Correlation between copy number variations of arm-level result and selected clinical features
Esophageal Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1T15300
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1T15300
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, 23 significant findings detected with Q value < 0.25.

  • 3q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 12p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 13q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 20q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • 3p loss cnv correlated to 'HISTOLOGICAL_TYPE' 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 'RACE'.

  • 13q loss cnv correlated to 'RACE'.

  • 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'.

  • 22q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

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, 23 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 0.682
(0.996) 		0.0356
(0.456) 		0.348
(0.89) 		0.185
(0.745) 		0.00618
(0.268) 		0.665
(0.996) 		0.578
(0.984) 		0.818
(1.00) 		0.239
(0.815) 		2.07e-06
(0.000635) 		0.931
(1.00) 		0.684
(0.996) 		0.739
(1.00) 		0.00195
(0.147) 		1
(1.00)
3p loss 92 (50%) 92 0.145
(0.722) 		0.0346
(0.456) 		0.111
(0.66) 		0.545
(0.974) 		0.125
(0.69) 		0.505
(0.962) 		0.211
(0.769) 		1
(1.00) 		0.875
(1.00) 		8.52e-07
(0.000635) 		0.682
(0.996) 		0.0206
(0.417) 		0.0116
(0.325) 		0.00078
(0.0738) 		0.199
(0.768)
5p loss 46 (25%) 138 0.798
(1.00) 		0.297
(0.862) 		0.00292
(0.18) 		0.0484
(0.485) 		0.446
(0.939) 		0.685
(0.996) 		0.478
(0.945) 		0.313
(0.863) 		0.606
(0.989) 		6.76e-05
(0.0119) 		0.765
(1.00) 		0.888
(1.00) 		0.468
(0.945) 		0.443
(0.939) 		0.622
(0.996)
10p loss 51 (28%) 133 0.499
(0.962) 		0.331
(0.881) 		0.483
(0.952) 		0.0949
(0.63) 		0.0475
(0.485) 		0.467
(0.945) 		0.818
(1.00) 		0.556
(0.978) 		0.0415
(0.479) 		0.00281
(0.18) 		0.569
(0.984) 		0.0188
(0.417) 		0.392
(0.91) 		0.00055
(0.0615) 		1
(1.00)
10q loss 50 (27%) 134 0.925
(1.00) 		0.148
(0.722) 		0.773
(1.00) 		0.0969
(0.63) 		0.967
(1.00) 		0.719
(1.00) 		1
(1.00) 		1
(1.00) 		0.522
(0.962) 		0.000429
(0.0528) 		0.38
(0.909) 		0.0767
(0.59) 		0.282
(0.851) 		3e-05
(0.00615) 		1
(1.00)
3q gain 77 (42%) 107 0.858
(1.00) 		0.00307
(0.18) 		0.923
(1.00) 		0.457
(0.943) 		0.828
(1.00) 		0.495
(0.961) 		1
(1.00) 		0.048
(0.485) 		0.884
(1.00) 		0.1
(0.634) 		0.172
(0.744) 		0.825
(1.00) 		0.531
(0.966) 		0.324
(0.874) 		1
(1.00)
12p gain 57 (31%) 127 0.359
(0.897) 		0.0974
(0.63) 		0.0947
(0.63) 		0.163
(0.742) 		0.873
(1.00) 		0.0237
(0.417) 		0.0697
(0.563) 		0.0518
(0.493) 		0.0518
(0.493) 		0.00134
(0.11) 		0.273
(0.845) 		0.89
(1.00) 		0.203
(0.769) 		0.00943
(0.325) 		1
(1.00)
13q gain 44 (24%) 140 0.204
(0.769) 		0.823
(1.00) 		0.156
(0.73) 		0.0534
(0.493) 		0.257
(0.837) 		0.37
(0.902) 		1
(1.00) 		0.0967
(0.63) 		0.73
(1.00) 		1.63e-06
(0.000635) 		0.081
(0.596) 		0.895
(1.00) 		0.186
(0.746) 		0.149
(0.722) 		0.082
(0.598)
20q gain 114 (62%) 70 0.0335
(0.453) 		0.224
(0.786) 		0.65
(0.996) 		0.0301
(0.441) 		0.101
(0.636) 		0.309
(0.863) 		0.0536
(0.493) 		0.467
(0.945) 		0.291
(0.86) 		0.000769
(0.0738) 		0.637
(0.996) 		0.449
(0.941) 		0.0309
(0.441) 		0.288
(0.857) 		1
(1.00)
7q loss 23 (12%) 161 0.78
(1.00) 		0.196
(0.767) 		0.225
(0.786) 		0.00455
(0.243) 		0.367
(0.9) 		0.357
(0.897) 		1
(1.00) 		1
(1.00) 		0.786
(1.00) 		1
(1.00) 		0.349
(0.89) 		0.123
(0.69) 		0.0544
(0.495) 		1
(1.00) 		1
(1.00)
12p loss 34 (18%) 150 0.267
(0.845) 		0.463
(0.945) 		0.488
(0.954) 		0.509
(0.962) 		0.484
(0.952) 		1
(1.00) 		0.595
(0.984) 		0.00587
(0.267) 		0.867
(1.00) 		0.00109
(0.0962) 		0.204
(0.769) 		0.301
(0.862) 		0.418
(0.926) 		0.174
(0.744) 		0.587
(0.984)
12q loss 32 (17%) 152 0.468
(0.945) 		0.498
(0.961) 		0.0305
(0.441) 		0.101
(0.636) 		0.586
(0.984) 		0.636
(0.996) 		0.268
(0.845) 		0.0572
(0.506) 		0.0378
(0.465) 		0.0112
(0.325) 		0.0839
(0.6) 		0.609
(0.99) 		0.0554
(0.497) 		0.00203
(0.147) 		1
(1.00)
13q loss 67 (36%) 117 0.235
(0.808) 		0.0789
(0.592) 		0.728
(1.00) 		0.705
(1.00) 		0.706
(1.00) 		0.483
(0.952) 		0.05
(0.489) 		0.0454
(0.485) 		0.121
(0.69) 		0.0331
(0.452) 		0.864
(1.00) 		0.413
(0.917) 		0.7
(1.00) 		0.00288
(0.18) 		1
(1.00)
16p loss 54 (29%) 130 0.578
(0.984) 		0.477
(0.945) 		0.464
(0.945) 		0.244
(0.815) 		0.18
(0.745) 		1
(1.00) 		0.82
(1.00) 		0.241
(0.815) 		0.976
(1.00) 		9.24e-05
(0.0142) 		0.585
(0.984) 		0.674
(0.996) 		0.788
(1.00) 		0.182
(0.745) 		0.171
(0.744)
16q loss 53 (29%) 131 0.751
(1.00) 		0.346
(0.89) 		0.731
(1.00) 		0.496
(0.961) 		0.287
(0.857) 		1
(1.00) 		1
(1.00) 		0.435
(0.934) 		0.828
(1.00) 		1.79e-06
(0.000635) 		0.548
(0.976) 		0.412
(0.917) 		0.141
(0.722) 		0.0695
(0.563) 		0.0353
(0.456)
17p loss 72 (39%) 112 0.758
(1.00) 		0.107
(0.654) 		0.225
(0.786) 		0.177
(0.745) 		0.456
(0.943) 		1
(1.00) 		0.67
(0.996) 		1
(1.00) 		0.0953
(0.63) 		0.000161
(0.0221) 		0.592
(0.984) 		0.567
(0.984) 		0.0681
(0.563) 		0.108
(0.654) 		0.179
(0.745)
18p loss 69 (38%) 115 0.841
(1.00) 		0.0901
(0.623) 		0.633
(0.996) 		0.0348
(0.456) 		0.64
(0.996) 		0.719
(1.00) 		0.519
(0.962) 		0.0428
(0.479) 		0.891
(1.00) 		0.00363
(0.203) 		0.128
(0.691) 		0.0918
(0.624) 		0.748
(1.00) 		0.0229
(0.417) 		0.662
(0.996)
22q loss 73 (40%) 111 0.0932
(0.63) 		0.243
(0.815) 		0.0446
(0.485) 		0.00935
(0.325) 		0.037
(0.459) 		0.164
(0.742) 		0.834
(1.00) 		0.471
(0.945) 		0.475
(0.945) 		2.37e-05
(0.00584) 		0.953
(1.00) 		0.42
(0.926) 		0.0822
(0.598) 		0.342
(0.887) 		1
(1.00)
1p gain 38 (21%) 146 0.191
(0.755) 		0.255
(0.837) 		0.581
(0.984) 		0.709
(1.00) 		0.941
(1.00) 		0.676
(0.996) 		0.607
(0.99) 		0.827
(1.00) 		0.752
(1.00) 		0.856
(1.00) 		0.996
(1.00) 		0.213
(0.773) 		0.627
(0.996) 		0.12
(0.69) 		0.643
(0.996)
1q gain 64 (35%) 120 0.0709
(0.563) 		0.277
(0.845) 		0.884
(1.00) 		0.676
(0.996) 		0.776
(1.00) 		0.284
(0.851) 		0.0786
(0.592) 		0.457
(0.943) 		0.818
(1.00) 		0.282
(0.851) 		0.534
(0.966) 		0.0426
(0.479) 		0.641
(0.996) 		0.294
(0.861) 		1
(1.00)
2p gain 61 (33%) 123 0.531
(0.966) 		0.143
(0.722) 		0.206
(0.769) 		0.378
(0.906) 		0.94
(1.00) 		0.703
(1.00) 		0.826
(1.00) 		0.263
(0.839) 		0.305
(0.863) 		0.212
(0.772) 		0.271
(0.845) 		0.0464
(0.485) 		0.781
(1.00) 		0.0118
(0.325) 		1
(1.00)
2q gain 47 (26%) 137 0.996
(1.00) 		0.186
(0.746) 		0.441
(0.937) 		0.144
(0.722) 		0.887
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.686
(0.997) 		0.703
(1.00) 		0.867
(1.00) 		0.955
(1.00) 		0.204
(0.769) 		0.829
(1.00) 		0.112
(0.66) 		1
(1.00)
3p gain 31 (17%) 153 0.391
(0.91) 		0.242
(0.815) 		0.171
(0.744) 		0.251
(0.829) 		0.122
(0.69) 		0.126
(0.69) 		0.578
(0.984) 		0.109
(0.658) 		0.929
(1.00) 		0.434
(0.934) 		0.875
(1.00) 		0.151
(0.725) 		0.13
(0.696) 		0.148
(0.722) 		0.243
(0.815)
4p gain 17 (9%) 167 0.209
(0.769) 		0.655
(0.996) 		0.677
(0.996) 		0.746
(1.00) 		0.643
(0.996) 		0.487
(0.954) 		0.475
(0.945) 		1
(1.00) 		0.389
(0.91) 		1
(1.00) 		0.638
(0.996) 		0.0996
(0.634) 		0.0538
(0.493) 		0.0362
(0.457) 		0.501
(0.962)
4q gain 17 (9%) 167 0.295
(0.861) 		0.505
(0.962) 		1
(1.00) 		0.609
(0.99) 		0.917
(1.00) 		1
(1.00) 		0.475
(0.945) 		0.764
(1.00) 		0.672
(0.996) 		0.317
(0.865) 		0.653
(0.996) 		1
(1.00) 		0.0227
(0.417) 		0.136
(0.711) 		1
(1.00)
5p gain 75 (41%) 109 0.344
(0.888) 		0.62
(0.996) 		0.387
(0.91) 		0.181
(0.745) 		0.62
(0.996) 		1
(1.00) 		0.405
(0.917) 		0.859
(1.00) 		0.817
(1.00) 		0.0105
(0.325) 		0.889
(1.00) 		0.154
(0.727) 		0.883
(1.00) 		0.172
(0.744) 		1
(1.00)
5q gain 20 (11%) 164 0.866
(1.00) 		0.366
(0.9) 		0.335
(0.884) 		0.44
(0.937) 		0.0534
(0.493) 		1
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.068
(0.563) 		0.817
(1.00) 		0.817
(1.00) 		0.11
(0.66) 		0.505
(0.962) 		0.533
(0.966) 		1
(1.00)
6p gain 39 (21%) 145 0.522
(0.962) 		0.673
(0.996) 		0.337
(0.884) 		0.923
(1.00) 		0.96
(1.00) 		0.111
(0.66) 		1
(1.00) 		1
(1.00) 		0.22
(0.78) 		0.0706
(0.563) 		0.393
(0.91) 		0.721
(1.00) 		0.958
(1.00) 		1
(1.00) 		0.585
(0.984)
6q gain 33 (18%) 151 0.513
(0.962) 		0.422
(0.926) 		0.0959
(0.63) 		0.609
(0.99) 		0.837
(1.00) 		0.012
(0.325) 		0.79
(1.00) 		1
(1.00) 		0.0849
(0.6) 		0.125
(0.69) 		0.218
(0.779) 		0.072
(0.565) 		0.383
(0.909) 		0.852
(1.00) 		0.587
(0.984)
7p gain 109 (59%) 75 0.723
(1.00) 		0.557
(0.978) 		0.55
(0.976) 		0.0259
(0.425) 		0.193
(0.757) 		0.185
(0.745) 		0.0548
(0.495) 		0.595
(0.984) 		0.797
(1.00) 		0.177
(0.745) 		0.191
(0.755) 		0.74
(1.00) 		0.639
(0.996) 		0.198
(0.768) 		0.401
(0.911)
7q gain 87 (47%) 97 0.817
(1.00) 		0.665
(0.996) 		0.596
(0.984) 		0.0288
(0.438) 		0.411
(0.917) 		0.174
(0.744) 		0.021
(0.417) 		0.723
(1.00) 		0.345
(0.888) 		0.555
(0.978) 		0.695
(1.00) 		0.33
(0.881) 		0.307
(0.863) 		0.466
(0.945) 		0.677
(0.996)
8p gain 67 (36%) 117 0.0364
(0.457) 		0.984
(1.00) 		0.843
(1.00) 		0.259
(0.837) 		0.467
(0.945) 		0.719
(1.00) 		1
(1.00) 		0.854
(1.00) 		0.722
(1.00) 		1
(1.00) 		0.122
(0.69) 		0.289
(0.857) 		0.172
(0.744) 		1
(1.00) 		0.661
(0.996)
8q gain 102 (55%) 82 0.361
(0.898) 		0.949
(1.00) 		0.244
(0.815) 		0.0287
(0.438) 		0.0597
(0.513) 		0.732
(1.00) 		0.682
(0.996) 		0.154
(0.727) 		0.707
(1.00) 		0.657
(0.996) 		0.786
(1.00) 		0.528
(0.964) 		0.0206
(0.417) 		0.385
(0.909) 		0.398
(0.911)
9p gain 17 (9%) 167 0.259
(0.837) 		0.571
(0.984) 		0.667
(0.996) 		0.35
(0.89) 		0.0236
(0.417) 		0.6
(0.984) 		0.475
(0.945) 		0.0253
(0.425) 		0.309
(0.863) 		0.317
(0.865) 		0.117
(0.686) 		0.736
(1.00) 		0.401
(0.911) 		0.125
(0.69) 		1
(1.00)
9q gain 34 (18%) 150 0.491
(0.956) 		0.343
(0.888) 		0.769
(1.00) 		0.242
(0.815) 		0.521
(0.962) 		1
(1.00) 		0.0318
(0.444) 		0.0595
(0.513) 		0.0527
(0.493) 		0.256
(0.837) 		0.0423
(0.479) 		0.314
(0.863) 		0.396
(0.911) 		0.00493
(0.253) 		1
(1.00)
10p gain 40 (22%) 144 0.516
(0.962) 		0.924
(1.00) 		0.0179
(0.416) 		0.0826
(0.598) 		0.129
(0.696) 		0.0808
(0.596) 		0.207
(0.769) 		1
(1.00) 		0.175
(0.744) 		0.0485
(0.485) 		0.274
(0.845) 		0.933
(1.00) 		0.506
(0.962) 		0.274
(0.845) 		0.336
(0.884)
10q gain 31 (17%) 153 0.873
(1.00) 		0.84
(1.00) 		0.0353
(0.456) 		0.0396
(0.473) 		0.329
(0.881) 		0.141
(0.722) 		0.263
(0.839) 		0.35
(0.89) 		0.538
(0.967) 		0.0494
(0.489) 		0.0475
(0.485) 		0.912
(1.00) 		0.312
(0.863) 		0.305
(0.863) 		0.587
(0.984)
11p gain 39 (21%) 145 0.377
(0.906) 		0.533
(0.966) 		0.843
(1.00) 		0.389
(0.91) 		0.217
(0.778) 		0.395
(0.911) 		1
(1.00) 		0.394
(0.911) 		0.76
(1.00) 		0.719
(1.00) 		0.16
(0.742) 		0.0283
(0.438) 		0.264
(0.842) 		0.755
(1.00) 		0.592
(0.984)
11q gain 29 (16%) 155 0.905
(1.00) 		0.0678
(0.563) 		0.605
(0.989) 		0.409
(0.917) 		0.0916
(0.624) 		1
(1.00) 		1
(1.00) 		0.088
(0.612) 		0.581
(0.984) 		0.108
(0.654) 		0.6
(0.984) 		0.0158
(0.406) 		0.602
(0.986) 		0.852
(1.00) 		0.585
(0.984)
12q gain 37 (20%) 147 0.514
(0.962) 		0.332
(0.881) 		0.0176
(0.416) 		0.441
(0.937) 		0.569
(0.984) 		0.0167
(0.411) 		0.299
(0.862) 		0.371
(0.902) 		0.0245
(0.425) 		0.361
(0.898) 		0.0469
(0.485) 		0.56
(0.979) 		0.0124
(0.325) 		0.019
(0.417) 		1
(1.00)
14q gain 49 (27%) 135 0.738
(1.00) 		0.126
(0.69) 		0.983
(1.00) 		0.012
(0.325) 		0.547
(0.976) 		0.445
(0.939) 		0.0167
(0.411) 		0.432
(0.934) 		0.73
(1.00) 		0.00721
(0.286) 		0.75
(1.00) 		0.375
(0.903) 		0.864
(1.00) 		0.0707
(0.563) 		0.66
(0.996)
15q gain 31 (17%) 153 0.595
(0.984) 		0.679
(0.996) 		0.584
(0.984) 		0.457
(0.943) 		0.979
(1.00) 		0.355
(0.897) 		0.578
(0.984) 		1
(1.00) 		0.524
(0.963) 		0.434
(0.934) 		0.0999
(0.634) 		0.429
(0.934) 		0.732
(1.00) 		0.303
(0.863) 		0.218
(0.778)
16p gain 40 (22%) 144 0.711
(1.00) 		0.921
(1.00) 		0.141
(0.722) 		0.275
(0.845) 		0.249
(0.826) 		0.428
(0.934) 		0.0111
(0.325) 		0.521
(0.962) 		0.235
(0.809) 		0.0124
(0.325) 		0.929
(1.00) 		0.541
(0.969) 		0.634
(0.996) 		0.00653
(0.268) 		1
(1.00)
16q gain 38 (21%) 146 0.103
(0.642) 		0.807
(1.00) 		0.0693
(0.563) 		0.338
(0.884) 		0.318
(0.865) 		0.0226
(0.417) 		0.0744
(0.579) 		0.662
(0.996) 		0.786
(1.00) 		0.0106
(0.325) 		0.843
(1.00) 		0.834
(1.00) 		0.359
(0.897) 		0.0419
(0.479) 		1
(1.00)
17p gain 32 (17%) 152 0.778
(1.00) 		0.456
(0.943) 		0.792
(1.00) 		0.82
(1.00) 		0.311
(0.863) 		1
(1.00) 		0.424
(0.929) 		0.0973
(0.63) 		0.957
(1.00) 		0.244
(0.815) 		0.923
(1.00) 		0.133
(0.71) 		0.439
(0.937) 		0.858
(1.00) 		0.585
(0.984)
17q gain 44 (24%) 140 0.559
(0.978) 		0.526
(0.964) 		0.781
(1.00) 		0.987
(1.00) 		0.474
(0.945) 		1
(1.00) 		0.329
(0.881) 		0.00534
(0.263) 		0.661
(0.996) 		1
(1.00) 		0.339
(0.884) 		0.223
(0.786) 		0.539
(0.968) 		0.693
(1.00) 		0.33
(0.881)
18p gain 50 (27%) 134 0.413
(0.917) 		0.505
(0.962) 		0.549
(0.976) 		0.639
(0.996) 		0.876
(1.00) 		0.253
(0.833) 		0.16
(0.742) 		0.163
(0.742) 		0.76
(1.00) 		0.407
(0.917) 		0.87
(1.00) 		0.453
(0.943) 		0.272
(0.845) 		0.187
(0.746) 		0.632
(0.996)
18q gain 24 (13%) 160 0.689
(1) 		0.855
(1.00) 		0.233
(0.806) 		0.698
(1.00) 		0.774
(1.00) 		1
(1.00) 		0.538
(0.967) 		0.445
(0.939) 		0.349
(0.89) 		1
(1.00) 		0.612
(0.992) 		0.91
(1.00) 		0.962
(1.00) 		1
(1.00) 		1
(1.00)
19p gain 28 (15%) 156 0.399
(0.911) 		0.353
(0.894) 		0.754
(1.00) 		0.809
(1.00) 		0.0796
(0.593) 		1
(1.00) 		0.0844
(0.6) 		0.636
(0.996) 		0.722
(1.00) 		1
(1.00) 		0.514
(0.962) 		0.91
(1.00) 		0.364
(0.9) 		0.126
(0.69) 		1
(1.00)
19q gain 40 (22%) 144 0.839
(1.00) 		0.269
(0.845) 		0.431
(0.934) 		1
(1.00) 		0.454
(0.943) 		0.665
(0.996) 		0.0111
(0.325) 		0.14
(0.722) 		0.931
(1.00) 		0.211
(0.769) 		0.934
(1.00) 		0.489
(0.954) 		0.37
(0.902) 		0.382
(0.909) 		1
(1.00)
20p gain 107 (58%) 77 0.0463
(0.485) 		0.432
(0.934) 		0.515
(0.962) 		0.595
(0.984) 		0.411
(0.917) 		0.299
(0.862) 		0.141
(0.722) 		0.476
(0.945) 		0.079
(0.592) 		0.1
(0.634) 		0.614
(0.994) 		0.934
(1.00) 		0.106
(0.65) 		0.313
(0.863) 		0.693
(1.00)
21q gain 16 (9%) 168 0.34
(0.884) 		0.916
(1.00) 		0.858
(1.00) 		0.767
(1.00) 		0.595
(0.984) 		1
(1.00) 		1
(1.00) 		0.198
(0.768) 		0.392
(0.91) 		0.197
(0.768) 		0.772
(1.00) 		0.793
(1.00) 		0.837
(1.00) 		0.163
(0.742) 		1
(1.00)
xp gain 25 (14%) 159 0.654
(0.996) 		0.884
(1.00) 		0.498
(0.961) 		0.954
(1.00) 		0.0231
(0.417) 		0.598
(0.984) 		0.541
(0.969) 		0.311
(0.863) 		0.973
(1.00) 		0.519
(0.962) 		0.553
(0.978) 		0.292
(0.86) 		0.715
(1.00) 		0.165
(0.743) 		0.587
(0.984)
xq gain 41 (22%) 143 0.725
(1.00) 		0.215
(0.776) 		0.362
(0.899) 		0.622
(0.996) 		0.183
(0.745) 		0.684
(0.996) 		0.209
(0.769) 		0.531
(0.966) 		0.686
(0.997) 		0.0216
(0.417) 		0.636
(0.996) 		0.173
(0.744) 		0.227
(0.788) 		0.0308
(0.441) 		1
(1.00)
1p loss 38 (21%) 146 0.836
(1.00) 		1
(1.00) 		0.515
(0.962) 		1
(1.00) 		0.407
(0.917) 		0.207
(0.769) 		1
(1.00) 		0.658
(0.996) 		0.312
(0.863) 		0.0173
(0.416) 		0.791
(1.00) 		0.0277
(0.438) 		0.774
(1.00) 		0.386
(0.91) 		1
(1.00)
1q loss 22 (12%) 162 0.0324
(0.448) 		0.15
(0.722) 		0.177
(0.745) 		0.557
(0.978) 		0.248
(0.824) 		0.142
(0.722) 		1
(1.00) 		0.784
(1.00) 		0.321
(0.871) 		0.0669
(0.563) 		0.359
(0.897) 		0.0124
(0.325) 		0.189
(0.751) 		0.324
(0.874) 		1
(1.00)
2p loss 10 (5%) 174 0.0707
(0.563) 		0.327
(0.88) 		0.436
(0.934) 		0.475
(0.945) 		1
(1.00) 		1
(1.00) 		0.643
(0.996) 		0.24
(0.815) 		0.729
(1.00) 		0.103
(0.642) 		0.629
(0.996) 		0.734
(1.00) 		0.181
(0.745) 		0.799
(1.00) 		1
(1.00)
2q loss 18 (10%) 166 0.527
(0.964) 		0.339
(0.884) 		0.857
(1.00) 		0.452
(0.943) 		0.694
(1.00) 		0.599
(0.984) 		0.732
(1.00) 		0.384
(0.909) 		0.294
(0.861) 		0.0258
(0.425) 		0.453
(0.943) 		0.752
(1.00) 		0.284
(0.851) 		1
(1.00) 		1
(1.00)
3q loss 33 (18%) 151 0.803
(1.00) 		0.809
(1.00) 		0.192
(0.757) 		0.766
(1.00) 		0.78
(1.00) 		1
(1.00) 		0.421
(0.926) 		0.496
(0.961) 		0.364
(0.9) 		0.566
(0.984) 		0.665
(0.996) 		0.505
(0.962) 		0.95
(1.00) 		0.289
(0.857) 		1
(1.00)
4p loss 105 (57%) 79 0.0849
(0.6) 		0.149
(0.722) 		0.591
(0.984) 		0.127
(0.69) 		0.366
(0.9) 		1
(1.00) 		0.4
(0.911) 		0.475
(0.945) 		0.947
(1.00) 		0.373
(0.903) 		0.221
(0.78) 		0.227
(0.788) 		0.04
(0.473) 		0.0196
(0.417) 		0.677
(0.996)
4q loss 88 (48%) 96 0.0568
(0.506) 		0.181
(0.745) 		0.148
(0.722) 		0.31
(0.863) 		0.704
(1.00) 		0.312
(0.863) 		0.144
(0.722) 		0.375
(0.903) 		0.558
(0.978) 		0.184
(0.745) 		0.565
(0.984) 		0.446
(0.939) 		0.0086
(0.325) 		0.146
(0.722) 		1
(1.00)
5q loss 87 (47%) 97 0.433
(0.934) 		0.923
(1.00) 		0.174
(0.744) 		0.47
(0.945) 		0.217
(0.778) 		0.735
(1.00) 		0.534
(0.966) 		0.859
(1.00) 		0.303
(0.863) 		0.076
(0.588) 		0.901
(1.00) 		0.745
(1.00) 		0.283
(0.851) 		1
(1.00) 		1
(1.00)
6p loss 38 (21%) 146 0.372
(0.902) 		0.668
(0.996) 		0.706
(1.00) 		0.64
(0.996) 		0.0453
(0.485) 		0.209
(0.769) 		1
(1.00) 		0.657
(0.996) 		0.891
(1.00) 		0.278
(0.845) 		0.178
(0.745) 		0.76
(1.00) 		0.272
(0.845) 		0.18
(0.745) 		0.622
(0.996)
6q loss 40 (22%) 144 0.581
(0.984) 		0.868
(1.00) 		0.716
(1.00) 		0.317
(0.865) 		0.487
(0.954) 		1
(1.00) 		0.207
(0.769) 		1
(1.00) 		0.838
(1.00) 		0.723
(1.00) 		0.162
(0.742) 		0.625
(0.996) 		0.241
(0.815) 		0.276
(0.845) 		0.622
(0.996)
7p loss 13 (7%) 171 0.591
(0.984) 		0.808
(1.00) 		0.967
(1.00) 		0.446
(0.939) 		0.666
(0.996) 		1
(1.00) 		0.411
(0.917) 		1
(1.00) 		0.644
(0.996) 		0.572
(0.984) 		0.0236
(0.417) 		0.555
(0.978) 		0.151
(0.725) 		0.827
(1.00) 		1
(1.00)
8p loss 62 (34%) 122 0.806
(1.00) 		0.971
(1.00) 		0.517
(0.962) 		0.633
(0.996) 		0.201
(0.769) 		0.486
(0.954) 		1
(1.00) 		0.454
(0.943) 		0.77
(1.00) 		0.438
(0.937) 		0.128
(0.691) 		0.577
(0.984) 		0.492
(0.958) 		0.643
(0.996) 		0.664
(0.996)
8q loss 21 (11%) 163 0.174
(0.744) 		0.944
(1.00) 		0.298
(0.862) 		0.782
(1.00) 		0.644
(0.996) 		1
(1.00) 		1
(1.00) 		0.027
(0.436) 		0.844
(1.00) 		0.817
(1.00) 		0.858
(1.00) 		0.677
(0.996) 		0.807
(1.00) 		0.136
(0.711) 		0.423
(0.926)
9p loss 100 (54%) 84 0.624
(0.996) 		0.401
(0.911) 		0.277
(0.845) 		0.51
(0.962) 		0.148
(0.722) 		1
(1.00) 		0.0608
(0.519) 		0.214
(0.773) 		0.375
(0.903) 		0.555
(0.978) 		0.923
(1.00) 		0.0881
(0.612) 		0.261
(0.837) 		0.0579
(0.509) 		0.398
(0.911)
9q loss 65 (35%) 119 0.535
(0.966) 		0.417
(0.925) 		0.0415
(0.479) 		0.537
(0.967) 		0.9
(1.00) 		0.276
(0.845) 		0.383
(0.909) 		0.855
(1.00) 		0.301
(0.862) 		0.358
(0.897) 		0.164
(0.742) 		0.844
(1.00) 		0.932
(1.00) 		0.259
(0.837) 		0.396
(0.911)
11p loss 52 (28%) 132 0.665
(0.996) 		0.581
(0.984) 		0.135
(0.711) 		0.73
(1.00) 		0.126
(0.69) 		0.448
(0.939) 		0.257
(0.837) 		0.0501
(0.489) 		0.169
(0.744) 		1
(1.00) 		0.893
(1.00) 		0.839
(1.00) 		0.823
(1.00) 		0.135
(0.711) 		0.368
(0.902)
11q loss 60 (33%) 124 0.526
(0.964) 		0.267
(0.845) 		0.174
(0.744) 		0.704
(1.00) 		0.0398
(0.473) 		1
(1.00) 		0.826
(1.00) 		0.0386
(0.47) 		0.661
(0.996) 		0.0184
(0.417) 		0.476
(0.945) 		0.517
(0.962) 		0.766
(1.00) 		0.0531
(0.493) 		0.184
(0.745)
14q loss 45 (24%) 139 0.682
(0.996) 		0.158
(0.738) 		0.204
(0.769) 		0.318
(0.865) 		0.303
(0.863) 		0.428
(0.934) 		0.812
(1.00) 		0.413
(0.917) 		0.477
(0.945) 		0.00566
(0.267) 		0.41
(0.917) 		0.697
(1.00) 		0.94
(1.00) 		0.173
(0.744) 		1
(1.00)
15q loss 56 (30%) 128 0.333
(0.882) 		0.371
(0.902) 		0.939
(1.00) 		0.293
(0.861) 		0.716
(1.00) 		0.152
(0.725) 		0.657
(0.996) 		0.703
(1.00) 		0.955
(1.00) 		0.0249
(0.425) 		0.757
(1.00) 		0.163
(0.742) 		0.858
(1.00) 		0.847
(1.00) 		0.67
(0.996)
17q loss 26 (14%) 158 0.123
(0.69) 		0.828
(1.00) 		0.632
(0.996) 		0.612
(0.992) 		0.348
(0.89) 		1
(1.00) 		0.772
(1.00) 		0.799
(1.00) 		0.105
(0.65) 		0.835
(1.00) 		0.721
(1.00) 		0.799
(1.00) 		0.462
(0.945) 		0.706
(1.00) 		0.0595
(0.513)
18q loss 103 (56%) 81 0.621
(0.996) 		0.205
(0.769) 		0.599
(0.984) 		0.434
(0.934) 		0.388
(0.91) 		0.513
(0.962) 		0.834
(1.00) 		0.86
(1.00) 		0.505
(0.962) 		0.0115
(0.325) 		0.319
(0.867) 		0.26
(0.837) 		0.51
(0.962) 		0.749
(1.00) 		0.681
(0.996)
19p loss 64 (35%) 120 0.775
(1.00) 		0.143
(0.722) 		0.515
(0.962) 		0.282
(0.851) 		0.0874
(0.612) 		0.728
(1.00) 		0.383
(0.909) 		1
(1.00) 		0.518
(0.962) 		0.757
(1.00) 		0.0221
(0.417) 		0.617
(0.996) 		0.17
(0.744) 		0.27
(0.845) 		1
(1.00)
19q loss 52 (28%) 132 0.476
(0.945) 		0.0919
(0.624) 		0.887
(1.00) 		0.335
(0.884) 		0.297
(0.862) 		1
(1.00) 		0.644
(0.996) 		0.55
(0.976) 		0.74
(1.00) 		0.252
(0.83) 		0.0789
(0.592) 		0.279
(0.846) 		0.988
(1.00) 		0.047
(0.485) 		0.667
(0.996)
20p loss 19 (10%) 165 0.0317
(0.444) 		0.884
(1.00) 		0.896
(1.00) 		0.883
(1.00) 		0.969
(1.00) 		0.598
(0.984) 		0.744
(1.00) 		1
(1.00) 		0.392
(0.91) 		0.809
(1.00) 		0.704
(1.00) 		0.502
(0.962) 		0.339
(0.884) 		0.22
(0.78) 		0.423
(0.926)
20q loss 6 (3%) 178 0.632
(0.996) 		0.734
(1.00) 		0.722
(1.00) 		0.153
(0.725) 		0.567
(0.984) 		1
(1.00) 		1
(1.00) 		0.65
(0.996) 		0.684
(0.996) 		0.353
(0.894) 		0.366
(0.9) 		0.265
(0.844) 		1
(1.00)
21q loss 108 (59%) 76 0.226
(0.787) 		0.295
(0.861) 		0.679
(0.996) 		0.709
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.677
(0.996) 		0.858
(1.00) 		0.117
(0.686) 		0.0721
(0.565) 		0.149
(0.722) 		0.0288
(0.438) 		0.883
(1.00) 		0.308
(0.863) 		0.209
(0.769)
xp loss 60 (33%) 124 0.787
(1.00) 		0.583
(0.984) 		0.385
(0.909) 		0.559
(0.978) 		0.122
(0.69) 		0.167
(0.744) 		0.044
(0.485) 		0.704
(1.00) 		0.917
(1.00) 		1
(1.00) 		0.00634
(0.268) 		0.93
(1.00) 		0.94
(1.00) 		0.122
(0.69) 		0.664
(0.996)
xq loss 39 (21%) 145 0.888
(1.00) 		0.566
(0.984) 		0.753
(1.00) 		0.905
(1.00) 		0.665
(0.996) 		0.209
(0.769) 		0.208
(0.769) 		1
(1.00) 		0.511
(0.962) 		0.0297
(0.441) 		0.0197
(0.417) 		0.821
(1.00) 		0.872
(1.00) 		0.478
(0.945) 		0.597
(0.984)
'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00307 (Wilcoxon-test), Q value = 0.18

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'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00134 (Fisher's exact test), Q value = 0.11

Table S2.  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 40
12P GAIN WILD-TYPE 71 56

Figure S2.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1.63e-06 (Fisher's exact test), Q value = 0.00064

Table S3.  Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA, NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
13Q GAIN MUTATED 35 9
13Q GAIN WILD-TYPE 53 87

Figure S3.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.000769 (Fisher's exact test), Q value = 0.074

Table S4.  Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA, NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
20Q GAIN MUTATED 66 48
20Q GAIN WILD-TYPE 22 48

Figure S4.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 2.07e-06 (Fisher's exact test), Q value = 0.00064

Table S5.  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 S5.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'22q gain' versus 'RACE'

P value = 0.00195 (Fisher's exact test), Q value = 0.15

Table S6.  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 S6.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #14: 'RACE'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 8.52e-07 (Fisher's exact test), Q value = 0.00064

Table S7.  Gene #46: '3p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA, NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
3P LOSS MUTATED 27 65
3P LOSS WILD-TYPE 61 31

Figure S7.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'RACE'

P value = 0.00078 (Fisher's exact test), Q value = 0.074

Table S8.  Gene #46: '3p loss' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
3P LOSS MUTATED 34 2 49
3P LOSS WILD-TYPE 12 3 65

Figure S8.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #14: 'RACE'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00292 (Fisher's exact test), Q value = 0.18

Table S9.  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 S9.  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 = 0.012

Table S10.  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 S10.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'7q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00455 (Fisher's exact test), Q value = 0.24

Table S11.  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 16 2
7Q LOSS WILD-TYPE 32 40 71 3

Figure S11.  Get High-res Image Gene #55: '7q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00281 (Fisher's exact test), Q value = 0.18

Table S12.  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 36
10P LOSS WILD-TYPE 73 60

Figure S12.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RACE'

P value = 0.00055 (Fisher's exact test), Q value = 0.061

Table S13.  Gene #60: '10p loss' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
10P LOSS MUTATED 19 4 22
10P LOSS WILD-TYPE 27 1 92

Figure S13.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #14: 'RACE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.000429 (Fisher's exact test), Q value = 0.053

Table S14.  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 37
10Q LOSS WILD-TYPE 75 59

Figure S14.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RACE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0061

Table S15.  Gene #61: '10q loss' versus Clinical Feature #14: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 46 5 114
10Q LOSS MUTATED 21 4 20
10Q LOSS WILD-TYPE 25 1 94

Figure S15.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #14: 'RACE'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00109 (Fisher's exact test), Q value = 0.096

Table S16.  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 9
12P LOSS WILD-TYPE 63 87

Figure S16.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'RACE'

P value = 0.00203 (Fisher's exact test), Q value = 0.15

Table S17.  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 23
12Q LOSS WILD-TYPE 44 2 91

Figure S17.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #14: 'RACE'

'13q loss' versus 'RACE'

P value = 0.00288 (Fisher's exact test), Q value = 0.18

Table S18.  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 S18.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #14: 'RACE'

'16p loss' versus 'HISTOLOGICAL_TYPE'

P value = 9.24e-05 (Fisher's exact test), Q value = 0.014

Table S19.  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 S19.  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 = 0.00064

Table S20.  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 S20.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.000161 (Fisher's exact test), Q value = 0.022

Table S21.  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 25
17P LOSS WILD-TYPE 41 71

Figure S21.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00363 (Fisher's exact test), Q value = 0.2

Table S22.  Gene #73: '18p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA, NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
18P LOSS MUTATED 43 26
18P LOSS WILD-TYPE 45 70

Figure S22.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 2.37e-05 (Fisher's exact test), Q value = 0.0058

Table S23.  Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients ESOPHAGUS ADENOCARCINOMA, NOS ESOPHAGUS SQUAMOUS CELL CARCINOMA
ALL 88 96
22Q LOSS MUTATED 49 24
22Q LOSS WILD-TYPE 39 72

Figure S23.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

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/22519067/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/22506419/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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