Correlation between copy number variation genes (focal) and selected clinical features
Cervical Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1Z60M1Q
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1Z60M1Q
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 52 arm-level results and 8 clinical features across 42 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 52 arm-level results 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 RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test Fisher's exact test Fisher's exact test t-test t-test
Amp Peak 1(1q21 3) 0 (0%) 15 0.158
(1.00) 		0.417
(1.00) 		0.739
(1.00) 		0.939
(1.00) 		0.0395
(1.00) 		0.729
(1.00) 		0.15
(1.00)
Amp Peak 2(1q44) 0 (0%) 17 0.203
(1.00) 		0.289
(1.00) 		0.505
(1.00) 		0.939
(1.00) 		0.169
(1.00) 		1
(1.00) 		0.224
(1.00)
Amp Peak 3(2p24 3) 0 (0%) 29 0.0862
(1.00) 		0.282
(1.00) 		0.719
(1.00) 		0.491
(1.00) 		0.71
(1.00) 		0.488
(1.00) 		0.207
(1.00)
Amp Peak 4(2q32 3) 0 (0%) 36 0.364
(1.00) 		0.3
(1.00) 		0.647
(1.00) 		0.63
(1.00) 		0.633
(1.00) 		0.912
(1.00)
Amp Peak 5(3q26 2) 0 (0%) 10 0.569
(1.00) 		0.59
(1.00) 		0.466
(1.00) 		0.66
(1.00) 		0.215
(1.00) 		0.699
(1.00) 		0.652
(1.00)
Amp Peak 6(3q28) 0 (0%) 11 0.113
(1.00) 		0.472
(1.00) 		1
(1.00) 		0.66
(1.00) 		0.0569
(1.00) 		0.449
(1.00) 		0.468
(1.00)
Amp Peak 7(4q12) 0 (0%) 37 0.925
(1.00) 		0.229
(1.00) 		0.162
(1.00) 		0.544
(1.00) 		0.542
(1.00) 		0.769
(1.00)
Amp Peak 8(6p21 33) 0 (0%) 30 0.879
(1.00) 		0.253
(1.00) 		0.722
(1.00) 		0.836
(1.00) 		0.26
(1.00) 		1
(1.00) 		0.604
(1.00)
Amp Peak 9(6q12) 0 (0%) 36 0.394
(1.00) 		0.319
(1.00) 		1
(1.00) 		0.376
(1.00) 		1
(1.00) 		0.577
(1.00)
Amp Peak 10(8q24 21) 0 (0%) 25 0.803
(1.00) 		0.641
(1.00) 		0.505
(1.00) 		0.366
(1.00) 		0.733
(1.00) 		1
(1.00) 		0.517
(1.00)
Amp Peak 11(8q24 21) 0 (0%) 25 0.471
(1.00) 		0.789
(1.00) 		0.505
(1.00) 		0.366
(1.00) 		0.733
(1.00) 		0.51
(1.00) 		0.761
(1.00)
Amp Peak 12(9p24 1) 0 (0%) 35 0.124
(1.00) 		0.205
(1.00) 		0.405
(1.00) 		0.687
(1.00) 		0.387
(1.00) 		0.946
(1.00)
Amp Peak 13(11q13 3) 0 (0%) 38 0.461
(1.00) 		0.369
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.522
(1.00)
Amp Peak 14(11q22 1) 0 (0%) 33 0.643
(1.00) 		0.00368
(1.00) 		1
(1.00) 		0.683
(1.00) 		0.684
(1.00) 		0.869
(1.00)
Amp Peak 15(13q22 1) 0 (0%) 38 0.667
(1.00) 		0.877
(1.00) 		1
(1.00) 		1
(1.00) 		0.542
(1.00) 		0.769
(1.00)
Amp Peak 16(14q24 1) 0 (0%) 33 0.394
(1.00) 		0.967
(1.00) 		0.232
(1.00) 		0.683
(1.00) 		1
(1.00) 		0.957
(1.00)
Amp Peak 17(15q26 3) 0 (0%) 32 0.805
(1.00) 		0.327
(1.00) 		0.466
(1.00) 		1
(1.00) 		0.684
(1.00) 		0.155
(1.00)
Amp Peak 18(16p13 2) 0 (0%) 32 0.306
(1.00) 		0.0442
(1.00) 		1
(1.00) 		0.705
(1.00) 		0.699
(1.00) 		0.514
(1.00)
Amp Peak 19(16p13 13) 0 (0%) 32 0.548
(1.00) 		0.0199
(1.00) 		0.466
(1.00) 		0.255
(1.00) 		0.699
(1.00) 		0.514
(1.00)
Amp Peak 20(17q12) 0 (0%) 37 0.981
(1.00) 		0.901
(1.00) 		0.637
(1.00) 		0.135
(1.00) 		0.337
(1.00) 		0.873
(1.00)
Amp Peak 21(17q25 1) 0 (0%) 30 0.359
(1.00) 		0.48
(1.00) 		0.722
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.266
(1.00) 		0.316
(1.00)
Amp Peak 22(19q13 31) 0 (0%) 28 0.0411
(1.00) 		0.802
(1.00) 		0.0148
(1.00) 		0.807
(1.00) 		1
(1.00) 		0.728
(1.00) 		0.381
(1.00)
Amp Peak 23(20q11 21) 0 (0%) 21 0.0091
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.383
(1.00) 		1
(1.00) 		0.179
(1.00) 		0.254
(1.00)
Amp Peak 24(Xq28) 0 (0%) 34 0.221
(1.00) 		0.385
(1.00) 		1
(1.00) 		0.445
(1.00) 		0.684
(1.00) 		0.669
(1.00)
Del Peak 1(1p36 23) 0 (0%) 35 0.824
(1.00) 		0.0757
(1.00) 		1
(1.00) 		0.403
(1.00) 		1
(1.00) 		1
(1.00) 		0.577
(1.00)
Del Peak 2(1p13 1) 0 (0%) 35 0.62
(1.00) 		0.506
(1.00) 		0.657
(1.00) 		0.376
(1.00) 		1
(1.00) 		0.869
(1.00)
Del Peak 3(2q22 1) 0 (0%) 36 0.365
(1.00) 		0.245
(1.00) 		0.00744
(1.00) 		0.63
(1.00) 		0.337
(1.00) 		0.472
(1.00)
Del Peak 4(2q37 1) 0 (0%) 23 0.198
(1.00) 		0.00433
(1.00) 		0.739
(1.00) 		0.115
(1.00) 		1
(1.00) 		0.506
(1.00) 		0.779
(1.00)
Del Peak 5(3p11 1) 0 (0%) 21 0.567
(1.00) 		0.399
(1.00) 		0.505
(1.00) 		0.139
(1.00) 		1
(1.00) 		0.179
(1.00) 		0.0691
(1.00)
Del Peak 6(4q22 1) 0 (0%) 31 0.216
(1.00) 		0.594
(1.00) 		0.713
(1.00) 		0.84
(1.00) 		0.71
(1.00) 		0.449
(1.00) 		0.1
(1.00)
Del Peak 7(4q35 2) 0 (0%) 27 0.0338
(1.00) 		0.665
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.306
(1.00) 		0.728
(1.00) 		0.267
(1.00)
Del Peak 8(5q14 3) 0 (0%) 24 0.174
(1.00) 		0.285
(1.00) 		0.748
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.51
(1.00) 		0.105
(1.00)
Del Peak 9(6p24 3) 0 (0%) 35 0.828
(1.00) 		0.3
(1.00) 		0.405
(1.00) 		1
(1.00) 		0.167
(1.00) 		0.654
(1.00)
Del Peak 10(6p12 1) 0 (0%) 39 0.29
(1.00) 		0.54
(1.00) 		0.137
(1.00) 		1
(1.00)
Del Peak 11(6q26) 0 (0%) 29 0.395
(1.00) 		0.775
(1.00) 		0.278
(1.00) 		0.0612
(1.00) 		1
(1.00) 		0.728
(1.00) 		0.45
(1.00)
Del Peak 12(7q34) 0 (0%) 33 0.00155
(0.525) 		0.911
(1.00) 		0.107
(1.00) 		0.827
(1.00) 		1
(1.00) 		1
(1.00) 		0.22
(1.00)
Del Peak 13(10q23 31) 0 (0%) 32 0.0242
(1.00) 		0.584
(1.00) 		0.697
(1.00) 		0.338
(1.00) 		0.445
(1.00) 		0.0516
(1.00) 		0.0456
(1.00)
Del Peak 14(10q26 3) 0 (0%) 33 0.0324
(1.00) 		0.614
(1.00) 		0.422
(1.00) 		0.338
(1.00) 		0.0801
(1.00) 		0.0337
(1.00) 		0.0208
(1.00)
Del Peak 15(11p15 1) 0 (0%) 27 0.725
(1.00) 		0.836
(1.00) 		0.739
(1.00) 		0.995
(1.00) 		1
(1.00) 		0.729
(1.00) 		0.387
(1.00)
Del Peak 16(11q25) 0 (0%) 14 0.689
(1.00) 		0.9
(1.00) 		1
(1.00) 		0.889
(1.00) 		1
(1.00) 		0.728
(1.00) 		0.0369
(1.00)
Del Peak 17(13q13 3) 0 (0%) 26 0.998
(1.00) 		0.598
(1.00) 		1
(1.00) 		0.381
(1.00) 		1
(1.00) 		0.298
(1.00) 		0.0418
(1.00)
Del Peak 18(14q32 31) 0 (0%) 38 0.502
(1.00) 		0.201
(1.00) 		1
(1.00) 		0.625
(1.00) 		0.276
(1.00) 		0.00241
(0.815)
Del Peak 19(15q15 1) 0 (0%) 34 0.491
(1.00) 		0.65
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.64
(1.00)
Del Peak 20(16q11 2) 0 (0%) 37 0.765
(1.00) 		0.802
(1.00) 		0.302
(1.00) 		1
(1.00) 		0.276
(1.00) 		0.00241
(0.815)
Del Peak 21(16q23 1) 0 (0%) 36 0.665
(1.00) 		0.957
(1.00) 		0.647
(1.00) 		0.346
(1.00) 		1
(1.00) 		0.911
(1.00)
Del Peak 22(17p12) 0 (0%) 29 0.718
(1.00) 		0.426
(1.00) 		0.495
(1.00) 		0.812
(1.00) 		0.477
(1.00) 		0.488
(1.00) 		0.67
(1.00)
Del Peak 23(17q25 3) 0 (0%) 33 0.129
(1.00) 		0.736
(1.00) 		1
(1.00) 		0.788
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.362
(1.00)
Del Peak 24(19p13 3) 0 (0%) 31 0.575
(1.00) 		0.879
(1.00) 		0.27
(1.00) 		0.954
(1.00) 		0.683
(1.00) 		0.684
(1.00) 		0.239
(1.00)
Del Peak 25(20p12 1) 0 (0%) 35 0.256
(1.00) 		0.746
(1.00) 		0.0791
(1.00) 		0.907
(1.00) 		0.173
(1.00) 		1
(1.00) 		0.374
(1.00)
Del Peak 26(21q21 1) 0 (0%) 31 0.997
(1.00) 		0.77
(1.00) 		0.127
(1.00) 		1
(1.00) 		0.488
(1.00) 		0.67
(1.00)
Del Peak 27(Xp11 3) 0 (0%) 28 0.749
(1.00) 		0.317
(1.00) 		0.298
(1.00) 		0.0407
(1.00) 		0.713
(1.00) 		1
(1.00) 		0.684
(1.00)
Del Peak 28(Xq21 33) 0 (0%) 31 0.0218
(1.00) 		0.953
(1.00) 		0.27
(1.00) 		0.0847
(1.00) 		1
(1.00) 		1
(1.00) 		0.643
(1.00)
Methods & Data
Input

  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

  • Clinical data file = CESC-TP.clin.merged.picked.txt

  • Number of patients = 42

  • Number of significantly arm-level cnvs = 52

  • 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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] 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)
[4] 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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