Correlation between copy number variation genes (focal) and selected clinical features
Bladder Urothelial Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1GH9FZX
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/C1GH9FZX
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 62 arm-level results and 10 clinical features across 134 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 62 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 GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBERPACKYEARSSMOKED DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test t-test Fisher's exact test Chi-square test t-test t-test Fisher's exact test
Amp Peak 1(1p34 2) 0 (0%) 92 0.693
(1.00) 		0.19
(1.00) 		0.669
(1.00) 		0.151
(1.00) 		0.197
(1.00) 		0.739
(1.00) 		0.442
(1.00) 		0.442
(1.00) 		0.402
(1.00)
Amp Peak 2(1p22 3) 0 (0%) 92 0.356
(1.00) 		0.1
(1.00) 		0.834
(1.00) 		0.586
(1.00) 		0.0948
(1.00) 		0.211
(1.00) 		0.424
(1.00) 		0.196
(1.00) 		0.659
(1.00)
Amp Peak 3(1q21 3) 0 (0%) 63 0.409
(1.00) 		0.307
(1.00) 		0.696
(1.00) 		0.413
(1.00) 		0.0593
(1.00) 		0.289
(1.00) 		0.0204
(1.00) 		0.0901
(1.00) 		0.0629
(1.00)
Amp Peak 4(1q23 3) 0 (0%) 59 0.692
(1.00) 		0.328
(1.00) 		0.431
(1.00) 		0.352
(1.00) 		0.285
(1.00) 		0.03
(1.00) 		0.0695
(1.00) 		0.0785
(1.00) 		0.0713
(1.00)
Amp Peak 5(3p25 2) 0 (0%) 68 0.0742
(1.00) 		0.37
(1.00) 		0.0289
(1.00) 		0.115
(1.00) 		0.83
(1.00) 		0.913
(1.00) 		0.567
(1.00) 		0.428
(1.00) 		0.455
(1.00)
Amp Peak 6(3q26 32) 0 (0%) 56 0.0272
(1.00) 		0.762
(1.00) 		0.841
(1.00) 		0.795
(1.00) 		0.799
(1.00) 		0.659
(1.00) 		0.319
(1.00) 		0.952
(1.00) 		0.765
(1.00)
Amp Peak 7(4p16 3) 0 (0%) 107 0.0567
(1.00) 		0.545
(1.00) 		0.0815
(1.00) 		0.414
(1.00) 		0.483
(1.00) 		0.0158
(1.00) 		0.157
(1.00) 		0.94
(1.00) 		0.0286
(1.00)
Amp Peak 8(4q13 3) 0 (0%) 115 0.407
(1.00) 		0.0375
(1.00) 		0.0242
(1.00) 		0.224
(1.00) 		0.997
(1.00) 		1
(1.00) 		0.878
(1.00) 		0.803
(1.00) 		0.747
(1.00)
Amp Peak 9(5p15 1) 0 (0%) 69 0.71
(1.00) 		0.389
(1.00) 		0.427
(1.00) 		0.722
(1.00) 		0.348
(1.00) 		0.478
(1.00) 		0.00125
(0.698) 		0.0779
(1.00) 		0.677
(1.00)
Amp Peak 10(6p22 3) 0 (0%) 78 0.458
(1.00) 		0.505
(1.00) 		0.841
(1.00) 		0.754
(1.00) 		0.655
(1.00) 		0.905
(1.00) 		0.281
(1.00) 		0.0141
(1.00) 		0.543
(1.00)
Amp Peak 11(6q12) 0 (0%) 111 0.707
(1.00) 		0.14
(1.00) 		0.189
(1.00) 		0.229
(1.00) 		0.102
(1.00) 		1
(1.00) 		0.992
(1.00) 		0.0844
(1.00) 		0.764
(1.00)
Amp Peak 12(6q21) 0 (0%) 118 0.845
(1.00) 		0.479
(1.00) 		1
(1.00) 		0.377
(1.00) 		0.233
(1.00) 		0.508
(1.00) 		0.555
(1.00) 		0.919
(1.00) 		0.721
(1.00)
Amp Peak 13(7p11 2) 0 (0%) 61 0.588
(1.00) 		0.0395
(1.00) 		1
(1.00) 		0.64
(1.00) 		0.488
(1.00) 		0.848
(1.00) 		0.0982
(1.00) 		0.307
(1.00) 		0.784
(1.00)
Amp Peak 14(8p11 23) 0 (0%) 87 0.988
(1.00) 		0.983
(1.00) 		0.534
(1.00) 		0.941
(1.00) 		0.201
(1.00) 		0.581
(1.00) 		0.765
(1.00) 		0.876
(1.00) 		0.605
(1.00)
Amp Peak 15(8p11 21) 0 (0%) 88 0.0531
(1.00) 		0.608
(1.00) 		0.147
(1.00) 		0.489
(1.00) 		0.0734
(1.00) 		0.164
(1.00) 		0.953
(1.00) 		0.749
(1.00) 		0.923
(1.00)
Amp Peak 16(8q22 3) 0 (0%) 49 0.28
(1.00) 		0.838
(1.00) 		0.0669
(1.00) 		0.516
(1.00) 		0.206
(1.00) 		0.774
(1.00) 		0.319
(1.00) 		0.0919
(1.00) 		0.973
(1.00)
Amp Peak 17(8q24 21) 0 (0%) 51 0.164
(1.00) 		0.84
(1.00) 		0.106
(1.00) 		0.551
(1.00) 		0.706
(1.00) 		0.389
(1.00) 		0.658
(1.00) 		0.112
(1.00) 		0.776
(1.00)
Amp Peak 18(10p15 1) 0 (0%) 77 0.681
(1.00) 		0.0757
(1.00) 		0.843
(1.00) 		0.739
(1.00) 		0.74
(1.00) 		0.58
(1.00) 		0.0848
(1.00) 		0.579
(1.00) 		0.662
(1.00)
Amp Peak 19(11q13 3) 0 (0%) 81 0.954
(1.00) 		0.222
(1.00) 		0.548
(1.00) 		0.629
(1.00) 		0.456
(1.00) 		0.09
(1.00) 		0.0738
(1.00) 		0.386
(1.00) 		0.453
(1.00)
Amp Peak 20(12q15) 0 (0%) 90 0.765
(1.00) 		0.864
(1.00) 		0.678
(1.00) 		0.645
(1.00) 		0.0854
(1.00) 		0.533
(1.00) 		0.183
(1.00) 		0.52
(1.00) 		0.178
(1.00)
Amp Peak 21(13q34) 0 (0%) 82 0.992
(1.00) 		0.752
(1.00) 		0.839
(1.00) 		0.72
(1.00) 		0.166
(1.00) 		0.635
(1.00) 		0.586
(1.00) 		0.518
(1.00) 		0.336
(1.00)
Amp Peak 22(16p12 1) 0 (0%) 97 0.621
(1.00) 		0.675
(1.00) 		0.826
(1.00) 		0.35
(1.00) 		0.846
(1.00) 		0.277
(1.00) 		0.169
(1.00) 		0.933
(1.00) 		0.291
(1.00)
Amp Peak 23(17q11 2) 0 (0%) 70 0.692
(1.00) 		0.273
(1.00) 		1
(1.00) 		0.0247
(1.00) 		0.984
(1.00) 		0.118
(1.00) 		0.0598
(1.00) 		0.72
(1.00) 		0.0441
(1.00)
Amp Peak 24(17q12) 0 (0%) 76 0.256
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.0911
(1.00) 		0.15
(1.00) 		0.22
(1.00) 		0.156
(1.00) 		0.829
(1.00) 		0.0756
(1.00)
Amp Peak 25(19q12) 0 (0%) 75 0.152
(1.00) 		0.42
(1.00) 		1
(1.00) 		0.449
(1.00) 		0.371
(1.00) 		0.602
(1.00) 		0.412
(1.00) 		0.171
(1.00) 		0.38
(1.00)
Amp Peak 26(19q13 43) 0 (0%) 77 0.219
(1.00) 		0.579
(1.00) 		0.843
(1.00) 		0.531
(1.00) 		0.539
(1.00) 		0.321
(1.00) 		0.0884
(1.00) 		0.0703
(1.00) 		0.123
(1.00)
Amp Peak 27(20q11 21) 0 (0%) 39 0.842
(1.00) 		0.339
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.0362
(1.00) 		0.872
(1.00) 		0.512
(1.00) 		0.645
(1.00) 		0.638
(1.00)
Amp Peak 28(22q11 23) 0 (0%) 102 0.111
(1.00) 		0.347
(1.00) 		0.169
(1.00) 		0.635
(1.00) 		0.419
(1.00) 		0.828
(1.00) 		0.81
(1.00) 		0.767
(1.00) 		0.353
(1.00)
Del Peak 1(1p36 11) 0 (0%) 110 0.158
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.916
(1.00) 		0.744
(1.00) 		0.858
(1.00) 		0.00152
(0.843) 		0.393
(1.00) 		0.583
(1.00)
Del Peak 2(1q32 1) 0 (0%) 108 0.406
(1.00) 		0.0977
(1.00) 		0.0824
(1.00) 		0.631
(1.00) 		0.00307
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.349
(1.00) 		0.409
(1.00)
Del Peak 3(2q22 1) 0 (0%) 93 0.176
(1.00) 		0.804
(1.00) 		0.136
(1.00) 		0.612
(1.00) 		0.893
(1.00) 		0.158
(1.00) 		0.682
(1.00) 		0.597
(1.00) 		0.431
(1.00)
Del Peak 4(2q34) 0 (0%) 77 0.368
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.693
(1.00) 		0.584
(1.00) 		0.354
(1.00) 		0.778
(1.00) 		0.411
(1.00) 		0.686
(1.00)
Del Peak 5(2q37 1) 0 (0%) 66 0.339
(1.00) 		0.556
(1.00) 		0.0472
(1.00) 		0.473
(1.00) 		0.233
(1.00) 		0.266
(1.00) 		0.411
(1.00) 		0.909
(1.00) 		0.286
(1.00)
Del Peak 6(3p21 31) 0 (0%) 90 0.915
(1.00) 		0.678
(1.00) 		0.527
(1.00) 		0.594
(1.00) 		0.843
(1.00) 		0.415
(1.00) 		0.828
(1.00) 		0.223
(1.00) 		0.749
(1.00)
Del Peak 7(3p14 2) 0 (0%) 89 0.328
(1.00) 		0.398
(1.00) 		0.533
(1.00) 		0.594
(1.00) 		0.604
(1.00) 		0.483
(1.00) 		0.333
(1.00) 		0.0646
(1.00) 		0.813
(1.00)
Del Peak 8(3p12 3) 0 (0%) 96 0.758
(1.00) 		0.0399
(1.00) 		0.66
(1.00) 		0.0937
(1.00) 		0.957
(1.00) 		0.197
(1.00) 		0.27
(1.00) 		0.246
(1.00) 		0.788
(1.00)
Del Peak 9(4q22 1) 0 (0%) 81 0.75
(1.00) 		0.0987
(1.00) 		0.317
(1.00) 		0.939
(1.00) 		0.896
(1.00) 		0.124
(1.00) 		0.616
(1.00) 		0.159
(1.00) 		0.617
(1.00)
Del Peak 10(4q34 2) 0 (0%) 75 0.388
(1.00) 		0.119
(1.00) 		0.842
(1.00) 		0.575
(1.00) 		0.541
(1.00) 		0.924
(1.00) 		0.613
(1.00) 		0.464
(1.00) 		0.147
(1.00)
Del Peak 11(5q11 2) 0 (0%) 63 0.549
(1.00) 		0.00991
(1.00) 		0.241
(1.00) 		0.377
(1.00) 		0.438
(1.00) 		0.289
(1.00) 		0.123
(1.00) 		0.278
(1.00) 		0.0178
(1.00)
Del Peak 12(5q35 1) 0 (0%) 66 0.277
(1.00) 		0.114
(1.00) 		0.113
(1.00) 		0.205
(1.00) 		0.418
(1.00) 		0.0371
(1.00) 		0.284
(1.00) 		0.189
(1.00) 		0.0235
(1.00)
Del Peak 13(6p25 3) 0 (0%) 96 0.103
(1.00) 		0.562
(1.00) 		0.186
(1.00) 		0.234
(1.00) 		0.323
(1.00) 		0.73
(1.00) 		0.0515
(1.00) 		0.0822
(1.00) 		0.0966
(1.00)
Del Peak 14(6q21) 0 (0%) 77 0.0705
(1.00) 		0.105
(1.00) 		1
(1.00) 		0.967
(1.00) 		0.857
(1.00) 		0.852
(1.00) 		0.00868
(1.00) 		0.00313
(1.00) 		0.000513
(0.286)
Del Peak 15(8p23 1) 0 (0%) 59 0.501
(1.00) 		0.516
(1.00) 		0.0486
(1.00) 		0.844
(1.00) 		0.628
(1.00) 		0.0802
(1.00) 		0.499
(1.00) 		0.45
(1.00) 		0.27
(1.00)
Del Peak 16(9p23) 0 (0%) 73 0.487
(1.00) 		0.975
(1.00) 		0.691
(1.00) 		0.693
(1.00) 		0.767
(1.00) 		0.655
(1.00) 		0.542
(1.00) 		0.606
(1.00) 		0.875
(1.00)
Del Peak 17(9p21 3) 0 (0%) 55 0.507
(1.00) 		0.642
(1.00) 		0.426
(1.00) 		0.975
(1.00) 		0.179
(1.00) 		1
(1.00) 		0.0912
(1.00) 		0.56
(1.00) 		0.765
(1.00)
Del Peak 18(10p12 1) 0 (0%) 106 0.989
(1.00) 		0.239
(1.00) 		1
(1.00) 		0.596
(1.00) 		0.986
(1.00) 		0.321
(1.00) 		0.287
(1.00) 		0.321
(1.00) 		0.859
(1.00)
Del Peak 19(10q23 31) 0 (0%) 76 0.769
(1.00) 		0.0148
(1.00) 		0.843
(1.00) 		0.0726
(1.00) 		0.616
(1.00) 		0.806
(1.00) 		0.0295
(1.00) 		0.177
(1.00) 		0.073
(1.00)
Del Peak 20(11p15 5) 0 (0%) 66 0.384
(1.00) 		0.00885
(1.00) 		0.693
(1.00) 		0.00602
(1.00) 		0.843
(1.00) 		0.416
(1.00) 		0.12
(1.00) 		0.166
(1.00) 		0.0246
(1.00)
Del Peak 21(11q25) 0 (0%) 92 0.585
(1.00) 		0.635
(1.00) 		0.834
(1.00) 		0.908
(1.00) 		0.228
(1.00) 		0.53
(1.00) 		0.202
(1.00) 		0.0498
(1.00) 		0.22
(1.00)
Del Peak 22(13q14 2) 0 (0%) 82 0.319
(1.00) 		0.0801
(1.00) 		0.226
(1.00) 		0.84
(1.00) 		0.598
(1.00) 		0.679
(1.00) 		0.143
(1.00) 		0.205
(1.00) 		0.0482
(1.00)
Del Peak 23(14q12) 0 (0%) 95 0.28
(1.00) 		0.142
(1.00) 		0.275
(1.00) 		0.597
(1.00) 		0.0455
(1.00) 		0.91
(1.00) 		0.114
(1.00) 		0.186
(1.00) 		0.102
(1.00)
Del Peak 24(14q32 31) 0 (0%) 96 0.631
(1.00) 		0.148
(1.00) 		0.0482
(1.00) 		0.283
(1.00) 		0.603
(1.00) 		0.411
(1.00) 		0.975
(1.00) 		0.674
(1.00) 		0.745
(1.00)
Del Peak 25(15q13 1) 0 (0%) 84 0.251
(1.00) 		0.0978
(1.00) 		0.31
(1.00) 		0.34
(1.00) 		0.716
(1.00) 		0.122
(1.00) 		0.317
(1.00) 		0.482
(1.00) 		0.277
(1.00)
Del Peak 26(16p13 3) 0 (0%) 85 0.443
(1.00) 		0.21
(1.00) 		0.681
(1.00) 		0.94
(1.00) 		0.722
(1.00) 		0.622
(1.00) 		0.462
(1.00) 		0.724
(1.00) 		0.529
(1.00)
Del Peak 27(16q23 1) 0 (0%) 96 0.279
(1.00) 		0.705
(1.00) 		0.517
(1.00) 		0.169
(1.00) 		0.74
(1.00) 		0.615
(1.00) 		0.0943
(1.00) 		0.2
(1.00) 		0.213
(1.00)
Del Peak 28(17p12) 0 (0%) 63 0.0709
(1.00) 		0.37
(1.00) 		0.435
(1.00) 		0.876
(1.00) 		0.949
(1.00) 		0.928
(1.00) 		0.187
(1.00) 		0.552
(1.00) 		0.00786
(1.00)
Del Peak 29(18q23) 0 (0%) 76 0.105
(1.00) 		0.0934
(1.00) 		0.69
(1.00) 		0.148
(1.00) 		0.379
(1.00) 		0.58
(1.00) 		0.829
(1.00) 		0.423
(1.00) 		0.896
(1.00)
Del Peak 30(19p13 3) 0 (0%) 80 0.819
(1.00) 		0.457
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.232
(1.00) 		0.0189
(1.00) 		0.147
(1.00) 		0.578
(1.00) 		0.106
(1.00)
Del Peak 31(22q13 32) 0 (0%) 80 0.853
(1.00) 		0.298
(1.00) 		1
(1.00) 		0.14
(1.00) 		0.758
(1.00) 		0.0407
(1.00) 		0.77
(1.00) 		0.404
(1.00) 		0.338
(1.00)
Del Peak 32(Xp11 3) 0 (0%) 97 0.858
(1.00) 		0.131
(1.00) 		0.376
(1.00) 		0.832
(1.00) 		0.205
(1.00) 		0.884
(1.00) 		0.147
(1.00) 		0.979
(1.00) 		0.276
(1.00)
Del Peak 33(Xq21 33) 0 (0%) 103 0.706
(1.00) 		0.991
(1.00) 		1
(1.00) 		0.477
(1.00) 		0.673
(1.00) 		0.361
(1.00) 		0.278
(1.00) 		0.913
(1.00) 		0.597
(1.00)
Del Peak 34(Xq23) 0 (0%) 104 0.66
(1.00) 		0.7
(1.00) 		1
(1.00) 		0.809
(1.00) 		0.791
(1.00) 		0.268
(1.00) 		0.39
(1.00) 		0.956
(1.00) 		0.795
(1.00)
Methods & Data
Input

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

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

  • Number of patients = 134

  • Number of significantly arm-level cnvs = 62

  • 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

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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