Correlation between copy number variations of arm-level result and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1K35SWF
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1K35SWF
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 515 patients, 5 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 7p gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 17p 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'.

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, 5 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 150 (29%) 365 0.767
(0.995) 		0.0115
(0.313) 		0.154
(0.702) 		0.608
(0.961) 		0.0008
(0.204) 		0.822
(1.00) 		0.698
(0.979) 		0.873
(1.00) 		0.703
(0.979) 		0.742
(0.989) 		0.545
(0.959) 		0.598
(0.96) 		0.929
(1.00) 		0.0928
(0.579) 		0.679
(0.979)
7p gain 258 (50%) 257 0.0736
(0.548) 		0.0388
(0.498) 		0.193
(0.739) 		0.221
(0.762) 		0.00083
(0.204) 		0.301
(0.833) 		0.724
(0.979) 		0.47
(0.916) 		0.369
(0.857) 		0.0393
(0.499) 		0.0217
(0.375) 		0.51
(0.945) 		0.726
(0.979) 		0.408
(0.88) 		0.721
(0.979)
17p gain 83 (16%) 432 0.203
(0.746) 		0.0205
(0.37) 		0.0826
(0.574) 		0.272
(0.815) 		0.133
(0.657) 		0.174
(0.725) 		0.0925
(0.579) 		0.066
(0.535) 		1
(1.00) 		0.585
(0.96) 		2.41e-05
(0.0297) 		0.544
(0.959) 		0.194
(0.739) 		0.0778
(0.559) 		0.604
(0.961)
20q gain 191 (37%) 324 0.698
(0.979) 		0.107
(0.608) 		0.349
(0.851) 		0.227
(0.762) 		0.231
(0.762) 		0.663
(0.979) 		0.315
(0.846) 		0.448
(0.908) 		0.0059
(0.311) 		0.122
(0.639) 		0.000132
(0.0813) 		0.731
(0.981) 		0.857
(1.00) 		0.173
(0.725) 		0.716
(0.979)
5q loss 152 (30%) 363 0.0526
(0.521) 		0.000456
(0.187) 		0.688
(0.979) 		0.811
(1.00) 		0.457
(0.911) 		0.654
(0.976) 		0.0202
(0.37) 		0.631
(0.972) 		0.291
(0.827) 		0.324
(0.848) 		0.00718
(0.311) 		0.388
(0.865) 		0.514
(0.945) 		0.175
(0.725) 		0.0312
(0.428)
1q gain 309 (60%) 206 0.594
(0.96) 		0.172
(0.725) 		0.682
(0.979) 		0.754
(0.992) 		0.238
(0.77) 		0.679
(0.979) 		0.241
(0.774) 		0.375
(0.862) 		0.969
(1.00) 		0.194
(0.739) 		0.351
(0.853) 		0.463
(0.914) 		0.649
(0.975) 		0.919
(1.00) 		0.124
(0.639)
2p gain 153 (30%) 362 0.942
(1.00) 		0.176
(0.725) 		0.708
(0.979) 		0.85
(1.00) 		0.452
(0.909) 		0.264
(0.81) 		0.562
(0.96) 		0.0248
(0.398) 		0.966
(1.00) 		0.565
(0.96) 		0.0159
(0.344) 		0.509
(0.945) 		0.169
(0.72) 		0.272
(0.815) 		0.0212
(0.375)
2q gain 141 (27%) 374 0.763
(0.995) 		0.75
(0.992) 		0.439
(0.902) 		0.995
(1.00) 		0.584
(0.96) 		0.367
(0.857) 		0.921
(1.00) 		0.0298
(0.428) 		0.882
(1.00) 		0.663
(0.979) 		0.018
(0.363) 		0.423
(0.89) 		0.583
(0.96) 		0.85
(1.00) 		0.0805
(0.566)
3p gain 40 (8%) 475 0.489
(0.935) 		0.175
(0.725) 		0.626
(0.969) 		0.289
(0.827) 		0.059
(0.525) 		1
(1.00) 		0.51
(0.945) 		0.0658
(0.535) 		0.616
(0.966) 		0.76
(0.994) 		0.222
(0.762) 		0.183
(0.738) 		0.0482
(0.502) 		0.762
(0.995) 		0.0892
(0.579)
3q gain 88 (17%) 427 0.563
(0.96) 		0.952
(1.00) 		0.565
(0.96) 		0.854
(1.00) 		0.529
(0.948) 		1
(1.00) 		0.816
(1.00) 		0.564
(0.96) 		0.512
(0.945) 		0.741
(0.988) 		0.112
(0.615) 		0.764
(0.995) 		0.117
(0.627) 		0.736
(0.985) 		0.0982
(0.601)
4p gain 77 (15%) 438 0.994
(1.00) 		0.0166
(0.346) 		0.0782
(0.559) 		0.301
(0.833) 		1
(1.00) 		0.0422
(0.502) 		0.902
(1.00) 		0.303
(0.833) 		0.886
(1.00) 		0.495
(0.94) 		0.0219
(0.375) 		0.934
(1.00) 		0.931
(1.00) 		0.212
(0.757) 		1
(1.00)
4q gain 44 (9%) 471 0.446
(0.908) 		0.639
(0.972) 		0.109
(0.608) 		0.345
(0.848) 		0.646
(0.973) 		0.487
(0.934) 		0.64
(0.972) 		0.067
(0.535) 		0.5
(0.943) 		0.575
(0.96) 		0.0105
(0.313) 		0.873
(1.00) 		0.923
(1.00) 		0.224
(0.762) 		1
(1.00)
5p gain 270 (52%) 245 0.688
(0.979) 		0.0473
(0.502) 		0.47
(0.916) 		0.598
(0.96) 		0.568
(0.96) 		1
(1.00) 		0.25
(0.786) 		0.885
(1.00) 		0.607
(0.961) 		0.393
(0.865) 		0.00293
(0.278) 		0.495
(0.94) 		0.973
(1.00) 		0.868
(1.00) 		0.71
(0.979)
5q gain 125 (24%) 390 0.816
(1.00) 		0.651
(0.975) 		0.893
(1.00) 		0.966
(1.00) 		0.579
(0.96) 		0.634
(0.972) 		0.0995
(0.603) 		0.619
(0.966) 		0.792
(1.00) 		0.41
(0.88) 		0.561
(0.96) 		0.683
(0.979) 		0.562
(0.96) 		0.732
(0.981) 		1
(1.00)
6p gain 143 (28%) 372 0.175
(0.725) 		0.908
(1.00) 		0.337
(0.848) 		0.532
(0.952) 		0.696
(0.979) 		0.108
(0.608) 		0.43
(0.894) 		0.517
(0.946) 		0.342
(0.848) 		0.552
(0.96) 		0.234
(0.766) 		0.527
(0.948) 		0.681
(0.979) 		0.0203
(0.37) 		0.112
(0.615)
6q gain 61 (12%) 454 0.915
(1.00) 		0.617
(0.966) 		0.695
(0.979) 		0.903
(1.00) 		0.805
(1.00) 		0.517
(0.946) 		0.785
(1.00) 		0.821
(1.00) 		0.669
(0.979) 		0.959
(1.00) 		0.977
(1.00) 		0.645
(0.973) 		0.767
(0.995) 		0.877
(1.00) 		0.223
(0.762)
7q gain 211 (41%) 304 0.425
(0.892) 		0.00728
(0.311) 		0.0925
(0.579) 		0.873
(1.00) 		0.00474
(0.311) 		0.091
(0.579) 		0.929
(1.00) 		0.0745
(0.549) 		0.145
(0.681) 		0.065
(0.535) 		0.223
(0.762) 		0.873
(1.00) 		0.374
(0.862) 		0.89
(1.00) 		0.704
(0.979)
8p gain 129 (25%) 386 0.895
(1.00) 		0.157
(0.702) 		0.893
(1.00) 		0.221
(0.762) 		0.684
(0.979) 		0.486
(0.934) 		0.0107
(0.313) 		1
(1.00) 		0.335
(0.848) 		0.755
(0.992) 		0.75
(0.992) 		0.505
(0.945) 		0.214
(0.758) 		0.212
(0.757) 		0.199
(0.742)
8q gain 243 (47%) 272 0.00512
(0.311) 		0.0317
(0.428) 		0.864
(1.00) 		0.305
(0.833) 		0.337
(0.848) 		0.68
(0.979) 		0.426
(0.892) 		0.77
(0.998) 		0.52
(0.947) 		0.00426
(0.311) 		0.999
(1.00) 		0.139
(0.677) 		0.403
(0.874) 		0.0118
(0.315) 		1
(1.00)
9p gain 45 (9%) 470 0.639
(0.972) 		0.177
(0.725) 		0.872
(1.00) 		0.448
(0.908) 		0.587
(0.96) 		0.487
(0.934) 		0.159
(0.702) 		0.619
(0.966) 		0.0664
(0.535) 		0.358
(0.856) 		0.827
(1.00) 		0.623
(0.968) 		0.472
(0.917) 		0.235
(0.766) 		1
(1.00)
9q gain 32 (6%) 483 0.791
(1.00) 		0.289
(0.827) 		0.449
(0.908) 		0.866
(1.00) 		1
(1.00) 		0.0848
(0.576) 		0.584
(0.96) 		0.391
(0.865) 		0.125
(0.644) 		0.672
(0.979) 		0.95
(1.00) 		0.609
(0.961) 		0.709
(0.979) 		0.293
(0.827) 		1
(1.00)
10p gain 111 (22%) 404 0.787
(1.00) 		0.0433
(0.502) 		0.804
(1.00) 		0.0427
(0.502) 		0.08
(0.566) 		0.622
(0.968) 		0.00515
(0.311) 		0.86
(1.00) 		0.805
(1.00) 		0.793
(1.00) 		0.228
(0.762) 		0.487
(0.934) 		0.321
(0.848) 		0.071
(0.548) 		0.624
(0.968)
10q gain 77 (15%) 438 0.929
(1.00) 		0.219
(0.762) 		0.511
(0.945) 		0.0238
(0.398) 		0.0987
(0.601) 		0.276
(0.816) 		0.00294
(0.278) 		1
(1.00) 		0.334
(0.848) 		0.698
(0.979) 		0.666
(0.979) 		0.91
(1.00) 		0.873
(1.00) 		0.0921
(0.579) 		1
(1.00)
11p gain 94 (18%) 421 0.0608
(0.525) 		0.276
(0.816) 		0.457
(0.911) 		0.228
(0.762) 		0.127
(0.648) 		0.786
(1.00) 		0.0863
(0.576) 		0.187
(0.739) 		0.396
(0.868) 		0.344
(0.848) 		0.0124
(0.322) 		0.292
(0.827) 		0.948
(1.00) 		0.952
(1.00) 		1
(1.00)
11q gain 114 (22%) 401 0.191
(0.739) 		0.0462
(0.502) 		0.518
(0.946) 		0.849
(1.00) 		0.447
(0.908) 		0.0716
(0.548) 		0.137
(0.673) 		0.861
(1.00) 		0.524
(0.948) 		0.111
(0.615) 		0.048
(0.502) 		0.249
(0.786) 		0.958
(1.00) 		0.222
(0.762) 		0.659
(0.977)
12p gain 137 (27%) 378 0.0764
(0.558) 		0.0679
(0.535) 		0.0301
(0.428) 		0.785
(1.00) 		0.233
(0.763) 		0.155
(0.702) 		0.231
(0.762) 		0.865
(1.00) 		0.725
(0.979) 		0.692
(0.979) 		0.153
(0.702) 		0.13
(0.653) 		0.722
(0.979) 		0.545
(0.959) 		0.683
(0.979)
12q gain 130 (25%) 385 0.119
(0.629) 		0.208
(0.748) 		0.201
(0.746) 		0.596
(0.96) 		0.273
(0.815) 		0.232
(0.762) 		0.416
(0.885) 		0.609
(0.961) 		0.962
(1.00) 		0.596
(0.96) 		0.676
(0.979) 		0.0145
(0.343) 		0.708
(0.979) 		0.599
(0.96) 		0.671
(0.979)
13q gain 44 (9%) 471 0.93
(1.00) 		0.579
(0.96) 		0.00765
(0.311) 		0.342
(0.848) 		0.474
(0.917) 		0.00784
(0.311) 		1
(1.00) 		0.423
(0.89) 		0.0866
(0.576) 		0.971
(1.00) 		0.24
(0.773) 		0.217
(0.762) 		0.227
(0.762) 		1
(1.00) 		0.421
(0.889)
14q gain 130 (25%) 385 0.585
(0.96) 		0.41
(0.88) 		0.762
(0.995) 		0.856
(1.00) 		0.383
(0.865) 		0.452
(0.909) 		0.188
(0.739) 		0.501
(0.943) 		0.00173
(0.278) 		0.52
(0.947) 		0.347
(0.848) 		0.201
(0.746) 		0.269
(0.815) 		0.632
(0.972) 		1
(1.00)
15q gain 38 (7%) 477 0.0089
(0.313) 		0.53
(0.949) 		0.0255
(0.398) 		0.383
(0.865) 		0.016
(0.344) 		0.474
(0.917) 		0.312
(0.842) 		0.767
(0.995) 		0.0589
(0.525) 		0.0544
(0.525) 		0.42
(0.887) 		0.832
(1.00) 		0.561
(0.96) 		0.501
(0.943) 		1
(1.00)
16p gain 131 (25%) 384 0.623
(0.968) 		0.547
(0.96) 		0.379
(0.865) 		0.47
(0.916) 		0.988
(1.00) 		0.0938
(0.581) 		1
(1.00) 		0.738
(0.986) 		0.26
(0.806) 		0.0736
(0.548) 		0.345
(0.848) 		0.991
(1.00) 		0.961
(1.00) 		0.284
(0.826) 		0.197
(0.742)
16q gain 99 (19%) 416 0.946
(1.00) 		0.248
(0.786) 		0.427
(0.892) 		0.391
(0.865) 		0.986
(1.00) 		0.598
(0.96) 		0.575
(0.96) 		1
(1.00) 		0.721
(0.979) 		0.0601
(0.525) 		0.166
(0.718) 		0.333
(0.848) 		0.596
(0.96) 		0.265
(0.81) 		0.353
(0.853)
17q gain 191 (37%) 324 0.376
(0.862) 		0.0641
(0.535) 		0.165
(0.716) 		0.454
(0.911) 		0.198
(0.742) 		0.204
(0.746) 		0.784
(1.00) 		0.363
(0.857) 		0.0374
(0.484) 		0.194
(0.739) 		0.00413
(0.311) 		0.547
(0.96) 		0.0194
(0.37) 		0.0455
(0.502) 		0.702
(0.979)
18p gain 91 (18%) 424 0.0611
(0.525) 		0.364
(0.857) 		0.368
(0.857) 		0.798
(1.00) 		0.985
(1.00) 		0.592
(0.96) 		0.299
(0.833) 		1
(1.00) 		0.306
(0.833) 		0.693
(0.979) 		0.00225
(0.278) 		0.646
(0.973) 		0.599
(0.96) 		0.0463
(0.502) 		0.36
(0.857)
18q gain 69 (13%) 446 0.529
(0.948) 		0.0587
(0.525) 		0.354
(0.853) 		0.612
(0.963) 		0.981
(1.00) 		0.553
(0.96) 		0.154
(0.702) 		0.83
(1.00) 		0.208
(0.748) 		0.46
(0.912) 		0.00698
(0.311) 		0.337
(0.848) 		0.0664
(0.535) 		0.11
(0.61) 		0.6
(0.96)
19p gain 30 (6%) 485 0.877
(1.00) 		0.92
(1.00) 		0.545
(0.959) 		0.178
(0.726) 		0.502
(0.943) 		0.228
(0.762) 		0.265
(0.81) 		0.536
(0.956) 		0.593
(0.96) 		0.00609
(0.311) 		0.0693
(0.54) 		0.834
(1.00) 		0.443
(0.908) 		1
(1.00) 		0.374
(0.862)
19q gain 75 (15%) 440 0.203
(0.746) 		0.799
(1.00) 		0.446
(0.908) 		0.237
(0.77) 		0.391
(0.865) 		0.391
(0.865) 		0.046
(0.502) 		1
(1.00) 		0.275
(0.816) 		0.0634
(0.535) 		0.142
(0.679) 		0.976
(1.00) 		0.839
(1.00) 		0.709
(0.979) 		0.295
(0.827)
20p gain 172 (33%) 343 0.352
(0.853) 		0.176
(0.725) 		0.631
(0.972) 		0.334
(0.848) 		0.142
(0.677) 		1
(1.00) 		0.512
(0.945) 		0.64
(0.972) 		0.0406
(0.502) 		0.158
(0.702) 		0.00682
(0.311) 		0.181
(0.736) 		0.352
(0.853) 		0.0541
(0.525) 		0.101
(0.606)
21q gain 96 (19%) 419 0.171
(0.725) 		0.303
(0.833) 		0.0864
(0.576) 		0.551
(0.96) 		0.0722
(0.548) 		1
(1.00) 		0.0311
(0.428) 		1
(1.00) 		0.731
(0.981) 		0.538
(0.957) 		0.116
(0.627) 		0.282
(0.824) 		1
(1.00) 		0.389
(0.865) 		0.358
(0.856)
22q gain 62 (12%) 453 0.105
(0.608) 		0.0371
(0.484) 		0.562
(0.96) 		0.342
(0.848) 		0.459
(0.912) 		0.752
(0.992) 		0.135
(0.665) 		0.369
(0.857) 		0.195
(0.739) 		0.339
(0.848) 		0.368
(0.857) 		0.157
(0.702) 		0.36
(0.857) 		0.599
(0.96) 		0.58
(0.96)
xp gain 51 (10%) 464 0.304
(0.833) 		0.939
(1.00) 		0.0152
(0.344) 		0.0787
(0.559) 		0.106
(0.608) 		0.0067
(0.311) 		0.376
(0.862) 		0.434
(0.896) 		0.0912
(0.579) 		0.868
(1.00) 		0.0046
(0.311) 		0.108
(0.608) 		0.395
(0.867) 		0.837
(1.00) 		1
(1.00)
xq gain 83 (16%) 432 0.856
(1.00) 		0.919
(1.00) 		0.325
(0.848) 		0.392
(0.865) 		0.936
(1.00) 		0.047
(0.502) 		0.337
(0.848) 		0.202
(0.746) 		0.448
(0.908) 		0.225
(0.762) 		0.0246
(0.398) 		0.207
(0.748) 		0.916
(1.00) 		0.894
(1.00) 		0.6
(0.96)
1p loss 82 (16%) 433 0.305
(0.833) 		0.89
(1.00) 		0.0443
(0.502) 		0.0875
(0.576) 		0.00812
(0.311) 		1
(1.00) 		0.399
(0.869) 		0.559
(0.96) 		0.489
(0.935) 		0.645
(0.973) 		0.977
(1.00) 		0.783
(1.00) 		0.475
(0.917) 		0.845
(1.00) 		0.288
(0.827)
1q loss 33 (6%) 482 0.329
(0.848) 		0.859
(1.00) 		0.7
(0.979) 		0.985
(1.00) 		0.291
(0.827) 		1
(1.00) 		0.858
(1.00) 		0.781
(1.00) 		0.919
(1.00) 		0.573
(0.96) 		0.528
(0.948) 		0.601
(0.96) 		1
(1.00) 		1
(1.00) 		0.0733
(0.548)
2p loss 28 (5%) 487 0.928
(1.00) 		0.0678
(0.535) 		0.555
(0.96) 		0.514
(0.945) 		0.466
(0.914) 		1
(1.00) 		0.25
(0.786) 		0.335
(0.848) 		0.499
(0.943) 		0.608
(0.961) 		0.195
(0.739) 		0.456
(0.911) 		0.711
(0.979) 		0.474
(0.917) 		0.311
(0.842)
2q loss 29 (6%) 486 0.0825
(0.574) 		0.0922
(0.579) 		0.571
(0.96) 		0.837
(1.00) 		0.708
(0.979) 		1
(1.00) 		0.444
(0.908) 		0.343
(0.848) 		0.0624
(0.533) 		0.188
(0.739) 		0.0479
(0.502) 		0.194
(0.739) 		1
(1.00) 		0.427
(0.892) 		0.324
(0.848)
3p loss 212 (41%) 303 0.964
(1.00) 		0.129
(0.653) 		0.627
(0.969) 		0.0316
(0.428) 		0.376
(0.862) 		1
(1.00) 		1
(1.00) 		0.883
(1.00) 		0.882
(1.00) 		0.13
(0.653) 		0.191
(0.739) 		0.0419
(0.502) 		0.107
(0.608) 		0.959
(1.00) 		0.704
(0.979)
3q loss 146 (28%) 369 0.226
(0.762) 		0.0575
(0.525) 		0.305
(0.833) 		0.777
(1.00) 		0.0445
(0.502) 		0.653
(0.976) 		0.696
(0.979) 		0.263
(0.81) 		0.361
(0.857) 		0.507
(0.945) 		0.0466
(0.502) 		0.0113
(0.313) 		0.355
(0.853) 		0.699
(0.979) 		0.109
(0.608)
4p loss 123 (24%) 392 0.695
(0.979) 		0.157
(0.702) 		0.502
(0.943) 		0.983
(1.00) 		0.219
(0.762) 		0.811
(1.00) 		0.757
(0.992) 		0.31
(0.842) 		0.131
(0.653) 		0.277
(0.816) 		0.386
(0.865) 		0.0719
(0.548) 		0.558
(0.96) 		0.637
(0.972) 		1
(1.00)
4q loss 140 (27%) 375 0.792
(1.00) 		0.103
(0.608) 		0.312
(0.842) 		0.983
(1.00) 		0.00835
(0.311) 		0.641
(0.972) 		0.921
(1.00) 		0.192
(0.739) 		0.188
(0.739) 		0.327
(0.848) 		0.575
(0.96) 		0.132
(0.655) 		0.408
(0.88) 		0.781
(1.00) 		1
(1.00)
5p loss 52 (10%) 463 0.342
(0.848) 		0.0562
(0.525) 		0.618
(0.966) 		0.674
(0.979) 		0.365
(0.857) 		1
(1.00) 		0.0564
(0.525) 		1
(1.00) 		0.789
(1.00) 		0.405
(0.878) 		0.643
(0.973) 		0.0193
(0.37) 		1
(1.00) 		0.341
(0.848) 		0.169
(0.72)
6p loss 106 (21%) 409 0.16
(0.703) 		0.329
(0.848) 		0.246
(0.782) 		0.0847
(0.576) 		0.298
(0.831) 		0.797
(1.00) 		1
(1.00) 		0.857
(1.00) 		0.584
(0.96) 		0.802
(1.00) 		0.0162
(0.344) 		0.211
(0.756) 		0.935
(1.00) 		1
(1.00) 		0.639
(0.972)
6q loss 216 (42%) 299 0.893
(1.00) 		0.158
(0.702) 		0.744
(0.99) 		0.522
(0.948) 		0.712
(0.979) 		1
(1.00) 		0.591
(0.96) 		0.658
(0.977) 		0.553
(0.96) 		0.866
(1.00) 		0.159
(0.702) 		0.0675
(0.535) 		0.669
(0.979) 		0.94
(1.00) 		1
(1.00)
7p loss 39 (8%) 476 0.544
(0.959) 		0.339
(0.848) 		0.989
(1.00) 		0.884
(1.00) 		0.907
(1.00) 		0.712
(0.979) 		0.243
(0.776) 		0.603
(0.96) 		0.266
(0.81) 		0.88
(1.00) 		0.194
(0.739) 		0.118
(0.629) 		0.694
(0.979) 		0.632
(0.972) 		0.465
(0.914)
7q loss 47 (9%) 468 0.387
(0.865) 		0.756
(0.992) 		0.528
(0.948) 		0.838
(1.00) 		0.432
(0.895) 		0.0922
(0.579) 		0.878
(1.00) 		0.14
(0.677) 		0.429
(0.894) 		0.868
(1.00) 		0.824
(1.00) 		0.144
(0.68) 		1
(1.00) 		0.231
(0.762) 		0.506
(0.945)
8p loss 202 (39%) 313 0.779
(1.00) 		0.865
(1.00) 		0.362
(0.857) 		0.633
(0.972) 		0.852
(1.00) 		0.394
(0.867) 		0.0302
(0.428) 		0.881
(1.00) 		0.876
(1.00) 		0.022
(0.375) 		0.608
(0.961) 		0.929
(1.00) 		0.155
(0.702) 		0.593
(0.96) 		0.12
(0.632)
8q loss 60 (12%) 455 0.462
(0.914) 		0.694
(0.979) 		0.433
(0.896) 		0.334
(0.848) 		0.419
(0.887) 		0.753
(0.992) 		0.492
(0.936) 		1
(1.00) 		0.346
(0.848) 		0.104
(0.608) 		0.99
(1.00) 		0.366
(0.857) 		0.702
(0.979) 		0.191
(0.739) 		0.589
(0.96)
9p loss 270 (52%) 245 0.204
(0.746) 		0.29
(0.827) 		0.523
(0.948) 		0.665
(0.979) 		0.0316
(0.428) 		0.838
(1.00) 		0.0773
(0.559) 		0.188
(0.739) 		0.0425
(0.502) 		0.781
(1.00) 		0.756
(0.992) 		0.957
(1.00) 		0.948
(1.00) 		0.416
(0.885) 		1
(1.00)
9q loss 254 (49%) 261 0.928
(1.00) 		0.672
(0.979) 		0.839
(1.00) 		0.456
(0.911) 		0.277
(0.816) 		0.681
(0.979) 		0.93
(1.00) 		0.382
(0.865) 		0.238
(0.77) 		0.489
(0.935) 		0.231
(0.762) 		0.59
(0.96) 		1
(1.00) 		0.466
(0.914) 		0.724
(0.979)
10p loss 114 (22%) 401 0.108
(0.608) 		0.836
(1.00) 		0.9
(1.00) 		0.222
(0.762) 		0.617
(0.966) 		1
(1.00) 		0.00566
(0.311) 		0.0579
(0.525) 		0.419
(0.887) 		0.0327
(0.432) 		0.986
(1.00) 		0.788
(1.00) 		0.689
(0.979) 		0.0456
(0.502) 		0.204
(0.746)
10q loss 136 (26%) 379 0.0454
(0.502) 		0.273
(0.815) 		0.649
(0.975) 		0.113
(0.62) 		0.603
(0.96) 		0.251
(0.787) 		0.0449
(0.502) 		0.511
(0.945) 		0.386
(0.865) 		0.0272
(0.407) 		0.345
(0.848) 		0.577
(0.96) 		0.391
(0.865) 		0.119
(0.629) 		0.0831
(0.574)
11p loss 116 (23%) 399 0.692
(0.979) 		0.018
(0.363) 		0.0855
(0.576) 		0.26
(0.806) 		0.214
(0.758) 		0.47
(0.916) 		0.00209
(0.278) 		0.295
(0.827) 		0.327
(0.848) 		0.297
(0.831) 		0.867
(1.00) 		0.0527
(0.521) 		0.279
(0.82) 		0.388
(0.865) 		0.00989
(0.313)
11q loss 91 (18%) 424 0.71
(0.979) 		0.355
(0.853) 		0.266
(0.81) 		0.737
(0.985) 		0.969
(1.00) 		0.797
(1.00) 		0.00781
(0.311) 		0.851
(1.00) 		0.719
(0.979) 		0.601
(0.96) 		0.882
(1.00) 		0.239
(0.772) 		0.416
(0.885) 		0.573
(0.96) 		0.618
(0.966)
12p loss 114 (22%) 401 0.925
(1.00) 		0.0843
(0.576) 		0.717
(0.979) 		0.859
(1.00) 		0.843
(1.00) 		0.438
(0.902) 		0.00286
(0.278) 		0.609
(0.961) 		0.588
(0.96) 		0.654
(0.976) 		0.0649
(0.535) 		0.562
(0.96) 		0.792
(1.00) 		0.319
(0.848) 		0.684
(0.979)
12q loss 102 (20%) 413 0.677
(0.979) 		0.162
(0.708) 		0.777
(1.00) 		0.75
(0.992) 		0.71
(0.979) 		0.781
(1.00) 		0.00564
(0.311) 		0.6
(0.96) 		0.266
(0.81) 		0.534
(0.954) 		0.00963
(0.313) 		0.439
(0.902) 		0.743
(0.989) 		0.255
(0.794) 		0.65
(0.975)
13q loss 257 (50%) 258 0.829
(1.00) 		0.127
(0.648) 		0.655
(0.976) 		0.518
(0.946) 		0.316
(0.846) 		0.301
(0.833) 		0.659
(0.977) 		0.885
(1.00) 		0.881
(1.00) 		0.7
(0.979) 		0.092
(0.579) 		0.168
(0.72) 		0.793
(1.00) 		0.324
(0.848) 		0.45
(0.908)
14q loss 114 (22%) 401 0.944
(1.00) 		0.0517
(0.521) 		0.571
(0.96) 		0.292
(0.827) 		0.0282
(0.418) 		0.81
(1.00) 		0.338
(0.848) 		0.502
(0.943) 		0.0113
(0.313) 		0.872
(1.00) 		0.249
(0.786) 		0.541
(0.959) 		0.184
(0.739) 		0.0567
(0.525) 		0.671
(0.979)
15q loss 241 (47%) 274 0.339
(0.848) 		0.00152
(0.278) 		0.913
(1.00) 		0.878
(1.00) 		0.801
(1.00) 		0.542
(0.959) 		0.288
(0.827) 		0.143
(0.68) 		0.141
(0.677) 		0.0131
(0.322) 		0.592
(0.96) 		0.291
(0.827) 		0.925
(1.00) 		0.714
(0.979) 		1
(1.00)
16p loss 117 (23%) 398 0.636
(0.972) 		0.526
(0.948) 		0.0875
(0.576) 		0.384
(0.865) 		0.13
(0.653) 		0.47
(0.916) 		0.399
(0.869) 		1
(1.00) 		0.576
(0.96) 		0.683
(0.979) 		0.713
(0.979) 		0.626
(0.969) 		0.75
(0.992) 		1
(1.00) 		0.053
(0.521)
16q loss 144 (28%) 371 0.883
(1.00) 		0.362
(0.857) 		0.712
(0.979) 		0.986
(1.00) 		0.4
(0.87) 		1
(1.00) 		0.491
(0.936) 		1
(1.00) 		0.944
(1.00) 		0.599
(0.96) 		0.674
(0.979) 		0.777
(1.00) 		0.434
(0.896) 		0.94
(1.00) 		0.0204
(0.37)
17p loss 216 (42%) 299 0.68
(0.979) 		0.216
(0.762) 		0.283
(0.824) 		0.397
(0.868) 		0.783
(1.00) 		0.676
(0.979) 		0.0605
(0.525) 		0.141
(0.677) 		0.415
(0.885) 		0.161
(0.703) 		0.013
(0.322) 		0.0252
(0.398) 		0.724
(0.979) 		0.905
(1.00) 		0.0203
(0.37)
17q loss 57 (11%) 458 0.356
(0.854) 		0.996
(1.00) 		0.0566
(0.525) 		0.0269
(0.407) 		0.252
(0.787) 		1
(1.00) 		0.328
(0.848) 		0.655
(0.976) 		0.0739
(0.548) 		0.922
(1.00) 		0.229
(0.762) 		0.0242
(0.398) 		0.856
(1.00) 		0.796
(1.00) 		0.182
(0.738)
18p loss 177 (34%) 338 0.57
(0.96) 		0.107
(0.608) 		0.0127
(0.322) 		0.385
(0.865) 		0.1
(0.605) 		0.118
(0.629) 		0.0255
(0.398) 		1
(1.00) 		0.955
(1.00) 		0.563
(0.96) 		0.0767
(0.558) 		0.0108
(0.313) 		0.107
(0.608) 		0.168
(0.72) 		1
(1.00)
18q loss 212 (41%) 303 0.0693
(0.54) 		0.418
(0.887) 		0.0103
(0.313) 		0.346
(0.848) 		0.0515
(0.521) 		0.206
(0.748) 		0.0595
(0.525) 		1
(1.00) 		0.718
(0.979) 		0.634
(0.972) 		0.158
(0.702) 		0.177
(0.725) 		0.0114
(0.313) 		0.847
(1.00) 		1
(1.00)
19p loss 247 (48%) 268 0.195
(0.739) 		0.0502
(0.519) 		0.589
(0.96) 		0.514
(0.945) 		0.295
(0.827) 		0.409
(0.88) 		0.027
(0.407) 		0.466
(0.914) 		0.89
(1.00) 		0.826
(1.00) 		0.725
(0.979) 		0.374
(0.862) 		0.106
(0.608) 		0.809
(1.00) 		1
(1.00)
19q loss 160 (31%) 355 0.511
(0.945) 		0.117
(0.627) 		0.293
(0.827) 		0.383
(0.865) 		0.339
(0.848) 		0.272
(0.815) 		0.567
(0.96) 		0.875
(1.00) 		0.578
(0.96) 		0.381
(0.865) 		0.765
(0.995) 		0.803
(1.00) 		0.199
(0.742) 		0.399
(0.869) 		1
(1.00)
20p loss 113 (22%) 402 0.27
(0.815) 		0.369
(0.857) 		0.123
(0.639) 		0.282
(0.824) 		0.0607
(0.525) 		1
(1.00) 		0.456
(0.911) 		0.73
(0.981) 		0.104
(0.608) 		0.317
(0.846) 		0.094
(0.581) 		0.518
(0.946) 		0.816
(1.00) 		0.295
(0.827) 		1
(1.00)
20q loss 69 (13%) 446 0.551
(0.96) 		0.61
(0.961) 		0.34
(0.848) 		0.411
(0.88) 		0.316
(0.846) 		1
(1.00) 		1
(1.00) 		0.538
(0.957) 		0.0154
(0.344) 		0.0949
(0.583) 		0.466
(0.914) 		0.66
(0.977) 		0.684
(0.979) 		0.15
(0.702) 		0.23
(0.762)
21q loss 167 (32%) 348 0.971
(1.00) 		0.153
(0.702) 		0.78
(1.00) 		0.551
(0.96) 		0.96
(1.00) 		0.664
(0.979) 		0.132
(0.655) 		0.159
(0.702) 		0.0516
(0.521) 		0.0102
(0.313) 		0.755
(0.992) 		0.0322
(0.43) 		0.559
(0.96) 		0.189
(0.739) 		1
(1.00)
22q loss 217 (42%) 298 0.728
(0.979) 		0.00272
(0.278) 		0.863
(1.00) 		0.916
(1.00) 		0.845
(1.00) 		1
(1.00) 		0.245
(0.781) 		0.459
(0.912) 		0.015
(0.344) 		0.272
(0.815) 		0.973
(1.00) 		0.0139
(0.336) 		0.818
(1.00) 		0.276
(0.816) 		1
(1.00)
xp loss 104 (20%) 411 0.756
(0.992) 		0.977
(1.00) 		0.524
(0.948) 		0.794
(1.00) 		0.242
(0.776) 		0.318
(0.848) 		0.155
(0.702) 		1
(1.00) 		0.863
(1.00) 		0.728
(0.979) 		0.116
(0.627) 		0.123
(0.639) 		0.759
(0.994) 		0.429
(0.894) 		0.353
(0.853)
xq loss 62 (12%) 453 0.644
(0.973) 		0.334
(0.848) 		0.326
(0.848) 		0.877
(1.00) 		0.721
(0.979) 		0.225
(0.762) 		0.0582
(0.525) 		0.184
(0.739) 		0.7
(0.979) 		0.172
(0.725) 		0.207
(0.748) 		0.14
(0.677) 		0.722
(0.979) 		0.159
(0.702) 		1
(1.00)
'1p gain' versus 'PATHOLOGY_N_STAGE'

P value = 8e-04 (Fisher's exact test), Q value = 0.2

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

nPatients N0 N1 N2+N3
ALL 332 96 76
1P GAIN MUTATED 88 43 16
1P GAIN WILD-TYPE 244 53 60

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 = 0.00083 (Fisher's exact test), Q value = 0.2

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

nPatients N0 N1 N2+N3
ALL 332 96 76
7P GAIN MUTATED 153 46 53
7P GAIN WILD-TYPE 179 50 23

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

'17p gain' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 2.41e-05 (Wilcoxon-test), Q value = 0.03

Table S3.  Gene #30: '17p gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 355 41.6 (27.3)
17P GAIN MUTATED 56 55.3 (30.8)
17P GAIN WILD-TYPE 299 39.0 (25.9)

Figure S3.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'20q gain' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.000132 (Wilcoxon-test), Q value = 0.081

Table S4.  Gene #37: '20q gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 355 41.6 (27.3)
20Q GAIN MUTATED 142 47.5 (27.9)
20Q GAIN WILD-TYPE 213 37.7 (26.2)

Figure S4.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'5q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000456 (Wilcoxon-test), Q value = 0.19

Table S5.  Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 484 65.2 (10.0)
5Q LOSS MUTATED 145 62.7 (10.0)
5Q LOSS WILD-TYPE 339 66.3 (9.8)

Figure S5.  Get High-res Image Gene #51: '5q 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/19782226/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LUAD-TP/19775350/LUAD-TP.merged_data.txt

  • Number of patients = 515

  • 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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle