Correlation between copy number variation genes (focal events) and selected clinical features
Pancreatic Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1QZ28MC
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/C1QZ28MC
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 42 focal events and 12 clinical features across 72 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 42 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 YEAROFTOBACCOSMOKINGONSET COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
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 t-test t-test Fisher's exact test t-test
amp 1p34 2 4 (6%) 68 0.461
(1.00) 		0.06
(1.00) 		0.353
(1.00) 		1
(1.00) 		0.566
(1.00) 		0.0187
(1.00) 		0.614
(1.00) 		0.346
(1.00) 		0.0755
(1.00) 		0.000904
(0.434)
amp 1p12 10 (14%) 62 0.956
(1.00) 		0.841
(1.00) 		0.131
(1.00) 		0.583
(1.00) 		1
(1.00) 		0.0279
(1.00) 		1
(1.00) 		1
(1.00) 		0.497
(1.00) 		0.643
(1.00)
amp 7q22 1 19 (26%) 53 0.535
(1.00) 		0.845
(1.00) 		0.298
(1.00) 		0.178
(1.00) 		0.362
(1.00) 		0.312
(1.00) 		0.594
(1.00) 		1
(1.00) 		0.348
(1.00) 		0.371
(1.00) 		0.00105
(0.504) 		0.396
(1.00)
amp 8q24 21 27 (38%) 45 0.238
(1.00) 		0.795
(1.00) 		0.701
(1.00) 		0.704
(1.00) 		0.58
(1.00) 		0.216
(1.00) 		0.627
(1.00) 		0.834
(1.00) 		0.13
(1.00) 		0.72
(1.00) 		0.452
(1.00) 		0.247
(1.00)
amp 9p13 3 8 (11%) 64 0.116
(1.00) 		0.124
(1.00) 		0.273
(1.00) 		1
(1.00) 		0.409
(1.00) 		0.389
(1.00) 		0.71
(1.00) 		0.584
(1.00) 		1
(1.00) 		0.458
(1.00)
amp 11p11 2 8 (11%) 64 0.319
(1.00) 		0.626
(1.00) 		0.853
(1.00) 		1
(1.00) 		1
(1.00) 		0.0227
(1.00) 		0.26
(1.00) 		1
(1.00) 		0.00315
(1.00) 		0.905
(1.00) 		0.113
(1.00) 		0.214
(1.00)
amp 12p13 33 9 (12%) 63 0.181
(1.00) 		0.6
(1.00) 		0.593
(1.00) 		1
(1.00) 		0.432
(1.00) 		1
(1.00) 		0.151
(1.00) 		0.584
(1.00) 		0.0014
(0.669) 		0.284
(1.00) 		0.0599
(1.00) 		0.161
(1.00)
amp 12p11 21 12 (17%) 60 0.0464
(1.00) 		0.49
(1.00) 		0.521
(1.00) 		1
(1.00) 		0.718
(1.00) 		0.621
(1.00) 		0.0238
(1.00) 		0.453
(1.00) 		0.00315
(1.00) 		0.905
(1.00) 		0.0116
(1.00) 		0.259
(1.00)
amp 12q15 9 (12%) 63 0.00452
(1.00) 		0.713
(1.00) 		0.476
(1.00) 		0.585
(1.00) 		0.0997
(1.00) 		1
(1.00) 		0.151
(1.00) 		0.214
(1.00) 		0.556
(1.00) 		0.515
(1.00) 		0.0599
(1.00) 		0.142
(1.00)
amp 17q21 32 8 (11%) 64 0.857
(1.00) 		0.567
(1.00) 		0.853
(1.00) 		1
(1.00) 		1
(1.00) 		0.805
(1.00) 		0.26
(1.00) 		0.175
(1.00) 		0.265
(1.00) 		0.786
(1.00)
amp 18q11 2 22 (31%) 50 0.451
(1.00) 		0.822
(1.00) 		0.0713
(1.00) 		0.0924
(1.00) 		1
(1.00) 		0.00202
(0.962) 		0.798
(1.00) 		0.821
(1.00) 		0.564
(1.00) 		0.556
(1.00) 		0.0653
(1.00) 		0.951
(1.00)
amp 19q13 2 18 (25%) 54 0.685
(1.00) 		0.489
(1.00) 		0.559
(1.00) 		0.181
(1.00) 		0.531
(1.00) 		0.435
(1.00) 		0.173
(1.00) 		0.245
(1.00) 		0.421
(1.00) 		0.285
(1.00) 		0.737
(1.00) 		0.0685
(1.00)
amp 20q13 2 17 (24%) 55 0.549
(1.00) 		0.131
(1.00) 		0.355
(1.00) 		0.665
(1.00) 		0.531
(1.00) 		1
(1.00) 		0.0942
(1.00) 		0.598
(1.00) 		0.0365
(1.00) 		0.191
(1.00) 		0.0403
(1.00) 		0.17
(1.00)
amp xp22 11 4 (6%) 68 0.961
(1.00) 		0.332
(1.00) 		0.868
(1.00) 		1
(1.00) 		0.566
(1.00) 		1
(1.00) 		0.614
(1.00) 		1
(1.00) 		1
(1.00) 		0.382
(1.00)
amp xq27 1 8 (11%) 64 0.469
(1.00) 		0.745
(1.00) 		0.308
(1.00) 		1
(1.00) 		0.67
(1.00) 		1
(1.00) 		0.71
(1.00) 		0.533
(1.00) 		0.316
(1.00) 		0.408
(1.00)
del 1p36 32 15 (21%) 57 0.384
(1.00) 		0.168
(1.00) 		0.745
(1.00) 		0.332
(1.00) 		0.494
(1.00) 		0.0284
(1.00) 		0.0182
(1.00) 		0.564
(1.00) 		0.9
(1.00) 		0.0442
(1.00) 		0.37
(1.00) 		0.126
(1.00)
del 1p36 11 21 (29%) 51 0.428
(1.00) 		0.481
(1.00) 		0.237
(1.00) 		0.0982
(1.00) 		1
(1.00) 		0.0314
(1.00) 		0.00862
(1.00) 		0.502
(1.00) 		0.748
(1.00) 		0.0172
(1.00) 		0.8
(1.00) 		0.353
(1.00)
del 1q42 2 3 (4%) 69 0.201
(1.00) 		0.0167
(1.00) 		0.95
(1.00) 		1
(1.00) 		1
(1.00) 		0.627
(1.00) 		0.239
(1.00) 		1
(1.00) 		0.0849
(1.00) 		0.861
(1.00)
del 2p23 3 10 (14%) 62 0.519
(1.00) 		0.725
(1.00) 		0.648
(1.00) 		1
(1.00) 		0.261
(1.00) 		0.68
(1.00) 		0.735
(1.00) 		0.254
(1.00) 		0.564
(1.00) 		0.804
(1.00) 		0.307
(1.00) 		0.0617
(1.00)
del 3p24 1 15 (21%) 57 0.846
(1.00) 		0.409
(1.00) 		0.816
(1.00) 		1
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.245
(1.00) 		1
(1.00) 		0.0954
(1.00) 		0.513
(1.00) 		0.0751
(1.00) 		0.139
(1.00)
del 4q35 2 14 (19%) 58 0.785
(1.00) 		0.967
(1.00) 		0.572
(1.00) 		0.615
(1.00) 		0.726
(1.00) 		0.878
(1.00) 		0.135
(1.00) 		0.528
(1.00) 		0.381
(1.00) 		0.886
(1.00) 		0.713
(1.00) 		0.0489
(1.00)
del 5q14 2 14 (19%) 58 0.706
(1.00) 		0.367
(1.00) 		0.851
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.767
(1.00) 		1
(1.00) 		0.027
(1.00) 		0.0175
(1.00) 		0.393
(1.00) 		0.278
(1.00)
del 6p25 2 27 (38%) 45 0.261
(1.00) 		0.145
(1.00) 		0.574
(1.00) 		0.244
(1.00) 		1
(1.00) 		0.173
(1.00) 		0.627
(1.00) 		0.344
(1.00) 		0.403
(1.00) 		0.679
(1.00) 		0.339
(1.00) 		0.213
(1.00)
del 7q36 1 6 (8%) 66 0.96
(1.00) 		0.361
(1.00) 		0.658
(1.00) 		0.471
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.883
(1.00)
del 8p21 3 19 (26%) 53 0.364
(1.00) 		0.106
(1.00) 		0.817
(1.00) 		0.667
(1.00) 		0.531
(1.00) 		0.513
(1.00) 		0.285
(1.00) 		0.348
(1.00) 		0.182
(1.00) 		0.751
(1.00) 		0.00696
(1.00) 		0.238
(1.00)
del 8q12 1 6 (8%) 66 0.384
(1.00) 		0.302
(1.00) 		0.424
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.293
(1.00) 		0.674
(1.00) 		0.104
(1.00) 		0.716
(1.00) 		0.783
(1.00)
del 9p21 3 44 (61%) 28 0.454
(1.00) 		0.45
(1.00) 		0.107
(1.00) 		0.419
(1.00) 		0.781
(1.00) 		0.178
(1.00) 		0.809
(1.00) 		1
(1.00) 		0.384
(1.00) 		0.768
(1.00) 		0.00983
(1.00) 		0.914
(1.00)
del 9q22 33 17 (24%) 55 0.38
(1.00) 		0.659
(1.00) 		0.473
(1.00) 		1
(1.00) 		1
(1.00) 		0.481
(1.00) 		1
(1.00) 		0.764
(1.00) 		0.442
(1.00) 		0.306
(1.00) 		0.87
(1.00) 		0.53
(1.00)
del 9q32 18 (25%) 54 0.603
(1.00) 		0.77
(1.00) 		0.458
(1.00) 		0.672
(1.00) 		1
(1.00) 		0.644
(1.00) 		1
(1.00) 		0.778
(1.00) 		0.442
(1.00) 		0.306
(1.00) 		0.585
(1.00) 		0.373
(1.00)
del 10q23 2 10 (14%) 62 0.619
(1.00) 		0.187
(1.00) 		0.857
(1.00) 		1
(1.00) 		1
(1.00) 		0.245
(1.00) 		0.735
(1.00) 		0.672
(1.00) 		0.151
(1.00) 		0.352
(1.00) 		0.387
(1.00)
del 11p15 4 13 (18%) 59 0.109
(1.00) 		0.802
(1.00) 		0.519
(1.00) 		0.337
(1.00) 		0.161
(1.00) 		0.0448
(1.00) 		1
(1.00) 		0.717
(1.00) 		0.182
(1.00) 		0.249
(1.00) 		0.54
(1.00) 		0.152
(1.00)
del 12p12 1 9 (12%) 63 0.149
(1.00) 		0.708
(1.00) 		0.849
(1.00) 		0.585
(1.00) 		1
(1.00) 		1
(1.00) 		0.151
(1.00) 		0.584
(1.00) 		0.0599
(1.00) 		0.567
(1.00)
del 12q12 8 (11%) 64 0.228
(1.00) 		0.629
(1.00) 		0.717
(1.00) 		0.578
(1.00) 		0.409
(1.00) 		0.078
(1.00) 		0.71
(1.00) 		1
(1.00) 		0.986
(1.00) 		0.451
(1.00) 		0.387
(1.00) 		0.675
(1.00)
del 12q24 33 16 (22%) 56 0.924
(1.00) 		0.543
(1.00) 		0.771
(1.00) 		1
(1.00) 		0.324
(1.00) 		0.401
(1.00) 		0.778
(1.00) 		0.598
(1.00) 		0.935
(1.00) 		0.631
(1.00) 		0.0505
(1.00) 		0.692
(1.00)
del 16q23 1 4 (6%) 68 0.528
(1.00) 		0.871
(1.00) 		0.372
(1.00) 		1
(1.00) 		0.566
(1.00) 		0.186
(1.00) 		0.115
(1.00) 		0.0459
(1.00) 		0.0755
(1.00) 		0.693
(1.00)
del 17q22 20 (28%) 52 0.414
(1.00) 		0.764
(1.00) 		0.362
(1.00) 		0.179
(1.00) 		0.762
(1.00) 		0.174
(1.00) 		1
(1.00) 		1
(1.00) 		0.0399
(1.00) 		0.455
(1.00) 		0.00254
(1.00) 		0.885
(1.00)
del 18p11 32 24 (33%) 48 0.755
(1.00) 		0.0137
(1.00) 		0.31
(1.00) 		0.212
(1.00) 		0.565
(1.00) 		0.221
(1.00) 		1
(1.00) 		1
(1.00) 		0.749
(1.00) 		0.8
(1.00) 		0.902
(1.00) 		0.475
(1.00)
del 18q21 2 47 (65%) 25 0.53
(1.00) 		0.704
(1.00) 		0.249
(1.00) 		0.688
(1.00) 		0.778
(1.00) 		0.0634
(1.00) 		0.621
(1.00) 		0.839
(1.00) 		0.948
(1.00) 		0.0115
(1.00) 		0.292
(1.00)
del 19p13 3 11 (15%) 61 0.361
(1.00) 		0.889
(1.00) 		0.411
(1.00) 		0.585
(1.00) 		0.269
(1.00) 		0.594
(1.00) 		1
(1.00) 		1
(1.00) 		0.858
(1.00) 		0.614
(1.00) 		0.352
(1.00) 		0.0767
(1.00)
del 19q13 41 9 (12%) 63 0.69
(1.00) 		0.807
(1.00) 		0.814
(1.00) 		0.585
(1.00) 		0.105
(1.00) 		0.815
(1.00) 		0.478
(1.00) 		0.333
(1.00) 		0.172
(1.00) 		0.362
(1.00) 		0.445
(1.00) 		0.131
(1.00)
del 21q21 1 25 (35%) 47 0.131
(1.00) 		0.319
(1.00) 		0.261
(1.00) 		0.0877
(1.00) 		0.256
(1.00) 		0.124
(1.00) 		0.621
(1.00) 		0.839
(1.00) 		0.494
(1.00) 		0.911
(1.00) 		0.0338
(1.00) 		0.049
(1.00)
del 22q13 31 20 (28%) 52 0.205
(1.00) 		0.17
(1.00) 		0.332
(1.00) 		0.179
(1.00) 		0.762
(1.00) 		0.0718
(1.00) 		0.064
(1.00) 		0.792
(1.00) 		0.441
(1.00) 		0.199
(1.00) 		0.0312
(1.00) 		0.285
(1.00)
Methods & Data
Input

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

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

  • Number of patients = 72

  • Number of significantly focal cnvs = 42

  • 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

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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle