Correlation between copy number variations of arm-level result and selected clinical features
Skin Cutaneous Melanoma (Metastatic)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1HT2MSH
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1HT2MSH
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 79 arm-level events and 12 clinical features across 260 patients, 2 significant findings detected with Q value < 0.25.

  • 5q gain cnv correlated to 'BRESLOW.THICKNESS'.

  • 10q loss cnv correlated to 'AGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.

Clinical
Features 		Time
from
Specimen
Diagnosis
to
Death 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		MELANOMA
ULCERATION 		MELANOMA
PRIMARY
KNOWN 		BRESLOW
THICKNESS 		GENDER
nCNV (%) nWild-Type logrank test logrank test t-test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test t-test Fisher's exact test
5q gain 31 (12%) 229 0.268
(1.00) 		0.106
(1.00) 		0.955
(1.00) 		0.34
(1.00) 		0.447
(1.00) 		0.289
(1.00) 		0.787
(1.00) 		0.123
(1.00) 		0.105
(1.00) 		0.231
(1.00) 		0.000181
(0.171) 		0.556
(1.00)
10q loss 157 (60%) 103 0.614
(1.00) 		0.359
(1.00) 		8.81e-05
(0.0835) 		0.125
(1.00) 		0.859
(1.00) 		0.0343
(1.00) 		0.583
(1.00) 		0.147
(1.00) 		0.744
(1.00) 		0.437
(1.00) 		0.649
(1.00) 		0.121
(1.00)
1p gain 59 (23%) 201 0.68
(1.00) 		0.607
(1.00) 		0.617
(1.00) 		0.19
(1.00) 		0.109
(1.00) 		0.761
(1.00) 		0.439
(1.00) 		0.0789
(1.00) 		0.57
(1.00) 		0.82
(1.00) 		0.713
(1.00) 		1
(1.00)
1q gain 116 (45%) 144 0.469
(1.00) 		0.756
(1.00) 		0.711
(1.00) 		0.194
(1.00) 		0.562
(1.00) 		0.845
(1.00) 		0.167
(1.00) 		0.272
(1.00) 		0.631
(1.00) 		0.848
(1.00) 		0.592
(1.00) 		0.611
(1.00)
2p gain 52 (20%) 208 0.204
(1.00) 		0.105
(1.00) 		0.529
(1.00) 		0.381
(1.00) 		0.902
(1.00) 		0.144
(1.00) 		0.896
(1.00) 		0.57
(1.00) 		0.434
(1.00) 		0.348
(1.00) 		0.833
(1.00) 		0.528
(1.00)
2q gain 50 (19%) 210 0.0357
(1.00) 		0.0383
(1.00) 		0.632
(1.00) 		0.409
(1.00) 		0.817
(1.00) 		0.0366
(1.00) 		0.802
(1.00) 		0.668
(1.00) 		0.839
(1.00) 		0.81
(1.00) 		0.907
(1.00) 		1
(1.00)
3p gain 43 (17%) 217 0.627
(1.00) 		0.0246
(1.00) 		0.116
(1.00) 		0.237
(1.00) 		0.166
(1.00) 		0.0678
(1.00) 		0.218
(1.00) 		0.428
(1.00) 		0.652
(1.00) 		0.797
(1.00) 		0.00235
(1.00) 		1
(1.00)
3q gain 52 (20%) 208 0.386
(1.00) 		0.0193
(1.00) 		0.0175
(1.00) 		0.258
(1.00) 		0.0974
(1.00) 		0.0097
(1.00) 		0.0364
(1.00) 		0.407
(1.00) 		0.0617
(1.00) 		0.811
(1.00) 		0.00145
(1.00) 		0.874
(1.00)
4p gain 38 (15%) 222 0.764
(1.00) 		0.675
(1.00) 		0.368
(1.00) 		0.786
(1.00) 		0.0992
(1.00) 		0.134
(1.00) 		0.806
(1.00) 		0.52
(1.00) 		1
(1.00) 		0.182
(1.00) 		0.897
(1.00) 		0.473
(1.00)
4q gain 32 (12%) 228 0.893
(1.00) 		0.505
(1.00) 		0.28
(1.00) 		0.779
(1.00) 		0.356
(1.00) 		0.238
(1.00) 		0.659
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.558
(1.00) 		0.852
(1.00) 		1
(1.00)
5p gain 51 (20%) 209 0.159
(1.00) 		0.0189
(1.00) 		0.0899
(1.00) 		0.45
(1.00) 		0.0341
(1.00) 		0.455
(1.00) 		0.066
(1.00) 		0.386
(1.00) 		0.0437
(1.00) 		0.225
(1.00) 		0.000523
(0.494) 		0.75
(1.00)
6p gain 105 (40%) 155 0.21
(1.00) 		0.902
(1.00) 		0.449
(1.00) 		0.143
(1.00) 		0.177
(1.00) 		0.16
(1.00) 		0.119
(1.00) 		0.0733
(1.00) 		0.744
(1.00) 		0.337
(1.00) 		0.537
(1.00) 		0.438
(1.00)
6q gain 32 (12%) 228 0.492
(1.00) 		0.387
(1.00) 		0.799
(1.00) 		0.38
(1.00) 		0.136
(1.00) 		0.00856
(1.00) 		0.0176
(1.00) 		0.352
(1.00) 		0.368
(1.00) 		0.778
(1.00) 		0.201
(1.00) 		0.565
(1.00)
7p gain 139 (53%) 121 0.766
(1.00) 		0.626
(1.00) 		0.409
(1.00) 		0.187
(1.00) 		0.0311
(1.00) 		0.347
(1.00) 		0.197
(1.00) 		0.499
(1.00) 		0.425
(1.00) 		0.25
(1.00) 		0.482
(1.00) 		0.206
(1.00)
7q gain 137 (53%) 123 0.909
(1.00) 		0.84
(1.00) 		0.151
(1.00) 		0.342
(1.00) 		0.0356
(1.00) 		0.709
(1.00) 		0.612
(1.00) 		0.742
(1.00) 		0.425
(1.00) 		0.569
(1.00) 		0.446
(1.00) 		0.0979
(1.00)
8p gain 84 (32%) 176 0.939
(1.00) 		0.932
(1.00) 		0.182
(1.00) 		0.00785
(1.00) 		0.705
(1.00) 		0.746
(1.00) 		0.438
(1.00) 		0.58
(1.00) 		0.387
(1.00) 		0.419
(1.00) 		0.973
(1.00) 		0.223
(1.00)
8q gain 118 (45%) 142 0.622
(1.00) 		0.691
(1.00) 		0.0217
(1.00) 		0.0121
(1.00) 		0.638
(1.00) 		0.137
(1.00) 		0.279
(1.00) 		0.768
(1.00) 		1
(1.00) 		0.0825
(1.00) 		0.735
(1.00) 		0.898
(1.00)
9p gain 14 (5%) 246 0.858
(1.00) 		0.461
(1.00) 		0.802
(1.00) 		0.0425
(1.00) 		0.0978
(1.00) 		0.254
(1.00) 		0.902
(1.00) 		0.663
(1.00) 		0.203
(1.00) 		0.386
(1.00) 		0.00285
(1.00) 		1
(1.00)
9q gain 19 (7%) 241 0.381
(1.00) 		0.988
(1.00) 		0.338
(1.00) 		0.0427
(1.00) 		0.228
(1.00) 		0.379
(1.00) 		0.981
(1.00) 		0.786
(1.00) 		0.164
(1.00) 		0.141
(1.00) 		0.000311
(0.294) 		0.469
(1.00)
10p gain 7 (3%) 253 0.557
(1.00) 		0.228
(1.00) 		0.657
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.81
(1.00) 		0.685
(1.00) 		0.0115
(1.00) 		1
(1.00) 		0.0387
(1.00) 		0.0263
(1.00) 		1
(1.00)
11p gain 26 (10%) 234 0.897
(1.00) 		0.676
(1.00) 		0.976
(1.00) 		0.805
(1.00) 		0.116
(1.00) 		0.0966
(1.00) 		0.351
(1.00) 		0.841
(1.00) 		1
(1.00) 		0.101
(1.00) 		0.43
(1.00) 		0.406
(1.00)
11q gain 22 (8%) 238 0.955
(1.00) 		0.949
(1.00) 		0.926
(1.00) 		0.63
(1.00) 		0.0943
(1.00) 		0.11
(1.00) 		0.397
(1.00) 		0.876
(1.00) 		0.741
(1.00) 		0.0327
(1.00) 		0.0769
(1.00) 		0.648
(1.00)
12p gain 45 (17%) 215 0.331
(1.00) 		0.336
(1.00) 		0.497
(1.00) 		0.586
(1.00) 		0.0318
(1.00) 		0.106
(1.00) 		0.0258
(1.00) 		0.546
(1.00) 		0.832
(1.00) 		0.8
(1.00) 		0.835
(1.00) 		0.737
(1.00)
12q gain 29 (11%) 231 0.72
(1.00) 		0.375
(1.00) 		0.838
(1.00) 		0.539
(1.00) 		0.399
(1.00) 		0.525
(1.00) 		0.0314
(1.00) 		0.843
(1.00) 		0.808
(1.00) 		0.22
(1.00) 		0.506
(1.00) 		0.423
(1.00)
13q gain 66 (25%) 194 0.0557
(1.00) 		0.143
(1.00) 		0.702
(1.00) 		0.0541
(1.00) 		0.367
(1.00) 		0.192
(1.00) 		0.282
(1.00) 		0.554
(1.00) 		0.458
(1.00) 		0.381
(1.00) 		0.575
(1.00) 		0.885
(1.00)
14q gain 29 (11%) 231 0.938
(1.00) 		0.782
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.867
(1.00) 		0.241
(1.00) 		0.533
(1.00) 		0.817
(1.00) 		0.808
(1.00) 		1
(1.00) 		0.535
(1.00) 		0.228
(1.00)
15q gain 58 (22%) 202 0.342
(1.00) 		0.285
(1.00) 		0.464
(1.00) 		0.673
(1.00) 		0.391
(1.00) 		0.365
(1.00) 		0.484
(1.00) 		0.62
(1.00) 		0.551
(1.00) 		0.17
(1.00) 		0.666
(1.00) 		1
(1.00)
16p gain 37 (14%) 223 0.568
(1.00) 		0.762
(1.00) 		0.292
(1.00) 		0.0981
(1.00) 		0.479
(1.00) 		0.0164
(1.00) 		0.0106
(1.00) 		0.408
(1.00) 		0.63
(1.00) 		1
(1.00) 		0.938
(1.00) 		0.857
(1.00)
16q gain 31 (12%) 229 0.3
(1.00) 		0.719
(1.00) 		0.567
(1.00) 		0.196
(1.00) 		0.579
(1.00) 		0.0158
(1.00) 		0.0199
(1.00) 		0.368
(1.00) 		0.799
(1.00) 		1
(1.00) 		0.928
(1.00) 		0.44
(1.00)
17p gain 31 (12%) 229 0.891
(1.00) 		0.891
(1.00) 		0.419
(1.00) 		0.928
(1.00) 		0.831
(1.00) 		0.536
(1.00) 		0.526
(1.00) 		0.378
(1.00) 		0.148
(1.00) 		0.773
(1.00) 		0.414
(1.00) 		0.44
(1.00)
17q gain 54 (21%) 206 0.322
(1.00) 		0.407
(1.00) 		0.00248
(1.00) 		0.529
(1.00) 		0.501
(1.00) 		0.931
(1.00) 		0.446
(1.00) 		0.545
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.896
(1.00) 		1
(1.00)
18p gain 42 (16%) 218 0.634
(1.00) 		0.898
(1.00) 		0.262
(1.00) 		0.757
(1.00) 		0.00468
(1.00) 		0.0381
(1.00) 		0.289
(1.00) 		0.0186
(1.00) 		0.186
(1.00) 		0.605
(1.00) 		0.412
(1.00) 		0.389
(1.00)
18q gain 37 (14%) 223 0.609
(1.00) 		0.339
(1.00) 		0.855
(1.00) 		0.558
(1.00) 		0.00397
(1.00) 		0.0393
(1.00) 		0.223
(1.00) 		0.505
(1.00) 		0.234
(1.00) 		0.411
(1.00) 		0.53
(1.00) 		0.587
(1.00)
19p gain 39 (15%) 221 0.984
(1.00) 		0.954
(1.00) 		0.697
(1.00) 		0.319
(1.00) 		0.837
(1.00) 		0.753
(1.00) 		0.655
(1.00) 		0.147
(1.00) 		0.379
(1.00) 		0.431
(1.00) 		0.66
(1.00) 		0.373
(1.00)
19q gain 41 (16%) 219 0.72
(1.00) 		0.689
(1.00) 		0.356
(1.00) 		0.222
(1.00) 		0.908
(1.00) 		0.554
(1.00) 		0.438
(1.00) 		0.171
(1.00) 		0.186
(1.00) 		0.599
(1.00) 		0.504
(1.00) 		0.166
(1.00)
20p gain 108 (42%) 152 0.27
(1.00) 		0.682
(1.00) 		0.194
(1.00) 		0.818
(1.00) 		0.143
(1.00) 		0.0699
(1.00) 		0.0877
(1.00) 		0.25
(1.00) 		0.105
(1.00) 		0.562
(1.00) 		0.0306
(1.00) 		1
(1.00)
20q gain 129 (50%) 131 0.958
(1.00) 		0.283
(1.00) 		0.0512
(1.00) 		0.553
(1.00) 		0.0681
(1.00) 		0.0546
(1.00) 		0.428
(1.00) 		0.134
(1.00) 		0.198
(1.00) 		0.344
(1.00) 		0.0334
(1.00) 		0.8
(1.00)
21q gain 45 (17%) 215 0.422
(1.00) 		0.325
(1.00) 		0.358
(1.00) 		0.315
(1.00) 		0.0546
(1.00) 		0.238
(1.00) 		0.123
(1.00) 		0.533
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.0591
(1.00) 		0.618
(1.00)
22q gain 92 (35%) 168 0.242
(1.00) 		0.167
(1.00) 		0.793
(1.00) 		0.247
(1.00) 		0.794
(1.00) 		0.482
(1.00) 		0.124
(1.00) 		0.959
(1.00) 		0.506
(1.00) 		0.692
(1.00) 		0.24
(1.00) 		0.595
(1.00)
xq gain 28 (11%) 232 0.0622
(1.00) 		0.0842
(1.00) 		0.113
(1.00) 		0.233
(1.00) 		0.422
(1.00) 		0.916
(1.00) 		0.436
(1.00) 		0.805
(1.00) 		0.808
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.838
(1.00)
1p loss 35 (13%) 225 0.111
(1.00) 		0.0211
(1.00) 		0.0368
(1.00) 		0.463
(1.00) 		0.0332
(1.00) 		0.675
(1.00) 		0.179
(1.00) 		0.839
(1.00) 		0.335
(1.00) 		0.779
(1.00) 		0.496
(1.00) 		1
(1.00)
1q loss 18 (7%) 242 0.778
(1.00) 		0.35
(1.00) 		0.667
(1.00) 		0.732
(1.00) 		0.363
(1.00) 		0.92
(1.00) 		0.386
(1.00) 		0.749
(1.00) 		1
(1.00) 		1
(1.00) 		0.232
(1.00) 		0.624
(1.00)
2p loss 33 (13%) 227 0.744
(1.00) 		0.176
(1.00) 		0.719
(1.00) 		0.965
(1.00) 		0.565
(1.00) 		0.187
(1.00) 		0.324
(1.00) 		0.454
(1.00) 		0.652
(1.00) 		0.777
(1.00) 		0.594
(1.00) 		0.704
(1.00)
2q loss 33 (13%) 227 0.261
(1.00) 		0.612
(1.00) 		0.853
(1.00) 		0.641
(1.00) 		0.879
(1.00) 		0.365
(1.00) 		0.329
(1.00) 		0.221
(1.00) 		0.652
(1.00) 		0.391
(1.00) 		0.929
(1.00) 		0.704
(1.00)
3p loss 38 (15%) 222 0.55
(1.00) 		0.432
(1.00) 		0.27
(1.00) 		0.855
(1.00) 		0.446
(1.00) 		0.226
(1.00) 		0.323
(1.00) 		0.829
(1.00) 		0.818
(1.00) 		0.788
(1.00) 		0.135
(1.00) 		0.72
(1.00)
3q loss 31 (12%) 229 0.76
(1.00) 		0.308
(1.00) 		0.619
(1.00) 		0.766
(1.00) 		0.525
(1.00) 		0.182
(1.00) 		0.241
(1.00) 		0.843
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.217
(1.00) 		0.7
(1.00)
4p loss 53 (20%) 207 0.702
(1.00) 		0.752
(1.00) 		0.371
(1.00) 		0.322
(1.00) 		0.578
(1.00) 		0.755
(1.00) 		0.824
(1.00) 		0.411
(1.00) 		0.443
(1.00) 		0.64
(1.00) 		0.0293
(1.00) 		0.114
(1.00)
4q loss 55 (21%) 205 0.683
(1.00) 		0.902
(1.00) 		0.168
(1.00) 		0.417
(1.00) 		0.5
(1.00) 		0.335
(1.00) 		0.488
(1.00) 		0.0592
(1.00) 		0.172
(1.00) 		0.488
(1.00) 		0.0148
(1.00) 		0.0437
(1.00)
5p loss 60 (23%) 200 0.968
(1.00) 		0.943
(1.00) 		0.502
(1.00) 		0.813
(1.00) 		0.655
(1.00) 		0.384
(1.00) 		0.234
(1.00) 		0.387
(1.00) 		0.192
(1.00) 		0.179
(1.00) 		0.422
(1.00) 		0.452
(1.00)
5q loss 76 (29%) 184 0.556
(1.00) 		0.967
(1.00) 		0.461
(1.00) 		0.85
(1.00) 		0.967
(1.00) 		0.254
(1.00) 		0.762
(1.00) 		0.606
(1.00) 		0.479
(1.00) 		0.528
(1.00) 		0.495
(1.00) 		0.678
(1.00)
6p loss 48 (18%) 212 0.294
(1.00) 		0.341
(1.00) 		0.863
(1.00) 		0.47
(1.00) 		0.679
(1.00) 		0.21
(1.00) 		0.58
(1.00) 		0.744
(1.00) 		0.536
(1.00) 		1
(1.00) 		0.269
(1.00) 		0.417
(1.00)
6q loss 127 (49%) 133 0.351
(1.00) 		0.741
(1.00) 		0.124
(1.00) 		0.548
(1.00) 		0.973
(1.00) 		0.222
(1.00) 		0.727
(1.00) 		0.88
(1.00) 		0.631
(1.00) 		0.849
(1.00) 		0.156
(1.00) 		0.526
(1.00)
7p loss 14 (5%) 246 0.952
(1.00) 		0.736
(1.00) 		0.133
(1.00) 		0.563
(1.00) 		0.199
(1.00) 		0.000517
(0.489) 		0.377
(1.00) 		0.935
(1.00) 		1
(1.00) 		1
(1.00) 		0.393
(1.00) 		0.576
(1.00)
7q loss 13 (5%) 247 0.685
(1.00) 		0.801
(1.00) 		0.824
(1.00) 		0.425
(1.00) 		0.313
(1.00) 		0.104
(1.00) 		0.567
(1.00) 		0.943
(1.00) 		1
(1.00) 		1
(1.00) 		0.986
(1.00) 		0.772
(1.00)
8p loss 45 (17%) 215 0.62
(1.00) 		0.382
(1.00) 		0.161
(1.00) 		0.0724
(1.00) 		0.403
(1.00) 		0.164
(1.00) 		1
(1.00) 		0.415
(1.00) 		0.0348
(1.00) 		1
(1.00) 		0.0712
(1.00) 		0.618
(1.00)
8q loss 18 (7%) 242 0.289
(1.00) 		0.279
(1.00) 		0.384
(1.00) 		0.184
(1.00) 		0.856
(1.00) 		0.221
(1.00) 		0.576
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.614
(1.00) 		0.624
(1.00)
9p loss 171 (66%) 89 0.333
(1.00) 		0.769
(1.00) 		0.543
(1.00) 		0.262
(1.00) 		0.727
(1.00) 		0.638
(1.00) 		0.688
(1.00) 		0.707
(1.00) 		0.315
(1.00) 		1
(1.00) 		0.98
(1.00) 		0.0453
(1.00)
9q loss 133 (51%) 127 0.829
(1.00) 		0.366
(1.00) 		0.299
(1.00) 		0.143
(1.00) 		0.497
(1.00) 		0.948
(1.00) 		0.434
(1.00) 		0.477
(1.00) 		0.873
(1.00) 		0.449
(1.00) 		0.898
(1.00) 		0.203
(1.00)
10p loss 143 (55%) 117 0.44
(1.00) 		0.976
(1.00) 		0.0121
(1.00) 		0.214
(1.00) 		0.8
(1.00) 		0.0629
(1.00) 		0.523
(1.00) 		0.596
(1.00) 		0.518
(1.00) 		1
(1.00) 		0.654
(1.00) 		0.0405
(1.00)
11p loss 90 (35%) 170 0.619
(1.00) 		0.292
(1.00) 		0.0504
(1.00) 		0.562
(1.00) 		0.386
(1.00) 		0.738
(1.00) 		0.187
(1.00) 		0.173
(1.00) 		0.184
(1.00) 		0.843
(1.00) 		0.487
(1.00) 		0.0108
(1.00)
11q loss 101 (39%) 159 0.942
(1.00) 		0.386
(1.00) 		0.335
(1.00) 		0.923
(1.00) 		0.226
(1.00) 		0.831
(1.00) 		0.184
(1.00) 		0.633
(1.00) 		0.0233
(1.00) 		1
(1.00) 		0.818
(1.00) 		0.00108
(1.00)
12p loss 35 (13%) 225 0.966
(1.00) 		0.589
(1.00) 		0.733
(1.00) 		0.44
(1.00) 		0.967
(1.00) 		0.992
(1.00) 		0.975
(1.00) 		0.0411
(1.00) 		0.64
(1.00) 		0.276
(1.00) 		0.133
(1.00) 		0.263
(1.00)
12q loss 42 (16%) 218 0.637
(1.00) 		0.995
(1.00) 		0.669
(1.00) 		0.482
(1.00) 		0.9
(1.00) 		0.868
(1.00) 		0.783
(1.00) 		0.31
(1.00) 		1
(1.00) 		1
(1.00) 		0.0904
(1.00) 		0.228
(1.00)
13q loss 58 (22%) 202 0.373
(1.00) 		0.222
(1.00) 		0.265
(1.00) 		0.463
(1.00) 		0.698
(1.00) 		0.205
(1.00) 		0.484
(1.00) 		0.0134
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.0452
(1.00) 		0.359
(1.00)
14q loss 81 (31%) 179 0.927
(1.00) 		0.899
(1.00) 		0.212
(1.00) 		0.357
(1.00) 		0.25
(1.00) 		0.427
(1.00) 		0.402
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.68
(1.00) 		0.281
(1.00) 		0.34
(1.00)
15q loss 35 (13%) 225 0.523
(1.00) 		0.589
(1.00) 		0.663
(1.00) 		0.54
(1.00) 		0.184
(1.00) 		0.0457
(1.00) 		0.637
(1.00) 		0.408
(1.00) 		0.368
(1.00) 		0.779
(1.00) 		0.134
(1.00) 		0.855
(1.00)
16p loss 52 (20%) 208 0.974
(1.00) 		0.443
(1.00) 		0.0891
(1.00) 		0.472
(1.00) 		0.873
(1.00) 		0.514
(1.00) 		0.773
(1.00) 		0.512
(1.00) 		0.846
(1.00) 		0.348
(1.00) 		0.908
(1.00) 		0.0384
(1.00)
16q loss 76 (29%) 184 0.416
(1.00) 		0.228
(1.00) 		0.193
(1.00) 		0.417
(1.00) 		0.248
(1.00) 		0.237
(1.00) 		0.635
(1.00) 		0.813
(1.00) 		1
(1.00) 		0.528
(1.00) 		0.477
(1.00) 		0.0928
(1.00)
17p loss 92 (35%) 168 0.295
(1.00) 		0.238
(1.00) 		0.141
(1.00) 		0.134
(1.00) 		0.729
(1.00) 		0.868
(1.00) 		0.996
(1.00) 		0.601
(1.00) 		0.41
(1.00) 		0.842
(1.00) 		0.343
(1.00) 		0.144
(1.00)
17q loss 43 (17%) 217 0.466
(1.00) 		0.123
(1.00) 		0.694
(1.00) 		0.642
(1.00) 		0.179
(1.00) 		0.851
(1.00) 		0.6
(1.00) 		0.0967
(1.00) 		0.406
(1.00) 		1
(1.00) 		0.0366
(1.00) 		0.611
(1.00)
18p loss 76 (29%) 184 0.0892
(1.00) 		0.118
(1.00) 		0.509
(1.00) 		0.85
(1.00) 		0.154
(1.00) 		0.588
(1.00) 		0.687
(1.00) 		0.215
(1.00) 		0.585
(1.00) 		0.139
(1.00) 		0.727
(1.00) 		1
(1.00)
18q loss 70 (27%) 190 0.201
(1.00) 		0.0695
(1.00) 		0.582
(1.00) 		0.731
(1.00) 		0.195
(1.00) 		0.561
(1.00) 		0.323
(1.00) 		0.311
(1.00) 		0.853
(1.00) 		0.132
(1.00) 		0.523
(1.00) 		0.568
(1.00)
19p loss 54 (21%) 206 0.773
(1.00) 		0.531
(1.00) 		0.561
(1.00) 		0.666
(1.00) 		0.329
(1.00) 		0.197
(1.00) 		0.4
(1.00) 		0.093
(1.00) 		0.418
(1.00) 		0.481
(1.00) 		0.239
(1.00) 		0.0621
(1.00)
19q loss 51 (20%) 209 0.701
(1.00) 		0.878
(1.00) 		0.41
(1.00) 		0.676
(1.00) 		0.696
(1.00) 		0.209
(1.00) 		0.748
(1.00) 		0.0611
(1.00) 		0.837
(1.00) 		0.634
(1.00) 		0.408
(1.00) 		0.0551
(1.00)
20p loss 14 (5%) 246 0.991
(1.00) 		0.753
(1.00) 		0.268
(1.00) 		0.2
(1.00) 		0.984
(1.00) 		1
(1.00) 		0.274
(1.00) 		0.0921
(1.00) 		0.32
(1.00) 		0.225
(1.00) 		0.734
(1.00) 		1
(1.00)
20q loss 4 (2%) 256 0.773
(1.00) 		0.71
(1.00) 		0.936
(1.00) 		0.171
(1.00) 		0.551
(1.00) 		0.747
(1.00) 		0.196
(1.00) 		0.994
(1.00) 		1
(1.00) 		0.4
(1.00) 		0.717
(1.00) 		0.16
(1.00)
21q loss 52 (20%) 208 0.844
(1.00) 		0.454
(1.00) 		0.144
(1.00) 		0.601
(1.00) 		0.441
(1.00) 		0.634
(1.00) 		0.406
(1.00) 		0.42
(1.00) 		0.698
(1.00) 		0.155
(1.00) 		0.338
(1.00) 		0.427
(1.00)
22q loss 27 (10%) 233 0.297
(1.00) 		0.331
(1.00) 		0.408
(1.00) 		0.687
(1.00) 		0.0717
(1.00) 		0.214
(1.00) 		0.21
(1.00) 		0.317
(1.00) 		0.105
(1.00) 		1
(1.00) 		0.122
(1.00) 		0.837
(1.00)
xq loss 67 (26%) 193 0.592
(1.00) 		0.997
(1.00) 		0.501
(1.00) 		0.247
(1.00) 		0.147
(1.00) 		0.637
(1.00) 		0.121
(1.00) 		0.00373
(1.00) 		0.281
(1.00) 		0.513
(1.00) 		0.508
(1.00) 		0.0286
(1.00)
'5q gain' versus 'BRESLOW.THICKNESS'

P value = 0.000181 (t-test), Q value = 0.17

Table S1.  Gene #10: '5q gain' versus Clinical Feature #11: 'BRESLOW.THICKNESS'

nPatients Mean (Std.Dev)
ALL 192 3.6 (5.1)
5Q GAIN MUTATED 21 1.8 (1.5)
5Q GAIN WILD-TYPE 171 3.8 (5.3)

Figure S1.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #11: 'BRESLOW.THICKNESS'

'10q loss' versus 'AGE'

P value = 8.81e-05 (t-test), Q value = 0.083

Table S2.  Gene #59: '10q loss' versus Clinical Feature #3: 'AGE'

nPatients Mean (Std.Dev)
ALL 256 55.6 (15.8)
10Q LOSS MUTATED 153 52.5 (16.3)
10Q LOSS WILD-TYPE 103 60.1 (13.8)

Figure S2.  Get High-res Image Gene #59: '10q loss' versus Clinical Feature #3: 'AGE'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = SKCM-TM.merged_data.txt

  • Number of patients = 260

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 12

  • Exclude regions 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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