Correlation between copy number variations of arm-level result and selected clinical features
Skin Cutaneous Melanoma (Metastatic)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1CZ35VJ
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/C1CZ35VJ
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 274 patients, 3 significant findings detected with Q value < 0.25.

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

  • 9q 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, 3 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 33 (12%) 241 0.322
(1.00) 		0.118
(1.00) 		0.986
(1.00) 		0.402
(1.00) 		0.563
(1.00) 		0.317
(1.00) 		0.867
(1.00) 		0.135
(1.00) 		0.193
(1.00) 		0.255
(1.00) 		0.000131
(0.124) 		0.573
(1.00)
9q gain 20 (7%) 254 0.25
(1.00) 		0.984
(1.00) 		0.269
(1.00) 		0.0672
(1.00) 		0.279
(1.00) 		0.31
(1.00) 		0.921
(1.00) 		0.787
(1.00) 		0.105
(1.00) 		0.145
(1.00) 		0.000188
(0.178) 		0.634
(1.00)
10q loss 167 (61%) 107 0.479
(1.00) 		0.287
(1.00) 		7.2e-05
(0.0683) 		0.0455
(1.00) 		0.771
(1.00) 		0.0861
(1.00) 		0.329
(1.00) 		0.149
(1.00) 		0.751
(1.00) 		0.57
(1.00) 		0.6
(1.00) 		0.161
(1.00)
1p gain 62 (23%) 212 0.634
(1.00) 		0.444
(1.00) 		0.465
(1.00) 		0.078
(1.00) 		0.197
(1.00) 		0.646
(1.00) 		0.549
(1.00) 		0.0794
(1.00) 		0.588
(1.00) 		0.659
(1.00) 		0.67
(1.00) 		1
(1.00)
1q gain 121 (44%) 153 0.849
(1.00) 		0.623
(1.00) 		0.894
(1.00) 		0.445
(1.00) 		0.606
(1.00) 		0.953
(1.00) 		0.0722
(1.00) 		0.271
(1.00) 		0.436
(1.00) 		1
(1.00) 		0.543
(1.00) 		0.617
(1.00)
2p gain 53 (19%) 221 0.132
(1.00) 		0.0611
(1.00) 		0.516
(1.00) 		0.421
(1.00) 		0.926
(1.00) 		0.129
(1.00) 		0.963
(1.00) 		0.568
(1.00) 		0.558
(1.00) 		0.35
(1.00) 		0.792
(1.00) 		0.531
(1.00)
2q gain 51 (19%) 223 0.0206
(1.00) 		0.0204
(1.00) 		0.614
(1.00) 		0.457
(1.00) 		0.831
(1.00) 		0.0349
(1.00) 		0.792
(1.00) 		0.68
(1.00) 		1
(1.00) 		0.811
(1.00) 		0.867
(1.00) 		1
(1.00)
3p gain 44 (16%) 230 0.571
(1.00) 		0.0294
(1.00) 		0.13
(1.00) 		0.374
(1.00) 		0.124
(1.00) 		0.0656
(1.00) 		0.195
(1.00) 		0.426
(1.00) 		0.385
(1.00) 		0.621
(1.00) 		0.00288
(1.00) 		0.736
(1.00)
3q gain 54 (20%) 220 0.284
(1.00) 		0.0176
(1.00) 		0.0155
(1.00) 		0.395
(1.00) 		0.0521
(1.00) 		0.0061
(1.00) 		0.0214
(1.00) 		0.413
(1.00) 		0.0488
(1.00) 		0.642
(1.00) 		0.00135
(1.00) 		0.755
(1.00)
4p gain 40 (15%) 234 0.906
(1.00) 		0.599
(1.00) 		0.53
(1.00) 		0.448
(1.00) 		0.0439
(1.00) 		0.0707
(1.00) 		0.64
(1.00) 		0.524
(1.00) 		1
(1.00) 		0.29
(1.00) 		0.765
(1.00) 		0.599
(1.00)
4q gain 34 (12%) 240 0.987
(1.00) 		0.451
(1.00) 		0.426
(1.00) 		0.531
(1.00) 		0.168
(1.00) 		0.0963
(1.00) 		0.499
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.578
(1.00) 		0.709
(1.00) 		0.851
(1.00)
5p gain 53 (19%) 221 0.181
(1.00) 		0.0255
(1.00) 		0.0899
(1.00) 		0.555
(1.00) 		0.0551
(1.00) 		0.498
(1.00) 		0.0891
(1.00) 		0.38
(1.00) 		0.0533
(1.00) 		0.241
(1.00) 		0.000446
(0.422) 		0.638
(1.00)
6p gain 109 (40%) 165 0.164
(1.00) 		0.651
(1.00) 		0.722
(1.00) 		0.182
(1.00) 		0.173
(1.00) 		0.06
(1.00) 		0.123
(1.00) 		0.0702
(1.00) 		0.636
(1.00) 		0.343
(1.00) 		0.607
(1.00) 		0.447
(1.00)
6q gain 36 (13%) 238 0.428
(1.00) 		0.501
(1.00) 		0.863
(1.00) 		0.392
(1.00) 		0.102
(1.00) 		0.0053
(1.00) 		0.0055
(1.00) 		0.382
(1.00) 		0.191
(1.00) 		0.591
(1.00) 		0.174
(1.00) 		0.714
(1.00)
7p gain 148 (54%) 126 0.874
(1.00) 		0.804
(1.00) 		0.424
(1.00) 		0.161
(1.00) 		0.0149
(1.00) 		0.364
(1.00) 		0.274
(1.00) 		0.411
(1.00) 		0.642
(1.00) 		0.138
(1.00) 		0.556
(1.00) 		0.213
(1.00)
7q gain 146 (53%) 128 0.878
(1.00) 		0.873
(1.00) 		0.16
(1.00) 		0.294
(1.00) 		0.0398
(1.00) 		0.763
(1.00) 		0.781
(1.00) 		0.619
(1.00) 		0.642
(1.00) 		0.458
(1.00) 		0.518
(1.00) 		0.0829
(1.00)
8p gain 88 (32%) 186 0.931
(1.00) 		0.958
(1.00) 		0.181
(1.00) 		0.00537
(1.00) 		0.457
(1.00) 		0.734
(1.00) 		0.644
(1.00) 		0.579
(1.00) 		0.183
(1.00) 		0.427
(1.00) 		0.889
(1.00) 		0.353
(1.00)
8q gain 129 (47%) 145 0.492
(1.00) 		0.363
(1.00) 		0.0132
(1.00) 		0.0164
(1.00) 		0.453
(1.00) 		0.115
(1.00) 		0.36
(1.00) 		0.74
(1.00) 		0.876
(1.00) 		0.0617
(1.00) 		0.638
(1.00) 		0.804
(1.00)
9p gain 14 (5%) 260 0.802
(1.00) 		0.497
(1.00) 		0.817
(1.00) 		0.0446
(1.00) 		0.102
(1.00) 		0.249
(1.00) 		0.879
(1.00) 		0.638
(1.00) 		0.203
(1.00) 		0.388
(1.00) 		0.00345
(1.00) 		1
(1.00)
10p gain 8 (3%) 266 0.975
(1.00) 		0.521
(1.00) 		0.86
(1.00) 		0.878
(1.00) 		0.471
(1.00) 		0.537
(1.00) 		0.435
(1.00) 		0.0205
(1.00) 		1
(1.00) 		0.0586
(1.00) 		0.00537
(1.00) 		1
(1.00)
11p gain 26 (9%) 248 0.945
(1.00) 		0.713
(1.00) 		1
(1.00) 		0.744
(1.00) 		0.113
(1.00) 		0.0874
(1.00) 		0.346
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.104
(1.00) 		0.467
(1.00) 		0.526
(1.00)
11q gain 23 (8%) 251 0.965
(1.00) 		0.633
(1.00) 		0.891
(1.00) 		0.516
(1.00) 		0.0428
(1.00) 		0.0855
(1.00) 		0.299
(1.00) 		0.876
(1.00) 		0.528
(1.00) 		0.0428
(1.00) 		0.0506
(1.00) 		0.825
(1.00)
12p gain 47 (17%) 227 0.324
(1.00) 		0.408
(1.00) 		0.547
(1.00) 		0.485
(1.00) 		0.00861
(1.00) 		0.117
(1.00) 		0.0104
(1.00) 		0.545
(1.00) 		0.686
(1.00) 		0.809
(1.00) 		0.856
(1.00) 		0.869
(1.00)
12q gain 32 (12%) 242 0.959
(1.00) 		0.802
(1.00) 		0.773
(1.00) 		0.426
(1.00) 		0.297
(1.00) 		0.598
(1.00) 		0.0263
(1.00) 		0.843
(1.00) 		1
(1.00) 		0.146
(1.00) 		0.575
(1.00) 		0.443
(1.00)
13q gain 70 (26%) 204 0.102
(1.00) 		0.592
(1.00) 		0.348
(1.00) 		0.0579
(1.00) 		0.215
(1.00) 		0.134
(1.00) 		0.208
(1.00) 		0.554
(1.00) 		0.587
(1.00) 		0.526
(1.00) 		0.631
(1.00) 		0.887
(1.00)
14q gain 29 (11%) 245 0.992
(1.00) 		0.587
(1.00) 		0.365
(1.00) 		0.962
(1.00) 		0.806
(1.00) 		0.481
(1.00) 		0.526
(1.00) 		0.832
(1.00) 		1
(1.00) 		1
(1.00) 		0.556
(1.00) 		0.232
(1.00)
15q gain 61 (22%) 213 0.371
(1.00) 		0.203
(1.00) 		0.586
(1.00) 		0.519
(1.00) 		0.427
(1.00) 		0.295
(1.00) 		0.5
(1.00) 		0.617
(1.00) 		0.56
(1.00) 		0.265
(1.00) 		0.551
(1.00) 		0.882
(1.00)
16p gain 40 (15%) 234 0.596
(1.00) 		0.474
(1.00) 		0.137
(1.00) 		0.0315
(1.00) 		0.136
(1.00) 		0.00613
(1.00) 		0.00388
(1.00) 		0.415
(1.00) 		0.647
(1.00) 		0.798
(1.00) 		0.815
(1.00) 		0.861
(1.00)
16q gain 34 (12%) 240 0.324
(1.00) 		0.873
(1.00) 		0.295
(1.00) 		0.0678
(1.00) 		0.175
(1.00) 		0.00616
(1.00) 		0.00806
(1.00) 		0.383
(1.00) 		0.809
(1.00) 		0.779
(1.00) 		0.946
(1.00) 		0.458
(1.00)
17p gain 31 (11%) 243 0.931
(1.00) 		0.871
(1.00) 		0.404
(1.00) 		0.929
(1.00) 		0.767
(1.00) 		0.538
(1.00) 		0.42
(1.00) 		0.364
(1.00) 		0.225
(1.00) 		0.775
(1.00) 		0.458
(1.00) 		0.436
(1.00)
17q gain 54 (20%) 220 0.561
(1.00) 		0.539
(1.00) 		0.00296
(1.00) 		0.455
(1.00) 		0.439
(1.00) 		0.939
(1.00) 		0.448
(1.00) 		0.521
(1.00) 		0.457
(1.00) 		0.817
(1.00) 		0.676
(1.00) 		1
(1.00)
18p gain 46 (17%) 228 0.659
(1.00) 		0.979
(1.00) 		0.391
(1.00) 		0.781
(1.00) 		0.00355
(1.00) 		0.0216
(1.00) 		0.296
(1.00) 		0.0212
(1.00) 		0.297
(1.00) 		0.805
(1.00) 		0.507
(1.00) 		0.319
(1.00)
18q gain 38 (14%) 236 0.467
(1.00) 		0.229
(1.00) 		0.729
(1.00) 		0.721
(1.00) 		0.00206
(1.00) 		0.0371
(1.00) 		0.227
(1.00) 		0.496
(1.00) 		0.36
(1.00) 		0.426
(1.00) 		0.584
(1.00) 		0.376
(1.00)
19p gain 40 (15%) 234 0.898
(1.00) 		0.806
(1.00) 		0.823
(1.00) 		0.428
(1.00) 		0.751
(1.00) 		0.888
(1.00) 		0.743
(1.00) 		0.137
(1.00) 		0.525
(1.00) 		0.598
(1.00) 		0.688
(1.00) 		0.22
(1.00)
19q gain 41 (15%) 233 0.789
(1.00) 		0.75
(1.00) 		0.338
(1.00) 		0.306
(1.00) 		0.886
(1.00) 		0.543
(1.00) 		0.478
(1.00) 		0.149
(1.00) 		0.27
(1.00) 		0.603
(1.00) 		0.482
(1.00) 		0.164
(1.00)
20p gain 115 (42%) 159 0.383
(1.00) 		0.409
(1.00) 		0.0953
(1.00) 		0.804
(1.00) 		0.0748
(1.00) 		0.0202
(1.00) 		0.0981
(1.00) 		0.238
(1.00) 		0.116
(1.00) 		0.574
(1.00) 		0.0259
(1.00) 		0.803
(1.00)
20q gain 137 (50%) 137 0.809
(1.00) 		0.136
(1.00) 		0.019
(1.00) 		0.663
(1.00) 		0.0288
(1.00) 		0.0161
(1.00) 		0.425
(1.00) 		0.131
(1.00) 		0.159
(1.00) 		0.458
(1.00) 		0.0249
(1.00) 		0.804
(1.00)
21q gain 51 (19%) 223 0.495
(1.00) 		0.261
(1.00) 		0.265
(1.00) 		0.334
(1.00) 		0.0256
(1.00) 		0.164
(1.00) 		0.155
(1.00) 		0.555
(1.00) 		0.078
(1.00) 		1
(1.00) 		0.0538
(1.00) 		0.875
(1.00)
22q gain 98 (36%) 176 0.276
(1.00) 		0.193
(1.00) 		0.584
(1.00) 		0.206
(1.00) 		0.767
(1.00) 		0.288
(1.00) 		0.109
(1.00) 		0.959
(1.00) 		0.747
(1.00) 		0.7
(1.00) 		0.186
(1.00) 		0.437
(1.00)
xq gain 31 (11%) 243 0.167
(1.00) 		0.21
(1.00) 		0.559
(1.00) 		0.344
(1.00) 		0.644
(1.00) 		0.647
(1.00) 		0.227
(1.00) 		0.785
(1.00) 		0.817
(1.00) 		0.775
(1.00) 		0.631
(1.00) 		0.845
(1.00)
1p loss 36 (13%) 238 0.177
(1.00) 		0.0252
(1.00) 		0.0234
(1.00) 		0.757
(1.00) 		0.0466
(1.00) 		0.345
(1.00) 		0.218
(1.00) 		0.84
(1.00) 		0.323
(1.00) 		0.591
(1.00) 		0.496
(1.00) 		1
(1.00)
1q loss 20 (7%) 254 0.693
(1.00) 		0.58
(1.00) 		0.545
(1.00) 		0.947
(1.00) 		0.641
(1.00) 		0.963
(1.00) 		0.574
(1.00) 		0.771
(1.00) 		0.771
(1.00) 		0.485
(1.00) 		0.198
(1.00) 		0.634
(1.00)
2p loss 35 (13%) 239 0.845
(1.00) 		0.175
(1.00) 		0.802
(1.00) 		0.969
(1.00) 		0.627
(1.00) 		0.27
(1.00) 		0.188
(1.00) 		0.463
(1.00) 		0.665
(1.00) 		0.78
(1.00) 		0.639
(1.00) 		0.854
(1.00)
2q loss 35 (13%) 239 0.214
(1.00) 		0.586
(1.00) 		0.929
(1.00) 		0.731
(1.00) 		0.961
(1.00) 		0.455
(1.00) 		0.304
(1.00) 		0.23
(1.00) 		0.665
(1.00) 		0.277
(1.00) 		0.977
(1.00) 		0.854
(1.00)
3p loss 42 (15%) 232 0.514
(1.00) 		0.395
(1.00) 		0.239
(1.00) 		0.706
(1.00) 		0.411
(1.00) 		0.398
(1.00) 		0.433
(1.00) 		0.818
(1.00) 		0.826
(1.00) 		1
(1.00) 		0.0959
(1.00) 		0.605
(1.00)
3q loss 33 (12%) 241 0.893
(1.00) 		0.334
(1.00) 		0.598
(1.00) 		0.619
(1.00) 		0.616
(1.00) 		0.349
(1.00) 		0.397
(1.00) 		0.843
(1.00) 		0.808
(1.00) 		0.778
(1.00) 		0.178
(1.00) 		0.703
(1.00)
4p loss 57 (21%) 217 0.791
(1.00) 		0.998
(1.00) 		0.523
(1.00) 		0.221
(1.00) 		0.524
(1.00) 		0.863
(1.00) 		0.658
(1.00) 		0.405
(1.00) 		0.708
(1.00) 		0.821
(1.00) 		0.0553
(1.00) 		0.127
(1.00)
4q loss 59 (22%) 215 0.749
(1.00) 		0.867
(1.00) 		0.266
(1.00) 		0.421
(1.00) 		0.52
(1.00) 		0.527
(1.00) 		0.341
(1.00) 		0.064
(1.00) 		0.344
(1.00) 		0.375
(1.00) 		0.0303
(1.00) 		0.0692
(1.00)
5p loss 64 (23%) 210 0.908
(1.00) 		0.965
(1.00) 		0.657
(1.00) 		0.932
(1.00) 		0.582
(1.00) 		0.429
(1.00) 		0.34
(1.00) 		0.375
(1.00) 		0.144
(1.00) 		0.126
(1.00) 		0.444
(1.00) 		0.467
(1.00)
5q loss 80 (29%) 194 0.792
(1.00) 		0.928
(1.00) 		0.364
(1.00) 		0.805
(1.00) 		0.938
(1.00) 		0.307
(1.00) 		0.882
(1.00) 		0.605
(1.00) 		0.305
(1.00) 		0.316
(1.00) 		0.529
(1.00) 		0.785
(1.00)
6p loss 50 (18%) 224 0.23
(1.00) 		0.23
(1.00) 		0.825
(1.00) 		0.421
(1.00) 		0.538
(1.00) 		0.171
(1.00) 		0.582
(1.00) 		0.748
(1.00) 		0.54
(1.00) 		0.811
(1.00) 		0.28
(1.00) 		0.338
(1.00)
6q loss 132 (48%) 142 0.427
(1.00) 		0.746
(1.00) 		0.215
(1.00) 		0.323
(1.00) 		0.966
(1.00) 		0.214
(1.00) 		0.702
(1.00) 		0.882
(1.00) 		0.439
(1.00) 		0.463
(1.00) 		0.176
(1.00) 		0.804
(1.00)
7p loss 15 (5%) 259 0.955
(1.00) 		0.758
(1.00) 		0.11
(1.00) 		0.389
(1.00) 		0.357
(1.00) 		0.000556
(0.525) 		0.684
(1.00) 		0.932
(1.00) 		0.74
(1.00) 		0.699
(1.00) 		0.422
(1.00) 		0.421
(1.00)
7q loss 14 (5%) 260 0.773
(1.00) 		0.742
(1.00) 		0.915
(1.00) 		0.456
(1.00) 		0.281
(1.00) 		0.102
(1.00) 		0.518
(1.00) 		0.948
(1.00) 		1
(1.00) 		1
(1.00) 		0.891
(1.00) 		1
(1.00)
8p loss 50 (18%) 224 0.464
(1.00) 		0.309
(1.00) 		0.0819
(1.00) 		0.0444
(1.00) 		0.285
(1.00) 		0.0881
(1.00) 		0.97
(1.00) 		0.459
(1.00) 		0.0613
(1.00) 		1
(1.00) 		0.0657
(1.00) 		1
(1.00)
8q loss 19 (7%) 255 0.189
(1.00) 		0.431
(1.00) 		0.293
(1.00) 		0.113
(1.00) 		0.514
(1.00) 		0.21
(1.00) 		0.454
(1.00) 		0.184
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.647
(1.00) 		0.808
(1.00)
9p loss 180 (66%) 94 0.391
(1.00) 		0.548
(1.00) 		0.339
(1.00) 		0.273
(1.00) 		0.78
(1.00) 		0.761
(1.00) 		0.66
(1.00) 		0.706
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.914
(1.00) 		0.019
(1.00)
9q loss 140 (51%) 134 0.968
(1.00) 		0.193
(1.00) 		0.277
(1.00) 		0.162
(1.00) 		0.275
(1.00) 		0.885
(1.00) 		0.273
(1.00) 		0.464
(1.00) 		1
(1.00) 		0.713
(1.00) 		0.918
(1.00) 		0.0818
(1.00)
10p loss 152 (55%) 122 0.292
(1.00) 		0.861
(1.00) 		0.00842
(1.00) 		0.0406
(1.00) 		0.75
(1.00) 		0.0796
(1.00) 		0.36
(1.00) 		0.592
(1.00) 		0.638
(1.00) 		1
(1.00) 		0.718
(1.00) 		0.061
(1.00)
11p loss 93 (34%) 181 0.685
(1.00) 		0.197
(1.00) 		0.0462
(1.00) 		0.769
(1.00) 		0.441
(1.00) 		0.437
(1.00) 		0.136
(1.00) 		0.119
(1.00) 		0.33
(1.00) 		0.699
(1.00) 		0.565
(1.00) 		0.00856
(1.00)
11q loss 107 (39%) 167 0.833
(1.00) 		0.298
(1.00) 		0.483
(1.00) 		0.893
(1.00) 		0.277
(1.00) 		0.653
(1.00) 		0.203
(1.00) 		0.628
(1.00) 		0.0583
(1.00) 		1
(1.00) 		0.815
(1.00) 		0.00139
(1.00)
12p loss 38 (14%) 236 0.878
(1.00) 		0.266
(1.00) 		0.524
(1.00) 		0.252
(1.00) 		0.942
(1.00) 		0.987
(1.00) 		0.89
(1.00) 		0.0481
(1.00) 		0.497
(1.00) 		0.279
(1.00) 		0.0878
(1.00) 		0.376
(1.00)
12q loss 45 (16%) 229 0.708
(1.00) 		0.578
(1.00) 		0.873
(1.00) 		0.332
(1.00) 		0.813
(1.00) 		0.845
(1.00) 		0.612
(1.00) 		0.325
(1.00) 		0.832
(1.00) 		1
(1.00) 		0.0628
(1.00) 		0.403
(1.00)
13q loss 60 (22%) 214 0.385
(1.00) 		0.307
(1.00) 		0.411
(1.00) 		0.326
(1.00) 		0.761
(1.00) 		0.208
(1.00) 		0.548
(1.00) 		0.0124
(1.00) 		0.366
(1.00) 		1
(1.00) 		0.0428
(1.00) 		0.652
(1.00)
14q loss 86 (31%) 188 0.871
(1.00) 		0.757
(1.00) 		0.218
(1.00) 		0.182
(1.00) 		0.347
(1.00) 		0.656
(1.00) 		0.319
(1.00) 		0.294
(1.00) 		0.74
(1.00) 		0.842
(1.00) 		0.274
(1.00) 		0.425
(1.00)
15q loss 38 (14%) 236 0.478
(1.00) 		0.446
(1.00) 		0.741
(1.00) 		0.334
(1.00) 		0.0916
(1.00) 		0.0577
(1.00) 		0.833
(1.00) 		0.415
(1.00) 		0.665
(1.00) 		0.591
(1.00) 		0.151
(1.00) 		0.72
(1.00)
16p loss 53 (19%) 221 0.815
(1.00) 		0.713
(1.00) 		0.0928
(1.00) 		0.415
(1.00) 		0.84
(1.00) 		0.475
(1.00) 		0.638
(1.00) 		0.506
(1.00) 		0.702
(1.00) 		0.35
(1.00) 		0.991
(1.00) 		0.0412
(1.00)
16q loss 81 (30%) 193 0.473
(1.00) 		0.402
(1.00) 		0.184
(1.00) 		0.589
(1.00) 		0.368
(1.00) 		0.279
(1.00) 		0.682
(1.00) 		0.811
(1.00) 		0.869
(1.00) 		0.547
(1.00) 		0.507
(1.00) 		0.0763
(1.00)
17p loss 96 (35%) 178 0.499
(1.00) 		0.335
(1.00) 		0.182
(1.00) 		0.138
(1.00) 		0.632
(1.00) 		0.839
(1.00) 		0.987
(1.00) 		0.6
(1.00) 		0.424
(1.00) 		0.698
(1.00) 		0.318
(1.00) 		0.242
(1.00)
17q loss 47 (17%) 227 0.575
(1.00) 		0.208
(1.00) 		0.58
(1.00) 		0.756
(1.00) 		0.123
(1.00) 		0.875
(1.00) 		0.503
(1.00) 		0.117
(1.00) 		0.842
(1.00) 		1
(1.00) 		0.267
(1.00) 		0.869
(1.00)
18p loss 79 (29%) 195 0.115
(1.00) 		0.109
(1.00) 		0.462
(1.00) 		0.835
(1.00) 		0.158
(1.00) 		0.583
(1.00) 		0.654
(1.00) 		0.23
(1.00) 		0.374
(1.00) 		0.0992
(1.00) 		0.722
(1.00) 		1
(1.00)
18q loss 75 (27%) 199 0.343
(1.00) 		0.0917
(1.00) 		0.486
(1.00) 		0.574
(1.00) 		0.149
(1.00) 		0.612
(1.00) 		0.355
(1.00) 		0.313
(1.00) 		0.476
(1.00) 		0.143
(1.00) 		0.551
(1.00) 		0.677
(1.00)
19p loss 55 (20%) 219 0.784
(1.00) 		0.413
(1.00) 		0.592
(1.00) 		0.653
(1.00) 		0.203
(1.00) 		0.214
(1.00) 		0.396
(1.00) 		0.0812
(1.00) 		0.32
(1.00) 		0.494
(1.00) 		0.299
(1.00) 		0.0873
(1.00)
19q loss 53 (19%) 221 0.774
(1.00) 		0.842
(1.00) 		0.525
(1.00) 		0.81
(1.00) 		0.6
(1.00) 		0.25
(1.00) 		0.659
(1.00) 		0.0593
(1.00) 		0.552
(1.00) 		0.814
(1.00) 		0.527
(1.00) 		0.0843
(1.00)
20p loss 15 (5%) 259 0.903
(1.00) 		0.726
(1.00) 		0.223
(1.00) 		0.126
(1.00) 		0.981
(1.00) 		1
(1.00) 		0.307
(1.00) 		0.0786
(1.00) 		0.529
(1.00) 		0.403
(1.00) 		0.587
(1.00) 		1
(1.00)
20q loss 4 (1%) 270 0.793
(1.00) 		0.713
(1.00) 		0.928
(1.00) 		0.186
(1.00) 		0.527
(1.00) 		0.747
(1.00) 		0.2
(1.00) 		0.995
(1.00) 		1
(1.00) 		0.403
(1.00) 		0.699
(1.00) 		0.301
(1.00)
21q loss 53 (19%) 221 0.755
(1.00) 		0.762
(1.00) 		0.149
(1.00) 		0.624
(1.00) 		0.475
(1.00) 		0.613
(1.00) 		0.298
(1.00) 		0.405
(1.00) 		0.847
(1.00) 		0.157
(1.00) 		0.392
(1.00) 		0.433
(1.00)
22q loss 27 (10%) 247 0.346
(1.00) 		0.334
(1.00) 		0.432
(1.00) 		0.812
(1.00) 		0.078
(1.00) 		0.202
(1.00) 		0.212
(1.00) 		0.298
(1.00) 		0.0675
(1.00) 		1
(1.00) 		0.137
(1.00) 		0.836
(1.00)
xq loss 70 (26%) 204 0.505
(1.00) 		0.9
(1.00) 		0.586
(1.00) 		0.0574
(1.00) 		0.0703
(1.00) 		0.435
(1.00) 		0.0432
(1.00) 		0.00369
(1.00) 		0.288
(1.00) 		0.396
(1.00) 		0.603
(1.00) 		0.0229
(1.00)
'5q gain' versus 'BRESLOW.THICKNESS'

P value = 0.000131 (t-test), Q value = 0.12

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

nPatients Mean (Std.Dev)
ALL 200 3.5 (5.0)
5Q GAIN MUTATED 23 1.8 (1.5)
5Q GAIN WILD-TYPE 177 3.7 (5.2)

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

'9q gain' versus 'BRESLOW.THICKNESS'

P value = 0.000188 (t-test), Q value = 0.18

Table S2.  Gene #18: '9q gain' versus Clinical Feature #11: 'BRESLOW.THICKNESS'

nPatients Mean (Std.Dev)
ALL 200 3.5 (5.0)
9Q GAIN MUTATED 19 1.8 (1.4)
9Q GAIN WILD-TYPE 181 3.7 (5.2)

Figure S2.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #11: 'BRESLOW.THICKNESS'

'10q loss' versus 'AGE'

P value = 7.2e-05 (t-test), Q value = 0.068

Table S3.  Gene #59: '10q loss' versus Clinical Feature #3: 'AGE'

nPatients Mean (Std.Dev)
ALL 270 55.5 (15.6)
10Q LOSS MUTATED 163 52.6 (16.1)
10Q LOSS WILD-TYPE 107 59.9 (13.6)

Figure S3.  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 = 274

  • 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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