Correlation between copy number variations of arm-level result and selected clinical features
Esophageal Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1GH9H5F
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1GH9H5F
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 82 arm-level events and 15 clinical features across 184 patients, 34 significant findings detected with Q value < 0.25.

  • 3q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 5p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 5q gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 9q gain cnv correlated to 'RACE'.

  • 12p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 13q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 16p gain cnv correlated to 'RACE'.

  • 16q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 20q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 22q gain cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 3p loss cnv correlated to 'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • 5p loss cnv correlated to 'PATHOLOGIC_STAGE' and 'HISTOLOGICAL_TYPE'.

  • 7q loss cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 10p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 10q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 12p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 12q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 13q loss cnv correlated to 'RACE'.

  • 14q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 16p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 16q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 17p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 18p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 19q loss cnv correlated to 'RACE'.

  • 22q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • xp loss cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 34 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
22q gain 31 (17%) 153 0.733
(0.989) 		0.0356
(0.444) 		0.35
(0.873) 		0.186
(0.71) 		0.00646
(0.241) 		0.665
(0.989) 		0.578
(0.962) 		1
(1.00) 		0.239
(0.791) 		2.07e-06
(0.000847) 		0.931
(1.00) 		0.682
(0.989) 		0.739
(0.99) 		0.00173
(0.125) 		1
(1.00)
3p loss 93 (51%) 91 0.0914
(0.589) 		0.0429
(0.469) 		0.117
(0.649) 		0.551
(0.962) 		0.0439
(0.469) 		0.499
(0.935) 		0.212
(0.737) 		1
(1.00) 		0.666
(0.989) 		1.83e-06
(0.000847) 		0.586
(0.962) 		0.018
(0.374) 		0.00642
(0.241) 		0.00025
(0.0298) 		0.199
(0.731)
5p loss 46 (25%) 138 0.786
(1.00) 		0.297
(0.834) 		0.00285
(0.156) 		0.0489
(0.469) 		0.441
(0.923) 		0.685
(0.989) 		0.478
(0.923) 		0.41
(0.91) 		0.606
(0.967) 		6.76e-05
(0.0126) 		0.765
(1.00) 		0.889
(1.00) 		0.468
(0.923) 		0.439
(0.923) 		0.622
(0.975)
10p loss 50 (27%) 134 0.458
(0.923) 		0.428
(0.92) 		0.485
(0.927) 		0.116
(0.649) 		0.0288
(0.419) 		0.461
(0.923) 		0.816
(1.00) 		0.426
(0.92) 		0.0415
(0.469) 		0.00454
(0.207) 		0.538
(0.956) 		0.0131
(0.335) 		0.502
(0.935) 		0.00118
(0.0968) 		1
(1.00)
10q loss 49 (27%) 135 0.945
(1.00) 		0.204
(0.731) 		0.721
(0.989) 		0.131
(0.668) 		0.965
(1.00) 		0.72
(0.989) 		1
(1.00) 		0.84
(1.00) 		0.522
(0.948) 		0.000743
(0.0703) 		0.353
(0.873) 		0.0585
(0.49) 		0.373
(0.875) 		9e-05
(0.0126) 		1
(1.00)
12q loss 31 (17%) 153 0.695
(0.989) 		0.483
(0.926) 		0.0327
(0.444) 		0.0777
(0.552) 		0.562
(0.962) 		0.627
(0.978) 		0.173
(0.71) 		0.0888
(0.581) 		0.083
(0.558) 		0.00562
(0.224) 		0.0352
(0.444) 		0.643
(0.986) 		0.0346
(0.444) 		0.00249
(0.15) 		1
(1.00)
3q gain 77 (42%) 107 0.886
(1.00) 		0.00307
(0.156) 		0.923
(1.00) 		0.457
(0.923) 		0.829
(1.00) 		0.495
(0.934) 		1
(1.00) 		0.0707
(0.528) 		0.884
(1.00) 		0.1
(0.598) 		0.172
(0.71) 		0.828
(1.00) 		0.531
(0.954) 		0.322
(0.856) 		1
(1.00)
5p gain 76 (41%) 108 0.332
(0.862) 		0.657
(0.989) 		0.236
(0.788) 		0.143
(0.682) 		0.284
(0.834) 		0.487
(0.928) 		0.29
(0.834) 		0.718
(0.989) 		0.969
(1.00) 		0.00686
(0.248) 		0.889
(1.00) 		0.174
(0.71) 		0.899
(1.00) 		0.198
(0.731) 		1
(1.00)
5q gain 20 (11%) 164 0.557
(0.962) 		0.331
(0.861) 		0.167
(0.71) 		0.623
(0.975) 		0.00151
(0.116) 		0.584
(0.962) 		0.503
(0.935) 		0.408
(0.91) 		0.294
(0.834) 		0.817
(1.00) 		0.417
(0.916) 		0.254
(0.801) 		0.339
(0.866) 		0.536
(0.956) 		1
(1.00)
9q gain 33 (18%) 151 0.578
(0.962) 		0.298
(0.834) 		0.946
(1.00) 		0.504
(0.935) 		0.865
(1.00) 		1
(1.00) 		0.0531
(0.484) 		0.0356
(0.444) 		0.12
(0.656) 		0.179
(0.71) 		0.0423
(0.469) 		0.305
(0.834) 		0.59
(0.962) 		0.00206
(0.133) 		1
(1.00)
12p gain 58 (32%) 126 0.53
(0.954) 		0.0966
(0.595) 		0.117
(0.649) 		0.14
(0.681) 		0.908
(1.00) 		0.0267
(0.419) 		0.0458
(0.469) 		0.119
(0.656) 		0.0996
(0.598) 		0.000803
(0.0706) 		0.181
(0.71) 		0.926
(1.00) 		0.16
(0.705) 		0.0133
(0.335) 		1
(1.00)
13q gain 43 (23%) 141 0.189
(0.715) 		0.975
(1.00) 		0.153
(0.696) 		0.0444
(0.469) 		0.28
(0.834) 		0.207
(0.731) 		0.628
(0.978) 		0.14
(0.681) 		0.73
(0.989) 		3.35e-06
(0.00103) 		0.046
(0.469) 		0.84
(1.00) 		0.295
(0.834) 		0.15
(0.696) 		0.082
(0.558)
16p gain 41 (22%) 143 0.639
(0.985) 		0.8
(1.00) 		0.145
(0.685) 		0.232
(0.777) 		0.548
(0.961) 		0.441
(0.923) 		0.0108
(0.329) 		0.286
(0.834) 		0.396
(0.901) 		0.00788
(0.277) 		1
(1.00) 		0.549
(0.961) 		0.822
(1.00) 		0.00188
(0.128) 		1
(1.00)
16q gain 38 (21%) 146 0.193
(0.723) 		0.933
(1.00) 		0.0999
(0.598) 		0.184
(0.71) 		0.462
(0.923) 		0.1
(0.598) 		0.0744
(0.538) 		0.384
(0.883) 		1
(1.00) 		0.00338
(0.16) 		0.843
(1.00) 		0.833
(1.00) 		0.43
(0.922) 		0.0306
(0.43) 		1
(1.00)
20q gain 115 (62%) 69 0.0669
(0.524) 		0.317
(0.851) 		0.862
(1.00) 		0.02
(0.375) 		0.291
(0.834) 		0.305
(0.834) 		0.131
(0.668) 		0.275
(0.831) 		0.291
(0.834) 		0.000266
(0.0298) 		0.423
(0.919) 		0.449
(0.923) 		0.102
(0.6) 		0.259
(0.81) 		1
(1.00)
7q loss 22 (12%) 162 0.703
(0.989) 		0.271
(0.829) 		0.366
(0.875) 		0.00526
(0.224) 		0.284
(0.834) 		0.361
(0.875) 		1
(1.00) 		0.785
(1.00) 		0.365
(0.875) 		1
(1.00) 		0.424
(0.919) 		0.123
(0.663) 		0.0389
(0.461) 		0.875
(1.00) 		1
(1.00)
12p loss 33 (18%) 151 0.423
(0.919) 		0.449
(0.923) 		0.641
(0.986) 		0.553
(0.962) 		0.491
(0.932) 		1
(1.00) 		0.587
(0.962) 		0.00995
(0.322) 		0.743
(0.99) 		0.000456
(0.0468) 		0.0963
(0.595) 		0.254
(0.801) 		0.329
(0.861) 		0.21
(0.732) 		0.587
(0.962)
13q loss 67 (36%) 117 0.249
(0.799) 		0.0789
(0.552) 		0.729
(0.989) 		0.704
(0.989) 		0.708
(0.989) 		0.483
(0.926) 		0.05
(0.469) 		0.0686
(0.528) 		0.121
(0.656) 		0.0331
(0.444) 		0.864
(1.00) 		0.416
(0.916) 		0.7
(0.989) 		0.00296
(0.156) 		1
(1.00)
14q loss 45 (24%) 139 0.695
(0.989) 		0.158
(0.703) 		0.201
(0.731) 		0.316
(0.851) 		0.303
(0.834) 		0.428
(0.92) 		0.812
(1.00) 		0.53
(0.954) 		0.477
(0.923) 		0.00566
(0.224) 		0.41
(0.91) 		0.693
(0.989) 		0.94
(1.00) 		0.174
(0.71) 		1
(1.00)
16p loss 54 (29%) 130 0.591
(0.962) 		0.477
(0.923) 		0.468
(0.923) 		0.247
(0.797) 		0.182
(0.71) 		1
(1.00) 		0.82
(1.00) 		0.243
(0.791) 		0.976
(1.00) 		9.24e-05
(0.0126) 		0.585
(0.962) 		0.673
(0.989) 		0.788
(1.00) 		0.182
(0.71) 		0.171
(0.71)
16q loss 53 (29%) 131 0.765
(1.00) 		0.346
(0.873) 		0.731
(0.989) 		0.494
(0.934) 		0.289
(0.834) 		1
(1.00) 		1
(1.00) 		0.438
(0.923) 		0.828
(1.00) 		1.79e-06
(0.000847) 		0.548
(0.961) 		0.412
(0.912) 		0.141
(0.682) 		0.0702
(0.528) 		0.0353
(0.444)
17p loss 71 (39%) 113 0.674
(0.989) 		0.111
(0.632) 		0.163
(0.71) 		0.231
(0.777) 		0.351
(0.873) 		1
(1.00) 		0.67
(0.989) 		1
(1.00) 		0.0953
(0.595) 		8.39e-05
(0.0126) 		0.592
(0.962) 		0.514
(0.94) 		0.0681
(0.528) 		0.0485
(0.469) 		0.175
(0.71)
18p loss 71 (39%) 113 0.713
(0.989) 		0.0386
(0.461) 		0.718
(0.989) 		0.0466
(0.469) 		0.349
(0.873) 		0.721
(0.989) 		0.29
(0.834) 		0.0277
(0.419) 		0.891
(1.00) 		0.00257
(0.15) 		0.12
(0.656) 		0.0593
(0.49) 		0.508
(0.935) 		0.0507
(0.472) 		0.662
(0.989)
19q loss 52 (28%) 132 0.726
(0.989) 		0.0967
(0.595) 		0.924
(1.00) 		0.356
(0.875) 		0.268
(0.825) 		0.72
(0.989) 		0.644
(0.986) 		0.156
(0.703) 		0.74
(0.99) 		0.0711
(0.528) 		0.0592
(0.49) 		0.298
(0.834) 		0.929
(1.00) 		0.00317
(0.156) 		1
(1.00)
22q loss 72 (39%) 112 0.113
(0.638) 		0.271
(0.829) 		0.0818
(0.558) 		0.012
(0.329) 		0.0606
(0.497) 		0.16
(0.705) 		1
(1.00) 		0.36
(0.875) 		0.475
(0.923) 		4.51e-05
(0.0111) 		0.953
(1.00) 		0.652
(0.989) 		0.136
(0.675) 		0.339
(0.866) 		1
(1.00)
xp loss 60 (33%) 124 0.837
(1.00) 		0.636
(0.985) 		0.38
(0.883) 		0.555
(0.962) 		0.103
(0.602) 		0.167
(0.71) 		0.044
(0.469) 		0.847
(1.00) 		0.671
(0.989) 		1
(1.00) 		0.00531
(0.224) 		0.931
(1.00) 		0.955
(1.00) 		0.0947
(0.595) 		1
(1.00)
1p gain 37 (20%) 147 0.144
(0.684) 		0.128
(0.668) 		0.461
(0.923) 		0.483
(0.926) 		0.923
(1.00) 		0.665
(0.989) 		0.606
(0.967) 		0.376
(0.878) 		0.84
(1.00) 		1
(1.00) 		0.91
(1.00) 		0.226
(0.766) 		0.783
(1.00) 		0.0906
(0.586) 		0.643
(0.986)
1q gain 63 (34%) 121 0.0577
(0.49) 		0.207
(0.731) 		0.87
(1.00) 		0.588
(0.962) 		0.723
(0.989) 		0.28
(0.834) 		0.079
(0.552) 		0.346
(0.873) 		0.818
(1.00) 		0.216
(0.746) 		0.534
(0.956) 		0.0488
(0.469) 		0.493
(0.934) 		0.215
(0.744) 		1
(1.00)
2p gain 61 (33%) 123 0.365
(0.875) 		0.0566
(0.49) 		0.299
(0.834) 		0.279
(0.834) 		0.932
(1.00) 		0.703
(0.989) 		0.826
(1.00) 		0.253
(0.801) 		0.465
(0.923) 		0.212
(0.737) 		0.167
(0.71) 		0.0481
(0.469) 		0.781
(1.00) 		0.012
(0.329) 		1
(1.00)
2q gain 46 (25%) 138 0.907
(1.00) 		0.179
(0.71) 		0.473
(0.923) 		0.304
(0.834) 		0.842
(1.00) 		1
(1.00) 		0.478
(0.923) 		1
(1.00) 		0.926
(1.00) 		0.737
(0.99) 		0.705
(0.989) 		0.202
(0.731) 		0.814
(1.00) 		0.232
(0.777) 		1
(1.00)
3p gain 31 (17%) 153 0.349
(0.873) 		0.283
(0.834) 		0.121
(0.656) 		0.25
(0.799) 		0.0563
(0.49) 		0.126
(0.664) 		0.578
(0.962) 		0.241
(0.791) 		0.8
(1.00) 		0.434
(0.923) 		0.712
(0.989) 		0.151
(0.696) 		0.13
(0.668) 		0.0925
(0.593) 		0.243
(0.791)
4p gain 19 (10%) 165 0.459
(0.923) 		0.593
(0.962) 		0.776
(1.00) 		0.96
(1.00) 		0.693
(0.989) 		0.521
(0.948) 		0.317
(0.851) 		1
(1.00) 		0.692
(0.989) 		1
(1.00) 		0.494
(0.934) 		0.143
(0.682) 		0.0538
(0.486) 		0.0815
(0.558) 		0.168
(0.71)
4q gain 18 (10%) 166 0.37
(0.875) 		0.395
(0.9) 		1
(1.00) 		0.715
(0.989) 		0.963
(1.00) 		1
(1.00) 		0.48
(0.924) 		0.565
(0.962) 		0.415
(0.916) 		0.222
(0.758) 		0.573
(0.962) 		1
(1.00) 		0.0475
(0.469) 		0.0179
(0.374) 		0.536
(0.956)
6p gain 38 (21%) 146 0.856
(1.00) 		0.428
(0.92) 		0.408
(0.91) 		0.809
(1.00) 		0.986
(1.00) 		0.1
(0.598) 		1
(1.00) 		1
(1.00) 		0.0849
(0.562) 		0.202
(0.731) 		0.727
(0.989) 		0.647
(0.988) 		0.739
(0.99) 		0.858
(1.00) 		0.585
(0.962)
6q gain 33 (18%) 151 0.773
(1.00) 		0.315
(0.849) 		0.0933
(0.595) 		0.451
(0.923) 		0.783
(1.00) 		0.012
(0.329) 		0.421
(0.919) 		1
(1.00) 		0.0849
(0.562) 		0.251
(0.799) 		0.502
(0.935) 		0.0712
(0.528) 		0.33
(0.861) 		0.654
(0.989) 		0.585
(0.962)
7p gain 110 (60%) 74 0.56
(0.962) 		0.589
(0.962) 		0.549
(0.961) 		0.0255
(0.413) 		0.193
(0.723) 		0.185
(0.71) 		0.0346
(0.444) 		0.471
(0.923) 		0.797
(1.00) 		0.132
(0.672) 		0.285
(0.834) 		0.741
(0.99) 		0.639
(0.985) 		0.186
(0.71) 		0.406
(0.91)
7q gain 89 (48%) 95 0.945
(1.00) 		0.735
(0.99) 		0.655
(0.989) 		0.0258
(0.413) 		0.424
(0.919) 		0.18
(0.71) 		0.0127
(0.333) 		0.721
(0.989) 		0.178
(0.71) 		0.555
(0.962) 		0.963
(1.00) 		0.33
(0.861) 		0.278
(0.834) 		0.531
(0.954) 		0.678
(0.989)
8p gain 68 (37%) 116 0.0461
(0.469) 		0.825
(1.00) 		0.65
(0.989) 		0.0896
(0.583) 		0.165
(0.71) 		0.719
(0.989) 		1
(1.00) 		0.578
(0.962) 		0.922
(1.00) 		1
(1.00) 		0.0992
(0.598) 		0.303
(0.834) 		0.0952
(0.595) 		1
(1.00) 		0.66
(0.989)
8q gain 101 (55%) 83 0.35
(0.873) 		0.994
(1.00) 		0.137
(0.675) 		0.00914
(0.304) 		0.0493
(0.469) 		0.732
(0.989) 		0.835
(1.00) 		0.153
(0.696) 		0.717
(0.989) 		0.767
(1.00) 		0.946
(1.00) 		0.508
(0.935) 		0.0155
(0.374) 		0.585
(0.962) 		0.402
(0.904)
9p gain 16 (9%) 168 0.291
(0.834) 		0.537
(0.956) 		0.866
(1.00) 		0.464
(0.923) 		0.065
(0.518) 		0.6
(0.964) 		0.474
(0.923) 		0.0478
(0.469) 		0.309
(0.841) 		0.197
(0.731) 		0.117
(0.649) 		0.616
(0.975) 		0.156
(0.703) 		0.0653
(0.518) 		1
(1.00)
10p gain 40 (22%) 144 0.506
(0.935) 		0.924
(1.00) 		0.0184
(0.374) 		0.0825
(0.558) 		0.128
(0.668) 		0.0808
(0.558) 		0.207
(0.731) 		0.835
(1.00) 		0.175
(0.71) 		0.0485
(0.469) 		0.274
(0.831) 		0.933
(1.00) 		0.506
(0.935) 		0.272
(0.831) 		0.336
(0.866)
10q gain 30 (16%) 154 0.98
(1.00) 		0.859
(1.00) 		0.0354
(0.444) 		0.0384
(0.461) 		0.295
(0.834) 		0.126
(0.664) 		0.26
(0.81) 		0.473
(0.923) 		0.454
(0.923) 		0.0284
(0.419) 		0.0592
(0.49) 		0.911
(1.00) 		0.329
(0.861) 		0.35
(0.873) 		0.585
(0.962)
11p gain 39 (21%) 145 0.242
(0.791) 		0.386
(0.883) 		0.885
(1.00) 		0.262
(0.811) 		0.294
(0.834) 		0.385
(0.883) 		1
(1.00) 		0.201
(0.731) 		0.76
(1.00) 		0.471
(0.923) 		0.133
(0.672) 		0.0278
(0.419) 		0.188
(0.715) 		0.867
(1.00) 		0.587
(0.962)
11q gain 29 (16%) 155 0.898
(1.00) 		0.0357
(0.444) 		0.585
(0.962) 		0.139
(0.681) 		0.0828
(0.558) 		1
(1.00) 		1
(1.00) 		0.134
(0.672) 		0.581
(0.962) 		0.0439
(0.469) 		0.522
(0.948) 		0.0159
(0.374) 		0.455
(0.923) 		0.781
(1.00) 		0.587
(0.962)
12q gain 38 (21%) 146 0.736
(0.99) 		0.33
(0.861) 		0.0201
(0.375) 		0.373
(0.875) 		0.618
(0.975) 		0.0195
(0.374) 		0.301
(0.834) 		0.658
(0.989) 		0.0616
(0.5) 		0.278
(0.834) 		0.0249
(0.413) 		0.607
(0.967) 		0.00867
(0.296) 		0.0256
(0.413) 		1
(1.00)
14q gain 48 (26%) 136 0.71
(0.989) 		0.182
(0.71) 		0.977
(1.00) 		0.0109
(0.329) 		0.464
(0.923) 		0.445
(0.923) 		0.0168
(0.374) 		0.55
(0.961) 		0.73
(0.989) 		0.0113
(0.329) 		0.974
(1.00) 		0.364
(0.875) 		0.953
(1.00) 		0.0618
(0.5) 		0.66
(0.989)
15q gain 30 (16%) 154 0.619
(0.975) 		0.561
(0.962) 		0.331
(0.861) 		0.6
(0.964) 		0.916
(1.00) 		0.357
(0.875) 		0.578
(0.962) 		0.811
(1.00) 		0.788
(1.00) 		0.322
(0.856) 		0.0734
(0.534) 		0.438
(0.923) 		0.863
(1.00) 		0.919
(1.00) 		1
(1.00)
17p gain 33 (18%) 151 0.703
(0.989) 		0.477
(0.923) 		0.794
(1.00) 		0.888
(1.00) 		0.399
(0.903) 		1
(1.00) 		0.421
(0.919) 		0.101
(0.598) 		0.957
(1.00) 		0.179
(0.71) 		0.923
(1.00) 		0.147
(0.69) 		0.439
(0.923) 		0.691
(0.989) 		0.587
(0.962)
17q gain 45 (24%) 139 0.543
(0.959) 		0.514
(0.94) 		0.811
(1.00) 		0.95
(1.00) 		0.592
(0.962) 		1
(1.00) 		0.237
(0.79) 		0.0192
(0.374) 		0.661
(0.989) 		0.866
(1.00) 		0.339
(0.866) 		0.244
(0.791) 		0.539
(0.956) 		0.58
(0.962) 		0.33
(0.861)
18p gain 50 (27%) 134 0.31
(0.841) 		0.478
(0.923) 		0.282
(0.834) 		0.969
(1.00) 		0.617
(0.975) 		0.264
(0.815) 		0.0589
(0.49) 		0.106
(0.609) 		0.76
(1.00) 		0.407
(0.91) 		0.823
(1.00) 		0.147
(0.69) 		0.385
(0.883) 		0.426
(0.92) 		0.622
(0.975)
18q gain 26 (14%) 158 0.374
(0.875) 		0.981
(1.00) 		0.0565
(0.49) 		0.571
(0.962) 		0.455
(0.923) 		1
(1.00) 		0.772
(1.00) 		0.444
(0.923) 		0.349
(0.873) 		0.835
(1.00) 		0.698
(0.989) 		0.518
(0.946) 		0.931
(1.00) 		0.897
(1.00) 		1
(1.00)
19p gain 28 (15%) 156 0.602
(0.964) 		0.611
(0.972) 		0.701
(0.989) 		0.874
(1.00) 		0.025
(0.413) 		1
(1.00) 		0.0844
(0.562) 		0.811
(1.00) 		0.971
(1.00) 		0.839
(1.00) 		0.651
(0.989) 		0.469
(0.923) 		0.513
(0.94) 		0.622
(0.975) 		1
(1.00)
19q gain 38 (21%) 146 0.955
(1.00) 		0.351
(0.873) 		0.301
(0.834) 		1
(1.00) 		0.348
(0.873) 		0.655
(0.989) 		0.0187
(0.374) 		0.0301
(0.43) 		0.931
(1.00) 		0.101
(0.598) 		0.934
(1.00) 		0.433
(0.923) 		0.338
(0.866) 		0.638
(0.985) 		1
(1.00)
20p gain 108 (59%) 76 0.0472
(0.469) 		0.392
(0.895) 		0.707
(0.989) 		0.565
(0.962) 		0.474
(0.923) 		0.299
(0.834) 		0.29
(0.834) 		0.371
(0.875) 		0.079
(0.552) 		0.0721
(0.531) 		0.628
(0.978) 		0.935
(1.00) 		0.157
(0.703) 		0.311
(0.841) 		0.693
(0.989)
21q gain 18 (10%) 166 0.323
(0.856) 		0.771
(1.00) 		0.742
(0.99) 		0.803
(1.00) 		0.501
(0.935) 		0.6
(0.964) 		1
(1.00) 		0.239
(0.791) 		0.687
(0.989) 		0.222
(0.758) 		0.681
(0.989) 		0.82
(1.00) 		0.727
(0.989) 		0.0582
(0.49) 		1
(1.00)
xp gain 23 (12%) 161 0.979
(1.00) 		0.765
(1.00) 		0.54
(0.956) 		0.795
(1.00) 		0.0309
(0.43) 		0.6
(0.964) 		0.537
(0.956) 		0.18
(0.71) 		0.711
(0.989) 		0.504
(0.935) 		0.228
(0.769) 		0.268
(0.825) 		0.715
(0.989) 		0.184
(0.71) 		1
(1.00)
xq gain 38 (21%) 146 0.976
(1.00) 		0.464
(0.923) 		0.442
(0.923) 		0.691
(0.989) 		0.18
(0.71) 		0.685
(0.989) 		0.301
(0.834) 		0.376
(0.878) 		0.703
(0.989) 		0.0289
(0.419) 		1
(1.00) 		0.185
(0.71) 		0.14
(0.681) 		0.0254
(0.413) 		1
(1.00)
1p loss 38 (21%) 146 0.793
(1.00) 		0.867
(1.00) 		0.413
(0.912) 		1
(1.00) 		0.528
(0.953) 		0.207
(0.731) 		1
(1.00) 		0.18
(0.71) 		0.238
(0.791) 		0.0173
(0.374) 		0.695
(0.989) 		0.0288
(0.419) 		0.732
(0.989) 		0.385
(0.883) 		1
(1.00)
1q loss 22 (12%) 162 0.0224
(0.4) 		0.15
(0.696) 		0.178
(0.71) 		0.563
(0.962) 		0.248
(0.797) 		0.142
(0.682) 		1
(1.00) 		1
(1.00) 		0.321
(0.856) 		0.0669
(0.524) 		0.359
(0.875) 		0.0117
(0.329) 		0.189
(0.715) 		0.324
(0.857) 		1
(1.00)
2p loss 11 (6%) 173 0.028
(0.419) 		0.182
(0.71) 		0.554
(0.962) 		0.356
(0.875) 		1
(1.00) 		1
(1.00) 		0.666
(0.989) 		0.275
(0.831) 		0.729
(0.989) 		0.217
(0.747) 		1
(1.00) 		0.771
(1.00) 		0.181
(0.71) 		0.657
(0.989) 		1
(1.00)
2q loss 18 (10%) 166 0.522
(0.948) 		0.339
(0.866) 		0.856
(1.00) 		0.45
(0.923) 		0.695
(0.989) 		0.599
(0.964) 		0.732
(0.989) 		0.377
(0.879) 		0.294
(0.834) 		0.0258
(0.413) 		0.453
(0.923) 		0.753
(1) 		0.284
(0.834) 		1
(1.00) 		1
(1.00)
3q loss 33 (18%) 151 0.815
(1.00) 		0.809
(1.00) 		0.194
(0.725) 		0.766
(1.00) 		0.779
(1.00) 		1
(1.00) 		0.421
(0.919) 		0.496
(0.935) 		0.364
(0.875) 		0.566
(0.962) 		0.665
(0.989) 		0.504
(0.935) 		0.95
(1.00) 		0.289
(0.834) 		1
(1.00)
4p loss 105 (57%) 79 0.128
(0.668) 		0.159
(0.705) 		0.594
(0.962) 		0.126
(0.664) 		0.368
(0.875) 		1
(1.00) 		0.4
(0.903) 		0.474
(0.923) 		0.717
(0.989) 		0.373
(0.875) 		0.131
(0.668) 		0.226
(0.766) 		0.04
(0.468) 		0.0188
(0.374) 		0.207
(0.731)
4q loss 87 (47%) 97 0.0711
(0.528) 		0.0641
(0.515) 		0.103
(0.6) 		0.409
(0.91) 		0.684
(0.989) 		0.304
(0.834) 		0.145
(0.685) 		0.37
(0.875) 		0.558
(0.962) 		0.076
(0.547) 		0.509
(0.935) 		0.397
(0.901) 		0.0123
(0.33) 		0.0498
(0.469) 		0.684
(0.989)
5q loss 86 (47%) 98 0.452
(0.923) 		0.998
(1.00) 		0.157
(0.703) 		0.451
(0.923) 		0.206
(0.731) 		0.734
(0.989) 		0.537
(0.956) 		0.722
(0.989) 		0.303
(0.834) 		0.0544
(0.488) 		0.883
(1.00) 		0.743
(0.99) 		0.283
(0.834) 		0.953
(1.00) 		1
(1.00)
6p loss 39 (21%) 145 0.484
(0.926) 		0.55
(0.961) 		0.801
(1.00) 		0.528
(0.953) 		0.0879
(0.578) 		0.206
(0.731) 		0.804
(1.00) 		0.658
(0.989) 		0.656
(0.989) 		0.371
(0.875) 		0.178
(0.71) 		0.768
(1.00) 		0.439
(0.923) 		0.241
(0.791) 		0.622
(0.975)
6q loss 39 (21%) 145 0.684
(0.989) 		0.636
(0.985) 		0.797
(1.00) 		0.371
(0.875) 		0.487
(0.928) 		1
(1.00) 		0.208
(0.731) 		1
(1.00) 		0.838
(1.00) 		0.858
(1.00) 		0.288
(0.834) 		0.581
(0.962) 		0.241
(0.791) 		0.354
(0.874) 		0.613
(0.972)
7p loss 13 (7%) 171 0.585
(0.962) 		0.808
(1.00) 		0.967
(1.00) 		0.444
(0.923) 		0.669
(0.989) 		1
(1.00) 		0.411
(0.91) 		1
(1.00) 		0.644
(0.986) 		0.572
(0.962) 		0.0236
(0.413) 		0.553
(0.962) 		0.151
(0.696) 		0.827
(1.00) 		1
(1.00)
8p loss 63 (34%) 121 0.886
(1.00) 		0.867
(1.00) 		0.362
(0.875) 		0.708
(0.989) 		0.133
(0.672) 		1
(1.00) 		1
(1.00) 		0.26
(0.81) 		0.563
(0.962) 		0.216
(0.746) 		0.0705
(0.528) 		0.602
(0.964) 		0.507
(0.935) 		0.645
(0.986) 		0.664
(0.989)
8q loss 23 (12%) 161 0.185
(0.71) 		0.677
(0.989) 		0.123
(0.663) 		0.502
(0.935) 		0.57
(0.962) 		0.613
(0.972) 		1
(1.00) 		0.0683
(0.528) 		0.837
(1.00) 		1
(1.00) 		0.668
(0.989) 		0.798
(1.00) 		1
(1.00) 		0.0956
(0.595) 		0.463
(0.923)
9p loss 101 (55%) 83 0.573
(0.962) 		0.546
(0.961) 		0.431
(0.922) 		0.728
(0.989) 		0.199
(0.731) 		1
(1.00) 		0.0588
(0.49) 		0.153
(0.696) 		0.262
(0.811) 		0.46
(0.923) 		0.775
(1.00) 		0.0772
(0.552) 		0.166
(0.71) 		0.153
(0.696) 		0.401
(0.904)
9q loss 65 (35%) 119 0.773
(1.00) 		0.46
(0.923) 		0.0527
(0.484) 		0.629
(0.978) 		0.9
(1.00) 		0.274
(0.831) 		0.383
(0.883) 		0.855
(1.00) 		0.599
(0.964) 		0.358
(0.875) 		0.112
(0.634) 		0.788
(1.00) 		0.816
(1.00) 		0.556
(0.962) 		0.398
(0.902)
11p loss 52 (28%) 132 0.68
(0.989) 		0.581
(0.962) 		0.135
(0.674) 		0.732
(0.989) 		0.125
(0.664) 		0.448
(0.923) 		0.257
(0.807) 		0.0453
(0.469) 		0.169
(0.71) 		1
(1.00) 		0.893
(1.00) 		0.839
(1.00) 		0.823
(1.00) 		0.135
(0.674) 		0.368
(0.875)
11q loss 58 (32%) 126 0.313
(0.846) 		0.438
(0.923) 		0.143
(0.682) 		0.878
(1.00) 		0.0469
(0.469) 		1
(1.00) 		1
(1.00) 		0.0206
(0.379) 		0.622
(0.975) 		0.0172
(0.374) 		0.463
(0.923) 		0.47
(0.923) 		0.74
(0.99) 		0.053
(0.484) 		0.179
(0.71)
15q loss 57 (31%) 127 0.374
(0.875) 		0.447
(0.923) 		0.936
(1.00) 		0.351
(0.873) 		0.634
(0.984) 		0.16
(0.705) 		0.655
(0.989) 		0.703
(0.989) 		0.689
(0.989) 		0.0382
(0.461) 		0.827
(1.00) 		0.209
(0.732) 		0.964
(1.00) 		0.715
(0.989) 		1
(1.00)
17q loss 25 (14%) 159 0.179
(0.71) 		0.83
(1.00) 		0.581
(0.962) 		0.631
(0.98) 		0.459
(0.923) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.105
(0.609) 		0.673
(0.989) 		0.947
(1.00) 		1
(1.00) 		0.726
(0.989) 		0.479
(0.924) 		0.0497
(0.469)
18q loss 102 (55%) 82 0.721
(0.989) 		0.163
(0.71) 		0.604
(0.967) 		0.385
(0.883) 		0.322
(0.856) 		0.508
(0.935) 		1
(1.00) 		1
(1.00) 		0.343
(0.873) 		0.0177
(0.374) 		0.289
(0.834) 		0.47
(0.923) 		0.333
(0.864) 		0.907
(1.00) 		0.681
(0.989)
19p loss 65 (35%) 119 0.991
(1.00) 		0.362
(0.875) 		0.44
(0.923) 		0.251
(0.799) 		0.0581
(0.49) 		0.728
(0.989) 		0.383
(0.883) 		0.192
(0.723) 		0.371
(0.875) 		0.54
(0.956) 		0.0363
(0.446) 		0.931
(1.00) 		0.185
(0.71) 		0.0189
(0.374) 		1
(1.00)
20p loss 19 (10%) 165 0.0311
(0.43) 		0.884
(1.00) 		0.896
(1.00) 		0.882
(1.00) 		0.97
(1.00) 		0.598
(0.964) 		0.744
(0.99) 		1
(1.00) 		0.392
(0.895) 		0.809
(1.00) 		0.704
(0.989) 		0.499
(0.935) 		0.339
(0.866) 		0.22
(0.753) 		0.423
(0.919)
20q loss 8 (4%) 176 0.31
(0.841) 		0.724
(0.989) 		0.509
(0.935) 		0.111
(0.632) 		0.244
(0.791) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.666
(0.989) 		0.459
(0.923) 		0.11
(0.63) 		0.527
(0.953) 		1
(1.00)
21q loss 106 (58%) 78 0.195
(0.727) 		0.247
(0.797) 		0.593
(0.962) 		0.62
(0.975) 		0.769
(1.00) 		1
(1.00) 		0.674
(0.989) 		0.858
(1.00) 		0.199
(0.731) 		0.0733
(0.534) 		0.129
(0.668) 		0.0218
(0.395) 		0.957
(1.00) 		0.258
(0.81) 		0.679
(0.989)
xq loss 40 (22%) 144 0.941
(1.00) 		0.625
(0.977) 		0.745
(0.99) 		0.84
(1.00) 		0.544
(0.96) 		0.206
(0.731) 		0.207
(0.731) 		1
(1.00) 		0.352
(0.873) 		0.0485
(0.469) 		0.0164
(0.374) 		0.826
(1.00) 		0.797
(1.00) 		1
(1.00) 		1
(1.00)
'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00307 (Wilcoxon-test), Q value = 0.16

Table S1.  Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 184 62.4 (11.9)
3Q GAIN MUTATED 77 59.4 (11.5)
3Q GAIN WILD-TYPE 107 64.6 (11.8)

Figure S1.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00686 (Fisher's exact test), Q value = 0.25

Table S2.  Gene #9: '5p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
5P GAIN MUTATED 27 49
5P GAIN WILD-TYPE 61 47

Figure S2.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00151 (Fisher's exact test), Q value = 0.12

Table S3.  Gene #10: '5q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 77 68 12 8
5Q GAIN MUTATED 10 2 1 4
5Q GAIN WILD-TYPE 67 66 11 4

Figure S3.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9q gain' versus 'RACE'

P value = 0.00206 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #18: '9q gain' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
9Q GAIN MUTATED 15 2 13
9Q GAIN WILD-TYPE 31 3 101

Figure S4.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #14: 'RACE'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.000803 (Fisher's exact test), Q value = 0.071

Table S5.  Gene #23: '12p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
12P GAIN MUTATED 17 41
12P GAIN WILD-TYPE 71 55

Figure S5.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 3.35e-06 (Fisher's exact test), Q value = 0.001

Table S6.  Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
13Q GAIN MUTATED 34 9
13Q GAIN WILD-TYPE 54 87

Figure S6.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'RACE'

P value = 0.00188 (Fisher's exact test), Q value = 0.13

Table S7.  Gene #28: '16p gain' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
16P GAIN MUTATED 17 3 18
16P GAIN WILD-TYPE 29 2 96

Figure S7.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #14: 'RACE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00338 (Fisher's exact test), Q value = 0.16

Table S8.  Gene #29: '16q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
16Q GAIN MUTATED 10 28
16Q GAIN WILD-TYPE 78 68

Figure S8.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.000266 (Fisher's exact test), Q value = 0.03

Table S9.  Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
20Q GAIN MUTATED 67 48
20Q GAIN WILD-TYPE 21 48

Figure S9.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'22q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00646 (Fisher's exact test), Q value = 0.24

Table S10.  Gene #39: '22q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 77 68 12 8
22Q GAIN MUTATED 19 4 3 2
22Q GAIN WILD-TYPE 58 64 9 6

Figure S10.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.00085

Table S11.  Gene #39: '22q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
22Q GAIN MUTATED 3 28
22Q GAIN WILD-TYPE 85 68

Figure S11.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'22q gain' versus 'RACE'

P value = 0.00173 (Fisher's exact test), Q value = 0.13

Table S12.  Gene #39: '22q gain' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
22Q GAIN MUTATED 16 1 13
22Q GAIN WILD-TYPE 30 4 101

Figure S12.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #14: 'RACE'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1.83e-06 (Fisher's exact test), Q value = 0.00085

Table S13.  Gene #46: '3p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
3P LOSS MUTATED 28 65
3P LOSS WILD-TYPE 60 31

Figure S13.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00642 (Wilcoxon-test), Q value = 0.24

Table S14.  Gene #46: '3p loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 134 2.5 (3.4)
3P LOSS MUTATED 66 1.8 (3.0)
3P LOSS WILD-TYPE 68 3.2 (3.7)

Figure S14.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #13: 'NUMBER_OF_LYMPH_NODES'

'3p loss' versus 'RACE'

P value = 0.00025 (Fisher's exact test), Q value = 0.03

Table S15.  Gene #46: '3p loss' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
3P LOSS MUTATED 35 2 49
3P LOSS WILD-TYPE 11 3 65

Figure S15.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #14: 'RACE'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00285 (Fisher's exact test), Q value = 0.16

Table S16.  Gene #50: '5p loss' 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
5P LOSS MUTATED 7 0 0 0 8 6 9 2 3 0 0 1
5P LOSS WILD-TYPE 1 5 6 1 39 25 16 12 6 7 5 3

Figure S16.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 6.76e-05 (Fisher's exact test), Q value = 0.013

Table S17.  Gene #50: '5p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
5P LOSS MUTATED 34 12
5P LOSS WILD-TYPE 54 84

Figure S17.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'7q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00526 (Fisher's exact test), Q value = 0.22

Table S18.  Gene #55: '7q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 32 43 87 5
7Q LOSS MUTATED 0 3 15 2
7Q LOSS WILD-TYPE 32 40 72 3

Figure S18.  Get High-res Image Gene #55: '7q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00454 (Fisher's exact test), Q value = 0.21

Table S19.  Gene #60: '10p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
10P LOSS MUTATED 15 35
10P LOSS WILD-TYPE 73 61

Figure S19.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RACE'

P value = 0.00118 (Fisher's exact test), Q value = 0.097

Table S20.  Gene #60: '10p loss' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
10P LOSS MUTATED 18 4 22
10P LOSS WILD-TYPE 28 1 92

Figure S20.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #14: 'RACE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.000743 (Fisher's exact test), Q value = 0.07

Table S21.  Gene #61: '10q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
10Q LOSS MUTATED 13 36
10Q LOSS WILD-TYPE 75 60

Figure S21.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RACE'

P value = 9e-05 (Fisher's exact test), Q value = 0.013

Table S22.  Gene #61: '10q loss' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
10Q LOSS MUTATED 20 4 20
10Q LOSS WILD-TYPE 26 1 94

Figure S22.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #14: 'RACE'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.000456 (Fisher's exact test), Q value = 0.047

Table S23.  Gene #64: '12p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
12P LOSS MUTATED 25 8
12P LOSS WILD-TYPE 63 88

Figure S23.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00562 (Fisher's exact test), Q value = 0.22

Table S24.  Gene #65: '12q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
12Q LOSS MUTATED 22 9
12Q LOSS WILD-TYPE 66 87

Figure S24.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'RACE'

P value = 0.00249 (Fisher's exact test), Q value = 0.15

Table S25.  Gene #65: '12q loss' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
12Q LOSS MUTATED 2 3 22
12Q LOSS WILD-TYPE 44 2 92

Figure S25.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #14: 'RACE'

'13q loss' versus 'RACE'

P value = 0.00296 (Fisher's exact test), Q value = 0.16

Table S26.  Gene #66: '13q loss' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
13Q LOSS MUTATED 26 2 33
13Q LOSS WILD-TYPE 20 3 81

Figure S26.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #14: 'RACE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00566 (Fisher's exact test), Q value = 0.22

Table S27.  Gene #67: '14q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
14Q LOSS MUTATED 30 15
14Q LOSS WILD-TYPE 58 81

Figure S27.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16p loss' versus 'HISTOLOGICAL_TYPE'

P value = 9.24e-05 (Fisher's exact test), Q value = 0.013

Table S28.  Gene #69: '16p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
16P LOSS MUTATED 38 16
16P LOSS WILD-TYPE 50 80

Figure S28.  Get High-res Image Gene #69: '16p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1.79e-06 (Fisher's exact test), Q value = 0.00085

Table S29.  Gene #70: '16q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
16Q LOSS MUTATED 40 13
16Q LOSS WILD-TYPE 48 83

Figure S29.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 8.39e-05 (Fisher's exact test), Q value = 0.013

Table S30.  Gene #71: '17p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
17P LOSS MUTATED 47 24
17P LOSS WILD-TYPE 41 72

Figure S30.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00257 (Fisher's exact test), Q value = 0.15

Table S31.  Gene #73: '18p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
18P LOSS MUTATED 44 27
18P LOSS WILD-TYPE 44 69

Figure S31.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'RACE'

P value = 0.00317 (Fisher's exact test), Q value = 0.16

Table S32.  Gene #76: '19q loss' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
19Q LOSS MUTATED 18 4 24
19Q LOSS WILD-TYPE 28 1 90

Figure S32.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #14: 'RACE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 4.51e-05 (Fisher's exact test), Q value = 0.011

Table S33.  Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
22Q LOSS MUTATED 48 24
22Q LOSS WILD-TYPE 40 72

Figure S33.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'xp loss' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00531 (Wilcoxon-test), Q value = 0.22

Table S34.  Gene #81: 'xp loss' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 98 34.5 (21.5)
XP LOSS MUTATED 30 25.7 (16.0)
XP LOSS WILD-TYPE 68 38.4 (22.6)

Figure S34.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/19782631/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 arm-level cnvs = 82

  • Number of selected clinical features = 15

  • Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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