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 85 focal events and 10 clinical features across 173 patients, 21 significant findings detected with Q value < 0.25.

  • amp_1q42.3 cnv correlated to 'GENDER'.

  • amp_3q26.2 cnv correlated to 'RACE'.

  • amp_5p15.33 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_6q23.3 cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_M_STAGE'.

  • amp_8q24.21 cnv correlated to 'RACE'.

  • amp_9q34.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_12p12.1 cnv correlated to 'GENDER'.

  • amp_14q21.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'GENDER', and 'RACE'.

  • amp_xq28 cnv correlated to 'RACE'.

  • del_3p14.3 cnv correlated to 'RACE'.

  • del_3p14.2 cnv correlated to 'RACE'.

  • del_9p21.3 cnv correlated to 'RACE'.

  • del_10p11.21 cnv correlated to 'RACE'.

  • del_10q21.1 cnv correlated to 'RACE'.

  • del_13q14.2 cnv correlated to 'RACE'.

  • del_xp21.1 cnv correlated to 'NEOPLASM_DISEASESTAGE'.

  • del_xp11.3 cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 85 focal events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 21 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER NUMBER
PACK
YEARS
SMOKED 		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 Wilcoxon-test Fisher's exact test Fisher's exact test
amp 14q21 1 55 (32%) 118 0.357
(0.908) 		0.223
(0.773) 		0.967
(1.00) 		0.00368
(0.177) 		0.513
(0.937) 		0.717
(0.993) 		0.000828
(0.103) 		0.64
(0.981) 		0.00438
(0.193) 		0.276
(0.865)
amp 6q23 3 40 (23%) 133 0.694
(0.991) 		0.42
(0.931) 		0.00374
(0.177) 		0.5
(0.936) 		0.206
(0.772) 		0.00093
(0.103) 		1
(1.00) 		0.846
(1.00) 		0.629
(0.977) 		1
(1.00)
del xp11 3 69 (40%) 104 0.815
(1.00) 		0.97
(1.00) 		0.00319
(0.177) 		0.189
(0.763) 		0.0172
(0.354) 		0.08
(0.615) 		0.122
(0.685) 		0.703
(0.993) 		0.00092
(0.103) 		1
(1.00)
amp 1q42 3 87 (50%) 86 0.514
(0.937) 		0.0148
(0.341) 		0.515
(0.937) 		0.331
(0.908) 		0.136
(0.715) 		0.165
(0.732) 		0.00197
(0.12) 		0.975
(1.00) 		0.731
(0.993) 		0.58
(0.961)
amp 3q26 2 118 (68%) 55 0.331
(0.908) 		0.035
(0.474) 		0.324
(0.908) 		0.0572
(0.546) 		0.768
(1.00) 		0.717
(0.993) 		0.155
(0.732) 		0.179
(0.751) 		2e-05
(0.017) 		0.14
(0.721)
amp 5p15 33 89 (51%) 84 0.0954
(0.639) 		0.0452
(0.506) 		0.317
(0.906) 		0.0035
(0.177) 		0.57
(0.958) 		1
(1.00) 		1
(1.00) 		0.612
(0.97) 		0.0262
(0.416) 		0.0815
(0.616)
amp 8q24 21 136 (79%) 37 0.778
(1.00) 		0.145
(0.732) 		0.372
(0.908) 		0.659
(0.987) 		0.155
(0.732) 		0.684
(0.987) 		0.0148
(0.341) 		0.371
(0.908) 		0.00097
(0.103) 		0.474
(0.935)
amp 9q34 3 59 (34%) 114 0.164
(0.732) 		0.00117
(0.11) 		0.636
(0.981) 		0.181
(0.751) 		0.417
(0.928) 		0.161
(0.732) 		0.0192
(0.354) 		0.0281
(0.418) 		0.0173
(0.354) 		0.549
(0.952)
amp 12p12 1 74 (43%) 99 0.183
(0.752) 		0.148
(0.732) 		0.0209
(0.379) 		0.00712
(0.275) 		0.253
(0.84) 		0.158
(0.732) 		0.00141
(0.11) 		0.33
(0.908) 		0.0133
(0.332) 		0.603
(0.965)
amp xq28 64 (37%) 109 0.481
(0.935) 		0.0452
(0.506) 		0.368
(0.908) 		0.48
(0.935) 		0.107
(0.649) 		0.721
(0.993) 		0.11
(0.649) 		0.239
(0.808) 		0.00453
(0.193) 		0.603
(0.965)
del 3p14 3 116 (67%) 57 0.886
(1.00) 		0.6
(0.965) 		0.412
(0.924) 		0.909
(1.00) 		0.528
(0.946) 		1
(1.00) 		0.485
(0.935) 		0.91
(1.00) 		0.0006
(0.103) 		0.166
(0.732)
del 3p14 2 114 (66%) 59 0.407
(0.922) 		0.371
(0.908) 		0.465
(0.935) 		0.919
(1.00) 		0.486
(0.935) 		0.722
(0.993) 		0.361
(0.908) 		0.81
(1.00) 		0.00185
(0.12) 		0.181
(0.751)
del 9p21 3 131 (76%) 42 0.398
(0.918) 		0.226
(0.777) 		0.177
(0.751) 		0.172
(0.738) 		0.865
(1.00) 		0.207
(0.772) 		0.0182
(0.354) 		0.181
(0.751) 		0.00026
(0.103) 		1
(1.00)
del 10p11 21 45 (26%) 128 0.162
(0.732) 		0.22
(0.772) 		0.572
(0.959) 		0.0525
(0.531) 		0.731
(0.993) 		0.459
(0.935) 		1
(1.00) 		0.158
(0.732) 		0.00149
(0.11) 		0.554
(0.952)
del 10q21 1 40 (23%) 133 0.366
(0.908) 		0.62
(0.975) 		0.504
(0.936) 		0.89
(1.00) 		0.319
(0.908) 		0.691
(0.989) 		0.798
(1.00) 		0.751
(0.993) 		0.00078
(0.103) 		0.554
(0.952)
del 13q14 2 69 (40%) 104 0.423
(0.934) 		0.00834
(0.29) 		0.744
(0.993) 		0.739
(0.993) 		0.475
(0.935) 		0.298
(0.882) 		0.122
(0.685) 		0.362
(0.908) 		0.00156
(0.11) 		1
(1.00)
del xp21 1 65 (38%) 108 0.487
(0.935) 		0.568
(0.958) 		0.0059
(0.239) 		0.531
(0.946) 		0.0664
(0.582) 		0.155
(0.732) 		0.256
(0.841) 		0.73
(0.993) 		0.0293
(0.425) 		0.595
(0.965)
amp 1p34 2 37 (21%) 136 0.925
(1.00) 		0.186
(0.757) 		0.715
(0.993) 		0.748
(0.993) 		0.75
(0.993) 		0.374
(0.908) 		0.789
(1.00) 		0.336
(0.908) 		0.501
(0.936) 		0.497
(0.936)
amp 1q23 3 84 (49%) 89 0.5
(0.936) 		0.164
(0.732) 		0.6
(0.965) 		0.18
(0.751) 		0.67
(0.987) 		0.0918
(0.63) 		0.0153
(0.342) 		0.687
(0.987) 		0.733
(0.993) 		0.595
(0.965)
amp 2q14 2 55 (32%) 118 0.611
(0.97) 		0.0498
(0.531) 		0.797
(1.00) 		0.589
(0.965) 		0.92
(1.00) 		0.446
(0.935) 		1
(1.00) 		0.802
(1.00) 		0.0618
(0.562) 		1
(1.00)
amp 2q31 1 55 (32%) 118 0.966
(1.00) 		0.307
(0.892) 		0.452
(0.935) 		0.794
(1.00) 		0.364
(0.908) 		1
(1.00) 		0.102
(0.648) 		0.672
(0.987) 		0.0608
(0.562) 		1
(1.00)
amp 4q21 1 31 (18%) 142 0.0264
(0.416) 		0.792
(1.00) 		0.351
(0.908) 		0.458
(0.935) 		0.409
(0.922) 		1
(1.00) 		0.774
(1.00) 		0.249
(0.829) 		0.401
(0.921) 		1
(1.00)
amp 6p21 1 65 (38%) 108 0.834
(1.00) 		0.35
(0.908) 		0.378
(0.908) 		0.794
(1.00) 		0.472
(0.935) 		0.719
(0.993) 		0.496
(0.936) 		0.967
(1.00) 		0.865
(1.00) 		0.548
(0.952)
amp 7p11 2 117 (68%) 56 0.639
(0.981) 		0.217
(0.772) 		0.834
(1.00) 		0.0804
(0.615) 		0.563
(0.956) 		0.726
(0.993) 		0.348
(0.908) 		0.722
(0.993) 		1
(1.00) 		0.547
(0.952)
amp 7q21 2 107 (62%) 66 0.891
(1.00) 		0.298
(0.882) 		0.875
(1.00) 		0.0172
(0.354) 		0.482
(0.935) 		0.482
(0.935) 		0.498
(0.936) 		0.497
(0.936) 		0.384
(0.908) 		0.284
(0.875)
amp 8p23 1 50 (29%) 123 0.779
(1.00) 		0.107
(0.649) 		0.836
(1.00) 		0.35
(0.908) 		0.463
(0.935) 		0.257
(0.841) 		0.0559
(0.54) 		0.389
(0.908) 		0.14
(0.721) 		0.542
(0.952)
amp 8p11 21 81 (47%) 92 0.688
(0.987) 		0.814
(1.00) 		0.378
(0.908) 		0.749
(0.993) 		0.781
(1.00) 		1
(1.00) 		0.663
(0.987) 		0.519
(0.937) 		0.134
(0.715) 		1
(1.00)
amp 9p13 3 34 (20%) 139 0.522
(0.938) 		0.764
(1.00) 		0.58
(0.961) 		0.2
(0.772) 		0.628
(0.977) 		1
(1.00) 		0.05
(0.531) 		0.17
(0.738) 		1
(1.00) 		1
(1.00)
amp 11p13 49 (28%) 124 0.199
(0.772) 		0.962
(1.00) 		0.481
(0.935) 		0.0533
(0.533) 		0.841
(1.00) 		0.114
(0.667) 		0.225
(0.777) 		0.376
(0.908) 		0.512
(0.937) 		0.558
(0.953)
amp 11p13 46 (27%) 127 0.0997
(0.648) 		0.809
(1.00) 		0.38
(0.908) 		0.297
(0.882) 		0.84
(1.00) 		0.013
(0.332) 		0.322
(0.908) 		0.0719
(0.601) 		0.0404
(0.498) 		0.563
(0.956)
amp 11q13 3 95 (55%) 78 0.505
(0.936) 		0.384
(0.908) 		0.772
(1.00) 		0.415
(0.925) 		0.891
(1.00) 		0.733
(0.993) 		1
(1.00) 		0.194
(0.764) 		0.0859
(0.628) 		0.0628
(0.562)
amp 12q15 49 (28%) 124 0.223
(0.773) 		0.808
(1.00) 		0.0728
(0.601) 		0.148
(0.732) 		0.16
(0.732) 		0.00954
(0.29) 		0.47
(0.935) 		0.762
(1.00) 		0.368
(0.908) 		1
(1.00)
amp 13q22 1 62 (36%) 111 0.713
(0.993) 		0.952
(1.00) 		0.442
(0.935) 		0.214
(0.772) 		0.681
(0.987) 		1
(1.00) 		1
(1.00) 		0.166
(0.732) 		1
(1.00) 		0.0426
(0.504)
amp 15q26 1 54 (31%) 119 0.743
(0.993) 		0.381
(0.908) 		0.481
(0.935) 		0.216
(0.772) 		0.612
(0.97) 		0.247
(0.826) 		1
(1.00) 		0.0188
(0.354) 		0.202
(0.772) 		0.542
(0.952)
amp 17q12 71 (41%) 102 0.869
(1.00) 		0.858
(1.00) 		0.101
(0.648) 		0.289
(0.876) 		0.156
(0.732) 		0.154
(0.732) 		0.117
(0.672) 		0.123
(0.687) 		0.119
(0.676) 		1
(1.00)
amp 18p11 32 64 (37%) 109 0.436
(0.935) 		0.217
(0.772) 		0.193
(0.764) 		0.0332
(0.463) 		0.395
(0.915) 		0.0763
(0.612) 		0.0385
(0.496) 		0.585
(0.965) 		0.0218
(0.386) 		1
(1.00)
amp 18q11 2 56 (32%) 117 0.383
(0.908) 		0.551
(0.952) 		0.461
(0.935) 		0.72
(0.993) 		0.683
(0.987) 		1
(1.00) 		0.817
(1.00) 		0.99
(1.00) 		0.291
(0.88) 		1
(1.00)
amp 19p13 2 30 (17%) 143 0.57
(0.958) 		0.545
(0.952) 		0.317
(0.906) 		0.586
(0.965) 		0.0272
(0.418) 		0.622
(0.975) 		0.0819
(0.616) 		0.538
(0.952) 		0.381
(0.908) 		1
(1.00)
amp 19q12 51 (29%) 122 0.167
(0.732) 		0.677
(0.987) 		0.885
(1.00) 		0.989
(1.00) 		0.813
(1.00) 		1
(1.00) 		0.156
(0.732) 		0.508
(0.937) 		0.469
(0.935) 		1
(1.00)
del 1p36 11 70 (40%) 103 0.669
(0.987) 		0.734
(0.993) 		0.131
(0.715) 		0.531
(0.946) 		0.0521
(0.531) 		0.738
(0.993) 		0.825
(1.00) 		0.807
(1.00) 		0.36
(0.908) 		0.549
(0.952)
del 1p13 2 58 (34%) 115 0.107
(0.649) 		0.241
(0.811) 		0.275
(0.865) 		0.936
(1.00) 		0.106
(0.649) 		1
(1.00) 		0.485
(0.935) 		0.304
(0.891) 		0.664
(0.987) 		0.548
(0.952)
del 1q44 17 (10%) 156 0.877
(1.00) 		0.334
(0.908) 		0.212
(0.772) 		0.372
(0.908) 		0.0253
(0.416) 		0.6
(0.965) 		1
(1.00) 		0.813
(1.00) 		0.635
(0.981) 		1
(1.00)
del 2q22 1 52 (30%) 121 0.853
(1.00) 		0.194
(0.764) 		0.653
(0.987) 		0.155
(0.732) 		0.931
(1.00) 		1
(1.00) 		0.472
(0.935) 		0.867
(1.00) 		0.488
(0.935) 		1
(1.00)
del 2q33 3 32 (18%) 141 0.405
(0.921) 		0.568
(0.958) 		0.505
(0.936) 		0.0257
(0.416) 		0.862
(1.00) 		0.206
(0.772) 		1
(1.00) 		0.45
(0.935) 		1
(1.00) 		1
(1.00)
del 3p26 2 101 (58%) 72 0.454
(0.935) 		0.846
(1.00) 		0.673
(0.987) 		0.667
(0.987) 		0.731
(0.993) 		0.482
(0.935) 		0.504
(0.936) 		0.462
(0.935) 		0.0437
(0.504) 		0.273
(0.865)
del 3q11 1 32 (18%) 141 0.662
(0.987) 		0.38
(0.908) 		0.473
(0.935) 		0.354
(0.908) 		0.265
(0.852) 		1
(1.00) 		0.575
(0.959) 		0.617
(0.975) 		0.496
(0.936) 		0.52
(0.937)
del 3q26 31 15 (9%) 158 0.2
(0.772) 		0.533
(0.946) 		0.0438
(0.504) 		0.0384
(0.496) 		0.0839
(0.626) 		0.209
(0.772) 		0.697
(0.993) 		0.338
(0.908) 		0.062
(0.562) 		1
(1.00)
del 4p15 2 100 (58%) 73 0.0313
(0.444) 		0.94
(1.00) 		0.927
(1.00) 		0.152
(0.732) 		0.877
(1.00) 		1
(1.00) 		0.824
(1.00) 		0.218
(0.772) 		0.59
(0.965) 		1
(1.00)
del 4q22 1 100 (58%) 73 0.125
(0.692) 		0.0554
(0.54) 		0.0847
(0.626) 		0.0506
(0.531) 		0.195
(0.764) 		0.0784
(0.615) 		0.266
(0.852) 		0.466
(0.935) 		0.347
(0.908) 		1
(1.00)
del 4q34 3 94 (54%) 79 0.0919
(0.63) 		0.0108
(0.29) 		0.172
(0.738) 		0.625
(0.975) 		0.0611
(0.562) 		0.496
(0.936) 		0.665
(0.987) 		0.994
(1.00) 		0.414
(0.925) 		0.611
(0.97)
del 5q12 1 105 (61%) 68 0.887
(1.00) 		0.381
(0.908) 		0.0295
(0.425) 		0.821
(1.00) 		0.804
(1.00) 		0.153
(0.732) 		0.267
(0.853) 		0.946
(1.00) 		0.792
(1.00) 		1
(1.00)
del 6p25 3 70 (40%) 103 0.211
(0.772) 		0.376
(0.908) 		0.618
(0.975) 		0.682
(0.987) 		0.164
(0.732) 		0.726
(0.993) 		1
(1.00) 		0.899
(1.00) 		0.133
(0.715) 		0.0472
(0.514)
del 6q16 3 51 (29%) 122 0.705
(0.993) 		0.52
(0.937) 		0.991
(1.00) 		0.933
(1.00) 		0.731
(0.993) 		1
(1.00) 		0.0554
(0.54) 		0.0869
(0.628) 		0.106
(0.649) 		1
(1.00)
del 6q26 48 (28%) 125 0.532
(0.946) 		0.728
(0.993) 		0.256
(0.841) 		0.35
(0.908) 		0.587
(0.965) 		0.446
(0.935) 		0.228
(0.78) 		0.22
(0.772) 		0.158
(0.732) 		1
(1.00)
del 7q31 1 55 (32%) 118 0.00855
(0.29) 		0.0351
(0.474) 		0.0717
(0.601) 		0.621
(0.975) 		0.619
(0.975) 		1
(1.00) 		0.102
(0.648) 		0.216
(0.772) 		0.642
(0.981) 		1
(1.00)
del 7q36 3 66 (38%) 107 0.389
(0.908) 		0.47
(0.935) 		0.141
(0.724) 		0.721
(0.993) 		0.31
(0.901) 		0.314
(0.906) 		1
(1.00) 		0.864
(1.00) 		0.736
(0.993) 		1
(1.00)
del 8p23 2 81 (47%) 92 0.852
(1.00) 		0.0439
(0.504) 		0.279
(0.868) 		0.654
(0.987) 		0.216
(0.772) 		1
(1.00) 		0.188
(0.763) 		0.066
(0.582) 		0.133
(0.715) 		1
(1.00)
del 8p12 68 (39%) 105 0.56
(0.955) 		0.83
(1.00) 		0.074
(0.605) 		1
(1.00) 		0.0899
(0.63) 		0.51
(0.937) 		0.369
(0.908) 		0.152
(0.732) 		0.578
(0.961) 		1
(1.00)
del 9p23 102 (59%) 71 0.934
(1.00) 		0.733
(0.993) 		0.102
(0.648) 		0.136
(0.715) 		0.134
(0.715) 		1
(1.00) 		0.00744
(0.275) 		0.596
(0.965) 		0.0187
(0.354) 		0.284
(0.875)
del 10p15 3 48 (28%) 125 0.136
(0.715) 		0.636
(0.981) 		0.844
(1.00) 		0.0775
(0.615) 		0.259
(0.843) 		0.724
(0.993) 		1
(1.00) 		0.745
(0.993) 		0.0256
(0.416) 		1
(1.00)
del 10q23 31 59 (34%) 114 0.876
(1.00) 		0.439
(0.935) 		0.914
(1.00) 		0.364
(0.908) 		0.625
(0.975) 		1
(1.00) 		0.487
(0.935) 		0.429
(0.934) 		0.0105
(0.29) 		0.293
(0.88)
del 11p15 4 74 (43%) 99 0.95
(1.00) 		0.355
(0.908) 		0.81
(1.00) 		0.368
(0.908) 		0.885
(1.00) 		1
(1.00) 		0.0752
(0.609) 		0.441
(0.935) 		0.0106
(0.29) 		1
(1.00)
del 11q25 73 (42%) 100 0.0944
(0.637) 		0.0718
(0.601) 		0.391
(0.909) 		0.662
(0.987) 		0.601
(0.965) 		0.489
(0.935) 		0.381
(0.908) 		0.612
(0.97) 		0.219
(0.772) 		1
(1.00)
del 12q23 1 47 (27%) 126 0.14
(0.721) 		0.427
(0.934) 		0.598
(0.965) 		0.481
(0.935) 		0.886
(1.00) 		0.7
(0.993) 		0.135
(0.715) 		0.357
(0.908) 		0.101
(0.648) 		1
(1.00)
del 13q12 11 71 (41%) 102 0.596
(0.965) 		0.0886
(0.628) 		0.739
(0.993) 		0.287
(0.876) 		0.82
(1.00) 		1
(1.00) 		0.265
(0.852) 		0.365
(0.908) 		0.0181
(0.354) 		1
(1.00)
del 13q21 31 64 (37%) 109 0.672
(0.987) 		0.279
(0.868) 		0.934
(1.00) 		0.679
(0.987) 		0.681
(0.987) 		0.482
(0.935) 		0.11
(0.649) 		0.673
(0.987) 		0.0108
(0.29) 		0.568
(0.958)
del 14q23 3 49 (28%) 124 0.553
(0.952) 		0.69
(0.988) 		0.577
(0.961) 		0.285
(0.875) 		0.387
(0.908) 		0.257
(0.841) 		1
(1.00) 		0.641
(0.981) 		0.388
(0.908) 		0.52
(0.937)
del 15q11 2 59 (34%) 114 0.987
(1.00) 		0.337
(0.908) 		0.699
(0.993) 		0.452
(0.935) 		0.655
(0.987) 		0.276
(0.865) 		1
(1.00) 		0.379
(0.908) 		1
(1.00) 		1
(1.00)
del 16p13 3 63 (36%) 110 0.11
(0.649) 		0.652
(0.987) 		0.543
(0.952) 		0.483
(0.935) 		0.0399
(0.498) 		1
(1.00) 		0.499
(0.936) 		0.674
(0.987) 		0.231
(0.788) 		0.0383
(0.496)
del 16q23 1 80 (46%) 93 0.676
(0.987) 		0.751
(0.993) 		0.305
(0.891) 		0.211
(0.772) 		0.203
(0.772) 		1
(1.00) 		0.386
(0.908) 		0.925
(1.00) 		0.103
(0.648) 		0.0628
(0.562)
del 17p12 81 (47%) 92 0.951
(1.00) 		0.0404
(0.498) 		0.3
(0.885) 		0.452
(0.935) 		0.452
(0.935) 		1
(1.00) 		0.382
(0.908) 		0.881
(1.00) 		0.0109
(0.29) 		0.558
(0.953)
del 17q25 3 40 (23%) 133 0.0521
(0.531) 		0.272
(0.865) 		0.41
(0.922) 		0.392
(0.909) 		0.362
(0.908) 		1
(1.00) 		0.798
(1.00) 		0.155
(0.732) 		0.182
(0.751) 		1
(1.00)
del 18p11 23 56 (32%) 117 0.656
(0.987) 		0.0883
(0.628) 		0.43
(0.934) 		0.0684
(0.594) 		0.381
(0.908) 		1
(1.00) 		0.348
(0.908) 		0.0418
(0.504) 		0.292
(0.88) 		1
(1.00)
del 18q12 2 103 (60%) 70 0.193
(0.764) 		0.212
(0.772) 		0.784
(1.00) 		0.47
(0.935) 		0.487
(0.935) 		0.741
(0.993) 		1
(1.00) 		0.109
(0.649) 		0.586
(0.965) 		1
(1.00)
del 18q21 2 110 (64%) 63 0.456
(0.935) 		0.383
(0.908) 		0.801
(1.00) 		0.861
(1.00) 		0.726
(0.993) 		1
(1.00) 		0.649
(0.987) 		0.155
(0.732) 		0.116
(0.669) 		0.262
(0.85)
del 18q22 3 103 (60%) 70 0.83
(1.00) 		0.315
(0.906) 		0.661
(0.987) 		0.215
(0.772) 		0.333
(0.908) 		1
(1.00) 		0.825
(1.00) 		0.171
(0.738) 		0.0989
(0.648) 		0.241
(0.811)
del 19p13 3 88 (51%) 85 0.739
(0.993) 		0.463
(0.935) 		0.638
(0.981) 		0.324
(0.908) 		0.472
(0.935) 		1
(1.00) 		0.0793
(0.615) 		0.0878
(0.628) 		0.28
(0.868) 		1
(1.00)
del 19q11 46 (27%) 127 0.947
(1.00) 		0.234
(0.794) 		0.849
(1.00) 		0.425
(0.934) 		0.218
(0.772) 		0.7
(0.993) 		0.322
(0.908) 		0.0728
(0.601) 		0.303
(0.891) 		1
(1.00)
del 20p12 1 32 (18%) 141 0.0279
(0.418) 		0.53
(0.946) 		0.833
(1.00) 		0.425
(0.934) 		0.518
(0.937) 		1
(1.00) 		0.575
(0.959) 		0.63
(0.977) 		1
(1.00) 		0.426
(0.934)
del 21q11 2 99 (57%) 74 0.708
(0.993) 		0.468
(0.935) 		0.404
(0.921) 		0.885
(1.00) 		0.791
(1.00) 		0.507
(0.936) 		1
(1.00) 		0.404
(0.921) 		0.175
(0.749) 		1
(1.00)
del 21q21 1 101 (58%) 72 0.398
(0.918) 		0.516
(0.937) 		0.745
(0.993) 		0.852
(1.00) 		0.906
(1.00) 		1
(1.00) 		0.662
(0.987) 		0.296
(0.882) 		0.593
(0.965) 		1
(1.00)
del 21q22 12 101 (58%) 72 0.336
(0.908) 		0.437
(0.935) 		0.685
(0.987) 		0.897
(1.00) 		0.749
(0.993) 		1
(1.00) 		0.504
(0.936) 		0.0908
(0.63) 		0.428
(0.934) 		1
(1.00)
del 22q11 1 76 (44%) 97 0.0464
(0.512) 		0.409
(0.922) 		0.115
(0.669) 		0.0103
(0.29) 		0.0141
(0.341) 		0.185
(0.757) 		1
(1.00) 		0.625
(0.975) 		0.0933
(0.634) 		1
(1.00)
del xq11 2 40 (23%) 133 0.55
(0.952) 		0.372
(0.908) 		0.387
(0.908) 		0.685
(0.987) 		0.403
(0.921) 		0.683
(0.987) 		0.442
(0.935) 		0.704
(0.993) 		0.44
(0.935) 		0.542
(0.952)
del xq21 33 39 (23%) 134 0.807
(1.00) 		0.558
(0.953) 		0.0229
(0.397) 		0.759
(1.00) 		0.221
(0.772) 		0.687
(0.987) 		0.191
(0.764) 		0.288
(0.876) 		0.347
(0.908) 		1
(1.00)
'amp_1q42.3' versus 'GENDER'

P value = 0.00197 (Fisher's exact test), Q value = 0.12

Table S1.  Gene #3: 'amp_1q42.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 24 149
AMP PEAK 3(1Q42.3) MUTATED 5 82
AMP PEAK 3(1Q42.3) WILD-TYPE 19 67

Figure S1.  Get High-res Image Gene #3: 'amp_1q42.3' versus Clinical Feature #7: 'GENDER'

'amp_3q26.2' versus 'RACE'

P value = 2e-05 (Fisher's exact test), Q value = 0.017

Table S2.  Gene #6: 'amp_3q26.2' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
AMP PEAK 6(3Q26.2) MUTATED 38 1 66
AMP PEAK 6(3Q26.2) WILD-TYPE 3 1 45

Figure S2.  Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #9: 'RACE'

'amp_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.0035 (Fisher's exact test), Q value = 0.18

Table S3.  Gene #8: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 31 36 85 5
AMP PEAK 8(5P15.33) MUTATED 9 19 54 1
AMP PEAK 8(5P15.33) WILD-TYPE 22 17 31 4

Figure S3.  Get High-res Image Gene #8: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6q23.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00374 (Fisher's exact test), Q value = 0.18

Table S4.  Gene #10: 'amp_6q23.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 8 5 7 1 39 29 25 12 10 7 5 4
AMP PEAK 10(6Q23.3) MUTATED 5 0 1 0 7 7 4 1 1 3 4 3
AMP PEAK 10(6Q23.3) WILD-TYPE 3 5 6 1 32 22 21 11 9 4 1 1

Figure S4.  Get High-res Image Gene #10: 'amp_6q23.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_6q23.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.00093 (Fisher's exact test), Q value = 0.1

Table S5.  Gene #10: 'amp_6q23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 126 9
AMP PEAK 10(6Q23.3) MUTATED 27 7
AMP PEAK 10(6Q23.3) WILD-TYPE 99 2

Figure S5.  Get High-res Image Gene #10: 'amp_6q23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_8q24.21' versus 'RACE'

P value = 0.00097 (Fisher's exact test), Q value = 0.1

Table S6.  Gene #15: 'amp_8q24.21' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
AMP PEAK 15(8Q24.21) MUTATED 39 1 79
AMP PEAK 15(8Q24.21) WILD-TYPE 2 1 32

Figure S6.  Get High-res Image Gene #15: 'amp_8q24.21' versus Clinical Feature #9: 'RACE'

'amp_9q34.3' versus 'YEARS_TO_BIRTH'

P value = 0.00117 (Wilcoxon-test), Q value = 0.11

Table S7.  Gene #17: 'amp_9q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 173 62.6 (12.1)
AMP PEAK 17(9Q34.3) MUTATED 59 58.5 (12.7)
AMP PEAK 17(9Q34.3) WILD-TYPE 114 64.7 (11.3)

Figure S7.  Get High-res Image Gene #17: 'amp_9q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12p12.1' versus 'GENDER'

P value = 0.00141 (Fisher's exact test), Q value = 0.11

Table S8.  Gene #21: 'amp_12p12.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 24 149
AMP PEAK 21(12P12.1) MUTATED 3 71
AMP PEAK 21(12P12.1) WILD-TYPE 21 78

Figure S8.  Get High-res Image Gene #21: 'amp_12p12.1' versus Clinical Feature #7: 'GENDER'

'amp_14q21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00368 (Fisher's exact test), Q value = 0.18

Table S9.  Gene #24: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 31 36 85 5
AMP PEAK 24(14Q21.1) MUTATED 4 16 26 4
AMP PEAK 24(14Q21.1) WILD-TYPE 27 20 59 1

Figure S9.  Get High-res Image Gene #24: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_14q21.1' versus 'GENDER'

P value = 0.000828 (Fisher's exact test), Q value = 0.1

Table S10.  Gene #24: 'amp_14q21.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 24 149
AMP PEAK 24(14Q21.1) MUTATED 1 54
AMP PEAK 24(14Q21.1) WILD-TYPE 23 95

Figure S10.  Get High-res Image Gene #24: 'amp_14q21.1' versus Clinical Feature #7: 'GENDER'

'amp_14q21.1' versus 'RACE'

P value = 0.00438 (Fisher's exact test), Q value = 0.19

Table S11.  Gene #24: 'amp_14q21.1' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
AMP PEAK 24(14Q21.1) MUTATED 21 0 28
AMP PEAK 24(14Q21.1) WILD-TYPE 20 2 83

Figure S11.  Get High-res Image Gene #24: 'amp_14q21.1' versus Clinical Feature #9: 'RACE'

'amp_xq28' versus 'RACE'

P value = 0.00453 (Fisher's exact test), Q value = 0.19

Table S12.  Gene #31: 'amp_xq28' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
AMP PEAK 31(XQ28) MUTATED 24 1 35
AMP PEAK 31(XQ28) WILD-TYPE 17 1 76

Figure S12.  Get High-res Image Gene #31: 'amp_xq28' versus Clinical Feature #9: 'RACE'

'del_3p14.3' versus 'RACE'

P value = 6e-04 (Fisher's exact test), Q value = 0.1

Table S13.  Gene #38: 'del_3p14.3' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
DEL PEAK 7(3P14.3) MUTATED 36 1 65
DEL PEAK 7(3P14.3) WILD-TYPE 5 1 46

Figure S13.  Get High-res Image Gene #38: 'del_3p14.3' versus Clinical Feature #9: 'RACE'

'del_3p14.2' versus 'RACE'

P value = 0.00185 (Fisher's exact test), Q value = 0.12

Table S14.  Gene #39: 'del_3p14.2' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
DEL PEAK 8(3P14.2) MUTATED 35 1 64
DEL PEAK 8(3P14.2) WILD-TYPE 6 1 47

Figure S14.  Get High-res Image Gene #39: 'del_3p14.2' versus Clinical Feature #9: 'RACE'

'del_9p21.3' versus 'RACE'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S15.  Gene #54: 'del_9p21.3' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
DEL PEAK 23(9P21.3) MUTATED 39 1 75
DEL PEAK 23(9P21.3) WILD-TYPE 2 1 36

Figure S15.  Get High-res Image Gene #54: 'del_9p21.3' versus Clinical Feature #9: 'RACE'

'del_10p11.21' versus 'RACE'

P value = 0.00149 (Fisher's exact test), Q value = 0.11

Table S16.  Gene #56: 'del_10p11.21' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
DEL PEAK 25(10P11.21) MUTATED 19 1 21
DEL PEAK 25(10P11.21) WILD-TYPE 22 1 90

Figure S16.  Get High-res Image Gene #56: 'del_10p11.21' versus Clinical Feature #9: 'RACE'

'del_10q21.1' versus 'RACE'

P value = 0.00078 (Fisher's exact test), Q value = 0.1

Table S17.  Gene #57: 'del_10q21.1' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
DEL PEAK 26(10Q21.1) MUTATED 18 1 18
DEL PEAK 26(10Q21.1) WILD-TYPE 23 1 93

Figure S17.  Get High-res Image Gene #57: 'del_10q21.1' versus Clinical Feature #9: 'RACE'

'del_13q14.2' versus 'RACE'

P value = 0.00156 (Fisher's exact test), Q value = 0.11

Table S18.  Gene #63: 'del_13q14.2' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
DEL PEAK 32(13Q14.2) MUTATED 26 0 38
DEL PEAK 32(13Q14.2) WILD-TYPE 15 2 73

Figure S18.  Get High-res Image Gene #63: 'del_13q14.2' versus Clinical Feature #9: 'RACE'

'del_xp21.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0059 (Fisher's exact test), Q value = 0.24

Table S19.  Gene #82: 'del_xp21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 8 5 7 1 39 29 25 12 10 7 5 4
DEL PEAK 51(XP21.1) MUTATED 1 2 0 0 16 14 6 7 8 1 1 0
DEL PEAK 51(XP21.1) WILD-TYPE 7 3 7 1 23 15 19 5 2 6 4 4

Figure S19.  Get High-res Image Gene #82: 'del_xp21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_xp11.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00319 (Fisher's exact test), Q value = 0.18

Table S20.  Gene #83: 'del_xp11.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 8 5 7 1 39 29 25 12 10 7 5 4
DEL PEAK 52(XP11.3) MUTATED 1 2 1 0 18 13 10 7 9 0 1 0
DEL PEAK 52(XP11.3) WILD-TYPE 7 3 6 1 21 16 15 5 1 7 4 4

Figure S20.  Get High-res Image Gene #83: 'del_xp11.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_xp11.3' versus 'RACE'

P value = 0.00092 (Fisher's exact test), Q value = 0.1

Table S21.  Gene #83: 'del_xp11.3' versus Clinical Feature #9: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 41 2 111
DEL PEAK 52(XP11.3) MUTATED 26 0 36
DEL PEAK 52(XP11.3) WILD-TYPE 15 2 75

Figure S21.  Get High-res Image Gene #83: 'del_xp11.3' versus Clinical Feature #9: '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/ESCA-TP/15084414/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/15078602/ESCA-TP.merged_data.txt

  • Number of patients = 173

  • Number of significantly focal cnvs = 85

  • Number of selected clinical features = 10

  • 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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