Correlation between copy number variations of arm-level result and selected clinical features
Pancreatic Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C16W99HR
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C16W99HR
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 80 arm-level events and 15 clinical features across 184 patients, 2 significant findings detected with Q value < 0.25.

  • 3q gain cnv correlated to 'Time to Death'.

  • 17p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
3q gain 20 (11%) 164 0.000395
(0.237) 		0.933
(1.00) 		0.495
(1.00) 		1
(1.00) 		0.788
(1.00) 		0.0931
(0.896) 		0.0611
(0.824) 		0.00404
(0.387) 		0.86
(1.00) 		0.688
(1.00) 		0.221
(0.959) 		0.492
(1.00) 		0.172
(0.924) 		1
(1.00) 		1
(1.00)
17p gain 10 (5%) 174 0.00239
(0.387) 		0.0252
(0.676) 		0.0154
(0.597) 		0.206
(0.942) 		0.401
(1.00) 		1
(1.00) 		0.35
(1.00) 		0.288
(0.988) 		0.00022
(0.237) 		1
(1.00) 		0.629
(1.00) 		0.42
(1.00) 		1
(1.00)
1p gain 22 (12%) 162 0.955
(1.00) 		0.167
(0.924) 		0.175
(0.924) 		0.593
(1.00) 		0.446
(1.00) 		0.192
(0.94) 		0.254
(0.976) 		1
(1.00) 		0.0554
(0.817) 		0.0695
(0.845) 		0.874
(1.00) 		0.295
(0.988) 		0.395
(1.00) 		0.694
(1.00) 		0.388
(1.00)
1q gain 52 (28%) 132 0.562
(1.00) 		0.252
(0.976) 		0.0162
(0.606) 		0.338
(1.00) 		0.0971
(0.906) 		0.129
(0.906) 		0.0995
(0.906) 		1
(1.00) 		0.383
(1.00) 		0.889
(1.00) 		0.933
(1.00) 		0.799
(1.00) 		0.285
(0.988) 		0.134
(0.906) 		0.602
(1.00)
2p gain 16 (9%) 168 0.963
(1.00) 		0.854
(1.00) 		0.508
(1.00) 		0.894
(1.00) 		0.562
(1.00) 		0.487
(1.00) 		0.0344
(0.731) 		1
(1.00) 		0.803
(1.00) 		0.773
(1.00) 		0.0666
(0.845) 		0.511
(1.00) 		0.208
(0.942) 		0.795
(1.00) 		1
(1.00)
2q gain 18 (10%) 166 0.656
(1.00) 		0.73
(1.00) 		0.546
(1.00) 		0.706
(1.00) 		0.783
(1.00) 		0.52
(1.00) 		0.0121
(0.495) 		1
(1.00) 		1
(1.00) 		0.359
(1.00) 		0.197
(0.94) 		0.484
(1.00) 		0.46
(1.00) 		0.663
(1.00) 		1
(1.00)
3p gain 10 (5%) 174 0.372
(1.00) 		0.585
(1.00) 		0.314
(0.998) 		0.464
(1.00) 		0.145
(0.924) 		0.339
(1.00) 		0.0239
(0.676) 		0.114
(0.906) 		1
(1.00) 		0.71
(1.00) 		0.421
(1.00) 		1
(1.00) 		1
(1.00)
4p gain 11 (6%) 173 0.178
(0.933) 		0.485
(1.00) 		0.181
(0.934) 		0.513
(1.00) 		0.469
(1.00) 		0.159
(0.924) 		0.548
(1.00) 		0.241
(0.972) 		0.00678
(0.473) 		1
(1.00) 		0.37
(1.00) 		1
(1.00) 		0.257
(0.976)
4q gain 9 (5%) 175 0.121
(0.906) 		0.391
(1.00) 		0.0765
(0.85) 		0.349
(1.00) 		0.688
(1.00) 		0.0556
(0.817) 		0.733
(1.00) 		0.0762
(0.85) 		0.0752
(0.85) 		1
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.257
(0.976)
5p gain 28 (15%) 156 0.686
(1.00) 		0.847
(1.00) 		0.273
(0.988) 		0.402
(1.00) 		1
(1.00) 		1
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.0331
(0.731) 		0.507
(1.00) 		0.0482
(0.784) 		0.575
(1.00) 		0.625
(1.00) 		1
(1.00) 		0.54
(1.00)
5q gain 22 (12%) 162 0.232
(0.966) 		0.66
(1.00) 		0.165
(0.924) 		0.161
(0.924) 		0.788
(1.00) 		1
(1.00) 		0.82
(1.00) 		0.597
(1.00) 		0.258
(0.978) 		0.208
(0.942) 		0.219
(0.959) 		0.763
(1.00) 		0.828
(1.00) 		0.847
(1.00) 		0.479
(1.00)
6p gain 7 (4%) 177 0.128
(0.906) 		0.939
(1.00) 		0.231
(0.966) 		1
(1.00) 		0.351
(1.00) 		0.109
(0.906) 		0.13
(0.906) 		1
(1.00) 		0.0781
(0.859) 		1
(1.00) 		0.387
(1.00) 		0.298
(0.988) 		1
(1.00)
6q gain 5 (3%) 179 0.462
(1.00) 		0.512
(1.00) 		0.271
(0.988) 		1
(1.00) 		0.311
(0.998) 		0.109
(0.906) 		0.38
(1.00) 		0.606
(1.00) 		0.257
(0.976) 		0.74
(1.00) 		0.898
(1.00) 		0.208
(0.942) 		1
(1.00)
7p gain 53 (29%) 131 0.638
(1.00) 		0.447
(1.00) 		0.3
(0.988) 		0.444
(1.00) 		0.578
(1.00) 		0.615
(1.00) 		0.414
(1.00) 		0.337
(1.00) 		0.0353
(0.731) 		0.133
(0.906) 		0.285
(0.988) 		0.103
(0.906) 		0.277
(0.988) 		0.522
(1.00) 		0.322
(1.00)
7q gain 49 (27%) 135 0.619
(1.00) 		0.636
(1.00) 		0.329
(1.00) 		0.399
(1.00) 		0.569
(1.00) 		0.599
(1.00) 		0.319
(1.00) 		0.557
(1.00) 		0.0433
(0.784) 		0.118
(0.906) 		0.179
(0.933) 		0.0652
(0.845) 		0.149
(0.924) 		0.283
(0.988) 		0.326
(1.00)
8p gain 25 (14%) 159 0.583
(1.00) 		0.76
(1.00) 		0.904
(1.00) 		0.94
(1.00) 		0.625
(1.00) 		1
(1.00) 		0.39
(1.00) 		0.019
(0.653) 		1
(1.00) 		0.387
(1.00) 		0.654
(1.00) 		0.27
(0.988) 		0.688
(1.00) 		0.851
(1.00) 		0.134
(0.906)
8q gain 48 (26%) 136 0.353
(1.00) 		0.22
(0.959) 		0.743
(1.00) 		0.972
(1.00) 		0.57
(1.00) 		1
(1.00) 		0.241
(0.972) 		0.553
(1.00) 		0.26
(0.98) 		0.802
(1.00) 		0.553
(1.00) 		0.119
(0.906) 		0.714
(1.00) 		0.37
(1.00) 		0.0906
(0.896)
9p gain 8 (4%) 176 0.38
(1.00) 		0.0839
(0.891) 		0.794
(1.00) 		0.588
(1.00) 		0.688
(1.00) 		1
(1.00) 		0.297
(0.988) 		0.43
(1.00) 		0.0737
(0.845) 		0.532
(1.00) 		0.575
(1.00) 		1
(1.00) 		0.167
(0.924)
9q gain 12 (7%) 172 0.216
(0.953) 		0.31
(0.997) 		0.322
(1.00) 		0.253
(0.976) 		0.184
(0.94) 		1
(1.00) 		0.551
(1.00) 		0.479
(1.00) 		0.562
(1.00) 		0.127
(0.906) 		0.328
(1.00) 		1
(1.00) 		0.257
(0.976)
10p gain 10 (5%) 174 0.74
(1.00) 		0.527
(1.00) 		0.523
(1.00) 		0.641
(1.00) 		0.711
(1.00) 		0.298
(0.988) 		0.117
(0.906) 		1
(1.00) 		0.362
(1.00) 		0.369
(1.00) 		0.729
(1.00) 		0.00343
(0.387) 		1
(1.00)
10q gain 13 (7%) 171 0.174
(0.924) 		0.461
(1.00) 		0.663
(1.00) 		0.224
(0.959) 		0.514
(1.00) 		0.379
(1.00) 		0.0397
(0.769) 		0.518
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.462
(1.00) 		0.355
(1.00) 		0.127
(0.906) 		0.0102
(0.473) 		1
(1.00)
11p gain 14 (8%) 170 0.182
(0.934) 		0.307
(0.997) 		0.501
(1.00) 		0.488
(1.00) 		0.539
(1.00) 		1
(1.00) 		0.0924
(0.896) 		0.518
(1.00) 		0.175
(0.924) 		0.806
(1.00) 		0.0372
(0.744) 		0.358
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 17 (9%) 167 0.00162
(0.387) 		0.695
(1.00) 		0.643
(1.00) 		0.753
(1.00) 		1
(1.00) 		1
(1.00) 		0.207
(0.942) 		0.564
(1.00) 		0.28
(0.988) 		0.155
(0.924) 		0.725
(1.00) 		0.0488
(0.784) 		0.369
(1.00) 		0.48
(1.00) 		0.0672
(0.845)
12p gain 32 (17%) 152 0.619
(1.00) 		0.834
(1.00) 		0.172
(0.924) 		0.582
(1.00) 		0.821
(1.00) 		0.417
(1.00) 		0.117
(0.906) 		0.821
(1.00) 		0.0124
(0.495) 		0.829
(1.00) 		0.584
(1.00) 		0.0289
(0.693) 		0.0908
(0.896) 		0.464
(1.00) 		0.586
(1.00)
12q gain 24 (13%) 160 0.579
(1.00) 		0.427
(1.00) 		0.154
(0.924) 		0.723
(1.00) 		0.597
(1.00) 		1
(1.00) 		0.0465
(0.784) 		0.799
(1.00) 		0.0356
(0.731) 		0.352
(1.00) 		0.385
(1.00) 		0.01
(0.473) 		0.0328
(0.731) 		0.856
(1.00) 		1
(1.00)
13q gain 28 (15%) 156 0.3
(0.988) 		0.314
(0.998) 		0.317
(1.00) 		0.482
(1.00) 		0.642
(1.00) 		0.55
(1.00) 		0.542
(1.00) 		0.323
(1.00) 		0.0033
(0.387) 		0.0359
(0.731) 		0.182
(0.934) 		0.869
(1.00) 		0.638
(1.00) 		1
(1.00)
14q gain 26 (14%) 158 0.532
(1.00) 		0.707
(1.00) 		0.7
(1.00) 		1
(1.00) 		0.473
(1.00) 		0.487
(1.00) 		0.527
(1.00) 		0.314
(0.998) 		0.893
(1.00) 		0.794
(1.00) 		0.909
(1.00) 		0.577
(1.00) 		0.37
(1.00) 		0.744
(1.00) 		0.52
(1.00)
15q gain 15 (8%) 169 0.815
(1.00) 		0.369
(1.00) 		0.195
(0.94) 		0.33
(1.00) 		0.117
(0.906) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.61
(1.00) 		0.394
(1.00) 		0.0579
(0.817) 		1
(1.00) 		0.284
(0.988)
16p gain 23 (12%) 161 0.285
(0.988) 		0.0565
(0.817) 		0.892
(1.00) 		0.94
(1.00) 		0.621
(1.00) 		0.453
(1.00) 		0.0718
(0.845) 		0.793
(1.00) 		0.871
(1.00) 		0.719
(1.00) 		0.137
(0.906) 		0.0647
(0.845) 		0.622
(1.00) 		0.487
(1.00) 		1
(1.00)
16q gain 23 (12%) 161 0.816
(1.00) 		0.166
(0.924) 		0.555
(1.00) 		0.739
(1.00) 		1
(1.00) 		0.13
(0.906) 		0.0718
(0.845) 		0.793
(1.00) 		0.872
(1.00) 		0.719
(1.00) 		0.137
(0.906) 		0.415
(1.00) 		0.913
(1.00) 		0.487
(1.00) 		1
(1.00)
17q gain 19 (10%) 165 0.00306
(0.387) 		0.0339
(0.731) 		0.0739
(0.845) 		0.824
(1.00) 		0.152
(0.924) 		0.339
(1.00) 		0.627
(1.00) 		0.0218
(0.676) 		0.0181
(0.638) 		0.412
(1.00) 		0.672
(1.00) 		0.92
(1.00) 		0.775
(1.00) 		0.532
(1.00) 		1
(1.00)
18p gain 29 (16%) 155 0.275
(0.988) 		0.0725
(0.845) 		0.986
(1.00) 		0.806
(1.00) 		0.821
(1.00) 		0.55
(1.00) 		0.108
(0.906) 		0.812
(1.00) 		0.0271
(0.677) 		0.367
(1.00) 		0.584
(1.00) 		0.6
(1.00) 		0.345
(1.00) 		0.752
(1.00) 		1
(1.00)
18q gain 13 (7%) 171 0.294
(0.988) 		0.823
(1.00) 		0.894
(1.00) 		0.66
(1.00) 		1
(1.00) 		1
(1.00) 		0.389
(1.00) 		1
(1.00) 		0.00792
(0.473) 		0.756
(1.00) 		0.522
(1.00) 		1
(1.00) 		1
(1.00)
19p gain 19 (10%) 165 0.133
(0.906) 		0.864
(1.00) 		0.454
(1.00) 		0.331
(1.00) 		0.783
(1.00) 		0.453
(1.00) 		0.0933
(0.896) 		1
(1.00) 		0.175
(0.924) 		0.0611
(0.824) 		1
(1.00) 		0.203
(0.942) 		0.271
(0.988) 		0.446
(1.00) 		1
(1.00)
19q gain 29 (16%) 155 0.126
(0.906) 		0.893
(1.00) 		0.746
(1.00) 		0.331
(1.00) 		0.493
(1.00) 		1
(1.00) 		0.0435
(0.784) 		0.811
(1.00) 		0.395
(1.00) 		0.121
(0.906) 		0.552
(1.00) 		0.265
(0.988) 		0.364
(1.00) 		0.162
(0.924) 		0.5
(1.00)
20p gain 36 (20%) 148 0.39
(1.00) 		0.102
(0.906) 		0.576
(1.00) 		0.522
(1.00) 		1
(1.00) 		1
(1.00) 		0.136
(0.906) 		0.663
(1.00) 		0.0514
(0.811) 		0.391
(1.00) 		0.383
(1.00) 		0.301
(0.988) 		0.686
(1.00) 		0.286
(0.988) 		1
(1.00)
20q gain 46 (25%) 138 0.393
(1.00) 		0.337
(1.00) 		0.983
(1.00) 		0.775
(1.00) 		0.7
(1.00) 		1
(1.00) 		0.0601
(0.824) 		0.553
(1.00) 		0.15
(0.924) 		0.17
(0.924) 		0.459
(1.00) 		0.707
(1.00) 		0.748
(1.00) 		0.552
(1.00) 		1
(1.00)
22q gain 7 (4%) 177 0.0654
(0.845) 		0.212
(0.942) 		1
(1.00) 		0.739
(1.00) 		0.675
(1.00) 		1
(1.00) 		0.0471
(0.784) 		0.651
(1.00) 		0.0574
(0.817) 		1
(1.00) 		0.518
(1.00) 		0.253
(0.976) 		1
(1.00)
xp gain 8 (4%) 176 0.00985
(0.473) 		0.192
(0.94) 		0.495
(1.00) 		0.157
(0.924) 		0.672
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.678
(1.00) 		0.00373
(0.387) 		0.532
(1.00) 		0.871
(1.00) 		0.339
(1.00) 		1
(1.00)
xq gain 15 (8%) 169 0.0124
(0.495) 		0.779
(1.00) 		0.197
(0.94) 		0.268
(0.988) 		0.758
(1.00) 		0.159
(0.924) 		1
(1.00) 		1
(1.00) 		0.0446
(0.784) 		0.532
(1.00) 		0.756
(1.00) 		0.453
(1.00) 		0.412
(1.00)
1p loss 34 (18%) 150 0.308
(0.997) 		0.192
(0.94) 		0.346
(1.00) 		0.761
(1.00) 		0.389
(1.00) 		1
(1.00) 		0.253
(0.976) 		0.658
(1.00) 		0.654
(1.00) 		0.225
(0.959) 		0.491
(1.00) 		0.692
(1.00) 		0.401
(1.00) 		0.786
(1.00) 		1
(1.00)
1q loss 8 (4%) 176 0.539
(1.00) 		0.0902
(0.896) 		0.156
(0.924) 		0.447
(1.00) 		1
(1.00) 		1
(1.00) 		0.297
(0.988) 		0.113
(0.906) 		0.453
(1.00) 		0.177
(0.932) 		0.815
(1.00) 		0.852
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 10 (5%) 174 0.0724
(0.845) 		0.456
(1.00) 		0.128
(0.906) 		0.554
(1.00) 		0.268
(0.988) 		1
(1.00) 		0.756
(1.00) 		0.721
(1.00) 		0.00318
(0.387) 		0.29
(0.988) 		0.0852
(0.896) 		0.266
(0.988) 		1
(1.00)
2q loss 4 (2%) 180 0.0277
(0.679) 		0.131
(0.906) 		0.0252
(0.676) 		0.1
(0.906) 		0.189
(0.94) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.00925
(0.473) 		0.44
(1.00) 		0.442
(1.00) 		1
(1.00) 		1
(1.00)
3p loss 36 (20%) 148 0.929
(1.00) 		0.677
(1.00) 		0.789
(1.00) 		0.759
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.0247
(0.676) 		0.279
(0.988) 		0.234
(0.97) 		0.563
(1.00) 		0.782
(1.00) 		0.918
(1.00) 		0.29
(0.988) 		0.631
(1.00) 		0.584
(1.00)
3q loss 19 (10%) 165 0.416
(1.00) 		0.933
(1.00) 		0.986
(1.00) 		0.598
(1.00) 		1
(1.00) 		1
(1.00) 		0.0933
(0.896) 		1
(1.00) 		0.192
(0.94) 		0.385
(1.00) 		0.11
(0.906) 		1
(1.00) 		0.975
(1.00) 		0.0271
(0.677) 		1
(1.00)
4p loss 25 (14%) 159 0.691
(1.00) 		0.889
(1.00) 		0.839
(1.00) 		0.756
(1.00) 		0.228
(0.965) 		1
(1.00) 		0.0297
(0.698) 		1
(1.00) 		0.305
(0.997) 		0.763
(1.00) 		0.646
(1.00) 		0.869
(1.00) 		0.172
(0.924) 		0.328
(1.00) 		0.52
(1.00)
4q loss 24 (13%) 160 0.591
(1.00) 		0.552
(1.00) 		0.915
(1.00) 		0.885
(1.00) 		0.32
(1.00) 		1
(1.00) 		0.00353
(0.387) 		0.8
(1.00) 		0.324
(1.00) 		0.32
(1.00) 		0.366
(1.00) 		0.781
(1.00) 		0.314
(0.998) 		0.306
(0.997) 		0.5
(1.00)
5p loss 9 (5%) 175 0.554
(1.00) 		0.596
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.208
(0.942) 		1
(1.00) 		0.477
(1.00) 		0.558
(1.00) 		0.533
(1.00) 		0.0887
(0.896) 		0.625
(1.00) 		0.198
(0.94)
5q loss 11 (6%) 173 0.993
(1.00) 		0.757
(1.00) 		0.617
(1.00) 		1
(1.00) 		0.295
(0.988) 		1
(1.00) 		0.757
(1.00) 		0.288
(0.988) 		0.0731
(0.845) 		0.572
(1.00) 		0.654
(1.00) 		0.255
(0.976) 		0.0931
(0.896) 		0.7
(1.00) 		0.257
(0.976)
6p loss 64 (35%) 120 0.139
(0.909) 		0.285
(0.988) 		0.34
(1.00) 		0.905
(1.00) 		0.295
(0.988) 		0.171
(0.924) 		0.162
(0.924) 		0.855
(1.00) 		0.155
(0.924) 		0.193
(0.94) 		0.991
(1.00) 		0.622
(1.00) 		0.115
(0.906) 		1
(1.00) 		0.661
(1.00)
6q loss 82 (45%) 102 0.131
(0.906) 		0.238
(0.972) 		0.398
(1.00) 		0.522
(1.00) 		0.868
(1.00) 		0.392
(1.00) 		0.18
(0.933) 		1
(1.00) 		0.625
(1.00) 		0.229
(0.965) 		0.589
(1.00) 		0.834
(1.00) 		0.985
(1.00) 		0.646
(1.00) 		0.651
(1.00)
7q loss 3 (2%) 181 0.308
(0.997) 		0.827
(1.00) 		0.488
(1.00) 		0.476
(1.00) 		1
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.454
(1.00) 		1
(1.00) 		1
(1.00) 		0.614
(1.00) 		0.274
(0.988) 		0.0699
(0.845)
8p loss 42 (23%) 142 0.947
(1.00) 		0.358
(1.00) 		0.385
(1.00) 		0.453
(1.00) 		0.161
(0.924) 		1
(1.00) 		0.597
(1.00) 		0.295
(0.988) 		0.166
(0.924) 		0.538
(1.00) 		1
(1.00) 		0.925
(1.00) 		0.0456
(0.784) 		0.905
(1.00) 		0.588
(1.00)
8q loss 16 (9%) 168 0.957
(1.00) 		0.793
(1.00) 		0.386
(1.00) 		0.735
(1.00) 		0.76
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.359
(1.00) 		0.0948
(0.903) 		0.655
(1.00) 		0.56
(1.00) 		0.893
(1.00) 		0.626
(1.00) 		1
(1.00)
9p loss 74 (40%) 110 0.15
(0.924) 		0.831
(1.00) 		0.00145
(0.387) 		0.109
(0.906) 		0.499
(1.00) 		0.646
(1.00) 		0.881
(1.00) 		0.158
(0.924) 		0.0557
(0.817) 		0.294
(0.988) 		0.366
(1.00) 		0.949
(1.00) 		0.708
(1.00) 		0.928
(1.00) 		1
(1.00)
9q loss 43 (23%) 141 0.749
(1.00) 		0.676
(1.00) 		0.335
(1.00) 		0.826
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.0123
(0.495) 		0.397
(1.00) 		0.599
(1.00) 		0.36
(1.00) 		0.795
(1.00) 		0.2
(0.94) 		0.125
(0.906) 		0.594
(1.00)
10p loss 36 (20%) 148 0.455
(1.00) 		0.787
(1.00) 		0.0443
(0.784) 		0.522
(1.00) 		0.297
(0.988) 		0.307
(0.997) 		1
(1.00) 		1
(1.00) 		0.217
(0.953) 		0.938
(1.00) 		0.417
(1.00) 		0.816
(1.00) 		0.589
(1.00) 		0.43
(1.00) 		1
(1.00)
10q loss 30 (16%) 154 0.629
(1.00) 		0.672
(1.00) 		0.112
(0.906) 		1
(1.00) 		0.498
(1.00) 		0.237
(0.972) 		1
(1.00) 		0.819
(1.00) 		0.0838
(0.891) 		0.222
(0.959) 		0.339
(1.00) 		0.805
(1.00) 		0.772
(1.00) 		0.752
(1.00) 		0.559
(1.00)
11p loss 17 (9%) 167 0.0264
(0.677) 		0.121
(0.906) 		0.346
(1.00) 		0.626
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.387
(1.00) 		0.548
(1.00) 		0.777
(1.00) 		0.277
(0.988) 		0.275
(0.988) 		0.435
(1.00)
11q loss 15 (8%) 169 0.0207
(0.676) 		0.1
(0.906) 		0.274
(0.988) 		0.71
(1.00) 		1
(1.00) 		1
(1.00) 		0.0568
(0.817) 		0.541
(1.00) 		0.00786
(0.473) 		0.384
(1.00) 		0.634
(1.00) 		1
(1.00) 		0.388
(1.00)
12p loss 19 (10%) 165 0.82
(1.00) 		0.249
(0.976) 		0.645
(1.00) 		0.719
(1.00) 		0.783
(1.00) 		0.58
(1.00) 		0.0933
(0.896) 		0.244
(0.976) 		0.0717
(0.845) 		0.133
(0.906) 		0.412
(1.00) 		0.632
(1.00) 		0.998
(1.00) 		0.0466
(0.784) 		1
(1.00)
12q loss 28 (15%) 156 0.413
(1.00) 		0.85
(1.00) 		0.662
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.284
(0.988) 		0.542
(1.00) 		0.228
(0.965) 		0.457
(1.00) 		0.231
(0.966) 		0.696
(1.00) 		0.367
(1.00) 		0.982
(1.00) 		0.00876
(0.473) 		1
(1.00)
13q loss 20 (11%) 164 0.241
(0.972) 		0.815
(1.00) 		0.171
(0.924) 		0.407
(1.00) 		0.198
(0.94) 		0.453
(1.00) 		1
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.427
(1.00) 		0.862
(1.00) 		0.255
(0.976) 		0.227
(0.965) 		0.214
(0.949) 		0.5
(1.00)
14q loss 15 (8%) 169 0.983
(1.00) 		0.649
(1.00) 		0.652
(1.00) 		0.711
(1.00) 		0.539
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.2
(0.94) 		0.612
(1.00) 		0.495
(1.00) 		0.645
(1.00) 		0.00996
(0.473) 		1
(1.00)
15q loss 30 (16%) 154 0.404
(1.00) 		0.38
(1.00) 		0.128
(0.906) 		0.81
(1.00) 		0.17
(0.924) 		1
(1.00) 		0.167
(0.924) 		0.814
(1.00) 		0.127
(0.906) 		0.637
(1.00) 		0.783
(1.00) 		0.753
(1.00) 		0.222
(0.959) 		0.0823
(0.891) 		0.134
(0.906)
16p loss 10 (5%) 174 0.0253
(0.676) 		0.105
(0.906) 		0.0831
(0.891) 		0.174
(0.924) 		1
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.721
(1.00) 		0.00419
(0.387) 		1
(1.00) 		0.502
(1.00) 		0.663
(1.00) 		0.198
(0.94)
16q loss 13 (7%) 171 0.129
(0.906) 		0.476
(1.00) 		0.195
(0.94) 		0.586
(1.00) 		1
(1.00) 		1
(1.00) 		0.389
(1.00) 		1
(1.00) 		0.00516
(0.413) 		0.0666
(0.845) 		0.686
(1.00) 		0.255
(0.976) 		0.198
(0.94)
17p loss 79 (43%) 105 0.00866
(0.473) 		0.516
(1.00) 		0.132
(0.906) 		0.5
(1.00) 		0.616
(1.00) 		0.385
(1.00) 		0.457
(1.00) 		0.86
(1.00) 		0.105
(0.906) 		0.0563
(0.817) 		0.412
(1.00) 		0.0987
(0.906) 		0.846
(1.00) 		0.862
(1.00) 		1
(1.00)
17q loss 19 (10%) 165 0.495
(1.00) 		0.415
(1.00) 		0.937
(1.00) 		0.721
(1.00) 		1
(1.00) 		0.487
(1.00) 		0.0933
(0.896) 		0.773
(1.00) 		0.191
(0.94) 		0.0216
(0.676) 		0.911
(1.00) 		0.00504
(0.413) 		0.567
(1.00) 		0.828
(1.00) 		0.388
(1.00)
18p loss 54 (29%) 130 0.848
(1.00) 		0.0244
(0.676) 		0.268
(0.988) 		0.579
(1.00) 		0.467
(1.00) 		0.323
(1.00) 		0.516
(1.00) 		0.848
(1.00) 		0.771
(1.00) 		0.0597
(0.824) 		0.31
(0.997) 		0.914
(1.00) 		0.439
(1.00) 		0.913
(1.00) 		0.156
(0.924)
18q loss 104 (57%) 80 0.205
(0.942) 		0.0981
(0.906) 		0.0091
(0.473) 		0.189
(0.94) 		0.737
(1.00) 		0.152
(0.924) 		0.455
(1.00) 		1
(1.00) 		0.123
(0.906) 		0.762
(1.00) 		0.991
(1.00) 		0.332
(1.00) 		0.255
(0.976) 		0.0382
(0.751) 		0.681
(1.00)
19p loss 17 (9%) 167 0.826
(1.00) 		0.367
(1.00) 		0.655
(1.00) 		0.752
(1.00) 		0.405
(1.00) 		0.453
(1.00) 		1
(1.00) 		0.541
(1.00) 		0.138
(0.907) 		0.968
(1.00) 		0.935
(1.00) 		0.673
(1.00) 		0.161
(0.924) 		0.506
(1.00) 		0.412
(1.00)
19q loss 11 (6%) 173 0.603
(1.00) 		0.209
(0.942) 		0.592
(1.00) 		0.688
(1.00) 		0.73
(1.00) 		0.339
(1.00) 		1
(1.00) 		0.288
(0.988) 		1
(1.00) 		0.403
(1.00) 		0.331
(1.00) 		0.551
(1.00) 		0.211
(0.942) 		1
(1.00) 		1
(1.00)
20p loss 19 (10%) 165 0.879
(1.00) 		0.203
(0.942) 		0.722
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.453
(1.00) 		0.813
(1.00) 		0.57
(1.00) 		0.849
(1.00) 		0.432
(1.00) 		0.56
(1.00) 		0.212
(0.942) 		0.58
(1.00) 		0.172
(0.924) 		0.435
(1.00)
20q loss 5 (3%) 179 0.747
(1.00) 		0.233
(0.968) 		0.628
(1.00) 		0.661
(1.00) 		1
(1.00) 		1
(1.00) 		0.38
(1.00) 		0.278
(0.988) 		1
(1.00) 		0.572
(1.00) 		0.489
(1.00) 		0.461
(1.00) 		0.21
(0.942) 		0.136
(0.906)
21q loss 58 (32%) 126 0.46
(1.00) 		0.387
(1.00) 		0.0464
(0.784) 		0.025
(0.676) 		0.0326
(0.731) 		0.398
(1.00) 		0.205
(0.942) 		0.35
(1.00) 		0.3
(0.988) 		0.466
(1.00) 		0.239
(0.972) 		0.257
(0.976) 		0.0471
(0.784) 		0.778
(1.00) 		0.156
(0.924)
22q loss 47 (26%) 137 0.824
(1.00) 		0.129
(0.906) 		0.255
(0.976) 		0.535
(1.00) 		0.701
(1.00) 		1
(1.00) 		0.0174
(0.631) 		0.683
(1.00) 		0.939
(1.00) 		0.757
(1.00) 		0.488
(1.00) 		0.689
(1.00) 		0.577
(1.00) 		0.913
(1.00) 		1
(1.00)
xp loss 27 (15%) 157 0.14
(0.91) 		0.57
(1.00) 		0.193
(0.94) 		0.442
(1.00) 		0.237
(0.972) 		1
(1.00) 		1
(1.00) 		0.331
(1.00) 		0.796
(1.00) 		0.476
(1.00) 		0.173
(0.924) 		0.276
(0.988) 		0.115
(0.906) 		0.65
(1.00) 		0.578
(1.00)
xq loss 16 (9%) 168 0.241
(0.972) 		0.734
(1.00) 		0.049
(0.784) 		0.195
(0.94) 		0.129
(0.906) 		1
(1.00) 		0.605
(1.00) 		0.541
(1.00) 		0.452
(1.00) 		0.152
(0.924) 		0.223
(0.959) 		0.83
(1.00) 		0.0551
(0.817) 		0.351
(1.00) 		1
(1.00)
'3q gain' versus 'Time to Death'

P value = 0.000395 (logrank test), Q value = 0.24

Table S1.  Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 183 100 0.1 - 90.1 (15.3)
3Q GAIN MUTATED 20 16 0.1 - 24.4 (8.9)
3Q GAIN WILD-TYPE 163 84 0.2 - 90.1 (15.6)

Figure S1.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00022 (Fisher's exact test), Q value = 0.24

Table S2.  Gene #30: '17p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients PANCREAS-ADENOCARCINOMA DUCTAL TYPE PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA PANCREAS-UNDIFFERENTIATED CARCINOMA
ALL 153 25 4 1
17P GAIN MUTATED 3 5 0 1
17P GAIN WILD-TYPE 150 20 4 0

Figure S2.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/22533737/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PAAD-TP/22507097/PAAD-TP.merged_data.txt

  • Number of patients = 184

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 15

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

Survival analysis

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

Fisher's exact test

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

Q value calculation

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

Download Results

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

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