Correlation between copy number variation genes (focal) and selected clinical features
Skin Cutaneous Melanoma (Metastatic)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1CC0XPD
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Skin Cutaneous Melanoma (Metastatic cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1CC0XPD
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 8 clinical features across 173 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 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%) 122 0.0127
(1.00) 		0.583
(1.00) 		0.4
(1.00) 		0.61
(1.00) 		0.703
(1.00) 		0.282
(1.00) 		0.289
(1.00)
Amp Peak 2(1q21 3) 0 (0%) 83 0.693
(1.00) 		0.97
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.259
(1.00) 		0.899
(1.00)
Amp Peak 3(1q44) 0 (0%) 81 0.11
(1.00) 		0.886
(1.00) 		0.256
(1.00) 		0.532
(1.00) 		0.472
(1.00) 		0.34
(1.00) 		0.655
(1.00)
Amp Peak 4(3p13) 0 (0%) 131 0.191
(1.00) 		0.0604
(1.00) 		0.163
(1.00) 		0.204
(1.00) 		0.611
(1.00) 		0.825
(1.00) 		0.277
(1.00)
Amp Peak 5(4q12) 0 (0%) 141 0.537
(1.00) 		0.281
(1.00) 		0.442
(1.00) 		0.55
(1.00) 		0.443
(1.00) 		0.791
(1.00) 		0.791
(1.00)
Amp Peak 6(5p15 33) 0 (0%) 125 0.0884
(1.00) 		0.331
(1.00) 		0.132
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.322
(1.00) 		0.334
(1.00)
Amp Peak 7(5q35 3) 0 (0%) 151 0.519
(1.00) 		0.162
(1.00) 		0.12
(1.00) 		0.252
(1.00) 		0.11
(1.00) 		0.72
(1.00) 		0.427
(1.00)
Amp Peak 8(6p25 1) 0 (0%) 72 0.0832
(1.00) 		0.018
(1.00) 		0.203
(1.00) 		0.874
(1.00) 		0.542
(1.00) 		0.0487
(1.00) 		0.556
(1.00)
Amp Peak 9(6q12) 0 (0%) 136 0.4
(1.00) 		0.68
(1.00) 		0.585
(1.00) 		0.705
(1.00) 		0.725
(1.00) 		0.271
(1.00) 		0.192
(1.00)
Amp Peak 10(7p22 3) 0 (0%) 77 0.786
(1.00) 		0.756
(1.00) 		0.749
(1.00) 		0.348
(1.00) 		0.277
(1.00) 		0.395
(1.00) 		0.191
(1.00)
Amp Peak 11(7q34) 0 (0%) 74 0.989
(1.00) 		0.343
(1.00) 		0.549
(1.00) 		0.433
(1.00) 		0.328
(1.00) 		0.249
(1.00) 		0.0169
(1.00)
Amp Peak 12(8q11 21) 0 (0%) 103 0.294
(1.00) 		0.104
(1.00) 		0.326
(1.00) 		0.753
(1.00) 		0.135
(1.00) 		0.846
(1.00) 		0.733
(1.00)
Amp Peak 13(8q24 21) 0 (0%) 91 0.366
(1.00) 		0.198
(1.00) 		0.453
(1.00) 		0.64
(1.00) 		0.208
(1.00) 		0.936
(1.00) 		0.88
(1.00)
Amp Peak 14(9p24 1) 0 (0%) 160 0.522
(1.00) 		0.869
(1.00) 		0.0575
(1.00) 		0.568
(1.00) 		0.0294
(1.00) 		0.371
(1.00) 		0.0933
(1.00)
Amp Peak 15(11q13 3) 0 (0%) 144 0.307
(1.00) 		0.199
(1.00) 		0.531
(1.00) 		0.213
(1.00) 		0.798
(1.00) 		0.571
(1.00) 		0.787
(1.00)
Amp Peak 16(11q13 4) 0 (0%) 145 0.554
(1.00) 		0.622
(1.00) 		0.519
(1.00) 		0.291
(1.00) 		0.565
(1.00) 		0.312
(1.00) 		0.835
(1.00)
Amp Peak 17(12q14 1) 0 (0%) 143 0.45
(1.00) 		0.423
(1.00) 		0.777
(1.00) 		1
(1.00) 		0.604
(1.00) 		0.217
(1.00) 		0.0704
(1.00)
Amp Peak 18(12q15) 0 (0%) 149 0.934
(1.00) 		0.379
(1.00) 		0.687
(1.00) 		0.501
(1.00) 		0.838
(1.00) 		0.0548
(1.00) 		0.12
(1.00)
Amp Peak 19(15q24 3) 0 (0%) 115 0.464
(1.00) 		0.544
(1.00) 		0.825
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.27
(1.00) 		0.0479
(1.00)
Amp Peak 20(17q25 3) 0 (0%) 107 0.612
(1.00) 		0.0124
(1.00) 		1
(1.00) 		0.152
(1.00) 		0.812
(1.00) 		0.542
(1.00) 		0.652
(1.00)
Amp Peak 21(19p13 2) 0 (0%) 139 0.378
(1.00) 		0.792
(1.00) 		0.517
(1.00) 		0.438
(1.00) 		0.00193
(0.69) 		0.73
(1.00) 		0.342
(1.00)
Amp Peak 22(20q13 2) 0 (0%) 83 0.254
(1.00) 		0.197
(1.00) 		0.423
(1.00) 		0.435
(1.00) 		0.208
(1.00) 		0.687
(1.00) 		0.0667
(1.00)
Amp Peak 23(22q13 2) 0 (0%) 94 0.516
(1.00) 		0.982
(1.00) 		0.445
(1.00) 		1
(1.00) 		0.999
(1.00) 		0.311
(1.00) 		0.585
(1.00)
Amp Peak 24(Xq28) 0 (0%) 143 0.842
(1.00) 		0.255
(1.00) 		0.556
(1.00) 		0.0982
(1.00) 		0.597
(1.00) 		0.907
(1.00) 		0.663
(1.00)
Del Peak 1(1p36 31) 0 (0%) 127 0.839
(1.00) 		0.679
(1.00) 		0.584
(1.00) 		0.159
(1.00) 		0.102
(1.00) 		0.583
(1.00) 		0.855
(1.00)
Del Peak 2(1p22 1) 0 (0%) 127 0.129
(1.00) 		0.0166
(1.00) 		0.277
(1.00) 		1
(1.00) 		0.102
(1.00) 		0.393
(1.00) 		0.361
(1.00)
Del Peak 3(2q37 3) 0 (0%) 129 0.325
(1.00) 		0.312
(1.00) 		0.15
(1.00) 		0.37
(1.00) 		0.0637
(1.00) 		0.641
(1.00) 		0.456
(1.00)
Del Peak 4(3q23) 0 (0%) 149 0.519
(1.00) 		0.135
(1.00) 		1
(1.00) 		0.261
(1.00) 		0.00274
(0.976) 		0.582
(1.00) 		0.251
(1.00)
Del Peak 5(4q22 1) 0 (0%) 138 0.442
(1.00) 		0.0309
(1.00) 		0.0689
(1.00) 		0.119
(1.00) 		0.0413
(1.00) 		0.164
(1.00) 		0.372
(1.00)
Del Peak 6(4q34 3) 0 (0%) 129 0.318
(1.00) 		0.155
(1.00) 		0.0847
(1.00) 		0.0192
(1.00) 		0.102
(1.00) 		0.902
(1.00) 		0.125
(1.00)
Del Peak 7(5q11 2) 0 (0%) 119 0.306
(1.00) 		0.269
(1.00) 		0.485
(1.00) 		0.738
(1.00) 		0.204
(1.00) 		0.668
(1.00) 		0.499
(1.00)
Del Peak 8(5q31 3) 0 (0%) 104 0.0887
(1.00) 		0.825
(1.00) 		0.736
(1.00) 		0.751
(1.00) 		0.354
(1.00) 		0.589
(1.00) 		0.835
(1.00)
Del Peak 9(6q26) 0 (0%) 69 0.703
(1.00) 		0.158
(1.00) 		0.231
(1.00) 		0.634
(1.00) 		0.812
(1.00) 		0.285
(1.00) 		0.91
(1.00)
Del Peak 10(8p23 3) 0 (0%) 131 0.881
(1.00) 		0.0978
(1.00) 		0.156
(1.00) 		0.146
(1.00) 		0.554
(1.00) 		0.286
(1.00) 		0.422
(1.00)
Del Peak 11(9p23) 0 (0%) 52 0.646
(1.00) 		0.901
(1.00) 		0.208
(1.00) 		0.311
(1.00) 		0.192
(1.00) 		0.351
(1.00) 		0.495
(1.00)
Del Peak 12(9p21 3) 0 (0%) 36 0.178
(1.00) 		0.46
(1.00) 		0.187
(1.00) 		0.178
(1.00) 		0.622
(1.00) 		0.275
(1.00) 		0.595
(1.00)
Del Peak 13(10p15 3) 0 (0%) 81 0.251
(1.00) 		0.18
(1.00) 		0.121
(1.00) 		0.349
(1.00) 		0.396
(1.00) 		0.611
(1.00) 		0.876
(1.00)
Del Peak 14(10q23 31) 0 (0%) 66 0.591
(1.00) 		0.0421
(1.00) 		0.123
(1.00) 		0.0065
(1.00) 		0.589
(1.00) 		0.87
(1.00) 		0.612
(1.00)
Del Peak 15(10q26 3) 0 (0%) 66 0.326
(1.00) 		0.00584
(1.00) 		0.0151
(1.00) 		0.0065
(1.00) 		0.216
(1.00) 		0.948
(1.00) 		0.814
(1.00)
Del Peak 16(11q23 3) 0 (0%) 72 0.401
(1.00) 		0.416
(1.00) 		0.0578
(1.00) 		0.429
(1.00) 		0.802
(1.00) 		0.0117
(1.00) 		0.215
(1.00)
Del Peak 17(12p13 31) 0 (0%) 150 0.495
(1.00) 		0.206
(1.00) 		0.783
(1.00) 		0.65
(1.00) 		0.516
(1.00) 		0.238
(1.00) 		0.551
(1.00)
Del Peak 18(12q23 3) 0 (0%) 135 0.428
(1.00) 		0.453
(1.00) 		0.247
(1.00) 		0.452
(1.00) 		0.479
(1.00) 		0.18
(1.00) 		0.996
(1.00)
Del Peak 19(12q24 33) 0 (0%) 134 0.606
(1.00) 		0.588
(1.00) 		0.242
(1.00) 		0.351
(1.00) 		0.554
(1.00) 		0.182
(1.00) 		0.82
(1.00)
Del Peak 20(13q34) 0 (0%) 131 0.339
(1.00) 		0.796
(1.00) 		0.155
(1.00) 		0.469
(1.00) 		0.00845
(1.00) 		0.157
(1.00) 		0.0897
(1.00)
Del Peak 21(14q32 2) 0 (0%) 115 0.715
(1.00) 		0.669
(1.00) 		0.608
(1.00) 		0.741
(1.00) 		0.193
(1.00) 		0.51
(1.00) 		0.0918
(1.00)
Del Peak 22(15q13 3) 0 (0%) 133 0.458
(1.00) 		0.665
(1.00) 		0.749
(1.00) 		0.361
(1.00) 		0.568
(1.00) 		0.566
(1.00) 		0.737
(1.00)
Del Peak 23(15q15 3) 0 (0%) 134 0.268
(1.00) 		0.858
(1.00) 		0.631
(1.00) 		0.191
(1.00) 		0.554
(1.00) 		0.808
(1.00) 		0.74
(1.00)
Del Peak 24(16p13 3) 0 (0%) 141 0.854
(1.00) 		0.187
(1.00) 		0.2
(1.00) 		0.0728
(1.00) 		0.77
(1.00) 		0.21
(1.00) 		0.706
(1.00)
Del Peak 25(16q12 1) 0 (0%) 115 0.358
(1.00) 		0.634
(1.00) 		0.149
(1.00) 		0.252
(1.00) 		0.646
(1.00) 		0.759
(1.00) 		0.289
(1.00)
Del Peak 26(16q24 3) 0 (0%) 111 0.0981
(1.00) 		0.306
(1.00) 		0.28
(1.00) 		0.199
(1.00) 		0.629
(1.00) 		0.093
(1.00) 		0.0994
(1.00)
Del Peak 27(19p13 3) 0 (0%) 120 0.882
(1.00) 		0.911
(1.00) 		0.186
(1.00) 		0.31
(1.00) 		0.18
(1.00) 		0.819
(1.00) 		0.607
(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 = 173

  • Number of significantly arm-level cnvs = 51

  • 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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