Correlation between copy number variations of arm-level result and selected clinical features
Cholangiocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C12806RS
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/C12806RS
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 66 arm-level events and 10 clinical features across 36 patients, no significant finding detected with Q value < 0.25.

  • No arm-level cnvs related to clinical features.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 66 arm-level events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR 		RACE
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
1p gain 10 (28%) 26 0.748
(1.00) 		0.596
(1.00) 		0.787
(1.00) 		0.343
(1.00) 		0.286
(1.00) 		0.291
(1.00) 		0.285
(1.00) 		0.455
(1.00) 		0.215
(1.00) 		0.763
(1.00)
1q gain 21 (58%) 15 0.785
(1.00) 		0.413
(1.00) 		0.198
(1.00) 		0.336
(1.00) 		0.368
(1.00) 		0.36
(1.00) 		0.741
(1.00) 		0.207
(1.00) 		0.607
(1.00) 		0.777
(1.00)
2p gain 6 (17%) 30 0.582
(1.00) 		0.432
(1.00) 		0.927
(1.00) 		0.585
(1.00) 		1
(1.00) 		1
(1.00) 		0.672
(1.00) 		0.698
(1.00) 		0.399
(1.00) 		0.187
(1.00)
2q gain 6 (17%) 30 0.501
(1.00) 		0.51
(1.00) 		0.505
(1.00) 		0.475
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.672
(1.00) 		0.693
(1.00) 		0.556
(1.00) 		0.184
(1.00)
3p gain 3 (8%) 33 0.478
(1.00) 		0.277
(1.00) 		0.551
(1.00) 		0.24
(1.00) 		0.422
(1.00) 		0.4
(1.00) 		0.574
(1.00) 		0.186
(1.00) 		1
(1.00) 		0.37
(1.00)
3q gain 8 (22%) 28 0.325
(1.00) 		0.159
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.574
(1.00) 		0.103
(1.00) 		0.128
(1.00) 		0.127
(1.00) 		0.16
(1.00)
4p gain 3 (8%) 33 0.0435
(1.00) 		0.0758
(1.00) 		0.137
(1.00) 		0.124
(1.00) 		0.422
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.188
(1.00) 		0.277
(1.00) 		0.368
(1.00)
5p gain 12 (33%) 24 0.961
(1.00) 		0.775
(1.00) 		0.606
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.63
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.23
(1.00)
5q gain 12 (33%) 24 0.961
(1.00) 		0.775
(1.00) 		0.605
(1.00) 		0.706
(1.00) 		1
(1.00) 		0.63
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.228
(1.00)
6p gain 7 (19%) 29 0.0851
(1.00) 		0.764
(1.00) 		1
(1.00) 		0.717
(1.00) 		1
(1.00) 		1
(1.00) 		0.0298
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.422
(1.00)
7p gain 7 (19%) 29 0.276
(1.00) 		0.81
(1.00) 		0.161
(1.00) 		0.524
(1.00) 		0.241
(1.00) 		0.282
(1.00) 		1
(1.00) 		0.0892
(1.00) 		0.774
(1.00) 		0.419
(1.00)
7q gain 6 (17%) 30 0.44
(1.00) 		0.718
(1.00) 		0.177
(1.00) 		0.706
(1.00) 		0.173
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.0598
(1.00) 		0.553
(1.00) 		0.363
(1.00)
8p gain 6 (17%) 30 0.443
(1.00) 		0.581
(1.00) 		0.256
(1.00) 		0.475
(1.00) 		0.241
(1.00) 		0.216
(1.00) 		0.374
(1.00) 		0.143
(1.00) 		0.554
(1.00) 		0.623
(1.00)
8q gain 12 (33%) 24 0.349
(1.00) 		0.392
(1.00) 		0.749
(1.00) 		0.894
(1.00) 		1
(1.00) 		1
(1.00) 		0.298
(1.00) 		0.634
(1.00) 		0.835
(1.00) 		0.231
(1.00)
10p gain 5 (14%) 31 0.875
(1.00) 		0.945
(1.00) 		0.746
(1.00) 		0.678
(1.00) 		1
(1.00) 		1
(1.00) 		0.149
(1.00) 		1
(1.00) 		1
(1.00) 		0.55
(1.00)
11p gain 4 (11%) 32 0.112
(1.00) 		0.743
(1.00) 		0.13
(1.00) 		0.61
(1.00) 		0.0601
(1.00) 		0.0993
(1.00) 		1
(1.00) 		0.12
(1.00) 		0.374
(1.00) 		0.0849
(1.00)
11q gain 4 (11%) 32 0.112
(1.00) 		0.743
(1.00) 		0.127
(1.00) 		0.611
(1.00) 		0.0601
(1.00) 		0.0993
(1.00) 		1
(1.00) 		0.122
(1.00) 		0.377
(1.00) 		0.0836
(1.00)
12p gain 9 (25%) 27 0.023
(1.00) 		0.798
(1.00) 		1
(1.00) 		0.43
(1.00) 		1
(1.00) 		1
(1.00) 		0.146
(1.00) 		1
(1.00) 		0.522
(1.00) 		0.0177
(1.00)
12q gain 8 (22%) 28 0.087
(1.00) 		0.805
(1.00) 		0.958
(1.00) 		0.733
(1.00) 		0.291
(1.00) 		0.302
(1.00) 		0.422
(1.00) 		0.731
(1.00) 		0.614
(1.00) 		0.011
(1.00)
13q gain 3 (8%) 33 0.952
(1.00) 		0.457
(1.00) 		0.0796
(1.00) 		0.538
(1.00) 		0.0601
(1.00) 		0.0532
(1.00) 		1
(1.00) 		0.0028
(1.00) 		0.276
(1.00) 		1
(1.00)
15q gain 6 (17%) 30 0.569
(1.00) 		0.687
(1.00) 		0.317
(1.00) 		0.835
(1.00) 		0.173
(1.00) 		1
(1.00) 		1
(1.00) 		0.143
(1.00) 		0.556
(1.00) 		0.362
(1.00)
16p gain 7 (19%) 29 0.444
(1.00) 		0.208
(1.00) 		0.698
(1.00) 		0.444
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.426
(1.00) 		0.328
(1.00) 		1
(1.00) 		0.683
(1.00)
16q gain 5 (14%) 31 0.213
(1.00) 		0.423
(1.00) 		0.813
(1.00) 		0.83
(1.00) 		1
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.186
(1.00) 		0.73
(1.00) 		0.547
(1.00)
17p gain 3 (8%) 33 0.0222
(1.00) 		0.797
(1.00) 		0.553
(1.00) 		0.713
(1.00) 		0.301
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.43
(1.00) 		0.278
(1.00) 		0.0438
(1.00)
17q gain 7 (19%) 29 0.00835
(1.00) 		0.873
(1.00) 		0.86
(1.00) 		0.616
(1.00) 		1
(1.00) 		1
(1.00) 		0.204
(1.00) 		1
(1.00) 		0.774
(1.00) 		0.0604
(1.00)
18p gain 7 (19%) 29 0.732
(1.00) 		0.119
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.426
(1.00) 		0.33
(1.00) 		0.6
(1.00) 		0.683
(1.00)
18q gain 6 (17%) 30 0.685
(1.00) 		0.226
(1.00) 		0.928
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.747
(1.00) 		0.619
(1.00)
19p gain 6 (17%) 30 0.689
(1.00) 		0.396
(1.00) 		0.313
(1.00) 		0.703
(1.00) 		0.173
(1.00) 		1
(1.00) 		1
(1.00) 		0.404
(1.00) 		0.746
(1.00) 		0.36
(1.00)
19q gain 6 (17%) 30 0.689
(1.00) 		0.396
(1.00) 		0.314
(1.00) 		0.706
(1.00) 		0.173
(1.00) 		1
(1.00) 		1
(1.00) 		0.405
(1.00) 		0.747
(1.00) 		0.361
(1.00)
20p gain 11 (31%) 25 0.384
(1.00) 		0.0304
(1.00) 		0.581
(1.00) 		0.694
(1.00) 		1
(1.00) 		1
(1.00) 		0.0335
(1.00) 		1
(1.00) 		0.371
(1.00) 		0.189
(1.00)
20q gain 12 (33%) 24 0.627
(1.00) 		0.0156
(1.00) 		0.504
(1.00) 		0.546
(1.00) 		1
(1.00) 		1
(1.00) 		0.0815
(1.00) 		0.637
(1.00) 		0.199
(1.00) 		0.231
(1.00)
21q gain 3 (8%) 33 0.373
(1.00) 		0.731
(1.00) 		0.411
(1.00) 		0.243
(1.00) 		0.422
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.543
(1.00) 		1
(1.00)
22q gain 5 (14%) 31 0.196
(1.00) 		0.252
(1.00) 		0.15
(1.00) 		0.83
(1.00) 		0.173
(1.00) 		0.155
(1.00) 		0.637
(1.00) 		0.187
(1.00) 		0.472
(1.00) 		1
(1.00)
1p loss 4 (11%) 32 0.608
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.436
(1.00) 		0.112
(1.00) 		0.0532
(1.00) 		1
(1.00) 		0.532
(1.00) 		0.377
(1.00) 		0.467
(1.00)
3p loss 22 (61%) 14 0.801
(1.00) 		0.346
(1.00) 		0.0596
(1.00) 		0.116
(1.00) 		0.06
(1.00) 		0.36
(1.00) 		0.307
(1.00) 		0.253
(1.00) 		0.338
(1.00) 		1
(1.00)
3q loss 3 (8%) 33 0.285
(1.00) 		0.886
(1.00) 		0.65
(1.00) 		0.714
(1.00) 		1
(1.00) 		1
(1.00) 		0.238
(1.00) 		1
(1.00) 		1
(1.00) 		0.0451
(1.00)
4p loss 10 (28%) 26 0.867
(1.00) 		0.888
(1.00) 		0.499
(1.00) 		0.145
(1.00) 		1
(1.00) 		1
(1.00) 		0.0732
(1.00) 		1
(1.00) 		1
(1.00) 		0.148
(1.00)
4q loss 13 (36%) 23 0.96
(1.00) 		0.692
(1.00) 		0.96
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.63
(1.00) 		0.493
(1.00) 		0.656
(1.00) 		0.599
(1.00) 		1
(1.00)
6p loss 5 (14%) 31 0.844
(1.00) 		0.731
(1.00) 		0.503
(1.00) 		0.11
(1.00) 		0.56
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.727
(1.00) 		1
(1.00)
6q loss 20 (56%) 16 0.496
(1.00) 		0.339
(1.00) 		0.895
(1.00) 		0.806
(1.00) 		0.636
(1.00) 		0.639
(1.00) 		0.091
(1.00) 		0.525
(1.00) 		0.847
(1.00) 		0.783
(1.00)
7p loss 4 (11%) 32 0.0272
(1.00) 		0.597
(1.00) 		0.297
(1.00) 		0.435
(1.00) 		0.422
(1.00) 		1
(1.00) 		0.613
(1.00) 		1
(1.00) 		0.655
(1.00) 		0.464
(1.00)
7q loss 4 (11%) 32 0.227
(1.00) 		0.821
(1.00) 		0.35
(1.00) 		0.249
(1.00) 		1
(1.00) 		1
(1.00) 		0.613
(1.00) 		1
(1.00) 		0.653
(1.00) 		0.465
(1.00)
8p loss 10 (28%) 26 0.379
(1.00) 		0.536
(1.00) 		0.195
(1.00) 		0.0286
(1.00) 		0.291
(1.00) 		0.29
(1.00) 		0.285
(1.00) 		0.454
(1.00) 		0.421
(1.00) 		0.763
(1.00)
8q loss 3 (8%) 33 0.536
(1.00) 		0.529
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.278
(1.00) 		1
(1.00)
9p loss 18 (50%) 18 0.99
(1.00) 		0.0515
(1.00) 		0.107
(1.00) 		0.356
(1.00) 		0.654
(1.00) 		0.0184
(1.00) 		0.315
(1.00) 		0.21
(1.00) 		1
(1.00) 		0.229
(1.00)
9q loss 19 (53%) 17 0.987
(1.00) 		0.0493
(1.00) 		0.39
(1.00) 		0.244
(1.00) 		0.172
(1.00) 		0.152
(1.00) 		1
(1.00) 		0.432
(1.00) 		0.495
(1.00) 		0.228
(1.00)
10p loss 6 (17%) 30 0.972
(1.00) 		0.983
(1.00) 		0.18
(1.00) 		0.706
(1.00) 		0.173
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.0597
(1.00) 		0.555
(1.00) 		0.36
(1.00)
10q loss 5 (14%) 31 0.641
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.83
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.637
(1.00) 		0.333
(1.00) 		1
(1.00) 		1
(1.00)
11p loss 8 (22%) 28 0.261
(1.00) 		0.985
(1.00) 		0.728
(1.00) 		0.413
(1.00) 		0.553
(1.00) 		1
(1.00) 		0.422
(1.00) 		1
(1.00) 		0.276
(1.00) 		1
(1.00)
11q loss 9 (25%) 27 0.153
(1.00) 		0.715
(1.00) 		0.862
(1.00) 		0.43
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.146
(1.00) 		1
(1.00) 		0.52
(1.00) 		1
(1.00)
12q loss 3 (8%) 33 0.363
(1.00) 		0.954
(1.00) 		0.0805
(1.00) 		0.536
(1.00) 		0.0601
(1.00) 		0.0532
(1.00) 		1
(1.00) 		0.066
(1.00) 		0.276
(1.00) 		1
(1.00)
13q loss 15 (42%) 21 0.449
(1.00) 		0.712
(1.00) 		0.495
(1.00) 		0.415
(1.00) 		0.368
(1.00) 		0.131
(1.00) 		0.741
(1.00) 		0.093
(1.00) 		1
(1.00) 		0.627
(1.00)
14q loss 13 (36%) 23 0.938
(1.00) 		0.961
(1.00) 		0.508
(1.00) 		0.799
(1.00) 		0.147
(1.00) 		0.63
(1.00) 		0.731
(1.00) 		0.654
(1.00) 		1
(1.00) 		1
(1.00)
15q loss 5 (14%) 31 0.212
(1.00) 		0.537
(1.00) 		0.501
(1.00) 		0.193
(1.00) 		0.525
(1.00) 		0.5
(1.00) 		0.637
(1.00) 		0.332
(1.00) 		0.729
(1.00) 		1
(1.00)
16p loss 4 (11%) 32 0.311
(1.00) 		0.84
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.303
(1.00) 		1
(1.00) 		0.651
(1.00) 		0.467
(1.00)
16q loss 7 (19%) 29 0.909
(1.00) 		0.889
(1.00) 		0.825
(1.00) 		1
(1.00) 		1
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.715
(1.00) 		0.0569
(1.00) 		0.685
(1.00)
17p loss 10 (28%) 26 0.244
(1.00) 		0.958
(1.00) 		0.881
(1.00) 		0.524
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.774
(1.00) 		0.542
(1.00) 		0.241
(1.00)
18p loss 6 (17%) 30 0.585
(1.00) 		0.47
(1.00) 		0.929
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.374
(1.00) 		1
(1.00) 		1
(1.00) 		0.0893
(1.00)
18q loss 8 (22%) 28 0.534
(1.00) 		0.849
(1.00) 		0.958
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.537
(1.00) 		1
(1.00) 		0.159
(1.00)
19p loss 4 (11%) 32 0.505
(1.00) 		0.94
(1.00) 		0.497
(1.00) 		1
(1.00) 		0.525
(1.00) 		0.5
(1.00) 		1
(1.00) 		0.0621
(1.00) 		0.377
(1.00) 		1
(1.00)
19q loss 3 (8%) 33 0.436
(1.00) 		0.567
(1.00) 		0.785
(1.00) 		0.375
(1.00) 		1
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.431
(1.00) 		1
(1.00) 		1
(1.00)
20p loss 5 (14%) 31 0.422
(1.00) 		0.537
(1.00) 		0.815
(1.00) 		0.829
(1.00) 		1
(1.00) 		0.5
(1.00) 		1
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.548
(1.00)
21q loss 15 (42%) 21 0.403
(1.00) 		0.199
(1.00) 		0.603
(1.00) 		0.414
(1.00) 		0.368
(1.00) 		0.625
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.835
(1.00) 		0.778
(1.00)
22q loss 5 (14%) 31 0.22
(1.00) 		1
(1.00) 		0.502
(1.00) 		0.108
(1.00) 		1
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.621
(1.00) 		0.729
(1.00) 		0.299
(1.00)
xp loss 15 (42%) 21 0.946
(1.00) 		0.885
(1.00) 		0.23
(1.00) 		0.588
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.32
(1.00) 		0.642
(1.00) 		0.836
(1.00) 		0.199
(1.00)
xq loss 15 (42%) 21 0.946
(1.00) 		0.885
(1.00) 		0.227
(1.00) 		0.589
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.32
(1.00) 		0.642
(1.00) 		0.833
(1.00) 		0.201
(1.00)
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/CHOL-TP/19780560/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CHOL-TP/19775070/CHOL-TP.merged_data.txt

  • Number of patients = 36

  • Number of significantly arm-level cnvs = 66

  • Number of selected clinical features = 10

  • 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)
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