Correlation between copy number variation genes (focal) and selected clinical features
Skin Cutaneous Melanoma (Metastatic)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1PN93PF
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/C1PN93PF
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 54 arm-level results and 8 clinical features across 180 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 54 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 PRIMARY
SITE
OF
DISEASE 		GENDER DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Chi-square test Chi-square test t-test Chi-square test
Amp Peak 1(1p12) 0 (0%) 127 0.00909
(1.00) 		0.73
(1.00) 		0.284
(1.00) 		0.619
(1.00) 		0.703
(1.00) 		0.52
(1.00) 		0.227
(1.00)
Amp Peak 2(1q44) 0 (0%) 85 0.0902
(1.00) 		0.931
(1.00) 		0.262
(1.00) 		0.544
(1.00) 		0.464
(1.00) 		0.44
(1.00) 		0.477
(1.00)
Amp Peak 3(3p13) 0 (0%) 136 0.126
(1.00) 		0.0383
(1.00) 		0.256
(1.00) 		0.213
(1.00) 		0.613
(1.00) 		0.914
(1.00) 		0.323
(1.00)
Amp Peak 4(4q12) 0 (0%) 147 0.638
(1.00) 		0.186
(1.00) 		0.411
(1.00) 		0.432
(1.00) 		0.438
(1.00) 		0.865
(1.00) 		0.792
(1.00)
Amp Peak 5(5p15 33) 0 (0%) 130 0.186
(1.00) 		0.629
(1.00) 		0.277
(1.00) 		1
(1.00) 		0.613
(1.00) 		0.227
(1.00) 		0.462
(1.00)
Amp Peak 6(5q35 3) 0 (0%) 157 0.672
(1.00) 		0.0974
(1.00) 		0.192
(1.00) 		0.176
(1.00) 		0.112
(1.00) 		0.692
(1.00) 		0.452
(1.00)
Amp Peak 7(6p25 1) 0 (0%) 75 0.126
(1.00) 		0.0183
(1.00) 		0.21
(1.00) 		0.758
(1.00) 		0.543
(1.00) 		0.0795
(1.00) 		0.443
(1.00)
Amp Peak 8(6q12) 0 (0%) 142 0.349
(1.00) 		0.695
(1.00) 		0.642
(1.00) 		0.577
(1.00) 		0.732
(1.00) 		0.334
(1.00) 		0.157
(1.00)
Amp Peak 9(7p22 3) 0 (0%) 80 0.785
(1.00) 		0.862
(1.00) 		0.684
(1.00) 		0.442
(1.00) 		0.28
(1.00) 		0.509
(1.00) 		0.171
(1.00)
Amp Peak 10(7q34) 0 (0%) 77 0.935
(1.00) 		0.493
(1.00) 		0.481
(1.00) 		0.44
(1.00) 		0.329
(1.00) 		0.366
(1.00) 		0.0352
(1.00)
Amp Peak 11(8q11 21) 0 (0%) 103 0.337
(1.00) 		0.0968
(1.00) 		0.318
(1.00) 		0.877
(1.00) 		0.129
(1.00) 		0.871
(1.00) 		0.804
(1.00)
Amp Peak 12(8q24 21) 0 (0%) 91 0.391
(1.00) 		0.185
(1.00) 		0.457
(1.00) 		0.649
(1.00) 		0.195
(1.00) 		0.953
(1.00) 		0.854
(1.00)
Amp Peak 13(9p24 1) 0 (0%) 166 0.625
(1.00) 		0.825
(1.00) 		0.0194
(1.00) 		0.78
(1.00) 		0.0359
(1.00) 		0.447
(1.00) 		0.0674
(1.00)
Amp Peak 14(11q13 3) 0 (0%) 149 0.453
(1.00) 		0.336
(1.00) 		0.567
(1.00) 		0.233
(1.00) 		0.787
(1.00) 		0.81
(1.00) 		0.941
(1.00)
Amp Peak 15(11q13 4) 0 (0%) 150 0.738
(1.00) 		0.828
(1.00) 		0.574
(1.00) 		0.311
(1.00) 		0.576
(1.00) 		0.525
(1.00) 		0.957
(1.00)
Amp Peak 16(12q14 1) 0 (0%) 148 0.364
(1.00) 		0.318
(1.00) 		0.619
(1.00) 		0.554
(1.00) 		0.609
(1.00) 		0.33
(1.00) 		0.0767
(1.00)
Amp Peak 17(12q15) 0 (0%) 155 0.799
(1.00) 		0.252
(1.00) 		0.496
(1.00) 		0.378
(1.00) 		0.839
(1.00) 		0.116
(1.00) 		0.145
(1.00)
Amp Peak 18(15q26 2) 0 (0%) 117 0.253
(1.00) 		0.332
(1.00) 		0.528
(1.00) 		0.749
(1.00) 		0.494
(1.00) 		0.329
(1.00) 		0.0568
(1.00)
Amp Peak 19(17q25 3) 0 (0%) 112 0.454
(1.00) 		0.0209
(1.00) 		0.967
(1.00) 		0.115
(1.00) 		0.811
(1.00) 		0.561
(1.00) 		0.49
(1.00)
Amp Peak 20(19p13 2) 0 (0%) 145 0.448
(1.00) 		0.986
(1.00) 		0.418
(1.00) 		0.568
(1.00) 		0.00174
(0.659) 		0.737
(1.00) 		0.444
(1.00)
Amp Peak 21(20q13 33) 0 (0%) 89 0.4
(1.00) 		0.292
(1.00) 		0.332
(1.00) 		0.221
(1.00) 		0.199
(1.00) 		0.528
(1.00) 		0.0647
(1.00)
Amp Peak 22(22q13 2) 0 (0%) 98 0.533
(1.00) 		0.855
(1.00) 		0.399
(1.00) 		1
(1.00) 		0.998
(1.00) 		0.386
(1.00) 		0.603
(1.00)
Del Peak 1(1p36 31) 0 (0%) 132 0.629
(1.00) 		0.554
(1.00) 		0.542
(1.00) 		0.3
(1.00) 		0.103
(1.00) 		0.654
(1.00) 		0.785
(1.00)
Del Peak 2(1p22 1) 0 (0%) 132 0.108
(1.00) 		0.0147
(1.00) 		0.418
(1.00) 		0.864
(1.00) 		0.103
(1.00) 		0.301
(1.00) 		0.306
(1.00)
Del Peak 3(2q37 3) 0 (0%) 134 0.346
(1.00) 		0.348
(1.00) 		0.155
(1.00) 		0.487
(1.00) 		0.0669
(1.00) 		0.694
(1.00) 		0.518
(1.00)
Del Peak 4(3q23) 0 (0%) 153 0.432
(1.00) 		0.195
(1.00) 		0.833
(1.00) 		0.528
(1.00) 		0.00554
(1.00) 		0.642
(1.00) 		0.303
(1.00)
Del Peak 5(4p16 3) 0 (0%) 140 0.683
(1.00) 		0.387
(1.00) 		0.0285
(1.00) 		0.141
(1.00) 		0.622
(1.00) 		0.808
(1.00) 		0.957
(1.00)
Del Peak 6(4q34 3) 0 (0%) 135 0.289
(1.00) 		0.152
(1.00) 		0.115
(1.00) 		0.0334
(1.00) 		0.0957
(1.00) 		0.871
(1.00) 		0.107
(1.00)
Del Peak 7(5p15 31) 0 (0%) 141 0.552
(1.00) 		0.537
(1.00) 		0.851
(1.00) 		0.194
(1.00) 		0.622
(1.00) 		0.57
(1.00) 		0.194
(1.00)
Del Peak 8(5q11 2) 0 (0%) 124 0.365
(1.00) 		0.23
(1.00) 		0.441
(1.00) 		0.742
(1.00) 		0.202
(1.00) 		0.589
(1.00) 		0.576
(1.00)
Del Peak 9(5q31 3) 0 (0%) 108 0.148
(1.00) 		0.91
(1.00) 		0.739
(1.00) 		0.537
(1.00) 		0.355
(1.00) 		0.614
(1.00) 		0.895
(1.00)
Del Peak 10(6q22 31) 0 (0%) 73 0.663
(1.00) 		0.068
(1.00) 		0.17
(1.00) 		0.534
(1.00) 		0.812
(1.00) 		0.124
(1.00) 		0.849
(1.00)
Del Peak 11(6q25 3) 0 (0%) 68 0.783
(1.00) 		0.135
(1.00) 		0.408
(1.00) 		1
(1.00) 		0.807
(1.00) 		0.16
(1.00) 		0.94
(1.00)
Del Peak 12(6q26) 0 (0%) 73 0.585
(1.00) 		0.126
(1.00) 		0.232
(1.00) 		0.534
(1.00) 		0.812
(1.00) 		0.206
(1.00) 		0.925
(1.00)
Del Peak 13(8p22) 0 (0%) 137 0.335
(1.00) 		0.0208
(1.00) 		0.131
(1.00) 		0.108
(1.00) 		0.492
(1.00) 		0.239
(1.00) 		0.52
(1.00)
Del Peak 14(9p23) 0 (0%) 54 0.859
(1.00) 		0.944
(1.00) 		0.191
(1.00) 		0.243
(1.00) 		0.191
(1.00) 		0.397
(1.00) 		0.357
(1.00)
Del Peak 15(9p21 3) 0 (0%) 37 0.27
(1.00) 		0.585
(1.00) 		0.145
(1.00) 		0.13
(1.00) 		0.622
(1.00) 		0.291
(1.00) 		0.613
(1.00)
Del Peak 16(10p15 3) 0 (0%) 85 0.216
(1.00) 		0.301
(1.00) 		0.0787
(1.00) 		0.363
(1.00) 		0.399
(1.00) 		0.781
(1.00) 		0.874
(1.00)
Del Peak 17(10q23 31) 0 (0%) 69 0.79
(1.00) 		0.0735
(1.00) 		0.0905
(1.00) 		0.00732
(1.00) 		0.588
(1.00) 		0.791
(1.00) 		0.448
(1.00)
Del Peak 18(10q26 3) 0 (0%) 68 0.386
(1.00) 		0.00719
(1.00) 		0.0125
(1.00) 		0.0113
(1.00) 		0.215
(1.00) 		0.932
(1.00) 		0.828
(1.00)
Del Peak 19(11q23 3) 0 (0%) 73 0.371
(1.00) 		0.388
(1.00) 		0.0373
(1.00) 		0.534
(1.00) 		0.808
(1.00) 		0.0423
(1.00) 		0.265
(1.00)
Del Peak 20(12p13 31) 0 (0%) 156 0.624
(1.00) 		0.129
(1.00) 		0.54
(1.00) 		0.503
(1.00) 		0.517
(1.00) 		0.222
(1.00) 		0.733
(1.00)
Del Peak 21(12q23 3) 0 (0%) 140 0.674
(1.00) 		0.383
(1.00) 		0.154
(1.00) 		0.27
(1.00) 		0.492
(1.00) 		0.135
(1.00) 		0.982
(1.00)
Del Peak 22(13q12 11) 0 (0%) 139 0.983
(1.00) 		0.985
(1.00) 		0.236
(1.00) 		0.202
(1.00) 		0.00354
(1.00) 		0.369
(1.00) 		0.182
(1.00)
Del Peak 23(13q34) 0 (0%) 137 0.362
(1.00) 		0.714
(1.00) 		0.347
(1.00) 		0.373
(1.00) 		0.00753
(1.00) 		0.152
(1.00) 		0.143
(1.00)
Del Peak 24(14q32 2) 0 (0%) 119 0.76
(1.00) 		0.786
(1.00) 		0.509
(1.00) 		0.63
(1.00) 		0.195
(1.00) 		0.738
(1.00) 		0.112
(1.00)
Del Peak 25(15q13 3) 0 (0%) 136 0.542
(1.00) 		0.947
(1.00) 		0.883
(1.00) 		0.594
(1.00) 		0.595
(1.00) 		0.409
(1.00) 		0.675
(1.00)
Del Peak 26(15q15 1) 0 (0%) 135 0.316
(1.00) 		0.878
(1.00) 		0.901
(1.00) 		0.223
(1.00) 		0.605
(1.00) 		0.686
(1.00) 		0.307
(1.00)
Del Peak 27(16p13 3) 0 (0%) 147 0.811
(1.00) 		0.197
(1.00) 		0.189
(1.00) 		0.116
(1.00) 		0.774
(1.00) 		0.239
(1.00) 		0.68
(1.00)
Del Peak 28(16q12 1) 0 (0%) 120 0.359
(1.00) 		0.583
(1.00) 		0.117
(1.00) 		0.42
(1.00) 		0.647
(1.00) 		0.751
(1.00) 		0.253
(1.00)
Del Peak 29(16q24 3) 0 (0%) 116 0.102
(1.00) 		0.274
(1.00) 		0.239
(1.00) 		0.341
(1.00) 		0.632
(1.00) 		0.0789
(1.00) 		0.0773
(1.00)
Del Peak 30(17q21 31) 0 (0%) 138 0.274
(1.00) 		0.839
(1.00) 		0.0756
(1.00) 		1
(1.00) 		0.0745
(1.00) 		0.715
(1.00) 		0.543
(1.00)
Del Peak 31(19p13 3) 0 (0%) 124 0.857
(1.00) 		0.71
(1.00) 		0.134
(1.00) 		0.323
(1.00) 		0.191
(1.00) 		0.752
(1.00) 		0.536
(1.00)
Del Peak 32(22q12 1) 0 (0%) 154 0.485
(1.00) 		0.513
(1.00) 		0.67
(1.00) 		0.67
(1.00) 		0.564
(1.00) 		0.798
(1.00) 		0.699
(1.00)
Methods & Data
Input

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

  • Clinical data file = SKCM-TM.clin.merged.picked.txt

  • Number of patients = 180

  • Number of significantly arm-level cnvs = 54

  • 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

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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)
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