Skin Cutaneous Melanoma: Correlation between copy number variations of arm-level result and selected clinical features
(All_Samples cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 77 arm-level results and 9 clinical features across 202 patients, one significant finding detected with Q value < 0.25.

  • 18q gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 77 arm-level results and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		GENDER RADIATIONS
RADIATION
REGIMENINDICATION 		DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Chi-square test t-test Chi-square test
18q gain 15 (7%) 187 0.731
(1.00) 		0.282
(1.00) 		0.169
(1.00) 		0.581
(1.00) 		1
(1.00) 		0.949
(1.00) 		0.509
(1.00) 		0.000104
(0.0636)
1p gain 26 (13%) 176 0.168
(1.00) 		0.0899
(1.00) 		0.68
(1.00) 		0.83
(1.00) 		0.34
(1.00) 		0.831
(1.00) 		0.0742
(1.00) 		0.0214
(1.00)
1q gain 67 (33%) 135 0.749
(1.00) 		0.924
(1.00) 		0.0191
(1.00) 		1
(1.00) 		0.552
(1.00) 		0.683
(1.00) 		0.0348
(1.00) 		0.149
(1.00)
2p gain 19 (9%) 183 0.315
(1.00) 		0.0188
(1.00) 		0.692
(1.00) 		0.33
(1.00) 		0.258
(1.00) 		0.907
(1.00) 		0.245
(1.00) 		0.657
(1.00)
2q gain 17 (8%) 185 0.445
(1.00) 		0.118
(1.00) 		0.631
(1.00) 		0.297
(1.00) 		0.233
(1.00) 		0.925
(1.00) 		0.32
(1.00) 		0.648
(1.00)
3p gain 20 (10%) 182 0.345
(1.00) 		0.804
(1.00) 		0.0128
(1.00) 		0.235
(1.00) 		0.27
(1.00) 		0.907
(1.00) 		0.786
(1.00) 		0.613
(1.00)
3q gain 25 (12%) 177 0.318
(1.00) 		0.52
(1.00) 		0.0196
(1.00) 		0.275
(1.00) 		0.329
(1.00) 		0.854
(1.00) 		0.525
(1.00) 		0.696
(1.00)
4p gain 17 (8%) 185 0.194
(1.00) 		0.0762
(1.00) 		0.342
(1.00) 		0.439
(1.00) 		1
(1.00) 		0.934
(1.00) 		0.289
(1.00) 		0.529
(1.00)
4q gain 13 (6%) 189 0.173
(1.00) 		0.0689
(1.00) 		0.466
(1.00) 		1
(1.00) 		1
(1.00) 		0.969
(1.00) 		0.409
(1.00) 		0.642
(1.00)
5p gain 24 (12%) 178 0.913
(1.00) 		0.492
(1.00) 		0.0842
(1.00) 		0.379
(1.00) 		1
(1.00) 		0.204
(1.00) 		0.787
(1.00) 		0.51
(1.00)
5q gain 7 (3%) 195 0.139
(1.00) 		0.125
(1.00) 		0.713
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.579
(1.00) 		0.433
(1.00)
6p gain 67 (33%) 135 0.0819
(1.00) 		0.525
(1.00) 		0.163
(1.00) 		0.441
(1.00) 		0.552
(1.00) 		0.14
(1.00) 		0.193
(1.00) 		0.263
(1.00)
6q gain 16 (8%) 186 0.796
(1.00) 		0.768
(1.00) 		0.348
(1.00) 		1
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.927
(1.00) 		0.54
(1.00)
7p gain 85 (42%) 117 0.118
(1.00) 		0.897
(1.00) 		0.428
(1.00) 		0.105
(1.00) 		1
(1.00) 		0.104
(1.00) 		0.471
(1.00) 		0.336
(1.00)
7q gain 86 (43%) 116 0.341
(1.00) 		0.516
(1.00) 		0.627
(1.00) 		0.379
(1.00) 		1
(1.00) 		0.12
(1.00) 		0.444
(1.00) 		0.0766
(1.00)
8p gain 39 (19%) 163 0.713
(1.00) 		0.784
(1.00) 		0.127
(1.00) 		0.362
(1.00) 		0.476
(1.00) 		0.0371
(1.00) 		0.473
(1.00) 		0.818
(1.00)
8q gain 63 (31%) 139 0.413
(1.00) 		0.37
(1.00) 		0.338
(1.00) 		0.64
(1.00) 		0.554
(1.00) 		0.137
(1.00) 		0.396
(1.00) 		0.794
(1.00)
9p gain 3 (1%) 199 0.0392
(1.00) 		1
(1.00) 		0.558
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.0339
(1.00) 		0.439
(1.00)
9q gain 4 (2%) 198 0.406
(1.00) 		0.662
(1.00) 		0.51
(1.00) 		0.633
(1.00) 		1
(1.00) 		0.995
(1.00) 		0.303
(1.00) 		0.65
(1.00)
11p gain 13 (6%) 189 0.882
(1.00) 		0.123
(1.00) 		0.794
(1.00) 		0.378
(1.00) 		0.182
(1.00) 		0.957
(1.00) 		0.349
(1.00) 		0.951
(1.00)
11q gain 9 (4%) 193 0.977
(1.00) 		0.212
(1.00) 		0.903
(1.00) 		1
(1.00) 		1
(1.00) 		0.98
(1.00) 		0.945
(1.00) 		0.713
(1.00)
12p gain 19 (9%) 183 0.465
(1.00) 		0.464
(1.00) 		0.155
(1.00) 		0.628
(1.00) 		1
(1.00) 		0.0913
(1.00) 		0.16
(1.00) 		0.0969
(1.00)
12q gain 7 (3%) 195 0.947
(1.00) 		0.816
(1.00) 		0.827
(1.00) 		0.259
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.0166
(1.00) 		0.0881
(1.00)
13q gain 35 (17%) 167 0.514
(1.00) 		0.925
(1.00) 		0.0432
(1.00) 		1
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.161
(1.00) 		0.613
(1.00)
14q gain 14 (7%) 188 0.587
(1.00) 		0.91
(1.00) 		0.548
(1.00) 		0.575
(1.00) 		1
(1.00) 		0.957
(1.00) 		0.766
(1.00) 		0.983
(1.00)
15q gain 26 (13%) 176 0.533
(1.00) 		0.506
(1.00) 		0.125
(1.00) 		1
(1.00) 		1
(1.00) 		0.842
(1.00) 		0.453
(1.00) 		0.906
(1.00)
16p gain 14 (7%) 188 0.223
(1.00) 		0.703
(1.00) 		0.369
(1.00) 		1
(1.00) 		1
(1.00) 		0.942
(1.00) 		0.591
(1.00) 		0.463
(1.00)
16q gain 13 (6%) 189 0.39
(1.00) 		0.979
(1.00) 		0.643
(1.00) 		0.77
(1.00) 		1
(1.00) 		0.949
(1.00) 		0.243
(1.00) 		0.692
(1.00)
17p gain 15 (7%) 187 0.9
(1.00) 		0.915
(1.00) 		0.233
(1.00) 		0.267
(1.00) 		1
(1.00) 		0.185
(1.00) 		0.937
(1.00) 		0.546
(1.00)
17q gain 24 (12%) 178 0.0853
(1.00) 		0.102
(1.00) 		0.129
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.446
(1.00) 		0.69
(1.00) 		0.868
(1.00)
18p gain 25 (12%) 177 0.838
(1.00) 		0.0322
(1.00) 		0.662
(1.00) 		0.275
(1.00) 		0.329
(1.00) 		0.465
(1.00) 		0.615
(1.00) 		0.0185
(1.00)
19p gain 12 (6%) 190 0.607
(1.00) 		0.227
(1.00) 		0.086
(1.00) 		0.767
(1.00) 		0.169
(1.00) 		0.963
(1.00) 		0.989
(1.00) 		0.0497
(1.00)
19q gain 15 (7%) 187 0.5
(1.00) 		0.152
(1.00) 		0.229
(1.00) 		0.094
(1.00) 		1
(1.00) 		0.942
(1.00) 		0.883
(1.00) 		0.0741
(1.00)
20p gain 57 (28%) 145 0.78
(1.00) 		0.486
(1.00) 		0.314
(1.00) 		0.519
(1.00) 		1
(1.00) 		0.114
(1.00) 		0.788
(1.00) 		0.668
(1.00)
20q gain 70 (35%) 132 0.69
(1.00) 		0.863
(1.00) 		0.245
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.0508
(1.00) 		0.943
(1.00) 		0.809
(1.00)
21q gain 22 (11%) 180 0.0174
(1.00) 		0.915
(1.00) 		0.384
(1.00) 		0.487
(1.00) 		1
(1.00) 		0.134
(1.00) 		0.344
(1.00) 		0.0996
(1.00)
22q gain 50 (25%) 152 0.372
(1.00) 		0.898
(1.00) 		0.313
(1.00) 		0.315
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.14
(1.00) 		0.1
(1.00)
Xq gain 4 (2%) 198 0.0323
(1.00) 		0.296
(1.00) 		1
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.989
(1.00) 		0.384
(1.00)
1p loss 16 (8%) 186 0.564
(1.00) 		0.697
(1.00) 		0.779
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.949
(1.00) 		0.421
(1.00) 		0.622
(1.00)
1q loss 7 (3%) 195 0.591
(1.00) 		0.252
(1.00) 		0.179
(1.00) 		0.429
(1.00) 		0.101
(1.00) 		0.989
(1.00) 		0.724
(1.00) 		0.857
(1.00)
2p loss 19 (9%) 183 0.632
(1.00) 		0.676
(1.00) 		0.982
(1.00) 		1
(1.00) 		0.258
(1.00) 		0.934
(1.00) 		0.713
(1.00) 		0.378
(1.00)
2q loss 17 (8%) 185 0.697
(1.00) 		0.344
(1.00) 		0.87
(1.00) 		0.797
(1.00) 		0.233
(1.00) 		0.22
(1.00) 		0.926
(1.00) 		0.307
(1.00)
3p loss 13 (6%) 189 0.259
(1.00) 		0.207
(1.00) 		0.352
(1.00) 		1
(1.00) 		1
(1.00) 		0.963
(1.00) 		0.23
(1.00) 		0.0422
(1.00)
3q loss 13 (6%) 189 0.253
(1.00) 		0.449
(1.00) 		0.375
(1.00) 		0.561
(1.00) 		1
(1.00) 		0.963
(1.00) 		0.23
(1.00) 		0.365
(1.00)
4p loss 22 (11%) 180 0.978
(1.00) 		0.379
(1.00) 		0.4
(1.00) 		0.103
(1.00) 		1
(1.00) 		0.376
(1.00) 		0.869
(1.00) 		0.658
(1.00)
4q loss 23 (11%) 179 0.896
(1.00) 		0.592
(1.00) 		0.303
(1.00) 		0.169
(1.00) 		1
(1.00) 		0.00161
(0.981) 		0.807
(1.00) 		0.199
(1.00)
5p loss 25 (12%) 177 0.604
(1.00) 		0.639
(1.00) 		1
(1.00) 		1
(1.00) 		0.329
(1.00) 		0.887
(1.00) 		0.912
(1.00) 		0.879
(1.00)
5q loss 41 (20%) 161 0.772
(1.00) 		0.416
(1.00) 		0.824
(1.00) 		0.471
(1.00) 		0.496
(1.00) 		0.12
(1.00) 		0.464
(1.00) 		0.487
(1.00)
6p loss 16 (8%) 186 0.749
(1.00) 		0.956
(1.00) 		0.532
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.934
(1.00) 		0.854
(1.00) 		0.517
(1.00)
6q loss 74 (37%) 128 0.767
(1.00) 		0.084
(1.00) 		0.11
(1.00) 		0.764
(1.00) 		0.3
(1.00) 		0.982
(1.00) 		0.892
(1.00) 		0.534
(1.00)
7p loss 3 (1%) 199 0.621
(1.00) 		0.418
(1.00) 		0.558
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.965
(1.00) 		0.583
(1.00)
7q loss 3 (1%) 199 0.621
(1.00) 		0.418
(1.00) 		0.558
(1.00) 		1
(1.00) 		0.997
(1.00) 		0.965
(1.00) 		0.583
(1.00)
8p loss 27 (13%) 175 0.403
(1.00) 		0.823
(1.00) 		0.0953
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.648
(1.00) 		0.558
(1.00)
8q loss 6 (3%) 196 1
(1.00) 		0.179
(1.00) 		0.0477
(1.00) 		0.674
(1.00) 		1
(1.00) 		0.989
(1.00) 		0.327
(1.00) 		0.555
(1.00)
9p loss 117 (58%) 85 0.0344
(1.00) 		0.606
(1.00) 		0.0869
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.441
(1.00) 		0.0633
(1.00) 		0.0283
(1.00)
9q loss 83 (41%) 119 0.253
(1.00) 		0.178
(1.00) 		0.0868
(1.00) 		0.0552
(1.00) 		1
(1.00) 		0.101
(1.00) 		0.499
(1.00) 		0.00977
(1.00)
10p loss 88 (44%) 114 0.089
(1.00) 		0.0748
(1.00) 		0.428
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.688
(1.00) 		0.551
(1.00) 		0.751
(1.00)
10q loss 100 (50%) 102 0.253
(1.00) 		0.00193
(1.00) 		0.167
(1.00) 		0.245
(1.00) 		1
(1.00) 		0.354
(1.00) 		0.767
(1.00) 		0.83
(1.00)
11p loss 51 (25%) 151 0.867
(1.00) 		0.345
(1.00) 		0.791
(1.00) 		0.242
(1.00) 		0.573
(1.00) 		0.277
(1.00) 		0.108
(1.00) 		0.0254
(1.00)
11q loss 55 (27%) 147 0.578
(1.00) 		0.893
(1.00) 		0.884
(1.00) 		0.103
(1.00) 		0.564
(1.00) 		0.352
(1.00) 		0.323
(1.00) 		0.049
(1.00)
12p loss 13 (6%) 189 0.265
(1.00) 		0.964
(1.00) 		0.456
(1.00) 		0.561
(1.00) 		0.182
(1.00) 		0.406
(1.00) 		0.405
(1.00) 		0.489
(1.00)
12q loss 24 (12%) 178 0.904
(1.00) 		0.842
(1.00) 		0.141
(1.00) 		0.187
(1.00) 		0.317
(1.00) 		0.322
(1.00) 		0.671
(1.00) 		0.787
(1.00)
13q loss 29 (14%) 173 0.743
(1.00) 		0.348
(1.00) 		0.229
(1.00) 		1
(1.00) 		0.373
(1.00) 		0.00746
(1.00) 		0.00859
(1.00) 		0.286
(1.00)
14q loss 47 (23%) 155 0.798
(1.00) 		0.718
(1.00) 		0.872
(1.00) 		0.865
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.494
(1.00) 		0.595
(1.00)
15q loss 12 (6%) 190 0.467
(1.00) 		0.138
(1.00) 		0.158
(1.00) 		0.767
(1.00) 		1
(1.00) 		0.0843
(1.00) 		0.48
(1.00) 		0.869
(1.00)
16p loss 15 (7%) 187 0.441
(1.00) 		0.326
(1.00) 		0.642
(1.00) 		0.581
(1.00) 		1
(1.00) 		0.957
(1.00) 		0.785
(1.00) 		0.211
(1.00)
16q loss 38 (19%) 164 0.0962
(1.00) 		0.633
(1.00) 		0.403
(1.00) 		0.853
(1.00) 		1
(1.00) 		0.434
(1.00) 		0.748
(1.00) 		0.206
(1.00)
17p loss 41 (20%) 161 0.99
(1.00) 		0.501
(1.00) 		0.677
(1.00) 		0.719
(1.00) 		1
(1.00) 		0.604
(1.00) 		0.76
(1.00) 		0.551
(1.00)
17q loss 20 (10%) 182 0.322
(1.00) 		0.647
(1.00) 		0.803
(1.00) 		1
(1.00) 		1
(1.00) 		0.224
(1.00) 		0.152
(1.00) 		0.617
(1.00)
18p loss 39 (19%) 163 0.834
(1.00) 		0.661
(1.00) 		0.551
(1.00) 		0.713
(1.00) 		0.476
(1.00) 		0.698
(1.00) 		0.628
(1.00) 		0.145
(1.00)
18q loss 36 (18%) 166 0.938
(1.00) 		0.566
(1.00) 		0.567
(1.00) 		0.852
(1.00) 		0.447
(1.00) 		0.567
(1.00) 		0.281
(1.00) 		0.0446
(1.00)
19p loss 18 (9%) 184 0.821
(1.00) 		0.697
(1.00) 		0.78
(1.00) 		0.127
(1.00) 		1
(1.00) 		0.159
(1.00) 		0.862
(1.00) 		0.349
(1.00)
19q loss 19 (9%) 183 0.51
(1.00) 		0.742
(1.00) 		0.21
(1.00) 		0.456
(1.00) 		1
(1.00) 		0.129
(1.00) 		0.785
(1.00) 		0.484
(1.00)
20p loss 8 (4%) 194 0.188
(1.00) 		0.213
(1.00) 		0.111
(1.00) 		0.713
(1.00) 		1
(1.00) 		0.0335
(1.00) 		0.94
(1.00) 		0.774
(1.00)
21q loss 24 (12%) 178 0.881
(1.00) 		0.843
(1.00) 		0.901
(1.00) 		1
(1.00) 		1
(1.00) 		0.854
(1.00) 		0.585
(1.00) 		0.105
(1.00)
22q loss 15 (7%) 187 0.305
(1.00) 		0.824
(1.00) 		0.468
(1.00) 		0.581
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.973
(1.00) 		0.37
(1.00)
Xq loss 5 (2%) 197 0.65
(1.00) 		0.932
(1.00) 		0.914
(1.00) 		0.0676
(1.00) 		1
(1.00) 		0.995
(1.00) 		0.97
(1.00) 		0.126
(1.00)
'18q gain mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000104 (Chi-square test), Q value = 0.064

Table S1.  Gene #31: '18q gain mutation analysis' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'

nPatients I OR II NOS STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
ALL 4 17 10 15 20 9 10 23 9 7 21 27 7
18Q GAIN MUTATED 2 1 0 0 0 0 0 7 0 2 0 2 0
18Q GAIN WILD-TYPE 2 16 10 15 20 9 10 16 9 5 21 25 7

Figure S1.  Get High-res Image Gene #31: '18q gain mutation analysis' versus Clinical Feature #9: 'NEOPLASM.DISEASESTAGE'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

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

  • Number of patients = 202

  • Number of significantly arm-level cnvs = 77

  • Number of selected clinical features = 9

  • 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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