Correlation between copy number variations of arm-level result and selected clinical features
Cholangiocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1QZ290Q
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/C1QZ290Q
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 8 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 8 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 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER 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
1p gain 10 (28%) 26 0.782
(1.00) 		0.596
(1.00) 		0.787
(1.00) 		0.345
(1.00) 		0.286
(1.00) 		0.291
(1.00) 		0.285
(1.00) 		0.761
(1.00)
1q gain 21 (58%) 15 0.833
(1.00) 		0.413
(1.00) 		0.198
(1.00) 		0.335
(1.00) 		0.368
(1.00) 		0.36
(1.00) 		0.741
(1.00) 		0.778
(1.00)
2p gain 6 (17%) 30 0.554
(1.00) 		0.432
(1.00) 		0.927
(1.00) 		0.586
(1.00) 		1
(1.00) 		1
(1.00) 		0.672
(1.00) 		0.184
(1.00)
2q gain 6 (17%) 30 0.454
(1.00) 		0.51
(1.00) 		0.506
(1.00) 		0.476
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.672
(1.00) 		0.184
(1.00)
3p gain 3 (8%) 33 0.434
(1.00) 		0.277
(1.00) 		0.555
(1.00) 		0.243
(1.00) 		0.422
(1.00) 		0.4
(1.00) 		0.574
(1.00) 		0.371
(1.00)
3q gain 8 (22%) 28 0.244
(1.00) 		0.159
(1.00) 		0.527
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.574
(1.00) 		0.103
(1.00) 		0.158
(1.00)
4p gain 3 (8%) 33 0.026
(1.00) 		0.0758
(1.00) 		0.139
(1.00) 		0.122
(1.00) 		0.422
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.372
(1.00)
5p gain 12 (33%) 24 0.899
(1.00) 		0.775
(1.00) 		0.606
(1.00) 		0.703
(1.00) 		1
(1.00) 		0.63
(1.00) 		1
(1.00) 		0.228
(1.00)
5q gain 12 (33%) 24 0.899
(1.00) 		0.775
(1.00) 		0.606
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.63
(1.00) 		1
(1.00) 		0.229
(1.00)
6p gain 7 (19%) 29 0.066
(1.00) 		0.764
(1.00) 		1
(1.00) 		0.719
(1.00) 		1
(1.00) 		1
(1.00) 		0.0298
(1.00) 		0.421
(1.00)
7p gain 7 (19%) 29 0.272
(1.00) 		0.81
(1.00) 		0.162
(1.00) 		0.525
(1.00) 		0.241
(1.00) 		0.282
(1.00) 		1
(1.00) 		0.418
(1.00)
7q gain 6 (17%) 30 0.432
(1.00) 		0.718
(1.00) 		0.181
(1.00) 		0.704
(1.00) 		0.173
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.358
(1.00)
8p gain 6 (17%) 30 0.491
(1.00) 		0.581
(1.00) 		0.256
(1.00) 		0.476
(1.00) 		0.241
(1.00) 		0.216
(1.00) 		0.374
(1.00) 		0.623
(1.00)
8q gain 12 (33%) 24 0.385
(1.00) 		0.392
(1.00) 		0.747
(1.00) 		0.891
(1.00) 		1
(1.00) 		1
(1.00) 		0.298
(1.00) 		0.231
(1.00)
10p gain 5 (14%) 31 0.922
(1.00) 		0.945
(1.00) 		0.745
(1.00) 		0.677
(1.00) 		1
(1.00) 		1
(1.00) 		0.149
(1.00) 		0.549
(1.00)
11p gain 4 (11%) 32 0.0916
(1.00) 		0.743
(1.00) 		0.128
(1.00) 		0.613
(1.00) 		0.0601
(1.00) 		0.0993
(1.00) 		1
(1.00) 		0.0841
(1.00)
11q gain 4 (11%) 32 0.0916
(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) 		0.0843
(1.00)
12p gain 9 (25%) 27 0.0116
(1.00) 		0.798
(1.00) 		1
(1.00) 		0.435
(1.00) 		1
(1.00) 		1
(1.00) 		0.146
(1.00) 		0.0172
(1.00)
12q gain 8 (22%) 28 0.0562
(1.00) 		0.805
(1.00) 		0.958
(1.00) 		0.734
(1.00) 		0.291
(1.00) 		0.302
(1.00) 		0.422
(1.00) 		0.0113
(1.00)
13q gain 3 (8%) 33 0.974
(1.00) 		0.457
(1.00) 		0.0793
(1.00) 		0.537
(1.00) 		0.0601
(1.00) 		0.0532
(1.00) 		1
(1.00) 		1
(1.00)
15q gain 6 (17%) 30 0.561
(1.00) 		0.687
(1.00) 		0.313
(1.00) 		0.837
(1.00) 		0.173
(1.00) 		1
(1.00) 		1
(1.00) 		0.363
(1.00)
16p gain 7 (19%) 29 0.474
(1.00) 		0.208
(1.00) 		0.697
(1.00) 		0.441
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.426
(1.00) 		0.685
(1.00)
16q gain 5 (14%) 31 0.223
(1.00) 		0.423
(1.00) 		0.815
(1.00) 		0.83
(1.00) 		1
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.549
(1.00)
17p gain 3 (8%) 33 0.0148
(1.00) 		0.797
(1.00) 		0.552
(1.00) 		0.71
(1.00) 		0.301
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.044
(1.00)
17q gain 7 (19%) 29 0.00598
(1.00) 		0.873
(1.00) 		0.86
(1.00) 		0.614
(1.00) 		1
(1.00) 		1
(1.00) 		0.204
(1.00) 		0.0596
(1.00)
18p gain 7 (19%) 29 0.704
(1.00) 		0.119
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.426
(1.00) 		0.682
(1.00)
18q gain 6 (17%) 30 0.654
(1.00) 		0.226
(1.00) 		0.929
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.621
(1.00)
19p gain 6 (17%) 30 0.698
(1.00) 		0.396
(1.00) 		0.314
(1.00) 		0.705
(1.00) 		0.173
(1.00) 		1
(1.00) 		1
(1.00) 		0.363
(1.00)
19q gain 6 (17%) 30 0.698
(1.00) 		0.396
(1.00) 		0.315
(1.00) 		0.704
(1.00) 		0.173
(1.00) 		1
(1.00) 		1
(1.00) 		0.359
(1.00)
20p gain 11 (31%) 25 0.341
(1.00) 		0.0304
(1.00) 		0.576
(1.00) 		0.693
(1.00) 		1
(1.00) 		1
(1.00) 		0.0335
(1.00) 		0.188
(1.00)
20q gain 12 (33%) 24 0.577
(1.00) 		0.0156
(1.00) 		0.502
(1.00) 		0.543
(1.00) 		1
(1.00) 		1
(1.00) 		0.0815
(1.00) 		0.231
(1.00)
21q gain 3 (8%) 33 0.394
(1.00) 		0.731
(1.00) 		0.408
(1.00) 		0.242
(1.00) 		0.422
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
22q gain 5 (14%) 31 0.199
(1.00) 		0.252
(1.00) 		0.15
(1.00) 		0.832
(1.00) 		0.173
(1.00) 		0.155
(1.00) 		0.637
(1.00) 		1
(1.00)
1p loss 4 (11%) 32 0.565
(1.00) 		1
(1.00) 		0.128
(1.00) 		0.436
(1.00) 		0.112
(1.00) 		0.0532
(1.00) 		1
(1.00) 		0.465
(1.00)
3p loss 22 (61%) 14 0.747
(1.00) 		0.338
(1.00) 		0.06
(1.00) 		0.117
(1.00) 		0.06
(1.00) 		0.36
(1.00) 		0.307
(1.00) 		1
(1.00)
3q loss 3 (8%) 33 0.273
(1.00) 		0.886
(1.00) 		0.646
(1.00) 		0.714
(1.00) 		1
(1.00) 		1
(1.00) 		0.238
(1.00) 		0.0441
(1.00)
4p loss 10 (28%) 26 0.83
(1.00) 		0.888
(1.00) 		0.498
(1.00) 		0.147
(1.00) 		1
(1.00) 		1
(1.00) 		0.0732
(1.00) 		0.151
(1.00)
4q loss 13 (36%) 23 0.988
(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) 		1
(1.00)
6p loss 5 (14%) 31 0.834
(1.00) 		0.731
(1.00) 		0.499
(1.00) 		0.107
(1.00) 		0.56
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
6q loss 20 (56%) 16 0.484
(1.00) 		0.347
(1.00) 		0.895
(1.00) 		0.804
(1.00) 		0.636
(1.00) 		0.639
(1.00) 		0.091
(1.00) 		0.783
(1.00)
7p loss 4 (11%) 32 0.0428
(1.00) 		0.632
(1.00) 		0.295
(1.00) 		0.44
(1.00) 		0.422
(1.00) 		1
(1.00) 		0.613
(1.00) 		0.466
(1.00)
7q loss 4 (11%) 32 0.308
(1.00) 		0.86
(1.00) 		0.349
(1.00) 		0.25
(1.00) 		1
(1.00) 		1
(1.00) 		0.613
(1.00) 		0.468
(1.00)
8p loss 10 (28%) 26 0.382
(1.00) 		0.536
(1.00) 		0.196
(1.00) 		0.029
(1.00) 		0.291
(1.00) 		0.29
(1.00) 		0.285
(1.00) 		0.763
(1.00)
8q loss 3 (8%) 33 0.541
(1.00) 		0.529
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
9p loss 18 (50%) 18 0.953
(1.00) 		0.0515
(1.00) 		0.107
(1.00) 		0.357
(1.00) 		0.654
(1.00) 		0.0184
(1.00) 		0.315
(1.00) 		0.227
(1.00)
9q loss 19 (53%) 17 0.976
(1.00) 		0.0475
(1.00) 		0.39
(1.00) 		0.245
(1.00) 		0.172
(1.00) 		0.152
(1.00) 		1
(1.00) 		0.231
(1.00)
10p loss 6 (17%) 30 0.98
(1.00) 		0.983
(1.00) 		0.18
(1.00) 		0.703
(1.00) 		0.173
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.36
(1.00)
10q loss 5 (14%) 31 0.634
(1.00) 		1
(1.00) 		0.815
(1.00) 		0.828
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.637
(1.00) 		1
(1.00)
11p loss 8 (22%) 28 0.255
(1.00) 		0.97
(1.00) 		0.727
(1.00) 		0.41
(1.00) 		0.553
(1.00) 		1
(1.00) 		0.422
(1.00) 		1
(1.00)
11q loss 9 (25%) 27 0.149
(1.00) 		0.701
(1.00) 		0.86
(1.00) 		0.432
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.146
(1.00) 		1
(1.00)
12q loss 3 (8%) 33 0.371
(1.00) 		0.954
(1.00) 		0.0818
(1.00) 		0.537
(1.00) 		0.0601
(1.00) 		0.0532
(1.00) 		1
(1.00) 		1
(1.00)
13q loss 15 (42%) 21 0.414
(1.00) 		0.736
(1.00) 		0.494
(1.00) 		0.414
(1.00) 		0.368
(1.00) 		0.131
(1.00) 		0.741
(1.00) 		0.626
(1.00)
14q loss 13 (36%) 23 0.925
(1.00) 		0.974
(1.00) 		0.508
(1.00) 		0.8
(1.00) 		0.147
(1.00) 		0.63
(1.00) 		0.731
(1.00) 		1
(1.00)
15q loss 5 (14%) 31 0.181
(1.00) 		0.567
(1.00) 		0.5
(1.00) 		0.193
(1.00) 		0.525
(1.00) 		0.5
(1.00) 		0.637
(1.00) 		1
(1.00)
16p loss 4 (11%) 32 0.317
(1.00) 		0.84
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.303
(1.00) 		0.465
(1.00)
16q loss 7 (19%) 29 0.954
(1.00) 		0.889
(1.00) 		0.822
(1.00) 		1
(1.00) 		1
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.686
(1.00)
17p loss 10 (28%) 26 0.252
(1.00) 		0.958
(1.00) 		0.882
(1.00) 		0.524
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.241
(1.00)
18p loss 6 (17%) 30 0.605
(1.00) 		0.47
(1.00) 		0.929
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.374
(1.00) 		0.0883
(1.00)
18q loss 8 (22%) 28 0.552
(1.00) 		0.849
(1.00) 		0.958
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.158
(1.00)
19p loss 4 (11%) 32 0.513
(1.00) 		0.94
(1.00) 		0.499
(1.00) 		1
(1.00) 		0.525
(1.00) 		0.5
(1.00) 		1
(1.00) 		1
(1.00)
19q loss 3 (8%) 33 0.583
(1.00) 		0.529
(1.00) 		0.783
(1.00) 		0.378
(1.00) 		1
(1.00) 		1
(1.00) 		0.574
(1.00) 		1
(1.00)
20p loss 5 (14%) 31 0.429
(1.00) 		0.537
(1.00) 		0.815
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.5
(1.00) 		1
(1.00) 		0.55
(1.00)
21q loss 15 (42%) 21 0.433
(1.00) 		0.21
(1.00) 		0.601
(1.00) 		0.419
(1.00) 		0.368
(1.00) 		0.625
(1.00) 		1
(1.00) 		0.777
(1.00)
22q loss 5 (14%) 31 0.223
(1.00) 		1
(1.00) 		0.502
(1.00) 		0.11
(1.00) 		1
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.299
(1.00)
xp loss 15 (42%) 21 0.964
(1.00) 		0.911
(1.00) 		0.226
(1.00) 		0.59
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.32
(1.00) 		0.201
(1.00)
xq loss 15 (42%) 21 0.964
(1.00) 		0.911
(1.00) 		0.227
(1.00) 		0.587
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.32
(1.00) 		0.2
(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/15082092/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CHOL-TP/15076818/CHOL-TP.merged_data.txt

  • Number of patients = 36

  • Number of significantly arm-level cnvs = 66

  • Number of selected clinical features = 8

  • 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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