Correlation between copy number variations of arm-level result and selected clinical features
Lung Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1251G7Q
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1251G7Q
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 80 arm-level results and 13 clinical features across 389 patients, 9 significant findings detected with Q value < 0.25.

  • 9q gain cnv correlated to 'DISTANT.METASTASIS'.

  • 11q gain cnv correlated to 'AGE'.

  • 19p gain cnv correlated to 'DISTANT.METASTASIS'.

  • 2p loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 2q loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 7q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 8q loss cnv correlated to 'DISTANT.METASTASIS'.

  • 16p loss cnv correlated to 'DISTANT.METASTASIS'.

  • 18p loss cnv correlated to 'NUMBERPACKYEARSSMOKED'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level results and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 9 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED YEAROFTOBACCOSMOKINGONSET DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		COMPLETENESS
OF
RESECTION 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test Chi-square test Fisher's exact test t-test t-test Chi-square test Chi-square test Fisher's exact test t-test Chi-square test
9q gain 0 (0%) 384 0.0725
(1.00) 		0.16
(1.00) 		0.664
(1.00) 		0.997
(1.00) 		1
(1.00) 		0.312
(1.00) 		0.78
(1.00) 		6.69e-05
(0.0611) 		0.711
(1.00) 		1
(1.00) 		0.81
(1.00)
11q gain 0 (0%) 346 0.371
(1.00) 		0.000169
(0.154) 		0.194
(1.00) 		0.586
(1.00) 		0.767
(1.00) 		0.125
(1.00) 		0.255
(1.00) 		0.0617
(1.00) 		0.632
(1.00) 		0.445
(1.00) 		0.83
(1.00) 		0.271
(1.00)
19p gain 0 (0%) 383 0.926
(1.00) 		0.0498
(1.00) 		1
(1.00) 		0.999
(1.00) 		1
(1.00) 		0.45
(1.00) 		0.414
(1.00) 		0.000171
(0.156) 		0.0493
(1.00) 		0.412
(1.00) 		0.0707
(1.00)
2p loss 0 (0%) 384 0.219
(1.00) 		0.146
(1.00) 		1
(1.00) 		0.922
(1.00) 		1
(1.00) 		0.521
(1.00) 		0.977
(1.00) 		0.897
(1.00) 		1
(1.00) 		1.53e-19
(1.4e-16)
2q loss 0 (0%) 386 1
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.841
(1.00) 		0.792
(1.00) 		2.22e-07
(0.000203)
7q loss 0 (0%) 377 0.776
(1.00) 		0.204
(1.00) 		0.558
(1.00) 		0.000176
(0.16) 		0.438
(1.00) 		0.288
(1.00) 		0.576
(1.00) 		0.817
(1.00) 		0.986
(1.00) 		0.285
(1.00) 		0.914
(1.00)
8q loss 0 (0%) 375 0.606
(1.00) 		0.392
(1.00) 		0.79
(1.00) 		0.0667
(1.00) 		1
(1.00) 		0.173
(1.00) 		1.72e-05
(0.0158) 		0.62
(1.00) 		1
(1.00) 		0.851
(1.00)
16p loss 0 (0%) 358 0.322
(1.00) 		0.219
(1.00) 		0.189
(1.00) 		0.364
(1.00) 		0.646
(1.00) 		0.961
(1.00) 		0.659
(1.00) 		3.76e-05
(0.0344) 		0.953
(1.00) 		0.349
(1.00) 		0.00792
(1.00)
18p loss 0 (0%) 321 0.371
(1.00) 		0.0879
(1.00) 		0.182
(1.00) 		0.00533
(1.00) 		0.254
(1.00) 		0.335
(1.00) 		0.000136
(0.124) 		0.0289
(1.00) 		0.109
(1.00) 		0.471
(1.00) 		0.225
(1.00) 		0.257
(1.00)
1p gain 0 (0%) 340 0.861
(1.00) 		0.000928
(0.84) 		1
(1.00) 		0.475
(1.00) 		0.926
(1.00) 		0.713
(1.00) 		0.918
(1.00) 		0.824
(1.00) 		0.845
(1.00) 		0.0196
(1.00) 		0.36
(1.00) 		0.0694
(1.00)
1q gain 0 (0%) 237 0.628
(1.00) 		0.261
(1.00) 		0.532
(1.00) 		0.557
(1.00) 		0.399
(1.00) 		0.459
(1.00) 		0.521
(1.00) 		0.648
(1.00) 		0.392
(1.00) 		0.0552
(1.00) 		0.157
(1.00) 		0.151
(1.00)
2p gain 0 (0%) 344 0.181
(1.00) 		0.0408
(1.00) 		0.111
(1.00) 		0.558
(1.00) 		0.777
(1.00) 		0.45
(1.00) 		0.646
(1.00) 		0.755
(1.00) 		0.194
(1.00) 		0.87
(1.00) 		0.378
(1.00) 		0.0571
(1.00)
2q gain 0 (0%) 351 0.355
(1.00) 		0.145
(1.00) 		0.395
(1.00) 		0.836
(1.00) 		0.692
(1.00) 		0.707
(1.00) 		0.961
(1.00) 		0.16
(1.00) 		0.907
(1.00) 		1
(1.00) 		0.0893
(1.00)
3p gain 0 (0%) 379 0.0858
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.966
(1.00) 		0.381
(1.00) 		0.865
(1.00) 		0.252
(1.00) 		0.91
(1.00) 		0.516
(1.00) 		0.373
(1.00) 		0.532
(1.00)
3q gain 0 (0%) 366 0.321
(1.00) 		0.943
(1.00) 		0.527
(1.00) 		0.999
(1.00) 		0.288
(1.00) 		0.602
(1.00) 		0.365
(1.00) 		0.965
(1.00) 		0.629
(1.00) 		0.651
(1.00) 		0.175
(1.00)
4p gain 0 (0%) 363 0.342
(1.00) 		0.0149
(1.00) 		0.421
(1.00) 		0.691
(1.00) 		0.342
(1.00) 		0.0671
(1.00) 		0.968
(1.00) 		0.0542
(1.00) 		0.938
(1.00) 		0.642
(1.00) 		0.000338
(0.307)
4q gain 0 (0%) 382 0.673
(1.00) 		0.858
(1.00) 		0.254
(1.00) 		0.997
(1.00) 		0.284
(1.00) 		0.0571
(1.00) 		0.0235
(1.00) 		0.425
(1.00) 		0.657
(1.00) 		1
(1.00) 		0.00399
(1.00)
5p gain 0 (0%) 242 0.558
(1.00) 		0.0632
(1.00) 		0.6
(1.00) 		0.83
(1.00) 		0.143
(1.00) 		0.322
(1.00) 		0.0129
(1.00) 		0.664
(1.00) 		0.53
(1.00) 		0.423
(1.00) 		0.258
(1.00) 		0.552
(1.00)
5q gain 0 (0%) 343 0.979
(1.00) 		0.844
(1.00) 		0.533
(1.00) 		0.794
(1.00) 		0.249
(1.00) 		0.564
(1.00) 		0.752
(1.00) 		0.568
(1.00) 		0.623
(1.00) 		0.473
(1.00) 		0.832
(1.00)
6p gain 0 (0%) 330 0.508
(1.00) 		0.971
(1.00) 		0.779
(1.00) 		0.738
(1.00) 		0.252
(1.00) 		1
(1.00) 		0.697
(1.00) 		0.306
(1.00) 		0.17
(1.00) 		0.45
(1.00) 		0.936
(1.00) 		0.568
(1.00)
6q gain 0 (0%) 374 0.992
(1.00) 		0.262
(1.00) 		0.0147
(1.00) 		0.975
(1.00) 		0.515
(1.00) 		0.566
(1.00) 		0.413
(1.00) 		0.094
(1.00) 		0.934
(1.00) 		0.618
(1.00) 		0.0716
(1.00)
7p gain 0 (0%) 256 0.16
(1.00) 		0.039
(1.00) 		0.748
(1.00) 		0.23
(1.00) 		0.448
(1.00) 		0.622
(1.00) 		0.401
(1.00) 		0.721
(1.00) 		0.282
(1.00) 		0.0281
(1.00) 		0.547
(1.00) 		0.107
(1.00)
7q gain 0 (0%) 295 0.728
(1.00) 		0.0143
(1.00) 		0.479
(1.00) 		0.915
(1.00) 		0.262
(1.00) 		0.397
(1.00) 		0.744
(1.00) 		0.738
(1.00) 		0.0663
(1.00) 		0.415
(1.00) 		0.373
(1.00) 		0.0699
(1.00)
8p gain 0 (0%) 341 0.499
(1.00) 		0.00518
(1.00) 		0.125
(1.00) 		0.468
(1.00) 		0.475
(1.00) 		0.161
(1.00) 		0.0174
(1.00) 		0.887
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.677
(1.00)
8q gain 0 (0%) 266 0.945
(1.00) 		0.00377
(1.00) 		0.229
(1.00) 		0.309
(1.00) 		0.192
(1.00) 		0.801
(1.00) 		0.686
(1.00) 		0.0176
(1.00) 		0.615
(1.00) 		0.151
(1.00) 		0.767
(1.00) 		0.805
(1.00)
9p gain 0 (0%) 377 0.231
(1.00) 		0.217
(1.00) 		0.777
(1.00) 		0.798
(1.00) 		1
(1.00) 		0.308
(1.00) 		0.688
(1.00) 		0.0232
(1.00) 		0.577
(1.00) 		0.618
(1.00) 		0.965
(1.00)
10p gain 0 (0%) 345 0.909
(1.00) 		0.445
(1.00) 		0.036
(1.00) 		0.842
(1.00) 		0.823
(1.00) 		0.243
(1.00) 		0.0444
(1.00) 		0.873
(1.00) 		0.81
(1.00) 		0.362
(1.00) 		0.242
(1.00) 		0.366
(1.00)
10q gain 0 (0%) 366 0.999
(1.00) 		0.782
(1.00) 		0.0289
(1.00) 		0.383
(1.00) 		0.614
(1.00) 		0.171
(1.00) 		0.879
(1.00) 		0.612
(1.00) 		0.36
(1.00) 		0.118
(1.00) 		0.49
(1.00)
11p gain 0 (0%) 358 0.445
(1.00) 		0.0589
(1.00) 		0.574
(1.00) 		0.503
(1.00) 		0.725
(1.00) 		0.646
(1.00) 		0.427
(1.00) 		0.872
(1.00) 		0.533
(1.00) 		0.518
(1.00) 		0.502
(1.00) 		0.793
(1.00)
12p gain 0 (0%) 340 0.771
(1.00) 		0.00842
(1.00) 		1
(1.00) 		0.545
(1.00) 		0.484
(1.00) 		0.599
(1.00) 		0.111
(1.00) 		0.845
(1.00) 		0.241
(1.00) 		0.776
(1.00) 		0.0058
(1.00)
12q gain 0 (0%) 349 0.925
(1.00) 		0.0582
(1.00) 		1
(1.00) 		0.46
(1.00) 		0.414
(1.00) 		0.0289
(1.00) 		0.0464
(1.00) 		0.854
(1.00) 		0.326
(1.00) 		0.578
(1.00) 		0.161
(1.00)
13q gain 0 (0%) 374 0.883
(1.00) 		0.575
(1.00) 		1
(1.00) 		0.97
(1.00) 		0.149
(1.00) 		0.936
(1.00) 		0.806
(1.00) 		0.23
(1.00) 		0.731
(1.00) 		1
(1.00) 		0.297
(1.00)
14q gain 0 (0%) 348 0.404
(1.00) 		0.424
(1.00) 		0.409
(1.00) 		0.637
(1.00) 		0.426
(1.00) 		0.237
(1.00) 		0.579
(1.00) 		0.506
(1.00) 		0.728
(1.00) 		0.172
(1.00) 		0.729
(1.00) 		0.52
(1.00)
15q gain 0 (0%) 379 0.267
(1.00) 		0.411
(1.00) 		0.76
(1.00) 		0.127
(1.00) 		0.381
(1.00) 		0.878
(1.00) 		0.869
(1.00) 		0.739
(1.00) 		0.641
(1.00) 		0.575
(1.00) 		0.675
(1.00)
16p gain 0 (0%) 337 0.552
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.599
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.814
(1.00) 		0.711
(1.00) 		0.872
(1.00) 		0.258
(1.00) 		0.534
(1.00)
16q gain 0 (0%) 355 0.798
(1.00) 		0.0405
(1.00) 		0.472
(1.00) 		0.319
(1.00) 		0.231
(1.00) 		0.387
(1.00) 		0.0966
(1.00) 		0.644
(1.00) 		0.304
(1.00) 		0.425
(1.00) 		1
(1.00) 		0.0269
(1.00)
17p gain 0 (0%) 365 0.476
(1.00) 		0.56
(1.00) 		0.212
(1.00) 		0.284
(1.00) 		0.0759
(1.00) 		0.0191
(1.00) 		0.0542
(1.00) 		0.892
(1.00) 		0.302
(1.00) 		0.949
(1.00) 		0.496
(1.00) 		0.0391
(1.00)
17q gain 0 (0%) 322 0.273
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.344
(1.00) 		0.261
(1.00) 		0.1
(1.00) 		0.0812
(1.00) 		0.713
(1.00) 		0.0987
(1.00) 		0.87
(1.00) 		0.00878
(1.00) 		0.229
(1.00)
18p gain 0 (0%) 349 0.81
(1.00) 		0.0689
(1.00) 		0.243
(1.00) 		0.613
(1.00) 		0.0722
(1.00) 		0.706
(1.00) 		0.103
(1.00) 		0.627
(1.00) 		0.712
(1.00) 		0.731
(1.00) 		0.741
(1.00) 		0.0583
(1.00)
18q gain 0 (0%) 365 0.238
(1.00) 		0.0441
(1.00) 		0.407
(1.00) 		0.613
(1.00) 		0.243
(1.00) 		0.306
(1.00) 		0.357
(1.00) 		0.0709
(1.00) 		0.944
(1.00) 		0.59
(1.00) 		0.377
(1.00) 		0.215
(1.00)
19q gain 0 (0%) 369 0.295
(1.00) 		0.777
(1.00) 		0.491
(1.00) 		0.468
(1.00) 		0.613
(1.00) 		0.445
(1.00) 		0.219
(1.00) 		0.118
(1.00) 		0.278
(1.00) 		0.725
(1.00) 		0.127
(1.00)
20p gain 0 (0%) 337 0.934
(1.00) 		0.663
(1.00) 		0.882
(1.00) 		0.548
(1.00) 		0.734
(1.00) 		0.72
(1.00) 		0.886
(1.00) 		0.595
(1.00) 		0.459
(1.00) 		0.597
(1.00) 		0.516
(1.00) 		0.338
(1.00)
20q gain 0 (0%) 323 0.8
(1.00) 		0.2
(1.00) 		0.343
(1.00) 		0.138
(1.00) 		0.617
(1.00) 		0.749
(1.00) 		0.0332
(1.00) 		0.806
(1.00) 		0.65
(1.00) 		0.803
(1.00) 		0.898
(1.00) 		0.251
(1.00)
21q gain 0 (0%) 355 0.802
(1.00) 		0.844
(1.00) 		0.213
(1.00) 		0.72
(1.00) 		1
(1.00) 		0.939
(1.00) 		0.554
(1.00) 		0.874
(1.00) 		0.193
(1.00) 		1
(1.00) 		0.978
(1.00)
22q gain 0 (0%) 374 0.659
(1.00) 		0.354
(1.00) 		0.793
(1.00) 		0.254
(1.00) 		0.515
(1.00) 		0.248
(1.00) 		0.481
(1.00) 		0.922
(1.00) 		0.29
(1.00) 		0.754
(1.00) 		0.264
(1.00)
Xq gain 0 (0%) 373 0.178
(1.00) 		0.167
(1.00) 		0.448
(1.00) 		0.675
(1.00) 		1
(1.00) 		0.406
(1.00) 		0.163
(1.00) 		0.154
(1.00) 		0.934
(1.00) 		0.658
(1.00) 		0.0127
(1.00)
1p loss 0 (0%) 363 0.207
(1.00) 		0.707
(1.00) 		0.226
(1.00) 		0.514
(1.00) 		1
(1.00) 		0.224
(1.00) 		0.959
(1.00) 		0.414
(1.00) 		0.907
(1.00) 		0.315
(1.00) 		0.196
(1.00)
1q loss 0 (0%) 380 0.000374
(0.339) 		0.743
(1.00) 		0.738
(1.00) 		0.00754
(1.00) 		0.35
(1.00) 		0.372
(1.00) 		0.706
(1.00) 		0.952
(1.00) 		0.172
(1.00) 		1
(1.00) 		0.00431
(1.00)
3p loss 0 (0%) 314 0.159
(1.00) 		0.732
(1.00) 		0.797
(1.00) 		0.0141
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.16
(1.00) 		0.116
(1.00) 		0.369
(1.00) 		0.532
(1.00) 		0.899
(1.00) 		0.347
(1.00)
3q loss 0 (0%) 344 0.346
(1.00) 		0.801
(1.00) 		1
(1.00) 		0.0171
(1.00) 		0.507
(1.00) 		0.707
(1.00) 		0.0362
(1.00) 		0.593
(1.00) 		0.642
(1.00) 		0.478
(1.00) 		0.91
(1.00) 		0.634
(1.00)
4p loss 0 (0%) 354 0.564
(1.00) 		0.012
(1.00) 		0.484
(1.00) 		0.625
(1.00) 		0.56
(1.00) 		0.214
(1.00) 		0.8
(1.00) 		0.227
(1.00) 		0.948
(1.00) 		0.114
(1.00) 		0.781
(1.00) 		0.317
(1.00)
4q loss 0 (0%) 347 0.616
(1.00) 		0.0473
(1.00) 		0.14
(1.00) 		0.851
(1.00) 		0.917
(1.00) 		0.427
(1.00) 		0.414
(1.00) 		0.982
(1.00) 		0.598
(1.00) 		0.0129
(1.00) 		0.628
(1.00) 		0.0207
(1.00)
5p loss 0 (0%) 380 0.689
(1.00) 		0.555
(1.00) 		0.738
(1.00) 		0.04
(1.00) 		0.35
(1.00) 		0.362
(1.00) 		0.75
(1.00) 		0.895
(1.00) 		0.829
(1.00) 		0.24
(1.00) 		0.674
(1.00)
5q loss 0 (0%) 340 0.694
(1.00) 		0.0229
(1.00) 		0.0473
(1.00) 		0.705
(1.00) 		0.0324
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.421
(1.00) 		0.387
(1.00) 		0.182
(1.00) 		0.185
(1.00) 		0.629
(1.00)
6p loss 0 (0%) 357 0.829
(1.00) 		0.0474
(1.00) 		0.138
(1.00) 		0.12
(1.00) 		0.755
(1.00) 		0.652
(1.00) 		0.139
(1.00) 		0.266
(1.00) 		0.392
(1.00) 		0.729
(1.00) 		0.357
(1.00) 		0.668
(1.00)
6q loss 0 (0%) 304 0.886
(1.00) 		0.058
(1.00) 		0.462
(1.00) 		0.0285
(1.00) 		0.576
(1.00) 		0.56
(1.00) 		0.0627
(1.00) 		0.238
(1.00) 		0.286
(1.00) 		0.74
(1.00) 		0.779
(1.00) 		0.864
(1.00)
7p loss 0 (0%) 378 0.835
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.461
(1.00) 		0.41
(1.00) 		0.625
(1.00) 		0.397
(1.00) 		0.683
(1.00) 		0.906
(1.00) 		0.33
(1.00) 		0.953
(1.00)
8p loss 0 (0%) 291 0.633
(1.00) 		0.919
(1.00) 		0.725
(1.00) 		0.254
(1.00) 		0.159
(1.00) 		0.579
(1.00) 		0.604
(1.00) 		0.89
(1.00) 		0.222
(1.00) 		0.53
(1.00) 		0.663
(1.00) 		0.885
(1.00)
9p loss 0 (0%) 274 0.00797
(1.00) 		0.395
(1.00) 		0.0743
(1.00) 		0.87
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.764
(1.00) 		0.503
(1.00) 		0.0342
(1.00) 		0.688
(1.00) 		0.262
(1.00)
9q loss 0 (0%) 293 0.52
(1.00) 		0.638
(1.00) 		1
(1.00) 		0.99
(1.00) 		0.646
(1.00) 		0.579
(1.00) 		0.284
(1.00) 		0.891
(1.00) 		0.416
(1.00) 		0.318
(1.00) 		0.295
(1.00) 		0.616
(1.00)
10p loss 0 (0%) 362 0.26
(1.00) 		0.716
(1.00) 		0.108
(1.00) 		0.167
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.708
(1.00) 		0.882
(1.00) 		0.617
(1.00) 		0.663
(1.00) 		0.956
(1.00)
10q loss 0 (0%) 356 0.302
(1.00) 		0.201
(1.00) 		0.719
(1.00) 		0.000405
(0.367) 		1
(1.00) 		0.0607
(1.00) 		0.975
(1.00) 		0.968
(1.00) 		0.256
(1.00) 		0.81
(1.00) 		0.371
(1.00)
11p loss 0 (0%) 360 0.291
(1.00) 		0.00725
(1.00) 		0.563
(1.00) 		0.584
(1.00) 		1
(1.00) 		0.0624
(1.00) 		0.0173
(1.00) 		0.108
(1.00) 		0.416
(1.00) 		0.892
(1.00) 		0.129
(1.00)
11q loss 0 (0%) 364 0.163
(1.00) 		0.883
(1.00) 		0.307
(1.00) 		0.705
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.0328
(1.00) 		0.354
(1.00) 		0.0355
(1.00) 		0.714
(1.00) 		0.748
(1.00) 		0.5
(1.00)
12p loss 0 (0%) 355 0.384
(1.00) 		0.554
(1.00) 		1
(1.00) 		0.533
(1.00) 		0.723
(1.00) 		1
(1.00) 		0.705
(1.00) 		0.0672
(1.00) 		0.527
(1.00) 		0.865
(1.00) 		0.772
(1.00) 		0.547
(1.00)
12q loss 0 (0%) 368 0.0565
(1.00) 		0.947
(1.00) 		0.654
(1.00) 		0.782
(1.00) 		0.612
(1.00) 		0.978
(1.00) 		0.26
(1.00) 		0.651
(1.00) 		0.706
(1.00) 		1
(1.00) 		0.269
(1.00)
13q loss 0 (0%) 302 0.329
(1.00) 		0.149
(1.00) 		0.542
(1.00) 		0.562
(1.00) 		0.147
(1.00) 		0.774
(1.00) 		0.707
(1.00) 		0.155
(1.00) 		0.628
(1.00) 		0.0739
(1.00) 		0.471
(1.00) 		0.261
(1.00)
14q loss 0 (0%) 348 0.484
(1.00) 		0.47
(1.00) 		1
(1.00) 		0.798
(1.00) 		0.412
(1.00) 		0.421
(1.00) 		0.233
(1.00) 		0.322
(1.00) 		0.301
(1.00) 		0.835
(1.00) 		0.487
(1.00) 		0.616
(1.00)
15q loss 0 (0%) 308 0.732
(1.00) 		0.0563
(1.00) 		0.319
(1.00) 		0.773
(1.00) 		0.149
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.831
(1.00) 		0.949
(1.00) 		0.841
(1.00) 		0.312
(1.00) 		0.484
(1.00)
16q loss 0 (0%) 337 0.325
(1.00) 		0.299
(1.00) 		0.551
(1.00) 		0.724
(1.00) 		0.0195
(1.00) 		1
(1.00) 		0.945
(1.00) 		0.519
(1.00) 		0.013
(1.00) 		0.911
(1.00) 		0.515
(1.00) 		0.416
(1.00)
17p loss 0 (0%) 293 0.781
(1.00) 		0.245
(1.00) 		0.723
(1.00) 		0.107
(1.00) 		0.651
(1.00) 		0.579
(1.00) 		0.449
(1.00) 		0.0588
(1.00) 		0.831
(1.00) 		0.54
(1.00) 		0.183
(1.00) 		0.722
(1.00)
17q loss 0 (0%) 375 0.0251
(1.00) 		0.205
(1.00) 		0.275
(1.00) 		0.395
(1.00) 		1
(1.00) 		0.517
(1.00) 		0.0539
(1.00) 		0.978
(1.00) 		0.742
(1.00) 		0.693
(1.00) 		0.125
(1.00)
18q loss 0 (0%) 294 0.0162
(1.00) 		0.476
(1.00) 		0.636
(1.00) 		0.486
(1.00) 		0.237
(1.00) 		0.262
(1.00) 		0.215
(1.00) 		0.383
(1.00) 		0.521
(1.00) 		0.586
(1.00) 		0.0192
(1.00) 		0.0991
(1.00)
19p loss 0 (0%) 288 0.0562
(1.00) 		0.28
(1.00) 		0.0818
(1.00) 		0.562
(1.00) 		0.829
(1.00) 		1
(1.00) 		0.715
(1.00) 		0.444
(1.00) 		0.0326
(1.00) 		0.283
(1.00) 		0.135
(1.00) 		0.0172
(1.00)
19q loss 0 (0%) 330 0.0669
(1.00) 		0.495
(1.00) 		0.779
(1.00) 		0.00559
(1.00) 		0.463
(1.00) 		0.744
(1.00) 		0.457
(1.00) 		0.612
(1.00) 		0.0166
(1.00) 		0.868
(1.00) 		0.0401
(1.00) 		0.0918
(1.00)
20p loss 0 (0%) 336 0.0657
(1.00) 		0.896
(1.00) 		0.882
(1.00) 		0.0151
(1.00) 		0.684
(1.00) 		0.487
(1.00) 		0.636
(1.00) 		0.0686
(1.00) 		0.371
(1.00) 		0.267
(1.00) 		1
(1.00) 		0.523
(1.00)
20q loss 0 (0%) 368 0.183
(1.00) 		0.346
(1.00) 		0.826
(1.00) 		0.425
(1.00) 		0.612
(1.00) 		0.871
(1.00) 		0.257
(1.00) 		0.73
(1.00) 		0.909
(1.00) 		0.525
(1.00) 		0.576
(1.00)
21q loss 0 (0%) 335 1
(1.00) 		0.285
(1.00) 		0.0182
(1.00) 		0.124
(1.00) 		0.439
(1.00) 		1
(1.00) 		0.299
(1.00) 		0.8
(1.00) 		0.858
(1.00) 		0.715
(1.00) 		0.634
(1.00) 		0.146
(1.00)
22q loss 0 (0%) 310 0.544
(1.00) 		0.0263
(1.00) 		0.0575
(1.00) 		0.657
(1.00) 		0.781
(1.00) 		0.381
(1.00) 		0.184
(1.00) 		0.0362
(1.00) 		0.0395
(1.00) 		0.879
(1.00) 		0.21
(1.00) 		0.646
(1.00)
Xq loss 0 (0%) 379 0.275
(1.00) 		0.0652
(1.00) 		0.0486
(1.00) 		0.0157
(1.00) 		0.0731
(1.00) 		0.304
(1.00) 		0.909
(1.00) 		0.919
(1.00) 		0.397
(1.00) 		1
(1.00) 		0.00114
(1.00)
'9q gain' versus 'DISTANT.METASTASIS'

P value = 6.69e-05 (Chi-square test), Q value = 0.061

Table S1.  Gene #18: '9q gain' versus Clinical Feature #9: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 262 17 1 3 102
9Q GAIN CNV 3 0 0 1 1
9Q GAIN WILD-TYPE 259 17 1 2 101

Figure S1.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #9: 'DISTANT.METASTASIS'

'11q gain' versus 'AGE'

P value = 0.000169 (t-test), Q value = 0.15

Table S2.  Gene #22: '11q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 358 65.2 (9.8)
11Q GAIN CNV 40 59.5 (9.5)
11Q GAIN WILD-TYPE 318 65.9 (9.6)

Figure S2.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'AGE'

'19p gain' versus 'DISTANT.METASTASIS'

P value = 0.000171 (Chi-square test), Q value = 0.16

Table S3.  Gene #34: '19p gain' versus Clinical Feature #9: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 262 17 1 3 102
19P GAIN CNV 3 1 0 1 1
19P GAIN WILD-TYPE 259 16 1 2 101

Figure S3.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #9: 'DISTANT.METASTASIS'

'2p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.53e-19 (Chi-square test), Q value = 1.4e-16

Table S4.  Gene #43: '2p loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
ALL 3 97 113 32 53 57 11 21
2P LOSS CNV 2 0 1 1 1 0 0 0
2P LOSS WILD-TYPE 1 97 112 31 52 57 11 21

Figure S4.  Get High-res Image Gene #43: '2p loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'2q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.22e-07 (Chi-square test), Q value = 2e-04

Table S5.  Gene #44: '2q loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
ALL 3 97 113 32 53 57 11 21
2Q LOSS CNV 1 0 1 0 1 0 0 0
2Q LOSS WILD-TYPE 2 97 112 32 52 57 11 21

Figure S5.  Get High-res Image Gene #44: '2q loss' versus Clinical Feature #13: 'NEOPLASM.DISEASESTAGE'

'7q loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000176 (Chi-square test), Q value = 0.16

Table S6.  Gene #54: '7q loss' versus Clinical Feature #5: '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 SOLID PATTERN PREDOMINANT ADENOCARCINOMA MUCINOUS (COLLOID) CARCINOMA
ALL 11 79 243 4 17 2 3 2 18 3 7
7Q LOSS CNV 0 0 8 0 0 1 0 0 1 0 2
7Q LOSS WILD-TYPE 11 79 235 4 17 1 3 2 17 3 5

Figure S6.  Get High-res Image Gene #54: '7q loss' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'8q loss' versus 'DISTANT.METASTASIS'

P value = 1.72e-05 (Chi-square test), Q value = 0.016

Table S7.  Gene #56: '8q loss' versus Clinical Feature #9: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 262 17 1 3 102
8Q LOSS CNV 9 0 1 0 4
8Q LOSS WILD-TYPE 253 17 0 3 98

Figure S7.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #9: 'DISTANT.METASTASIS'

'16p loss' versus 'DISTANT.METASTASIS'

P value = 3.76e-05 (Chi-square test), Q value = 0.034

Table S8.  Gene #68: '16p loss' versus Clinical Feature #9: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 262 17 1 3 102
16P LOSS CNV 18 5 1 1 6
16P LOSS WILD-TYPE 244 12 0 2 96

Figure S8.  Get High-res Image Gene #68: '16p loss' versus Clinical Feature #9: 'DISTANT.METASTASIS'

'18p loss' versus 'NUMBERPACKYEARSSMOKED'

P value = 0.000136 (t-test), Q value = 0.12

Table S9.  Gene #72: '18p loss' versus Clinical Feature #7: 'NUMBERPACKYEARSSMOKED'

nPatients Mean (Std.Dev)
ALL 272 41.6 (26.9)
18P LOSS CNV 46 31.5 (16.5)
18P LOSS WILD-TYPE 226 43.7 (28.1)

Figure S9.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #7: 'NUMBERPACKYEARSSMOKED'

Methods & Data
Input

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

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

  • Number of patients = 389

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 13

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle