Correlation between copy number variation genes (focal events) and selected clinical features
Pancreatic Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1319TN6
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/C1319TN6
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 47 focal events and 12 clinical features across 86 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 47 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 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		NUMBERPACKYEARSSMOKED COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		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 Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test
amp 1p34 2 5 (6%) 81 0.499
(1.00) 		0.314
(1.00) 		0.364
(1.00) 		1
(1.00) 		1
(1.00) 		0.026
(1.00) 		0.197
(1.00) 		0.0669
(1.00) 		0.0974
(1.00) 		0.115
(1.00) 		1
(1.00)
amp 1p12 13 (15%) 73 0.755
(1.00) 		0.408
(1.00) 		0.106
(1.00) 		0.601
(1.00) 		0.293
(1.00) 		0.039
(1.00) 		1
(1.00) 		0.329
(1.00) 		0.846
(1.00) 		0.359
(1.00) 		0.392
(1.00)
amp 6p21 31 5 (6%) 81 0.631
(1.00) 		0.625
(1.00) 		0.162
(1.00) 		0.394
(1.00) 		0.094
(1.00) 		0.0271
(1.00) 		1
(1.00) 		0.23
(1.00) 		0.708
(1.00) 		0.531
(1.00) 		0.409
(1.00)
amp 7q22 1 25 (29%) 61 0.345
(1.00) 		0.604
(1.00) 		0.47
(1.00) 		0.428
(1.00) 		0.591
(1.00) 		0.316
(1.00) 		0.479
(1.00) 		1
(1.00) 		0.239
(1.00) 		0.00109
(0.598) 		0.297
(1.00) 		0.526
(1.00)
amp 8q24 21 35 (41%) 51 0.0892
(1.00) 		0.923
(1.00) 		0.771
(1.00) 		1
(1.00) 		0.611
(1.00) 		0.326
(1.00) 		0.511
(1.00) 		0.764
(1.00) 		0.0604
(1.00) 		0.453
(1.00) 		0.724
(1.00) 		0.0939
(1.00)
amp 9p13 3 10 (12%) 76 0.435
(1.00) 		0.028
(1.00) 		0.152
(1.00) 		0.588
(1.00) 		0.254
(1.00) 		0.301
(1.00) 		0.516
(1.00) 		1
(1.00) 		0.807
(1.00) 		0.663
(1.00) 		0.626
(1.00)
amp 11p11 2 12 (14%) 74 0.612
(1.00) 		0.197
(1.00) 		0.268
(1.00) 		0.593
(1.00) 		0.16
(1.00) 		0.153
(1.00) 		0.223
(1.00) 		0.296
(1.00) 		0.107
(1.00) 		0.26
(1.00) 		0.818
(1.00) 		0.397
(1.00)
amp 12p13 33 12 (14%) 74 0.803
(1.00) 		0.736
(1.00) 		0.826
(1.00) 		0.309
(1.00) 		0.722
(1.00) 		0.844
(1.00) 		0.0652
(1.00) 		0.389
(1.00) 		0.076
(1.00) 		0.285
(1.00) 		0.0759
(1.00) 		1
(1.00)
amp 12p12 1 17 (20%) 69 0.82
(1.00) 		0.761
(1.00) 		0.214
(1.00) 		0.654
(1.00) 		0.219
(1.00) 		0.472
(1.00) 		0.0593
(1.00) 		0.816
(1.00) 		0.107
(1.00) 		0.00456
(1.00) 		0.124
(1.00) 		1
(1.00)
amp 12p11 21 14 (16%) 72 0.83
(1.00) 		0.475
(1.00) 		0.289
(1.00) 		0.611
(1.00) 		0.501
(1.00) 		0.641
(1.00) 		0.0196
(1.00) 		0.78
(1.00) 		0.107
(1.00) 		0.0235
(1.00) 		0.0513
(1.00) 		1
(1.00)
amp 12q15 10 (12%) 76 0.202
(1.00) 		0.962
(1.00) 		0.651
(1.00) 		0.588
(1.00) 		0.0611
(1.00) 		1
(1.00) 		0.0466
(1.00) 		0.488
(1.00) 		0.519
(1.00) 		0.106
(1.00) 		0.0182
(1.00) 		0.666
(1.00)
amp 17p11 2 3 (3%) 83 0.645
(1.00) 		0.621
(1.00) 		0.326
(1.00) 		1
(1.00) 		0.15
(1.00) 		1
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.346
(1.00) 		0.268
(1.00)
amp 17q21 32 11 (13%) 75 0.301
(1.00) 		0.573
(1.00) 		0.525
(1.00) 		0.589
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.346
(1.00) 		0.535
(1.00) 		0.197
(1.00) 		0.364
(1.00) 		0.71
(1.00) 		0.665
(1.00)
amp 18q11 2 27 (31%) 59 0.419
(1.00) 		0.579
(1.00) 		0.0885
(1.00) 		0.426
(1.00) 		0.429
(1.00) 		0.0116
(1.00) 		0.488
(1.00) 		0.741
(1.00) 		0.0833
(1.00) 		0.259
(1.00) 		0.432
(1.00) 		0.209
(1.00)
amp 19q13 2 21 (24%) 65 0.0661
(1.00) 		0.243
(1.00) 		0.7
(1.00) 		0.191
(1.00) 		0.769
(1.00) 		0.324
(1.00) 		0.0799
(1.00) 		0.0567
(1.00) 		0.485
(1.00) 		0.271
(1.00) 		0.031
(1.00) 		0.494
(1.00)
amp 20q13 2 26 (30%) 60 0.294
(1.00) 		0.535
(1.00) 		0.602
(1.00) 		0.693
(1.00) 		0.587
(1.00) 		0.643
(1.00) 		0.35
(1.00) 		0.274
(1.00) 		0.0294
(1.00) 		0.116
(1.00) 		0.368
(1.00) 		1
(1.00)
amp xp22 11 5 (6%) 81 0.49
(1.00) 		0.817
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.197
(1.00) 		0.231
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.409
(1.00)
amp xq27 1 9 (10%) 77 0.942
(1.00) 		0.977
(1.00) 		0.322
(1.00) 		0.592
(1.00) 		0.441
(1.00) 		0.813
(1.00) 		0.308
(1.00) 		0.688
(1.00) 		0.329
(1.00) 		0.495
(1.00) 		0.315
(1.00)
del 1p36 32 23 (27%) 63 0.31
(1.00) 		0.187
(1.00) 		0.517
(1.00) 		0.676
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.0889
(1.00) 		0.208
(1.00) 		0.194
(1.00) 		0.786
(1.00) 		0.406
(1.00) 		0.507
(1.00)
del 1p36 11 28 (33%) 58 0.00556
(1.00) 		0.274
(1.00) 		0.204
(1.00) 		0.265
(1.00) 		1
(1.00) 		0.464
(1.00) 		0.0209
(1.00) 		0.432
(1.00) 		0.155
(1.00) 		0.772
(1.00) 		0.77
(1.00) 		0.268
(1.00)
del 1p21 2 20 (23%) 66 0.0137
(1.00) 		0.846
(1.00) 		0.846
(1.00) 		0.675
(1.00) 		0.137
(1.00) 		0.24
(1.00) 		0.312
(1.00) 		0.719
(1.00) 		0.213
(1.00) 		0.263
(1.00) 		0.0331
(1.00) 		0.0634
(1.00)
del 1q42 2 4 (5%) 82 0.0119
(1.00) 		0.753
(1.00) 		1
(1.00) 		1
(1.00) 		0.665
(1.00) 		0.0527
(1.00) 		0.43
(1.00) 		0.215
(1.00) 		0.784
(1.00) 		1
(1.00)
del 2p23 3 11 (13%) 75 0.337
(1.00) 		0.688
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.57
(1.00) 		0.346
(1.00) 		0.164
(1.00) 		0.642
(1.00) 		0.395
(1.00) 		0.0666
(1.00) 		0.147
(1.00)
del 2q37 3 3 (3%) 83 0.519
(1.00) 		0.0697
(1.00) 		0.648
(1.00) 		1
(1.00) 		1
(1.00) 		0.657
(1.00) 		1
(1.00) 		0.124
(1.00) 		0.0435
(1.00) 		0.352
(1.00) 		1
(1.00)
del 3p24 1 20 (23%) 66 0.367
(1.00) 		0.645
(1.00) 		0.967
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.613
(1.00) 		0.592
(1.00) 		0.0498
(1.00) 		0.134
(1.00) 		0.247
(1.00) 		0.765
(1.00)
del 4q35 2 15 (17%) 71 0.414
(1.00) 		0.923
(1.00) 		0.769
(1.00) 		0.624
(1.00) 		0.74
(1.00) 		1
(1.00) 		0.048
(1.00) 		0.634
(1.00) 		0.556
(1.00) 		0.746
(1.00) 		0.584
(1.00) 		0.0402
(1.00)
del 5q14 2 20 (23%) 66 0.459
(1.00) 		0.428
(1.00) 		0.983
(1.00) 		1
(1.00) 		0.769
(1.00) 		1
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.0316
(1.00) 		0.19
(1.00) 		0.606
(1.00) 		0.603
(1.00)
del 6p25 2 33 (38%) 53 0.0506
(1.00) 		0.194
(1.00) 		0.675
(1.00) 		0.705
(1.00) 		0.614
(1.00) 		0.346
(1.00) 		0.507
(1.00) 		0.167
(1.00) 		0.34
(1.00) 		0.75
(1.00) 		0.321
(1.00) 		0.71
(1.00)
del 7q36 1 8 (9%) 78 0.552
(1.00) 		0.466
(1.00) 		0.55
(1.00) 		0.16
(1.00) 		0.673
(1.00) 		0.786
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.149
(1.00) 		1
(1.00)
del 8p21 3 26 (30%) 60 0.476
(1.00) 		0.267
(1.00) 		1
(1.00) 		0.426
(1.00) 		0.591
(1.00) 		0.917
(1.00) 		0.16
(1.00) 		0.226
(1.00) 		0.112
(1.00) 		0.042
(1.00) 		0.973
(1.00) 		0.0909
(1.00)
del 8q12 1 8 (9%) 78 0.582
(1.00) 		0.178
(1.00) 		0.258
(1.00) 		1
(1.00) 		0.357
(1.00) 		0.298
(1.00) 		0.479
(1.00) 		0.168
(1.00) 		0.78
(1.00) 		0.548
(1.00) 		0.0952
(1.00)
del 9p21 3 54 (63%) 32 0.262
(1.00) 		0.491
(1.00) 		0.0956
(1.00) 		0.463
(1.00) 		0.61
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.666
(1.00) 		0.163
(1.00) 		0.0133
(1.00) 		0.709
(1.00) 		0.589
(1.00)
del 9q22 33 22 (26%) 64 0.554
(1.00) 		0.968
(1.00) 		0.457
(1.00) 		1
(1.00) 		0.778
(1.00) 		0.481
(1.00) 		0.463
(1.00) 		0.858
(1.00) 		0.117
(1.00) 		0.839
(1.00) 		0.518
(1.00) 		0.78
(1.00)
del 10q23 2 13 (15%) 73 0.326
(1.00) 		0.362
(1.00) 		0.956
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.624
(1.00) 		0.769
(1.00) 		0.237
(1.00) 		0.0865
(1.00) 		0.487
(1.00) 		0.519
(1.00) 		0.699
(1.00)
del 11p15 4 15 (17%) 71 0.344
(1.00) 		0.711
(1.00) 		0.916
(1.00) 		0.341
(1.00) 		0.338
(1.00) 		0.018
(1.00) 		0.573
(1.00) 		0.391
(1.00) 		0.313
(1.00) 		0.337
(1.00) 		0.0724
(1.00) 		0.119
(1.00)
del 12p12 3 11 (13%) 75 0.719
(1.00) 		0.539
(1.00) 		0.756
(1.00) 		0.589
(1.00) 		1
(1.00) 		0.321
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.00787
(1.00) 		0.884
(1.00) 		0.393
(1.00)
del 12q12 8 (9%) 78 0.653
(1.00) 		0.71
(1.00) 		0.363
(1.00) 		0.558
(1.00) 		0.402
(1.00) 		0.0395
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.972
(1.00) 		0.387
(1.00) 		0.97
(1.00) 		0.526
(1.00)
del 12q24 33 20 (23%) 66 0.0674
(1.00) 		0.919
(1.00) 		0.983
(1.00) 		1
(1.00) 		0.379
(1.00) 		0.66
(1.00) 		0.613
(1.00) 		0.716
(1.00) 		0.588
(1.00) 		0.122
(1.00) 		0.542
(1.00) 		0.0015
(0.822)
del 15q15 1 17 (20%) 69 0.899
(1.00) 		0.484
(1.00) 		0.428
(1.00) 		1
(1.00) 		0.528
(1.00) 		0.789
(1.00) 		0.0593
(1.00) 		0.11
(1.00) 		0.0671
(1.00) 		0.236
(1.00) 		0.995
(1.00) 		0.383
(1.00)
del 16q23 1 4 (5%) 82 0.699
(1.00) 		0.75
(1.00) 		0.27
(1.00) 		1
(1.00) 		0.571
(1.00) 		0.133
(1.00) 		0.0527
(1.00) 		0.0413
(1.00) 		0.106
(1.00) 		0.856
(1.00) 		0.12
(1.00)
del 17q22 24 (28%) 62 0.834
(1.00) 		0.644
(1.00) 		0.408
(1.00) 		0.433
(1.00) 		0.404
(1.00) 		0.148
(1.00) 		0.812
(1.00) 		0.429
(1.00) 		0.0316
(1.00) 		0.00271
(1.00) 		0.344
(1.00) 		0.316
(1.00)
del 18p11 32 30 (35%) 56 0.789
(1.00) 		0.0551
(1.00) 		0.393
(1.00) 		0.442
(1.00) 		0.792
(1.00) 		0.298
(1.00) 		0.652
(1.00) 		0.747
(1.00) 		0.696
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.691
(1.00)
del 18q21 2 59 (69%) 27 0.735
(1.00) 		0.592
(1.00) 		0.323
(1.00) 		0.702
(1.00) 		0.59
(1.00) 		0.173
(1.00) 		0.358
(1.00) 		1
(1.00) 		0.568
(1.00) 		0.0553
(1.00) 		0.572
(1.00) 		0.439
(1.00)
del 19p13 3 16 (19%) 70 0.142
(1.00) 		0.629
(1.00) 		0.602
(1.00) 		1
(1.00) 		0.336
(1.00) 		0.68
(1.00) 		1
(1.00) 		0.292
(1.00) 		0.844
(1.00) 		0.211
(1.00) 		0.0139
(1.00) 		1
(1.00)
del 19q13 41 11 (13%) 75 0.0926
(1.00) 		0.623
(1.00) 		0.936
(1.00) 		0.589
(1.00) 		0.0611
(1.00) 		0.839
(1.00) 		0.113
(1.00) 		0.265
(1.00) 		0.42
(1.00) 		0.549
(1.00) 		0.0117
(1.00) 		0.0162
(1.00)
del 21q21 1 32 (37%) 54 0.117
(1.00) 		0.993
(1.00) 		0.264
(1.00) 		0.249
(1.00) 		0.194
(1.00) 		0.313
(1.00) 		0.509
(1.00) 		0.585
(1.00) 		0.584
(1.00) 		0.0574
(1.00) 		0.00598
(1.00) 		0.844
(1.00)
del 22q13 31 28 (33%) 58 0.892
(1.00) 		0.189
(1.00) 		0.422
(1.00) 		0.265
(1.00) 		0.184
(1.00) 		0.352
(1.00) 		0.168
(1.00) 		1
(1.00) 		0.134
(1.00) 		0.144
(1.00) 		0.131
(1.00) 		0.696
(1.00)
Methods & Data
Input

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

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

  • Number of patients = 86

  • Number of significantly focal cnvs = 47

  • 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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