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 278 patients, 14 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'.

  • 18q gain cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.

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

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

  • Xq gain cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.

  • 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'.

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, 14 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 30 (11%) 248 0.431
(1.00) 		0.46
(1.00) 		0.828
(1.00) 		7.92e-06
(0.00672) 		1.44e-05
(0.0121) 		0.828
(1.00) 		0.736
(1.00) 		0.673
(1.00) 		0.685
(1.00) 		0.294
(1.00) 		1
(1.00)
1p gain 18 (6%) 260 0.867
(1.00) 		0.154
(1.00) 		0.097
(1.00) 		3.73e-06
(0.00317) 		0.0354
(1.00) 		0.647
(1.00) 		0.278
(1.00) 		0.345
(1.00) 		0.494
(1.00) 		0.415
(1.00)
2q gain 34 (12%) 244 0.564
(1.00) 		0.542
(1.00) 		0.836
(1.00) 		0.591
(1.00) 		2.92e-06
(0.00248) 		0.339
(1.00) 		0.422
(1.00) 		0.324
(1.00) 		0.029
(1.00) 		0.11
(1.00) 		0.766
(1.00)
11p gain 17 (6%) 261 0.962
(1.00) 		0.511
(1.00) 		0.255
(1.00) 		8.74e-06
(0.0074) 		0.954
(1.00) 		0.00121
(1.00) 		0.409
(1.00) 		1
(1.00) 		0.589
(1.00) 		0.474
(1.00) 		0.694
(1.00)
17p gain 6 (2%) 272 0.444
(1.00) 		0.48
(1.00) 		0.347
(1.00) 		2.93e-09
(2.49e-06) 		0.233
(1.00) 		0.558
(1.00) 		0.456
(1.00) 		0.126
(1.00) 		1
(1.00) 		1
(1.00)
18q gain 32 (12%) 246 0.326
(1.00) 		0.91
(1.00) 		1
(1.00) 		9.14e-06
(0.00772) 		0.122
(1.00) 		0.558
(1.00) 		0.594
(1.00) 		0.167
(1.00) 		0.909
(1.00) 		1
(1.00) 		0.757
(1.00)
21q gain 15 (5%) 263 0.675
(1.00) 		0.994
(1.00) 		1
(1.00) 		0.996
(1.00) 		4.07e-05
(0.0343) 		0.383
(1.00) 		0.334
(1.00) 		0.417
(1.00) 		0.383
(1.00) 		0.431
(1.00) 		0.0125
(1.00)
Xq gain 8 (3%) 270 0.901
(1.00) 		0.363
(1.00) 		1
(1.00) 		9.14e-06
(0.00772) 		0.989
(1.00) 		0.408
(1.00) 		1
(1.00) 		1
(1.00) 		0.468
(1.00) 		1
(1.00) 		0.198
(1.00)
12p loss 4 (1%) 274 0.499
(1.00) 		0.0133
(1.00) 		0.289
(1.00) 		4.02e-14
(3.43e-11) 		0.522
(1.00) 		1
(1.00) 		0.333
(1.00) 		0.554
(1.00) 		1
(1.00) 		0.358
(1.00)
12q loss 3 (1%) 275 0.41
(1.00) 		0.174
(1.00) 		4.85e-19
(4.14e-16) 		0.395
(1.00) 		0.678
(1.00) 		0.261
(1.00) 		0.454
(1.00) 		1
(1.00) 		0.282
(1.00)
16p loss 38 (14%) 240 0.0958
(1.00) 		0.411
(1.00) 		1
(1.00) 		8.74e-06
(0.0074) 		0.801
(1.00) 		0.74
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.889
(1.00) 		1
(1.00) 		0.393
(1.00)
16q loss 51 (18%) 227 0.0552
(1.00) 		0.0642
(1.00) 		0.226
(1.00) 		7.92e-06
(0.00672) 		0.675
(1.00) 		0.917
(1.00) 		0.324
(1.00) 		0.149
(1.00) 		0.916
(1.00) 		0.398
(1.00) 		0.619
(1.00)
17q loss 13 (5%) 265 0.729
(1.00) 		0.433
(1.00) 		0.341
(1.00) 		9.14e-06
(0.00772) 		0.973
(1.00) 		0.154
(1.00) 		0.853
(1.00) 		0.245
(1.00) 		0.0697
(1.00) 		1
(1.00) 		0.633
(1.00)
1q gain 60 (22%) 218 0.284
(1.00) 		0.451
(1.00) 		0.743
(1.00) 		0.446
(1.00) 		0.00517
(1.00) 		0.257
(1.00) 		0.786
(1.00) 		0.245
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.347
(1.00)
2p gain 70 (25%) 208 0.713
(1.00) 		0.733
(1.00) 		0.0424
(1.00) 		0.198
(1.00) 		0.0186
(1.00) 		0.173
(1.00) 		0.141
(1.00) 		0.0923
(1.00) 		0.194
(1.00) 		0.128
(1.00) 		0.258
(1.00)
3p gain 33 (12%) 245 0.41
(1.00) 		0.0427
(1.00) 		0.142
(1.00) 		0.264
(1.00) 		0.979
(1.00) 		0.0531
(1.00) 		0.956
(1.00) 		0.491
(1.00) 		0.5
(1.00) 		1
(1.00) 		0.549
(1.00)
3q gain 124 (45%) 154 0.705
(1.00) 		0.249
(1.00) 		0.891
(1.00) 		0.31
(1.00) 		0.348
(1.00) 		0.695
(1.00) 		0.93
(1.00) 		0.261
(1.00) 		0.722
(1.00) 		1
(1.00) 		0.0743
(1.00)
4p gain 10 (4%) 268 0.997
(1.00) 		0.506
(1.00) 		0.0672
(1.00) 		0.796
(1.00) 		0.651
(1.00) 		0.047
(1.00) 		0.908
(1.00) 		0.64
(1.00) 		0.434
(1.00) 		1
(1.00) 		0.606
(1.00)
4q gain 7 (3%) 271 0.317
(1.00) 		0.286
(1.00) 		0.679
(1.00) 		0.391
(1.00) 		0.0698
(1.00) 		1
(1.00) 		1
(1.00) 		0.591
(1.00) 		1
(1.00) 		1
(1.00)
5p gain 131 (47%) 147 0.435
(1.00) 		0.0771
(1.00) 		0.497
(1.00) 		0.693
(1.00) 		0.332
(1.00) 		0.0368
(1.00) 		0.612
(1.00) 		0.162
(1.00) 		0.65
(1.00) 		1
(1.00) 		1
(1.00)
5q gain 31 (11%) 247 0.857
(1.00) 		0.454
(1.00) 		1
(1.00) 		0.523
(1.00) 		0.979
(1.00) 		0.816
(1.00) 		0.441
(1.00) 		0.554
(1.00) 		0.56
(1.00) 		0.309
(1.00) 		1
(1.00)
6p gain 27 (10%) 251 0.739
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.225
(1.00) 		0.0362
(1.00) 		0.0826
(1.00) 		0.795
(1.00) 		0.351
(1.00) 		0.0664
(1.00) 		0.252
(1.00) 		1
(1.00)
6q gain 15 (5%) 263 0.83
(1.00) 		0.32
(1.00) 		0.766
(1.00) 		0.428
(1.00) 		0.0012
(1.00) 		0.493
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.863
(1.00) 		0.431
(1.00) 		0.661
(1.00)
7p gain 82 (29%) 196 0.399
(1.00) 		0.548
(1.00) 		0.656
(1.00) 		0.619
(1.00) 		0.762
(1.00) 		0.00711
(1.00) 		0.718
(1.00) 		0.534
(1.00) 		0.337
(1.00) 		0.728
(1.00) 		0.832
(1.00)
7q gain 77 (28%) 201 0.528
(1.00) 		0.873
(1.00) 		0.544
(1.00) 		0.333
(1.00) 		0.496
(1.00) 		0.0223
(1.00) 		0.67
(1.00) 		0.326
(1.00) 		0.18
(1.00) 		0.732
(1.00) 		1
(1.00)
8p gain 42 (15%) 236 0.481
(1.00) 		0.714
(1.00) 		0.85
(1.00) 		0.0289
(1.00) 		0.134
(1.00) 		0.532
(1.00) 		0.664
(1.00) 		0.134
(1.00) 		0.239
(1.00) 		0.18
(1.00) 		0.17
(1.00)
8q gain 85 (31%) 193 0.533
(1.00) 		0.905
(1.00) 		0.662
(1.00) 		0.31
(1.00) 		0.852
(1.00) 		0.159
(1.00) 		0.67
(1.00) 		0.124
(1.00) 		0.0853
(1.00) 		0.18
(1.00) 		0.672
(1.00)
9p gain 18 (6%) 260 0.209
(1.00) 		0.545
(1.00) 		0.269
(1.00) 		0.00323
(1.00) 		0.706
(1.00) 		0.619
(1.00) 		0.518
(1.00) 		0.634
(1.00) 		1
(1.00) 		1
(1.00)
9q gain 27 (10%) 251 0.223
(1.00) 		0.429
(1.00) 		0.819
(1.00) 		0.602
(1.00) 		0.524
(1.00) 		0.526
(1.00) 		0.773
(1.00) 		0.269
(1.00) 		0.673
(1.00) 		0.605
(1.00) 		0.502
(1.00)
10p gain 13 (5%) 265 0.631
(1.00) 		0.955
(1.00) 		0.524
(1.00) 		0.852
(1.00) 		0.973
(1.00) 		0.131
(1.00) 		0.132
(1.00) 		0.159
(1.00) 		0.0113
(1.00) 		0.386
(1.00) 		0.143
(1.00)
10q gain 6 (2%) 272 0.349
(1.00) 		0.733
(1.00) 		1
(1.00) 		0.994
(1.00) 		0.429
(1.00) 		0.463
(1.00) 		1
(1.00) 		0.523
(1.00) 		0.199
(1.00) 		0.121
(1.00)
11q gain 19 (7%) 259 0.569
(1.00) 		0.956
(1.00) 		0.419
(1.00) 		0.452
(1.00) 		0.934
(1.00) 		0.0064
(1.00) 		0.241
(1.00) 		0.527
(1.00) 		0.0404
(1.00) 		0.513
(1.00) 		0.431
(1.00)
12p gain 78 (28%) 200 0.615
(1.00) 		0.804
(1.00) 		0.023
(1.00) 		0.368
(1.00) 		0.881
(1.00) 		0.057
(1.00) 		0.725
(1.00) 		0.918
(1.00) 		0.672
(1.00) 		0.474
(1.00) 		0.274
(1.00)
12q gain 36 (13%) 242 0.733
(1.00) 		0.642
(1.00) 		0.0706
(1.00) 		0.958
(1.00) 		0.977
(1.00) 		0.0725
(1.00) 		0.108
(1.00) 		0.253
(1.00) 		0.212
(1.00) 		1
(1.00) 		0.237
(1.00)
13q gain 6 (2%) 272 0.112
(1.00) 		0.567
(1.00) 		1
(1.00) 		0.994
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.456
(1.00) 		0.759
(1.00) 		1
(1.00) 		1
(1.00)
14q gain 29 (10%) 249 0.0929
(1.00) 		0.0403
(1.00) 		0.513
(1.00) 		0.937
(1.00) 		0.977
(1.00) 		0.439
(1.00) 		0.897
(1.00) 		0.669
(1.00) 		1
(1.00) 		1
(1.00) 		0.203
(1.00)
15q gain 25 (9%) 253 0.618
(1.00) 		0.85
(1.00) 		0.817
(1.00) 		0.365
(1.00) 		0.458
(1.00) 		0.647
(1.00) 		0.255
(1.00) 		0.799
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.733
(1.00)
16p gain 16 (6%) 262 0.516
(1.00) 		0.315
(1.00) 		0.251
(1.00) 		0.0584
(1.00) 		0.889
(1.00) 		0.0252
(1.00) 		0.473
(1.00) 		1
(1.00) 		0.549
(1.00) 		1
(1.00) 		0.389
(1.00)
16q gain 19 (7%) 259 0.838
(1.00) 		0.107
(1.00) 		0.114
(1.00) 		0.305
(1.00) 		0.944
(1.00) 		0.00727
(1.00) 		0.17
(1.00) 		0.296
(1.00) 		0.139
(1.00) 		1
(1.00) 		1
(1.00)
17q gain 34 (12%) 244 0.133
(1.00) 		0.238
(1.00) 		0.0386
(1.00) 		0.326
(1.00) 		0.703
(1.00) 		0.662
(1.00) 		0.00659
(1.00) 		0.345
(1.00) 		0.0663
(1.00) 		0.11
(1.00) 		0.55
(1.00)
18p gain 45 (16%) 233 0.0651
(1.00) 		0.101
(1.00) 		0.357
(1.00) 		0.577
(1.00) 		0.367
(1.00) 		0.39
(1.00) 		0.0579
(1.00) 		0.278
(1.00) 		0.219
(1.00) 		0.667
(1.00) 		0.436
(1.00)
19q gain 42 (15%) 236 0.731
(1.00) 		0.833
(1.00) 		0.85
(1.00) 		0.183
(1.00) 		0.00113
(0.945) 		0.963
(1.00) 		0.281
(1.00) 		0.134
(1.00) 		0.121
(1.00) 		0.651
(1.00) 		0.41
(1.00)
20p gain 82 (29%) 196 0.848
(1.00) 		0.137
(1.00) 		0.011
(1.00) 		0.19
(1.00) 		0.209
(1.00) 		0.808
(1.00) 		0.461
(1.00) 		0.115
(1.00) 		0.147
(1.00) 		0.166
(1.00) 		0.832
(1.00)
20q gain 70 (25%) 208 0.482
(1.00) 		0.424
(1.00) 		0.162
(1.00) 		0.764
(1.00) 		0.109
(1.00) 		0.989
(1.00) 		0.535
(1.00) 		0.0531
(1.00) 		0.132
(1.00) 		0.128
(1.00) 		0.371
(1.00)
22q gain 64 (23%) 214 0.0325
(1.00) 		0.419
(1.00) 		0.42
(1.00) 		0.674
(1.00) 		0.907
(1.00) 		0.231
(1.00) 		0.922
(1.00) 		0.5
(1.00) 		0.431
(1.00) 		0.701
(1.00) 		1
(1.00)
1p loss 41 (15%) 237 0.676
(1.00) 		0.572
(1.00) 		0.00703
(1.00) 		0.541
(1.00) 		0.119
(1.00) 		0.43
(1.00) 		0.531
(1.00) 		0.349
(1.00) 		0.435
(1.00) 		0.17
(1.00) 		1
(1.00)
1q loss 7 (3%) 271 0.435
(1.00) 		0.0138
(1.00) 		0.679
(1.00) 		0.992
(1.00) 		0.0926
(1.00) 		0.425
(1.00) 		0.509
(1.00) 		0.452
(1.00) 		0.228
(1.00) 		1
(1.00)
2q loss 8 (3%) 270 0.0509
(1.00) 		0.0687
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.562
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.612
(1.00) 		1
(1.00) 		0.591
(1.00)
3p loss 120 (43%) 158 0.45
(1.00) 		0.0522
(1.00) 		1
(1.00) 		0.116
(1.00) 		0.406
(1.00) 		0.968
(1.00) 		0.732
(1.00) 		0.764
(1.00) 		0.98
(1.00) 		0.75
(1.00) 		0.173
(1.00)
3q loss 24 (9%) 254 0.164
(1.00) 		0.541
(1.00) 		0.81
(1.00) 		0.745
(1.00) 		0.0221
(1.00) 		0.19
(1.00) 		0.0778
(1.00) 		0.463
(1.00) 		0.0856
(1.00) 		1
(1.00) 		0.293
(1.00)
4p loss 116 (42%) 162 0.146
(1.00) 		0.88
(1.00) 		0.891
(1.00) 		0.227
(1.00) 		0.405
(1.00) 		0.672
(1.00) 		0.337
(1.00) 		0.164
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.32
(1.00)
4q loss 99 (36%) 179 0.102
(1.00) 		0.549
(1.00) 		0.323
(1.00) 		0.0968
(1.00) 		0.234
(1.00) 		0.793
(1.00) 		0.742
(1.00) 		0.0746
(1.00) 		0.297
(1.00) 		0.748
(1.00) 		0.153
(1.00)
5p loss 17 (6%) 261 0.0341
(1.00) 		0.417
(1.00) 		0.572
(1.00) 		0.787
(1.00) 		0.00309
(1.00) 		0.112
(1.00) 		0.523
(1.00) 		1
(1.00) 		0.717
(1.00) 		0.474
(1.00) 		0.087
(1.00)
5q loss 97 (35%) 181 0.0894
(1.00) 		0.817
(1.00) 		0.67
(1.00) 		0.285
(1.00) 		0.233
(1.00) 		0.0481
(1.00) 		0.328
(1.00) 		0.168
(1.00) 		0.0357
(1.00) 		0.743
(1.00) 		0.537
(1.00)
6p loss 28 (10%) 250 0.837
(1.00) 		0.5
(1.00) 		0.0447
(1.00) 		0.939
(1.00) 		0.0176
(1.00) 		0.139
(1.00) 		0.322
(1.00) 		0.814
(1.00) 		0.246
(1.00) 		0.606
(1.00) 		0.511
(1.00)
6q loss 32 (12%) 246 0.731
(1.00) 		0.809
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.0392
(1.00) 		0.221
(1.00) 		0.225
(1.00) 		0.839
(1.00) 		0.666
(1.00) 		0.611
(1.00) 		0.549
(1.00)
7p loss 17 (6%) 261 0.573
(1.00) 		0.612
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.954
(1.00) 		0.654
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.66
(1.00) 		0.474
(1.00) 		1
(1.00)
7q loss 9 (3%) 269 0.584
(1.00) 		0.724
(1.00) 		0.453
(1.00) 		0.987
(1.00) 		0.222
(1.00) 		0.382
(1.00) 		1
(1.00) 		1
(1.00) 		0.284
(1.00) 		0.604
(1.00)
8p loss 80 (29%) 198 0.419
(1.00) 		0.315
(1.00) 		0.37
(1.00) 		0.221
(1.00) 		0.874
(1.00) 		0.0309
(1.00) 		0.672
(1.00) 		0.395
(1.00) 		0.561
(1.00) 		0.0676
(1.00) 		0.668
(1.00)
8q loss 8 (3%) 270 0.696
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.428
(1.00) 		0.491
(1.00) 		0.715
(1.00) 		0.764
(1.00) 		0.557
(1.00) 		0.906
(1.00) 		1
(1.00) 		0.198
(1.00)
9p loss 113 (41%) 165 0.598
(1.00) 		0.501
(1.00) 		0.17
(1.00) 		0.0888
(1.00) 		0.402
(1.00) 		0.764
(1.00) 		0.542
(1.00) 		0.938
(1.00) 		0.538
(1.00) 		1
(1.00) 		0.552
(1.00)
9q loss 71 (26%) 207 0.603
(1.00) 		0.0141
(1.00) 		0.437
(1.00) 		0.527
(1.00) 		0.156
(1.00) 		0.225
(1.00) 		0.6
(1.00) 		0.459
(1.00) 		0.771
(1.00) 		0.719
(1.00) 		0.823
(1.00)
10p loss 58 (21%) 220 0.408
(1.00) 		0.792
(1.00) 		0.181
(1.00) 		0.708
(1.00) 		0.332
(1.00) 		0.525
(1.00) 		0.0886
(1.00) 		0.591
(1.00) 		0.11
(1.00) 		0.128
(1.00) 		0.469
(1.00)
10q loss 58 (21%) 220 0.368
(1.00) 		0.993
(1.00) 		0.505
(1.00) 		0.708
(1.00) 		0.342
(1.00) 		0.899
(1.00) 		0.711
(1.00) 		0.586
(1.00) 		0.192
(1.00) 		0.128
(1.00) 		0.469
(1.00)
11p loss 45 (16%) 233 0.179
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.62
(1.00) 		0.232
(1.00) 		0.775
(1.00) 		0.946
(1.00) 		0.443
(1.00) 		0.829
(1.00) 		0.209
(1.00) 		0.794
(1.00)
11q loss 25 (9%) 253 0.49
(1.00) 		0.046
(1.00) 		0.817
(1.00) 		0.915
(1.00) 		0.906
(1.00) 		0.621
(1.00) 		0.346
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.224
(1.00) 		0.0882
(1.00)
13q loss 101 (36%) 177 0.124
(1.00) 		0.614
(1.00) 		0.574
(1.00) 		0.135
(1.00) 		0.354
(1.00) 		0.972
(1.00) 		0.193
(1.00) 		0.363
(1.00) 		0.0171
(1.00) 		1
(1.00) 		0.316
(1.00)
14q loss 50 (18%) 228 0.146
(1.00) 		0.239
(1.00) 		0.0524
(1.00) 		0.316
(1.00) 		0.162
(1.00) 		0.044
(1.00) 		0.238
(1.00) 		0.375
(1.00) 		0.675
(1.00) 		0.393
(1.00) 		1
(1.00)
15q loss 34 (12%) 244 0.954
(1.00) 		0.507
(1.00) 		0.145
(1.00) 		0.446
(1.00) 		0.077
(1.00) 		0.104
(1.00) 		0.0157
(1.00) 		0.517
(1.00) 		0.00474
(1.00) 		1
(1.00) 		1
(1.00)
17p loss 99 (36%) 179 0.538
(1.00) 		0.784
(1.00) 		0.672
(1.00) 		0.0303
(1.00) 		0.545
(1.00) 		0.47
(1.00) 		0.14
(1.00) 		0.641
(1.00) 		0.779
(1.00) 		1
(1.00) 		0.541
(1.00)
18p loss 30 (11%) 248 0.972
(1.00) 		0.91
(1.00) 		0.274
(1.00) 		0.416
(1.00) 		0.869
(1.00) 		0.871
(1.00) 		0.15
(1.00) 		0.369
(1.00) 		0.0713
(1.00) 		0.607
(1.00) 		0.752
(1.00)
18q loss 54 (19%) 224 0.835
(1.00) 		0.21
(1.00) 		0.0854
(1.00) 		0.382
(1.00) 		0.175
(1.00) 		0.384
(1.00) 		0.953
(1.00) 		0.489
(1.00) 		0.982
(1.00) 		0.218
(1.00) 		1
(1.00)
19p loss 44 (16%) 234 0.101
(1.00) 		0.908
(1.00) 		0.71
(1.00) 		0.0806
(1.00) 		0.135
(1.00) 		0.281
(1.00) 		0.672
(1.00) 		0.365
(1.00) 		0.338
(1.00) 		0.0559
(1.00) 		0.426
(1.00)
19q loss 30 (11%) 248 0.17
(1.00) 		0.295
(1.00) 		0.665
(1.00) 		0.405
(1.00) 		0.00152
(1.00) 		0.251
(1.00) 		0.558
(1.00) 		0.82
(1.00) 		0.735
(1.00) 		0.294
(1.00) 		1
(1.00)
20p loss 12 (4%) 266 0.0975
(1.00) 		0.546
(1.00) 		0.526
(1.00) 		0.977
(1.00) 		0.952
(1.00) 		0.267
(1.00) 		1
(1.00) 		0.0927
(1.00) 		1
(1.00) 		1
(1.00)
20q loss 14 (5%) 264 0.39
(1.00) 		0.542
(1.00) 		0.367
(1.00) 		0.968
(1.00) 		0.925
(1.00) 		0.404
(1.00) 		1
(1.00) 		0.805
(1.00) 		1
(1.00) 		1
(1.00)
21q loss 91 (33%) 187 0.497
(1.00) 		0.356
(1.00) 		0.00898
(1.00) 		0.747
(1.00) 		0.544
(1.00) 		0.301
(1.00) 		0.68
(1.00) 		0.234
(1.00) 		0.211
(1.00) 		0.733
(1.00) 		0.403
(1.00)
22q loss 29 (10%) 249 0.605
(1.00) 		0.196
(1.00) 		0.0745
(1.00) 		0.275
(1.00) 		0.00151
(1.00) 		0.43
(1.00) 		0.000743
(0.623) 		0.299
(1.00) 		0.00859
(1.00) 		0.606
(1.00) 		0.521
(1.00)
Xq loss 14 (5%) 264 0.878
(1.00) 		0.143
(1.00) 		0.534
(1.00) 		0.00067
(0.563) 		0.313
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.544
(1.00) 		1
(1.00) 		0.0458
(1.00)
'1p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.73e-06 (Chi-square test), Q value = 0.0032

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 1 268
1P GAIN MUTATED 4 0 0 0 14
1P GAIN WILD-TYPE 3 1 1 1 254

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 = 2.92e-06 (Chi-square test), Q value = 0.0025

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 1 268
2Q GAIN MUTATED 5 1 0 0 28
2Q GAIN WILD-TYPE 2 0 1 1 240

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 = 2.93e-09 (Chi-square test), Q value = 2.5e-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 1 268
17P GAIN MUTATED 0 1 0 0 5
17P GAIN WILD-TYPE 7 0 1 1 263

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

'18q gain mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 9.14e-06 (t-test), Q value = 0.0077

Table S5.  Gene #33: '18q gain mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 52 26.5 (39.1)
18Q GAIN MUTATED 3 0.0 (0.0)
18Q GAIN WILD-TYPE 49 28.2 (39.7)

Figure S5.  Get High-res Image Gene #33: '18q gain mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

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

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

Table S6.  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 S6.  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 = 1.44e-05 (Chi-square test), Q value = 0.012

Table S7.  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 1 268
19P GAIN MUTATED 5 0 0 0 25
19P GAIN WILD-TYPE 2 1 1 1 243

Figure S7.  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 = 4.07e-05 (Chi-square test), Q value = 0.034

Table S8.  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 1 268
21Q GAIN MUTATED 2 0 0 1 12
21Q GAIN WILD-TYPE 5 1 1 0 256

Figure S8.  Get High-res Image Gene #38: '21q gain mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Xq gain mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 9.14e-06 (t-test), Q value = 0.0077

Table S9.  Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

nPatients Mean (Std.Dev)
ALL 52 26.5 (39.1)
XQ GAIN MUTATED 3 0.0 (0.0)
XQ GAIN WILD-TYPE 49 28.2 (39.7)

Figure S9.  Get High-res Image Gene #40: 'Xq gain mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

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

P value = 4.02e-14 (Chi-square test), Q value = 3.4e-11

Table S10.  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 1 268
12P LOSS MUTATED 0 0 0 1 3
12P LOSS WILD-TYPE 7 1 1 0 265

Figure S10.  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 = 4.85e-19 (Chi-square test), Q value = 4.1e-16

Table S11.  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 1 268
12Q LOSS MUTATED 0 0 0 1 2
12Q LOSS WILD-TYPE 7 1 1 0 266

Figure S11.  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 S12.  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 S12.  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 S13.  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 S13.  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 = 9.14e-06 (t-test), Q value = 0.0077

Table S14.  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 3 0.0 (0.0)
17Q LOSS WILD-TYPE 49 28.2 (39.7)

Figure S14.  Get High-res Image Gene #70: '17q loss mutation analysis' versus Clinical Feature #4: 'KARNOFSKY.PERFORMANCE.SCORE'

Methods & Data
Input

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

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

  • Number of patients = 278

  • 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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