Correlation between copy number variations of arm-level result and molecular subtypes
Skin Cutaneous Melanoma (Metastatic)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1M907K8
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 molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1M907K8
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 80 arm-level events and 10 molecular subtypes across 366 patients, 29 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q gain cnv correlated to 'CN_CNMF'.

  • 2p gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.

  • 2q gain cnv correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • 6p gain cnv correlated to 'METHLYATION_CNMF'.

  • 7p gain cnv correlated to 'CN_CNMF'.

  • 7q gain cnv correlated to 'CN_CNMF'.

  • 8p gain cnv correlated to 'CN_CNMF'.

  • 8q gain cnv correlated to 'CN_CNMF'.

  • 11q gain cnv correlated to 'CN_CNMF'.

  • 13q gain cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • 15q gain cnv correlated to 'CN_CNMF'.

  • 16q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 19q gain cnv correlated to 'MRNASEQ_CNMF'.

  • 20p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 20q gain cnv correlated to 'CN_CNMF'.

  • xq gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • 1p loss cnv correlated to 'METHLYATION_CNMF'.

  • 6q loss cnv correlated to 'CN_CNMF'.

  • 9p loss cnv correlated to 'CN_CNMF'.

  • 10p loss cnv correlated to 'CN_CNMF'.

  • 10q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 14q loss cnv correlated to 'CN_CNMF'.

  • xq loss cnv correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 29 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) nWild-Type 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 Fisher's exact test Fisher's exact test Fisher's exact test
2q gain 65 (18%) 301 0.00818
(1.00) 		0.465
(1.00) 		0.775
(1.00) 		0.344
(1.00) 		0.0002
(0.154) 		0.00209
(1.00) 		0.138
(1.00) 		4e-05
(0.0312) 		0.0526
(1.00) 		0.00236
(1.00)
13q gain 94 (26%) 272 1e-05
(0.00796) 		1e-05
(0.00796) 		0.459
(1.00) 		0.313
(1.00) 		0.00051
(0.389) 		0.231
(1.00) 		0.498
(1.00) 		0.839
(1.00) 		0.0896
(1.00) 		0.684
(1.00)
16q gain 44 (12%) 322 0.00028
(0.215) 		0.0228
(1.00) 		0.274
(1.00) 		0.628
(1.00) 		1e-05
(0.00796) 		0.0016
(1.00) 		0.785
(1.00) 		0.101
(1.00) 		0.054
(1.00) 		0.149
(1.00)
20p gain 147 (40%) 219 1e-05
(0.00796) 		0.0114
(1.00) 		0.843
(1.00) 		0.985
(1.00) 		0.00017
(0.131) 		0.0208
(1.00) 		0.487
(1.00) 		0.267
(1.00) 		0.272
(1.00) 		0.0659
(1.00)
xq gain 42 (11%) 324 7e-05
(0.0543) 		0.00036
(0.276) 		0.584
(1.00) 		0.986
(1.00) 		0.00484
(1.00) 		0.0155
(1.00) 		0.44
(1.00) 		0.348
(1.00) 		0.00019
(0.147) 		0.647
(1.00)
10q loss 224 (61%) 142 1e-05
(0.00796) 		0.237
(1.00) 		0.919
(1.00) 		0.201
(1.00) 		5e-05
(0.0389) 		0.00048
(0.367) 		0.021
(1.00) 		0.365
(1.00) 		0.332
(1.00) 		0.5
(1.00)
1q gain 171 (47%) 195 1e-05
(0.00796) 		0.592
(1.00) 		0.27
(1.00) 		0.51
(1.00) 		0.0176
(1.00) 		0.138
(1.00) 		0.124
(1.00) 		0.316
(1.00) 		0.0471
(1.00) 		0.285
(1.00)
2p gain 67 (18%) 299 0.0115
(1.00) 		0.367
(1.00) 		0.801
(1.00) 		0.813
(1.00) 		0.00162
(1.00) 		0.00418
(1.00) 		0.105
(1.00) 		0.00012
(0.093) 		0.0384
(1.00) 		0.0277
(1.00)
6p gain 144 (39%) 222 0.00053
(0.404) 		6e-05
(0.0466) 		0.988
(1.00) 		0.144
(1.00) 		0.223
(1.00) 		0.152
(1.00) 		0.0021
(1.00) 		0.0573
(1.00) 		0.00041
(0.314) 		0.00169
(1.00)
7p gain 203 (55%) 163 1e-05
(0.00796) 		0.91
(1.00) 		0.461
(1.00) 		0.373
(1.00) 		0.0236
(1.00) 		0.104
(1.00) 		0.074
(1.00) 		0.738
(1.00) 		0.174
(1.00) 		0.569
(1.00)
7q gain 200 (55%) 166 3e-05
(0.0234) 		0.877
(1.00) 		0.693
(1.00) 		0.519
(1.00) 		0.00886
(1.00) 		0.0488
(1.00) 		0.685
(1.00) 		0.57
(1.00) 		0.00889
(1.00) 		0.3
(1.00)
8p gain 121 (33%) 245 1e-05
(0.00796) 		0.225
(1.00) 		0.611
(1.00) 		0.842
(1.00) 		0.0169
(1.00) 		0.0134
(1.00) 		0.523
(1.00) 		0.844
(1.00) 		0.852
(1.00) 		0.44
(1.00)
8q gain 169 (46%) 197 1e-05
(0.00796) 		0.00212
(1.00) 		0.695
(1.00) 		0.797
(1.00) 		0.00414
(1.00) 		0.0434
(1.00) 		0.626
(1.00) 		0.891
(1.00) 		0.807
(1.00) 		0.375
(1.00)
11q gain 29 (8%) 337 0.00021
(0.161) 		0.165
(1.00) 		0.0758
(1.00) 		0.0872
(1.00) 		0.0119
(1.00) 		0.0218
(1.00) 		0.00612
(1.00) 		0.00082
(0.619) 		0.0568
(1.00) 		0.0133
(1.00)
15q gain 85 (23%) 281 4e-05
(0.0312) 		0.176
(1.00) 		0.945
(1.00) 		0.817
(1.00) 		0.00922
(1.00) 		0.00597
(1.00) 		0.192
(1.00) 		0.172
(1.00) 		0.375
(1.00) 		0.0565
(1.00)
19q gain 56 (15%) 310 0.0112
(1.00) 		0.0411
(1.00) 		0.292
(1.00) 		1
(1.00) 		1e-05
(0.00796) 		0.00767
(1.00) 		0.523
(1.00) 		0.431
(1.00) 		0.154
(1.00) 		0.853
(1.00)
20q gain 179 (49%) 187 1e-05
(0.00796) 		0.0198
(1.00) 		0.941
(1.00) 		0.974
(1.00) 		0.00364
(1.00) 		0.124
(1.00) 		0.478
(1.00) 		0.259
(1.00) 		0.914
(1.00) 		0.28
(1.00)
1p loss 53 (14%) 313 0.0491
(1.00) 		0.00019
(0.147) 		0.587
(1.00) 		0.313
(1.00) 		0.0141
(1.00) 		0.004
(1.00) 		0.00922
(1.00) 		0.693
(1.00) 		0.178
(1.00) 		0.0552
(1.00)
6q loss 172 (47%) 194 1e-05
(0.00796) 		0.0185
(1.00) 		0.978
(1.00) 		0.483
(1.00) 		0.00412
(1.00) 		0.0317
(1.00) 		0.219
(1.00) 		0.215
(1.00) 		0.404
(1.00) 		0.162
(1.00)
9p loss 236 (64%) 130 0.00013
(0.101) 		0.106
(1.00) 		0.648
(1.00) 		0.45
(1.00) 		0.00557
(1.00) 		0.123
(1.00) 		0.0759
(1.00) 		0.218
(1.00) 		0.737
(1.00) 		0.59
(1.00)
10p loss 204 (56%) 162 1e-05
(0.00796) 		0.151
(1.00) 		0.923
(1.00) 		0.411
(1.00) 		0.00095
(0.715) 		0.00532
(1.00) 		0.0613
(1.00) 		0.345
(1.00) 		0.369
(1.00) 		0.56
(1.00)
14q loss 112 (31%) 254 2e-05
(0.0156) 		0.44
(1.00) 		0.413
(1.00) 		0.268
(1.00) 		0.0103
(1.00) 		0.0593
(1.00) 		0.00527
(1.00) 		0.212
(1.00) 		0.335
(1.00) 		0.238
(1.00)
xq loss 94 (26%) 272 0.0276
(1.00) 		1e-05
(0.00796) 		0.239
(1.00) 		0.0771
(1.00) 		0.00094
(0.709) 		0.00062
(0.471) 		0.0554
(1.00) 		0.682
(1.00) 		0.0247
(1.00) 		0.687
(1.00)
1p gain 87 (24%) 279 0.134
(1.00) 		0.126
(1.00) 		0.798
(1.00) 		0.978
(1.00) 		0.871
(1.00) 		0.751
(1.00) 		0.569
(1.00) 		0.923
(1.00) 		0.801
(1.00) 		0.495
(1.00)
3p gain 63 (17%) 303 0.22
(1.00) 		0.224
(1.00) 		0.0451
(1.00) 		0.0209
(1.00) 		0.427
(1.00) 		0.732
(1.00) 		0.333
(1.00) 		0.558
(1.00) 		0.755
(1.00) 		0.976
(1.00)
3q gain 72 (20%) 294 0.563
(1.00) 		0.415
(1.00) 		0.0187
(1.00) 		0.0455
(1.00) 		0.0486
(1.00) 		0.396
(1.00) 		0.135
(1.00) 		0.529
(1.00) 		0.201
(1.00) 		0.618
(1.00)
4p gain 56 (15%) 310 0.00201
(1.00) 		0.253
(1.00) 		0.305
(1.00) 		0.857
(1.00) 		0.569
(1.00) 		0.563
(1.00) 		0.303
(1.00) 		0.0461
(1.00) 		0.729
(1.00) 		0.564
(1.00)
4q gain 47 (13%) 319 0.0118
(1.00) 		0.29
(1.00) 		0.264
(1.00) 		0.935
(1.00) 		0.266
(1.00) 		0.747
(1.00) 		0.689
(1.00) 		0.0419
(1.00) 		0.773
(1.00) 		0.943
(1.00)
5p gain 76 (21%) 290 0.00055
(0.419) 		0.129
(1.00) 		0.89
(1.00) 		0.397
(1.00) 		0.172
(1.00) 		0.284
(1.00) 		0.0875
(1.00) 		0.499
(1.00) 		0.984
(1.00) 		0.0973
(1.00)
5q gain 52 (14%) 314 0.0105
(1.00) 		0.129
(1.00) 		0.36
(1.00) 		0.138
(1.00) 		0.965
(1.00) 		1
(1.00) 		0.103
(1.00) 		0.522
(1.00) 		0.334
(1.00) 		0.0714
(1.00)
6q gain 48 (13%) 318 0.309
(1.00) 		0.492
(1.00) 		0.859
(1.00) 		0.331
(1.00) 		0.924
(1.00) 		0.507
(1.00) 		0.356
(1.00) 		0.404
(1.00) 		0.835
(1.00) 		0.644
(1.00)
9p gain 16 (4%) 350 0.306
(1.00) 		0.203
(1.00) 		0.377
(1.00) 		0.837
(1.00) 		0.344
(1.00) 		0.547
(1.00) 		0.903
(1.00) 		0.608
(1.00) 		0.128
(1.00) 		0.262
(1.00)
9q gain 21 (6%) 345 0.664
(1.00) 		0.656
(1.00) 		0.135
(1.00) 		0.929
(1.00) 		0.537
(1.00) 		0.295
(1.00) 		0.886
(1.00) 		0.417
(1.00) 		0.48
(1.00) 		0.553
(1.00)
10p gain 12 (3%) 354 0.499
(1.00) 		0.932
(1.00) 		0.866
(1.00) 		0.548
(1.00) 		0.705
(1.00) 		0.93
(1.00) 		0.26
(1.00) 		0.557
(1.00) 		1
(1.00) 		0.906
(1.00)
10q gain 3 (1%) 363 0.378
(1.00) 		0.359
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.777
(1.00) 		0.721
(1.00) 		0.269
(1.00) 		0.691
(1.00)
11p gain 35 (10%) 331 0.00634
(1.00) 		0.0874
(1.00) 		0.0865
(1.00) 		0.187
(1.00) 		0.00185
(1.00) 		0.054
(1.00) 		0.024
(1.00) 		0.00628
(1.00) 		0.23
(1.00) 		0.018
(1.00)
12p gain 65 (18%) 301 0.00081
(0.612) 		0.18
(1.00) 		0.538
(1.00) 		0.426
(1.00) 		0.00467
(1.00) 		0.295
(1.00) 		0.873
(1.00) 		0.492
(1.00) 		0.165
(1.00) 		0.368
(1.00)
12q gain 39 (11%) 327 0.0163
(1.00) 		0.931
(1.00) 		0.618
(1.00) 		0.057
(1.00) 		0.342
(1.00) 		0.274
(1.00) 		0.818
(1.00) 		0.0611
(1.00) 		0.422
(1.00) 		0.678
(1.00)
14q gain 41 (11%) 325 0.394
(1.00) 		0.328
(1.00) 		0.348
(1.00) 		0.156
(1.00) 		0.934
(1.00) 		0.908
(1.00) 		0.511
(1.00) 		0.506
(1.00) 		0.764
(1.00) 		0.966
(1.00)
16p gain 58 (16%) 308 0.00162
(1.00) 		0.0173
(1.00) 		0.987
(1.00) 		0.658
(1.00) 		0.00063
(0.478) 		0.054
(1.00) 		0.782
(1.00) 		0.0742
(1.00) 		0.0716
(1.00) 		0.123
(1.00)
17p gain 37 (10%) 329 0.00924
(1.00) 		0.00163
(1.00) 		0.581
(1.00) 		0.528
(1.00) 		0.118
(1.00) 		0.101
(1.00) 		0.57
(1.00) 		0.296
(1.00) 		0.975
(1.00) 		0.139
(1.00)
17q gain 65 (18%) 301 0.0521
(1.00) 		0.0556
(1.00) 		0.104
(1.00) 		0.276
(1.00) 		0.883
(1.00) 		0.569
(1.00) 		0.477
(1.00) 		0.671
(1.00) 		0.556
(1.00) 		0.764
(1.00)
18p gain 55 (15%) 311 0.00216
(1.00) 		0.616
(1.00) 		0.21
(1.00) 		0.387
(1.00) 		0.202
(1.00) 		0.599
(1.00) 		0.933
(1.00) 		0.966
(1.00) 		0.0606
(1.00) 		0.469
(1.00)
18q gain 44 (12%) 322 0.00074
(0.56) 		0.708
(1.00) 		0.352
(1.00) 		0.467
(1.00) 		0.304
(1.00) 		0.602
(1.00) 		0.675
(1.00) 		0.77
(1.00) 		0.646
(1.00) 		0.796
(1.00)
19p gain 57 (16%) 309 0.00489
(1.00) 		0.0492
(1.00) 		0.248
(1.00) 		0.799
(1.00) 		0.00056
(0.426) 		0.0112
(1.00) 		0.908
(1.00) 		0.542
(1.00) 		0.172
(1.00) 		0.901
(1.00)
21q gain 67 (18%) 299 0.165
(1.00) 		0.0522
(1.00) 		0.889
(1.00) 		0.531
(1.00) 		0.252
(1.00) 		0.763
(1.00) 		0.11
(1.00) 		0.997
(1.00) 		0.949
(1.00) 		0.508
(1.00)
22q gain 126 (34%) 240 0.00033
(0.253) 		0.166
(1.00) 		0.893
(1.00) 		0.945
(1.00) 		0.0875
(1.00) 		0.119
(1.00) 		0.615
(1.00) 		0.161
(1.00) 		0.701
(1.00) 		0.501
(1.00)
1q loss 28 (8%) 338 0.0645
(1.00) 		0.0225
(1.00) 		0.968
(1.00) 		0.462
(1.00) 		0.163
(1.00) 		0.0929
(1.00) 		0.368
(1.00) 		0.939
(1.00) 		0.284
(1.00) 		0.357
(1.00)
2p loss 51 (14%) 315 0.372
(1.00) 		0.292
(1.00) 		0.0473
(1.00) 		0.0151
(1.00) 		0.845
(1.00) 		0.26
(1.00) 		0.0029
(1.00) 		0.0633
(1.00) 		0.224
(1.00) 		0.211
(1.00)
2q loss 52 (14%) 314 0.816
(1.00) 		0.278
(1.00) 		0.0105
(1.00) 		0.00195
(1.00) 		0.556
(1.00) 		0.184
(1.00) 		0.00835
(1.00) 		0.117
(1.00) 		0.17
(1.00) 		0.226
(1.00)
3p loss 61 (17%) 305 0.061
(1.00) 		0.86
(1.00) 		0.493
(1.00) 		0.328
(1.00) 		0.228
(1.00) 		0.331
(1.00) 		0.06
(1.00) 		0.66
(1.00) 		0.519
(1.00) 		0.408
(1.00)
3q loss 53 (14%) 313 0.0474
(1.00) 		0.0796
(1.00) 		0.515
(1.00) 		0.374
(1.00) 		0.267
(1.00) 		0.409
(1.00) 		0.126
(1.00) 		0.633
(1.00) 		0.331
(1.00) 		0.768
(1.00)
4p loss 80 (22%) 286 0.528
(1.00) 		0.176
(1.00) 		0.352
(1.00) 		0.969
(1.00) 		0.105
(1.00) 		0.074
(1.00) 		0.544
(1.00) 		0.0134
(1.00) 		0.879
(1.00) 		0.318
(1.00)
4q loss 85 (23%) 281 0.529
(1.00) 		0.0635
(1.00) 		0.483
(1.00) 		0.749
(1.00) 		0.139
(1.00) 		0.0479
(1.00) 		0.903
(1.00) 		0.00556
(1.00) 		0.604
(1.00) 		0.242
(1.00)
5p loss 79 (22%) 287 0.85
(1.00) 		0.111
(1.00) 		0.882
(1.00) 		0.86
(1.00) 		0.686
(1.00) 		0.668
(1.00) 		0.513
(1.00) 		0.26
(1.00) 		0.207
(1.00) 		0.389
(1.00)
5q loss 99 (27%) 267 0.591
(1.00) 		0.0393
(1.00) 		0.651
(1.00) 		0.364
(1.00) 		0.751
(1.00) 		0.25
(1.00) 		0.907
(1.00) 		0.578
(1.00) 		0.418
(1.00) 		0.608
(1.00)
6p loss 68 (19%) 298 0.00548
(1.00) 		0.526
(1.00) 		0.874
(1.00) 		0.276
(1.00) 		0.0106
(1.00) 		0.0297
(1.00) 		0.0419
(1.00) 		0.0906
(1.00) 		0.0257
(1.00) 		0.0275
(1.00)
7p loss 18 (5%) 348 0.83
(1.00) 		0.0572
(1.00) 		0.0958
(1.00) 		0.561
(1.00) 		0.495
(1.00) 		0.947
(1.00) 		0.653
(1.00) 		0.709
(1.00) 		0.17
(1.00) 		0.749
(1.00)
7q loss 17 (5%) 349 0.361
(1.00) 		0.0104
(1.00) 		0.339
(1.00) 		0.438
(1.00) 		0.425
(1.00) 		0.488
(1.00) 		0.523
(1.00) 		0.771
(1.00) 		0.0957
(1.00) 		0.926
(1.00)
8p loss 67 (18%) 299 0.125
(1.00) 		0.486
(1.00) 		0.0583
(1.00) 		0.294
(1.00) 		0.0928
(1.00) 		0.953
(1.00) 		0.458
(1.00) 		0.0297
(1.00) 		0.439
(1.00) 		0.182
(1.00)
8q loss 27 (7%) 339 0.52
(1.00) 		0.00845
(1.00) 		0.319
(1.00) 		0.537
(1.00) 		0.275
(1.00) 		0.787
(1.00) 		0.408
(1.00) 		0.504
(1.00) 		0.0146
(1.00) 		0.147
(1.00)
9q loss 185 (51%) 181 0.272
(1.00) 		0.0547
(1.00) 		0.992
(1.00) 		0.15
(1.00) 		0.0385
(1.00) 		0.808
(1.00) 		0.0401
(1.00) 		0.138
(1.00) 		0.97
(1.00) 		0.466
(1.00)
11p loss 126 (34%) 240 0.0182
(1.00) 		0.0474
(1.00) 		0.585
(1.00) 		0.294
(1.00) 		0.586
(1.00) 		0.617
(1.00) 		0.525
(1.00) 		0.337
(1.00) 		0.0844
(1.00) 		0.568
(1.00)
11q loss 148 (40%) 218 0.0125
(1.00) 		0.309
(1.00) 		0.952
(1.00) 		0.7
(1.00) 		0.349
(1.00) 		0.414
(1.00) 		0.74
(1.00) 		0.157
(1.00) 		0.0751
(1.00) 		0.547
(1.00)
12p loss 59 (16%) 307 0.221
(1.00) 		0.115
(1.00) 		0.855
(1.00) 		0.872
(1.00) 		0.0186
(1.00) 		0.623
(1.00) 		0.125
(1.00) 		0.435
(1.00) 		0.982
(1.00) 		0.579
(1.00)
12q loss 67 (18%) 299 0.034
(1.00) 		0.0124
(1.00) 		0.983
(1.00) 		0.874
(1.00) 		0.125
(1.00) 		0.379
(1.00) 		0.133
(1.00) 		0.5
(1.00) 		0.449
(1.00) 		0.696
(1.00)
13q loss 80 (22%) 286 0.937
(1.00) 		0.0192
(1.00) 		0.0661
(1.00) 		0.56
(1.00) 		0.563
(1.00) 		0.402
(1.00) 		0.8
(1.00) 		0.202
(1.00) 		0.323
(1.00) 		0.47
(1.00)
15q loss 52 (14%) 314 0.183
(1.00) 		0.285
(1.00) 		0.286
(1.00) 		0.062
(1.00) 		0.65
(1.00) 		0.118
(1.00) 		0.645
(1.00) 		0.421
(1.00) 		0.29
(1.00) 		0.458
(1.00)
16p loss 68 (19%) 298 0.205
(1.00) 		0.105
(1.00) 		0.0629
(1.00) 		0.363
(1.00) 		0.05
(1.00) 		0.52
(1.00) 		0.233
(1.00) 		0.194
(1.00) 		0.134
(1.00) 		0.302
(1.00)
16q loss 106 (29%) 260 0.303
(1.00) 		0.345
(1.00) 		0.0158
(1.00) 		0.756
(1.00) 		0.0187
(1.00) 		0.12
(1.00) 		0.327
(1.00) 		0.105
(1.00) 		0.0678
(1.00) 		0.184
(1.00)
17p loss 127 (35%) 239 0.0772
(1.00) 		0.00637
(1.00) 		0.446
(1.00) 		0.512
(1.00) 		0.204
(1.00) 		0.146
(1.00) 		0.879
(1.00) 		0.518
(1.00) 		0.622
(1.00) 		0.444
(1.00)
17q loss 64 (17%) 302 0.142
(1.00) 		0.141
(1.00) 		0.129
(1.00) 		0.545
(1.00) 		0.8
(1.00) 		0.184
(1.00) 		0.508
(1.00) 		0.871
(1.00) 		0.0614
(1.00) 		1
(1.00)
18p loss 104 (28%) 262 0.73
(1.00) 		0.587
(1.00) 		0.377
(1.00) 		0.512
(1.00) 		0.023
(1.00) 		0.366
(1.00) 		0.0272
(1.00) 		0.391
(1.00) 		0.545
(1.00) 		0.152
(1.00)
18q loss 100 (27%) 266 0.446
(1.00) 		0.819
(1.00) 		0.296
(1.00) 		0.488
(1.00) 		0.393
(1.00) 		0.847
(1.00) 		0.75
(1.00) 		0.232
(1.00) 		0.561
(1.00) 		0.178
(1.00)
19p loss 77 (21%) 289 0.0724
(1.00) 		0.603
(1.00) 		0.784
(1.00) 		0.035
(1.00) 		0.117
(1.00) 		0.786
(1.00) 		0.572
(1.00) 		0.887
(1.00) 		0.238
(1.00) 		0.513
(1.00)
19q loss 73 (20%) 293 0.0242
(1.00) 		0.0529
(1.00) 		0.979
(1.00) 		0.0822
(1.00) 		0.0523
(1.00) 		0.538
(1.00) 		0.486
(1.00) 		0.989
(1.00) 		0.0547
(1.00) 		0.529
(1.00)
20p loss 26 (7%) 340 0.37
(1.00) 		0.662
(1.00) 		0.236
(1.00) 		0.772
(1.00) 		0.282
(1.00) 		0.0538
(1.00) 		0.134
(1.00) 		0.0173
(1.00) 		0.89
(1.00) 		0.187
(1.00)
20q loss 9 (2%) 357 0.399
(1.00) 		0.183
(1.00) 		0.0763
(1.00) 		0.00729
(1.00) 		0.685
(1.00) 		0.557
(1.00) 		0.362
(1.00) 		0.686
(1.00)
21q loss 70 (19%) 296 0.0996
(1.00) 		0.311
(1.00) 		0.471
(1.00) 		0.93
(1.00) 		0.803
(1.00) 		0.327
(1.00) 		0.335
(1.00) 		0.746
(1.00) 		0.593
(1.00) 		0.768
(1.00)
22q loss 39 (11%) 327 0.403
(1.00) 		0.407
(1.00) 		0.955
(1.00) 		0.94
(1.00) 		0.179
(1.00) 		0.658
(1.00) 		0.867
(1.00) 		0.701
(1.00) 		0.708
(1.00) 		0.773
(1.00)
'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S1.  Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
1Q GAIN MUTATED 77 44 50
1Q GAIN WILD-TYPE 24 95 76

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #1: 'CN_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.093

Table S2.  Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
2P GAIN MUTATED 7 23 24 11
2P GAIN WILD-TYPE 84 124 50 27

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.15

Table S3.  Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
2Q GAIN MUTATED 18 11 36
2Q GAIN WILD-TYPE 124 91 85

Figure S3.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.031

Table S4.  Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 91 147 74 38
2Q GAIN MUTATED 6 22 24 11
2Q GAIN WILD-TYPE 85 125 50 27

Figure S4.  Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.047

Table S5.  Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
6P GAIN MUTATED 52 38 51
6P GAIN WILD-TYPE 77 104 41

Figure S5.  Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S6.  Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
7P GAIN MUTATED 57 56 90
7P GAIN WILD-TYPE 44 83 36

Figure S6.  Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #1: 'CN_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.023

Table S7.  Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
7Q GAIN MUTATED 54 58 88
7Q GAIN WILD-TYPE 47 81 38

Figure S7.  Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'CN_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S8.  Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
8P GAIN MUTATED 25 28 68
8P GAIN WILD-TYPE 76 111 58

Figure S8.  Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #1: 'CN_CNMF'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S9.  Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
8Q GAIN MUTATED 41 42 86
8Q GAIN WILD-TYPE 60 97 40

Figure S9.  Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'CN_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.16

Table S10.  Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
11Q GAIN MUTATED 2 7 20
11Q GAIN WILD-TYPE 99 132 106

Figure S10.  Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S11.  Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
13Q GAIN MUTATED 31 17 46
13Q GAIN WILD-TYPE 70 122 80

Figure S11.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #1: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S12.  Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
13Q GAIN MUTATED 31 22 40
13Q GAIN WILD-TYPE 98 120 52

Figure S12.  Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.031

Table S13.  Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
15Q GAIN MUTATED 15 23 47
15Q GAIN WILD-TYPE 86 116 79

Figure S13.  Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.22

Table S14.  Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
16Q GAIN MUTATED 12 6 26
16Q GAIN WILD-TYPE 89 133 100

Figure S14.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #1: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S15.  Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
16Q GAIN MUTATED 8 7 29
16Q GAIN WILD-TYPE 134 95 92

Figure S15.  Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S16.  Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
19Q GAIN MUTATED 19 5 32
19Q GAIN WILD-TYPE 123 97 89

Figure S16.  Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S17.  Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
20P GAIN MUTATED 48 29 70
20P GAIN WILD-TYPE 53 110 56

Figure S17.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.13

Table S18.  Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
20P GAIN MUTATED 47 33 67
20P GAIN WILD-TYPE 95 69 54

Figure S18.  Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S19.  Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
20Q GAIN MUTATED 64 37 78
20Q GAIN WILD-TYPE 37 102 48

Figure S19.  Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.054

Table S20.  Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
XQ GAIN MUTATED 22 5 15
XQ GAIN WILD-TYPE 79 134 111

Figure S20.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'CN_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.15

Table S21.  Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 105 139
XQ GAIN MUTATED 1 13 22
XQ GAIN WILD-TYPE 91 92 117

Figure S21.  Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.15

Table S22.  Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
1P LOSS MUTATED 12 14 26
1P LOSS WILD-TYPE 117 128 66

Figure S22.  Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S23.  Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
6Q LOSS MUTATED 61 38 73
6Q LOSS WILD-TYPE 40 101 53

Figure S23.  Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'CN_CNMF'

'9p loss' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.1

Table S24.  Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
9P LOSS MUTATED 60 77 99
9P LOSS WILD-TYPE 41 62 27

Figure S24.  Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S25.  Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
10P LOSS MUTATED 55 51 98
10P LOSS WILD-TYPE 46 88 28

Figure S25.  Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S26.  Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
10Q LOSS MUTATED 51 63 110
10Q LOSS WILD-TYPE 50 76 16

Figure S26.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #1: 'CN_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.039

Table S27.  Gene #60: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 142 102 121
10Q LOSS MUTATED 77 54 93
10Q LOSS WILD-TYPE 65 48 28

Figure S27.  Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.016

Table S28.  Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 101 139 126
14Q LOSS MUTATED 26 27 59
14Q LOSS WILD-TYPE 75 112 67

Figure S28.  Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S29.  Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 129 142 92
XQ LOSS MUTATED 49 17 27
XQ LOSS WILD-TYPE 80 125 65

Figure S29.  Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data
Input

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

  • Molecular subtypes file = SKCM-TM.transferedmergedcluster.txt

  • Number of patients = 366

  • Number of significantly arm-level cnvs = 80

  • Number of molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

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] 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)
[2] 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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