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 15 clinical features across 184 patients, 65 significant findings detected with Q value < 0.25.

  • amp_1q42.3 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.

  • amp_3q26.2 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • amp_5p15.33 cnv correlated to 'PATHOLOGY_T_STAGE' and 'HISTOLOGICAL_TYPE'.

  • amp_6p21.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • amp_8p23.1 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RESIDUAL_TUMOR'.

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

  • amp_9p13.3 cnv correlated to 'GENDER'.

  • amp_9q34.3 cnv correlated to 'YEARS_TO_BIRTH' and 'NUMBER_PACK_YEARS_SMOKED'.

  • amp_11q13.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_12p12.1 cnv correlated to 'GENDER'.

  • amp_12q15 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • amp_13q22.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • amp_15q26.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_17q12 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_18q11.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_xq28 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • del_2q22.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_2q33.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_3p26.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_3p14.3 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • del_3p14.2 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • del_3q26.31 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_4q34.3 cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_7q31.1 cnv correlated to 'Time to Death'.

  • del_9p21.3 cnv correlated to 'GENDER' and 'RACE'.

  • del_10p15.3 cnv correlated to 'RACE'.

  • del_10p11.21 cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • del_10q21.1 cnv correlated to 'RACE'.

  • del_10q23.31 cnv correlated to 'RESIDUAL_TUMOR' and 'RACE'.

  • del_11p15.4 cnv correlated to 'RACE'.

  • del_11q25 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_13q12.11 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_13q14.2 cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • del_13q21.31 cnv correlated to 'RACE'.

  • del_16p13.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_16q23.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_17p12 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_18q21.2 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_22q11.1 cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • del_xp11.3 cnv correlated to 'PATHOLOGIC_STAGE' 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 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 65 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 		KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		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 Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
amp 14q21 1 61 (33%) 123 0.412
(0.853) 		0.0995
(0.593) 		0.937
(1.00) 		0.00788
(0.193) 		0.624
(0.957) 		0.492
(0.883) 		0.00157
(0.0714) 		0.346
(0.829) 		0.664
(0.957) 		0.00169
(0.0744) 		0.593
(0.948) 		1
(1.00) 		0.35
(0.83) 		0.00366
(0.111) 		1
(1.00)
del 4q34 3 99 (54%) 85 0.0967
(0.59) 		0.0114
(0.229) 		0.0527
(0.463) 		0.501
(0.889) 		0.0654
(0.509) 		0.495
(0.884) 		0.305
(0.801) 		0.154
(0.674) 		0.889
(1.00) 		0.0019
(0.0809) 		0.897
(1.00) 		0.294
(0.792) 		0.00215
(0.0885) 		0.359
(0.845) 		1
(1.00)
del 13q14 2 74 (40%) 110 0.337
(0.821) 		0.00574
(0.163) 		0.646
(0.957) 		0.656
(0.957) 		0.469
(0.87) 		0.299
(0.8) 		0.137
(0.664) 		0.0299
(0.35) 		0.0905
(0.569) 		0.00659
(0.172) 		0.305
(0.801) 		0.0485
(0.442) 		0.884
(1.00) 		0.00144
(0.0706) 		0.688
(0.957)
del 22q11 1 79 (43%) 105 0.0474
(0.436) 		0.305
(0.801) 		0.0662
(0.511) 		0.00285
(0.0956) 		0.00939
(0.21) 		0.174
(0.681) 		1
(1.00) 		0.365
(0.847) 		0.684
(0.957) 		1.56e-06
(0.000248) 		0.82
(1.00) 		0.45
(0.865) 		0.182
(0.693) 		0.106
(0.602) 		1
(1.00)
amp 1q42 3 96 (52%) 88 0.379
(0.847) 		0.00598
(0.166) 		0.732
(0.969) 		0.238
(0.736) 		0.162
(0.674) 		0.172
(0.681) 		0.00349
(0.11) 		1
(1.00) 		0.522
(0.897) 		0.46
(0.865) 		0.892
(1.00) 		0.185
(0.693) 		0.156
(0.674) 		0.171
(0.68) 		0.683
(0.957)
amp 3q26 2 128 (70%) 56 0.623
(0.957) 		0.0153
(0.268) 		0.372
(0.847) 		0.0547
(0.475) 		0.79
(1.00) 		0.703
(0.959) 		0.257
(0.75) 		0.337
(0.821) 		0.197
(0.707) 		1.11e-06
(0.000248) 		0.0964
(0.59) 		0.419
(0.853) 		0.451
(0.865) 		2e-05
(0.00255) 		0.604
(0.948)
amp 5p15 33 98 (53%) 86 0.14
(0.664) 		0.0282
(0.336) 		0.227
(0.72) 		0.00246
(0.0956) 		0.622
(0.957) 		1
(1.00) 		0.677
(0.957) 		0.474
(0.872) 		0.167
(0.68) 		0.000636
(0.0427) 		0.602
(0.948) 		0.634
(0.957) 		0.403
(0.853) 		0.0138
(0.263) 		0.229
(0.721)
amp 6q23 3 42 (23%) 142 0.384
(0.847) 		0.594
(0.948) 		0.00264
(0.0956) 		0.466
(0.87) 		0.184
(0.693) 		0.000743
(0.0451) 		1
(1.00) 		0.834
(1.00) 		0.952
(1.00) 		0.0524
(0.463) 		0.965
(1.00) 		0.133
(0.664) 		0.787
(0.999) 		0.803
(1.00) 		0.585
(0.948)
amp 8p23 1 52 (28%) 132 0.658
(0.957) 		0.0757
(0.544) 		0.81
(1.00) 		0.459
(0.865) 		0.479
(0.875) 		0.244
(0.74) 		0.163
(0.674) 		0.326
(0.819) 		0.444
(0.863) 		0.00322
(0.105) 		0.279
(0.773) 		0.00707
(0.18) 		0.462
(0.865) 		0.0648
(0.507) 		0.604
(0.948)
amp 8q24 21 145 (79%) 39 0.611
(0.954) 		0.199
(0.707) 		0.459
(0.865) 		0.432
(0.858) 		0.189
(0.698) 		0.687
(0.957) 		0.0111
(0.228) 		0.829
(1.00) 		0.128
(0.664) 		0.471
(0.87) 		0.392
(0.849) 		0.142
(0.664) 		0.0181
(0.282) 		0.00269
(0.0956) 		0.323
(0.819)
amp 9q34 3 64 (35%) 120 0.0857
(0.555) 		0.00043
(0.0304) 		0.6
(0.948) 		0.281
(0.775) 		0.486
(0.877) 		0.157
(0.674) 		0.027
(0.336) 		0.253
(0.743) 		0.727
(0.966) 		0.442
(0.863) 		0.011
(0.228) 		0.466
(0.87) 		0.244
(0.74) 		0.0371
(0.373) 		1
(1.00)
amp xq28 69 (38%) 115 0.493
(0.883) 		0.0628
(0.496) 		0.139
(0.664) 		0.592
(0.948) 		0.174
(0.681) 		0.723
(0.963) 		0.0877
(0.559) 		0.855
(1.00) 		0.374
(0.847) 		0.00646
(0.172) 		0.316
(0.816) 		0.662
(0.957) 		0.218
(0.72) 		0.00558
(0.163) 		0.414
(0.853)
del 3p14 3 126 (68%) 58 0.664
(0.957) 		0.401
(0.853) 		0.158
(0.674) 		0.85
(1.00) 		0.389
(0.849) 		1
(1.00) 		0.37
(0.847) 		0.565
(0.936) 		0.107
(0.602) 		2.46e-07
(0.000157) 		0.638
(0.957) 		0.714
(0.963) 		0.241
(0.739) 		0.00027
(0.0215) 		0.622
(0.957)
del 3p14 2 125 (68%) 59 0.516
(0.893) 		0.312
(0.811) 		0.176
(0.681) 		0.937
(1.00) 		0.39
(0.849) 		1
(1.00) 		0.272
(0.772) 		0.334
(0.821) 		0.385
(0.847) 		6.67e-07
(0.000248) 		0.671
(0.957) 		0.83
(1.00) 		0.29
(0.792) 		0.00117
(0.0622) 		0.632
(0.957)
del 9p21 3 141 (77%) 43 0.258
(0.75) 		0.165
(0.678) 		0.201
(0.707) 		0.165
(0.678) 		0.833
(1.00) 		0.205
(0.707) 		0.0117
(0.229) 		0.41
(0.853) 		0.171
(0.68) 		0.0357
(0.365) 		0.25
(0.743) 		1
(1.00) 		0.375
(0.847) 		0.00151
(0.0713) 		0.587
(0.948)
del 10p11 21 52 (28%) 132 0.21
(0.707) 		0.113
(0.612) 		0.515
(0.893) 		0.0695
(0.524) 		0.679
(0.957) 		0.481
(0.877) 		1
(1.00) 		0.844
(1.00) 		0.407
(0.853) 		1.21e-06
(0.000248) 		0.0561
(0.48) 		0.292
(0.792) 		0.872
(1.00) 		7e-05
(0.00687) 		0.392
(0.849)
del 10q23 31 65 (35%) 119 0.916
(1.00) 		0.715
(0.963) 		0.923
(1.00) 		0.341
(0.826) 		0.586
(0.948) 		1
(1.00) 		0.521
(0.897) 		0.853
(1.00) 		0.136
(0.664) 		0.22
(0.72) 		0.635
(0.957) 		0.00877
(0.21) 		0.641
(0.957) 		0.00283
(0.0956) 		1
(1.00)
del xp11 3 74 (40%) 110 0.858
(1.00) 		0.957
(1.00) 		0.00617
(0.167) 		0.275
(0.773) 		0.016
(0.268) 		0.0802
(0.549) 		0.137
(0.664) 		1
(1.00) 		0.183
(0.693) 		0.0158
(0.268) 		0.684
(0.957) 		0.224
(0.72) 		0.428
(0.856) 		0.0008
(0.0464) 		0.679
(0.957)
amp 6p21 1 69 (38%) 115 0.457
(0.865) 		0.344
(0.829) 		0.445
(0.863) 		0.84
(1.00) 		0.454
(0.865) 		0.719
(0.963) 		0.398
(0.853) 		0.853
(1.00) 		0.0806
(0.549) 		0.00933
(0.21) 		0.87
(1.00) 		0.462
(0.865) 		0.749
(0.98) 		0.532
(0.906) 		0.42
(0.853)
amp 9p13 3 40 (22%) 144 0.854
(1.00) 		0.996
(1.00) 		0.836
(1.00) 		0.206
(0.707) 		0.675
(0.957) 		0.685
(0.957) 		0.0111
(0.228) 		0.829
(1.00) 		0.796
(1.00) 		0.592
(0.948) 		0.223
(0.72) 		0.248
(0.743) 		0.674
(0.957) 		0.87
(1.00) 		1
(1.00)
amp 11q13 3 104 (57%) 80 0.601
(0.948) 		0.369
(0.847) 		0.696
(0.957) 		0.428
(0.856) 		0.944
(1.00) 		0.737
(0.972) 		0.835
(1.00) 		0.367
(0.847) 		0.6
(0.948) 		0.000189
(0.0161) 		0.19
(0.699) 		0.283
(0.778) 		0.672
(0.957) 		0.135
(0.664) 		0.672
(0.957)
amp 12p12 1 79 (43%) 105 0.246
(0.741) 		0.114
(0.615) 		0.0165
(0.269) 		0.0185
(0.284) 		0.274
(0.773) 		0.16
(0.674) 		0.00134
(0.0683) 		0.279
(0.773) 		0.0587
(0.492) 		0.0254
(0.321) 		0.381
(0.847) 		0.904
(1.00) 		0.198
(0.707) 		0.0576
(0.486) 		0.421
(0.853)
amp 12q15 51 (28%) 133 0.36
(0.845) 		0.75
(0.98) 		0.0374
(0.373) 		0.143
(0.665) 		0.158
(0.674) 		0.00922
(0.21) 		0.643
(0.957) 		0.423
(0.853) 		0.346
(0.829) 		0.742
(0.975) 		0.877
(1.00) 		0.143
(0.665) 		0.0226
(0.305) 		0.485
(0.877) 		1
(1.00)
amp 13q22 1 65 (35%) 119 0.836
(1.00) 		0.902
(1.00) 		0.349
(0.829) 		0.156
(0.674) 		0.548
(0.92) 		1
(1.00) 		0.663
(0.957) 		0.579
(0.947) 		0.0968
(0.59) 		0.000349
(0.0262) 		0.173
(0.681) 		0.928
(1.00) 		0.294
(0.792) 		0.517
(0.893) 		0.0191
(0.284)
amp 15q26 1 58 (32%) 126 0.902
(1.00) 		0.405
(0.853) 		0.43
(0.856) 		0.151
(0.674) 		0.599
(0.948) 		0.253
(0.743) 		1
(1.00) 		0.251
(0.743) 		0.571
(0.942) 		0.011
(0.228) 		0.0346
(0.362) 		0.928
(1.00) 		0.427
(0.856) 		0.149
(0.674) 		0.154
(0.674)
amp 17q12 75 (41%) 109 0.974
(1.00) 		0.703
(0.959) 		0.11
(0.605) 		0.605
(0.948) 		0.14
(0.664) 		0.0907
(0.569) 		0.0957
(0.59) 		0.366
(0.847) 		0.691
(0.957) 		0.00273
(0.0956) 		0.221
(0.72) 		0.502
(0.889) 		0.0616
(0.496) 		0.39
(0.849) 		1
(1.00)
amp 18q11 2 59 (32%) 125 0.416
(0.853) 		0.414
(0.853) 		0.274
(0.773) 		0.516
(0.893) 		0.616
(0.957) 		1
(1.00) 		0.827
(1.00) 		0.563
(0.933) 		0.379
(0.847) 		0.000852
(0.0472) 		0.699
(0.957) 		0.404
(0.853) 		0.567
(0.938) 		0.102
(0.6) 		1
(1.00)
del 2q22 1 59 (32%) 125 0.991
(1.00) 		0.106
(0.602) 		0.581
(0.948) 		0.154
(0.674) 		1
(1.00) 		1
(1.00) 		0.372
(0.847) 		0.455
(0.865) 		0.0233
(0.305) 		1.5e-06
(0.000248) 		0.603
(0.948) 		0.322
(0.819) 		0.992
(1.00) 		0.539
(0.91) 		0.207
(0.707)
del 2q33 3 36 (20%) 148 0.276
(0.773) 		0.986
(1.00) 		0.303
(0.801) 		0.0212
(0.295) 		0.794
(1.00) 		0.204
(0.707) 		0.607
(0.95) 		1
(1.00) 		0.592
(0.948) 		0.00892
(0.21) 		0.341
(0.826) 		0.578
(0.946) 		0.324
(0.819) 		1
(1.00) 		1
(1.00)
del 3p26 2 111 (60%) 73 0.243
(0.74) 		0.598
(0.948) 		0.458
(0.865) 		0.831
(1.00) 		0.582
(0.948) 		0.492
(0.883) 		0.292
(0.792) 		1
(1.00) 		0.817
(1.00) 		2.37e-05
(0.00275) 		0.749
(0.98) 		0.797
(1.00) 		0.11
(0.605) 		0.0169
(0.269) 		1
(1.00)
del 3q26 31 16 (9%) 168 0.141
(0.664) 		0.836
(1.00) 		0.0391
(0.381) 		0.0624
(0.496) 		0.0417
(0.4) 		0.189
(0.697) 		0.474
(0.872) 		1
(1.00) 		9.14e-05
(0.00832) 		0.558
(0.93) 		0.491
(0.883) 		0.263
(0.758) 		0.042
(0.4) 		1
(1.00)
del 7q31 1 56 (30%) 128 0.00721
(0.18) 		0.0155
(0.268) 		0.0358
(0.365) 		0.255
(0.745) 		0.514
(0.893) 		0.72
(0.963) 		0.07
(0.524) 		0.334
(0.821) 		1
(1.00) 		0.201
(0.707) 		0.105
(0.602) 		0.333
(0.821) 		0.931
(1.00) 		0.269
(0.769) 		1
(1.00)
del 10p15 3 54 (29%) 130 0.112
(0.609) 		0.372
(0.847) 		0.821
(1.00) 		0.145
(0.67) 		0.32
(0.819) 		1
(1.00) 		0.494
(0.884) 		0.435
(0.861) 		0.294
(0.792) 		0.0349
(0.362) 		0.514
(0.893) 		0.0789
(0.547) 		0.854
(1.00) 		0.00069
(0.044) 		0.406
(0.853)
del 10q21 1 46 (25%) 138 0.377
(0.847) 		0.347
(0.829) 		0.642
(0.957) 		0.877
(1.00) 		0.383
(0.847) 		0.703
(0.959) 		1
(1.00) 		0.841
(1.00) 		0.293
(0.792) 		0.018
(0.282) 		0.507
(0.889) 		0.476
(0.872) 		0.407
(0.853) 		5e-05
(0.00531) 		1
(1.00)
del 11p15 4 79 (43%) 105 0.839
(1.00) 		0.383
(0.847) 		0.949
(1.00) 		0.336
(0.821) 		0.874
(1.00) 		1
(1.00) 		0.0602
(0.496) 		0.107
(0.602) 		0.152
(0.674) 		0.457
(0.865) 		0.447
(0.863) 		0.527
(0.901) 		0.619
(0.957) 		0.00353
(0.11) 		1
(1.00)
del 11q25 81 (44%) 103 0.137
(0.664) 		0.0591
(0.493) 		0.515
(0.893) 		0.655
(0.957) 		0.647
(0.957) 		0.505
(0.889) 		0.834
(1.00) 		0.154
(0.674) 		0.297
(0.798) 		0.0115
(0.229) 		0.457
(0.865) 		0.878
(1.00) 		0.433
(0.858) 		0.077
(0.545) 		0.678
(0.957)
del 13q12 11 76 (41%) 108 0.421
(0.853) 		0.0612
(0.496) 		0.637
(0.957) 		0.475
(0.872) 		0.781
(0.995) 		1
(1.00) 		0.209
(0.707) 		0.105
(0.602) 		0.593
(0.948) 		0.00264
(0.0956) 		0.196
(0.707) 		0.535
(0.907) 		0.896
(1.00) 		0.0307
(0.356) 		1
(1.00)
del 13q21 31 69 (38%) 115 0.626
(0.957) 		0.21
(0.707) 		0.91
(1.00) 		0.622
(0.957) 		0.64
(0.957) 		0.483
(0.877) 		0.0877
(0.559) 		0.103
(0.602) 		0.163
(0.674) 		0.0345
(0.362) 		0.57
(0.941) 		0.102
(0.599) 		0.725
(0.964) 		0.0105
(0.228) 		0.697
(0.957)
del 16p13 3 65 (35%) 119 0.11
(0.605) 		0.501
(0.889) 		0.329
(0.819) 		0.392
(0.849) 		0.0347
(0.362) 		1
(1.00) 		0.383
(0.847) 		0.14
(0.664) 		0.626
(0.957) 		5.88e-06
(0.000833) 		0.458
(0.865) 		0.0726
(0.529) 		0.251
(0.743) 		0.185
(0.693) 		0.38
(0.847)
del 16q23 1 84 (46%) 100 0.774
(0.994) 		0.555
(0.927) 		0.453
(0.865) 		0.182
(0.693) 		0.128
(0.664) 		1
(1.00) 		0.21
(0.707) 		0.211
(0.707) 		0.967
(1.00) 		8.74e-11
(1.11e-07) 		0.69
(0.957) 		0.663
(0.957) 		0.151
(0.674) 		0.171
(0.68) 		0.207
(0.707)
del 17p12 86 (47%) 98 0.721
(0.963) 		0.0475
(0.436) 		0.234
(0.734) 		0.3
(0.8) 		0.345
(0.829) 		1
(1.00) 		0.148
(0.674) 		1
(1.00) 		0.163
(0.674) 		8.21e-07
(0.000248) 		0.781
(0.995) 		0.559
(0.93) 		0.135
(0.664) 		0.0383
(0.378) 		0.207
(0.707)
del 18q21 2 119 (65%) 65 0.536
(0.908) 		0.325
(0.819) 		0.865
(1.00) 		0.873
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.831
(1.00) 		0.577
(0.946) 		0.914
(1.00) 		0.00562
(0.163) 		0.235
(0.734) 		0.694
(0.957) 		0.757
(0.982) 		0.697
(0.957) 		0.0779
(0.546)
amp 1p34 2 40 (22%) 144 0.861
(1.00) 		0.204
(0.707) 		0.755
(0.982) 		0.781
(0.995) 		0.747
(0.979) 		0.377
(0.847) 		0.803
(1.00) 		0.829
(1.00) 		0.884
(1.00) 		0.592
(0.948) 		0.325
(0.819) 		0.203
(0.707) 		0.224
(0.72) 		0.141
(0.664) 		0.604
(0.948)
amp 1q23 3 93 (51%) 91 0.385
(0.847) 		0.0822
(0.549) 		0.724
(0.963) 		0.175
(0.681) 		0.653
(0.957) 		0.167
(0.68) 		0.0221
(0.303) 		0.859
(1.00) 		0.817
(1.00) 		1
(1.00) 		0.85
(1.00) 		0.0838
(0.549) 		0.674
(0.957) 		0.142
(0.664) 		0.697
(0.957)
amp 2q14 2 60 (33%) 124 0.455
(0.865) 		0.0385
(0.378) 		0.817
(1.00) 		0.443
(0.863) 		0.909
(1.00) 		0.276
(0.773) 		0.826
(1.00) 		0.707
(0.96) 		0.777
(0.994) 		0.158
(0.674) 		0.879
(1.00) 		0.0317
(0.359) 		0.631
(0.957) 		0.133
(0.664) 		1
(1.00)
amp 2q31 1 60 (33%) 124 0.953
(1.00) 		0.399
(0.853) 		0.775
(0.994) 		0.765
(0.989) 		0.485
(0.877) 		1
(1.00) 		0.12
(0.637) 		0.253
(0.743) 		1
(1.00) 		0.273
(0.773) 		0.887
(1.00) 		0.763
(0.987) 		0.804
(1.00) 		0.211
(0.707) 		1
(1.00)
amp 4q21 1 34 (18%) 150 0.0597
(0.494) 		0.505
(0.889) 		0.412
(0.853) 		0.37
(0.847) 		0.401
(0.853) 		0.687
(0.957) 		1
(1.00) 		0.496
(0.884) 		0.939
(1.00) 		0.705
(0.96) 		0.423
(0.853) 		0.807
(1.00) 		0.803
(1.00) 		0.368
(0.847) 		0.592
(0.948)
amp 7p11 2 126 (68%) 58 0.849
(1.00) 		0.221
(0.72) 		0.867
(1.00) 		0.0987
(0.593) 		0.43
(0.856) 		0.723
(0.963) 		0.27
(0.769) 		0.253
(0.743) 		0.535
(0.907) 		0.0812
(0.549) 		0.506
(0.889) 		0.903
(1.00) 		0.817
(1.00) 		0.47
(0.87) 		0.661
(0.957)
amp 7q21 2 114 (62%) 70 0.992
(1.00) 		0.402
(0.853) 		0.868
(1.00) 		0.0163
(0.269) 		0.484
(0.877) 		0.483
(0.877) 		0.285
(0.782) 		0.854
(1.00) 		0.178
(0.685) 		1
(1.00) 		0.262
(0.756) 		0.325
(0.819) 		0.253
(0.743) 		0.561
(0.932) 		1
(1.00)
amp 8p11 21 85 (46%) 99 0.644
(0.957) 		0.925
(1.00) 		0.428
(0.856) 		0.689
(0.957) 		0.831
(1.00) 		1
(1.00) 		0.677
(0.957) 		1
(1.00) 		0.235
(0.734) 		1
(1.00) 		0.816
(1.00) 		0.711
(0.963) 		0.0375
(0.373) 		0.0923
(0.577) 		0.227
(0.72)
amp 11p13 52 (28%) 132 0.167
(0.68) 		0.995
(1.00) 		0.442
(0.863) 		0.0823
(0.549) 		0.881
(1.00) 		0.0608
(0.496) 		0.109
(0.605) 		0.845
(1.00) 		0.0776
(0.546) 		0.193
(0.702) 		0.449
(0.865) 		0.259
(0.75) 		0.0994
(0.593) 		0.699
(0.957) 		0.188
(0.697)
amp 11p13 50 (27%) 134 0.108
(0.602) 		0.871
(1.00) 		0.323
(0.819) 		0.251
(0.743) 		0.935
(1.00) 		0.0142
(0.266) 		0.16
(0.674) 		1
(1.00) 		0.0968
(0.59) 		0.868
(1.00) 		0.0992
(0.593) 		0.392
(0.849) 		0.0282
(0.336) 		0.0275
(0.336) 		0.188
(0.697)
amp 18p11 32 69 (38%) 115 0.624
(0.957) 		0.139
(0.664) 		0.279
(0.773) 		0.0254
(0.321) 		0.33
(0.819) 		0.0851
(0.554) 		0.0315
(0.359) 		0.461
(0.865) 		0.414
(0.853) 		0.17
(0.68) 		0.577
(0.946) 		0.966
(1.00) 		0.0153
(0.268) 		0.0233
(0.305) 		0.667
(0.957)
amp 19p13 2 32 (17%) 152 0.326
(0.819) 		0.435
(0.861) 		0.127
(0.664) 		0.764
(0.988) 		0.0157
(0.268) 		0.627
(0.957) 		0.175
(0.681) 		0.641
(0.957) 		0.237
(0.736) 		0.244
(0.74) 		0.42
(0.853) 		0.396
(0.853) 		0.0152
(0.268) 		0.668
(0.957) 		0.592
(0.948)
amp 19q12 54 (29%) 130 0.369
(0.847) 		0.622
(0.957) 		0.909
(1.00) 		0.989
(1.00) 		0.767
(0.99) 		1
(1.00) 		0.107
(0.602) 		0.241
(0.739) 		0.635
(0.957) 		0.0526
(0.463) 		0.56
(0.931) 		0.695
(0.957) 		0.444
(0.863) 		0.222
(0.72) 		1
(1.00)
del 1p36 11 75 (41%) 109 0.721
(0.963) 		0.94
(1.00) 		0.137
(0.664) 		0.486
(0.877) 		0.0318
(0.359) 		1
(1.00) 		0.525
(0.9) 		0.0666
(0.512) 		0.0202
(0.292) 		0.0167
(0.269) 		0.78
(0.995) 		0.713
(0.963) 		0.63
(0.957) 		0.313
(0.812) 		1
(1.00)
del 1p13 2 64 (35%) 120 0.185
(0.693) 		0.46
(0.865) 		0.381
(0.847) 		0.884
(1.00) 		0.124
(0.655) 		1
(1.00) 		0.383
(0.847) 		1
(1.00) 		0.856
(1.00) 		0.757
(0.982) 		0.401
(0.853) 		0.817
(1.00) 		0.983
(1.00) 		0.539
(0.91) 		0.42
(0.853)
del 1q44 17 (9%) 167 0.719
(0.963) 		0.304
(0.801) 		0.184
(0.693) 		0.372
(0.847) 		0.0199
(0.292) 		1
(1.00) 		1
(1.00) 		0.754
(0.98) 		0.133
(0.664) 		0.8
(1.00) 		0.886
(1.00) 		0.844
(1.00) 		0.0213
(0.295) 		0.855
(1.00) 		1
(1.00)
del 3q11 1 33 (18%) 151 0.797
(1.00) 		0.442
(0.863) 		0.354
(0.835) 		0.36
(0.845) 		0.325
(0.819) 		0.687
(0.957) 		0.421
(0.853) 		1
(1.00) 		0.0688
(0.524) 		0.444
(0.863) 		0.739
(0.973) 		0.402
(0.853) 		0.3
(0.8) 		0.415
(0.853) 		1
(1.00)
del 4p15 2 106 (58%) 78 0.084
(0.549) 		0.715
(0.963) 		0.926
(1.00) 		0.213
(0.71) 		0.881
(1.00) 		0.74
(0.974) 		0.533
(0.907) 		1
(1.00) 		0.705
(0.96) 		0.882
(1.00) 		0.201
(0.707) 		0.224
(0.72) 		0.114
(0.615) 		0.33
(0.819) 		0.677
(0.957)
del 4q22 1 105 (57%) 79 0.221
(0.72) 		0.0833
(0.549) 		0.0708
(0.524) 		0.103
(0.602) 		0.199
(0.707) 		0.0788
(0.547) 		0.206
(0.707) 		0.282
(0.778) 		0.824
(1.00) 		0.0254
(0.321) 		0.505
(0.889) 		0.662
(0.957) 		0.0277
(0.336) 		0.713
(0.963) 		0.684
(0.957)
del 5q12 1 112 (61%) 72 0.96
(1.00) 		0.468
(0.87) 		0.0433
(0.408) 		0.924
(1.00) 		0.84
(1.00) 		0.153
(0.674) 		0.2
(0.707) 		0.587
(0.948) 		0.484
(0.877) 		0.226
(0.72) 		0.928
(1.00) 		0.577
(0.946) 		0.768
(0.99) 		0.555
(0.927) 		1
(1.00)
del 6p25 3 74 (40%) 110 0.112
(0.609) 		0.501
(0.889) 		0.625
(0.957) 		0.721
(0.963) 		0.161
(0.674) 		0.728
(0.966) 		0.833
(1.00) 		0.857
(1.00) 		0.597
(0.948) 		0.0999
(0.593) 		0.989
(1.00) 		0.776
(0.994) 		0.855
(1.00) 		0.514
(0.893) 		0.191
(0.699)
del 6q16 3 55 (30%) 129 0.602
(0.948) 		0.365
(0.847) 		0.995
(1.00) 		0.915
(1.00) 		0.676
(0.957) 		1
(1.00) 		0.0715
(0.524) 		0.69
(0.957) 		0.663
(0.957) 		0.52
(0.897) 		0.0697
(0.524) 		0.959
(1.00) 		0.417
(0.853) 		0.0415
(0.4) 		0.662
(0.957)
del 6q26 50 (27%) 134 0.505
(0.889) 		0.846
(1.00) 		0.206
(0.707) 		0.469
(0.87) 		0.65
(0.957) 		0.448
(0.863) 		0.16
(0.674) 		0.537
(0.908) 		0.148
(0.674) 		0.619
(0.957) 		0.238
(0.736) 		0.913
(1.00) 		0.446
(0.863) 		0.154
(0.674) 		1
(1.00)
del 7q36 3 67 (36%) 117 0.308
(0.804) 		0.692
(0.957) 		0.0815
(0.549) 		0.446
(0.863) 		0.293
(0.792) 		0.29
(0.792) 		0.83
(1.00) 		0.269
(0.769) 		0.669
(0.957) 		0.878
(1.00) 		0.544
(0.916) 		0.752
(0.98) 		0.85
(1.00) 		0.373
(0.847) 		0.662
(0.957)
del 8p23 2 90 (49%) 94 0.743
(0.975) 		0.0713
(0.524) 		0.228
(0.721) 		0.393
(0.85) 		0.348
(0.829) 		1
(1.00) 		0.409
(0.853) 		0.154
(0.674) 		0.651
(0.957) 		0.019
(0.284) 		0.0834
(0.549) 		0.254
(0.743) 		0.0765
(0.545) 		0.13
(0.664) 		1
(1.00)
del 8p12 75 (41%) 109 0.532
(0.906) 		0.929
(1.00) 		0.134
(0.664) 		0.983
(1.00) 		0.142
(0.664) 		0.732
(0.969) 		0.525
(0.9) 		1
(1.00) 		0.697
(0.957) 		0.453
(0.865) 		0.17
(0.68) 		0.329
(0.819) 		0.313
(0.812) 		0.376
(0.847) 		0.697
(0.957)
del 9p23 108 (59%) 76 0.683
(0.957) 		0.719
(0.963) 		0.153
(0.674) 		0.199
(0.707) 		0.115
(0.618) 		1
(1.00) 		0.0191
(0.284) 		0.277
(0.773) 		0.177
(0.683) 		0.549
(0.921) 		0.616
(0.957) 		0.105
(0.602) 		0.156
(0.674) 		0.0759
(0.544) 		0.398
(0.853)
del 12q23 1 51 (28%) 133 0.213
(0.71) 		0.333
(0.821) 		0.491
(0.883) 		0.241
(0.74) 		0.924
(1.00) 		0.699
(0.957) 		0.251
(0.743) 		0.689
(0.957) 		0.329
(0.819) 		0.033
(0.362) 		0.304
(0.801) 		0.955
(1.00) 		0.0338
(0.362) 		0.0349
(0.362) 		1
(1.00)
del 14q23 3 51 (28%) 133 0.327
(0.819) 		0.447
(0.863) 		0.62
(0.957) 		0.225
(0.72) 		0.259
(0.75) 		0.235
(0.734) 		1
(1.00) 		0.689
(0.957) 		0.747
(0.979) 		0.0138
(0.263) 		0.904
(1.00) 		0.869
(1.00) 		0.61
(0.953) 		0.305
(0.801) 		1
(1.00)
del 15q11 2 63 (34%) 121 0.984
(1.00) 		0.328
(0.819) 		0.869
(1.00) 		0.389
(0.849) 		0.662
(0.957) 		0.276
(0.773) 		0.665
(0.957) 		0.354
(0.835) 		0.876
(1.00) 		0.162
(0.674) 		0.423
(0.853) 		0.0888
(0.563) 		0.864
(1.00) 		0.951
(1.00) 		1
(1.00)
del 17q25 3 41 (22%) 143 0.0345
(0.362) 		0.223
(0.72) 		0.341
(0.826) 		0.504
(0.889) 		0.385
(0.847) 		1
(1.00) 		1
(1.00) 		0.67
(0.957) 		0.192
(0.702) 		0.861
(1.00) 		0.116
(0.619) 		0.175
(0.681) 		0.348
(0.829) 		0.323
(0.819) 		1
(1.00)
del 18p11 23 60 (33%) 124 0.642
(0.957) 		0.0329
(0.362) 		0.309
(0.804) 		0.0512
(0.46) 		0.474
(0.872) 		1
(1.00) 		0.184
(0.693) 		0.0207
(0.295) 		0.731
(0.969) 		0.0274
(0.336) 		0.0451
(0.42) 		0.134
(0.664) 		0.698
(0.957) 		0.141
(0.664) 		1
(1.00)
del 18q12 2 111 (60%) 73 0.16
(0.674) 		0.128
(0.664) 		0.735
(0.971) 		0.423
(0.853) 		0.585
(0.948) 		1
(1.00) 		0.834
(1.00) 		1
(1.00) 		1
(1.00) 		0.0234
(0.305) 		0.125
(0.657) 		0.53
(0.904) 		0.347
(0.829) 		0.822
(1.00) 		0.684
(0.957)
del 18q22 3 112 (61%) 72 0.685
(0.957) 		0.278
(0.773) 		0.699
(0.957) 		0.269
(0.769) 		0.43
(0.856) 		1
(1.00) 		0.67
(0.957) 		0.715
(0.963) 		0.401
(0.853) 		0.226
(0.72) 		0.259
(0.75) 		0.238
(0.736) 		0.644
(0.957) 		0.643
(0.957) 		0.0296
(0.35)
del 19p13 3 93 (51%) 91 0.813
(1.00) 		0.387
(0.849) 		0.608
(0.95) 		0.372
(0.847) 		0.41
(0.853) 		1
(1.00) 		0.0621
(0.496) 		0.0746
(0.54) 		0.585
(0.948) 		0.188
(0.697) 		0.063
(0.496) 		0.416
(0.853) 		0.221
(0.72) 		0.131
(0.664) 		1
(1.00)
del 19q11 48 (26%) 136 0.907
(1.00) 		0.145
(0.67) 		0.769
(0.99) 		0.516
(0.893) 		0.208
(0.707) 		0.699
(0.957) 		0.234
(0.734) 		0.225
(0.72) 		0.807
(1.00) 		0.867
(1.00) 		0.0503
(0.454) 		0.662
(0.957) 		0.0546
(0.475) 		0.439
(0.863) 		0.643
(0.957)
del 20p12 1 33 (18%) 151 0.0349
(0.362) 		0.665
(0.957) 		0.715
(0.963) 		0.718
(0.963) 		0.479
(0.875) 		1
(1.00) 		0.421
(0.853) 		1
(1.00) 		0.471
(0.87) 		0.0208
(0.295) 		0.753
(0.98) 		0.373
(0.847) 		0.0566
(0.481) 		1
(1.00) 		0.243
(0.74)
del 21q11 2 107 (58%) 77 0.663
(0.957) 		0.517
(0.893) 		0.685
(0.957) 		0.856
(1.00) 		0.785
(0.998) 		0.513
(0.893) 		0.834
(1.00) 		0.476
(0.872) 		0.707
(0.96) 		0.179
(0.686) 		0.551
(0.922) 		0.548
(0.92) 		0.268
(0.769) 		0.818
(1.00) 		0.22
(0.72)
del 21q21 1 107 (58%) 77 0.416
(0.853) 		0.427
(0.856) 		0.871
(1.00) 		0.545
(0.916) 		0.894
(1.00) 		1
(1.00) 		0.529
(0.904) 		0.858
(1.00) 		0.33
(0.819) 		0.1
(0.593) 		0.354
(0.835) 		0.16
(0.674) 		0.604
(0.948) 		0.447
(0.863) 		0.679
(0.957)
del 21q22 12 108 (59%) 76 0.414
(0.853) 		0.605
(0.948) 		0.848
(1.00) 		0.934
(1.00) 		0.733
(0.969) 		1
(1.00) 		0.677
(0.957) 		0.471
(0.87) 		0.0435
(0.408) 		0.134
(0.664) 		0.2
(0.707) 		0.211
(0.707) 		0.877
(1.00) 		0.342
(0.826) 		0.209
(0.707)
del xp21 1 69 (38%) 115 0.674
(0.957) 		0.582
(0.948) 		0.016
(0.268) 		0.633
(0.957) 		0.0817
(0.549) 		0.157
(0.674) 		0.0877
(0.559) 		0.577
(0.946) 		0.839
(1.00) 		0.17
(0.68) 		0.758
(0.982) 		0.245
(0.741) 		0.308
(0.804) 		0.0557
(0.48) 		1
(1.00)
del xq11 2 42 (23%) 142 0.525
(0.9) 		0.414
(0.853) 		0.441
(0.863) 		0.598
(0.948) 		0.334
(0.821) 		0.684
(0.957) 		0.629
(0.957) 		0.829
(1.00) 		0.305
(0.801) 		0.38
(0.847) 		0.775
(0.994) 		0.168
(0.68) 		0.921
(1.00) 		0.753
(0.98) 		1
(1.00)
del xq21 33 40 (22%) 144 0.782
(0.995) 		0.361
(0.845) 		0.0235
(0.305) 		0.769
(0.99) 		0.354
(0.835) 		1
(1.00) 		0.314
(0.812) 		0.824
(1.00) 		0.0704
(0.524) 		0.211
(0.707) 		0.502
(0.889) 		0.937
(1.00) 		0.776
(0.994) 		0.869
(1.00) 		0.336
(0.821)
'amp_1q42.3' versus 'YEARS_TO_BIRTH'

P value = 0.00598 (Wilcoxon-test), Q value = 0.17

Table S1.  Gene #3: 'amp_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 184 62.4 (11.9)
AMP PEAK 3(1Q42.3) MUTATED 96 59.8 (10.0)
AMP PEAK 3(1Q42.3) WILD-TYPE 88 65.4 (13.2)

Figure S1.  Get High-res Image Gene #3: 'amp_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q42.3' versus 'GENDER'

P value = 0.00349 (Fisher's exact test), Q value = 0.11

Table S2.  Gene #3: 'amp_1q42.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 27 157
AMP PEAK 3(1Q42.3) MUTATED 7 89
AMP PEAK 3(1Q42.3) WILD-TYPE 20 68

Figure S2.  Get High-res Image Gene #3: 'amp_1q42.3' versus Clinical Feature #7: 'GENDER'

'amp_3q26.2' versus 'HISTOLOGICAL_TYPE'

P value = 1.11e-06 (Fisher's exact test), Q value = 0.00025

Table S3.  Gene #6: 'amp_3q26.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 6(3Q26.2) MUTATED 46 82
AMP PEAK 6(3Q26.2) WILD-TYPE 42 14

Figure S3.  Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_3q26.2' versus 'RACE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0025

Table S4.  Gene #6: 'amp_3q26.2' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
AMP PEAK 6(3Q26.2) MUTATED 43 4 68
AMP PEAK 6(3Q26.2) WILD-TYPE 3 1 46

Figure S4.  Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #14: 'RACE'

'amp_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.00246 (Fisher's exact test), Q value = 0.096

Table S5.  Gene #8: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 32 43 87 5
AMP PEAK 8(5P15.33) MUTATED 10 23 57 1
AMP PEAK 8(5P15.33) WILD-TYPE 22 20 30 4

Figure S5.  Get High-res Image Gene #8: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.000636 (Fisher's exact test), Q value = 0.043

Table S6.  Gene #8: 'amp_5p15.33' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 8(5P15.33) MUTATED 35 63
AMP PEAK 8(5P15.33) WILD-TYPE 53 33

Figure S6.  Get High-res Image Gene #8: 'amp_5p15.33' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_6p21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00933 (Fisher's exact test), Q value = 0.21

Table S7.  Gene #9: 'amp_6p21.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 9(6P21.1) MUTATED 42 27
AMP PEAK 9(6P21.1) WILD-TYPE 46 69

Figure S7.  Get High-res Image Gene #9: 'amp_6p21.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_6q23.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00264 (Fisher's exact test), Q value = 0.096

Table S8.  Gene #10: 'amp_6q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 6 1 47 31 25 14 9 7 5 4
AMP PEAK 10(6Q23.3) MUTATED 5 0 1 0 8 7 4 1 1 3 4 3
AMP PEAK 10(6Q23.3) WILD-TYPE 3 5 5 1 39 24 21 13 8 4 1 1

Figure S8.  Get High-res Image Gene #10: 'amp_6q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_6q23.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.000743 (Fisher's exact test), Q value = 0.045

Table S9.  Gene #10: 'amp_6q23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 135 9
AMP PEAK 10(6Q23.3) MUTATED 28 7
AMP PEAK 10(6Q23.3) WILD-TYPE 107 2

Figure S9.  Get High-res Image Gene #10: 'amp_6q23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_8p23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00322 (Fisher's exact test), Q value = 0.11

Table S10.  Gene #13: 'amp_8p23.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 13(8P23.1) MUTATED 34 18
AMP PEAK 13(8P23.1) WILD-TYPE 54 78

Figure S10.  Get High-res Image Gene #13: 'amp_8p23.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_8p23.1' versus 'RESIDUAL_TUMOR'

P value = 0.00707 (Fisher's exact test), Q value = 0.18

Table S11.  Gene #13: 'amp_8p23.1' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 137 12 2 7
AMP PEAK 13(8P23.1) MUTATED 39 8 0 0
AMP PEAK 13(8P23.1) WILD-TYPE 98 4 2 7

Figure S11.  Get High-res Image Gene #13: 'amp_8p23.1' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

'amp_8q24.21' versus 'GENDER'

P value = 0.0111 (Fisher's exact test), Q value = 0.23

Table S12.  Gene #15: 'amp_8q24.21' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 27 157
AMP PEAK 15(8Q24.21) MUTATED 16 129
AMP PEAK 15(8Q24.21) WILD-TYPE 11 28

Figure S12.  Get High-res Image Gene #15: 'amp_8q24.21' versus Clinical Feature #7: 'GENDER'

'amp_8q24.21' versus 'RACE'

P value = 0.00269 (Fisher's exact test), Q value = 0.096

Table S13.  Gene #15: 'amp_8q24.21' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
AMP PEAK 15(8Q24.21) MUTATED 43 3 82
AMP PEAK 15(8Q24.21) WILD-TYPE 3 2 32

Figure S13.  Get High-res Image Gene #15: 'amp_8q24.21' versus Clinical Feature #14: 'RACE'

'amp_9p13.3' versus 'GENDER'

P value = 0.0111 (Fisher's exact test), Q value = 0.23

Table S14.  Gene #16: 'amp_9p13.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 27 157
AMP PEAK 16(9P13.3) MUTATED 1 39
AMP PEAK 16(9P13.3) WILD-TYPE 26 118

Figure S14.  Get High-res Image Gene #16: 'amp_9p13.3' versus Clinical Feature #7: 'GENDER'

'amp_9q34.3' versus 'YEARS_TO_BIRTH'

P value = 0.00043 (Wilcoxon-test), Q value = 0.03

Table S15.  Gene #17: 'amp_9q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 184 62.4 (11.9)
AMP PEAK 17(9Q34.3) MUTATED 64 58.3 (12.3)
AMP PEAK 17(9Q34.3) WILD-TYPE 120 64.7 (11.1)

Figure S15.  Get High-res Image Gene #17: 'amp_9q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_9q34.3' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.011 (Wilcoxon-test), Q value = 0.23

Table S16.  Gene #17: 'amp_9q34.3' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 98 34.5 (21.5)
AMP PEAK 17(9Q34.3) MUTATED 39 27.8 (18.8)
AMP PEAK 17(9Q34.3) WILD-TYPE 59 38.9 (22.2)

Figure S16.  Get High-res Image Gene #17: 'amp_9q34.3' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'amp_11q13.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.000189 (Fisher's exact test), Q value = 0.016

Table S17.  Gene #20: 'amp_11q13.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 20(11Q13.3) MUTATED 37 67
AMP PEAK 20(11Q13.3) WILD-TYPE 51 29

Figure S17.  Get High-res Image Gene #20: 'amp_11q13.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_12p12.1' versus 'GENDER'

P value = 0.00134 (Fisher's exact test), Q value = 0.068

Table S18.  Gene #21: 'amp_12p12.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 27 157
AMP PEAK 21(12P12.1) MUTATED 4 75
AMP PEAK 21(12P12.1) WILD-TYPE 23 82

Figure S18.  Get High-res Image Gene #21: 'amp_12p12.1' versus Clinical Feature #7: 'GENDER'

'amp_12q15' versus 'PATHOLOGY_M_STAGE'

P value = 0.00922 (Fisher's exact test), Q value = 0.21

Table S19.  Gene #22: 'amp_12q15' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 135 9
AMP PEAK 22(12Q15) MUTATED 31 6
AMP PEAK 22(12Q15) WILD-TYPE 104 3

Figure S19.  Get High-res Image Gene #22: 'amp_12q15' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_13q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.000349 (Fisher's exact test), Q value = 0.026

Table S20.  Gene #23: 'amp_13q22.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 23(13Q22.1) MUTATED 43 22
AMP PEAK 23(13Q22.1) WILD-TYPE 45 74

Figure S20.  Get High-res Image Gene #23: 'amp_13q22.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_14q21.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00788 (Fisher's exact test), Q value = 0.19

Table S21.  Gene #24: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 32 43 87 5
AMP PEAK 24(14Q21.1) MUTATED 5 19 28 4
AMP PEAK 24(14Q21.1) WILD-TYPE 27 24 59 1

Figure S21.  Get High-res Image Gene #24: 'amp_14q21.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_14q21.1' versus 'GENDER'

P value = 0.00157 (Fisher's exact test), Q value = 0.071

Table S22.  Gene #24: 'amp_14q21.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 27 157
AMP PEAK 24(14Q21.1) MUTATED 2 59
AMP PEAK 24(14Q21.1) WILD-TYPE 25 98

Figure S22.  Get High-res Image Gene #24: 'amp_14q21.1' versus Clinical Feature #7: 'GENDER'

'amp_14q21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00169 (Fisher's exact test), Q value = 0.074

Table S23.  Gene #24: 'amp_14q21.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 24(14Q21.1) MUTATED 19 42
AMP PEAK 24(14Q21.1) WILD-TYPE 69 54

Figure S23.  Get High-res Image Gene #24: 'amp_14q21.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_14q21.1' versus 'RACE'

P value = 0.00366 (Fisher's exact test), Q value = 0.11

Table S24.  Gene #24: 'amp_14q21.1' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
AMP PEAK 24(14Q21.1) MUTATED 24 2 29
AMP PEAK 24(14Q21.1) WILD-TYPE 22 3 85

Figure S24.  Get High-res Image Gene #24: 'amp_14q21.1' versus Clinical Feature #14: 'RACE'

'amp_15q26.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.011 (Fisher's exact test), Q value = 0.23

Table S25.  Gene #25: 'amp_15q26.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 25(15Q26.1) MUTATED 36 22
AMP PEAK 25(15Q26.1) WILD-TYPE 52 74

Figure S25.  Get High-res Image Gene #25: 'amp_15q26.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_17q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00273 (Fisher's exact test), Q value = 0.096

Table S26.  Gene #26: 'amp_17q12' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 26(17Q12) MUTATED 46 29
AMP PEAK 26(17Q12) WILD-TYPE 42 67

Figure S26.  Get High-res Image Gene #26: 'amp_17q12' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_18q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.000852 (Fisher's exact test), Q value = 0.047

Table S27.  Gene #28: 'amp_18q11.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 28(18Q11.2) MUTATED 39 20
AMP PEAK 28(18Q11.2) WILD-TYPE 49 76

Figure S27.  Get High-res Image Gene #28: 'amp_18q11.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_xq28' versus 'HISTOLOGICAL_TYPE'

P value = 0.00646 (Fisher's exact test), Q value = 0.17

Table S28.  Gene #31: 'amp_xq28' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
AMP PEAK 31(XQ28) MUTATED 24 45
AMP PEAK 31(XQ28) WILD-TYPE 64 51

Figure S28.  Get High-res Image Gene #31: 'amp_xq28' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_xq28' versus 'RACE'

P value = 0.00558 (Fisher's exact test), Q value = 0.16

Table S29.  Gene #31: 'amp_xq28' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
AMP PEAK 31(XQ28) MUTATED 26 3 36
AMP PEAK 31(XQ28) WILD-TYPE 20 2 78

Figure S29.  Get High-res Image Gene #31: 'amp_xq28' versus Clinical Feature #14: 'RACE'

'del_2q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 1.5e-06 (Fisher's exact test), Q value = 0.00025

Table S30.  Gene #35: 'del_2q22.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 4(2Q22.1) MUTATED 13 46
DEL PEAK 4(2Q22.1) WILD-TYPE 75 50

Figure S30.  Get High-res Image Gene #35: 'del_2q22.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_2q33.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00892 (Fisher's exact test), Q value = 0.21

Table S31.  Gene #36: 'del_2q33.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 5(2Q33.3) MUTATED 10 26
DEL PEAK 5(2Q33.3) WILD-TYPE 78 70

Figure S31.  Get High-res Image Gene #36: 'del_2q33.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p26.2' versus 'HISTOLOGICAL_TYPE'

P value = 2.37e-05 (Fisher's exact test), Q value = 0.0028

Table S32.  Gene #37: 'del_3p26.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 6(3P26.2) MUTATED 39 72
DEL PEAK 6(3P26.2) WILD-TYPE 49 24

Figure S32.  Get High-res Image Gene #37: 'del_3p26.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p14.3' versus 'HISTOLOGICAL_TYPE'

P value = 2.46e-07 (Fisher's exact test), Q value = 0.00016

Table S33.  Gene #38: 'del_3p14.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 7(3P14.3) MUTATED 44 82
DEL PEAK 7(3P14.3) WILD-TYPE 44 14

Figure S33.  Get High-res Image Gene #38: 'del_3p14.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p14.3' versus 'RACE'

P value = 0.00027 (Fisher's exact test), Q value = 0.022

Table S34.  Gene #38: 'del_3p14.3' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 7(3P14.3) MUTATED 41 4 67
DEL PEAK 7(3P14.3) WILD-TYPE 5 1 47

Figure S34.  Get High-res Image Gene #38: 'del_3p14.3' versus Clinical Feature #14: 'RACE'

'del_3p14.2' versus 'HISTOLOGICAL_TYPE'

P value = 6.67e-07 (Fisher's exact test), Q value = 0.00025

Table S35.  Gene #39: 'del_3p14.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 8(3P14.2) MUTATED 44 81
DEL PEAK 8(3P14.2) WILD-TYPE 44 15

Figure S35.  Get High-res Image Gene #39: 'del_3p14.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p14.2' versus 'RACE'

P value = 0.00117 (Fisher's exact test), Q value = 0.062

Table S36.  Gene #39: 'del_3p14.2' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 8(3P14.2) MUTATED 40 4 67
DEL PEAK 8(3P14.2) WILD-TYPE 6 1 47

Figure S36.  Get High-res Image Gene #39: 'del_3p14.2' versus Clinical Feature #14: 'RACE'

'del_3q26.31' versus 'HISTOLOGICAL_TYPE'

P value = 9.14e-05 (Fisher's exact test), Q value = 0.0083

Table S37.  Gene #41: 'del_3q26.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 10(3Q26.31) MUTATED 15 1
DEL PEAK 10(3Q26.31) WILD-TYPE 73 95

Figure S37.  Get High-res Image Gene #41: 'del_3q26.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_4q34.3' versus 'YEARS_TO_BIRTH'

P value = 0.0114 (Wilcoxon-test), Q value = 0.23

Table S38.  Gene #44: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 184 62.4 (11.9)
DEL PEAK 13(4Q34.3) MUTATED 99 64.6 (11.5)
DEL PEAK 13(4Q34.3) WILD-TYPE 85 60.0 (12.0)

Figure S38.  Get High-res Image Gene #44: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0019 (Fisher's exact test), Q value = 0.081

Table S39.  Gene #44: 'del_4q34.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 13(4Q34.3) MUTATED 58 41
DEL PEAK 13(4Q34.3) WILD-TYPE 30 55

Figure S39.  Get High-res Image Gene #44: 'del_4q34.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_4q34.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00215 (Wilcoxon-test), Q value = 0.089

Table S40.  Gene #44: 'del_4q34.3' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 134 2.5 (3.4)
DEL PEAK 13(4Q34.3) MUTATED 74 3.1 (3.8)
DEL PEAK 13(4Q34.3) WILD-TYPE 60 1.7 (2.8)

Figure S40.  Get High-res Image Gene #44: 'del_4q34.3' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'del_7q31.1' versus 'Time to Death'

P value = 0.00721 (logrank test), Q value = 0.18

Table S41.  Gene #49: 'del_7q31.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 183 76 0.1 - 122.1 (13.2)
DEL PEAK 18(7Q31.1) MUTATED 56 28 0.1 - 55.5 (12.5)
DEL PEAK 18(7Q31.1) WILD-TYPE 127 48 0.3 - 122.1 (13.4)

Figure S41.  Get High-res Image Gene #49: 'del_7q31.1' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'GENDER'

P value = 0.0117 (Fisher's exact test), Q value = 0.23

Table S42.  Gene #54: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 27 157
DEL PEAK 23(9P21.3) MUTATED 15 126
DEL PEAK 23(9P21.3) WILD-TYPE 12 31

Figure S42.  Get High-res Image Gene #54: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'RACE'

P value = 0.00151 (Fisher's exact test), Q value = 0.071

Table S43.  Gene #54: 'del_9p21.3' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 23(9P21.3) MUTATED 43 4 78
DEL PEAK 23(9P21.3) WILD-TYPE 3 1 36

Figure S43.  Get High-res Image Gene #54: 'del_9p21.3' versus Clinical Feature #14: 'RACE'

'del_10p15.3' versus 'RACE'

P value = 0.00069 (Fisher's exact test), Q value = 0.044

Table S44.  Gene #55: 'del_10p15.3' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 24(10P15.3) MUTATED 20 4 24
DEL PEAK 24(10P15.3) WILD-TYPE 26 1 90

Figure S44.  Get High-res Image Gene #55: 'del_10p15.3' versus Clinical Feature #14: 'RACE'

'del_10p11.21' versus 'HISTOLOGICAL_TYPE'

P value = 1.21e-06 (Fisher's exact test), Q value = 0.00025

Table S45.  Gene #56: 'del_10p11.21' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 25(10P11.21) MUTATED 10 42
DEL PEAK 25(10P11.21) WILD-TYPE 78 54

Figure S45.  Get High-res Image Gene #56: 'del_10p11.21' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_10p11.21' versus 'RACE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0069

Table S46.  Gene #56: 'del_10p11.21' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 25(10P11.21) MUTATED 22 4 22
DEL PEAK 25(10P11.21) WILD-TYPE 24 1 92

Figure S46.  Get High-res Image Gene #56: 'del_10p11.21' versus Clinical Feature #14: 'RACE'

'del_10q21.1' versus 'RACE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0053

Table S47.  Gene #57: 'del_10q21.1' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 26(10Q21.1) MUTATED 20 4 19
DEL PEAK 26(10Q21.1) WILD-TYPE 26 1 95

Figure S47.  Get High-res Image Gene #57: 'del_10q21.1' versus Clinical Feature #14: 'RACE'

'del_10q23.31' versus 'RESIDUAL_TUMOR'

P value = 0.00877 (Fisher's exact test), Q value = 0.21

Table S48.  Gene #58: 'del_10q23.31' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 137 12 2 7
DEL PEAK 27(10Q23.31) MUTATED 44 8 0 5
DEL PEAK 27(10Q23.31) WILD-TYPE 93 4 2 2

Figure S48.  Get High-res Image Gene #58: 'del_10q23.31' versus Clinical Feature #12: 'RESIDUAL_TUMOR'

'del_10q23.31' versus 'RACE'

P value = 0.00283 (Fisher's exact test), Q value = 0.096

Table S49.  Gene #58: 'del_10q23.31' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 27(10Q23.31) MUTATED 22 4 30
DEL PEAK 27(10Q23.31) WILD-TYPE 24 1 84

Figure S49.  Get High-res Image Gene #58: 'del_10q23.31' versus Clinical Feature #14: 'RACE'

'del_11p15.4' versus 'RACE'

P value = 0.00353 (Fisher's exact test), Q value = 0.11

Table S50.  Gene #59: 'del_11p15.4' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 28(11P15.4) MUTATED 27 4 40
DEL PEAK 28(11P15.4) WILD-TYPE 19 1 74

Figure S50.  Get High-res Image Gene #59: 'del_11p15.4' versus Clinical Feature #14: 'RACE'

'del_11q25' versus 'HISTOLOGICAL_TYPE'

P value = 0.0115 (Fisher's exact test), Q value = 0.23

Table S51.  Gene #60: 'del_11q25' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 29(11Q25) MUTATED 30 51
DEL PEAK 29(11Q25) WILD-TYPE 58 45

Figure S51.  Get High-res Image Gene #60: 'del_11q25' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_13q12.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.00264 (Fisher's exact test), Q value = 0.096

Table S52.  Gene #62: 'del_13q12.11' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 31(13Q12.11) MUTATED 26 50
DEL PEAK 31(13Q12.11) WILD-TYPE 62 46

Figure S52.  Get High-res Image Gene #62: 'del_13q12.11' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_13q14.2' versus 'YEARS_TO_BIRTH'

P value = 0.00574 (Wilcoxon-test), Q value = 0.16

Table S53.  Gene #63: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 184 62.4 (11.9)
DEL PEAK 32(13Q14.2) MUTATED 74 59.5 (11.1)
DEL PEAK 32(13Q14.2) WILD-TYPE 110 64.4 (12.1)

Figure S53.  Get High-res Image Gene #63: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00659 (Fisher's exact test), Q value = 0.17

Table S54.  Gene #63: 'del_13q14.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 32(13Q14.2) MUTATED 26 48
DEL PEAK 32(13Q14.2) WILD-TYPE 62 48

Figure S54.  Get High-res Image Gene #63: 'del_13q14.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_13q14.2' versus 'RACE'

P value = 0.00144 (Fisher's exact test), Q value = 0.071

Table S55.  Gene #63: 'del_13q14.2' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 32(13Q14.2) MUTATED 29 2 38
DEL PEAK 32(13Q14.2) WILD-TYPE 17 3 76

Figure S55.  Get High-res Image Gene #63: 'del_13q14.2' versus Clinical Feature #14: 'RACE'

'del_13q21.31' versus 'RACE'

P value = 0.0105 (Fisher's exact test), Q value = 0.23

Table S56.  Gene #64: 'del_13q21.31' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 33(13Q21.31) MUTATED 26 2 36
DEL PEAK 33(13Q21.31) WILD-TYPE 20 3 78

Figure S56.  Get High-res Image Gene #64: 'del_13q21.31' versus Clinical Feature #14: 'RACE'

'del_16p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 5.88e-06 (Fisher's exact test), Q value = 0.00083

Table S57.  Gene #67: 'del_16p13.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 36(16P13.3) MUTATED 46 19
DEL PEAK 36(16P13.3) WILD-TYPE 42 77

Figure S57.  Get High-res Image Gene #67: 'del_16p13.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_16q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 8.74e-11 (Fisher's exact test), Q value = 1.1e-07

Table S58.  Gene #68: 'del_16q23.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 37(16Q23.1) MUTATED 62 22
DEL PEAK 37(16Q23.1) WILD-TYPE 26 74

Figure S58.  Get High-res Image Gene #68: 'del_16q23.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_17p12' versus 'HISTOLOGICAL_TYPE'

P value = 8.21e-07 (Fisher's exact test), Q value = 0.00025

Table S59.  Gene #69: 'del_17p12' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 38(17P12) MUTATED 58 28
DEL PEAK 38(17P12) WILD-TYPE 30 68

Figure S59.  Get High-res Image Gene #69: 'del_17p12' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_18q21.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00562 (Fisher's exact test), Q value = 0.16

Table S60.  Gene #73: 'del_18q21.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 42(18Q21.2) MUTATED 66 53
DEL PEAK 42(18Q21.2) WILD-TYPE 22 43

Figure S60.  Get High-res Image Gene #73: 'del_18q21.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_22q11.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00285 (Fisher's exact test), Q value = 0.096

Table S61.  Gene #81: 'del_22q11.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 32 43 87 5
DEL PEAK 50(22Q11.1) MUTATED 19 11 42 0
DEL PEAK 50(22Q11.1) WILD-TYPE 13 32 45 5

Figure S61.  Get High-res Image Gene #81: 'del_22q11.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_22q11.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00939 (Fisher's exact test), Q value = 0.21

Table S62.  Gene #81: 'del_22q11.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 77 68 12 8
DEL PEAK 50(22Q11.1) MUTATED 27 39 2 4
DEL PEAK 50(22Q11.1) WILD-TYPE 50 29 10 4

Figure S62.  Get High-res Image Gene #81: 'del_22q11.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_22q11.1' versus 'HISTOLOGICAL_TYPE'

P value = 1.56e-06 (Fisher's exact test), Q value = 0.00025

Table S63.  Gene #81: 'del_22q11.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
DEL PEAK 50(22Q11.1) MUTATED 54 25
DEL PEAK 50(22Q11.1) WILD-TYPE 34 71

Figure S63.  Get High-res Image Gene #81: 'del_22q11.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_xp11.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00617 (Fisher's exact test), Q value = 0.17

Table S64.  Gene #83: 'del_xp11.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

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 6 1 47 31 25 14 9 7 5 4
DEL PEAK 52(XP11.3) MUTATED 1 2 1 0 23 13 10 8 8 0 1 0
DEL PEAK 52(XP11.3) WILD-TYPE 7 3 5 1 24 18 15 6 1 7 4 4

Figure S64.  Get High-res Image Gene #83: 'del_xp11.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_xp11.3' versus 'RACE'

P value = 8e-04 (Fisher's exact test), Q value = 0.046

Table S65.  Gene #83: 'del_xp11.3' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
DEL PEAK 52(XP11.3) MUTATED 29 1 37
DEL PEAK 52(XP11.3) WILD-TYPE 17 4 77

Figure S65.  Get High-res Image Gene #83: 'del_xp11.3' versus Clinical Feature #14: '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/19782630/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/19775149/ESCA-TP.merged_data.txt

  • Number of patients = 184

  • Number of significantly focal cnvs = 85

  • Number of selected clinical features = 15

  • 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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