Correlation between copy number variations of arm-level result and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1K0727Z
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 Adenocarcinoma (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/C1K0727Z
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 80 arm-level results and 14 clinical features across 389 patients, 2 significant findings detected with Q value < 0.25.

  • 1q loss cnv correlated to 'Time to Death'.

  • 18p loss cnv correlated to 'NUMBERPACKYEARSSMOKED'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 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
1q loss 0 (0%) 379 3.02e-05
(0.0323) 		0.684
(1.00) 		1
(1.00) 		0.0269
(1.00) 		0.792
(1.00) 		0.0653
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.0882
(1.00) 		0.37
(1.00) 		0.516
(1.00) 		1
(1.00)
18p loss 0 (0%) 322 0.493
(1.00) 		0.096
(1.00) 		0.14
(1.00) 		0.00533
(1.00) 		0.317
(1.00) 		0.273
(1.00) 		0.451
(1.00) 		0.0481
(1.00) 		0.00756
(1.00) 		0.221
(1.00) 		9.54e-05
(0.102) 		0.579
(1.00) 		0.0345
(1.00) 		0.23
(1.00)
1p gain 0 (0%) 340 0.839
(1.00) 		0.000928
(0.987) 		1
(1.00) 		0.475
(1.00) 		0.911
(1.00) 		0.662
(1.00) 		0.0036
(1.00) 		0.626
(1.00) 		0.00241
(1.00) 		0.49
(1.00) 		0.849
(1.00) 		0.866
(1.00) 		0.902
(1.00) 		0.308
(1.00)
1q gain 0 (0%) 238 0.768
(1.00) 		0.172
(1.00) 		0.465
(1.00) 		0.557
(1.00) 		0.325
(1.00) 		0.426
(1.00) 		0.0263
(1.00) 		0.185
(1.00) 		0.0258
(1.00) 		0.242
(1.00) 		0.537
(1.00) 		0.405
(1.00) 		0.454
(1.00) 		0.145
(1.00)
2p gain 0 (0%) 343 0.0933
(1.00) 		0.0304
(1.00) 		0.0822
(1.00) 		0.558
(1.00) 		0.828
(1.00) 		0.132
(1.00) 		0.775
(1.00) 		0.0927
(1.00) 		0.151
(1.00) 		1
(1.00) 		0.851
(1.00) 		0.136
(1.00) 		0.778
(1.00) 		0.437
(1.00)
2q gain 0 (0%) 351 0.204
(1.00) 		0.145
(1.00) 		0.395
(1.00) 		0.889
(1.00) 		0.27
(1.00) 		0.962
(1.00) 		0.0969
(1.00) 		0.228
(1.00) 		0.707
(1.00) 		0.659
(1.00) 		0.236
(1.00) 		0.893
(1.00) 		1
(1.00)
3p gain 0 (0%) 379 0.0991
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.982
(1.00) 		0.0854
(1.00) 		0.623
(1.00) 		0.545
(1.00) 		0.426
(1.00) 		0.414
(1.00) 		0.844
(1.00) 		0.362
(1.00) 		0.262
(1.00) 		0.386
(1.00)
3q gain 0 (0%) 366 0.132
(1.00) 		0.943
(1.00) 		0.527
(1.00) 		1
(1.00) 		0.79
(1.00) 		0.155
(1.00) 		0.91
(1.00) 		0.383
(1.00) 		0.334
(1.00) 		0.569
(1.00) 		0.592
(1.00) 		0.388
(1.00) 		0.64
(1.00)
4p gain 0 (0%) 362 0.615
(1.00) 		0.0149
(1.00) 		0.321
(1.00) 		0.517
(1.00) 		0.221
(1.00) 		0.896
(1.00) 		0.0902
(1.00) 		0.271
(1.00) 		1
(1.00) 		0.042
(1.00) 		0.125
(1.00) 		0.905
(1.00) 		0.679
(1.00)
4q gain 0 (0%) 380 0.592
(1.00) 		0.702
(1.00) 		0.311
(1.00) 		0.182
(1.00) 		0.0825
(1.00) 		0.364
(1.00) 		0.505
(1.00) 		0.644
(1.00) 		0.381
(1.00) 		0.0195
(1.00) 		0.448
(1.00) 		0.171
(1.00) 		1
(1.00)
5p gain 0 (0%) 244 0.302
(1.00) 		0.089
(1.00) 		0.6
(1.00) 		0.83
(1.00) 		0.194
(1.00) 		0.494
(1.00) 		0.78
(1.00) 		0.674
(1.00) 		1
(1.00) 		0.101
(1.00) 		0.0448
(1.00) 		0.567
(1.00) 		0.619
(1.00) 		0.113
(1.00)
5q gain 0 (0%) 344 0.685
(1.00) 		0.962
(1.00) 		0.637
(1.00) 		0.852
(1.00) 		0.551
(1.00) 		0.686
(1.00) 		0.546
(1.00) 		0.803
(1.00) 		0.0677
(1.00) 		0.52
(1.00) 		0.159
(1.00) 		0.702
(1.00) 		0.77
(1.00)
6p gain 0 (0%) 330 0.62
(1.00) 		0.971
(1.00) 		0.779
(1.00) 		0.738
(1.00) 		0.326
(1.00) 		0.479
(1.00) 		0.193
(1.00) 		0.792
(1.00) 		0.762
(1.00) 		0.751
(1.00) 		0.64
(1.00) 		0.104
(1.00) 		0.249
(1.00) 		0.939
(1.00)
6q gain 0 (0%) 374 0.618
(1.00) 		0.262
(1.00) 		0.0147
(1.00) 		0.987
(1.00) 		0.845
(1.00) 		0.504
(1.00) 		0.53
(1.00) 		0.414
(1.00) 		1
(1.00) 		0.55
(1.00) 		0.00542
(1.00) 		0.435
(1.00) 		0.633
(1.00)
7p gain 0 (0%) 257 0.293
(1.00) 		0.0461
(1.00) 		0.83
(1.00) 		0.23
(1.00) 		0.431
(1.00) 		0.2
(1.00) 		0.00916
(1.00) 		0.088
(1.00) 		0.0298
(1.00) 		0.473
(1.00) 		0.565
(1.00) 		0.57
(1.00) 		0.64
(1.00) 		0.528
(1.00)
7q gain 0 (0%) 295 0.678
(1.00) 		0.0143
(1.00) 		0.479
(1.00) 		0.915
(1.00) 		0.337
(1.00) 		0.393
(1.00) 		0.191
(1.00) 		0.0467
(1.00) 		0.0318
(1.00) 		0.592
(1.00) 		0.983
(1.00) 		0.784
(1.00) 		0.85
(1.00) 		0.338
(1.00)
8p gain 0 (0%) 340 0.902
(1.00) 		0.00444
(1.00) 		0.287
(1.00) 		0.55
(1.00) 		0.706
(1.00) 		0.869
(1.00) 		0.108
(1.00) 		0.767
(1.00) 		0.728
(1.00) 		0.195
(1.00) 		0.0992
(1.00) 		0.0391
(1.00) 		0.732
(1.00)
8q gain 0 (0%) 266 0.666
(1.00) 		0.00236
(1.00) 		0.326
(1.00) 		0.309
(1.00) 		0.256
(1.00) 		0.524
(1.00) 		0.391
(1.00) 		0.168
(1.00) 		0.23
(1.00) 		0.626
(1.00) 		0.472
(1.00) 		0.178
(1.00) 		0.0382
(1.00) 		0.833
(1.00)
9p gain 0 (0%) 377 0.19
(1.00) 		0.217
(1.00) 		0.777
(1.00) 		0.86
(1.00) 		0.251
(1.00) 		0.731
(1.00) 		0.741
(1.00) 		0.899
(1.00) 		1
(1.00) 		0.297
(1.00) 		0.181
(1.00) 		0.661
(1.00) 		0.633
(1.00)
9q gain 0 (0%) 384 0.0586
(1.00) 		0.16
(1.00) 		0.664
(1.00) 		0.999
(1.00) 		0.709
(1.00) 		1
(1.00) 		0.63
(1.00) 		1
(1.00) 		1
(1.00) 		0.307
(1.00) 		0.75
(1.00) 		0.796
(1.00) 		1
(1.00)
10p gain 0 (0%) 346 0.871
(1.00) 		0.67
(1.00) 		0.0509
(1.00) 		0.842
(1.00) 		0.862
(1.00) 		0.634
(1.00) 		0.173
(1.00) 		0.891
(1.00) 		0.522
(1.00) 		0.711
(1.00) 		0.0302
(1.00) 		0.0108
(1.00) 		0.447
(1.00) 		0.199
(1.00)
10q gain 0 (0%) 366 0.717
(1.00) 		0.717
(1.00) 		0.0823
(1.00) 		0.47
(1.00) 		0.398
(1.00) 		0.227
(1.00) 		0.551
(1.00) 		0.32
(1.00) 		1
(1.00) 		0.122
(1.00) 		0.0949
(1.00) 		0.261
(1.00) 		0.0946
(1.00)
11p gain 0 (0%) 357 0.44
(1.00) 		0.0826
(1.00) 		0.46
(1.00) 		0.503
(1.00) 		0.824
(1.00) 		0.712
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.441
(1.00) 		0.675
(1.00) 		0.223
(1.00) 		0.794
(1.00) 		0.835
(1.00) 		0.523
(1.00)
11q gain 0 (0%) 345 0.22
(1.00) 		0.000304
(0.325) 		0.148
(1.00) 		0.586
(1.00) 		0.81
(1.00) 		0.618
(1.00) 		0.579
(1.00) 		0.519
(1.00) 		0.155
(1.00) 		0.264
(1.00) 		0.123
(1.00) 		0.0659
(1.00) 		0.132
(1.00) 		0.84
(1.00)
12p gain 0 (0%) 340 0.74
(1.00) 		0.00842
(1.00) 		1
(1.00) 		0.545
(1.00) 		0.147
(1.00) 		0.065
(1.00) 		1
(1.00) 		0.0281
(1.00) 		1
(1.00) 		0.484
(1.00) 		0.0247
(1.00) 		0.131
(1.00) 		0.768
(1.00)
12q gain 0 (0%) 349 0.955
(1.00) 		0.0582
(1.00) 		1
(1.00) 		0.448
(1.00) 		0.145
(1.00) 		0.0801
(1.00) 		0.683
(1.00) 		0.0414
(1.00) 		0.708
(1.00) 		0.0189
(1.00) 		0.0518
(1.00) 		0.0556
(1.00) 		0.6
(1.00)
13q gain 0 (0%) 375 0.827
(1.00) 		0.496
(1.00) 		0.79
(1.00) 		0.976
(1.00) 		0.131
(1.00) 		0.468
(1.00) 		0.136
(1.00) 		0.422
(1.00) 		0.529
(1.00) 		0.715
(1.00) 		0.458
(1.00) 		0.904
(1.00) 		1
(1.00)
14q gain 0 (0%) 348 0.43
(1.00) 		0.424
(1.00) 		0.409
(1.00) 		0.637
(1.00) 		0.516
(1.00) 		0.412
(1.00) 		0.321
(1.00) 		0.47
(1.00) 		0.644
(1.00) 		0.249
(1.00) 		0.583
(1.00) 		0.71
(1.00) 		0.583
(1.00) 		0.728
(1.00)
15q gain 0 (0%) 379 0.303
(1.00) 		0.411
(1.00) 		0.76
(1.00) 		0.177
(1.00) 		0.678
(1.00) 		0.351
(1.00) 		0.442
(1.00) 		0.209
(1.00) 		1
(1.00) 		0.864
(1.00) 		0.0993
(1.00) 		0.842
(1.00) 		0.589
(1.00)
16p gain 0 (0%) 336 0.464
(1.00) 		0.164
(1.00) 		0.882
(1.00) 		0.356
(1.00) 		0.52
(1.00) 		0.459
(1.00) 		0.511
(1.00) 		0.626
(1.00) 		0.513
(1.00) 		0.744
(1.00) 		0.586
(1.00) 		0.141
(1.00) 		0.781
(1.00) 		0.249
(1.00)
16q gain 0 (0%) 354 0.616
(1.00) 		0.067
(1.00) 		0.293
(1.00) 		0.319
(1.00) 		0.166
(1.00) 		0.344
(1.00) 		0.517
(1.00) 		0.418
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.0871
(1.00) 		0.462
(1.00) 		0.597
(1.00) 		1
(1.00)
17p gain 0 (0%) 366 0.762
(1.00) 		0.56
(1.00) 		0.195
(1.00) 		0.284
(1.00) 		0.46
(1.00) 		0.966
(1.00) 		0.506
(1.00) 		0.394
(1.00) 		0.34
(1.00) 		0.0239
(1.00) 		0.0495
(1.00) 		0.648
(1.00) 		0.895
(1.00) 		0.516
(1.00)
17q gain 0 (0%) 322 0.24
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.344
(1.00) 		0.336
(1.00) 		0.0301
(1.00) 		0.332
(1.00) 		0.0198
(1.00) 		0.0184
(1.00) 		0.0598
(1.00) 		0.0666
(1.00) 		0.543
(1.00) 		0.651
(1.00) 		0.0106
(1.00)
18p gain 0 (0%) 351 0.775
(1.00) 		0.0871
(1.00) 		0.0605
(1.00) 		0.613
(1.00) 		0.203
(1.00) 		0.947
(1.00) 		0.644
(1.00) 		0.837
(1.00) 		0.98
(1.00) 		0.707
(1.00) 		0.104
(1.00) 		0.755
(1.00) 		0.827
(1.00) 		0.83
(1.00)
18q gain 0 (0%) 366 0.526
(1.00) 		0.0441
(1.00) 		0.195
(1.00) 		0.613
(1.00) 		0.847
(1.00) 		0.889
(1.00) 		0.797
(1.00) 		0.891
(1.00) 		0.867
(1.00) 		1
(1.00) 		0.381
(1.00) 		0.732
(1.00) 		0.113
(1.00) 		0.425
(1.00)
19p gain 0 (0%) 383 0.337
(1.00) 		0.0498
(1.00) 		1
(1.00) 		1
(1.00) 		0.335
(1.00) 		0.336
(1.00) 		0.244
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.821
(1.00) 		0.431
(1.00) 		0.425
(1.00)
19q gain 0 (0%) 370 0.991
(1.00) 		0.897
(1.00) 		0.639
(1.00) 		0.568
(1.00) 		0.46
(1.00) 		0.49
(1.00) 		0.333
(1.00) 		0.703
(1.00) 		0.613
(1.00) 		0.335
(1.00) 		0.235
(1.00) 		0.277
(1.00) 		0.74
(1.00)
20p gain 0 (0%) 337 0.896
(1.00) 		0.663
(1.00) 		0.882
(1.00) 		0.548
(1.00) 		0.806
(1.00) 		0.424
(1.00) 		0.629
(1.00) 		0.9
(1.00) 		0.148
(1.00) 		0.74
(1.00) 		0.907
(1.00) 		0.149
(1.00) 		0.463
(1.00) 		0.553
(1.00)
20q gain 0 (0%) 322 0.725
(1.00) 		0.224
(1.00) 		0.419
(1.00) 		0.138
(1.00) 		0.706
(1.00) 		0.139
(1.00) 		0.873
(1.00) 		0.678
(1.00) 		0.823
(1.00) 		0.221
(1.00) 		0.0305
(1.00) 		0.0902
(1.00) 		0.659
(1.00) 		0.901
(1.00)
21q gain 0 (0%) 355 0.8
(1.00) 		0.844
(1.00) 		0.213
(1.00) 		0.794
(1.00) 		0.626
(1.00) 		0.557
(1.00) 		0.418
(1.00) 		0.934
(1.00) 		1
(1.00) 		0.885
(1.00) 		0.0151
(1.00) 		0.593
(1.00) 		1
(1.00)
22q gain 0 (0%) 374 0.34
(1.00) 		0.354
(1.00) 		0.793
(1.00) 		0.328
(1.00) 		0.2
(1.00) 		0.0324
(1.00) 		0.465
(1.00) 		0.287
(1.00) 		0.554
(1.00) 		0.268
(1.00) 		0.463
(1.00) 		0.454
(1.00) 		0.74
(1.00)
Xq gain 0 (0%) 371 0.355
(1.00) 		0.471
(1.00) 		0.228
(1.00) 		0.81
(1.00) 		0.649
(1.00) 		0.593
(1.00) 		0.724
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.263
(1.00) 		0.316
(1.00) 		0.509
(1.00) 		0.74
(1.00)
1p loss 0 (0%) 363 0.192
(1.00) 		0.707
(1.00) 		0.226
(1.00) 		0.586
(1.00) 		0.907
(1.00) 		0.692
(1.00) 		0.387
(1.00) 		0.0861
(1.00) 		0.141
(1.00) 		0.214
(1.00) 		0.0823
(1.00) 		0.945
(1.00) 		0.271
(1.00)
2p loss 0 (0%) 384 0.237
(1.00) 		0.146
(1.00) 		1
(1.00) 		0.953
(1.00) 		1
(1.00) 		1
(1.00) 		0.63
(1.00) 		1
(1.00) 		1
(1.00) 		0.512
(1.00) 		0.0769
(1.00) 		1
(1.00)
2q loss 0 (0%) 386 1
(1.00) 		0.443
(1.00) 		1
(1.00)
3p loss 0 (0%) 312 0.446
(1.00) 		0.756
(1.00) 		1
(1.00) 		0.0141
(1.00) 		0.789
(1.00) 		0.617
(1.00) 		0.504
(1.00) 		0.169
(1.00) 		0.00483
(1.00) 		1
(1.00) 		0.424
(1.00) 		0.036
(1.00) 		0.165
(1.00) 		0.78
(1.00)
3q loss 0 (0%) 342 0.42
(1.00) 		0.724
(1.00) 		0.644
(1.00) 		0.0171
(1.00) 		0.464
(1.00) 		0.465
(1.00) 		0.8
(1.00) 		0.458
(1.00) 		0.349
(1.00) 		1
(1.00) 		0.0647
(1.00) 		0.365
(1.00) 		0.591
(1.00) 		0.851
(1.00)
4p loss 0 (0%) 354 0.465
(1.00) 		0.012
(1.00) 		0.484
(1.00) 		0.625
(1.00) 		0.528
(1.00) 		0.32
(1.00) 		0.265
(1.00) 		0.65
(1.00) 		0.479
(1.00) 		0.409
(1.00) 		0.795
(1.00) 		0.138
(1.00) 		0.283
(1.00) 		0.78
(1.00)
4q loss 0 (0%) 347 0.578
(1.00) 		0.0473
(1.00) 		0.14
(1.00) 		0.851
(1.00) 		0.892
(1.00) 		0.155
(1.00) 		0.00814
(1.00) 		0.514
(1.00) 		0.0645
(1.00) 		0.254
(1.00) 		0.6
(1.00) 		0.125
(1.00) 		0.907
(1.00) 		0.628
(1.00)
5p loss 0 (0%) 377 0.737
(1.00) 		0.918
(1.00) 		0.154
(1.00) 		0.0604
(1.00) 		0.937
(1.00) 		0.733
(1.00) 		0.0966
(1.00) 		0.606
(1.00) 		1
(1.00) 		0.778
(1.00) 		0.446
(1.00) 		0.492
(1.00) 		0.342
(1.00)
5q loss 0 (0%) 339 0.642
(1.00) 		0.0227
(1.00) 		0.0691
(1.00) 		0.705
(1.00) 		0.0648
(1.00) 		0.884
(1.00) 		0.0709
(1.00) 		0.501
(1.00) 		0.263
(1.00) 		0.492
(1.00) 		0.244
(1.00) 		0.0906
(1.00) 		0.504
(1.00) 		0.214
(1.00)
6p loss 0 (0%) 357 0.661
(1.00) 		0.0805
(1.00) 		0.138
(1.00) 		0.12
(1.00) 		0.707
(1.00) 		0.478
(1.00) 		0.614
(1.00) 		0.173
(1.00) 		0.632
(1.00) 		0.221
(1.00) 		0.283
(1.00) 		0.568
(1.00) 		0.308
(1.00) 		0.271
(1.00)
6q loss 0 (0%) 303 0.665
(1.00) 		0.136
(1.00) 		0.541
(1.00) 		0.0285
(1.00) 		0.565
(1.00) 		0.2
(1.00) 		0.246
(1.00) 		0.638
(1.00) 		0.49
(1.00) 		0.407
(1.00) 		0.16
(1.00) 		0.859
(1.00) 		0.312
(1.00) 		0.779
(1.00)
7p loss 0 (0%) 378 0.848
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.117
(1.00) 		1
(1.00) 		0.282
(1.00) 		0.442
(1.00) 		0.254
(1.00) 		0.445
(1.00) 		0.507
(1.00) 		0.299
(1.00) 		0.297
(1.00) 		0.296
(1.00)
7q loss 0 (0%) 377 0.682
(1.00) 		0.204
(1.00) 		0.558
(1.00) 		0.000297
(0.317) 		0.894
(1.00) 		0.691
(1.00) 		1
(1.00) 		0.677
(1.00) 		0.474
(1.00) 		0.158
(1.00) 		0.172
(1.00) 		0.249
(1.00)
8p loss 0 (0%) 291 0.758
(1.00) 		0.844
(1.00) 		0.558
(1.00) 		0.254
(1.00) 		0.187
(1.00) 		0.069
(1.00) 		0.675
(1.00) 		0.678
(1.00) 		0.84
(1.00) 		1
(1.00) 		0.546
(1.00) 		0.0551
(1.00) 		0.68
(1.00) 		0.62
(1.00)
8q loss 0 (0%) 377 0.185
(1.00) 		0.633
(1.00) 		0.395
(1.00) 		0.0425
(1.00) 		0.512
(1.00) 		0.801
(1.00) 		0.284
(1.00) 		1
(1.00) 		1
(1.00) 		0.167
(1.00) 		0.21
(1.00) 		1
(1.00)
9p loss 0 (0%) 272 0.0149
(1.00) 		0.419
(1.00) 		0.0456
(1.00) 		0.87
(1.00) 		0.58
(1.00) 		0.154
(1.00) 		0.0129
(1.00) 		0.762
(1.00) 		0.0227
(1.00) 		1
(1.00) 		0.685
(1.00) 		0.104
(1.00) 		0.815
(1.00) 		0.504
(1.00)
9q loss 0 (0%) 290 0.396
(1.00) 		0.582
(1.00) 		0.727
(1.00) 		0.99
(1.00) 		0.694
(1.00) 		0.314
(1.00) 		0.147
(1.00) 		0.513
(1.00) 		0.187
(1.00) 		0.428
(1.00) 		0.405
(1.00) 		0.0569
(1.00) 		0.999
(1.00) 		0.273
(1.00)
10p loss 0 (0%) 362 0.285
(1.00) 		0.716
(1.00) 		0.108
(1.00) 		0.106
(1.00) 		0.898
(1.00) 		0.483
(1.00) 		0.424
(1.00) 		0.892
(1.00) 		0.382
(1.00) 		0.633
(1.00) 		0.0877
(1.00) 		0.815
(1.00) 		0.636
(1.00)
10q loss 0 (0%) 356 0.337
(1.00) 		0.201
(1.00) 		0.719
(1.00) 		0.000308
(0.328) 		0.321
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.161
(1.00) 		0.397
(1.00) 		0.0649
(1.00) 		0.287
(1.00) 		0.856
(1.00) 		0.81
(1.00)
11p loss 0 (0%) 362 0.289
(1.00) 		0.0115
(1.00) 		0.843
(1.00) 		0.611
(1.00) 		0.907
(1.00) 		0.135
(1.00) 		0.128
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.134
(1.00) 		0.000842
(0.897) 		0.0199
(1.00) 		0.883
(1.00)
11q loss 0 (0%) 365 0.347
(1.00) 		0.966
(1.00) 		0.407
(1.00) 		0.705
(1.00) 		0.297
(1.00) 		0.968
(1.00) 		0.599
(1.00) 		0.0324
(1.00) 		0.819
(1.00) 		0.354
(1.00) 		0.0372
(1.00) 		0.281
(1.00) 		0.383
(1.00) 		0.743
(1.00)
12p loss 0 (0%) 355 0.336
(1.00) 		0.554
(1.00) 		1
(1.00) 		0.533
(1.00) 		0.797
(1.00) 		0.612
(1.00) 		1
(1.00) 		0.307
(1.00) 		0.544
(1.00) 		0.69
(1.00) 		0.688
(1.00) 		0.0348
(1.00) 		0.0247
(1.00) 		0.77
(1.00)
12q loss 0 (0%) 368 0.0612
(1.00) 		0.947
(1.00) 		0.654
(1.00) 		0.847
(1.00) 		0.481
(1.00) 		0.375
(1.00) 		0.365
(1.00) 		0.293
(1.00) 		0.615
(1.00) 		0.995
(1.00) 		0.166
(1.00) 		0.261
(1.00) 		1
(1.00)
13q loss 0 (0%) 301 0.194
(1.00) 		0.166
(1.00) 		0.467
(1.00) 		0.562
(1.00) 		0.172
(1.00) 		0.952
(1.00) 		0.156
(1.00) 		0.439
(1.00) 		0.211
(1.00) 		0.786
(1.00) 		0.903
(1.00) 		0.487
(1.00) 		0.0981
(1.00) 		0.473
(1.00)
14q loss 0 (0%) 347 0.671
(1.00) 		0.436
(1.00) 		0.87
(1.00) 		0.798
(1.00) 		0.531
(1.00) 		0.509
(1.00) 		1
(1.00) 		0.263
(1.00) 		0.941
(1.00) 		0.465
(1.00) 		0.392
(1.00) 		0.405
(1.00) 		0.355
(1.00) 		0.475
(1.00)
15q loss 0 (0%) 308 0.834
(1.00) 		0.0563
(1.00) 		0.319
(1.00) 		0.773
(1.00) 		0.204
(1.00) 		0.775
(1.00) 		0.979
(1.00) 		0.934
(1.00) 		0.891
(1.00) 		0.581
(1.00) 		0.23
(1.00) 		0.215
(1.00) 		0.752
(1.00) 		0.313
(1.00)
16p loss 0 (0%) 358 0.619
(1.00) 		0.219
(1.00) 		0.189
(1.00) 		0.336
(1.00) 		0.939
(1.00) 		0.953
(1.00) 		0.00845
(1.00) 		0.0615
(1.00) 		0.207
(1.00) 		0.815
(1.00) 		0.125
(1.00) 		0.687
(1.00) 		0.366
(1.00)
16q loss 0 (0%) 338 0.24
(1.00) 		0.299
(1.00) 		0.653
(1.00) 		0.724
(1.00) 		0.0193
(1.00) 		0.187
(1.00) 		0.531
(1.00) 		0.127
(1.00) 		0.176
(1.00) 		0.735
(1.00) 		0.986
(1.00) 		0.451
(1.00) 		0.543
(1.00) 		0.536
(1.00)
17p loss 0 (0%) 292 0.998
(1.00) 		0.245
(1.00) 		0.638
(1.00) 		0.107
(1.00) 		0.731
(1.00) 		0.688
(1.00) 		0.771
(1.00) 		0.661
(1.00) 		0.503
(1.00) 		0.427
(1.00) 		0.365
(1.00) 		0.00391
(1.00) 		0.0442
(1.00) 		0.184
(1.00)
17q loss 0 (0%) 373 0.181
(1.00) 		0.371
(1.00) 		0.308
(1.00) 		0.646
(1.00) 		0.531
(1.00) 		0.593
(1.00) 		0.75
(1.00) 		0.457
(1.00) 		1
(1.00) 		0.523
(1.00) 		0.131
(1.00) 		0.0566
(1.00) 		0.708
(1.00)
18q loss 0 (0%) 294 0.031
(1.00) 		0.41
(1.00) 		0.477
(1.00) 		0.486
(1.00) 		0.291
(1.00) 		0.107
(1.00) 		0.294
(1.00) 		0.229
(1.00) 		0.00304
(1.00) 		0.18
(1.00) 		0.115
(1.00) 		0.698
(1.00) 		0.383
(1.00) 		0.0198
(1.00)
19p loss 0 (0%) 288 0.0341
(1.00) 		0.28
(1.00) 		0.0818
(1.00) 		0.562
(1.00) 		0.708
(1.00) 		0.151
(1.00) 		0.032
(1.00) 		0.0985
(1.00) 		0.281
(1.00) 		1
(1.00) 		0.495
(1.00) 		0.0725
(1.00) 		0.408
(1.00) 		0.137
(1.00)
19q loss 0 (0%) 331 0.0757
(1.00) 		0.495
(1.00) 		0.775
(1.00) 		0.00559
(1.00) 		0.45
(1.00) 		0.287
(1.00) 		0.276
(1.00) 		0.0602
(1.00) 		0.345
(1.00) 		0.518
(1.00) 		0.325
(1.00) 		0.242
(1.00) 		0.533
(1.00) 		0.034
(1.00)
20p loss 0 (0%) 337 0.151
(1.00) 		0.852
(1.00) 		0.766
(1.00) 		0.0151
(1.00) 		0.681
(1.00) 		0.201
(1.00) 		0.1
(1.00) 		0.205
(1.00) 		0.119
(1.00) 		0.74
(1.00) 		0.51
(1.00) 		0.852
(1.00) 		0.0777
(1.00) 		1
(1.00)
20q loss 0 (0%) 368 0.305
(1.00) 		0.346
(1.00) 		0.826
(1.00) 		0.344
(1.00) 		0.872
(1.00) 		0.714
(1.00) 		0.212
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.432
(1.00) 		0.268
(1.00) 		0.516
(1.00)
21q loss 0 (0%) 335 0.838
(1.00) 		0.285
(1.00) 		0.0182
(1.00) 		0.124
(1.00) 		0.529
(1.00) 		0.877
(1.00) 		0.728
(1.00) 		0.831
(1.00) 		0.768
(1.00) 		0.501
(1.00) 		0.407
(1.00) 		0.0213
(1.00) 		0.703
(1.00) 		0.629
(1.00)
22q loss 0 (0%) 310 0.805
(1.00) 		0.0263
(1.00) 		0.0575
(1.00) 		0.657
(1.00) 		0.795
(1.00) 		0.831
(1.00) 		0.979
(1.00) 		0.16
(1.00) 		0.991
(1.00) 		0.147
(1.00) 		0.136
(1.00) 		0.00651
(1.00) 		0.0513
(1.00) 		0.21
(1.00)
Xq loss 0 (0%) 379 0.283
(1.00) 		0.0652
(1.00) 		0.0486
(1.00) 		0.0253
(1.00) 		0.349
(1.00) 		1
(1.00) 		1
(1.00) 		0.537
(1.00) 		0.0882
(1.00) 		0.295
(1.00) 		0.633
(1.00) 		0.928
(1.00) 		1
(1.00)
'1q loss' versus 'Time to Death'

P value = 3.02e-05 (logrank test), Q value = 0.032

Table S1.  Gene #42: '1q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 349 85 0.0 - 224.0 (8.1)
1Q LOSS CNV 8 4 0.1 - 21.5 (7.0)
1Q LOSS WILD-TYPE 341 81 0.0 - 224.0 (8.1)

Figure S1.  Get High-res Image Gene #42: '1q loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'NUMBERPACKYEARSSMOKED'

P value = 9.54e-05 (t-test), Q value = 0.1

Table S2.  Gene #72: '18p loss' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'

nPatients Mean (Std.Dev)
ALL 274 41.3 (27.0)
18P LOSS CNV 47 30.8 (17.0)
18P LOSS WILD-TYPE 227 43.4 (28.2)

Figure S2.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'

Methods & Data
Input

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

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

  • Number of patients = 389

  • Number of significantly arm-level cnvs = 80

  • 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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