Correlation between copy number variations of arm-level result and selected clinical features
Skin Cutaneous Melanoma (Metastatic)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1348JG9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1348JG9
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 82 arm-level events and 14 clinical features across 358 patients, 2 significant findings detected with Q value < 0.25.

  • 17q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 10q loss cnv correlated to 'YEARS_TO_BIRTH'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 14 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 		YEARS
TO
BIRTH 		PRIMARY
SITE
OF
DISEASE 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		MELANOMA
ULCERATION 		MELANOMA
PRIMARY
KNOWN 		BRESLOW
THICKNESS 		GENDER RACE ETHNICITY
nCNV (%) nWild-Type logrank test logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
17q gain 65 (18%) 293 0.337
(0.982) 		0.552
(0.984) 		0.000119
(0.129) 		0.222
(0.982) 		0.714
(0.998) 		0.93
(1.00) 		0.2
(0.982) 		1
(1.00) 		0.163
(0.982) 		0.407
(0.982) 		0.243
(0.982) 		0.674
(0.989) 		0.218
(0.982) 		1
(1.00)
10q loss 219 (61%) 139 0.446
(0.982) 		0.488
(0.982) 		0.000225
(0.129) 		0.0986
(0.982) 		0.418
(0.982) 		0.0511
(0.939) 		0.18
(0.982) 		0.363
(0.982) 		1
(1.00) 		1
(1.00) 		0.205
(0.982) 		0.0733
(0.939) 		0.0352
(0.939) 		1
(1.00)
1p gain 85 (24%) 273 0.516
(0.982) 		0.794
(1.00) 		0.197
(0.982) 		0.147
(0.982) 		0.072
(0.939) 		0.671
(0.989) 		0.411
(0.982) 		0.428
(0.982) 		0.434
(0.982) 		0.707
(0.995) 		0.294
(0.982) 		0.446
(0.982) 		1
(1.00) 		0.664
(0.989)
1q gain 169 (47%) 189 0.975
(1.00) 		0.732
(1.00) 		0.371
(0.982) 		0.0394
(0.939) 		0.129
(0.982) 		0.531
(0.982) 		0.459
(0.982) 		0.259
(0.982) 		0.338
(0.982) 		0.423
(0.982) 		0.96
(1.00) 		0.586
(0.989) 		1
(1.00) 		0.26
(0.982)
2p gain 66 (18%) 292 0.586
(0.989) 		0.521
(0.982) 		0.817
(1.00) 		0.549
(0.984) 		0.876
(1.00) 		0.488
(0.982) 		0.996
(1.00) 		0.39
(0.982) 		0.586
(0.989) 		1
(1.00) 		0.199
(0.982) 		0.888
(1.00) 		0.664
(0.989) 		0.358
(0.982)
2q gain 64 (18%) 294 0.238
(0.982) 		0.319
(0.982) 		0.648
(0.989) 		0.59
(0.989) 		0.695
(0.995) 		0.176
(0.982) 		0.972
(1.00) 		0.143
(0.982) 		0.854
(1.00) 		0.675
(0.989) 		0.0708
(0.939) 		0.67
(0.989) 		0.663
(0.989) 		0.612
(0.989)
3p gain 62 (17%) 296 0.00368
(0.522) 		0.036
(0.939) 		0.684
(0.989) 		0.391
(0.982) 		0.0779
(0.939) 		0.503
(0.982) 		0.161
(0.982) 		0.143
(0.982) 		0.719
(0.998) 		0.394
(0.982) 		0.557
(0.984) 		0.315
(0.982) 		0.663
(0.989) 		0.607
(0.989)
3q gain 71 (20%) 287 0.0133
(0.668) 		0.0179
(0.791) 		0.328
(0.982) 		0.343
(0.982) 		0.11
(0.982) 		0.232
(0.982) 		0.0994
(0.982) 		0.09
(0.967) 		0.491
(0.982) 		0.843
(1.00) 		0.0934
(0.982) 		0.585
(0.989) 		0.669
(0.989) 		0.354
(0.982)
4p gain 55 (15%) 303 0.741
(1.00) 		0.45
(0.982) 		0.204
(0.982) 		0.639
(0.989) 		0.149
(0.982) 		0.136
(0.982) 		0.68
(0.989) 		0.221
(0.982) 		1
(1.00) 		1
(1.00) 		0.944
(1.00) 		1
(1.00) 		0.63
(0.989) 		1
(1.00)
4q gain 47 (13%) 311 1
(1.00) 		0.436
(0.982) 		0.335
(0.982) 		0.691
(0.994) 		0.275
(0.982) 		0.237
(0.982) 		0.863
(1.00) 		0.332
(0.982) 		1
(1.00) 		0.816
(1.00) 		0.543
(0.984) 		1
(1.00) 		0.574
(0.989) 		1
(1.00)
5p gain 75 (21%) 283 0.082
(0.939) 		0.256
(0.982) 		0.504
(0.982) 		0.0116
(0.665) 		0.575
(0.989) 		0.437
(0.982) 		0.0705
(0.939) 		0.416
(0.982) 		0.0835
(0.939) 		0.553
(0.984) 		0.156
(0.982) 		1
(1.00) 		1
(1.00) 		0.641
(0.989)
5q gain 50 (14%) 308 0.535
(0.982) 		0.697
(0.995) 		0.505
(0.982) 		0.0806
(0.939) 		0.953
(1.00) 		0.449
(0.982) 		0.465
(0.982) 		0.514
(0.982) 		0.694
(0.995) 		0.647
(0.989) 		0.174
(0.982) 		0.638
(0.989) 		0.583
(0.989) 		0.0596
(0.939)
6p gain 140 (39%) 218 0.394
(0.982) 		0.273
(0.982) 		0.405
(0.982) 		0.683
(0.989) 		0.138
(0.982) 		0.075
(0.939) 		0.336
(0.982) 		0.817
(1.00) 		1
(1.00) 		0.622
(0.989) 		0.779
(1.00) 		0.372
(0.982) 		0.787
(1.00) 		0.707
(0.995)
6q gain 48 (13%) 310 0.151
(0.982) 		0.153
(0.982) 		0.885
(1.00) 		0.416
(0.982) 		0.0992
(0.982) 		0.0458
(0.939) 		0.0103
(0.632) 		0.742
(1.00) 		0.251
(0.982) 		0.637
(0.989) 		0.831
(1.00) 		0.752
(1.00) 		1
(1.00) 		0.6
(0.989)
7p gain 197 (55%) 161 0.242
(0.982) 		0.726
(1.00) 		0.984
(1.00) 		0.547
(0.984) 		0.0339
(0.939) 		0.497
(0.982) 		0.227
(0.982) 		0.652
(0.989) 		0.411
(0.982) 		0.258
(0.982) 		0.999
(1.00) 		0.229
(0.982) 		0.274
(0.982) 		0.463
(0.982)
7q gain 194 (54%) 164 0.134
(0.982) 		0.453
(0.982) 		0.321
(0.982) 		0.579
(0.989) 		0.0565
(0.939) 		0.751
(1.00) 		0.602
(0.989) 		0.825
(1.00) 		0.337
(0.982) 		0.335
(0.982) 		0.777
(1.00) 		0.0628
(0.939) 		0.821
(1.00) 		0.458
(0.982)
8p gain 118 (33%) 240 0.612
(0.989) 		0.985
(1.00) 		0.327
(0.982) 		0.114
(0.982) 		0.376
(0.982) 		0.862
(1.00) 		0.206
(0.982) 		0.812
(1.00) 		0.307
(0.982) 		0.612
(0.989) 		0.249
(0.982) 		0.487
(0.982) 		0.0407
(0.939) 		1
(1.00)
8q gain 165 (46%) 193 0.189
(0.982) 		0.353
(0.982) 		0.0443
(0.939) 		0.0692
(0.939) 		0.274
(0.982) 		0.204
(0.982) 		0.331
(0.982) 		0.823
(1.00) 		0.89
(1.00) 		0.0765
(0.939) 		0.08
(0.939) 		0.827
(1.00) 		0.184
(0.982) 		1
(1.00)
9p gain 16 (4%) 342 0.586
(0.989) 		0.404
(0.982) 		0.86
(1.00) 		0.329
(0.982) 		0.265
(0.982) 		0.471
(0.982) 		0.705
(0.995) 		1
(1.00) 		0.57
(0.989) 		0.237
(0.982) 		0.264
(0.982) 		1
(1.00) 		1
(1.00) 		1
(1.00)
9q gain 21 (6%) 337 0.86
(1.00) 		0.945
(1.00) 		0.424
(0.982) 		0.217
(0.982) 		0.417
(0.982) 		0.389
(0.982) 		0.534
(0.982) 		1
(1.00) 		0.414
(0.982) 		0.0902
(0.967) 		0.0538
(0.939) 		0.647
(0.989) 		0.0898
(0.967) 		1
(1.00)
10p gain 12 (3%) 346 0.289
(0.982) 		0.532
(0.982) 		0.337
(0.982) 		0.215
(0.982) 		0.94
(1.00) 		0.663
(0.989) 		0.283
(0.982) 		0.147
(0.982) 		1
(1.00) 		0.00931
(0.632) 		0.684
(0.989) 		0.546
(0.984) 		1
(1.00) 		1
(1.00)
10q gain 3 (1%) 355 0.757
(1.00) 		0.634
(0.989) 		0.705
(0.995) 		1
(1.00) 		0.688
(0.993) 		0.0493
(0.939) 		1
(1.00) 		0.4
(0.982) 		0.327
(0.982) 		1
(1.00) 		1
(1.00) 		1
(1.00)
11p gain 35 (10%) 323 0.141
(0.982) 		0.507
(0.982) 		0.83
(1.00) 		0.302
(0.982) 		0.0502
(0.939) 		0.611
(0.989) 		0.616
(0.989) 		0.242
(0.982) 		1
(1.00) 		0.164
(0.982) 		0.71
(0.995) 		1
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 29 (8%) 329 0.0613
(0.939) 		0.254
(0.982) 		0.454
(0.982) 		0.131
(0.982) 		0.0504
(0.939) 		0.427
(0.982) 		0.796
(1.00) 		0.237
(0.982) 		0.414
(0.982) 		0.0637
(0.939) 		0.131
(0.982) 		0.842
(1.00) 		1
(1.00) 		1
(1.00)
12p gain 62 (17%) 296 0.256
(0.982) 		0.265
(0.982) 		0.488
(0.982) 		0.299
(0.982) 		0.00473
(0.522) 		0.373
(0.982) 		0.00427
(0.522) 		0.552
(0.984) 		0.374
(0.982) 		0.529
(0.982) 		0.249
(0.982) 		0.774
(1.00) 		0.0645
(0.939) 		0.35
(0.982)
12q gain 36 (10%) 322 0.407
(0.982) 		0.48
(0.982) 		0.399
(0.982) 		0.602
(0.989) 		0.212
(0.982) 		0.513
(0.982) 		0.0103
(0.632) 		0.707
(0.995) 		0.658
(0.989) 		0.284
(0.982) 		0.156
(0.982) 		0.21
(0.982) 		0.172
(0.982) 		0.524
(0.982)
13q gain 93 (26%) 265 0.0282
(0.939) 		0.166
(0.982) 		0.879
(1.00) 		0.242
(0.982) 		0.117
(0.982) 		0.0352
(0.939) 		0.147
(0.982) 		0.305
(0.982) 		0.337
(0.982) 		0.855
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.708
(0.995) 		0.684
(0.989)
14q gain 41 (11%) 317 0.706
(0.995) 		0.759
(1.00) 		0.103
(0.982) 		0.57
(0.989) 		0.811
(1.00) 		0.618
(0.989) 		0.187
(0.982) 		0.147
(0.982) 		0.537
(0.982) 		1
(1.00) 		0.749
(1.00) 		0.733
(1.00) 		1
(1.00) 		1
(1.00)
15q gain 84 (23%) 274 0.388
(0.982) 		0.493
(0.982) 		0.304
(0.982) 		0.552
(0.984) 		0.523
(0.982) 		0.708
(0.995) 		0.799
(1.00) 		0.428
(0.982) 		0.609
(0.989) 		0.34
(0.982) 		0.408
(0.982) 		0.701
(0.995) 		1
(1.00) 		1
(1.00)
16p gain 55 (15%) 303 0.787
(1.00) 		0.792
(1.00) 		0.585
(0.989) 		0.367
(0.982) 		0.0697
(0.939) 		0.033
(0.939) 		0.0646
(0.939) 		0.22
(0.982) 		0.837
(1.00) 		0.51
(0.982) 		0.00188
(0.471) 		0.546
(0.984) 		0.635
(0.989) 		1
(1.00)
16q gain 43 (12%) 315 0.369
(0.982) 		0.86
(1.00) 		0.798
(1.00) 		0.282
(0.982) 		0.175
(0.982) 		0.0163
(0.758) 		0.152
(0.982) 		0.491
(0.982) 		0.823
(1.00) 		0.328
(0.982) 		0.00532
(0.522) 		0.241
(0.982) 		0.538
(0.982) 		0.575
(0.989)
17p gain 37 (10%) 321 0.384
(0.982) 		0.437
(0.982) 		0.154
(0.982) 		0.202
(0.982) 		0.962
(1.00) 		0.668
(0.989) 		0.262
(0.982) 		1
(1.00) 		0.362
(0.982) 		0.793
(1.00) 		0.467
(0.982) 		0.478
(0.982) 		0.487
(0.982) 		0.534
(0.982)
18p gain 53 (15%) 305 0.354
(0.982) 		0.648
(0.989) 		0.106
(0.982) 		0.36
(0.982) 		0.0132
(0.668) 		0.00932
(0.632) 		0.485
(0.982) 		1
(1.00) 		0.327
(0.982) 		0.651
(0.989) 		0.117
(0.982) 		0.223
(0.982) 		0.624
(0.989) 		1
(1.00)
18q gain 44 (12%) 314 0.0836
(0.939) 		0.165
(0.982) 		0.548
(0.984) 		0.721
(0.999) 		0.00564
(0.522) 		0.00223
(0.471) 		0.499
(0.982) 		1
(1.00) 		0.201
(0.982) 		1
(1.00) 		0.278
(0.982) 		0.319
(0.982) 		1
(1.00) 		0.594
(0.989)
19p gain 55 (15%) 303 0.983
(1.00) 		0.83
(1.00) 		0.638
(0.989) 		0.332
(0.982) 		0.601
(0.989) 		0.85
(1.00) 		0.774
(1.00) 		1
(1.00) 		1
(1.00) 		0.371
(0.982) 		1
(1.00) 		0.365
(0.982) 		0.621
(0.989) 		1
(1.00)
19q gain 55 (15%) 303 0.792
(1.00) 		0.822
(1.00) 		0.149
(0.982) 		0.314
(0.982) 		0.613
(0.989) 		0.464
(0.982) 		0.327
(0.982) 		1
(1.00) 		0.336
(0.982) 		0.371
(0.982) 		0.163
(0.982) 		0.365
(0.982) 		0.615
(0.989) 		1
(1.00)
20p gain 145 (41%) 213 0.224
(0.982) 		0.641
(0.989) 		0.303
(0.982) 		0.334
(0.982) 		0.111
(0.982) 		0.0402
(0.939) 		0.615
(0.989) 		0.113
(0.982) 		0.21
(0.982) 		0.414
(0.982) 		0.0375
(0.939) 		0.824
(1.00) 		1
(1.00) 		0.706
(0.995)
20q gain 177 (49%) 181 0.129
(0.982) 		0.59
(0.989) 		0.272
(0.982) 		0.438
(0.982) 		0.0208
(0.852) 		0.0296
(0.939) 		0.791
(1.00) 		0.175
(0.982) 		0.335
(0.982) 		0.748
(1.00) 		0.0793
(0.939) 		0.913
(1.00) 		1
(1.00) 		1
(1.00)
21q gain 67 (19%) 291 0.262
(0.982) 		0.15
(0.982) 		0.563
(0.989) 		0.592
(0.989) 		0.0287
(0.939) 		0.467
(0.982) 		0.465
(0.982) 		0.389
(0.982) 		0.056
(0.939) 		1
(1.00) 		0.641
(0.989) 		0.889
(1.00) 		1
(1.00) 		1
(1.00)
22q gain 124 (35%) 234 0.572
(0.989) 		0.794
(1.00) 		0.469
(0.982) 		0.0423
(0.939) 		0.493
(0.982) 		0.41
(0.982) 		0.046
(0.939) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.591
(0.989) 		0.36
(0.982) 		0.572
(0.989) 		0.429
(0.982)
xp gain 39 (11%) 319 0.389
(0.982) 		0.0596
(0.939) 		0.523
(0.982) 		0.0382
(0.939) 		0.254
(0.982) 		0.891
(1.00) 		0.307
(0.982) 		0.146
(0.982) 		0.67
(0.989) 		1
(1.00) 		0.953
(1.00) 		0.223
(0.982) 		0.512
(0.982) 		1
(1.00)
xq gain 41 (11%) 317 0.00287
(0.471) 		0.00123
(0.469) 		0.298
(0.982) 		0.144
(0.982) 		0.46
(0.982) 		0.824
(1.00) 		0.347
(0.982) 		0.489
(0.982) 		0.677
(0.989) 		1
(1.00) 		0.928
(1.00) 		1
(1.00) 		0.529
(0.982) 		1
(1.00)
1p loss 52 (15%) 306 0.604
(0.989) 		0.204
(0.982) 		0.14
(0.982) 		0.778
(1.00) 		0.165
(0.982) 		0.317
(0.982) 		0.0836
(0.939) 		0.75
(1.00) 		0.437
(0.982) 		0.363
(0.982) 		0.815
(1.00) 		0.536
(0.982) 		0.606
(0.989) 		1
(1.00)
1q loss 27 (8%) 331 0.894
(1.00) 		0.851
(1.00) 		0.746
(1.00) 		0.736
(1.00) 		0.856
(1.00) 		0.951
(1.00) 		0.182
(0.982) 		1
(1.00) 		0.61
(0.989) 		1
(1.00) 		0.661
(0.989) 		1
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 50 (14%) 308 0.677
(0.989) 		0.232
(0.982) 		0.654
(0.989) 		0.373
(0.982) 		0.889
(1.00) 		0.362
(0.982) 		0.36
(0.982) 		0.747
(1.00) 		0.852
(1.00) 		0.169
(0.982) 		0.0766
(0.939) 		0.754
(1.00) 		1
(1.00) 		0.246
(0.982)
2q loss 51 (14%) 307 0.221
(0.982) 		0.551
(0.984) 		0.859
(1.00) 		0.0604
(0.939) 		0.925
(1.00) 		0.536
(0.982) 		0.438
(0.982) 		0.509
(0.982) 		0.852
(1.00) 		0.0627
(0.939) 		0.37
(0.982) 		0.876
(1.00) 		1
(1.00) 		0.254
(0.982)
3p loss 60 (17%) 298 0.684
(0.989) 		0.333
(0.982) 		0.446
(0.982) 		0.363
(0.982) 		0.15
(0.982) 		0.838
(1.00) 		0.191
(0.982) 		0.548
(0.984) 		1
(1.00) 		1
(1.00) 		0.645
(0.989) 		0.243
(0.982) 		1
(1.00) 		1
(1.00)
3q loss 51 (14%) 307 0.783
(1.00) 		0.808
(1.00) 		0.936
(1.00) 		0.343
(0.982) 		0.226
(0.982) 		0.539
(0.982) 		0.535
(0.982) 		0.331
(0.982) 		0.842
(1.00) 		0.652
(0.989) 		0.441
(0.982) 		0.436
(0.982) 		0.605
(0.989) 		1
(1.00)
4p loss 78 (22%) 280 0.502
(0.982) 		0.666
(0.989) 		0.621
(0.989) 		0.167
(0.982) 		0.412
(0.982) 		0.534
(0.982) 		0.311
(0.982) 		1
(1.00) 		0.624
(0.989) 		0.847
(1.00) 		0.782
(1.00) 		0.511
(0.982) 		0.45
(0.982) 		1
(1.00)
4q loss 82 (23%) 276 0.266
(0.982) 		0.418
(0.982) 		0.588
(0.989) 		0.646
(0.989) 		0.163
(0.982) 		0.42
(0.982) 		0.151
(0.982) 		0.793
(1.00) 		0.413
(0.982) 		0.258
(0.982) 		0.746
(1.00) 		0.438
(0.982) 		0.132
(0.982) 		1
(1.00)
5p loss 78 (22%) 280 0.489
(0.982) 		0.843
(1.00) 		0.923
(1.00) 		0.59
(0.989) 		0.427
(0.982) 		0.868
(1.00) 		0.0643
(0.939) 		0.0105
(0.632) 		0.244
(0.982) 		0.178
(0.982) 		0.56
(0.989) 		0.511
(0.982) 		0.119
(0.982) 		0.352
(0.982)
5q loss 98 (27%) 260 0.788
(1.00) 		0.718
(0.998) 		0.392
(0.982) 		0.674
(0.989) 		0.869
(1.00) 		0.852
(1.00) 		0.348
(0.982) 		0.458
(0.982) 		0.64
(0.989) 		0.154
(0.982) 		0.744
(1.00) 		0.808
(1.00) 		0.264
(0.982) 		0.197
(0.982)
6p loss 66 (18%) 292 0.384
(0.982) 		0.167
(0.982) 		0.815
(1.00) 		0.0942
(0.982) 		0.319
(0.982) 		0.807
(1.00) 		0.717
(0.998) 		0.776
(1.00) 		0.22
(0.982) 		0.682
(0.989) 		0.258
(0.982) 		0.483
(0.982) 		1
(1.00) 		1
(1.00)
6q loss 167 (47%) 191 0.47
(0.982) 		0.912
(1.00) 		0.212
(0.982) 		0.369
(0.982) 		0.932
(1.00) 		0.569
(0.989) 		0.478
(0.982) 		0.5
(0.982) 		0.0986
(0.982) 		0.873
(1.00) 		0.181
(0.982) 		0.277
(0.982) 		0.275
(0.982) 		1
(1.00)
7p loss 18 (5%) 340 0.99
(1.00) 		0.381
(0.982) 		0.297
(0.982) 		0.653
(0.989) 		0.19
(0.982) 		0.0134
(0.668) 		0.541
(0.983) 		0.616
(0.989) 		1
(1.00) 		1
(1.00) 		0.196
(0.982) 		0.46
(0.982) 		0.272
(0.982) 		1
(1.00)
7q loss 17 (5%) 341 0.715
(0.998) 		0.365
(0.982) 		0.766
(1.00) 		0.538
(0.982) 		0.131
(0.982) 		0.126
(0.982) 		0.303
(0.982) 		0.611
(0.989) 		1
(1.00) 		0.706
(0.995) 		0.669
(0.989) 		1
(1.00) 		0.258
(0.982) 		1
(1.00)
8p loss 67 (19%) 291 0.665
(0.989) 		0.872
(1.00) 		0.496
(0.982) 		0.121
(0.982) 		0.44
(0.982) 		0.463
(0.982) 		0.427
(0.982) 		1
(1.00) 		0.211
(0.982) 		1
(1.00) 		0.189
(0.982) 		0.578
(0.989) 		1
(1.00) 		1
(1.00)
8q loss 27 (8%) 331 0.655
(0.989) 		0.613
(0.989) 		0.524
(0.982) 		0.239
(0.982) 		0.616
(0.989) 		0.0992
(0.982) 		0.471
(0.982) 		1
(1.00) 		1
(1.00) 		0.226
(0.982) 		0.876
(1.00) 		1
(1.00) 		1
(1.00) 		0.419
(0.982)
9p loss 232 (65%) 126 0.283
(0.982) 		0.425
(0.982) 		0.514
(0.982) 		0.129
(0.982) 		0.834
(1.00) 		0.857
(1.00) 		0.862
(1.00) 		0.639
(0.989) 		0.669
(0.989) 		0.405
(0.982) 		0.693
(0.995) 		0.00882
(0.632) 		1
(1.00) 		0.102
(0.982)
9q loss 183 (51%) 175 0.688
(0.993) 		0.795
(1.00) 		0.43
(0.982) 		0.189
(0.982) 		0.31
(0.982) 		0.978
(1.00) 		0.456
(0.982) 		0.369
(0.982) 		0.68
(0.989) 		0.873
(1.00) 		0.966
(1.00) 		0.038
(0.939) 		0.525
(0.982) 		0.719
(0.998)
10p loss 199 (56%) 159 0.601
(0.989) 		0.827
(1.00) 		0.0323
(0.939) 		0.203
(0.982) 		0.519
(0.982) 		0.00591
(0.522) 		0.64
(0.989) 		0.498
(0.982) 		0.581
(0.989) 		0.517
(0.982) 		0.463
(0.982) 		0.0369
(0.939) 		0.117
(0.982) 		1
(1.00)
11p loss 124 (35%) 234 0.221
(0.982) 		0.195
(0.982) 		0.0165
(0.758) 		0.356
(0.982) 		0.0591
(0.939) 		0.357
(0.982) 		0.208
(0.982) 		0.238
(0.982) 		0.156
(0.982) 		0.501
(0.982) 		0.138
(0.982) 		0.022
(0.87) 		0.338
(0.982) 		1
(1.00)
11q loss 146 (41%) 212 0.519
(0.982) 		0.721
(0.999) 		0.676
(0.989) 		0.731
(1.00) 		0.116
(0.982) 		0.523
(0.982) 		0.145
(0.982) 		0.499
(0.982) 		0.128
(0.982) 		0.624
(0.989) 		0.151
(0.982) 		0.00267
(0.471) 		0.639
(0.989) 		1
(1.00)
12p loss 58 (16%) 300 0.164
(0.982) 		0.164
(0.982) 		0.565
(0.989) 		0.0818
(0.939) 		0.842
(1.00) 		0.538
(0.982) 		0.946
(1.00) 		0.114
(0.982) 		0.58
(0.989) 		0.51
(0.982) 		0.328
(0.982) 		0.377
(0.982) 		1
(1.00) 		0.603
(0.989)
12q loss 66 (18%) 292 0.45
(0.982) 		0.342
(0.982) 		0.764
(1.00) 		0.0853
(0.942) 		0.924
(1.00) 		0.63
(0.989) 		0.853
(1.00) 		0.777
(1.00) 		0.719
(0.998) 		1
(1.00) 		0.594
(0.989) 		0.401
(0.982) 		0.664
(0.989) 		0.358
(0.982)
13q loss 77 (22%) 281 0.244
(0.982) 		0.388
(0.982) 		0.287
(0.982) 		0.367
(0.982) 		0.94
(1.00) 		0.218
(0.982) 		0.935
(1.00) 		0.0964
(0.982) 		0.0747
(0.939) 		0.696
(0.995) 		0.113
(0.982) 		0.691
(0.994) 		0.674
(0.989) 		0.648
(0.989)
14q loss 111 (31%) 247 0.458
(0.982) 		0.498
(0.982) 		0.243
(0.982) 		0.258
(0.982) 		0.412
(0.982) 		0.636
(0.989) 		0.246
(0.982) 		0.329
(0.982) 		0.654
(0.989) 		0.605
(0.989) 		0.909
(1.00) 		0.481
(0.982) 		1
(1.00) 		0.682
(0.989)
15q loss 50 (14%) 308 0.601
(0.989) 		0.379
(0.982) 		0.956
(1.00) 		0.669
(0.989) 		0.079
(0.939) 		0.0458
(0.939) 		0.802
(1.00) 		0.333
(0.982) 		1
(1.00) 		0.816
(1.00) 		0.499
(0.982) 		0.875
(1.00) 		0.265
(0.982) 		0.599
(0.989)
16p loss 67 (19%) 291 0.643
(0.989) 		0.701
(0.995) 		0.124
(0.982) 		0.0419
(0.939) 		0.347
(0.982) 		0.269
(0.982) 		0.902
(1.00) 		0.561
(0.989) 		0.403
(0.982) 		0.0983
(0.982) 		0.0298
(0.939) 		0.329
(0.982) 		0.214
(0.982) 		0.126
(0.982)
16q loss 103 (29%) 255 0.865
(1.00) 		0.746
(1.00) 		0.315
(0.982) 		0.214
(0.982) 		0.49
(0.982) 		0.139
(0.982) 		0.657
(0.989) 		0.616
(0.989) 		0.658
(0.989) 		0.379
(0.982) 		0.06
(0.939) 		0.23
(0.982) 		0.387
(0.982) 		0.419
(0.982)
17p loss 126 (35%) 232 0.851
(1.00) 		0.448
(0.982) 		0.238
(0.982) 		0.0697
(0.939) 		0.505
(0.982) 		0.805
(1.00) 		0.991
(1.00) 		0.347
(0.982) 		0.483
(0.982) 		0.737
(1.00) 		0.455
(0.982) 		0.0534
(0.939) 		0.341
(0.982) 		0.429
(0.982)
17q loss 64 (18%) 294 0.191
(0.982) 		0.29
(0.982) 		0.844
(1.00) 		0.324
(0.982) 		0.126
(0.982) 		0.862
(1.00) 		0.706
(0.995) 		0.555
(0.984) 		0.233
(0.982) 		0.835
(1.00) 		0.0843
(0.939) 		0.397
(0.982) 		0.662
(0.989) 		1
(1.00)
18p loss 103 (29%) 255 0.682
(0.989) 		0.52
(0.982) 		0.314
(0.982) 		0.818
(1.00) 		0.356
(0.982) 		0.332
(0.982) 		0.723
(1.00) 		0.0481
(0.939) 		1
(1.00) 		0.218
(0.982) 		0.448
(0.982) 		0.81
(1.00) 		0.518
(0.982) 		1
(1.00)
18q loss 98 (27%) 260 0.907
(1.00) 		0.412
(0.982) 		0.513
(0.982) 		0.682
(0.989) 		0.586
(0.989) 		0.49
(0.982) 		0.71
(0.995) 		0.61
(0.989) 		0.528
(0.982) 		0.476
(0.982) 		0.29
(0.982) 		1
(1.00) 		0.514
(0.982) 		1
(1.00)
19p loss 75 (21%) 283 0.842
(1.00) 		0.556
(0.984) 		0.506
(0.982) 		0.491
(0.982) 		0.496
(0.982) 		0.828
(1.00) 		0.255
(0.982) 		0.411
(0.982) 		0.395
(0.982) 		1
(1.00) 		0.537
(0.982) 		0.229
(0.982) 		1
(1.00) 		1
(1.00)
19q loss 70 (20%) 288 0.551
(0.984) 		0.848
(1.00) 		0.966
(1.00) 		0.654
(0.989) 		0.744
(1.00) 		0.302
(0.982) 		0.278
(0.982) 		0.148
(0.982) 		0.383
(0.982) 		1
(1.00) 		0.795
(1.00) 		0.338
(0.982) 		1
(1.00) 		1
(1.00)
20p loss 25 (7%) 333 0.702
(0.995) 		0.762
(1.00) 		0.33
(0.982) 		0.0489
(0.939) 		0.896
(1.00) 		0.94
(1.00) 		0.429
(0.982) 		0.167
(0.982) 		0.444
(0.982) 		1
(1.00) 		0.871
(1.00) 		0.67
(0.989) 		1
(1.00) 		0.0762
(0.939)
20q loss 9 (3%) 349 0.724
(1.00) 		0.972
(1.00) 		0.817
(1.00) 		0.0462
(0.939) 		0.569
(0.989) 		0.572
(0.989) 		0.15
(0.982) 		0.104
(0.982) 		0.247
(0.982) 		1
(1.00) 		0.34
(0.982) 		0.492
(0.982) 		1
(1.00) 		0.168
(0.982)
21q loss 68 (19%) 290 0.226
(0.982) 		0.845
(1.00) 		0.118
(0.982) 		0.516
(0.982) 		0.752
(1.00) 		0.84
(1.00) 		0.478
(0.982) 		1
(1.00) 		0.61
(0.989) 		0.684
(0.989) 		0.778
(1.00) 		0.781
(1.00) 		0.0827
(0.939) 		1
(1.00)
22q loss 38 (11%) 320 0.312
(0.982) 		0.19
(0.982) 		0.224
(0.982) 		0.516
(0.982) 		0.206
(0.982) 		0.446
(0.982) 		0.261
(0.982) 		0.716
(0.998) 		0.181
(0.982) 		0.797
(1.00) 		0.393
(0.982) 		0.86
(1.00) 		0.0534
(0.939) 		0.555
(0.984)
xp loss 96 (27%) 262 0.118
(0.982) 		0.956
(1.00) 		0.875
(1.00) 		0.534
(0.982) 		0.136
(0.982) 		0.533
(0.982) 		0.271
(0.982) 		0.204
(0.982) 		0.348
(0.982) 		0.366
(0.982) 		0.0713
(0.939) 		0.0193
(0.819) 		1
(1.00) 		1
(1.00)
xq loss 92 (26%) 266 0.554
(0.984) 		0.618
(0.989) 		0.525
(0.982) 		0.255
(0.982) 		0.115
(0.982) 		0.316
(0.982) 		0.159
(0.982) 		0.435
(0.982) 		0.346
(0.982) 		0.271
(0.982) 		0.079
(0.939) 		0.0806
(0.939) 		1
(1.00) 		1
(1.00)
'17q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000119 (Wilcoxon-test), Q value = 0.13

Table S1.  Gene #31: '17q gain' versus Clinical Feature #3: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 350 56.2 (15.6)
17Q GAIN MUTATED 64 63.1 (15.4)
17Q GAIN WILD-TYPE 286 54.7 (15.3)

Figure S1.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #3: 'YEARS_TO_BIRTH'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000225 (Wilcoxon-test), Q value = 0.13

Table S2.  Gene #61: '10q loss' versus Clinical Feature #3: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 350 56.2 (15.6)
10Q LOSS MUTATED 212 53.8 (15.9)
10Q LOSS WILD-TYPE 138 60.0 (14.4)

Figure S2.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #3: 'YEARS_TO_BIRTH'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/15098586/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SKCM-TM/15087681/SKCM-TM.merged_data.txt

  • Number of patients = 358

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 14

  • 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

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

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] 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)
[3] 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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