Correlation between copy number variations of arm-level result and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1ZC829F
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1ZC829F
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 82 arm-level events and 15 clinical features across 516 patients, 14 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 7p gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 7q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 12q gain cnv correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • 17p gain cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • 17q gain cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • 18p gain cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • 20q gain cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • 5q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 11p loss cnv correlated to 'GENDER'.

  • 12p loss cnv correlated to 'GENDER'.

  • 12q loss cnv correlated to 'GENDER'.

  • 15q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 22q loss cnv correlated to 'YEARS_TO_BIRTH'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 15 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 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		RESIDUAL
TUMOR 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-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 Wilcoxon-test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 142 (28%) 374 0.761
(0.991) 		0.0429
(0.503) 		0.0734
(0.551) 		0.574
(0.97) 		0.00137
(0.239) 		1
(1.00) 		1
(1.00) 		0.762
(0.991) 		0.992
(1.00) 		0.62
(0.97) 		0.682
(0.978) 		0.655
(0.978) 		0.76
(0.991) 		0.2
(0.778) 		1
(1.00)
7p gain 267 (52%) 249 0.0527
(0.532) 		0.0119
(0.356) 		0.382
(0.918) 		0.393
(0.918) 		0.00185
(0.239) 		0.408
(0.92) 		0.724
(0.988) 		0.679
(0.978) 		0.496
(0.935) 		0.012
(0.356) 		0.0197
(0.371) 		0.205
(0.778) 		0.824
(1.00) 		0.127
(0.655) 		0.713
(0.987)
7q gain 220 (43%) 296 0.106
(0.595) 		0.00278
(0.248) 		0.241
(0.802) 		0.786
(0.998) 		0.0102
(0.351) 		0.144
(0.697) 		1
(1.00) 		0.21
(0.778) 		0.104
(0.595) 		0.0429
(0.503) 		0.129
(0.659) 		0.479
(0.935) 		0.518
(0.949) 		0.501
(0.935) 		0.467
(0.934)
12q gain 133 (26%) 383 0.187
(0.766) 		0.0545
(0.532) 		0.174
(0.743) 		0.569
(0.97) 		0.484
(0.935) 		0.156
(0.713) 		0.227
(0.791) 		0.436
(0.929) 		1
(1.00) 		0.545
(0.965) 		0.603
(0.97) 		0.00282
(0.248) 		0.71
(0.985) 		0.62
(0.97) 		0.682
(0.978)
17p gain 84 (16%) 432 0.144
(0.697) 		0.0212
(0.379) 		0.0721
(0.551) 		0.198
(0.778) 		0.053
(0.532) 		0.186
(0.766) 		0.0726
(0.551) 		0.0654
(0.537) 		0.807
(1.00) 		0.466
(0.934) 		1.6e-05
(0.0197) 		0.676
(0.978) 		0.0837
(0.569) 		0.0758
(0.552) 		0.602
(0.97)
17q gain 191 (37%) 325 0.34
(0.882) 		0.0601
(0.537) 		0.157
(0.713) 		0.524
(0.953) 		0.167
(0.729) 		0.204
(0.778) 		0.715
(0.988) 		0.392
(0.918) 		0.0303
(0.425) 		0.149
(0.709) 		0.00258
(0.248) 		0.338
(0.882) 		0.0142
(0.356) 		0.0162
(0.356) 		0.7
(0.983)
18p gain 92 (18%) 424 0.0538
(0.532) 		0.421
(0.926) 		0.416
(0.924) 		0.945
(1.00) 		1
(1.00) 		0.593
(0.97) 		0.25
(0.806) 		1
(1.00) 		0.404
(0.92) 		0.488
(0.935) 		0.00248
(0.248) 		0.542
(0.965) 		0.593
(0.97) 		0.0405
(0.494) 		0.359
(0.899)
20q gain 201 (39%) 315 0.613
(0.97) 		0.0882
(0.571) 		0.108
(0.6) 		0.158
(0.713) 		0.106
(0.595) 		0.83
(1.00) 		0.321
(0.878) 		0.888
(1.00) 		0.0667
(0.537) 		0.0483
(0.528) 		0.00111
(0.239) 		0.765
(0.992) 		0.948
(1.00) 		0.229
(0.791) 		1
(1.00)
5q loss 143 (28%) 373 0.0298
(0.425) 		0.00103
(0.239) 		0.754
(0.991) 		0.993
(1.00) 		0.637
(0.975) 		0.492
(0.935) 		0.0299
(0.425) 		0.878
(1.00) 		0.731
(0.988) 		0.332
(0.881) 		0.0249
(0.406) 		0.486
(0.935) 		0.429
(0.926) 		0.0883
(0.571) 		0.101
(0.595)
11p loss 111 (22%) 405 0.507
(0.938) 		0.0438
(0.508) 		0.0997
(0.595) 		0.606
(0.97) 		0.201
(0.778) 		0.465
(0.934) 		0.00122
(0.239) 		0.243
(0.806) 		0.329
(0.878) 		0.575
(0.97) 		0.847
(1.00) 		0.0496
(0.528) 		0.389
(0.918) 		0.466
(0.934) 		0.192
(0.77)
12p loss 109 (21%) 407 0.85
(1.00) 		0.174
(0.743) 		0.539
(0.965) 		0.789
(1) 		0.961
(1.00) 		0.28
(0.843) 		0.00167
(0.239) 		0.867
(1.00) 		0.309
(0.868) 		0.821
(1.00) 		0.0953
(0.583) 		0.778
(0.998) 		0.707
(0.985) 		0.274
(0.839) 		0.669
(0.978)
12q loss 94 (18%) 422 0.873
(1.00) 		0.502
(0.935) 		0.782
(0.998) 		0.742
(0.99) 		0.625
(0.971) 		0.556
(0.97) 		0.00194
(0.239) 		1
(1.00) 		0.326
(0.878) 		0.73
(0.988) 		0.0286
(0.425) 		0.929
(1.00) 		0.643
(0.975) 		0.468
(0.934) 		1
(1.00)
15q loss 244 (47%) 272 0.248
(0.806) 		0.000705
(0.239) 		0.637
(0.975) 		0.856
(1.00) 		0.727
(0.988) 		0.537
(0.963) 		0.48
(0.935) 		0.0543
(0.532) 		0.183
(0.766) 		0.00726
(0.334) 		0.39
(0.918) 		0.16
(0.715) 		0.908
(1.00) 		0.646
(0.977) 		1
(1.00)
22q loss 221 (43%) 295 0.799
(1.00) 		0.00191
(0.239) 		0.91
(1.00) 		0.95
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.212
(0.778) 		0.579
(0.97) 		0.0199
(0.371) 		0.319
(0.877) 		0.818
(1.00) 		0.00542
(0.303) 		0.815
(1.00) 		0.302
(0.868) 		1
(1.00)
1q gain 319 (62%) 197 0.46
(0.934) 		0.147
(0.708) 		0.502
(0.935) 		0.736
(0.988) 		0.258
(0.823) 		0.833
(1.00) 		0.319
(0.877) 		0.887
(1.00) 		0.924
(1.00) 		0.282
(0.843) 		0.683
(0.978) 		0.603
(0.97) 		0.514
(0.946) 		0.543
(0.965) 		0.436
(0.929)
2p gain 154 (30%) 362 0.956
(1.00) 		0.12
(0.627) 		0.641
(0.975) 		0.709
(0.985) 		0.641
(0.975) 		0.369
(0.913) 		0.501
(0.935) 		0.00984
(0.351) 		0.904
(1.00) 		0.613
(0.97) 		0.0652
(0.537) 		0.263
(0.826) 		0.277
(0.839) 		0.41
(0.921) 		0.0234
(0.401)
2q gain 143 (28%) 373 0.902
(1.00) 		0.967
(1.00) 		0.463
(0.934) 		0.982
(1.00) 		0.72
(0.988) 		0.495
(0.935) 		0.922
(1.00) 		0.0298
(0.425) 		0.703
(0.983) 		0.826
(1.00) 		0.0453
(0.516) 		0.702
(0.983) 		0.663
(0.978) 		0.91
(1.00) 		0.087
(0.571)
3p gain 44 (9%) 472 0.672
(0.978) 		0.207
(0.778) 		0.468
(0.934) 		0.133
(0.673) 		0.187
(0.766) 		1
(1.00) 		0.434
(0.929) 		0.0238
(0.401) 		0.758
(0.991) 		0.594
(0.97) 		0.265
(0.827) 		0.27
(0.833) 		0.0493
(0.528) 		0.891
(1.00) 		0.105
(0.595)
3q gain 90 (17%) 426 0.883
(1.00) 		0.484
(0.935) 		0.47
(0.935) 		0.733
(0.988) 		0.433
(0.929) 		1
(1.00) 		0.643
(0.975) 		0.59
(0.97) 		0.348
(0.889) 		0.71
(0.985) 		0.11
(0.603) 		0.363
(0.903) 		0.19
(0.77) 		0.678
(0.978) 		0.104
(0.595)
4p gain 83 (16%) 433 0.893
(1.00) 		0.0132
(0.356) 		0.0668
(0.537) 		0.157
(0.713) 		0.859
(1.00) 		0.0529
(0.532) 		0.905
(1.00) 		0.192
(0.77) 		0.875
(1.00) 		0.363
(0.903) 		0.0572
(0.537) 		0.985
(1.00) 		0.814
(1.00) 		0.253
(0.815) 		0.264
(0.826)
4q gain 49 (9%) 467 0.467
(0.934) 		0.521
(0.953) 		0.0941
(0.583) 		0.258
(0.823) 		0.922
(1.00) 		0.726
(0.988) 		0.764
(0.992) 		0.0189
(0.368) 		0.515
(0.947) 		0.422
(0.926) 		0.0683
(0.537) 		0.814
(1.00) 		0.932
(1.00) 		0.287
(0.849) 		0.494
(0.935)
5p gain 279 (54%) 237 0.337
(0.882) 		0.0252
(0.406) 		0.396
(0.918) 		0.298
(0.868) 		0.691
(0.981) 		1
(1.00) 		0.184
(0.766) 		0.89
(1.00) 		0.794
(1.00) 		0.157
(0.713) 		0.00655
(0.334) 		0.404
(0.92) 		0.94
(1.00) 		0.621
(0.97) 		1
(1.00)
5q gain 132 (26%) 384 0.756
(0.991) 		0.789
(1) 		0.854
(1.00) 		0.777
(0.998) 		0.768
(0.994) 		0.479
(0.935) 		0.105
(0.595) 		0.876
(1.00) 		0.628
(0.972) 		0.434
(0.929) 		0.535
(0.963) 		0.637
(0.975) 		0.673
(0.978) 		0.586
(0.97) 		0.683
(0.978)
6p gain 146 (28%) 370 0.186
(0.766) 		0.911
(1.00) 		0.261
(0.825) 		0.454
(0.934) 		0.607
(0.97) 		0.116
(0.618) 		0.696
(0.983) 		0.542
(0.965) 		0.384
(0.918) 		0.301
(0.868) 		0.404
(0.92) 		0.794
(1.00) 		0.839
(1.00) 		0.0172
(0.365) 		0.202
(0.778)
6q gain 60 (12%) 456 0.983
(1.00) 		0.776
(0.998) 		0.603
(0.97) 		0.639
(0.975) 		0.687
(0.978) 		0.523
(0.953) 		0.891
(1.00) 		0.673
(0.978) 		0.572
(0.97) 		0.96
(1.00) 		0.921
(1.00) 		0.958
(1.00) 		0.769
(0.994) 		0.7
(0.983) 		0.208
(0.778)
8p gain 125 (24%) 391 0.783
(0.998) 		0.06
(0.537) 		0.501
(0.935) 		0.0944
(0.583) 		0.672
(0.978) 		1
(1.00) 		0.0304
(0.425) 		0.635
(0.975) 		0.463
(0.934) 		0.787
(0.998) 		0.673
(0.978) 		0.257
(0.823) 		0.258
(0.823) 		0.479
(0.935) 		1
(1.00)
8q gain 245 (47%) 271 0.0174
(0.365) 		0.00734
(0.334) 		0.87
(1.00) 		0.312
(0.871) 		0.522
(0.953) 		1
(1.00) 		0.597
(0.97) 		0.49
(0.935) 		0.871
(1.00) 		0.00542
(0.303) 		0.628
(0.972) 		0.0388
(0.485) 		0.287
(0.849) 		0.1
(0.595) 		0.709
(0.985)
9p gain 45 (9%) 471 0.527
(0.957) 		0.265
(0.827) 		0.872
(1.00) 		0.463
(0.934) 		0.613
(0.97) 		0.487
(0.935) 		0.159
(0.715) 		1
(1.00) 		0.101
(0.595) 		0.393
(0.918) 		0.826
(1.00) 		0.68
(0.978) 		0.472
(0.935) 		0.372
(0.915) 		1
(1.00)
9q gain 34 (7%) 482 0.807
(1.00) 		0.207
(0.778) 		0.412
(0.921) 		0.833
(1.00) 		1
(1.00) 		0.0951
(0.583) 		0.86
(1.00) 		0.595
(0.97) 		0.239
(0.802) 		0.72
(0.988) 		0.743
(0.99) 		0.574
(0.97) 		0.913
(1.00) 		0.327
(0.878) 		1
(1.00)
10p gain 112 (22%) 404 0.9
(1.00) 		0.0745
(0.552) 		0.761
(0.991) 		0.0605
(0.537) 		0.0726
(0.551) 		0.622
(0.97) 		0.00374
(0.275) 		1
(1.00) 		0.82
(1.00) 		0.796
(1.00) 		0.115
(0.617) 		0.714
(0.987) 		0.329
(0.878) 		0.387
(0.918) 		0.626
(0.971)
10q gain 79 (15%) 437 0.957
(1.00) 		0.305
(0.868) 		0.496
(0.935) 		0.0589
(0.537) 		0.102
(0.595) 		0.276
(0.839) 		0.00316
(0.259) 		1
(1.00) 		0.32
(0.877) 		0.747
(0.991) 		0.352
(0.891) 		0.876
(1.00) 		0.91
(1.00) 		0.373
(0.916) 		1
(1.00)
11p gain 94 (18%) 422 0.0584
(0.537) 		0.351
(0.891) 		0.513
(0.945) 		0.448
(0.934) 		0.0805
(0.563) 		1
(1.00) 		0.0866
(0.571) 		0.21
(0.778) 		0.234
(0.794) 		0.306
(0.868) 		0.0104
(0.351) 		0.281
(0.843) 		0.841
(1.00) 		1
(1.00) 		0.615
(0.97)
11q gain 118 (23%) 398 0.234
(0.794) 		0.0261
(0.406) 		0.798
(1.00) 		0.94
(1.00) 		0.363
(0.903) 		0.448
(0.934) 		0.172
(0.742) 		1
(1.00) 		0.615
(0.97) 		0.0786
(0.555) 		0.0395
(0.485) 		0.16
(0.715) 		0.808
(1.00) 		0.27
(0.833) 		0.364
(0.903)
12p gain 138 (27%) 378 0.111
(0.603) 		0.0178
(0.365) 		0.0498
(0.528) 		0.886
(1.00) 		0.38
(0.918) 		0.16
(0.715) 		0.195
(0.774) 		0.758
(0.991) 		0.47
(0.935) 		0.667
(0.978) 		0.111
(0.603) 		0.0428
(0.503) 		0.686
(0.978) 		0.625
(0.971) 		0.683
(0.978)
13q gain 43 (8%) 473 0.732
(0.988) 		0.533
(0.962) 		0.00607
(0.325) 		0.393
(0.918) 		0.512
(0.945) 		0.027
(0.415) 		1
(1.00) 		0.327
(0.878) 		0.0901
(0.574) 		0.974
(1.00) 		0.263
(0.826) 		0.211
(0.778) 		0.203
(0.778) 		1
(1.00) 		0.408
(0.92)
14q gain 129 (25%) 387 0.701
(0.983) 		0.21
(0.778) 		0.856
(1.00) 		0.87
(1.00) 		0.425
(0.926) 		0.62
(0.97) 		0.359
(0.899) 		0.528
(0.958) 		0.00943
(0.351) 		0.638
(0.975) 		0.217
(0.778) 		0.153
(0.713) 		0.136
(0.673) 		0.63
(0.972) 		0.683
(0.978)
15q gain 38 (7%) 478 0.00836
(0.343) 		0.685
(0.978) 		0.0224
(0.393) 		0.531
(0.962) 		0.0146
(0.356) 		0.462
(0.934) 		0.5
(0.935) 		0.595
(0.97) 		0.0607
(0.537) 		0.076
(0.552) 		0.671
(0.978) 		0.796
(1.00) 		0.561
(0.97) 		0.353
(0.891) 		1
(1.00)
16p gain 137 (27%) 379 0.472
(0.935) 		0.755
(0.991) 		0.3
(0.868) 		0.405
(0.92) 		0.966
(1.00) 		0.103
(0.595) 		0.921
(1.00) 		1
(1.00) 		0.643
(0.975) 		0.123
(0.637) 		0.105
(0.595) 		0.611
(0.97) 		0.863
(1.00) 		0.303
(0.868) 		0.679
(0.978)
16q gain 101 (20%) 415 0.889
(1.00) 		0.353
(0.891) 		0.417
(0.926) 		0.41
(0.921) 		1
(1.00) 		0.601
(0.97) 		0.507
(0.938) 		0.497
(0.935) 		0.969
(1.00) 		0.0685
(0.537) 		0.088
(0.571) 		0.319
(0.877) 		0.387
(0.918) 		0.281
(0.843) 		0.353
(0.891)
18q gain 69 (13%) 447 0.0526
(0.532) 		0.0809
(0.563) 		0.476
(0.935) 		0.743
(0.99) 		0.981
(1.00) 		0.545
(0.965) 		0.364
(0.903) 		1
(1.00) 		0.12
(0.627) 		0.427
(0.926) 		0.00492
(0.303) 		0.455
(0.934) 		0.0669
(0.537) 		0.0597
(0.537) 		0.6
(0.97)
19p gain 33 (6%) 483 0.942
(1.00) 		0.903
(1.00) 		0.736
(0.988) 		0.216
(0.778) 		0.474
(0.935) 		0.419
(0.926) 		0.371
(0.914) 		1
(1.00) 		0.59
(0.97) 		0.0038
(0.275) 		0.0893
(0.572) 		0.61
(0.97) 		0.581
(0.97) 		1
(1.00) 		0.408
(0.92)
19q gain 78 (15%) 438 0.224
(0.786) 		0.989
(1.00) 		0.661
(0.978) 		0.146
(0.705) 		0.414
(0.923) 		0.559
(0.97) 		0.0648
(0.537) 		0.706
(0.985) 		0.232
(0.792) 		0.0585
(0.537) 		0.107
(0.599) 		0.806
(1.00) 		0.881
(1.00) 		0.651
(0.978) 		0.314
(0.873)
20p gain 175 (34%) 341 0.791
(1.00) 		0.294
(0.864) 		0.548
(0.967) 		0.286
(0.848) 		0.0748
(0.552) 		0.826
(1.00) 		0.78
(0.998) 		0.665
(0.978) 		0.395
(0.918) 		0.127
(0.655) 		0.0178
(0.365) 		0.245
(0.806) 		0.431
(0.929) 		0.0783
(0.555) 		0.429
(0.926)
21q gain 98 (19%) 418 0.544
(0.965) 		0.268
(0.832) 		0.155
(0.713) 		0.567
(0.97) 		0.0886
(0.571) 		1
(1.00) 		0.0329
(0.45) 		1
(1.00) 		0.548
(0.967) 		0.557
(0.97) 		0.131
(0.667) 		0.169
(0.732) 		0.869
(1.00) 		0.385
(0.918) 		1
(1.00)
22q gain 62 (12%) 454 0.0481
(0.528) 		0.0366
(0.473) 		0.667
(0.978) 		0.337
(0.882) 		0.455
(0.934) 		0.752
(0.991) 		0.135
(0.673) 		0.521
(0.953) 		0.199
(0.778) 		0.343
(0.882) 		0.249
(0.806) 		0.151
(0.712) 		0.673
(0.978) 		0.56
(0.97) 		0.578
(0.97)
xp gain 53 (10%) 463 0.319
(0.877) 		0.807
(1.00) 		0.0111
(0.356) 		0.0188
(0.368) 		0.12
(0.627) 		0.0106
(0.351) 		0.245
(0.806) 		0.35
(0.891) 		0.0734
(0.551) 		0.872
(1.00) 		0.0162
(0.356) 		0.0596
(0.537) 		0.217
(0.778) 		0.245
(0.806) 		1
(1.00)
xq gain 86 (17%) 430 0.732
(0.988) 		0.676
(0.978) 		0.0963
(0.586) 		0.224
(0.786) 		0.952
(1.00) 		0.025
(0.406) 		0.347
(0.888) 		0.449
(0.934) 		0.664
(0.978) 		0.279
(0.843) 		0.0992
(0.595) 		0.29
(0.854) 		0.727
(0.988) 		0.603
(0.97) 		0.6
(0.97)
1p loss 80 (16%) 436 0.182
(0.766) 		0.989
(1.00) 		0.016
(0.356) 		0.0917
(0.576) 		0.00482
(0.303) 		1
(1.00) 		0.394
(0.918) 		0.45
(0.934) 		0.492
(0.935) 		0.816
(1.00) 		0.456
(0.934) 		0.643
(0.975) 		0.759
(0.991) 		1
(1.00) 		0.6
(0.97)
1q loss 28 (5%) 488 0.224
(0.786) 		0.456
(0.934) 		0.298
(0.868) 		1
(1.00) 		0.233
(0.794) 		0.66
(0.978) 		0.703
(0.983) 		0.76
(0.991) 		0.493
(0.935) 		0.851
(1.00) 		0.0935
(0.583) 		0.651
(0.978) 		0.825
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 24 (5%) 492 0.549
(0.967) 		0.229
(0.791) 		0.732
(0.988) 		0.669
(0.978) 		0.782
(0.998) 		1
(1.00) 		0.408
(0.92) 		0.499
(0.935) 		0.408
(0.92) 		0.424
(0.926) 		0.756
(0.991) 		0.866
(1.00) 		0.533
(0.962) 		0.305
(0.868) 		1
(1.00)
2q loss 25 (5%) 491 0.028
(0.425) 		0.441
(0.932) 		0.702
(0.983) 		0.944
(1.00) 		0.622
(0.97) 		1
(1.00) 		0.31
(0.868) 		0.338
(0.882) 		0.0369
(0.473) 		0.14
(0.689) 		0.0505
(0.531) 		0.388
(0.918) 		1
(1.00) 		0.0909
(0.574) 		1
(1.00)
3p loss 211 (41%) 305 0.921
(1.00) 		0.177
(0.751) 		0.594
(0.97) 		0.0141
(0.356) 		0.324
(0.878) 		0.838
(1.00) 		1
(1.00) 		0.78
(0.998) 		0.748
(0.991) 		0.356
(0.895) 		0.195
(0.774) 		0.0489
(0.528) 		0.0837
(0.569) 		0.96
(1.00) 		0.704
(0.983)
3q loss 144 (28%) 372 0.403
(0.92) 		0.0629
(0.537) 		0.203
(0.778) 		0.504
(0.937) 		0.0259
(0.406) 		0.653
(0.978) 		0.922
(1.00) 		0.285
(0.848) 		0.31
(0.868) 		0.306
(0.868) 		0.0152
(0.356) 		0.0133
(0.356) 		0.621
(0.97) 		0.611
(0.97) 		0.112
(0.604)
4p loss 119 (23%) 397 0.729
(0.988) 		0.328
(0.878) 		0.677
(0.978) 		0.994
(1.00) 		0.217
(0.778) 		1
(1.00) 		0.754
(0.991) 		0.331
(0.88) 		0.0541
(0.532) 		0.381
(0.918) 		0.307
(0.868) 		0.136
(0.673) 		0.491
(0.935) 		0.63
(0.972) 		1
(1.00)
4q loss 136 (26%) 380 0.681
(0.978) 		0.235
(0.795) 		0.187
(0.766) 		0.902
(1.00) 		0.00885
(0.351) 		0.482
(0.935) 		0.92
(1.00) 		0.0863
(0.571) 		0.0866
(0.571) 		0.389
(0.918) 		0.327
(0.878) 		0.23
(0.791) 		0.387
(0.918) 		0.774
(0.998) 		1
(1.00)
5p loss 45 (9%) 471 0.602
(0.97) 		0.0671
(0.537) 		0.805
(1.00) 		0.67
(0.978) 		0.482
(0.935) 		1
(1.00) 		0.12
(0.627) 		0.616
(0.97) 		0.937
(1.00) 		0.568
(0.97) 		0.809
(1.00) 		0.029
(0.425) 		1
(1.00) 		0.0767
(0.552) 		0.484
(0.935)
6p loss 101 (20%) 415 0.5
(0.935) 		0.413
(0.922) 		0.231
(0.791) 		0.0678
(0.537) 		0.393
(0.918) 		0.798
(1.00) 		0.507
(0.938) 		0.605
(0.97) 		0.611
(0.97) 		0.857
(1.00) 		0.00795
(0.337) 		0.105
(0.595) 		1
(1.00) 		1
(1.00) 		1
(1.00)
6q loss 217 (42%) 299 0.9
(1.00) 		0.109
(0.601) 		0.654
(0.978) 		0.545
(0.965) 		0.481
(0.935) 		1
(1.00) 		0.593
(0.97) 		0.78
(0.998) 		0.439
(0.93) 		0.823
(1.00) 		0.166
(0.729) 		0.0149
(0.356) 		0.576
(0.97) 		0.923
(1.00) 		1
(1.00)
7p loss 34 (7%) 482 0.89
(1.00) 		0.83
(1.00) 		0.925
(1.00) 		0.764
(0.992) 		0.837
(1.00) 		0.709
(0.985) 		0.288
(0.851) 		0.408
(0.92) 		0.331
(0.88) 		0.878
(1.00) 		0.297
(0.868) 		0.502
(0.935) 		0.578
(0.97) 		0.443
(0.934) 		0.408
(0.92)
7q loss 41 (8%) 475 0.437
(0.929) 		0.437
(0.929) 		0.695
(0.983) 		0.95
(1.00) 		0.541
(0.965) 		0.149
(0.709) 		0.747
(0.991) 		0.205
(0.778) 		0.821
(1.00) 		0.827
(1.00) 		0.599
(0.97) 		0.482
(0.935) 		0.914
(1.00) 		0.192
(0.77) 		0.453
(0.934)
8p loss 200 (39%) 316 0.94
(1.00) 		0.593
(0.97) 		0.283
(0.844) 		0.301
(0.868) 		0.781
(0.998) 		0.671
(0.978) 		0.0188
(0.368) 		0.887
(1.00) 		0.853
(1.00) 		0.0391
(0.485) 		0.473
(0.935) 		0.808
(1.00) 		0.24
(0.802) 		0.408
(0.92) 		0.439
(0.93)
8q loss 56 (11%) 460 0.535
(0.963) 		0.224
(0.786) 		0.213
(0.778) 		0.609
(0.97) 		0.156
(0.713) 		0.74
(0.99) 		0.574
(0.97) 		0.827
(1.00) 		0.595
(0.97) 		0.25
(0.806) 		0.307
(0.868) 		0.222
(0.786) 		0.247
(0.806) 		0.081
(0.563) 		1
(1.00)
9p loss 269 (52%) 247 0.164
(0.723) 		0.26
(0.825) 		0.384
(0.918) 		0.728
(0.988) 		0.0238
(0.401) 		0.838
(1.00) 		0.0635
(0.537) 		0.216
(0.778) 		0.0662
(0.537) 		0.901
(1.00) 		0.9
(1.00) 		0.881
(1.00) 		0.987
(1.00) 		0.39
(0.918) 		1
(1.00)
9q loss 249 (48%) 267 0.852
(1.00) 		0.746
(0.991) 		0.685
(0.978) 		0.517
(0.949) 		0.111
(0.603) 		1
(1.00) 		1
(1.00) 		0.217
(0.778) 		0.421
(0.926) 		0.664
(0.978) 		0.275
(0.839) 		0.55
(0.967) 		0.962
(1.00) 		0.555
(0.97) 		0.716
(0.988)
10p loss 110 (21%) 406 0.264
(0.826) 		0.734
(0.988) 		0.828
(1.00) 		0.309
(0.868) 		0.327
(0.878) 		1
(1.00) 		0.00967
(0.351) 		0.401
(0.92) 		0.336
(0.882) 		0.0478
(0.528) 		0.67
(0.978) 		0.382
(0.918) 		0.633
(0.975) 		0.0575
(0.537) 		0.652
(0.978)
10q loss 132 (26%) 384 0.248
(0.806) 		0.555
(0.97) 		0.735
(0.988) 		0.167
(0.729) 		0.481
(0.935) 		0.345
(0.885) 		0.0685
(0.537) 		0.753
(0.991) 		0.447
(0.934) 		0.0355
(0.465) 		0.185
(0.766) 		0.26
(0.825) 		0.329
(0.878) 		0.267
(0.829) 		0.376
(0.918)
11q loss 87 (17%) 429 0.832
(1.00) 		0.912
(1.00) 		0.23
(0.791) 		0.754
(0.991) 		0.868
(1.00) 		1
(1.00) 		0.00685
(0.334) 		0.586
(0.97) 		0.938
(1.00) 		0.809
(1.00) 		0.846
(1.00) 		0.425
(0.926) 		0.588
(0.97) 		0.454
(0.934) 		0.61
(0.97)
13q loss 251 (49%) 265 0.561
(0.97) 		0.149
(0.709) 		0.821
(1.00) 		0.785
(0.998) 		0.468
(0.934) 		0.308
(0.868) 		0.537
(0.963) 		1
(1.00) 		0.899
(1.00) 		0.585
(0.97) 		0.0518
(0.532) 		0.117
(0.624) 		0.703
(0.983) 		0.21
(0.778) 		0.724
(0.988)
14q loss 114 (22%) 402 0.616
(0.97) 		0.069
(0.537) 		0.605
(0.97) 		0.37
(0.913) 		0.0261
(0.406) 		0.81
(1.00) 		0.338
(0.882) 		0.87
(1.00) 		0.0335
(0.453) 		0.901
(1.00) 		0.139
(0.686) 		0.452
(0.934) 		0.141
(0.691) 		0.0622
(0.537) 		0.669
(0.978)
16p loss 107 (21%) 409 0.566
(0.97) 		0.884
(1.00) 		0.0637
(0.537) 		0.46
(0.934) 		0.0859
(0.571) 		0.443
(0.934) 		0.277
(0.839) 		0.865
(1.00) 		0.733
(0.988) 		0.78
(0.998) 		0.558
(0.97) 		0.834
(1.00) 		0.687
(0.978) 		1
(1.00) 		0.15
(0.709)
16q loss 137 (27%) 379 0.503
(0.935) 		0.719
(0.988) 		0.58
(0.97) 		0.988
(1.00) 		0.249
(0.806) 		1
(1.00) 		0.424
(0.926) 		1
(1.00) 		0.859
(1.00) 		0.618
(0.97) 		0.336
(0.882) 		0.386
(0.918) 		0.404
(0.92) 		0.969
(1.00) 		0.0148
(0.356)
17p loss 219 (42%) 297 0.743
(0.99) 		0.22
(0.783) 		0.448
(0.934) 		0.459
(0.934) 		0.91
(1.00) 		0.676
(0.978) 		0.0608
(0.537) 		0.0708
(0.548) 		0.468
(0.934) 		0.154
(0.713) 		0.0157
(0.356) 		0.0158
(0.356) 		0.896
(1.00) 		0.924
(1.00) 		0.136
(0.673)
17q loss 60 (12%) 456 0.184
(0.766) 		0.857
(1.00) 		0.00782
(0.337) 		0.0451
(0.516) 		0.225
(0.787) 		1
(1.00) 		0.335
(0.882) 		1
(1.00) 		0.0983
(0.595) 		0.812
(1.00) 		0.218
(0.778) 		0.0206
(0.373) 		0.625
(0.971) 		0.694
(0.983) 		0.587
(0.97)
18p loss 180 (35%) 336 0.654
(0.978) 		0.0381
(0.483) 		0.0571
(0.537) 		0.593
(0.97) 		0.0873
(0.571) 		0.12
(0.627) 		0.0124
(0.356) 		0.885
(1.00) 		0.925
(1.00) 		0.743
(0.99) 		0.0307
(0.425) 		0.00492
(0.303) 		0.208
(0.778) 		0.275
(0.839) 		0.698
(0.983)
18q loss 215 (42%) 301 0.343
(0.882) 		0.302
(0.868) 		0.0144
(0.356) 		0.422
(0.926) 		0.0414
(0.499) 		0.211
(0.778) 		0.0497
(0.528) 		1
(1.00) 		0.852
(1.00) 		0.396
(0.918) 		0.0679
(0.537) 		0.156
(0.713) 		0.0162
(0.356) 		1
(1.00) 		0.449
(0.934)
19p loss 245 (47%) 271 0.199
(0.778) 		0.0193
(0.371) 		0.245
(0.806) 		0.39
(0.918) 		0.194
(0.774) 		0.213
(0.778) 		0.0344
(0.455) 		0.784
(0.998) 		0.688
(0.978) 		0.821
(1.00) 		0.613
(0.97) 		0.169
(0.732) 		0.236
(0.796) 		0.796
(1.00) 		1
(1.00)
19q loss 159 (31%) 357 0.315
(0.873) 		0.0785
(0.555) 		0.189
(0.77) 		0.305
(0.868) 		0.191
(0.77) 		0.275
(0.839) 		0.341
(0.882) 		0.55
(0.967) 		0.685
(0.978) 		0.428
(0.926) 		0.58
(0.97) 		0.702
(0.983) 		0.133
(0.673) 		0.392
(0.918) 		1
(1.00)
20p loss 113 (22%) 403 0.175
(0.743) 		0.585
(0.97) 		0.164
(0.723) 		0.391
(0.918) 		0.1
(0.595) 		1
(1.00) 		0.596
(0.97) 		0.742
(0.99) 		0.682
(0.978) 		0.533
(0.962) 		0.0907
(0.574) 		0.428
(0.926) 		0.412
(0.921) 		0.501
(0.935) 		1
(1.00)
20q loss 67 (13%) 449 0.557
(0.97) 		0.722
(0.988) 		0.802
(1.00) 		0.584
(0.97) 		0.433
(0.929) 		0.777
(0.998) 		0.601
(0.97) 		1
(1.00) 		0.135
(0.673) 		0.0834
(0.569) 		0.462
(0.934) 		0.561
(0.97) 		0.727
(0.988) 		0.567
(0.97) 		0.215
(0.778)
21q loss 166 (32%) 350 0.967
(1.00) 		0.164
(0.723) 		0.858
(1.00) 		0.559
(0.97) 		0.98
(1.00) 		0.665
(0.978) 		0.108
(0.601) 		0.238
(0.801) 		0.0767
(0.552) 		0.0204
(0.373) 		0.758
(0.991) 		0.034
(0.455) 		0.498
(0.935) 		0.22
(0.783) 		1
(1.00)
xp loss 106 (21%) 410 0.429
(0.926) 		0.965
(1.00) 		0.342
(0.882) 		0.391
(0.918) 		0.18
(0.759) 		0.318
(0.877) 		0.327
(0.878) 		0.726
(0.988) 		0.63
(0.972) 		0.637
(0.975) 		0.0831
(0.569) 		0.0611
(0.537) 		0.72
(0.988) 		0.468
(0.934) 		0.353
(0.891)
xq loss 61 (12%) 455 0.769
(0.994) 		0.229
(0.791) 		0.423
(0.926) 		0.566
(0.97) 		0.77
(0.994) 		0.343
(0.882) 		0.0764
(0.552) 		0.2
(0.778) 		0.926
(1.00) 		0.144
(0.697) 		0.174
(0.743) 		0.2
(0.778) 		0.721
(0.988) 		0.154
(0.713) 		1
(1.00)
'1p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00137 (Fisher's exact test), Q value = 0.24

Table S1.  Gene #1: '1p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 333 96 76
1P GAIN MUTATED 85 40 14
1P GAIN WILD-TYPE 248 56 62

Figure S1.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00185 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2+N3
ALL 333 96 76
7P GAIN MUTATED 158 48 53
7P GAIN WILD-TYPE 175 48 23

Figure S2.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00278 (Wilcoxon-test), Q value = 0.25

Table S3.  Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
7Q GAIN MUTATED 209 63.8 (10.0)
7Q GAIN WILD-TYPE 276 66.4 (9.9)

Figure S3.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00282 (Wilcoxon-test), Q value = 0.25

Table S4.  Gene #24: '12q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 277 1965.0 (12.5)
12Q GAIN MUTATED 75 1968.5 (12.5)
12Q GAIN WILD-TYPE 202 1963.8 (12.4)

Figure S4.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'17p gain' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 1.6e-05 (Wilcoxon-test), Q value = 0.02

Table S5.  Gene #30: '17p gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 354 41.8 (27.2)
17P GAIN MUTATED 57 55.4 (30.6)
17P GAIN WILD-TYPE 297 39.2 (25.7)

Figure S5.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'17q gain' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00258 (Wilcoxon-test), Q value = 0.25

Table S6.  Gene #31: '17q gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 354 41.8 (27.2)
17Q GAIN MUTATED 128 46.6 (27.6)
17Q GAIN WILD-TYPE 226 39.1 (26.6)

Figure S6.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'18p gain' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00248 (Wilcoxon-test), Q value = 0.25

Table S7.  Gene #32: '18p gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 354 41.8 (27.2)
18P GAIN MUTATED 71 50.0 (28.7)
18P GAIN WILD-TYPE 283 39.8 (26.4)

Figure S7.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'20q gain' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00111 (Wilcoxon-test), Q value = 0.24

Table S8.  Gene #37: '20q gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 354 41.8 (27.2)
20Q GAIN MUTATED 149 46.6 (27.8)
20Q GAIN WILD-TYPE 205 38.4 (26.2)

Figure S8.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'5q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00103 (Wilcoxon-test), Q value = 0.24

Table S9.  Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
5Q LOSS MUTATED 136 62.8 (10.1)
5Q LOSS WILD-TYPE 349 66.2 (9.8)

Figure S9.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p loss' versus 'GENDER'

P value = 0.00122 (Fisher's exact test), Q value = 0.24

Table S10.  Gene #62: '11p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 276 240
11P LOSS MUTATED 44 67
11P LOSS WILD-TYPE 232 173

Figure S10.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #7: 'GENDER'

'12p loss' versus 'GENDER'

P value = 0.00167 (Fisher's exact test), Q value = 0.24

Table S11.  Gene #64: '12p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 276 240
12P LOSS MUTATED 73 36
12P LOSS WILD-TYPE 203 204

Figure S11.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #7: 'GENDER'

'12q loss' versus 'GENDER'

P value = 0.00194 (Fisher's exact test), Q value = 0.24

Table S12.  Gene #65: '12q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 276 240
12Q LOSS MUTATED 64 30
12Q LOSS WILD-TYPE 212 210

Figure S12.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #7: 'GENDER'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000705 (Wilcoxon-test), Q value = 0.24

Table S13.  Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
15Q LOSS MUTATED 226 63.7 (10.3)
15Q LOSS WILD-TYPE 259 66.6 (9.6)

Figure S13.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00191 (Wilcoxon-test), Q value = 0.24

Table S14.  Gene #80: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 485 65.2 (10.0)
22Q LOSS MUTATED 209 63.7 (10.0)
22Q LOSS WILD-TYPE 276 66.4 (9.9)

Figure S14.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/22531211/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/22506767/LUAD-TP.merged_data.txt

  • Number of patients = 516

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 15

  • 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

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] 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)
[3] 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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