Correlation between copy number variation genes (focal events) and selected clinical features
Skin Cutaneous Melanoma (Metastatic)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1ZC81ZJ
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1ZC81ZJ
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 55 focal events and 14 clinical features across 358 patients, 3 significant findings detected with Q value < 0.25.

  • amp_3p13 cnv correlated to 'Time from Specimen Diagnosis to Death'.

  • del_10q26.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_11p15.5 cnv correlated to 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 55 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 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
amp 3p13 101 (28%) 257 0.000394
(0.152) 		0.00477
(0.618) 		0.221
(0.878) 		0.856
(1.00) 		0.393
(0.945) 		0.511
(0.956) 		0.484
(0.956) 		0.455
(0.956) 		1
(1.00) 		0.476
(0.956) 		0.372
(0.945) 		0.0689
(0.852) 		0.73
(1.00) 		0.197
(0.878)
del 10q26 3 230 (64%) 128 0.172
(0.878) 		0.232
(0.878) 		0.000144
(0.111) 		0.0457
(0.831) 		0.505
(0.956) 		0.158
(0.878) 		0.417
(0.956) 		0.251
(0.878) 		0.888
(1.00) 		0.503
(0.956) 		0.143
(0.878) 		0.0689
(0.852) 		0.0247
(0.793) 		0.703
(1.00)
del 11p15 5 112 (31%) 246 0.578
(0.994) 		0.403
(0.953) 		0.105
(0.861) 		0.228
(0.878) 		0.383
(0.945) 		0.243
(0.878) 		0.205
(0.878) 		1
(1.00) 		0.108
(0.861) 		0.39
(0.945) 		0.177
(0.878) 		0.00064
(0.164) 		1
(1.00) 		0.103
(0.861)
amp 1p12 120 (34%) 238 0.25
(0.878) 		0.0587
(0.838) 		0.489
(0.956) 		0.167
(0.878) 		0.144
(0.878) 		0.38
(0.945) 		0.86
(1.00) 		0.812
(1.00) 		0.563
(0.994) 		0.866
(1.00) 		0.607
(1.00) 		0.489
(0.956) 		1
(1.00) 		0.691
(1.00)
amp 1q21 3 200 (56%) 158 0.859
(1.00) 		0.572
(0.994) 		0.443
(0.956) 		0.0523
(0.838) 		0.441
(0.956) 		0.992
(1.00) 		0.689
(1.00) 		0.821
(1.00) 		0.779
(1.00) 		0.631
(1.00) 		0.971
(1.00) 		0.913
(1.00) 		0.812
(1.00) 		0.471
(0.956)
amp 1q44 198 (55%) 160 0.559
(0.994) 		0.198
(0.878) 		0.786
(1.00) 		0.124
(0.865) 		0.825
(1.00) 		0.905
(1.00) 		0.883
(1.00) 		0.821
(1.00) 		0.49
(0.956) 		1
(1.00) 		0.598
(1.00) 		0.827
(1.00) 		0.815
(1.00) 		0.467
(0.956)
amp 4q12 64 (18%) 294 0.117
(0.861) 		0.471
(0.956) 		0.34
(0.917) 		0.991
(1.00) 		0.347
(0.925) 		0.283
(0.896) 		0.849
(1.00) 		0.39
(0.945) 		0.374
(0.945) 		0.835
(1.00) 		0.51
(0.956) 		0.887
(1.00) 		1
(1.00) 		0.616
(1.00)
amp 5p15 33 107 (30%) 251 0.196
(0.878) 		0.525
(0.967) 		0.99
(1.00) 		0.00772
(0.639) 		0.847
(1.00) 		0.159
(0.878) 		0.0851
(0.861) 		1
(1.00) 		0.881
(1.00) 		0.598
(1.00) 		0.617
(1.00) 		0.634
(1.00) 		0.3
(0.898) 		0.431
(0.956)
amp 5q35 3 57 (16%) 301 0.962
(1.00) 		0.711
(1.00) 		0.392
(0.945) 		0.00797
(0.639) 		0.994
(1.00) 		0.886
(1.00) 		0.428
(0.956) 		0.368
(0.945) 		0.583
(0.994) 		0.827
(1.00) 		0.61
(1.00) 		0.46
(0.956) 		0.639
(1.00) 		0.084
(0.861)
amp 6p24 3 205 (57%) 153 0.16
(0.878) 		0.036
(0.827) 		0.0399
(0.827) 		0.0551
(0.838) 		0.17
(0.878) 		0.111
(0.861) 		0.9
(1.00) 		1
(1.00) 		0.486
(0.956) 		0.872
(1.00) 		0.117
(0.861) 		0.583
(0.994) 		1
(1.00) 		1
(1.00)
amp 6q12 78 (22%) 280 0.118
(0.861) 		0.528
(0.967) 		0.29
(0.896) 		0.112
(0.861) 		0.00551
(0.618) 		0.305
(0.9) 		0.371
(0.945) 		0.0104
(0.667) 		0.328
(0.917) 		0.564
(0.994) 		0.723
(1.00) 		0.186
(0.878) 		0.443
(0.956) 		1
(1.00)
amp 7p22 1 202 (56%) 156 0.0975
(0.861) 		0.66
(1.00) 		0.995
(1.00) 		0.699
(1.00) 		0.17
(0.878) 		0.323
(0.917) 		0.244
(0.878) 		0.656
(1.00) 		0.679
(1.00) 		0.196
(0.878) 		0.89
(1.00) 		1
(1.00) 		0.0398
(0.827) 		0.473
(0.956)
amp 7q34 219 (61%) 139 0.075
(0.852) 		0.366
(0.945) 		0.341
(0.917) 		0.12
(0.861) 		0.022
(0.77) 		0.272
(0.894) 		0.334
(0.917) 		0.651
(1.00) 		0.395
(0.945) 		0.514
(0.956) 		0.582
(0.994) 		0.0438
(0.827) 		0.356
(0.94) 		1
(1.00)
amp 8q11 21 159 (44%) 199 0.0166
(0.77) 		0.143
(0.878) 		0.0372
(0.827) 		0.123
(0.865) 		0.148
(0.878) 		0.341
(0.917) 		0.405
(0.953) 		0.366
(0.945) 		1
(1.00) 		0.195
(0.878) 		0.25
(0.878) 		0.913
(1.00) 		0.0154
(0.77) 		0.704
(1.00)
amp 8q24 21 186 (52%) 172 0.044
(0.827) 		0.246
(0.878) 		0.114
(0.861) 		0.201
(0.878) 		0.204
(0.878) 		0.26
(0.883) 		0.452
(0.956) 		0.66
(1.00) 		1
(1.00) 		0.524
(0.967) 		0.139
(0.878) 		0.514
(0.956) 		0.0438
(0.827) 		1
(1.00)
amp 11q13 3 67 (19%) 291 0.224
(0.878) 		0.971
(1.00) 		0.276
(0.894) 		0.0752
(0.852) 		0.232
(0.878) 		0.12
(0.861) 		0.236
(0.878) 		0.143
(0.878) 		0.859
(1.00) 		1
(1.00) 		0.799
(1.00) 		0.676
(1.00) 		0.0785
(0.852) 		1
(1.00)
amp 12q14 1 54 (15%) 304 0.0738
(0.852) 		0.183
(0.878) 		0.192
(0.878) 		0.398
(0.945) 		0.474
(0.956) 		0.468
(0.956) 		0.278
(0.894) 		0.753
(1.00) 		0.856
(1.00) 		0.118
(0.861) 		0.33
(0.917) 		0.879
(1.00) 		0.291
(0.896) 		0.286
(0.896)
amp 12q15 55 (15%) 303 0.138
(0.878) 		0.624
(1.00) 		0.129
(0.878) 		0.32
(0.917) 		0.877
(1.00) 		0.732
(1.00) 		0.297
(0.898) 		0.753
(1.00) 		0.711
(1.00) 		0.118
(0.861) 		0.764
(1.00) 		0.452
(0.956) 		0.638
(1.00) 		0.294
(0.898)
amp 13q31 3 103 (29%) 255 0.00367
(0.618) 		0.0232
(0.775) 		0.821
(1.00) 		0.161
(0.878) 		0.192
(0.878) 		0.0633
(0.838) 		0.507
(0.956) 		0.456
(0.956) 		0.285
(0.896) 		0.722
(1.00) 		0.789
(1.00) 		0.718
(1.00) 		0.736
(1.00) 		0.678
(1.00)
amp 15q26 2 118 (33%) 240 0.274
(0.894) 		0.686
(1.00) 		0.95
(1.00) 		0.22
(0.878) 		0.0125
(0.685) 		0.482
(0.956) 		0.718
(1.00) 		0.23
(0.878) 		0.291
(0.896) 		0.233
(0.878) 		0.486
(0.956) 		0.564
(0.994) 		1
(1.00) 		1
(1.00)
amp 17q25 3 119 (33%) 239 0.672
(1.00) 		0.735
(1.00) 		0.0083
(0.639) 		0.231
(0.878) 		0.717
(1.00) 		0.286
(0.896) 		0.809
(1.00) 		1
(1.00) 		0.307
(0.9) 		1
(1.00) 		0.908
(1.00) 		0.132
(0.878) 		0.564
(0.994) 		0.432
(0.956)
amp 19p13 2 68 (19%) 290 0.586
(0.994) 		0.785
(1.00) 		0.538
(0.98) 		0.11
(0.861) 		0.117
(0.861) 		0.735
(1.00) 		0.85
(1.00) 		0.257
(0.883) 		0.233
(0.878) 		0.838
(1.00) 		0.434
(0.956) 		0.679
(1.00) 		1
(1.00) 		1
(1.00)
amp 20q13 33 186 (52%) 172 0.034
(0.827) 		0.296
(0.898) 		0.129
(0.878) 		0.451
(0.956) 		0.0765
(0.852) 		0.0839
(0.861) 		0.671
(1.00) 		0.076
(0.852) 		0.168
(0.878) 		0.872
(1.00) 		0.175
(0.878) 		1
(1.00) 		0.519
(0.961) 		1
(1.00)
amp 22q13 2 149 (42%) 209 0.416
(0.956) 		0.745
(1.00) 		0.297
(0.898) 		0.0335
(0.827) 		0.617
(1.00) 		0.503
(0.956) 		0.185
(0.878) 		0.822
(1.00) 		0.678
(1.00) 		1
(1.00) 		0.8
(1.00) 		0.581
(0.994) 		0.371
(0.945) 		0.246
(0.878)
del 1p36 31 80 (22%) 278 0.326
(0.917) 		0.71
(1.00) 		0.242
(0.878) 		0.695
(1.00) 		0.22
(0.878) 		0.276
(0.894) 		0.896
(1.00) 		0.793
(1.00) 		1
(1.00) 		0.849
(1.00) 		0.256
(0.883) 		0.36
(0.945) 		1
(1.00) 		1
(1.00)
del 1p22 1 95 (27%) 263 0.478
(0.956) 		0.828
(1.00) 		0.0918
(0.861) 		0.921
(1.00) 		0.0097
(0.667) 		0.741
(1.00) 		0.0549
(0.838) 		0.441
(0.956) 		0.0859
(0.861) 		0.715
(1.00) 		0.339
(0.917) 		0.0486
(0.831) 		0.71
(1.00) 		1
(1.00)
del 2q37 3 91 (25%) 267 0.177
(0.878) 		0.552
(0.988) 		0.962
(1.00) 		0.103
(0.861) 		0.685
(1.00) 		0.148
(0.878) 		0.502
(0.956) 		0.121
(0.861) 		0.44
(0.956) 		0.0641
(0.838) 		0.197
(0.878) 		1
(1.00) 		1
(1.00) 		0.0122
(0.685)
del 3p25 1 69 (19%) 289 0.177
(0.878) 		0.341
(0.917) 		0.197
(0.878) 		0.498
(0.956) 		0.216
(0.878) 		0.325
(0.917) 		0.392
(0.945) 		0.389
(0.945) 		0.47
(0.956) 		1
(1.00) 		0.0309
(0.827) 		0.273
(0.894) 		0.396
(0.945) 		1
(1.00)
del 3q13 31 60 (17%) 298 0.465
(0.956) 		0.865
(1.00) 		0.138
(0.878) 		0.362
(0.945) 		0.979
(1.00) 		0.879
(1.00) 		0.479
(0.956) 		0.548
(0.984) 		1
(1.00) 		0.196
(0.878) 		0.828
(1.00) 		1
(1.00) 		0.335
(0.917) 		0.334
(0.917)
del 4p16 3 89 (25%) 269 0.279
(0.894) 		0.225
(0.878) 		0.643
(1.00) 		0.192
(0.878) 		0.182
(0.878) 		0.865
(1.00) 		0.457
(0.956) 		0.308
(0.9) 		1
(1.00) 		0.853
(1.00) 		0.602
(1.00) 		1
(1.00) 		0.7
(1.00) 		1
(1.00)
del 4q34 3 107 (30%) 251 0.921
(1.00) 		0.768
(1.00) 		0.981
(1.00) 		0.483
(0.956) 		0.269
(0.894) 		0.947
(1.00) 		0.263
(0.883) 		1
(1.00) 		0.761
(1.00) 		0.218
(0.878) 		0.338
(0.917) 		0.191
(0.878) 		0.745
(1.00) 		0.679
(1.00)
del 5p15 31 77 (22%) 281 0.44
(0.956) 		0.424
(0.956) 		0.771
(1.00) 		0.391
(0.945) 		0.297
(0.898) 		0.238
(0.878) 		0.287
(0.896) 		0.27
(0.894) 		0.0189
(0.77) 		0.239
(0.878) 		0.304
(0.9) 		0.144
(0.878) 		0.0203
(0.77) 		0.352
(0.933)
del 5q12 1 96 (27%) 262 0.785
(1.00) 		0.771
(1.00) 		0.229
(0.878) 		0.63
(1.00) 		0.753
(1.00) 		0.918
(1.00) 		0.553
(0.988) 		0.61
(1.00) 		0.53
(0.969) 		0.366
(0.945) 		0.862
(1.00) 		1
(1.00) 		1
(1.00) 		0.197
(0.878)
del 5q31 3 129 (36%) 229 0.881
(1.00) 		0.871
(1.00) 		0.612
(1.00) 		0.808
(1.00) 		0.83
(1.00) 		0.443
(0.956) 		0.688
(1.00) 		1
(1.00) 		0.669
(1.00) 		0.0642
(0.838) 		0.669
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.0537
(0.838)
del 6q22 31 209 (58%) 149 0.29
(0.896) 		0.912
(1.00) 		0.464
(0.956) 		0.782
(1.00) 		0.699
(1.00) 		0.444
(0.956) 		0.755
(1.00) 		0.168
(0.878) 		0.0699
(0.852) 		0.745
(1.00) 		0.448
(0.956) 		0.27
(0.894) 		0.797
(1.00) 		0.458
(0.956)
del 6q26 215 (60%) 143 0.7
(1.00) 		0.687
(1.00) 		0.543
(0.981) 		0.655
(1.00) 		0.383
(0.945) 		0.25
(0.878) 		0.748
(1.00) 		0.109
(0.861) 		0.0928
(0.861) 		0.416
(0.956) 		0.975
(1.00) 		0.0948
(0.861) 		0.162
(0.878) 		1
(1.00)
del 8p23 3 86 (24%) 272 0.619
(1.00) 		0.388
(0.945) 		0.727
(1.00) 		0.131
(0.878) 		0.627
(1.00) 		0.145
(0.878) 		0.121
(0.861) 		0.606
(1.00) 		1
(1.00) 		0.573
(0.994) 		0.408
(0.956) 		0.61
(1.00) 		1
(1.00) 		1
(1.00)
del 9p23 244 (68%) 114 0.317
(0.917) 		0.226
(0.878) 		0.417
(0.956) 		0.803
(1.00) 		0.737
(1.00) 		0.777
(1.00) 		0.82
(1.00) 		1
(1.00) 		0.662
(1.00) 		0.733
(1.00) 		0.506
(0.956) 		0.198
(0.878) 		0.771
(1.00) 		0.0375
(0.827)
del 9p21 3 273 (76%) 85 0.75
(1.00) 		0.584
(0.994) 		0.254
(0.883) 		0.214
(0.878) 		0.511
(0.956) 		0.687
(1.00) 		0.799
(1.00) 		0.121
(0.861) 		0.876
(1.00) 		0.256
(0.883) 		0.432
(0.956) 		0.0214
(0.77) 		1
(1.00) 		0.0616
(0.838)
del 10p15 3 195 (54%) 163 0.794
(1.00) 		0.948
(1.00) 		0.0527
(0.838) 		0.173
(0.878) 		0.719
(1.00) 		0.041
(0.827) 		0.88
(1.00) 		0.366
(0.945) 		0.581
(0.994) 		0.628
(1.00) 		0.326
(0.917) 		0.189
(0.878) 		0.12
(0.861) 		1
(1.00)
del 10q21 1 213 (59%) 145 0.803
(1.00) 		0.685
(1.00) 		0.00562
(0.618) 		0.113
(0.861) 		0.601
(1.00) 		0.0912
(0.861) 		0.263
(0.883) 		0.502
(0.956) 		0.78
(1.00) 		0.745
(1.00) 		0.807
(1.00) 		0.0594
(0.838) 		0.0738
(0.852) 		1
(1.00)
del 10q23 31 224 (63%) 134 0.455
(0.956) 		0.548
(0.984) 		0.0199
(0.77) 		0.348
(0.925) 		0.625
(1.00) 		0.0702
(0.852) 		0.128
(0.878) 		0.101
(0.861) 		0.672
(1.00) 		1
(1.00) 		0.585
(0.994) 		0.033
(0.827) 		0.241
(0.878) 		1
(1.00)
del 11q23 3 197 (55%) 161 0.388
(0.945) 		0.54
(0.98) 		0.246
(0.878) 		0.155
(0.878) 		0.698
(1.00) 		0.636
(1.00) 		0.582
(0.994) 		0.504
(0.956) 		0.89
(1.00) 		0.518
(0.961) 		0.738
(1.00) 		0.155
(0.878) 		1
(1.00) 		0.706
(1.00)
del 12q23 3 91 (25%) 267 0.981
(1.00) 		0.445
(0.956) 		0.877
(1.00) 		0.138
(0.878) 		0.942
(1.00) 		0.654
(1.00) 		0.499
(0.956) 		0.795
(1.00) 		0.753
(1.00) 		1
(1.00) 		0.232
(0.878) 		0.382
(0.945) 		0.502
(0.956) 		0.198
(0.878)
del 13q34 82 (23%) 276 0.507
(0.956) 		0.527
(0.967) 		0.586
(0.994) 		0.689
(1.00) 		0.906
(1.00) 		0.152
(0.878) 		0.835
(1.00) 		0.108
(0.861) 		0.114
(0.861) 		0.566
(0.994) 		0.338
(0.917) 		0.897
(1.00) 		0.684
(1.00) 		0.664
(1.00)
del 14q23 3 120 (34%) 238 0.234
(0.878) 		0.397
(0.945) 		0.545
(0.983) 		0.153
(0.878) 		0.235
(0.878) 		0.868
(1.00) 		0.317
(0.917) 		0.231
(0.878) 		0.466
(0.956) 		1
(1.00) 		0.618
(1.00) 		0.299
(0.898) 		1
(1.00) 		1
(1.00)
del 14q32 31 116 (32%) 242 0.495
(0.956) 		0.372
(0.945) 		0.467
(0.956) 		0.391
(0.945) 		0.401
(0.95) 		0.513
(0.956) 		0.137
(0.878) 		0.476
(0.956) 		0.558
(0.994) 		0.606
(1.00) 		0.594
(1.00) 		1
(1.00) 		0.769
(1.00) 		1
(1.00)
del 15q13 3 83 (23%) 275 0.261
(0.883) 		0.047
(0.831) 		0.663
(1.00) 		0.731
(1.00) 		0.661
(1.00) 		0.0478
(0.831) 		0.723
(1.00) 		1
(1.00) 		0.872
(1.00) 		0.707
(1.00) 		0.944
(1.00) 		0.606
(1.00) 		0.484
(0.956) 		0.207
(0.878)
del 15q21 1 89 (25%) 269 0.188
(0.878) 		0.0627
(0.838) 		0.631
(1.00) 		0.746
(1.00) 		0.384
(0.945) 		0.327
(0.917) 		0.585
(0.994) 		1
(1.00) 		0.874
(1.00) 		0.578
(0.994) 		0.941
(1.00) 		0.614
(1.00) 		0.22
(0.878) 		1
(1.00)
del 16p13 3 61 (17%) 297 0.233
(0.878) 		0.865
(1.00) 		0.245
(0.878) 		0.307
(0.9) 		0.647
(1.00) 		0.309
(0.9) 		0.74
(1.00) 		0.383
(0.945) 		1
(1.00) 		0.0172
(0.77) 		0.412
(0.956) 		0.25
(0.878) 		0.202
(0.878) 		0.104
(0.861)
del 16q12 1 114 (32%) 244 0.501
(0.956) 		0.531
(0.97) 		0.324
(0.917) 		0.34
(0.917) 		0.503
(0.956) 		0.512
(0.956) 		0.782
(1.00) 		0.47
(0.956) 		0.773
(1.00) 		0.863
(1.00) 		0.203
(0.878) 		0.485
(0.956) 		0.541
(0.98) 		0.684
(1.00)
del 16q24 3 129 (36%) 229 0.804
(1.00) 		0.718
(1.00) 		0.103
(0.861) 		0.221
(0.878) 		0.0783
(0.852) 		0.289
(0.896) 		0.506
(0.956) 		0.816
(1.00) 		1
(1.00) 		0.616
(1.00) 		0.202
(0.878) 		0.82
(1.00) 		0.342
(0.917) 		0.707
(1.00)
del 17p13 3 135 (38%) 223 0.725
(1.00) 		0.431
(0.956) 		0.043
(0.827) 		0.115
(0.861) 		0.584
(0.994) 		0.803
(1.00) 		0.998
(1.00) 		0.487
(0.956) 		0.675
(1.00) 		0.411
(0.956) 		0.89
(1.00) 		0.0556
(0.838) 		0.348
(0.925) 		0.262
(0.883)
del 19p13 3 101 (28%) 257 0.631
(1.00) 		0.195
(0.878) 		0.739
(1.00) 		0.684
(1.00) 		0.633
(1.00) 		0.838
(1.00) 		0.481
(0.956) 		0.804
(1.00) 		0.88
(1.00) 		0.476
(0.956) 		0.733
(1.00) 		0.275
(0.894) 		1
(1.00) 		0.678
(1.00)
del xp21 1 86 (24%) 272 0.0323
(0.827) 		0.879
(1.00) 		0.661
(1.00) 		0.202
(0.878) 		0.0325
(0.827) 		0.306
(0.9) 		0.441
(0.956) 		0.0573
(0.838) 		0.186
(0.878) 		0.707
(1.00) 		0.0424
(0.827) 		0.162
(0.878) 		0.501
(0.956) 		0.674
(1.00)
'amp_3p13' versus 'Time from Specimen Diagnosis to Death'

P value = 0.000394 (logrank test), Q value = 0.15

Table S1.  Gene #4: 'amp_3p13' versus Clinical Feature #1: 'Time from Specimen Diagnosis to Death'

nPatients nDeath Duration Range (Median), Month
ALL 239 118 0.0 - 346.5 (46.0)
AMP PEAK 4(3P13) MUTATED 68 24 0.8 - 346.5 (61.1)
AMP PEAK 4(3P13) WILD-TYPE 171 94 0.0 - 312.1 (36.3)

Figure S1.  Get High-res Image Gene #4: 'amp_3p13' versus Clinical Feature #1: 'Time from Specimen Diagnosis to Death'

'del_10q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.000144 (Wilcoxon-test), Q value = 0.11

Table S2.  Gene #41: 'del_10q26.3' versus Clinical Feature #3: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 350 56.2 (15.6)
DEL PEAK 19(10Q26.3) MUTATED 222 53.8 (16.0)
DEL PEAK 19(10Q26.3) WILD-TYPE 128 60.4 (14.1)

Figure S2.  Get High-res Image Gene #41: 'del_10q26.3' versus Clinical Feature #3: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'GENDER'

P value = 0.00064 (Fisher's exact test), Q value = 0.16

Table S3.  Gene #42: 'del_11p15.5' versus Clinical Feature #12: 'GENDER'

nPatients FEMALE MALE
ALL 135 223
DEL PEAK 20(11P15.5) MUTATED 57 55
DEL PEAK 20(11P15.5) WILD-TYPE 78 168

Figure S3.  Get High-res Image Gene #42: 'del_11p15.5' versus Clinical Feature #12: 'GENDER'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SKCM-TM/15098585/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 focal cnvs = 55

  • Number of selected clinical features = 14

  • 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

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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