Correlation between copy number variations of arm-level result and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1FB51CS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1FB51CS
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 events and 13 clinical features across 455 patients, 2 significant findings detected with Q value < 0.25.

  • 17p gain cnv correlated to 'NUMBERPACKYEARSSMOKED'.

  • 19p gain 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 80 arm-level events and 13 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 NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED YEAROFTOBACCOSMOKINGONSET COMPLETENESS
OF
RESECTION
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test t-test Chi-square test Fisher's exact test t-test t-test Fisher's exact test
17p gain 76 (17%) 379 0.122
(1.00) 		0.0269
(1.00) 		0.567
(1.00) 		0.478
(1.00) 		0.256
(1.00) 		0.207
(1.00) 		0.0587
(1.00) 		0.623
(1.00) 		0.366
(1.00) 		0.139
(1.00) 		0.000172
(0.179) 		0.613
(1.00) 		0.147
(1.00)
19p gain 29 (6%) 426 0.215
(1.00) 		0.508
(1.00) 		0.71
(1.00) 		0.128
(1.00) 		0.549
(1.00) 		0.319
(1.00) 		0.343
(1.00) 		0.655
(1.00) 		0.000139
(0.145) 		1
(1.00) 		0.22
(1.00) 		0.943
(1.00) 		0.655
(1.00)
1p gain 122 (27%) 333 0.738
(1.00) 		0.00741
(1.00) 		0.85
(1.00) 		0.807
(1.00) 		0.0351
(1.00) 		0.536
(1.00) 		0.751
(1.00) 		0.579
(1.00) 		0.505
(1.00) 		0.614
(1.00) 		0.855
(1.00) 		0.651
(1.00) 		0.569
(1.00)
1q gain 269 (59%) 186 0.75
(1.00) 		0.287
(1.00) 		0.741
(1.00) 		0.863
(1.00) 		0.599
(1.00) 		0.599
(1.00) 		0.34
(1.00) 		0.324
(1.00) 		0.242
(1.00) 		0.364
(1.00) 		0.953
(1.00) 		0.626
(1.00) 		0.752
(1.00)
2p gain 141 (31%) 314 0.349
(1.00) 		0.0489
(1.00) 		0.801
(1.00) 		0.86
(1.00) 		0.312
(1.00) 		0.895
(1.00) 		0.684
(1.00) 		0.537
(1.00) 		0.494
(1.00) 		0.63
(1.00) 		0.234
(1.00) 		0.147
(1.00) 		0.495
(1.00)
2q gain 127 (28%) 328 0.468
(1.00) 		0.699
(1.00) 		0.654
(1.00) 		0.945
(1.00) 		0.338
(1.00) 		0.923
(1.00) 		0.676
(1.00) 		0.417
(1.00) 		0.526
(1.00) 		0.806
(1.00) 		0.153
(1.00) 		0.654
(1.00) 		0.735
(1.00)
3p gain 36 (8%) 419 0.807
(1.00) 		0.575
(1.00) 		0.826
(1.00) 		0.235
(1.00) 		0.193
(1.00) 		0.949
(1.00) 		1
(1.00) 		0.289
(1.00) 		0.603
(1.00) 		0.226
(1.00) 		0.315
(1.00) 		0.295
(1.00) 		0.0265
(1.00)
3q gain 75 (16%) 380 0.453
(1.00) 		0.649
(1.00) 		0.665
(1.00) 		0.758
(1.00) 		0.563
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.427
(1.00) 		0.786
(1.00) 		0.763
(1.00) 		0.173
(1.00) 		0.278
(1.00) 		0.23
(1.00)
4p gain 75 (16%) 380 0.969
(1.00) 		0.0193
(1.00) 		0.0864
(1.00) 		0.31
(1.00) 		0.578
(1.00) 		0.601
(1.00) 		0.801
(1.00) 		0.456
(1.00) 		0.285
(1.00) 		0.551
(1.00) 		0.202
(1.00) 		0.894
(1.00) 		1
(1.00)
4q gain 42 (9%) 413 0.125
(1.00) 		0.418
(1.00) 		0.0519
(1.00) 		0.199
(1.00) 		0.862
(1.00) 		0.925
(1.00) 		0.63
(1.00) 		0.695
(1.00) 		0.51
(1.00) 		0.709
(1.00) 		0.0878
(1.00) 		0.74
(1.00) 		0.762
(1.00)
5p gain 249 (55%) 206 0.209
(1.00) 		0.0779
(1.00) 		0.253
(1.00) 		0.13
(1.00) 		0.98
(1.00) 		0.515
(1.00) 		0.131
(1.00) 		0.217
(1.00) 		0.334
(1.00) 		0.37
(1.00) 		0.0159
(1.00) 		0.307
(1.00) 		0.498
(1.00)
5q gain 109 (24%) 346 0.853
(1.00) 		0.662
(1.00) 		0.947
(1.00) 		0.454
(1.00) 		0.675
(1.00) 		0.691
(1.00) 		0.037
(1.00) 		0.462
(1.00) 		0.368
(1.00) 		0.123
(1.00) 		0.676
(1.00) 		0.99
(1.00) 		0.949
(1.00)
6p gain 129 (28%) 326 0.135
(1.00) 		0.377
(1.00) 		0.204
(1.00) 		0.362
(1.00) 		0.294
(1.00) 		0.297
(1.00) 		0.835
(1.00) 		0.738
(1.00) 		0.535
(1.00) 		0.806
(1.00) 		0.624
(1.00) 		0.724
(1.00) 		0.465
(1.00)
6q gain 56 (12%) 399 0.419
(1.00) 		0.302
(1.00) 		0.751
(1.00) 		1
(1.00) 		0.87
(1.00) 		0.709
(1.00) 		0.668
(1.00) 		0.388
(1.00) 		0.956
(1.00) 		0.495
(1.00) 		0.834
(1.00) 		0.708
(1.00) 		0.663
(1.00)
7p gain 236 (52%) 219 0.406
(1.00) 		0.044
(1.00) 		0.337
(1.00) 		0.374
(1.00) 		0.00316
(1.00) 		0.699
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.0993
(1.00) 		0.504
(1.00) 		0.119
(1.00) 		0.312
(1.00) 		0.672
(1.00)
7q gain 195 (43%) 260 0.982
(1.00) 		0.00488
(1.00) 		0.179
(1.00) 		0.793
(1.00) 		0.00483
(1.00) 		0.318
(1.00) 		0.776
(1.00) 		0.922
(1.00) 		0.245
(1.00) 		0.184
(1.00) 		0.278
(1.00) 		0.536
(1.00) 		0.319
(1.00)
8p gain 113 (25%) 342 0.488
(1.00) 		0.0719
(1.00) 		0.815
(1.00) 		0.0753
(1.00) 		0.793
(1.00) 		0.956
(1.00) 		0.00662
(1.00) 		0.287
(1.00) 		0.812
(1.00) 		0.436
(1.00) 		0.487
(1.00) 		0.195
(1.00) 		0.233
(1.00)
8q gain 219 (48%) 236 0.0356
(1.00) 		0.0292
(1.00) 		0.901
(1.00) 		0.218
(1.00) 		0.123
(1.00) 		0.783
(1.00) 		0.452
(1.00) 		0.909
(1.00) 		0.0608
(1.00) 		0.824
(1.00) 		0.928
(1.00) 		0.0784
(1.00) 		0.645
(1.00)
9p gain 40 (9%) 415 0.238
(1.00) 		0.569
(1.00) 		0.833
(1.00) 		0.204
(1.00) 		0.363
(1.00) 		0.632
(1.00) 		0.251
(1.00) 		0.392
(1.00) 		0.159
(1.00) 		0.706
(1.00) 		0.674
(1.00) 		0.635
(1.00) 		0.332
(1.00)
9q gain 28 (6%) 427 0.121
(1.00) 		0.509
(1.00) 		0.281
(1.00) 		0.727
(1.00) 		0.956
(1.00) 		0.308
(1.00) 		0.845
(1.00) 		0.765
(1.00) 		0.993
(1.00) 		1
(1.00) 		0.389
(1.00) 		0.911
(1.00) 		1
(1.00)
10p gain 101 (22%) 354 0.794
(1.00) 		0.131
(1.00) 		0.611
(1.00) 		0.11
(1.00) 		0.0234
(1.00) 		0.713
(1.00) 		0.00152
(1.00) 		0.37
(1.00) 		0.65
(1.00) 		0.187
(1.00) 		0.229
(1.00) 		0.824
(1.00) 		0.111
(1.00)
10q gain 72 (16%) 383 0.876
(1.00) 		0.142
(1.00) 		0.391
(1.00) 		0.179
(1.00) 		0.0377
(1.00) 		0.19
(1.00) 		0.00305
(1.00) 		0.171
(1.00) 		0.448
(1.00) 		0.552
(1.00) 		0.913
(1.00) 		0.659
(1.00) 		0.458
(1.00)
11p gain 87 (19%) 368 0.452
(1.00) 		0.896
(1.00) 		0.313
(1.00) 		0.377
(1.00) 		0.0814
(1.00) 		0.704
(1.00) 		0.0556
(1.00) 		0.393
(1.00) 		0.571
(1.00) 		0.778
(1.00) 		0.141
(1.00) 		0.435
(1.00) 		0.937
(1.00)
11q gain 107 (24%) 348 0.789
(1.00) 		0.0293
(1.00) 		0.439
(1.00) 		0.679
(1.00) 		0.521
(1.00) 		0.375
(1.00) 		0.32
(1.00) 		0.261
(1.00) 		0.266
(1.00) 		0.6
(1.00) 		0.0585
(1.00) 		0.121
(1.00) 		1
(1.00)
12p gain 123 (27%) 332 0.337
(1.00) 		0.0191
(1.00) 		0.0969
(1.00) 		0.898
(1.00) 		0.628
(1.00) 		0.504
(1.00) 		0.112
(1.00) 		0.981
(1.00) 		0.501
(1.00) 		1
(1.00) 		0.159
(1.00) 		0.0618
(1.00) 		0.378
(1.00)
12q gain 118 (26%) 337 0.885
(1.00) 		0.108
(1.00) 		0.72
(1.00) 		0.735
(1.00) 		0.648
(1.00) 		0.322
(1.00) 		0.284
(1.00) 		0.896
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.384
(1.00) 		0.00258
(1.00) 		0.359
(1.00)
13q gain 41 (9%) 414 0.592
(1.00) 		0.793
(1.00) 		0.203
(1.00) 		0.536
(1.00) 		0.427
(1.00) 		0.0178
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.98
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.539
(1.00) 		0.398
(1.00)
14q gain 111 (24%) 344 0.0964
(1.00) 		0.212
(1.00) 		0.974
(1.00) 		0.975
(1.00) 		0.244
(1.00) 		0.00465
(1.00) 		0.381
(1.00) 		0.287
(1.00) 		0.693
(1.00) 		0.123
(1.00) 		0.124
(1.00) 		0.533
(1.00) 		0.357
(1.00)
15q gain 32 (7%) 423 0.161
(1.00) 		0.892
(1.00) 		0.0326
(1.00) 		0.474
(1.00) 		0.0148
(1.00) 		0.283
(1.00) 		0.273
(1.00) 		0.909
(1.00) 		0.335
(1.00) 		0.652
(1.00) 		0.634
(1.00) 		0.619
(1.00) 		0.884
(1.00)
16p gain 115 (25%) 340 0.359
(1.00) 		0.912
(1.00) 		0.886
(1.00) 		0.687
(1.00) 		0.559
(1.00) 		0.509
(1.00) 		0.914
(1.00) 		0.201
(1.00) 		0.371
(1.00) 		0.614
(1.00) 		0.187
(1.00) 		0.959
(1.00) 		0.906
(1.00)
16q gain 86 (19%) 369 0.285
(1.00) 		0.768
(1.00) 		0.87
(1.00) 		0.728
(1.00) 		0.742
(1.00) 		0.92
(1.00) 		0.633
(1.00) 		0.993
(1.00) 		0.317
(1.00) 		0.778
(1.00) 		0.15
(1.00) 		0.576
(1.00) 		0.556
(1.00)
17q gain 172 (38%) 283 0.562
(1.00) 		0.0799
(1.00) 		0.228
(1.00) 		0.311
(1.00) 		0.403
(1.00) 		0.454
(1.00) 		0.846
(1.00) 		0.503
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.0308
(1.00) 		0.878
(1.00) 		0.0174
(1.00)
18p gain 87 (19%) 368 0.615
(1.00) 		0.423
(1.00) 		0.316
(1.00) 		0.905
(1.00) 		0.937
(1.00) 		0.496
(1.00) 		0.404
(1.00) 		0.571
(1.00) 		0.666
(1.00) 		0.778
(1.00) 		0.00419
(1.00) 		0.595
(1.00) 		0.599
(1.00)
18q gain 62 (14%) 393 0.49
(1.00) 		0.0808
(1.00) 		0.794
(1.00) 		0.907
(1.00) 		0.629
(1.00) 		0.788
(1.00) 		0.412
(1.00) 		0.233
(1.00) 		0.267
(1.00) 		0.753
(1.00) 		0.011
(1.00) 		0.579
(1.00) 		0.0561
(1.00)
19q gain 65 (14%) 390 0.638
(1.00) 		0.925
(1.00) 		0.55
(1.00) 		0.117
(1.00) 		0.72
(1.00) 		0.872
(1.00) 		0.0104
(1.00) 		0.282
(1.00) 		0.25
(1.00) 		0.336
(1.00) 		0.0881
(1.00) 		0.999
(1.00) 		0.936
(1.00)
20p gain 151 (33%) 304 0.611
(1.00) 		0.997
(1.00) 		0.336
(1.00) 		0.264
(1.00) 		0.265
(1.00) 		0.204
(1.00) 		0.921
(1.00) 		0.138
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.0367
(1.00) 		0.0439
(1.00) 		0.643
(1.00)
20q gain 174 (38%) 281 0.531
(1.00) 		0.155
(1.00) 		0.421
(1.00) 		0.27
(1.00) 		0.59
(1.00) 		0.36
(1.00) 		0.562
(1.00) 		0.035
(1.00) 		0.189
(1.00) 		0.25
(1.00) 		0.00271
(1.00) 		0.416
(1.00) 		0.796
(1.00)
21q gain 84 (18%) 371 0.169
(1.00) 		0.366
(1.00) 		0.656
(1.00) 		0.873
(1.00) 		0.0509
(1.00) 		0.914
(1.00) 		0.115
(1.00) 		0.409
(1.00) 		0.343
(1.00) 		1
(1.00) 		0.525
(1.00) 		0.655
(1.00) 		0.94
(1.00)
22q gain 58 (13%) 397 0.117
(1.00) 		0.197
(1.00) 		0.517
(1.00) 		0.232
(1.00) 		0.307
(1.00) 		0.745
(1.00) 		0.205
(1.00) 		0.356
(1.00) 		0.53
(1.00) 		0.498
(1.00) 		0.759
(1.00) 		0.13
(1.00) 		0.496
(1.00)
xq gain 66 (15%) 389 0.498
(1.00) 		0.847
(1.00) 		0.723
(1.00) 		0.633
(1.00) 		0.85
(1.00) 		0.722
(1.00) 		0.286
(1.00) 		0.356
(1.00) 		0.436
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.312
(1.00) 		0.527
(1.00)
1p loss 74 (16%) 381 0.156
(1.00) 		0.616
(1.00) 		0.0133
(1.00) 		0.139
(1.00) 		0.00376
(1.00) 		0.268
(1.00) 		0.162
(1.00) 		0.729
(1.00) 		0.376
(1.00) 		0.761
(1.00) 		0.38
(1.00) 		0.475
(1.00) 		0.644
(1.00)
1q loss 27 (6%) 428 0.836
(1.00) 		0.579
(1.00) 		0.103
(1.00) 		1
(1.00) 		0.217
(1.00) 		0.382
(1.00) 		0.559
(1.00) 		0.257
(1.00) 		0.96
(1.00) 		0.121
(1.00) 		0.0525
(1.00) 		0.898
(1.00) 		1
(1.00)
2p loss 24 (5%) 431 0.71
(1.00) 		0.281
(1.00) 		0.00085
(0.881) 		0.777
(1.00) 		0.711
(1.00) 		0.969
(1.00) 		0.407
(1.00) 		0.983
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.963
(1.00) 		0.784
(1.00) 		0.366
(1.00)
2q loss 23 (5%) 432 0.341
(1.00) 		0.942
(1.00) 		0.34
(1.00) 		0.828
(1.00) 		0.775
(1.00) 		0.893
(1.00) 		0.526
(1.00) 		0.621
(1.00) 		0.0763
(1.00) 		0.615
(1.00) 		0.00306
(1.00) 		0.717
(1.00) 		0.726
(1.00)
3p loss 191 (42%) 264 0.231
(1.00) 		0.355
(1.00) 		0.531
(1.00) 		0.0659
(1.00) 		0.379
(1.00) 		0.709
(1.00) 		1
(1.00) 		0.17
(1.00) 		0.641
(1.00) 		1
(1.00) 		0.241
(1.00) 		0.0599
(1.00) 		0.204
(1.00)
3q loss 132 (29%) 323 0.244
(1.00) 		0.252
(1.00) 		0.586
(1.00) 		0.635
(1.00) 		0.0874
(1.00) 		0.449
(1.00) 		0.756
(1.00) 		0.137
(1.00) 		0.496
(1.00) 		1
(1.00) 		0.134
(1.00) 		0.0454
(1.00) 		0.504
(1.00)
4p loss 106 (23%) 349 0.428
(1.00) 		0.177
(1.00) 		0.523
(1.00) 		0.967
(1.00) 		0.207
(1.00) 		0.824
(1.00) 		0.579
(1.00) 		0.2
(1.00) 		0.461
(1.00) 		0.598
(1.00) 		0.321
(1.00) 		0.039
(1.00) 		0.15
(1.00)
4q loss 121 (27%) 334 0.827
(1.00) 		0.203
(1.00) 		0.0999
(1.00) 		0.963
(1.00) 		0.0112
(1.00) 		0.729
(1.00) 		0.457
(1.00) 		0.0869
(1.00) 		0.489
(1.00) 		0.804
(1.00) 		0.275
(1.00) 		0.227
(1.00) 		0.125
(1.00)
5p loss 38 (8%) 417 0.394
(1.00) 		0.352
(1.00) 		0.719
(1.00) 		0.975
(1.00) 		0.679
(1.00) 		0.916
(1.00) 		0.0165
(1.00) 		0.191
(1.00) 		0.286
(1.00) 		1
(1.00) 		0.586
(1.00) 		0.206
(1.00) 		0.72
(1.00)
5q loss 133 (29%) 322 0.0401
(1.00) 		0.00481
(1.00) 		0.749
(1.00) 		0.974
(1.00) 		0.416
(1.00) 		0.482
(1.00) 		0.013
(1.00) 		0.377
(1.00) 		0.32
(1.00) 		0.339
(1.00) 		0.0254
(1.00) 		0.898
(1.00) 		0.0568
(1.00)
6p loss 94 (21%) 361 0.144
(1.00) 		0.733
(1.00) 		0.265
(1.00) 		0.134
(1.00) 		0.514
(1.00) 		0.876
(1.00) 		0.486
(1.00) 		0.0922
(1.00) 		0.946
(1.00) 		0.782
(1.00) 		0.107
(1.00) 		0.419
(1.00) 		0.851
(1.00)
6q loss 193 (42%) 262 0.924
(1.00) 		0.122
(1.00) 		0.719
(1.00) 		0.671
(1.00) 		0.519
(1.00) 		0.825
(1.00) 		0.298
(1.00) 		0.137
(1.00) 		0.942
(1.00) 		0.656
(1.00) 		0.325
(1.00) 		0.042
(1.00) 		0.878
(1.00)
7p loss 30 (7%) 425 0.541
(1.00) 		0.792
(1.00) 		0.958
(1.00) 		0.911
(1.00) 		0.887
(1.00) 		0.772
(1.00) 		0.261
(1.00) 		0.659
(1.00) 		0.829
(1.00) 		0.641
(1.00) 		0.844
(1.00) 		0.71
(1.00) 		0.414
(1.00)
7q loss 35 (8%) 420 0.323
(1.00) 		0.199
(1.00) 		0.87
(1.00) 		0.885
(1.00) 		0.759
(1.00) 		0.427
(1.00) 		0.861
(1.00) 		0.713
(1.00) 		0.678
(1.00) 		1
(1.00) 		0.973
(1.00) 		0.377
(1.00) 		0.626
(1.00)
8p loss 176 (39%) 279 0.991
(1.00) 		0.814
(1.00) 		0.927
(1.00) 		0.541
(1.00) 		0.979
(1.00) 		0.417
(1.00) 		0.0673
(1.00) 		0.802
(1.00) 		0.0292
(1.00) 		0.175
(1.00) 		0.212
(1.00) 		0.663
(1.00) 		0.163
(1.00)
8q loss 49 (11%) 406 0.748
(1.00) 		0.572
(1.00) 		0.125
(1.00) 		0.503
(1.00) 		0.202
(1.00) 		0.0721
(1.00) 		0.29
(1.00) 		0.102
(1.00) 		0.136
(1.00) 		0.715
(1.00) 		0.389
(1.00) 		0.297
(1.00) 		0.926
(1.00)
9p loss 235 (52%) 220 0.104
(1.00) 		0.345
(1.00) 		0.583
(1.00) 		0.931
(1.00) 		0.0524
(1.00) 		0.527
(1.00) 		0.0609
(1.00) 		0.434
(1.00) 		0.635
(1.00) 		0.824
(1.00) 		0.538
(1.00) 		0.789
(1.00) 		0.965
(1.00)
9q loss 221 (49%) 234 0.657
(1.00) 		0.849
(1.00) 		0.844
(1.00) 		0.352
(1.00) 		0.376
(1.00) 		0.787
(1.00) 		0.779
(1.00) 		0.741
(1.00) 		0.351
(1.00) 		0.659
(1.00) 		0.257
(1.00) 		0.518
(1.00) 		0.935
(1.00)
10p loss 98 (22%) 357 0.523
(1.00) 		0.98
(1.00) 		0.609
(1.00) 		0.161
(1.00) 		0.371
(1.00) 		0.906
(1.00) 		0.0116
(1.00) 		0.611
(1.00) 		0.0471
(1.00) 		0.274
(1.00) 		0.545
(1.00) 		0.62
(1.00) 		0.82
(1.00)
10q loss 118 (26%) 337 0.293
(1.00) 		0.675
(1.00) 		0.509
(1.00) 		0.2
(1.00) 		0.189
(1.00) 		0.782
(1.00) 		0.108
(1.00) 		0.468
(1.00) 		0.0193
(1.00) 		0.122
(1.00) 		0.11
(1.00) 		0.264
(1.00) 		0.612
(1.00)
11p loss 104 (23%) 351 0.902
(1.00) 		0.0555
(1.00) 		0.397
(1.00) 		0.416
(1.00) 		0.445
(1.00) 		0.426
(1.00) 		0.000497
(0.516) 		0.809
(1.00) 		0.542
(1.00) 		0.433
(1.00) 		0.689
(1.00) 		0.137
(1.00) 		0.427
(1.00)
11q loss 83 (18%) 372 0.604
(1.00) 		0.702
(1.00) 		0.525
(1.00) 		0.904
(1.00) 		0.983
(1.00) 		0.31
(1.00) 		0.00332
(1.00) 		0.875
(1.00) 		0.783
(1.00) 		0.394
(1.00) 		0.896
(1.00) 		0.337
(1.00) 		0.705
(1.00)
12p loss 97 (21%) 358 0.177
(1.00) 		0.415
(1.00) 		0.522
(1.00) 		0.637
(1.00) 		0.942
(1.00) 		0.127
(1.00) 		0.0119
(1.00) 		0.0709
(1.00) 		0.866
(1.00) 		0.588
(1.00) 		0.126
(1.00) 		0.443
(1.00) 		0.88
(1.00)
12q loss 85 (19%) 370 0.149
(1.00) 		0.739
(1.00) 		0.652
(1.00) 		0.56
(1.00) 		0.308
(1.00) 		0.102
(1.00) 		0.00773
(1.00) 		0.217
(1.00) 		0.39
(1.00) 		0.393
(1.00) 		0.121
(1.00) 		0.906
(1.00) 		0.852
(1.00)
13q loss 218 (48%) 237 0.846
(1.00) 		0.184
(1.00) 		0.614
(1.00) 		0.362
(1.00) 		0.443
(1.00) 		0.509
(1.00) 		0.851
(1.00) 		0.804
(1.00) 		0.521
(1.00) 		0.381
(1.00) 		0.0509
(1.00) 		0.164
(1.00) 		0.582
(1.00)
14q loss 103 (23%) 352 0.477
(1.00) 		0.136
(1.00) 		0.505
(1.00) 		0.363
(1.00) 		0.0532
(1.00) 		0.701
(1.00) 		0.262
(1.00) 		0.552
(1.00) 		0.784
(1.00) 		0.796
(1.00) 		0.132
(1.00) 		0.38
(1.00) 		0.225
(1.00)
15q loss 214 (47%) 241 0.639
(1.00) 		0.000984
(1.00) 		0.756
(1.00) 		0.986
(1.00) 		0.715
(1.00) 		0.713
(1.00) 		0.573
(1.00) 		0.22
(1.00) 		0.0277
(1.00) 		0.659
(1.00) 		0.324
(1.00) 		0.175
(1.00) 		0.746
(1.00)
16p loss 100 (22%) 355 0.553
(1.00) 		0.726
(1.00) 		0.0415
(1.00) 		0.418
(1.00) 		0.0349
(1.00) 		0.312
(1.00) 		0.428
(1.00) 		0.961
(1.00) 		0.861
(1.00) 		0.791
(1.00) 		0.61
(1.00) 		0.78
(1.00) 		0.615
(1.00)
16q loss 127 (28%) 328 0.629
(1.00) 		0.404
(1.00) 		0.556
(1.00) 		0.986
(1.00) 		0.286
(1.00) 		0.621
(1.00) 		0.403
(1.00) 		0.274
(1.00) 		0.439
(1.00) 		0.806
(1.00) 		0.395
(1.00) 		0.886
(1.00) 		0.283
(1.00)
17p loss 191 (42%) 264 0.923
(1.00) 		0.15
(1.00) 		0.393
(1.00) 		0.459
(1.00) 		0.739
(1.00) 		0.451
(1.00) 		0.154
(1.00) 		0.631
(1.00) 		0.351
(1.00) 		0.0396
(1.00) 		0.0213
(1.00) 		0.0139
(1.00) 		0.951
(1.00)
17q loss 51 (11%) 404 0.335
(1.00) 		0.477
(1.00) 		0.295
(1.00) 		0.226
(1.00) 		0.286
(1.00) 		0.973
(1.00) 		0.657
(1.00) 		0.681
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.914
(1.00) 		0.109
(1.00) 		0.617
(1.00)
18p loss 155 (34%) 300 0.403
(1.00) 		0.0638
(1.00) 		0.0335
(1.00) 		0.345
(1.00) 		0.331
(1.00) 		0.0343
(1.00) 		0.00732
(1.00) 		0.296
(1.00) 		0.706
(1.00) 		0.356
(1.00) 		0.0172
(1.00) 		0.00469
(1.00) 		0.149
(1.00)
18q loss 190 (42%) 265 0.0505
(1.00) 		0.49
(1.00) 		0.0176
(1.00) 		0.217
(1.00) 		0.0717
(1.00) 		0.308
(1.00) 		0.0364
(1.00) 		0.929
(1.00) 		0.646
(1.00) 		0.26
(1.00) 		0.0869
(1.00) 		0.125
(1.00) 		0.00345
(1.00)
19p loss 221 (49%) 234 0.0309
(1.00) 		0.0784
(1.00) 		0.0631
(1.00) 		0.477
(1.00) 		0.15
(1.00) 		0.0514
(1.00) 		0.0114
(1.00) 		0.619
(1.00) 		0.749
(1.00) 		0.183
(1.00) 		0.946
(1.00) 		0.369
(1.00) 		0.245
(1.00)
19q loss 142 (31%) 313 0.132
(1.00) 		0.131
(1.00) 		0.109
(1.00) 		0.143
(1.00) 		0.412
(1.00) 		0.0173
(1.00) 		0.225
(1.00) 		0.968
(1.00) 		0.688
(1.00) 		0.334
(1.00) 		0.51
(1.00) 		0.779
(1.00) 		0.254
(1.00)
20p loss 107 (24%) 348 0.213
(1.00) 		0.64
(1.00) 		0.6
(1.00) 		0.419
(1.00) 		0.256
(1.00) 		0.332
(1.00) 		0.825
(1.00) 		0.502
(1.00) 		0.382
(1.00) 		0.794
(1.00) 		0.433
(1.00) 		0.174
(1.00) 		0.863
(1.00)
20q loss 64 (14%) 391 0.762
(1.00) 		0.407
(1.00) 		0.374
(1.00) 		0.443
(1.00) 		0.411
(1.00) 		0.163
(1.00) 		0.787
(1.00) 		0.00245
(1.00) 		0.0655
(1.00) 		0.336
(1.00) 		0.795
(1.00) 		0.481
(1.00) 		0.571
(1.00)
21q loss 148 (33%) 307 0.492
(1.00) 		0.448
(1.00) 		0.686
(1.00) 		0.808
(1.00) 		0.912
(1.00) 		0.665
(1.00) 		0.108
(1.00) 		0.877
(1.00) 		0.0752
(1.00) 		0.153
(1.00) 		0.16
(1.00) 		0.176
(1.00) 		0.781
(1.00)
22q loss 194 (43%) 261 0.506
(1.00) 		0.00174
(1.00) 		0.624
(1.00) 		0.998
(1.00) 		0.98
(1.00) 		0.272
(1.00) 		0.0371
(1.00) 		0.0442
(1.00) 		0.294
(1.00) 		0.822
(1.00) 		0.915
(1.00) 		0.00449
(1.00) 		0.732
(1.00)
xq loss 55 (12%) 400 0.632
(1.00) 		0.268
(1.00) 		0.26
(1.00) 		0.711
(1.00) 		0.953
(1.00) 		0.464
(1.00) 		0.199
(1.00) 		0.945
(1.00) 		0.0757
(1.00) 		0.158
(1.00) 		0.543
(1.00) 		0.528
(1.00) 		0.808
(1.00)
'17p gain' versus 'NUMBERPACKYEARSSMOKED'

P value = 0.000172 (t-test), Q value = 0.18

Table S1.  Gene #30: '17p gain' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'

nPatients Mean (Std.Dev)
ALL 315 42.2 (27.3)
17P GAIN MUTATED 53 56.7 (29.6)
17P GAIN WILD-TYPE 262 39.3 (25.9)

Figure S1.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #11: 'NUMBERPACKYEARSSMOKED'

'19p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000139 (Chi-square test), Q value = 0.14

Table S2.  Gene #34: '19p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA LUNG SIGNET RING ADENOCARCINOMA LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA MUCINOUS (COLLOID) CARCINOMA
ALL 13 92 292 4 17 2 3 2 18 1 4 7
19P GAIN MUTATED 2 4 17 0 0 0 1 0 2 1 2 0
19P GAIN WILD-TYPE 11 88 275 4 17 2 2 2 16 0 2 7

Figure S2.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = LUAD-TP.merged_data.txt

  • Number of patients = 455

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 13

  • Exclude regions 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

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

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

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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[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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