Correlation between copy number variation genes (focal) and selected clinical features
Cervical Squamous Cell Carcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1ZW1HVH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Cervical Squamous Cell Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1ZW1HVH
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 51 arm-level results and 10 clinical features across 34 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 51 arm-level results and 10 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 HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED TOBACCOSMOKINGHISTORYINDICATOR DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test t-test t-test Fisher's exact test Fisher's exact test t-test t-test
Amp Peak 1(1q21 3) 0 (0%) 10 0.298
(1.00) 		0.581
(1.00) 		0.746
(1.00) 		1
(1.00) 		0.287
(1.00) 		0.792
(1.00) 		0.675
(1.00) 		0.687
(1.00) 		0.35
(1.00)
Amp Peak 2(1q44) 0 (0%) 12 0.35
(1.00) 		0.368
(1.00) 		0.598
(1.00) 		0.705
(1.00) 		0.287
(1.00) 		0.953
(1.00) 		1
(1.00) 		1
(1.00) 		0.503
(1.00)
Amp Peak 3(2p24 3) 0 (0%) 24 0.0352
(1.00) 		0.238
(1.00) 		0.532
(1.00) 		1
(1.00) 		0.646
(1.00) 		0.544
(1.00) 		1
(1.00) 		1
(1.00) 		0.654
(1.00)
Amp Peak 4(2q32 3) 0 (0%) 30 0.395
(1.00) 		0.198
(1.00) 		1
(1.00) 		1
(1.00) 		0.693
(1.00) 		1
(1.00) 		1
(1.00) 		0.774
(1.00)
Amp Peak 5(3q26 2) 0 (0%) 7 0.423
(1.00) 		0.525
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.608
(1.00) 		0.287
(1.00) 		0.641
(1.00) 		0.566
(1.00)
Amp Peak 6(3q28) 0 (0%) 7 0.423
(1.00) 		0.525
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.608
(1.00) 		0.287
(1.00) 		0.641
(1.00) 		0.566
(1.00)
Amp Peak 7(4q12) 0 (0%) 29 0.857
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.3
(1.00) 		0.321
(1.00) 		0.22
(1.00) 		0.537
(1.00) 		0.593
(1.00)
Amp Peak 8(6p21 33) 0 (0%) 24 0.959
(1.00) 		0.138
(1.00) 		0.193
(1.00) 		1
(1.00) 		0.612
(1.00) 		0.891
(1.00) 		1
(1.00) 		0.417
(1.00) 		0.872
(1.00)
Amp Peak 9(6q12) 0 (0%) 30 0.285
(1.00) 		0.388
(1.00) 		1
(1.00) 		0.58
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.611
(1.00) 		0.914
(1.00)
Amp Peak 10(8q24 21) 0 (0%) 18 0.988
(1.00) 		0.748
(1.00) 		1
(1.00) 		0.477
(1.00) 		0.783
(1.00) 		0.186
(1.00) 		0.427
(1.00) 		1
(1.00) 		1
(1.00)
Amp Peak 11(8q24 21) 0 (0%) 18 0.305
(1.00) 		0.911
(1.00) 		1
(1.00) 		0.477
(1.00) 		0.783
(1.00) 		0.729
(1.00) 		0.427
(1.00) 		0.45
(1.00) 		0.68
(1.00)
Amp Peak 12(9p24 1) 0 (0%) 27 0.129
(1.00) 		0.122
(1.00) 		0.67
(1.00) 		0.384
(1.00) 		0.805
(1.00) 		1
(1.00) 		0.372
(1.00) 		0.634
(1.00)
Amp Peak 13(11q13 3) 0 (0%) 30 0.423
(1.00) 		0.28
(1.00) 		1
(1.00) 		0.58
(1.00) 		0.589
(1.00) 		0.532
(1.00) 		0.52
(1.00)
Amp Peak 14(11q22 1) 0 (0%) 27 0.9
(1.00) 		0.00543
(1.00) 		1
(1.00) 		1
(1.00) 		0.528
(1.00) 		0.633
(1.00) 		0.372
(1.00) 		0.154
(1.00)
Amp Peak 15(13q22 1) 0 (0%) 30 0.634
(1.00) 		0.981
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.537
(1.00) 		0.593
(1.00)
Amp Peak 16(14q24 1) 0 (0%) 27 0.285
(1.00) 		0.715
(1.00) 		0.19
(1.00) 		0.384
(1.00) 		0.555
(1.00) 		1
(1.00) 		0.641
(1.00) 		0.527
(1.00)
Amp Peak 17(15q26 3) 0 (0%) 24 0.829
(1.00) 		0.441
(1.00) 		1
(1.00) 		0.437
(1.00) 		0.676
(1.00) 		0.675
(1.00) 		0.672
(1.00) 		0.271
(1.00)
Amp Peak 18(16p13 2) 0 (0%) 26 0.317
(1.00) 		0.206
(1.00) 		0.242
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.642
(1.00) 		1
(1.00) 		0.704
(1.00)
Amp Peak 19(16p13 13) 0 (0%) 26 0.552
(1.00) 		0.112
(1.00) 		0.0374
(1.00) 		1
(1.00) 		0.388
(1.00) 		0.158
(1.00) 		1
(1.00) 		0.704
(1.00)
Amp Peak 20(17q12) 0 (0%) 29 0.932
(1.00) 		0.89
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.589
(1.00) 		0.153
(1.00) 		0.327
(1.00) 		0.613
(1.00)
Amp Peak 21(17q25 1) 0 (0%) 24 0.28
(1.00) 		0.914
(1.00) 		0.0477
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.24
(1.00) 		1
(1.00) 		0.225
(1.00) 		0.367
(1.00)
Amp Peak 22(19q13 31) 0 (0%) 23 0.149
(1.00) 		0.9
(1.00) 		0.577
(1.00) 		0.016
(1.00) 		0.985
(1.00) 		0.524
(1.00) 		0.396
(1.00) 		0.687
(1.00) 		0.692
(1.00)
Amp Peak 23(20q11 21) 0 (0%) 15 0.0234
(1.00) 		0.373
(1.00) 		0.813
(1.00) 		0.475
(1.00) 		0.113
(1.00) 		0.293
(1.00) 		0.454
(1.00) 		0.142
(1.00) 		0.54
(1.00)
Amp Peak 24(Xq28) 0 (0%) 27 0.241
(1.00) 		0.691
(1.00) 		0.67
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.158
(1.00) 		1
(1.00) 		0.89
(1.00)
Del Peak 1(1p36 23) 0 (0%) 28 0.916
(1.00) 		0.242
(1.00) 		0.146
(1.00) 		1
(1.00) 		0.277
(1.00) 		0.728
(1.00) 		0.633
(1.00) 		1
(1.00) 		0.8
(1.00)
Del Peak 2(1p13 1) 0 (0%) 27 0.719
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.235
(1.00) 		0.633
(1.00) 		1
(1.00) 		0.917
(1.00)
Del Peak 3(2q22 1) 0 (0%) 30 0.747
(1.00) 		0.569
(1.00) 		1
(1.00) 		0.0889
(1.00) 		0.888
(1.00) 		0.532
(1.00) 		1
(1.00) 		0.718
(1.00)
Del Peak 4(2q37 1) 0 (0%) 20 0.0924
(1.00) 		0.0168
(1.00) 		1
(1.00) 		0.295
(1.00) 		0.0503
(1.00) 		0.206
(1.00) 		1
(1.00) 		0.442
(1.00) 		0.463
(1.00)
Del Peak 5(3p11 1) 0 (0%) 17 0.68
(1.00) 		0.559
(1.00) 		0.398
(1.00) 		1
(1.00) 		0.534
(1.00) 		0.354
(1.00) 		0.7
(1.00) 		0.257
(1.00) 		0.0769
(1.00)
Del Peak 6(4q22 1) 0 (0%) 26 0.559
(1.00) 		0.535
(1.00) 		0.707
(1.00) 		1
(1.00) 		0.881
(1.00) 		0.86
(1.00) 		1
(1.00) 		0.372
(1.00) 		0.164
(1.00)
Del Peak 7(4q35 2) 0 (0%) 22 0.0897
(1.00) 		0.529
(1.00) 		0.769
(1.00) 		1
(1.00) 		0.838
(1.00) 		0.769
(1.00) 		0.675
(1.00) 		0.702
(1.00) 		0.441
(1.00)
Del Peak 8(5q14 3) 0 (0%) 18 0.327
(1.00) 		0.135
(1.00) 		0.66
(1.00) 		0.477
(1.00) 		0.627
(1.00) 		0.977
(1.00) 		0.688
(1.00) 		0.707
(1.00) 		0.171
(1.00)
Del Peak 9(6p24 3) 0 (0%) 28 0.986
(1.00) 		0.324
(1.00) 		0.42
(1.00) 		0.638
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.0472
(1.00) 		0.165
(1.00)
Del Peak 11(6q26) 0 (0%) 26 0.602
(1.00) 		0.114
(1.00) 		0.707
(1.00) 		0.227
(1.00) 		0.696
(1.00) 		0.642
(1.00) 		0.372
(1.00) 		0.634
(1.00)
Del Peak 12(7q34) 0 (0%) 27 0.00723
(1.00) 		0.811
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.838
(1.00) 		0.608
(1.00) 		1
(1.00) 		1
(1.00) 		0.458
(1.00)
Del Peak 13(10q23 31) 0 (0%) 27 0.108
(1.00) 		0.903
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.77
(1.00) 		0.0211
(1.00) 		0.633
(1.00) 		0.156
(1.00) 		0.208
(1.00)
Del Peak 14(10q26 3) 0 (0%) 28 0.285
(1.00) 		0.91
(1.00) 		0.42
(1.00) 		0.363
(1.00) 		0.77
(1.00) 		0.076
(1.00) 		0.076
(1.00) 		0.0472
(1.00) 		0.115
(1.00)
Del Peak 15(11p15 1) 0 (0%) 22 0.87
(1.00) 		0.938
(1.00) 		0.598
(1.00) 		1
(1.00) 		0.881
(1.00) 		0.953
(1.00) 		0.694
(1.00) 		0.238
(1.00) 		0.0926
(1.00)
Del Peak 16(11q25) 0 (0%) 11 0.954
(1.00) 		0.644
(1.00) 		0.422
(1.00) 		1
(1.00) 		0.304
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.702
(1.00) 		0.134
(1.00)
Del Peak 17(13q13 3) 0 (0%) 21 0.63
(1.00) 		0.968
(1.00) 		0.471
(1.00) 		1
(1.00) 		0.881
(1.00) 		0.769
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.182
(1.00)
Del Peak 18(14q32 31) 0 (0%) 31 0.523
(1.00) 		0.099
(1.00) 		1
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.22
(1.00) 		0.279
(1.00) 		0.00565
(1.00)
Del Peak 19(15q15 1) 0 (0%) 29 0.986
(1.00) 		0.529
(1.00) 		1
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.568
(1.00) 		1
(1.00) 		0.443
(1.00)
Del Peak 20(16q11 2) 0 (0%) 31 0.734
(1.00) 		1
(1.00) 		0.535
(1.00) 		1
(1.00) 		0.52
(1.00)
Del Peak 21(16q23 1) 0 (0%) 31 0.893
(1.00) 		0.0329
(1.00) 		1
(1.00) 		0.532
(1.00) 		1
(1.00)
Del Peak 22(17p12) 0 (0%) 22 0.644
(1.00) 		0.194
(1.00) 		0.235
(1.00) 		0.459
(1.00) 		0.533
(1.00) 		0.276
(1.00) 		1
(1.00) 		0.702
(1.00) 		0.441
(1.00)
Del Peak 23(17q25 3) 0 (0%) 26 0.0882
(1.00) 		0.307
(1.00) 		0.707
(1.00) 		1
(1.00) 		0.373
(1.00) 		0.86
(1.00) 		1
(1.00) 		0.641
(1.00) 		0.527
(1.00)
Del Peak 24(19p13 3) 0 (0%) 25 0.447
(1.00) 		0.612
(1.00) 		0.278
(1.00) 		0.111
(1.00) 		0.764
(1.00) 		0.837
(1.00) 		1
(1.00) 		1
(1.00) 		0.566
(1.00)
Del Peak 25(20p12 1) 0 (0%) 28 0.296
(1.00) 		0.804
(1.00) 		0.224
(1.00) 		0.145
(1.00) 		0.733
(1.00) 		0.728
(1.00) 		0.287
(1.00) 		1
(1.00) 		0.8
(1.00)
Del Peak 26(21q21 1) 0 (0%) 25 0.337
(1.00) 		0.605
(1.00) 		0.492
(1.00) 		0.0172
(1.00) 		0.03
(1.00) 		1
(1.00) 		0.419
(1.00) 		0.547
(1.00)
Del Peak 27(Xp11 3) 0 (0%) 21 0.844
(1.00) 		0.187
(1.00) 		0.789
(1.00) 		0.262
(1.00) 		0.0867
(1.00) 		0.268
(1.00) 		0.205
(1.00) 		1
(1.00) 		0.323
(1.00)
Del Peak 28(Xq21 33) 0 (0%) 24 0.00867
(1.00) 		0.897
(1.00) 		0.746
(1.00) 		0.232
(1.00) 		0.166
(1.00) 		0.549
(1.00) 		1
(1.00) 		1
(1.00) 		0.4
(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 = 34

  • Number of significantly arm-level cnvs = 51

  • Number of selected clinical features = 10

  • 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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