Correlation between copy number variation genes (focal events) and selected clinical features
Adrenocortical Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1474973
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1474973
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 44 focal events and 12 clinical features across 90 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 44 focal events and 12 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 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
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 Wilcoxon-test Fisher's exact test Fisher's exact test
amp 1q22 17 (19%) 73 0.00231
(0.406) 		0.595
(1.00) 		0.684
(1.00) 		0.686
(1.00) 		0.679
(1.00) 		0.779
(1.00) 		0.506
(1.00) 		1
(1.00) 		0.131
(0.722) 		0.0645
(0.686) 		0.499
(1.00) 		0.613
(1.00)
amp 4p16 3 41 (46%) 49 0.136
(0.722) 		0.789
(1.00) 		0.932
(1.00) 		0.972
(1.00) 		0.75
(1.00) 		0.505
(1.00) 		0.599
(1.00) 		0.213
(0.79) 		0.14
(0.722) 		0.877
(1.00) 		1
(1.00) 		0.693
(1.00)
amp 5p15 33 65 (72%) 25 0.967
(1.00) 		0.675
(1.00) 		0.584
(1.00) 		0.59
(1.00) 		0.721
(1.00) 		0.469
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.806
(1.00) 		1
(1.00) 		0.0813
(0.686) 		0.403
(1.00)
amp 5q35 3 63 (70%) 27 0.206
(0.79) 		0.685
(1.00) 		0.772
(1.00) 		0.905
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.392
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.878
(1.00) 		1
(1.00) 		0.694
(1.00)
amp 6p21 31 19 (21%) 71 0.778
(1.00) 		0.00597
(0.49) 		0.865
(1.00) 		0.64
(1.00) 		0.68
(1.00) 		0.188
(0.79) 		0.104
(0.715) 		1
(1.00) 		0.0438
(0.686) 		0.407
(1.00) 		0.104
(0.715) 		0.374
(1.00)
amp 6q24 3 19 (21%) 71 0.977
(1.00) 		0.355
(0.999) 		0.722
(1.00) 		0.366
(0.999) 		0.115
(0.722) 		0.792
(1.00) 		0.342
(0.985) 		1
(1.00) 		0.41
(1.00) 		0.0912
(0.713) 		0.0915
(0.713) 		0.645
(1.00)
amp 7p22 1 54 (60%) 36 0.579
(1.00) 		0.683
(1.00) 		0.09
(0.713) 		0.0977
(0.713) 		0.305
(0.941) 		1
(1.00) 		0.295
(0.93) 		0.787
(1.00) 		0.6
(1.00) 		0.475
(1.00) 		1
(1.00) 		1
(1.00)
amp 9q31 3 34 (38%) 56 0.00944
(0.554) 		0.861
(1.00) 		0.0256
(0.686) 		0.0787
(0.686) 		0.0413
(0.686) 		0.498
(1.00) 		0.174
(0.79) 		0.559
(1.00) 		0.0683
(0.686) 		0.206
(0.79) 		1
(1.00) 		0.439
(1.00)
amp 12q14 1 70 (78%) 20 0.538
(1.00) 		0.614
(1.00) 		0.89
(1.00) 		0.875
(1.00) 		0.683
(1.00) 		0.791
(1.00) 		0.528
(1.00) 		1
(1.00) 		0.672
(1.00) 		0.625
(1.00) 		0.545
(1.00) 		0.171
(0.79)
amp 14q11 2 27 (30%) 63 0.388
(1.00) 		0.067
(0.686) 		0.384
(1.00) 		0.395
(1.00) 		0.0585
(0.686) 		0.631
(1.00) 		0.254
(0.863) 		0.518
(1.00) 		0.438
(1.00) 		0.0567
(0.686) 		0.65
(1.00) 		0.407
(1.00)
amp 16p13 3 50 (56%) 40 0.205
(0.79) 		0.968
(1.00) 		0.799
(1.00) 		0.924
(1.00) 		1
(1.00) 		0.119
(0.722) 		0.425
(1.00) 		1
(1.00) 		0.737
(1.00) 		0.168
(0.79) 		0.717
(1.00) 		1
(1.00)
amp 16q22 1 56 (62%) 34 0.905
(1.00) 		0.68
(1.00) 		0.686
(1.00) 		0.662
(1.00) 		0.737
(1.00) 		0.257
(0.863) 		0.0303
(0.686) 		0.773
(1.00) 		0.215
(0.79) 		0.321
(0.968) 		0.0516
(0.686) 		1
(1.00)
amp 16q24 2 49 (54%) 41 0.18
(0.79) 		0.903
(1.00) 		0.738
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.187
(0.79) 		0.188
(0.79) 		1
(1.00) 		1
(1.00) 		0.515
(1.00) 		0.73
(1.00) 		0.699
(1.00)
amp 17q25 3 18 (20%) 72 0.186
(0.79) 		0.232
(0.811) 		0.791
(1.00) 		0.491
(1.00) 		0.68
(1.00) 		0.588
(1.00) 		0.754
(1.00) 		0.137
(0.722) 		0.874
(1.00) 		0.265
(0.863) 		0.474
(1.00) 		0.664
(1.00)
amp 19p13 12 58 (64%) 32 0.212
(0.79) 		0.129
(0.722) 		0.138
(0.722) 		0.19
(0.79) 		0.484
(1.00) 		1
(1.00) 		0.0576
(0.686) 		1
(1.00) 		0.816
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.23
(0.809)
amp 19q12 56 (62%) 34 0.0515
(0.686) 		0.0457
(0.686) 		0.0819
(0.686) 		0.118
(0.722) 		0.737
(1.00) 		0.498
(1.00) 		0.0303
(0.686) 		1
(1.00) 		0.367
(0.999) 		0.979
(1.00) 		1
(1.00) 		0.226
(0.802)
amp xp11 22 49 (54%) 41 0.838
(1.00) 		0.906
(1.00) 		0.674
(1.00) 		0.856
(1.00) 		0.502
(1.00) 		0.505
(1.00) 		0.6
(1.00) 		0.213
(0.79) 		0.785
(1.00) 		0.399
(1.00) 		1
(1.00) 		0.0399
(0.686)
amp xq28 46 (51%) 44 0.401
(1.00) 		0.707
(1.00) 		0.882
(1.00) 		0.937
(1.00) 		1
(1.00) 		1
(1.00) 		0.441
(1.00) 		0.804
(1.00) 		0.375
(1.00) 		0.554
(1.00) 		0.745
(1.00) 		1
(1.00)
del 1p36 23 38 (42%) 52 0.187
(0.79) 		0.49
(1.00) 		0.617
(1.00) 		0.469
(1.00) 		0.736
(1.00) 		0.823
(1.00) 		1
(1.00) 		0.601
(1.00) 		0.296
(0.93) 		0.939
(1.00) 		0.506
(1.00) 		0.407
(1.00)
del 2q22 1 18 (20%) 72 0.0679
(0.686) 		0.948
(1.00) 		0.432
(1.00) 		0.733
(1.00) 		1
(1.00) 		1
(1.00) 		0.331
(0.985) 		0.0524
(0.686) 		0.95
(1.00) 		0.814
(1.00) 		1
(1.00) 		1
(1.00)
del 2q37 3 21 (23%) 69 0.446
(1.00) 		0.8
(1.00) 		0.182
(0.79) 		0.977
(1.00) 		1
(1.00) 		1
(1.00) 		0.549
(1.00) 		0.0793
(0.686) 		0.847
(1.00) 		0.77
(1.00) 		1
(1.00) 		0.277
(0.88)
del 3q13 31 25 (28%) 65 0.116
(0.722) 		0.474
(1.00) 		0.361
(0.999) 		0.66
(1.00) 		1
(1.00) 		0.0464
(0.686) 		0.55
(1.00) 		0.692
(1.00) 		0.219
(0.79) 		0.883
(1.00) 		0.319
(0.968) 		0.374
(1.00)
del 4q34 3 25 (28%) 65 0.00224
(0.406) 		0.479
(1.00) 		0.0985
(0.713) 		0.0876
(0.713) 		1
(1.00) 		1
(1.00) 		0.562
(1.00) 		0.694
(1.00) 		0.0065
(0.49) 		0.611
(1.00) 		0.631
(1.00) 		1
(1.00)
del 4q34 3 28 (31%) 62 0.015
(0.66) 		0.717
(1.00) 		0.206
(0.79) 		0.168
(0.79) 		1
(1.00) 		0.815
(1.00) 		0.251
(0.862) 		0.161
(0.778) 		0.0358
(0.686) 		0.361
(0.999) 		0.652
(1.00) 		0.412
(1.00)
del 4q35 1 30 (33%) 60 0.0131
(0.628) 		0.535
(1.00) 		0.263
(0.863) 		0.205
(0.79) 		1
(1.00) 		0.485
(1.00) 		0.0241
(0.686) 		0.396
(1.00) 		0.0809
(0.686) 		0.716
(1.00) 		0.685
(1.00) 		0.669
(1.00)
del 6p24 3 20 (22%) 70 0.22
(0.79) 		0.197
(0.79) 		0.221
(0.79) 		0.759
(1.00) 		1
(1.00) 		1
(1.00) 		0.339
(0.985) 		0.0709
(0.686) 		0.265
(0.863) 		0.854
(1.00) 		1
(1.00) 		1
(1.00)
del 6q26 21 (23%) 69 0.102
(0.715) 		0.116
(0.722) 		0.022
(0.686) 		0.0455
(0.686) 		0.697
(1.00) 		0.301
(0.939) 		1
(1.00) 		0.081
(0.686) 		0.126
(0.722) 		0.671
(1.00) 		1
(1.00) 		1
(1.00)
del 7q36 3 11 (12%) 79 0.00753
(0.497) 		0.402
(1.00) 		0.133
(0.722) 		0.0456
(0.686) 		1
(1.00) 		1
(1.00) 		0.678
(1.00) 		1
(1.00) 		0.0225
(0.686) 		0.896
(1.00) 		0.335
(0.985) 		1
(1.00)
del 9p23 23 (26%) 67 0.0338
(0.686) 		0.608
(1.00) 		0.837
(1.00) 		0.567
(1.00) 		0.44
(1.00) 		0.617
(1.00) 		0.221
(0.79) 		0.679
(1.00) 		0.625
(1.00) 		0.0961
(0.713) 		1
(1.00) 		0.412
(1.00)
del 9p21 3 26 (29%) 64 0.0292
(0.686) 		0.26
(0.863) 		0.719
(1.00) 		0.686
(1.00) 		0.27
(0.865) 		1
(1.00) 		0.142
(0.722) 		0.511
(1.00) 		0.885
(1.00) 		0.065
(0.686) 		1
(1.00) 		0.669
(1.00)
del 10q23 1 10 (11%) 80 0.615
(1.00) 		0.138
(0.722) 		0.597
(1.00) 		0.333
(0.985) 		0.317
(0.968) 		1
(1.00) 		1
(1.00) 		0.0414
(0.686) 		0.0798
(0.686) 		0.338
(0.985) 		0.341
(0.985) 		1
(1.00)
del 11p15 5 26 (29%) 64 0.386
(1.00) 		0.485
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.128
(0.722) 		0.15
(0.74) 		0.562
(1.00) 		0.142
(0.722) 		0.619
(1.00) 		0.147
(0.734) 		1
(1.00) 		1
(1.00)
del 11q14 1 24 (27%) 66 0.484
(1.00) 		0.139
(0.722) 		0.139
(0.722) 		0.467
(1.00) 		1
(1.00) 		0.212
(0.79) 		0.768
(1.00) 		0.116
(0.722) 		0.636
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
del 12q14 2 5 (6%) 85 0.0311
(0.686) 		0.311
(0.955) 		0.391
(1.00) 		0.468
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.503
(1.00) 		1
(1.00) 		1
(1.00)
del 13q14 2 42 (47%) 48 0.108
(0.722) 		0.269
(0.865) 		0.202
(0.79) 		0.695
(1.00) 		0.75
(1.00) 		0.828
(1.00) 		1
(1.00) 		0.219
(0.79) 		0.909
(1.00) 		0.939
(1.00) 		0.496
(1.00) 		0.694
(1.00)
del 14q21 2 20 (22%) 70 0.619
(1.00) 		0.58
(1.00) 		0.813
(1.00) 		0.891
(1.00) 		0.11
(0.722) 		0.599
(1.00) 		0.339
(0.985) 		0.0707
(0.686) 		1
(1.00) 		0.0645
(0.686) 		0.235
(0.817) 		0.344
(0.988)
del 15q15 1 25 (28%) 65 0.446
(1.00) 		0.896
(1.00) 		0.632
(1.00) 		0.831
(1.00) 		0.718
(1.00) 		0.81
(1.00) 		0.572
(1.00) 		0.128
(0.722) 		1
(1.00) 		0.178
(0.79) 		1
(1.00) 		0.658
(1.00)
del 16p13 3 8 (9%) 82 0.0786
(0.686) 		0.697
(1.00) 		0.133
(0.722) 		0.0753
(0.686) 		1
(1.00) 		1
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.0447
(0.686) 		0.818
(1.00) 		0.0973
(0.713) 		0.203
(0.79)
del 16q23 1 11 (12%) 79 0.00333
(0.408) 		0.108
(0.722) 		0.359
(0.999) 		0.159
(0.777) 		0.35
(0.995) 		1
(1.00) 		0.68
(1.00) 		1
(1.00) 		0.0474
(0.686) 		0.173
(0.79) 		1
(1.00) 		1
(1.00)
del 17q11 2 24 (27%) 66 0.0277
(0.686) 		0.975
(1.00) 		0.189
(0.79) 		0.0968
(0.713) 		0.706
(1.00) 		0.0243
(0.686) 		0.759
(1.00) 		0.687
(1.00) 		0.103
(0.715) 		0.583
(1.00) 		1
(1.00) 		1
(1.00)
del 17q21 2 26 (29%) 64 0.00386
(0.408) 		0.94
(1.00) 		0.129
(0.722) 		0.217
(0.79) 		0.451
(1.00) 		0.055
(0.686) 		1
(1.00) 		0.512
(1.00) 		0.0544
(0.686) 		0.399
(1.00) 		1
(1.00) 		1
(1.00)
del 17q24 2 24 (27%) 66 0.0198
(0.686) 		0.971
(1.00) 		0.0112
(0.593) 		0.304
(0.941) 		0.26
(0.863) 		0.0802
(0.686) 		0.377
(1.00) 		0.686
(1.00) 		0.0412
(0.686) 		0.187
(0.79) 		1
(1.00) 		1
(1.00)
del 20p12 1 12 (13%) 78 0.116
(0.722) 		0.357
(0.999) 		0.454
(1.00) 		0.426
(1.00) 		0.35
(0.995) 		0.206
(0.79) 		0.69
(1.00) 		1
(1.00) 		0.00098
(0.406) 		0.173
(0.79) 		0.366
(0.999) 		0.203
(0.79)
del 22q12 1 50 (56%) 40 0.0645
(0.686) 		0.0943
(0.713) 		0.184
(0.79) 		0.147
(0.734) 		0.745
(1.00) 		0.267
(0.864) 		0.793
(1.00) 		1
(1.00) 		0.784
(1.00) 		0.26
(0.863) 		1
(1.00) 		0.243
(0.838)
Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/22522857/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/22489368/ACC-TP.merged_data.txt

  • Number of patients = 90

  • Number of significantly focal cnvs = 44

  • Number of selected clinical features = 12

  • 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

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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