Lung Adenocarcinoma: Correlation between copy number variations of arm-level result and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
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 77 arm-level results and 10 clinical features across 265 patients, 3 significant findings detected with Q value < 0.25.

  • 8q gain cnv correlated to 'AGE'.

  • 4q loss cnv correlated to 'GENDER'.

  • 7q loss 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 77 arm-level results and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) RADIATIONS
RADIATION
REGIMENINDICATION 		NEOADJUVANT
THERAPY
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
8q gain 79 (30%) 186 0.882
(1.00) 		9.09e-05
(0.0664) 		1
(1.00) 		0.413
(1.00) 		0.632
(1.00) 		0.457
(1.00) 		0.199
(1.00) 		0.248
(1.00) 		0.761
(1.00) 		0.852
(1.00)
4q loss 30 (11%) 235 0.744
(1.00) 		0.0657
(1.00) 		0.000327
(0.238) 		0.926
(1.00) 		0.713
(1.00) 		0.064
(1.00) 		0.0988
(1.00) 		0.578
(1.00) 		0.171
(1.00) 		0.42
(1.00)
7q loss 13 (5%) 252 0.355
(1.00) 		0.72
(1.00) 		0.777
(1.00) 		3.91e-05
(0.0286) 		0.908
(1.00) 		0.925
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.699
(1.00)
1p gain 42 (16%) 223 0.94
(1.00) 		0.00869
(1.00) 		1
(1.00) 		0.68
(1.00) 		0.806
(1.00) 		0.585
(1.00) 		0.0255
(1.00) 		0.287
(1.00) 		0.699
(1.00) 		0.643
(1.00)
1q gain 111 (42%) 154 0.875
(1.00) 		0.878
(1.00) 		0.533
(1.00) 		0.51
(1.00) 		0.331
(1.00) 		0.717
(1.00) 		0.0377
(1.00) 		0.34
(1.00) 		0.779
(1.00) 		0.488
(1.00)
2p gain 39 (15%) 226 0.101
(1.00) 		0.0543
(1.00) 		0.081
(1.00) 		0.343
(1.00) 		0.902
(1.00) 		0.146
(1.00) 		0.942
(1.00) 		0.195
(1.00) 		0.415
(1.00) 		1
(1.00)
2q gain 28 (11%) 237 0.041
(1.00) 		0.442
(1.00) 		0.423
(1.00) 		0.238
(1.00) 		0.573
(1.00) 		0.854
(1.00) 		0.393
(1.00) 		1
(1.00) 		0.588
(1.00)
3p gain 9 (3%) 256 0.343
(1.00) 		0.675
(1.00) 		1
(1.00) 		0.157
(1.00) 		0.0526
(1.00) 		0.356
(1.00) 		0.431
(1.00) 		0.369
(1.00) 		1
(1.00)
3q gain 22 (8%) 243 0.195
(1.00) 		0.486
(1.00) 		1
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.913
(1.00) 		0.294
(1.00) 		1
(1.00)
4p gain 19 (7%) 246 0.884
(1.00) 		0.138
(1.00) 		1
(1.00) 		0.934
(1.00) 		0.342
(1.00) 		0.556
(1.00) 		0.119
(1.00) 		1
(1.00) 		0.747
(1.00)
4q gain 8 (3%) 257 0.581
(1.00) 		0.469
(1.00) 		0.474
(1.00) 		1
(1.00) 		0.111
(1.00) 		0.754
(1.00) 		0.438
(1.00) 		0.335
(1.00) 		1
(1.00)
5p gain 116 (44%) 149 0.192
(1.00) 		0.07
(1.00) 		0.711
(1.00) 		0.935
(1.00) 		0.316
(1.00) 		0.489
(1.00) 		0.984
(1.00) 		0.922
(1.00) 		0.569
(1.00) 		1
(1.00)
5q gain 35 (13%) 230 0.613
(1.00) 		0.84
(1.00) 		0.363
(1.00) 		0.803
(1.00) 		0.691
(1.00) 		0.934
(1.00) 		0.692
(1.00) 		0.39
(1.00) 		0.202
(1.00)
6p gain 44 (17%) 221 0.879
(1.00) 		0.401
(1.00) 		0.408
(1.00) 		0.928
(1.00) 		0.378
(1.00) 		0.969
(1.00) 		0.292
(1.00) 		0.127
(1.00) 		1
(1.00) 		0.163
(1.00)
6q gain 12 (5%) 253 0.701
(1.00) 		0.306
(1.00) 		0.071
(1.00) 		0.991
(1.00) 		0.947
(1.00) 		0.764
(1.00) 		0.299
(1.00) 		1
(1.00) 		0.699
(1.00)
7p gain 92 (35%) 173 0.439
(1.00) 		0.136
(1.00) 		0.897
(1.00) 		0.395
(1.00) 		0.483
(1.00) 		0.677
(1.00) 		0.0164
(1.00) 		0.862
(1.00) 		1
(1.00) 		1
(1.00)
7q gain 65 (25%) 200 0.978
(1.00) 		0.00103
(0.748) 		0.477
(1.00) 		0.75
(1.00) 		0.67
(1.00) 		0.697
(1.00) 		0.0426
(1.00) 		0.198
(1.00) 		0.0923
(1.00) 		0.69
(1.00)
8p gain 29 (11%) 236 0.361
(1.00) 		0.00904
(1.00) 		0.323
(1.00) 		0.543
(1.00) 		0.21
(1.00) 		0.804
(1.00) 		0.435
(1.00) 		0.199
(1.00) 		0.641
(1.00) 		0.408
(1.00)
9p gain 5 (2%) 260 0.21
(1.00) 		0.853
(1.00) 		0.179
(1.00) 		0.999
(1.00) 		0.208
(1.00) 		0.825
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
9q gain 4 (2%) 261 0.0589
(1.00) 		0.338
(1.00) 		1
(1.00) 		1
(1.00) 		0.383
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
10p gain 31 (12%) 234 0.84
(1.00) 		0.85
(1.00) 		0.337
(1.00) 		0.0799
(1.00) 		0.478
(1.00) 		0.235
(1.00) 		1
(1.00) 		0.375
(1.00) 		1
(1.00)
10q gain 16 (6%) 249 0.822
(1.00) 		0.432
(1.00) 		0.441
(1.00) 		0.0757
(1.00) 		0.613
(1.00) 		0.282
(1.00) 		0.804
(1.00) 		1
(1.00) 		1
(1.00)
11p gain 20 (8%) 245 0.4
(1.00) 		0.238
(1.00) 		0.484
(1.00) 		0.658
(1.00) 		0.461
(1.00) 		0.215
(1.00) 		0.192
(1.00) 		0.682
(1.00) 		0.256
(1.00) 		0.199
(1.00)
11q gain 28 (11%) 237 0.335
(1.00) 		0.00603
(1.00) 		0.229
(1.00) 		0.658
(1.00) 		0.818
(1.00) 		0.765
(1.00) 		0.921
(1.00) 		0.406
(1.00) 		0.635
(1.00) 		0.588
(1.00)
12p gain 39 (15%) 226 0.56
(1.00) 		0.17
(1.00) 		0.487
(1.00) 		0.775
(1.00) 		0.0226
(1.00) 		0.224
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.628
(1.00)
12q gain 30 (11%) 235 0.914
(1.00) 		0.0163
(1.00) 		1
(1.00) 		0.713
(1.00) 		0.0378
(1.00) 		0.143
(1.00) 		0.114
(1.00) 		1
(1.00) 		0.42
(1.00)
13q gain 17 (6%) 248 0.948
(1.00) 		0.835
(1.00) 		0.617
(1.00) 		0.00592
(1.00) 		0.233
(1.00) 		0.281
(1.00) 		0.119
(1.00) 		0.586
(1.00) 		0.728
(1.00)
14q gain 36 (14%) 229 0.589
(1.00) 		0.429
(1.00) 		0.281
(1.00) 		0.451
(1.00) 		0.101
(1.00) 		0.761
(1.00) 		0.0886
(1.00) 		0.71
(1.00) 		0.226
(1.00) 		0.619
(1.00)
15q gain 9 (3%) 256 0.319
(1.00) 		0.126
(1.00) 		0.518
(1.00) 		0.333
(1.00) 		0.742
(1.00) 		0.376
(1.00) 		0.0611
(1.00) 		1
(1.00) 		1
(1.00)
16p gain 37 (14%) 228 0.943
(1.00) 		0.0619
(1.00) 		1
(1.00) 		0.286
(1.00) 		0.834
(1.00) 		0.853
(1.00) 		0.937
(1.00) 		0.52
(1.00) 		0.7
(1.00) 		0.224
(1.00)
16q gain 20 (8%) 245 0.678
(1.00) 		0.12
(1.00) 		0.816
(1.00) 		0.811
(1.00) 		0.922
(1.00) 		0.43
(1.00) 		1
(1.00) 		0.608
(1.00) 		1
(1.00)
17p gain 19 (7%) 246 0.441
(1.00) 		0.219
(1.00) 		0.339
(1.00) 		0.653
(1.00) 		0.476
(1.00) 		0.178
(1.00) 		0.713
(1.00) 		1
(1.00) 		0.237
(1.00) 		0.747
(1.00)
17q gain 51 (19%) 214 0.521
(1.00) 		0.0643
(1.00) 		0.876
(1.00) 		0.526
(1.00) 		0.124
(1.00) 		0.0609
(1.00) 		0.883
(1.00) 		0.548
(1.00) 		0.284
(1.00) 		1
(1.00)
18p gain 22 (8%) 243 0.501
(1.00) 		0.363
(1.00) 		1
(1.00) 		0.283
(1.00) 		0.771
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.419
(1.00) 		0.0823
(1.00) 		0.754
(1.00)
18q gain 14 (5%) 251 0.403
(1.00) 		0.0792
(1.00) 		0.787
(1.00) 		0.96
(1.00) 		0.00268
(1.00) 		0.644
(1.00) 		0.744
(1.00) 		0.676
(1.00) 		0.514
(1.00) 		0.239
(1.00)
19p gain 6 (2%) 259 0.532
(1.00) 		0.0675
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.726
(1.00) 		0.245
(1.00) 		0.369
(1.00) 		1
(1.00) 		1
(1.00)
19q gain 18 (7%) 247 0.197
(1.00) 		0.00165
(1.00) 		0.807
(1.00) 		0.968
(1.00) 		0.939
(1.00) 		0.0712
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.326
(1.00)
20p gain 32 (12%) 233 0.849
(1.00) 		0.247
(1.00) 		0.576
(1.00) 		0.371
(1.00) 		0.646
(1.00) 		0.669
(1.00) 		0.51
(1.00) 		0.933
(1.00) 		0.197
(1.00) 		0.0608
(1.00)
20q gain 40 (15%) 225 0.196
(1.00) 		0.113
(1.00) 		0.12
(1.00) 		0.379
(1.00) 		0.359
(1.00) 		0.67
(1.00) 		0.693
(1.00) 		0.699
(1.00) 		0.472
(1.00)
21q gain 27 (10%) 238 0.567
(1.00) 		0.546
(1.00) 		0.103
(1.00) 		0.477
(1.00) 		0.642
(1.00) 		0.6
(1.00) 		0.301
(1.00) 		1
(1.00) 		0.15
(1.00)
22q gain 12 (5%) 253 0.184
(1.00) 		0.527
(1.00) 		1
(1.00) 		0.119
(1.00) 		0.152
(1.00) 		0.105
(1.00) 		0.187
(1.00) 		0.46
(1.00) 		0.399
(1.00)
1p loss 29 (11%) 236 0.83
(1.00) 		0.186
(1.00) 		0.323
(1.00) 		0.879
(1.00) 		0.841
(1.00) 		0.537
(1.00) 		0.0731
(1.00) 		0.641
(1.00) 		1
(1.00)
1q loss 10 (4%) 255 0.76
(1.00) 		0.79
(1.00) 		0.193
(1.00) 		0.427
(1.00) 		0.371
(1.00) 		0.262
(1.00) 		1
(1.00) 		0.401
(1.00) 		1
(1.00)
2p loss 3 (1%) 262 0.0257
(1.00) 		1
(1.00) 		0.998
(1.00) 		0.482
(1.00) 		1
(1.00) 		0.149
(1.00) 		1
(1.00) 		0.389
(1.00)
3p loss 50 (19%) 215 0.402
(1.00) 		0.418
(1.00) 		1
(1.00) 		0.013
(1.00) 		0.684
(1.00) 		0.536
(1.00) 		0.246
(1.00) 		0.115
(1.00) 		0.716
(1.00) 		0.279
(1.00)
3q loss 32 (12%) 233 0.794
(1.00) 		0.403
(1.00) 		0.351
(1.00) 		0.0394
(1.00) 		0.76
(1.00) 		0.929
(1.00) 		0.0967
(1.00) 		0.573
(1.00) 		1
(1.00) 		1
(1.00)
4p loss 33 (12%) 232 0.875
(1.00) 		0.0363
(1.00) 		0.026
(1.00) 		0.926
(1.00) 		0.0516
(1.00) 		0.839
(1.00) 		0.594
(1.00) 		0.733
(1.00) 		0.669
(1.00) 		0.0639
(1.00)
5p loss 8 (3%) 257 0.21
(1.00) 		0.173
(1.00) 		0.732
(1.00) 		0.992
(1.00) 		0.00864
(1.00) 		0.332
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.611
(1.00)
5q loss 46 (17%) 219 0.256
(1.00) 		0.293
(1.00) 		0.105
(1.00) 		0.73
(1.00) 		0.42
(1.00) 		0.866
(1.00) 		0.0293
(1.00) 		0.909
(1.00) 		0.477
(1.00) 		0.822
(1.00)
6p loss 31 (12%) 234 0.77
(1.00) 		0.349
(1.00) 		0.565
(1.00) 		0.0207
(1.00) 		0.958
(1.00) 		0.863
(1.00) 		0.124
(1.00) 		0.578
(1.00) 		0.184
(1.00) 		1
(1.00)
6q loss 63 (24%) 202 0.879
(1.00) 		0.714
(1.00) 		0.147
(1.00) 		0.0207
(1.00) 		0.515
(1.00) 		0.803
(1.00) 		0.233
(1.00) 		0.218
(1.00) 		0.515
(1.00) 		0.688
(1.00)
7p loss 11 (4%) 254 0.57
(1.00) 		0.43
(1.00) 		1
(1.00) 		0.148
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.575
(1.00) 		0.431
(1.00) 		0.674
(1.00)
8p loss 78 (29%) 187 0.725
(1.00) 		0.741
(1.00) 		0.893
(1.00) 		0.175
(1.00) 		0.238
(1.00) 		0.241
(1.00) 		0.678
(1.00) 		0.541
(1.00) 		0.534
(1.00) 		0.452
(1.00)
8q loss 13 (5%) 252 0.368
(1.00) 		0.591
(1.00) 		1
(1.00) 		0.00062
(0.451) 		0.731
(1.00) 		0.495
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
9p loss 83 (31%) 182 0.127
(1.00) 		0.192
(1.00) 		0.287
(1.00) 		0.833
(1.00) 		0.652
(1.00) 		0.94
(1.00) 		0.0486
(1.00) 		0.496
(1.00) 		1
(1.00) 		1
(1.00)
9q loss 69 (26%) 196 0.301
(1.00) 		0.616
(1.00) 		0.888
(1.00) 		0.982
(1.00) 		0.801
(1.00) 		0.603
(1.00) 		0.142
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.116
(1.00)
10p loss 31 (12%) 234 0.122
(1.00) 		0.211
(1.00) 		0.0572
(1.00) 		0.00324
(1.00) 		0.984
(1.00) 		0.359
(1.00) 		0.0396
(1.00) 		1
(1.00) 		1
(1.00)
10q loss 26 (10%) 239 0.879
(1.00) 		0.0392
(1.00) 		0.837
(1.00) 		0.00658
(1.00) 		0.56
(1.00) 		0.0775
(1.00) 		0.74
(1.00) 		1
(1.00) 		1
(1.00)
11p loss 23 (9%) 242 0.994
(1.00) 		0.0409
(1.00) 		0.129
(1.00) 		0.632
(1.00) 		0.472
(1.00) 		0.954
(1.00) 		0.122
(1.00) 		0.014
(1.00) 		1
(1.00) 		0.761
(1.00)
11q loss 18 (7%) 247 0.46
(1.00) 		0.913
(1.00) 		0.631
(1.00) 		0.379
(1.00) 		0.675
(1.00) 		0.886
(1.00) 		0.459
(1.00) 		0.0554
(1.00) 		0.218
(1.00) 		0.163
(1.00)
12p loss 27 (10%) 238 0.622
(1.00) 		0.785
(1.00) 		0.686
(1.00) 		0.928
(1.00) 		0.086
(1.00) 		0.66
(1.00) 		0.586
(1.00) 		0.93
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 19 (7%) 246 0.758
(1.00) 		0.147
(1.00) 		0.816
(1.00) 		0.0015
(1.00) 		0.548
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.608
(1.00) 		0.747
(1.00)
13q loss 60 (23%) 205 0.729
(1.00) 		0.139
(1.00) 		0.883
(1.00) 		0.0194
(1.00) 		0.0771
(1.00) 		0.903
(1.00) 		0.111
(1.00) 		0.219
(1.00) 		0.499
(1.00) 		0.418
(1.00)
14q loss 28 (11%) 237 0.548
(1.00) 		0.494
(1.00) 		0.229
(1.00) 		0.73
(1.00) 		0.33
(1.00) 		0.773
(1.00) 		0.596
(1.00) 		0.75
(1.00) 		0.147
(1.00) 		0.399
(1.00)
15q loss 57 (22%) 208 0.536
(1.00) 		0.131
(1.00) 		0.454
(1.00) 		0.00887
(1.00) 		0.0498
(1.00) 		0.569
(1.00) 		0.935
(1.00) 		0.922
(1.00) 		0.741
(1.00) 		0.305
(1.00)
16p loss 29 (11%) 236 0.62
(1.00) 		0.143
(1.00) 		0.844
(1.00) 		0.273
(1.00) 		0.893
(1.00) 		0.787
(1.00) 		0.0276
(1.00) 		0.159
(1.00) 		0.589
(1.00)
16q loss 37 (14%) 228 0.372
(1.00) 		0.479
(1.00) 		0.86
(1.00) 		0.273
(1.00) 		0.0783
(1.00) 		0.344
(1.00) 		0.0813
(1.00) 		0.401
(1.00) 		0.621
(1.00)
17p loss 68 (26%) 197 0.984
(1.00) 		0.221
(1.00) 		0.673
(1.00) 		0.819
(1.00) 		0.503
(1.00) 		0.58
(1.00) 		0.251
(1.00) 		0.19
(1.00) 		0.525
(1.00) 		0.556
(1.00)
17q loss 13 (5%) 252 0.753
(1.00) 		0.59
(1.00) 		0.577
(1.00) 		0.279
(1.00) 		0.531
(1.00) 		0.791
(1.00) 		0.652
(1.00) 		0.488
(1.00) 		0.115
(1.00)
18p loss 49 (18%) 216 0.204
(1.00) 		0.0337
(1.00) 		1
(1.00) 		0.00667
(1.00) 		0.92
(1.00) 		0.464
(1.00) 		0.111
(1.00) 		0.0125
(1.00) 		0.473
(1.00) 		1
(1.00)
18q loss 72 (27%) 193 0.0941
(1.00) 		0.247
(1.00) 		0.782
(1.00) 		0.833
(1.00) 		0.345
(1.00) 		0.176
(1.00) 		0.286
(1.00) 		0.219
(1.00) 		0.524
(1.00) 		0.701
(1.00)
19p loss 83 (31%) 182 0.00781
(1.00) 		0.742
(1.00) 		0.00134
(0.973) 		0.833
(1.00) 		0.241
(1.00) 		0.033
(1.00) 		0.0715
(1.00) 		0.0924
(1.00) 		1
(1.00) 		0.267
(1.00)
19q loss 44 (17%) 221 0.116
(1.00) 		0.369
(1.00) 		0.048
(1.00) 		0.0903
(1.00) 		0.184
(1.00) 		0.161
(1.00) 		0.0471
(1.00) 		0.458
(1.00) 		1
(1.00)
20p loss 37 (14%) 228 0.0217
(1.00) 		0.125
(1.00) 		1
(1.00) 		0.251
(1.00) 		0.398
(1.00) 		0.128
(1.00) 		0.113
(1.00) 		1
(1.00) 		1
(1.00)
20q loss 20 (8%) 245 0.189
(1.00) 		0.359
(1.00) 		0.649
(1.00) 		0.573
(1.00) 		0.425
(1.00) 		0.853
(1.00) 		0.127
(1.00) 		0.608
(1.00) 		0.327
(1.00)
21q loss 38 (14%) 227 0.61
(1.00) 		0.951
(1.00) 		0.0216
(1.00) 		0.0869
(1.00) 		0.54
(1.00) 		0.781
(1.00) 		0.687
(1.00) 		1
(1.00) 		1
(1.00)
22q loss 60 (23%) 205 0.748
(1.00) 		0.148
(1.00) 		0.055
(1.00) 		0.655
(1.00) 		0.743
(1.00) 		0.898
(1.00) 		0.674
(1.00) 		0.504
(1.00) 		0.499
(1.00) 		0.838
(1.00)
'8q gain mutation analysis' versus 'AGE'

P value = 9.09e-05 (t-test), Q value = 0.066

Table S1.  Gene #16: '8q gain mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 234 65.2 (9.8)
8Q GAIN MUTATED 68 61.5 (8.7)
8Q GAIN WILD-TYPE 166 66.7 (9.8)

Figure S1.  Get High-res Image Gene #16: '8q gain mutation analysis' versus Clinical Feature #2: 'AGE'

'4q loss mutation analysis' versus 'GENDER'

P value = 0.000327 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #46: '4q loss mutation analysis' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 145 120
4Q LOSS MUTATED 7 23
4Q LOSS WILD-TYPE 138 97

Figure S2.  Get High-res Image Gene #46: '4q loss mutation analysis' versus Clinical Feature #3: 'GENDER'

'7q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.91e-05 (Chi-square test), Q value = 0.029

Table S3.  Gene #52: '7q loss mutation analysis' 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) ADENOCARCINOMA
ALL 3 60 171 3 8 2 2 2 10 1 3
7Q LOSS MUTATED 0 0 9 0 0 1 0 0 1 0 2
7Q LOSS WILD-TYPE 3 60 162 3 8 1 2 2 9 1 1

Figure S3.  Get High-res Image Gene #52: '7q loss mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

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

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

  • Number of patients = 265

  • Number of significantly arm-level cnvs = 77

  • Number of selected clinical features = 10

  • 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)
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