Correlation between copy number variation genes (focal events) and selected clinical features
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 61 focal events and 12 clinical features across 370 patients, 46 significant findings detected with Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_2p24.1 cnv correlated to 'GENDER'.

  • amp_2q33.1 cnv correlated to 'GENDER'.

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

  • amp_10p15.1 cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.

  • amp_17p11.2 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • amp_17q25.3 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • amp_19p13.12 cnv correlated to 'GENDER'.

  • amp_xq28 cnv correlated to 'GENDER'.

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

  • del_4p16.3 cnv correlated to 'GENDER'.

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

  • del_4q24 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_7q36.3 cnv correlated to 'Time to Death' and 'GENDER'.

  • del_10q23.31 cnv correlated to 'RACE'.

  • del_12p12.1 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_N_STAGE'.

  • del_12q24.33 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' and 'PATHOLOGY_T_STAGE'.

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

  • del_19p13.3 cnv correlated to 'RACE'.

  • del_22q12.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_22q13.32 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 61 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 46 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 22q13 32 83 (22%) 287 0.565
(0.883) 		0.287
(0.747) 		0.00958
(0.2) 		0.00356
(0.133) 		0.121
(0.587) 		1
(1.00) 		0.352
(0.779) 		1
(1.00) 		0.0134
(0.233) 		0.0413
(0.428) 		0.00103
(0.0838) 		0.112
(0.587)
amp 10p15 1 72 (19%) 298 0.0146
(0.233) 		0.295
(0.747) 		0.00616
(0.167) 		0.00508
(0.155) 		1
(1.00) 		0.18
(0.661) 		0.779
(0.977) 		0.687
(0.925) 		0.805
(0.991) 		0.685
(0.924) 		0.484
(0.861) 		0.53
(0.882)
del 3p13 73 (20%) 297 0.591
(0.884) 		0.137
(0.61) 		0.00129
(0.0858) 		0.00352
(0.133) 		0.0977
(0.568) 		0.174
(0.66) 		0.0173
(0.264) 		0.217
(0.661) 		0.00271
(0.124) 		1
(1.00) 		0.608
(0.892) 		0.747
(0.959)
del 4q35 1 172 (46%) 198 0.00606
(0.167) 		0.000583
(0.0567) 		0.487
(0.861) 		0.241
(0.686) 		1
(1.00) 		0.623
(0.893) 		0.0572
(0.483) 		0.514
(0.863) 		0.351
(0.779) 		0.216
(0.661) 		4e-05
(0.0122) 		1
(1.00)
del 22q12 1 79 (21%) 291 0.754
(0.962) 		0.166
(0.648) 		0.0507
(0.47) 		0.0135
(0.233) 		0.487
(0.861) 		1
(1.00) 		0.341
(0.777) 		1
(1.00) 		0.0121
(0.227) 		0.0781
(0.539) 		0.00676
(0.171) 		0.105
(0.585)
amp 8q24 21 231 (62%) 139 0.651
(0.899) 		0.128
(0.592) 		0.0287
(0.339) 		0.59
(0.884) 		0.0329
(0.37) 		0.601
(0.889) 		0.000211
(0.0257) 		0.492
(0.863) 		0.75
(0.96) 		0.566
(0.883) 		1e-05
(0.00732) 		0.117
(0.587)
amp 17p11 2 46 (12%) 324 0.602
(0.889) 		0.361
(0.783) 		0.0132
(0.233) 		0.00463
(0.147) 		1
(1.00) 		0.447
(0.842) 		0.867
(1.00) 		0.606
(0.892) 		1
(1.00) 		0.0196
(0.274) 		0.647
(0.898) 		0.421
(0.83)
amp 17q25 3 145 (39%) 225 0.236
(0.684) 		0.739
(0.958) 		0.00889
(0.191) 		0.00363
(0.133) 		1
(1.00) 		1
(1.00) 		0.11
(0.587) 		0.491
(0.863) 		0.449
(0.842) 		0.0522
(0.478) 		0.232
(0.681) 		0.299
(0.747)
del 4q21 3 171 (46%) 199 0.301
(0.747) 		0.000187
(0.0257) 		0.781
(0.977) 		0.641
(0.897) 		1
(1.00) 		0.622
(0.893) 		0.317
(0.747) 		1
(1.00) 		0.392
(0.814) 		0.399
(0.82) 		0.00225
(0.11) 		0.0751
(0.53)
del 4q24 173 (47%) 197 0.107
(0.587) 		0.00195
(0.102) 		0.679
(0.924) 		0.549
(0.883) 		1
(1.00) 		0.623
(0.893) 		0.373
(0.787) 		1
(1.00) 		0.347
(0.779) 		0.342
(0.777) 		0.0101
(0.205) 		0.122
(0.587)
del 7q36 3 34 (9%) 336 0.00637
(0.167) 		0.683
(0.924) 		0.859
(1.00) 		0.542
(0.883) 		1
(1.00) 		1
(1.00) 		0.00315
(0.133) 		0.574
(0.883) 		0.623
(0.893) 		0.0433
(0.432) 		0.887
(1.00) 		1
(1.00)
del 12p12 1 78 (21%) 292 0.339
(0.777) 		0.873
(1.00) 		0.0108
(0.209) 		0.47
(0.86) 		0.00887
(0.191) 		0.215
(0.661) 		0.892
(1.00) 		0.213
(0.661) 		0.149
(0.63) 		0.0704
(0.522) 		0.638
(0.897) 		1
(1.00)
del 16q23 1 162 (44%) 208 0.218
(0.661) 		0.00148
(0.0903) 		0.308
(0.747) 		0.151
(0.63) 		1
(1.00) 		1
(1.00) 		0.261
(0.708) 		0.308
(0.747) 		0.443
(0.842) 		0.85
(1.00) 		5e-05
(0.0122) 		0.798
(0.985)
del 17p13 1 226 (61%) 144 0.00787
(0.18) 		0.542
(0.883) 		0.0629
(0.5) 		0.0145
(0.233) 		0.287
(0.747) 		0.3
(0.747) 		0.649
(0.898) 		0.743
(0.959) 		0.874
(1.00) 		0.313
(0.747) 		0.254
(0.704) 		0.607
(0.892)
del 17p11 2 195 (53%) 175 0.00412
(0.137) 		0.726
(0.95) 		0.0168
(0.262) 		0.014
(0.233) 		0.249
(0.696) 		0.625
(0.893) 		0.911
(1.00) 		1
(1.00) 		0.591
(0.884) 		0.138
(0.61) 		0.952
(1.00) 		0.453
(0.847)
amp 1q21 3 271 (73%) 99 0.0406
(0.428) 		0.943
(1.00) 		0.574
(0.883) 		0.823
(1.00) 		0.163
(0.641) 		0.575
(0.883) 		0.614
(0.893) 		0.699
(0.936) 		0.0108
(0.209) 		0.429
(0.836) 		0.22
(0.661) 		1
(1.00)
amp 2p24 1 65 (18%) 305 0.0485
(0.459) 		0.0915
(0.551) 		0.219
(0.661) 		0.153
(0.63) 		0.0768
(0.535) 		0.131
(0.598) 		0.00187
(0.102) 		1
(1.00) 		0.643
(0.897) 		0.515
(0.863) 		0.156
(0.633) 		1
(1.00)
amp 2q33 1 64 (17%) 306 0.162
(0.64) 		0.695
(0.932) 		0.0531
(0.48) 		0.073
(0.524) 		0.479
(0.861) 		0.168
(0.65) 		0.000109
(0.0199) 		0.366
(0.783) 		0.634
(0.896) 		0.624
(0.893) 		0.275
(0.735) 		0.495
(0.863)
amp 19p13 12 69 (19%) 301 0.372
(0.787) 		0.628
(0.896) 		0.207
(0.661) 		0.855
(1.00) 		1
(1.00) 		0.021
(0.274) 		0.00621
(0.167) 		1
(1.00) 		0.204
(0.661) 		0.22
(0.661) 		0.335
(0.773) 		0.515
(0.863)
amp xq28 87 (24%) 283 0.35
(0.779) 		0.191
(0.661) 		0.98
(1.00) 		0.931
(1.00) 		1
(1.00) 		0.578
(0.883) 		0.00062
(0.0567) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.563
(0.883) 		0.379
(0.796)
del 4p16 3 85 (23%) 285 0.204
(0.661) 		0.436
(0.841) 		0.345
(0.778) 		0.59
(0.884) 		0.544
(0.883) 		0.245
(0.691) 		0.00784
(0.18) 		1
(1.00) 		0.848
(1.00) 		0.194
(0.661) 		0.0311
(0.356) 		0.219
(0.661)
del 6q27 136 (37%) 234 0.926
(1.00) 		0.00124
(0.0858) 		0.449
(0.842) 		0.973
(1.00) 		0.557
(0.883) 		0.305
(0.747) 		0.299
(0.747) 		0.496
(0.863) 		0.387
(0.808) 		0.245
(0.691) 		0.51
(0.863) 		0.184
(0.661)
del 10q23 31 97 (26%) 273 0.241
(0.686) 		0.418
(0.83) 		0.24
(0.686) 		0.0188
(0.274) 		1
(1.00) 		0.577
(0.883) 		1
(1.00) 		0.454
(0.847) 		0.086
(0.547) 		0.544
(0.883) 		0.007
(0.171) 		1
(1.00)
del 12q24 33 59 (16%) 311 0.114
(0.587) 		0.291
(0.747) 		0.004
(0.137) 		0.232
(0.681) 		0.424
(0.834) 		0.152
(0.63) 		0.128
(0.592) 		1
(1.00) 		0.594
(0.884) 		0.949
(1.00) 		0.386
(0.807) 		0.724
(0.95)
del 19p13 3 87 (24%) 283 0.185
(0.661) 		0.259
(0.708) 		0.353
(0.779) 		0.148
(0.63) 		0.572
(0.883) 		1
(1.00) 		0.513
(0.863) 		0.69
(0.928) 		1
(1.00) 		0.81
(0.995) 		0.0138
(0.233) 		0.77
(0.973)
amp 1q42 2 268 (72%) 102 0.48
(0.861) 		0.98
(1.00) 		0.192
(0.661) 		0.595
(0.884) 		1
(1.00) 		0.575
(0.883) 		0.618
(0.893) 		0.706
(0.941) 		0.51
(0.863) 		0.859
(1.00) 		0.311
(0.747) 		0.777
(0.975)
amp 3q26 31 77 (21%) 293 0.356
(0.782) 		0.41
(0.826) 		0.835
(1.00) 		0.735
(0.957) 		0.471
(0.86) 		0.587
(0.884) 		0.784
(0.979) 		1
(1.00) 		0.822
(1.00) 		0.583
(0.884) 		0.205
(0.661) 		0.345
(0.778)
amp 4p14 54 (15%) 316 0.214
(0.661) 		0.0431
(0.432) 		0.559
(0.883) 		0.257
(0.708) 		1
(1.00) 		1
(1.00) 		0.269
(0.721) 		1
(1.00) 		1
(1.00) 		0.547
(0.883) 		0.87
(1.00) 		0.718
(0.95)
amp 5p15 33 163 (44%) 207 0.0687
(0.522) 		0.558
(0.883) 		0.168
(0.65) 		0.0436
(0.432) 		0.259
(0.708) 		0.632
(0.896) 		0.736
(0.957) 		0.193
(0.661) 		0.443
(0.842) 		0.91
(1.00) 		0.22
(0.661) 		0.798
(0.985)
amp 5q35 3 135 (36%) 235 0.386
(0.807) 		0.113
(0.587) 		0.472
(0.86) 		0.694
(0.932) 		0.555
(0.883) 		0.631
(0.896) 		0.249
(0.696) 		0.299
(0.747) 		0.105
(0.585) 		0.12
(0.587) 		0.489
(0.863) 		1
(1.00)
amp 6p25 2 159 (43%) 211 0.133
(0.605) 		0.983
(1.00) 		0.117
(0.587) 		0.0836
(0.547) 		1
(1.00) 		0.317
(0.747) 		0.368
(0.784) 		0.311
(0.747) 		0.445
(0.842) 		0.723
(0.95) 		0.913
(1.00) 		0.123
(0.59)
amp 6p21 1 158 (43%) 212 0.365
(0.783) 		0.0928
(0.552) 		0.403
(0.826) 		0.409
(0.826) 		0.266
(0.719) 		0.315
(0.747) 		0.0918
(0.551) 		0.085
(0.547) 		0.302
(0.747) 		0.721
(0.95) 		0.882
(1.00) 		0.3
(0.747)
amp 6q12 109 (29%) 261 0.407
(0.826) 		0.637
(0.897) 		0.018
(0.269) 		0.0561
(0.483) 		0.195
(0.661) 		0.583
(0.884) 		0.328
(0.76) 		0.0667
(0.514) 		0.144
(0.63) 		0.337
(0.775) 		0.455
(0.847) 		0.255
(0.706)
amp 6q12 83 (22%) 287 0.281
(0.74) 		0.313
(0.747) 		0.399
(0.82) 		0.148
(0.63) 		1
(1.00) 		0.203
(0.661) 		0.352
(0.779) 		0.214
(0.661) 		0.299
(0.747) 		0.395
(0.816) 		0.305
(0.747) 		0.056
(0.483)
amp 7q31 2 120 (32%) 250 0.989
(1.00) 		0.0819
(0.547) 		0.368
(0.784) 		0.543
(0.883) 		0.234
(0.681) 		1
(1.00) 		0.476
(0.861) 		0.48
(0.861) 		0.411
(0.826) 		0.762
(0.968) 		0.145
(0.63) 		0.414
(0.826)
amp 9q34 2 47 (13%) 323 0.619
(0.893) 		0.393
(0.816) 		0.181
(0.661) 		0.037
(0.41) 		1
(1.00) 		0.438
(0.841) 		0.74
(0.958) 		1
(1.00) 		1
(1.00) 		0.157
(0.633) 		0.633
(0.896) 		0.443
(0.842)
amp 11q13 3 57 (15%) 313 0.748
(0.959) 		0.414
(0.826) 		0.207
(0.661) 		0.0984
(0.568) 		1
(1.00) 		0.511
(0.863) 		0.643
(0.897) 		0.366
(0.783) 		0.759
(0.966) 		0.0574
(0.483) 		0.893
(1.00) 		0.483
(0.861)
amp 13q32 3 67 (18%) 303 0.115
(0.587) 		0.345
(0.778) 		0.568
(0.883) 		0.509
(0.863) 		0.448
(0.842) 		0.577
(0.883) 		0.0304
(0.353) 		0.205
(0.661) 		0.189
(0.661) 		0.408
(0.826) 		0.776
(0.975) 		1
(1.00)
amp 13q33 3 67 (18%) 303 0.109
(0.587) 		0.366
(0.783) 		0.881
(1.00) 		0.954
(1.00) 		0.448
(0.842) 		0.569
(0.883) 		0.112
(0.587) 		0.212
(0.661) 		0.191
(0.661) 		0.753
(0.962) 		0.218
(0.661) 		1
(1.00)
amp 15q26 3 54 (15%) 316 0.946
(1.00) 		0.0482
(0.459) 		0.486
(0.861) 		0.234
(0.681) 		1
(1.00) 		0.494
(0.863) 		0.43
(0.836) 		1
(1.00) 		0.548
(0.883) 		0.706
(0.941) 		0.843
(1.00) 		0.0613
(0.499)
amp 19q13 11 91 (25%) 279 0.669
(0.915) 		0.292
(0.747) 		0.0753
(0.53) 		0.373
(0.787) 		1
(1.00) 		0.0407
(0.428) 		0.198
(0.661) 		1
(1.00) 		0.462
(0.85) 		0.0895
(0.551) 		0.207
(0.661) 		0.557
(0.883)
amp 20q13 13 124 (34%) 246 0.047
(0.458) 		0.0489
(0.459) 		0.112
(0.587) 		0.0809
(0.547) 		0.26
(0.708) 		0.617
(0.893) 		0.156
(0.633) 		0.724
(0.95) 		1
(1.00) 		0.216
(0.661) 		0.534
(0.883) 		0.787
(0.981)
amp 20q13 33 128 (35%) 242 0.0892
(0.551) 		0.0912
(0.551) 		0.105
(0.585) 		0.122
(0.587) 		1
(1.00) 		0.153
(0.63) 		0.0611
(0.499) 		0.724
(0.95) 		0.745
(0.959) 		0.514
(0.863) 		0.658
(0.903) 		0.792
(0.985)
del 1p36 31 162 (44%) 208 0.529
(0.882) 		0.478
(0.861) 		0.912
(1.00) 		0.729
(0.953) 		1
(1.00) 		0.342
(0.777) 		0.177
(0.66) 		0.0834
(0.547) 		0.135
(0.61) 		0.17
(0.65) 		0.0707
(0.522) 		0.314
(0.747)
del 1p36 11 142 (38%) 228 0.949
(1.00) 		0.91
(1.00) 		0.545
(0.883) 		0.53
(0.882) 		0.566
(0.883) 		0.314
(0.747) 		0.731
(0.954) 		1
(1.00) 		0.279
(0.74) 		0.15
(0.63) 		0.115
(0.587) 		0.298
(0.747)
del 2q22 1 52 (14%) 318 0.137
(0.61) 		0.148
(0.63) 		0.649
(0.898) 		1
(1.00) 		0.357
(0.782) 		1
(1.00) 		1
(1.00) 		0.36
(0.783) 		0.533
(0.883) 		0.303
(0.747) 		0.537
(0.883) 		1
(1.00)
del 2q37 3 62 (17%) 308 0.548
(0.883) 		0.0664
(0.514) 		0.412
(0.826) 		0.431
(0.836) 		0.0641
(0.504) 		1
(1.00) 		0.766
(0.971) 		1
(1.00) 		0.09
(0.551) 		0.458
(0.849) 		0.196
(0.661) 		0.721
(0.95)
del 8p23 2 247 (67%) 123 0.815
(0.999) 		0.0541
(0.48) 		0.128
(0.592) 		0.411
(0.826) 		1
(1.00) 		0.304
(0.747) 		0.408
(0.826) 		1
(1.00) 		0.16
(0.639) 		0.905
(1.00) 		0.652
(0.899) 		1
(1.00)
del 8p12 242 (65%) 128 0.67
(0.915) 		0.21
(0.661) 		0.323
(0.757) 		0.645
(0.897) 		1
(1.00) 		0.301
(0.747) 		0.64
(0.897) 		0.504
(0.863) 		0.432
(0.836) 		0.775
(0.975) 		0.621
(0.893) 		0.592
(0.884)
del 9p21 3 150 (41%) 220 0.1
(0.573) 		0.0796
(0.545) 		0.601
(0.889) 		0.561
(0.883) 		0.568
(0.883) 		1
(1.00) 		0.427
(0.836) 		0.327
(0.76) 		1
(1.00) 		0.201
(0.661) 		0.233
(0.681) 		0.0713
(0.522)
del 9q31 3 119 (32%) 251 0.226
(0.671) 		0.903
(1.00) 		0.0695
(0.522) 		0.182
(0.661) 		0.0262
(0.314) 		0.085
(0.547) 		0.905
(1.00) 		0.725
(0.95) 		1
(1.00) 		0.176
(0.66) 		0.975
(1.00) 		0.281
(0.74)
del 10q26 13 105 (28%) 265 0.113
(0.587) 		0.794
(0.985) 		0.42
(0.83) 		0.0386
(0.422) 		1
(1.00) 		0.581
(0.884) 		0.712
(0.948) 		0.456
(0.847) 		0.213
(0.661) 		0.365
(0.783) 		0.0205
(0.274) 		1
(1.00)
del 11q14 1 77 (21%) 293 0.481
(0.861) 		0.205
(0.661) 		0.126
(0.592) 		0.0874
(0.551) 		0.129
(0.592) 		1
(1.00) 		0.683
(0.924) 		1
(1.00) 		0.0415
(0.428) 		0.499
(0.863) 		0.502
(0.863) 		0.0252
(0.308)
del 11q23 3 93 (25%) 277 0.674
(0.918) 		0.151
(0.63) 		0.362
(0.783) 		0.507
(0.863) 		0.172
(0.655) 		1
(1.00) 		1
(1.00) 		0.461
(0.85) 		0.103
(0.582) 		0.661
(0.906) 		0.187
(0.661) 		0.245
(0.691)
del 13q14 2 179 (48%) 191 0.0208
(0.274) 		0.237
(0.684) 		0.285
(0.747) 		0.0219
(0.276) 		0.622
(0.893) 		1
(1.00) 		0.094
(0.555) 		0.744
(0.959) 		0.682
(0.924) 		0.427
(0.836) 		0.157
(0.633) 		0.614
(0.893)
del 14q23 3 131 (35%) 239 0.25
(0.696) 		0.186
(0.661) 		0.461
(0.85) 		0.437
(0.841) 		0.56
(0.883) 		0.64
(0.897) 		0.415
(0.826) 		1
(1.00) 		0.178
(0.66) 		0.794
(0.985) 		0.02
(0.274) 		0.593
(0.884)
del 14q32 33 133 (36%) 237 0.805
(0.991) 		0.0986
(0.568) 		0.177
(0.66) 		0.0726
(0.524) 		0.557
(0.883) 		0.634
(0.896) 		0.908
(1.00) 		0.496
(0.863) 		0.0626
(0.5) 		0.87
(1.00) 		0.12
(0.587) 		0.795
(0.985)
del 15q26 3 79 (21%) 291 0.0214
(0.274) 		0.938
(1.00) 		0.0856
(0.547) 		0.0205
(0.274) 		0.121
(0.587) 		0.575
(0.883) 		0.892
(1.00) 		1
(1.00) 		0.268
(0.721) 		0.767
(0.972) 		0.225
(0.671) 		1
(1.00)
del 18q21 2 94 (25%) 276 0.821
(1.00) 		0.824
(1.00) 		0.328
(0.76) 		0.937
(1.00) 		0.158
(0.634) 		0.277
(0.737) 		0.126
(0.592) 		0.228
(0.676) 		0.0244
(0.302) 		0.505
(0.863) 		0.966
(1.00) 		0.56
(0.883)
del 20p12 1 29 (8%) 341 0.501
(0.863) 		0.314
(0.747) 		0.186
(0.661) 		0.656
(0.902) 		1
(1.00) 		0.324
(0.757) 		0.534
(0.883) 		0.15
(0.63) 		0.18
(0.661) 		0.59
(0.884) 		0.169
(0.65) 		0.353
(0.779)
del xq26 2 67 (18%) 303 0.116
(0.587) 		0.0603
(0.499) 		0.507
(0.863) 		0.317
(0.747) 		0.464
(0.851) 		0.587
(0.884) 		0.773
(0.975) 		0.22
(0.661) 		0.192
(0.661) 		0.483
(0.861) 		0.0545
(0.48) 		0.747
(0.959)
'amp_1q21.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0108 (Fisher's exact test), Q value = 0.21

Table S1.  Gene #1: 'amp_1q21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA HEPATOCHOLANGIOCARCINOMA (MIXED)
ALL 3 360 7
AMP PEAK 1(1Q21.3) MUTATED 0 267 4
AMP PEAK 1(1Q21.3) WILD-TYPE 3 93 3

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_2p24.1' versus 'GENDER'

P value = 0.00187 (Fisher's exact test), Q value = 0.1

Table S2.  Gene #3: 'amp_2p24.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 118 252
AMP PEAK 3(2P24.1) MUTATED 32 33
AMP PEAK 3(2P24.1) WILD-TYPE 86 219

Figure S2.  Get High-res Image Gene #3: 'amp_2p24.1' versus Clinical Feature #7: 'GENDER'

'amp_2q33.1' versus 'GENDER'

P value = 0.000109 (Fisher's exact test), Q value = 0.02

Table S3.  Gene #4: 'amp_2q33.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 118 252
AMP PEAK 4(2Q33.1) MUTATED 34 30
AMP PEAK 4(2Q33.1) WILD-TYPE 84 222

Figure S3.  Get High-res Image Gene #4: 'amp_2q33.1' versus Clinical Feature #7: 'GENDER'

'amp_8q24.21' versus 'GENDER'

P value = 0.000211 (Fisher's exact test), Q value = 0.026

Table S4.  Gene #14: 'amp_8q24.21' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 118 252
AMP PEAK 14(8Q24.21) MUTATED 57 174
AMP PEAK 14(8Q24.21) WILD-TYPE 61 78

Figure S4.  Get High-res Image Gene #14: 'amp_8q24.21' versus Clinical Feature #7: 'GENDER'

'amp_8q24.21' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0073

Table S5.  Gene #14: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 158 17 183
AMP PEAK 14(8Q24.21) MUTATED 2 119 11 92
AMP PEAK 14(8Q24.21) WILD-TYPE 0 39 6 91

Figure S5.  Get High-res Image Gene #14: 'amp_8q24.21' versus Clinical Feature #11: 'RACE'

'amp_10p15.1' versus 'Time to Death'

P value = 0.0146 (logrank test), Q value = 0.23

Table S6.  Gene #16: 'amp_10p15.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 364 129 0.0 - 120.8 (19.8)
AMP PEAK 16(10P15.1) MUTATED 71 32 0.3 - 114.3 (15.5)
AMP PEAK 16(10P15.1) WILD-TYPE 293 97 0.0 - 120.8 (20.8)

Figure S6.  Get High-res Image Gene #16: 'amp_10p15.1' versus Clinical Feature #1: 'Time to Death'

'amp_10p15.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00616 (Fisher's exact test), Q value = 0.17

Table S7.  Gene #16: 'amp_10p15.1' 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 173 87 3 62 9 7 2 1 2
AMP PEAK 16(10P15.1) MUTATED 23 22 0 19 2 0 0 0 2
AMP PEAK 16(10P15.1) WILD-TYPE 150 65 3 43 7 7 2 1 0

Figure S7.  Get High-res Image Gene #16: 'amp_10p15.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_10p15.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00508 (Fisher's exact test), Q value = 0.15

Table S8.  Gene #16: 'amp_10p15.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 183 95 77 12
AMP PEAK 16(10P15.1) MUTATED 23 24 22 3
AMP PEAK 16(10P15.1) WILD-TYPE 160 71 55 9

Figure S8.  Get High-res Image Gene #16: 'amp_10p15.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_17p11.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0132 (Fisher's exact test), Q value = 0.23

Table S9.  Gene #21: 'amp_17p11.2' 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 173 87 3 62 9 7 2 1 2
AMP PEAK 21(17P11.2) MUTATED 17 7 1 15 3 1 1 0 0
AMP PEAK 21(17P11.2) WILD-TYPE 156 80 2 47 6 6 1 1 2

Figure S9.  Get High-res Image Gene #21: 'amp_17p11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_17p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00463 (Fisher's exact test), Q value = 0.15

Table S10.  Gene #21: 'amp_17p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 183 95 77 12
AMP PEAK 21(17P11.2) MUTATED 17 8 19 2
AMP PEAK 21(17P11.2) WILD-TYPE 166 87 58 10

Figure S10.  Get High-res Image Gene #21: 'amp_17p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_17q25.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00889 (Fisher's exact test), Q value = 0.19

Table S11.  Gene #22: 'amp_17q25.3' 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 173 87 3 62 9 7 2 1 2
AMP PEAK 22(17Q25.3) MUTATED 54 37 0 32 7 3 1 0 1
AMP PEAK 22(17Q25.3) WILD-TYPE 119 50 3 30 2 4 1 1 1

Figure S11.  Get High-res Image Gene #22: 'amp_17q25.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_17q25.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00363 (Fisher's exact test), Q value = 0.13

Table S12.  Gene #22: 'amp_17q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 183 95 77 12
AMP PEAK 22(17Q25.3) MUTATED 57 41 39 8
AMP PEAK 22(17Q25.3) WILD-TYPE 126 54 38 4

Figure S12.  Get High-res Image Gene #22: 'amp_17q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_19p13.12' versus 'GENDER'

P value = 0.00621 (Fisher's exact test), Q value = 0.17

Table S13.  Gene #23: 'amp_19p13.12' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 118 252
AMP PEAK 23(19P13.12) MUTATED 32 37
AMP PEAK 23(19P13.12) WILD-TYPE 86 215

Figure S13.  Get High-res Image Gene #23: 'amp_19p13.12' versus Clinical Feature #7: 'GENDER'

'amp_xq28' versus 'GENDER'

P value = 0.00062 (Fisher's exact test), Q value = 0.057

Table S14.  Gene #27: 'amp_xq28' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 118 252
AMP PEAK 27(XQ28) MUTATED 15 72
AMP PEAK 27(XQ28) WILD-TYPE 103 180

Figure S14.  Get High-res Image Gene #27: 'amp_xq28' versus Clinical Feature #7: 'GENDER'

'del_3p13' versus 'PATHOLOGIC_STAGE'

P value = 0.00129 (Fisher's exact test), Q value = 0.086

Table S15.  Gene #32: 'del_3p13' 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 173 87 3 62 9 7 2 1 2
DEL PEAK 5(3P13) MUTATED 20 22 0 17 3 3 1 1 1
DEL PEAK 5(3P13) WILD-TYPE 153 65 3 45 6 4 1 0 1

Figure S15.  Get High-res Image Gene #32: 'del_3p13' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p13' versus 'PATHOLOGY_T_STAGE'

P value = 0.00352 (Fisher's exact test), Q value = 0.13

Table S16.  Gene #32: 'del_3p13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 183 95 77 12
DEL PEAK 5(3P13) MUTATED 23 25 21 4
DEL PEAK 5(3P13) WILD-TYPE 160 70 56 8

Figure S16.  Get High-res Image Gene #32: 'del_3p13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p13' versus 'HISTOLOGICAL_TYPE'

P value = 0.00271 (Fisher's exact test), Q value = 0.12

Table S17.  Gene #32: 'del_3p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA HEPATOCHOLANGIOCARCINOMA (MIXED)
ALL 3 360 7
DEL PEAK 5(3P13) MUTATED 1 67 5
DEL PEAK 5(3P13) WILD-TYPE 2 293 2

Figure S17.  Get High-res Image Gene #32: 'del_3p13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_4p16.3' versus 'GENDER'

P value = 0.00784 (Fisher's exact test), Q value = 0.18

Table S18.  Gene #33: 'del_4p16.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 118 252
DEL PEAK 6(4P16.3) MUTATED 17 68
DEL PEAK 6(4P16.3) WILD-TYPE 101 184

Figure S18.  Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #7: 'GENDER'

'del_4q21.3' versus 'YEARS_TO_BIRTH'

P value = 0.000187 (Wilcoxon-test), Q value = 0.026

Table S19.  Gene #34: 'del_4q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 366 59.4 (13.2)
DEL PEAK 7(4Q21.3) MUTATED 169 57.1 (13.4)
DEL PEAK 7(4Q21.3) WILD-TYPE 197 61.4 (12.7)

Figure S19.  Get High-res Image Gene #34: 'del_4q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q21.3' versus 'RACE'

P value = 0.00225 (Fisher's exact test), Q value = 0.11

Table S20.  Gene #34: 'del_4q21.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 158 17 183
DEL PEAK 7(4Q21.3) MUTATED 1 89 9 68
DEL PEAK 7(4Q21.3) WILD-TYPE 1 69 8 115

Figure S20.  Get High-res Image Gene #34: 'del_4q21.3' versus Clinical Feature #11: 'RACE'

'del_4q24' versus 'YEARS_TO_BIRTH'

P value = 0.00195 (Wilcoxon-test), Q value = 0.1

Table S21.  Gene #35: 'del_4q24' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 366 59.4 (13.2)
DEL PEAK 8(4Q24) MUTATED 171 57.5 (13.5)
DEL PEAK 8(4Q24) WILD-TYPE 195 61.1 (12.6)

Figure S21.  Get High-res Image Gene #35: 'del_4q24' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q24' versus 'RACE'

P value = 0.0101 (Fisher's exact test), Q value = 0.2

Table S22.  Gene #35: 'del_4q24' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 158 17 183
DEL PEAK 8(4Q24) MUTATED 1 88 9 71
DEL PEAK 8(4Q24) WILD-TYPE 1 70 8 112

Figure S22.  Get High-res Image Gene #35: 'del_4q24' versus Clinical Feature #11: 'RACE'

'del_4q35.1' versus 'Time to Death'

P value = 0.00606 (logrank test), Q value = 0.17

Table S23.  Gene #36: 'del_4q35.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 364 129 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 196 60 0.0 - 114.3 (21.1)

Figure S23.  Get High-res Image Gene #36: 'del_4q35.1' versus Clinical Feature #1: 'Time to Death'

'del_4q35.1' versus 'YEARS_TO_BIRTH'

P value = 0.000583 (Wilcoxon-test), Q value = 0.057

Table S24.  Gene #36: 'del_4q35.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 366 59.4 (13.2)
DEL PEAK 9(4Q35.1) MUTATED 169 57.2 (13.2)
DEL PEAK 9(4Q35.1) WILD-TYPE 197 61.3 (12.9)

Figure S24.  Get High-res Image Gene #36: 'del_4q35.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q35.1' versus 'RACE'

P value = 4e-05 (Fisher's exact test), Q value = 0.012

Table S25.  Gene #36: 'del_4q35.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 158 17 183
DEL PEAK 9(4Q35.1) MUTATED 1 95 10 66
DEL PEAK 9(4Q35.1) WILD-TYPE 1 63 7 117

Figure S25.  Get High-res Image Gene #36: 'del_4q35.1' versus Clinical Feature #11: 'RACE'

'del_6q27' versus 'YEARS_TO_BIRTH'

P value = 0.00124 (Wilcoxon-test), Q value = 0.086

Table S26.  Gene #37: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 366 59.4 (13.2)
DEL PEAK 10(6Q27) MUTATED 135 62.6 (12.3)
DEL PEAK 10(6Q27) WILD-TYPE 231 57.6 (13.4)

Figure S26.  Get High-res Image Gene #37: 'del_6q27' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_7q36.3' versus 'Time to Death'

P value = 0.00637 (logrank test), Q value = 0.17

Table S27.  Gene #38: 'del_7q36.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 364 129 0.0 - 120.8 (19.8)
DEL PEAK 11(7Q36.3) MUTATED 34 18 0.2 - 90.3 (12.9)
DEL PEAK 11(7Q36.3) WILD-TYPE 330 111 0.0 - 120.8 (20.5)

Figure S27.  Get High-res Image Gene #38: 'del_7q36.3' versus Clinical Feature #1: 'Time to Death'

'del_7q36.3' versus 'GENDER'

P value = 0.00315 (Fisher's exact test), Q value = 0.13

Table S28.  Gene #38: 'del_7q36.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 118 252
DEL PEAK 11(7Q36.3) MUTATED 19 15
DEL PEAK 11(7Q36.3) WILD-TYPE 99 237

Figure S28.  Get High-res Image Gene #38: 'del_7q36.3' versus Clinical Feature #7: 'GENDER'

'del_10q23.31' versus 'RACE'

P value = 0.007 (Fisher's exact test), Q value = 0.17

Table S29.  Gene #43: 'del_10q23.31' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 158 17 183
DEL PEAK 16(10Q23.31) MUTATED 0 46 10 40
DEL PEAK 16(10Q23.31) WILD-TYPE 2 112 7 143

Figure S29.  Get High-res Image Gene #43: 'del_10q23.31' versus Clinical Feature #11: 'RACE'

'del_12p12.1' versus 'PATHOLOGIC_STAGE'

P value = 0.0108 (Fisher's exact test), Q value = 0.21

Table S30.  Gene #47: '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 173 87 3 62 9 7 2 1 2
DEL PEAK 20(12P12.1) MUTATED 30 20 1 11 5 2 2 1 0
DEL PEAK 20(12P12.1) WILD-TYPE 143 67 2 51 4 5 0 0 2

Figure S30.  Get High-res Image Gene #47: 'del_12p12.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_12p12.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00887 (Fisher's exact test), Q value = 0.19

Table S31.  Gene #47: 'del_12p12.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 254 3
DEL PEAK 20(12P12.1) MUTATED 51 3
DEL PEAK 20(12P12.1) WILD-TYPE 203 0

Figure S31.  Get High-res Image Gene #47: 'del_12p12.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_12q24.33' versus 'PATHOLOGIC_STAGE'

P value = 0.004 (Fisher's exact test), Q value = 0.14

Table S32.  Gene #48: 'del_12q24.33' 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 173 87 3 62 9 7 2 1 2
DEL PEAK 21(12Q24.33) MUTATED 20 16 2 10 4 1 1 1 1
DEL PEAK 21(12Q24.33) WILD-TYPE 153 71 1 52 5 6 1 0 1

Figure S32.  Get High-res Image Gene #48: 'del_12q24.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_16q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.00148 (Wilcoxon-test), Q value = 0.09

Table S33.  Gene #53: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 366 59.4 (13.2)
DEL PEAK 26(16Q23.1) MUTATED 161 57.5 (12.8)
DEL PEAK 26(16Q23.1) WILD-TYPE 205 61.0 (13.3)

Figure S33.  Get High-res Image Gene #53: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q23.1' versus 'RACE'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S34.  Gene #53: 'del_16q23.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 158 17 183
DEL PEAK 26(16Q23.1) MUTATED 0 91 7 60
DEL PEAK 26(16Q23.1) WILD-TYPE 2 67 10 123

Figure S34.  Get High-res Image Gene #53: 'del_16q23.1' versus Clinical Feature #11: 'RACE'

'del_17p13.1' versus 'Time to Death'

P value = 0.00787 (logrank test), Q value = 0.18

Table S35.  Gene #54: 'del_17p13.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 364 129 0.0 - 120.8 (19.8)
DEL PEAK 27(17P13.1) MUTATED 222 90 0.0 - 120.8 (19.0)
DEL PEAK 27(17P13.1) WILD-TYPE 142 39 0.3 - 114.3 (20.9)

Figure S35.  Get High-res Image Gene #54: 'del_17p13.1' versus Clinical Feature #1: 'Time to Death'

'del_17p13.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0145 (Fisher's exact test), Q value = 0.23

Table S36.  Gene #54: 'del_17p13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 183 95 77 12
DEL PEAK 27(17P13.1) MUTATED 100 65 49 11
DEL PEAK 27(17P13.1) WILD-TYPE 83 30 28 1

Figure S36.  Get High-res Image Gene #54: 'del_17p13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_17p11.2' versus 'Time to Death'

P value = 0.00412 (logrank test), Q value = 0.14

Table S37.  Gene #55: 'del_17p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 364 129 0.0 - 120.8 (19.8)
DEL PEAK 28(17P11.2) MUTATED 191 81 0.0 - 120.8 (19.1)
DEL PEAK 28(17P11.2) WILD-TYPE 173 48 0.2 - 114.3 (20.8)

Figure S37.  Get High-res Image Gene #55: 'del_17p11.2' versus Clinical Feature #1: 'Time to Death'

'del_17p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.014 (Fisher's exact test), Q value = 0.23

Table S38.  Gene #55: 'del_17p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 183 95 77 12
DEL PEAK 28(17P11.2) MUTATED 82 58 45 9
DEL PEAK 28(17P11.2) WILD-TYPE 101 37 32 3

Figure S38.  Get High-res Image Gene #55: 'del_17p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'RACE'

P value = 0.0138 (Fisher's exact test), Q value = 0.23

Table S39.  Gene #57: 'del_19p13.3' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 158 17 183
DEL PEAK 30(19P13.3) MUTATED 0 51 3 33
DEL PEAK 30(19P13.3) WILD-TYPE 2 107 14 150

Figure S39.  Get High-res Image Gene #57: 'del_19p13.3' versus Clinical Feature #11: 'RACE'

'del_22q12.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0135 (Fisher's exact test), Q value = 0.23

Table S40.  Gene #59: 'del_22q12.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 183 95 77 12
DEL PEAK 32(22Q12.1) MUTATED 29 31 16 3
DEL PEAK 32(22Q12.1) WILD-TYPE 154 64 61 9

Figure S40.  Get High-res Image Gene #59: 'del_22q12.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_22q12.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0121 (Fisher's exact test), Q value = 0.23

Table S41.  Gene #59: 'del_22q12.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA HEPATOCHOLANGIOCARCINOMA (MIXED)
ALL 3 360 7
DEL PEAK 32(22Q12.1) MUTATED 3 74 2
DEL PEAK 32(22Q12.1) WILD-TYPE 0 286 5

Figure S41.  Get High-res Image Gene #59: 'del_22q12.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_22q12.1' versus 'RACE'

P value = 0.00676 (Fisher's exact test), Q value = 0.17

Table S42.  Gene #59: 'del_22q12.1' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 158 17 183
DEL PEAK 32(22Q12.1) MUTATED 1 25 8 44
DEL PEAK 32(22Q12.1) WILD-TYPE 1 133 9 139

Figure S42.  Get High-res Image Gene #59: 'del_22q12.1' versus Clinical Feature #11: 'RACE'

'del_22q13.32' versus 'PATHOLOGIC_STAGE'

P value = 0.00958 (Fisher's exact test), Q value = 0.2

Table S43.  Gene #60: 'del_22q13.32' 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 173 87 3 62 9 7 2 1 2
DEL PEAK 33(22Q13.32) MUTATED 26 25 1 16 4 3 1 1 0
DEL PEAK 33(22Q13.32) WILD-TYPE 147 62 2 46 5 4 1 0 2

Figure S43.  Get High-res Image Gene #60: 'del_22q13.32' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_22q13.32' versus 'PATHOLOGY_T_STAGE'

P value = 0.00356 (Fisher's exact test), Q value = 0.13

Table S44.  Gene #60: 'del_22q13.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 183 95 77 12
DEL PEAK 33(22Q13.32) MUTATED 28 30 20 5
DEL PEAK 33(22Q13.32) WILD-TYPE 155 65 57 7

Figure S44.  Get High-res Image Gene #60: 'del_22q13.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_22q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 0.0134 (Fisher's exact test), Q value = 0.23

Table S45.  Gene #60: 'del_22q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA HEPATOCHOLANGIOCARCINOMA (MIXED)
ALL 3 360 7
DEL PEAK 33(22Q13.32) MUTATED 3 78 2
DEL PEAK 33(22Q13.32) WILD-TYPE 0 282 5

Figure S45.  Get High-res Image Gene #60: 'del_22q13.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'RACE'

P value = 0.00103 (Fisher's exact test), Q value = 0.084

Table S46.  Gene #60: 'del_22q13.32' versus Clinical Feature #11: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 158 17 183
DEL PEAK 33(22Q13.32) MUTATED 2 24 7 48
DEL PEAK 33(22Q13.32) WILD-TYPE 0 134 10 135

Figure S46.  Get High-res Image Gene #60: '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/22531241/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/22506983/LIHC-TP.merged_data.txt

  • Number of patients = 370

  • Number of significantly focal cnvs = 61

  • 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.

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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