Correlation between copy number variation genes (focal events) and selected clinical features
Liver Hepatocellular Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1P26X63
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/C1P26X63
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 357 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' and 'COMPLETENESS_OF_RESECTION'.

  • 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 '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 'NEOPLASM_DISEASESTAGE'.

  • del_13q14.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

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

  • del_17p11.2 cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_T_STAGE'.

  • 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 11 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 		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 21 224 (63%) 133 0.318
(0.782) 		0.0514
(0.428) 		0.104
(0.566) 		0.681
(0.927) 		0.237
(0.739) 		0.598
(0.886) 		0.00025
(0.0214) 		1
(1.00) 		0.609
(0.886) 		5e-05
(0.0112) 		0.541
(0.886)
amp 17p11 2 46 (13%) 311 0.638
(0.889) 		0.311
(0.782) 		0.0125
(0.266) 		0.00361
(0.152) 		1
(1.00) 		0.455
(0.873) 		1
(1.00) 		1
(1.00) 		0.00988
(0.249) 		0.715
(0.94) 		0.143
(0.59)
del 3p13 69 (19%) 288 0.864
(1.00) 		0.114
(0.566) 		0.0113
(0.256) 		0.00384
(0.152) 		0.471
(0.873) 		0.163
(0.613) 		0.0215
(0.326) 		0.00422
(0.152) 		0.578
(0.886) 		0.882
(1.00) 		1
(1.00)
del 4q21 3 165 (46%) 192 0.942
(1.00) 		8.22e-05
(0.0112) 		0.468
(0.873) 		0.476
(0.873) 		0.606
(0.886) 		0.622
(0.886) 		0.495
(0.884) 		0.629
(0.886) 		0.729
(0.94) 		0.00162
(0.0921) 		0.121
(0.571)
del 4q22 3 166 (46%) 191 0.855
(1.00) 		0.000248
(0.0214) 		0.543
(0.886) 		0.667
(0.913) 		0.609
(0.886) 		0.623
(0.886) 		0.427
(0.873) 		0.629
(0.886) 		0.732
(0.94) 		0.005
(0.155) 		0.122
(0.572)
del 4q35 1 168 (47%) 189 0.0863
(0.531) 		0.000198
(0.0214) 		0.195
(0.675) 		0.102
(0.566) 		0.621
(0.886) 		0.623
(0.886) 		0.0687
(0.488) 		0.631
(0.886) 		0.467
(0.873) 		7e-05
(0.0112) 		0.764
(0.96)
del 16q23 1 159 (45%) 198 0.739
(0.94) 		0.000578
(0.0394) 		0.171
(0.625) 		0.126
(0.579) 		0.609
(0.886) 		1
(1.00) 		0.209
(0.684) 		0.627
(0.886) 		0.597
(0.886) 		4e-05
(0.0112) 		0.554
(0.886)
del 17p11 2 186 (52%) 171 0.0196
(0.309) 		0.712
(0.94) 		0.00849
(0.226) 		0.0086
(0.226) 		0.248
(0.756) 		0.623
(0.886) 		1
(1.00) 		0.727
(0.94) 		0.338
(0.79) 		0.791
(0.971) 		0.546
(0.886)
del 22q13 32 79 (22%) 278 0.725
(0.94) 		0.404
(0.858) 		0.0379
(0.392) 		0.00496
(0.155) 		0.509
(0.886) 		1
(1.00) 		0.414
(0.867) 		0.0506
(0.428) 		0.0199
(0.309) 		0.00376
(0.152) 		0.0564
(0.437)
amp 2p24 1 64 (18%) 293 0.102
(0.566) 		0.0975
(0.563) 		0.211
(0.684) 		0.0896
(0.541) 		0.0797
(0.531) 		0.131
(0.579) 		0.000963
(0.0597) 		0.739
(0.94) 		0.385
(0.841) 		0.125
(0.579) 		1
(1.00)
amp 2q33 1 62 (17%) 295 0.184
(0.653) 		0.439
(0.873) 		0.0914
(0.546) 		0.0972
(0.563) 		0.471
(0.873) 		0.169
(0.624) 		3.65e-05
(0.0112) 		0.56
(0.886) 		0.546
(0.886) 		0.495
(0.884) 		0.418
(0.869)
amp 8q13 3 200 (56%) 157 0.774
(0.966) 		0.0833
(0.531) 		0.158
(0.604) 		0.307
(0.782) 		0.569
(0.886) 		1
(1.00) 		0.000566
(0.0394) 		0.854
(1.00) 		0.786
(0.971) 		0.085
(0.531) 		1
(1.00)
amp 17q25 3 141 (39%) 216 0.735
(0.94) 		0.872
(1.00) 		0.0174
(0.297) 		0.00447
(0.152) 		1
(1.00) 		1
(1.00) 		0.132
(0.579) 		0.622
(0.886) 		0.0337
(0.384) 		0.217
(0.697) 		0.537
(0.886)
amp 19p13 12 66 (18%) 291 0.82
(0.987) 		0.578
(0.886) 		0.131
(0.579) 		0.716
(0.94) 		0.463
(0.873) 		0.0199
(0.309) 		0.0019
(0.0997) 		0.152
(0.597) 		0.3
(0.782) 		0.605
(0.886) 		0.133
(0.58)
amp xq28 83 (23%) 274 0.306
(0.782) 		0.322
(0.782) 		0.928
(1.00) 		0.91
(1.00) 		1
(1.00) 		0.576
(0.886) 		0.00286
(0.139) 		0.305
(0.782) 		1
(1.00) 		0.288
(0.782) 		0.468
(0.873)
del 6q27 133 (37%) 224 0.581
(0.886) 		0.00431
(0.152) 		0.71
(0.94) 		0.96
(1.00) 		0.559
(0.886) 		0.306
(0.782) 		0.29
(0.782) 		0.732
(0.94) 		0.441
(0.873) 		0.563
(0.886) 		0.219
(0.7)
del 10q23 31 95 (27%) 262 0.38
(0.834) 		0.517
(0.886) 		0.105
(0.566) 		0.0237
(0.344) 		0.169
(0.624) 		0.577
(0.886) 		1
(1.00) 		0.151
(0.596) 		0.426
(0.873) 		0.00723
(0.213) 		1
(1.00)
del 12p12 1 73 (20%) 284 0.615
(0.886) 		0.973
(1.00) 		0.00748
(0.213) 		0.669
(0.914) 		0.109
(0.566) 		0.205
(0.684) 		0.78
(0.966) 		0.466
(0.873) 		0.117
(0.57) 		0.577
(0.886) 		0.459
(0.873)
del 13q14 2 169 (47%) 188 0.0537
(0.431) 		0.315
(0.782) 		0.332
(0.789) 		0.0102
(0.249) 		1
(1.00) 		1
(1.00) 		0.141
(0.59) 		0.855
(1.00) 		0.605
(0.886) 		0.0467
(0.428) 		1
(1.00)
amp 1p22 3 85 (24%) 272 0.972
(1.00) 		0.0944
(0.555) 		0.0893
(0.541) 		0.0618
(0.458) 		0.573
(0.886) 		0.056
(0.437) 		0.425
(0.873) 		1
(1.00) 		0.0356
(0.386) 		0.157
(0.604) 		0.469
(0.873)
amp 1q22 272 (76%) 85 0.203
(0.684) 		0.726
(0.94) 		0.915
(1.00) 		0.914
(1.00) 		0.538
(0.886) 		0.579
(0.886) 		0.505
(0.886) 		0.0293
(0.37) 		0.792
(0.971) 		0.244
(0.753) 		0.73
(0.94)
amp 1q42 3 261 (73%) 96 0.803
(0.977) 		0.939
(1.00) 		0.397
(0.854) 		0.629
(0.886) 		0.575
(0.886) 		0.575
(0.886) 		0.608
(0.886) 		0.437
(0.873) 		0.9
(1.00) 		0.532
(0.886) 		0.501
(0.886)
amp 3q26 31 74 (21%) 283 0.373
(0.826) 		0.428
(0.873) 		0.654
(0.901) 		0.632
(0.886) 		0.471
(0.873) 		1
(1.00) 		0.779
(0.966) 		0.776
(0.966) 		0.731
(0.94) 		0.192
(0.67) 		0.705
(0.94)
amp 4p14 52 (15%) 305 0.0735
(0.509) 		0.0507
(0.428) 		0.479
(0.877) 		0.21
(0.684) 		1
(1.00) 		1
(1.00) 		0.262
(0.768) 		1
(1.00) 		0.432
(0.873) 		0.798
(0.973) 		1
(1.00)
amp 5p15 33 158 (44%) 199 0.201
(0.684) 		0.499
(0.886) 		0.0747
(0.51) 		0.0254
(0.357) 		1
(1.00) 		0.632
(0.886) 		0.909
(1.00) 		0.626
(0.886) 		1
(1.00) 		0.367
(0.818) 		0.548
(0.886)
amp 5q35 3 131 (37%) 226 0.377
(0.829) 		0.131
(0.579) 		0.743
(0.942) 		0.705
(0.94) 		0.555
(0.886) 		0.635
(0.888) 		0.345
(0.79) 		0.103
(0.566) 		0.113
(0.566) 		0.794
(0.971) 		0.538
(0.886)
amp 6p25 2 150 (42%) 207 0.0699
(0.492) 		0.946
(1.00) 		0.111
(0.566) 		0.11
(0.566) 		1
(1.00) 		0.315
(0.782) 		0.302
(0.782) 		0.632
(0.886) 		0.734
(0.94) 		0.858
(1.00) 		1
(1.00)
amp 6p21 1 151 (42%) 206 0.364
(0.817) 		0.0834
(0.531) 		0.324
(0.782) 		0.474
(0.873) 		0.27
(0.776) 		0.315
(0.782) 		0.107
(0.566) 		0.452
(0.873) 		0.694
(0.939) 		0.865
(1.00) 		0.766
(0.96)
amp 6q12 102 (29%) 255 0.467
(0.873) 		0.551
(0.886) 		0.0273
(0.36) 		0.121
(0.571) 		0.183
(0.653) 		0.327
(0.782) 		0.258
(0.768) 		0.22
(0.7) 		0.317
(0.782) 		0.566
(0.886) 		0.508
(0.886)
amp 6q12 78 (22%) 279 0.598
(0.886) 		0.476
(0.873) 		0.303
(0.782) 		0.208
(0.684) 		1
(1.00) 		0.193
(0.67) 		0.271
(0.776) 		0.28
(0.782) 		0.421
(0.872) 		0.486
(0.882) 		0.259
(0.768)
amp 7q31 2 115 (32%) 242 0.82
(0.987) 		0.0789
(0.531) 		0.297
(0.782) 		0.698
(0.939) 		0.227
(0.711) 		1
(1.00) 		0.808
(0.979) 		0.494
(0.884) 		0.842
(1.00) 		0.263
(0.768) 		0.348
(0.793)
amp 9q34 2 44 (12%) 313 0.616
(0.886) 		0.482
(0.879) 		0.028
(0.36) 		0.0167
(0.297) 		0.327
(0.782) 		0.416
(0.867) 		0.491
(0.884) 		1
(1.00) 		0.159
(0.605) 		0.584
(0.886) 		0.633
(0.886)
amp 11q13 3 56 (16%) 301 0.434
(0.873) 		0.466
(0.873) 		0.051
(0.428) 		0.0524
(0.428) 		1
(1.00) 		0.52
(0.886) 		0.532
(0.886) 		0.717
(0.94) 		0.0468
(0.428) 		0.948
(1.00) 		1
(1.00)
amp 13q32 3 63 (18%) 294 0.32
(0.782) 		0.287
(0.782) 		0.649
(0.901) 		0.495
(0.884) 		0.455
(0.873) 		0.571
(0.886) 		0.0379
(0.392) 		0.137
(0.586) 		0.538
(0.886) 		0.628
(0.886) 		0.698
(0.939)
amp 13q33 3 64 (18%) 293 0.391
(0.844) 		0.41
(0.866) 		0.962
(1.00) 		0.974
(1.00) 		0.455
(0.873) 		0.571
(0.886) 		0.182
(0.653) 		0.141
(0.59) 		0.85
(1.00) 		0.151
(0.596) 		0.697
(0.939)
amp 15q26 3 53 (15%) 304 0.652
(0.901) 		0.0589
(0.446) 		0.277
(0.782) 		0.261
(0.768) 		1
(1.00) 		0.502
(0.886) 		0.523
(0.886) 		0.325
(0.782) 		0.568
(0.886) 		0.816
(0.986) 		0.012
(0.264)
amp 19q12 75 (21%) 282 0.799
(0.973) 		0.2
(0.684) 		0.289
(0.782) 		0.917
(1.00) 		0.494
(0.884) 		0.0279
(0.36) 		0.163
(0.613) 		0.265
(0.768) 		0.361
(0.815) 		0.592
(0.886) 		0.0628
(0.461)
amp 19q13 11 87 (24%) 270 0.317
(0.782) 		0.372
(0.825) 		0.0528
(0.428) 		0.337
(0.79) 		0.524
(0.886) 		0.0378
(0.392) 		0.111
(0.566) 		0.404
(0.858) 		0.144
(0.593) 		0.209
(0.684) 		0.475
(0.873)
amp 20q13 13 118 (33%) 239 0.0921
(0.546) 		0.0504
(0.428) 		0.0803
(0.531) 		0.0437
(0.428) 		0.253
(0.76) 		0.61
(0.886) 		0.117
(0.57) 		1
(1.00) 		0.278
(0.782) 		0.698
(0.939) 		1
(1.00)
amp 20q13 33 123 (34%) 234 0.224
(0.705) 		0.142
(0.59) 		0.0333
(0.384) 		0.0865
(0.531) 		0.296
(0.782) 		0.146
(0.593) 		0.0319
(0.384) 		0.862
(1.00) 		0.608
(0.886) 		0.778
(0.966) 		0.755
(0.954)
del 1p36 31 159 (45%) 198 0.738
(0.94) 		0.805
(0.977) 		0.971
(1.00) 		0.79
(0.971) 		0.591
(0.886) 		0.351
(0.797) 		0.138
(0.586) 		0.15
(0.596) 		0.186
(0.656) 		0.0824
(0.531) 		0.76
(0.958)
del 1p36 11 139 (39%) 218 0.538
(0.886) 		0.723
(0.94) 		0.521
(0.886) 		0.343
(0.79) 		0.0671
(0.482) 		0.316
(0.782) 		0.486
(0.882) 		0.434
(0.873) 		0.184
(0.653) 		0.111
(0.566) 		0.536
(0.886)
del 2q22 1 51 (14%) 306 0.254
(0.76) 		0.188
(0.66) 		0.976
(1.00) 		0.974
(1.00) 		1
(1.00) 		1
(1.00) 		0.748
(0.947) 		1
(1.00) 		0.299
(0.782) 		0.461
(0.873) 		0.654
(0.901)
del 2q37 3 60 (17%) 297 0.559
(0.886) 		0.131
(0.579) 		0.822
(0.987) 		0.426
(0.873) 		0.389
(0.844) 		1
(1.00) 		0.763
(0.959) 		0.12
(0.571) 		0.364
(0.817) 		0.439
(0.873) 		0.391
(0.844)
del 4p16 3 80 (22%) 277 0.302
(0.782) 		0.399
(0.856) 		0.0301
(0.373) 		0.367
(0.818) 		0.129
(0.579) 		0.242
(0.75) 		0.0136
(0.273) 		0.795
(0.971) 		0.39
(0.844) 		0.0352
(0.386) 		0.278
(0.782)
del 8p23 2 240 (67%) 117 0.905
(1.00) 		0.0991
(0.566) 		0.222
(0.7) 		0.415
(0.867) 		0.553
(0.886) 		0.304
(0.782) 		0.336
(0.79) 		0.25
(0.757) 		0.919
(1.00) 		0.722
(0.94) 		1
(1.00)
del 8p12 234 (66%) 123 0.659
(0.904) 		0.252
(0.76) 		0.469
(0.873) 		0.608
(0.886) 		0.553
(0.886) 		0.301
(0.782) 		0.475
(0.873) 		0.733
(0.94) 		0.876
(1.00) 		0.731
(0.94) 		0.342
(0.79)
del 9p21 3 146 (41%) 211 0.43
(0.873) 		0.0235
(0.344) 		0.537
(0.886) 		0.473
(0.873) 		0.569
(0.886) 		1
(1.00) 		0.356
(0.806) 		0.732
(0.94) 		0.475
(0.873) 		0.104
(0.566) 		0.13
(0.579)
del 9q31 3 116 (32%) 241 0.343
(0.79) 		0.909
(1.00) 		0.0578
(0.443) 		0.173
(0.627) 		0.0256
(0.357) 		0.0815
(0.531) 		0.717
(0.94) 		1
(1.00) 		0.162
(0.613) 		0.987
(1.00) 		0.345
(0.79)
del 10q26 13 102 (29%) 255 0.206
(0.684) 		0.938
(1.00) 		0.279
(0.782) 		0.0545
(0.432) 		0.197
(0.679) 		0.58
(0.886) 		0.9
(1.00) 		0.137
(0.586) 		0.47
(0.873) 		0.0173
(0.297) 		1
(1.00)
del 11q14 1 72 (20%) 285 0.965
(1.00) 		0.328
(0.783) 		0.052
(0.428) 		0.11
(0.566) 		0.121
(0.571) 		1
(1.00) 		1
(1.00) 		0.109
(0.566) 		0.55
(0.886) 		0.651
(0.901) 		0.0475
(0.428)
del 11q24 2 90 (25%) 267 0.683
(0.928) 		0.222
(0.7) 		0.171
(0.625) 		0.375
(0.827) 		0.169
(0.624) 		1
(1.00) 		0.896
(1.00) 		0.245
(0.753) 		0.655
(0.901) 		0.323
(0.782) 		0.154
(0.597)
del 12q24 33 54 (15%) 303 0.21
(0.684) 		0.338
(0.79) 		0.0161
(0.297) 		0.34
(0.79) 		1
(1.00) 		0.136
(0.586) 		0.266
(0.768) 		1
(1.00) 		0.879
(1.00) 		0.458
(0.873) 		0.678
(0.925)
del 14q23 3 126 (35%) 231 0.819
(0.987) 		0.151
(0.596) 		0.288
(0.782) 		0.202
(0.684) 		1
(1.00) 		0.638
(0.889) 		0.405
(0.858) 		0.34
(0.79) 		0.874
(1.00) 		0.0168
(0.297) 		1
(1.00)
del 14q32 33 129 (36%) 228 0.792
(0.971) 		0.0672
(0.482) 		0.153
(0.597) 		0.0355
(0.386) 		1
(1.00) 		0.632
(0.886) 		0.906
(1.00) 		0.147
(0.595) 		0.879
(1.00) 		0.14
(0.59) 		1
(1.00)
del 15q26 3 75 (21%) 282 0.0618
(0.458) 		0.947
(1.00) 		0.0854
(0.531) 		0.027
(0.36) 		0.117
(0.57) 		0.575
(0.886) 		0.78
(0.966) 		0.264
(0.768) 		0.739
(0.94) 		0.453
(0.873) 		0.705
(0.94)
del 17p13 1 217 (61%) 140 0.0327
(0.384) 		0.509
(0.886) 		0.0425
(0.428) 		0.0107
(0.251) 		0.284
(0.782) 		0.301
(0.782) 		0.561
(0.886) 		0.861
(1.00) 		0.588
(0.886) 		0.105
(0.566) 		0.538
(0.886)
del 18q21 2 88 (25%) 269 0.872
(1.00) 		0.939
(1.00) 		0.741
(0.941) 		0.944
(1.00) 		1
(1.00) 		0.274
(0.781) 		0.292
(0.782) 		0.0519
(0.428) 		0.615
(0.886) 		0.921
(1.00) 		0.473
(0.873)
del 19p13 3 84 (24%) 273 0.322
(0.782) 		0.114
(0.566) 		0.501
(0.886) 		0.215
(0.694) 		0.573
(0.886) 		1
(1.00) 		0.506
(0.886) 		1
(1.00) 		1
(1.00) 		0.0163
(0.297) 		0.733
(0.94)
del 20p12 1 27 (8%) 330 0.32
(0.782) 		0.57
(0.886) 		0.317
(0.782) 		0.781
(0.966) 		1
(1.00) 		0.307
(0.782) 		0.525
(0.886) 		0.0739
(0.509) 		0.613
(0.886) 		0.557
(0.886) 		0.589
(0.886)
del 22q12 1 75 (21%) 282 0.999
(1.00) 		0.247
(0.755) 		0.121
(0.571) 		0.0194
(0.309) 		1
(1.00) 		1
(1.00) 		0.402
(0.858) 		0.0427
(0.428) 		0.0502
(0.428) 		0.0135
(0.273) 		0.0504
(0.428)
del xq26 2 65 (18%) 292 0.907
(1.00) 		0.0448
(0.428) 		0.603
(0.886) 		0.413
(0.867) 		0.471
(0.873) 		0.585
(0.886) 		0.556
(0.886) 		0.146
(0.593) 		0.326
(0.782) 		0.0337
(0.384) 		1
(1.00)
'amp_2p24.1' versus 'GENDER'

P value = 0.000963 (Fisher's exact test), Q value = 0.06

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

nPatients FEMALE MALE
ALL 113 244
AMP PEAK 4(2P24.1) MUTATED 32 32
AMP PEAK 4(2P24.1) WILD-TYPE 81 212

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

'amp_2q33.1' versus 'GENDER'

P value = 3.65e-05 (Fisher's exact test), Q value = 0.011

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

nPatients FEMALE MALE
ALL 113 244
AMP PEAK 5(2Q33.1) MUTATED 34 28
AMP PEAK 5(2Q33.1) WILD-TYPE 79 216

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

'amp_8q13.3' versus 'GENDER'

P value = 0.000566 (Fisher's exact test), Q value = 0.039

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

nPatients FEMALE MALE
ALL 113 244
AMP PEAK 15(8Q13.3) MUTATED 48 152
AMP PEAK 15(8Q13.3) WILD-TYPE 65 92

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

'amp_8q24.21' versus 'GENDER'

P value = 0.00025 (Fisher's exact test), Q value = 0.021

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

nPatients FEMALE MALE
ALL 113 244
AMP PEAK 16(8Q24.21) MUTATED 55 169
AMP PEAK 16(8Q24.21) WILD-TYPE 58 75

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

'amp_8q24.21' versus 'RACE'

P value = 5e-05 (Fisher's exact test), Q value = 0.011

Table S5.  Gene #16: 'amp_8q24.21' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 156 17 173
AMP PEAK 16(8Q24.21) MUTATED 1 117 11 88
AMP PEAK 16(8Q24.21) WILD-TYPE 0 39 6 85

Figure S5.  Get High-res Image Gene #16: 'amp_8q24.21' versus Clinical Feature #10: 'RACE'

'amp_17p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00361 (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 179 91 73 12
AMP PEAK 22(17P11.2) MUTATED 17 8 19 2
AMP PEAK 22(17P11.2) WILD-TYPE 162 83 54 10

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

'amp_17p11.2' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.00988 (Fisher's exact test), Q value = 0.25

Table S7.  Gene #22: 'amp_17p11.2' versus Clinical Feature #9: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 315 15 1 19
AMP PEAK 22(17P11.2) MUTATED 37 5 1 3
AMP PEAK 22(17P11.2) WILD-TYPE 278 10 0 16

Figure S7.  Get High-res Image Gene #22: 'amp_17p11.2' versus Clinical Feature #9: 'COMPLETENESS_OF_RESECTION'

'amp_17q25.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00447 (Fisher's exact test), Q value = 0.15

Table S8.  Gene #23: 'amp_17q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 179 91 73 12
AMP PEAK 23(17Q25.3) MUTATED 57 38 38 8
AMP PEAK 23(17Q25.3) WILD-TYPE 122 53 35 4

Figure S8.  Get High-res Image Gene #23: 'amp_17q25.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_19p13.12' versus 'GENDER'

P value = 0.0019 (Fisher's exact test), Q value = 0.1

Table S9.  Gene #24: 'amp_19p13.12' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 113 244
AMP PEAK 24(19P13.12) MUTATED 32 34
AMP PEAK 24(19P13.12) WILD-TYPE 81 210

Figure S9.  Get High-res Image Gene #24: 'amp_19p13.12' versus Clinical Feature #7: 'GENDER'

'amp_xq28' versus 'GENDER'

P value = 0.00286 (Fisher's exact test), Q value = 0.14

Table S10.  Gene #29: 'amp_xq28' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 113 244
AMP PEAK 29(XQ28) MUTATED 15 68
AMP PEAK 29(XQ28) WILD-TYPE 98 176

Figure S10.  Get High-res Image Gene #29: 'amp_xq28' versus Clinical Feature #7: 'GENDER'

'del_3p13' versus 'PATHOLOGY_T_STAGE'

P value = 0.00384 (Fisher's exact test), Q value = 0.15

Table S11.  Gene #34: 'del_3p13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 179 91 73 12
DEL PEAK 5(3P13) MUTATED 22 23 20 4
DEL PEAK 5(3P13) WILD-TYPE 157 68 53 8

Figure S11.  Get High-res Image Gene #34: 'del_3p13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p13' versus 'HISTOLOGICAL_TYPE'

P value = 0.00422 (Fisher's exact test), Q value = 0.15

Table S12.  Gene #34: 'del_3p13' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA HEPATOCHOLANGIOCARCINOMA (MIXED)
ALL 2 348 7
DEL PEAK 5(3P13) MUTATED 0 64 5
DEL PEAK 5(3P13) WILD-TYPE 2 284 2

Figure S12.  Get High-res Image Gene #34: 'del_3p13' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_4q21.3' versus 'YEARS_TO_BIRTH'

P value = 8.22e-05 (Wilcoxon-test), Q value = 0.011

Table S13.  Gene #36: 'del_4q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 354 59.8 (12.7)
DEL PEAK 7(4Q21.3) MUTATED 163 57.2 (13.3)
DEL PEAK 7(4Q21.3) WILD-TYPE 191 62.0 (11.8)

Figure S13.  Get High-res Image Gene #36: 'del_4q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q21.3' versus 'RACE'

P value = 0.00162 (Fisher's exact test), Q value = 0.092

Table S14.  Gene #36: 'del_4q21.3' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 156 17 173
DEL PEAK 7(4Q21.3) MUTATED 0 88 9 64
DEL PEAK 7(4Q21.3) WILD-TYPE 1 68 8 109

Figure S14.  Get High-res Image Gene #36: 'del_4q21.3' versus Clinical Feature #10: 'RACE'

'del_4q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.000248 (Wilcoxon-test), Q value = 0.021

Table S15.  Gene #37: 'del_4q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 354 59.8 (12.7)
DEL PEAK 8(4Q22.3) MUTATED 164 57.3 (13.3)
DEL PEAK 8(4Q22.3) WILD-TYPE 190 61.8 (11.8)

Figure S15.  Get High-res Image Gene #37: 'del_4q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q22.3' versus 'RACE'

P value = 0.005 (Fisher's exact test), Q value = 0.15

Table S16.  Gene #37: 'del_4q22.3' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 156 17 173
DEL PEAK 8(4Q22.3) MUTATED 0 87 9 66
DEL PEAK 8(4Q22.3) WILD-TYPE 1 69 8 107

Figure S16.  Get High-res Image Gene #37: 'del_4q22.3' versus Clinical Feature #10: 'RACE'

'del_4q35.1' versus 'YEARS_TO_BIRTH'

P value = 0.000198 (Wilcoxon-test), Q value = 0.021

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

nPatients Mean (Std.Dev)
ALL 354 59.8 (12.7)
DEL PEAK 9(4Q35.1) MUTATED 165 57.3 (13.0)
DEL PEAK 9(4Q35.1) WILD-TYPE 189 61.9 (12.1)

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 = 7e-05 (Fisher's exact test), Q value = 0.011

Table S18.  Gene #38: 'del_4q35.1' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 156 17 173
DEL PEAK 9(4Q35.1) MUTATED 0 95 10 63
DEL PEAK 9(4Q35.1) WILD-TYPE 1 61 7 110

Figure S18.  Get High-res Image Gene #38: 'del_4q35.1' versus Clinical Feature #10: 'RACE'

'del_6q27' versus 'YEARS_TO_BIRTH'

P value = 0.00431 (Wilcoxon-test), Q value = 0.15

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

nPatients Mean (Std.Dev)
ALL 354 59.8 (12.7)
DEL PEAK 10(6Q27) MUTATED 132 62.4 (12.3)
DEL PEAK 10(6Q27) WILD-TYPE 222 58.2 (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 = 0.00723 (Fisher's exact test), Q value = 0.21

Table S20.  Gene #44: 'del_10q23.31' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 156 17 173
DEL PEAK 15(10Q23.31) MUTATED 0 46 10 38
DEL PEAK 15(10Q23.31) WILD-TYPE 1 110 7 135

Figure S20.  Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #10: 'RACE'

'del_12p12.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00748 (Fisher's exact test), Q value = 0.21

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

nPatients STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 168 84 3 59 8 7 3 1 2
DEL PEAK 19(12P12.1) MUTATED 30 17 1 10 5 2 3 0 0
DEL PEAK 19(12P12.1) WILD-TYPE 138 67 2 49 3 5 0 1 2

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

'del_13q14.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0102 (Fisher's exact test), Q value = 0.25

Table S22.  Gene #50: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 179 91 73 12
DEL PEAK 21(13Q14.2) MUTATED 75 51 33 10
DEL PEAK 21(13Q14.2) WILD-TYPE 104 40 40 2

Figure S22.  Get High-res Image Gene #50: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_16q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.000578 (Wilcoxon-test), Q value = 0.039

Table S23.  Gene #54: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 354 59.8 (12.7)
DEL PEAK 25(16Q23.1) MUTATED 158 57.4 (12.8)
DEL PEAK 25(16Q23.1) WILD-TYPE 196 61.6 (12.3)

Figure S23.  Get High-res Image Gene #54: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q23.1' versus 'RACE'

P value = 4e-05 (Fisher's exact test), Q value = 0.011

Table S24.  Gene #54: 'del_16q23.1' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 156 17 173
DEL PEAK 25(16Q23.1) MUTATED 0 90 7 58
DEL PEAK 25(16Q23.1) WILD-TYPE 1 66 10 115

Figure S24.  Get High-res Image Gene #54: 'del_16q23.1' versus Clinical Feature #10: 'RACE'

'del_17p11.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00849 (Fisher's exact test), Q value = 0.23

Table S25.  Gene #56: 'del_17p11.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 168 84 3 59 8 7 3 1 2
DEL PEAK 27(17P11.2) MUTATED 71 49 1 35 6 6 3 1 1
DEL PEAK 27(17P11.2) WILD-TYPE 97 35 2 24 2 1 0 0 1

Figure S25.  Get High-res Image Gene #56: 'del_17p11.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_17p11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0086 (Fisher's exact test), Q value = 0.23

Table S26.  Gene #56: 'del_17p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 179 91 73 12
DEL PEAK 27(17P11.2) MUTATED 78 55 43 9
DEL PEAK 27(17P11.2) WILD-TYPE 101 36 30 3

Figure S26.  Get High-res Image Gene #56: 'del_17p11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_22q13.32' versus 'PATHOLOGY_T_STAGE'

P value = 0.00496 (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 179 91 73 12
DEL PEAK 32(22Q13.32) MUTATED 27 28 19 5
DEL PEAK 32(22Q13.32) WILD-TYPE 152 63 54 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 = 0.00376 (Fisher's exact test), Q value = 0.15

Table S28.  Gene #61: 'del_22q13.32' versus Clinical Feature #10: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 156 17 173
DEL PEAK 32(22Q13.32) MUTATED 1 24 7 45
DEL PEAK 32(22Q13.32) WILD-TYPE 0 132 10 128

Figure S28.  Get High-res Image Gene #61: 'del_22q13.32' versus Clinical Feature #10: '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/15089885/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/15082975/LIHC-TP.merged_data.txt

  • Number of patients = 357

  • 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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle