Correlation between copy number variation genes (focal events) and selected clinical features
Liver Hepatocellular Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1GF0SR8
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/C1GF0SR8
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 12 clinical features across 362 patients, 28 significant findings detected with Q value < 0.25.

  • amp_2p24.1 cnv correlated to 'GENDER'.

  • amp_2q33.1 cnv correlated to 'GENDER'.

  • amp_8q13.3 cnv correlated to 'GENDER'.

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

  • amp_17p11.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_17q25.3 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_19p13.12 cnv correlated to 'GENDER'.

  • amp_xq28 cnv correlated to 'GENDER'.

  • del_3p13 cnv correlated to 'PATHOLOGY_T_STAGE' and 'HISTOLOGICAL_TYPE'.

  • del_4q21.3 cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.

  • del_4q22.3 cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.

  • del_4q35.1 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'RACE'.

  • del_6q27 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_10q23.31 cnv correlated to 'RACE'.

  • del_12p12.1 cnv correlated to 'PATHOLOGIC_STAGE'.

  • del_16q23.1 cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.

  • del_17p13.1 cnv correlated to 'Time to Death'.

  • del_17p11.2 cnv correlated to 'Time to Death'.

  • del_19p13.3 cnv correlated to 'RACE'.

  • del_22q13.32 cnv correlated to 'PATHOLOGY_T_STAGE' and '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 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 28 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR 		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 Fisher's exact test
del 4q35 1 171 (47%) 191 0.00868
(0.231) 		0.000436
(0.0411) 		0.289
(0.785) 		0.172
(0.644) 		0.619
(0.912) 		0.623
(0.912) 		0.0704
(0.53) 		1
(1.00) 		0.631
(0.912) 		0.367
(0.824) 		5e-05
(0.0093) 		0.403
(0.866)
amp 8q24 21 227 (63%) 135 0.553
(0.912) 		0.0527
(0.458) 		0.112
(0.599) 		0.68
(0.931) 		0.236
(0.746) 		0.598
(0.912) 		0.000274
(0.034) 		0.264
(0.758) 		1
(1.00) 		0.762
(0.973) 		3e-05
(0.0093) 		0.561
(0.912)
del 3p13 69 (19%) 293 0.643
(0.912) 		0.119
(0.606) 		0.0112
(0.253) 		0.00374
(0.148) 		0.47
(0.891) 		0.162
(0.636) 		0.0304
(0.39) 		0.354
(0.808) 		0.00437
(0.148) 		0.641
(0.912) 		0.862
(1.00) 		1
(1.00)
del 4q21 3 169 (47%) 193 0.333
(0.796) 		0.000154
(0.0229) 		0.507
(0.912) 		0.55
(0.912) 		0.608
(0.912) 		0.622
(0.912) 		0.43
(0.866) 		1
(1.00) 		0.629
(0.912) 		0.54
(0.912) 		0.00252
(0.144) 		0.0435
(0.443)
del 4q22 3 170 (47%) 192 0.282
(0.78) 		0.000442
(0.0411) 		0.575
(0.912) 		0.729
(0.955) 		0.611
(0.912) 		0.623
(0.912) 		0.429
(0.866) 		1
(1.00) 		0.63
(0.912) 		0.562
(0.912) 		0.00672
(0.2) 		0.0442
(0.443)
del 16q23 1 161 (44%) 201 0.213
(0.72) 		0.000979
(0.0677) 		0.128
(0.606) 		0.0972
(0.569) 		0.611
(0.912) 		1
(1.00) 		0.307
(0.785) 		0.47
(0.891) 		0.627
(0.912) 		0.889
(1.00) 		2e-05
(0.0093) 		0.578
(0.912)
del 22q13 32 79 (22%) 283 0.57
(0.912) 		0.418
(0.866) 		0.0343
(0.419) 		0.00424
(0.148) 		0.508
(0.912) 		1
(1.00) 		0.495
(0.912) 		0.653
(0.92) 		0.0467
(0.457) 		0.0402
(0.433) 		0.00418
(0.148) 		0.152
(0.606)
amp 2p24 1 64 (18%) 298 0.043
(0.443) 		0.095
(0.569) 		0.207
(0.718) 		0.0891
(0.568) 		0.0791
(0.55) 		0.13
(0.606) 		0.001
(0.0677) 		0.611
(0.912) 		0.737
(0.955) 		0.423
(0.866) 		0.15
(0.606) 		1
(1.00)
amp 2q33 1 62 (17%) 300 0.148
(0.606) 		0.432
(0.866) 		0.0837
(0.561) 		0.093
(0.569) 		0.47
(0.891) 		0.168
(0.641) 		3.94e-05
(0.0093) 		0.606
(0.912) 		0.553
(0.912) 		0.506
(0.912) 		0.521
(0.912) 		0.48
(0.899)
amp 8q13 3 203 (56%) 159 0.84
(1.00) 		0.0837
(0.561) 		0.165
(0.641) 		0.301
(0.785) 		0.568
(0.912) 		1
(1.00) 		0.000613
(0.0507) 		0.138
(0.606) 		0.852
(1.00) 		0.836
(1.00) 		0.0705
(0.53) 		1
(1.00)
amp 17p11 2 46 (13%) 316 0.643
(0.912) 		0.318
(0.79) 		0.0125
(0.263) 		0.0036
(0.148) 		1
(1.00) 		0.454
(0.882) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0131
(0.263) 		0.687
(0.931) 		0.202
(0.714)
amp 17q25 3 142 (39%) 220 0.245
(0.747) 		0.89
(1.00) 		0.0166
(0.299) 		0.0036
(0.148) 		1
(1.00) 		1
(1.00) 		0.107
(0.593) 		0.711
(0.95) 		0.626
(0.912) 		0.0491
(0.458) 		0.144
(0.606) 		0.263
(0.758)
amp 19p13 12 67 (19%) 295 0.351
(0.807) 		0.573
(0.912) 		0.128
(0.606) 		0.712
(0.95) 		0.462
(0.891) 		0.0197
(0.305) 		0.00337
(0.148) 		1
(1.00) 		0.152
(0.606) 		0.272
(0.762) 		0.596
(0.912) 		0.277
(0.773)
amp xq28 83 (23%) 279 0.409
(0.866) 		0.314
(0.79) 		0.927
(1.00) 		0.918
(1.00) 		1
(1.00) 		0.577
(0.912) 		0.00199
(0.123) 		0.66
(0.925) 		0.392
(0.866) 		0.962
(1.00) 		0.25
(0.748) 		0.312
(0.79)
del 6q27 133 (37%) 229 0.954
(1.00) 		0.00413
(0.148) 		0.683
(0.931) 		0.955
(1.00) 		0.558
(0.912) 		0.305
(0.785) 		0.293
(0.785) 		0.429
(0.866) 		0.616
(0.912) 		0.336
(0.796) 		0.563
(0.912) 		0.143
(0.606)
del 10q23 31 95 (26%) 267 0.241
(0.747) 		0.505
(0.912) 		0.1
(0.577) 		0.0209
(0.317) 		0.168
(0.641) 		0.576
(0.912) 		1
(1.00) 		0.68
(0.931) 		0.142
(0.606) 		0.574
(0.912) 		0.00502
(0.162) 		1
(1.00)
del 12p12 1 74 (20%) 288 0.331
(0.796) 		0.934
(1.00) 		0.00639
(0.198) 		0.536
(0.912) 		0.112
(0.599) 		0.209
(0.72) 		0.78
(0.973) 		0.352
(0.807) 		0.467
(0.891) 		0.146
(0.606) 		0.542
(0.912) 		0.726
(0.955)
del 17p13 1 220 (61%) 142 0.00718
(0.205) 		0.511
(0.912) 		0.0446
(0.443) 		0.0107
(0.251) 		0.285
(0.78) 		0.301
(0.785) 		0.563
(0.912) 		1
(1.00) 		0.864
(1.00) 		0.38
(0.849) 		0.0906
(0.568) 		0.773
(0.973)
del 17p11 2 189 (52%) 173 0.00342
(0.148) 		0.721
(0.953) 		0.0105
(0.251) 		0.00978
(0.251) 		0.248
(0.748) 		0.623
(0.912) 		1
(1.00) 		1
(1.00) 		0.724
(0.955) 		0.206
(0.716) 		0.767
(0.973) 		0.579
(0.912)
del 19p13 3 85 (23%) 277 0.215
(0.72) 		0.106
(0.591) 		0.412
(0.866) 		0.16
(0.629) 		1
(1.00) 		1
(1.00) 		0.506
(0.912) 		1
(1.00) 		1
(1.00) 		0.926
(1.00) 		0.00774
(0.213) 		1
(1.00)
amp 1p22 3 88 (24%) 274 0.67
(0.928) 		0.135
(0.606) 		0.129
(0.606) 		0.0951
(0.569) 		1
(1.00) 		0.0577
(0.477) 		0.432
(0.866) 		0.674
(0.93) 		1
(1.00) 		0.0341
(0.419) 		0.169
(0.641) 		1
(1.00)
amp 1q22 277 (77%) 85 0.0619
(0.495) 		0.743
(0.959) 		0.919
(1.00) 		0.918
(1.00) 		0.537
(0.912) 		0.579
(0.912) 		0.506
(0.912) 		0.663
(0.926) 		0.0189
(0.299) 		0.769
(0.973) 		0.293
(0.785) 		1
(1.00)
amp 1q42 3 266 (73%) 96 0.553
(0.912) 		0.955
(1.00) 		0.421
(0.866) 		0.638
(0.912) 		0.576
(0.912) 		0.575
(0.912) 		0.609
(0.912) 		1
(1.00) 		0.431
(0.866) 		0.966
(1.00) 		0.593
(0.912) 		0.754
(0.967)
amp 3q26 31 76 (21%) 286 0.366
(0.824) 		0.441
(0.87) 		0.62
(0.912) 		0.603
(0.912) 		0.477
(0.897) 		0.587
(0.912) 		0.783
(0.975) 		1
(1.00) 		0.778
(0.973) 		0.66
(0.925) 		0.215
(0.72) 		0.485
(0.905)
amp 4p14 52 (14%) 310 0.259
(0.755) 		0.0526
(0.458) 		0.471
(0.891) 		0.211
(0.72) 		1
(1.00) 		1
(1.00) 		0.264
(0.758) 		0.599
(0.912) 		1
(1.00) 		0.543
(0.912) 		0.777
(0.973) 		0.701
(0.939)
amp 5p15 33 161 (44%) 201 0.0777
(0.55) 		0.533
(0.912) 		0.0529
(0.458) 		0.017
(0.299) 		1
(1.00) 		0.631
(0.912) 		0.821
(1.00) 		0.249
(0.748) 		0.628
(0.912) 		0.923
(1.00) 		0.367
(0.824) 		0.575
(0.912)
amp 5q35 3 134 (37%) 228 0.4
(0.866) 		0.149
(0.606) 		0.73
(0.955) 		0.638
(0.912) 		0.556
(0.912) 		0.637
(0.912) 		0.296
(0.785) 		0.431
(0.866) 		0.124
(0.606) 		0.0744
(0.543) 		0.768
(0.973) 		0.561
(0.912)
amp 6p25 2 153 (42%) 209 0.0956
(0.569) 		0.825
(1.00) 		0.121
(0.606) 		0.135
(0.606) 		1
(1.00) 		0.316
(0.79) 		0.361
(0.821) 		0.246
(0.747) 		0.63
(0.912) 		0.732
(0.955) 		0.859
(1.00) 		0.403
(0.866)
amp 6p21 1 154 (43%) 208 0.33
(0.796) 		0.0612
(0.495) 		0.342
(0.8) 		0.512
(0.912) 		0.269
(0.758) 		0.316
(0.79) 		0.111
(0.599) 		0.246
(0.747) 		0.453
(0.882) 		0.764
(0.973) 		0.882
(1.00) 		0.398
(0.866)
amp 6q12 104 (29%) 258 0.34
(0.8) 		0.473
(0.891) 		0.0285
(0.379) 		0.129
(0.606) 		0.186
(0.689) 		0.582
(0.912) 		0.322
(0.795) 		0.196
(0.709) 		0.218
(0.72) 		0.343
(0.8) 		0.59
(0.912) 		0.529
(0.912)
amp 6q12 80 (22%) 282 0.205
(0.716) 		0.565
(0.912) 		0.317
(0.79) 		0.223
(0.732) 		1
(1.00) 		0.197
(0.709) 		0.343
(0.8) 		0.353
(0.807) 		0.284
(0.78) 		0.438
(0.866) 		0.472
(0.891) 		0.166
(0.641)
amp 7q31 2 117 (32%) 245 1
(1.00) 		0.0619
(0.495) 		0.3
(0.785) 		0.654
(0.92) 		0.231
(0.743) 		1
(1.00) 		0.631
(0.912) 		0.687
(0.931) 		0.496
(0.912) 		0.826
(1.00) 		0.307
(0.785) 		0.367
(0.824)
amp 9q34 2 45 (12%) 317 0.635
(0.912) 		0.532
(0.912) 		0.0315
(0.397) 		0.0177
(0.299) 		0.335
(0.796) 		0.425
(0.866) 		0.609
(0.912) 		1
(1.00) 		1
(1.00) 		0.238
(0.747) 		0.65
(0.917) 		0.67
(0.928)
amp 11q13 3 56 (15%) 306 0.685
(0.931) 		0.46
(0.891) 		0.0521
(0.458) 		0.0542
(0.463) 		1
(1.00) 		0.518
(0.912) 		0.533
(0.912) 		0.6
(0.912) 		0.715
(0.951) 		0.0385
(0.428) 		0.947
(1.00) 		0.7
(0.939)
amp 13q32 3 65 (18%) 297 0.0915
(0.568) 		0.225
(0.734) 		0.628
(0.912) 		0.473
(0.891) 		0.454
(0.882) 		0.569
(0.912) 		0.0183
(0.299) 		0.612
(0.912) 		0.143
(0.606) 		0.45
(0.882) 		0.677
(0.931) 		1
(1.00)
amp 13q33 3 66 (18%) 296 0.086
(0.565) 		0.33
(0.796) 		0.964
(1.00) 		0.98
(1.00) 		0.454
(0.882) 		0.569
(0.912) 		0.0814
(0.556) 		0.614
(0.912) 		0.146
(0.606) 		0.779
(0.973) 		0.229
(0.739) 		1
(1.00)
amp 15q26 3 54 (15%) 308 0.968
(1.00) 		0.0367
(0.428) 		0.214
(0.72) 		0.202
(0.714) 		1
(1.00) 		0.501
(0.912) 		0.428
(0.866) 		1
(1.00) 		0.329
(0.796) 		0.62
(0.912) 		0.865
(1.00) 		0.0272
(0.379)
amp 19q12 77 (21%) 285 0.246
(0.747) 		0.18
(0.67) 		0.285
(0.78) 		0.92
(1.00) 		0.5
(0.912) 		0.0291
(0.38) 		0.217
(0.72) 		1
(1.00) 		0.269
(0.758) 		0.302
(0.785) 		0.645
(0.912) 		0.166
(0.641)
amp 19q13 11 89 (25%) 273 0.669
(0.928) 		0.341
(0.8) 		0.0481
(0.458) 		0.318
(0.79) 		0.529
(0.912) 		0.0392
(0.428) 		0.15
(0.606) 		1
(1.00) 		0.409
(0.866) 		0.11
(0.599) 		0.269
(0.758) 		0.744
(0.959)
amp 20q13 13 120 (33%) 242 0.0387
(0.428) 		0.039
(0.428) 		0.0972
(0.569) 		0.0574
(0.477) 		0.257
(0.755) 		0.612
(0.912) 		0.187
(0.689) 		0.435
(0.866) 		1
(1.00) 		0.24
(0.747) 		0.721
(0.953) 		1
(1.00)
amp 20q13 33 125 (35%) 237 0.0764
(0.547) 		0.115
(0.601) 		0.0363
(0.428) 		0.0955
(0.569) 		0.3
(0.785) 		0.148
(0.606) 		0.0575
(0.477) 		0.43
(0.866) 		0.863
(1.00) 		0.523
(0.912) 		0.774
(0.973) 		1
(1.00)
del 1p36 31 161 (44%) 201 0.604
(0.912) 		0.692
(0.935) 		0.967
(1.00) 		0.788
(0.977) 		0.59
(0.912) 		0.349
(0.807) 		0.212
(0.72) 		0.14
(0.606) 		0.151
(0.606) 		0.19
(0.695) 		0.0896
(0.568) 		0.779
(0.973)
del 1p36 11 141 (39%) 221 0.972
(1.00) 		0.84
(1.00) 		0.592
(0.912) 		0.452
(0.882) 		0.0663
(0.514) 		0.316
(0.79) 		0.644
(0.912) 		1
(1.00) 		0.437
(0.866) 		0.172
(0.644) 		0.135
(0.606) 		0.575
(0.912)
del 2q22 1 51 (14%) 311 0.146
(0.606) 		0.194
(0.706) 		0.975
(1.00) 		0.967
(1.00) 		1
(1.00) 		1
(1.00) 		0.748
(0.961) 		0.255
(0.755) 		1
(1.00) 		0.325
(0.796) 		0.437
(0.866) 		0.693
(0.935)
del 2q37 3 60 (17%) 302 0.543
(0.912) 		0.136
(0.606) 		0.812
(1.00) 		0.421
(0.866) 		0.388
(0.861) 		1
(1.00) 		0.764
(0.973) 		1
(1.00) 		0.118
(0.606) 		0.467
(0.891) 		0.428
(0.866) 		0.437
(0.866)
del 4p16 3 84 (23%) 278 0.223
(0.732) 		0.481
(0.9) 		0.053
(0.458) 		0.537
(0.912) 		0.132
(0.606) 		0.247
(0.747) 		0.0108
(0.251) 		0.667
(0.928) 		0.805
(0.996) 		0.227
(0.739) 		0.0663
(0.514) 		0.0865
(0.565)
del 8p23 2 241 (67%) 121 0.823
(1.00) 		0.0862
(0.565) 		0.217
(0.72) 		0.423
(0.866) 		0.554
(0.912) 		0.303
(0.785) 		0.404
(0.866) 		1
(1.00) 		0.259
(0.755) 		0.973
(1.00) 		0.733
(0.955) 		1
(1.00)
del 8p12 236 (65%) 126 0.7
(0.939) 		0.297
(0.785) 		0.517
(0.912) 		0.682
(0.931) 		0.554
(0.912) 		0.301
(0.785) 		0.638
(0.912) 		0.429
(0.866) 		0.735
(0.955) 		0.882
(1.00) 		0.727
(0.955) 		0.555
(0.912)
del 9p21 3 147 (41%) 215 0.133
(0.606) 		0.0381
(0.428) 		0.569
(0.912) 		0.511
(0.912) 		0.568
(0.912) 		1
(1.00) 		0.302
(0.785) 		0.706
(0.945) 		0.733
(0.955) 		0.42
(0.866) 		0.103
(0.584) 		0.252
(0.75)
del 9q31 3 116 (32%) 246 0.235
(0.746) 		0.886
(1.00) 		0.0514
(0.458) 		0.159
(0.629) 		0.0253
(0.369) 		0.0807
(0.556) 		0.717
(0.951) 		1
(1.00) 		1
(1.00) 		0.198
(0.709) 		0.939
(1.00) 		0.233
(0.746)
del 10q26 13 102 (28%) 260 0.113
(0.599) 		0.953
(1.00) 		0.264
(0.758) 		0.0493
(0.458) 		0.196
(0.709) 		0.58
(0.912) 		0.901
(1.00) 		0.678
(0.931) 		0.132
(0.606) 		0.628
(0.912) 		0.013
(0.263) 		1
(1.00)
del 11q14 1 72 (20%) 290 0.381
(0.849) 		0.336
(0.796) 		0.051
(0.458) 		0.113
(0.599) 		0.12
(0.606) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.104
(0.584) 		0.523
(0.912) 		0.626
(0.912) 		0.145
(0.606)
del 11q24 2 92 (25%) 270 0.573
(0.912) 		0.274
(0.767) 		0.204
(0.716) 		0.415
(0.866) 		0.172
(0.644) 		1
(1.00) 		1
(1.00) 		0.683
(0.931) 		0.247
(0.747) 		0.787
(0.977) 		0.298
(0.785) 		0.103
(0.584)
del 12q24 33 54 (15%) 308 0.0998
(0.577) 		0.345
(0.803) 		0.0139
(0.271) 		0.327
(0.796) 		1
(1.00) 		0.135
(0.606) 		0.267
(0.758) 		1
(1.00) 		1
(1.00) 		0.835
(1.00) 		0.423
(0.866) 		1
(1.00)
del 13q14 2 174 (48%) 188 0.0161
(0.299) 		0.299
(0.785) 		0.368
(0.824) 		0.0126
(0.263) 		1
(1.00) 		1
(1.00) 		0.143
(0.606) 		0.716
(0.951) 		0.857
(1.00) 		0.41
(0.866) 		0.0727
(0.536) 		0.782
(0.974)
del 14q23 3 129 (36%) 233 0.244
(0.747) 		0.203
(0.714) 		0.335
(0.796) 		0.234
(0.746) 		1
(1.00) 		0.64
(0.912) 		0.409
(0.866) 		1
(1.00) 		0.347
(0.805) 		0.821
(1.00) 		0.0181
(0.299) 		0.556
(0.912)
del 14q32 33 131 (36%) 231 0.771
(0.973) 		0.0691
(0.53) 		0.129
(0.606) 		0.0282
(0.379) 		1
(1.00) 		0.634
(0.912) 		0.907
(1.00) 		1
(1.00) 		0.146
(0.606) 		0.847
(1.00) 		0.117
(0.606) 		1
(1.00)
del 15q26 3 77 (21%) 285 0.0262
(0.375) 		0.886
(1.00) 		0.0786
(0.55) 		0.0252
(0.369) 		0.12
(0.606) 		0.575
(0.912) 		0.891
(1.00) 		1
(1.00) 		0.268
(0.758) 		0.671
(0.928) 		0.425
(0.866) 		0.742
(0.959)
del 18q21 2 92 (25%) 270 0.815
(1.00) 		0.763
(0.973) 		0.735
(0.955) 		0.944
(1.00) 		1
(1.00) 		0.279
(0.774) 		0.244
(0.747) 		0.064
(0.506) 		0.0765
(0.547) 		0.391
(0.866) 		0.953
(1.00) 		0.326
(0.796)
del 20p12 1 27 (7%) 335 0.425
(0.866) 		0.58
(0.912) 		0.311
(0.79) 		0.771
(0.973) 		1
(1.00) 		0.306
(0.785) 		0.527
(0.912) 		0.0917
(0.568) 		0.0718
(0.534) 		0.694
(0.935) 		0.496
(0.912) 		1
(1.00)
del 22q12 1 75 (21%) 287 0.745
(0.959) 		0.257
(0.755) 		0.113
(0.599) 		0.0188
(0.299) 		1
(1.00) 		1
(1.00) 		0.404
(0.866) 		0.635
(0.912) 		0.0418
(0.443) 		0.0875
(0.566) 		0.0166
(0.299) 		0.147
(0.606)
del xq26 2 66 (18%) 296 0.139
(0.606) 		0.028
(0.379) 		0.514
(0.912) 		0.324
(0.796) 		0.47
(0.891) 		0.585
(0.912) 		0.661
(0.925) 		0.124
(0.606) 		0.146
(0.606) 		0.415
(0.866) 		0.0425
(0.443) 		1
(1.00)
'amp_2p24.1' versus 'GENDER'

P value = 0.001 (Fisher's exact test), Q value = 0.068

Table S1.  Gene #4: 'amp_2p24.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 115 247
AMP PEAK 4(2P24.1) MUTATED 32 32
AMP PEAK 4(2P24.1) WILD-TYPE 83 215

Figure S1.  Get High-res Image Gene #4: 'amp_2p24.1' versus Clinical Feature #7: 'GENDER'

'amp_2q33.1' versus 'GENDER'

P value = 3.94e-05 (Fisher's exact test), Q value = 0.0093

Table S2.  Gene #5: 'amp_2q33.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 115 247
AMP PEAK 5(2Q33.1) MUTATED 34 28
AMP PEAK 5(2Q33.1) WILD-TYPE 81 219

Figure S2.  Get High-res Image Gene #5: 'amp_2q33.1' versus Clinical Feature #7: 'GENDER'

'amp_8q13.3' versus 'GENDER'

P value = 0.000613 (Fisher's exact test), Q value = 0.051

Table S3.  Gene #15: 'amp_8q13.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 115 247
AMP PEAK 15(8Q13.3) MUTATED 49 154
AMP PEAK 15(8Q13.3) WILD-TYPE 66 93

Figure S3.  Get High-res Image Gene #15: 'amp_8q13.3' versus Clinical Feature #7: 'GENDER'

'amp_8q24.21' versus 'GENDER'

P value = 0.000274 (Fisher's exact test), Q value = 0.034

Table S4.  Gene #16: 'amp_8q24.21' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 115 247
AMP PEAK 16(8Q24.21) MUTATED 56 171
AMP PEAK 16(8Q24.21) WILD-TYPE 59 76

Figure S4.  Get High-res Image Gene #16: 'amp_8q24.21' versus Clinical Feature #7: 'GENDER'

'amp_8q24.21' versus 'RACE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0093

Table S5.  Gene #16: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 157 17 177
AMP PEAK 16(8Q24.21) MUTATED 1 118 11 90
AMP PEAK 16(8Q24.21) WILD-TYPE 0 39 6 87

Figure S5.  Get High-res Image Gene #16: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'

'amp_17p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0036 (Fisher's exact test), Q value = 0.15

Table S6.  Gene #22: 'amp_17p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 182 92 74 12
AMP PEAK 22(17P11.2) MUTATED 17 8 19 2
AMP PEAK 22(17P11.2) WILD-TYPE 165 84 55 10

Figure S6.  Get High-res Image Gene #22: 'amp_17p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_17q25.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0036 (Fisher's exact test), Q value = 0.15

Table S7.  Gene #23: 'amp_17q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 182 92 74 12
AMP PEAK 23(17Q25.3) MUTATED 57 39 38 8
AMP PEAK 23(17Q25.3) WILD-TYPE 125 53 36 4

Figure S7.  Get High-res Image Gene #23: 'amp_17q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_19p13.12' versus 'GENDER'

P value = 0.00337 (Fisher's exact test), Q value = 0.15

Table S8.  Gene #24: 'amp_19p13.12' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 115 247
AMP PEAK 24(19P13.12) MUTATED 32 35
AMP PEAK 24(19P13.12) WILD-TYPE 83 212

Figure S8.  Get High-res Image Gene #24: 'amp_19p13.12' versus Clinical Feature #7: 'GENDER'

'amp_xq28' versus 'GENDER'

P value = 0.00199 (Fisher's exact test), Q value = 0.12

Table S9.  Gene #29: 'amp_xq28' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 115 247
AMP PEAK 29(XQ28) MUTATED 15 68
AMP PEAK 29(XQ28) WILD-TYPE 100 179

Figure S9.  Get High-res Image Gene #29: 'amp_xq28' versus Clinical Feature #7: 'GENDER'

'del_3p13' versus 'PATHOLOGY_T_STAGE'

P value = 0.00374 (Fisher's exact test), Q value = 0.15

Table S10.  Gene #34: 'del_3p13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 182 92 74 12
DEL PEAK 5(3P13) MUTATED 22 23 20 4
DEL PEAK 5(3P13) WILD-TYPE 160 69 54 8

Figure S10.  Get High-res Image Gene #34: 'del_3p13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p13' versus 'HISTOLOGICAL_TYPE'

P value = 0.00437 (Fisher's exact test), Q value = 0.15

Table S11.  Gene #34: 'del_3p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA HEPATOCHOLANGIOCARCINOMA (MIXED)
ALL 2 353 7
DEL PEAK 5(3P13) MUTATED 0 64 5
DEL PEAK 5(3P13) WILD-TYPE 2 289 2

Figure S11.  Get High-res Image Gene #34: 'del_3p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_4q21.3' versus 'YEARS_TO_BIRTH'

P value = 0.000154 (Wilcoxon-test), Q value = 0.023

Table S12.  Gene #36: 'del_4q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 359 59.7 (12.7)
DEL PEAK 7(4Q21.3) MUTATED 167 57.3 (13.2)
DEL PEAK 7(4Q21.3) WILD-TYPE 192 61.8 (11.9)

Figure S12.  Get High-res Image Gene #36: 'del_4q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q21.3' versus 'RACE'

P value = 0.00252 (Fisher's exact test), Q value = 0.14

Table S13.  Gene #36: 'del_4q21.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 157 17 177
DEL PEAK 7(4Q21.3) MUTATED 0 89 9 67
DEL PEAK 7(4Q21.3) WILD-TYPE 1 68 8 110

Figure S13.  Get High-res Image Gene #36: 'del_4q21.3' versus Clinical Feature #11: 'RACE'

'del_4q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.000442 (Wilcoxon-test), Q value = 0.041

Table S14.  Gene #37: 'del_4q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 359 59.7 (12.7)
DEL PEAK 8(4Q22.3) MUTATED 168 57.5 (13.3)
DEL PEAK 8(4Q22.3) WILD-TYPE 191 61.7 (11.9)

Figure S14.  Get High-res Image Gene #37: 'del_4q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q22.3' versus 'RACE'

P value = 0.00672 (Fisher's exact test), Q value = 0.2

Table S15.  Gene #37: 'del_4q22.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 157 17 177
DEL PEAK 8(4Q22.3) MUTATED 0 88 9 69
DEL PEAK 8(4Q22.3) WILD-TYPE 1 69 8 108

Figure S15.  Get High-res Image Gene #37: 'del_4q22.3' versus Clinical Feature #11: 'RACE'

'del_4q35.1' versus 'Time to Death'

P value = 0.00868 (logrank test), Q value = 0.23

Table S16.  Gene #38: 'del_4q35.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 358 129 0.0 - 120.8 (19.8)
DEL PEAK 9(4Q35.1) MUTATED 168 69 0.2 - 120.8 (17.1)
DEL PEAK 9(4Q35.1) WILD-TYPE 190 60 0.0 - 114.3 (21.0)

Figure S16.  Get High-res Image Gene #38: 'del_4q35.1' versus Clinical Feature #1: 'Time to Death'

'del_4q35.1' versus 'YEARS_TO_BIRTH'

P value = 0.000436 (Wilcoxon-test), Q value = 0.041

Table S17.  Gene #38: 'del_4q35.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 359 59.7 (12.7)
DEL PEAK 9(4Q35.1) MUTATED 168 57.4 (13.0)
DEL PEAK 9(4Q35.1) WILD-TYPE 191 61.7 (12.2)

Figure S17.  Get High-res Image Gene #38: 'del_4q35.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q35.1' versus 'RACE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0093

Table S18.  Gene #38: 'del_4q35.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 157 17 177
DEL PEAK 9(4Q35.1) MUTATED 0 95 10 66
DEL PEAK 9(4Q35.1) WILD-TYPE 1 62 7 111

Figure S18.  Get High-res Image Gene #38: 'del_4q35.1' versus Clinical Feature #11: 'RACE'

'del_6q27' versus 'YEARS_TO_BIRTH'

P value = 0.00413 (Wilcoxon-test), Q value = 0.15

Table S19.  Gene #39: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 359 59.7 (12.7)
DEL PEAK 10(6Q27) MUTATED 132 62.4 (12.3)
DEL PEAK 10(6Q27) WILD-TYPE 227 58.1 (12.7)

Figure S19.  Get High-res Image Gene #39: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'RACE'

P value = 0.00502 (Fisher's exact test), Q value = 0.16

Table S20.  Gene #44: 'del_10q23.31' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 157 17 177
DEL PEAK 15(10Q23.31) MUTATED 0 46 10 38
DEL PEAK 15(10Q23.31) WILD-TYPE 1 111 7 139

Figure S20.  Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #11: 'RACE'

'del_12p12.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00639 (Fisher's exact test), Q value = 0.2

Table S21.  Gene #48: 'del_12p12.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 171 85 3 60 8 7 3 1 2
DEL PEAK 19(12P12.1) MUTATED 30 18 1 10 5 2 3 0 0
DEL PEAK 19(12P12.1) WILD-TYPE 141 67 2 50 3 5 0 1 2

Figure S21.  Get High-res Image Gene #48: 'del_12p12.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_16q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.000979 (Wilcoxon-test), Q value = 0.068

Table S22.  Gene #54: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 359 59.7 (12.7)
DEL PEAK 25(16Q23.1) MUTATED 160 57.5 (12.8)
DEL PEAK 25(16Q23.1) WILD-TYPE 199 61.5 (12.4)

Figure S22.  Get High-res Image Gene #54: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q23.1' versus 'RACE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0093

Table S23.  Gene #54: 'del_16q23.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 157 17 177
DEL PEAK 25(16Q23.1) MUTATED 0 91 7 59
DEL PEAK 25(16Q23.1) WILD-TYPE 1 66 10 118

Figure S23.  Get High-res Image Gene #54: 'del_16q23.1' versus Clinical Feature #11: 'RACE'

'del_17p13.1' versus 'Time to Death'

P value = 0.00718 (logrank test), Q value = 0.21

Table S24.  Gene #55: 'del_17p13.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 358 129 0.0 - 120.8 (19.8)
DEL PEAK 26(17P13.1) MUTATED 217 90 0.0 - 120.8 (19.1)
DEL PEAK 26(17P13.1) WILD-TYPE 141 39 0.3 - 114.3 (20.6)

Figure S24.  Get High-res Image Gene #55: 'del_17p13.1' versus Clinical Feature #1: 'Time to Death'

'del_17p11.2' versus 'Time to Death'

P value = 0.00342 (logrank test), Q value = 0.15

Table S25.  Gene #56: 'del_17p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 358 129 0.0 - 120.8 (19.8)
DEL PEAK 27(17P11.2) MUTATED 186 81 0.0 - 120.8 (19.2)
DEL PEAK 27(17P11.2) WILD-TYPE 172 48 0.2 - 114.3 (20.3)

Figure S25.  Get High-res Image Gene #56: 'del_17p11.2' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'RACE'

P value = 0.00774 (Fisher's exact test), Q value = 0.21

Table S26.  Gene #58: 'del_19p13.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 157 17 177
DEL PEAK 29(19P13.3) MUTATED 0 51 3 31
DEL PEAK 29(19P13.3) WILD-TYPE 1 106 14 146

Figure S26.  Get High-res Image Gene #58: 'del_19p13.3' versus Clinical Feature #11: 'RACE'

'del_22q13.32' versus 'PATHOLOGY_T_STAGE'

P value = 0.00424 (Fisher's exact test), Q value = 0.15

Table S27.  Gene #61: 'del_22q13.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 182 92 74 12
DEL PEAK 32(22Q13.32) MUTATED 27 28 19 5
DEL PEAK 32(22Q13.32) WILD-TYPE 155 64 55 7

Figure S27.  Get High-res Image Gene #61: 'del_22q13.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_22q13.32' versus 'RACE'

P value = 0.00418 (Fisher's exact test), Q value = 0.15

Table S28.  Gene #61: 'del_22q13.32' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 157 17 177
DEL PEAK 32(22Q13.32) MUTATED 1 24 7 45
DEL PEAK 32(22Q13.32) WILD-TYPE 0 133 10 132

Figure S28.  Get High-res Image Gene #61: 'del_22q13.32' versus Clinical Feature #11: 'RACE'

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/LIHC-TP/19782292/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/19775332/LIHC-TP.merged_data.txt

  • Number of patients = 362

  • Number of significantly focal cnvs = 62

  • Number of selected clinical features = 12

  • 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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