Correlation between copy number variations of arm-level result and selected clinical features
Cholangiocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1N8795B
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1N8795B
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 65 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 65 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 0.348
(1.00) 		0.596
(1.00) 		0.785
(1.00) 		0.345
(1.00) 		0.286
(1.00) 		0.291
(1.00) 		0.285
(1.00) 		0.452
(1.00) 		0.217
(1.00) 		0.764
(1.00)
1q gain 22 (61%) 14 0.924
(1.00) 		0.236
(1.00) 		0.0535
(1.00) 		0.149
(1.00) 		0.624
(1.00) 		0.328
(1.00) 		1
(1.00) 		0.141
(1.00) 		0.83
(1.00) 		1
(1.00)
2p gain 5 (14%) 31 0.344
(1.00) 		0.436
(1.00) 		0.815
(1.00) 		1
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.62
(1.00) 		0.465
(1.00) 		0.134
(1.00)
2q gain 6 (17%) 30 0.309
(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) 		0.696
(1.00) 		0.555
(1.00) 		0.186
(1.00)
3q gain 7 (19%) 29 0.467
(1.00) 		0.223
(1.00) 		0.443
(1.00) 		0.847
(1.00) 		0.562
(1.00) 		0.282
(1.00) 		0.204
(1.00) 		0.0911
(1.00) 		0.0931
(1.00) 		0.123
(1.00)
5p gain 12 (33%) 24 0.807
(1.00) 		0.775
(1.00) 		0.605
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.63
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.23
(1.00)
5q gain 11 (31%) 25 0.983
(1.00) 		0.548
(1.00) 		0.504
(1.00) 		0.599
(1.00) 		1
(1.00) 		0.643
(1.00) 		1
(1.00) 		0.35
(1.00) 		0.829
(1.00) 		0.189
(1.00)
6p gain 8 (22%) 28 0.205
(1.00) 		0.53
(1.00) 		1
(1.00) 		0.733
(1.00) 		1
(1.00) 		1
(1.00) 		0.103
(1.00) 		0.245
(1.00) 		0.173
(1.00) 		0.474
(1.00)
6q gain 3 (8%) 33 0.198
(1.00) 		0.144
(1.00) 		0.555
(1.00) 		0.712
(1.00) 		0.422
(1.00) 		0.4
(1.00) 		0.574
(1.00) 		0.0324
(1.00) 		0.02
(1.00) 		1
(1.00)
7p gain 7 (19%) 29 0.164
(1.00) 		0.81
(1.00) 		0.16
(1.00) 		0.527
(1.00) 		0.241
(1.00) 		0.282
(1.00) 		1
(1.00) 		0.0906
(1.00) 		0.774
(1.00) 		0.419
(1.00)
7q gain 6 (17%) 30 0.294
(1.00) 		0.718
(1.00) 		0.181
(1.00) 		0.703
(1.00) 		0.173
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.0589
(1.00) 		0.551
(1.00) 		0.359
(1.00)
8p gain 5 (14%) 31 0.349
(1.00) 		0.478
(1.00) 		0.746
(1.00) 		0.402
(1.00) 		1
(1.00) 		1
(1.00) 		0.637
(1.00) 		0.1
(1.00) 		0.305
(1.00) 		0.546
(1.00)
8q gain 11 (31%) 25 0.276
(1.00) 		0.514
(1.00) 		0.742
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.483
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.191
(1.00)
10p gain 5 (14%) 31 0.465
(1.00) 		0.945
(1.00) 		0.745
(1.00) 		0.676
(1.00) 		1
(1.00) 		1
(1.00) 		0.149
(1.00) 		1
(1.00) 		1
(1.00) 		0.553
(1.00)
11p gain 4 (11%) 32 0.0785
(1.00) 		0.743
(1.00) 		0.129
(1.00) 		0.61
(1.00) 		0.0601
(1.00) 		0.0993
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.373
(1.00) 		0.0847
(1.00)
11q gain 4 (11%) 32 0.0785
(1.00) 		0.743
(1.00) 		0.128
(1.00) 		0.61
(1.00) 		0.0601
(1.00) 		0.0993
(1.00) 		1
(1.00) 		0.12
(1.00) 		0.372
(1.00) 		0.0835
(1.00)
12p gain 9 (25%) 27 0.223
(1.00) 		0.798
(1.00) 		1
(1.00) 		0.431
(1.00) 		1
(1.00) 		1
(1.00) 		0.146
(1.00) 		1
(1.00) 		0.52
(1.00) 		0.0165
(1.00)
12q gain 8 (22%) 28 0.473
(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) 		0.73
(1.00) 		0.616
(1.00) 		0.0109
(1.00)
13q gain 3 (8%) 33 0.968
(1.00) 		0.457
(1.00) 		0.0789
(1.00) 		0.537
(1.00) 		0.0601
(1.00) 		0.0532
(1.00) 		1
(1.00) 		0.0029
(0.985) 		0.278
(1.00) 		1
(1.00)
15q gain 6 (17%) 30 0.42
(1.00) 		0.687
(1.00) 		0.31
(1.00) 		0.836
(1.00) 		0.173
(1.00) 		1
(1.00) 		1
(1.00) 		0.145
(1.00) 		0.555
(1.00) 		0.359
(1.00)
16p gain 7 (19%) 29 0.557
(1.00) 		0.208
(1.00) 		0.698
(1.00) 		0.441
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.426
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.686
(1.00)
16q gain 5 (14%) 31 0.274
(1.00) 		0.423
(1.00) 		0.816
(1.00) 		0.831
(1.00) 		1
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.185
(1.00) 		0.73
(1.00) 		0.549
(1.00)
17p gain 3 (8%) 33 0.0127
(1.00) 		0.797
(1.00) 		0.554
(1.00) 		0.713
(1.00) 		0.301
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.433
(1.00) 		0.28
(1.00) 		0.0444
(1.00)
17q gain 7 (19%) 29 0.00303
(0.985) 		0.873
(1.00) 		0.86
(1.00) 		0.619
(1.00) 		1
(1.00) 		1
(1.00) 		0.204
(1.00) 		1
(1.00) 		0.773
(1.00) 		0.062
(1.00)
18p gain 7 (19%) 29 0.599
(1.00) 		0.119
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.426
(1.00) 		0.331
(1.00) 		0.599
(1.00) 		0.686
(1.00)
18q gain 6 (17%) 30 0.596
(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) 		0.622
(1.00)
19p gain 6 (17%) 30 0.687
(1.00) 		0.396
(1.00) 		0.314
(1.00) 		0.704
(1.00) 		0.173
(1.00) 		1
(1.00) 		1
(1.00) 		0.401
(1.00) 		0.747
(1.00) 		0.358
(1.00)
19q gain 6 (17%) 30 0.687
(1.00) 		0.396
(1.00) 		0.316
(1.00) 		0.703
(1.00) 		0.173
(1.00) 		1
(1.00) 		1
(1.00) 		0.402
(1.00) 		0.748
(1.00) 		0.361
(1.00)
20p gain 11 (31%) 25 0.353
(1.00) 		0.0304
(1.00) 		0.577
(1.00) 		0.693
(1.00) 		1
(1.00) 		1
(1.00) 		0.0335
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.188
(1.00)
20q gain 12 (33%) 24 0.557
(1.00) 		0.0156
(1.00) 		0.504
(1.00) 		0.545
(1.00) 		1
(1.00) 		1
(1.00) 		0.0815
(1.00) 		0.634
(1.00) 		0.2
(1.00) 		0.229
(1.00)
22q gain 5 (14%) 31 0.287
(1.00) 		0.252
(1.00) 		0.15
(1.00) 		0.831
(1.00) 		0.173
(1.00) 		0.155
(1.00) 		0.637
(1.00) 		0.185
(1.00) 		0.467
(1.00) 		1
(1.00)
1p loss 3 (8%) 33 0.651
(1.00) 		0.529
(1.00) 		0.0806
(1.00) 		0.536
(1.00) 		0.0601
(1.00) 		0.0189
(1.00) 		0.574
(1.00) 		0.43
(1.00) 		0.278
(1.00) 		1
(1.00)
3p loss 24 (67%) 12 0.615
(1.00) 		0.135
(1.00) 		0.0347
(1.00) 		0.0908
(1.00) 		0.0274
(1.00) 		0.304
(1.00) 		0.729
(1.00) 		0.194
(1.00) 		0.253
(1.00) 		0.588
(1.00)
3q loss 4 (11%) 32 0.155
(1.00) 		0.65
(1.00) 		0.852
(1.00) 		0.801
(1.00) 		1
(1.00) 		1
(1.00) 		0.613
(1.00) 		1
(1.00) 		1
(1.00) 		0.0858
(1.00)
4p loss 11 (31%) 25 0.488
(1.00) 		0.481
(1.00) 		0.767
(1.00) 		0.165
(1.00) 		1
(1.00) 		0.643
(1.00) 		0.0335
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.188
(1.00)
4q loss 13 (36%) 23 0.845
(1.00) 		0.692
(1.00) 		0.961
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.63
(1.00) 		0.493
(1.00) 		0.654
(1.00) 		0.597
(1.00) 		1
(1.00)
5q loss 3 (8%) 33 0.749
(1.00) 		0.129
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.422
(1.00) 		0.4
(1.00) 		0.574
(1.00) 		0.0315
(1.00) 		0.279
(1.00) 		1
(1.00)
6p loss 5 (14%) 31 0.669
(1.00) 		0.731
(1.00) 		0.502
(1.00) 		0.109
(1.00) 		0.56
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.728
(1.00) 		1
(1.00)
6q loss 20 (56%) 16 0.532
(1.00) 		0.339
(1.00) 		0.897
(1.00) 		0.802
(1.00) 		0.636
(1.00) 		0.639
(1.00) 		0.091
(1.00) 		0.524
(1.00) 		0.847
(1.00) 		0.783
(1.00)
7p loss 4 (11%) 32 0.00941
(1.00) 		0.597
(1.00) 		0.296
(1.00) 		0.438
(1.00) 		0.422
(1.00) 		1
(1.00) 		0.613
(1.00) 		1
(1.00) 		0.655
(1.00) 		0.467
(1.00)
7q loss 4 (11%) 32 0.256
(1.00) 		0.821
(1.00) 		0.348
(1.00) 		0.25
(1.00) 		1
(1.00) 		1
(1.00) 		0.613
(1.00) 		1
(1.00) 		0.654
(1.00) 		0.463
(1.00)
8p loss 10 (28%) 26 0.454
(1.00) 		0.536
(1.00) 		0.197
(1.00) 		0.0287
(1.00) 		0.291
(1.00) 		0.29
(1.00) 		0.285
(1.00) 		0.452
(1.00) 		0.419
(1.00) 		0.763
(1.00)
8q loss 5 (14%) 31 0.832
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.527
(1.00) 		1
(1.00) 		1
(1.00) 		0.637
(1.00) 		1
(1.00) 		0.469
(1.00) 		1
(1.00)
9p loss 18 (50%) 18 0.709
(1.00) 		0.0515
(1.00) 		0.106
(1.00) 		0.357
(1.00) 		0.654
(1.00) 		0.0184
(1.00) 		0.315
(1.00) 		0.209
(1.00) 		1
(1.00) 		0.228
(1.00)
9q loss 19 (53%) 17 0.825
(1.00) 		0.0493
(1.00) 		0.388
(1.00) 		0.245
(1.00) 		0.172
(1.00) 		0.152
(1.00) 		1
(1.00) 		0.433
(1.00) 		0.491
(1.00) 		0.231
(1.00)
10p loss 6 (17%) 30 0.74
(1.00) 		0.983
(1.00) 		0.184
(1.00) 		0.705
(1.00) 		0.173
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.0585
(1.00) 		0.556
(1.00) 		0.359
(1.00)
10q loss 5 (14%) 31 0.897
(1.00) 		1
(1.00) 		0.814
(1.00) 		0.829
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.637
(1.00) 		0.33
(1.00) 		1
(1.00) 		1
(1.00)
11p loss 8 (22%) 28 0.158
(1.00) 		0.985
(1.00) 		0.727
(1.00) 		0.413
(1.00) 		0.553
(1.00) 		1
(1.00) 		0.422
(1.00) 		1
(1.00) 		0.272
(1.00) 		1
(1.00)
11q loss 9 (25%) 27 0.0995
(1.00) 		0.715
(1.00) 		0.86
(1.00) 		0.432
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.146
(1.00) 		1
(1.00) 		0.518
(1.00) 		1
(1.00)
12q loss 3 (8%) 33 0.481
(1.00) 		0.954
(1.00) 		0.0816
(1.00) 		0.535
(1.00) 		0.0601
(1.00) 		0.0532
(1.00) 		1
(1.00) 		0.065
(1.00) 		0.277
(1.00) 		1
(1.00)
13q loss 16 (44%) 20 0.558
(1.00) 		0.899
(1.00) 		0.316
(1.00) 		0.243
(1.00) 		0.344
(1.00) 		0.0574
(1.00) 		1
(1.00) 		0.072
(1.00) 		0.846
(1.00) 		0.613
(1.00)
14q loss 13 (36%) 23 0.91
(1.00) 		0.961
(1.00) 		0.507
(1.00) 		0.799
(1.00) 		0.147
(1.00) 		0.63
(1.00) 		0.731
(1.00) 		0.655
(1.00) 		1
(1.00) 		1
(1.00)
15q loss 5 (14%) 31 0.31
(1.00) 		0.537
(1.00) 		0.5
(1.00) 		0.194
(1.00) 		0.525
(1.00) 		0.5
(1.00) 		0.637
(1.00) 		0.331
(1.00) 		0.728
(1.00) 		1
(1.00)
16p loss 4 (11%) 32 0.281
(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) 		0.653
(1.00) 		0.467
(1.00)
16q loss 7 (19%) 29 0.529
(1.00) 		0.889
(1.00) 		0.824
(1.00) 		1
(1.00) 		1
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.719
(1.00) 		0.0567
(1.00) 		0.685
(1.00)
17p loss 10 (28%) 26 0.188
(1.00) 		0.958
(1.00) 		0.882
(1.00) 		0.523
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.774
(1.00) 		0.54
(1.00) 		0.242
(1.00)
18p loss 6 (17%) 30 0.665
(1.00) 		0.47
(1.00) 		0.93
(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 0.638
(1.00) 		0.849
(1.00) 		0.958
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.535
(1.00) 		1
(1.00) 		0.159
(1.00)
19p loss 4 (11%) 32 0.696
(1.00) 		0.94
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.525
(1.00) 		0.5
(1.00) 		1
(1.00) 		0.0616
(1.00) 		0.374
(1.00) 		1
(1.00)
19q loss 3 (8%) 33 0.334
(1.00) 		0.567
(1.00) 		0.783
(1.00) 		0.376
(1.00) 		1
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.432
(1.00) 		1
(1.00) 		1
(1.00)
20p loss 5 (14%) 31 0.326
(1.00) 		0.537
(1.00) 		0.814
(1.00) 		0.83
(1.00) 		1
(1.00) 		0.5
(1.00) 		1
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.548
(1.00)
21q loss 15 (42%) 21 0.867
(1.00) 		0.199
(1.00) 		0.601
(1.00) 		0.412
(1.00) 		0.368
(1.00) 		0.625
(1.00) 		1
(1.00) 		0.814
(1.00) 		0.836
(1.00) 		0.778
(1.00)
22q loss 5 (14%) 31 0.243
(1.00) 		1
(1.00) 		0.501
(1.00) 		0.108
(1.00) 		1
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.622
(1.00) 		0.728
(1.00) 		0.298
(1.00)
xp loss 15 (42%) 21 0.619
(1.00) 		0.885
(1.00) 		0.227
(1.00) 		0.587
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.32
(1.00) 		0.642
(1.00) 		0.834
(1.00) 		0.202
(1.00)
xq loss 15 (42%) 21 0.619
(1.00) 		0.885
(1.00) 		0.229
(1.00) 		0.588
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.32
(1.00) 		0.641
(1.00) 		0.836
(1.00) 		0.199
(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/22519028/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CHOL-TP/22489349/CHOL-TP.merged_data.txt

  • Number of patients = 36

  • Number of significantly arm-level cnvs = 65

  • 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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