Correlation between copy number variation genes (focal events) and selected clinical features
Liver Hepatocellular Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1TT4PVS
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1TT4PVS
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 62 focal events and 11 clinical features across 311 patients, 7 significant findings detected with Q value < 0.25.

  • amp_2q33.1 cnv correlated to 'GENDER'.

  • amp_8q13.3 cnv correlated to 'GENDER'.

  • amp_8q24.21 cnv correlated to 'GENDER' and 'RACE'.

  • del_4q21.3 cnv correlated to 'AGE'.

  • del_4q35.1 cnv correlated to 'RACE'.

  • del_16q23.1 cnv correlated to 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 62 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 7 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		COMPLETENESS
OF
RESECTION 		RACE ETHNICITY
nCNV (%) nWild-Type 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 Fisher's exact test Fisher's exact test
amp 8q24 21 199 (64%) 112 0.435
(1.00) 		0.0623
(1.00) 		0.0892
(1.00) 		0.617
(1.00) 		0.241
(1.00) 		0.0427
(1.00) 		0.000226
(0.154) 		1
(1.00) 		0.544
(1.00) 		0.00032
(0.217) 		0.267
(1.00)
amp 2q33 1 57 (18%) 254 0.319
(1.00) 		0.218
(1.00) 		0.23
(1.00) 		0.228
(1.00) 		0.481
(1.00) 		0.113
(1.00) 		0.000135
(0.0919) 		0.54
(1.00) 		0.616
(1.00) 		0.612
(1.00) 		0.646
(1.00)
amp 8q13 3 177 (57%) 134 0.678
(1.00) 		0.0551
(1.00) 		0.109
(1.00) 		0.26
(1.00) 		0.571
(1.00) 		0.621
(1.00) 		0.000356
(0.241) 		0.518
(1.00) 		0.83
(1.00) 		0.126
(1.00) 		0.144
(1.00)
del 4q21 3 148 (48%) 163 0.518
(1.00) 		0.000178
(0.121) 		0.566
(1.00) 		0.652
(1.00) 		0.618
(1.00) 		0.0108
(1.00) 		0.546
(1.00) 		0.608
(1.00) 		0.896
(1.00) 		0.00362
(1.00) 		0.486
(1.00)
del 4q35 1 151 (49%) 160 0.0974
(1.00) 		0.000587
(0.395) 		0.45
(1.00) 		0.222
(1.00) 		1
(1.00) 		0.0142
(1.00) 		0.0698
(1.00) 		0.61
(1.00) 		0.632
(1.00) 		0.00014
(0.0953) 		0.723
(1.00)
del 16q23 1 143 (46%) 168 0.964
(1.00) 		0.000584
(0.394) 		0.249
(1.00) 		0.0995
(1.00) 		0.615
(1.00) 		0.17
(1.00) 		0.226
(1.00) 		0.614
(1.00) 		0.473
(1.00) 		0.00035
(0.237) 		0.153
(1.00)
amp 1p22 3 77 (25%) 234 0.227
(1.00) 		0.0773
(1.00) 		0.0165
(1.00) 		0.0331
(1.00) 		1
(1.00) 		0.0386
(1.00) 		0.574
(1.00) 		1
(1.00) 		0.0552
(1.00) 		0.276
(1.00) 		1
(1.00)
amp 1q22 241 (77%) 70 0.0889
(1.00) 		0.95
(1.00) 		0.721
(1.00) 		0.479
(1.00) 		0.523
(1.00) 		0.419
(1.00) 		0.771
(1.00) 		0.0543
(1.00) 		0.908
(1.00) 		0.214
(1.00) 		1
(1.00)
amp 1q42 3 231 (74%) 80 0.422
(1.00) 		0.677
(1.00) 		0.261
(1.00) 		0.174
(1.00) 		1
(1.00) 		0.172
(1.00) 		0.679
(1.00) 		0.808
(1.00) 		0.817
(1.00) 		0.383
(1.00) 		0.213
(1.00)
amp 2p24 1 57 (18%) 254 0.147
(1.00) 		0.143
(1.00) 		0.0643
(1.00) 		0.0266
(1.00) 		0.0823
(1.00) 		0.182
(1.00) 		0.00787
(1.00) 		0.54
(1.00) 		0.285
(1.00) 		0.368
(1.00) 		0.65
(1.00)
amp 3q26 31 66 (21%) 245 0.335
(1.00) 		0.589
(1.00) 		0.86
(1.00) 		0.791
(1.00) 		0.481
(1.00) 		0.526
(1.00) 		0.768
(1.00) 		0.759
(1.00) 		0.862
(1.00) 		0.616
(1.00) 		1
(1.00)
amp 4p14 43 (14%) 268 0.0802
(1.00) 		0.0179
(1.00) 		0.562
(1.00) 		0.135
(1.00) 		1
(1.00) 		0.175
(1.00) 		0.726
(1.00) 		1
(1.00) 		0.799
(1.00) 		0.343
(1.00) 		0.607
(1.00)
amp 5p15 33 137 (44%) 174 0.117
(1.00) 		0.949
(1.00) 		0.08
(1.00) 		0.0186
(1.00) 		1
(1.00) 		0.717
(1.00) 		1
(1.00) 		0.709
(1.00) 		0.976
(1.00) 		0.653
(1.00) 		0.735
(1.00)
amp 5q35 3 112 (36%) 199 0.274
(1.00) 		0.283
(1.00) 		0.599
(1.00) 		0.695
(1.00) 		0.554
(1.00) 		0.326
(1.00) 		0.527
(1.00) 		0.249
(1.00) 		0.0257
(1.00) 		0.675
(1.00) 		1
(1.00)
amp 6p25 2 134 (43%) 177 0.199
(1.00) 		0.768
(1.00) 		0.173
(1.00) 		0.0985
(1.00) 		1
(1.00) 		0.373
(1.00) 		0.713
(1.00) 		0.707
(1.00) 		0.727
(1.00) 		0.782
(1.00) 		0.729
(1.00)
amp 6p21 1 133 (43%) 178 0.867
(1.00) 		0.189
(1.00) 		0.286
(1.00) 		0.483
(1.00) 		0.265
(1.00) 		0.369
(1.00) 		0.327
(1.00) 		0.359
(1.00) 		0.725
(1.00) 		0.955
(1.00) 		0.723
(1.00)
amp 6q12 89 (29%) 222 0.893
(1.00) 		0.846
(1.00) 		0.0438
(1.00) 		0.0775
(1.00) 		0.201
(1.00) 		0.42
(1.00) 		0.42
(1.00) 		0.107
(1.00) 		0.285
(1.00) 		0.685
(1.00) 		0.691
(1.00)
amp 6q12 67 (22%) 244 0.801
(1.00) 		0.205
(1.00) 		0.342
(1.00) 		0.152
(1.00) 		1
(1.00) 		0.374
(1.00) 		0.465
(1.00) 		0.159
(1.00) 		0.421
(1.00) 		0.426
(1.00) 		0.374
(1.00)
amp 7q31 2 99 (32%) 212 0.508
(1.00) 		0.234
(1.00) 		0.447
(1.00) 		0.828
(1.00) 		0.223
(1.00) 		0.863
(1.00) 		0.696
(1.00) 		0.7
(1.00) 		0.774
(1.00) 		0.231
(1.00) 		0.276
(1.00)
amp 9q34 2 38 (12%) 273 0.901
(1.00) 		0.627
(1.00) 		0.00689
(1.00) 		0.00792
(1.00) 		0.32
(1.00) 		0.588
(1.00) 		0.579
(1.00) 		0.653
(1.00) 		0.0464
(1.00) 		0.758
(1.00) 		1
(1.00)
amp 11q13 3 50 (16%) 261 0.364
(1.00) 		0.425
(1.00) 		0.0438
(1.00) 		0.00581
(1.00) 		1
(1.00) 		0.352
(1.00) 		0.328
(1.00) 		0.714
(1.00) 		0.0344
(1.00) 		0.885
(1.00) 		0.615
(1.00)
amp 13q32 3 58 (19%) 253 0.368
(1.00) 		0.188
(1.00) 		0.507
(1.00) 		0.526
(1.00) 		0.472
(1.00) 		0.48
(1.00) 		0.0609
(1.00) 		0.114
(1.00) 		0.449
(1.00) 		0.586
(1.00) 		0.638
(1.00)
amp 13q33 3 60 (19%) 251 0.468
(1.00) 		0.226
(1.00) 		0.93
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.577
(1.00) 		0.282
(1.00) 		0.121
(1.00) 		0.755
(1.00) 		0.103
(1.00) 		0.646
(1.00)
amp 15q26 3 46 (15%) 265 0.838
(1.00) 		0.0829
(1.00) 		0.395
(1.00) 		0.178
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.306
(1.00) 		0.307
(1.00) 		0.416
(1.00) 		0.935
(1.00) 		0.319
(1.00)
amp 17p11 2 40 (13%) 271 0.887
(1.00) 		0.263
(1.00) 		0.0562
(1.00) 		0.0399
(1.00) 		1
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.67
(1.00) 		0.0108
(1.00) 		0.821
(1.00) 		0.254
(1.00)
amp 17q25 3 127 (41%) 184 0.697
(1.00) 		0.777
(1.00) 		0.12
(1.00) 		0.0262
(1.00) 		1
(1.00) 		0.591
(1.00) 		0.108
(1.00) 		0.35
(1.00) 		0.0344
(1.00) 		0.206
(1.00) 		1
(1.00)
amp 19p13 12 58 (19%) 253 0.968
(1.00) 		0.559
(1.00) 		0.0667
(1.00) 		0.644
(1.00) 		0.472
(1.00) 		0.0407
(1.00) 		0.00177
(1.00) 		0.116
(1.00) 		0.337
(1.00) 		0.521
(1.00) 		0.179
(1.00)
amp 19q12 65 (21%) 246 0.547
(1.00) 		0.436
(1.00) 		0.148
(1.00) 		0.86
(1.00) 		0.49
(1.00) 		0.0382
(1.00) 		0.137
(1.00) 		0.147
(1.00) 		0.339
(1.00) 		0.461
(1.00) 		0.374
(1.00)
amp 19q13 11 79 (25%) 232 0.195
(1.00) 		0.443
(1.00) 		0.044
(1.00) 		0.342
(1.00) 		0.547
(1.00) 		0.0329
(1.00) 		0.127
(1.00) 		0.804
(1.00) 		0.298
(1.00) 		0.181
(1.00) 		0.429
(1.00)
amp 20q13 13 104 (33%) 207 0.0728
(1.00) 		0.189
(1.00) 		0.0251
(1.00) 		0.0154
(1.00) 		0.264
(1.00) 		0.39
(1.00) 		0.159
(1.00) 		0.853
(1.00) 		0.471
(1.00) 		0.825
(1.00) 		1
(1.00)
amp 20q13 33 111 (36%) 200 0.38
(1.00) 		0.387
(1.00) 		0.0168
(1.00) 		0.049
(1.00) 		0.558
(1.00) 		0.0461
(1.00) 		0.0426
(1.00) 		0.847
(1.00) 		0.705
(1.00) 		0.856
(1.00) 		1
(1.00)
amp xq28 71 (23%) 240 0.392
(1.00) 		0.417
(1.00) 		0.941
(1.00) 		1
(1.00) 		1
(1.00) 		0.796
(1.00) 		0.00145
(0.972) 		0.476
(1.00) 		0.955
(1.00) 		0.293
(1.00) 		0.689
(1.00)
del 1p36 31 146 (47%) 165 0.272
(1.00) 		0.764
(1.00) 		0.913
(1.00) 		0.881
(1.00) 		0.603
(1.00) 		0.139
(1.00) 		0.147
(1.00) 		0.0674
(1.00) 		0.409
(1.00) 		0.0594
(1.00) 		1
(1.00)
del 1p36 11 126 (41%) 185 0.987
(1.00) 		0.755
(1.00) 		0.249
(1.00) 		0.185
(1.00) 		0.0739
(1.00) 		0.0142
(1.00) 		0.539
(1.00) 		0.285
(1.00) 		0.353
(1.00) 		0.0995
(1.00) 		1
(1.00)
del 2q22 1 42 (14%) 269 0.0611
(1.00) 		0.0885
(1.00) 		0.853
(1.00) 		0.584
(1.00) 		1
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.691
(1.00) 		0.504
(1.00) 		0.506
(1.00) 		1
(1.00)
del 2q37 3 54 (17%) 257 0.281
(1.00) 		0.12
(1.00) 		0.903
(1.00) 		0.407
(1.00) 		0.418
(1.00) 		0.42
(1.00) 		0.873
(1.00) 		0.0956
(1.00) 		0.785
(1.00) 		0.564
(1.00) 		0.621
(1.00)
del 3p13 62 (20%) 249 0.915
(1.00) 		0.135
(1.00) 		0.0112
(1.00) 		0.00406
(1.00) 		0.481
(1.00) 		0.278
(1.00) 		0.0346
(1.00) 		0.00201
(1.00) 		0.635
(1.00) 		0.976
(1.00) 		1
(1.00)
del 4p16 3 73 (23%) 238 0.207
(1.00) 		0.416
(1.00) 		0.0725
(1.00) 		0.35
(1.00) 		0.134
(1.00) 		0.384
(1.00) 		0.0327
(1.00) 		0.782
(1.00) 		0.448
(1.00) 		0.288
(1.00) 		0.4
(1.00)
del 4q22 3 149 (48%) 162 0.647
(1.00) 		0.000512
(0.346) 		0.661
(1.00) 		0.83
(1.00) 		0.622
(1.00) 		0.00365
(1.00) 		0.544
(1.00) 		0.606
(1.00) 		0.897
(1.00) 		0.0114
(1.00) 		0.488
(1.00)
del 6q27 117 (38%) 194 0.811
(1.00) 		0.0292
(1.00) 		0.461
(1.00) 		0.962
(1.00) 		0.557
(1.00) 		0.0726
(1.00) 		0.616
(1.00) 		0.599
(1.00) 		0.429
(1.00) 		0.717
(1.00) 		0.715
(1.00)
del 8p23 2 210 (68%) 101 0.816
(1.00) 		0.215
(1.00) 		0.636
(1.00) 		0.595
(1.00) 		0.553
(1.00) 		0.425
(1.00) 		0.519
(1.00) 		0.116
(1.00) 		1
(1.00) 		0.818
(1.00) 		1
(1.00)
del 8p12 205 (66%) 106 0.592
(1.00) 		0.596
(1.00) 		0.889
(1.00) 		0.711
(1.00) 		0.553
(1.00) 		0.474
(1.00) 		0.701
(1.00) 		0.483
(1.00) 		0.913
(1.00) 		0.873
(1.00) 		0.27
(1.00)
del 9p21 3 127 (41%) 184 0.318
(1.00) 		0.0315
(1.00) 		0.433
(1.00) 		0.338
(1.00) 		0.571
(1.00) 		0.924
(1.00) 		0.108
(1.00) 		0.605
(1.00) 		0.293
(1.00) 		0.111
(1.00) 		0.145
(1.00)
del 9q31 3 101 (32%) 210 0.317
(1.00) 		0.963
(1.00) 		0.101
(1.00) 		0.113
(1.00) 		0.0268
(1.00) 		0.0566
(1.00) 		0.604
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.956
(1.00) 		0.273
(1.00)
del 10q23 31 86 (28%) 225 0.303
(1.00) 		0.401
(1.00) 		0.0658
(1.00) 		0.0184
(1.00) 		0.169
(1.00) 		0.698
(1.00) 		0.786
(1.00) 		0.0991
(1.00) 		0.177
(1.00) 		0.0177
(1.00) 		1
(1.00)
del 10q26 13 90 (29%) 221 0.191
(1.00) 		0.835
(1.00) 		0.19
(1.00) 		0.0359
(1.00) 		0.19
(1.00) 		0.613
(1.00) 		1
(1.00) 		0.0574
(1.00) 		0.172
(1.00) 		0.0288
(1.00) 		0.691
(1.00)
del 11q14 1 62 (20%) 249 0.761
(1.00) 		0.74
(1.00) 		0.0805
(1.00) 		0.183
(1.00) 		0.12
(1.00) 		0.369
(1.00) 		1
(1.00) 		0.0803
(1.00) 		0.466
(1.00) 		0.813
(1.00) 		0.193
(1.00)
del 11q24 2 79 (25%) 232 0.915
(1.00) 		0.643
(1.00) 		0.311
(1.00) 		0.497
(1.00) 		0.169
(1.00) 		0.8
(1.00) 		0.89
(1.00) 		0.152
(1.00) 		0.653
(1.00) 		0.528
(1.00) 		0.424
(1.00)
del 12p12 1 64 (21%) 247 0.387
(1.00) 		0.745
(1.00) 		0.0483
(1.00) 		0.618
(1.00) 		0.12
(1.00) 		0.166
(1.00) 		0.656
(1.00) 		0.224
(1.00) 		0.271
(1.00) 		0.776
(1.00) 		0.662
(1.00)
del 12q24 33 46 (15%) 265 0.331
(1.00) 		0.409
(1.00) 		0.0439
(1.00) 		0.428
(1.00) 		1
(1.00) 		0.0082
(1.00) 		0.306
(1.00) 		1
(1.00) 		0.928
(1.00) 		0.553
(1.00) 		1
(1.00)
del 13q14 2 151 (49%) 160 0.114
(1.00) 		0.246
(1.00) 		0.156
(1.00) 		0.00701
(1.00) 		0.622
(1.00) 		0.917
(1.00) 		0.224
(1.00) 		0.718
(1.00) 		0.417
(1.00) 		0.0996
(1.00) 		1
(1.00)
del 14q23 3 115 (37%) 196 0.738
(1.00) 		0.192
(1.00) 		0.0955
(1.00) 		0.0456
(1.00) 		1
(1.00) 		0.0434
(1.00) 		0.53
(1.00) 		0.307
(1.00) 		0.576
(1.00) 		0.0124
(1.00) 		0.715
(1.00)
del 14q32 33 117 (38%) 194 0.97
(1.00) 		0.0835
(1.00) 		0.027
(1.00) 		0.00449
(1.00) 		1
(1.00) 		0.364
(1.00) 		0.901
(1.00) 		0.0386
(1.00) 		0.735
(1.00) 		0.124
(1.00) 		0.714
(1.00)
del 15q26 3 70 (23%) 241 0.157
(1.00) 		0.757
(1.00) 		0.118
(1.00) 		0.0249
(1.00) 		0.134
(1.00) 		0.0192
(1.00) 		0.885
(1.00) 		0.175
(1.00) 		0.872
(1.00) 		0.652
(1.00) 		0.384
(1.00)
del 17p13 1 191 (61%) 120 0.121
(1.00) 		0.292
(1.00) 		0.0528
(1.00) 		0.0183
(1.00) 		0.285
(1.00) 		0.283
(1.00) 		0.618
(1.00) 		1
(1.00) 		0.517
(1.00) 		0.0861
(1.00) 		0.16
(1.00)
del 17p11 2 163 (52%) 148 0.0696
(1.00) 		0.944
(1.00) 		0.017
(1.00) 		0.0154
(1.00) 		0.248
(1.00) 		0.72
(1.00) 		1
(1.00) 		0.843
(1.00) 		0.248
(1.00) 		0.441
(1.00) 		0.287
(1.00)
del 18q21 2 79 (25%) 232 0.895
(1.00) 		0.32
(1.00) 		0.718
(1.00) 		0.865
(1.00) 		1
(1.00) 		0.436
(1.00) 		0.211
(1.00) 		0.076
(1.00) 		0.705
(1.00) 		0.779
(1.00) 		0.419
(1.00)
del 19p13 3 72 (23%) 239 0.878
(1.00) 		0.183
(1.00) 		0.6
(1.00) 		0.274
(1.00) 		1
(1.00) 		0.0176
(1.00) 		0.391
(1.00) 		1
(1.00) 		0.955
(1.00) 		0.00463
(1.00) 		0.685
(1.00)
del 20p12 1 23 (7%) 288 0.263
(1.00) 		0.705
(1.00) 		0.303
(1.00) 		1
(1.00) 		1
(1.00) 		0.0969
(1.00) 		0.818
(1.00) 		0.0596
(1.00) 		0.863
(1.00) 		0.386
(1.00) 		0.466
(1.00)
del 22q12 1 66 (21%) 245 0.841
(1.00) 		0.404
(1.00) 		0.445
(1.00) 		0.0529
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.182
(1.00) 		0.0638
(1.00) 		0.137
(1.00) 		0.0444
(1.00) 		0.667
(1.00)
del 22q13 32 70 (23%) 241 0.453
(1.00) 		0.833
(1.00) 		0.0911
(1.00) 		0.00772
(1.00) 		0.515
(1.00) 		0.891
(1.00) 		0.194
(1.00) 		0.0758
(1.00) 		0.0653
(1.00) 		0.00677
(1.00) 		0.676
(1.00)
del xq26 2 57 (18%) 254 0.683
(1.00) 		0.231
(1.00) 		0.63
(1.00) 		0.242
(1.00) 		0.464
(1.00) 		0.516
(1.00) 		1
(1.00) 		0.108
(1.00) 		0.401
(1.00) 		0.258
(1.00) 		1
(1.00)
'amp_2q33.1' versus 'GENDER'

P value = 0.000135 (Fisher's exact test), Q value = 0.092

Table S1.  Gene #5: 'amp_2q33.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 100 211
AMP PEAK 5(2Q33.1) MUTATED 31 26
AMP PEAK 5(2Q33.1) WILD-TYPE 69 185

Figure S1.  Get High-res Image Gene #5: 'amp_2q33.1' versus Clinical Feature #7: 'GENDER'

'amp_8q13.3' versus 'GENDER'

P value = 0.000356 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #15: 'amp_8q13.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 100 211
AMP PEAK 15(8Q13.3) MUTATED 42 135
AMP PEAK 15(8Q13.3) WILD-TYPE 58 76

Figure S2.  Get High-res Image Gene #15: 'amp_8q13.3' versus Clinical Feature #7: 'GENDER'

'amp_8q24.21' versus 'GENDER'

P value = 0.000226 (Fisher's exact test), Q value = 0.15

Table S3.  Gene #16: 'amp_8q24.21' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 100 211
AMP PEAK 16(8Q24.21) MUTATED 49 150
AMP PEAK 16(8Q24.21) WILD-TYPE 51 61

Figure S3.  Get High-res Image Gene #16: 'amp_8q24.21' versus Clinical Feature #7: 'GENDER'

'amp_8q24.21' versus 'RACE'

P value = 0.00032 (Fisher's exact test), Q value = 0.22

Table S4.  Gene #16: 'amp_8q24.21' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 141 15 145
AMP PEAK 16(8Q24.21) MUTATED 1 106 9 76
AMP PEAK 16(8Q24.21) WILD-TYPE 0 35 6 69

Figure S4.  Get High-res Image Gene #16: 'amp_8q24.21' versus Clinical Feature #10: 'RACE'

'del_4q21.3' versus 'AGE'

P value = 0.000178 (Wilcoxon-test), Q value = 0.12

Table S5.  Gene #36: 'del_4q21.3' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 308 59.8 (12.7)
DEL PEAK 7(4Q21.3) MUTATED 146 57.1 (13.5)
DEL PEAK 7(4Q21.3) WILD-TYPE 162 62.2 (11.4)

Figure S5.  Get High-res Image Gene #36: 'del_4q21.3' versus Clinical Feature #2: 'AGE'

'del_4q35.1' versus 'RACE'

P value = 0.00014 (Fisher's exact test), Q value = 0.095

Table S6.  Gene #38: 'del_4q35.1' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 141 15 145
DEL PEAK 9(4Q35.1) MUTATED 0 88 9 54
DEL PEAK 9(4Q35.1) WILD-TYPE 1 53 6 91

Figure S6.  Get High-res Image Gene #38: 'del_4q35.1' versus Clinical Feature #10: 'RACE'

'del_16q23.1' versus 'RACE'

P value = 0.00035 (Fisher's exact test), Q value = 0.24

Table S7.  Gene #54: 'del_16q23.1' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 141 15 145
DEL PEAK 25(16Q23.1) MUTATED 0 82 7 50
DEL PEAK 25(16Q23.1) WILD-TYPE 1 59 8 95

Figure S7.  Get High-res Image Gene #54: 'del_16q23.1' versus Clinical Feature #10: 'RACE'

Methods & Data
Input

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

  • Clinical data file = LIHC-TP.merged_data.txt

  • Number of patients = 311

  • Number of significantly focal cnvs = 62

  • Number of selected clinical features = 11

  • 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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