Correlation between copy number variations of arm-level result and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1M0442Q
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/C1M0442Q
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 461 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 78 (17%) 383 0.087
(1.00) 		0.0177
(1.00) 		0.302
(1.00) 		0.52
(1.00) 		0.237
(1.00) 		0.217
(1.00) 		0.105
(1.00) 		0.625
(1.00) 		0.548
(1.00) 		0.144
(1.00) 		0.000166
(0.173) 		0.589
(1.00) 		0.177
(1.00)
19p gain 29 (6%) 432 0.209
(1.00) 		0.478
(1.00) 		0.731
(1.00) 		0.136
(1.00) 		0.527
(1.00) 		0.299
(1.00) 		0.341
(1.00) 		0.68
(1.00) 		0.000182
(0.189) 		1
(1.00) 		0.218
(1.00) 		0.926
(1.00) 		0.681
(1.00)
1p gain 123 (27%) 338 0.781
(1.00) 		0.00383
(1.00) 		0.73
(1.00) 		0.759
(1.00) 		0.0295
(1.00) 		0.548
(1.00) 		0.752
(1.00) 		0.542
(1.00) 		0.589
(1.00) 		0.614
(1.00) 		0.869
(1.00) 		0.622
(1.00) 		0.518
(1.00)
1q gain 271 (59%) 190 0.689
(1.00) 		0.193
(1.00) 		0.728
(1.00) 		0.752
(1.00) 		0.452
(1.00) 		0.598
(1.00) 		0.297
(1.00) 		0.381
(1.00) 		0.196
(1.00) 		0.365
(1.00) 		0.924
(1.00) 		0.69
(1.00) 		0.696
(1.00)
2p gain 142 (31%) 319 0.313
(1.00) 		0.0486
(1.00) 		0.859
(1.00) 		0.902
(1.00) 		0.355
(1.00) 		0.857
(1.00) 		0.614
(1.00) 		0.474
(1.00) 		0.485
(1.00) 		0.63
(1.00) 		0.246
(1.00) 		0.181
(1.00) 		0.517
(1.00)
2q gain 128 (28%) 333 0.43
(1.00) 		0.7
(1.00) 		0.758
(1.00) 		0.95
(1.00) 		0.393
(1.00) 		0.882
(1.00) 		0.755
(1.00) 		0.35
(1.00) 		0.522
(1.00) 		0.806
(1.00) 		0.163
(1.00) 		0.58
(1.00) 		0.691
(1.00)
3p gain 36 (8%) 425 0.786
(1.00) 		0.534
(1.00) 		0.819
(1.00) 		0.234
(1.00) 		0.173
(1.00) 		0.954
(1.00) 		1
(1.00) 		0.279
(1.00) 		0.581
(1.00) 		0.22
(1.00) 		0.311
(1.00) 		0.286
(1.00) 		0.0274
(1.00)
3q gain 77 (17%) 384 0.37
(1.00) 		0.816
(1.00) 		0.74
(1.00) 		0.815
(1.00) 		0.583
(1.00) 		0.793
(1.00) 		1
(1.00) 		0.305
(1.00) 		0.747
(1.00) 		0.765
(1.00) 		0.192
(1.00) 		0.358
(1.00) 		0.251
(1.00)
4p gain 76 (16%) 385 0.879
(1.00) 		0.0105
(1.00) 		0.0214
(1.00) 		0.4
(1.00) 		0.522
(1.00) 		0.613
(1.00) 		0.9
(1.00) 		0.437
(1.00) 		0.336
(1.00) 		0.551
(1.00) 		0.197
(1.00) 		0.922
(1.00) 		1
(1.00)
4q gain 44 (10%) 417 0.111
(1.00) 		0.4
(1.00) 		0.0065
(1.00) 		0.267
(1.00) 		0.946
(1.00) 		0.973
(1.00) 		0.635
(1.00) 		0.68
(1.00) 		0.496
(1.00) 		0.709
(1.00) 		0.089
(1.00) 		0.725
(1.00) 		0.844
(1.00)
5p gain 253 (55%) 208 0.156
(1.00) 		0.0756
(1.00) 		0.183
(1.00) 		0.0888
(1.00) 		0.913
(1.00) 		0.463
(1.00) 		0.111
(1.00) 		0.201
(1.00) 		0.316
(1.00) 		0.37
(1.00) 		0.015
(1.00) 		0.272
(1.00) 		0.486
(1.00)
5q gain 112 (24%) 349 0.818
(1.00) 		0.697
(1.00) 		0.982
(1.00) 		0.396
(1.00) 		0.627
(1.00) 		0.711
(1.00) 		0.0385
(1.00) 		0.475
(1.00) 		0.376
(1.00) 		0.189
(1.00) 		0.682
(1.00) 		0.956
(1.00) 		0.95
(1.00)
6p gain 131 (28%) 330 0.17
(1.00) 		0.446
(1.00) 		0.256
(1.00) 		0.371
(1.00) 		0.289
(1.00) 		0.299
(1.00) 		0.836
(1.00) 		0.793
(1.00) 		0.586
(1.00) 		0.806
(1.00) 		0.657
(1.00) 		0.645
(1.00) 		0.458
(1.00)
6q gain 56 (12%) 405 0.406
(1.00) 		0.271
(1.00) 		0.84
(1.00) 		0.993
(1.00) 		0.831
(1.00) 		0.721
(1.00) 		0.669
(1.00) 		0.369
(1.00) 		0.94
(1.00) 		0.494
(1.00) 		0.826
(1.00) 		0.689
(1.00) 		0.738
(1.00)
7p gain 241 (52%) 220 0.341
(1.00) 		0.0526
(1.00) 		0.405
(1.00) 		0.33
(1.00) 		0.00184
(1.00) 		0.693
(1.00) 		0.852
(1.00) 		0.761
(1.00) 		0.0966
(1.00) 		0.503
(1.00) 		0.124
(1.00) 		0.348
(1.00) 		0.803
(1.00)
7q gain 199 (43%) 262 0.943
(1.00) 		0.00475
(1.00) 		0.268
(1.00) 		0.806
(1.00) 		0.00611
(1.00) 		0.335
(1.00) 		0.851
(1.00) 		0.993
(1.00) 		0.2
(1.00) 		0.259
(1.00) 		0.29
(1.00) 		0.592
(1.00) 		0.411
(1.00)
8p gain 115 (25%) 346 0.639
(1.00) 		0.0584
(1.00) 		0.66
(1.00) 		0.108
(1.00) 		0.829
(1.00) 		0.969
(1.00) 		0.00684
(1.00) 		0.262
(1.00) 		0.825
(1.00) 		0.437
(1.00) 		0.492
(1.00) 		0.18
(1.00) 		0.208
(1.00)
8q gain 222 (48%) 239 0.042
(1.00) 		0.0253
(1.00) 		0.935
(1.00) 		0.281
(1.00) 		0.151
(1.00) 		0.783
(1.00) 		0.455
(1.00) 		0.863
(1.00) 		0.0443
(1.00) 		0.824
(1.00) 		0.951
(1.00) 		0.0911
(1.00) 		0.627
(1.00)
9p gain 40 (9%) 421 0.211
(1.00) 		0.531
(1.00) 		0.818
(1.00) 		0.189
(1.00) 		0.386
(1.00) 		0.624
(1.00) 		0.32
(1.00) 		0.419
(1.00) 		0.145
(1.00) 		0.702
(1.00) 		0.669
(1.00) 		0.619
(1.00) 		0.35
(1.00)
9q gain 28 (6%) 433 0.106
(1.00) 		0.478
(1.00) 		0.287
(1.00) 		0.688
(1.00) 		0.956
(1.00) 		0.292
(1.00) 		0.845
(1.00) 		0.794
(1.00) 		0.993
(1.00) 		1
(1.00) 		0.386
(1.00) 		0.894
(1.00) 		1
(1.00)
10p gain 101 (22%) 360 0.747
(1.00) 		0.11
(1.00) 		0.636
(1.00) 		0.12
(1.00) 		0.0266
(1.00) 		0.666
(1.00) 		0.00151
(1.00) 		0.412
(1.00) 		0.698
(1.00) 		0.277
(1.00) 		0.223
(1.00) 		0.789
(1.00) 		0.15
(1.00)
10q gain 73 (16%) 388 0.916
(1.00) 		0.166
(1.00) 		0.491
(1.00) 		0.185
(1.00) 		0.0422
(1.00) 		0.163
(1.00) 		0.00474
(1.00) 		0.119
(1.00) 		0.516
(1.00) 		0.552
(1.00) 		0.871
(1.00) 		0.787
(1.00) 		0.618
(1.00)
11p gain 88 (19%) 373 0.417
(1.00) 		0.856
(1.00) 		0.352
(1.00) 		0.358
(1.00) 		0.111
(1.00) 		0.788
(1.00) 		0.0436
(1.00) 		0.452
(1.00) 		0.577
(1.00) 		0.778
(1.00) 		0.154
(1.00) 		0.358
(1.00) 		0.969
(1.00)
11q gain 108 (23%) 353 0.822
(1.00) 		0.0326
(1.00) 		0.454
(1.00) 		0.647
(1.00) 		0.587
(1.00) 		0.469
(1.00) 		0.321
(1.00) 		0.305
(1.00) 		0.343
(1.00) 		0.599
(1.00) 		0.0638
(1.00) 		0.154
(1.00) 		1
(1.00)
12p gain 126 (27%) 335 0.299
(1.00) 		0.0162
(1.00) 		0.086
(1.00) 		0.96
(1.00) 		0.611
(1.00) 		0.513
(1.00) 		0.116
(1.00) 		0.974
(1.00) 		0.502
(1.00) 		0.807
(1.00) 		0.154
(1.00) 		0.0559
(1.00) 		0.414
(1.00)
12q gain 120 (26%) 341 0.957
(1.00) 		0.0837
(1.00) 		0.692
(1.00) 		0.894
(1.00) 		0.742
(1.00) 		0.324
(1.00) 		0.244
(1.00) 		0.841
(1.00) 		0.523
(1.00) 		1
(1.00) 		0.394
(1.00) 		0.00225
(1.00) 		0.378
(1.00)
13q gain 42 (9%) 419 0.563
(1.00) 		0.706
(1.00) 		0.0675
(1.00) 		0.487
(1.00) 		0.398
(1.00) 		0.0164
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.973
(1.00) 		1
(1.00) 		0.316
(1.00) 		0.419
(1.00) 		0.39
(1.00)
14q gain 112 (24%) 349 0.105
(1.00) 		0.219
(1.00) 		0.95
(1.00) 		0.975
(1.00) 		0.235
(1.00) 		0.00477
(1.00) 		0.447
(1.00) 		0.262
(1.00) 		0.63
(1.00) 		0.124
(1.00) 		0.123
(1.00) 		0.509
(1.00) 		0.38
(1.00)
15q gain 34 (7%) 427 0.181
(1.00) 		0.977
(1.00) 		0.00338
(1.00) 		0.646
(1.00) 		0.0278
(1.00) 		0.589
(1.00) 		0.285
(1.00) 		0.931
(1.00) 		0.235
(1.00) 		0.662
(1.00) 		0.629
(1.00) 		0.632
(1.00) 		0.891
(1.00)
16p gain 117 (25%) 344 0.376
(1.00) 		0.977
(1.00) 		0.775
(1.00) 		0.547
(1.00) 		0.578
(1.00) 		0.491
(1.00) 		0.915
(1.00) 		0.182
(1.00) 		0.355
(1.00) 		0.614
(1.00) 		0.182
(1.00) 		0.994
(1.00) 		0.737
(1.00)
16q gain 88 (19%) 373 0.223
(1.00) 		0.681
(1.00) 		0.663
(1.00) 		0.531
(1.00) 		0.81
(1.00) 		0.947
(1.00) 		0.635
(1.00) 		0.962
(1.00) 		0.233
(1.00) 		0.778
(1.00) 		0.147
(1.00) 		0.553
(1.00) 		0.608
(1.00)
17q gain 176 (38%) 285 0.512
(1.00) 		0.0856
(1.00) 		0.242
(1.00) 		0.32
(1.00) 		0.304
(1.00) 		0.473
(1.00) 		1
(1.00) 		0.438
(1.00) 		0.191
(1.00) 		1
(1.00) 		0.0332
(1.00) 		0.802
(1.00) 		0.0391
(1.00)
18p gain 88 (19%) 373 0.685
(1.00) 		0.306
(1.00) 		0.101
(1.00) 		0.832
(1.00) 		0.938
(1.00) 		0.504
(1.00) 		0.476
(1.00) 		0.528
(1.00) 		0.646
(1.00) 		0.778
(1.00) 		0.00401
(1.00) 		0.622
(1.00) 		0.701
(1.00)
18q gain 63 (14%) 398 0.373
(1.00) 		0.0519
(1.00) 		0.413
(1.00) 		0.97
(1.00) 		0.673
(1.00) 		0.757
(1.00) 		0.497
(1.00) 		0.211
(1.00) 		0.349
(1.00) 		0.753
(1.00) 		0.0107
(1.00) 		0.559
(1.00) 		0.0708
(1.00)
19q gain 66 (14%) 395 0.757
(1.00) 		0.873
(1.00) 		0.614
(1.00) 		0.134
(1.00) 		0.801
(1.00) 		0.878
(1.00) 		0.0073
(1.00) 		0.27
(1.00) 		0.267
(1.00) 		0.337
(1.00) 		0.0877
(1.00) 		0.971
(1.00) 		0.941
(1.00)
20p gain 155 (34%) 306 0.669
(1.00) 		0.937
(1.00) 		0.179
(1.00) 		0.306
(1.00) 		0.158
(1.00) 		0.143
(1.00) 		0.843
(1.00) 		0.165
(1.00) 		0.332
(1.00) 		1
(1.00) 		0.0406
(1.00) 		0.0353
(1.00) 		0.673
(1.00)
20q gain 178 (39%) 283 0.618
(1.00) 		0.172
(1.00) 		0.218
(1.00) 		0.265
(1.00) 		0.416
(1.00) 		0.275
(1.00) 		0.502
(1.00) 		0.0422
(1.00) 		0.264
(1.00) 		0.175
(1.00) 		0.00304
(1.00) 		0.371
(1.00) 		0.731
(1.00)
21q gain 85 (18%) 376 0.183
(1.00) 		0.504
(1.00) 		0.716
(1.00) 		0.846
(1.00) 		0.0721
(1.00) 		0.917
(1.00) 		0.0918
(1.00) 		0.447
(1.00) 		0.359
(1.00) 		1
(1.00) 		0.517
(1.00) 		0.678
(1.00) 		0.971
(1.00)
22q gain 60 (13%) 401 0.145
(1.00) 		0.228
(1.00) 		0.518
(1.00) 		0.297
(1.00) 		0.358
(1.00) 		0.597
(1.00) 		0.213
(1.00) 		0.382
(1.00) 		0.552
(1.00) 		0.501
(1.00) 		0.761
(1.00) 		0.138
(1.00) 		0.509
(1.00)
xq gain 66 (14%) 395 0.577
(1.00) 		0.798
(1.00) 		0.773
(1.00) 		0.623
(1.00) 		0.85
(1.00) 		0.716
(1.00) 		0.234
(1.00) 		0.32
(1.00) 		0.446
(1.00) 		1
(1.00) 		0.378
(1.00) 		0.327
(1.00) 		0.495
(1.00)
1p loss 75 (16%) 386 0.182
(1.00) 		0.565
(1.00) 		0.0242
(1.00) 		0.135
(1.00) 		0.0055
(1.00) 		0.208
(1.00) 		0.206
(1.00) 		0.823
(1.00) 		0.386
(1.00) 		0.761
(1.00) 		0.404
(1.00) 		0.394
(1.00) 		0.678
(1.00)
1q loss 28 (6%) 433 0.881
(1.00) 		0.444
(1.00) 		0.246
(1.00) 		1
(1.00) 		0.284
(1.00) 		0.379
(1.00) 		0.7
(1.00) 		0.325
(1.00) 		0.975
(1.00) 		0.128
(1.00) 		0.0597
(1.00) 		0.912
(1.00) 		0.809
(1.00)
2p loss 24 (5%) 437 0.525
(1.00) 		0.261
(1.00) 		0.0105
(1.00) 		0.763
(1.00) 		0.711
(1.00) 		0.961
(1.00) 		0.409
(1.00) 		0.986
(1.00) 		0.81
(1.00) 		1
(1.00) 		0.968
(1.00) 		0.799
(1.00) 		0.371
(1.00)
2q loss 23 (5%) 438 0.231
(1.00) 		0.91
(1.00) 		0.513
(1.00) 		0.845
(1.00) 		0.775
(1.00) 		0.877
(1.00) 		0.527
(1.00) 		0.597
(1.00) 		0.114
(1.00) 		0.615
(1.00) 		0.00314
(1.00) 		0.709
(1.00) 		0.757
(1.00)
3p loss 193 (42%) 268 0.292
(1.00) 		0.361
(1.00) 		0.456
(1.00) 		0.0536
(1.00) 		0.342
(1.00) 		0.686
(1.00) 		0.925
(1.00) 		0.184
(1.00) 		0.536
(1.00) 		1
(1.00) 		0.248
(1.00) 		0.0527
(1.00) 		0.153
(1.00)
3q loss 133 (29%) 328 0.258
(1.00) 		0.23
(1.00) 		0.593
(1.00) 		0.609
(1.00) 		0.0644
(1.00) 		0.388
(1.00) 		0.758
(1.00) 		0.144
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.138
(1.00) 		0.0409
(1.00) 		0.565
(1.00)
4p loss 107 (23%) 354 0.302
(1.00) 		0.183
(1.00) 		0.525
(1.00) 		0.971
(1.00) 		0.241
(1.00) 		0.819
(1.00) 		0.441
(1.00) 		0.185
(1.00) 		0.405
(1.00) 		0.597
(1.00) 		0.318
(1.00) 		0.0358
(1.00) 		0.201
(1.00)
4q loss 121 (26%) 340 0.998
(1.00) 		0.165
(1.00) 		0.126
(1.00) 		0.95
(1.00) 		0.0162
(1.00) 		0.724
(1.00) 		0.397
(1.00) 		0.0784
(1.00) 		0.457
(1.00) 		0.802
(1.00) 		0.267
(1.00) 		0.211
(1.00) 		0.152
(1.00)
5p loss 38 (8%) 423 0.381
(1.00) 		0.325
(1.00) 		0.788
(1.00) 		0.975
(1.00) 		0.66
(1.00) 		0.9
(1.00) 		0.0165
(1.00) 		0.213
(1.00) 		0.264
(1.00) 		1
(1.00) 		0.594
(1.00) 		0.199
(1.00) 		0.719
(1.00)
5q loss 133 (29%) 328 0.0258
(1.00) 		0.00333
(1.00) 		0.692
(1.00) 		0.984
(1.00) 		0.357
(1.00) 		0.518
(1.00) 		0.0102
(1.00) 		0.347
(1.00) 		0.369
(1.00) 		0.46
(1.00) 		0.0244
(1.00) 		0.861
(1.00) 		0.0775
(1.00)
6p loss 95 (21%) 366 0.163
(1.00) 		0.773
(1.00) 		0.205
(1.00) 		0.133
(1.00) 		0.412
(1.00) 		0.868
(1.00) 		0.49
(1.00) 		0.107
(1.00) 		0.961
(1.00) 		0.782
(1.00) 		0.11
(1.00) 		0.402
(1.00) 		0.83
(1.00)
6q loss 194 (42%) 267 0.756
(1.00) 		0.118
(1.00) 		0.598
(1.00) 		0.723
(1.00) 		0.458
(1.00) 		0.822
(1.00) 		0.344
(1.00) 		0.163
(1.00) 		0.937
(1.00) 		0.654
(1.00) 		0.338
(1.00) 		0.0368
(1.00) 		0.83
(1.00)
7p loss 30 (7%) 431 0.528
(1.00) 		0.751
(1.00) 		0.956
(1.00) 		0.925
(1.00) 		0.887
(1.00) 		0.747
(1.00) 		0.26
(1.00) 		0.637
(1.00) 		0.813
(1.00) 		0.639
(1.00) 		0.85
(1.00) 		0.697
(1.00) 		0.416
(1.00)
7q loss 35 (8%) 426 0.313
(1.00) 		0.218
(1.00) 		0.849
(1.00) 		0.885
(1.00) 		0.787
(1.00) 		0.405
(1.00) 		0.86
(1.00) 		0.74
(1.00) 		0.654
(1.00) 		1
(1.00) 		0.98
(1.00) 		0.366
(1.00) 		0.695
(1.00)
8p loss 178 (39%) 283 0.981
(1.00) 		0.739
(1.00) 		0.958
(1.00) 		0.539
(1.00) 		0.969
(1.00) 		0.429
(1.00) 		0.0552
(1.00) 		0.851
(1.00) 		0.0165
(1.00) 		0.175
(1.00) 		0.223
(1.00) 		0.598
(1.00) 		0.132
(1.00)
8q loss 50 (11%) 411 0.703
(1.00) 		0.483
(1.00) 		0.165
(1.00) 		0.587
(1.00) 		0.136
(1.00) 		0.0743
(1.00) 		0.233
(1.00) 		0.115
(1.00) 		0.0145
(1.00) 		0.716
(1.00) 		0.384
(1.00) 		0.308
(1.00) 		0.926
(1.00)
9p loss 239 (52%) 222 0.0962
(1.00) 		0.355
(1.00) 		0.584
(1.00) 		0.953
(1.00) 		0.0437
(1.00) 		0.587
(1.00) 		0.0765
(1.00) 		0.465
(1.00) 		0.551
(1.00) 		0.824
(1.00) 		0.525
(1.00) 		0.845
(1.00) 		0.967
(1.00)
9q loss 225 (49%) 236 0.609
(1.00) 		0.85
(1.00) 		0.736
(1.00) 		0.333
(1.00) 		0.341
(1.00) 		0.781
(1.00) 		0.852
(1.00) 		0.777
(1.00) 		0.296
(1.00) 		0.658
(1.00) 		0.249
(1.00) 		0.476
(1.00) 		0.909
(1.00)
10p loss 101 (22%) 360 0.38
(1.00) 		0.821
(1.00) 		0.634
(1.00) 		0.223
(1.00) 		0.348
(1.00) 		0.941
(1.00) 		0.00935
(1.00) 		0.617
(1.00) 		0.0236
(1.00) 		0.277
(1.00) 		0.543
(1.00) 		0.644
(1.00) 		0.825
(1.00)
10q loss 121 (26%) 340 0.203
(1.00) 		0.841
(1.00) 		0.559
(1.00) 		0.223
(1.00) 		0.267
(1.00) 		0.789
(1.00) 		0.111
(1.00) 		0.471
(1.00) 		0.0113
(1.00) 		0.0804
(1.00) 		0.108
(1.00) 		0.282
(1.00) 		0.633
(1.00)
11p loss 104 (23%) 357 0.997
(1.00) 		0.0427
(1.00) 		0.466
(1.00) 		0.453
(1.00) 		0.4
(1.00) 		0.399
(1.00) 		0.000496
(0.515) 		0.753
(1.00) 		0.482
(1.00) 		0.435
(1.00) 		0.677
(1.00) 		0.127
(1.00) 		0.516
(1.00)
11q loss 83 (18%) 378 0.55
(1.00) 		0.623
(1.00) 		0.509
(1.00) 		0.922
(1.00) 		0.984
(1.00) 		0.265
(1.00) 		0.00235
(1.00) 		0.823
(1.00) 		0.731
(1.00) 		0.395
(1.00) 		0.883
(1.00) 		0.319
(1.00) 		0.787
(1.00)
12p loss 98 (21%) 363 0.15
(1.00) 		0.433
(1.00) 		0.424
(1.00) 		0.609
(1.00) 		0.902
(1.00) 		0.121
(1.00) 		0.0222
(1.00) 		0.0653
(1.00) 		0.87
(1.00) 		0.588
(1.00) 		0.127
(1.00) 		0.425
(1.00) 		0.858
(1.00)
12q loss 87 (19%) 374 0.0749
(1.00) 		0.814
(1.00) 		0.593
(1.00) 		0.468
(1.00) 		0.31
(1.00) 		0.11
(1.00) 		0.00852
(1.00) 		0.22
(1.00) 		0.486
(1.00) 		0.393
(1.00) 		0.121
(1.00) 		0.93
(1.00) 		0.927
(1.00)
13q loss 222 (48%) 239 0.915
(1.00) 		0.184
(1.00) 		0.628
(1.00) 		0.404
(1.00) 		0.422
(1.00) 		0.438
(1.00) 		0.78
(1.00) 		0.759
(1.00) 		0.544
(1.00) 		0.379
(1.00) 		0.0487
(1.00) 		0.146
(1.00) 		0.582
(1.00)
14q loss 103 (22%) 358 0.442
(1.00) 		0.111
(1.00) 		0.623
(1.00) 		0.4
(1.00) 		0.0509
(1.00) 		0.637
(1.00) 		0.262
(1.00) 		0.587
(1.00) 		0.734
(1.00) 		1
(1.00) 		0.137
(1.00) 		0.359
(1.00) 		0.26
(1.00)
15q loss 217 (47%) 244 0.574
(1.00) 		0.00139
(1.00) 		0.802
(1.00) 		0.986
(1.00) 		0.718
(1.00) 		0.743
(1.00) 		0.575
(1.00) 		0.258
(1.00) 		0.0591
(1.00) 		0.66
(1.00) 		0.339
(1.00) 		0.2
(1.00) 		0.87
(1.00)
16p loss 101 (22%) 360 0.628
(1.00) 		0.754
(1.00) 		0.032
(1.00) 		0.439
(1.00) 		0.047
(1.00) 		0.343
(1.00) 		0.498
(1.00) 		0.868
(1.00) 		0.909
(1.00) 		0.79
(1.00) 		0.643
(1.00) 		0.867
(1.00) 		0.593
(1.00)
16q loss 128 (28%) 333 0.558
(1.00) 		0.411
(1.00) 		0.532
(1.00) 		0.994
(1.00) 		0.367
(1.00) 		0.61
(1.00) 		0.466
(1.00) 		0.316
(1.00) 		0.48
(1.00) 		0.806
(1.00) 		0.415
(1.00) 		0.808
(1.00) 		0.234
(1.00)
17p loss 194 (42%) 267 0.772
(1.00) 		0.213
(1.00) 		0.394
(1.00) 		0.369
(1.00) 		0.742
(1.00) 		0.459
(1.00) 		0.157
(1.00) 		0.577
(1.00) 		0.246
(1.00) 		0.0396
(1.00) 		0.0195
(1.00) 		0.0183
(1.00) 		0.952
(1.00)
17q loss 52 (11%) 409 0.425
(1.00) 		0.544
(1.00) 		0.433
(1.00) 		0.213
(1.00) 		0.332
(1.00) 		0.969
(1.00) 		0.883
(1.00) 		0.635
(1.00) 		0.688
(1.00) 		1
(1.00) 		0.91
(1.00) 		0.105
(1.00) 		0.787
(1.00)
18p loss 156 (34%) 305 0.33
(1.00) 		0.0675
(1.00) 		0.0223
(1.00) 		0.344
(1.00) 		0.328
(1.00) 		0.0347
(1.00) 		0.00577
(1.00) 		0.336
(1.00) 		0.51
(1.00) 		0.479
(1.00) 		0.0182
(1.00) 		0.00413
(1.00) 		0.124
(1.00)
18q loss 191 (41%) 270 0.0338
(1.00) 		0.489
(1.00) 		0.0151
(1.00) 		0.225
(1.00) 		0.0627
(1.00) 		0.313
(1.00) 		0.037
(1.00) 		0.998
(1.00) 		0.543
(1.00) 		0.262
(1.00) 		0.0914
(1.00) 		0.113
(1.00) 		0.00236
(1.00)
19p loss 222 (48%) 239 0.0413
(1.00) 		0.0705
(1.00) 		0.127
(1.00) 		0.453
(1.00) 		0.163
(1.00) 		0.0433
(1.00) 		0.00879
(1.00) 		0.707
(1.00) 		0.809
(1.00) 		0.185
(1.00) 		0.962
(1.00) 		0.334
(1.00) 		0.233
(1.00)
19q loss 142 (31%) 319 0.133
(1.00) 		0.107
(1.00) 		0.0793
(1.00) 		0.149
(1.00) 		0.405
(1.00) 		0.0124
(1.00) 		0.225
(1.00) 		0.974
(1.00) 		0.674
(1.00) 		0.334
(1.00) 		0.523
(1.00) 		0.75
(1.00) 		0.245
(1.00)
20p loss 108 (23%) 353 0.185
(1.00) 		0.66
(1.00) 		0.511
(1.00) 		0.413
(1.00) 		0.197
(1.00) 		0.264
(1.00) 		0.826
(1.00) 		0.491
(1.00) 		0.382
(1.00) 		0.795
(1.00) 		0.441
(1.00) 		0.165
(1.00) 		0.828
(1.00)
20q loss 64 (14%) 397 0.8
(1.00) 		0.427
(1.00) 		0.362
(1.00) 		0.448
(1.00) 		0.42
(1.00) 		0.138
(1.00) 		0.787
(1.00) 		0.00286
(1.00) 		0.0753
(1.00) 		0.335
(1.00) 		0.803
(1.00) 		0.469
(1.00) 		0.616
(1.00)
21q loss 149 (32%) 312 0.377
(1.00) 		0.45
(1.00) 		0.819
(1.00) 		0.801
(1.00) 		0.923
(1.00) 		0.624
(1.00) 		0.111
(1.00) 		0.959
(1.00) 		0.052
(1.00) 		0.152
(1.00) 		0.169
(1.00) 		0.212
(1.00) 		0.736
(1.00)
22q loss 197 (43%) 264 0.466
(1.00) 		0.00272
(1.00) 		0.826
(1.00) 		1
(1.00) 		0.894
(1.00) 		0.253
(1.00) 		0.0727
(1.00) 		0.0555
(1.00) 		0.31
(1.00) 		0.822
(1.00) 		0.933
(1.00) 		0.00586
(1.00) 		0.69
(1.00)
xq loss 56 (12%) 405 0.669
(1.00) 		0.222
(1.00) 		0.4
(1.00) 		0.705
(1.00) 		0.889
(1.00) 		0.551
(1.00) 		0.255
(1.00) 		0.915
(1.00) 		0.0818
(1.00) 		0.159
(1.00) 		0.55
(1.00) 		0.514
(1.00) 		0.758
(1.00)
'17p gain' versus 'NUMBERPACKYEARSSMOKED'

P value = 0.000166 (t-test), Q value = 0.17

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

nPatients Mean (Std.Dev)
ALL 317 42.2 (27.2)
17P GAIN MUTATED 53 56.7 (29.6)
17P GAIN WILD-TYPE 264 39.2 (25.8)

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

'19p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000182 (Chi-square test), Q value = 0.19

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 93 294 4 19 2 4 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 89 277 4 19 2 3 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 = 461

  • 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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