Correlation between copy number variations of arm-level result and selected clinical features
Mesothelioma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C13J3C23
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/C13J3C23
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 73 arm-level events and 8 clinical features across 77 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 73 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 KARNOFSKY
PERFORMANCE
SCORE
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 Wilcoxon-test
1p gain 8 (10%) 69 0.0573
(0.885) 		0.701
(1.00) 		0.408
(1.00) 		0.95
(1.00) 		0.672
(1.00) 		1
(1.00) 		0.649
(1.00)
1q gain 18 (23%) 59 0.158
(1.00) 		0.796
(1.00) 		0.638
(1.00) 		0.703
(1.00) 		0.929
(1.00) 		0.547
(1.00) 		0.323
(1.00)
2p gain 4 (5%) 73 0.723
(1.00) 		0.662
(1.00) 		0.197
(1.00) 		0.308
(1.00) 		0.779
(1.00) 		1
(1.00) 		1
(1.00)
2q gain 6 (8%) 71 0.478
(1.00) 		0.621
(1.00) 		0.179
(1.00) 		0.301
(1.00) 		0.858
(1.00) 		1
(1.00) 		1
(1.00)
3p gain 17 (22%) 60 0.705
(1.00) 		0.453
(1.00) 		0.085
(0.886) 		0.331
(1.00) 		0.358
(1.00) 		1
(1.00) 		0.73
(1.00)
3q gain 19 (25%) 58 0.429
(1.00) 		0.523
(1.00) 		0.0754
(0.885) 		0.386
(1.00) 		0.388
(1.00) 		1
(1.00) 		0.505
(1.00)
5p gain 19 (25%) 58 0.658
(1.00) 		0.309
(1.00) 		0.885
(1.00) 		0.246
(1.00) 		0.93
(1.00) 		1
(1.00) 		1
(1.00)
5q gain 12 (16%) 65 0.984
(1.00) 		0.5
(1.00) 		0.503
(1.00) 		0.0385
(0.885) 		0.901
(1.00) 		1
(1.00) 		0.693
(1.00)
6p gain 6 (8%) 71 0.195
(1.00) 		0.318
(1.00) 		0.506
(1.00) 		0.264
(1.00) 		0.127
(1.00) 		1
(1.00) 		1
(1.00)
6q gain 4 (5%) 73 0.585
(1.00) 		0.25
(1.00) 		0.0759
(0.885) 		0.0151
(0.847) 		0.777
(1.00) 		1
(1.00) 		0.581
(1.00)
7p gain 22 (29%) 55 0.673
(1.00) 		0.502
(1.00) 		0.425
(1.00) 		0.804
(1.00) 		0.00149
(0.269) 		0.534
(1.00) 		0.752
(1.00)
7q gain 19 (25%) 58 0.636
(1.00) 		0.421
(1.00) 		0.506
(1.00) 		0.54
(1.00) 		0.00052
(0.269) 		0.547
(1.00) 		0.505
(1.00)
8p gain 11 (14%) 66 0.63
(1.00) 		0.89
(1.00) 		0.655
(1.00) 		0.0839
(0.886) 		0.554
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.0722
(0.885)
8q gain 12 (16%) 65 0.962
(1.00) 		0.795
(1.00) 		0.175
(1.00) 		0.0985
(0.928) 		0.555
(1.00) 		1
(1.00) 		0.442
(1.00) 		0.0722
(0.885)
9q gain 3 (4%) 74 0.0133
(0.847) 		0.589
(1.00) 		0.279
(1.00) 		0.228
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
10p gain 3 (4%) 74 0.959
(1.00) 		0.329
(1.00) 		0.134
(1.00) 		0.228
(1.00) 		0.52
(1.00) 		1
(1.00) 		0.483
(1.00)
10q gain 3 (4%) 74 0.959
(1.00) 		0.329
(1.00) 		0.134
(1.00) 		0.226
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.483
(1.00)
11p gain 11 (14%) 66 0.971
(1.00) 		0.462
(1.00) 		0.883
(1.00) 		0.616
(1.00) 		0.0122
(0.847) 		1
(1.00) 		0.681
(1.00)
11q gain 11 (14%) 66 0.262
(1.00) 		0.362
(1.00) 		0.884
(1.00) 		0.476
(1.00) 		0.0813
(0.885) 		1
(1.00) 		0.681
(1.00)
12p gain 18 (23%) 59 0.515
(1.00) 		0.722
(1.00) 		0.472
(1.00) 		0.715
(1.00) 		0.0584
(0.885) 		1
(1.00) 		0.498
(1.00)
12q gain 18 (23%) 59 0.515
(1.00) 		0.722
(1.00) 		0.473
(1.00) 		0.716
(1.00) 		0.0596
(0.885) 		1
(1.00) 		0.498
(1.00)
13q gain 4 (5%) 73 0.338
(1.00) 		0.25
(1.00) 		0.632
(1.00) 		0.702
(1.00) 		0.777
(1.00) 		1
(1.00) 		1
(1.00)
15q gain 10 (13%) 67 0.719
(1.00) 		0.519
(1.00) 		0.327
(1.00) 		0.298
(1.00) 		0.797
(1.00) 		1
(1.00) 		0.399
(1.00)
16p gain 16 (21%) 61 0.848
(1.00) 		0.336
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.0431
(0.885) 		1
(1.00) 		0.723
(1.00)
16q gain 15 (19%) 62 0.87
(1.00) 		0.315
(1.00) 		0.3
(1.00) 		0.786
(1.00) 		0.175
(1.00) 		1
(1.00) 		1
(1.00)
17p gain 6 (8%) 71 0.936
(1.00) 		0.0768
(0.885) 		0.287
(1.00) 		0.63
(1.00) 		0.856
(1.00) 		1
(1.00) 		0.591
(1.00)
17q gain 16 (21%) 61 0.767
(1.00) 		0.542
(1.00) 		0.589
(1.00) 		0.976
(1.00) 		0.105
(0.957) 		1
(1.00) 		0.723
(1.00)
18p gain 7 (9%) 70 0.79
(1.00) 		0.352
(1.00) 		0.435
(1.00) 		1
(1.00) 		0.543
(1.00) 		1
(1.00) 		0.617
(1.00)
18q gain 4 (5%) 73 0.245
(1.00) 		0.89
(1.00) 		0.163
(1.00) 		0.635
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
19p gain 13 (17%) 64 0.945
(1.00) 		0.395
(1.00) 		0.731
(1.00) 		0.913
(1.00) 		0.264
(1.00) 		1
(1.00) 		1
(1.00)
19q gain 9 (12%) 68 0.319
(1.00) 		0.284
(1.00) 		0.322
(1.00) 		0.747
(1.00) 		0.672
(1.00) 		1
(1.00) 		0.68
(1.00)
20p gain 8 (10%) 69 0.235
(1.00) 		0.462
(1.00) 		0.165
(1.00) 		0.6
(1.00) 		0.857
(1.00) 		1
(1.00) 		1
(1.00)
20q gain 10 (13%) 67 0.883
(1.00) 		0.665
(1.00) 		0.219
(1.00) 		0.707
(1.00) 		0.688
(1.00) 		1
(1.00) 		0.195
(1.00)
21q gain 5 (6%) 72 0.0622
(0.885) 		0.286
(1.00) 		0.719
(1.00) 		0.668
(1.00) 		0.679
(1.00) 		1
(1.00) 		1
(1.00)
xp gain 7 (9%) 70 0.836
(1.00) 		0.338
(1.00) 		0.817
(1.00) 		0.456
(1.00) 		0.252
(1.00) 		1
(1.00) 		0.617
(1.00)
xq gain 6 (8%) 71 0.694
(1.00) 		0.452
(1.00) 		0.485
(1.00) 		0.302
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.331
(1.00)
1p loss 8 (10%) 69 0.263
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.384
(1.00) 		0.366
(1.00) 		1
(1.00) 		0.182
(1.00)
2p loss 3 (4%) 74 0.0816
(0.885) 		0.626
(1.00) 		1
(1.00) 		0.857
(1.00) 		0.713
(1.00) 		1
(1.00) 		0.0952
(0.916)
2q loss 3 (4%) 74 0.0776
(0.885) 		0.429
(1.00) 		1
(1.00) 		0.855
(1.00) 		0.71
(1.00) 		1
(1.00) 		0.00622
(0.519)
3p loss 5 (6%) 72 0.0635
(0.885) 		0.983
(1.00) 		0.145
(1.00) 		0.724
(1.00) 		0.239
(1.00) 		1
(1.00) 		0.576
(1.00)
3q loss 3 (4%) 74 0.324
(1.00) 		0.732
(1.00) 		0.0516
(0.885) 		0.317
(1.00) 		1
(1.00) 		1
(1.00)
4p loss 29 (38%) 48 0.142
(1.00) 		0.636
(1.00) 		0.945
(1.00) 		0.665
(1.00) 		0.59
(1.00) 		0.506
(1.00) 		0.554
(1.00)
4q loss 30 (39%) 47 0.156
(1.00) 		0.653
(1.00) 		0.833
(1.00) 		0.0724
(0.885) 		0.421
(1.00) 		0.506
(1.00) 		0.245
(1.00)
5p loss 3 (4%) 74 0.0343
(0.885) 		0.206
(1.00) 		1
(1.00) 		0.853
(1.00) 		1
(1.00) 		1
(1.00) 		0.483
(1.00)
5q loss 8 (10%) 69 0.0786
(0.885) 		0.385
(1.00) 		0.918
(1.00) 		0.893
(1.00) 		0.095
(0.916) 		1
(1.00) 		1
(1.00)
6p loss 9 (12%) 68 0.0818
(0.885) 		0.0547
(0.885) 		0.00562
(0.519) 		0.485
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.192
(1.00)
6q loss 26 (34%) 51 0.197
(1.00) 		0.94
(1.00) 		0.00184
(0.269) 		0.173
(1.00) 		0.101
(0.935) 		1
(1.00) 		0.762
(1.00) 		0.0722
(0.885)
8p loss 10 (13%) 67 0.0919
(0.916) 		0.417
(1.00) 		0.0634
(0.885) 		0.506
(1.00) 		0.886
(1.00) 		1
(1.00) 		1
(1.00)
8q loss 4 (5%) 73 0.441
(1.00) 		0.646
(1.00) 		0.0258
(0.885) 		0.0805
(0.885) 		1
(1.00) 		1
(1.00) 		1
(1.00)
9p loss 26 (34%) 51 0.00486
(0.519) 		0.521
(1.00) 		0.475
(1.00) 		0.35
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.243
(1.00)
9q loss 18 (23%) 59 0.0502
(0.885) 		0.455
(1.00) 		0.199
(1.00) 		0.935
(1.00) 		0.196
(1.00) 		1
(1.00) 		0.498
(1.00)
10p loss 22 (29%) 55 0.029
(0.885) 		0.312
(1.00) 		0.46
(1.00) 		0.465
(1.00) 		0.743
(1.00) 		0.388
(1.00) 		0.0537
(0.885) 		0.261
(1.00)
10q loss 17 (22%) 60 0.00137
(0.269) 		0.576
(1.00) 		0.139
(1.00) 		0.316
(1.00) 		0.477
(1.00) 		0.357
(1.00) 		0.499
(1.00)
11p loss 4 (5%) 73 0.26
(1.00) 		0.144
(1.00) 		0.0174
(0.847) 		0.397
(1.00) 		0.524
(1.00) 		1
(1.00) 		1
(1.00)
11q loss 5 (6%) 72 0.0397
(0.885) 		0.352
(1.00) 		0.0259
(0.885) 		0.251
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
12p loss 3 (4%) 74 0.168
(1.00) 		0.166
(1.00) 		0.341
(1.00) 		1
(1.00) 		0.71
(1.00) 		1
(1.00) 		0.483
(1.00)
13q loss 32 (42%) 45 0.0404
(0.885) 		0.971
(1.00) 		0.468
(1.00) 		0.932
(1.00) 		0.634
(1.00) 		0.198
(1.00) 		0.567
(1.00) 		0.653
(1.00)
14q loss 31 (40%) 46 0.0346
(0.885) 		0.289
(1.00) 		0.298
(1.00) 		0.0463
(0.885) 		0.23
(1.00) 		0.506
(1.00) 		0.0375
(0.885)
15q loss 10 (13%) 67 0.0164
(0.847) 		0.688
(1.00) 		0.14
(1.00) 		0.682
(1.00) 		0.686
(1.00) 		1
(1.00) 		0.676
(1.00)
16p loss 7 (9%) 70 0.396
(1.00) 		0.153
(1.00) 		0.118
(1.00) 		0.301
(1.00) 		0.074
(0.885) 		1
(1.00) 		1
(1.00)
16q loss 10 (13%) 67 0.252
(1.00) 		0.219
(1.00) 		0.0344
(0.885) 		0.333
(1.00) 		0.0697
(0.885) 		1
(1.00) 		1
(1.00)
17p loss 21 (27%) 56 0.545
(1.00) 		0.0956
(0.916) 		0.331
(1.00) 		0.11
(0.99) 		0.0448
(0.885) 		1
(1.00) 		0.537
(1.00)
17q loss 7 (9%) 70 0.836
(1.00) 		0.777
(1.00) 		0.0957
(0.916) 		0.0779
(0.885) 		0.858
(1.00) 		1
(1.00) 		0.617
(1.00)
18p loss 8 (10%) 69 0.325
(1.00) 		0.304
(1.00) 		0.627
(1.00) 		0.944
(1.00) 		0.674
(1.00) 		1
(1.00) 		1
(1.00)
18q loss 14 (18%) 63 0.45
(1.00) 		0.879
(1.00) 		0.683
(1.00) 		0.566
(1.00) 		0.916
(1.00) 		1
(1.00) 		0.132
(1.00)
19p loss 3 (4%) 74 0.648
(1.00) 		0.702
(1.00) 		0.0748
(0.885) 		1
(1.00) 		1
(1.00)
19q loss 6 (8%) 71 0.173
(1.00) 		0.487
(1.00) 		0.15
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
20p loss 14 (18%) 63 0.264
(1.00) 		0.958
(1.00) 		0.503
(1.00) 		0.914
(1.00) 		0.303
(1.00) 		1
(1.00) 		0.725
(1.00)
20q loss 3 (4%) 74 0.242
(1.00) 		0.175
(1.00) 		0.204
(1.00) 		0.507
(1.00) 		1
(1.00) 		1
(1.00) 		0.483
(1.00)
21q loss 10 (13%) 67 0.292
(1.00) 		0.58
(1.00) 		0.0785
(0.885) 		0.506
(1.00) 		0.673
(1.00) 		1
(1.00) 		0.676
(1.00)
22q loss 59 (77%) 18 0.21
(1.00) 		0.638
(1.00) 		0.54
(1.00) 		0.469
(1.00) 		0.858
(1.00) 		0.419
(1.00) 		0.741
(1.00) 		0.0722
(0.885)
xp loss 22 (29%) 55 0.688
(1.00) 		0.194
(1.00) 		0.933
(1.00) 		0.93
(1.00) 		0.674
(1.00) 		0.478
(1.00) 		1
(1.00)
xq loss 23 (30%) 54 0.614
(1.00) 		0.263
(1.00) 		0.864
(1.00) 		0.932
(1.00) 		0.555
(1.00) 		0.506
(1.00) 		1
(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/MESO-TP/15089879/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/MESO-TP/15084766/MESO-TP.merged_data.txt

  • Number of patients = 77

  • Number of significantly arm-level cnvs = 73

  • 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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