Correlation between copy number variation genes (focal events) and selected clinical features
Stomach and Esophageal carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1000165
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1000165
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 99 focal events and 14 clinical features across 609 patients, 79 significant findings detected with Q value < 0.25.

  • amp_1p36.22 cnv correlated to 'GENDER'.

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

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

  • amp_5p15.33 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_5p13.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_6p21.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_6q12 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_7p22.3 cnv correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.

  • amp_7p11.2 cnv correlated to 'GENDER'.

  • amp_7q21.2 cnv correlated to 'GENDER'.

  • amp_8p23.1 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.

  • amp_9p13.3 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_12p12.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • amp_13q22.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_14q13.3 cnv correlated to 'GENDER'.

  • amp_17q12 cnv correlated to 'PATHOLOGY_M_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE',  'COMPLETENESS_OF_RESECTION', and 'RACE'.

  • amp_20q13.2 cnv correlated to 'PATHOLOGY_N_STAGE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • del_1p36.11 cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • del_4p15.2 cnv correlated to 'Time to Death'.

  • del_4q22.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

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

  • del_5q12.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_6q26 cnv correlated to 'PATHOLOGY_T_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • del_7q31.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'GENDER'.

  • del_7q36.3 cnv correlated to 'NEOPLASM_DISEASESTAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • del_8p23.2 cnv correlated to 'GENDER' and 'NUMBER_OF_LYMPH_NODES'.

  • del_9p21.3 cnv correlated to 'PATHOLOGY_T_STAGE',  'GENDER', and 'HISTOLOGICAL_TYPE'.

  • del_10p15.3 cnv correlated to 'Time to Death' and 'NUMBER_OF_LYMPH_NODES'.

  • del_10p11.21 cnv correlated to 'PATHOLOGY_T_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • del_10q21.1 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • del_10q22.3 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • del_10q23.31 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_11p15.5 cnv correlated to 'GENDER'.

  • del_11q25 cnv correlated to 'GENDER'.

  • del_12p13.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_12q23.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_13q12.11 cnv correlated to 'GENDER'.

  • del_13q14.2 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'GENDER', and 'RACE'.

  • del_14q32.32 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • del_16p13.3 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_17p12 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_17q24.3 cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • del_18q12.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_18q21.2 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_19p13.3 cnv correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.

  • del_19q13.11 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_22q11.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_22q13.31 cnv correlated to 'NEOPLASM_DISEASESTAGE'.

  • del_xp22.2 cnv correlated to 'GENDER'.

  • del_xp21.1 cnv correlated to 'GENDER'.

  • del_xp11.3 cnv correlated to 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 99 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 79 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
PACK
YEARS
SMOKED 		COMPLETENESS
OF
RESECTION 		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 Fisher's exact test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
amp 17q12 216 (35%) 393 0.219
(0.667) 		0.452
(0.809) 		0.0524
(0.393) 		0.59
(0.906) 		0.724
(0.941) 		0.00826
(0.188) 		0.00412
(0.156) 		2e-05
(0.00924) 		1
(1.00) 		0.123
(0.524) 		0.00015
(0.0224) 		0.438
(0.808) 		0.00226
(0.115) 		0.437
(0.808)
del 13q14 2 119 (20%) 490 0.549
(0.87) 		0.00547
(0.165) 		9e-05
(0.0156) 		0.00439
(0.156) 		0.0167
(0.26) 		0.204
(0.647) 		0.00246
(0.115) 		0.571
(0.892) 		0.0923
(0.48) 		0.362
(0.774) 		0.146
(0.572) 		0.286
(0.732) 		0.00546
(0.165) 		1
(1.00)
amp 20q13 2 407 (67%) 202 0.126
(0.53) 		0.0618
(0.418) 		0.492
(0.828) 		0.205
(0.647) 		0.0129
(0.232) 		0.862
(1.00) 		0.00256
(0.115) 		6e-05
(0.0121) 		1
(1.00) 		0.457
(0.813) 		0.44
(0.808) 		0.447
(0.809) 		0.834
(0.991) 		0.429
(0.808)
del 4q34 3 292 (48%) 317 0.0775
(0.449) 		0.00977
(0.199) 		0.00428
(0.156) 		0.238
(0.688) 		0.412
(0.803) 		0.319
(0.751) 		0.723
(0.94) 		0.00498
(0.165) 		0.434
(0.808) 		0.984
(1.00) 		0.118
(0.515) 		0.238
(0.688) 		0.835
(0.991) 		1
(1.00)
del 7q31 1 125 (21%) 484 0.235
(0.686) 		0.0834
(0.46) 		0.00139
(0.0869) 		0.00623
(0.173) 		0.0214
(0.288) 		0.303
(0.739) 		0.00144
(0.0869) 		0.298
(0.737) 		1
(1.00) 		0.216
(0.665) 		0.427
(0.808) 		0.307
(0.742) 		0.294
(0.734) 		1
(1.00)
del 9p21 3 320 (53%) 289 0.51
(0.834) 		0.998
(1.00) 		0.0161
(0.26) 		0.00435
(0.156) 		0.142
(0.562) 		1
(1.00) 		0.00604
(0.171) 		0.00783
(0.185) 		1
(1.00) 		0.181
(0.612) 		0.267
(0.722) 		0.311
(0.746) 		0.276
(0.726) 		0.722
(0.94)
amp 1q42 3 234 (38%) 375 0.292
(0.732) 		0.00909
(0.195) 		0.469
(0.815) 		0.0426
(0.37) 		0.978
(1.00) 		0.732
(0.944) 		0.0228
(0.295) 		0.0029
(0.122) 		0.68
(0.935) 		0.699
(0.935) 		0.741
(0.947) 		0.431
(0.808) 		0.115
(0.515) 		0.258
(0.71)
amp 3q26 2 276 (45%) 333 0.576
(0.893) 		0.0426
(0.37) 		0.00773
(0.185) 		0.992
(1.00) 		0.698
(0.935) 		0.74
(0.947) 		0.0503
(0.393) 		0.623
(0.913) 		0.694
(0.935) 		0.179
(0.611) 		0.942
(1.00) 		0.118
(0.515) 		0.00539
(0.165) 		0.466
(0.814)
amp 7p22 3 344 (56%) 265 0.507
(0.831) 		0.265
(0.721) 		0.154
(0.582) 		0.0659
(0.425) 		0.845
(0.993) 		1
(1.00) 		0.000487
(0.0422) 		0.00913
(0.195) 		1
(1.00) 		0.27
(0.725) 		0.89
(1.00) 		0.0889
(0.475) 		0.766
(0.965) 		0.126
(0.53)
amp 8p23 1 225 (37%) 384 0.385
(0.787) 		0.00786
(0.185) 		0.533
(0.856) 		0.385
(0.787) 		0.806
(0.983) 		1
(1.00) 		0.000346
(0.0368) 		0.771
(0.965) 		0.2
(0.647) 		0.389
(0.788) 		0.34
(0.763) 		0.5
(0.831) 		0.609
(0.913) 		0.26
(0.711)
del 3p14 2 269 (44%) 340 0.0867
(0.469) 		0.443
(0.808) 		0.0684
(0.431) 		0.102
(0.507) 		0.0611
(0.418) 		0.241
(0.69) 		0.476
(0.818) 		0.0324
(0.343) 		0.699
(0.935) 		0.81
(0.984) 		0.0126
(0.229) 		0.827
(0.99) 		0.0102
(0.202) 		1
(1.00)
del 6q26 149 (24%) 460 0.526
(0.849) 		0.583
(0.899) 		0.202
(0.647) 		0.0105
(0.204) 		0.881
(1.00) 		1
(1.00) 		0.0811
(0.455) 		0.0378
(0.37) 		0.638
(0.92) 		0.22
(0.667) 		0.376
(0.781) 		0.00973
(0.199) 		0.431
(0.808) 		0.662
(0.935)
del 7q36 3 162 (27%) 447 0.369
(0.78) 		0.291
(0.732) 		0.00256
(0.115) 		0.0892
(0.475) 		0.163
(0.59) 		0.572
(0.892) 		0.229
(0.679) 		0.514
(0.839) 		0.195
(0.645) 		0.864
(1.00) 		0.118
(0.515) 		0.0125
(0.229) 		0.745
(0.948) 		0.678
(0.935)
del 8p23 2 200 (33%) 409 0.545
(0.868) 		0.28
(0.729) 		0.161
(0.587) 		0.0401
(0.37) 		0.217
(0.665) 		0.295
(0.734) 		0.000162
(0.0224) 		0.028
(0.327) 		1
(1.00) 		0.066
(0.425) 		0.149
(0.572) 		0.00127
(0.0838) 		0.165
(0.596) 		1
(1.00)
del 10p15 3 125 (21%) 484 0.00937
(0.197) 		0.612
(0.913) 		0.288
(0.732) 		0.308
(0.742) 		0.21
(0.654) 		0.838
(0.991) 		0.0792
(0.449) 		0.0471
(0.384) 		1
(1.00) 		0.745
(0.948) 		0.811
(0.984) 		0.00539
(0.165) 		0.312
(0.746) 		1
(1.00)
del 10p11 21 95 (16%) 514 0.0928
(0.48) 		0.916
(1.00) 		0.0808
(0.455) 		0.00571
(0.165) 		0.829
(0.99) 		1
(1.00) 		0.465
(0.814) 		0.13
(0.535) 		0.237
(0.688) 		0.158
(0.584) 		0.736
(0.946) 		0.00821
(0.188) 		0.0166
(0.26) 		0.601
(0.908)
del 19p13 3 242 (40%) 367 0.0521
(0.393) 		0.978
(1.00) 		0.807
(0.983) 		0.0428
(0.37) 		0.581
(0.899) 		1
(1.00) 		0.00206
(0.115) 		0.00288
(0.122) 		0.039
(0.37) 		0.436
(0.808) 		0.292
(0.732) 		0.173
(0.604) 		0.0196
(0.272) 		1
(1.00)
amp 1p36 22 98 (16%) 511 0.914
(1.00) 		0.891
(1.00) 		0.339
(0.763) 		0.0717
(0.434) 		0.973
(1.00) 		0.819
(0.985) 		0.00109
(0.0755) 		0.883
(1.00) 		0.596
(0.906) 		0.174
(0.604) 		1
(1.00) 		0.11
(0.508) 		0.208
(0.651) 		0.303
(0.739)
amp 5p15 33 217 (36%) 392 0.69
(0.935) 		0.998
(1.00) 		0.288
(0.732) 		3e-05
(0.0104) 		0.902
(1.00) 		1
(1.00) 		0.0521
(0.393) 		0.0188
(0.263) 		1
(1.00) 		0.612
(0.913) 		0.636
(0.92) 		0.0478
(0.387) 		0.0665
(0.426) 		0.432
(0.808)
amp 5p13 1 205 (34%) 404 0.899
(1.00) 		0.517
(0.841) 		0.553
(0.875) 		0.0131
(0.232) 		0.478
(0.818) 		0.48
(0.818) 		0.35
(0.772) 		0.2
(0.647) 		1
(1.00) 		0.922
(1.00) 		0.461
(0.814) 		0.191
(0.634) 		0.709
(0.938) 		0.443
(0.808)
amp 6p21 1 185 (30%) 424 0.452
(0.809) 		0.0187
(0.263) 		0.104
(0.507) 		0.0599
(0.413) 		0.187
(0.623) 		0.468
(0.814) 		0.124
(0.524) 		1e-05
(0.00693) 		0.375
(0.78) 		0.841
(0.992) 		0.528
(0.85) 		0.715
(0.938) 		0.129
(0.535) 		0.679
(0.935)
amp 6q12 137 (22%) 472 0.052
(0.393) 		0.647
(0.927) 		0.0653
(0.425) 		0.463
(0.814) 		0.328
(0.762) 		0.32
(0.751) 		0.458
(0.814) 		0.00047
(0.0422) 		0.621
(0.913) 		0.8
(0.982) 		0.33
(0.762) 		0.568
(0.891) 		0.362
(0.774) 		0.353
(0.772)
amp 7p11 2 330 (54%) 279 0.247
(0.7) 		0.0593
(0.411) 		0.235
(0.686) 		0.0173
(0.26) 		0.951
(1.00) 		0.184
(0.618) 		0.0034
(0.135) 		0.02
(0.275) 		0.42
(0.808) 		0.722
(0.94) 		0.857
(1) 		0.179
(0.611) 		0.0986
(0.501) 		1
(1.00)
amp 7q21 2 309 (51%) 300 0.773
(0.967) 		0.996
(1.00) 		0.942
(1.00) 		0.0789
(0.449) 		0.37
(0.78) 		0.741
(0.947) 		0.00257
(0.115) 		0.0638
(0.423) 		0.444
(0.808) 		0.497
(0.831) 		0.29
(0.732) 		0.0948
(0.485) 		0.0484
(0.388) 		0.267
(0.722)
amp 9p13 3 124 (20%) 485 0.452
(0.809) 		0.612
(0.913) 		0.163
(0.59) 		0.575
(0.893) 		0.619
(0.913) 		0.838
(0.991) 		0.913
(1.00) 		0.00318
(0.13) 		0.102
(0.507) 		0.17
(0.601) 		0.59
(0.906) 		0.957
(1.00) 		0.912
(1.00) 		0.618
(0.913)
amp 12p12 1 201 (33%) 408 0.104
(0.507) 		0.264
(0.721) 		0.0322
(0.343) 		0.00078
(0.0616) 		0.818
(0.985) 		0.599
(0.908) 		0.0387
(0.37) 		0.241
(0.69) 		1
(1.00) 		0.33
(0.762) 		0.488
(0.823) 		0.467
(0.814) 		0.116
(0.515) 		0.7
(0.935)
amp 13q22 1 238 (39%) 371 0.249
(0.703) 		0.688
(0.935) 		0.688
(0.935) 		0.766
(0.965) 		0.166
(0.597) 		1
(1.00) 		0.0701
(0.432) 		0.00721
(0.185) 		0.412
(0.803) 		0.186
(0.623) 		0.52
(0.843) 		0.359
(0.772) 		0.358
(0.772) 		0.435
(0.808)
amp 14q13 3 106 (17%) 503 0.113
(0.514) 		0.251
(0.704) 		0.175
(0.609) 		0.445
(0.808) 		0.838
(0.991) 		0.828
(0.99) 		0.0139
(0.245) 		0.256
(0.71) 		1
(1.00) 		0.81
(0.984) 		0.907
(1.00) 		0.0382
(0.37) 		0.479
(0.818) 		1
(1.00)
del 1p36 11 203 (33%) 406 0.202
(0.647) 		0.777
(0.969) 		0.269
(0.724) 		0.299
(0.739) 		0.499
(0.831) 		1
(1.00) 		0.223
(0.674) 		0.00239
(0.115) 		0.406
(0.803) 		0.807
(0.983) 		0.108
(0.507) 		0.381
(0.787) 		0.523
(0.846) 		0.198
(0.647)
del 4p15 2 260 (43%) 349 0.00908
(0.195) 		0.488
(0.823) 		0.271
(0.725) 		0.105
(0.507) 		0.704
(0.938) 		0.313
(0.746) 		0.0397
(0.37) 		0.302
(0.739) 		1
(1.00) 		0.218
(0.666) 		0.975
(1.00) 		0.173
(0.604) 		0.329
(0.762) 		1
(1.00)
del 4q22 1 290 (48%) 319 0.0673
(0.428) 		0.166
(0.597) 		0.0327
(0.343) 		0.00656
(0.178) 		0.236
(0.686) 		1
(1.00) 		0.0926
(0.48) 		0.16
(0.587) 		0.431
(0.808) 		0.466
(0.814) 		0.368
(0.779) 		0.0257
(0.314) 		0.375
(0.78) 		1
(1.00)
del 5q12 1 271 (44%) 338 0.498
(0.831) 		0.549
(0.87) 		0.0313
(0.343) 		0.0636
(0.423) 		0.339
(0.763) 		0.867
(1.00) 		0.0905
(0.48) 		5e-05
(0.0121) 		1
(1.00) 		0.946
(1.00) 		0.171
(0.603) 		0.0735
(0.44) 		0.48
(0.818) 		1
(1.00)
del 10q21 1 106 (17%) 503 0.978
(1.00) 		0.268
(0.724) 		0.554
(0.875) 		0.257
(0.71) 		0.893
(1.00) 		0.376
(0.781) 		0.908
(1.00) 		0.13
(0.535) 		0.281
(0.729) 		0.751
(0.95) 		1
(1.00) 		0.0125
(0.229) 		0.0453
(0.377) 		1
(1.00)
del 10q22 3 128 (21%) 481 0.156
(0.582) 		0.0444
(0.375) 		0.564
(0.886) 		0.0305
(0.341) 		0.923
(1.00) 		0.839
(0.991) 		0.278
(0.729) 		0.0293
(0.336) 		1
(1.00) 		0.179
(0.611) 		0.881
(1.00) 		0.00725
(0.185) 		0.0149
(0.255) 		1
(1.00)
del 10q23 31 175 (29%) 434 0.0816
(0.455) 		0.023
(0.295) 		0.975
(1.00) 		0.0178
(0.262) 		0.941
(1.00) 		0.717
(0.938) 		0.696
(0.935) 		0.00221
(0.115) 		0.679
(0.935) 		0.646
(0.927) 		0.904
(1.00) 		0.0612
(0.418) 		0.0644
(0.425) 		0.68
(0.935)
del 11p15 5 170 (28%) 439 0.682
(0.935) 		0.202
(0.647) 		0.109
(0.507) 		0.0187
(0.263) 		0.639
(0.92) 		0.852
(0.998) 		0.00757
(0.185) 		0.0221
(0.294) 		1
(1.00) 		0.441
(0.808) 		0.228
(0.679) 		0.116
(0.515) 		0.518
(0.841) 		1
(1.00)
del 11q25 168 (28%) 441 0.11
(0.508) 		0.52
(0.843) 		0.0412
(0.37) 		0.101
(0.507) 		0.209
(0.652) 		0.71
(0.938) 		0.0099
(0.199) 		0.374
(0.78) 		1
(1.00) 		0.303
(0.739) 		0.343
(0.766) 		0.116
(0.515) 		0.718
(0.938) 		1
(1.00)
del 12p13 1 110 (18%) 499 0.29
(0.732) 		0.104
(0.507) 		0.421
(0.808) 		0.13
(0.535) 		0.969
(1.00) 		0.662
(0.935) 		0.818
(0.985) 		0.0003
(0.0346) 		0.0756
(0.446) 		0.15
(0.572) 		0.79
(0.978) 		0.135
(0.547) 		0.426
(0.808) 		1
(1.00)
del 12q23 1 104 (17%) 505 0.935
(1.00) 		0.315
(0.746) 		0.574
(0.893) 		0.00477
(0.165) 		0.918
(1.00) 		0.657
(0.934) 		0.815
(0.985) 		0.158
(0.584) 		0.596
(0.906) 		0.357
(0.772) 		0.872
(1.00) 		0.782
(0.972) 		0.573
(0.892) 		1
(1.00)
del 13q12 11 131 (22%) 478 0.521
(0.843) 		0.142
(0.562) 		0.115
(0.515) 		0.028
(0.327) 		0.412
(0.803) 		0.689
(0.935) 		6.09e-05
(0.0121) 		0.814
(0.985) 		0.117
(0.515) 		0.382
(0.787) 		0.638
(0.92) 		0.393
(0.789) 		0.161
(0.587) 		1
(1.00)
del 14q32 32 186 (31%) 423 0.709
(0.938) 		0.694
(0.935) 		0.15
(0.572) 		0.451
(0.809) 		0.499
(0.831) 		0.00566
(0.165) 		0.503
(0.831) 		0.45
(0.809) 		1
(1.00) 		0.914
(1.00) 		0.32
(0.751) 		0.305
(0.74) 		0.804
(0.983) 		0.2
(0.647)
del 16p13 3 175 (29%) 434 0.148
(0.572) 		0.124
(0.524) 		0.0508
(0.393) 		0.00767
(0.185) 		0.122
(0.524) 		0.356
(0.772) 		0.0312
(0.343) 		0.0262
(0.315) 		1
(1.00) 		0.674
(0.935) 		0.938
(1.00) 		0.816
(0.985) 		0.51
(0.834) 		0.385
(0.787)
del 17p12 258 (42%) 351 0.54
(0.862) 		0.195
(0.645) 		0.98
(1.00) 		0.257
(0.71) 		0.673
(0.935) 		0.315
(0.746) 		0.0318
(0.343) 		0.00027
(0.034) 		0.248
(0.701) 		0.881
(1.00) 		0.155
(0.582) 		0.432
(0.808) 		0.292
(0.732) 		0.714
(0.938)
del 17q24 3 102 (17%) 507 0.757
(0.957) 		0.0577
(0.408) 		0.373
(0.78) 		0.199
(0.647) 		0.281
(0.729) 		0.658
(0.934) 		0.409
(0.803) 		0.318
(0.75) 		0.596
(0.906) 		0.687
(0.935) 		0.191
(0.634) 		0.00524
(0.165) 		0.256
(0.71) 		1
(1.00)
del 18q12 2 283 (46%) 326 0.234
(0.685) 		0.335
(0.763) 		0.438
(0.808) 		1e-05
(0.00693) 		0.609
(0.913) 		0.868
(1.00) 		0.063
(0.423) 		0.157
(0.584) 		0.691
(0.935) 		0.109
(0.507) 		0.482
(0.821) 		0.0847
(0.464) 		0.483
(0.821) 		0.471
(0.817)
del 18q21 2 313 (51%) 296 0.585
(0.9) 		0.453
(0.809) 		0.666
(0.935) 		0.00039
(0.0386) 		0.668
(0.935) 		0.869
(1.00) 		0.0422
(0.37) 		0.11
(0.508) 		0.439
(0.808) 		0.155
(0.582) 		0.466
(0.814) 		0.0573
(0.408) 		0.109
(0.507) 		0.275
(0.726)
del 19q13 11 118 (19%) 491 0.391
(0.788) 		0.997
(1.00) 		0.97
(1.00) 		0.248
(0.701) 		0.603
(0.909) 		0.146
(0.572) 		0.18
(0.611) 		0.00102
(0.0744) 		1
(1.00) 		0.301
(0.739) 		0.386
(0.788) 		0.141
(0.562) 		0.419
(0.808) 		1
(1.00)
del 22q11 1 224 (37%) 385 0.0487
(0.388) 		0.198
(0.647) 		0.0779
(0.449) 		0.0008
(0.0616) 		0.859
(1.00) 		0.733
(0.944) 		0.313
(0.746) 		0.39
(0.788) 		0.674
(0.935) 		0.625
(0.913) 		0.521
(0.843) 		0.0853
(0.465) 		0.332
(0.762) 		1
(1.00)
del 22q13 31 231 (38%) 378 0.0567
(0.408) 		0.829
(0.99) 		0.0108
(0.208) 		0.181
(0.612) 		0.241
(0.69) 		0.394
(0.789) 		0.412
(0.803) 		0.0402
(0.37) 		0.207
(0.651) 		0.582
(0.899) 		0.572
(0.892) 		0.0153
(0.258) 		0.412
(0.803) 		1
(1.00)
del xp22 2 143 (23%) 466 0.747
(0.948) 		0.0687
(0.431) 		0.292
(0.732) 		0.51
(0.834) 		0.407
(0.803) 		0.7
(0.935) 		0.00886
(0.195) 		0.131
(0.537) 		1
(1.00) 		0.106
(0.507) 		0.617
(0.913) 		0.272
(0.725) 		0.0164
(0.26) 		0.684
(0.935)
del xp21 1 136 (22%) 473 0.606
(0.911) 		0.392
(0.788) 		0.214
(0.663) 		0.854
(0.998) 		0.305
(0.74) 		0.225
(0.677) 		0.00773
(0.185) 		0.264
(0.721) 		1
(1.00) 		0.73
(0.944) 		0.348
(0.772) 		0.168
(0.601) 		0.539
(0.862) 		0.177
(0.611)
del xp11 3 138 (23%) 471 0.797
(0.982) 		0.204
(0.647) 		0.0534
(0.396) 		0.332
(0.762) 		0.294
(0.734) 		0.422
(0.808) 		0.011
(0.208) 		0.203
(0.647) 		1
(1.00) 		0.703
(0.937) 		0.623
(0.913) 		0.0426
(0.37) 		0.169
(0.601) 		0.654
(0.933)
amp 1p34 2 92 (15%) 517 0.747
(0.948) 		0.176
(0.609) 		0.104
(0.507) 		0.12
(0.516) 		0.446
(0.808) 		0.339
(0.763) 		0.137
(0.552) 		0.505
(0.831) 		1
(1.00) 		0.692
(0.935) 		0.103
(0.507) 		0.428
(0.808) 		0.615
(0.913) 		1
(1.00)
amp 1q21 3 238 (39%) 371 0.352
(0.772) 		0.172
(0.604) 		0.293
(0.732) 		0.0245
(0.309) 		0.894
(1.00) 		0.497
(0.831) 		0.148
(0.572) 		0.141
(0.562) 		0.0362
(0.369) 		0.944
(1.00) 		0.2
(0.647) 		0.292
(0.732) 		0.347
(0.772) 		0.253
(0.707)
amp 2q12 2 148 (24%) 461 0.865
(1.00) 		0.43
(0.808) 		0.0431
(0.37) 		0.0226
(0.295) 		0.569
(0.891) 		0.689
(0.935) 		0.149
(0.572) 		0.298
(0.737) 		0.344
(0.766) 		0.848
(0.994) 		0.664
(0.935) 		0.709
(0.938) 		0.424
(0.808) 		1
(1.00)
amp 6q21 108 (18%) 501 0.0174
(0.26) 		0.676
(0.935) 		0.0521
(0.393) 		0.561
(0.883) 		0.504
(0.831) 		0.0165
(0.26) 		0.488
(0.823) 		0.0433
(0.37) 		0.289
(0.732) 		0.828
(0.99) 		0.3
(0.739) 		0.112
(0.51) 		0.0767
(0.448) 		1
(1.00)
amp 8p11 21 266 (44%) 343 0.535
(0.859) 		0.607
(0.913) 		0.0521
(0.393) 		0.416
(0.808) 		0.117
(0.515) 		0.505
(0.831) 		0.0618
(0.418) 		0.615
(0.913) 		0.412
(0.803) 		0.667
(0.935) 		0.135
(0.547) 		0.0463
(0.38) 		0.904
(1.00) 		0.468
(0.814)
amp 8q24 21 441 (72%) 168 0.54
(0.862) 		0.363
(0.774) 		0.483
(0.821) 		0.229
(0.679) 		0.169
(0.601) 		0.711
(0.938) 		0.137
(0.552) 		0.349
(0.772) 		1
(1.00) 		0.371
(0.78) 		0.372
(0.78) 		0.717
(0.938) 		0.224
(0.675) 		1
(1.00)
amp 9p24 1 88 (14%) 521 0.668
(0.935) 		0.806
(0.983) 		0.934
(1.00) 		0.533
(0.856) 		0.28
(0.729) 		1
(1.00) 		0.451
(0.809) 		0.35
(0.772) 		0.0421
(0.37) 		0.695
(0.935) 		0.698
(0.935) 		0.465
(0.814) 		0.266
(0.722) 		0.282
(0.731)
amp 9q34 3 180 (30%) 429 0.0257
(0.314) 		0.0424
(0.37) 		0.714
(0.938) 		0.312
(0.746) 		0.253
(0.707) 		0.716
(0.938) 		0.0653
(0.425) 		0.0706
(0.433) 		0.368
(0.779) 		0.0281
(0.327) 		0.344
(0.766) 		0.44
(0.808) 		0.716
(0.938) 		0.408
(0.803)
amp 10p11 22 166 (27%) 443 0.862
(1.00) 		0.735
(0.946) 		0.169
(0.601) 		0.0917
(0.48) 		0.983
(1.00) 		0.576
(0.893) 		0.621
(0.913) 		0.213
(0.663) 		0.353
(0.772) 		0.221
(0.667) 		0.7
(0.935) 		0.635
(0.92) 		0.0385
(0.37) 		0.679
(0.935)
amp 10q22 2 124 (20%) 485 0.692
(0.935) 		0.496
(0.831) 		0.074
(0.44) 		0.173
(0.604) 		0.613
(0.913) 		0.676
(0.935) 		0.742
(0.947) 		0.639
(0.92) 		0.354
(0.772) 		0.053
(0.395) 		0.358
(0.772) 		0.33
(0.762) 		0.252
(0.707) 		0.353
(0.772)
amp 10q26 13 119 (20%) 490 0.438
(0.808) 		0.945
(1.00) 		0.0322
(0.343) 		0.149
(0.572) 		0.889
(1.00) 		0.4
(0.797) 		0.912
(1.00) 		0.256
(0.71) 		0.333
(0.763) 		0.0927
(0.48) 		0.804
(0.983) 		0.7
(0.935) 		0.12
(0.517) 		0.357
(0.772)
amp 11p13 133 (22%) 476 0.0292
(0.336) 		0.557
(0.879) 		0.197
(0.647) 		0.0171
(0.26) 		0.265
(0.721) 		0.0684
(0.431) 		0.0416
(0.37) 		0.505
(0.831) 		0.616
(0.913) 		0.0719
(0.434) 		0.248
(0.701) 		0.0558
(0.408) 		0.0717
(0.434) 		1
(1.00)
amp 11q13 3 209 (34%) 400 0.782
(0.973) 		0.734
(0.945) 		0.205
(0.647) 		0.937
(1.00) 		0.152
(0.579) 		0.487
(0.823) 		0.0401
(0.37) 		0.629
(0.915) 		1
(1.00) 		0.281
(0.729) 		0.743
(0.947) 		0.129
(0.535) 		0.07
(0.432) 		0.44
(0.808)
amp 12q15 158 (26%) 451 0.0222
(0.294) 		0.179
(0.611) 		0.277
(0.728) 		0.464
(0.814) 		0.383
(0.787) 		0.0575
(0.408) 		0.158
(0.584) 		0.21
(0.654) 		0.652
(0.932) 		0.762
(0.961) 		0.444
(0.808) 		0.955
(1.00) 		0.22
(0.667) 		0.385
(0.787)
amp 13q12 3 211 (35%) 398 0.474
(0.818) 		0.149
(0.572) 		0.363
(0.774) 		0.801
(0.982) 		0.167
(0.599) 		0.385
(0.787) 		0.926
(1.00) 		0.155
(0.582) 		0.422
(0.808) 		0.0447
(0.376) 		0.691
(0.935) 		0.203
(0.647) 		0.0296
(0.336) 		1
(1.00)
amp 15q26 1 162 (27%) 447 0.805
(0.983) 		0.955
(1.00) 		0.428
(0.808) 		0.22
(0.667) 		0.366
(0.778) 		0.128
(0.535) 		0.109
(0.507) 		0.118
(0.515) 		0.659
(0.935) 		0.018
(0.262) 		0.241
(0.69) 		0.31
(0.745) 		0.216
(0.665) 		0.66
(0.935)
amp 18p11 32 171 (28%) 438 0.157
(0.584) 		0.77
(0.965) 		0.074
(0.44) 		0.328
(0.762) 		0.301
(0.739) 		0.357
(0.772) 		0.239
(0.688) 		0.132
(0.538) 		0.357
(0.772) 		0.585
(0.9) 		0.831
(0.99) 		0.308
(0.742) 		0.0437
(0.372) 		0.405
(0.803)
amp 18q11 2 192 (32%) 417 0.392
(0.788) 		0.177
(0.611) 		0.478
(0.818) 		0.472
(0.817) 		0.649
(0.928) 		0.478
(0.818) 		1
(1.00) 		0.0299
(0.337) 		0.0822
(0.456) 		0.99
(1.00) 		0.39
(0.788) 		0.371
(0.78) 		0.616
(0.913) 		0.682
(0.935)
amp 19p13 2 76 (12%) 533 0.0785
(0.449) 		0.994
(1.00) 		0.288
(0.732) 		0.408
(0.803) 		0.332
(0.762) 		0.436
(0.808) 		0.23
(0.679) 		0.914
(1.00) 		1
(1.00) 		0.538
(0.862) 		0.456
(0.813) 		0.383
(0.787) 		0.207
(0.651) 		0.602
(0.909)
amp 19q12 181 (30%) 428 0.694
(0.935) 		0.564
(0.886) 		0.881
(1.00) 		0.138
(0.553) 		0.437
(0.808) 		1
(1.00) 		0.335
(0.763) 		0.657
(0.934) 		0.0673
(0.428) 		0.414
(0.805) 		0.746
(0.948) 		0.161
(0.587) 		0.112
(0.509) 		1
(1.00)
amp 19q13 43 157 (26%) 452 0.874
(1.00) 		0.944
(1.00) 		0.391
(0.788) 		0.274
(0.726) 		0.366
(0.778) 		0.848
(0.994) 		0.363
(0.774) 		0.785
(0.975) 		0.0411
(0.37) 		0.114
(0.514) 		0.337
(0.763) 		0.0584
(0.409) 		0.0339
(0.35) 		0.684
(0.935)
amp xq28 146 (24%) 463 0.73
(0.944) 		0.154
(0.582) 		0.463
(0.814) 		0.73
(0.944) 		0.844
(0.993) 		1
(1.00) 		0.0785
(0.449) 		0.0408
(0.37) 		0.344
(0.766) 		0.239
(0.688) 		0.786
(0.975) 		0.771
(0.965) 		0.0654
(0.425) 		0.373
(0.78)
del 1p13 2 150 (25%) 459 0.0998
(0.505) 		0.53
(0.854) 		0.128
(0.535) 		0.0569
(0.408) 		0.0759
(0.446) 		1
(1.00) 		0.0507
(0.393) 		0.0374
(0.37) 		1
(1.00) 		0.304
(0.74) 		0.227
(0.679) 		0.839
(0.991) 		0.368
(0.779) 		0.358
(0.772)
del 1q44 45 (7%) 564 0.476
(0.818) 		0.0373
(0.37) 		0.486
(0.823) 		0.674
(0.935) 		0.479
(0.818) 		0.758
(0.957) 		1
(1.00) 		0.877
(1.00) 		1
(1.00) 		0.836
(0.991) 		0.811
(0.984) 		0.107
(0.507) 		0.234
(0.685) 		1
(1.00)
del 1q44 43 (7%) 566 0.845
(0.993) 		0.775
(0.967) 		0.119
(0.516) 		0.832
(0.99) 		0.506
(0.831) 		0.506
(0.831) 		0.73
(0.944) 		0.638
(0.92) 		1
(1.00) 		0.813
(0.985) 		0.596
(0.906) 		0.391
(0.788) 		0.687
(0.935) 		1
(1.00)
del 2q22 1 118 (19%) 491 0.427
(0.808) 		0.229
(0.679) 		0.716
(0.938) 		0.805
(0.983) 		0.799
(0.982) 		0.835
(0.991) 		1
(1.00) 		0.797
(0.982) 		0.329
(0.762) 		0.867
(1.00) 		0.494
(0.831) 		0.569
(0.891) 		0.932
(1.00) 		1
(1.00)
del 2q32 1 84 (14%) 525 0.271
(0.725) 		0.591
(0.906) 		0.935
(1.00) 		0.536
(0.859) 		0.159
(0.584) 		0.338
(0.763) 		0.799
(0.982) 		0.3
(0.739) 		0.591
(0.906) 		0.424
(0.808) 		0.774
(0.967) 		0.422
(0.808) 		1
(1.00) 		0.601
(0.908)
del 2q33 3 81 (13%) 528 0.472
(0.817) 		0.792
(0.98) 		0.922
(1.00) 		0.124
(0.524) 		0.823
(0.987) 		0.459
(0.814) 		0.796
(0.982) 		0.0702
(0.432) 		0.184
(0.618) 		0.45
(0.809) 		0.0817
(0.455) 		0.406
(0.803) 		0.664
(0.935) 		0.604
(0.909)
del 2q37 2 118 (19%) 491 0.752
(0.951) 		0.233
(0.685) 		0.903
(1.00) 		0.853
(0.998) 		0.821
(0.985) 		0.0587
(0.409) 		0.737
(0.946) 		0.105
(0.507) 		0.329
(0.762) 		0.18
(0.611) 		0.0464
(0.38) 		0.331
(0.762) 		0.629
(0.915) 		0.612
(0.913)
del 3p26 2 237 (39%) 372 0.696
(0.935) 		0.675
(0.935) 		0.722
(0.94) 		0.406
(0.803) 		0.335
(0.763) 		0.312
(0.746) 		0.0845
(0.464) 		0.106
(0.507) 		1
(1.00) 		0.462
(0.814) 		0.646
(0.927) 		0.39
(0.788) 		0.465
(0.814) 		1
(1.00)
del 3q11 1 96 (16%) 513 0.214
(0.663) 		0.154
(0.582) 		0.817
(0.985) 		0.217
(0.665) 		0.314
(0.746) 		0.655
(0.933) 		0.397
(0.794) 		0.484
(0.821) 		0.597
(0.906) 		0.617
(0.913) 		0.451
(0.809) 		0.891
(1.00) 		0.946
(1.00) 		1
(1.00)
del 3q26 31 62 (10%) 547 0.628
(0.915) 		0.628
(0.915) 		0.871
(1.00) 		0.396
(0.791) 		0.436
(0.808) 		0.786
(0.975) 		0.77
(0.965) 		0.314
(0.746) 		0.476
(0.818) 		0.338
(0.763) 		0.419
(0.808) 		0.842
(0.992) 		0.229
(0.679) 		1
(1.00)
del 4p16 3 263 (43%) 346 0.102
(0.507) 		0.767
(0.965) 		0.389
(0.788) 		0.101
(0.507) 		0.141
(0.562) 		0.131
(0.537) 		0.0159
(0.26) 		0.34
(0.763) 		0.703
(0.937) 		0.418
(0.808) 		0.498
(0.831) 		0.777
(0.969) 		0.625
(0.913) 		1
(1.00)
del 6p25 3 182 (30%) 427 0.34
(0.763) 		0.275
(0.726) 		0.582
(0.899) 		0.12
(0.516) 		0.955
(1.00) 		0.356
(0.772) 		0.847
(0.994) 		0.0212
(0.288) 		0.675
(0.935) 		0.899
(1.00) 		0.258
(0.71) 		0.357
(0.772) 		0.957
(1.00) 		0.0961
(0.49)
del 6q16 3 142 (23%) 467 0.709
(0.938) 		0.812
(0.984) 		0.62
(0.913) 		0.0946
(0.485) 		0.515
(0.839) 		0.104
(0.507) 		0.0163
(0.26) 		0.057
(0.408) 		1
(1.00) 		0.0869
(0.469) 		0.229
(0.679) 		0.69
(0.935) 		0.547
(0.87) 		1
(1.00)
del 9p23 292 (48%) 317 0.953
(1.00) 		0.595
(0.906) 		0.0861
(0.468) 		0.049
(0.388) 		0.195
(0.645) 		0.409
(0.803) 		0.0335
(0.349) 		0.0548
(0.404) 		1
(1.00) 		0.596
(0.906) 		0.77
(0.965) 		0.0186
(0.263) 		0.793
(0.98) 		0.71
(0.938)
del 9q21 11 171 (28%) 438 0.285
(0.732) 		0.749
(0.949) 		0.278
(0.729) 		0.275
(0.726) 		0.814
(0.985) 		0.854
(0.998) 		0.0768
(0.448) 		0.233
(0.685) 		1
(1.00) 		0.0258
(0.314) 		0.838
(0.991) 		0.33
(0.762) 		0.109
(0.507) 		0.428
(0.808)
del 13q21 31 120 (20%) 489 0.778
(0.969) 		0.106
(0.507) 		0.0315
(0.343) 		0.0232
(0.295) 		0.425
(0.808) 		0.203
(0.647) 		0.0341
(0.35) 		0.985
(1.00) 		0.0943
(0.485) 		0.673
(0.935) 		0.823
(0.987) 		0.0915
(0.48) 		0.0257
(0.314) 		0.618
(0.913)
del 14q23 3 183 (30%) 426 0.615
(0.913) 		0.625
(0.913) 		0.363
(0.774) 		0.583
(0.899) 		0.0582
(0.409) 		0.274
(0.726) 		0.5
(0.831) 		0.0265
(0.317) 		0.674
(0.935) 		0.641
(0.922) 		0.111
(0.508) 		0.729
(0.944) 		0.654
(0.933) 		0.679
(0.935)
del 15q11 2 178 (29%) 431 0.455
(0.811) 		0.648
(0.928) 		0.403
(0.802) 		0.0144
(0.25) 		0.445
(0.808) 		0.855
(0.998) 		0.56
(0.883) 		0.0794
(0.449) 		0.0636
(0.423) 		0.379
(0.785) 		0.343
(0.766) 		0.863
(1.00) 		0.732
(0.944) 		0.679
(0.935)
del 16p13 3 146 (24%) 463 0.288
(0.732) 		0.259
(0.711) 		0.0429
(0.37) 		0.0751
(0.445) 		0.0488
(0.388) 		0.245
(0.698) 		0.121
(0.518) 		0.0694
(0.432) 		0.634
(0.919) 		0.708
(0.938) 		0.74
(0.947) 		0.707
(0.938) 		0.112
(0.509) 		0.181
(0.612)
del 16q23 1 259 (43%) 350 0.797
(0.982) 		0.554
(0.875) 		0.0508
(0.393) 		0.623
(0.913) 		0.203
(0.647) 		0.0175
(0.26) 		0.107
(0.507) 		0.137
(0.552) 		0.0884
(0.475) 		0.925
(1.00) 		0.258
(0.71) 		0.501
(0.831) 		0.675
(0.935) 		0.441
(0.808)
del 20p12 1 70 (11%) 539 0.873
(1.00) 		0.956
(1.00) 		0.884
(1.00) 		0.428
(0.808) 		0.981
(1.00) 		1
(1.00) 		0.678
(0.935) 		0.338
(0.763) 		0.144
(0.567) 		0.63
(0.915) 		0.624
(0.913) 		0.717
(0.938) 		0.962
(1.00) 		0.514
(0.839)
del 21q11 2 280 (46%) 329 0.799
(0.982) 		0.0721
(0.434) 		0.729
(0.944) 		0.324
(0.759) 		0.286
(0.732) 		0.739
(0.947) 		1
(1.00) 		0.0568
(0.408) 		0.421
(0.808) 		0.404
(0.803) 		0.291
(0.732) 		0.913
(1.00) 		0.669
(0.935) 		0.455
(0.811)
del 21q22 13 294 (48%) 315 0.462
(0.814) 		0.273
(0.726) 		0.593
(0.906) 		0.547
(0.87) 		0.954
(1.00) 		0.506
(0.831) 		0.929
(1.00) 		0.0407
(0.37) 		1
(1.00) 		0.0908
(0.48) 		0.55
(0.871) 		0.476
(0.818) 		0.296
(0.735) 		0.468
(0.814)
del xq11 2 98 (16%) 511 0.819
(0.985) 		0.952
(1.00) 		0.979
(1.00) 		0.719
(0.938) 		0.663
(0.935) 		0.246
(0.7) 		0.149
(0.572) 		0.745
(0.948) 		1
(1.00) 		0.896
(1.00) 		0.452
(0.809) 		0.0455
(0.377) 		0.943
(1.00) 		1
(1.00)
del xq21 33 94 (15%) 515 0.503
(0.831) 		0.897
(1.00) 		0.719
(0.938) 		0.497
(0.831) 		0.374
(0.78) 		0.636
(0.92) 		0.391
(0.788) 		0.83
(0.99) 		1
(1.00) 		0.288
(0.732) 		0.435
(0.808) 		0.911
(1.00) 		0.944
(1.00) 		0.6
(0.908)
'amp_1p36.22' versus 'GENDER'

P value = 0.00109 (Fisher's exact test), Q value = 0.075

Table S1.  Gene #1: 'amp_1p36.22' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
AMP PEAK 1(1P36.22) MUTATED 16 82
AMP PEAK 1(1P36.22) WILD-TYPE 166 345

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.22' versus Clinical Feature #7: 'GENDER'

'amp_1q42.3' versus 'YEARS_TO_BIRTH'

P value = 0.00909 (Wilcoxon-test), Q value = 0.19

Table S2.  Gene #4: 'amp_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 602 64.8 (11.3)
AMP PEAK 4(1Q42.3) MUTATED 231 63.5 (10.5)
AMP PEAK 4(1Q42.3) WILD-TYPE 371 65.7 (11.7)

Figure S2.  Get High-res Image Gene #4: 'amp_1q42.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q42.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0029 (Fisher's exact test), Q value = 0.12

Table S3.  Gene #4: 'amp_1q42.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 4(1Q42.3) MUTATED 12 53 29 39 7 3 5
AMP PEAK 4(1Q42.3) WILD-TYPE 59 109 52 39 14 5 8

Figure S3.  Get High-res Image Gene #4: 'amp_1q42.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_3q26.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00773 (Fisher's exact test), Q value = 0.18

Table S4.  Gene #6: 'amp_3q26.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 19 48 32 77 84 29 97 72 48 51 4
AMP PEAK 6(3Q26.2) MUTATED 3 9 17 12 38 41 23 40 28 27 20 3
AMP PEAK 6(3Q26.2) WILD-TYPE 8 10 31 20 39 43 6 57 44 21 31 1

Figure S4.  Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_3q26.2' versus 'RACE'

P value = 0.00539 (Fisher's exact test), Q value = 0.16

Table S5.  Gene #6: 'amp_3q26.2' versus Clinical Feature #13: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 129 13 1 385
AMP PEAK 6(3Q26.2) MUTATED 74 7 0 159
AMP PEAK 6(3Q26.2) WILD-TYPE 55 6 1 226

Figure S5.  Get High-res Image Gene #6: 'amp_3q26.2' versus Clinical Feature #13: 'RACE'

'amp_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.01

Table S6.  Gene #7: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
AMP PEAK 7(5P15.33) MUTATED 11 48 123 26
AMP PEAK 7(5P15.33) WILD-TYPE 42 78 157 98

Figure S6.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_5p13.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0131 (Fisher's exact test), Q value = 0.23

Table S7.  Gene #8: 'amp_5p13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
AMP PEAK 8(5P13.1) MUTATED 11 45 108 32
AMP PEAK 8(5P13.1) WILD-TYPE 42 81 172 92

Figure S7.  Get High-res Image Gene #8: 'amp_5p13.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_6p21.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0069

Table S8.  Gene #9: 'amp_6p21.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 9(6P21.1) MUTATED 4 50 30 30 3 2 2
AMP PEAK 9(6P21.1) WILD-TYPE 67 112 51 48 18 6 11

Figure S8.  Get High-res Image Gene #9: 'amp_6p21.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_6q12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00047 (Fisher's exact test), Q value = 0.042

Table S9.  Gene #10: 'amp_6q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 10(6Q12) MUTATED 4 36 27 15 1 1 2
AMP PEAK 10(6Q12) WILD-TYPE 67 126 54 63 20 7 11

Figure S9.  Get High-res Image Gene #10: 'amp_6q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_7p22.3' versus 'GENDER'

P value = 0.000487 (Fisher's exact test), Q value = 0.042

Table S10.  Gene #12: 'amp_7p22.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
AMP PEAK 12(7P22.3) MUTATED 83 261
AMP PEAK 12(7P22.3) WILD-TYPE 99 166

Figure S10.  Get High-res Image Gene #12: 'amp_7p22.3' versus Clinical Feature #7: 'GENDER'

'amp_7p22.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00913 (Fisher's exact test), Q value = 0.19

Table S11.  Gene #12: 'amp_7p22.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 12(7P22.3) MUTATED 24 80 51 44 9 5 9
AMP PEAK 12(7P22.3) WILD-TYPE 47 82 30 34 12 3 4

Figure S11.  Get High-res Image Gene #12: 'amp_7p22.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'GENDER'

P value = 0.0034 (Fisher's exact test), Q value = 0.13

Table S12.  Gene #13: 'amp_7p11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
AMP PEAK 13(7P11.2) MUTATED 82 248
AMP PEAK 13(7P11.2) WILD-TYPE 100 179

Figure S12.  Get High-res Image Gene #13: 'amp_7p11.2' versus Clinical Feature #7: 'GENDER'

'amp_7q21.2' versus 'GENDER'

P value = 0.00257 (Fisher's exact test), Q value = 0.11

Table S13.  Gene #14: 'amp_7q21.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
AMP PEAK 14(7Q21.2) MUTATED 75 234
AMP PEAK 14(7Q21.2) WILD-TYPE 107 193

Figure S13.  Get High-res Image Gene #14: 'amp_7q21.2' versus Clinical Feature #7: 'GENDER'

'amp_8p23.1' versus 'YEARS_TO_BIRTH'

P value = 0.00786 (Wilcoxon-test), Q value = 0.18

Table S14.  Gene #15: 'amp_8p23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 602 64.8 (11.3)
AMP PEAK 15(8P23.1) MUTATED 222 66.3 (11.1)
AMP PEAK 15(8P23.1) WILD-TYPE 380 64.0 (11.2)

Figure S14.  Get High-res Image Gene #15: 'amp_8p23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8p23.1' versus 'GENDER'

P value = 0.000346 (Fisher's exact test), Q value = 0.037

Table S15.  Gene #15: 'amp_8p23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
AMP PEAK 15(8P23.1) MUTATED 87 138
AMP PEAK 15(8P23.1) WILD-TYPE 95 289

Figure S15.  Get High-res Image Gene #15: 'amp_8p23.1' versus Clinical Feature #7: 'GENDER'

'amp_9p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00318 (Fisher's exact test), Q value = 0.13

Table S16.  Gene #19: 'amp_9p13.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 19(9P13.3) MUTATED 9 25 17 23 9 4 3
AMP PEAK 19(9P13.3) WILD-TYPE 62 137 64 55 12 4 10

Figure S16.  Get High-res Image Gene #19: 'amp_9p13.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_12p12.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00078 (Fisher's exact test), Q value = 0.062

Table S17.  Gene #26: 'amp_12p12.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
AMP PEAK 26(12P12.1) MUTATED 12 37 115 29
AMP PEAK 26(12P12.1) WILD-TYPE 41 89 165 95

Figure S17.  Get High-res Image Gene #26: 'amp_12p12.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_13q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00721 (Fisher's exact test), Q value = 0.18

Table S18.  Gene #29: 'amp_13q22.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 29(13Q22.1) MUTATED 16 68 38 38 10 5 3
AMP PEAK 29(13Q22.1) WILD-TYPE 55 94 43 40 11 3 10

Figure S18.  Get High-res Image Gene #29: 'amp_13q22.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_14q13.3' versus 'GENDER'

P value = 0.0139 (Fisher's exact test), Q value = 0.24

Table S19.  Gene #30: 'amp_14q13.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
AMP PEAK 30(14Q13.3) MUTATED 21 85
AMP PEAK 30(14Q13.3) WILD-TYPE 161 342

Figure S19.  Get High-res Image Gene #30: 'amp_14q13.3' versus Clinical Feature #7: 'GENDER'

'amp_17q12' versus 'PATHOLOGY_M_STAGE'

P value = 0.00826 (Fisher's exact test), Q value = 0.19

Table S20.  Gene #32: 'amp_17q12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 513 39
AMP PEAK 32(17Q12) MUTATED 166 21
AMP PEAK 32(17Q12) WILD-TYPE 347 18

Figure S20.  Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_17q12' versus 'GENDER'

P value = 0.00412 (Fisher's exact test), Q value = 0.16

Table S21.  Gene #32: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
AMP PEAK 32(17Q12) MUTATED 49 167
AMP PEAK 32(17Q12) WILD-TYPE 133 260

Figure S21.  Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #7: 'GENDER'

'amp_17q12' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0092

Table S22.  Gene #32: 'amp_17q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 32(17Q12) MUTATED 9 46 35 38 6 4 6
AMP PEAK 32(17Q12) WILD-TYPE 62 116 46 40 15 4 7

Figure S22.  Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_17q12' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.00015 (Fisher's exact test), Q value = 0.022

Table S23.  Gene #32: 'amp_17q12' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 347 18 19 25
AMP PEAK 32(17Q12) MUTATED 121 1 12 3
AMP PEAK 32(17Q12) WILD-TYPE 226 17 7 22

Figure S23.  Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'amp_17q12' versus 'RACE'

P value = 0.00226 (Fisher's exact test), Q value = 0.11

Table S24.  Gene #32: 'amp_17q12' versus Clinical Feature #13: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 129 13 1 385
AMP PEAK 32(17Q12) MUTATED 38 10 1 134
AMP PEAK 32(17Q12) WILD-TYPE 91 3 0 251

Figure S24.  Get High-res Image Gene #32: 'amp_17q12' versus Clinical Feature #13: 'RACE'

'amp_20q13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0129 (Fisher's exact test), Q value = 0.23

Table S25.  Gene #38: 'amp_20q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2 N3
ALL 200 182 96 97
AMP PEAK 38(20Q13.2) MUTATED 118 134 68 60
AMP PEAK 38(20Q13.2) WILD-TYPE 82 48 28 37

Figure S25.  Get High-res Image Gene #38: 'amp_20q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_20q13.2' versus 'GENDER'

P value = 0.00256 (Fisher's exact test), Q value = 0.11

Table S26.  Gene #38: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
AMP PEAK 38(20Q13.2) MUTATED 105 302
AMP PEAK 38(20Q13.2) WILD-TYPE 77 125

Figure S26.  Get High-res Image Gene #38: 'amp_20q13.2' versus Clinical Feature #7: 'GENDER'

'amp_20q13.2' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.012

Table S27.  Gene #38: 'amp_20q13.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
AMP PEAK 38(20Q13.2) MUTATED 32 101 63 64 13 6 9
AMP PEAK 38(20Q13.2) WILD-TYPE 39 61 18 14 8 2 4

Figure S27.  Get High-res Image Gene #38: 'amp_20q13.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_1p36.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.00239 (Fisher's exact test), Q value = 0.11

Table S28.  Gene #40: 'del_1p36.11' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 1(1P36.11) MUTATED 11 42 31 35 7 2 5
DEL PEAK 1(1P36.11) WILD-TYPE 60 120 50 43 14 6 8

Figure S28.  Get High-res Image Gene #40: 'del_1p36.11' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_3p14.2' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0126 (Fisher's exact test), Q value = 0.23

Table S29.  Gene #49: 'del_3p14.2' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 347 18 19 25
DEL PEAK 10(3P14.2) MUTATED 134 3 7 3
DEL PEAK 10(3P14.2) WILD-TYPE 213 15 12 22

Figure S29.  Get High-res Image Gene #49: 'del_3p14.2' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'del_3p14.2' versus 'RACE'

P value = 0.0102 (Fisher's exact test), Q value = 0.2

Table S30.  Gene #49: 'del_3p14.2' versus Clinical Feature #13: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 129 13 1 385
DEL PEAK 10(3P14.2) MUTATED 68 2 0 160
DEL PEAK 10(3P14.2) WILD-TYPE 61 11 1 225

Figure S30.  Get High-res Image Gene #49: 'del_3p14.2' versus Clinical Feature #13: 'RACE'

'del_4p15.2' versus 'Time to Death'

P value = 0.00908 (logrank test), Q value = 0.19

Table S31.  Gene #53: 'del_4p15.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 575 221 0.0 - 122.3 (12.8)
DEL PEAK 14(4P15.2) MUTATED 247 105 0.1 - 115.7 (12.0)
DEL PEAK 14(4P15.2) WILD-TYPE 328 116 0.0 - 122.3 (13.4)

Figure S31.  Get High-res Image Gene #53: 'del_4p15.2' versus Clinical Feature #1: 'Time to Death'

'del_4q22.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00656 (Fisher's exact test), Q value = 0.18

Table S32.  Gene #54: 'del_4q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 15(4Q22.1) MUTATED 16 59 148 50
DEL PEAK 15(4Q22.1) WILD-TYPE 37 67 132 74

Figure S32.  Get High-res Image Gene #54: 'del_4q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4q34.3' versus 'YEARS_TO_BIRTH'

P value = 0.00977 (Wilcoxon-test), Q value = 0.2

Table S33.  Gene #55: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 602 64.8 (11.3)
DEL PEAK 16(4Q34.3) MUTATED 288 66.1 (10.5)
DEL PEAK 16(4Q34.3) WILD-TYPE 314 63.6 (11.8)

Figure S33.  Get High-res Image Gene #55: 'del_4q34.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q34.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00428 (Fisher's exact test), Q value = 0.16

Table S34.  Gene #55: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 19 48 32 77 84 29 97 72 48 51 4
DEL PEAK 16(4Q34.3) MUTATED 2 5 20 21 34 35 20 48 37 28 17 3
DEL PEAK 16(4Q34.3) WILD-TYPE 9 14 28 11 43 49 9 49 35 20 34 1

Figure S34.  Get High-res Image Gene #55: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_4q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00498 (Fisher's exact test), Q value = 0.16

Table S35.  Gene #55: 'del_4q34.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 16(4Q34.3) MUTATED 21 66 48 42 8 4 7
DEL PEAK 16(4Q34.3) WILD-TYPE 50 96 33 36 13 4 6

Figure S35.  Get High-res Image Gene #55: 'del_4q34.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_5q12.1' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S36.  Gene #56: 'del_5q12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 17(5Q12.1) MUTATED 11 59 33 44 10 4 4
DEL PEAK 17(5Q12.1) WILD-TYPE 60 103 48 34 11 4 9

Figure S36.  Get High-res Image Gene #56: 'del_5q12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_6q26' versus 'PATHOLOGY_T_STAGE'

P value = 0.0105 (Fisher's exact test), Q value = 0.2

Table S37.  Gene #59: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 20(6Q26) MUTATED 7 27 84 23
DEL PEAK 20(6Q26) WILD-TYPE 46 99 196 101

Figure S37.  Get High-res Image Gene #59: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q26' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00973 (Wilcoxon-test), Q value = 0.2

Table S38.  Gene #59: 'del_6q26' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
DEL PEAK 20(6Q26) MUTATED 90 6.6 (7.7)
DEL PEAK 20(6Q26) WILD-TYPE 297 5.4 (8.7)

Figure S38.  Get High-res Image Gene #59: 'del_6q26' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_7q31.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00139 (Fisher's exact test), Q value = 0.087

Table S39.  Gene #60: 'del_7q31.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 19 48 32 77 84 29 97 72 48 51 4
DEL PEAK 21(7Q31.1) MUTATED 1 5 4 8 18 21 15 21 9 6 8 2
DEL PEAK 21(7Q31.1) WILD-TYPE 10 14 44 24 59 63 14 76 63 42 43 2

Figure S39.  Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_7q31.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00623 (Fisher's exact test), Q value = 0.17

Table S40.  Gene #60: 'del_7q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 21(7Q31.1) MUTATED 14 22 70 14
DEL PEAK 21(7Q31.1) WILD-TYPE 39 104 210 110

Figure S40.  Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_7q31.1' versus 'GENDER'

P value = 0.00144 (Fisher's exact test), Q value = 0.087

Table S41.  Gene #60: 'del_7q31.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 21(7Q31.1) MUTATED 23 102
DEL PEAK 21(7Q31.1) WILD-TYPE 159 325

Figure S41.  Get High-res Image Gene #60: 'del_7q31.1' versus Clinical Feature #7: 'GENDER'

'del_7q36.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00256 (Fisher's exact test), Q value = 0.11

Table S42.  Gene #61: 'del_7q36.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 19 48 32 77 84 29 97 72 48 51 4
DEL PEAK 22(7Q36.3) MUTATED 1 5 6 9 20 32 15 27 13 11 13 3
DEL PEAK 22(7Q36.3) WILD-TYPE 10 14 42 23 57 52 14 70 59 37 38 1

Figure S42.  Get High-res Image Gene #61: 'del_7q36.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_7q36.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0125 (Wilcoxon-test), Q value = 0.23

Table S43.  Gene #61: 'del_7q36.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
DEL PEAK 22(7Q36.3) MUTATED 84 7.0 (9.4)
DEL PEAK 22(7Q36.3) WILD-TYPE 303 5.3 (8.1)

Figure S43.  Get High-res Image Gene #61: 'del_7q36.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_8p23.2' versus 'GENDER'

P value = 0.000162 (Fisher's exact test), Q value = 0.022

Table S44.  Gene #62: 'del_8p23.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 23(8P23.2) MUTATED 40 160
DEL PEAK 23(8P23.2) WILD-TYPE 142 267

Figure S44.  Get High-res Image Gene #62: 'del_8p23.2' versus Clinical Feature #7: 'GENDER'

'del_8p23.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00127 (Wilcoxon-test), Q value = 0.084

Table S45.  Gene #62: 'del_8p23.2' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
DEL PEAK 23(8P23.2) MUTATED 105 7.7 (10.5)
DEL PEAK 23(8P23.2) WILD-TYPE 282 4.9 (7.4)

Figure S45.  Get High-res Image Gene #62: 'del_8p23.2' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00435 (Fisher's exact test), Q value = 0.16

Table S46.  Gene #64: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 25(9P21.3) MUTATED 29 70 159 47
DEL PEAK 25(9P21.3) WILD-TYPE 24 56 121 77

Figure S46.  Get High-res Image Gene #64: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.00604 (Fisher's exact test), Q value = 0.17

Table S47.  Gene #64: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 25(9P21.3) MUTATED 80 240
DEL PEAK 25(9P21.3) WILD-TYPE 102 187

Figure S47.  Get High-res Image Gene #64: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00783 (Fisher's exact test), Q value = 0.18

Table S48.  Gene #64: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 25(9P21.3) MUTATED 18 67 45 40 9 4 5
DEL PEAK 25(9P21.3) WILD-TYPE 53 95 36 38 12 4 8

Figure S48.  Get High-res Image Gene #64: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_10p15.3' versus 'Time to Death'

P value = 0.00937 (logrank test), Q value = 0.2

Table S49.  Gene #66: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 575 221 0.0 - 122.3 (12.8)
DEL PEAK 27(10P15.3) MUTATED 118 55 0.1 - 115.7 (11.5)
DEL PEAK 27(10P15.3) WILD-TYPE 457 166 0.0 - 122.3 (12.8)

Figure S49.  Get High-res Image Gene #66: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p15.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00539 (Wilcoxon-test), Q value = 0.16

Table S50.  Gene #66: 'del_10p15.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
DEL PEAK 27(10P15.3) MUTATED 66 7.3 (9.2)
DEL PEAK 27(10P15.3) WILD-TYPE 321 5.3 (8.2)

Figure S50.  Get High-res Image Gene #66: 'del_10p15.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_10p11.21' versus 'PATHOLOGY_T_STAGE'

P value = 0.00571 (Fisher's exact test), Q value = 0.16

Table S51.  Gene #67: 'del_10p11.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 28(10P11.21) MUTATED 5 25 52 9
DEL PEAK 28(10P11.21) WILD-TYPE 48 101 228 115

Figure S51.  Get High-res Image Gene #67: 'del_10p11.21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10p11.21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00821 (Wilcoxon-test), Q value = 0.19

Table S52.  Gene #67: 'del_10p11.21' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
DEL PEAK 28(10P11.21) MUTATED 42 7.5 (7.7)
DEL PEAK 28(10P11.21) WILD-TYPE 345 5.4 (8.5)

Figure S52.  Get High-res Image Gene #67: 'del_10p11.21' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_10q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0125 (Wilcoxon-test), Q value = 0.23

Table S53.  Gene #68: 'del_10q21.1' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
DEL PEAK 29(10Q21.1) MUTATED 58 6.6 (6.1)
DEL PEAK 29(10Q21.1) WILD-TYPE 329 5.5 (8.8)

Figure S53.  Get High-res Image Gene #68: 'del_10q21.1' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_10q22.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00725 (Wilcoxon-test), Q value = 0.18

Table S54.  Gene #69: 'del_10q22.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
DEL PEAK 30(10Q22.3) MUTATED 64 8.6 (11.9)
DEL PEAK 30(10Q22.3) WILD-TYPE 323 5.1 (7.5)

Figure S54.  Get High-res Image Gene #69: 'del_10q22.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_10q23.31' versus 'HISTOLOGICAL_TYPE'

P value = 0.00221 (Fisher's exact test), Q value = 0.11

Table S55.  Gene #70: 'del_10q23.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 31(10Q23.31) MUTATED 7 39 31 25 5 3 4
DEL PEAK 31(10Q23.31) WILD-TYPE 64 123 50 53 16 5 9

Figure S55.  Get High-res Image Gene #70: 'del_10q23.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_11p15.5' versus 'GENDER'

P value = 0.00757 (Fisher's exact test), Q value = 0.18

Table S56.  Gene #71: 'del_11p15.5' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 32(11P15.5) MUTATED 37 133
DEL PEAK 32(11P15.5) WILD-TYPE 145 294

Figure S56.  Get High-res Image Gene #71: 'del_11p15.5' versus Clinical Feature #7: 'GENDER'

'del_11q25' versus 'GENDER'

P value = 0.0099 (Fisher's exact test), Q value = 0.2

Table S57.  Gene #72: 'del_11q25' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 33(11Q25) MUTATED 37 131
DEL PEAK 33(11Q25) WILD-TYPE 145 296

Figure S57.  Get High-res Image Gene #72: 'del_11q25' versus Clinical Feature #7: 'GENDER'

'del_12p13.1' versus 'HISTOLOGICAL_TYPE'

P value = 3e-04 (Fisher's exact test), Q value = 0.035

Table S58.  Gene #73: 'del_12p13.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 34(12P13.1) MUTATED 3 30 15 20 0 4 2
DEL PEAK 34(12P13.1) WILD-TYPE 68 132 66 58 21 4 11

Figure S58.  Get High-res Image Gene #73: 'del_12p13.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_12q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00477 (Fisher's exact test), Q value = 0.16

Table S59.  Gene #74: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 35(12Q23.1) MUTATED 15 16 56 12
DEL PEAK 35(12Q23.1) WILD-TYPE 38 110 224 112

Figure S59.  Get High-res Image Gene #74: 'del_12q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q12.11' versus 'GENDER'

P value = 6.09e-05 (Fisher's exact test), Q value = 0.012

Table S60.  Gene #75: 'del_13q12.11' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 36(13Q12.11) MUTATED 21 110
DEL PEAK 36(13Q12.11) WILD-TYPE 161 317

Figure S60.  Get High-res Image Gene #75: 'del_13q12.11' versus Clinical Feature #7: 'GENDER'

'del_13q14.2' versus 'YEARS_TO_BIRTH'

P value = 0.00547 (Wilcoxon-test), Q value = 0.16

Table S61.  Gene #76: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 602 64.8 (11.3)
DEL PEAK 37(13Q14.2) MUTATED 117 62.2 (11.4)
DEL PEAK 37(13Q14.2) WILD-TYPE 485 65.5 (11.1)

Figure S61.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.016

Table S62.  Gene #76: 'del_13q14.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 19 48 32 77 84 29 97 72 48 51 4
DEL PEAK 37(13Q14.2) MUTATED 4 2 7 4 23 17 15 22 8 5 4 1
DEL PEAK 37(13Q14.2) WILD-TYPE 7 17 41 28 54 67 14 75 64 43 47 3

Figure S62.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_13q14.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00439 (Fisher's exact test), Q value = 0.16

Table S63.  Gene #76: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 37(13Q14.2) MUTATED 12 27 64 11
DEL PEAK 37(13Q14.2) WILD-TYPE 41 99 216 113

Figure S63.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q14.2' versus 'GENDER'

P value = 0.00246 (Fisher's exact test), Q value = 0.11

Table S64.  Gene #76: 'del_13q14.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 37(13Q14.2) MUTATED 22 97
DEL PEAK 37(13Q14.2) WILD-TYPE 160 330

Figure S64.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #7: 'GENDER'

'del_13q14.2' versus 'RACE'

P value = 0.00546 (Fisher's exact test), Q value = 0.16

Table S65.  Gene #76: 'del_13q14.2' versus Clinical Feature #13: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
ALL 129 13 1 385
DEL PEAK 37(13Q14.2) MUTATED 38 0 0 69
DEL PEAK 37(13Q14.2) WILD-TYPE 91 13 1 316

Figure S65.  Get High-res Image Gene #76: 'del_13q14.2' versus Clinical Feature #13: 'RACE'

'del_14q32.32' versus 'PATHOLOGY_M_STAGE'

P value = 0.00566 (Fisher's exact test), Q value = 0.16

Table S66.  Gene #79: 'del_14q32.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 513 39
DEL PEAK 40(14Q32.32) MUTATED 161 4
DEL PEAK 40(14Q32.32) WILD-TYPE 352 35

Figure S66.  Get High-res Image Gene #79: 'del_14q32.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_16p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00767 (Fisher's exact test), Q value = 0.18

Table S67.  Gene #81: 'del_16p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 42(16P13.3) MUTATED 20 28 88 23
DEL PEAK 42(16P13.3) WILD-TYPE 33 98 192 101

Figure S67.  Get High-res Image Gene #81: 'del_16p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_17p12' versus 'HISTOLOGICAL_TYPE'

P value = 0.00027 (Fisher's exact test), Q value = 0.034

Table S68.  Gene #84: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 45(17P12) MUTATED 15 58 42 41 9 4 8
DEL PEAK 45(17P12) WILD-TYPE 56 104 39 37 12 4 5

Figure S68.  Get High-res Image Gene #84: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_17q24.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00524 (Wilcoxon-test), Q value = 0.16

Table S69.  Gene #85: 'del_17q24.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 387 5.7 (8.4)
DEL PEAK 46(17Q24.3) MUTATED 63 9.7 (13.3)
DEL PEAK 46(17Q24.3) WILD-TYPE 324 4.9 (6.9)

Figure S69.  Get High-res Image Gene #85: 'del_17q24.3' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'del_18q12.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0069

Table S70.  Gene #86: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 47(18Q12.2) MUTATED 22 56 156 36
DEL PEAK 47(18Q12.2) WILD-TYPE 31 70 124 88

Figure S70.  Get High-res Image Gene #86: 'del_18q12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_18q21.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.039

Table S71.  Gene #87: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 48(18Q21.2) MUTATED 26 63 165 45
DEL PEAK 48(18Q21.2) WILD-TYPE 27 63 115 79

Figure S71.  Get High-res Image Gene #87: 'del_18q21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'GENDER'

P value = 0.00206 (Fisher's exact test), Q value = 0.11

Table S72.  Gene #88: 'del_19p13.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 49(19P13.3) MUTATED 55 187
DEL PEAK 49(19P13.3) WILD-TYPE 127 240

Figure S72.  Get High-res Image Gene #88: 'del_19p13.3' versus Clinical Feature #7: 'GENDER'

'del_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.00288 (Fisher's exact test), Q value = 0.12

Table S73.  Gene #88: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 49(19P13.3) MUTATED 15 53 41 34 5 4 4
DEL PEAK 49(19P13.3) WILD-TYPE 56 109 40 44 16 4 9

Figure S73.  Get High-res Image Gene #88: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_19q13.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.00102 (Fisher's exact test), Q value = 0.074

Table S74.  Gene #89: 'del_19q13.11' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients STOMACH ADENOCARCINOMA DIFFUSE TYPE STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE STOMACH ADENOCARCINOMA SIGNET RING TYPE
ALL 71 162 81 78 21 8 13
DEL PEAK 50(19Q13.11) MUTATED 5 24 17 25 1 2 1
DEL PEAK 50(19Q13.11) WILD-TYPE 66 138 64 53 20 6 12

Figure S74.  Get High-res Image Gene #89: 'del_19q13.11' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_22q11.1' versus 'PATHOLOGY_T_STAGE'

P value = 8e-04 (Fisher's exact test), Q value = 0.062

Table S75.  Gene #93: 'del_22q11.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T0+T1 T2 T3 T4
ALL 53 126 280 124
DEL PEAK 54(22Q11.1) MUTATED 26 40 118 30
DEL PEAK 54(22Q11.1) WILD-TYPE 27 86 162 94

Figure S75.  Get High-res Image Gene #93: 'del_22q11.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_22q13.31' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0108 (Fisher's exact test), Q value = 0.21

Table S76.  Gene #94: 'del_22q13.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
ALL 11 19 48 32 77 84 29 97 72 48 51 4
DEL PEAK 55(22Q13.31) MUTATED 6 1 19 11 27 28 18 42 30 16 17 3
DEL PEAK 55(22Q13.31) WILD-TYPE 5 18 29 21 50 56 11 55 42 32 34 1

Figure S76.  Get High-res Image Gene #94: 'del_22q13.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_xp22.2' versus 'GENDER'

P value = 0.00886 (Fisher's exact test), Q value = 0.19

Table S77.  Gene #95: 'del_xp22.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 56(XP22.2) MUTATED 30 113
DEL PEAK 56(XP22.2) WILD-TYPE 152 314

Figure S77.  Get High-res Image Gene #95: 'del_xp22.2' versus Clinical Feature #7: 'GENDER'

'del_xp21.1' versus 'GENDER'

P value = 0.00773 (Fisher's exact test), Q value = 0.18

Table S78.  Gene #96: 'del_xp21.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 57(XP21.1) MUTATED 28 108
DEL PEAK 57(XP21.1) WILD-TYPE 154 319

Figure S78.  Get High-res Image Gene #96: 'del_xp21.1' versus Clinical Feature #7: 'GENDER'

'del_xp11.3' versus 'GENDER'

P value = 0.011 (Fisher's exact test), Q value = 0.21

Table S79.  Gene #97: 'del_xp11.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 182 427
DEL PEAK 58(XP11.3) MUTATED 29 109
DEL PEAK 58(XP11.3) WILD-TYPE 153 318

Figure S79.  Get High-res Image Gene #97: 'del_xp11.3' versus Clinical Feature #7: 'GENDER'

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/STES-TP/15101925/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/STES-TP/15090071/STES-TP.merged_data.txt

  • Number of patients = 609

  • Number of significantly focal cnvs = 99

  • Number of selected clinical features = 14

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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