Correlation between copy number variations of arm-level result and selected clinical features
Stomach Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C10K2785
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/C10K2785
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 309 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%) 267 0.45
(1.00) 		0.246
(1.00) 		0.0101
(1.00) 		0.374
(1.00) 		0.564
(1.00) 		0.000153
(0.132) 		0.734
(1.00) 		0.901
(1.00) 		0.0554
(1.00) 		0.17
(1.00) 		0.174
(1.00)
16q gain 33 (11%) 276 0.194
(1.00) 		0.524
(1.00) 		0.00313
(1.00) 		0.595
(1.00) 		0.748
(1.00) 		6.59e-06
(0.00573) 		0.711
(1.00) 		0.813
(1.00) 		0.165
(1.00) 		0.0707
(1.00) 		0.161
(1.00)
xq gain 39 (13%) 270 0.603
(1.00) 		0.675
(1.00) 		0.000573
(0.496) 		0.0131
(1.00) 		0.048
(1.00) 		1
(1.00) 		0.117
(1.00) 		0.00329
(1.00) 		0.602
(1.00) 		0.74
(1.00) 		1.76e-05
(0.0153)
1p gain 30 (10%) 279 0.126
(1.00) 		0.379
(1.00) 		0.825
(1.00) 		0.432
(1.00) 		0.898
(1.00) 		0.325
(1.00) 		0.169
(1.00) 		0.0145
(1.00) 		1
(1.00) 		0.173
(1.00) 		0.234
(1.00)
1q gain 74 (24%) 235 0.42
(1.00) 		0.898
(1.00) 		0.967
(1.00) 		0.551
(1.00) 		0.774
(1.00) 		0.12
(1.00) 		0.174
(1.00) 		0.00937
(1.00) 		0.364
(1.00) 		0.644
(1.00) 		0.407
(1.00)
2p gain 50 (16%) 259 0.651
(1.00) 		0.996
(1.00) 		0.742
(1.00) 		0.342
(1.00) 		0.764
(1.00) 		0.204
(1.00) 		0.528
(1.00) 		0.22
(1.00) 		0.603
(1.00) 		0.277
(1.00) 		0.23
(1.00)
2q gain 44 (14%) 265 0.858
(1.00) 		0.991
(1.00) 		0.723
(1.00) 		0.68
(1.00) 		0.524
(1.00) 		0.625
(1.00) 		0.408
(1.00) 		0.716
(1.00) 		0.599
(1.00) 		0.317
(1.00) 		0.229
(1.00)
3p gain 36 (12%) 273 0.16
(1.00) 		0.643
(1.00) 		0.939
(1.00) 		0.946
(1.00) 		0.687
(1.00) 		1
(1.00) 		0.856
(1.00) 		0.888
(1.00) 		1
(1.00) 		0.733
(1.00) 		0.0838
(1.00)
3q gain 59 (19%) 250 0.153
(1.00) 		0.12
(1.00) 		0.739
(1.00) 		0.501
(1.00) 		0.604
(1.00) 		0.232
(1.00) 		0.883
(1.00) 		0.998
(1.00) 		1
(1.00) 		0.418
(1.00) 		0.11
(1.00)
4p gain 11 (4%) 298 0.284
(1.00) 		0.899
(1.00) 		0.038
(1.00) 		0.142
(1.00) 		0.329
(1.00) 		0.74
(1.00) 		0.211
(1.00) 		0.934
(1.00) 		1
(1.00) 		0.281
(1.00) 		0.494
(1.00)
4q gain 8 (3%) 301 0.897
(1.00) 		0.43
(1.00) 		0.544
(1.00) 		0.678
(1.00) 		0.272
(1.00) 		0.226
(1.00) 		0.486
(1.00) 		0.0183
(1.00) 		1
(1.00) 		0.558
(1.00) 		0.59
(1.00)
5p gain 69 (22%) 240 0.512
(1.00) 		0.408
(1.00) 		0.35
(1.00) 		0.599
(1.00) 		0.786
(1.00) 		0.642
(1.00) 		0.889
(1.00) 		0.00796
(1.00) 		0.188
(1.00) 		0.453
(1.00) 		0.349
(1.00)
5q gain 29 (9%) 280 0.99
(1.00) 		0.478
(1.00) 		0.403
(1.00) 		0.699
(1.00) 		0.489
(1.00) 		0.713
(1.00) 		1
(1.00) 		0.0135
(1.00) 		0.502
(1.00) 		0.457
(1.00) 		0.908
(1.00)
6p gain 56 (18%) 253 0.822
(1.00) 		0.727
(1.00) 		0.529
(1.00) 		0.305
(1.00) 		0.923
(1.00) 		0.217
(1.00) 		0.45
(1.00) 		0.0422
(1.00) 		0.0223
(1.00) 		0.423
(1.00) 		0.0442
(1.00)
6q gain 47 (15%) 262 0.422
(1.00) 		0.876
(1.00) 		0.287
(1.00) 		0.617
(1.00) 		0.713
(1.00) 		0.436
(1.00) 		0.424
(1.00) 		0.0678
(1.00) 		0.0117
(1.00) 		0.423
(1.00) 		0.175
(1.00)
7p gain 136 (44%) 173 0.0939
(1.00) 		0.218
(1.00) 		0.887
(1.00) 		0.793
(1.00) 		0.701
(1.00) 		0.184
(1.00) 		0.128
(1.00) 		0.919
(1.00) 		0.703
(1.00) 		0.865
(1.00) 		0.262
(1.00)
7q gain 117 (38%) 192 0.154
(1.00) 		0.375
(1.00) 		0.807
(1.00) 		0.997
(1.00) 		0.393
(1.00) 		0.0229
(1.00) 		0.151
(1.00) 		0.902
(1.00) 		1
(1.00) 		0.612
(1.00) 		0.195
(1.00)
8p gain 126 (41%) 183 0.466
(1.00) 		0.0276
(1.00) 		0.486
(1.00) 		0.106
(1.00) 		0.846
(1.00) 		0.0746
(1.00) 		0.156
(1.00) 		0.672
(1.00) 		0.449
(1.00) 		0.2
(1.00) 		0.947
(1.00)
8q gain 169 (55%) 140 0.553
(1.00) 		0.0117
(1.00) 		0.332
(1.00) 		0.0453
(1.00) 		0.997
(1.00) 		0.194
(1.00) 		0.641
(1.00) 		0.336
(1.00) 		0.462
(1.00) 		0.314
(1.00) 		0.354
(1.00)
9p gain 38 (12%) 271 0.95
(1.00) 		0.761
(1.00) 		0.313
(1.00) 		0.0706
(1.00) 		0.171
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.092
(1.00) 		0.208
(1.00) 		0.777
(1.00) 		0.683
(1.00)
9q gain 47 (15%) 262 0.801
(1.00) 		0.916
(1.00) 		0.402
(1.00) 		0.241
(1.00) 		0.404
(1.00) 		0.804
(1.00) 		0.517
(1.00) 		0.0635
(1.00) 		0.289
(1.00) 		0.6
(1.00) 		0.0825
(1.00)
10p gain 75 (24%) 234 0.566
(1.00) 		0.828
(1.00) 		0.485
(1.00) 		0.478
(1.00) 		0.911
(1.00) 		0.81
(1.00) 		0.786
(1.00) 		0.473
(1.00) 		0.678
(1.00) 		0.638
(1.00) 		0.468
(1.00)
10q gain 52 (17%) 257 0.935
(1.00) 		0.278
(1.00) 		0.182
(1.00) 		0.789
(1.00) 		0.587
(1.00) 		0.873
(1.00) 		0.644
(1.00) 		0.899
(1.00) 		0.335
(1.00) 		0.608
(1.00) 		0.332
(1.00)
11p gain 32 (10%) 277 0.33
(1.00) 		0.528
(1.00) 		0.768
(1.00) 		0.117
(1.00) 		0.269
(1.00) 		0.351
(1.00) 		0.445
(1.00) 		0.741
(1.00) 		0.538
(1.00) 		0.592
(1.00) 		0.478
(1.00)
11q gain 38 (12%) 271 0.838
(1.00) 		0.817
(1.00) 		0.762
(1.00) 		0.605
(1.00) 		0.0228
(1.00) 		0.696
(1.00) 		0.294
(1.00) 		0.666
(1.00) 		1
(1.00) 		0.935
(1.00) 		0.677
(1.00)
12p gain 59 (19%) 250 0.161
(1.00) 		0.215
(1.00) 		0.405
(1.00) 		0.0242
(1.00) 		0.0689
(1.00) 		0.473
(1.00) 		0.768
(1.00) 		0.109
(1.00) 		0.354
(1.00) 		0.0648
(1.00) 		0.93
(1.00)
12q gain 55 (18%) 254 0.583
(1.00) 		0.255
(1.00) 		0.445
(1.00) 		0.0515
(1.00) 		0.0181
(1.00) 		0.821
(1.00) 		0.449
(1.00) 		0.12
(1.00) 		1
(1.00) 		0.31
(1.00) 		0.831
(1.00)
13q gain 102 (33%) 207 0.0463
(1.00) 		0.963
(1.00) 		0.855
(1.00) 		0.439
(1.00) 		0.926
(1.00) 		0.174
(1.00) 		1
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.886
(1.00) 		0.846
(1.00)
14q gain 15 (5%) 294 0.00298
(1.00) 		0.168
(1.00) 		0.854
(1.00) 		0.532
(1.00) 		0.0352
(1.00) 		0.378
(1.00) 		0.287
(1.00) 		0.225
(1.00) 		1
(1.00) 		0.0327
(1.00) 		0.168
(1.00)
15q gain 25 (8%) 284 0.617
(1.00) 		0.791
(1.00) 		0.538
(1.00) 		0.909
(1.00) 		0.0458
(1.00) 		0.391
(1.00) 		0.524
(1.00) 		0.948
(1.00) 		1
(1.00) 		0.444
(1.00) 		0.988
(1.00)
17p gain 19 (6%) 290 0.613
(1.00) 		0.191
(1.00) 		0.238
(1.00) 		0.859
(1.00) 		0.87
(1.00) 		0.00343
(1.00) 		1
(1.00) 		0.0791
(1.00) 		0.362
(1.00) 		0.0195
(1.00) 		0.864
(1.00)
17q gain 36 (12%) 273 0.495
(1.00) 		0.86
(1.00) 		0.807
(1.00) 		0.578
(1.00) 		0.825
(1.00) 		0.00469
(1.00) 		0.72
(1.00) 		0.668
(1.00) 		0.584
(1.00) 		0.0633
(1.00) 		0.871
(1.00)
18p gain 53 (17%) 256 0.00577
(1.00) 		0.0185
(1.00) 		0.729
(1.00) 		0.605
(1.00) 		0.374
(1.00) 		0.545
(1.00) 		0.759
(1.00) 		0.0162
(1.00) 		0.002
(1.00) 		0.162
(1.00) 		0.191
(1.00)
18q gain 40 (13%) 269 0.00854
(1.00) 		0.0549
(1.00) 		0.43
(1.00) 		0.243
(1.00) 		0.529
(1.00) 		0.292
(1.00) 		0.605
(1.00) 		0.00156
(1.00) 		0.0487
(1.00) 		0.32
(1.00) 		0.476
(1.00)
19p gain 40 (13%) 269 0.337
(1.00) 		0.479
(1.00) 		0.212
(1.00) 		0.0829
(1.00) 		0.0291
(1.00) 		0.064
(1.00) 		0.49
(1.00) 		0.044
(1.00) 		0.226
(1.00) 		0.0495
(1.00) 		0.0502
(1.00)
19q gain 53 (17%) 256 0.4
(1.00) 		0.983
(1.00) 		0.4
(1.00) 		0.379
(1.00) 		0.0232
(1.00) 		0.13
(1.00) 		0.54
(1.00) 		0.153
(1.00) 		0.1
(1.00) 		0.208
(1.00) 		0.0156
(1.00)
20p gain 165 (53%) 144 0.535
(1.00) 		0.965
(1.00) 		0.587
(1.00) 		0.21
(1.00) 		0.386
(1.00) 		0.446
(1.00) 		0.0199
(1.00) 		0.188
(1.00) 		0.709
(1.00) 		0.575
(1.00) 		0.0899
(1.00)
20q gain 193 (62%) 116 0.4
(1.00) 		0.545
(1.00) 		0.453
(1.00) 		0.214
(1.00) 		0.325
(1.00) 		0.11
(1.00) 		0.00825
(1.00) 		0.0225
(1.00) 		1
(1.00) 		0.0987
(1.00) 		0.223
(1.00)
21q gain 19 (6%) 290 0.57
(1.00) 		0.969
(1.00) 		0.732
(1.00) 		0.506
(1.00) 		0.72
(1.00) 		0.852
(1.00) 		1
(1.00) 		0.155
(1.00) 		0.362
(1.00) 		0.519
(1.00) 		0.936
(1.00)
22q gain 24 (8%) 285 0.279
(1.00) 		0.786
(1.00) 		0.0871
(1.00) 		0.296
(1.00) 		0.539
(1.00) 		1
(1.00) 		1
(1.00) 		0.697
(1.00) 		1
(1.00) 		0.806
(1.00) 		0.99
(1.00)
1p loss 40 (13%) 269 0.568
(1.00) 		0.998
(1.00) 		0.225
(1.00) 		0.641
(1.00) 		0.494
(1.00) 		0.0783
(1.00) 		0.49
(1.00) 		0.503
(1.00) 		1
(1.00) 		0.155
(1.00) 		0.384
(1.00)
1q loss 19 (6%) 290 0.22
(1.00) 		0.747
(1.00) 		0.347
(1.00) 		0.469
(1.00) 		0.631
(1.00) 		0.0624
(1.00) 		0.477
(1.00) 		0.878
(1.00) 		1
(1.00) 		0.275
(1.00) 		0.945
(1.00)
2p loss 16 (5%) 293 0.13
(1.00) 		0.73
(1.00) 		0.765
(1.00) 		0.95
(1.00) 		0.421
(1.00) 		0.187
(1.00) 		0.192
(1.00) 		0.0384
(1.00) 		0.0454
(1.00) 		0.151
(1.00) 		0.307
(1.00)
2q loss 19 (6%) 290 0.499
(1.00) 		0.778
(1.00) 		0.93
(1.00) 		0.604
(1.00) 		0.517
(1.00) 		0.258
(1.00) 		1
(1.00) 		0.0187
(1.00) 		0.0626
(1.00) 		0.155
(1.00) 		0.317
(1.00)
3p loss 59 (19%) 250 0.693
(1.00) 		0.748
(1.00) 		0.979
(1.00) 		0.652
(1.00) 		0.187
(1.00) 		0.203
(1.00) 		0.883
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.141
(1.00) 		0.0452
(1.00)
3q loss 35 (11%) 274 0.778
(1.00) 		0.242
(1.00) 		0.937
(1.00) 		0.0152
(1.00) 		0.598
(1.00) 		0.825
(1.00) 		1
(1.00) 		0.523
(1.00) 		1
(1.00) 		0.57
(1.00) 		0.194
(1.00)
4p loss 111 (36%) 198 0.643
(1.00) 		0.371
(1.00) 		0.197
(1.00) 		0.0455
(1.00) 		0.869
(1.00) 		0.219
(1.00) 		0.333
(1.00) 		0.503
(1.00) 		0.256
(1.00) 		0.428
(1.00) 		0.224
(1.00)
4q loss 110 (36%) 199 0.578
(1.00) 		0.168
(1.00) 		0.442
(1.00) 		0.147
(1.00) 		0.435
(1.00) 		0.634
(1.00) 		0.0397
(1.00) 		0.462
(1.00) 		0.252
(1.00) 		0.556
(1.00) 		0.263
(1.00)
5p loss 37 (12%) 272 0.191
(1.00) 		0.543
(1.00) 		0.0407
(1.00) 		0.78
(1.00) 		0.396
(1.00) 		0.631
(1.00) 		0.86
(1.00) 		0.273
(1.00) 		1
(1.00) 		1
(1.00) 		0.901
(1.00)
5q loss 64 (21%) 245 0.466
(1.00) 		0.577
(1.00) 		0.00838
(1.00) 		0.782
(1.00) 		0.388
(1.00) 		0.224
(1.00) 		0.775
(1.00) 		0.177
(1.00) 		0.637
(1.00) 		0.517
(1.00) 		0.957
(1.00)
6p loss 30 (10%) 279 0.968
(1.00) 		0.271
(1.00) 		0.662
(1.00) 		0.742
(1.00) 		0.603
(1.00) 		0.0761
(1.00) 		0.327
(1.00) 		0.0719
(1.00) 		1
(1.00) 		0.887
(1.00) 		0.617
(1.00)
6q loss 40 (13%) 269 0.573
(1.00) 		0.604
(1.00) 		0.608
(1.00) 		0.351
(1.00) 		0.822
(1.00) 		0.0139
(1.00) 		0.226
(1.00) 		0.353
(1.00) 		0.601
(1.00) 		0.969
(1.00) 		0.745
(1.00)
7p loss 10 (3%) 299 0.121
(1.00) 		0.913
(1.00) 		0.228
(1.00) 		0.186
(1.00) 		0.943
(1.00) 		0.483
(1.00) 		0.325
(1.00) 		0.778
(1.00) 		1
(1.00) 		1
(1.00) 		0.687
(1.00)
7q loss 20 (6%) 289 0.079
(1.00) 		0.345
(1.00) 		0.222
(1.00) 		0.119
(1.00) 		0.56
(1.00) 		0.724
(1.00) 		0.48
(1.00) 		0.114
(1.00) 		1
(1.00) 		1
(1.00) 		0.323
(1.00)
8p loss 51 (17%) 258 0.997
(1.00) 		0.341
(1.00) 		0.236
(1.00) 		0.545
(1.00) 		0.147
(1.00) 		0.461
(1.00) 		0.351
(1.00) 		0.0753
(1.00) 		0.326
(1.00) 		0.27
(1.00) 		0.0595
(1.00)
8q loss 16 (5%) 293 0.791
(1.00) 		0.57
(1.00) 		0.825
(1.00) 		0.0201
(1.00) 		0.533
(1.00) 		0.319
(1.00) 		0.795
(1.00) 		0.493
(1.00) 		0.313
(1.00) 		0.151
(1.00) 		0.217
(1.00)
9p loss 94 (30%) 215 0.544
(1.00) 		0.229
(1.00) 		0.256
(1.00) 		0.413
(1.00) 		0.458
(1.00) 		0.267
(1.00) 		0.527
(1.00) 		0.258
(1.00) 		0.206
(1.00) 		0.381
(1.00) 		0.952
(1.00)
9q loss 64 (21%) 245 0.656
(1.00) 		0.885
(1.00) 		0.257
(1.00) 		0.27
(1.00) 		0.931
(1.00) 		0.0152
(1.00) 		0.775
(1.00) 		0.936
(1.00) 		0.0358
(1.00) 		0.212
(1.00) 		0.187
(1.00)
10p loss 35 (11%) 274 0.403
(1.00) 		0.377
(1.00) 		0.0255
(1.00) 		0.12
(1.00) 		0.177
(1.00) 		0.222
(1.00) 		0.855
(1.00) 		0.248
(1.00) 		0.182
(1.00) 		0.229
(1.00) 		0.22
(1.00)
10q loss 40 (13%) 269 0.407
(1.00) 		0.0169
(1.00) 		0.409
(1.00) 		0.23
(1.00) 		0.476
(1.00) 		1
(1.00) 		1
(1.00) 		0.199
(1.00) 		0.226
(1.00) 		0.575
(1.00) 		0.545
(1.00)
11p loss 43 (14%) 266 0.4
(1.00) 		0.839
(1.00) 		0.736
(1.00) 		0.0655
(1.00) 		0.782
(1.00) 		0.19
(1.00) 		0.615
(1.00) 		0.00616
(1.00) 		1
(1.00) 		0.118
(1.00) 		0.3
(1.00)
11q loss 40 (13%) 269 0.0301
(1.00) 		0.73
(1.00) 		0.138
(1.00) 		0.674
(1.00) 		0.271
(1.00) 		0.19
(1.00) 		0.388
(1.00) 		0.351
(1.00) 		1
(1.00) 		0.182
(1.00) 		0.159
(1.00)
12p loss 43 (14%) 266 0.342
(1.00) 		0.102
(1.00) 		0.362
(1.00) 		0.149
(1.00) 		0.112
(1.00) 		0.44
(1.00) 		0.506
(1.00) 		0.0264
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.542
(1.00)
12q loss 33 (11%) 276 0.0828
(1.00) 		0.204
(1.00) 		0.896
(1.00) 		0.326
(1.00) 		0.293
(1.00) 		0.109
(1.00) 		0.711
(1.00) 		0.37
(1.00) 		0.55
(1.00) 		0.959
(1.00) 		0.712
(1.00)
13q loss 28 (9%) 281 0.427
(1.00) 		0.462
(1.00) 		0.692
(1.00) 		0.918
(1.00) 		0.527
(1.00) 		0.0676
(1.00) 		0.311
(1.00) 		0.834
(1.00) 		0.125
(1.00) 		0.0565
(1.00) 		0.448
(1.00)
14q loss 71 (23%) 238 0.938
(1.00) 		0.223
(1.00) 		0.119
(1.00) 		0.251
(1.00) 		0.269
(1.00) 		0.0148
(1.00) 		1
(1.00) 		0.883
(1.00) 		0.663
(1.00) 		0.166
(1.00) 		0.676
(1.00)
15q loss 58 (19%) 251 0.937
(1.00) 		0.339
(1.00) 		0.703
(1.00) 		0.00609
(1.00) 		0.795
(1.00) 		0.295
(1.00) 		0.374
(1.00) 		0.00192
(1.00) 		0.0253
(1.00) 		0.652
(1.00) 		0.167
(1.00)
16p loss 62 (20%) 247 0.73
(1.00) 		0.0114
(1.00) 		0.523
(1.00) 		0.36
(1.00) 		0.155
(1.00) 		0.548
(1.00) 		0.885
(1.00) 		0.122
(1.00) 		0.631
(1.00) 		0.637
(1.00) 		0.535
(1.00)
16q loss 71 (23%) 238 0.291
(1.00) 		0.161
(1.00) 		0.179
(1.00) 		0.321
(1.00) 		0.716
(1.00) 		0.112
(1.00) 		0.411
(1.00) 		0.0686
(1.00) 		0.201
(1.00) 		0.505
(1.00) 		0.985
(1.00)
17p loss 106 (34%) 203 0.756
(1.00) 		0.89
(1.00) 		0.55
(1.00) 		0.142
(1.00) 		0.866
(1.00) 		0.811
(1.00) 		0.391
(1.00) 		0.0116
(1.00) 		0.0491
(1.00) 		0.14
(1.00) 		0.258
(1.00)
17q loss 48 (16%) 261 0.951
(1.00) 		0.64
(1.00) 		0.3
(1.00) 		0.54
(1.00) 		0.0987
(1.00) 		0.928
(1.00) 		0.202
(1.00) 		0.534
(1.00) 		0.298
(1.00) 		0.928
(1.00) 		0.318
(1.00)
18p loss 84 (27%) 225 0.318
(1.00) 		0.93
(1.00) 		0.236
(1.00) 		0.264
(1.00) 		0.89
(1.00) 		0.867
(1.00) 		0.298
(1.00) 		0.637
(1.00) 		0.196
(1.00) 		0.754
(1.00) 		0.147
(1.00)
18q loss 103 (33%) 206 0.482
(1.00) 		0.559
(1.00) 		0.171
(1.00) 		0.0183
(1.00) 		0.852
(1.00) 		0.774
(1.00) 		0.459
(1.00) 		0.806
(1.00) 		1
(1.00) 		0.806
(1.00) 		0.0641
(1.00)
19p loss 72 (23%) 237 0.0276
(1.00) 		0.106
(1.00) 		0.966
(1.00) 		0.774
(1.00) 		0.855
(1.00) 		0.899
(1.00) 		1
(1.00) 		0.0332
(1.00) 		0.36
(1.00) 		0.723
(1.00) 		0.274
(1.00)
19q loss 56 (18%) 253 0.196
(1.00) 		0.0239
(1.00) 		0.843
(1.00) 		0.469
(1.00) 		0.519
(1.00) 		0.881
(1.00) 		1
(1.00) 		0.013
(1.00) 		0.115
(1.00) 		0.722
(1.00) 		0.706
(1.00)
20p loss 16 (5%) 293 0.0832
(1.00) 		0.509
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.559
(1.00) 		0.00589
(1.00) 		0.0667
(1.00) 		0.681
(1.00) 		0.0454
(1.00) 		0.192
(1.00) 		0.95
(1.00)
21q loss 108 (35%) 201 0.961
(1.00) 		0.0269
(1.00) 		0.479
(1.00) 		0.0232
(1.00) 		0.943
(1.00) 		0.631
(1.00) 		0.0875
(1.00) 		0.966
(1.00) 		0.244
(1.00) 		0.969
(1.00) 		0.765
(1.00)
22q loss 91 (29%) 218 0.179
(1.00) 		0.87
(1.00) 		0.52
(1.00) 		0.0485
(1.00) 		0.644
(1.00) 		0.633
(1.00) 		0.446
(1.00) 		0.85
(1.00) 		0.0251
(1.00) 		0.451
(1.00) 		0.166
(1.00)
xq loss 35 (11%) 274 0.851
(1.00) 		0.447
(1.00) 		0.994
(1.00) 		0.475
(1.00) 		0.876
(1.00) 		1
(1.00) 		0.0424
(1.00) 		0.645
(1.00) 		0.182
(1.00) 		0.0105
(1.00) 		0.383
(1.00)
'16p gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.000153 (Fisher's exact test), Q value = 0.13

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

nPatients M0 M1 MX
ALL 274 20 15
16P GAIN MUTATED 29 6 7
16P GAIN WILD-TYPE 245 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 = 6.59e-06 (Fisher's exact test), Q value = 0.0057

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

nPatients M0 M1 MX
ALL 274 20 15
16Q GAIN MUTATED 20 6 7
16Q GAIN WILD-TYPE 254 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 = 1.76e-05 (t-test), Q value = 0.015

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

nPatients Mean (Std.Dev)
ALL 270 5.0 (7.5)
XQ GAIN MUTATED 34 2.1 (3.2)
XQ GAIN WILD-TYPE 236 5.4 (7.8)

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 = 309

  • 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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