Correlation between copy number variation genes (focal events) and selected clinical features
Liver Hepatocellular Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C11834X1
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C11834X1
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 57 focal events and 8 clinical features across 123 patients, no significant finding detected with Q value < 0.25.

  • No focal 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 57 focal 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 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER COMPLETENESS
OF
RESECTION
nCNV (%) nWild-Type logrank 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
amp 1p22 3 31 (25%) 92 0.287
(1.00) 		0.495
(1.00) 		0.165
(1.00) 		0.633
(1.00) 		0.525
(1.00) 		0.0836
(1.00) 		0.834
(1.00) 		0.0413
(1.00)
amp 1q22 90 (73%) 33 0.0601
(1.00) 		0.54
(1.00) 		0.547
(1.00) 		0.407
(1.00) 		1
(1.00) 		0.895
(1.00) 		0.297
(1.00) 		0.695
(1.00)
amp 1q42 3 84 (68%) 39 0.0673
(1.00) 		0.483
(1.00) 		0.1
(1.00) 		0.012
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.689
(1.00) 		0.849
(1.00)
amp 2p24 1 25 (20%) 98 0.934
(1.00) 		0.442
(1.00) 		0.0703
(1.00) 		0.0467
(1.00) 		0.0936
(1.00) 		0.19
(1.00) 		0.491
(1.00) 		0.418
(1.00)
amp 2q31 2 26 (21%) 97 0.291
(1.00) 		0.451
(1.00) 		0.235
(1.00) 		0.628
(1.00) 		0.479
(1.00) 		0.478
(1.00) 		0.0679
(1.00) 		0.456
(1.00)
amp 3q26 31 24 (20%) 99 0.434
(1.00) 		0.435
(1.00) 		0.628
(1.00) 		0.35
(1.00) 		0.351
(1.00) 		0.526
(1.00) 		1
(1.00) 		1
(1.00)
amp 4q13 3 12 (10%) 111 0.425
(1.00) 		0.289
(1.00) 		0.503
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.404
(1.00) 		0.761
(1.00) 		0.0276
(1.00)
amp 4q32 3 10 (8%) 113 0.148
(1.00) 		0.885
(1.00) 		0.167
(1.00) 		0.264
(1.00) 		0.0235
(1.00) 		1
(1.00) 		0.499
(1.00) 		0.52
(1.00)
amp 5p15 33 59 (48%) 64 0.957
(1.00) 		0.783
(1.00) 		0.114
(1.00) 		0.0449
(1.00) 		1
(1.00) 		0.273
(1.00) 		0.713
(1.00) 		0.928
(1.00)
amp 5q35 3 46 (37%) 77 0.389
(1.00) 		0.215
(1.00) 		0.396
(1.00) 		0.336
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.703
(1.00) 		0.189
(1.00)
amp 6p25 2 50 (41%) 73 0.175
(1.00) 		0.865
(1.00) 		0.444
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.276
(1.00) 		0.256
(1.00) 		0.849
(1.00)
amp 6p21 1 50 (41%) 73 0.528
(1.00) 		0.808
(1.00) 		0.293
(1.00) 		0.965
(1.00) 		0.289
(1.00) 		0.247
(1.00) 		0.256
(1.00) 		0.849
(1.00)
amp 7q21 2 47 (38%) 76 0.771
(1.00) 		0.0885
(1.00) 		0.381
(1.00) 		0.321
(1.00) 		0.278
(1.00) 		0.761
(1.00) 		0.571
(1.00) 		0.443
(1.00)
amp 7q31 2 44 (36%) 79 0.768
(1.00) 		0.228
(1.00) 		0.257
(1.00) 		0.337
(1.00) 		0.214
(1.00) 		0.685
(1.00) 		0.565
(1.00) 		0.695
(1.00)
amp 8q13 3 67 (54%) 56 0.904
(1.00) 		0.549
(1.00) 		0.0994
(1.00) 		0.266
(1.00) 		0.598
(1.00) 		1
(1.00) 		0.0644
(1.00) 		0.663
(1.00)
amp 8q24 21 74 (60%) 49 0.363
(1.00) 		0.93
(1.00) 		0.32
(1.00) 		0.885
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.0372
(1.00) 		0.956
(1.00)
amp 9q34 2 17 (14%) 106 0.524
(1.00) 		0.35
(1.00) 		0.178
(1.00) 		0.381
(1.00) 		0.323
(1.00) 		0.512
(1.00) 		1
(1.00) 		0.0543
(1.00)
amp 10p15 1 25 (20%) 98 0.703
(1.00) 		0.167
(1.00) 		0.0849
(1.00) 		0.0186
(1.00) 		1
(1.00) 		0.332
(1.00) 		0.646
(1.00) 		1
(1.00)
amp 11q13 3 24 (20%) 99 0.493
(1.00) 		0.705
(1.00) 		0.11
(1.00) 		0.0366
(1.00) 		1
(1.00) 		0.265
(1.00) 		0.815
(1.00) 		0.072
(1.00)
amp 12q23 1 23 (19%) 100 0.88
(1.00) 		0.0868
(1.00) 		0.0899
(1.00) 		0.0846
(1.00) 		0.455
(1.00) 		0.308
(1.00) 		0.0544
(1.00) 		0.255
(1.00)
amp 13q32 3 21 (17%) 102 0.152
(1.00) 		0.854
(1.00) 		0.97
(1.00) 		0.893
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.327
(1.00) 		0.0847
(1.00)
amp 15q26 3 21 (17%) 102 0.788
(1.00) 		0.236
(1.00) 		0.712
(1.00) 		0.185
(1.00) 		1
(1.00) 		1
(1.00) 		0.327
(1.00) 		1
(1.00)
amp 17p11 2 21 (17%) 102 0.701
(1.00) 		0.52
(1.00) 		0.0605
(1.00) 		0.0207
(1.00) 		1
(1.00) 		0.181
(1.00) 		0.806
(1.00) 		0.0986
(1.00)
amp 17q25 3 57 (46%) 66 0.226
(1.00) 		0.684
(1.00) 		0.263
(1.00) 		0.191
(1.00) 		1
(1.00) 		0.334
(1.00) 		0.135
(1.00) 		0.0809
(1.00)
amp 19p13 12 31 (25%) 92 0.47
(1.00) 		0.909
(1.00) 		0.147
(1.00) 		0.798
(1.00) 		0.547
(1.00) 		0.0153
(1.00) 		0.0851
(1.00) 		0.402
(1.00)
amp 19q13 11 39 (32%) 84 0.73
(1.00) 		0.26
(1.00) 		0.091
(1.00) 		0.253
(1.00) 		1
(1.00) 		0.0337
(1.00) 		0.229
(1.00) 		0.218
(1.00)
amp 20q13 33 44 (36%) 79 0.856
(1.00) 		0.487
(1.00) 		0.204
(1.00) 		0.873
(1.00) 		0.295
(1.00) 		0.214
(1.00) 		0.338
(1.00) 		0.505
(1.00)
amp 22q13 1 26 (21%) 97 0.974
(1.00) 		0.374
(1.00) 		0.827
(1.00) 		0.516
(1.00) 		0.455
(1.00) 		0.867
(1.00) 		0.363
(1.00) 		0.545
(1.00)
del 1p36 23 60 (49%) 63 0.167
(1.00) 		0.333
(1.00) 		0.576
(1.00) 		0.0724
(1.00) 		0.583
(1.00) 		0.539
(1.00) 		0.581
(1.00) 		0.271
(1.00)
del 1p35 2 47 (38%) 76 0.514
(1.00) 		0.324
(1.00) 		0.189
(1.00) 		0.238
(1.00) 		0.0357
(1.00) 		0.142
(1.00) 		0.702
(1.00) 		0.412
(1.00)
del 2q22 1 13 (11%) 110 0.0415
(1.00) 		0.639
(1.00) 		0.625
(1.00) 		0.141
(1.00) 		1
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.722
(1.00)
del 2q34 15 (12%) 108 0.706
(1.00) 		0.987
(1.00) 		0.825
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.795
(1.00) 		0.254
(1.00) 		1
(1.00)
del 3p13 22 (18%) 101 0.419
(1.00) 		0.916
(1.00) 		0.124
(1.00) 		0.0577
(1.00) 		0.455
(1.00) 		0.421
(1.00) 		0.0888
(1.00) 		0.827
(1.00)
del 4p16 3 23 (19%) 100 0.714
(1.00) 		0.733
(1.00) 		0.198
(1.00) 		0.982
(1.00) 		0.0534
(1.00) 		0.437
(1.00) 		0.242
(1.00) 		0.337
(1.00)
del 4q21 23 51 (41%) 72 0.331
(1.00) 		0.139
(1.00) 		0.247
(1.00) 		0.68
(1.00) 		0.565
(1.00) 		0.225
(1.00) 		0.709
(1.00) 		0.707
(1.00)
del 4q24 53 (43%) 70 0.135
(1.00) 		0.194
(1.00) 		0.166
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.259
(1.00) 		0.348
(1.00) 		0.159
(1.00)
del 4q35 1 53 (43%) 70 0.0141
(1.00) 		0.212
(1.00) 		0.631
(1.00) 		0.934
(1.00) 		0.57
(1.00) 		0.259
(1.00) 		0.574
(1.00) 		0.398
(1.00)
del 5q23 1 16 (13%) 107 0.105
(1.00) 		0.683
(1.00) 		0.448
(1.00) 		0.117
(1.00) 		0.323
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.681
(1.00)
del 6q16 3 45 (37%) 78 0.732
(1.00) 		0.546
(1.00) 		0.59
(1.00) 		0.569
(1.00) 		0.553
(1.00) 		0.277
(1.00) 		0.249
(1.00) 		0.473
(1.00)
del 6q27 47 (38%) 76 0.913
(1.00) 		0.326
(1.00) 		0.607
(1.00) 		0.654
(1.00) 		0.556
(1.00) 		0.0574
(1.00) 		0.702
(1.00) 		0.518
(1.00)
del 8p23 2 79 (64%) 44 0.0829
(1.00) 		0.0564
(1.00) 		0.436
(1.00) 		0.792
(1.00) 		0.273
(1.00) 		0.835
(1.00) 		0.338
(1.00) 		1
(1.00)
del 9p21 3 50 (41%) 73 0.157
(1.00) 		0.628
(1.00) 		0.13
(1.00) 		0.209
(1.00) 		0.553
(1.00) 		0.0708
(1.00) 		0.346
(1.00) 		0.0771
(1.00)
del 10q23 31 37 (30%) 86 0.985
(1.00) 		0.999
(1.00) 		0.0899
(1.00) 		0.0555
(1.00) 		0.184
(1.00) 		0.585
(1.00) 		0.84
(1.00) 		0.129
(1.00)
del 10q24 33 35 (28%) 88 0.374
(1.00) 		0.852
(1.00) 		0.321
(1.00) 		0.288
(1.00) 		0.17
(1.00) 		0.81
(1.00) 		0.685
(1.00) 		0.344
(1.00)
del 11q23 3 25 (20%) 98 0.98
(1.00) 		0.0571
(1.00) 		0.468
(1.00) 		0.435
(1.00) 		0.0827
(1.00) 		0.862
(1.00) 		1
(1.00) 		0.418
(1.00)
del 12p12 1 27 (22%) 96 0.117
(1.00) 		0.804
(1.00) 		0.231
(1.00) 		0.825
(1.00) 		0.105
(1.00) 		0.562
(1.00) 		0.66
(1.00) 		0.104
(1.00)
del 12q24 33 21 (17%) 102 0.497
(1.00) 		0.55
(1.00) 		0.0437
(1.00) 		0.38
(1.00) 		1
(1.00) 		0.146
(1.00) 		0.327
(1.00) 		1
(1.00)
del 13q14 2 57 (46%) 66 0.0897
(1.00) 		0.835
(1.00) 		0.16
(1.00) 		0.000603
(0.275) 		1
(1.00) 		0.754
(1.00) 		0.353
(1.00) 		0.264
(1.00)
del 13q22 2 45 (37%) 78 0.421
(1.00) 		0.162
(1.00) 		0.596
(1.00) 		0.00181
(0.824) 		0.548
(1.00) 		0.836
(1.00) 		0.249
(1.00) 		0.526
(1.00)
del 14q23 3 43 (35%) 80 0.911
(1.00) 		0.809
(1.00) 		0.28
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.547
(1.00) 		0.442
(1.00) 		0.252
(1.00)
del 14q32 33 45 (37%) 78 0.221
(1.00) 		0.961
(1.00) 		0.197
(1.00) 		0.121
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.847
(1.00) 		0.366
(1.00)
del 16q23 1 54 (44%) 69 0.0996
(1.00) 		0.179
(1.00) 		0.277
(1.00) 		0.189
(1.00) 		0.598
(1.00) 		0.911
(1.00) 		0.574
(1.00) 		0.187
(1.00)
del 17p13 3 65 (53%) 58 0.185
(1.00) 		0.391
(1.00) 		0.086
(1.00) 		0.287
(1.00) 		1
(1.00) 		0.307
(1.00) 		0.71
(1.00) 		0.129
(1.00)
del 17p11 2 66 (54%) 57 0.375
(1.00) 		0.701
(1.00) 		0.159
(1.00) 		0.197
(1.00) 		0.246
(1.00) 		1
(1.00) 		0.353
(1.00) 		0.21
(1.00)
del 18q12 2 24 (20%) 99 0.201
(1.00) 		0.37
(1.00) 		0.481
(1.00) 		0.788
(1.00) 		0.404
(1.00) 		0.385
(1.00) 		0.356
(1.00) 		1
(1.00)
del 19p13 3 32 (26%) 91 0.812
(1.00) 		0.517
(1.00) 		0.137
(1.00) 		0.147
(1.00) 		0.568
(1.00) 		0.252
(1.00) 		0.525
(1.00) 		0.679
(1.00)
del 22q13 32 33 (27%) 90 0.166
(1.00) 		0.957
(1.00) 		0.743
(1.00) 		0.119
(1.00) 		1
(1.00) 		0.304
(1.00) 		0.297
(1.00) 		0.218
(1.00)
Methods & Data
Input

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

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

  • Number of patients = 123

  • Number of significantly focal cnvs = 57

  • Number of selected clinical features = 8

  • 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

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

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[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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