q value = 0.0067

Table S11.  Gene #68: '16q loss mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 52 26.5 (39.1)
16Q LOSS MUTATED 6 0.0 (0.0)
16Q LOSS WILD-TYPE 46 30.0 (40.3)

Figure S11.  Get High-res Image Gene #68: '16q loss mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

'17q loss mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 8.74e-06 (t-test), Q value = 0.0074

Table S12.  Gene #70: '17q loss mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 52 26.5 (39.1)
17Q LOSS MUTATED 4 0.0 (0.0)
17Q LOSS WILD-TYPE 48 28.8 (39.9)

Figure S12.  Get High-res Image Gene #70: '17q loss mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

'Xq loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.07e-05 (Chi-square test), Q value = 0.043

Table S13.  Gene #79: 'Xq loss mutation analysis' 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 1 297
XQ LOSS MUTATED 0 0 0 1 11
XQ LOSS WILD-TYPE 7 1 1 0 286

Figure S13.  Get High-res Image Gene #79: 'Xq loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

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

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

  • Number of patients = 307

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 11

  • 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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