Correlation between copy number variations of arm-level result and selected clinical features
Stomach Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1862DXF
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1862DXF
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 79 arm-level events and 11 clinical features across 306 patients, 3 significant findings detected with Q value < 0.25.

  • 16p gain cnv correlated to 'PATHOLOGY.M.STAGE'.

  • 16q gain cnv correlated to 'PATHOLOGY.M.STAGE'.

  • xq gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test t-test
16p gain 42 (14%) 264 0.279
(1.00) 		0.212
(1.00) 		0.00861
(1.00) 		0.411
(1.00) 		0.562
(1.00) 		0.000167
(0.145) 		0.613
(1.00) 		0.894
(1.00) 		0.0568
(1.00) 		0.177
(1.00) 		0.182
(1.00)
16q gain 32 (10%) 274 0.174
(1.00) 		0.438
(1.00) 		0.00194
(1.00) 		0.536
(1.00) 		0.72
(1.00) 		5.01e-06
(0.00435) 		0.851
(1.00) 		0.814
(1.00) 		0.16
(1.00) 		0.0627
(1.00) 		0.139
(1.00)
xq gain 39 (13%) 267 0.493
(1.00) 		0.438
(1.00) 		0.00217
(1.00) 		0.0101
(1.00) 		0.0728
(1.00) 		0.843
(1.00) 		0.0537
(1.00) 		0.00592
(1.00) 		0.601
(1.00) 		0.383
(1.00) 		5.3e-05
(0.046)
1p gain 32 (10%) 274 0.0294
(1.00) 		0.756
(1.00) 		0.673
(1.00) 		0.517
(1.00) 		0.851
(1.00) 		0.355
(1.00) 		0.187
(1.00) 		0.0149
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.298
(1.00)
1q gain 75 (25%) 231 0.296
(1.00) 		0.757
(1.00) 		0.966
(1.00) 		0.463
(1.00) 		0.82
(1.00) 		0.131
(1.00) 		0.173
(1.00) 		0.0091
(1.00) 		0.368
(1.00) 		0.679
(1.00) 		0.46
(1.00)
2p gain 51 (17%) 255 0.428
(1.00) 		0.885
(1.00) 		0.729
(1.00) 		0.297
(1.00) 		0.648
(1.00) 		0.17
(1.00) 		0.534
(1.00) 		0.154
(1.00) 		0.605
(1.00) 		0.264
(1.00) 		0.27
(1.00)
2q gain 45 (15%) 261 0.851
(1.00) 		0.869
(1.00) 		0.705
(1.00) 		0.6
(1.00) 		0.425
(1.00) 		0.688
(1.00) 		0.509
(1.00) 		0.751
(1.00) 		0.599
(1.00) 		0.316
(1.00) 		0.268
(1.00)
3p gain 36 (12%) 270 0.279
(1.00) 		0.697
(1.00) 		0.929
(1.00) 		0.964
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.856
(1.00) 		0.866
(1.00) 		1
(1.00) 		0.735
(1.00) 		0.0858
(1.00)
3q gain 59 (19%) 247 0.222
(1.00) 		0.148
(1.00) 		0.729
(1.00) 		0.531
(1.00) 		0.749
(1.00) 		0.22
(1.00) 		0.882
(1.00) 		0.998
(1.00) 		1
(1.00) 		0.397
(1.00) 		0.114
(1.00)
4p gain 10 (3%) 296 0.372
(1.00) 		0.623
(1.00) 		0.101
(1.00) 		0.128
(1.00) 		0.452
(1.00) 		0.709
(1.00) 		0.325
(1.00) 		0.954
(1.00) 		1
(1.00) 		0.242
(1.00) 		0.449
(1.00)
4q gain 7 (2%) 299 0.896
(1.00) 		0.707
(1.00) 		0.632
(1.00) 		0.791
(1.00) 		0.551
(1.00) 		0.185
(1.00) 		0.709
(1.00) 		0.0138
(1.00) 		1
(1.00) 		0.506
(1.00) 		0.537
(1.00)
5p gain 69 (23%) 237 0.464
(1.00) 		0.249
(1.00) 		0.487
(1.00) 		0.563
(1.00) 		0.828
(1.00) 		0.946
(1.00) 		0.889
(1.00) 		0.0314
(1.00) 		0.192
(1.00) 		0.456
(1.00) 		0.433
(1.00)
5q gain 28 (9%) 278 0.745
(1.00) 		0.512
(1.00) 		0.496
(1.00) 		0.681
(1.00) 		0.604
(1.00) 		0.707
(1.00) 		1
(1.00) 		0.0541
(1.00) 		0.493
(1.00) 		0.516
(1.00) 		0.836
(1.00)
6p gain 55 (18%) 251 0.497
(1.00) 		0.577
(1.00) 		0.366
(1.00) 		0.283
(1.00) 		0.853
(1.00) 		0.215
(1.00) 		0.36
(1.00) 		0.0472
(1.00) 		0.0216
(1.00) 		0.407
(1.00) 		0.0309
(1.00)
6q gain 46 (15%) 260 0.193
(1.00) 		0.715
(1.00) 		0.157
(1.00) 		0.546
(1.00) 		0.707
(1.00) 		0.402
(1.00) 		0.332
(1.00) 		0.0833
(1.00) 		0.0112
(1.00) 		0.394
(1.00) 		0.136
(1.00)
7p gain 138 (45%) 168 0.0585
(1.00) 		0.256
(1.00) 		0.795
(1.00) 		0.845
(1.00) 		0.764
(1.00) 		0.147
(1.00) 		0.101
(1.00) 		0.93
(1.00) 		0.705
(1.00) 		0.763
(1.00) 		0.304
(1.00)
7q gain 118 (39%) 188 0.0665
(1.00) 		0.334
(1.00) 		0.866
(1.00) 		0.981
(1.00) 		0.449
(1.00) 		0.0236
(1.00) 		0.149
(1.00) 		0.916
(1.00) 		1
(1.00) 		0.625
(1.00) 		0.208
(1.00)
8p gain 127 (42%) 179 0.652
(1.00) 		0.0488
(1.00) 		0.643
(1.00) 		0.108
(1.00) 		0.821
(1.00) 		0.106
(1.00) 		0.236
(1.00) 		0.677
(1.00) 		0.455
(1.00) 		0.199
(1.00) 		0.79
(1.00)
8q gain 168 (55%) 138 0.629
(1.00) 		0.0204
(1.00) 		0.265
(1.00) 		0.0423
(1.00) 		0.993
(1.00) 		0.193
(1.00) 		0.639
(1.00) 		0.446
(1.00) 		0.464
(1.00) 		0.311
(1.00) 		0.371
(1.00)
9p gain 38 (12%) 268 0.682
(1.00) 		0.709
(1.00) 		0.28
(1.00) 		0.0695
(1.00) 		0.164
(1.00) 		0.37
(1.00) 		1
(1.00) 		0.099
(1.00) 		0.211
(1.00) 		0.725
(1.00) 		0.694
(1.00)
9q gain 47 (15%) 259 0.904
(1.00) 		0.981
(1.00) 		0.351
(1.00) 		0.247
(1.00) 		0.404
(1.00) 		0.749
(1.00) 		0.517
(1.00) 		0.0712
(1.00) 		0.293
(1.00) 		0.603
(1.00) 		0.0775
(1.00)
10p gain 75 (25%) 231 0.442
(1.00) 		0.92
(1.00) 		0.648
(1.00) 		0.486
(1.00) 		0.876
(1.00) 		0.811
(1.00) 		0.685
(1.00) 		0.447
(1.00) 		0.681
(1.00) 		0.621
(1.00) 		0.484
(1.00)
10q gain 51 (17%) 255 0.706
(1.00) 		0.275
(1.00) 		0.255
(1.00) 		0.679
(1.00) 		0.655
(1.00) 		0.872
(1.00) 		0.534
(1.00) 		0.864
(1.00) 		0.33
(1.00) 		0.614
(1.00) 		0.381
(1.00)
11p gain 32 (10%) 274 0.179
(1.00) 		0.48
(1.00) 		0.755
(1.00) 		0.114
(1.00) 		0.287
(1.00) 		0.355
(1.00) 		0.347
(1.00) 		0.761
(1.00) 		0.542
(1.00) 		0.598
(1.00) 		0.485
(1.00)
11q gain 37 (12%) 269 0.749
(1.00) 		0.788
(1.00) 		0.88
(1.00) 		0.526
(1.00) 		0.0507
(1.00) 		0.694
(1.00) 		0.215
(1.00) 		0.702
(1.00) 		0.598
(1.00) 		0.933
(1.00) 		0.743
(1.00)
12p gain 59 (19%) 247 0.0529
(1.00) 		0.179
(1.00) 		0.403
(1.00) 		0.0217
(1.00) 		0.0784
(1.00) 		0.507
(1.00) 		0.769
(1.00) 		0.0814
(1.00) 		0.353
(1.00) 		0.0607
(1.00) 		0.905
(1.00)
12q gain 55 (18%) 251 0.235
(1.00) 		0.301
(1.00) 		0.445
(1.00) 		0.0489
(1.00) 		0.0215
(1.00) 		0.822
(1.00) 		0.451
(1.00) 		0.0885
(1.00) 		1
(1.00) 		0.305
(1.00) 		0.805
(1.00)
13q gain 102 (33%) 204 0.148
(1.00) 		0.851
(1.00) 		0.826
(1.00) 		0.435
(1.00) 		0.879
(1.00) 		0.167
(1.00) 		1
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.886
(1.00) 		0.812
(1.00)
14q gain 16 (5%) 290 0.0117
(1.00) 		0.0804
(1.00) 		0.865
(1.00) 		0.491
(1.00) 		0.0954
(1.00) 		0.418
(1.00) 		0.433
(1.00) 		0.221
(1.00) 		1
(1.00) 		0.0447
(1.00) 		0.187
(1.00)
15q gain 25 (8%) 281 0.874
(1.00) 		0.832
(1.00) 		0.573
(1.00) 		0.909
(1.00) 		0.0478
(1.00) 		0.395
(1.00) 		0.525
(1.00) 		0.948
(1.00) 		1
(1.00) 		0.469
(1.00) 		0.995
(1.00)
17p gain 19 (6%) 287 0.522
(1.00) 		0.17
(1.00) 		0.233
(1.00) 		0.83
(1.00) 		0.912
(1.00) 		0.00362
(1.00) 		1
(1.00) 		0.0792
(1.00) 		0.364
(1.00) 		0.0205
(1.00) 		0.874
(1.00)
17q gain 35 (11%) 271 0.556
(1.00) 		0.902
(1.00) 		0.769
(1.00) 		0.529
(1.00) 		0.84
(1.00) 		0.0035
(1.00) 		0.585
(1.00) 		0.724
(1.00) 		0.577
(1.00) 		0.0629
(1.00) 		0.915
(1.00)
18p gain 53 (17%) 253 0.00181
(1.00) 		0.0189
(1.00) 		0.803
(1.00) 		0.608
(1.00) 		0.326
(1.00) 		0.548
(1.00) 		0.758
(1.00) 		0.0277
(1.00) 		0.00209
(1.00) 		0.17
(1.00) 		0.203
(1.00)
18q gain 40 (13%) 266 0.0414
(1.00) 		0.0454
(1.00) 		0.471
(1.00) 		0.27
(1.00) 		0.475
(1.00) 		0.296
(1.00) 		0.606
(1.00) 		0.00178
(1.00) 		0.0499
(1.00) 		0.339
(1.00) 		0.486
(1.00)
19p gain 39 (13%) 267 0.522
(1.00) 		0.361
(1.00) 		0.245
(1.00) 		0.0996
(1.00) 		0.0416
(1.00) 		0.0607
(1.00) 		0.382
(1.00) 		0.0284
(1.00) 		0.22
(1.00) 		0.0422
(1.00) 		0.0526
(1.00)
19q gain 52 (17%) 254 0.666
(1.00) 		0.817
(1.00) 		0.452
(1.00) 		0.437
(1.00) 		0.0225
(1.00) 		0.127
(1.00) 		0.438
(1.00) 		0.109
(1.00) 		0.0981
(1.00) 		0.197
(1.00) 		0.0165
(1.00)
20p gain 165 (54%) 141 0.527
(1.00) 		0.8
(1.00) 		0.679
(1.00) 		0.171
(1.00) 		0.422
(1.00) 		0.426
(1.00) 		0.0258
(1.00) 		0.189
(1.00) 		0.707
(1.00) 		0.555
(1.00) 		0.0996
(1.00)
20q gain 192 (63%) 114 0.282
(1.00) 		0.338
(1.00) 		0.472
(1.00) 		0.117
(1.00) 		0.403
(1.00) 		0.109
(1.00) 		0.0154
(1.00) 		0.0215
(1.00) 		0.714
(1.00) 		0.087
(1.00) 		0.223
(1.00)
21q gain 19 (6%) 287 0.845
(1.00) 		0.931
(1.00) 		0.668
(1.00) 		0.508
(1.00) 		0.765
(1.00) 		0.853
(1.00) 		1
(1.00) 		0.15
(1.00) 		0.364
(1.00) 		0.524
(1.00) 		0.943
(1.00)
22q gain 24 (8%) 282 0.404
(1.00) 		0.824
(1.00) 		0.106
(1.00) 		0.291
(1.00) 		0.495
(1.00) 		1
(1.00) 		1
(1.00) 		0.675
(1.00) 		1
(1.00) 		0.722
(1.00) 		0.996
(1.00)
1p loss 40 (13%) 266 0.366
(1.00) 		0.934
(1.00) 		0.223
(1.00) 		0.638
(1.00) 		0.543
(1.00) 		0.0809
(1.00) 		0.488
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.372
(1.00)
1q loss 19 (6%) 287 0.141
(1.00) 		0.787
(1.00) 		0.334
(1.00) 		0.45
(1.00) 		0.648
(1.00) 		0.0646
(1.00) 		0.474
(1.00) 		0.877
(1.00) 		1
(1.00) 		0.28
(1.00) 		0.954
(1.00)
2p loss 16 (5%) 290 0.0926
(1.00) 		0.764
(1.00) 		0.76
(1.00) 		0.951
(1.00) 		0.388
(1.00) 		0.191
(1.00) 		0.19
(1.00) 		0.0392
(1.00) 		0.0462
(1.00) 		0.155
(1.00) 		0.309
(1.00)
2q loss 19 (6%) 287 0.432
(1.00) 		0.817
(1.00) 		0.922
(1.00) 		0.586
(1.00) 		0.516
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.0179
(1.00) 		0.0637
(1.00) 		0.148
(1.00) 		0.32
(1.00)
3p loss 59 (19%) 247 0.703
(1.00) 		0.668
(1.00) 		0.978
(1.00) 		0.658
(1.00) 		0.0918
(1.00) 		0.235
(1.00) 		0.882
(1.00) 		0.452
(1.00) 		1
(1.00) 		0.134
(1.00) 		0.0417
(1.00)
3q loss 35 (11%) 271 0.849
(1.00) 		0.213
(1.00) 		0.925
(1.00) 		0.0157
(1.00) 		0.625
(1.00) 		0.826
(1.00) 		1
(1.00) 		0.558
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.184
(1.00)
4p loss 112 (37%) 194 0.961
(1.00) 		0.313
(1.00) 		0.159
(1.00) 		0.0179
(1.00) 		0.894
(1.00) 		0.231
(1.00) 		0.333
(1.00) 		0.435
(1.00) 		0.264
(1.00) 		0.422
(1.00) 		0.254
(1.00)
4q loss 112 (37%) 194 0.704
(1.00) 		0.131
(1.00) 		0.387
(1.00) 		0.105
(1.00) 		0.346
(1.00) 		0.538
(1.00) 		0.0528
(1.00) 		0.455
(1.00) 		0.264
(1.00) 		0.524
(1.00) 		0.27
(1.00)
5p loss 37 (12%) 269 0.224
(1.00) 		0.707
(1.00) 		0.0605
(1.00) 		0.793
(1.00) 		0.611
(1.00) 		1
(1.00) 		1
(1.00) 		0.25
(1.00) 		1
(1.00) 		1
(1.00) 		0.796
(1.00)
5q loss 65 (21%) 241 0.736
(1.00) 		0.462
(1.00) 		0.0109
(1.00) 		0.653
(1.00) 		0.486
(1.00) 		0.192
(1.00) 		0.775
(1.00) 		0.0799
(1.00) 		0.643
(1.00) 		0.464
(1.00) 		0.865
(1.00)
6p loss 30 (10%) 276 0.659
(1.00) 		0.303
(1.00) 		0.611
(1.00) 		0.704
(1.00) 		0.633
(1.00) 		0.079
(1.00) 		0.328
(1.00) 		0.0667
(1.00) 		1
(1.00) 		0.888
(1.00) 		0.627
(1.00)
6q loss 40 (13%) 266 0.334
(1.00) 		0.659
(1.00) 		0.601
(1.00) 		0.338
(1.00) 		0.881
(1.00) 		0.0147
(1.00) 		0.227
(1.00) 		0.338
(1.00) 		0.6
(1.00) 		0.97
(1.00) 		0.763
(1.00)
7p loss 10 (3%) 296 0.104
(1.00) 		0.267
(1.00) 		0.29
(1.00) 		0.105
(1.00) 		0.804
(1.00) 		0.487
(1.00) 		0.325
(1.00) 		0.469
(1.00) 		1
(1.00) 		1
(1.00) 		0.579
(1.00)
7q loss 19 (6%) 287 0.0265
(1.00) 		0.0584
(1.00) 		0.344
(1.00) 		0.0569
(1.00) 		0.434
(1.00) 		0.714
(1.00) 		0.332
(1.00) 		0.0777
(1.00) 		1
(1.00) 		1
(1.00) 		0.311
(1.00)
8p loss 51 (17%) 255 0.973
(1.00) 		0.298
(1.00) 		0.345
(1.00) 		0.539
(1.00) 		0.144
(1.00) 		0.464
(1.00) 		0.432
(1.00) 		0.075
(1.00) 		0.33
(1.00) 		0.271
(1.00) 		0.0617
(1.00)
8q loss 17 (6%) 289 0.747
(1.00) 		0.407
(1.00) 		0.894
(1.00) 		0.0112
(1.00) 		0.671
(1.00) 		0.358
(1.00) 		1
(1.00) 		0.489
(1.00) 		0.332
(1.00) 		0.183
(1.00) 		0.254
(1.00)
9p loss 93 (30%) 213 0.597
(1.00) 		0.202
(1.00) 		0.165
(1.00) 		0.39
(1.00) 		0.484
(1.00) 		0.267
(1.00) 		0.527
(1.00) 		0.207
(1.00) 		0.205
(1.00) 		0.386
(1.00) 		0.913
(1.00)
9q loss 65 (21%) 241 0.821
(1.00) 		0.712
(1.00) 		0.192
(1.00) 		0.246
(1.00) 		0.945
(1.00) 		0.0158
(1.00) 		0.775
(1.00) 		0.923
(1.00) 		0.0391
(1.00) 		0.304
(1.00) 		0.193
(1.00)
10p loss 34 (11%) 272 0.221
(1.00) 		0.268
(1.00) 		0.0168
(1.00) 		0.166
(1.00) 		0.153
(1.00) 		0.215
(1.00) 		1
(1.00) 		0.198
(1.00) 		0.176
(1.00) 		0.209
(1.00) 		0.279
(1.00)
10q loss 41 (13%) 265 0.221
(1.00) 		0.0106
(1.00) 		0.406
(1.00) 		0.149
(1.00) 		0.645
(1.00) 		1
(1.00) 		1
(1.00) 		0.238
(1.00) 		0.238
(1.00) 		0.673
(1.00) 		0.618
(1.00)
11p loss 44 (14%) 262 0.503
(1.00) 		0.981
(1.00) 		0.873
(1.00) 		0.0928
(1.00) 		0.633
(1.00) 		0.235
(1.00) 		0.507
(1.00) 		0.00933
(1.00) 		1
(1.00) 		0.149
(1.00) 		0.325
(1.00)
11q loss 40 (13%) 266 0.0613
(1.00) 		0.665
(1.00) 		0.213
(1.00) 		0.674
(1.00) 		0.259
(1.00) 		0.231
(1.00) 		0.389
(1.00) 		0.351
(1.00) 		1
(1.00) 		0.209
(1.00) 		0.163
(1.00)
12p loss 43 (14%) 263 0.231
(1.00) 		0.0857
(1.00) 		0.334
(1.00) 		0.141
(1.00) 		0.107
(1.00) 		0.409
(1.00) 		0.503
(1.00) 		0.0297
(1.00) 		1
(1.00) 		0.507
(1.00) 		0.527
(1.00)
12q loss 33 (11%) 273 0.0387
(1.00) 		0.18
(1.00) 		0.913
(1.00) 		0.321
(1.00) 		0.284
(1.00) 		0.0985
(1.00) 		0.709
(1.00) 		0.396
(1.00) 		0.554
(1.00) 		0.959
(1.00) 		0.698
(1.00)
13q loss 28 (9%) 278 0.41
(1.00) 		0.419
(1.00) 		0.658
(1.00) 		0.908
(1.00) 		0.531
(1.00) 		0.07
(1.00) 		0.23
(1.00) 		0.822
(1.00) 		0.127
(1.00) 		0.0588
(1.00) 		0.458
(1.00)
14q loss 71 (23%) 235 0.97
(1.00) 		0.268
(1.00) 		0.0714
(1.00) 		0.232
(1.00) 		0.323
(1.00) 		0.0135
(1.00) 		1
(1.00) 		0.902
(1.00) 		0.665
(1.00) 		0.161
(1.00) 		0.654
(1.00)
15q loss 58 (19%) 248 0.696
(1.00) 		0.29
(1.00) 		0.61
(1.00) 		0.00514
(1.00) 		0.748
(1.00) 		0.298
(1.00) 		0.371
(1.00) 		0.00168
(1.00) 		0.0261
(1.00) 		0.655
(1.00) 		0.172
(1.00)
16p loss 62 (20%) 244 0.715
(1.00) 		0.00837
(1.00) 		0.503
(1.00) 		0.335
(1.00) 		0.168
(1.00) 		0.521
(1.00) 		0.885
(1.00) 		0.128
(1.00) 		0.633
(1.00) 		0.649
(1.00) 		0.519
(1.00)
16q loss 72 (24%) 234 0.392
(1.00) 		0.146
(1.00) 		0.179
(1.00) 		0.32
(1.00) 		0.711
(1.00) 		0.0934
(1.00) 		0.335
(1.00) 		0.0801
(1.00) 		0.361
(1.00) 		0.477
(1.00) 		0.954
(1.00)
17p loss 106 (35%) 200 0.673
(1.00) 		0.772
(1.00) 		0.645
(1.00) 		0.122
(1.00) 		0.906
(1.00) 		0.812
(1.00) 		0.392
(1.00) 		0.0142
(1.00) 		0.0512
(1.00) 		0.136
(1.00) 		0.273
(1.00)
17q loss 49 (16%) 257 0.517
(1.00) 		0.571
(1.00) 		0.421
(1.00) 		0.512
(1.00) 		0.174
(1.00) 		0.929
(1.00) 		0.151
(1.00) 		0.468
(1.00) 		0.312
(1.00) 		1
(1.00) 		0.504
(1.00)
18p loss 84 (27%) 222 0.107
(1.00) 		0.911
(1.00) 		0.337
(1.00) 		0.241
(1.00) 		0.947
(1.00) 		0.828
(1.00) 		0.359
(1.00) 		0.686
(1.00) 		0.196
(1.00) 		0.741
(1.00) 		0.151
(1.00)
18q loss 103 (34%) 203 0.435
(1.00) 		0.466
(1.00) 		0.298
(1.00) 		0.014
(1.00) 		0.945
(1.00) 		0.775
(1.00) 		0.388
(1.00) 		0.778
(1.00) 		1
(1.00) 		0.837
(1.00) 		0.0683
(1.00)
19p loss 72 (24%) 234 0.0666
(1.00) 		0.116
(1.00) 		0.9
(1.00) 		0.782
(1.00) 		0.883
(1.00) 		0.9
(1.00) 		0.783
(1.00) 		0.0283
(1.00) 		0.361
(1.00) 		0.707
(1.00) 		0.251
(1.00)
19q loss 55 (18%) 251 0.524
(1.00) 		0.0225
(1.00) 		0.869
(1.00) 		0.538
(1.00) 		0.58
(1.00) 		0.88
(1.00) 		1
(1.00) 		0.00859
(1.00) 		0.113
(1.00) 		0.744
(1.00) 		0.659
(1.00)
20p loss 16 (5%) 290 0.0463
(1.00) 		0.487
(1.00) 		0.235
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.00618
(1.00) 		0.0652
(1.00) 		0.685
(1.00) 		0.0462
(1.00) 		0.197
(1.00) 		0.966
(1.00)
21q loss 109 (36%) 197 0.785
(1.00) 		0.0281
(1.00) 		0.361
(1.00) 		0.0163
(1.00) 		0.912
(1.00) 		0.584
(1.00) 		0.0506
(1.00) 		0.976
(1.00) 		0.252
(1.00) 		0.98
(1.00) 		0.718
(1.00)
22q loss 91 (30%) 215 0.153
(1.00) 		0.772
(1.00) 		0.511
(1.00) 		0.0425
(1.00) 		0.694
(1.00) 		0.607
(1.00) 		0.443
(1.00) 		0.857
(1.00) 		0.0263
(1.00) 		0.464
(1.00) 		0.173
(1.00)
xq loss 34 (11%) 272 0.842
(1.00) 		0.832
(1.00) 		0.955
(1.00) 		0.205
(1.00) 		0.805
(1.00) 		0.823
(1.00) 		0.00825
(1.00) 		0.753
(1.00) 		0.176
(1.00) 		0.00741
(1.00) 		0.407
(1.00)
'16p gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.000167 (Fisher's exact test), Q value = 0.15

Table S1.  Gene #28: '16p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 271 20 15
16P GAIN MUTATED 29 6 7
16P GAIN WILD-TYPE 242 14 8

Figure S1.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'16q gain' versus 'PATHOLOGY.M.STAGE'

P value = 5.01e-06 (Fisher's exact test), Q value = 0.0044

Table S2.  Gene #29: '16q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 271 20 15
16Q GAIN MUTATED 19 6 7
16Q GAIN WILD-TYPE 252 14 8

Figure S2.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'xq gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 5.3e-05 (t-test), Q value = 0.046

Table S3.  Gene #40: 'xq gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 267 5.0 (7.5)
XQ GAIN MUTATED 34 2.2 (3.2)
XQ GAIN WILD-TYPE 233 5.4 (7.9)

Figure S3.  Get High-res Image Gene #40: 'xq gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = STAD-TP.merged_data.txt

  • Number of patients = 306

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 11

  • 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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' 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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[5] 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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