Lung Squamous Cell Carcinoma: Correlation between copy number variations of arm-level result and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/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 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 STOPPEDSMOKINGYEAR TOBACCOSMOKINGHISTORYINDICATOR YEAROFTOBACCOSMOKINGONSET
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 t-test Fisher's exact test t-test
19p gain 33 (10%) 292 0.438
(1.00) 		0.227
(1.00) 		0.675
(1.00) 		1.77e-06
(0.00192) 		5.63e-06
(0.00609) 		0.634
(1.00) 		0.378
(1.00) 		0.566
(1.00) 		0.63
(1.00) 		0.309
(1.00) 		0.592
(1.00) 		0.954
(1.00) 		0.656
(1.00) 		0.83
(1.00)
1p gain 21 (6%) 304 0.876
(1.00) 		0.574
(1.00) 		0.197
(1.00) 		3.79e-06
(0.0041) 		0.0675
(1.00) 		0.915
(1.00) 		0.268
(1.00) 		0.232
(1.00) 		0.526
(1.00) 		0.353
(1.00) 		0.285
(1.00) 		0.408
(1.00) 		0.409
(1.00)
2q gain 34 (10%) 291 0.166
(1.00) 		0.886
(1.00) 		1
(1.00) 		0.831
(1.00) 		3.8e-05
(0.0411) 		0.111
(1.00) 		0.58
(1.00) 		0.225
(1.00) 		0.00397
(1.00) 		0.0963
(1.00) 		0.243
(1.00) 		0.328
(1.00) 		0.979
(1.00) 		0.641
(1.00)
11p gain 19 (6%) 306 0.954
(1.00) 		0.426
(1.00) 		0.422
(1.00) 		2e-06
(0.00217) 		0.958
(1.00) 		0.0101
(1.00) 		0.363
(1.00) 		1
(1.00) 		0.641
(1.00) 		0.49
(1.00) 		0.148
(1.00) 		0.873
(1.00) 		0.851
(1.00) 		0.541
(1.00)
17p gain 9 (3%) 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) 		0.581
(1.00) 		0.143
(1.00) 		0.0232
(1.00)
21q gain 18 (6%) 307 0.268
(1.00) 		0.682
(1.00) 		1
(1.00) 		0.949
(1.00) 		5.96e-05
(0.0644) 		0.239
(1.00) 		0.249
(1.00) 		0.72
(1.00) 		0.191
(1.00) 		0.471
(1.00) 		0.865
(1.00) 		0.515
(1.00) 		0.488
(1.00) 		0.631
(1.00)
12p loss 5 (2%) 320 0.505
(1.00) 		0.00216
(1.00) 		0.605
(1.00) 		3.63e-13
(3.95e-10) 		0.185
(1.00) 		0.789
(1.00) 		0.433
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.23
(1.00) 		0.916
(1.00) 		0.378
(1.00) 		0.273
(1.00)
12q loss 4 (1%) 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)
16q loss 60 (18%) 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) 		0.739
(1.00) 		0.299
(1.00) 		0.59
(1.00)
Xq loss 13 (4%) 312 0.884
(1.00) 		0.284
(1.00) 		0.329
(1.00) 		0.949
(1.00) 		6.63e-05
(0.0715) 		0.729
(1.00) 		0.15
(1.00) 		1
(1.00) 		0.449
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.841
(1.00) 		1
(1.00) 		0.788
(1.00)
1q gain 68 (21%) 257 0.514
(1.00) 		0.636
(1.00) 		1
(1.00) 		0.358
(1.00) 		0.00395
(1.00) 		0.12
(1.00) 		0.688
(1.00) 		0.291
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.868
(1.00) 		0.828
(1.00) 		0.903
(1.00)
2p gain 76 (23%) 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) 		0.392
(1.00) 		0.726
(1.00) 		0.0201
(1.00)
3p gain 35 (11%) 290 0.393
(1.00) 		0.137
(1.00) 		0.149
(1.00) 		0.197
(1.00) 		0.978
(1.00) 		0.0564
(1.00) 		0.871
(1.00) 		0.507
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.256
(1.00) 		0.113
(1.00) 		0.0561
(1.00)
3q gain 146 (45%) 179 0.784
(1.00) 		0.191
(1.00) 		1
(1.00) 		0.127
(1.00) 		0.35
(1.00) 		0.486
(1.00) 		0.9
(1.00) 		0.436
(1.00) 		0.708
(1.00) 		1
(1.00) 		0.736
(1.00) 		0.838
(1.00) 		0.0623
(1.00) 		0.0154
(1.00)
4p gain 13 (4%) 312 0.662
(1.00) 		0.588
(1.00) 		0.0445
(1.00) 		0.712
(1.00) 		0.72
(1.00) 		0.0695
(1.00) 		0.924
(1.00) 		0.455
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.303
(1.00) 		0.59
(1.00) 		0.78
(1.00) 		0.404
(1.00)
4q gain 5 (2%) 320 0.558
(1.00) 		0.512
(1.00) 		0.334
(1.00) 		0.103
(1.00) 		0.0324
(1.00) 		0.789
(1.00) 		1
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.0948
(1.00) 		0.343
(1.00)
5p gain 147 (45%) 178 0.537
(1.00) 		0.0819
(1.00) 		0.526
(1.00) 		0.663
(1.00) 		0.305
(1.00) 		0.0487
(1.00) 		0.443
(1.00) 		0.525
(1.00) 		0.611
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.54
(1.00) 		0.0592
(1.00) 		0.943
(1.00)
5q gain 33 (10%) 292 0.81
(1.00) 		0.396
(1.00) 		0.834
(1.00) 		0.453
(1.00) 		0.976
(1.00) 		0.942
(1.00) 		0.392
(1.00) 		0.482
(1.00) 		0.374
(1.00) 		0.309
(1.00) 		0.752
(1.00) 		0.777
(1.00) 		0.296
(1.00) 		0.499
(1.00)
6p gain 30 (9%) 295 0.755
(1.00) 		0.343
(1.00) 		0.83
(1.00) 		0.286
(1.00) 		0.0295
(1.00) 		0.118
(1.00) 		0.915
(1.00) 		0.452
(1.00) 		0.178
(1.00) 		0.269
(1.00) 		0.279
(1.00) 		0.15
(1.00) 		0.787
(1.00) 		0.0131
(1.00)
6q gain 17 (5%) 308 0.779
(1.00) 		0.455
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.000929
(1.00) 		0.611
(1.00) 		0.74
(1.00) 		0.735
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.164
(1.00) 		0.733
(1.00) 		0.87
(1.00) 		0.189
(1.00)
7p gain 88 (27%) 237 0.23
(1.00) 		0.25
(1.00) 		0.567
(1.00) 		0.465
(1.00) 		0.736
(1.00) 		0.00945
(1.00) 		0.783
(1.00) 		0.319
(1.00) 		0.583
(1.00) 		0.734
(1.00) 		0.0725
(1.00) 		0.253
(1.00) 		0.708
(1.00) 		0.503
(1.00)
7q gain 83 (26%) 242 0.401
(1.00) 		0.414
(1.00) 		0.385
(1.00) 		0.232
(1.00) 		0.457
(1.00) 		0.0112
(1.00) 		0.7
(1.00) 		0.126
(1.00) 		0.304
(1.00) 		0.736
(1.00) 		0.809
(1.00) 		0.0372
(1.00) 		0.852
(1.00) 		0.566
(1.00)
8p gain 45 (14%) 280 0.885
(1.00) 		0.441
(1.00) 		0.855
(1.00) 		0.00638
(1.00) 		0.0959
(1.00) 		0.55
(1.00) 		0.713
(1.00) 		0.0706
(1.00) 		0.241
(1.00) 		0.184
(1.00) 		0.898
(1.00) 		0.855
(1.00) 		0.667
(1.00) 		0.502
(1.00)
8q gain 91 (28%) 234 0.262
(1.00) 		0.608
(1.00) 		0.573
(1.00) 		0.295
(1.00) 		0.882
(1.00) 		0.162
(1.00) 		0.744
(1.00) 		0.0642
(1.00) 		0.0617
(1.00) 		0.19
(1.00) 		0.23
(1.00) 		0.86
(1.00) 		0.235
(1.00) 		0.503
(1.00)
9p gain 19 (6%) 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) 		0.205
(1.00) 		0.879
(1.00) 		0.882
(1.00)
9q gain 28 (9%) 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) 		0.892
(1.00) 		0.619
(1.00) 		0.74
(1.00)
10p gain 16 (5%) 309 0.802
(1.00) 		0.774
(1.00) 		0.769
(1.00) 		0.936
(1.00) 		0.97
(1.00) 		0.681
(1.00) 		0.0771
(1.00) 		0.212
(1.00) 		0.0312
(1.00) 		0.431
(1.00) 		0.179
(1.00) 		0.975
(1.00) 		0.271
(1.00) 		0.327
(1.00)
10q gain 6 (2%) 319 0.354
(1.00) 		0.734
(1.00) 		1
(1.00) 		0.996
(1.00) 		0.481
(1.00) 		0.452
(1.00) 		1
(1.00) 		0.52
(1.00) 		0.188
(1.00) 		0.582
(1.00) 		0.459
(1.00) 		0.112
(1.00) 		0.771
(1.00)
11q gain 22 (7%) 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) 		0.822
(1.00) 		0.478
(1.00) 		0.987
(1.00)
12p gain 91 (28%) 234 0.808
(1.00) 		0.864
(1.00) 		0.00435
(1.00) 		0.268
(1.00) 		0.882
(1.00) 		0.126
(1.00) 		0.835
(1.00) 		0.862
(1.00) 		0.933
(1.00) 		0.509
(1.00) 		0.979
(1.00) 		0.525
(1.00) 		0.46
(1.00) 		0.342
(1.00)
12q gain 40 (12%) 285 0.645
(1.00) 		0.724
(1.00) 		0.0519
(1.00) 		0.859
(1.00) 		0.978
(1.00) 		0.151
(1.00) 		0.164
(1.00) 		0.353
(1.00) 		0.291
(1.00) 		1
(1.00) 		0.636
(1.00) 		0.715
(1.00) 		0.152
(1.00) 		0.809
(1.00)
13q gain 7 (2%) 318 0.117
(1.00) 		0.944
(1.00) 		0.683
(1.00) 		0.994
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.21
(1.00) 		0.637
(1.00) 		1
(1.00) 		0.293
(1.00) 		0.843
(1.00) 		0.0536
(1.00) 		0.798
(1.00)
14q gain 31 (10%) 294 0.0683
(1.00) 		0.0833
(1.00) 		0.518
(1.00) 		0.858
(1.00) 		0.974
(1.00) 		0.273
(1.00) 		0.629
(1.00) 		0.552
(1.00) 		0.9
(1.00) 		1
(1.00) 		0.608
(1.00) 		0.251
(1.00) 		0.358
(1.00) 		0.657
(1.00)
15q gain 29 (9%) 296 0.687
(1.00) 		0.993
(1.00) 		1
(1.00) 		0.389
(1.00) 		0.453
(1.00) 		0.733
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.644
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.441
(1.00) 		0.0126
(1.00) 		0.463
(1.00)
16p gain 14 (4%) 311 0.205
(1.00) 		0.204
(1.00) 		0.531
(1.00) 		0.0681
(1.00) 		0.763
(1.00) 		0.0245
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.806
(1.00) 		0.688
(1.00) 		0.536
(1.00) 		0.121
(1.00)
16q gain 18 (6%) 307 0.612
(1.00) 		0.0607
(1.00) 		0.176
(1.00) 		0.366
(1.00) 		0.963
(1.00) 		0.00615
(1.00) 		0.188
(1.00) 		0.271
(1.00) 		0.093
(1.00) 		1
(1.00) 		0.94
(1.00) 		0.174
(1.00) 		0.978
(1.00) 		0.0125
(1.00)
17q gain 34 (10%) 291 0.548
(1.00) 		0.316
(1.00) 		0.0609
(1.00) 		0.271
(1.00) 		0.586
(1.00) 		0.52
(1.00) 		0.0358
(1.00) 		0.198
(1.00) 		0.0823
(1.00) 		0.323
(1.00) 		0.777
(1.00) 		0.401
(1.00) 		0.681
(1.00) 		0.0558
(1.00)
18p gain 51 (16%) 274 0.183
(1.00) 		0.13
(1.00) 		0.22
(1.00) 		0.321
(1.00) 		0.837
(1.00) 		0.123
(1.00) 		0.0196
(1.00) 		0.097
(1.00) 		0.179
(1.00) 		0.685
(1.00) 		0.344
(1.00) 		0.498
(1.00) 		0.191
(1.00) 		0.636
(1.00)
18q gain 37 (11%) 288 0.421
(1.00) 		0.378
(1.00) 		0.55
(1.00) 		0.567
(1.00) 		0.652
(1.00) 		0.209
(1.00) 		0.0995
(1.00) 		0.316
(1.00) 		0.79
(1.00) 		0.362
(1.00) 		0.0847
(1.00) 		0.691
(1.00) 		0.646
(1.00) 		0.205
(1.00)
19q gain 46 (14%) 279 0.667
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.139
(1.00) 		0.000565
(0.608) 		0.854
(1.00) 		0.112
(1.00) 		0.0747
(1.00) 		0.0574
(1.00) 		0.659
(1.00) 		0.879
(1.00) 		0.742
(1.00) 		0.863
(1.00) 		0.162
(1.00)
20p gain 91 (28%) 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) 		0.683
(1.00) 		0.779
(1.00) 		0.198
(1.00)
20q gain 80 (25%) 245 0.659
(1.00) 		0.266
(1.00) 		0.139
(1.00) 		0.77
(1.00) 		0.0159
(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) 		0.516
(1.00) 		0.798
(1.00) 		0.632
(1.00)
22q gain 77 (24%) 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) 		0.0869
(1.00) 		0.328
(1.00) 		0.604
(1.00)
Xq gain 9 (3%) 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) 		0.753
(1.00) 		1
(1.00) 		0.964
(1.00)
1p loss 48 (15%) 277 0.566
(1.00) 		0.764
(1.00) 		0.0021
(1.00) 		0.45
(1.00) 		0.119
(1.00) 		0.537
(1.00) 		0.496
(1.00) 		0.121
(1.00) 		0.258
(1.00) 		0.212
(1.00) 		0.519
(1.00) 		0.76
(1.00) 		0.511
(1.00) 		0.572
(1.00)
1q loss 10 (3%) 315 0.679
(1.00) 		0.198
(1.00) 		0.462
(1.00) 		0.988
(1.00) 		0.506
(1.00) 		0.903
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.295
(1.00) 		0.239
(1.00) 		0.545
(1.00) 		0.0525
(1.00) 		0.942
(1.00)
2q loss 9 (3%) 316 0.0514
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.99
(1.00) 		0.663
(1.00) 		0.89
(1.00) 		1
(1.00) 		0.766
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.556
(1.00) 		0.111
(1.00) 		0.731
(1.00)
3p loss 144 (44%) 181 0.408
(1.00) 		0.206
(1.00) 		0.798
(1.00) 		0.138
(1.00) 		0.404
(1.00) 		0.949
(1.00) 		0.908
(1.00) 		0.891
(1.00) 		0.959
(1.00) 		0.547
(1.00) 		0.583
(1.00) 		0.308
(1.00) 		0.671
(1.00) 		0.655
(1.00)
3q loss 27 (8%) 298 0.562
(1.00) 		0.254
(1.00) 		1
(1.00) 		0.65
(1.00) 		0.0185
(1.00) 		0.379
(1.00) 		0.12
(1.00) 		0.177
(1.00) 		0.177
(1.00) 		0.609
(1.00) 		0.0845
(1.00) 		0.204
(1.00) 		0.972
(1.00) 		0.137
(1.00)
4p loss 137 (42%) 188 0.113
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.406
(1.00) 		0.362
(1.00) 		0.31
(1.00) 		0.264
(1.00) 		0.0526
(1.00) 		1
(1.00) 		0.512
(1.00) 		0.962
(1.00) 		0.926
(1.00) 		0.202
(1.00)
4q loss 118 (36%) 207 0.0797
(1.00) 		0.566
(1.00) 		0.146
(1.00) 		0.138
(1.00) 		0.235
(1.00) 		0.483
(1.00) 		0.846
(1.00) 		0.34
(1.00) 		0.209
(1.00) 		0.536
(1.00) 		0.514
(1.00) 		0.601
(1.00) 		0.685
(1.00) 		0.522
(1.00)
5p loss 23 (7%) 302 0.0659
(1.00) 		0.285
(1.00) 		0.461
(1.00) 		0.491
(1.00) 		0.00789
(1.00) 		0.264
(1.00) 		0.313
(1.00) 		0.358
(1.00) 		0.7
(1.00) 		0.178
(1.00) 		0.858
(1.00) 		0.295
(1.00) 		0.675
(1.00) 		0.174
(1.00)
5q loss 121 (37%) 204 0.128
(1.00) 		0.766
(1.00) 		0.511
(1.00) 		0.684
(1.00) 		0.235
(1.00) 		0.0317
(1.00) 		0.371
(1.00) 		0.204
(1.00) 		0.0222
(1.00) 		0.546
(1.00) 		0.491
(1.00) 		0.708
(1.00) 		0.354
(1.00) 		0.0127
(1.00)
6p loss 35 (11%) 290 0.562
(1.00) 		0.416
(1.00) 		0.149
(1.00) 		0.818
(1.00) 		0.027
(1.00) 		0.0325
(1.00) 		0.245
(1.00) 		0.848
(1.00) 		0.0431
(1.00) 		0.616
(1.00) 		0.712
(1.00) 		0.994
(1.00) 		0.771
(1.00) 		0.903
(1.00)
6q loss 38 (12%) 287 0.991
(1.00) 		0.581
(1.00) 		1
(1.00) 		0.789
(1.00) 		0.043
(1.00) 		0.0445
(1.00) 		0.226
(1.00) 		0.862
(1.00) 		0.104
(1.00) 		0.374
(1.00) 		0.257
(1.00) 		0.564
(1.00) 		0.574
(1.00) 		0.175
(1.00)
7p loss 19 (6%) 306 0.745
(1.00) 		0.542
(1.00) 		0.79
(1.00) 		0.796
(1.00) 		0.958
(1.00) 		0.312
(1.00) 		0.177
(1.00) 		1
(1.00) 		0.528
(1.00) 		0.49
(1.00) 		0.101
(1.00) 		0.0191
(1.00) 		0.532
(1.00) 		0.366
(1.00)
7q loss 11 (3%) 314 0.649
(1.00) 		0.973
(1.00) 		0.736
(1.00) 		0.986
(1.00) 		0.0846
(1.00) 		0.464
(1.00) 		0.654
(1.00) 		0.653
(1.00) 		0.319
(1.00) 		0.122
(1.00) 		0.893
(1.00) 		0.361
(1.00) 		0.596
(1.00)
8p loss 99 (30%) 226 0.743
(1.00) 		0.142
(1.00) 		0.582
(1.00) 		0.519
(1.00) 		0.854
(1.00) 		0.182
(1.00) 		0.687
(1.00) 		0.346
(1.00) 		0.601
(1.00) 		0.183
(1.00) 		0.0854
(1.00) 		0.0759
(1.00) 		0.0711
(1.00) 		0.342
(1.00)
8q loss 11 (3%) 314 0.493
(1.00) 		0.706
(1.00) 		0.301
(1.00) 		0.463
(1.00) 		0.611
(1.00) 		0.641
(1.00) 		1
(1.00) 		0.66
(1.00) 		0.928
(1.00) 		1
(1.00) 		0.44
(1.00) 		0.158
(1.00) 		0.381
(1.00) 		0.35
(1.00)
9p loss 134 (41%) 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) 		0.776
(1.00) 		0.736
(1.00) 		0.312
(1.00)
9q loss 84 (26%) 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) 		0.92
(1.00) 		0.609
(1.00) 		0.0714
(1.00)
10p loss 72 (22%) 253 0.39
(1.00) 		0.622
(1.00) 		0.221
(1.00) 		0.963
(1.00) 		0.372
(1.00) 		0.845
(1.00) 		0.301
(1.00) 		0.373
(1.00) 		0.326
(1.00) 		0.131
(1.00) 		0.918
(1.00) 		0.0328
(1.00) 		0.48
(1.00) 		0.553
(1.00)
10q loss 71 (22%) 254 0.341
(1.00) 		0.969
(1.00) 		0.878
(1.00) 		0.832
(1.00) 		0.358
(1.00) 		0.99
(1.00) 		0.845
(1.00) 		0.194
(1.00) 		0.318
(1.00) 		0.13
(1.00) 		0.182
(1.00) 		0.0568
(1.00) 		0.781
(1.00) 		0.0792
(1.00)
11p loss 51 (16%) 274 0.309
(1.00) 		0.732
(1.00) 		0.6
(1.00) 		0.712
(1.00) 		0.218
(1.00) 		0.535
(1.00) 		0.271
(1.00) 		0.247
(1.00) 		0.709
(1.00) 		0.388
(1.00) 		0.475
(1.00) 		0.847
(1.00) 		0.487
(1.00) 		0.755
(1.00)
11q loss 32 (10%) 293 0.663
(1.00) 		0.0338
(1.00) 		0.402
(1.00) 		0.963
(1.00) 		0.89
(1.00) 		0.693
(1.00) 		0.106
(1.00) 		1
(1.00) 		0.509
(1.00) 		0.296
(1.00) 		0.864
(1.00) 		0.639
(1.00) 		0.406
(1.00) 		0.792
(1.00)
13q loss 124 (38%) 201 0.011
(1.00) 		0.529
(1.00) 		0.601
(1.00) 		0.0744
(1.00) 		0.332
(1.00) 		0.935
(1.00) 		0.166
(1.00) 		0.4
(1.00) 		0.0275
(1.00) 		0.754
(1.00) 		0.786
(1.00) 		0.046
(1.00) 		0.194
(1.00) 		0.0138
(1.00)
14q loss 60 (18%) 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) 		0.899
(1.00) 		0.427
(1.00) 		0.19
(1.00)
15q loss 39 (12%) 286 0.696
(1.00) 		0.495
(1.00) 		0.0761
(1.00) 		0.734
(1.00) 		0.073
(1.00) 		0.0518
(1.00) 		0.0369
(1.00) 		0.472
(1.00) 		0.0103
(1.00) 		1
(1.00) 		0.341
(1.00) 		0.198
(1.00) 		0.164
(1.00) 		0.959
(1.00)
16p loss 49 (15%) 276 0.188
(1.00) 		0.754
(1.00) 		0.86
(1.00) 		0.453
(1.00) 		0.767
(1.00) 		0.738
(1.00) 		0.611
(1.00) 		0.793
(1.00) 		0.956
(1.00) 		1
(1.00) 		0.313
(1.00) 		0.639
(1.00) 		0.901
(1.00) 		0.684
(1.00)
17p loss 117 (36%) 208 0.255
(1.00) 		0.773
(1.00) 		0.428
(1.00) 		0.0249
(1.00) 		0.55
(1.00) 		0.411
(1.00) 		0.174
(1.00) 		0.362
(1.00) 		0.907
(1.00) 		0.533
(1.00) 		0.392
(1.00) 		0.0314
(1.00) 		0.279
(1.00) 		0.654
(1.00)
17q loss 21 (6%) 304 0.48
(1.00) 		0.925
(1.00) 		0.0714
(1.00) 		0.453
(1.00) 		0.95
(1.00) 		0.5
(1.00) 		0.734
(1.00) 		0.143
(1.00) 		0.254
(1.00) 		0.526
(1.00) 		0.244
(1.00) 		0.868
(1.00) 		0.691
(1.00) 		0.206
(1.00)
18p loss 35 (11%) 290 0.526
(1.00) 		0.651
(1.00) 		0.838
(1.00) 		0.997
(1.00) 		0.871
(1.00) 		0.966
(1.00) 		0.251
(1.00) 		0.162
(1.00) 		0.275
(1.00) 		0.616
(1.00) 		0.0644
(1.00) 		0.78
(1.00) 		0.822
(1.00) 		0.235
(1.00)
18q loss 65 (20%) 260 0.574
(1.00) 		0.0876
(1.00) 		0.271
(1.00) 		0.768
(1.00) 		0.326
(1.00) 		0.468
(1.00) 		0.907
(1.00) 		0.237
(1.00) 		0.908
(1.00) 		0.7
(1.00) 		0.136
(1.00) 		0.276
(1.00) 		0.354
(1.00) 		0.294
(1.00)
19p loss 53 (16%) 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) 		0.975
(1.00) 		0.146
(1.00) 		0.111
(1.00)
19q loss 36 (11%) 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) 		0.794
(1.00) 		0.261
(1.00) 		0.035
(1.00)
20p loss 16 (5%) 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) 		0.0366
(1.00) 		0.795
(1.00) 		0.705
(1.00)
20q loss 17 (5%) 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) 		0.906
(1.00) 		0.89
(1.00) 		0.178
(1.00)
21q loss 100 (31%) 225 0.4
(1.00) 		0.373
(1.00) 		0.0194
(1.00) 		0.862
(1.00) 		0.532
(1.00) 		0.359
(1.00) 		0.698
(1.00) 		0.293
(1.00) 		0.135
(1.00) 		0.743
(1.00) 		0.204
(1.00) 		0.124
(1.00) 		0.869
(1.00) 		0.3
(1.00)
22q loss 33 (10%) 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) 		0.0676
(1.00) 		0.402
(1.00) 		0.0836
(1.00)
'1p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.79e-06 (Chi-square test), Q value = 0.0041

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 1 315
1P GAIN MUTATED 4 0 0 0 17
1P GAIN WILD-TYPE 3 1 1 1 298

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 = 3.8e-05 (Chi-square test), Q value = 0.041

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 1 315
2Q GAIN MUTATED 4 1 0 0 29
2Q GAIN WILD-TYPE 3 0 1 1 286

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

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

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

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

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 1 315
17P GAIN MUTATED 0 1 0 0 8
17P GAIN WILD-TYPE 7 0 1 1 307

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

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

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

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

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 1 315
19P GAIN MUTATED 5 0 0 0 28
19P GAIN WILD-TYPE 2 1 1 1 287

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

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 1 315
21Q GAIN MUTATED 2 0 0 1 15
21Q GAIN WILD-TYPE 5 1 1 0 300

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 = 3.63e-13 (Chi-square test), Q value = 3.9e-10

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 1 315
12P LOSS MUTATED 0 0 0 1 4
12P LOSS WILD-TYPE 7 1 1 0 311

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

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 1 315
12Q LOSS MUTATED 0 0 0 1 3
12Q LOSS WILD-TYPE 7 1 1 0 312

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

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

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

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

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

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

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

P value = 6.63e-05 (Chi-square test), Q value = 0.071

Table S11.  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 1 315
XQ LOSS MUTATED 0 0 0 1 12
XQ LOSS WILD-TYPE 7 1 1 0 303

Figure S11.  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-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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle