Correlation between copy number variations of arm-level result and selected clinical features
Pancreatic Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1513X99
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1513X99
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 14 clinical features across 173 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 79 arm-level events and 14 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 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		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 Wilcoxon-test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
3q gain 18 (10%) 155 0.000323
(0.178) 		0.777
(1.00) 		0.765
(1.00) 		0.851
(1.00) 		1
(1.00) 		0.37
(1.00) 		0.139
(0.912) 		0.698
(1.00) 		0.705
(1.00) 		0.236
(0.977) 		0.414
(1.00) 		0.148
(0.912) 		1
(1.00) 		1
(1.00)
17p gain 9 (5%) 164 0.00238
(0.439) 		0.00829
(0.612) 		0.0163
(0.65) 		0.0352
(0.762) 		0.193
(0.952) 		1
(1.00) 		0.733
(1.00) 		0.00015
(0.166) 		1
(1.00) 		0.877
(1.00) 		0.432
(1.00) 		1
(1.00)
1p gain 16 (9%) 157 0.739
(1.00) 		0.326
(0.996) 		0.52
(1.00) 		0.458
(1.00) 		1
(1.00) 		0.404
(1.00) 		0.604
(1.00) 		0.0649
(0.793) 		0.227
(0.976) 		0.549
(1.00) 		0.492
(1.00) 		0.89
(1.00) 		1
(1.00) 		0.222
(0.975)
1q gain 45 (26%) 128 0.713
(1.00) 		0.392
(1.00) 		0.183
(0.952) 		0.373
(1.00) 		0.12
(0.912) 		0.259
(0.977) 		0.0818
(0.852) 		0.191
(0.952) 		0.707
(1.00) 		0.698
(1.00) 		0.902
(1.00) 		0.258
(0.977) 		1
(1.00) 		0.158
(0.931)
2p gain 13 (8%) 160 0.73
(1.00) 		0.927
(1.00) 		0.748
(1.00) 		1
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.147
(0.912) 		0.563
(1.00) 		0.811
(1.00) 		0.0662
(0.793) 		0.455
(1.00) 		0.167
(0.944) 		1
(1.00) 		1
(1.00)
2q gain 15 (9%) 158 0.437
(1.00) 		0.522
(1.00) 		0.694
(1.00) 		0.902
(1.00) 		0.762
(1.00) 		1
(1.00) 		0.0562
(0.793) 		0.801
(1.00) 		0.385
(1.00) 		0.193
(0.952) 		0.411
(1.00) 		0.424
(1.00) 		1
(1.00) 		1
(1.00)
3p gain 9 (5%) 164 0.193
(0.952) 		0.697
(1.00) 		0.511
(1.00) 		0.262
(0.977) 		0.249
(0.977) 		1
(1.00) 		0.0422
(0.788) 		0.703
(1.00) 		0.802
(1.00) 		0.669
(1.00) 		1
(1.00) 		1
(1.00)
4p gain 11 (6%) 162 0.105
(0.912) 		0.472
(1.00) 		0.143
(0.912) 		0.407
(1.00) 		0.459
(1.00) 		0.138
(0.912) 		0.547
(1.00) 		0.00664
(0.612) 		1
(1.00) 		0.359
(1.00) 		1
(1.00) 		0.165
(0.943)
4q gain 8 (5%) 165 0.0619
(0.793) 		0.184
(0.952) 		0.0377
(0.762) 		0.18
(0.952) 		0.385
(1.00) 		0.0476
(0.793) 		1
(1.00) 		0.0442
(0.788) 		0.788
(1.00) 		0.87
(1.00) 		1
(1.00) 		1
(1.00)
5p gain 27 (16%) 146 0.43
(1.00) 		0.888
(1.00) 		0.197
(0.956) 		0.311
(0.983) 		0.804
(1.00) 		1
(1.00) 		0.405
(1.00) 		0.0153
(0.65) 		0.473
(1.00) 		0.0505
(0.793) 		0.564
(1.00) 		0.636
(1.00) 		1
(1.00) 		0.377
(1.00)
5q gain 20 (12%) 153 0.134
(0.912) 		0.747
(1.00) 		0.089
(0.888) 		0.0578
(0.793) 		0.395
(1.00) 		1
(1.00) 		0.812
(1.00) 		0.118
(0.912) 		0.363
(1.00) 		0.145
(0.912) 		0.748
(1.00) 		0.926
(1.00) 		0.71
(1.00) 		0.311
(0.983)
6p gain 6 (3%) 167 0.17
(0.945) 		0.771
(1.00) 		0.539
(1.00) 		0.661
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.224
(0.976) 		0.129
(0.912) 		1
(1.00) 		0.701
(1.00) 		0.31
(0.983) 		1
(1.00)
6q gain 4 (2%) 169 0.611
(1.00) 		0.628
(1.00) 		0.688
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.499
(1.00) 		0.65
(1.00) 		0.572
(1.00) 		0.219
(0.975) 		1
(1.00)
7p gain 50 (29%) 123 0.678
(1.00) 		0.531
(1.00) 		0.338
(1.00) 		0.478
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.244
(0.977) 		0.0299
(0.762) 		0.113
(0.912) 		0.302
(0.983) 		0.0383
(0.762) 		0.228
(0.976) 		0.512
(1.00) 		0.564
(1.00)
7q gain 47 (27%) 126 0.604
(1.00) 		0.747
(1.00) 		0.383
(1.00) 		0.448
(1.00) 		0.557
(1.00) 		1
(1.00) 		0.306
(0.983) 		0.0437
(0.788) 		0.104
(0.912) 		0.191
(0.952) 		0.0288
(0.762) 		0.119
(0.912) 		0.488
(1.00) 		0.571
(1.00)
8p gain 24 (14%) 149 0.668
(1.00) 		0.667
(1.00) 		0.804
(1.00) 		0.941
(1.00) 		0.622
(1.00) 		1
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.52
(1.00) 		0.8
(1.00) 		0.361
(1.00) 		0.974
(1.00) 		0.737
(1.00) 		0.361
(1.00)
8q gain 45 (26%) 128 0.262
(0.977) 		0.269
(0.977) 		0.664
(1.00) 		1
(1.00) 		0.428
(1.00) 		1
(1.00) 		0.298
(0.983) 		0.327
(0.996) 		0.484
(1.00) 		0.588
(1.00) 		0.128
(0.912) 		0.78
(1.00) 		0.32
(0.996) 		0.142
(0.912)
9p gain 7 (4%) 166 0.601
(1.00) 		0.054
(0.793) 		0.823
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.46
(1.00) 		0.0434
(0.788) 		0.756
(1.00) 		0.905
(1.00) 		1
(1.00) 		1
(1.00)
9q gain 11 (6%) 162 0.312
(0.983) 		0.253
(0.977) 		0.497
(1.00) 		0.407
(1.00) 		0.459
(1.00) 		1
(1.00) 		0.756
(1.00) 		0.401
(1.00) 		0.204
(0.957) 		0.53
(1.00) 		1
(1.00) 		1
(1.00)
10p gain 8 (5%) 165 0.662
(1.00) 		0.797
(1.00) 		0.824
(1.00) 		0.759
(1.00) 		1
(1.00) 		1
(1.00) 		0.297
(0.983) 		1
(1.00) 		0.254
(0.977) 		0.732
(1.00) 		0.00365
(0.449) 		1
(1.00)
10q gain 12 (7%) 161 0.0667
(0.793) 		0.603
(1.00) 		0.592
(1.00) 		0.269
(0.977) 		0.729
(1.00) 		0.299
(0.983) 		0.0676
(0.793) 		1
(1.00) 		0.38
(1.00) 		0.466
(1.00) 		0.298
(0.983) 		0.251
(0.977) 		0.0135
(0.65) 		1
(1.00)
11p gain 13 (8%) 160 0.341
(1.00) 		0.491
(1.00) 		0.381
(1.00) 		0.541
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.0393
(0.762) 		0.235
(0.977) 		0.0614
(0.793) 		0.643
(1.00) 		1
(1.00) 		1
(1.00)
11q gain 15 (9%) 158 0.0165
(0.65) 		0.73
(1.00) 		0.485
(1.00) 		0.902
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.0562
(0.793) 		0.361
(1.00) 		0.187
(0.952) 		0.894
(1.00) 		1
(1.00) 		0.0167
(0.65)
12p gain 28 (16%) 145 0.662
(1.00) 		0.717
(1.00) 		0.0699
(0.793) 		0.199
(0.956) 		1
(1.00) 		1
(1.00) 		0.306
(0.983) 		0.0462
(0.793) 		0.868
(1.00) 		0.563
(1.00) 		0.0385
(0.762) 		0.0862
(0.875) 		0.764
(1.00) 		1
(1.00)
12q gain 21 (12%) 152 0.405
(1.00) 		0.367
(1.00) 		0.0591
(0.793) 		0.271
(0.978) 		0.783
(1.00) 		1
(1.00) 		0.159
(0.931) 		0.0404
(0.771) 		0.0176
(0.65) 		0.0732
(0.809) 		0.729
(1.00) 		1
(1.00)
13q gain 26 (15%) 147 0.498
(1.00) 		0.533
(1.00) 		0.451
(1.00) 		0.75
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.525
(1.00) 		0.0152
(0.65) 		0.039
(0.762) 		0.268
(0.977) 		0.991
(1.00) 		0.745
(1.00) 		1
(1.00)
14q gain 25 (14%) 148 0.365
(1.00) 		0.752
(1.00) 		0.766
(1.00) 		1
(1.00) 		0.8
(1.00) 		0.404
(1.00) 		0.388
(1.00) 		0.888
(1.00) 		0.727
(1.00) 		0.88
(1.00) 		0.607
(1.00) 		0.375
(1.00) 		0.748
(1.00) 		0.361
(1.00)
15q gain 13 (8%) 160 0.78
(1.00) 		0.128
(0.912) 		0.245
(0.977) 		0.485
(1.00) 		0.185
(0.952) 		1
(1.00) 		1
(1.00) 		0.3
(0.983) 		0.643
(1.00) 		0.334
(1.00) 		0.0609
(0.793) 		1
(1.00) 		1
(1.00)
16p gain 22 (13%) 151 0.156
(0.931) 		0.082
(0.852) 		0.861
(1.00) 		0.88
(1.00) 		0.799
(1.00) 		0.404
(1.00) 		0.107
(0.912) 		0.502
(1.00) 		0.651
(1.00) 		0.146
(0.912) 		0.0898
(0.888) 		0.638
(1.00) 		1
(1.00) 		1
(1.00)
16q gain 22 (13%) 151 0.627
(1.00) 		0.209
(0.964) 		0.863
(1.00) 		0.641
(1.00) 		0.799
(1.00) 		0.436
(1.00) 		0.107
(0.912) 		0.501
(1.00) 		0.651
(1.00) 		0.146
(0.912) 		0.362
(1.00) 		0.719
(1.00) 		1
(1.00) 		1
(1.00)
17q gain 16 (9%) 157 0.0014
(0.386) 		0.0102
(0.65) 		0.135
(0.912) 		0.279
(0.983) 		0.335
(1.00) 		1
(1.00) 		0.432
(1.00) 		0.0237
(0.748) 		0.373
(1.00) 		0.649
(1.00) 		0.757
(1.00) 		0.913
(1.00) 		0.619
(1.00) 		1
(1.00)
18p gain 26 (15%) 147 0.614
(1.00) 		0.0369
(0.762) 		0.843
(1.00) 		0.699
(1.00) 		0.812
(1.00) 		0.436
(1.00) 		0.136
(0.912) 		0.0333
(0.762) 		0.288
(0.983) 		0.425
(1.00) 		0.749
(1.00) 		0.236
(0.977) 		0.752
(1.00) 		1
(1.00)
18q gain 12 (7%) 161 0.152
(0.931) 		0.862
(1.00) 		0.794
(1.00) 		0.504
(1.00) 		0.729
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.00758
(0.612) 		0.56
(1.00) 		0.77
(1.00) 		1
(1.00) 		1
(1.00)
19p gain 15 (9%) 158 0.111
(0.912) 		0.873
(1.00) 		0.517
(1.00) 		0.104
(0.912) 		0.762
(1.00) 		1
(1.00) 		0.0562
(0.793) 		0.127
(0.912) 		0.082
(0.852) 		0.936
(1.00) 		0.143
(0.912) 		0.269
(0.977) 		1
(1.00) 		1
(1.00)
19q gain 23 (13%) 150 0.146
(0.912) 		0.998
(1.00) 		0.782
(1.00) 		0.248
(0.977) 		1
(1.00) 		1
(1.00) 		0.0705
(0.793) 		0.304
(0.983) 		0.107
(0.912) 		0.562
(1.00) 		0.267
(0.977) 		0.19
(0.952) 		1
(1.00) 		1
(1.00)
20p gain 34 (20%) 139 0.23
(0.977) 		0.102
(0.912) 		0.567
(1.00) 		0.306
(0.983) 		0.827
(1.00) 		1
(1.00) 		0.25
(0.977) 		0.025
(0.748) 		0.699
(1.00) 		0.676
(1.00) 		0.373
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.482
(1.00)
20q gain 43 (25%) 130 0.249
(0.977) 		0.175
(0.952) 		0.837
(1.00) 		0.536
(1.00) 		0.687
(1.00) 		0.578
(1.00) 		0.157
(0.931) 		0.155
(0.931) 		0.14
(0.912) 		0.485
(1.00) 		0.371
(1.00) 		0.52
(1.00) 		1
(1.00) 		1
(1.00)
22q gain 8 (5%) 165 0.0172
(0.65) 		0.0899
(0.888) 		1
(1.00) 		0.776
(1.00) 		0.683
(1.00) 		1
(1.00) 		0.142
(0.912) 		0.0747
(0.819) 		1
(1.00) 		0.269
(0.977) 		0.353
(1.00) 		1
(1.00)
xp gain 8 (5%) 165 0.00831
(0.612) 		0.182
(0.952) 		0.448
(1.00) 		0.132
(0.912) 		0.657
(1.00) 		1
(1.00) 		0.731
(1.00) 		0.00311
(0.449) 		0.461
(1.00) 		0.884
(1.00) 		0.395
(1.00) 		1
(1.00)
xq gain 12 (7%) 161 0.0127
(0.65) 		0.597
(1.00) 		0.113
(0.912) 		0.0825
(0.852) 		1
(1.00) 		1
(1.00) 		0.38
(1.00) 		0.168
(0.945) 		0.384
(1.00) 		0.523
(1.00) 		0.532
(1.00) 		0.222
(0.975)
1p loss 34 (20%) 139 0.526
(1.00) 		0.2
(0.956) 		0.294
(0.983) 		0.937
(1.00) 		0.127
(0.912) 		1
(1.00) 		0.124
(0.912) 		1
(1.00) 		0.191
(0.952) 		0.464
(1.00) 		0.792
(1.00) 		0.259
(0.977) 		0.525
(1.00) 		0.468
(1.00)
1q loss 8 (5%) 165 0.488
(1.00) 		0.0962
(0.907) 		0.169
(0.945) 		0.486
(1.00) 		1
(1.00) 		1
(1.00) 		0.297
(0.983) 		0.437
(1.00) 		0.161
(0.933) 		0.785
(1.00) 		0.87
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 11 (6%) 162 0.145
(0.912) 		0.363
(1.00) 		0.156
(0.931) 		0.719
(1.00) 		0.459
(1.00) 		1
(1.00) 		1
(1.00) 		0.00513
(0.567) 		0.461
(1.00) 		0.197
(0.956) 		0.13
(0.912) 		1
(1.00)
2q loss 5 (3%) 168 0.0848
(0.869) 		0.102
(0.912) 		0.0523
(0.793) 		0.216
(0.974) 		0.288
(0.983) 		1
(1.00) 		1
(1.00) 		0.0189
(0.676) 		1
(1.00) 		0.877
(1.00) 		1
(1.00) 		1
(1.00)
3p loss 35 (20%) 138 0.923
(1.00) 		0.515
(1.00) 		0.733
(1.00) 		0.451
(1.00) 		0.828
(1.00) 		1
(1.00) 		0.0129
(0.65) 		0.309
(0.983) 		0.504
(1.00) 		0.809
(1.00) 		0.916
(1.00) 		0.347
(1.00) 		0.824
(1.00) 		1
(1.00)
3q loss 19 (11%) 154 0.305
(0.983) 		0.952
(1.00) 		0.974
(1.00) 		0.547
(1.00) 		1
(1.00) 		1
(1.00) 		0.0923
(0.894) 		0.177
(0.952) 		0.339
(1.00) 		0.116
(0.912) 		1
(1.00) 		1
(1.00) 		0.0654
(0.793) 		1
(1.00)
4p loss 23 (13%) 150 0.281
(0.983) 		0.975
(1.00) 		0.973
(1.00) 		0.944
(1.00) 		0.442
(1.00) 		1
(1.00) 		0.0229
(0.746) 		0.118
(0.912) 		0.736
(1.00) 		0.649
(1.00) 		0.621
(1.00) 		0.278
(0.983) 		0.518
(1.00) 		0.361
(1.00)
4q loss 23 (13%) 150 0.367
(1.00) 		0.591
(1.00) 		0.974
(1.00) 		0.657
(1.00) 		0.442
(1.00) 		1
(1.00) 		0.00594
(0.597) 		0.12
(0.912) 		0.302
(0.983) 		0.38
(1.00) 		0.62
(1.00) 		0.567
(1.00) 		0.523
(1.00) 		0.0497
(0.793)
5p loss 7 (4%) 166 0.779
(1.00) 		0.339
(1.00) 		0.753
(1.00) 		0.757
(1.00) 		0.191
(0.952) 		1
(1.00) 		1
(1.00) 		0.675
(1.00) 		0.438
(1.00) 		0.549
(1.00) 		0.508
(1.00) 		0.0615
(0.793) 		1
(1.00) 		1
(1.00)
5q loss 10 (6%) 163 0.53
(1.00) 		0.827
(1.00) 		0.66
(1.00) 		0.697
(1.00) 		0.064
(0.793) 		1
(1.00) 		1
(1.00) 		0.113
(0.912) 		0.289
(0.983) 		0.638
(1.00) 		0.207
(0.96) 		0.0631
(0.793) 		1
(1.00) 		1
(1.00)
6p loss 59 (34%) 114 0.177
(0.952) 		0.316
(0.99) 		0.262
(0.977) 		0.711
(1.00) 		0.272
(0.978) 		0.296
(0.983) 		0.263
(0.977) 		0.0561
(0.793) 		0.322
(0.996) 		0.923
(1.00) 		1
(1.00) 		0.148
(0.912) 		0.743
(1.00) 		1
(1.00)
6q loss 78 (45%) 95 0.122
(0.912) 		0.259
(0.977) 		0.542
(1.00) 		0.279
(0.983) 		0.863
(1.00) 		1
(1.00) 		0.36
(1.00) 		0.7
(1.00) 		0.294
(0.983) 		0.854
(1.00) 		0.694
(1.00) 		0.89
(1.00) 		0.262
(0.977) 		0.58
(1.00)
8p loss 40 (23%) 133 0.832
(1.00) 		0.361
(1.00) 		0.218
(0.975) 		0.473
(1.00) 		0.0595
(0.793) 		1
(1.00) 		0.476
(1.00) 		0.175
(0.952) 		0.692
(1.00) 		0.955
(1.00) 		0.543
(1.00) 		0.0203
(0.681) 		0.181
(0.952) 		1
(1.00)
8q loss 16 (9%) 157 0.807
(1.00) 		0.765
(1.00) 		0.369
(1.00) 		0.909
(1.00) 		0.762
(1.00) 		1
(1.00) 		0.604
(1.00) 		0.097
(0.907) 		0.643
(1.00) 		0.548
(1.00) 		0.876
(1.00) 		0.244
(0.977) 		1
(1.00)
9p loss 71 (41%) 102 0.215
(0.974) 		0.826
(1.00) 		0.00082
(0.302) 		0.063
(0.793) 		0.598
(1.00) 		0.293
(0.983) 		1
(1.00) 		0.0976
(0.907) 		0.23
(0.977) 		0.395
(1.00) 		0.793
(1.00) 		0.788
(1.00) 		0.76
(1.00) 		0.558
(1.00)
9q loss 42 (24%) 131 0.577
(1.00) 		0.773
(1.00) 		0.333
(1.00) 		0.97
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.725
(1.00) 		0.206
(0.96) 		0.67
(1.00) 		0.383
(1.00) 		1
(1.00) 		0.141
(0.912) 		0.852
(1.00) 		0.142
(0.912)
10p loss 34 (20%) 139 0.324
(0.996) 		0.851
(1.00) 		0.0555
(0.793) 		0.654
(1.00) 		0.276
(0.983) 		0.2
(0.956) 		1
(1.00) 		0.176
(0.952) 		0.991
(1.00) 		0.389
(1.00) 		1
(1.00) 		0.442
(1.00) 		0.51
(1.00) 		1
(1.00)
10q loss 27 (16%) 146 0.766
(1.00) 		0.781
(1.00) 		0.262
(0.977) 		1
(1.00) 		0.228
(0.976) 		0.525
(1.00) 		1
(1.00) 		0.0929
(0.894) 		0.235
(0.977) 		0.328
(0.996) 		0.81
(1.00) 		0.417
(1.00) 		0.751
(1.00) 		1
(1.00)
11p loss 15 (9%) 158 0.158
(0.931) 		0.547
(1.00) 		0.303
(0.983) 		0.812
(1.00) 		0.358
(1.00) 		1
(1.00) 		0.789
(1.00) 		0.636
(1.00) 		0.75
(1.00) 		0.754
(1.00) 		0.121
(0.912) 		0.22
(0.975) 		1
(1.00)
11q loss 14 (8%) 159 0.111
(0.912) 		0.376
(1.00) 		0.364
(1.00) 		0.792
(1.00) 		1
(1.00) 		1
(1.00) 		0.265
(0.977) 		0.0162
(0.65) 		0.891
(1.00) 		0.355
(1.00) 		0.202
(0.957) 		0.589
(1.00) 		1
(1.00)
12p loss 18 (10%) 155 0.857
(1.00) 		0.302
(0.983) 		0.491
(1.00) 		0.79
(1.00) 		0.777
(1.00) 		0.496
(1.00) 		0.327
(0.996) 		0.0552
(0.793) 		0.308
(0.983) 		0.425
(1.00) 		0.8
(1.00) 		0.415
(1.00) 		0.0908
(0.888) 		1
(1.00)
12q loss 24 (14%) 149 0.204
(0.957) 		0.845
(1.00) 		0.796
(1.00) 		0.893
(1.00) 		0.622
(1.00) 		0.578
(1.00) 		1
(1.00) 		0.668
(1.00) 		0.486
(1.00) 		0.69
(1.00) 		0.791
(1.00) 		0.584
(1.00) 		0.0197
(0.68) 		1
(1.00)
13q loss 20 (12%) 153 0.194
(0.952) 		0.798
(1.00) 		0.192
(0.952) 		0.358
(1.00) 		0.285
(0.983) 		0.404
(1.00) 		1
(1.00) 		0.855
(1.00) 		0.394
(1.00) 		0.882
(1.00) 		0.103
(0.912) 		0.242
(0.977) 		0.339
(1.00) 		0.345
(1.00)
14q loss 14 (8%) 159 0.818
(1.00) 		0.632
(1.00) 		0.313
(0.984) 		0.709
(1.00) 		0.335
(1.00) 		1
(1.00) 		0.783
(1.00) 		0.377
(1.00) 		0.183
(0.952) 		0.632
(1.00) 		0.363
(1.00) 		0.564
(1.00) 		0.0495
(0.793) 		1
(1.00)
15q loss 26 (15%) 147 0.619
(1.00) 		0.325
(0.996) 		0.0707
(0.793) 		0.793
(1.00) 		0.139
(0.912) 		0.525
(1.00) 		0.289
(0.983) 		0.136
(0.912) 		0.596
(1.00) 		0.766
(1.00) 		0.789
(1.00) 		0.117
(0.912) 		0.285
(0.983) 		0.345
(1.00)
16p loss 9 (5%) 164 0.0469
(0.793) 		0.071
(0.793) 		0.136
(0.912) 		0.359
(1.00) 		0.683
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.00219
(0.439) 		0.788
(1.00) 		0.514
(1.00) 		1
(1.00) 		1
(1.00)
16q loss 10 (6%) 163 0.337
(1.00) 		0.178
(0.952) 		0.16
(0.931) 		0.586
(1.00) 		0.447
(1.00) 		1
(1.00) 		0.515
(1.00) 		0.00357
(0.449) 		0.0388
(0.762) 		0.55
(1.00) 		1
(1.00) 		1
(1.00)
17p loss 74 (43%) 99 0.0109
(0.65) 		0.542
(1.00) 		0.124
(0.912) 		0.265
(0.977) 		0.384
(1.00) 		0.644
(1.00) 		0.758
(1.00) 		0.135
(0.912) 		0.0386
(0.762) 		0.385
(1.00) 		0.0321
(0.762) 		0.885
(1.00) 		0.68
(1.00) 		1
(1.00)
17q loss 21 (12%) 152 0.722
(1.00) 		0.676
(1.00) 		0.533
(1.00) 		0.212
(0.969) 		1
(1.00) 		0.467
(1.00) 		0.159
(0.931) 		0.21
(0.964) 		0.0774
(0.84) 		0.891
(1.00) 		0.032
(0.762) 		0.849
(1.00) 		0.478
(1.00) 		1
(1.00)
18p loss 51 (29%) 122 0.969
(1.00) 		0.0694
(0.793) 		0.684
(1.00) 		0.667
(1.00) 		1
(1.00) 		0.591
(1.00) 		0.402
(1.00) 		0.629
(1.00) 		0.0682
(0.793) 		0.366
(1.00) 		0.861
(1.00) 		0.896
(1.00) 		1
(1.00) 		0.22
(0.975)
18q loss 97 (56%) 76 0.0822
(0.852) 		0.299
(0.983) 		0.0131
(0.65) 		0.116
(0.912) 		0.726
(1.00) 		0.293
(0.983) 		0.283
(0.983) 		0.109
(0.912) 		0.647
(1.00) 		0.954
(1.00) 		0.163
(0.938) 		0.251
(0.977) 		0.341
(1.00) 		1
(1.00)
19p loss 17 (10%) 156 0.498
(1.00) 		0.322
(0.996) 		0.453
(1.00) 		0.266
(0.977) 		0.245
(0.977) 		0.404
(1.00) 		1
(1.00) 		0.141
(0.912) 		0.698
(1.00) 		0.938
(1.00) 		0.299
(0.983) 		0.033
(0.762) 		0.665
(1.00) 		1
(1.00)
19q loss 11 (6%) 162 0.76
(1.00) 		0.204
(0.957) 		0.573
(1.00) 		0.62
(1.00) 		0.729
(1.00) 		0.299
(0.983) 		1
(1.00) 		1
(1.00) 		0.419
(1.00) 		0.311
(0.983) 		0.233
(0.977) 		0.223
(0.976) 		1
(1.00) 		1
(1.00)
20p loss 18 (10%) 155 0.834
(1.00) 		0.267
(0.977) 		0.669
(1.00) 		0.451
(1.00) 		0.406
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.852
(1.00) 		0.324
(0.996) 		0.324
(0.996) 		0.305
(0.983) 		0.264
(0.977) 		1
(1.00)
20q loss 4 (2%) 169 0.236
(0.977) 		0.241
(0.977) 		1
(1.00) 		1
(1.00) 		0.574
(1.00) 		1
(1.00) 		0.628
(1.00) 		1
(1.00) 		0.557
(1.00) 		0.654
(1.00) 		0.147
(0.912) 		0.22
(0.975) 		1
(1.00)
21q loss 53 (31%) 120 0.169
(0.945) 		0.483
(1.00) 		0.0381
(0.762) 		0.0175
(0.65) 		0.0246
(0.748) 		0.633
(1.00) 		0.246
(0.977) 		0.195
(0.955) 		0.408
(1.00) 		0.226
(0.976) 		0.377
(1.00) 		0.0274
(0.762) 		0.458
(1.00) 		0.201
(0.957)
22q loss 43 (25%) 130 0.579
(1.00) 		0.0566
(0.793) 		0.171
(0.946) 		0.478
(1.00) 		0.544
(1.00) 		1
(1.00) 		0.0333
(0.762) 		0.819
(1.00) 		0.662
(1.00) 		0.461
(1.00) 		0.812
(1.00) 		0.619
(1.00) 		0.864
(1.00) 		1
(1.00)
xp loss 25 (14%) 148 0.165
(0.943) 		0.762
(1.00) 		0.231
(0.977) 		0.479
(1.00) 		0.216
(0.974) 		1
(1.00) 		0.829
(1.00) 		1
(1.00) 		0.425
(1.00) 		0.191
(0.952) 		0.413
(1.00) 		0.0945
(0.901) 		0.297
(0.983) 		0.393
(1.00)
xq loss 17 (10%) 156 0.207
(0.96) 		0.621
(1.00) 		0.0667
(0.793) 		0.246
(0.977) 		0.0369
(0.762) 		1
(1.00) 		0.45
(1.00) 		0.34
(1.00) 		0.133
(0.912) 		0.247
(0.977) 		0.786
(1.00) 		0.0321
(0.762) 		0.386
(1.00) 		1
(1.00)
'3q gain' versus 'Time to Death'

P value = 0.000323 (logrank test), Q value = 0.18

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

nPatients nDeath Duration Range (Median), Month
ALL 171 92 0.1 - 84.1 (14.2)
3Q GAIN MUTATED 18 14 0.1 - 23.5 (8.9)
3Q GAIN WILD-TYPE 153 78 0.2 - 84.1 (14.9)

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

'17p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00015 (Fisher's exact test), Q value = 0.17

Table S2.  Gene #30: '17p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients PANCREAS-ADENOCARCINOMA DUCTAL TYPE PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA PANCREAS-UNDIFFERENTIATED CARCINOMA
ALL 145 22 4 1
17P GAIN MUTATED 3 5 0 1
17P GAIN WILD-TYPE 142 17 4 0

Figure S2.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #8: '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/15096459/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PAAD-TP/15087151/PAAD-TP.merged_data.txt

  • Number of patients = 173

  • Number of significantly arm-level cnvs = 79

  • Number of selected clinical features = 14

  • 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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