Correlation between copy number variations of arm-level result and selected clinical features
Liver Hepatocellular Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1ZK5FKH
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/C1ZK5FKH
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 11 clinical features across 311 patients, 2 significant findings detected with Q value < 0.25.

  • 16q loss cnv correlated to 'AGE' and 'RACE'.

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 11 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 HISTOLOGICAL
TYPE 		COMPLETENESS
OF
RESECTION 		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 Fisher's exact test Fisher's exact test Fisher's exact test
16q loss 129 (41%) 182 0.781
(1.00) 		5.01e-05
(0.0441) 		0.179
(1.00) 		0.0788
(1.00) 		0.586
(1.00) 		0.0398
(1.00) 		0.391
(1.00) 		0.609
(1.00) 		0.307
(1.00) 		3e-05
(0.0264) 		0.0748
(1.00)
1p gain 49 (16%) 262 0.975
(1.00) 		0.185
(1.00) 		0.252
(1.00) 		0.0496
(1.00) 		1
(1.00) 		0.927
(1.00) 		0.246
(1.00) 		1
(1.00) 		0.48
(1.00) 		0.0834
(1.00) 		1
(1.00)
1q gain 192 (62%) 119 0.843
(1.00) 		0.328
(1.00) 		0.148
(1.00) 		0.116
(1.00) 		0.558
(1.00) 		0.197
(1.00) 		0.533
(1.00) 		0.173
(1.00) 		0.23
(1.00) 		0.0899
(1.00) 		0.161
(1.00)
2p gain 38 (12%) 273 0.372
(1.00) 		0.131
(1.00) 		0.032
(1.00) 		0.0462
(1.00) 		0.0444
(1.00) 		0.104
(1.00) 		0.00253
(1.00) 		0.351
(1.00) 		0.0713
(1.00) 		0.536
(1.00) 		0.275
(1.00)
2q gain 37 (12%) 274 0.404
(1.00) 		0.408
(1.00) 		0.125
(1.00) 		0.144
(1.00) 		0.35
(1.00) 		0.0789
(1.00) 		0.00118
(1.00) 		0.343
(1.00) 		0.254
(1.00) 		0.756
(1.00) 		0.264
(1.00)
3p gain 33 (11%) 278 0.984
(1.00) 		0.594
(1.00) 		0.715
(1.00) 		0.743
(1.00) 		0.267
(1.00) 		0.48
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.167
(1.00) 		0.733
(1.00) 		1
(1.00)
3q gain 36 (12%) 275 0.336
(1.00) 		0.661
(1.00) 		0.728
(1.00) 		0.744
(1.00) 		0.288
(1.00) 		0.454
(1.00) 		0.19
(1.00) 		0.632
(1.00) 		0.199
(1.00) 		0.597
(1.00) 		0.243
(1.00)
4p gain 21 (7%) 290 0.0317
(1.00) 		0.263
(1.00) 		0.372
(1.00) 		0.167
(1.00) 		1
(1.00) 		0.104
(1.00) 		0.629
(1.00) 		1
(1.00) 		1
(1.00) 		0.576
(1.00) 		1
(1.00)
4q gain 7 (2%) 304 0.631
(1.00) 		0.236
(1.00) 		0.76
(1.00) 		0.696
(1.00) 		1
(1.00) 		0.415
(1.00) 		1
(1.00) 		1
(1.00) 		0.162
(1.00) 		0.597
(1.00) 		0.177
(1.00)
5p gain 116 (37%) 195 0.331
(1.00) 		0.296
(1.00) 		0.332
(1.00) 		0.0732
(1.00) 		0.554
(1.00) 		0.806
(1.00) 		0.802
(1.00) 		0.598
(1.00) 		0.868
(1.00) 		0.9
(1.00) 		1
(1.00)
5q gain 91 (29%) 220 0.484
(1.00) 		0.165
(1.00) 		0.924
(1.00) 		0.518
(1.00) 		0.561
(1.00) 		0.904
(1.00) 		0.183
(1.00) 		1
(1.00) 		0.784
(1.00) 		0.783
(1.00) 		1
(1.00)
6p gain 97 (31%) 214 0.985
(1.00) 		0.358
(1.00) 		0.748
(1.00) 		0.385
(1.00) 		0.553
(1.00) 		0.396
(1.00) 		0.192
(1.00) 		0.44
(1.00) 		0.534
(1.00) 		0.194
(1.00) 		0.715
(1.00)
6q gain 53 (17%) 258 0.239
(1.00) 		0.696
(1.00) 		0.267
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.191
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.315
(1.00) 		0.302
(1.00) 		0.634
(1.00)
7p gain 94 (30%) 217 0.955
(1.00) 		0.124
(1.00) 		0.67
(1.00) 		0.804
(1.00) 		0.201
(1.00) 		0.511
(1.00) 		0.509
(1.00) 		0.841
(1.00) 		0.7
(1.00) 		0.346
(1.00) 		0.257
(1.00)
7q gain 91 (29%) 220 0.517
(1.00) 		0.0847
(1.00) 		0.644
(1.00) 		0.624
(1.00) 		0.196
(1.00) 		1
(1.00) 		1
(1.00) 		0.837
(1.00) 		0.836
(1.00) 		0.131
(1.00) 		0.249
(1.00)
8p gain 68 (22%) 243 0.701
(1.00) 		0.0853
(1.00) 		0.941
(1.00) 		0.787
(1.00) 		0.576
(1.00) 		0.0954
(1.00) 		0.027
(1.00) 		0.464
(1.00) 		0.324
(1.00) 		0.23
(1.00) 		0.377
(1.00)
8q gain 162 (52%) 149 0.744
(1.00) 		0.132
(1.00) 		0.118
(1.00) 		0.321
(1.00) 		0.597
(1.00) 		0.881
(1.00) 		0.000676
(0.593) 		0.162
(1.00) 		0.804
(1.00) 		0.0992
(1.00) 		0.0694
(1.00)
9p gain 17 (5%) 294 0.899
(1.00) 		0.26
(1.00) 		0.0388
(1.00) 		0.0974
(1.00) 		1
(1.00) 		0.259
(1.00) 		0.189
(1.00) 		0.0645
(1.00) 		0.139
(1.00) 		0.378
(1.00) 		0.345
(1.00)
9q gain 17 (5%) 294 0.552
(1.00) 		0.144
(1.00) 		0.058
(1.00) 		0.0682
(1.00) 		1
(1.00) 		0.262
(1.00) 		0.0289
(1.00) 		0.364
(1.00) 		0.138
(1.00) 		0.71
(1.00) 		0.363
(1.00)
10p gain 53 (17%) 258 0.793
(1.00) 		0.0024
(1.00) 		0.217
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.241
(1.00) 		0.523
(1.00) 		0.355
(1.00) 		0.831
(1.00) 		0.478
(1.00) 		0.151
(1.00)
10q gain 32 (10%) 279 0.524
(1.00) 		0.0425
(1.00) 		0.0667
(1.00) 		0.102
(1.00) 		1
(1.00) 		0.0719
(1.00) 		0.162
(1.00) 		0.585
(1.00) 		0.809
(1.00) 		0.604
(1.00) 		0.041
(1.00)
11p gain 16 (5%) 295 0.924
(1.00) 		0.858
(1.00) 		0.262
(1.00) 		0.164
(1.00) 		1
(1.00) 		0.157
(1.00) 		0.597
(1.00) 		1
(1.00) 		0.0136
(1.00) 		0.769
(1.00) 		1
(1.00)
11q gain 17 (5%) 294 0.625
(1.00) 		0.962
(1.00) 		0.116
(1.00) 		0.0391
(1.00) 		1
(1.00) 		0.065
(1.00) 		0.43
(1.00) 		1
(1.00) 		0.0178
(1.00) 		0.711
(1.00) 		1
(1.00)
12p gain 35 (11%) 276 0.163
(1.00) 		0.758
(1.00) 		0.158
(1.00) 		0.0591
(1.00) 		1
(1.00) 		0.499
(1.00) 		0.179
(1.00) 		0.0321
(1.00) 		0.907
(1.00) 		0.806
(1.00) 		0.604
(1.00)
12q gain 37 (12%) 274 0.433
(1.00) 		0.621
(1.00) 		0.0237
(1.00) 		0.0427
(1.00) 		0.32
(1.00) 		0.366
(1.00) 		0.0624
(1.00) 		0.342
(1.00) 		0.622
(1.00) 		0.887
(1.00) 		0.603
(1.00)
13q gain 19 (6%) 292 0.133
(1.00) 		0.875
(1.00) 		0.053
(1.00) 		0.467
(1.00) 		0.211
(1.00) 		0.132
(1.00) 		0.203
(1.00) 		1
(1.00) 		0.434
(1.00) 		0.434
(1.00) 		0.382
(1.00)
14q gain 17 (5%) 294 0.433
(1.00) 		0.649
(1.00) 		0.299
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.257
(1.00) 		0.43
(1.00) 		0.0637
(1.00) 		0.0583
(1.00) 		0.343
(1.00) 		0.363
(1.00)
15q gain 29 (9%) 282 0.0932
(1.00) 		0.652
(1.00) 		0.583
(1.00) 		0.367
(1.00) 		1
(1.00) 		0.562
(1.00) 		0.407
(1.00) 		0.262
(1.00) 		1
(1.00) 		0.615
(1.00) 		1
(1.00)
16p gain 24 (8%) 287 0.638
(1.00) 		0.136
(1.00) 		0.331
(1.00) 		0.505
(1.00) 		1
(1.00) 		0.597
(1.00) 		0.503
(1.00) 		0.0656
(1.00) 		0.584
(1.00) 		0.588
(1.00) 		0.466
(1.00)
16q gain 11 (4%) 300 0.686
(1.00) 		0.0425
(1.00) 		0.413
(1.00) 		0.288
(1.00) 		1
(1.00) 		0.754
(1.00) 		0.513
(1.00) 		0.0141
(1.00) 		0.7
(1.00) 		0.573
(1.00) 		0.222
(1.00)
17p gain 28 (9%) 283 0.533
(1.00) 		0.396
(1.00) 		0.58
(1.00) 		0.395
(1.00) 		1
(1.00) 		0.871
(1.00) 		1
(1.00) 		0.536
(1.00) 		0.108
(1.00) 		0.766
(1.00) 		0.541
(1.00)
17q gain 81 (26%) 230 0.903
(1.00) 		0.324
(1.00) 		0.741
(1.00) 		0.477
(1.00) 		1
(1.00) 		0.174
(1.00) 		0.0992
(1.00) 		1
(1.00) 		0.0293
(1.00) 		0.17
(1.00) 		0.445
(1.00)
18p gain 28 (9%) 283 0.745
(1.00) 		0.158
(1.00) 		0.332
(1.00) 		0.236
(1.00) 		1
(1.00) 		0.235
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.125
(1.00) 		0.0456
(1.00) 		1
(1.00)
18q gain 22 (7%) 289 0.993
(1.00) 		0.0602
(1.00) 		0.281
(1.00) 		0.311
(1.00) 		1
(1.00) 		0.168
(1.00) 		0.478
(1.00) 		1
(1.00) 		0.0497
(1.00) 		0.151
(1.00) 		1
(1.00)
19p gain 49 (16%) 262 0.968
(1.00) 		0.384
(1.00) 		0.0409
(1.00) 		0.701
(1.00) 		0.418
(1.00) 		0.0187
(1.00) 		0.0455
(1.00) 		0.464
(1.00) 		0.195
(1.00) 		0.33
(1.00) 		0.119
(1.00)
19q gain 62 (20%) 249 0.764
(1.00) 		0.389
(1.00) 		0.0626
(1.00) 		0.753
(1.00) 		0.481
(1.00) 		0.0458
(1.00) 		0.227
(1.00) 		0.581
(1.00) 		0.239
(1.00) 		0.616
(1.00) 		0.369
(1.00)
20p gain 91 (29%) 220 0.00716
(1.00) 		0.235
(1.00) 		0.11
(1.00) 		0.0793
(1.00) 		1
(1.00) 		0.0411
(1.00) 		0.23
(1.00) 		1
(1.00) 		0.444
(1.00) 		0.826
(1.00) 		0.694
(1.00)
20q gain 95 (31%) 216 0.0687
(1.00) 		0.299
(1.00) 		0.109
(1.00) 		0.0433
(1.00) 		1
(1.00) 		0.22
(1.00) 		0.513
(1.00) 		1
(1.00) 		0.506
(1.00) 		0.954
(1.00) 		1
(1.00)
21q gain 23 (7%) 288 0.419
(1.00) 		0.196
(1.00) 		0.038
(1.00) 		0.013
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.462
(1.00) 		0.0292
(1.00) 		0.628
(1.00) 		0.113
(1.00)
22q gain 41 (13%) 270 0.3
(1.00) 		0.587
(1.00) 		0.0522
(1.00) 		0.0077
(1.00) 		0.34
(1.00) 		1
(1.00) 		0.591
(1.00) 		0.385
(1.00) 		0.264
(1.00) 		0.682
(1.00) 		0.308
(1.00)
xq gain 50 (16%) 261 0.622
(1.00) 		0.468
(1.00) 		0.961
(1.00) 		0.905
(1.00) 		1
(1.00) 		0.793
(1.00) 		0.191
(1.00) 		0.716
(1.00) 		0.498
(1.00) 		0.253
(1.00) 		1
(1.00)
1p loss 72 (23%) 239 0.877
(1.00) 		0.375
(1.00) 		0.277
(1.00) 		0.435
(1.00) 		0.563
(1.00) 		0.00071
(0.622) 		0.314
(1.00) 		0.185
(1.00) 		0.445
(1.00) 		0.705
(1.00) 		1
(1.00)
1q loss 19 (6%) 292 0.247
(1.00) 		0.625
(1.00) 		0.307
(1.00) 		0.19
(1.00) 		0.176
(1.00) 		0.675
(1.00) 		0.8
(1.00) 		0.4
(1.00) 		0.198
(1.00) 		0.51
(1.00) 		0.382
(1.00)
2p loss 28 (9%) 283 0.634
(1.00) 		0.371
(1.00) 		0.787
(1.00) 		0.392
(1.00) 		1
(1.00) 		0.755
(1.00) 		0.289
(1.00) 		0.537
(1.00) 		0.884
(1.00) 		0.851
(1.00) 		1
(1.00)
2q loss 33 (11%) 278 0.464
(1.00) 		0.176
(1.00) 		0.908
(1.00) 		0.899
(1.00) 		1
(1.00) 		0.784
(1.00) 		0.694
(1.00) 		0.597
(1.00) 		0.317
(1.00) 		0.701
(1.00) 		0.581
(1.00)
3p loss 43 (14%) 268 0.484
(1.00) 		0.193
(1.00) 		0.0114
(1.00) 		0.00237
(1.00) 		0.36
(1.00) 		0.686
(1.00) 		0.483
(1.00) 		0.0015
(1.00) 		0.451
(1.00) 		0.846
(1.00) 		0.604
(1.00)
3q loss 32 (10%) 279 0.104
(1.00) 		0.2
(1.00) 		0.178
(1.00) 		0.0898
(1.00) 		0.288
(1.00) 		0.887
(1.00) 		0.55
(1.00) 		0.045
(1.00) 		0.662
(1.00) 		0.587
(1.00) 		1
(1.00)
4p loss 92 (30%) 219 0.542
(1.00) 		0.131
(1.00) 		0.11
(1.00) 		0.222
(1.00) 		0.196
(1.00) 		0.119
(1.00) 		0.235
(1.00) 		1
(1.00) 		0.448
(1.00) 		0.173
(1.00) 		0.701
(1.00)
4q loss 127 (41%) 184 0.707
(1.00) 		0.00412
(1.00) 		0.655
(1.00) 		0.566
(1.00) 		0.575
(1.00) 		0.0112
(1.00) 		0.388
(1.00) 		0.605
(1.00) 		0.202
(1.00) 		0.0043
(1.00) 		1
(1.00)
5p loss 26 (8%) 285 0.772
(1.00) 		0.0214
(1.00) 		0.394
(1.00) 		0.313
(1.00) 		0.267
(1.00) 		0.454
(1.00) 		0.383
(1.00) 		0.0262
(1.00) 		1
(1.00) 		0.351
(1.00) 		1
(1.00)
5q loss 37 (12%) 274 0.394
(1.00) 		0.0754
(1.00) 		0.255
(1.00) 		0.0212
(1.00) 		0.32
(1.00) 		0.807
(1.00) 		1
(1.00) 		0.0085
(1.00) 		0.766
(1.00) 		0.703
(1.00) 		0.602
(1.00)
6p loss 24 (8%) 287 0.607
(1.00) 		0.913
(1.00) 		0.293
(1.00) 		0.67
(1.00) 		0.222
(1.00) 		0.313
(1.00) 		0.0222
(1.00) 		1
(1.00) 		1
(1.00) 		0.156
(1.00) 		1
(1.00)
6q loss 80 (26%) 231 0.722
(1.00) 		0.0171
(1.00) 		0.336
(1.00) 		0.646
(1.00) 		0.164
(1.00) 		0.228
(1.00) 		0.0262
(1.00) 		0.299
(1.00) 		0.96
(1.00) 		0.725
(1.00) 		1
(1.00)
7p loss 14 (5%) 297 0.467
(1.00) 		0.664
(1.00) 		0.828
(1.00) 		0.537
(1.00) 		1
(1.00) 		0.607
(1.00) 		0.153
(1.00) 		1
(1.00) 		0.784
(1.00) 		0.655
(1.00) 		1
(1.00)
7q loss 19 (6%) 292 0.0132
(1.00) 		0.541
(1.00) 		0.905
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.675
(1.00) 		0.0205
(1.00) 		1
(1.00) 		0.198
(1.00) 		0.143
(1.00) 		1
(1.00)
8p loss 162 (52%) 149 0.905
(1.00) 		0.205
(1.00) 		0.515
(1.00) 		0.613
(1.00) 		0.115
(1.00) 		0.342
(1.00) 		0.903
(1.00) 		0.0468
(1.00) 		0.737
(1.00) 		0.193
(1.00) 		0.725
(1.00)
8q loss 36 (12%) 275 0.791
(1.00) 		0.994
(1.00) 		0.495
(1.00) 		0.384
(1.00) 		0.277
(1.00) 		0.566
(1.00) 		0.0217
(1.00) 		0.631
(1.00) 		0.683
(1.00) 		0.641
(1.00) 		0.603
(1.00)
9p loss 99 (32%) 212 0.324
(1.00) 		0.0383
(1.00) 		0.366
(1.00) 		0.806
(1.00) 		0.252
(1.00) 		0.127
(1.00) 		0.0264
(1.00) 		1
(1.00) 		0.393
(1.00) 		0.252
(1.00) 		0.445
(1.00)
9q loss 91 (29%) 220 0.196
(1.00) 		0.736
(1.00) 		0.126
(1.00) 		0.527
(1.00) 		0.0222
(1.00) 		0.108
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.336
(1.00) 		0.731
(1.00) 		0.442
(1.00)
10p loss 40 (13%) 271 0.581
(1.00) 		0.111
(1.00) 		0.0776
(1.00) 		0.167
(1.00) 		0.277
(1.00) 		0.668
(1.00) 		0.857
(1.00) 		0.0458
(1.00) 		0.43
(1.00) 		0.153
(1.00) 		1
(1.00)
10q loss 66 (21%) 245 0.181
(1.00) 		0.689
(1.00) 		0.415
(1.00) 		0.204
(1.00) 		0.481
(1.00) 		0.891
(1.00) 		0.768
(1.00) 		0.0126
(1.00) 		0.148
(1.00) 		0.00095
(0.831) 		1
(1.00)
11p loss 53 (17%) 258 0.815
(1.00) 		0.863
(1.00) 		0.0364
(1.00) 		0.0339
(1.00) 		0.0823
(1.00) 		0.414
(1.00) 		0.628
(1.00) 		0.0522
(1.00) 		0.53
(1.00) 		0.802
(1.00) 		0.624
(1.00)
11q loss 60 (19%) 251 0.739
(1.00) 		0.964
(1.00) 		0.0569
(1.00) 		0.135
(1.00) 		0.116
(1.00) 		0.287
(1.00) 		1
(1.00) 		0.0723
(1.00) 		0.455
(1.00) 		0.953
(1.00) 		0.179
(1.00)
12p loss 52 (17%) 259 0.415
(1.00) 		0.294
(1.00) 		0.0704
(1.00) 		0.341
(1.00) 		0.0785
(1.00) 		0.0941
(1.00) 		1
(1.00) 		1
(1.00) 		0.261
(1.00) 		0.774
(1.00) 		0.627
(1.00)
12q loss 30 (10%) 281 0.684
(1.00) 		0.135
(1.00) 		0.0337
(1.00) 		0.571
(1.00) 		1
(1.00) 		0.0186
(1.00) 		0.841
(1.00) 		0.56
(1.00) 		0.1
(1.00) 		0.395
(1.00) 		0.568
(1.00)
13q loss 107 (34%) 204 0.895
(1.00) 		0.633
(1.00) 		0.115
(1.00) 		0.00218
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.162
(1.00) 		0.279
(1.00) 		0.0813
(1.00) 		0.841
(1.00) 		1
(1.00)
14q loss 97 (31%) 214 0.601
(1.00) 		0.207
(1.00) 		0.0294
(1.00) 		0.00286
(1.00) 		1
(1.00) 		0.0428
(1.00) 		0.297
(1.00) 		0.343
(1.00) 		0.668
(1.00) 		0.0884
(1.00) 		1
(1.00)
15q loss 59 (19%) 252 0.0586
(1.00) 		0.67
(1.00) 		0.0642
(1.00) 		0.0165
(1.00) 		0.0943
(1.00) 		0.0633
(1.00) 		1
(1.00) 		0.555
(1.00) 		0.947
(1.00) 		0.463
(1.00) 		0.179
(1.00)
16p loss 99 (32%) 212 0.206
(1.00) 		0.000689
(0.605) 		0.304
(1.00) 		0.281
(1.00) 		0.27
(1.00) 		0.035
(1.00) 		0.298
(1.00) 		1
(1.00) 		0.0672
(1.00) 		0.00524
(1.00) 		0.281
(1.00)
17p loss 153 (49%) 158 0.185
(1.00) 		0.358
(1.00) 		0.00412
(1.00) 		0.0407
(1.00) 		0.122
(1.00) 		0.434
(1.00) 		0.904
(1.00) 		0.722
(1.00) 		0.285
(1.00) 		0.185
(1.00) 		0.17
(1.00)
17q loss 34 (11%) 277 0.108
(1.00) 		0.27
(1.00) 		0.00418
(1.00) 		0.0734
(1.00) 		0.0282
(1.00) 		0.385
(1.00) 		0.44
(1.00) 		0.00634
(1.00) 		1
(1.00) 		0.184
(1.00) 		0.201
(1.00)
18p loss 62 (20%) 249 0.932
(1.00) 		0.844
(1.00) 		0.691
(1.00) 		0.586
(1.00) 		0.507
(1.00) 		0.503
(1.00) 		0.227
(1.00) 		0.00468
(1.00) 		0.814
(1.00) 		0.888
(1.00) 		0.662
(1.00)
18q loss 66 (21%) 245 0.884
(1.00) 		0.24
(1.00) 		0.685
(1.00) 		0.98
(1.00) 		0.531
(1.00) 		0.207
(1.00) 		0.299
(1.00) 		0.0465
(1.00) 		0.574
(1.00) 		0.956
(1.00) 		0.371
(1.00)
19p loss 42 (14%) 269 0.135
(1.00) 		0.0769
(1.00) 		0.559
(1.00) 		0.17
(1.00) 		0.38
(1.00) 		0.206
(1.00) 		0.154
(1.00) 		0.394
(1.00) 		0.249
(1.00) 		0.0269
(1.00) 		0.605
(1.00)
19q loss 30 (10%) 281 0.974
(1.00) 		0.038
(1.00) 		0.437
(1.00) 		0.296
(1.00) 		0.299
(1.00) 		0.0881
(1.00) 		0.154
(1.00) 		0.561
(1.00) 		0.26
(1.00) 		0.0182
(1.00) 		1
(1.00)
20p loss 20 (6%) 291 0.675
(1.00) 		0.181
(1.00) 		0.196
(1.00) 		0.667
(1.00) 		1
(1.00) 		0.0945
(1.00) 		1
(1.00) 		0.0462
(1.00) 		0.857
(1.00) 		0.516
(1.00) 		0.417
(1.00)
20q loss 9 (3%) 302 0.553
(1.00) 		0.448
(1.00) 		0.295
(1.00) 		0.932
(1.00) 		1
(1.00) 		0.727
(1.00) 		1
(1.00) 		0.0648
(1.00) 		0.622
(1.00) 		1
(1.00) 		0.2
(1.00)
21q loss 94 (30%) 217 0.00596
(1.00) 		0.227
(1.00) 		0.15
(1.00) 		0.797
(1.00) 		0.229
(1.00) 		0.0353
(1.00) 		0.187
(1.00) 		0.0954
(1.00) 		0.35
(1.00) 		0.638
(1.00) 		1
(1.00)
22q loss 58 (19%) 253 0.311
(1.00) 		0.545
(1.00) 		0.438
(1.00) 		0.0631
(1.00) 		1
(1.00) 		0.614
(1.00) 		0.212
(1.00) 		0.047
(1.00) 		0.0411
(1.00) 		0.0217
(1.00) 		0.638
(1.00)
xq loss 59 (19%) 252 0.619
(1.00) 		0.202
(1.00) 		0.716
(1.00) 		0.336
(1.00) 		0.464
(1.00) 		0.449
(1.00) 		0.0877
(1.00) 		0.116
(1.00) 		0.594
(1.00) 		0.662
(1.00) 		0.642
(1.00)
'16q loss' versus 'AGE'

P value = 5.01e-05 (Wilcoxon-test), Q value = 0.044

Table S1.  Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 308 59.8 (12.7)
16Q LOSS MUTATED 128 56.5 (12.6)
16Q LOSS WILD-TYPE 180 62.2 (12.2)

Figure S1.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

'16q loss' versus 'RACE'

P value = 3e-05 (Fisher's exact test), Q value = 0.026

Table S2.  Gene #69: '16q loss' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 141 15 145
16Q LOSS MUTATED 0 78 7 41
16Q LOSS WILD-TYPE 1 63 8 104

Figure S2.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #10: 'RACE'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = LIHC-TP.merged_data.txt

  • Number of patients = 311

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 11

  • 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